University of New Hampshire University of New Hampshire Scholars' Repository

Master's Theses and Capstones Student Scholarship

Spring 2012

Ecosystem structure and function in an urban, piped

Amanda Hope University of New Hampshire, Durham

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Recommended Citation Hope, Amanda, "Ecosystem structure and function in an urban, piped stream" (2012). Master's Theses and Capstones. 701. https://scholars.unh.edu/thesis/701

This Thesis is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Master's Theses and Capstones by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. ECOSYSTEM STRUCTURE AND FUNCTION

IN AN URBAN, PIPED STREAM

BY

AMANDA HOPE

B.S., Eastern Nazarene College, 2002

THESIS

Submitted to the University of New Hampshire

in Partial Fulfillment of

the Requirements for the Degree of

Master of Science

in

Natural Resources

May, 2012 UMI Number: 1518004

All rights reserved

INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted.

In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion.

UMI 1518004 Published by ProQuest LLC 2012. Copyright in the Dissertation held by the Author. Microform Edition © ProQuest LLC. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code.

ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 This thesis has been examined and approved.

Thesis Director, Dr. William H. McDowell, Professor of Environmental Sciences

Dr. Wilfred Wollheim, Assistant Professor of Environmental Sciences and Earth, Oceans, and Space

A4-J1 Dr. Gretchen Gettel, Lecturer in Aquatic Biogeochemistry, UNESCO-IHE Institute for Water Education

M(5|qo|3-

Date ACKNOWLEDGEMENTS

I would like to thank my committee: Bill McDowell, Wil Wollheim, and Gretchen

Gettel. I appreciate their encouragement and the time they spent with me, providing research guidance and insight into the world of academic science. The opportunity to work with these outstanding individuals was a valued privilege.

I am very grateful to Jody Potter, Jeff Merriam, Adam Baumann, and Michelle

Daley from the NH Research Center lab. This research could not have been completed without the many hours they devoted to assisting me with equipment, sample analyses, and problem-solving.

Thank you to all the other fellow students and colleagues who offered moral support and helpful suggestions. I'd also like to thank Tom Dubois and Ruth Abelmann, as well as my friends, family, and God who sustained me throughout this process. My husband, James, never failed to believe in me with patient, unconditional love.

This research was funded by the NH Water Resources Research Center.

Additional graduate support was provided by the UNH Department of Natural Resources and the Environment, as well as the Plum Island Ecosystem Long Term Ecological

Research Program (NSF LTER OCE- 0423565).

iii TABLE OF CONTENTS

SECTION PAGE

ACKNOWLEDGEMENTS iii

LIST OF TABLES vii

LIST OF FIGURES viii

ABSTRACT ix

CHAPTER I: INTRODUCTION 1

Urban Threats to Stream Ecosystems 1

Prevalence of Buried and Piped 2

Ecological Studies Regarding Piped Streams 3

Importance of Ecosystem Processes 4

Ecosystem Metabolism 5

Nutrient Spiraling 7

Summary of Research Needs 11

Project Overview 13

CHAPTER II: METHODS 17

Study Site 17

Stream Characterization 21

Water Chemistry Analyses 23

iv Ecosystem Metabolism 24

Ecosystem Metabolism Calculations 27

Nutrient Uptake 31

Nutrient Uptake Calculations 33

Chlorophyll a and Ash Free Dry Mass of Epilithon & Benthic Organic Matter...35

Chlorophyll a and Ash Free Dry Mass Calculations 37

Statistical Analyses 39

CHAPTER III: RESULTS 40

Chemical and Physical Parameters 40

Reaeration 46

Ecosystem Metabolism 47

Benthic Ash Free Dry Mass and Pigment Biomass 50

Dissolved Organic Carbon (DOC) Uptake 53

Nitrate (NO3) Uptake 54

Ammonium (NH4) Uptake 55

Phosphate (PO4) Uptake 58

Entire Reach Nutrient Uptake Values 58

CHAPTER IV: DISCUSSION 61

Chemical and Physical Parameters 61

Reaeration 63

v Ecosystem Metabolism 64

Benthic Ash Free Dry Mass and Pigment Biomass 67

Nutrient Uptake 69

Strengths and Limitations of Study Results 75

Implications of the Results at the Stream and Landscape Scale 75

Ecological and Management Implications of the Results 77

CHAPTER V: CONCLUSION 81

REFERENCES 83

APPENDICES 94

APPENDIX A: LITERATURE REVIEW 95

APPENDIX B: BACKGROUND SAMPLING WATER CHEMISTRY DATA 107

APPENDIX C: EXPERIMENT WATER CHEMSITRY DATA 113

APPENDIX D: SUMMER EXPERIMENT WATER CHEMISTRY DATA 119

APPENDIX E: EXAMPLE ECOSYSTEM METABOLISM 02 GRAPHS 140

APPENDIX F: ECOSYSTEM METABOLISM VALUES 142

APPENDIX G: BENTHIC AFDM AND PIGMENT BIOMASS VALUES 143

APPENDIX H: EXAMPLE NUTRIENT UPTAKE GRAPHS 144

APPENDIX I: NUTRIENT UPTAKE VALUES 147

vi LIST OF TABLES

TABLE PAGE

Table 1. GPS coordinates for study reaches in Pettee Brook 21

Table 2. Stream chemistry during assessments of nutrient uptake and ecosystem metabolism 43

Table 3. Stream characteristics during assessments of nutrient uptake and ecosystem metabolism 44

Table 4. Ecosystem metabolism changes in piped reaches of Pettee Brook 67

Table 5. Observed anthropogenic impacts to Pettee Brook, 2009-2010 79

vii LIST OF FIGURES

FIGURE PAGE

Figure 1. Diagram of study reaches 20

Figure 2. Average ambient solute concentrations 40

Figure 3. Ambient nutrient concentrations 41

Figure 4. Daily PAR 42

Figure 5. Relationship between Reaeration rates derived from SF6 additions and equations 3,4,6,7 found in Raymond et al. (in press) 46

Figure 6. Standardized reaeration rates 47

Figure 7. Average GPP 48

Figure 8. Average ER 49

Figure 9. Average NEP 49

Figure 10. Average P/R ratios 50

Figure 11. Ash free dry mass of surface FBOM and epilithon 51

Figure 12. Chlorophyll a and pheophytin biomass of surface FBOM and epilithon 52

Figure 13. DOC uptake 54

Figure 14. Summer NH4 uptake 55

Figure 15. Spring NH4 uptake 56

Figure 16. Background corrected NH4-N and NOrN flux for Pipe 1, 8/18/2009 57

Figure 17. Nutrient uptake velocity in Reaches 1 and 2 of Pettee Brook 59

Figure 18. Areal uptake in Reaches 1 and 2 of Pettee Brook 59

viii ABSTRACT

ECOSYSTEM STRUCTURE AND FUNCTION

IN AN URBAN, PIPED STREAM

by

Amanda Hope

University of New Hampshire, May, 2012

Piped streams, or streams that run underground, are common features in urban areas. However, there is little empirical evidence regarding their ecological structure and function. This study measured ecosystem metabolism, nutrient uptake, and related characteristics of Pettee Brook - an that flows through several pipes under impervious surfaces near the UNH (Durham) campus.

Piped and open reaches of Pettee Brook had similar water quality, nutrient uptake, and ER. However, the absence of light in piped reaches led to their complete loss of

GPP. Benthic AFDM and chlorophyll a biomass were also significantly reduced in piped reaches. For both open and piped reaches, spring metabolism and nutrient uptake were elevated compared to summer rates.

The results suggest that ecological conditions in piped streams may be degraded beyond the extent of other urban stream reaches. However, piped stream reaches may still offer some ecosystem services such as nutrient uptake during ER.

ix CHAPTER I - INTRODUCTION

Urban Threats to Stream Ecosystems

Urban impairment of aquatic ecosystems (reviewed by Paul and Meyer 2001,

Walsh et al. 2005b) threatens the quality and diversity of life on Earth, including human health and well being (Palmer et al. 2004). Degraded urban streams fail to adequately support water uses such as drinking, sanitation, industry, protection, agriculture, fisheries, and recreation. There is an urgent need to find ecological solutions to this problem (Grimm et al. 2008).

Urban stream impairment is associated with development that covers watersheds with impervious surfaces, such as pavement and buildings. The impervious surfaces are connected to streams by efficient drainage systems (e.g. gutters and storm drains, Walsh et al. 2005a). This land use reduces and increases storm water flow into streams, resulting in streams that suffer from altered geomorphology, elevated concentrations of nutrients and contaminants, and reduced biodiversity. Stream ecological processes, such as organic matter retention, nutrient uptake, and ecosystem metabolism, may also be affected (Paul and Meyer 2001, Walsh et al. 2005b, Grimm et al. 2005, Meyer et al. 2005).

In addition to the problems caused by impervious surfaces and efficient drainage systems, urban streams are also directly impaired by channelization and burial (Elmore

1 and Kaushal 2008). Channelization involves straightening urban streams and/or lining stream beds with hard materials such as concrete. Burial occurs when urban streams are completely filled with material, as well as when streams are diverted through underground pipes (referred to as "stream piping" and "piped streams"). These practices create urban streams that may be extremely degraded; losses include aquatic habitat, and nutrient retention, and primary productivity (Elmore and Kaushal 2008,

Doyle and Bernhardt 2011).

Prevalence of Buried and Piped Streams

Buried streams (filled-in streams as well as piped streams) are prevalent in urban watersheds. Elmore and Kaushal (2008) found that buried streams comprised 20% to

70% of all streams in the region surrounding , MD (with the highest percentage in Baltimore City). Roy et al. (2009) estimated that 93% of ephemeral and 46% of intermittent stream length was buried in the region near Cincinnati, OH. Stream piping was widespread in perennial streams, with 40% of perennial streams originating from pipes. Twenty-eight percent of piped streams had continuous flow (Roy et al. 2009).

Piped streams are also common in New England. GIS analysis indicates that there are over 28,500 road crossings in Massachusetts ( and Stream Continuity

Partnership 2009) and over 17,000 road crossings in New Hampshire (Lemay 2008).

This suggests that there may be over 100,000 of meters of stream that flow through pipes under roads (MA and NH combined, calculations based on US DOT FHA 1997). Many more meters of stream are contained in pipes that flow under parking lots, buildings, and other surfaces. Whereas road crossings may only be 10-15 meters long, piped streams

2 under other urban surfaces can be hundreds of meters long. Additional assessment of the degree of stream piping in urban areas is needed (Elmore and Kaushal 2008, Wenger et al. 2009).

It is often headwater streams that are piped (Elmore and Kaushal 2008, Meyer et al. 2005b, Roy et al. 2009). Headwater streams are more likely to be intermittent, resulting in weak to non-existent legal protection (Doyle and Bernhardt 2011).

Furthermore, the expense and safety considerations associated with piping small streams are less prohibitive than for larger streams. Piping headwater streams degrades these important sites of ecological activity and substantially impairs downstream water quality

(Doyle and Bernhardt 2011, Elmore and Kaushal 2008, Freeman 2007).

Ecological Studies Regarding Piped Streams

Piped streams are assumed to function solely as conduits for transport, devoid of ecosystem structure or processes (Doyle and Bernhardt 2011, Bencala 1993). However, very few studies exist that examine the ecology within piped streams. These studies suggest that piped streams negatively affect aquatic organisms as well as water quality

(Meyer et al. 2005b, Simmons et al. 2002, Krueger 1998, Davies et al. 2010).

Meyer et al. (2005b) reported reduced abundance and diversity of aquatic organisms below a 58 m piped stream reach in Georgia. In contrast to other streams in the area, the piped stream samples only contained one EPT taxa (indicative of high water quality). The majority of organisms sampled from the piped stream were aquatic worms

(indicative of low water quality).

3 Simmons et al. (2002) and Krueger (1998) also found degraded water quality resulting from piped streams. Pipes provided a substrate for the growth of biofilms containing fecal coliform bacteria, increasing downstream E. coli concentrations

(Simmons et al. 2002). Krueger (1998) reported that pipes prevented groundwater from diluting high pesticide levels in piped stream reaches.

Davies et al. (2010) found that streamwater ion concentrations increased when water was diverted through PVC and concrete pipes. The concrete pipe had the greatest effect, adding bicarbonate, calcium, and potassium to the water. The pipes in this study were brand new, and the effect of concrete pipes on stream water chemistry may become less significant as the pipes age.

Additional research is needed to characterize ecological structure and function within piped streams (Elmore and Kaushal 2008, Wenger et al. 2009). Piped streams present an opportunity to study principles of stream ecology at the extreme end of the spectrum. Therefore, characterizing ecological structure and function in piped streams may increase our understanding of these characteristics in urban and less disturbed streams. This research is essential to the facilitation of effective stream management and restoration (Wenger et al. 2009, Elmore and Kaushal 2008, Doyle and Bernhardt 2011,

Walsh et al. 2005b, Bernhardt and Palmer 2007).

Importance of Ecosystem Processes

This paper addresses ecological function, specifically ecosystem metabolism and nutrient spiraling, in a stream degraded by urban land use that includes piping.

4 Ecosystem metabolism describes the flow of energy/organic matter throughout the stream. Nutrient spiraling refers to the transformation, retention, and removal of nutrients as they are transported downstream.

Ecosystem metabolism and nutrient spiraling are critical functions that influence the ability of streams to be self-sustaining. If ecosystem processes are not addressed in degraded streams, restoration attempts may be futile (Palmer 2009). Furthermore, the levels of ecosystem metabolism and nutrient uptake in streams affect the health of downstream water bodies. If downstream reaches receive no organic matter to support their food webs, aquatic organisms such as fish may suffer. Reduced nutrient uptake in headwater streams contributes to elevated downstream concentrations which can lead to eutrophication (Freeman et al. 2007).

Despite the importance of ecosystem metabolism and nutrient spiraling to the health of streams, there has been limited research on these processes in urban and piped streams. Young et al. (2008) suggested that monitoring these processes might provide more information about stream health than assessing only biota, water chemistry, and channel characteristics. Assessing ecosystem metabolism and nutrient spiraling is an important step towards understanding and improving the ecological condition of urban and piped streams (Wenger et al. 2009, Palmer et al. 2004).

Ecosystem Metabolism

Ecosystem metabolism is the combination of gross primary production (GPP or P) and ecosystem respiration (ER or R). GPP occurs when algae and aquatic plants use

5 sunlight as energy to convert inorganic compounds into organic carbon and oxygen. This provides autochthonous organic matter inputs to the stream. Streams also receive allochthonous carbon inputs from terrestrial sources. ER refers to the consumption of organic carbon by all autotrophs and heterotrophs in the stream. Net ecosystem production (NEP) is the difference between GPP and ER, while P/R refers to the ratio of

GPP to ER.

The majority of ecosystem metabolism studies have been conducted on relatively undisturbed streams. GPP at these sites ranged from 1-3 g C>2/m2/d, and ER ranged from

2-7 g C>2/m2/d (Young et al. 2008, Mulholland et al. 2001, Bernot et al. 2010). Most of these streams had negative NEP, indicating that they were heterotrophic.

Land use disturbance leads to varied stream ecosystem metabolism responses

(Tank et al. 2010). GPP may increase (Bernot et al. 2010), stay the same (Houser et al.

2005, Meyer et al. 2005), or decline (Izagirre et al. 2008) depending upon how the disturbance affects the stream. Likewise, ER may be higher (Izagirre et al. 2008), similar

(Bernot et al. 2010, Meyer et al. 2005), or lower (Houser et al. 2005) in disturbed streams than in pristine streams.

The variable response of ecosystem metabolism to land use disturbance reflects the many influences on GPP and ER. Main factors include light, nutrients, benthic organic matter supply, substrate, hydrology, and temperature (Bernot et al. 2010, Roberts et al. 2007, Young et al. 2008, Tank et al. 2010). Many of these factors interact with each other, making it difficult to determine their individual effects on stream ecosystem metabolism (Wenger et al. 2009, Young et al. 2008, Bernot et al. 2010).

6 Urbanization bolsters anthropogenic control over the factors that influence stream ecosystem metabolism. For instance, the amount of light reaching the benthos of an urban stream may increase if the is mowed or decrease if the stream becomes turbid due to and organic matter loading (Izagiree et al. 2008, Young et al. 2008). The elevated nutrient concentrations in urban streams may enhance GPP and

ER rates (Bernot et al. 2010). However, flashy hydrology in urban streams may decrease ecosystem metabolism by reducing organic matter supply and scouring the benthos

(Walsh et al. 2005b, Roberts et al. 2007, Atkinson et al. 2008). The mechanisms by which urbanization controls stream ecosystem metabolism are complex and are not yet fully understood (Wenger et al. 2009).

No research has been done on ecosystem metabolism in piped streams. Piped streams have no light and thus should have little GPP regardless of other factors. This reduced GPP may decrease ER (Bernot et al. 2010). There may also be little ER in piped streams if their lack of channel complexity and increased flow velocity decrease organic matter and sediment retention (the fuel and habitat for heterotrophs). However, pipes do become clogged with debris. Additionally, biofilms may grow on pipes (Simmons et al.

2002). It is not certain whether ER in piped streams would be significantly less than in urban streams.

Nutrient Spiraling

As autotrophs and heterotrophs produce and consume organic matter within streams, nutrients are retained, transformed, and removed. Abiotic processes, such as adsorption and precipitation, can also slow the downstream transport of nutrients.

7 Nutrient spiraling refers to the cycling of nutrients from their inorganic form in the water column, to an organic or particulate form in the benthos, and then back to a dissolved inorganic form again. This cycle is stretched into a spiral due to the downstream movement of water (Stream Solute Workshop 1990).

The metrics used to describe nutrient spiraling include Sw, Vf, and U. Sw, or uptake length, refers to the distance the nutrient travels in its dissolved inorganic form before it is taken into the benthos. Sw depends strongly on velocity (as well as and stream size), so ecologists often standardize Sw for these factors by converting Sw to

Vf. Vf, or uptake velocity, represents the speed at which the nutrient moves into the stream bottom due to biological and chemical demand. U, or areal uptake, combines Vf and nutrient concentration to provide a measure of the amount of inorganic nutrient immobilized per unit of stream bottom per time unit (Stream Solute Workshop 1990,

Newbold et al. 1981, Allan and Castillo 2007).

Healthy streams with a high nutrient retention capacity are expected to have short nutrient uptake lengths, high uptake velocities, and high areal uptake rates (Grimm et al.

2005). These spiraling metrics have been measured for nutrients including dissolved organic carbon (DOC), nitrate (NO3), ammonium (NH4), and phosphorous/phosphate (P,

SRP, or PO4).

Reported DOC Vf values range from 0.5-15 mm/min, depending on the type of

DOC added to the stream (Johnson et al. 2009, McDowell 1985, Newbold et al. 2006,

Munn and Meyer 1990, Bernhardt and Likens 2002). Only 2 studies have used nutrient spiraling methods to measure labile DOC uptake in streams of varying land use types

8 including urbanization (Johnson et al. 2009, Newbold et al. 2006). Neither study found a relationship between human land use and DOC Vf.

NO3 Sw and Vf values are variable, reflecting the growing trend to include urban and high NO3 streams in studies (Tank et al. 2008). Hall et al. (2009) reported a NO3 Sw interquartile range of 70-10,000 m and a Vf interquartile range of 0.7-10 mm/min. NO3 uptake is often reduced in urban streams compared to unaltered streams (Grimm et al.

2005, Klocker et al. 2009).

NH4 uptake rates are usually faster than NO3 uptake rates. Ensign and Doyle

(2006) reported an interquartile range of 36-250 m for NH4 Sw and 2.2-10.4 mm/min for

NH4 Vf. Values within these ranges were also reported by Newbold et al. (2006) and

Roberts et al. (2007), although some disturbed streams in these studies had longer Sw and slower Vf. Additional studies indicate that NH4 uptake may be compromised in urban streams (Meyer et al. 2005, Newbold et al. 2006).

PO4 Sw values range from 32-530 m, while Vf values range from 0.9-6.0 mm/ min

(Ensign and Doyle 2006, Withers and Jarvie 2008). The few studies that assessed PO4 uptake in urban streams indicated that PO4 Vf may be slower in urban streams than in forested streams (Newbold et al. 2006, Meyer et al. 2005).

Several factors influence nutrient uptake in streams, including: hydrology, channel geomorphology, nutrient concentration, biological activity, land use, and other anthropogenic activities. As with ecosystem metabolism, urbanization increases anthropogenic control over these factors. Urban land use results in rapid water velocity, as well as loss of channel complexity (Grimm et al. 2005, Walsh et al. 2005b). Urban

9 streams often lack debris which are hot spots of nutrient uptake because the dams trap water, nutrients, and organic matter while providing a stable habitat for biological communities (Groffman et al. 2005, Bernhardt et al. 2005a). Urban streams are also incised and disconnected from their where additional nutrient processing occurs (Klocker et al. 2009, Kaushal et al. 2008). Furthermore, the elevated solute concentrations in urban streams may saturate or otherwise inhibit nutrient uptake by overwhelming or killing the streams' biological communities (Mulholland et al. 2002,

Grimm et al. 2005, Newbold et al. 2006, Paul and Meyer 2001).

Due to the diverse interacting factors that affect nutrient spiraling, additional research is needed to elucidate the most effective ways to mitigate reduced nutrient retention in urban streams (Wenger et al. 2009, Grimm et al. 2005, Walsh et al. 2005b).

There have been no studies regarding nutrient spiraling in piped streams. Assessing nutrient uptake in piped streams is critical to understanding nutrient retention in urban watersheds (Elmore and Kaushal 2008).

Piped streams lack channel complexity, riparian connection, organic matter, and . Thus, there may be little habitat or fuel to support a benthic community capable of significant nutrient uptake. The severe light limitation within piped streams means that any respiration and associated nutrient assimilation must occur through heterotrophs rather than autotrophs. This may reduce total nutrient uptake (Hall et al.

2009, Kent et al. 2005, Mulholland et al. 2006, Fellows et al. 2006, Hall and Tank 2003).

Whatever benthic community exists in piped streams may be subject to frequent disturbance and scour. Hydrology may be especially flashy in piped streams, and high

10 discharges may be more frequent as there is no opportunity for flooding. Repeated benthic disturbance may inhibit nutrient assimilation (D'Angelo and Webster 1991).

However, this impact may be offset since the pipe itself may provide a very stable surface for biofilm attachment and growth (Simmons et al. 2002).

Even at base flow, water velocity may be faster in piped streams. This provides less opportunity for nutrients to come in contact with any benthic assimilation sites

(Stream Solute Workshop 1990). Nutrient uptake may also be diminished if chemical water quality is degraded in piped streams. While there are many factors which may reduce nutrient uptake in piped streams, it is not clear to what extent nutrient uptake may differ between piped and other urban stream reaches. This study addresses this research gap-

Summary of Research Needs

Human population and development are expanding, resulting in the increased prevalence of urban areas (United Nations 2008). Urban land use degrades the ecological structure and function of streams (Paul and Meyer 2001, Walsh et al. 2005b). A common, extreme example of urban stream degradation occurs when streams are diverted into pipes running under roads, parking lots, buildings, and other surfaces (Elmore and

Kaushal 2008). Legislators and other resource managers face increasing pressure to allow additional stream piping during development (Doyle and Bernhardt 2011, Meyer et al. 2005b).

11 Empirical evidence regarding the impact of piping on stream ecosystem structure and function is needed to support the effective protection and management of streams in urbanizing areas (Wenger et al. 2009). In particular, questions remain about the essential stream processes of ecosystem metabolism and nutrient spiraling. These processes describe the cycling of energy and materials in streams, which becomes especially important in light of anthropogenic loading of carbon and nutrients to aquatic ecosystems

(Palmer et al. 2004, Steele et al. 2010).

It is not clear whether ecosystem function can be restored in urban and piped streams (Craig et al. 2008, Palmer 2009, Bernhardt and Palmer 2007, Bernhardt et al.

2005b, Booth 2005). However, over SI billion each year is spent on attempts to restore degraded streams in the United States (Bernhardt et al. 2005b). Each daylighting project

(where a piped stream is removed from its pipe and placed in an open channel) costs between thousands and millions of dollars (not including donated materials and time,

Pinkham 2000).

Restoration projects may achieve some goals (e.g. flood relief, habitat creation), but there is no research to support the idea that removing streams from pipes enhances ecosystem processes including metabolism and nutrient retention. Furthermore, there is no research that assesses these processes in piped streams. It is impossible to properly mitigate the degradation associated with stream piping when this degradation is unknown and unqualified.

In order to restore and maintain ecosystem services in urban and piped streams, it is first necessary to understand the fundamental processes that sustain them (Palmer et al.

12 2004). This study addresses the need for additional assessments of ecosystem metabolism and nutrient uptake in urban streams. It also addresses the nearly complete lack of research about ecology in piped streams. Characterizing ecosystem metabolism and nutrient spiraling in urban and piped streams helps to improve our comprehension of these processes in other aquatic environments.

Project Overview

The objective of this study was to investigate ecosystem processes in an urban, piped stream (Pettee Brook) flowing through the University of New Hampshire campus.

I measured ecosystem metabolism and nutrient cycling in 2 piped stream reaches, as well as nearby open upstream and downstream reaches. I also assessed related stream characteristics including light, chlorophyll a, organic matter, and substrate.

Research Questions

1. Do chemical and physical characteristics such as water quality, temperature, light,

and substrate vary between piped and open reaches in Pettee Brook?

2. What is the magnitude of ecosystem metabolism (GPP, ER, and NEP) in piped

reaches of Pettee Brook? How does this compare to open reaches in Pettee Brook

and in the literature?

3. Do the chlorophyll a and ash free dry mass (AFDM) of epilithon and fine benthic

organic matter (FBOM) differ between piped and open reaches in Pettee Brook?

13 4. What is the magnitude of DOC, NO3, NH4, and PO4 uptake in piped reaches in

Pettee Brook? How does this compare to open reaches in Pettee Brook and in the

literature?

5. Are there any correlations between ecosystem metabolism, nutrient uptake, and

other descriptive characteristics measured in this study?

Hypotheses

1. Ambient solute concentrations may be higher in the piped reaches of Pettee

Brook. Shade will be greater in the piped reaches, and temperature may be

reduced in these reaches. Piped reaches will exhibit diminished channel

complexity, and sediments may be less prevalent. Velocity will likely be faster in

piped reaches than in open stream reaches.

