Freshwater Inflow Effects on Mobile Epifauna and Estuarine Dependent Crustaceans in Rincon Bayou in the Nueces Delta

FRESHWATER INFLOW EFFECTS ON MOBILE EPIFAUNA AND ESTUARINE DEPENDENT CRUSTACEANS IN RINCON BAYOU IN THE NUECES DELTA

A Thesis

AMANDA MAE GORDON

BS, Texas A&M University-San Antonio, 2012

Submitted in Partial Fulfillment of the Requirements for the Degree of

MASTER of SCIENCE

FISHERIES AND MARICULTURE

Texas A&M University-Corpus Christi Corpus Christi, Texas

August 2016

FRESHWATER INFLOW EFFECTS ON MOBILE EPIFAUNA AND ESTUARINE DEPENDENT CRUSTACEANS IN RINCON BAYOU IN THE NUECES DELTA

A Thesis

AMANDA MAE GORDON

This thesis meets the standards for scope and quality of Texas A&M University-Corpus Christi and is hereby approved.

Paul Montagna, PhD Jennifer Pollack, PhD Chair Committee Member

Anthony Siccardi, PhD Committee Member

August 2016 ABSTRACT

Rincon Bayou is a negative estuary located in the western region of the Nueces Delta, north of Nueces Bay in Corpus Christi, Texas, and has been affected by anthropogenic freshwater withdrawals, impacting the epifaunal community. For over two decades, there have been adaptive management activities to mitigate potential effects from water withdrawals, including establishment of inflow requirements, construction of a pipeline to enhance flow to the marsh, and monitoring to assess the extent the region has been affected. Salt marshes provide habitat and refuge to a multitude of species at various trophic levels. From a fisheries standpoint, this region serves as juvenile and refuge habitat for several recreationally and commercially valued marine species of the Texas coast. This study compared three sites and three years of sampling (2010, 2014-2015) in Rincon Bayou to determine spatial and temporal effects of natural and pumped inflows on the mobile epifauna, particularly, on post- larval and juvenile recruits of brown shrimp (Farfantepenaeus aztecus), white shrimp (Litopenaeus setiferus), and blue crab (Callinectes sapidus). The results indicated that physical variables, depth and dissolved oxygen, explained dissimilarities within the epibenthic community more than salinity, suggesting that Rincon Bayou exhibits signs of being more than just a salinity-stressed environment. Signs of disturbance were recognized with the presence of freshwater indicator species, particularly significant following the May and June 2015 spring freshets. The epifaunal community of Rincon Bayou experienced some enhancement, where abundance, biomass, species richness, and diversity were higher for the year 2015 in comparison to previous years of this study. Fish exhibited a trend in higher biomass and diversity, increasing each year of the study, but an overall decline in abundance. In the crustacean community, brown shrimp displayed declines in abundance and biomass from 2010-2015, and white shrimp experienced a decrease in biomass. Blue crab populations also experienced a reduction in biomass, but showed signs of improvement in 2015. The overall findings of this study indicate that the region is utilized by several commercially valued species, and current management practices are improving the ecosystem of Rincon Bayou at the epibenthic level. However, current pumping regimes may have a negative impact on the environment as a whole, where magnitude, timing, and duration of freshwater events may alter recruitment of estuarine-dependent species.

v ACKNOWLEDGEMENTS

This project was partially supported by Coastal Bend Bays & Estuaries Program grant numbers 1417 and 1617, and Texas Water Development Board Interagency Agreement number

1548311787 to Paul Montagna. Additional funding was also provided by the Harte Research

Institute and Texas A&M University-Corpus Christi’s Fisheries and Mariculture Program.

I would like to thank my committee members Dr. Paul Montagna, Dr. Jennifer Pollack, and Dr. Anthony Siccardi for advising me on this project. Additional recognition and appreciation are due to the myriad of technicians and students that have worked on this project.

Special thanks go to Larry Hyde, Elani Eckert-Morgan, Noe Barrera, Elizabeth Del Rosario,

Mike Grubbs, Jason Williams, and especially Crystal Chaloupka, my partner in grime, and Rick

Kalke, whom I have kindly dubbed “Rick-i-Pedia”. Finally, I would also like to thank my family and friends, whose support and guidance were crucial to my success.

vi TABLE OF CONTENTS

CONTENTS PAGE ABSTRACT ...... v ACKNOWLEDGEMENTS ...... vi TABLE OF CONTENTS ...... vii LIST OF FIGURES ...... viii LIST OF TABLES ...... xi INTRODUCTION ...... 1 METHODS ...... 6 Study Site ...... 6 Sampling ...... 7 Data Analysis ...... 10 RESULTS ...... 14 Hydrology of Rincon Bayou ...... 14 Community Structure ...... 17 Gear Type: Push Net ...... 21 Gear Type: Seine ...... 25 Rincon Bayou Fish Community ...... 27 Gear Type: Push Net ...... 31 Gear Type: Seine ...... 34 Rincon Bayou Penaeid Shrimp Populations ...... 37 Brown Shrimp (Farfantepenaeus aztecus) ...... 38 Gear Type: Push Net ...... 38 Gear Type: Seine ...... 41 White Shrimp (Litopenaeus setiferus) ...... 44 Gear Type: Push Net ...... 45 Gear Type: Seine ...... 47 Rincon Bayou Blue Crab (Callinectes sapidus) Population ...... 49 Gear Type: Push Net ...... 50 Gear Type: Seine ...... 52 Benthic Macrofauna Correlation to Epifauna ...... 55 DISCUSSION ...... 56 CONCLUSION ...... 71 REFERENCES ...... 72 APPENDIX I: FIGURES ...... A-1 APPENDIX II: TABLES ...... A-13

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LIST OF FIGURES FIGURES PAGE

Figure 1. Map of study area. a) State of Texas with the Nueces Basin highlighted. b) Location of Choke Canyon Reservoir, Lake Corpus Christi and Nueces Estuary (Nueces Bay) within the Nueces Basin. c) Location of the Nueces Delta marsh containing Rincon Bayou. Arrows indicate approximate sampling locations by gear type, where red arrows represent push nets and yellow arrows represent seines...... 6 Figure 2. Euclidian distance matrix PCA of physical variables recorded in Rincon Bayou during the study period, including depth (m), salinity (psu), temperature (°C), dissolved oxygen (DO mg L-1), and pH. PC1 is representative of the inflow axis and PC2 is representative of the seasonal axis. Top: Variable loads, and Bottom: PCA sample scores, where labels represent numeric months of the study...... 16 Figure 3. Time series showing changes in dissolved oxygen over time as it relates to benthic metrics. A) Abundance (N m-2), B) Biomass (g m-2), and C) Diversity (Hill’s N1) from pooled samples collected in Rincon Bayou during the study period (2010-2015)...... 18 Figure 4. A MDS plot of Bray-Curtis similarity matrix of log-transformed total abundance of all samples collected in Rincon Bayou (after removing outliers), comparing gear types (Method), push net (PN) and seine (RS). Symbols represent gear selection, and are labeled by station. This plot includes a subset of sampling events, where only coinciding dates for push net and seine samples are included (periods June-December 2015). See Appendix I, Figure 23 for MDS plot of all samples...... 21 Figure 5. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net samples collected in Rincon Bayou. Labels are periods of the study, with bubble plot overlay representing species composition for 8 and 22 Jun. 2015 (periods 35 and 36, bottom), and PCA overlay where depth and dissolved oxygen are representative of the inflow (PC1) axis...... 24 Figure 6. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine samples collected in Rincon Bayou with group average cluster overlay, identifying samples with less than 30 percent similarities. Labels are numeric months of the study, with bubble plot overlay representing species composition for 8 and 22 Jun. 2015 (bottom of graph)...... 26 Figure 7. A MDS ordination plot (after removing outliers) of pooled fish assemblage data from Rincon Bayou, identifying separation of fish structure by gear type, push net (PN) or seine (RS). Symbols are gear selection and labels are periods...... 30 Figure 8. A MDS ordination plot of Bray-Curtis similarity matrix for log-transformed abundance data from the push net sampled fish assemblage, with bubble plot overlay displaying fish species as they pertain to samples identified with greater variance...... 32 Figure 9. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from the seine sampled fish assemblage in Rincon Bayou with 30 percent similarity cluster overlay. Symbols represent stations (C, F, or G), and labels are periods. See Figure 28 for MDS plot with outliers...... 36

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Figure 10. Distribution of the means of abundance and lengths of brown and white shrimp encountered in Rincon Bayou, during the study period...... 37 Figure 11. Time series showing changes in temperature, over time as it relates to abundance of brown shrimp according to assigned sized class, including only brown shrimp collected in push nets from Rincon Bayou during the study period (2010-2015)...... 40 Figure 12. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net-sampled brown shrimp collected in Rincon Bayou where points are labeled by month with bubble indicating size class...... 41 Figure 13. Box plot of the log-transformed variables for brown shrimp from seine samples, Left: length and Right: weight...... 42 Figure 14. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine-sampled brown shrimp collected in Rincon Bayou, where points are labeled by month with bubble plot overlay indicating size class...... 43 Figure 15. Time series of push net sampled white shrimp by size classes compared to salinity. 46 Figure 16. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net-sampled white shrimp collected in ...... 47 Figure 17. Box plots of means of log-transformed white shrimp in seine samples, A. length and B. weight...... 48 Figure 18. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine-sampled white shrimp collected in ...... 49 Figure 19. Time series for push net sampled crab abundance by size class, compared against salinity and inflow regimes. Inflow is log-transformed for scale purposes...... 51 Figure 20. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net-sampled blue crab collected in ...... 52 Figure 21. Box plots of log-transformed blue crabs collected in seine samples, Left: length and Right: weight...... 53 Figure 22. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from the seine-sampled blue crab collected in ...... 54 Figure 23. Time series of physical variables recorded at each station, C, F, or G in Rincon Bayou during the study period. From top to bottom: Dissolved oxygen, Salinity, Depth, pH, and Temperature, where the physical variable is plotted on the y-axis and dates of the study are plotted on the x-axis, with trend lines added to variables pH and Temperature...... A-1 Figure 24. Time series showing changes in recorded physical variable, salinity, over time as it pertains to diversity indices A) Abundance (N m-2), B) Biomass (g m-2), and C) Diversity (Hill’s N1) from pooled samples collected in Rincon Bayou during the study period (2010-2015)...... A-2 Figure 25. A MDS of Bray-Curtis similarity matrix of log-transformed total abundance of all samples comparing gear types (Method), push net (PN) and seine (RS). A cluster overlay of significant groupings identifying samples with less than 30 percent similarities between samples...... A-3