2. Ecosystem metabolism will vary between piped and open stream reaches. I

expect this outcome because the absence of light in piped reaches will limit GPP.

ER may also be reduced in piped streams due to low amounts of sediment and

organic matter.

3. The chlorophyll a and AFDM of epilithon will be reduced in piped stream

reaches. I expect this outcome due to the absence of light and autotrophs. The

chlorophyll a and AFDM of FBOM will also be reduced in piped stream reaches.

My reasoning is that there are no direct riparian inputs to piped streams, and any

FBOM transported from upstream may not be retained because of the high water

velocity and low channel complexity in piped stream reaches.

14 4. DOC uptake may differ between piped and open stream reaches. Abiotic DOC

adsorption in piped stream reaches may be limited by the amount of sediments

and organic matter. These characteristics may also inhibit the heterotrophic

respiration of added DOC in piped streams.

There will not be measurable NO3 uptake in any of the reaches. I expect

this result because these reaches are all impacted by urbanization and have high

NO3 concentrations. Furthermore, the study reaches are shorter than common

NO3 uptake lengths so it may not be possible to see downstream NO3 decline.

NH4 and PO4 uptake will vary between piped and open stream reaches.

Piped reaches will not have autotrophic nutrient assimilation, and heterotrophic

nutrient assimilation may be compromised by a lack of benthic organic matter in

piped streams. Abiotic adsorption of NH4 and PO4 may also be reduced if

sediments are not present in piped stream reaches. However, the pipe materials

(calcium from concrete and aluminum or iron oxides from metal) may aid NH4 or

PO4 removal. Reduced channel complexity in piped reaches leads to faster water

velocity than in nearby open reaches, so nutrients have less time to interact with

assimilation sites in piped streams. Overall, I expect that NH4 and PO4 uptake

will be less in piped stream reaches than in open reaches.

5. There may not be any clear correlations between factors assessed in this study.

This study is descriptive and may not have enough repetition to find strong

relationships between variables. Also, the interaction of stressors in urban

streams is complex and often obscures correlations even in more extensive

15 studies. However, I still test for relationships due to their potential to increase our

understanding of ecosystem processes in urban and piped streams.

16 CHAPTER II - METHODS

Study Site

This study was conducted in piped and open reaches of Pettee Brook, a first order stream flowing through the University of New Hampshire (Durham) campus. The mean annual temperature of this area is ~9.5°C, and the mean annual precipitation is -120 cm

(Prusevich et al. 2011). The watershed is 1.3 km2, of which 28.9 % is covered by impervious surfaces (e.g. road pavement, Lemay 2010). Of the 1475 m of Pettee Brook located within the UNH campus, 42% (615 m) disappears into pipes under parking lots, buildings, roads, and other surfaces. This percentage increases to 57% of Pettee Brook flowing through the campus center. Overall, 25% (735 m) of Pettee Brook's entire length flows underground through pipes (Lemay 2010, UNH ECD GIS 2009, personal measurements).

The remaining open reaches of Pettee Brook have narrow or non-existent riparian buffers. Vegetation includes grasses, white pine (Pinus strobus), red maple (Acer rubrum), black locust (Robinia pseudoacacia), glossy buckthorn (Rhamnas frangula), and oak (Quercus sp.). Stream banks are typically incised, unless they are reinforced with concrete or rip-rap. The resulting substrate is variable; some areas have large chunks of broken rock and asphalt, while other areas are covered with eroded sand.

Trash is common in the stream channel, and there are a few debris dams.

17 I selected Pettee Brook for this study because it contained piped reaches that were appropriate for the methodology as well as physically accessible. I chose the piped reaches based on length, lack of other connected pipes, and the fewest possible number of connected catch basins/outfalls. I was limited to piped stream reaches that I could walk through with minimal disturbance to the benthos. It was impossible to take samples within the piped reaches by floating tubing downstream and using a peristaltic pump to obtain water (the tubing often became trapped and tangled). Also, there were not enough manholes in the area to access piped streams from above ground.

The first piped stream reach (Pipe 1) was 200 m long and flowed through a 1.8 m

(diameter) concrete pipe under UNH's Whittemore Center Arena. This pipe was fairly new and unobstructed, as UNH installed it in 1995 (Lynch 2009, pers. comm.).

The open reach upstream of this pipe (Upstream 1) was 170 m long and flowed through a forested riparian area. Due to access constraints, it was the only open stream reach that was not adjacent to its piped reach. This reach was lost after one set of experiments due to construction that re-routed its upper portion into a new channel.

The open reach downstream of the concrete pipe (Downstream 1) was 69 m long, and it meandered through a narrow forested buffer bounded by asphalt walkways and buildings. Results from the adjacent Pipe 1 and Downstream 1 were sometimes compiled into Reach 1 (269 m long).

The second piped stream reach (Pipe 2) was 129 m long and flowed through a 1.8 m corrugated metal pipe under UNH's Stoke Hall parking lot and Garrison Ave. This pipe was installed by the Durham, NH Department of Public Works at least 50 years ago

18 (Lynch 2009, pers. comm..). The metal was somewhat corroded, with a black and brown sticky slime on it. The benthos in many areas was covered with sand, asphalt chunks, and trash.

The open reach directly upstream of this pipe (Upstream 2) was 110 m long. This channel was lined with large square stones, although these stones had eroded over time so that the channel was rocky and somewhat heterogeneous with trapped sediments. One side of the channel had a narrow forested buffer bounded by a walking path. The other side of the channel was separated from the parking lot by a strip of vegetation that was removed 1-2 times a year (usually fall and spring).

The open reach directly downstream of the metal pipe (Downstream 2) was 71 m long. It flowed through an incised channel bordered on one side by a wet, grassy riparian zone that was regularly mowed. The other side of the channel had a narrow buffer of shrubs/saplings along with a small apartment building and a road. Reach 2 consisted of

Upstream 2, Pipe 2, and Downstream 2 (310 m long).

Experiments were conducted during the growing season of2009 and 2010. The weather during experiments was dry and mostly sunny. Pettee Brook's wetted width during this study ranged from 0.29-2.33 m, and the channel depth was between 3-23 cm.

Discharge ranged from 2.1-18.71 L/s. Discharge between the top and bottom of each reach was consistent during the experiments.

19 Pettee Brook. Durham. NH

Upstream 1

Pipe 1 -3 (Concrete)

Downstream 1

Upstream * 2 ' Pipe 2 (Metal) Downstream 2

250 m

Figure 1. Diagram of study reaches in Pettee Brook, Durham, NH. Light gray represents open reaches and dark gray represents piped reaches. Station Location (m) N W Notes -400 43°08.651 70°56.370 Reach lost due to replacement -205 43°08.586 70°56.279

180 43°08.430 70°56.127 Beginning Reach 1, beginning Pipe 1 380 43°08.379 70°55.999 End Pipe 1, beginning Downstream 1 399 43°08.379 70°56.003 418 43°08.372 70°55.994 449 43°08.360 70°55.974 End Downstream 1, end Reach 1

750 43°08.321 70°55.826 Beginning Reach 2 765 43°08.310 70°55.820 Beginning Upstream 2 790 43°08.306 70°55.806 825 43°08.298 70°55.787 850 43°08.285 70°55.769 875 43°08.280 70°55.750 End Upstream 2, beginning Pipe 2 1004 43°08.226 70°55.691 End Pipe 2, beginning Downstream 2 1035 43°08.218 70°55.675 1058 43°08.208 70°55.664 1075 43°08.201 70°55.655 End Downstream 2, end Reach 2 Table 1. GPS coordinates for study reaches in Pettee Brook (accuracy ± 3m). Gray highlighting denotes piped reaches. The location (m) of study reaches refers to the distance from Gables Way (Durham, NH).

Stream Characterization

Evenly spaced transects (-25 m apart, see Table 1) were established along the open and piped reaches of Pettee Brook, resulting in 4-7 sampling stations per reach. I assessed the following stream characteristics at each station one time during the summer: in-stream habitat, sediment size, debris dams, benthic cover, condition, riparian vegetation, and canopy cover.

The habitat type at each transect (e.g. pool, , run) was noted. In order to characterize sediment size, I used a gravelometer to measure 10 randomly selected sediments from each transect. I measured the dimensions of all debris dams in the study reaches, and I recorded what materials comprised the debris dams. I visually assessed the

21 presence of benthic algae and organic matter at each transect, as well as the bank/pipe condition. I also measured bank dimensions and incision/undercutting in open reach transects. I identified riparian vegetation and used a concave densiometer to estimate percent canopy cover in open reaches. Piped reaches had no riparian vegetation, and canopy cover was recorded as 100%.

The average canopy cover for each reach was used to select the most representative spot in the reach to place an Onset HOBO Pendant datalogger, which measured light and air temperature at 5 minute intervals. I first attempted to attach the dataloggers to cement blocks so that they could be deployed on the benthos in each reach.

This resulted in the loss and burial of some of the dataloggers. Therefore, it was necessary to attach the dataloggers to a tree or piece of rebar approximately 0.5m above the reach (these also were lost occasionally, most likely due to anthropogenic maintenance near the channel). It was not possible to secure dataloggers inside the piped reaches. However, several walkthroughs indicated that the piped reaches were completely dark except for the ~25 m near their beginning and end.

Stream discharge was measured using a Marsh-McBirney Flo-Mate meter or a

SonTek FlowTracker, as well as a staging rod and measuring tape. I measured discharge during preliminary field work and the day before each ecosystem metabolism/nutrient uptake experiment. I also measured transect channel dimensions, such as wetted width and depth, at these times.

Water temperature, pH, specific conductivity, and dissolved oxygen were measured using multiparameter water quality sensors (YSI or Hydro lab depending on

22 equipment availability, but not both types during one set of experiments). I calibrated the meters according to their manuals by using standard solutions in the lab or water saturated air for DO and accounting for barometric pressure. During ecosystem metabolism/nutrient uptake experiments, I also calibrated the meters next to each other in the stream to assess differences in readings due to the equipment. I rechecked this calibration during and after the experiments to account for meter fouling and drift.

Ambient stream water chemistry was sampled several times in each open and piped study reach. I sampled within the few weeks before the ecosystem metabolism/ nutrient uptake experiments, as well as on the day of these experiments. I used acid- washed plastic syringes, filter holders, and 60 mL HDPE bottles. I rinsed the syringe 3 times with stream water before rinsing a filter holder that contained a pre-combusted 0.7

|im glass fiber filter (Whatman GF/F). Then I rinsed the 60 mL bottles 3 times with filtered stream water. I obtained three 60 mL samples from the of each study reach transect. Samples were frozen until analysis.

Water Chemistry Analyses

Stream water samples were analyzed for NH4 and PO4 using robotic automated colorimetry (Westco SmartChem). Anions (NO3, Br, CI, SO4), as well as cations (Ca,

Mg, Na, K), were analyzed using ion chromatography (Dionex ICS-1000). DOC and total dissolved nitrogen (TDN) concentrations were determined by high temperature catalytic oxidation (Shimadzu TOC-V). All analyses were conducted at the UNH Water

Quality Analysis Laboratory.

23 For some 2010 samples, it was not possible to use the ion chromatograph due to an equipment malfunction that may have been caused by an unknown compound in the urban stream water. Furthermore, the stream water's high CI concentrations made it difficult to detect Br using ion chromatography. I used an ion-selective electrode (Cole-

Parmer) to analyze these samples for Br, and I used the SmartChem to determine corresponding NO3 concentrations. To confirm that the change in analysis methodology did not affect results, I compared values for a subset of samples that were tested both by the ion chromatograph and the Br electrode/SmartChem.

When using the Br electrode, it was necessary to account for CI interference. I used the linear relationship between specific conductivity and CI in Pettee Brook to estimate the CI of samples that were not analyzed by ion chromatography. After determining the relationship between CI and electrode response, I used the estimated CI concentration of samples to find the electrode response due to CI. This allowed me to determine the electrode response due to Br. I calibrated the Br electrode before testing water samples, and I included quality control samples throughout analysis to check for drift.

Ecosystem Metabolism

Ecosystem metabolism was determined using the modified open channel method

(Marzolf et al. 1994, Bott 2007). This method involves measuring the diel change in dissolved oxygen (O2) at an upstream and a downstream station. This O2 change is corrected for reaeration (the exchange of O2 between the stream and the atmosphere) in

24 order to estimate the O2 change due to GPP and ER. I assessed ecosystem metabolism on

4 occasions for each of the upstream open, piped, and downstream open stream reaches.

Laboratory and field calibrated YSIs or Hydro labs were deployed at the top and bottom of the stream reaches. When possible, I used the same meter for two reaches (e.g. the downstream station of a piped reach and the upstream station of an adjacent open reach). Although this approach resulted in variable travel times between meters, it was necessary due to the availability of equipment. I secured the meters using rebar and/or chain, and care was taken to ensure that the probes were in an area of flowing rather than stagnant water. The meters collected water temperature, O2 concentration, and % O2 saturation (as well as pH and specific conductivity) data at 5-15 minute intervals for 2-5 days (depending on battery life and weather).

Ecosystem metabolism experiments were conducted at the same time as nutrient uptake experiments so that the same conservative tracer addition could be used to measure groundwater dilution within the reach. I used bromide (Br) as the conservative tracer because ambient chloride concentrations in Pettee Brook are too high to be safely and feasibly elevated. I used rhodamine dye to visually determine reach travel time. The accuracy of this visual estimation was confirmed for several reaches, as one of the

Hydrolabs had a rhodamine probe.

In order to measure reaeration in the open and piped reaches, I added sulfur hexafluoride (SF6) gas at the same time as the Br during the combined ecosystem metabolism/nutrient uptake experiments (Wanninkhof et al. 1990, Bott 2007). The SF6 was pumped into the stream at a steady rate using a battery powered peristaltic pump,

25 tubing, and a gas diffusing stone. It was not possible to determine the rate at which SF6 was added. It was assumed that SF6 reached a plateau in stream reaches after 2.5x the travel time determined by rhodamine.

Once SF6 reached plateau conditions, 6-8 water samples were taken at the top and bottom of each reach using acid washed 60 mL syringes with attached stopcocks. I waited for lx the reach travel time between the top and bottom samples so that I could sample the same parcel of water. To take the samples, I rinsed each syringe twice before completely filling it with stream water. I then expelled any air bubbles and placed the syringe back into the stream. After pushing the water out, I obtained a 45 mL sample while ensuring that no air entered the syringe. Syringes were placed on ice and returned to the lab once sampling was complete.

In the lab, I pulled 15 mL of air into each syringe and shook them for 10 minutes to equilibrate the headspace. I injected this headspace gas into evacuated 15 mL glass vials. Silicone was placed over the seals, and vials were stored for a few weeks until analysis by gas chromatograph (GC, Hewlett Packard 5890 Series II).

Several problems were encountered when using SF6 to measure reaeration. The bag of SF6, the tubing, and the connection to the gas diffusing stone tended to leak. If a good seal was obtained, the rate of the peristaltic pump tended to change due to the vacuum. Therefore, I constantly monitored the equipment setup to ensure its proper function. Even so, several samples contained too little SF6 to be detected by the GC. It is possible that all the SF6 escaped to the atmosphere during these experiments.

Alternatively, the discharge was low during failed SF6 experiments and maybe the SF6

26 never made it to the bottom of the reaches. Another problem was that our GC became inoperable during 2010, and it took several months to replace it and adjust its settings for

SF6. This delay meant that my samples may have been too old for successful analysis.

Since SF6 additions often failed, I used equations presented by Raymond et al. (in press) to calculate reaeration for all experiments. I used the set of experiments where both SF6-based and equation-based reaeration rates were available to test for significant differences between the two methods. Also, I compared metabolism metrics obtained using the two types of reaeration values. After finding the equations that provided the best fit for my data and resulted in no significant differences between SF6-based and equation-based values, I calculated ecosystem metabolism using equation-based reaeration rates when SF6-based rates were not available.

Ecosystem Metabolism Calculations

Ecosystem metabolism was calculated according to the procedures described by

Bott (2007) as well as Grace and Imberger (2006). Provided that O2 inputs from surface and groundwater are negligible, the equation for ecosystem metabolism is:

GPP-ER = AO2±E where E is the reaeration flux.

To determine the change in dissolved oxygen, I used the data that I obtained from the upstream and downstream 02 probes (YSIs or Hydrolabs) and transferred into

Microsoft Excel spreadsheets. I corrected this data to offset any differences between the probes during the calibration period, as well as any probe drift during the experiment.

27 Next, I offset the downstream data by the reach travel time so that the AO2 was calculated for the same parcel of water (e.g. if the reach travel time was 30 minutes, then the upstream 7 a.m. O2 concentration was compared to the downstream 7:30 a.m. O2 concentration). In addition to the AO2 for each time period, I also calculated the average stream water temperature. Equations follow:

AO2 (mg O2/L) = Downstream O2 Cone. - Upstream O2 Cone.

Avg. Stream Water Temp. (°C) = (Upstream Temp. + Downstream Temp.) / 2

The AO2 for each time period must be corrected for reaeration flux (E) to determine ecosystem metabolism (i.e. we are only interested in the AO2 due to the stream's biological processes, not due to the stream's absorption of O2 from the atmosphere). E is calculated as follows (Young and Huryn 1998):

E = (O2 deficitup + O2 deficitdn)/2 * &02 * TT where the average stream water O2 saturation deficit measured at the top and bottom of the reach is multiplied by the reaeration coefficient (&02) and the reach travel time (Tt).

The average O2 saturation deficit for each time period is found from the following equation (units mg O2/L):

Average O2 Deficit = ((Up. 100% Sat. Cone. - Up. Measured Cone.) + (Dn.

100% Sat. Cone. - Dn. Measured Cone.)) / 2

The average O2 deficit is positive when the stream is undersaturated, and negative when the stream is oversaturated. I used the probe values for O2 concentration and % saturation to calculate the 100% saturation O2 concentrations at the upstream and downstream stations.

28 In order to obtain the ko2 value, I used data from the SF6 additions when it was available. Values for &sf6 were calculated as follows:

*SF6 (1/min) = 1/Tt * In (([SF6]up * [Br]dn) / ([SF6;U * [Br]up)) where the brackets refer to the percentages of SF6 and Br at the top and bottom of the reach. The reaeration coefficient of SF6 is related to the reaeration coefficient of oxygen by the following equation:

koi (1/min) = ksvt, * 1.35 where the value of 1.35 refers to the ratio of the molecular masses. Because O2 is a smaller molecule than SF6, O2 diffuses at a faster rate.

When data from SF6 additions was not available, I calculated &02 after using the following equations (Raymond et al. in press, note their definition of ko2 as k2):

Eq. 3: k*oo = 1162 * S0'77 V0'85

4: kooo = (VS)0'76 * 951.5

6: k6oo = 929 * (VS)0'75 * Q0 01

7: ksoo = 4725 * (VS)0'86 * Q"0'14 * D° 66 where k6oo (m/day) is the reaeration rate normalized for depth and temperature. S (m/m) is slope found from Google Earth as well as USGS Topographic map elevations (NH

GRANIT). V (m/s) is stream velocity determined by rhodamine tracer (reach length/tracer travel time). Q (m3/s) is stream discharge (see nutrient uptake calculations below), and D (m) is mean stream depth:

D = Q/V*W where W is the measured average stream width (m).

29 To convert the mean k6oo to koi, I used the following formula rearranged from

Raymond et al. (in press):

koi= (k6oo/(((600/Sco2)4'5) * D)

2 3 where Sc02 = 1801 + -120.1 T + 3.782 T + -0.0476 T .

T (°C) is the average stream temperature during the 24 hour metabolism period, and SC02 is the Schmidt number which reflects the temperature dependency of reaeration

(Raymond et al. in press, Wanninkhof 1992).

In cases where stream water temperature (t°C) varied by more than 2-3 °C during the ecosystem metabolism experiment, it was necessary to adjust koi for each time period as follows:

£o2(t°C) = £o2(i°C) * 1 -024 (t°c 1 C) where t°C is the average temperature for each time period (equation shown previously) and i°C is the average temperature during the SF6 injection or T.

Once I calculated E for each sampling period, I subtracted it from the AO2 for each sampling period: the resulting value was the reaeration corrected A02 change per unit volume in one travel time. I multiplied this value by the ratio of sampling period time to reach travel time to get the reaeration corrected A02 change per unit volume in one sampling period. Summing these values for a 24 hour period provided the net daily metabolism (NDM, NEP, GPP-ER) volumetric rate. To convert this rate to an areal rate,

I multiplied by mean reach depth (D). Volumetric metabolism values could also be converted to metabolism rates per meter of stream length by multiplying by Q/V (i.e.

W*D, Roberts et al. 2007).

30 In order to differentiate between GPP and ER, I assessed net metabolism values at night. I defined night as the period when the HOBO dataloggers reported zero light

(these times coincided well with reported sunrise and sunset times). It is assumed that only ER occurs at night due to the lack of light. Therefore, I designated as ER any reaeration corrected AO2 change that occurred at night. In order to estimate ER during the day, I averaged the ER rates for the hour before dawn and the hour after dusk and multiplied this average rate by the number of daylight hours. This daylight ER, added to the night ER, provided the daily ER value. I calculated daily GPP by finding the difference between the sum of the reaeration corrected AO2 change occurring during the day and the daylight ER value.

Nutrient Uptake

Nutrient uptake in open and piped stream reaches was measured using short-term elevated solute additions of NO3, DOC, or combined NH4/PO4. The methodology involves the release of a known concentration of the nutrient in question, as well as a conservative tracer, to the stream reach. After the stream water reaches a plateau concentration, samples are taken to determine the longitudinal pattern (e.g. decline) of the nutrient in comparison to the tracer (Webster and Valett 2007, Stream Solute Workshop

1990).

Nutrient uptake in adjacent open and piped reaches was measured by adding solutes at the beginning of the most upstream reach (vs. at the beginning of each individual reach). This maximized the use of limited personnel, materials, and days that were appropriate for solute additions (i.e. days with neither rain nor anthropogenic

31 impacts). Since individual open and piped reaches were fairly short, the plateau nutrient concentrations were similar in the downstream direction (Appendix I).

I assessed NO3, DOC, and NH4/PO4 uptake on 1 occasion per nutrient per reach during summer conditions. I allowed several days between the different addition types to ensure that ambient concentrations returned to baseline and that the experiments did not affect each other. I also measured NH4/PO4 uptake once during the spring open canopy period to test whether increased light availability would impact my results.

The target nutrient concentration elevation for my experiments was 3-5x the ambient concentration. I sampled stream reaches for ambient nutrient concentration as close as possible to the dates of the experiments. The day before the addition, I measured discharge and wetted stream width. I used the ambient nutrient concentrations and discharge/velocity values to calculate the mass of NaNCb, KCH3CO2 (DOC as potassium acetate), NH4CI, or KH2PO4 to add to a 20-L acid-washed carboy. I also added NaBr and rhodamine dye (the conservative tracers) to the solution, and I calculated the release rates necessary to achieve the desired plateau concentrations in the stream reaches. The spreadsheets used for these calculations were obtained from the LINX protocol (Lotic

Interstate Nitrogen Experiment, Potter 2009, pers. comm.).

The day of the experiment, I sampled for ambient stream water solute concentrations at the previously established evenly spaced transects (3 replicates per station). 1 placed these samples on ice while I began the solute addition. I used a battery powered peristaltic pump and tubing to drip the addition solution into the stream at the

32 desired release rate. Using a graduated cylinder, I checked this release rate periodically during the addition to confirm that the rate remained steady. The release site was located at a riffle ~50m above the first sampling transect in order to ensure that the solution was well mixed into the stream.

To determine the travel time in each reach, I timed the downstream movement of the rhodamine dye. I waited for 2.5x the travel time for the stream to achieve plateau concentration at the most downstream sampling station: I later confirmed that this was sufficient using the rhodamine concentration data from the Hydrolab. Once the stream reaches reached their plateau concentrations, I sampled at all the transects again and placed these samples on ice. All samples were taken back to the laboratory and frozen until analysis.

Nutrient Uptake Calculations

Nutrient uptake values were calculated using the procedures described by Webster and Valett (2007). First, I used the data obtained from the conservative tracer release to calculate stream discharge during experiments. The equation follows:

== Q ((CR - CB) * QR) / (CP - CB) where CR is the Br concentration of the release solution, CB is the ambient (background)

Br concentration, CP is the plateau Br concentration, and QR is the release rate of the solution. I compared the resulting Q values to those I obtained from field measurements.

I also plotted the calculated Q for each sampling station against distance and determined whether groundwater/ subsurface dilution was less than 10% from the top to the bottom of the reach. Ideally, dilution within the reach should be minimal so that the experiment

33 is not affected by the groundwater concentration which often varies from the stream water concentration.

To calculate Sw (nutrient uptake length), I corrected the plateau sample concentrations for each sampling station by subtracting the corresponding ambient concentrations. Then I divided the corrected nutrient concentration at each site by the corrected Br concentration to obtain normalized nutrient concentrations (CN):

Cn = (Nutrient Cp - Nutrient Cb) / (Br Cp - Br Cb).

I graphed the regression of In (CN) vs. the distance of the sample (meters) to produce a line with the slope kw and the standard error kw SE. Kw, the distance specific uptake rate, is an estimate of the stream reach's longitudinal nutrient uptake rate per unit distance.

Kw values were considered significant when p < 0.05, except for one set of additions when the cutoff was raised to p < 0.1. This higher cutoff is considered reasonable in urban streams, as variable ambient nutrient concentrations and other factors make it more difficult to measure nutrient uptake (Meyer et al. 2005, Potter 2009, personal communication). Only significant kw values were reported and used in statistical analyses (except for in Appendix 1). This decision was based on the idea that although nutrient uptake may not statistically detectable using the method, this uptake may not be zero or any other arbitrary number.

Kw is related to Sw (m) by the following equation:

Sw = -l/kw.

Because Sw is influenced by discharge and velocity, as well as concentration, I also calculated the related spiraling metrics Vf (mm/min) and U (ug/m2/min or mg/m2/min):

34 Vf= VD/Sw - (Q/W) / Sw

U = Vf * Nutrient Cb.

These equations were presented by the Stream Solute Workshop (1990), with additional information available from Webster and Valett (2007).