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Figure 26. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net samples collected in Rincon Bayou with non-significant group average cluster overlay, identifying samples with less than 30 percent similarities. Symbols represent study year, labeled by numeric month...... A-3 Figure 27. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net samples with bubble plot overlay displaying the most abundant species found in push net collections from Rincon Bayou. An additional PCA overlay depicting physical variable gradients...... A-4 Figure 28. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine samples with bubble plot overlay displaying the five most abundant species found in Rincon Bayou, with an additional PCA overlay depicting physical variable gradients...... A-4 Figure 29. Euclidian distance matrix PCA of physical variables recorded in Rincon Bayou during the study period, including Depth (m), Salinity (psu), Temperature (°C), Dissolved Oxygen (DO mg L-1), and pH as they pertain to the total fish assemblage of Rincon Bayou. PC1 is representative of the inflow axis, Left: PCA sample scores, where labels represent months of the study, and Right: Variable loads...... A-5 Figure 30. MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from the total fish assemblage in Rincon Bayou with bubble plot overlay displaying fish identified in outliers, with an additional PCA overlay depicting physical variable gradients...... A-5 Figure 31. A MDS ordination plot of Bray-Curtis similarity matrix for log-transformed abundance data from the push net sampled fish assemblage, with bubble plot overlay displaying the four most abundant fish species encountered in Rincon Bayou, with a PCA overlay, where dissolved oxygen, temperature, and depth represent the inflow axis (PC1)...... A-6 Figure 32. A MDS ordination plot (after removing outliers) of push net sampled fish assemblage data from Rincon Bayou, with trajectory overlay, identifying seasonal influence. Symbols represent stations (C, F, or G), and labels are periods...... A-6 Figure 33. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from the total fish assemblage in Rincon Bayou with bubble plot overlay displaying fish identified in highest abundance, with a PCA overlay depicting physical variable gradients...... A-7 Figure 34. Seasonal influence in fish assemblage for Subset of original MDS ordination plot (after removing outliers) of seine sampled fish assemblage data from Rincon Bayou, with trajectory overlay, identifying seasonal influence. Symbols represent stations (C, F, or G), and labels are periods...... A-7 Figure 35. Box plots of distribution of means of log-transformed variables, A. Length and B. Weight, for push net sampled brown shrimp collected in Rincon Bayou...... A-8 Figure 36. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Depth, over time as they pertain to abundance of brown shrimp collected in push nets from Rincon Bayou during the study period (2010-2015)...... A-8

Figure 37. Time series showing changes in recorded physical variables, Top: Depth, and Bottom: Temperature, over time as they pertain to abundance of brown shrimp collected in in seine nets from Rincon Bayou during 2015...... A-9 Figure 38. Box plots of distribution of means of log-transformed variables, A. Length and B. Weight, for push net sampled white shrimp collected in Rincon Bayou...... A-9 Figure 39. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Temperature, over time as they pertain to abundance of white shrimp collected in push nets from Rincon Bayou during the study period (2010-2015)...... A-10 Figure 40. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Temperature, over time as they pertain to abundance of white shrimp collected in in seine nets from Rincon Bayou during 2015...... A-10 Figure 41. Boxplot of log-transformed variable, carapace width and weights, as they pertain to push net sampled blue crab...... A-11 Figure 42. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Dissolved Oxygen, over time as they pertain to abundance of blue crab collected in push nets from Rincon Bayou during the study period (2010-2015)...... A-11 Figure 43. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Temperature, over time as they pertain to abundance of blue crab collected in in seine nets from Rincon Bayou during 2015...... A-12

LIST OF TABLES TABLES PAGE

Table 1. Summary of mean values for hydrographic variables, inflow, depth, temperature, salinity, dissolved oxygen, and pH, recorded in Rincon Bayou for each year and site of the study...... 14 Table 2. Mean values for diversity indices of Rincon Bayou epibenthos pooled by year. N. Obs. is the number of samples used for averaging replicates...... 17 Table 3. Summary of mean values for abundance, biomass, species richness, diversity and evenness for the push net sampled epifaunal community sampled in Rincon Bayou, displayed by years and stations...... 22 Table 4. Mean epibenthic metrics for abundance and biomass of seine samples by stations...... 25 Table 5. Mean values for epibenthic indices of Rincon Bayou pooled fish data displayed by year and gear selection...... 28 Table 6. Summary of variable means of push net and seine-sampled brown shrimp, and physical variables...... 38 Table 7. Summary of variable means of total white shrimp collected in push nets (PN) and seines (RS)...... 44 Table 8. Summary statistics for blue crab by year and station. Values are the total number of crab encountered (N) and their abundance (N m-2), biomass (g), biomass per tow (g m-2), carapace widths (mm) and individual weights (g)...... 50 Table 9. Pearson correlation values comparing benthic to epibenthic biotic and diversity variables...... 55 Table 10. Species composition for collective community (combined gears) displaying percent abundance and biomass. Table for collective data showing % contribution of abundance and biomass for push nets and seines, as well as the total contribution of each taxonomic category...... A-13 Table 11. Nested ANOVA output for factors year, month, and station comparing biotic and diversity variables as they pertain to the collective epifaunal community of Rincon Bayou...... A-15 Table 12.Summary of mean values of biotic and diversity variables for the overall community composition according to each year and station of the study. N. Obs. is the number of samples taken, determined from 1231 total species observations...... A-15 Table 13. One-way ANOVA output comparing gear type for the pooled community data sampled from Rincon Bayou...... A-15 Table 14. Nested ANOVA output for factors year, month, and station comparing biotic and diversity variables as they pertain to push net samples only for the epifaunal community of Rincon Bayou...... A-16

Table 15. Values for physical variables depth, temperature, salinity, dissolved oxygen, and pH as recorded in Rincon Bayou for sampling events where no specimen were found in push net collections...... A-16 Table 16. Two-way ANOVA output for factors month and station, comparing biotic and diversity variables as they pertain to the seine sampled epifaunal community of Rincon Bayou...... A-16 Table 17. Means of hydrographic variables as they pertain to the pooled fish community of Rincon Bayou, displayed by year and site selection...... A-17 Table 18. Nested ANOVA output for factors year, month, and station, comparing biotic and diversity variables as they pertain to the pooled fish community of Rincon Bayou. ... A-17 Table 19. One-way ANOVA output comparing gear type for the pooled fish community data sampled from Rincon Bayou...... A-17 Table 20. Nested ANOVA output for factors year, month, and station, comparing biotic and diversity variables as they pertain to the of push net sampled fish community of Rincon Bayou...... A-18 Table 21. Two-way ANOVA output for factors month and station, comparing biotic and diversity variables as they pertain to the seine sampled fish community...... A-18 Table 22. Two-way ANOVA output for factors gear selection and shrimp species, comparing lengths and weights of all brown and white shrimp collected in Rincon Bayou...... A-18 Table 23. One-way ANOVA output for factor gear selection, comparing biotic variables as they pertain to the collective total of brown shrimp collected in Rincon Bayou...... A-19 Table 24. Nested ANOVA output for factors year, month, and station, comparing biotic variables as they pertain to push net-sampled brown shrimp collected in Rincon Bayou...... A-19 Table 25. Two-way ANOVA output for factors month and station, comparing biotic variables as they pertain to the seine sampled brown shrimp community of Rincon Bayou...... A-19 Table 26. One-way ANOVA output for factor gear selection, comparing biotic variables as they pertain to the collective total of white shrimp collected in Rincon Bayou...... A-19 Table 27. Nested ANOVA output for factors year, month, and station, comparing biotic variables as they pertain to the push net sampled white shrimp community of Rincon Bayou. .. A-20 Table 28. Two-way ANOVA output for factors month and station, comparing biotic variables for seine sampled white shrimp collected in Rincon Bayou...... A-20 Table 29. Summary of total blue crab, selected by gear type and size class, encountered in Rincon Bayou. Values are the total number of crab encountered (N) and their abundance (N m-2), biomass (g), biomass per tow (g m-2), carapace widths (mm) and individual weights (g)...... A-20 Table 30. Summary of total blue crab, selected by sex and size class, encountered in Rincon Bayou. Values are the total number of crab encountered (N) and their relative abundance (Nm-2), the total biomass (B) and relative biomass (gm-2), average carapace widths (CW) and individual weights (Wt.) ...... A-21

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Table 31. Summary of physical variables for overall crab population of Rincon Bayou, selected by year and station of the study. Values are the total number of crab encountered (N) and their abundance (N m-2), biomass (g), biomass per tow (g m-2), carapace widths (mm) and individual weights (g)...... A-21 Table 32. One-way ANOVA output for log-transformed variables abundance, carapace width, and weight, comparing gear selection for pooled crab data from Rincon Bayou...... A-21 Table 33. Nested ANOVA output of factors year, month, and station, comparing biotic variables for push net sampled blue crab collected in Rincon Bayou...... A-22 Table 34. Complete summary of physical variables as they pertain to clustered events identified in the MDS ordination plot (Figure 20) of push net sampled crab population of Rincon Bayou...... A-22 Table 35. Two-way ANOVA output of factors date and station, comparing means of biotic variables as they pertain to seine sampled blue crab collected in Rincon Bayou...... A-22

INTRODUCTION

Rincon Bayou is a part of the Nueces River Delta and Nueces Bay Estuary system, secondary to Corpus Christi Bay, Corpus Christi, Texas, U.S.A. The delta region was once affected by multiple natural flood events per year and freshwater was typically delivered to these systems by way of river flows, or inflows. Inflow from the Nueces River once delivered water to

Rincon Bayou, which in turn delivered water to the western region of Nueces Bay (Ward et al

2002). Nueces River inflows first became restricted from Rincon Bayou in 1958 after the construction of the Wesley Seale Dam on Lake Corpus Christi, and again after construction of the Choke Canyon Dam to create the Choke Canyon Reservoir. The reservoir was completed in

1982, but water was not released until the post-1990 drought period (Montagna et al. 2009).

Completion of the Choke Canyon Dam caused a 99% reduction of inflow (Asquith et al. 1997,

Palmer et al. 2002), which affected the hydrological dynamics and regime in the marsh area.

Reduction of inflow can have negative impacts on the flora and fauna of the area by significantly reducing abundance and diversity of organisms, and habitat area.

A specific problem in Rincon Bayou is periods of hypersalinity, as the region has been documented as a reverse estuary over the past several years (Montagna et al 2002, Palmer et al

2002). This is especially problematic in periods of persistent hypersaline conditions, which is a strong disturbance that can alter overall species composition (Ritter et al 2005). Freshwater delivered to the delta region is necessary to reduce salinities and freshwater provides nutrients for primary producers and other estuary-dependent species (Montagna et al 2002). Adversely, over-inundation, i.e., floods into the delta creates hyposaline conditions incapable of supporting marine organisms as this region of the delta becomes a nearly freshwater environment (Palmer et al. 2002).

To mitigate the ecological impacts of altered flows on Rincon Bayou, an adaptive management strategy has been in place since 1992 (Montagna et al. 2009). An agreed order in

1995 mandated pass-through requirements, as well as the creation of a diversion channel (Nueces

Overflow Channel, Figure 1) that was placed at the entrance of Rincon Bayou (Montagna et al

2009, Ward et al 2002). It was subsequently closed in 2000, but reestablished in 2001 (Montagna et al. 2009). In addition to the improved Nueces Overflow Channel (Rincon Overflow Channel,

Figure 1), a diversion pipeline that pumps water from the Calallen Pool (Figure 1) directly into

Rincon Bayou was constructed in 2007 (Montagna and Nelson 2009). The diversion project included a pumping station with three pumps (Hodges et al. 2012). Later, a weir system to prevent backflow to the Nueces River during pumping events was constructed in 2014

(Montagna et al 2015). However, during the present study, the weir was washed out by a flood in

June 2015, and had not been replaced prior to completion of sampling for this study, but pumping continued.

Ecological monitoring studies have been performed in Rincon Bayou for two decades, with several sampling stations covering areas of the delta from the river to the bay. Community types ranging from avian to benthic macrofauna have been investigated, but focused primarily on the benthic infaunal communities. Because of their sessile nature and short life spans, benthic infauna can be ideal organisms to measure short term effects of environmental impacts. Benthic studies have received the most attention in Rincon Bayou, and investigation at higher trophic levels is required to understand the effects of the entire ecosystem and habitat. A study of the mobile epifauna has not been completed in Rincon Bayou since before pumping began.

An interdisciplinary study of Rincon Bayou was completed by Hill and Nicolau (2007), which addressed water quality, primary producers, and trophic dynamics for dominant taxa

including crustacean and fish. This study was performed between 2001 and 2006 and found that crustaceans were the dominant taxa contributing greater than 50 percent community abundance.

Additionally, the greatest biomass contributors alternated between crustacean and fish communities, and that during two years of the study, the decline in biomass was due to the reduction of three fish species (Cyprinodon.variegatus, Brevoortia.patronus, and

Anchoa.mitchilli). This study also identified seasonal entrance of larval and post-larval shrimp, crab, and fish, where spikes or peaks in abundance could be tied to changes in salinity within

Rincon Bayou.

A study covering the periods 1999 to 2004 was completed by Tolan and Newstead

(2005). This study was completed to identify the effects of freshwater inflow on the fish assemblage of Nueces Bay. While this study compared several sites within Nueces Bay, two of these stations were located within Rincon Bayou. This study found that fluctuations in the higher trophic-level community were strongly influenced by salinity regimes. There was some indication that the natural exchange of tidal flows could be altering recruitment events for larval estuarine-dependent species, as tidal exchanges can make emigration difficult. Species that can better exploit the lowered salinities were identified, and when flooding events caused short-term changes in community structure, marine organisms were unable to recover when freshwater pulses persisted.

Evidence that organisms are using Rincon Bayou as refuge and juvenile habitat has been provided in multiple studies (Hill and Nicolau 2007, Riera et al. 2000, Tolan and Newstead

2004B, Tolan and Newstead 2005). The Rincon Diversion project has propagated some significant changes in inflow regimes since those studies, so new studies are needed on the effects at higher trophic levels, especially since pumping began. Degradation of habitat, utilized

by commercially important species, can be directly correlated to reduced catch rates in the bay

(Jordan et al. 2009, Lellis-Dibble et al. 2008). In Texas, white shrimp, brown shrimp, and blue crab are all commercially important estuarine-dependent species (Sutton and Wagner 2007).

In south Texas, adult brown shrimp (Farfantepenaeus aztecus) mate and spawn in deeper nearshore waters of the Gulf of Mexico (Riera et al 2000, Turner and Brody 1983). Free- swimming larvae (approximately 8 - 10 mm in length) move into the shallow waters of estuaries and marshes, where migratory patterns are determined by temperature and tidal cues, typically in early spring (TPWD 2002, Turner and Brody 1983). They develop into juveniles (> 25 mm) over the course of several weeks, and then into sub-adults (> 65 mm) before returning to open waters

(Riera et al 2000, TPWD 2002). Emigration back to nearshore waters typically occurs once brown shrimp have reached approximately 60 - 70 mm in length, and the occurrence of shrimp >

90 mm should be minimal in the marsh region. Brown shrimp reach sexual maturity at lengths greater than 110 mm and should not be encountered in marsh habitat (TPWD 2002).

White shrimp (Litopenaeus setiferus) life history mimics that of brown, but their migration is highly temperature-dependent, and they do not move towards the shallower waters until bay waters are greater than 25 ºC (Turner and Brody 1983). This typically occurs later in the year, and new recruits are smaller than brown shrimp, and once in the marsh, white shrimp experience more rapid growth (Tolan 2013, Turner and Brody 1983). Additionally, white shrimp will attain larger sizes and move out towards the bay at lengths > 120 mm. Sexual maturity is reached at lengths greater than 150 mm (TPWD 2002) and they tend to move into farther reaches with lower salinities as well (Tolan 2013, Turner and Brody 1983).

Similar to shrimp, blue crab (Callinectes sapidus) spawn in deeper waters and free- swimming larvae move into estuarine water to complete development (SOURCE). Their life-

cycle, including migratory and molting cues, is dependent on salinity and temperature, where it is suggested that egg-hatching requires salinities > 20 psu and temperatures > 19 °C (Gandy et al.

2007). Larvae move towards estuarine waters with tidal flows and development of larval stages occur over 1-2 months. Blue crab enter the estuaries during their megalops stage and develop into juvenile, then sub-adult specimens, which occurs after a series of molts. Females mate after their final molt and move back towards offshore waters to spawn (Gandy et al. 2007, Ward

2012).

Fish can be good biological indicators of water quality, and there are some commercially and recreationally valued, estuarine-dependent fish that have been identified in Rincon Bayou, such as gulf menhaden (Brevoortia patronus) and ladyfish (Elops saurus) (Hill and Nicolau

2007, Moore et al 1997, Tolan 2008). Various fish have seasonal migration patterns where peaks in abundance are evident during typical times of the year (Hill and Nicolau 2007, Tolan and

Newstead 2004, Tolan and Newstead 2005). Heavy pulses of freshwater have been documented to wipe out epifaunal communities (Turner and Brody 1983).

The purpose of the current study was to determine whether current pumping regimes and natural freshwater inflow events were a factor for determining the abundance and distribution of the epifaunal community in Rincon Bayou. A diverse ecosystem can be indicative of a healthy ecosystem, whereas a lack of diversity, abundance, and richness can often be explained by poor water quality and anthropogenic effects. Additionally, habitat degradation and lack of nutrients can significantly alter the adult populations and future recruitment of estuary-dependent species.

Because of the economic and ecological importance crustaceans have for the coastal economy and ecology, a study to identify the community dynamics of a higher trophic level with a focus on Litopenaeus setiferus, Farfantepenaeus aztecus, Callinectes sapidus, and various

forage fish species was performed. In particular, the study was designed to identify estuarine- dependent juvenile shrimp, fish, and crab that are utilizing the region. These target organisms are benthic feeders (Gosselink 1984), and a healthy benthic community is required to support organisms of higher trophic levels, particularly post-larval and juvenile crustaceans and fish. A comparison of the benthic and epibenthic communities was made to determine if there is a correlation between each community.

METHODS

Study Site

The study was performed in Rincon Bayou, which is a tributary of the Nueces River that flows into the Nueces Delta area near Corpus Christi, Texas, USA. It receives freshwater from the Nueces River and from the pumping station that derives water from the Calallen Pool, which is fed by water flowing in the Nueces River from Lake Corpus Christi. Three stations were

sampled (Figure 1). Station 466C (C) is the station with closest proximity to the pump outfall, approximately 3 km downstream. The surrounding environment consists of muddy, clay sediments and vegetation that extends to the shoreline. Station 400F (F) is more centrally located in the bayou, approximately 6 km downstream and the environment is more open with small pool formations, less vegetation, which still extends to the shoreline, and sediment that is more silty than muddy. Station 463G (G), approximately 8 km downstream from the pump outfall, and 6 km from Nueces Bay, is adjacent to a train trestle and the sediment is sandy with shell litter and sparse coverage of vegetation. There are larger and deeper pool formations at this station in comparison to station F.

Sampling

All epibenthic samples were collected biweekly April-August 2010, and April 2014 to

December 2015. Samples prior to June 2015 were collected using a push net measuring 1.0 m x

1.0 m with 5.0 mm mesh. The push net was used to collect one sample by pushing towards the shore, in 5 m tows. In August 2015, and for all samples following, an additional two replicates were added to the push net sampling method. All three replicates were performed in 5 m tows towards the shore, in the same 50 m2 area, each replicate with 1-2 m separation between tow sites. Samples were taken from the northern bank of station C and southern bank of station F. At station G, a small channel flows under an adjacent train trestle. Two push net samples were taken on the northern side of the bridge and one on the southern side (Figure 1).

In June 2015, and for all samples after, one additional sample was collected by seine

(18.0 ft (≈ 5.5 m) x 1 m, 5.0 mm mesh). The seine was dragged perpendicular to the shoreline at each station, for 10 m tows from the same 50 ft2 area on the northern bank of station C, southern

bank of station F, and along the northwestern shoreline of station G, north of the train trestle.

Seine samples were taken approximately 50 m away from push net sampling areas.

All samples were labeled and immediately preserved in 5% buffered formalin and analyzed in the lab. Samples were rinsed, sieved (5.0 mm mesh), sorted, and each specimen identified to the lowest taxonomic classification possible. For the scope of this research, penaeid shrimp, crab, and fish species were of major concern, and were identified to species level with no exceptions.

Once identified, all fish standard lengths were measured (mm) and individual wet weights (mg) recorded. Penaeid specimens collected were measured (mm) from the tip of the rostrum to the tip of the telson. Individual wet weights (mg) were taken and recorded. Size classes for shrimp and crab were determined by using the individual lengths of each specimen.

For brown shrimp, size classes were determined based on anticipated sizes to be encountered. The first class was determined by the minimum length encountered up to 25.0 mm.

Class 2 consisted of shrimp ranging from > 25.0 mm to 60.0 mm. Class 3 consisted of shrimp with lengths > 60.0 mm to 90.0 mm. Class 4 was shrimp > 90.0 mm.

White shrimp size classes were determined similarly, but accounted for slightly larger size differences between the two species. Class one consisted of shrimp up to 35.0 mm. Lengths

> 35.0 mm and up to 70.0 mm represented class 2, and lengths > 70.0 mm and up to 120.0 mm represented class 3. Shrimp with lengths > 120.0 mm represented size class 4.

In an effort to preserve as many sub-adult and adult blue crab specimens as possible, a weight-length conversion was used for the blue crab collections, based on methods outlined by

Pullen and Trent. Crabs are subject to several molting/ecdysis stages and often lose regenerable limbs, which tends to cause much variability in crab weights. A study out of Galveston bay

determined a sex-specific length weight regression where the weights of female crabs were expressed as:

W=10^(3.54147+ 2.63954(Log(CW))) and weights of males were expressed as:

W=10^(3.74149 + 2.77478(Log(CW))), where W represents the wet weight and CW represents the carapace width of the specimen

(Pullen and Trent 1970). Carapace widths (mm) were measured at the widest portion (spine to spine) of the specimen. For consistency, no wet weights were recorded and larger crabs were measured in the field and immediately released. Crabs were size-classed by carapace width, where class 1 blue crab were determined by the smallest length encountered up to 20.0 mm, class

2 (juveniles) were > 20.0 mm to 80.0 mm, and size class 3 were crabs measuring > 80.0 mm, and were considered sub-adult and adult specimen (McClintock et al. 1993; Fitz and Wiegert 1991).

Lengths of bivalves were measured across the widest portion of the shell. Gastropod shells were measured from the apex across the aperture. Shells were dissolved in 10% HCl

(typically 5-10 minutes) and organism wet weights were recorded.

All other organisms found in samples were identified to the lowest possible taxonomic classifications and weight wets (mg) recorded for entire sample conspecifics. Weights for organisms > 0.01g were obtained and carried out to the nearest 0.01 gram. Weights for organisms

< 0.01g were obtained and carried out the nearest 0.00001 gram. All recorded measurements were according to scale used, but all calculated measurements were according to most significant figures (0.00001). Samples were disposed of according to Texas A&M University-Corpus

Christi’s Environmental Health and Safety regulations. Any samples that were kept were labeled and preserved in a 70% ethanol solution.