Chlorophyll a and Ash Free Dry Mass of Epilithon and Benthic Organic Matter

Chlorophyll a density and ash free dry mass (AFDM) are measures of the biomass of the stream's benthic community. Thus, these measures provide information about the organisms responsible for ecosystem metabolism and nutrient uptake. Chlorophyll a is the most abundant pigment found in plants, and chlorophyll a density indicates the importance of algae and other primary producers to the stream ecosystem. AFDM includes autotrophs, heterotrophs, and other organic material found in the bio film attached to benthic substrates. Chlorophyll a density and AFDM often exhibit a positive correlation with light, nutrients, and stream productivity. Other factors may also be important, including substrate type and velocity (Steinman et al. 2007, Fellows et al. 2006).

Samples for chlorophyll a density and AFDM analysis were obtained from the 2 main benthic substrates found in the open and piped reaches of Pettee Brook: rocks

(epilithon) and sediments (benthic organic matter). I sampled these substrates at 3 transects in each open and piped reach. Samples were not taken from the materials comprising the pipes themselves. The concrete pipe had very little visible biofilm, and benthos of the metal pipe was covered with sediment for the majority of its length. It was

35 also necessary to minimize sampling time within the piped reaches due to safety concerns.

To sample epilithon at each station, I placed 3-5 rocks into a plastic container with a known surface area. I repeated this procedure at all stations within the reach.

Next, I used a wire brush to scrape the tops of the rocks (thoroughly cleaning the wire brush with distilled water in between rocks from different stations). I created a slurry from each station by using a small amount of distilled water to wash the scraped biofilm from the rocks. After I measured the volume of each slurry, I filtered known amounts through pre-combusted glass fiber filters. Three filters from each station were folded in half, wrapped in tin foil, and frozen for chlorophyll a analysis. One pre-weighed filter was placed in its tin for AFDM analysis (Steinman et al. 2007).

To sample benthic organic matter at each station, I inserted a plastic bucket

(bottom removed) into the . I measured the water depth at 3 points within the bucket, and then I swirled the water within the bucket to suspend the surface sediments. I sampled this suspension using an acid-washed plastic container. I repeated this procedure at all stations within the reach. After measuring the volume of each sample, I filtered a known amount through pre-combusted glass fiber filters. One filter was frozen for chlorophyll a analysis as above. A second, pre-weighed filter was placed in its tin for

AFDM analysis (Steinman et al. 2007).

Chlorophyll a filters were analyzed within a few weeks of freezing. I used the hot ethanol extraction method (Sartory and Grobbelaar 1984). Working in the dark, I used tweezers to open each filter and place it in a washed and ashed glass test tube. Then I

36 added 10 mL of 95% ethanol to each tube, making sure to cover the filter. I loosely capped the tubes and placed them into a pre-heated, 79°C water bath for 5 minutes. Upon removing the tubes, I swirled their contents. I placed the tubes into a covered cardboard box where they were allowed to cool for 24 hours. The tube contents settled during this time.

A spectrophotometer (Thermo Scientific GENESYS 10) was used to analyze the extracted chlorophyll a. Throughout the analysis, I calibrated the spectrophotometer using a 1 cm glass cuvette filled with 3 mL of 95% ethanol. Another 1 cm glass cuvette was used for samples (rinsed with 95% ethanol in between samples). I pipetted 3 mL extract from the test tube into the cuvette and obtained readings at 750 and 665 nm.

Next, I added 0.03 mL hydrochloric acid (HC1) to the cuvette. After gently agitating the cuvette and waiting for 90 seconds, I took another set of readings at 750 and 665 nm

(Steinman et al. 2007).

To determine AFDM, I dried the pre-weighed filters in a 105°C oven for at least

24 hours. After the filters cooled to room temperature, I weighed them to find dry mass.

I checked to ensure that the filter tins were etched with their sample ids. Then I ashed the filters at 450°C for 6 hours, cooled them in the muffle furnace, and reweighed them to determine ash free dry mass (Steinman et al. 2007).

Chlorophyll a and Ash Free Dry Mass Calculations

The calculation of chlorophyll a density requires that absorbance values first be corrected for turbidity and color in the sample. I determined this correction by

37 subtracting each reading at 750 nm from the corresponding reading at 665 nm. I used the resulting values in the following equation:

2 Chi a (mg/m ) = 28.78 (665b - 665a) * VCxt / (A * 1)

where 665b is the corrected reading before the acid addition, 665a is the corrected reading after the acid addition, Vcxt is the volume of 95% ethanol used in the extraction (L), A is the benthic sampling area represented by the extracted filter (m2), and 1 is the path length of the cuvette (cm).

The use of data before and after the acid addition corrects the chlorophyll a value for pheophytin. Pheophytin, a degradation product of chlorophyll a, occurs when algal cells die or when detritus is present in the sample. I calculated pheophytin as follows:

2 Pheophytin (mg/m ) = 28.78 ((1,72*665a) - 665b) * Vcxt / (A*l).

Coefficients given in these equations represent absorbance corrections derived from

Sartory and Grobbelaar (1984). Additional information regarding chlorophyll a and pheophytin calculations can be found in Steinman et al. (2007).

In order to calculate the dry mass (DM) and AFDM of samples, I used the following equations:

2 DM (mg/cm ) = (Wd - Wf) / A

2 AFDM (mg/cm ) = ((Wd- Wf) - (W, - Wf)) / A

where Wd is the weight of the filter after drying, Wf is the weight of the filter, Wa is the weight of the filter after ashing, and A is the benthic sampling area represented by the filter (Steinman et al. 2007).

38 Statistical Analyses

Descriptive statistics, as well as linear regressions for nutrient uptake, were computed using Microsoft Excel. After log transforming non-normal data, I used analysis of variance (ANOVA, SPSS 19) to examine whether there were significant differences between open and piped stream reaches. Variables tested included stream characteristics such as substrate and light, ecosystem metabolism rates, nutrient uptake rates, chlorophyll a, and AFDM. Differences between open and piped stream reaches were considered significant at p < 0.05.

Regression analysis, along with Pearson correlation, was used to investigate whether there were relationships between measured hydrological, physical, and chemical variables and ecosystem processes. For example, I tested whether there was any correlation between light, ambient nutrient concentration, discharge, or benthic characteristics and ecosystem metabolism or nutrient uptake rates. I pooled data from all study reaches for this analysis. I considered correlations to be significant at p < 0.05, with higher r values indicating better relationships between the data in my study.

39 CHAPTER III - RESULTS

Chemical and Physical Parameters

Samples for ambient concentrations were obtained just before all solute additions

(Table 2), as well as on 4 additional dates. There were no significant differences in ambient solute concentrations between the open and piped stream reaches (Figures 2, 3).

Ambient solute concentrations were significantly higher (p < 0.05) in summer than in spring, with the exception of dissolved organic carbon (DOC) and nitrate (NO3).

275 250 • OPEN (Summer) 225 • PIPED (Summer) 200 • OPEN (Spring) 175 150 • PIPED (Spring) cuo E 125 100

a 75 a2 z 50 b, b 2 "2 a 25 a,3 a 3 4 b,3 b"3 b4 b4 0 CI Na Ca Mg K

Figure 2. Average ambient solute concentrations in open and piped reaches of Pettee Brook (April through September of 2009 as well as 2010). Letters denote values that are significantly different at p < 0.05.

40 12 • OPEN (Summer) 120 3 • PIPED (Summer) 10 • OPEN (Spring) 100 Z a || • piped (Spring) a g 8 • 80 £ ;V 6 T t { 60 ^

n..kDOC N03 NH4 P04

Figure 3. Ambient nutrient concentrations in open and piped reaches of Pettee Brook (April through September of 2009 as well as 2010). Letters denote values that are significantly different at p < 0.05.

Stream water pH and specific conductivity values were obtained from meter readings for the time periods when ambient solute concentration samples were taken.

Average pH, at 7.22 ± 0.06, did not vary between open and piped stream reaches.

Average specific conductivity, at 798 ± 368 (iS/cm, was not significantly different between open and piped stream reaches. However, specific conductivity was significantly higher (p < 0.05) in summer at 1018 ± 71 jiS/cm than in spring at 457 ± 135

US/cm.

The average daily concentration of dissolved oxygen (O2) was measured during all metabolism/nutrient uptake experiments. There were no significant differences between open and piped stream reaches. However, average daily O2 concentrations were

41 significantly lower (p < 0.05) in the summer at 7.56 ± 0.22 mg/L than in spring at 9.66 ±

0.33 mg/L (Table 3).

Average daily stream water temperatures, as measured during all metabolism/ nutrient uptake experiments, were not significantly different between open and piped stream reaches. However, these temperatures were significantly warmer (p < 0.01) in summer at 18.84 ± 0.42°C than in spring at 12.74 ± 1.88°C (Table 3).

Light was measured during all metabolism/nutrient uptake experiments and was reported as daily PAR (mol quanta/m2/d). Light was significantly higher in open reaches than in piped reaches (p <0.01, Figure 4). Also, light was significantly higher in spring than in summer when the canopy cover was fully developed (Figure 4, Table 3).

600 500

< *| 400 = | 300 n j o O- o 200 E a 100 -t-

OPEN PIPED OPEN PIPED (Summer) (Summer) (Spring) (Spring)

Figure 4. Daily PAR in open and piped reaches of Pettee Brook. Letters denote values that are significantly different (p < 0.01).

42 Reach Reach Solute(s) Addition Metabolism Ambient NH4 Ambient P04 Ambient N03 Ambient DOC Name Type Added Date Date(s) (ug N/L) (ug P/L) (mg N/L) (mg C/L)

Pipe 1 Piped NH4/PO4 8/18/2009 8/18/2009 78.13 4.55 0.53 5.91

Downstream 1 Open NH4/PO4 8/18/2009 8/18/2009 61.33 5.98 0.53 5.85

Upstream 2 Open NH4/PO4 8/14/2009 8/20/2009 28.62 15.96 0.41 5.83

Pipe 2 Piped NH4/PO4 8/14/2009 8/20/2009 29.88 10.52 0.47 5.96

Downstream 2 Open NH4/PO4 8/14/2009 ND 34.71 12.01 0.48 5.65

Pipe 1 Piped NH4/PO4 5/5/2010 5/6/2010 100.03 14.22 0.30 5.34

Downstream 1 Open NH4/PO4 5/5/2010 5/6/2010 80.19 10.50 0.31 5.22

Upstream 2 Open NH4/PO4 4/30/2010 4/30/2010 32.39 7.87 0.21 4.64

Pipe 2 Piped NH4/PO4 4/30/2010 4/30/2010 28.11 7.52 0.21 5.41

Downstream 2 Open NH4/PO4 4/30/2010 4/30, 5/1/2010 37.19 7.73 0.22 4.87

Pipe 1 Piped NO3 8/10/2010 8/11, 8/12/2010 60.22 52.12 0.46 5.44

Downstream 1 Open N03 8/10/2010 8/11, 8/12/2010 52.64 48.31 0.54 5.13

Upstream 2 Open N03 8/4/2010 8/7, 8/8/2010 88.25 19.77 0.81 8.29

Pipe 2 Piped NO3 8/4/2010 8/7, 8/8/2010 107.88 41.44 0.76 8.22

Downstream 2 Open NO3 8/4/2010 8/7, 8/8/2010 125.23 35.79 0.77 8.20

Pipe 1 Piped DOC 9/11/2010 9/11, 9/12/2010 188.72 41.59 0.78 4.00 Downstream 1 Open DOC 9/11/2010 9/11, 9/12/2010 149.22 51.70 0.83 3.92 Upstream 2 Open DOC 8/30/2010 8/29/2010 ND ND 0.95 2.45 Pipe 2 Piped DOC 8/30/2010 8/29/2010 ND ND 0.99 2.61 Downstream 2 Open DOC 8/30/2010 ND ND ND 0.96 2.61 Table 2. Stream chemistry during assessments of nutrient uptake and ecosystem metabolism. Reach Date(s) Q Velocity Width Depth 02 H20 Temp. Daily PAR Reaeration Stand. Reaeration 2 Name (L/s) (m/s) (m) (m) (mg/L) °C (mol quanta/m /d) (*02, 1/min) (kfioo.m/d) Pipe 1 8/18/2009 4.04 0.10 1.40 0.03 6.08 21.45 0 0.0165 0.73 Downstream 1 8/18/2009 4.17 0.06 1.40 0.05 7.15 21.55 60 0.0249 1.50 Upstream 2 8/14, 8/20/2009 12.16 0.14 1.04 0.08 7.26 21.78 75 0.0635 5.86 Pipe 2 8/14, 8/20/2009 12.13 0.10 1.04 0.11 6.33 21.71 0 0.0112 1.07 Downstream 2 8/14/2009 13.12 0.08 1.87 0.09 ND ND 75 0.0203 3.03

Pipe 1 5/5, 5/6/2010 8.93 0.13 1.10 0.06 9.02 15.45 0 0.0100 0.95 Downstream 1 5/5, 5/6/2010 10.19 0.05 2.33 0.10 9.40 15.00 315 0.0090 1.39 Upstream 2 4/30/2010 18.71 0.14 0.97 0.14 10.01 11.14 551 0.0258 6.24 Pipe 2 4/30/2010 17.59 0.12 1.45 0.10 10.76 11.01 0 0.0070 1.21 Downstream 2 4/30, 5/1/2010 18.06 0.12 2.03 0.08 9.09 11.92 506 0.0310 4.13

Pipe 1 8/10-8/12/2010 2.51 0.09 0.60 0.05 7.06 18.49 0 0.0100 0.71 Downstream 1 8/10-8/12/2010 3.04 0.02 1.85 0.07 7.00 18.68 201 0.0070 0.66 Upstream 2 8/4, 8/7, 8/8/2010 3.27 0.05 0.29 0.23 8.21 19.34 130 0.0100 3.28 Pipe 2 8/4, 8/7, 8/8/2010 3.37 0.04 0.51 0.18 8.35 19.23 0 0.0020 0.59 Downstream 2 8/4, 8/7, 8/8/2010 3.58 0.03 0.84 0.13 8.32 19.18 87 0.0090 1.55

Pipe 1 9/11,9/12/2010 2.20 0.05 0.54 0.09 8.17 15.72 0 0.0020 0.48 Downstream 1 9/11,9/12/2010 2.10 0.01 1.30 0.14 8.17 15.94 33 0.0020 0.43 Upstream 2 8/29, 8/30/2010 5.17 0.05 0.43 0.23 8.03 19.48 167 0.0100 3.21 Pipe 2 8/29, 8/30/2010 3.38 0.05 0.39 0.18 8.16 19.44 0 0.0030 0.70 Downstream 2 8/30/2010 3.44 0.03 0.90 0.11 ND ND 167 ND ND Table 3. Stream characteristics during assessments of nutrient uptake and ecosystem metabolism. Benthic sediments were measured once during the summer. Whereas open stream reaches had sediments covering 100% of reach length, sediments were present for only

31-76% of piped reaches' length. Sediment size (average D50 = 15.85 mm) was not significantly different between open and piped reaches. However, average sediment depth was significantly lower (p < 0.01) in piped reaches at 2.58 ± 1.09 cm than in open reaches at 12.10 ± 2.30 cm.

Debris dams were also measured once during the summer. No debris dams were present in piped stream reaches, while open reaches had an average of 1.40 ± 0.07 debris dams per 100 m. The average surface area of the debris dams in open reaches was 1.06 ±

0.44 m2. The debris dams were composed of different sizes of wood, leaves, and varied trash including food/ beverage packaging and sporting equipment. Although formal assessment of debris dams was only conducted once, the debris dams were noted to be present during all summer solute additions. However, their average surface area may have changed, especially after high discharge events.

Stream velocity, as measured during all solute additions, was significantly different between open and piped reaches during the summer only (p < 0.05). The average summer velocity in piped reaches was faster at 0.07 ± 0.01 m/s, while velocity in open reaches was 0.04 ± 0.01 m/s. The average spring velocity was 0.11 ±0.1 m/s for both reach types (Table 3).

Stream discharge during solute additions was not significantly different between open and piped stream reaches. Summer discharge, at 5.18 ± 1.71 L/s, was significantly less (p < 0.05) than spring discharge at 14.70 ± 2.11 L/s. No significant differences in

45 channel width or depth were found between open and piped stream reaches or between seasons (Table 3).

Reaeration

Reaeration values (&02) calculated from equations found in Raymond et al. (in press) corresponded well with reaeration values derived from SFg additions (Figure 5).

Equations 3, 4, 6, and 7 provided the best fit between calculated and measured reaeration coefficients. Therefore, these equations were used to calculate reaeration when SF6- derived values were not available. There were no significant differences between reaeration or metabolism values (GPP, ER, NEP) obtained using the two methods.

0.06 y = 0.8712x - 0.0005 0.05 r2 = 0.99 p < 0.01 E _ O i/t £ is 0.04 o 3 ai a m -c •4 •5 ^ 0.03 A6 h I o; c -O 0.02 E o ri I .. <0 0.01 cc

0.00 0.02 0.04 0.06 0.08

k02 (1/min) measured by SF6 addition

Figure 5. Relationship between reaeration rates derived from SF6 additions and equations 3,4,6,7 found in Raymond et al. (in press), note their definition of ko2 as IC2).

46 SF6 additions were successful for all reaches during summer 2009. Spring and summer 2010 SF6 additions failed. Since velocity, depth, and discharge were not significantly different between 2009 and 2010 (slope was the same for both years), the calculated reaeration values for 2010 were assumed to be valid as evidenced by the 2009 comparison. There were no significant differences in k6oo values between 2009 and 2010

(Table 3).

Reaeration (&02) was higher in open stream reaches (0.019 ± 0.005, 1/min) than in piped reaches (0.008 ± 0.002, 1/min), but this difference was not significant.

Standardized reaeration rates (k6oo, m/d) were also higher in open reaches than in piped reaches, with this difference being significant in summer only (p < 0.05, Figure 6).

OPEN P PED OPEN P PED (Summer) (Summer) Spring) (Spring)

Figure 6. Standardized reaeration rates (k6oo) for open and piped reaches of Pettee Brook. Letters denote values that are significantly different (p < 0.05).

Ecosystem Metabolism

Gross primary production (GPP) measured in open stream reaches was significantly higher than in piped reaches (p < 0.05). Whereas piped stream reaches'

47 GPP was negligible during all seasons at -0.01 ± 0.05 g C^/W/d, open reaches' GPP was

0.53 ± 0.04 g C>2/m2/d in the summer and 5.74 ± 1.16 g CVmVd in the spring (Figure 7).

Ecosystem respiration (ER) was also higher in open stream reaches than in piped reaches (Figure 8), but this difference was not significant during summer or spring.

Likewise, there was no significant difference in net ecosystem production (NEP) between open and piped stream reaches during summer or spring (Figure 9). NEP was negative in all reaches, except during the spring in open reaches. Therefore, the piped stream reaches were always heterotrophic and the open reaches were likely to be heterotrophic in the summer and autotrophic in the spring. This trend was confirmed by looking at the ratio of production to respiration (P/R, Figure 10). Open reaches had significantly higher P/R ratios than piped reaches in spring only (p < 0.01).

8 7 GPP

5 6

° 3 w> >y £ 1 a b b w r—1 0 1 1 -1 OPEN PIPED OPEN PIPED (Summer) (Summer) (Spring) (Spring)

Figure 7. Average GPP in open and piped reaches of Pettee Brook, in units of O2 produced per m2 of stream benthos per day. Letters denote values that are significantly different (at p < 0.05).

48 9 8 ER 7 6 5 fM O 4 «ss 3 cc 2 1 0 n i OPEN PIPED OPEN PIPED (Summer) (Summer) (Spring) (Spring)

Figure 8. Average ER in open and piped reaches of Pettee Brook, in units of O2 consumed per m of stream benthos per day.

5 1 NEP fM

Q. UJ , Z _3 -4 OPEN PIPED OPEN PIPED (Summer) (Summer) (Spring) (Spring)

Figure 9. Average NEP in open and piped reaches of Pettee Brook. Line at zero represents the transition between autotrophy (above zero; net O2 production) and heterotrophy (below zero; net O2 consumption).

49 a 3 P/R

2

1 b 1 0 1 1 - .... —- OPEN PIPED OPEN PIPED (Summer) (Summer) (Spring) (Spring)

Figure 10. Average P/R ratios in open and piped reaches of Pettee Brook. Letters denote values that are significantly different (at p < 0.01). When P/R exceeds 1, the stream reach has net O2 production and is autotrophic.

During both spring and summer, P/R was positively correlated with light (PAR, log-log, r = 0.79, r2 - 0.62, p < 0.01). GPP was also positively correlated with light (log- log, r = 0.76, r2 = 0.57, p < 0.01). A weaker positive correlation between ER and light was significant during summer only (log-log, r = 0.59, r2 = 0.35, p < 0.05).

No metabolism metrics (GPP, ER, NEP, P/R) were significantly correlated to stream temperature, discharge, specific conductivity, or ambient nutrient concentration

(DOC, no3, nh4, po4). Additionally, metabolism metrics were not correlated with sediment depth or percent reach covered by sediment.

Benthic Ash Free Dry Mass and Pigment Biomass

Benthic ash free dry mass (AFDM) and pigment biomass (chlorophyll a and pheophytin) were measured once during the summer. Measurements were conducted on

50 surface fine benthic organic matter (FBOM) and epilithon, as preliminary investigation indicated that these were the main biomass compartments on the stream benthos (coarse benthic organic matter was also present, but it was less common and not sampled).

There was significantly more surface FBOM and epilithon in open stream reaches than in piped reaches (p < 0.05, Figure 11). Both FBOM and epilithon samples had higher chlorophyll a levels in open reaches than in piped reaches (p < 0 05, Figure 12).

30 • Surface FBOM 25 • Epilithon E 20 60 5 15 o u. < 10

5

•f" 0 OPEN PIPED

Figure 11. Ash free dry mass of surface FBOM and epilithon in open and piped reaches of Pettee Brook. Letters denote values that are significantly different (p < 0.05).

51 20 • FBOM Chi a

• FBOM Pheop g> 15 • Epilithon Chi a V)m to • Epilithon Pheop £ 10 o 2 +•» c

OPEN PIPED

Figure 12. Chlorophyll a and pheophytin biomass of surface FBOM and epilithon in open and piped reaches of Pettee Brook. Letters denote values that are significantly different (p < 0.05).

FBOM chlorophyll a was significantly correlated to FBOM AFDM (r = 0.89, r2 =

0.80, p < 0.05). There were no other significant correlations found between FBOM characteristics and light, stream discharge, water temperature, ambient nutrient concentration, or metabolism metrics.

Epilithon chlorophyll a (log scale) was positively correlated with light (PAR, r =

0.89, r2 = 0.79, p < 0.05), as well as with GPP (r = 0.95, r2 = 0.90, p < 0.05) and ER (r

= 0.92, r2 = 0.84, p < 0.05). Epilithon chlorophyll a and epilithon pheophytin were positively correlated (log-log, r = 0.97, r2 = 0.95, p < 0.01), although epilithon pheophytin was not correlated to light. Epilithon pheophytin (log scale) was positively correlated to

GPP (r = 0.95, r2 = 0.90, p < 0.05) and ER (r = 0.89, r2 = 0.80, p < 0.01).

52 Epilithon AFDM was positively correlated with P/R (r = 0.95, r2 = 0.91, p < 0.05).

There were no other significant correlations found between epilithon characteristics and stream discharge, water temperature, or ambient nutrient concentrations.

Dissolved Organic Carbon (DOO Uptake

Statistically significant (p < 0.05) DOC uptake was detected in 2 of 3 open stream reaches and 2 of 2 piped stream reaches (Appendix Table 8). Due to increasing Q in the downstream direction of Pettee Brook, uptake velocity (vf) and areal uptake (U) were used when comparing nutrient uptake in open and piped stream reaches. DOC Vf was higher in open reaches (1.12 ± 0.44 mm/min) than in piped reaches (0.63 ± 0.22 mm/ min), but this difference was not significant (Figure 13). DOC U was also higher in open reaches (3.09 ± 1.07 mg/m2/min) than in piped reaches (1.73 ± 0.52 mg/m2/min), although this difference also failed to be significant (Figure 13).

53 4.5

c 4.0 I 3.5 IN ,E oo 3.0 E 2.5 2.0 c I 1.5 *E E 1.0 0.5 0.0 OPEN V, PIPED V, OPEN U PIPED U

Figure 13. DOC uptake velocity (vf, mm/min) and areal uptake (U, mg/m /min) in open and piped reaches of Pettee Brook (summer addition).

Nitrate (NCh) Uptake

Nitrate uptake was not detected in any of the open or piped stream reaches

(summer addition, Appendix I). Linear regressions used to find the distance specific uptake rate (kw) never produced negative slopes, resulting in infinitely long uptake rates

(Sw) and undetectable Vfand U.

54 Ammonium (NHa) Uptake

Summer NH4 uptake was detected in 1 of 3 open reaches and 1 of 2 piped reaches

(Appendix I). Linear regressions used to find NH4 uptake were considered statistically significant at p < 0.1 for this set of additions only. This is acceptable for urban streams where nutrient uptake is often difficult to detect (see Methods). At p < 0.05, NH4 uptake was not detectable in open reaches. At p < 0.1, NH4 Vf was significantly lower (p < 0.05) in the open reach (0.13 ± 0.04 mm/min) than the piped reach (0.24 ± 0.06 mm/min). nh4

U was also lower in the open reach (4.41 ±1.27 ug/m2/min) than in the piped reach (18.17

±4.49 ug/m2/min, Figure 14).

2.50 25 bi 2.25 2.00 20 1.75 Ic 1.50 1.1 1.25 *£ go E 1.00 10 3 0.75 0.50 5 a 0.25 0.00 r*-i 0

OPEN Vf PIPED V, OPENU PIPED U

Figure 14. Summer NH4 uptake velocity (vf, mm/min) and areal uptake (U, ug/m2/min) in open and piped reaches of Pettee Brook. Letters denote values that are significantly different (p < 0.05).

55 NH4 uptake was also measured in spring, with uptake detected in 1 of 3 open reaches and 1 of 2 piped reaches (Appendix I). NH4 Vf was higher in the open reach (3.74

± 0.35 mm/min) than in the piped reach (2.91 ± 0.77 mm/min), but this difference was

2 not significant. NH4 U was also higher in the open reach (109.51 ± 11.34 ug/m /min) than in the piped reach (91.10 ± 24.06 ug/m2/min), although this difference also was not significant (Figure 15).

14 140

12 120

10 100 c I E 8 80 E E E 6 60 003 4 40 3

2 20

0 i 0 OPEN V, PIPED V, OPEN U PIPED U

Figure 15. Spring NH4 uptake velocity (vf, mm/min) and areal uptake (U, ug/m2/min) in open and piped reaches of Pettee Brook.