Hydrographic data included inflow (m3 s-1), water temperature (°C), depth (m), salinity

(psu), pH, and dissolved oxygen (mg L-1). Inflow measurements were provided by Elizabeth

DelRosario (2016) and based on information gathered from United States Geological Survey

(USGS) and the Nueces River Authority (NRA). All other hydrographic values were the surface and bottom depth values of temperature, salinity, pH, and dissolved oxygen measurements for each station (C, F, and G) for each sampling event when weather conditions allowed. Except inflow, all water parameters were measured with an YSI6920 multiparameter sonde and recorded.

Data Analysis

Data were analyzed using Primer 7.0 and SAS 9.4 software and all significant results were reported at an α-0.05 level. Data transformations and analysis method adjustments were made as necessary to meet all required assumptions of the statistical procedures. Data management, summary statistics and statistical analysis were performed using SAS software.

Multivariate community structure analysis and diversity calculations were also completed, using

SAS software, to determine similarities among factors of the study design.

Diversity indices were calculated using abundance (N, N m-2), biomass (g, g m-2), richness (R), Shannon Diversity (H´), Hill’s Diversity (N1), and Pielou’s Evenness (J´). These indices can be useful tools to determine factors affecting the biodiversity of the overall community structures (Stirling 2001). Abundance is simply the total number of individuals encountered (or number per tow), biomass is the collective wet weight of organisms (or weight per tow), and richness is the number of species encountered.

Calculations for Shannon diversity were performed for calculating Hill’s diversity and

Pielou’s evenness. Shannon diversity results were not reported, but are represented as:

H´= -∑i pi log(pi), where i represents species and pi represents the proportion of those species (Hill 1973, Clarke et al 2014). Hill’s N1 diversity index is a measure of the number of dominant species in the community (Stirling 2001), expressed as:

N1= exp(H´).

Evenness is the measure in variation of individuals across species and was analyzed using

Pielou’s evenness index, represented as J´, where:

J´=H´/log(R).

The value of J’ will typically fall between 0 and 1, where the closer to 1 the J’ value falls, the more even species distribution is within a sample (Stirling 2001). Values closer to 0 indicate samples being dominated by one or a few species. A value of 1 would indicate even distribution of all species. Additionally, evenness will often decrease as richness increases. Additionally, low evenness values are often associated with high dominance (i.e., low J´, high N1) (Clarke et al

2014).

Additional analyses included one-way, two-way, and nested analysis of variance

(ANOVA) procedures, with Tukey post-hoc testing, to compare treatment means between gears, dates (years and months), and site selection. Biotic and physical variables were log-transformed to normalize data for analysis. An initial analysis was performed to determine if significant differences existed between the push net and seine sampling gears. This was completed by running a one-way ANOVA on pooled data obtained by gear type, seine (RS) or push net (PN).

The analysis was used to confirm whether differences in composition were significant enough for the data to be treated separately.

Nested and two-way ANOVAs were performed to identify the relationships between dates

(temporal) and stations (spatial), where the analysis of dates was completed using years of the study and months nested within years. For seine sampled events, only one year of data was included in the study, and two-way ANOVAs to test for interactions were employed instead. The variables included species abundance, abundance per tow, biomass, and biomass per tow, species richness, species diversity and species evenness. Biotic variables were log transformed for

ANOVA purposes and results were reported on per tow variables.

Pearson correlation coefficients were used to identify correlations between hydrographic, biotic, and/or diversity variables of epifaunal data collected during the study period. Values were reported as ρ values between -1 and 1, with significant p-values. Correlation coefficients > ǀ0.3ǀ are considered moderately strong, and coefficients > ǀ0.5ǀ are considered strong relationships

(Clarke et al 2014).

To add another level of understanding to this study, an additional Pearson correlation was performed to identify connections between the epifaunal and benthic infaunal communities. The benthic infauna data were provided by Crystal Chaloupka (2016). Collections occurred biweekly at station C in Rincon Bayou. Benthic cores were taken at sections 0-3 cm and 3-10 cm.

Similar methodology for lab procedures and species identification were followed, however, dry weights were recorded.

PRIMER-E 7.0 software was used to perform non-metric multidimensional scaling

(MDS) plots and primary component analysis (PCA) operations. Bray-Curtis and Euclidian matrices required for these analyses were also completed. Hierarchal cluster analysis was also performed on each dataset, based on group averaging. Cluster analysis for each dataset was performed using Bray-Curtis similarity resemblance matrices of the log-transformed data.

Cluster analyses were beneficial to determine similarities of communities between dates and stations, where clustered events sharing greater than 30 percent similarity were reported (Clarke et al 2006).

Utilization of MDS plots allowed for community composition to be depicted in two- dimensional space, where samples that are more similar have less distance between them. Plots with a stress value < 0.20 were indicative of accurate representation. The distance between samples in relation to each other is based on Bray-Curtis similarity matrices when biotic data were the source, and the data were log-transformed abundance (N) variables for each dataset.

Calculation of Bray-Curtis coefficients range between 0 and 100, where values closer to 0 represent samples less similar, and a value of 100 would be indicative of samples that are exactly the same (Clarke et al 2014).

Principle component analyses (PCA) were performed on hydrographic data using

Euclidean distance similarity matrices on the normalized and log-transformed hydrologic data.

Euclidian matrices were calculated from the original data, where the distance between samples is considered the natural distance (Clarke et al 2014). The results were then reported as the loading score, which is a linear coefficient of each variable. Only primary component (PC) axes that explained > 20 percent, and variable loads > than ǀ0.3ǀ were reported. Hydrographic values, for analysis purposes, were water depth, and the average of the top and bottom measurements of temperature, salinity, pH, and dissolved oxygen measurements to create one date and station combination for each sampling event. Inflow was calculated as the difference in the USGS gauge values and NRA values determined from pumping events from the Calallen pumping station and the Rincon pipeline, reported as monthly totals. PCA for water parameters aided in identifying

any relationship or driving of abiotic factors, such as salinity or dissolved oxygen, on the community structure.

RESULTS

Hydrology of Rincon Bayou

A total of 49 sampling events (117 observations) were analyzed to identify overall trends in the hydrology of Rincon Bayou. Data for one or more variables (either temperature, salinity,

DO, or pH) were missing for 4 of the 49 events, and these values were imputed using PRIMER and an expectation maximum likelihood algorithm. Data were analyzed to determine the differences in community structure that could be attributed to each physical variable, inflow, depth, temperature, salinity, dissolved oxygen and pH for the study period (Table 1).

Table 1. Summary of mean values for hydrographic variables, inflow, depth, temperature, salinity, dissolved oxygen, and pH, recorded in Rincon Bayou for each year and site of the study. Year Station N. Depth (m) Temperatu Salinity Dissolved pH Monthly Obs. re (°C) (psu) Oxygen (mg L-1) Inflow (m3 s-1) C 6 0.18 27.61 6.00 7.49 8.56 191.5 2010 F 8 0.16 29.62 19.83 8.63 8.67 183.62 G 5 0.29 31.05 15.29 7.65 8.63 200.84 C 16 0.16 27.12 9.37 8.59 8.37 84.97 2014 F 13 0.18 29.19 15.94 8.77 8.41 101.09 G 14 0.25 27.04 19.24 8.55 8.43 93.85 C 19 0.19 26.58 7.43 8.79 8.2 296.6 2015 F 18 0.15 25.62 13.44 9.63 8.28 135.58 G 18 0.26 25.00 14.42 9.22 8.35 136.12

Monthly inflows ranged from 0.16 (April 2014) to 1777.55 (May 2015) m3s-1 over the study period with a monthly average of 155.01 m3s-1, ± 342.84. The lowest depths in Rincon

Bayou were 0.03 m (18 Nov. 2014, station C; 16 Feb. 2015, station F), maximum depth of 0.80 m (8 June 2015, station C), mean of 0.21 m, ± 0.16. Water temperatures ranged from 10.15 ºC

(16 Jan. 2015, station G) to 39.17 ºC (11 Aug. 2015, station F), mean 27.72 °C, ± 5.61. The lowest salinity was 0.22 psu (8 June 2015, station C), highest 44.54 psu (28 Apr. 2014, station F), mean 12.95 psu, ± 9.92. Dissolved oxygen ranged from 3.67 mg L-1 (8 June 2015, station C) to

15.97 mg L-1 (27 July 2015, station C), mean 8.61 mg L-1, ± 1.83. Ranges in pH were from 7.54

(8 June 2015, station C) to 9.36 (28 Apr. 2010, station F), mean 8.37, ± 0.28 (Appendix I, Figure

23).

A PCA of the physical variables identified PC1 as the inflow indicator axis indicated by the load values of depth (0.571), dissolved oxygen (-0.610), and lesser contributing variables, salinity (-0.384) and pH (-0.381) (Figure 2, Top). The inflow axis accounted for 36.1 percent of the variation in overall physical data structure. PC2 is the seasonal indicator axis, as it was most highly explained temperature (0.769) and pH (0.575). It accounted for an additional 24.2 percent of variation in the overall community structure, for a total 60.3 percent variation in community structure. PCA scores from hydrologic variables compared by months of the study indicate a seasonal influence (Figure 2, Bottom), where cooler months are clustered towards the bottom and warmer months on top.

Figure 2. Euclidian distance matrix PCA of physical variables recorded in Rincon Bayou during the study period, including depth (m), salinity (psu), temperature (°C), dissolved oxygen (DO mg L-1), and pH. PC1 is representative of the inflow axis and PC2 is representative of the seasonal axis. Top: Variable loads, and Bottom: PCA sample scores, where labels represent numeric months of the study.

Community Structure

From 49 sampling events, 214 samples were collected (176 push net, 38 seine). A combined 1231 species observations were made from three stations (C, F, and G) located in the southern region of Rincon Bayou from April 2010 to December 2015. A total of 87 (72 in push nets, 63 in seines) organisms were identified, totaling 40,241 individuals, weighing a total of

7,866.23 grams (Appendix II, Table 10).

For both gear types, the diversity indices, abundance (N), abundance per tow (N m-2), biomass (g), biomass per tow (g m-2), richness (R), Hill’s N1 diversity (N1), and Pielou’s evenness index (J´) were calculated for the pooled data for the entire study period. For the entire epifaunal community there was a trend of increasing density, richness, and diversity. Average biomass declined from year 2010 to 2014, and then increased in 2015 (Table 2). Overall diversity, based on Hill’s NI diversity coefficient, indicated an increase of dominant species, showing the highest incidence in the seine samples. There were no significant variations in

Pielou’s evenness index.