NH4 Vf and U were significantly higher (p <0.01) in spring than in summer. NH4

Vf in open stream reaches was 30x higher in spring than summer, whereas NH4 Vf in piped reaches was 12x higher in spring. Open reach NH4 U was 25x higher in spring than in summer, and piped reach NH4 U was 5x higher in spring. Therefore, the spring increase in NH4 uptake was 2-5x more in open reaches than in piped reaches.

56 Nitrification. For all nh4 additions, I plotted the background corrected nh4-N and no3-N flux at each sampling station vs. the distance from the addition site.

Nitrification was determined to have occurred when graphs showed a decline in nh4 that was accompanied by a clear increase in no3. The only graph that evidenced nitrification was for the piped reach that had summer nh4 uptake. The graph suggested that the majority of nh4 uptake in this reach was due to nitrification, as the slope of the lines indicated that no3 was produced at least as fast as nh4 declined (Figure 16). The percentage of added NH4 that was nitrified appeared to be > 100%, which is not possible and was attributed to addition-induced remineralization of organic N forms (e.g. DON) or possible illicit no3 sources that occurred after the addition started (see Discussion).

1400 1200 O • • ^7T 1000 • Z 800 8 CUD •

X 600 400 O O • IMH4 200 O 0 N03 0 • 180 230 280 330 380 430

Distance (m)

Figure 16. Background corrected nh4-N and no3-N flux for Pipe 1, 8/18/2009. The addition "drip" site was at 180 m.

57 Phosphate (po4) Uptake

P04 uptake was not detected in any of the open or piped stream reaches during the summer (Appendices H, I). During the spring, po4 uptake was detected in 1 of 3 open reaches and 0 of 2 piped reaches. Spring po4 Vf in the open reach was 7.33 ± 2.02 mm/min, and U was 53.94 ± 14.83 mm/min.

Entire Reach Nutrient Uptake Values

Nutrient uptake in adjacent open and piped reaches was measured by adding solutes at the beginning of the most upstream reach (see Methods). This approach resulted in 2 urban stream reaches where nutrient uptake could be calculated (Appendix

I). These reaches are extreme examples of urban streams since a significant portion of their length flows underground through pipes. Seventy-four percent of Reach 1 's length is contained in a 15 year old concrete pipe, while 42% of Reach 2's length flows through a 50+ year old corrugated metal pipe. no3 uptake was not detected in Reach 1 or 2.

Other nutrient uptake values, with the exception of summer nh4, were lower for Reach 1 than Reach 2 (Figures 17, 18).

58 3.0

2.5 • DOC c 2.0 • NH4 I E i 5 • PO4 E. ^ u • NH4 (Spring) J 1.0 •

P04 (Spring) 0.5 1 0.0 i Reach 1 Reach 2

Figure 17. Nutrient uptake velocity (vf, mm/min) in Reaches 1 and 2 of Pettee Brook. In Reach 1, no spring NH4 or po4 uptake was detected. In Reach 2, no summer nh4 uptake was detected. Non-detectable uptake rates were excluded from statistical analysis (see Methods). Letters denote values that are significantly different (p < 0.05).

70

c c 60 I I • DOC 50 |! ,E • NH4 bfi &0 40 E = • P04 • • ^ % O 30 • NH4 (Spring) O a. • a 3- 20 P04 (Spring) => Zx bi 10

0 n Reach 1 Reach 2

Figure 18. Areal uptake (U, mg/m2/min for DOC, ug/m2/min for NH4 and P04) in Reaches 1 and 2 of Pettee Brook. In Reach 1, no spring nh4 or po4 uptake was detected. In Reach 2, no summer nh4 uptake was detected. Non-detectable uptake rates were excluded from statistical analysis (see Methods). Letters denote values that are significantly different (p < 0.05).

59 There were no significant differences in ambient nutrient chemistry, pH, specific conductivity, stream water temperature, or light between Reach 1 and Reach 2.

Differences in sediment also failed to be significant, although sediment was less prevalent (covering 50% of Reach 1 's length vs. 90% of Reach 2's length) and shallower

(Reach 1 average depth of 6 ± 2.66 cm vs. Reach 2 average depth of 12 ± 5.25 cm) in

Reach 1. FBOM AFDM was similar in both reaches, but epilithon AFDM was somewhat lower (p < 0.1) in Reach 1 (3.38 ± 1.69 g/m2) than in Reach 2 (11.19 ± 3.65 g/m2).

There were no significant differences in summer GPP or summer ER between

Reaches 1 and 2. Spring GPP was lower for Reach 1 (1.68 g 02/m2/d) than for Reach 2

(3.31 g 02/m2/d), but lack of replication during spring made it difficult to determine whether this difference was significant. Spring ER was also lower for Reach 1 (0.91 g

CVn^/d) than for Reach 2 (5.06 g Ch/nfc/d), with the same caveat regarding the significance of this difference.

In general, there were not enough nutrient uptake values (whether for open and piped reaches or for Reaches 1 and 2) to establish correlations between nutrient uptake and other factors such as discharge, light, sediments, or metabolism.

60 CHAPTER IV - DISCUSSION

This study provides some of the first quantification of ecosystem structure and function in piped stream reaches. This study also adds to the body of literature on ecosystem metabolism and nutrient uptake in urban streams.

Chemical and Physical Parameters

Ambient solute concentrations, pH, specific conductivity, and average daily 02 levels were not significantly different between the open and piped reaches of Pettee

Brook. Thus, the hypothesis that water quality would be degraded in piped stream reaches was rejected. This finding is contrary to results reported by Krueger (1998) and

Davies et al. (2010).

The pipe itself may not affect water quality in Pettee Brook, either because of the pipe's age or because water does not remain in contact with the pipe for a long time. The pipes in this study were 15-50+ years older than the pipes tested by Davies et al. (2010).

Pipes in Pettee Brook appeared dirty and were coated with slime or other unidentified substances. Furthermore, sediments covered 31-76% of the pipes' length. The slime and sediments possibly provided a barrier between the material composing the pipes and the stream water.

61 The data suggests that the physical reach type within the stream (i.e. open or piped) did not control ambient water chemistry. Rather, the surrounding watershed use and other factors probably were more important in determining stream water concentrations. Water quality degradation, as well as variability, introduced by these factors may have overwhelmed any differences caused by stream piping.

Whereas pH and O2 levels in Pettee Brook were within healthy ranges (Murdoch et al. 1999), specific conductivity was elevated. Average CI concentrations were quite high, approaching and exceeding the US EPA chronic toxicity standard of 230 mg/L and the US EPA maximum contaminant level for drinking water of 250 mg/L (US EPA

1988). Na and Ca concentrations were elevated too. These data confirm the trends reported by Daley et al. (2009) for Pettee Brook and other southern NH streams. Daley et al. (2009) found that specific conductivity was correlated to CI and Na concentrations. CI concentrations in Pettee Brook doubled from 1991 to 2005, while the percent of watershed covered by impervious surfaces increased 151% (Daley et al. 2009).

Impervious surfaces, and the road salt used to deice these surfaces, may pose a bigger threat to water quality in Pettee Brook than the practice of stream piping.

Ambient nutrient concentrations in Pettee Brook were somewhat elevated compared to more natural systems. Average DOC concentrations were slightly higher than reported for pristine streams (5 vs. 1-4 mg/L) and within the range reported for other streams (Allan and Castillo 2007, Johnson et al. 2009). Average no3 and NH4 concentrations were higher than reported for undisturbed streams (0.5 vs. 0.1 mg no3-

N/L and 63 vs. 15 ug nh4-N/L), but lower than concentrations found in agricultural

62 streams (Allan and Castillo 2007). po4 concentrations in Pettee Brook were higher than

undisturbed streams (20 vs. 10 ug/L) during the summer only.

Light was negligible in piped stream reaches, but this lack of solar energy did

not reduce average daily stream water temperatures (refuting my hypothesis). In a study

that included Pettee Brook, Lemay (2010) also found that road crossings (piped stream

reaches) did not impact stream water temperatures. There are several interacting factors

that affect water temperature in both open and piped reaches, obscuring differences

between the reaches (Lemay 2010).

Benthic sediments, as well as debris dams, were less common in piped reaches of

Pettee Brook. This finding supported the hypothesis that channel complexity and substrate would vary between open and piped stream reaches. The hypothesis that

velocity would be faster in piped reaches was supported during the summer only. The correlation between quicker velocity and fewer, shallower sediments (r = -0.87, p = 0.06) may have been significant if more frequent sediment assessments had been conducted.

Additional data regarding sediments would also offer insight into ecosystem metabolism and nutrient uptake results.

Reaeration

Standardized reaeration rates (k6oo) in this study ranged from 0 to 6.24 m/d. The k6oo of other first order streams in New England ranged from approximately 10 to 15 m/d

(Raymond et al. in press). Reaches in Pettee Brook had very little elevation change

(slopes ranging from 0 to 0.0090 m/m). Discharge and depth were also less than

63 averages reported by Raymond et al. (in press). Therefore, it is reasonable that k6oo in

Pettee Brook was low. The more gradual slope in piped stream reaches (0.0014-0.0015) than in open reaches (0.0040-0.0090) may explain why piped reaches had lower k6oo than open reaches.

The relationship between calculated k6oo and k6oo measured by SF6 evasion in this study offers support for the equations presented by Raymond et al. (in press). Future studies may find it useful to establish such a relationship over a range of discharges for their streams. Doing so would remove some of the expense and personnel hours that prohibit researchers from gathering more extensive ecosystem metabolism measurements

(Roberts et al. 2007, Young et al. 2008).

Ecosystem Metabolism

Gross primary production (GPP) was minimal in piped reaches compared to open reaches of Pettee Brook. This finding, as well as the strong correlation between GPP and light, supported the hypothesis that GPP in piped stream reaches would be suppressed by the absence of light. Other studies have also found that GPP is heavily influenced by light (Mulholland et al. 2001, Roberts et al. 2007, Bernot et al. 2010, Hill et al. 2001).

Hill et al. (2001) and Roberts et al. (2007) reported light-driven GPP increases during spring in first order streams. The influence of light on GPP in Pettee Brook was also especially evident in spring, when GPP in open reaches was lOx higher than during summer. Open reaches, typically heterotrophic during summer, were often autotrophic

64 during the spring. Piped reaches were never autotrophic. These results indicate that the impact of stream piping on GPP may be greatest during the spring.

GPP in piped reaches of Pettee Brook was always lower than expected for healthy streams (0 vs. 1-3 g Ch/W/d, Young et al. 2008). Summer GPP in open reaches was also on the low end of reported values (0.5 vs. 0.4-4 g 02/m2/d), as may be expected considering the well-developed canopy and the level of disturbance around the stream.

Spring GPP in open reaches was within the range found by Roberts et al. (2007) in

Walker Branch, a forested first order stream. Nutrient concentrations were higher in

Pettee Brook than Walker Branch. Increased nutrient availability may have offset the negative effects of land use disturbance on GPP rates in open reaches of Pettee Brook.

Whereas there was a significant difference in GPP between open and piped reaches of Pettee Brook, there was not a significant difference in ER. Piped stream reaches, although unable to sustain an autotrophic community, were still able to support heterotrophs. The hypothesis regarding reduced ER in piped stream reaches was rejected, even though sediments and surface FBOM were significantly less in piped reaches than in open reaches.

Simmons et al. (2002) also reported that piped stream reaches supported a heterotrophic community: the pipes provided a stable substrate for bacteria. The stability of pipes as substrate may offset the impact of reduced sediments and organic matter on

ER in piped reaches of Pettee Brook. Furthermore, the heterotrophic community in piped reaches may have adapted to the conditions. For example, the summer NH4 uptake

65 results suggest that nitrifying bacteria may be important to ER during periods of energy limitation in piped reaches.

ER in Pettee Brook was on the low end of the range expected for healthy streams

(2-6 g 02/m2/d, Young et al. 2008), with the exception of open reaches during the spring.

Increased GPP during the spring resulted in increased autotrophic respiration. The autochthonous carbon associated with increased spring GPP supported heterotrophic respiration, as indicated by the P/R ratio greater than 1. Roberts et al. (2007) reported a similar effect of spring GPP on ER in Walker Branch.

Autotrophic production enhanced ER in Pettee Brook even during periods of net heterotrophy. Summer ER was positively correlated to GPP and light. This suggests that higher light levels increased GPP, which in turn added autochthonous carbon to the stream that stimulated ER. Although summer NEP and P/R values indicate that both open and piped reaches were dependent on allochthonous carbon during the summer, there may have been insufficient allochthonous carbon to support demand. Thus, even small carbon inputs from GPP may have been important to ER.

The correlation between GPP and ER was stronger during the summer than during the spring. It is possible that the high spring GPP reduced carbon limitation to the point where any extra GPP was exported downstream rather than stimulating an increase in ER within the studied stream reach. However, fewer ecosystem metabolism measurements were taken in spring (once per reach vs. 3x per reach in summer). This may have reduced the statistical ability to detect a relationship between GPP and ER.

66 The results suggest that the loss of light may have been the most important factor controlling ecosystem metabolism in piped stream reaches. Light limitation inhibited

GPP. Reduced GPP was correlated with reduced ER. ER was lower in piped reaches than in open reaches, although this difference was not significant. The light limitation in piped reaches led to changes in the carbon balance of Pettee Brook (Table 4).

Average loss of autotrophic (g C/m/d) (kJ/m/d) inputs to pipe Summer 0.21 10.06 Less carbon produced Spring 3.00 143.51 in piped stream reaches.... Average decline of consumption in pipe Summer 0.73 110.28 but less carbon consumed Spring 1.69 254.24 in piped reaches. Average net change due to pipe Summer 0.51 24.66 Increased carbon output from piped reaches Spring -1.35 -64.74 Decreased carbon output from piped reaches Table 4. Ecosystem metabolism changes in piped reaches of Pettee Brook; based on average GPP, ER, and NEP differences between open and piped reaches. Conversions from g CVm/d to g C/m/d and kJ/m/d used equations from Bott (2007).

Benthic Ash Free Dry Mass and Pigment Biomass

The hypothesis that benthic AFDM and chlorophyll a would be reduced in piped stream reaches was supported by the results of this study, as there were significant differences in these metrics between open and piped reaches of Pettee Brook. The reduction of benthic AFDM and chlorophyll a in piped stream reaches may have been related to the absence of light in these reaches. This relationship was most apparent for epilithon chlorophyll a.

67 The positive correlation between surface FBOM chlorophyll a and AFDM suggests that autotrophic production increased organic matter availability within the stream. The finding that epilithon APDM and P/R were positively correlated also shows that autotrophs provided important inputs of energy and organic matter to the stream reaches. Epilithon chlorophyll a was positively correlated with light, GPP, and ER. This supports the idea that light enhances autotrophic growth and ecosystem metabolism

(Bernot et al. 2010, Mulholland et al. 2001).

The average surface FBOM in open reaches of Pettee Brook was comparable to that reported by Meyer et al. (2005) for urban streams (24 vs. 11-31 g AFDM/m2). Urban streams had significantly less FBOM than forested reaches, which Meyer et al. (2005) attributed to the flushing effect of high discharges from impervious surfaces. Piped reaches of Pettee Brook had even less FBOM (8.5 g AFDM/m2) than found in urban streams. The light limitation in the piped reaches augmented the FBOM losses that occurred due to urbanization.

Chlorophyll a in open reaches of Pettee Brook was comparable to values reported for 2 urban streams in Michigan with similar discharge (13 vs. 8-14 mg/m2, Johnson et al.

2009). Open reach chlorophyll a values were also within the range reported by Taylor et al. (2004) for streams with various levels of catchment disturbance (1-47 mg/m2), although Pettee Brook values were low when compared to reaches with similar % impervious cover in the watershed (25-28 mg/m2). Taylor et al. (2004) sampled benthic chlorophyll a more frequently and widely than was done in Pettee Brook. Additional chlorophyll a assessments in Pettee Brook, especially during spring, would likely increase average values for open reaches.

68 Chlorophyll a in piped reaches of Pettee Brook was very low compared to other urban streams, and this result would be expected even in spring due to the constant light limitation within the pipes. The presence of any chlorophyll a in piped reaches was probably due to the downstream movement of sediment and rocks from open reaches.

The pheophytin results also suggested that there was downstream movement of dead autotrophs. Surface FBOM pheophytin appeared to be transported downstream more than epilithon pheophytin, as would be expected since FBOM was smaller than rocks.

Taylor et al. (2004) reported that light explained 3-11% of the variation in their chlorophyll a values. Other controls on chlorophyll a included substrate, impervious surfaces, and efficient drainages that supplied phosphorous-rich water to urban streams.

While light was found to be an important determinant of chlorophyll a in Pettee Brook, managing light availability would be unlikely to achieve the desired results unless other factors were also considered.

Nutrient Uptake

Nutrient uptake velocities and areal uptake rates were not significantly different between piped and open reaches of Pettee Brook, with the exception of NH4 uptake during the summer. Summer NH4 uptake was higher in a piped reach than in open reaches, and this finding was attributed to nitrification within the pipe. These results failed to support the hypothesis that there would be diminished nutrient uptake in piped reaches compared to open stream reaches.

69 As is typical for urban streams, it was difficult to detect nutrient uptake in Pettee

Brook using the short-term elevated solute addition method (Meyer et al. 2005, Grimm et al. 2005). The number of usable experiments (i.e. experiments that detected statistically significant nutrient uptake) was similar for piped and open stream reaches. This supported the finding of similar nutrient uptake rates in piped and open stream reaches.

Piped reaches had detectable nutrient uptake rates as often as open stream reaches.

Other results in this study corroborated the finding of similar nutrient uptake rates in piped and open reaches of Pettee Brook. For instance, ambient nutrient concentrations were not significantly different between piped and open reaches. Neither were ecosystem metabolism metrics including ER and NEP.

The results suggest that heterotrophs in piped stream reaches were able to assimilate nutrients during metabolism at a similar rate to heterotrophs in open reaches.

Nitrifying bacteria in piped reaches may have compensated for any limitation of heterotrophic assimilation that occurred due to the pipes' reduced FBOM (carbon/energy) levels. Autotrophic nutrient assimilation did not occur in piped reaches, but this loss was not enough to significantly lower overall nutrient uptake rates compared to open reaches.

This seems reasonable considering that Pettee Brook is a first order stream with some remaining canopy cover.

During the spring open canopy period, there was a pulse of autotrophic production in open reaches that enhanced metabolism and nutrient uptake by the benthic community in both open and piped reaches. GPP in open reaches was lOx higher in spring than in summer (there was no increase in piped reaches). ER in both open and

70 piped reaches was 2.5x higher in spring. NH4 U in open reaches was 25x higher in spring, while nh4 U in piped reaches was 5x higher in spring than in summer. po4 U in

Reach 2 was 3x higher in spring. Open reaches experienced a greater spring increase in

nutrient uptake than was found for piped reaches. This may be attributed to the autotrophic activity within the open reaches.

Spring DOC uptake was not assessed in this study. Future research could address this issue. It is likely that spring DOC uptake would be similar in open and piped stream reaches, because ER was similar in both reach types. Spring GPP was higher in open reaches, but GPP uses co2 as its carbon source so it is not likely that open reaches would have significantly higher DOC uptake. Spring GPP may ease carbon limitation within open and piped stream reaches. Thus, spring DOC uptake may be lower than summer

DOC uptake. However, Johnson et al. (2009) reported that there were no significant differences in DOC uptake between seasons. Elevated nutrient concentrations (e.g. N)

result in streams that may be carbon limited despite seasonally-high carbon inputs

(Johnson et al. 2009).

Summer DOC Vf in Pettee Brook was within the range reported by Johnson et al.

(2009) for urban streams with similar discharge (1 vs. 1 -4 mm/min for acetate). Acetate vf in streams of varying land uses ranged from 0-21 mm/min (Johnson et al. 2009), with no correlation between DOC Vfand land use (Johnson et al. 2009, Newbold et al. 2006).

Results from Pettee Brook suggested that even extreme urban land use such as stream piping may not significantly lower DOC uptake (or the ER that leads to DOC uptake).

Other factors, such as elevated ambient N concentrations or toxins, may control DOC uptake in urban streams (Newbold et al. 2006, Johnson et al. 2009).

71 There was no evidence ofNC>3 uptake in any reaches of Pettee Brook during the

summer. This was not surprising considering that other studies have found diminished

no3 uptake in urban streams (Grimm et al. 2005, Klocker et al. 2009). Like other urban

streams (Meyer et al. 2005, Young et al. 2008), Pettee Brook had high no3

concentrations as well as low FBOM, GPP, and ER. Pettee Brook's capacity for no3

assimilation and denitrification may be saturated. Spring no3 additions were not

attempted. GPP and ER were higher during the spring, but the increased ecosystem

metabolism may not have been sufficient to raise no3 uptake to detectable levels. Future

experiments could address this question.

Summer nh4 Vf in open and piped reaches of Pettee Brook was on the low end of

reported values for urban streams (0.13-0.24 vs. 1-8 mm/min, Johnson et al. 2009, Meyer

et al. 2005, Newbold et al. 2006). Summer nh4 Vf and U were significantly lower in an open reach than in a piped reach, which was an unexpected result. Further investigation

indicated that nitrification was responsible for the majority of nh4 uptake within the

piped reach (no nitrification was detected in the open reach).

Nitrification in the piped reach during the summer nh4 addition was higher than

published elsewhere (> 100% vs. 20-50% of measured nh4 uptake, Peterson et al. 2001,

Ashkenas et al. 2004). More no3 was produced than was accounted for by nitrification of added NH4. There may have been an illicit source of no3 in the reach (e.g. an unseen

trickle of highly contaminated water entering the pipe sometime between the collection of ambient samples and plateau samples). However, plots of ions such as CI failed to clearly support an illicit discharge into the study reach during the addition.

72 Addition-induced remineralization of organic N sources may explain the excess nitrate production. DON concentrations in the reach declined during the summer NH4 addition, from an average of 240 ug N/L before the addition to an average of 79 ug N/L during the plateau of the addition. po4 was added at the same time as nh4, which may have stimulated the remineralization. Further studies using isotopes might clarify the pathway of N during nitrification in piped stream reaches.

Conditions in the piped reach during the summer may have supported high nitrification rates by promoting the growth of nitrifying bacteria. The temperature

(21°C), pH (7), and O2 concentration (6 mg/L) were within the range required to sustain nitrification, and the ambient nh4 concentration (78 ug N/L) was more than sufficient

(Kemp and Dodds 2002, Wetzel 2001). There was no autotrophic competition for nh4 due to the absence of light in the piped reach. Heterotrophic NH4 uptake was limited by the low levels of FBOM and other organic matter (ambient DOC concentration was 5.91 mg C/L but the DOC probably was not labile). Thus, the piped reach had few impediments to nitrifying bacteria's use of energy from nh4 and O2 to assimilate carbon from CO2. Conversely, nitrification in open reaches may have been inhibited by competition from autotrophs or heterotrophs (Bernhardt and Likens 2002).

Competition for NH4 from autotrophs and heterotrophs also limited nitrification during the spring. The augmented autotrophic production during spring provided enough organic carbon to sustain respiration and associated biotic NH4 assimilation (Butturini et al. 2000). Excess autochthonous carbon produced in open reaches flowed downstream, supporting heterotrophic respiration and nh4 assimilation in piped reaches. Nitrification was not detected in either open or piped reaches during the spring. Spring nh4 Vfwas

73 similar in both reach types, and it was within the range of values reported for other urban streams (3 vs. 1-8 mm/min, Johnson et al. 2009).

Spring po4 uptake, detected in an open reach but not any piped reaches of Pettee

Brook, was on the high end of the range reported for urban streams (7 vs. 1-8 mm/min,

Newbold et al. 2006, Meyer et al. 2005). It was especially high when compared to summer po4 uptake in low order urban streams (0.67 mm/min, Newbold et al. 2006, no studies available that addressed spring po4 uptake in low order urban streams). The results support the importance of spring autotrophic production to amplifying nutrient uptake.

po4 uptake was not detected during the summer in open and piped reaches of

Pettee Brook. However, statistically significant po4 uptake was detected for Reaches 1 and 2 (reaches consisting of adjacent open and piped sections, see Methods/Results).

These po4 Vfvalues were somewhat low compared to similar urban streams (0.23-0.45 vs. 0.67 mm/min, Newbold et al. 2006).

nh4 and DOC uptake detected in Reaches 1 and 2 was also lower than reported for similar urban streams. Spring nh4 Vf (1.7 mm/min for Reach 2) and summer NH4 Vf

(0.3 mm/min for Reach 1) were less than the range (1-4 mm/min) found by Johnson et al.

(2009) and Newbold et al. (2006). Summer DOC Vf(0.2 mm/min for Reach 1 and 0.96 mm/min for Reach 2) was also less than reported by Johnson et al. (2009).

With the exception of summer NH4 uptake, nutrient uptake was higher in Reach 2

(42% piped) than in Reach 1 (74% piped). This was difficult to explain using the available data. Higher epilithon AFDM, as well as higher spring GPP and ER, may be

74 reasons why there was more nutrient uptake in Reach 2. This corresponds well with other findings in this study that highlight the importance of light and spring autotrophic production to ecosystem processes in Pettee Brook.

Strengths and Limitations of Study Results

This was the first study of ecosystem structure and function in urban, piped stream reaches. Therefore, the study design emphasized the exploration of several factors and processes rather than focusing on replication. Some statistical power was lost in this approach, but this was accepted so that the limited resources could be used to cast a wide net in order to find the factors and processes that were important in piped stream reaches.

The advantage of this approach was that the results offered insight into how elements of ecosystem structure and function interacted in Pettee Brook.

This study addresses the ecosystem structure and function of piped stream reaches during base flow only. Most measurements were obtained during summer, although there were some spring assessments as well. Questions remain regarding conditions in piped streams during times of higher discharge including storm flow, or during other seasons

(e.g. autumn). The study results provide a snapshot, rather than a comprehensive overview, of ecosystem structure and function in open and piped reaches of Pettee Brook.

Implications of the Results at the Stream and Landscape Scale

Compared to open reaches of Pettee Brook, piped reaches had no GPP, reduced benthic AFDM and pigment biomass, and increased nitrification. Approximately 25%

75 (735 m) of Pettee Brook's entire length flows underground through pipes (Lemay 2010, confirmed by my own measurements). Therefore, the effects of stream piping may be substantial at the stream scale (meaning all of Pettee Brook, from headwaters to the with Oyster River).

Scaling this study's ecosystem metabolism results to the entire stream length suggested that inputs to Pettee Brook were reduced by 26% due to the lack of autotrophic production in pipes. This loss was 154 g C/d (7934 kJ/d) in the summer and 2203 g C/d

(105,480 kJ/d) in the spring. Losses were offset by reduced respiration in piped reaches

(see Table 4). During the summer, the net effect of stream piping was to increase outputs from Pettee Brook by 20% (387 g C/d or 18,122 kJ/d). However, outputs decreased by

84% (994 g C/d or 47,581 kJ/d) during the spring.

Scaling the summer AFDM and pigment biomass results indicated that stream piping in Pettee Brook reduced surface FBOM by 19% (27,432 g AFDM) and epilithon by 22% (13,878 g AFDM). Twenty-three percent (16 g) of chlorophyll a biomass, and

18% (13 g) of pheophytin biomass, were also lost due to the pipes.

Nutrient uptake results were not scaled to the entire stream length. There were several open and piped reaches with non-detectable nutrient uptake rates, and this resulted in a general lack of replication/consistency. Evidence of nitrification was only detected once, making it difficult to assert confidently that stream piping leads to NO3 production instead of no3 uptake. In most cases, there was no significant difference in nutrient uptake between open and piped reaches. It was assumed that the effect of stream

76 piping on nutrient uptake at the stream scale would be insignificant or obscured by variability and other factors.

Values obtained for scaling should be viewed with caution due to the assumption that the studied reaches (encompassing 20% of Pettee Brook's total length) were representative of the entire stream. However, the scaling results are important as they indicated that the effect of stream piping on energy flow and organic carbon production may be considerable.

In addition to Pettee Brook, Lemay (2010) assessed 8 other streams in the region that contain piped reaches. The piped reaches composed between 1 -29% of the total length in these streams (median 14% of total length). The implication is that stream piping may significantly disrupt ecosystem metabolism, as well as energy and biomass production, at the landscape scale.

Ecological and Management Implications of the Results

In some ways, piped stream reaches acted as longitudinal hyporheic zones in the urban stream. Piped reaches lacked light and GPP, but ER and nutrient uptake did occur.

This consumption of DOC, without any direct autochthonous or allochthonous carbon sources to replace the DOC, may have created a zone of energy limitation within the piped reaches. As in light and energy-limited hyporheic zones, NH4 was used as an alternative energy source during the process of nitrification (although this was only detected once). It is not known if there was accompanying denitrification, although it seems unlikely due to the low levels of organic matter on the benthos.

77 If urban, piped streams have reduced carbon production and increased

nitrification (no3 production), the ecological health of downstream receiving waters may

be impacted. Also, higher trophic levels may be affected. Further research is needed to answer questions about invertebrates and other animals within and downstream of piped stream reaches. Larger scale research is needed to clarify the ecological significance of

piped reaches to the river network.

The main differences between open and piped stream reaches in Pettee Brook

were the absence of light and the fewer, shallower sediments in piped reaches. The data suggested that the absence of light was the strongest factor driving the ecological changes in the piped reaches. However, simply increasing light by opening (or "daylighting") the piped reaches would not completely restore their ecological health. It is likely that GPP, as well as benthic AFDM and pigment biomass, would increase. However, the ecological condition of the reaches would still be harmed by other factors common to urban

watersheds (e.g. Table 5). Daylighting the piped reaches might only create stream

channels similar to the open reaches of Pettee Brook, which suffer from ecological degradation typical of urban streams (Walsh et al. 2005b).

Rather than spending a significant amount of time and money daylighting piped

reaches of Pettee Brook, it might be more cost-effective to protect the stream by reducing

anthropogenic inputs including trash, road salt (CI), and nutrients. Raising awareness

that Pettee Brook exists under the UNH campus center (where nearly 60% of the stream

flows underground through pipes) might be a relatively inexpensive way to inspire the

UNH community to reduce some of these inputs.

78 Trash thrown into stream Food and beverage containers Sporting equipment Construction materials Electronic waste

Pollutants applied near stream Road salt that covered the majority of impervious surfaces draining into the stream Snow plowed onto stream banks (later melted into the stream) Herbicides/pesticides applied near stream

In-Stream Construction Dam removal/replacement (involved substantial riparian cutting and excavation of a new channel replacement (no , resulted in downstream turbidity)

Near-Stream Construction Parking lot resurfacing (replaced asphalt with porous pavement, used erosion control) Tear down and rebuild of apartment building

Other Impacts Mowing/cutting of stream bank vegetation Large footbridge fell into stream (later removed) Numerous storm drain outlets Numerous illicit discharges Table 5. Observed anthropogenic impacts to Pettee Brook, 2009-2010 (experiments in this study avoided these impacts to the greatest extent possible).

On a more positive note, UNH recently installed porous pavement in 2 parking lots that drain into Pettee Brook (personal observation, personal communication with the

UNH Center). These projects were in line with ecologists' recommendation to redirect restoration funds from stream reach scale projects (e.g. daylighting) to better water management that mimics natural watershed hydrology (Bernhardt and Palmer

2007, Walsh et al. 2005a, Taylor et al. 2004). It may be impossible to restore urban streams without integrating infiltration opportunities throughout their watersheds. It is

79 also critical that impervious surfaces be disconnected from urban streams (Bernhardt and

Palmer 2007, Walsh et al. 2005b). These practices should be more restorative to Pettee

Brook than daylighting Pettee Brook's piped reaches. Additional research is needed to clarify the optimal ways to protect, manage, and restore streams in urban watersheds

(Wenger et al. 2009, Walsh et al. 2005b, Palmer 2009, Bernhardt and Palmer 2007,

Bernhardt et al. 2005b).

80 CHAPTER V - CONCLUSION

Like other urban streams, Pettee Brook had high concentrations of CI and nutrients. Summer GPP, ER, benthic biomass, and nutrient uptake values were low compared to other studies in the literature. Spring was an important time of ecological activity in Pettee Brook, as the open canopy increased light availability to the stream.

GPP, ER, nh4 uptake, and po4 uptake were substantially higher in spring.

Piped reaches of Pettee Brook were similar to open reaches in terms of water quality, dissolved O2 concentration, temperature, and discharge. However, piped reaches had significantly less light, sediments, and debris dams. The absence of light inhibited autotrophic activity in piped reaches, resulting in the complete loss of GPP as well as a significant reduction in benthic AFDM and chlorophyll a biomass.

Heterotrophic activity in piped reaches of Pettee Brook was not impaired to the same extent as autotrophic activity. ER and nutrient uptake values were not significantly lower in piped reaches than in open reaches. The presence of carbon consumption in piped reaches, without any direct autochthonous or allochthonous carbon replenishment, may have induced energy limitation at times. Nitrification was measured during the summer in a piped reach.

This study is an important first step toward understanding the ecosystem structure and function in urban, piped stream reaches. However, additional research is needed to confirm the results of this study in other piped streams. Would results be similar for first

81 order streams that flow through smaller diameter pipes (< 1.8 m)? Would the difference between open and piped reaches be more pronounced for urban streams that have little canopy cover in the open reaches? How would results change for piped streams in other regions and climates? Would results be different during other seasons (e.g. autumn, winter) or during periods of higher discharge (e.g. storm flows)? Would further research with more replication find correlations between sediments and other ecological characteristics of piped stream reaches?

Urban, piped stream reaches are prevalent in the landscape (Elmore and Kaushal

2008, Lemay 2010). It is likely that their prevalence will increase in the future due to expanding population and development. In NH alone, the population grew by 6.5% between 2000 and 2010 (US Census Bureau 2012). The extent of coverage in coastal NH increased by 18% between 2000 and 2005 (Lemay 2010).

Current development practices often allow stream piping (Doyle and Bernhardt 2011).

Therefore, it is important to understand the ecological structure and function of piped stream reaches.

The results of this study suggested that stream piping may have negative ecological impacts that extend beyond typical urban stream degradation. It is hoped that the empirical evidence contained in this study will lead to more effective protection and management of Pettee Brook and other streams. It is also hoped that this study will spur additional research on the ecology of urban, piped streams.

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93 APPENDICES

94 APPENDIX A - LITERATURE REVIEW

Importance of Urban Stream Ecology

Over half of the world's people, including 81% of the United States' population, live in cities (UN 2008). The number, size, and density of cities are projected to increase due to population growth and development. Although cities currently occupy less than 10% of the landscape area, their influence on ecosystem health is widespread. Urbanization degrades aquatic ecosystems in a drastic and potentially irreversible way (Grimm et al. 2008, Palmer et al. 2004).

In order to effectively manage stressors to urban watersheds and streams, ecologists must address the need for research on how urban ecosystems function (Wenger et al. 2009, Grimm et al. 2000). While research in undisturbed ecosystems is important, findings may not always be applicable to urban systems (Kaye et al. 2006). It may be impossible to preserve or restore "naturally" functioning stream ecosystems in urban areas. Rather ecologists may have to design urban streams to meet human needs in a way that protects ecosystem services (Palmer et al. 2004). Increased ecological study of urban streams, and the mechanisms controlling their health, is critical to identifying optimal stream management strategies (Wenger et al. 2009).

Urban ecology, with its inclusion of humans as organisms within the ecosystem, is also worthwhile from a purely scientific perspective. Research in urban ecosystems allows ecologists to test theories based upon patterns in undisturbed systems. For instance, studies regarding the relative importance of watershed vs. channel disturbance to urban streams' ecological function test the theory that rivers are the product of their landscapes (Hynes 1975). Studies on the flow of energy and materials in urban streams add to the knowledge regarding Vannote et al.'s River Continuum Concept (1980). Research on urban streams is essential to a more complete understanding of stream ecology.

Urban Stream Syndrome

A main concept in urban stream ecology is "urban stream syndrome", which refers to the common changes that occur in urban streams when watersheds are developed (Meyer et al. 2005, Walsh et al. 2005b).

95 Impervious surfaces prevent precipitation from infiltrating into the ground in urban areas, so increases and reaches streams more quickly by way of storm drains. The result is that storm flow peaks are earlier, higher, and of shorter duration than in forested watersheds (Paul and Meyer 2001). Additionally, water flows reach streams more frequently since even small amounts of water are piped to streams rather than soaking into the ground as in undisturbed watersheds (Walsh et al. 2005a,b).

The altered hydrology in urban watersheds causes changes to channel geometry through erosion. Urban stream channels become deeper and wider, resulting in incised streams that are cut off from riparian vegetation and floodplains. Channel complexity decreases, reducing the presence of instream habitat and transient water storage zones (Walsh et al. 2005b, Paul and Meyer 2001). Eroded sediments increase turbidity and degrade stream bottoms (Bernhardt and Palmer 2007).

Urbanization also degrades streams by increasing their nutrient and contaminant load. Wastewater and fertilizers used in the watershed lead to elevated nitrate, ammonium, and phosphate concentrations. Urban stormwater also efficiently conveys chloride, hydrocarbons, and metals from impervious surfaces to streams. Insecticides and herbicides are some of the other toxic compounds found in urban stream water (Paul and Meyer 2001).

Physical and chemical changes caused by urbanization impact urban streams' biological and ecological condition, although these areas are not as well researched (Paul and Meyer 2001, Walsh et al. 2005b). The abundance and diversity of fish and macro- invertebrates typically decrease in response to urbanization. Algal biomass sometimes increases when urbanization elevates nutrients and lights within streams, although scour associated with high water flows may negate this effect (Walsh et al. 2005b). also are a concern in urban watersheds (Paul and Meyer 2001).

Ecological processes may change due to urbanization. Flashy hydrology and simplified channels may reduce organic matter and nutrient uptake (Walsh et al. 2005b, Grimm et al. 2005, Meyer et al. 2005). It is not certain if ecosystem metabolism varies in a predictable manner with urban land use (Meyer et al. 2005). Additional study is required to assess and understand ecosystem function in urban streams (Paul and Meyer 2001, Walsh et al. 2005b, Wenger et al. 2009).

Piped Stream Syndrome

Urban stream syndrome results in degraded streams that are controlled by anthropogenic actions rather than differences in climate, geology, or vegetation (Bernhardt and Palmer 2007). An extreme example of this anthropogenic control occurs when urban streams are diverted though pipes (Elmore and Kaushal 2008).

96 Is there a "piped stream syndrome" that is similar to, or worse than, urban stream syndrome? The process of excavating the channel, placing the pipe, and then directing water through the pipe acutely impacts the stream. Once the stream is in the pipe, it likely suffers from many of the same physical, chemical, and ecological problems found in urban streams.

The channel morphology of piped streams is constrained in terms of dimension and pattern. It may be difficult for the piped stream to form and maintain , point bars, and debris dams. Because piped streams are straight and unable to flood, flow velocity within piped streams may be higher than in nearby urban streams. Scour may prevent sediments from accumulating on the bottom of piped streams. Hyporheic zones in piped streams are probably minimal due to the lack of sediments and the disconnection from surrounding soils and groundwater.

Pipes may protect the streams flowing through them from contaminated groundwater. However, catch basins and storm drains often empty directly into piped streams, bringing in water that is loaded with salt, hydrocarbons, and many other toxins (Steele et al. 2010). Piped streams may also receive illicit discharges. Without groundwater connection and sediments, piped streams may offer little chance of diluting and filtering these pollutants. Water quality may be degraded in piped streams (Kreuger 1998).

The biological community in piped streams may be altered in terms of abundance and diversity (Meyer et al. 2005b). Pipes may prevent organisms from entering or remaining in piped streams (Stream Continuity Partnership 2009). The lack of light inside piped streams prevents plant and algal growth, inhibiting primary production (Elmore and Kaushal 2008). It is uncertain if community respiration would also decrease in piped streams. Nutrient retention and removal may be compromised in piped streams, unless organic matter accumulates and creates anaerobic hotspots of denitrification (Elmore and Kaushal 2008, Walsh et al. 2005b). There is no data to indicate whether this happens. Many questions remain regarding the ecosystem structure and function of piped streams (Wenger et al. 2009). This paper focuses on ecosystem metabolism and nutrient spiraling in an urban, piped stream.

Ecosystem Metabolism

Expected ecosystem metabolism rates along a stream's longitudinal gradient from headwaters to mouth are described by the River Continuum Concept, or RCC (Vannote et al. 1980). Headwater streams are often heavily shaded, with low light levels inhibiting autotrophic production. Riparian vegetation fuels net heterotrophy (NEP < 0). In mid- order streams, shade is less prevalent so the metabolic balance shifts towards autotrophy (NEP > 1). Algal and rooted vascular plants become significant organic matter sources,

97 although fine particulate organic matter (FPOM) from upstream processing also supports aquatic organisms. In high-order streams, autotrophic production declines due to light limitation from depth and turbidity. FPOM from upstream processing sustains organisms living in high-order streams, and the metabolic balance returns to net heterotrophy.

Many studies have tested the RCC's predictions about ecosystem metabolism (reviewed by Young et al. 2008, Tank et al. 2010). Young et al. (2008) did a meta­ analysis of ecosystem metabolism data reported in the literature that included 213 relatively undisturbed sites. They found that most streams had a P/R ratio less than 1, meaning that the streams' ER was greater than the GPP. Young et al. (2008) suggested that a healthy stream's ER ranges from 2-6 g C>2/m2/d, and its GPP ranges from 1-3 g 2 02/m /d.

Mulholland et al. (2001) assessed ecosystem metabolism in eight undisturbed streams in several biomes (e.g. temperate, tropical). Most of the streams had negative NEP which indicated that they were heterotrophic. Bernot et al.'s (2010) study on 70 streams in the same biomes also found that NEP in undisturbed streams was negative (average approximately -6 g C>2/m2/d). Average ER in undisturbed streams was 7 g C>2/m2/d, and average GPP was 1 g C>2/m2/d (Bernot et al. 2010).

The Bernot et al. (2010) study included streams disturbed by agricultural and urban land use. While these streams had similar average ER values to the undisturbed streams, their average GPP values were significantly higher at approximately 4 g 2 2 02/m /d. Thus, the disturbed streams' average NEP values (-2 to -3 g 02/m /d) were significantly different from reference stream values. Disturbed streams also exhibited reduced inter-regional variability in ecosystem metabolism rates (Bernot et al. 2010).

Bernot et al.'s (2010) results contrast with those reported by Izagirre et al. (2008) who found that average stream ER increased to 19.14 ± 7.94 g C>2/m2/d in disturbed sites, potentially due to pollution. Wastewater treatment may curb such organic matter loading and thereby moderate ER increases in urban streams (Iwata et al. 2007). Izagirre et al. (2008) also found that average stream GPP decreased as population density, and associated turbidity, increased. Nearly all streams assessed by Izagirre et al. (2008) and Iwata et al. (2007) were net heterotrophic.

GPP was less than 0.5 g CVmVd in streams at a military base and was not noticeably changed by land use disturbance (Houser et al. 2005). Average ER rates 2 decreased in these disturbed streams, from 5.7 ± 1.9 g 02/m /d to 2.4 ± 0.6 g CVirrVd (Houser et al. 2005). Meanwhile, Meyer et al. (2005) found no effect of urban land use disturbance on any measure of ecosystem metabolism. Streams in this study had average 2 GPP values ranging from 0.43 to 2.38 g 02/m /d and average ER values ranging from

98 1.31 to 8.72 g 02/m2/d. Average NEP ranged from -0.39 to -7.96 g 02/m2/d (Meyer et al. 2005).

Factors Influencing Ecosystem Metabolism

Light, nutrients, benthic organic matter supply, substrate, hydrology, and temperature are some of the main factors that influence GPP and ER. In turn, these factors are controlled by stream location, climate, weather, geology, riparian vegetation, land use, and other anthropogenic impacts (Bernot et al. 2010, Roberts et al. 2007, Young et al. 2008, Tank et al. 2010).

The amount of light available to stream autotrophs influences GPP (Mulholland et al. 2001, Roberts et al. 2007, Bernot et al. 2010). Even strongly heterotrophic streams may have periods, such as spring, when extra light reaches the stream bottom and increases primary production (Hill et al. 2001, Roberts et al. 2007). In undisturbed streams, light depends on the location, climate, weather, and riparian vegetation. Urban land use introduces human control of light and thereby GPP. For instance, humans may remove riparian vegetation which may increase light. On the other hand, urban streams that flow through deeply incised channels or through pipes may experience light limitation.

Elevated stream nutrient concentrations are correlated with increases in ecosystem metabolism rates. Lamberti and Steinman (1997) reported that soluble reactive phosphorous (SRP) concentration was positively correlated with GPP in streams across several biomes. Mulholland et al. (2001) found that SRP concentration increased both GPP and ER. These findings were not corroborated by Bernot et al. (2010), who suggested that over-riding factors (e.g. light) may have masked any relationship between SRP and ecosystem metabolism or that streams in this study may have been N limited. Bernot et al. (2010) did find that ammonium (nh4) enhanced GPP rates. Also, nh4 and nitrate (no3) increased ER. It is likely a combination of soil, climate, and land use that controls the role of nutrients in determining stream metabolism (Bernot et al. 2010).

Dissolved organic carbon (DOC) and organic matter supply influence streams' ER rates (Bernot et al. 2010, Roberts et al. 2007, Houser et al. 2005). Therefore, organic carbon produced by GPP may increase ER (Bernot et al. 2010). that re-suspend benthic organic matter and bring in organic matter from the surrounding landscape also stimulate ER (Roberts et al. 2007). Coarse woody debris traps organic matter, providing hot spots of ecosystem metabolism in streams (Houser et al. 2005). Urbanization may alter the type and amount of organic matter supplied to and retained in streams. Although additional research is needed to clarify this process, the implication is that altered organic matter dynamics may result in altered ER (Walsh et al. 2005b).

99 While floods can stimulate ER, the associated scour of benthic algae may depress GPP (Roberts et al. 2007). Even low flows can inhibit benthic algae/GPP in sandy- bottomed streams by constantly moving the top layer of substrate (Atkinson et al. 2008). While autotrophs live mainly on lighted surfaces, heterotrophs are found deeper in the hyporheic zone and may not suffer as markedly from unstable benthic sediments (Atkinson et al. 2008). The hydrological and geomorphological changes that accompany urbanization increase channel scour and sediment instability within streams (Walsh et al. 2005b). In some cases this may be offset when humans cover stream bottoms with concrete or rip rap. Regardless, ecosystem metabolism may be related to urban land use through urbanization's effect on stream bottoms, flow velocity, and hyporheic zones.

Temperature may also influence stream ecosystem metabolism, because biological rates are thought to increase with increasing temperature up to the point where organisms become stressed. However, studies suggest that temperature may not be as important of a control to GPP and ER as light or nutrients (Young et al. 2008). The literature provides some support for the idea that temperature impacts ER, while there is little evidence pointing to a relationship between temperature and GPP (Young et al. 2008, Bernot et al. 2010). Urbanization often increases stream temperatures (Walsh et al. 2005b), so this may influence ER rates in urban streams. It may not be possible discern the effect of temperature on ER in urban streams due to all the other confounding factors controlling ecosystem metabolism.

There is very little data regarding how nutrients, organic matter, substrate, and temperature change as a result of stream piping. It is not known how ecosystem metabolism in piped streams compares to metabolism in other urban streams.

Nutrient Spiraling

Nutrient spiraling is an important indicator of stream health. It is an ecological process that is used to define streams as ecosystems vs. conveyances like gutters, pipes, and ditches (Stream Solute Workshop 1990, Doyle and Bernhardt 2011). Nutrient spiraling alters the magnitude, timing, and form of nutrients that are transported downstream (Doyle and Bernhardt 2011). Nutrient uptake may slow downstream nutrient transport by recycling and storing nutrients in the benthos, and some nutrients (e.g. nitrogen) can be removed from the stream through gaseous output.

Nutrient retention and removal are critical ecosystem services because they prevent downstream eutrophication, protecting fisheries and recreational uses. Nutrient retention and removal are also essential for maintaining water quality (especially in areas subject to high nutrient inputs from agriculture, sewage, and the like). Thus, there is a significant impetus to better understand and maximize nutrient processes in aquatic ecosystems (Craig et al. 2008, Grimm et al. 2005).

100 Dissolved Organic Carbon (DOC)

Dissolved organic carbon (DOC) is critical to stream ecosystems: it provides energy to support the food web and its availability regulates the cycling of other nutrients. Natural sources of DOC to streams include the decomposition of terrestrial vegetation and animals, as well as in-stream autotrophic production. Humans account for many more DOC sources. Examples of these novel organic compounds are hydrocarbons (from oil, lubricants, exhaust, and combustion), pesticides, drugs, and personal care products. Waste water effluent from treatment plants and septic systems is an important source of anthropogenic DOC. Humans change both the quantity and quality of DOC in streams (Steele et al. 2010, Allan and Castillo 2007).

Excess DOC in streams causes water quality problems. DOC stimulates the growth of pathogenic and nuisance bacterial populations, and it interacts with disinfection agents such as chlorine to produce carcinogenic and mutagenic compounds in drinking water (Escobar et al. 2001). DOC also influences the solubility of hazardous organic compounds and heavy metals. Resource managers and the general public are invested in the management of DOC in aquatic ecosystems, and additional research is needed to understand the mechanisms of DOC uptake and retention in streams (Edmonds and Grimm 2011, Kaplan et al. 2006, Escobar et al. 2001).

DOC enters streams through groundwater, sub-surface and surface flows, canopy throughfall, and through leaching of leaf litter that falls directly into the stream. DOC is stored in the soil underneath vegetated areas, and storms flush this DOC through and over the ground until it reaches streams (Allan and Castillo 2007). In urban areas, point sources of waste water as well as storm runoff from impervious surfaces elevate streams' DOC concentrations (Steele et al. 2010). Fates of allochthonous and autochthonous DOC in streams include heterotrophic assimilation, respiration, and transport (Edmonds and Grimm 2011, Bernhardt and Likens 2002). DOC can also be photodegraded by UV radiation (Findlay et al. 2001, Edmonds and Grimm 2011) and adsorbed to stream sediments and metal hydroxides (McDowell 1985).

DOC is chemically complex, consisting of numerous labile and refractory compounds. Labile DOC is readily available for heterotrophic uptake, whereas refractory DOC is not as easily assimilated (Battin et al. 2003). Nutrient spiraling studies often assess the uptake of labile DOC compounds such as acetate, glucose, and sucrose (Johnson et al. 2009, Bernhardt and Likens 2002, Newbold et al. 2006, Munn and Meyer 1990). However, studies have also measured uptake rates of the more complex arabinose (Newbold et al. 2006) and leaf leachate (McDowell 1985).

Reported DOC Vf values range from 0.5-15 mm/min (Johnson et al. 2009). Leaf leachate (McDowell 1985) and arabinose (Newbold et al. 2006) had the slowest Vf at

101 approximately 1.26 mm/min. Average glucose Vf was 3.3 mm/min (Newbold et al. 2006).

Murin and Meyer (1990) found that sucrose Sw was 87-357 m, which corresponds to a maximum Vf of 9 mm/min. Acetate had the highest Vf, ranging from 0-21 mm/min (Johnson et al. 2009). Bernhardt and Likens (2002) also found rapid uptake of acetate added to a stream.

Thus far, studies do not suggest that DOC uptake is related to human land uses such as urbanization (Johnson et al. 2009, Newbold et al. 2006). This may correspond with the variable response of ecosystem metabolism to urbanization (Tank et al. 2010, Walsh et al. 2005b). The mechanisms affecting DOC dynamics in urban streams are complex, as is DOC itself. DOC uptake in urban streams may not yet be saturated (especially since nutrient concentrations are also high in urban streams). The types of DOC measured in uptake studies are only a few of the possible DOC compounds found in streams. Additional research is needed to understand the manner in which urbanization affects DOC uptake (Johnson et al. 2009, Wenger et al. 2009).

DOC uptake values reflect both abiotic and biotic processes in streams. Abiotic adsorption to sediments and organic matter is rapid (Findlay and Sobczak 1996) and may account for a substantial proportion of DOC uptake at times (McDowell 1985). Abiotic adsorption initially traps DOC, making it available for later microbial utilization (Findlay and Sobczak 1996). While biotic uptake is typically slower than abiotic adsorption, it is equally as important to DOC retention in streams. Edmonds and Grimm (2011) reported that heterotrophic respiration accounted for 22-100% of downstream declines in DOC concentration. Newbold et al. (2006) found that DOC Vf correlated with ecosystem metabolism. Additional studies have shown that biofilm activity is important to DOC uptake (Battin et al. 2003, Findlay et al. 2003, Bernhardt et al. 2002).