Table 2. Mean values for diversity indices of Rincon Bayou epibenthos pooled by year. N. Obs. is the number of samples used for averaging replicates. N. Abundance Species Hill's N1 Pielou's Year Biomass (g m-2) Obs. (N m-2) Richness Diversity Evenness 2010 19 9.99 2.99 3.95 1.96 0.50 2014 43 20.87 1.83 4.05 2.27 0.56 2015 93 21.72 2.06 8.66 3.42 0.54

DO (mg/L) Abundance (N/m2)

18 450 16 400 14 350 12 300 10 250 8 200 6 150 4 100 Abundance

Dissolved Oxygen Dissolved 2 50

0 0

9/8/2014 7/6/2015 9/9/2015

2011 - ND - 2011 ND - 2012 ND - 2013

6/30/2014 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 5/15/2014 6/17/2014 7/14/2014 8/11/2014 8/25/2014 11/3/2014 12/2/2014 1/16/2015 3/16/2015 3/30/2015 4/10/2015 5/11/2015 7/27/2015 8/24/2015 9/21/2015

10/28/2015 11/11/2015 11/24/2015 12/21/2015 A 10/20/2014 Date DO (mg/L) Biomass (g/m2) 18 25 16 14 20 12 10 15 8 10 6 Biomass 4 5 Dissolved Oxygen Dissolved 2

0 0

9/8/2014 7/6/2015 9/9/2015

2011 - ND - 2011 ND - 2012 ND - 2013

4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 5/15/2014 6/17/2014 6/30/2014 7/14/2014 8/11/2014 8/25/2014 11/3/2014 12/2/2014 1/16/2015 3/16/2015 3/30/2015 4/10/2015 5/11/2015 7/27/2015 8/24/2015 9/21/2015

10/28/2015 11/11/2015 11/24/2015 12/21/2015 B 10/20/2014 Date

DO (mg/L) Hill's N1 Diversity 18 10 16 9 14 8 12 7 10 6 5 8 4 6 3 Diversity 4 2 Dissolved Oxygen Dissolved 2 1

0 0

9/8/2014 7/6/2015 9/9/2015

2011 - ND - 2011 ND - 2012 ND - 2013

4/10/2015 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 5/15/2014 6/17/2014 6/30/2014 7/14/2014 8/11/2014 8/25/2014 11/3/2014 12/2/2014 1/16/2015 3/16/2015 3/30/2015 5/11/2015 7/27/2015 8/24/2015 9/21/2015

10/28/2015 11/11/2015 11/24/2015 12/21/2015 C 10/20/2014 Date

Figure 3. Time series showing changes in dissolved oxygen over time as it relates to benthic metrics. A) Abundance (N m-2), B) Biomass (g m-2), and C) Diversity (Hill’s N1) from pooled samples collected in Rincon Bayou during the study period (2010-2015).

A comparison of diversity indices, biomass, abundance and Hill’s N1 depicted trends in biotic and diversity variables over time in relation to dissolved oxygen concentrations (Figure 3) and salinity levels (Appendix I, Figure 24). Dissolved oxygen was found to be the highest contributing factor to dissimilarities between samples. Abundance, biomass, and diversity are generally highest between 6 and 12 mg L-1, except following the June 2015 sampling events.

Biomass and abundance were low following this period, but diversity was higher. This period coincided with the lowest dissolved oxygen and salinity < 1 psu. There is some indication that the highest peaks in abundance and biomass occurred after salinities decreased and deficits in biotic and diversity variables were occurring when there were dramatic fluctuations in salinity.

Tests for significance were completed with a nested/blocked ANOVA (Appendix II, Table

11) to identify variations across years, months, and stations of the study. There were significant differences in abundance (p < 0.0001) between years, where the average abundance was significantly higher in 2015 than the other two years of the study, with substantial variation in abundance for the factor month (p = 0.0309). Differences were identified across years and stations for the means of biomass (p = 0.0159, p = 0.0585) and months and stations for biomass per tow (p = 0.0582, p = 0.0002). Average biomass was highest in 2015, where mean values for station G were substantially higher than station F, but station C did not greatly differ from other stations. Biomass per tow was also highest at station G, and means from station F were significantly lower than the other two stations (Appendix II, Table 12). Variations in the means were identified across years and between months for species richness (p < 0.0001, p = 0.0013) and Hill’s diversity (p = 0.0005, p = 0.0184), with no significant variation within any factor for evenness. Richness and diversity were significantly higher in 2015 and showed an increase each year of the study.

Pearson correlation procedures performed on the total community and hydrographic variables found strong positive correlations between richness and diversity (ρ = 0.62, p < 0.0001) and between diversity and evenness (ρ = 0.62, p < 0.0001). Moderately positive correlations were identified between abundance and richness (ρ = 0.45, p < 0.0001), biomass and richness (ρ

= 0.43, p < 0.0001), biomass and diversity (ρ = 0.41, p < 0.0001). No strong negative correlations were present but moderate negative relationships existed for abundance and evenness (ρ = -0.40, p < 0.0001), richness and pH (ρ = -0.34, p < 0.0001), diversity and pH (ρ = -

0.31, p < 0.0001), and diversity and inflow (ρ = -0.32, p < 0.0001).

A one-way ANOVA (Appendix II, Table 13) comparing gear type identified that abundance was higher seines, but density was higher in push nets (p < 0.0001, p = 0.0016).

Biomass and biomass per tow were also higher in seines (p < 0.0001, p < 0.0001), as well as species richness and diversity (p < 0.0001, p < 0.0001). There was no substantial variation in species evenness. This means that on average, push nets are encountering more organisms with lower biomass and seines are targeting larger organisms. Furthermore, comparing abundance counts and total weights of biomass in varying gears is difficult when considering that larger organisms will contribute significantly more to the biomass indices.

For the variables density (N m-2), biomass per tow (g m-2), species richness, and Hill’s

N1, significant differences in means did exist for each of the two sampling methods (push net or seine). There were not significant results showing that spatial differences between stations C, F, and G were a driving factor in overall species composition, but a seasonal influence was detected. Because of the timing of the addition of seines, there is not enough comparable data to determine any seasonal influence.

A MDS subset plot (stress 0.22) and cluster analysis were created from the Bray-Curtis similarity matrix of the total abundance (N) of the overall community (Figure 4). The resulting plot indicated clustering by gear type. An ANOSIM of the Bray-Curtis matrix indicated differences in gear type were significant enough (R = 0.183, p < 0.001) to not pool data between gear types.

Figure 4. A MDS plot of Bray-Curtis similarity matrix of log-transformed total abundance of all samples collected in Rincon Bayou (after removing outliers), comparing gear types (Method), push net (PN) and seine (RS). Symbols represent gear selection, and are labeled by station. This plot includes a subset of sampling events, where only coinciding dates for push net and seine samples are included (periods June-December 2015). See Appendix I, Figure 23 for MDS plot of all samples.

Gear Type: Push Net

A blocked ANOVA (Appendix II, Table 14) was used to identify trends between sampling years for the means of biotic and diversity variables for push net samples. Differences in the means of abundance were identified across years (p = 0.0001) and for months within years (p =

0.0309) of the study, where average counts were highest in 2015. For the month factor, this difference was due to sampling events in 2015 beginning in June, where the means were of

abundance were greater than any previous year. The highest average biomass occurred in year

2015 (p = 0.0159) and between stations (p = 0.0585), where the mean biomass of station C was similar to stations G and F, but with substantial difference between stations G and F. The lowest mean biomass was identified at station F. The average biomass decreased in each year at stations

C and G. Biomass at station F was highest in 2010, declining in 2014 and increasing in 2015.

The biomass per tow variable varied for months within years (p = 0.0582) and stations (p =

0.0002), where mean values were lowest at station F. Species richness and diversity were also significantly higher in 2015 (p < 0.0001, p = 0.0005) and months within 2015 (p = 0.0013, p =

0.0184). There was less variation in Hill’s diversity than in comparison to the pooled data, but there was still an increase in dominant species each year of the study (Table 3).

Table 3. Summary of mean values for abundance, biomass, species richness, diversity and evenness for the push net sampled epifaunal community sampled in Rincon Bayou, displayed by years and stations. Year Station N. Obs. Abundance Biomass Species Hill's Diversity Pielou's (N m-2) (g m-2) Richness (R) (N1) Evenness (J′) C 6 21.10 3.85 6.00 2.25 0.49 2010 F 8 3.63 1.51 2.50 1.53 0.44 G 5 6.84 4.32 3.80 2.28 0.60 C 16 41.94 2.36 5.63 2.34 0.46 2014 F 13 6.43 0.60 2.77 2.00 0.62 G 14 10.20 2.35 3.43 2.45 0.63 C 19 15.34 0.73 7.05 3.23 0.59 2015 F 18 38.20 0.91 7.17 2.72 0.54 G 18 54.70 2.26 6.56 2.36 0.40

Four events during the study period (28 Apr. and 11 Aug. 2010, station F; 18 Nov. 2014 and 11 Aug. 2015, station C) returned empty samples (Appendix II, Table 15). The mean depths, temperatures, salinity, dissolved oxygen, and pH values for these events did not indicate that variation in overall water quality was the driving factor. However, the depth for each of these events fell below the Rincon average and were some of the lowest depths encountered in the study period. The 28 Apr. 2010 event occurred simultaneously with the highest pH (9.36)

recorded, 18 Nov. 2014 with the lowest recorded depth (0.03 m), and 11 Aug. 2015 with highest recorded temperature (39.17 °C).

A MDS (stress 0.20) ordination plot (Appendix I, Figure 26) on remaining samples was used to identify differences in the species abundance between samples. The abundance data for push net samples showed the greatest distance between 6 Jul. 2015, station C from the rest of the samples. July 2015 inflows were 6.88 m3 s-1 for the month, and were subject to increases in salinity (from 0.34 to 5.06 psu) and dissolved oxygen (from 6.01 to 10.06 mg L-1). This sample contained only one gulf killifish.

An additional MDS (stress 0.22) ordination plot was created, after removing this outlier, to clearly depict the configuration of remaining samples (Figure 5). Two more samples were identified (8 and 22 Jun. 2015, station C) in this plot. These periods were subject to the highest monthly inflows than any other period. Large amounts of freshwater were delivered to the marsh during flooding events in May and June 2015 (inflow 1777.55 m3 s-1 and 1547.62 m3 s-1, respectively).

The 8 June event had the highest recorded depth (0.80 m), lowest recorded dissolved oxygen (3.9 mg L-1), salinity (0.22 psu), and pH (7.54) during the study period. The sample included Streblospio benedicti, ostracods, Trichocorixa sp., Ephemeroptera sp., Ceratopogonidae larvae, Americamysis almyra, and freshwater snails (Physidae, Planorbidae, and Lymnaeidae sp.), where the only species occurring in densities > 1 N m-2 were S. benedicti, Ceratopogonidae larvae, Ephmeroptera sp., and Physidae and Planorbidae gastropods. The 22 June event had comparable species composition, where the number of species identified was 23, with similar freshwater organisms. S. benedicti, ostracods, Ceratopogonidae larvae, damselfly nymphs, T.

louisianae, Ephemeroptera sp., and Lymnaeidae gastropods were the dominating species, and the rest occurred in smaller densities.

Depth and dissolved oxygen were the most significant driving factors in the species composition of push net samples. On PC1, depth and dissolved oxygen explained the greatest variance (0.576 and -0.611, respectively), and salinity and pH exhibited lower values (-0.393 and

-0.359). The PC2 axis was best explained by temperature and pH (-0.766 and -0.597).

Figure 5. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net samples collected in Rincon Bayou. Labels are periods of the study, with bubble plot overlay representing species composition for 8 and 22 Jun. 2015 (periods 35 and 36, bottom), and PCA overlay where depth and dissolved oxygen are representative of the inflow (PC1) axis.