Nitrogen (NOj and NFU)

Nitrogen (N) occurs naturally in aquatic ecosystems; however, anthropogenic activity in recent decades has more than doubled the amount of reactive N entering the environment (Vitousek et al. 1997). Major sources are industrial fixation of N for fertilizer, fossil fuel combustion, and leaky sewage lines. Humans also increase the mobility of N to surface waters by clearing land and destroying wetlands. It is likely that anthropogenic N loading to aquatic ecosystems will continue for the foreseeable future (Galloway et al. 2008). Excess N contributes to eutrophication, and elevated nitrate concentrations in drinking water cause cancer and methemoglobinemia (blue-baby syndrome). Therefore, it is important to understand and manage N retention in streams.

The main N compounds found in streams include the inorganic NH4 and no3, as well as dissolved organic nitrogen (DON) and particulate organic nitrogen. N enters the stream from terrestrial and atmospheric inputs, as well as from bacterial fixation. nh4

102 and no3 are assimilated by stream organisms including benthic algae and microbes. nh4 is easier for organisms to assimilate (because no3 must be converted to nh4 first). When organisms assimilate N, it becomes DON and particulate N. Mineralization is the process by which this organic N is excreted or decomposed back into nh4 (Allen and Castillo 2007).

nh4 is oxidized to no3 by bacteria in an energy yielding reaction known as nitrification. Denitrification is another energy yielding reaction, which uses no3 instead of O2 for the respiration of organic matter. Denitrification produces N2 as an end product, and this is the primary way that N can be permanently removed from the stream. Other fates of N include storage in the benthos and downstream transport (Allan and Castillo 2007). The abiotic adsorption of nh4 onto stream sediments can be substantial, representing nearly all of NH4 uptake at times (Richey et al. 1985).

Studies prior to 2006 found no3 uptake lengths (Sw) ranging from 102-758 m, which corresponds to uptake velocity (vf) values ranging from 0.5 to 4.3 mm/min (interquartile ranges, Ensign and Doyle 2006). Tank et al. (2008) included studies after

2006 and found a greater range of Sw and Vf values for no3. Hall et al. (2009) reported a no3 Sw interquartile range of 70-10,000 m and a Vf interquartile range of 0.7-10 mm/min.

no3 uptake is typically reduced in urban streams. Grimm et al. (2005) reported no3 Sw values of294-1245 m in urban streams vs. 67-90 m in unaltered streams. Corresponding Vf values were 0.021-0.120 mm/min for urban streams vs. 0.077-0.200 mm/min for unaltered streams. Klocker et al. (2009) found that no3 Sw ranged from 356-1341 m and Vf ranged from 0.077-0.540 mm/min in urban streams.

nh4 uptake may also be compromised in urban streams. Meyer et al. (2005) found that NH4 Vf in urban streams ranged from 1.15-8.00 mm/min, whereas forested streams had Vf values ranging from 6.03-9.75 mm/min. Newbold et al. (2006) also reported that urban streams' Vf (average 2.51 mm/min) was slower than forested streams' Vf (average 3.82 mm/min).

N uptake values represent the combination of biological assimilation, nitrification, denitrification, and abiotic adsorption. Studies indicate that autotrophic assimilation may account for a considerable portion of no3 and nh4 uptake (Hall et al. 2009, Kent et al. 2005, Mulholland et al. 2006, Fellows et al. 2006, Hall and Tank 2003). Heterotrophic assimilation is also important to no3 and nh4 retention (Arango et al. 2008, Richey et al. 1985, Ashkenas et al. 2004, Webster et al. 2003, Meyer et al. 2005, and Hall and Tank 2003).

Nitrification varies in its proportion of total nh4 uptake. Arango et al. (2008) found that nitrification rates were an order of magnitude lower than assimilation rates, and Hall and Tank (2003) found no evidence of nitrification. However, Ashkenas et al.

103 (2004) reported that 40-50% of added NH4 was converted to no3. Peterson et al. (2001) found that nitrification accounted for 20-30% of nh4 removal, with assimilatory uptake accounting for the other 70-80%.

Denitrification in streams can be minimal compared to assimilatory uptake (Richey et al. 1985, Arango et al. 2008). In a study assessing 72 streams in 8 regions representing different biomes, Mulholland et al. (2008) found that denitrification accounted for a median of 16% of no3 uptake. However, more than a quarter of streams in this study had denitrification amounts that exceeded 43% of no3 uptake (Mulholland et al. 2008). Denitrification requires adequate no3 concentrations, anoxic conditions, and organic matter. Because denitrification is the process by which no3 can be permanently removed from streams, there is a critical need for research addressing how streams' denitrification rates can be maximized (Craig et al. 2008).

Phosphorus (SRP or po4)

Like N, phosphorus (P) is a naturally occurring nutrient in stream ecosystems that is subject to anthropogenic increases in concentration. Rocks and sediments are the main source of P. Humans mine P for fertilizer, which eventually reaches streams through runoff and sewage. Terrestrial organic matter inputs to streams also contain P, as do eroded sediments. Excess P joins N as a cause of downstream eutrophication, especially in lakes. Therefore, it is important to understand P spiraling in streams (Allan and Castillo 2007, Withers and Jarvie 2008).

Soluble reactive phosphorous (SRP) is the amount of phosphorus that reacts with molybdate during analysis. SRP mainly consists of orthophosphate (po4), although polyphosphates may also be present. SRP and po4 are often used interchangeably to refer to the amount of dissolved inorganic phosphorous present in stream water. Other forms of P found in streams include particulate inorganic phosphorus as well as dissolved and particulate organic phosphorus (Allan and Castillo 2007).

Unlike N, there is not a large reservoir of P in the atmosphere and there are no processes analogous to N fixation, nitrification, or denitrification. Biological P uptake and assimilation convert po4 to organic P. Organic P is mineralized into po4 during decomposition and excretion. Abiotic P uptake is important and includes the adsorption of po4 onto charged sediments and organic matter. Dissolved inorganic and organic P may also precipitate through interactions with calcite or with metal oxides (Allan and Castillo 2007, Withers and Jarvie 2008).

Ensign and Doyle (2006) reviewed P spiraling studies and reported an interquartile range of 32-394 m for P04 Sw. Vf ranged from 0.9-6.0 mm/min (Ensign and

Doyle 2006). Another review included more recent studies and found that po4 Sw ranged

104 from 85-530 m in first order streams (Withers and Jarvie 2008). po4 Sw increases to thousands of meters in larger order streams (Ensign and Doyle 2006, Withers and Jarvie 2008).

Urban streams usually have slower P Vf values than forested streams. For instance, Newbold et al. (2006) found an average po4 Vf of 0.67 mm/min for urban streams vs. 1.37 mm/min for forested streams. Meyer et al. (2005) reported that SRP Vf ranged from 1.86-8.30 mm/min in urban streams, compared to 7.77-11.65 mm/min in forested streams. Additional study is needed to understand P uptake in urban streams (Wenger et al. 2009).

P uptake values represent the combination of biotic and abiotic processes in the stream. Studies suggest that biotic P uptake may be significant. For instance, McDaniel and David (2009) estimated that biotic retention accounted for 32% of P uptake. po4 uptake may be enhanced by the heterotrophic respiration of both fine and coarse benthic organic matter (Mulholland et al. 1985, Mulholland et al. 1997, Newbold et al. 2006, Meyer et al. 2005).

Some studies have reported that po4 uptake is controlled by abiotic adsorption onto stream sediments (Meyer and Likens 1979, Hall et al. 2002). Aldridge et al. (2010) found that abiotic adsorption accounted for more than 70% of total P uptake. The relative importance of adsorption may increase with elevated P concentrations (Mulholland et al. 1990, Davis and Minshall 1999, Aldridge et al. 2010). Due to the deleterious effects of excess P in aquatic ecosystems, it is essential that both the abiotic and biotic pathways of P retention be preserved and rehabilitated (Aldridge et al. 2010).

Factors Influencing Nutrient Spiraling

Managing the effects of anthropogenic nutrient loading to aquatic ecosystems requires an understanding of the mechanisms that drive nutrient uptake and retention in streams (Wenger et al. 2009). Several factors influence the abiotic and biotic uptake of N, P, and DOC. These factors include channel geomorphology, hydrology, nutrient concentration, biological activity, and land use.

The geomorphology of the stream channel controls the travel time of water through the reach. Channels that are heterogeneous and complex delay the passage of stream water, providing increased contact time between the nutrients and the benthos (Grimm et al. 2005, Ensign and Doyle 2006). The more opportunity that stream water has to interact with the stream bottom, the greater the likelihood that nutrients will be retained. This is because nutrient uptake occurs mainly on sediments and biofilms covering submerged surfaces, rather than in the water column (Stream Solute Workshop 1990, Peterson et al. 2001).

105 Channels that are small and shallow also have a greater chance that nutrients will come in contact with benthic uptake sites. Small channels typically have less discharge and slower water velocity than larger channels. Additionally, shallow channels have a greater proportion of their water volume in contact with the benthos (Ensign and Doyle 2006). Studies have found that small streams make a significant contribution to nutrient retention at the watershed scale (Peterson et al. 2001).

Hydrology affects nutrient retention because of the influence of water velocity and depth on uptake (Wollheim et al. 2001, Simon et al. 2005). High discharge periods are thought to be times of nutrient transport, whereas lower flow periods are expected to be times of nutrient uptake (Doyle 2005, Meyer and Likens 1979). Storms bring in additional nutrients from the watershed; these nutrients may pass through the stream so quickly that they have no opportunity to interact with benthic assimilation sites. High discharge can also slough biofilms and flush particulate nutrients away. Nutrient uptake is diminished during and after storms, whereas low discharges allow biofilms to grow and accumulate biomass that is stored on the stream bottom (D'Angelo and Webster 1991, Grimm 1987).

Another important determinant of nutrient retention is the stream's ambient nutrient concentration. At low nutrient concentrations, uptake increases linearly with concentration due to advective transport. The increased nutrient concentration gradient drives diffusion across the bio film's boundary layer, making the nutrient more available for uptake. The increased concentration gradient also enhances sorption onto sediments. However, at some point the stream's benthic assimilation sites begin to saturate. Stream organisms' ability to take up additional nutrients becomes overwhelmed, and further increases in the stream's nutrient concentration lead to decreased uptake rates (Dodds et al. 2002, Grimm et al. 2005). Several studies have reported that nutrient uptake is slower when streams are subject to higher nutrient concentrations (Mulholland et al. 2002, Grimm et al. 2005, Newbold et al. 2006).

Since stream organisms require nutrients for growth and energy, biological demand strongly influences nutrient retention. Ecosystem metabolism has been related to increases in N, P, and DOC uptake (Newbold et al. 2006, Meyer et al. 2005). Therefore, factors that affect ecosystem metabolism (e.g. light, temperature) also affect stream nutrient dynamics. Salts, metals, pesticides, antibiotics, and other toxins may inhibit biotic assimilation and growth (Paul and Meyer 2001). Human activities such as dredging or filling may destroy benthic communities. Without healthy communities of stream organisms, nutrient uptake capacity is reduced.

106 APPENDIX B - BACKGROUND SAMPLING WATER CHEMISTRY DATA

UNHID Sample Collection Br nh4 P04 no3 CI S04 Na K Mg Ca Name Date (mg Br/L) (ugN/L) (•fiP/L) (mgN/L) (mgCl/L) (mgS/L) (mg Na/L) (mgMg/L) (mgCa/L) 88102 PB400Up 5/19/2009 0.00 35.89 6.66 0.07 39.34 1.91 23.24 1.70 2.26 13.20

88101 PB300Up 5/19/2009 0.00 35.08 7.41 0.16 38.80 2.02 22.44 1.97 2.50 14.22

88119 PB205Up 5/19/2009 0.00 20.62 9.33 0.20 49.79 2.34 26.55 2.44 2.82 18.19

88118 PB200Up 5/19/2009 0.03 24.57 5.41 0.47 164.60 4.34 72.65 5.81 5.60 47.83

88117 PBlOOUp 5/19/2009 0.00 19.15 14.36 0.24 90.61 2.98 41.72 3.43 3.64 28.70

88116 PB6Up 5/19/2009 0.12 27.87 5.97 0.24 95.84 3.00 44.50 3.41 3.64 28.85

88115 PBO 5/19/2009 0.00 32.14 6.34 0.24 103.19 2.96 48.30 3.49 3.86 29.97

88106 PB180 5/19/2009 0.34 68.99 1.61 0.67 360.08 5.16 180.90 8.93 11.73 70.51

88107 PB380 5/19/2009 0.25 78.83 5.55 0.49 294.47 4.50 144.58 6.91 8.85 60.36

88108 PB449 5/19/2009 0.17 89.98 2.00 0.43 267.57 4.13 132.52 6.26 7.99 52.11

88111 PB750 5/19/2009 0.11 76.35 3.90 0.48 300.93 4.30 152.01 6.68 8.34 50.88

88112 PB875 5/19/2009 0.22 74.05 6.52 0.52 311.75 4.41 158.42 6.86 8.57 50.21

88113 PB1004 5/19/2009 0.14 86.33 2.79 0.47 300.67 4.37 152.42 6.57 8.47 56.95

88114 PB1075 5/19/2009 0.14 81.24 5.22 0.44 297.36 4.34 149.62 6.42 8.45 56.40 p04 S0 UNHID Sample Collection Br nh4 no3 CI 4 Na k Mg Ca Name (mg Br/L) U P/L (mg NIL) (mgCl/L) (mgS/L) (mg Na/L) (mgMg/L) (mg Ca/L) Date w ( S ) HKIl) 89266 PB180 7/15/2009 0.00 80.01 13.44 0.28 161.99 3.13 83.13 4.74 5,13 32.76

89267 PB380 7/15/2009 0.00 65.93 8.36 0.36 187.89 3.50 94.20 5.43 5.95 38.80

89268 PB449 7/15/2009 0.00 61.23 7.60 0.35 180.25 3.34 95.38 5.47 6.21 41.20

89192 PB765-1 7/15/2009 0.17 58.63 7.33 0.53 248.47 3.89 127.62 6.20 6.65 39.19

89193 PB765-2 7/15/2009 0.00 58.94 7.98 0.50 232.73 3.64 130.24 6.28 6.83 42.04

89194 PB765-3 7/15/2009 0.00 62.29 8.97 0.54 252.45 3.96 130.01 6.27 6.80 40.41

89198 PB790-1 7/15/2009 0.00 61.18 8.85 0.56 260.84 4.06 133.88 6.41 6.93 44.58

89199 PB790-2 7/15/2009 0.00 61.86 27.67 0.45 225.15 3.63 115.47 5.55 5.96 37.56

89200 PB790-3 7/15/2009 0.00 55.82 8.08 0.44 215.97 3.19 118.47 5.79 5.94 38.99

89201 PB824-1 7/15/2009 0.00 64.81 11.50 0.50 252.62 3.88 129.24 6.29 6.64 42.71

89202 PB824-2 7/15/2009 0.00 54.51 10.37 0.46 217.13 3.43 110.23 5.27 5.82 40.41

89203 PB824-3 7/15/2009 0.00 61.03 12.06 0.54 245.26 3.83 134.53 6.45 7.00 45.23

89204 PB848-1 7/15/2009 0.20 57.95 9.86 0.53 254.22 3.99 130.80 6.27 6.82 45.96

89205 PB848-2 7/15/2009 0.00 56.89 11.14 0.53 246.11 3.80 124.60 5.99 6.46 40.01

89206 PB848-3 7/15/2009 0.00 58.28 9.44 0.49 243.27 3.80 131.16 6.30 6.80 41.38

89195 PB875-1 7/15/2009 0.00 63.20 14.03 0.58 263.36 4.15 134.58 6.56 7.02 48.36

89196 PB875-2 7/15/2009 0.00 59.61 14.03 0.51 262.93 4.19 134.79 6.45 7.03 46.01

89197 PB875-3 7/15/2009 0.22 58.87 12.51 0.55 263.44 4.14 134.96 6.46 7.04 47.00 UNH ID Sample Collection Br nh4 P04 no3 CI S04 Na K Mg Ca Name Date (mgBr/L) (ugN/L) (u|?p/L) (mgN/L) (mgCi/L) (mgS/L) (mg Na/L) ^K/L) (mg Mg/L) (mg Ca/L)

89216 PB904-1 7/15/2009 0.00 56.51 12.92 0.56 266.70 4.14 137.05 6.54 7.05 46.36

89217 PB904-2 7/15/2009 0.18 62.37 13.86 0.52 256.38 3.89 131.54 6.35 6.67 41.40

89218 PB904-3 7/15/2009 0.00 55.04 16.87 0.58 261.40 4.01 133.97 6.38 6.88 43.19

89207 PB1004-1 7/15/2009 0.00 82.54 15.48 0.55 255.15 3.89 138.77 6.64 7.19 47.00

89208 PB1004-2 7/15/2009 0.00 64.41 19.25 0.57 271.50 4.21 139.11 6.64 7.22 50.79

89209 PB 1004-3 7/15/2009 0.21 67.78 14.71 0.57 271.14 4.23 139.14 6.68 7.22 50.60

89210 PB 1035-1 7/15/2009 0.00 90.02 11.14 0.57 271.55 4.22 138.98 6.66 7.20 44.74

89211 PB 1035-2 7/15/2009 0.27 62.34 6.98 0.59 272.06 4.21 139.41 6.68 7.23 45.68

89212 PB 1035-3 7/15/2009 0.00 71.64 4.89 0.58 262.84 4.04 138.70 6.65 7.17 44.35

89213 PB 1058-1 7/15/2009 0.00 70.36 9.46 0.59 275.65 4.25 140.74 6.77 7.36 45.10

89214 PB 1058-2 7/15/2009 0.18 58.29 10.97 0.54 292.54 4.38 141.91 6.78 7.48 52.05

89215 PB 1058-3 7/15/2009 0.00 82.69 12.10 0.56 259.51 3.98 141.28 6.73 7.44 48.80

92006 PB-Barton Hall 11/17/2009 0.00 102.05 0.49 192.29 4.56

92007 Barton/Mast 11/17/2009 0.00 16.26 0.04 106.76 3.69

92008 Horse Field 11/17/2009 0.00 26.53 0.07 90.77 3.62 Sample Collection Br nh4 p04 no3 CI S04 Na k Mg Ca UNHID l Name Date (mg Br/L) (ugN/L) W ) (mgN/L) (mgCl/L) (mgS/L) (mg Na/L) (mgK/L) (mg Mg/L) (mg Ca/L) 93993 PB400Up 4/21/2010 0.00 43.30 0.70 0.05 17.41 1.80 12.29 1.51 1.55 7.10

93994 PB375Up 4/21/2010 0.00 0.00 3.05 0.08 17.39 1.84 12.14 1.49 1.55 8.34

93995 PB350Up 4/21/2010 0.00 8.53 13.65 0.06 17.22 1.83 12.16 1.52 1.67 9.73

93996 PB325Up 4/21/2010 0.00 7.98 1.37 0.67 16.78 1.97 11.83 2.05 1.94 9.66

93997 PB300Up 4/21/2010 0.00 11.49 3.39 0.12 17.20 1.84 12.09 1.55 1.62 7.63

93998 PB275Up 4/21/2010 0.00 6.32 0.53 0.15 17.21 1.83 12.19 1.57 1.63 7.67

93999 PB250Up 4/21/2010 0.00 9.24 4.57 0.13 17.23 1.83 12.24 1.57 1.62 7.67

94000 PB225Up 4/21/2010 0.00 2.92 0.00 0.14 17.72 1.88 12.51 1.63 1.64 7.96

94001 PB205Up 4/21/2010 0.00 16.79 0.53 0.15 18.67 1.93 12.91 1.68 1.65 8.27

94002 PBlOOUp 4/21/2010 0.00 8.75 2.55 0.23 24.24 2.16 16.29 1.92 1.80 10.23

94003 PB15Up 4/21/2010 0.00 13.38 1.37 0.21 26.73 2.14 17.80 2.03 1.86 10.70

94004 PB180 4/21/2010 0.00 27.77 0.70 0.72 125.17 3.49 65.58 4.27 4.13 28.47

94005 PB380 4/21/2010 0.00 23.30 1.54 0.50 72.98 2.70 42.19 2.91 2.79 17.35

94006 PB399 4/21/2010 0.00 26.74 2.21 0.46 74.31 2.70 42.70 2.95 2.82 17.65

94007 PB418 4/21/2010 0.00 22.76 2.55 0.53 88.97 2.94 49.20 3.30 3.21 20.76

94008 PB449 4/21/2010 0.00 18.80 3.72 0.51 87.51 2.88 48.74 3.18 3.08 20.08 UNH ID Sample Collection Br NH4 P04 NO3 CI S04 Na K Mg Ca Name Date (mg Br/L) (ug N/L) (ugP/L) (mgN/L) (mgCI/L) (mgS/L) (mg Na/L) (mgK/L) (mgMg/L) (mg Ca/L) 94009 PB750 4/21/2010 0.00 19.96 3.56 0.60 101.05 3.05 56.33 3.40 3.26 20.50 94010 PB765 4/21/2010 0.00 24.52 -0.14 0.61 101.36 3.07 56.83 3.42 3.29 20.61 94011 PB790 4/21/2010 0.00 12.06 1.54 0.61 101.18 3.07 56.80 3.43 3.28 20.58 94012 PB824 4/21/2010 0.00 20.59 3.72 0.60 103.70 3.06 58.17 3.46 3.30 20.83 94013 PB848 4/21/2010 0.00 16.08 1.37 0.64 106.83 3.10 59.62 3.55 3.39 21.46 94014 PB875 4/21/2010 0.00 20.06 0.00 0.63 109.00 3.13 60.89 3.58 3.43 21.67 94015 PB1004 4/21/2010 0.00 35.38 2.88 0.69 118.20 3.26 65.35 3.71 3.56 22.71 94016 PB1035 4/21/2010 0.00 20.22 1.87 0.68 119.30 3.26 65.93 3.73 3.59 22.80 94017 PB1058 4/21/2010 0.00 26.98 7.59 0.68 116.41 3.24 64.76 3.69 3.56 22.32 94018 PB1075 4/21/2010 0.00 26.99 0.36 0.70 122.88 3.29 67.49 3.77 3.69 23.42

94019 PB-Barton Hall 4/21/2010 0.00 152.45 0.00 2.21 390.04 5.50 184.33 12.10 17.98 98.54 94020 Barton/Mast 4/21/2010 0.00 47.72 24.58 0.68 204.88 1.95 125.50 4.20 6.30 27.20 94021 Horse Field 4/21/2010 0.00 30.94 32.32 0.67 227.70 1.77 138.37 3.31 5.84 18.82 UNH ID Sample Collection Br NOj CI so4 Na K Mg Ca Name Date (mg Br/L) (mg N/L) (mg Cl/L) (mgS/L) (mg Na/L) (mg K/L) (mg Mg/L) (mg Ca/L) 95127 PB300Up 7/27/2010 0.00 0.17 27.31 5.12 21.72 3.54 3.61 20.89 95128 PB250Up 7/27/2010 0.00 0.23 25.67 5.30 20.48 3.54 3.82 21.44 95129 PB205Up 7/27/2010 0.00 0.49 36.08 5.27 26.55 4.34 4.00 24.96 95130 PB250 7/27/2010 0.00 0.62 194.39 6.32 103.78 7.54 7.81 55.17 95131 PB300 7/27/2010 0.00 0.60 187.15 6.26 101.01 7.09 7.43 52.86 95132 PB350 7/27/2010 0.00 0.64 194.12 6.60 104.71 7.51 7.53 53.75 95133 PB399 7/27/2010 0.00 0.54 189.60 6.00 102.32 7.11 6.77 49.56 95134 PB418 7/27/2010 0.00 0.55 195.06 6.27 105.57 7.25 7.46 50.61 95135 PB449 7/27/2010 0.00 0.59 205.60 6.22 112.03 7.55 7.56 56.85 95136 PB765 7/26/2010 0.00 0.73 262.56 5.27 150.18 6.79 6.84 50.43 95137 PB790 7/26/2010 0.00 0.73 266.18 5.35 151.69 6.69 6.91 49.22 95138 PB848 7/26/2010 0.00 0.28 63.48 1.98 39.29 2.06 2.11 18.42 95139 PB904 7/26/2010 0.00 0.73 272.24 5.29 156.93 6.98 7.05 52.29 95140 PB929 7/26/2010 0.00 0.71 256.17 5.12 148.59 6.40 6.34 49.19 95141 PB979 7/26/2010 0.00 0.68 253.00 4.93 145.96 6.29 6.08 43.95 95142 PB1004 7/26/2010 0.00 0.78 287.17 5.61 163.45 7.25 7.17 53.07 95143 PB1035 7/26/2010 0.00 0.75 272.14 5.30 156.71 6.81 6.61 47.77 95144 PB1075 7/26/2010 0.00 0.76 278.94 5.42 161.11 7.14 7.09 48.39