Crustaceans were found to be the most abundant taxa, accounting for > 90 % relative abundance. The most abundant species encountered in push net samples were A. almyra (64.42

%), Palaemonetes sp (24.25 %), Farfantepenaeus aztecus (1.96 %), Cyprinodon variegatus (1.63

%), S. benedicti (1.61 %), Trichocorixa sp. (1.12 %) and Ephemeroptera sp. (1.00 %) (Appendix

I, Figure 27). These were the only species of 72 that contributed at least one percent, and they collectively accounted for approximately 96 percent of the total abundance of push net samples.

The greatest biomass contributors were Palaemonetes sp. (39.00 %), F. aztecus (24.93 %), C. variegatus (9.77 %), Litopenaeus setiferus (6.86 %), A. almyra (6.59 %), C. sapidus (6.39 %),

Menidia beryllina (1.84 %), B. patronus (1.10 %) and Fundulus grandis (1.05 %). Again, these were the only species that contributed at least one percent to the collective biomass, accounting for over 97 percent of the total biomass.

Gear Type: Seine

The data obtained from seine samples were from June-December 2015 and consisted of one replicate at each station, C, F, and G. Due to flooding conditions in Rincon Bayou, the first

June 2015 events occurred only at station C. A two-way ANOVA (Appendix II, Table 16) of the biotic and diversity variables was used to determine differences in means of seine samples.

Differences in the means of biomass and biomass per tow were identified between site selections of samples (p < 0.0001, p = 0.0002). Biomass and biomass per tow were lowest at station F, but biomass was substantially lower at station F. Both variables were highest at station G. The month factor was also significant for the biomass variables of seine samples (p < 0.0001, p = 0.0049), where biomass displayed a decreasing trend from June to December. This indicates that seasonal patterns were influencing the overall biomass composition of the study area.

Table 4. Mean epibenthic metrics for abundance and biomass of seine samples by stations. Abundance Biomass Hill's Pielou's Station N. Obs. Richness (R) (N m-2) (g m-2) Diversity (N1) Evenness (J') C 14 1.23 3.02 10.79 4.51 0.61 F 12 1.09 2.00 10.42 4.26 0.60 G 12 2.18 4.49 12.33 4.21 0.58

Diversity and richness in seine samples were higher than in the push net samples (Table

4). A total of 38 seine sampling events occurred. Coefficients for Hill’s N1 diversity and Peilou’s evenness provided evidence that the community targeted by seines is dominated by more species

than the community of push net samples. However, as in the overall and push net data, there was little change in the evenness index.

A MDS (stress 0.17) ordination plot of the community structure based on abundance

(Figure 6) identified the samples taken 8 and 22 Jun. 2015 as samples with the greatest distance from others. Samples were only collected from station C for both events. There were 12 species identified in the 8 Jun. 2015 sample, where the biomass contributions of C. sapidus, E. saurus, L. xanthurus, M. cephalus, B. patronus, D. petenense, and unidentified hirudinea species. The remaining species accounted for < 0.1 g m-2, and all species contributed < 1 N m-2. The 22 Jun. sample contained only S. benedicti, in densities > 1 N m-2, but sample biomass was dominated by additional organisms, E. saurus, D. petenense, B. patronus, C. sapidus, unidentified decopod larvae, and ceratopogonidae larvae. Freshwater insect larvae were still present. Other samples are clustered with enough similarity to be considered to not have significant differences.

Figure 6. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine samples collected in Rincon Bayou with group average cluster overlay, identifying samples with less than 30 percent similarities. Labels are numeric months of the study, with bubble plot overlay representing species composition for 8 and 22 Jun. 2015 (bottom of graph).

The most abundant species encountered in seine samples were Palaemonetes sp (37.31

%), C. variegatus (25.93 %), F. aztecus (7.46 %), Anchoa mitchilli (6.09 %), F. grandis (5.45 %),

L. setiferus (4.98 %), C. sapidus (2.78 %), M. beryllina (1.19 %) and S. benedicti (1.49 %)

(Appendix I, Figure 28). The majority of the biomass measurements were taken from C. sapidus

(27.01 %), F. grandis (18.90 %), C. variegatus (15.66 %), and L. setiferus (10.95 %), F. aztecus

(7.03 %), Palaemonetes sp. (5.26 %), Elops saurus (4.07 %), Mugil cephalus (3.87 %), M. beryllina (2.02 %), A. mitchilli (1.82 %), and Poecilia latipinna (1.01 %). As with the push net samples, these were the species that contributed at least one percent to the total abundance and biomass. The dominant taxa in seine samples, however, was fish, contributing ≈ 55 percent to relative abundance, with crustaceans accounting for ≈ 40 percent.

Rincon Bayou Fish Community

A PCA (Appendix I, Figure 29) of the hydrological variables as they pertain to the fish community in Rincon Bayou identified minor differences in these variables than when considering the community as a whole (Appendix II, Table 17). Hydrology of fish explained 59.0 percent of the variance of the collective fish population. The PC1 axis accounted for 34.0 percent of variance. This axis was still representative of the inflow axis, where depth (0.571), dissolved oxygen (-0.601), pH (-0.446), and salinity (-0.318) were the highest explanatory variables. The

PC2 axis was, again, representative of the seasonal axis, where temperature (0.780), pH (0.502), dissolved oxygen (-0.303), accounted for an additional 25.0 percent of the variation. As was the case with entire community, dissolved oxygen was the greatest explanatory inflow variable and temperature was the most influential seasonal variable.

Fish were identified in samples 44 of the 49 events during the study period. A collective total of 5100 fish were identified, 4201 from seines and 899 from push nets. The mean fish

weight was 0.68 g with a standard deviation of ± 1.97 (seines: 0.78 g, ± 2.14; push nets: 0.21 g, ±

0.61). The total biomass of push net sampled fish was 191.26 g, seines 3291.60 g. The mean fish length was 24.92 mm with a standard deviation of ± 13.03 (seines: 26.34 mm, ± 13.48; push nets: 18.25 mm, ± 7.71). Fish measuring < 50.0 mm comprised more than 90 percent of the total fish assemblage and all fish from push net samples were < 50.0 mm.

From this study, a total of 22 different species of fish were identified in Rincon Bayou, 16 of which, were documented in both gear types. Fish identified in only push nets were striped anchovy (Anchoa hepsetus), pinfish (Lagodon rhomboides), and gulf pipefish (Syngnathys scovelli). Fish identified in only seines were threadfin shad (Dorosoma petenense), rainwater killifish (Fundulus pulvereus), and river carpsucker (Carpiodes carpio). Sheepshead minnow

(Cyprinodon variegatus) was identified as the most frequently occurring fish species for either sampling gear.

Table 5. Mean values for epibenthic indices of Rincon Bayou pooled fish data displayed by year and gear selection. Year Station N. Abundance Biomass Richness Hill's Pielou's Evenness Obs. (N m-2) (g m-2) (R) Diversity (N1) (J′) C 3 0.47 0.09 1.33 1.33 0.33 2010 F 6 0.50 0.11 1.00 1.00 0.00 G 4 1.35 0.42 2.00 1.62 0.52 C 11 3.80 0.52 1.55 1.24 0.19 2014 F 6 0.67 0.05 1.00 1.00 0.00 G 8 6.33 1.73 1.50 1.37 0.40 C 27 1.56 0.99 3.07 1.99 0.43 2015 F 23 0.98 0.44 2.43 1.64 0.46 G 30 1.67 1.05 3.00 1.90 0.53

Calculation of diversity indices for the pooled fish community identified higher species abundance in year 2014 and higher biomass in 2015. There was greater variance in the evenness index as compared to the overall community (Table 5). Pearson correlation coefficients produced from the fish community diversity indices indicated strong positive correlations between species richness and dominance (ρ = 0.82, p < 0.0001), species dominance and evenness (ρ = 0.76, p <

0.0001), and between abundance and biomass (ρ = 0.60, p < 0 .0001). Moderately positive

correlations between richness and evenness (ρ = 0.48, p < 0.0001) and richness and biomass (ρ =

0.38, p < 0.0001) were also identified. There were no significant correlations between the overall fish community and hydrographic variables.

A nested ANOVA (Appendix II, Table 18) comparing means of biotic and diversity indices identified differences between years for biomass (p = 0.0167), richness (p = 0.0158), and diversity (p = 0.0373), where both were substantially higher in 2015 than other years.

Differences between months were found in species abundance (N m-2) and biomass (g m-2) (p =

0.0293, p = 0.0320). Abundance was highest in 2014 and lowest in 2010, with the greatest dissimilarity between these two years. Tukey post hoc determined differences in biomass not great enough. A significant variation in abundance (N m-2) existed between stations (p = 0.0116), where station F exhibited the lowest means, substantially different from stations C and G.

A MDS ordination plot (stress 0.01) identified three events (2 June 2014, 27 Apr. 2015, and 22 June 2015, station C push nets) as significantly different from all other samples

(Appendix I, Figure 30). Each of the events were subject to nearly freshwater environment, during the wet season, and only contain one species of fish. The 2 June 2014 event (salinity 0.65 psu, dissolved oxygen 7.43 mg L-1, depth 0.18 m) was the only encounter of pinfish (Lagodon rhomboides, 24.3 mm, 0.36 g) during the study period. The 27 Apr. 2015 event (salinity 0.74 psu, dissolved oxygen 5.53 mg L-1, depth 0.3 m) contained one alligator gar (Atractosteus spatula, 16.9 mm, 0.03 g), a fish encountered three times during the months, April-June.

Alligator gar were only identified in samples from station C, but larger specimen were observed at all stations. The 22 June 2015 event (salinity 0.34 psu, dissolved oxygen 6.01 mg L-1, depth

0.35 m) had five bluegill (Lepomis macrochirus), being the only event in which they were identified.

After removing these outliers, the resulting MDS ordination plot (stress: 0.12) identified two additional sampling events with significant clustering (Figure 7), based on the group averages of samples in the overall fish assemblage. These two events were push net samples taken at station C (1 and 16 June 2010) and contained only rainwater killifish (Lucania parva), four and one, respectively. There were moderate environmental variances. Rainwater killifish were found in low numbers in two other push net samples (November 2014 and 2015), but always accompanying other fish, especially, sheepshead minnow. They were only found in samples the months of June, July, November, and December. Additional clustering of events from the pooled data was evident, but not at the 30 percent determination. However, gear- specific clusters were evident.

Figure 7. A MDS ordination plot (after removing outliers) of pooled fish assemblage data from Rincon Bayou, identifying separation of fish structure by gear type, push net (PN) or seine (RS). Symbols are gear selection and labels are periods.

Results from the ANOSIM of pooled fish data did not support the need for separate analysis, but a one-way ANOVA (Appendix II, Table 19) identified significantly higher differences in the means of abundance (p < 0.0001), biomass and biomass per tow (p < 0.0001, p

< 0.0001), richness (p < 0.0001), diversity (p < 0.0001), and evenness (p < 0.0029) in the seine sampling gear. This supported the same findings in the collective community, in that the seine gear type is targeting larger organisms. It was also targeting a higher number species. Additional analysis for fish abundance was completed on gear selections separately.

Gear Type: Push Net

A PCA of the hydrological variables for only push net samples was performed on the fish community. Axis identifiers (inflow or seasonal) remained the same. Push net sampled hydrology was similar to the overall analysis, where PC1 explained 31.8 percent and PC2 explained 24.9 percent. Dissolved oxygen was the greatest explanatory variable (-0.645), then depth (0.481), and temperature (0.481). Salinity (-0.183) had minimal effect on push net samples.

A nested ANOVA (Appendix II, Table 20) comparing means of diversity indices for push net samples showed differences occurred between stations for abundance and density (p =

0.0114, p = 0.0329), richness (p = 0.0196), diversity (p = 0.0154), and evenness (p = 0.0190).

Abundance, richness, diversity, and evenness were highest at station G, with similarity to station

C, and the greatest distance between means were from station F. Less significant differences were identified between years in the means of density (p = 0.0765), where density was lowest in

2010 and highest in 2014, with a decline in 2015. Effects within the month factor were evident for diversity (p = 0.0701) and evenness (p = 0.0947), where the means of both variable were higher in September-December 2015.

Pearson correlation coefficients produced from the fish community as they pertain to only push net diversity indices indicated strong positive correlations between species richness and evenness (ρ = 0.75, p < 0.0001), richness and dominance (ρ = 0.87, p < 0.0001), species dominance and evenness (ρ = 0.90, p < 0.0001), and between abundance and biomass (ρ = 0.88, p < 0.0001). There were no significant correlations between the push net fish community and hydrographic variables.

The four fish species found in highest densities in push net samples were sheepshead minnow (99.8 N m-2, 24.58 g m-2), inland silversides (32.6 N m-2, 4.46 g m-2), gulf menhaden

(15.4 N m-2, 2.74 g m-2) and bay anchovy (11.6 N m-2, 1.27 g m-2). Other fish species collected in push nets accounted for abundance values less than 10 N m-2 and biomass less than 1 g m-2, except for gulf killifish (2.63 g m-2), and occurred less than 50 times during the study period

(Appendix I, Figure 31).

Figure 8. A MDS ordination plot of Bray-Curtis similarity matrix for log-transformed abundance data from the push net sampled fish assemblage, with bubble plot overlay displaying fish species as they pertain to samples identified with greater variance.

A MDS (stress = 0.01) ordination plot was utilized to illustrate the structure of the push net sampled fish community independent of seines. The same three events were identified as in the pooled community, and were removed as outliers. The resulting MDS (stress = 0.07) plot identified additional events (Figure 8), as well an overall seasonal influence to the fish assemblage (Appendix I, Figure 32). For these groups of samples, groupings shared a common dominant species across each sample.

The first group (top left) included four events (4 May 2010, station C; 28 Apr. 2014, stations F and G; 30 Mar. 2015, station F) and an additional nested cluster which included the 1 and 16 June 2010 events, previously identified by the pooled MDS. The common fish identified in each of these samples was ladyfish (Elops saurus). A total of 31 ladyfish were identified in the course of this study, encountered in 11 events at an average of < 1 per tow. The clustered events are those in which lady fish were the dominant, or only, species encountered.

The 4 May 2010 event contained one ladyfish (18.5 mm, 0.02 g), and co-occurring species, alligator gar (18.2 mm, 0.02 g). The 28 Apr. 2014-F event contained one ladyfish (25.6 mm, 0.04 g) and four from 28 Apr. 2014-G (mean 25.55 mm, mean 0.03 g). The 30 Mar. 2015 event contained two ladyfish (mean 28.1 mm, mean 0.1 g), and one inland silverside (Menidia beryllina, 44.4 mm, 1.03 g) was a co-occurring species. Salinities of these events ranged from

3.48 to 44.54 psu, dissolved oxygen levels never fell below 6.48 mg L-1 and depths ranged from

0.1 to 0.3 m.

The second group (Figure 8, bottom left) identified an additional 10 events (11 May

2010, station G, 16 June 2010, station G, 2 June 2014, stations F and G, 17 June 2014, station G,

16 Mar. 2015, station G, 30 Mar. 2015, stations C and G, and 10 Apr. 2015, stations C and G),

where gulf menhaden were the dominant or only species encountered. Menhaden were collected in 14 samples March to July, and one instance in November 2014.

The 11 May 2010 event had 14 gulf menhaden (B. patronus) and 1 sheepshead minnow

(C. variegatus). Only menhaden were found in the 16 Jun. 2010, station G (N = 3), 2 June 2014, station F (N = 4), and 2 and 17 June 2014, station G (N = 1, 10) events. 16 Mar. 2015, station G contained one gulf menhaden and three spot croaker (L. xanthurus). The 30 Mar. 2015, station C event had only two gulf menhaden. 30 Mar. 2015, station G had 31 menhaden and two ladyfish

(E. saurus). The 10 Apr. 2015, station C event contained only one gulf menhaden and for station

G, five menhaden and one ladyfish. For these events, salinities ranged from 4.26 psu to 30.1 psu, dissolved oxygen levels were between 6.93 and 9.03 mg L-1, and depths were either 0.2 or 0.3 m.

Gear Type: Seine

A PCA for hydrologic variables, as they pertained to only the seine sampled community, indicated PC1 accounted for 45.0 percent of the variation, and PC2 contributed an additional

23.3 percent. Depth was the greatest explanatory variable (0.543) on PC1, followed by dissolved oxygen (-0.506), pH (-0.484), and salinity (-0.400).

A two-way ANOVA (Appendix II, Table 21) examined diversity indices calculated for seine samples only. Significant differences in variable means for factor month were identified in abundance and density (p = 0.0446, p = 0.0152) and biomass and biomass per tow (p < 0.0001, p

< 0.0001), where biomass was significantly higher for the months of June and July as compared to other months where seine samples were taken. Tukey post-hoc testing did not show variance in abundance to be sufficiently significant. Differences were also identified between stations for abundance and density (p = 0.0446, p = 0.0152), biomass and biomass per tow (p = 0.0026, p =

0.0166), where biomass was significantly lower at station F than stations C or G. An interaction was identified in biomass per tow (p = 0.0027), due to higher biomass at station G in July 2015.

Pearson correlation coefficients regarding seines indicated strong positive correlations between species richness and dominance (ρ = 0.69, p < .0001) and between species dominance and evenness (ρ = 0.71, p < 0.0001. Moderately positive correlations were found between abundance and biomass (ρ = 0.38, p = 0.0180) and richness and biomass (ρ = 0.35, p = 0.0336).

Strong negative relationship were identified between abundance and evenness (ρ = -0.66, p <

0.0001), and moderately negative correlations between abundance and diversity (ρ = -0.40, p =

0.0125). Correlations between hydrographic variables were also identified where salinity was moderately negatively correlated to species richness (ρ = -0.42, p = 0.0079) and diversity (ρ = -

0.36, p = 0.0259). Dissolved oxygen was strongly correlated to abundance (ρ = 0.50, p = 0.0014) and moderately negative relationships were identified between diversity (ρ = -0.37, p = 0.0211) and evenness (ρ = -0.39, p = 0.0163). Biomass also showed a moderately positive correlation to pH (ρ = 0.46, p = 0.0036).

In seine samples, the species found in greatest abundance were sheepshead minnow

(47.89 N m-2, 18.84 g m-2), bay anchovy (11.76 N m-2, 2.27 g m-2), gulf killifish (10.05 N m-2,

22.76 g m-2), inland silverside (2.2 N m-2, 2.42 g m-2) and sailfin molly (1.35 n m-2, 1.21 g m-2).

The remaining species encountered contributed less than 1 N m-2 and g m-2. Striped mullet and lady fish added more to the total fish biomass than abundance, contributing 4.65 and 4.90 g m-2, respectively, but still occurred less than 50 times during the study period (Appendix I, Figure

33).

Clusters were identified in an MDS ordination plot created for strictly seine samples

(Figure 9), as well a seasonal influence (Appendix I, Figure 34). This gear type lacked a full year

of samples, so a full seasonal cycle could not be clearly depicted. The first cluster (bottom right) contained only one sample (24 Aug. 2015, station G). This sample contained one striped mullet

(M. cephalus) and one Gulf killifish (F. grandis). Striped mullet were encountered seven times, and only found in seine samples June to November, in very low numbers. Salinity for this event was 19.26 psu, dissolved oxygen was 9.24 mg L-1, and depth was 0.25 m. Temperatures were highest at this event (36.14 °C) in comparison to other encounters of striped mullet.

Figure 9. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from the seine sampled fish assemblage in Rincon Bayou with 30 percent similarity cluster overlay. Symbols represent stations (C, F, or G), and labels are periods. See Figure 28 for MDS plot with outliers.

The second cluster (bottom left) contained two samples, both of which occurred at station

C (8 and 22 June 2015). The 8 June 2015 event included 15 silversides, 1 threadfin shad

(Dorosoma pretense), 13 ladyfish, 1 striped mullet, and 1 spot croaker. This event was subject to the lowest recorded dissolved oxygen (3.9 mg L-1) and salinity (0.22 psu) values. The 22 June

2015 event had 23 silversides, 12 threadfin shad, 1 bay anchovy, 2 gulf killifish, 4 ladyfish, 1 gar,

1 (Poecilia latipinna), 9 bluegill (Lepomis macrochirus), and 1 (Carpiodes carpio). These events had higher temperatures, lowered salinities and dissolved oxygen, and followed major flooding events and washing out of the weir in May 2015.

Rincon Bayou Penaeid Shrimp Populations

A total of 2169 penaeid shrimp were collected (1387 brown, 782 white) in push nets and seines over the study period, ranging in lengths from 6.9 mm to 141.9 mm. Multivariate analysis determined that shrimp > 100.0 mm in length only occurred in white shrimp. Additionally, the presence of white shrimp was non-existent in samples collected after September 2015.

Figure 10. Distribution of the means of abundance and lengths of brown and white shrimp encountered in Rincon Bayou, during the study period.

One-way ANOVAs (Appendix II, Table 22) comparing lengths and weights of shrimp between methods and species determined the mean length (p < 0.0001) and weight (p < 0.0001) of shrimp encountered in seine samples was significantly higher than those of push net-sampled shrimp. The mean length (p < 0.0001) and weight (p < 0.0001) of white shrimp was significantly higher than those of brown shrimp. Boxplots produced from means of brown shrimp and white

shrimp by abundance and size indicated that fewer white shrimp are encountered than brown shrimp, but white shrimp are larger (Figure 10).

Brown Shrimp (Farfantepenaeus aztecus)

A one-way ANOVA (Appendix II, Table 23) comparing gear types for the overall composition of brown shrimp indicated that there were no significant differences between sampling gears for the lengths and weights of brown shrimp. However, significant differences in the abundance, density, biomass and biomass per tow (p = 0.0022, p = 0.0004, p = 0.0003, p =

0.0043) variables of brown shrimp did indicate that treating gears separately should occur instead of pooling data for both sampling techniques (Table 6). Analysis of brown shrimp lengths compared by gear selection, determined that regardless of method, the 25 - 60 mm size class was the most common.