96275 PB300Up 9/6/2010 0.04 0.15 21.49 63.57 22.63 6.06 8.37 57.25 96276 PB205Up 9/6/2010 0.00 0.27 28.08 59.54 26.17 6.55 7.80 56.12 96277 PB180 9/6/2010 0.00 0.68 208.49 33.81 118.70 9.51 10.06 74.34 96278 PB380 9/6/2010 0.00 0.76 219.68 29.42 123.39 9.51 10.27 74.86 96279 PB449 9/6/2010 0.00 0.67 215.84 30.33 119.92 9.20 10.07 75.47 APPENDIX C - SPRING EXPERIMENT WATER CHEMISTRY DATA

po UNH ID Sample Collection Br nh4 4 no, TDN NPOC Name Date (mg Br/L) Cue N/L) («e P/L) (mR N/L) (me N/L) (me C/L) 95961 PB180-Prel 5/5/2010 92.95 13.00 0.69 5.04 95962 PB180-Pre2 5/5/2010 1 16.19 22.00 95963 PB 1 80-Pre3 5/5/2010 96.1 1 15.00 0.33 95964 PB230-Pre 1 5/5/2010 84.35 5.87 0.63 5.20 95965 PB230-Pre2 5/5/2010 90.95 17.00 95966 PB230-Pre3 5/5/2010 95.53 16.00 0.33 95967 PB264-Prel 5/5/2010 88.94 19.00 0.65 5.30 95968 PB264-Pre2 5/5/2010 94.96 12.00 95969 PB264-Pre3 5/5/2010 90.95 15.00 0.32 95970 PB297-Prel 5/5/2010 1 15.04 18.00 0.67 5.25 95971 PB297-Pre2 5/5/2010 1 1 1.88 19.00 95972 PB297-Pre3 5/5/2010 120.49 8.00 0.36 95973 PB330-Prel 5/5/2010 93.24 15.00 0.63 5.56 95974 PB330-Pre2 5/5/2010 104.43 15.00 95975 PB330-Pre3 5/5/2010 1 1 1.02 9.00 0.27 95976 PB350-Prel 5/5/2010 95.53 16.00 0.68 5.69 95977 PB350-Pre2 5/5/2010 84.92 12.00 95978 PB350-Pre3 5/5/2010 1 13.03 9.00 0.27 95979 PB380-Pre 1 5/5/2010 88.94 17.00 0.61 5.24 95980 PB380-Pre2 5/5/2010 93.81 10.00 95981 PB380-Pre3 5/5/2010 85.78 9.00 0.28 Note: Br concentration was assumed to be 0 mg Br/L for all "Pre" samples in this nh4/po4 addition (based on the average of all other ambient Br concentrations). nh4 N0 UNH ID Sample Collection Br P04 3 TDN NPOC Name Date (mg Br/L) (ug N/L) (ug P/L) (mg N/L) (mg N/L) (mg C/L) 95982 PB399-Prel 5/5/2010 76.32 9.00 0.64 5.29 95983 PB399-Pre2 5/5/2010 80.33 10.00 95984 PB399-Pre3 5/5/2010 83.20 9.00 0.30 95985 PB418-Pre 1 5/5/2010 99.26 16.00 0.63 5.04 95986 PB418-Pre2 5/5/2010 69.72 11.00 95987 PB418-Pre3 5/5/2010 70.58 9.00 0.31 95988 PB449-Prel 5/5/2010 69.72 10.00 0.63 5.31 95989 PB449-Pre2 5/5/2010 75.17 9.00 95990 PB449-Pre3 5/5/2010 69.43 7.00 0.31 95994 PB180-Platl 5/5/2010 201.37 16.00 0.70 5.64 95995 PB180-Plat2 5/5/2010 86.07 9.00 95996 PB180-Plat3 5/5/2010 100.41 9.00 0.32 96021 PB230-Platl 5/5/2010 0.80 213.13 19.00 0.78 5.53 96022 PB230-Plat2 5/5/2010 0.83 215.71 96023 PB230-Plat3 5/5/2010 0.85 271.64 17.18 0.32 96018 PB264-Platl 5/5/2010 0.83 187.32 13.00 0.76 5.02 96019 PB264-Plat2 5/5/2010 0.88 286.94 16.39 96020 PB264-Plat3 5/5/2010 0.79 235.44 15.21 0.33 96015 PB297-Platl 5/5/2010 0.92 178.71 14.00 0.81 4.97 96016 PB297-Plat2 5/5/2010 0.87 199.46 12.26 96017 PB297-Plat3 5/5/2010 0.91 187.60 15.41 0.38 Vote: Br concentration was assumed to be 0 mg Br/L for a 1 "Pre" samples in this nh4/po4 addition (based on the average of all other ambient Br concentrations). J 0 0 K CL. Z Z • U 5 « •- Q z s « V © Sample *6$ NPOC fc z

ID "W UNH Z "5 /•"S /^S w s s s H ex ex V 01 M W Name fi 01 ng C/L) m co o o o co o "3" oH oH (N © 00 in in r- n r- No VO NO NO NO | 96014 C3 16.02 CO o o o o o T (N (N oH cu r- CQ in in in ON ON in in NO (N NO +-»

| 96009 C3 16.00

o e i co o o o o oH co m © in in oH CQ n NO | 96011 cs 12.55 o o o o o o oH co 00 © Cu in CQ in r- r- NO n •HH | 96007 CS 19.00 115 o co o co 00 o o oH o o eu (N © O CQ in in f- ON en

|96008 C3

0 9 1 O 0 o oH oH o © o *n f> o o ON OQ

\ z ^ NO co ON rt CO CO Q z in ^ ON 0 i (N (N 0 z

w 1 0 0

0 0 0 cu © 7.45 6.00 7.00 7.62 9.00 4.32 15.97 17.32 13.64 15.19 14.22 14.22 12.08 13.05 0- W 11.31 13.25 3

/-•s ON (N

ON co 00 NO 0 ON 00 00 0 (N O r- 00 r- r-- 00 r-~ 00 00 00 00 00 00 Br O O 0 0 0 0 0 0 0 0 0 O 0 O 0 (mg Br/L)

O O 0 O O 0 0 0 0 0 0 0 0 0 O 0 O 0 O O 0 O 0 0 0 0 0 0 0 0 0 0 O 0 O 0

117 /"•s U e3 fN X n in rf •t Z P ** wC z g m n in H g o o O O o o o © wE /«•* tn m t fN 0 z (N fN fN fN fN fN fN fN Z W O O o o o © © © E

w 1 0 6 0 /"•s 0 0 0 o o 00 © o © © © 0 ft. o o \q o o © © © 00 8.00 5.49 NO 6.81 10.73 13.25 11.70 15.19 12.00 13.00 18.00 12.28 12.08 ft. Dl t' 00 15.00 00 t' 11.31 w3

/-—S fN fN X rt NO o in m fN X Tt fN r- X •3- NO © fN On X

00 ro m • NO o\ NO fN "t r-~ X fN r» o On r- X x X X X X X X X X X 00 X X h- X X X r» X X X Br o o o o o o o o O O o o o o o o © o o © o o © (mg Br/L)

o o o o o o o o o o o o o o o o © © © © © © o © g o © © © © © © © © o o o o © © © © © © © © © © fN (N fN fN ollection ro m m m ro m m co CO n m m V t •t "t TJ- 't "t "t rf- t 1 Name Sample 1 004-Plat3 1 004-Plat2 PB904-Platl PB904-Plat3 PB929-Plat2 PB929-Plat3 PB954-Platl PB954-Plat2 PB979-Plat2 PB979-Plat3 PB 1 004-Plat PB PB PB1035-Platl PB1035-Plat3 PB1058-Platl PB1058-Plat2 PB1058-Plat3 PB1075-Platl PB1075-Plat2 PB1075-Plat3 PB904-Plat2 PB929-Plat 1 PB954-Plat3 PB979-Platl PB1035-Plat2 95934 95935 95930 95932 95928 95929 95924 95925 95926 95921 95922 95923 95918 95919 95920 95939 95940 95941 95936 95937 95938 95933 95931 95927 UNH ID | | | | | | | | | | | | | | | | | | | | | | | I

118 APPENDIX D - SUMMER EXPERIMENT WATER CHEMISTRY DATA

Sample Collection Br nh4 P04 NO, TDN NPOC CI S04 Na k Mg Ca UNHID m Name Date (mg Br/L) (ufiN/l) (ufip/l) (mfiN/L) (•rn/l) (mfiC/L) (mgCI/L) (mgS/L) (mg Na/L) H ) (mg Mg/L) (mgCa/L) 91887 PB180-Prel 8/18/2009 0.00 81.33 4.52 0.53 0.89 6.02 199.72 3.58 104.97 6.07 6.15 30.88 91888 PB180-Pre2 8/18/2009 0.00 77.16 6.54 0.38 152.85 2.80 81.48 4.59 4.69 27.76 91889 PB180-Pre3 8/18/2009 0.00 85.67 3.32 0.49 187.54 3.32 99.94 5.49 5.71 29.09 91890 PB230-Prel 8/18/2009 0.00 77.80 4.80 0.53 0.86 5.91 195.79 3.47 102.34 6.06 6.17 31.34 91891 PB230-Pre2 8/18/2009 0.00 79.38 4.54 0.54 207.20 3.69 108.48 6.27 6.42 34.39 91892 PB230-Pre3 8/18/2009 0.00 77.25 4.82 0.53 206.96 3.69 108.32 6.42 6.53 30.61 91893 PB264-Prel 8/18/2009 0.00 78.83 6.84 0.52 0.91 6.06 199.86 3.52 104.63 6.05 6.17 31.73 91894 PB264-Pre2 8/18/2009 0.00 77.21 3.08 0.53 202.42 3.57 106.14 6.29 6.38 33.58 91895 PB264-Pre3 8/18/2009 0.00 78.11 5.24 0.55 205.05 3.68 107.65 6.35 6.48 36.89 91896 PB297-Prel 8/18/2009 0.00 81.38 4.03 0.55 0.87 5.76 204.37 3.60 107.02 6.31 6.46 36.05 91897 PB297-Pre2 8/18/2009 0.00 78.74 5.52 0.57 206.64 3.65 108.14 6.39 6.52 32.57 91898 PB297-Pre3 8/18/2009 0.00 74.47 4.99 0.50 184.34 3.38 96.28 5.40 5.81 34.00 91899 PB330-Prel 8/18/2009 0.00 72.37 3.81 0.59 0.78 5.81 218.83 3.72 113.79 6.71 6.83 32.31 91900 PB330-Pre2 8/18/2009 0.00 76.29 1.79 0.59 220.66 3.80 114.84 6.73 6.93 36.09 91901 PB330-Pre3 8/18/2009 0.00 76.02 4.37 0.57 220.22 3.84 114.60 6.72 6.92 36.89 *4ote: 8/18/2009 was a nh4/po4 addition. OO •n ON r-« oo CM OO OO OO oo m «o ON «n i— NO U«i <-> cm in OO •rrro orO ON oCO >nco CO CO COr-~' coNO COCM £ r-4 r-4

r~- ON r— oo *y~i r~~ r~- rsi r-- CN| r-- CO o> ON ON CM OO s s ON ON c~> m NO r— o_ On oo oo r-^ oo ON oo Mg NO NO NO NO NO NO NO NO en in «n NO NO NO NO NO NO (mg Mg/L) r- o NO in NO oo r-~- r~- Tt- Tf r-«- ON •^r OO ON o CO ON r~~- *6 * oo OS 3 NO NO s r— ON r~- C-l ON ON oo oo m «n NO r-» NO NO at in in NO NO NO NO NO NO NO NO •rf r-4 >n

cmt— OsO Tj"NO NO cm r-~-NO v> rs ONTt- OO"cr rnr-- r— r^i ooON •rfm oNO CO ON OO oNO -«3-NO ro ro fO NO NO oo r-^ csi CN c-4 co CO r^i Na oot—^ *D o> s (mg Na/L) o «« cor- co"«3" NO N©r-~ "rr ONr-^ ofO oo ON NO ON-**• CZ5 oo fO rn r4 rsi rn CO CO CO CO co co CO B

coOO innO cmOO r^iOO roNO «n •^rrsi Ofvi r—NO s •*1" »o «n in l> • 61 ON ONNO ONOn

<-> 5 cm ooo> ONNO r~~NO OCO Os inNO %« NO in uS NO in in z J. <=> Z Z *nOO oor— OONO OO ON in m g ~ <=> o < 5.

<=> <=> O Z »n m O"Tf*N inr-~- «n O^3-n u-1OO «n csNO rsMl «nNO CO«n min NO NO NO mON inOO CMNO Z M o O O ® O <=> <=> <=> <=> <=> <=> C3> <=> s.

<=> Ov r- NO CM r— «n w> O r-4 •^1" CN| r-• ON OJ On <3 CM<=> o ®- cm r-^ o CM NO ON oo rn <=> r^i ON ro in

OO OO ON oo oo oo r~~ r^i rn Tf ON On inoo NO«n NO •^rrvj C-J COCM 33 Z co r- o •«sf* oo >T) NO o rO r *n »n NO OO oo CO cO^r CO co co co

o o <=> <=> o o in "t CO in Br o <=> c> o o o c5 o o «o o g o 8rs s o o Sr^i

Collection OO OO OO oo oo oo oo oo oS oo oo oo oo oo oo oo oo oo oo oo oo

CM co cm m rsj rO C3 CO Oj CO rj co

Name <3> Sample o o Os OO oo OO On On GfN O) cr> OOro COOO COOO coON ONro ONPO 5 5 oo oo oo o>»CO CO CNCO CMNO CMNO sCM CQ CO CQ CO CQ CO CQ CQ CQ CQ CQ pa CQ PQ CQ CQ CO CO CQ CQ CO o. cu cu Cu cu cu Cu cu CU cu CU o. CU CU CU CU cu CU cu cu cu o CM rO m NO r-~- oo ON o> rs m NO r-» oo ON o CM s ONO ONO oON ON On oOn ON ON ON ON ON ON ON Os ONCNJ 04ON ONCM z ON ON ON ON §ON ON §ON ON ON ON ON ON s: ON ON ON ON ON ON ON

120 UNHID Sample Collection Br nh4 P04 no3 TDN NPOC CI S04 Na K Mg Ca Name Date (mgBr/L) (ugN/L) (UfP/L) (mgN/L) (mgC/L) Hm (mgS/L) (mg Na/L) (mfiK/L) (mgMg/L) (mgCa/L) 91923 PB297-Platl 8/18/2009 1.52 339.02 18.57 0.65 1.13 5.27 224.35 3.97 115.75 6.94 7.14 35.68 91924 PB297-Plat2 8/18/2009 1.54 340.91 15.69 0.66 225.55 3.99 116.35 6.98 7.20 36.27 91925 PB297-Plat3 8/18/2009 1.45 344.27 16.25 0.62 223.41 3.98 115.32 6.90 7.14 36.89 91926 PB330-Platl 8/18/2009 1.50 301.62 17.02 0.81 1.23 4.76 242.15 4.43 123.92 7.55 7.97 42.82 91927 PB330-Plat2 8/18/2009 1.49 307.29 15.24 0.82 235.05 4.29 120.19 7.30 7.74 38.44 91928 PB330-Plat3 8/18/2009 1.42 302.01 14.84 0.76 242.00 4.51 123.99 7.54 7.98 42.51 91929 PB-380-Platl 8/18/2009 1.44 240.80 15.69 0.80 1.18 4.54 251.70 4.46 127.28 7.63 8.26 45.88 91930 PB-380-Plat2 8/18/2009 1.41 244.06 16.38 0.82 249.11 4.48 127.49 7.66 8.26 44.88 91932 PB-399-Platl 8/18/2009 1.41 269.32 14.28 0.67 1.15 5.34 220.46 3.96 114.46 6.78 7.07 38.77 91933 PB-399-Plat2 8/18/2009 1.54 273.57 17.03 0.77 220.37 3.92 114.46 6.78 7.06 37.51 91934 PB-399-Plat3 8/18/2009 1.44 273.36 15.53 0.71 220.09 3.91 114.31 6.78 7.07 38.33 91935 PB-418-Platl 8/18/2009 1.39 264.32 12.61 0.69 1.13 5.16 223.17 3.96 115.43 6.90 7.17 38.05 91936 PB-418-Plat2 8/18/2009 1.45 255.07 14.95 0.74 223.12 3.95 115.52 6.88 7.17 36.28 91937 PB-418-Plat3 8/18/2009 1.50 248.13 11.95 0.72 223.21 3.91 115.52 6.89 7.16 32.79 91938 PB-449-Platl 8/18/2009 1.32 249.55 14.99 0.76 1.17 4.89 229.40 4.21 118.45 7.10 7.54 44.73 91939 PB-449-Plat2 8/18/2009 1.46 246.37 12.13 0.80 230.23 4.07 118.85 7.11 7.46 38.99 PO UNH ID Sample Collection Br NH4 4 NO3 TDN NPOC CI so4 Name Date (mg Br/L) (ugN/L) (ugP/L) (mg N/L) (mg N/L) (mgC/L) (mgCI/L) (mgS/L) 90199 PB750-Prel 8/14/2009 0.00 37.29 14.12 0.47 0.77 6.18 201.71 2.88 90200 PB750-Pre2 8/14/2009 0.00 39.05 12.74 0.53 202.56 2.95 90201 PB750-Pre3 8/14/2009 0.00 33.33 9.28 0.52 201.46 2.90 90121 PB765-Prel 8/14/2009 0.00 32.73 12.39 0.46 0.67 5.62 182.38 2.68 90122 PB765-Pre2 8/14/2009 0.00 32.62 8.59 0.43 180.90 2.67 90123 PB765-Pre3 8/14/2009 0.00 32.36 11.87 0.48 185.91 2.74 90124 PB790-Prel 8/14/2009 0.00 36.25 12.56 0.47 0.74 6.30 186.67 2.83 90125 PB790-Pre2 8/14/2009 0.00 32.29 8.93 0.48 186.85 2.75 90126 PB790-Pre3 8/14/2009 0.00 33.88 9.62 0.45 186.87 2.76 90127 PB824-Prel 8/14/2009 0.00 27.48 30.72 0.35 130.38 2.17 90128 PB824-Pre2 8/14/2009 0.00 32.81 13.60 0.46 0.73 6.14 189.80 2.78 90129 PB824-Pre3 8/14/2009 0.00 35.13 12.39 0.46 189.55 2.78 90130 PB848-Prel 8/14/2009 0.00 27.01 11.87 0.45 0.69 6.02 183.75 2.67 90131 PB848-Pre2 8/14/2009 0.00 32.01 13.43 0.43 171.94 2.58 90132 PB848-Pre3 8/14/2009 0.00 17.93 9.45 0.24 97.92 1.54 90133 PB875-Prel 8/14/2009 0.00 28.18 11.18 0.41 0.66 5.83 169.91 2.48 90134 PB875-Pre2 8/14/2009 0.00 28.67 27.43 0.34 142.92 2.16 90135 PB875-Pre3 8/14/2009 0.00 29.01 9.28 0.47 191.79 2.73 *«Jote: 8/14/2009 was a nh4/ po4 addition. 2 Tt O Os CO sO o OS wo o^ Tt o Os r- o 00 Tt (N CO r- (N O o (« r- 00 r- 00 sO r- 00 sO r- 00 00 m 00 r- 00 00 Os ON Os Os o Sf (N CN

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y*s (N C^i o o Os Os Tf fN SO so Tt 00 m r- r- m m SO in Os o Os CO OS r- cO 00 OS

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123 o o O SK C/3 Pm oS - UNHID Sample Collection - TDN NPOC CI Na K Mg Ca se Om ^ oa >& S, 9 3 or ox Name Date Dl ©JC (mgN/L) (mgC/L) (mg Cl/L) M (mg Na/L) (mgK/L) (mg Mg/L) (mg Ca/L) CD CD uS r~- c£ CD |90196 PB750-Platl 8/14/2009 35.39 209.67 r-4 CD CD CD O |90197 PB750-Plat2 8/14/2009 34.81 10.14 208.56 CN OO CD CD <=> •rj- SO SO Os sO OO

|90198 PB750-Plat3 8/14/2009 31.16 182.60 to

| W l l | | | 9 1 0 6 0 s CD SO TT CD to co to CD PB765-Platl 8/14/2009 386.18 61.33 211.84 116.66 to 3 rn oo OO OO oo CD OO Os CO 212.14 116.29 21.13 | •rr •rr CO CD to SO r-- CO CO CD <3> to r— |90164 PB790-Plat2 8/14/2009 365.13 72.57 to to to r*- 215.26 118.17 21.16 | 124 CD CD SO co

I 90165 PB790-Plat3 8/14/2009 379.73 69.11 215.62 118.37 r—- rsj r^i r-^ Os

|90167 PB-824-Plat2 8/14/2009 374.36 75.51 220.90 120.61 to 23.85 |

| | l l l SO 1— i CD CsJ CO SO to to oo Os Os CD CO CO <0 to |90168 PB-824-Plat3 8/14/2009 367.58 56.83 221.09 120.71 to o CD SO o> C5 r-4 sO OO oo rsi to r- to CO |90169 PB848-Platl 8/14/2009 73.78 220.58 120.87 to to to 23.28 | SO ?S) CO r-4 c> OO oo rf; CO |90170 PB848-Plat2 8/14/2009 383.91 71.88 220.47 120.78 to to 22.25 | o sO oo CO Os |90171 PB848-Plat3 8/14/2009 400.18 76.37 219.95 120.57 to to 24.47 | *o co co -rf SO OO sO r-4 <=> to oo CO CZ3 to to to to r- |90172 PB875-Platl 8/14/2009 384.54 r-~ 222.57 121.97 20.82 | (N co sO CD OO oo oo oo CO CO to |90173 PB875-Plat2 8/14/2009 384.53 73.78 222.43 to 22.48 [ 1— c^i SO oo co Os CO to to |90174 PB875-Plat3 8/14/2009 388.33 72.05

UNHID 1 .a. &• z it J= js at ox ox ox DX Name Date (mgBr/L) (mgN/L) gf (mg Na/L) (mgK/L) (mgMg/L) (mgCa/L) ® c-i rN CO OO OO OO OO <=> SO wS vS «"CJ- |90178 PB929-Platl 8/14/2009 349.93 69.80 224.94 uo 122.99 24.70 | o <=> so co O rN sO ON «n ON r—- i/S |90179 PB929-Plat2 8/14/2009 343.86 61.85 vo 226.37 123.84 wS 23.36 | so O vS SO <=> SO ON OO vS |90180 PB929-Plat3 8/14/2009 338.31 62.02 225.96 m 123.61 22.00 | O SO rN ® rN On OO i/S |90181 PB954-Platl 8/14/2009 335.20 58.04 225.28 123.14 wo 23.08 | rN O SO •n co co Tf- ON r-~ iO ON <=5 to i/o |90182 PB954-Plat2 8/14/2009 331.64 51.64 226.26 123.57 ® 22.01 |

•ri fN <=> WO <=5 so OO >n ON c«-> PO

|90183 PB954-Plat3 8/14/2009 349.59 57.01 226.60 123.90 WO 22.13 | z z z o m O CN in OO Os c*S w*> |90184 PB979-Platl 8/14/2009 304.75 59.25 vo OO 123.03 22.90 | o f- co rN «n C5 rN «tn ro sd sO r—

|90185 PB979-Plat2 8/14/2009 341.93 57.87 wo 230.14 125.89 23.76 |

m o m CN c r- SO CN o> Os sO sO Os wo wS 125 |90186 PB979-PIat3 8/14/2009 343.02 60.29 124.65 24.57 ON SO ® sO in co vS CN rN |90187 PB1004-Platl 8/14/2009 wo 369.12 62.54 226.63 •n ON ON •n OO m rO fN

|90188 PB1004-Plat2 8/14/2009 64.10 226.12 <=5

Z " 9 T C OO ON 9 <=> O ON «n |90189 PB1004-Plat3 8/14/2009 360.71 64.10 cO CN 00 OO rn rN CN CD ON in iri CO |90190 PB1035-Platl 8/14/2009 360.00 54.58 V) 225.31 !— -rr |90191 PB1035-Plat2 8/14/2009 296.34 61.67 0.44 166.74 rN sO oo OO sO O SO w->

|90192 PB1035-Plat3 8/14/2009 359.46 58.39 225.07 CO

6 0 9 8 o OO OO rN Os CO 1—

|90193 PB1058-Platl 8/14/2009 357.34 WO 230.07

0 9 0 00 0 rN iri sq I/O

|90194 PB1058-Plat2 8/14/2009 351.65 59.43 230.91 CO CO

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|90195 PB1058-Plat3 8/14/2009 359.21 62.89 231.45 CO CO

z z z rs o m ON SO CO ON so CO rN ON iri r-> |90286 PB1075-Platl 8/14/2009 352.22 60.12 124.25 wS 24.60 1 SO o CO OO cdi SO OO OO c«o ON OO ON OO CN rN |90287 PB1075-Plat2 8/14/2009 308.29 72.57 153.91 83.27 20.21 1 cO OO OO co os SO cO Os r-- in «n |90288 PB1075-Plat3 8/14/2009 361.39 47.49 226.94 123.28 m 25.26 | UNH ID Sample Collection Br NO, NH4 PO4 TDN NPOC Name Date (mg Br/L) (mg N/L) (ug N/L) (ue P/L) (mg N/L) (mg C/L) 95991 PB1 80-Pre 1 8/10/2010 0.65 76.38 0.90 3.86 95992 PB1 80-Pre2 8/10/2010 0.70 95993 PB1 80-Pre3 8/10/2010 0.76 48.18 96025 PB225-Pre 1 8/10/2010 0.36 45.45 0.72 5.88 96026 PB225-Pre2 8/10/2010 0.37 96027 PB225-Pre3 8/10/2010 0.36 64.87 96028 PB250-Prel 8/10/2010 0.38 67.49 0.72 5.71 96029 PB250-Pre2 8/10/2010 0.37 96030 PB250-Pre3 8/10/2010 0.37 66.82 96031 PB275-Prel 8/10/2010 0.41 33.18 0.73 5.65 96032 PB275-Pre2 8/10/2010 0.40 96033 PB275-Pre3 8/10/2010 0.41 66.04 96034 PB300-Pre 1 8/10/2010 0.58 44.21 0.85 4.98 96035 PB300-Pre2 8/10/2010 0.58 96036 PB300-Pre3 8/10/2010 53.42 96037 PB325-Prel 8/10/2010 0.66 46.68 0.88 5.05 96038 PB325-Pre2 8/10/2010 0.64 96039 PB325-Pre3 8/10/2010 0.64 50.51 96040 PB350~Prel 8/10/2010 0.46 75.71 0.73 5.37 96041 PB350-Pre2 8/10/2010 0.44 96042 PB350-Pre3 8/10/2010 0.44 59.63 96043 PB380-Prel 8/10/2010 0.50 48.93 0.74 5.18 96044 PB380-Pre2 8/10/2010 0.49 96045 PB380-Pre3 8/10/2010 0.51 56.14 Note: Br concentration was assumed to be 0 mg Br/L for all "Pre" samples in this NO3 addition (based on the average of all other ambient Br concentrations). UNH ID Sample Collection Br N03 NH4 PO4 TDN NPOC Name Date (mg Br/L) (mg N/L) (ug N/L) (ug P/L) (mg N/L) (mg C/L) 96046 PB399-Prel 8/10/2010 0.56 61.98 0.79 4.69 96047 PB399-Pre2 8/10/2010 0.62 96048 PB399-Pre3 8/10/2010 0.63 54.78 96049 PB418-Pre 1 8/10/2010 0.52 46.68 0.76 5.21 96050 PB418-Pre2 8/10/2010 0.50 96051 PB418-Pre3 8/10/2010 0.52 50.90 96052 PB449-Prel 8/10/2010 0.52 35.66 0.79 5.45 96053 PB449-Pre2 8/10/2010 0.54 96054 PB449-Pre3 8/10/2010 0.51 48.76 96085 PB180-Platl 8/10/2010 0.56 40.27 0.83 5.42 96086 PB180-Plat2 8/10/2010 0.56 96087 PB180-Plat3 8/10/2010 0.56 70.50 96082 PB225-Platl 8/10/2010 0.91 1.84 79.64 1.94 5.27 96083 PB225-Plat2 8/10/2010 1.01 1.91 96084 PB225-Plat3 8/10/2010 0.90 1.86 67.01 96079 PB250-Platl 8/10/2010 1.48 2.90 105.40 2.93 4.82 96080 PB250-Plat2 8/10/2010 1.48 2.96 96081 PB250-Plat3 8/10/2010 1.50 2.96 59.24 96076 PB275-Platl 8/10/2010 1.15 2.49 70.19 2.45 4.30 96077 PB275-Plat2 8/10/2010 1.18 2.49 96078 PB275-Plat3 8/10/2010 1.19 2.54 48.18 Note: Br concentration was assumed to be 0 mg Br/L for all "Pre" samples in this NO3 addition (based on the average of all other ambient Br concentrations). u 5? ^ r} o Ci en m m ON o W U cn O) 00 r-; r- ON 5: w i/S Tt" '^: •

z ss - «J 00 ON ON r- o ®< v© in ON r—i in VO ON in 00 Os r-H* ON C) ON ^p"* fcfw* ON r-~ VO in 00 VO w3 /—s , eJ ON ON in r- 00 rn rf; o o •

^t r- ON o vO VO VO m (N vO 00 r- 't in 00 00 r- r- #£o z IT, r-^ v~- r~ S in VO (N o o o ON ON ON z w —H «—H ^-4 "-C « O © o o O o o o o o O o O O O o o O O O O & «8

ro (N en (N m ® fl>V rj rj rj CO a, c 15 03 C3 ts ra e3 ej J§ s J3 e3 Ca « e ®r e e e e s ®T S e e CU ft. e CU oH e e e oH e 5 z © © © T in O

128 UNH ID Sample Collection Br NOJ NH4 P04 TDN NPOC CI S04 Na K Mg Ca Name Date (mg Br/L) (mgN/L) (ugN/L) (ugP/L) (mgN/L) (mgC/L) (mfiCl/L) (mg S/L) (mg Na/L) (mgK/L) (mgMg/L) (mgCa/L) 95217 PB750-Prel 8/4/2010 0.00 0.98 37.59 1.17 6.55 261.22 4.30 152.65 5.56 5.21 35.50 95218 PB750-Pre2 8/4/2010 0.00 0.88 40.60 258.01 4.14 154.18 4.64 4.94 35.70 95219 PB750-Pre3 8/4/2010 0.00 0.91 42.40 251.15 4.03 144.57 5.96 5.13 35.44 95220 PB765-Prel 8/4/2010 0.00 0.87 79.20 3.09 223.02 4.29 129.30 6.36 5.20 37.46 95221 PB765-Pre2 8/4/2010 0.00 0.82 95.10 215.96 4.10 126.22 5.51 4.91 36.04 95222 PB765-Pre3 8/4/2010 0.00 0.86 96.30 222.07 4.10 129.07 5.92 5.45 38.29 95223 PB790-Prel 8/4/2010 0.00 0.85 52.70 1.21 9.16 225.86 4.35 129.92 6.59 5.50 35.74 95224 PB790-Pre2 8/4/2010 0.00 0.82 109.20 219.19 4.11 127.96 6.00 5.39 31.97 95225 PB790-Pre3 8/4/2010 0.00 0.86 116.60 231.61 4.40 133.94 6.67 5.89 39.57 95226 PB824-Prel 8/4/2010 0.00 0.83 98.80 13.15 1.17 8.64 222.35 4.26 127.35 6.46 5.38 36.84 95227 PB824-Pre2 8/4/2010 0.00 0.85 109.90 228.75 4.29 132.12 6.23 5.53 44.39 95228 PB824-Pre3 8/4/2010 0.00 0.76 91.47 214.92 4.24 124.94 6.31 5.60 33.76 95229 PB848-Prel 8/4/2010 0.00 0.81 53.80 18.34 1.17 8.80 238.01 4.48 136.47 6.92 5.80 36.80 95230 PB848-Pre2 8/4/2010 0.00 0.33 90.30 109.25 2.31 63.94 3.09 2.96 26.72 95231 PB848-Pre3 8/4/2010 0.00 0.78 119.10 234.51 4.37 134.30 6.68 5.86 39.49 95232 PB875-Prel 8/4/2010 0.02 0.79 104.50 26.71 1.12 8.29 239.82 4.42 134.45 6.47 5.43 30.53 95233 PB875-Pre2 8/4/2010 0.00 0.77 103.90 235.72 4.31 136.21 6.17 5.79 40.01 95234 PB875-Pre3 8/4/2010 0.00 0.78 96.30 239.12 4.43 133.28 6.83 5.97 39.32 95235 PB904-Prel 8/4/2010 0.00 0.78 109.50 36.42 1.18 8.51 252.12 4.58 143.31 6.90 6.46 41.73 95236 PB904-Pre2 8/4/2010 0.00 0.76 118.80 243.33 4.37 140.86 6.52 6.12 41.00 95237 PB904-Pre3 8/4/2010 0.00 0.76 108.55 247.89 4.53 137.99 6.35 6.41 41.64 Note: 8/4/2010 was a NO3 addition. O £ C/3 z Z 35 cT <-> u o © u u O £- z Z z flu # a Sample Br CJ)

UNHID I 5 , ? a 5 <*) £ Z z 5" 5? pa Z t3 z £ £ £ £ "e3 a. a. ex ox en ox S. o> 9 ox Ol ox ox ox 3 M B

Name . (mg Cl/L) (mg Ca/L) 1 o o O W~t <=> ro oo r-j ON •t ro r-- oo CN rO oo -rf CN ON •*T r— r-- Tf r-* i/~i | 95238 PB929-Prel 97.30 W~> wo o o <=> <=> CD •A) c^l OO Tf- ro •T) r— r— cr> NO T co ro IT) ro Cs» rO ON rO ON ON OO ON | 95239 PB929-Pre2 w~> NO NO o o o o oo o> oo o> ON 5 ^r RS r- OO m ro oo ro "3- ro oo oo OJ NO iO r~- rr ON | 95242 PB954-Pre2 NO NO o o o o o o O oo oo r— ON ON TF "=f »D 1— ro r^j rO c> OO OO r— •*4" OO •*3- | 95243 PB954-Pre3 NO WO NO wo NO o o o o NO rs "Tj- r- oo o> « cs c- r- es CD r~- vj w~> NO NO NO | 95244 PB979-Prel Tj- s o o o oo C5 csl O-J ^r oo ro oo r- O *«** -rf- r-j oo ro ro R^I u~) rO ON ON ON NO NO lO 130 |95246 PB979-Pre3 o o o o o o rsi NO ro o o OO r— r-» oo oo ro Tf OJ rsi ro o> ro i— CN| •^r T r^i r^i TT CNI ON r- r- NO O NO |95249 PB1004-Pre3 w^> o o oo «rf o> oo ro •ri ro ro o W~i CD r~~ Tt- NO NO |95251 PB1035-Pre2 W> o o oo o> Ovl o O rs Tf oo r^i oo o> rsi oo ro ro w> NO NO NO o o <=> O O r- NO O rs O oo <=> ro ro CN| CNl ON ro ro oo cs CN r-4 OO *O CD NO CNI NO d> oo r~- r~~ w~> i— NO f 95253 PB1058-Prel NO o o oo o oo o> o> 0> rs| r— TT oo rs rs "^1- r- t r- ro CD OO •*r r~~ wo o o o o o oo r- S o> c— fN ON r- rs ro oo oo OS r^i OO r— Tj- r-Nj NO NO -rr W~1 w-» |95255 PB1058-Pre3 NO s o o o oo rs r- oo ro o ro rs ro ^r ^r oo w-» ON <=> -*a- r- "Tf O^L rO oo ro ON Tj- |95256 PB1075-Prel NO NO NO NO o o o o o oo CN| O oo •rf r^i o i CO —1 C-j rs CD co o wS r^ •**• <3* *5±- •^f •»^- Tf "Tj" CO co -3- co I

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|96401 PB979-Platl 8/30/2010 160.97 273.24 164.51 19.29 NO NO 49.36 |

0 0 0 0 ON rn rs CD CD NO NO NO |96402 PB979-Plat2 8/30/2010 10.39 327.49 NO 202.29 23.39 46.90 | [ oo O to m CD CD ON CD r-~- r-~* NO NO

139 |96403 PB979-Plat3 8/30/2010 10.36 0.00 327.34 220.30 45.75 |

n n i CD »o Tj- r-~ rn NO |96398 PB1004-Plat 1 8/30/2010 10.71 154.22 0.92 320.93 NO 193.17 21.63 47.83 | O C^l CD CD ON OO to CD NO NO to to r-^ |96399 PB1004-Plat2 8/30/2010 10.03 329.78 204.64 23.18 42.01 | O <=> m <=> CN oo to OO ON to m |96396 PB1035-Plat2 8/30/2010 276.66 167.13 18.29 NO 48.35 | r o so i CD ON CD CD oo OO CD to to Ti­ r— to NO r-^ |96397 PB1035-Plat3 8/30/2010 I— 325.54 200.95 21.77 53.71 | o CD ON oo oo oo ON «o ON CNj to m to rn r-^ NO r~- |96392 PB1058-Platl 8/30/2010 172.33 323.74 NO 194.89 20.76 ON CD CD O ON ON ON ON r^i r^i NO r-^ |96393 PB1058-Plat2 8/30/2010 NO 333.95 203.39 21.57 52.69 | CD CD o> ON oq ON CD ON ON rn to OO r—' NO NO |96394 PB1058-Plat3 8/30/2010 NO 335.38 202.16 20.95 47.29 1 ON to m NO CD CD ON ON to OO to |96389 PB1075-Platl 8/30/2010 176.83 323.81 NO NO 192.29 20.27 54.13 | CD CD C-sJ ON CD CD OO CD t-- r-^ NO rsi •O ON ON |96390 PB1075-Plat2 8/30/2010 274.93 to 167.18 17.88 NO r- 48.67 | s 8 cK cz> CD r- ON ONI m ON NO* r- |96391 PB1075-Plat3 8/30/2010 333.42 203.11 21.26 53.44 | APPENDIX E - EXAMPLE ECOSYSTEM METABOLISM O? GRAPHS

180 m (Beginning Pipe 1) • 380 m (End Pipe 1) 110 110 c o • 380 m (End Pipe 1) § 449 m(End 2 100 •jg 200 Downstream 1) 3 4-> i/i 90 90 oIS 80 80 o 5/6/10 0:00 12:00 24:00 5/6/10 0:00 12:00 24:00

130 • 1004 m (End Pipe 2) 120 1075 m (End Downstream 2) * no 2 to 100 to VP ^ 90 I 80 4/30/10 0:00 12:00 24:00 12:00 24:00 120 875 m (Beginning Pipe 2) • 1004 m (End Pipe 2)

•B no • 1004 m (End Pipe 2) c - - « 1075 m (End Downstream 2) re o 11U 3 ro $ 100 1100 re as to 90 * 90 O 80 80 8/7/10 0:00 12:00 24:00 12:00 24:00 8/7/10 0:00 12:00 24:00 12:00 24:00

110 875 m (Beginning Pipe 2) 110 • 380 m (End Pipe 1) 105 • 1004 m (End Pipe 2) c ? 449 m (End Downstream 1) o -100 *3 100 re K.re 4->3 95 re « 90 in as 90 N 80 o 85

80 70 8/29/10 0:00 12:00 24:00 9/11/10 0:00 12:00 24:00 12:00 24:00 APPENDIX F - ECOSYSTEM METABOLISM VALUES

Reach Name Reach Type Date NEP ER GPP NEP ER GPP 2 2 2 (g 02/m /day) (g 02/m /day) (g 02/m /day) (g 02/m/day) (g 02/m/day) (g 02/m/day) Upstream 1 Open 9/17/2009 -2.67 -2.51 -0.16 -3.05 -2.87 -0.18 Pipe 1 Piped 8/18/2009 -1.29 -1.31 0.02 -1.77 -1.79 0.02 Downstream 1 Open 8/18/2009 3.81 3.39 0.42 5.25 4.67 0.58

Pipe 1 Piped 5/6/2010 -1.15 -1.32 0.17 -1.34 -1.54 0.20 Downstream 1 Open 5/6/2010 2.18 -0.61 2.79 4.83 -1.35 6.18 Upstream 2 Open 4/30/2010 -3.48 -11.60 8.13 -3.28 -10.95 7.67 Pipe 2 Piped 4/30/2010 -3.16 -2.51 -0.65 -4.66 -3.70 -0.96 Downstream 2 Open 4/30/2010 0.17 -4.95 5.11 0.32 -9.44 9.76 Downstream 2 Open 5/1/2010 1.71 -5.23 6.94 3.26 -9.97 13.23

Pipe 1 Piped 8/11/2010 -1.47 -1.54 0.07 -0.82 -0.86 0.04 Pipe 1 Piped 8/12/2010 -1.34 -1.37 0.02 -0.75 -0.76 0.01 Downstream 1 Open 8/11/2010 -2.52 -3.17 0.66 -4.75 -5.99 1.24 Downstream 1 Open 8/12/2010 -2.28 -2.90 0.62 -4.30 -5.48 1.17 Upstream 2 Open 8/7/2010 0.80 0.47 0.34 0.23 0.14 0.10 Upstream 2 Open 8/8/2010 -0.80 -1.13 0.32 -0.23 -0.33 0.09 Pipe 2 Piped 8/7/2010 -0.21 -0.06 -0.15 -0.11 -0.03 -0.08 Downstream 2 Open 8/7/2010 -0.66 -1.15 0.49 -0.56 -0.96 0.41 Downstream 2 Open 8/8/2010 -0.46 -1.10 0.64 -0.39 -0.92 0.54

Downstream 1 Open 9/11/2010 -2.01 -2.50 0.49 -2.62 -3.27 0.64 Downstream 1 Open 9/12/2010 -1.97 -2.50 0.53 -2.95 -3.75 0.80 Upstream 2 Open 8/29/2010 -1.93 -2.52 0.59 -0.82 -1.08 0.25 Pipe 2 Piped 8/29/2010 -0.30 -0.08 -0.23 -0.12 -0.03 -0.09 APPENDIX G - BENTHIC AFDM AND PIGMENT BIOMASS VALUES

FBOM FBOM FBOM Epilithon Epilithon Epilithon Reach Name Location (m) AFDM (g/m2) Chi a (mg/m2) Pheophytin (mg/m2) AFDM (g/m2) Chi a (mg/m2) Pheophytin (mR/m2) Upstream 1 300Up 25.18 -2.11 6.05 12.27 1.26 4.90 250Up 3.80 2.95 3.44 5.96 2.21 4.50 205Up 21.15 10.36 6.86 7.43 1.73 2.50

Ppe 1 250 3.33 0.90 4.77 0.00 0.00 0.00 300 5.11 3.20 -0.96 3.90 0.90 4.29 350 1.56 1.15 -1.55 0.00 0.00 0.00

Downstream 1 400 27.13 12.59 18.55 9.69 3.78 3.62 425 32.20 3.84 16.04 6.71 5.30 17.21 450 36.06 23.50 9.40 0.00 11.15 39.73

Upstream 2 775 50.00 7.59 8.35 14.06 0.00 0.31 800 23.89 0.00 6.74 6.40 0.13 0.72 850 14.60 29.18 -22.37 14.36 0.61 1.69

Piped 2 900 18.49 1.50 7.93 6.90 0.20 0.25 925 8.41 -0.85 3.83 0.00 0.00 0.00 975 14.26 -3.31 5.63 0.00 0.00 0.00

Downstream 2 1000 11.63 11.44 5.64 14.25 0.67 4.36 1025 18.53 12.42 25.26 8.44 1.16 3.74 1075 25.78 51.47 48.83 36.30 0.95 6.61 Note: Values highlighted in gray were not included in reported averages or statistical analysis (because negative pigment biomass is not possible, and the highlighted values at 1075 m were outliers). APPENDIX H - EXAMPLE NUTRIENT UPTAKE GRAPHS

Spring NH4 Addition - Reach 1 Spring NH4 Addition - Reach 2 o o ^ 180 230 280 330 380 430 1^750 850 950 1050 ft t * i A # Z "2 ' * 1 J • W +

-4 -5

-6 -6

Distance (m) Distance (m)

Spring P04 Addition - Reach 1 Spring P04 Addition - Reach 2 o o 180 230 280 330 380 430 480 750 850 950 1050 -2

-4

-8 4

-10 -8 Distance (m) Distance (m) Summer NH4 Addition - Reach 1 Summer NH4 Addition - Reach 2

-1 230 280 330 380 430 700 800 900 1000 1100

X 1 * oL_ * 1* •,«** z _c

-3

Distance (m) Distance (m)

Summer P04 Addition - Reach 1 Summer P04 Addition - Reach 2 -3 230 280 330 380 430 700 800 900 1000 1100

0Q. i • • : • 1 -4 * • • o Z • c

-5 Distance (m) Distance (m) N03 Addition - Entire Reach 1 NO, Addition - Reach 2 1.0

o z "8 TJ £ 0.5 t • • *

DOC Addition - Reach 1 DOC Addition - Reach 2

o O Q 2 TS 0)N "5 E l

180 230 280 330 380 430 480

Distance (m) Distance (m) APPENDIX I - NUTRIENT UPTAKE VALUES

Spring NH, Uptake K kw SE P Sw Vf u Date Ambient Cone. Plat. Cone. Inc. Plat. Br Cone. 2 -l/m m mm/s ug/m /s ug/L NH4-N ug/L NH4-N mg/L Br

Reach 1 (180-449m) 0.0011 0.0011 0.32 0.05 inf. 0.000 0.000 5/5/2010 89.77 208.2 2.3 0.78 Pipe 1 (180-380m) -0.0010 0.0020 0.62 0.02 1000 0.008 0.796 5/5/2010 98.02 210.96 2.2 0.81 Downstream 1 (380-449m) 0.0008 0.0027 0.77 0.01 inf. 0.000 0.000 5/5/2010 78.46 204.81 2.6 0.72

Reach 2 (765-1075m) -0.0022 0.0007 <0.01 0.26 455 0.028 0.931 4/30/2010 32.85 75.05 2.3 0.82 Upstream 2 (765-875m) -0.0029 0.0005 <0.01 0.78 345 0.056 1.825 4/30/2010 32.46 82.57 2.5 0.80 Pipe 2 (875-1004m) -0.0040 0.0018 0.04 0.24 250 0.049 1.518 4/30/2010 31.29 73.69 2.4 0.84 Downstream 2 (1004-1075m) 0.0002 0.0031 0.94 0 inf. 0.000 0.000 4/30/2010 36.80 69.58 1.9 0.84

Spring P04 Uptake K kw SE P Sw Vf U Date Ambient Cone. Plat. Cone. Inc. Plat. Br Cone. 2 -l/m m mm/s ug/m /s ug/L POrP ug/L PO4-P mg/L Br

Reach 1 (180-449m) 0.0068 0.0028 0.02 0.28 inf. 0.000 0.000 5/5/2010 11.72 14.63 1.2 0.73 Pipe 1 (180-380m) 0.0098 0.0048 0.07 0.32 inf. 0.000 0.000 5/5/2010 13.27 15.57 1.2 0.74 Downstream 1 (380-449m) -0.0114 0.0080 0.20 0.22 88 0.050 0.510 5/5/2010 10.22 14.12 1.4 0.72

Reach 2 (765-1075m) -0.0029 0.0011 0.01 0.19 345 0.037 0.277 4/30/2010 7.41 12.30 1.7 0.80 Upstream 2 (765-875m) -0.0063 0.0030 0.07 0.36 159 0.122 0.899 4/30/2010 7.36 13.30 1.8 0.81 Pipe 2 (875-1004m) 0.0019 0.0037 0.61 0.02 inf. 0.000 0.000 4/30/2010 7.47 12.20 1.6 0.82 Downstream 2 (1004-1075m) -0.0052 0.0010 0.62 0.04 192 0.046 0.330 4/30/2010 7.13 10.89 1.5 0.84 Note: Only the values highlighted in gray were considered detectable and included in study figures/statistics. Summer NH4 Uptake kw kw SE P Sw Vf U Date Ambient Cone. Plat. Cone. Inc. Plat. Br Cone. 2 -1/m m mm/s ug/m /s ug/L NH4-N ug/L NH4-N mg/L Br

Reach 1 (180449m) -0.0017 0.0003 <0.001 0.70 588 0.005 0.3493 8/18/2009 70.16 299.27 4.3 1.46 Pipe 1 (180-38Qm) -0.0024 0.0005 <0.001 0.69 417 0.007 0.5190 8/18/2009 74.94 318.24 4.2 1.47 Downstream 1 (380-449m) -0.0008 0.0012 0.54 0.07 1250 0.002 0.1440 8/18/2009 60.43 259.96 4.3 1.44

Reach 2 (765-1075m) -0.0001 0.0001 0.34 0.03 10000 0.001 0.0298 8/14/2009 31.6 354.75 11.2 1.96 Upstream 2 (765-875m) -0.0007 0.0004 0.12 0.21 1429 0.008 0.2532 8/14/2009 30.94 375.20 12.1 2.01 Pipe 2(875-1004m) -0.001 0.0003 0.008 0.45 1000 0.012 0.3385 8/14/2009 29.09 340.92 11.7 2.02 Downstream 2 (1004-1075m) -0.0003 0.0002 0.098 0.27 3333 0.002 0.0735 8/14/2009 34.98 353.93 10.1 1.85

Summer P04 Uptake K kw SE P Sw Vf U Date Ambient Cone. Plat. Cone. Inc. Plat. Br Cone. 2 -l/m m mm/s ug/m /s ug/L P04-P ug/L P04-P mg/L Br Reach 1 (180-449m) -0.0013 0.0005 0.03 0.23 769 0.004 0.0202 8/18/2009 5.30 16 3.0 1.46 Pipe 1 (180-380m) -0.0009 0.0010 0.37 0.07 1111 0.003 0.0116 8/18/2009 4.47 16.85 3.8 1.47 Downstream 1 (380-449m) -0.0031 0.0033 0.39 0.15 323 0.009 0.0597 8/18/2009 6.47 14.18 2.2 1.44

Reach 2 (765-1075m) -0.0008 0.0003 0.02 0.15 1250 0.008 0.0906 8/14/2009 12.03 64.35 5.3 1.96 Upstream 2 (765-875m) -0.0012 0.0013 0.38 0.07 833 0.014 0.1567 8/14/2009 11.17 70.75 6.3 2.01 Pipe 2 (875-1004m) -0.0028 0.0010 0.02 0.37 357 0.033 0.4092 8/14/2009 12.56 62.43 5.0 2.02 Downstream 2 (1004-1075m) -0.0015 0.0018 0.44 0.07 667 0.011 0.1266 8/14/2009 12.05 60.79 5.0 1.85 Sote: Only the values highlighted in gray were considered detectable and included in study figures/statistics. Values for Pipe 2 were excluded from study figures/statistics because these values were only valid if the station at 1004 m was excluded (otherwise the values were non-detectable). Summer N03 Uptake K kw SE P Sw Vf u Date Ambient Cone. Plat. Cone. Inc. Plat. Br Cone. 2 -Mm m mm/s mg/m /s mg/L N03-N mg/L NOj-N mg/L Br

Reach 1 (180-449m) 0.0004 0.0002 0.09 0.11 inf. 0.000 0.00 8/10/2010 0.49 2.34 4.8 1.1 Pipe I (180-380m) 0.00001 0.0003 0.97 0 inf. 0.000 0.00 8/10/2010 0.47 2.47 5.3 1.2 Downstream 1 (380-449m) 0.0033 0.0009 0.004 0.59 inf. 0.000 0.00 8/10/2010 0.54 2.09 3.9 0.91

Reach 2 (765-1075m) 0.0009 0.0003 <0.001 0.28 inf. 0.000 0.00 8/4/2010 0.78 1.78 2.3 0.8 Upstream 2 (765-875m) 0.0004 0.0010 0.69 0.01 inf. 0.000 0.00 8/4/2010 0.82 1.76 2.1 0.83 Pipe 2 (875- 1004m) 0.0012 0.0010 0.25 0.09 inf. 0.000 0.00 8/4/2010 0.76 1.78 2.3 0.81 Downstream 2 (1004-1075m) 0.0008 0.0018 0.67 0.02 inf. 0.000 0.00 8/4/2010 0.77 1.8 2.3 0.73

Summer DOC Uptake kw kw SE P 1^ Sw Vf u Date Ambient Cone. Plat. Cone. Inc. Plat. Br Cone. -1/m m mm/s mg/m2/s mg/L DOC-C mg/L DOC-C mg/L Br

Reach 1 (180449m) -0.0012 0.0002 <0.001 0.71 833 0.004 0.014 9/11/2010 3.91 15.35 3.9 1.06 Pipe 1 (180-380m) -0.0007 0.0003 0.047 0.34 1429 0.003 0.011 9/11/2010 3.88 15.93 4.1 1.05 Downstream 1 (380-449m) -0.0029 0.0003 <0.001 0.95 345 0.005 0.018 9/11/2010 3.9 14.35 3.7 1.05

Reach 2 (765-1075m) -0.0023 0.0003 <0.001 0.62 435 0.016 0.042 8/30/2010 2.6 9.8 3.8 1.21 Upstream 2 (765-875m) -0.0031 0.0014 0.04 0.30 323 0.033 0.085 8/30/2010 2.60 10.04 3.9 0.9 Pipe 2 (875-1004m) -0.0021 0.0006 0.003 0.44 476 0.018 0.046 8/30/2010 2.57 9.89 3.8 1.39 Downstream 2 (1004-1075m) 0.00003 0.0016 0.99 0 inf. 0.000 0.000 8/30/2010 2.61 9.35 3.6 1.34 Vote: Only the values highlighted in gray were considered detectable and included in study figures/statistics.