Table 6. Summary of variable means of push net and seine-sampled brown shrimp, and physical variables. Size Length Weight Monthly Depth Temperature Salinity DO Gear N pH Class (mm) (g) Inflow (m3s-1) (m) (°C) (psu) (mg L-1) 1 171 17.17 0.04 96.31 0.21 30.42 22.48 8.27 8.45 2 367 40.58 0.53 268.45 0.23 28.03 16.00 7.86 8.43 PN 3 51 66.96 2.11 278.98 0.27 28.56 19.13 7.39 8.43 4 1 91.80 5.89 1777.55 0.40 28.56 15.07 8.76 8.23 1 207 19.73 0.06 18.02 0.22 30.91 22.89 8.91 8.21 2 513 38.49 0.51 29.85 0.23 28.94 18.21 8.33 8.20 RS 3 76 68.58 2.45 57.96 0.26 27.10 11.80 8.77 8.22 4 1 91.90 5.17 50.21 0.25 22.04 3.35 9.18 7.98

Gear Type: Push Net

For push net samples, the mean length of shrimp found was 36.16 mm, mean weight was

0.53 g, and total of 590 shrimp collected with this gear type (Appendix I, Figure 35). A nested/blocked ANOVA (Appendix II, Table 24) to identify differences in the means of variables pertaining to brown shrimp between dates and stations determined significant differences between years of the study in means of abundance and density (p < 0.0001, p < 0.0001), as well as biomass and biomass per tow (p = 0.0003, p = 0.0008). Biomass and abundance were

substantially higher in 2010, decreasing each year of the study. Significant differences were identified between factor months for length (p = 0.0151), weight (p = 0.0082), and abundance (p

= 0.0416). Differences were also identified between stations for the biomass and biomass per tow variables (p = 0.0505, p = 0.0347). Tukey post hoc testing of the variables indicated these differences were not substantial enough for biomass.

Pearson correlation procedures did identify a strong positive relationship between length and weight (ρ = 0.93, p < 0.0001) and abundance and biomass (ρ = 0.58, p < 0.0001). A moderate positive relationship between biomass and length was also present (ρ = 0.30, p =

0.0216). Correlation of hydrographic variables against the biotic variables of push net sampled shrimp were very weak, and only existed between abundance and salinity (ρ = 0.28, p = 0.0310), weight and depth (ρ = 0.28, p = 0.0343), and biomass and depth (ρ = 0.28, p = 0.0345).

Time series of push net sampled brown shrimp against salinity and depth (Appendix I,

Figure 36) depict changes in the brown shrimp population with fluctuations in weakly correlated hydrological parameters. A PCA of physical variables as they pertain to brown shrimp identified temperature (-0.547) as the highest explanatory variable for variances between samples. A time series of brown shrimp size classes against temperature (Figure 11) revealed the highest abundance of new recruits found in push net collections entered Rincon Bayou in the fall of

2014. Juvenile shrimp were typically entering the marsh following an increase in temperature. As temperatures decreased, fewer shrimp were collected. The presence of juvenile shrimp during the spring months of years 2014 and 2015, but lowered numbers of post-larval, indicated that the newly entering brown shrimp were not being captured in push nets.

60 45 SC1 SC2 SC3 SC4 Temperature (C) 40 50 35

40 30

25 30

20 Abundance 20 15 Temperature

10 10 5

0 0

9/8/2014 7/6/2015 9/9/2015

8/25/2014 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 5/15/2014 6/17/2014 6/30/2014 7/14/2014 8/11/2014 11/3/2014 12/2/2014 1/16/2015 3/16/2015 3/30/2015 4/10/2015 5/11/2015 7/27/2015 8/24/2015 9/21/2015

10/28/2015 11/11/2015 11/24/2015 12/21/2015 10/20/2014 Date Figure 11. Time series showing changes in temperature, over time as it relates to abundance of brown shrimp according to assigned sized class, including only brown shrimp collected in push nets from Rincon Bayou during the study period (2010-2015).

A MDS ordination plot (stress 0.13) of brown shrimp according to their assigned size class (Figure 12) depicted variation (similarity < 50 %) in several events (14 Jul. 2014, 28 Oct.

2015, 6 Jul. 2015, and 25 Aug. 2014, station G; 3 Nov. 2014, station C; and 3 Nov. 2014 and 11

Nov. 2015, station F). These events included some of the lowest abundance of brown shrimp, and the majority encountered were in the third size class (abundance ranges from only 1 - 3 total shrimp). Depths for these events ranged between 0.15 and 0.35 m. Salinities ranged from 3.70 to

29.94 psu.

Shrimp collected 14 Jul. 2014, station G, occurred in a period with higher than average inflows (234.45 m3 s-1) and temperature (30.98 °C), and lowered salinity (3.70 psu) and dissolved oxygen (6.48 mg L-1). Collections from 3 Nov. 2014, stations C and F, and events 25 Aug. 2014,

6 Jul. 2015, and 28 Oct. 2015, station G, shared similarities greater than 70 percent, with nearly

100 percent similarity between 25 Aug. 2014 and 3 Nov.14. There was also nearly 100 percent similarity between 6 Jul. 2015 and 28 Oct. 2015. Samples taken 25 Aug. 2014 and 6 Jul. 2015,

and 3 Nov. 2014 were subject to monthly inflows less than 7.0 m3 s-1, salinities greater than 23.0 psu, and a maximum depth of 0.25 m. Sampling events 6 Jul. 2015 and 28 Oct. 2015 were subject to inflows < 51.0 m3 s-1, depths lower than 0.5 m, salinities less than 4.5 psu, and dissolved oxygen greater than 8.0 mg L-1. The 11 Nov. 2015 event was the final event in which brown shrimp occurred during the study period.

Figure 12. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net-sampled brown shrimp collected in Rincon Bayou where points are labeled by month with bubble indicating size class.

Gear Type: Seine

A total of 797 brown shrimp were collected in seine nets June-December 2015 (Table 6).

There were a total of ten events, in which brown shrimp falling in category of size class 2 were the most frequently encountered size, as was the case for push net samples. Two-way ANOVA results (Appendix II, Table 25) for factors month and station determined no significant interactions. There were significant differences between months for the variables length (p =

0.0005), weight (p < 0.0001), abundance (p = 0.0238), density (p = 0.0060), biomass (p =

0.0429), and biomass per tow (p = 0.0577). Lengths and weights were greatest in November and

July, and lowest in August and September. Abundance was highest in September and lowest in

July. Tukey post hoc testing revealed that means were not significantly different enough for biomass. Differences were identified between stations for the variables length (p = 0.0501) and weight (p = 0.0137), but post hoc testing indicated not significant enough.

There was a seasonal pattern of lengths and weights evident (Figure 13), indicating that seines are effectively capturing juvenile shrimp beginning late July to early August. There is a steady increase over the summer months with clear indication that the larger shrimp begin to move out of the region around November, but there was still the presence of some smaller recruits. For 2015, no brown shrimp were encountered in seine samples in June or December.

Figure 13. Box plot of the log-transformed variables for brown shrimp from seine samples, Left: length and Right: weight.

A MDS (stress = 0.07) ordination plot (Figure 14) provided visualization of the separation of the seine sampled brown shrimp based on size class. Two events had > 30 percent differences from others. Samples taken 27 July 2015, station F and 11 Nov. 2015, station C share

> 70 percent similarities. Both events had low counts of brown shrimp (1 and 2, respectively), in

the third size class. Depths measured for these events were 0.1 and 0.25 m, dissolved oxygen was

9.41 and 8.52 mg L-1, and salinities were 9.71 and 2.34 psu.

Figure 14. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine- sampled brown shrimp collected in Rincon Bayou, where points are labeled by month with bubble plot overlay indicating size class.

A PCA of hydrographic variables as they pertain to only seine sampled brown shrimp indicated a strong response to depth and temperature, where PC1 accounted for 46.5 percent of overall variance, as explained by depth (-0.520) and temperature (0.559). Time series analysis of the abundance of brown shrimp against these variables showed a trend of increasing abundance when depths were between approximately 0.2 and 0.4 m, and for temperatures ranging between

20 and 30 ºC (Appendix I, Figure 37).

White Shrimp (Litopenaeus setiferus)

A total of 782 white shrimp were collected over the study period, in months ranging from

August 2010 to November 2015. The lowest inflow value was 1.91 m3 s-1 and maximum was

234.45 m3 s-1, averaging 18.55 m3 s-1, ± 23.59. Depths ranged from 0.05 to 0.35 m, mean of 0.08 m, ± 0.21. Salinities ranged from 0.44 psu to 29.94 psu, mean of 16.54 psu, ± 5.96.

Temperatures ranged from 22.04 to 36.14 °C, with a mean of 31.81 °C, ± 3.44. Dissolved oxygen ranged from 6.48 to 12.51 mg L-1, with an average of 8.93 mg L-1, ± 1.44. The minimum pH recorded was 7.95, maximum 8.88, with an average of 8.35, ± 0.25.

A one-way ANOVA was utilized to determine differences in push net and seine-sampled white shrimp (Appendix II, Table 26). The variance in means for push net sampled white shrimp and seine sampled white shrimp were significant for all variables, except biomass per tow. Gear selection in white shrimp populations differs from brown shrimp is that the seine samples are targeting more of the larger size classes than those of the brown shrimp (Table 7).

Table 7. Summary of variable means of total white shrimp collected in push nets (PN) and seines (RS). Gear Size N Length Weight Monthly Depth (m) Temperature Salinity DO pH Class (mm) (g) Inflow (m3 s-1) (°C) (psu) (mg L-1) 1 178 21.31 0.07 8.32 0.20 33.18 15.62 9.18 8.52 PN 2 89 46.32 0.59 11.41 0.22 33.91 16.70 8.54 8.43 3 9 78.07 2.91 6.21 0.22 33.51 15.90 8.45 8.45 1 117 25.46 0.11 13.54 0.18 32.76 16.78 8.93 8.41 2 279 53.54 1.02 23.26 0.23 30.85 16.33 9.20 8.25 RS 3 109 82.54 3.83 35.49 0.23 29.10 18.17 8.22 8.20 4 1 141.90 10.16 7.45 0.25 36.14 19.26 9.24 8.30

Analysis of biotic and hydrographic variables implementing Pearson correlation procedures identified strong positive relationships in biotic variables abundance and biomass (ρ

= 0.72, p = 0.0003) and between lengths and weights (ρ = 0.83, p < 0.0001). There were no correlations identified between white shrimp and hydrographic variables. However, a PCA analysis of physical variables identified a strong seasonal influence as explained by temperature

(-0.557) and dissolved oxygen (-0.593) on the PC1 axis. The PC2 axis was best explained by salinity (-0.931).

Gear Type: Push Net

A total of 276 white shrimp specimen were collected in push net samples in 12 sampling events (Table 7). The mean length of white shrimp found in push net samples was 36.16 mm, weight was 0.53 g. A nested ANOVA (Appendix II, Table 27) identified a significant differences across years for biomass and biomass per tow only (p = 0.0477, p = 0.0315), where average biomass was significantly higher in 2010. The average length of white shrimp decreased from year 2010 to 2014 and again slightly in 2015, with an overall trend of size reduction (Appendix I,

Figure 38). Positive correlations were identified in variables abundance and biomass (ρ = 0.72, p

= 0.0003) and lengths and weights (ρ = 0.83, p < 0.0001), with no correlation to physical variables.

A time series of each size class of white shrimp encountered in push net samples, compared with salinity, showed that abundance of white shrimp peaked July-August, shortly after freshwater reduced salinities, and then began to decrease as salinities increased (Figure 15).

For sampling events in 2010, white shrimp were only found in the month of August (two events).

Four events in 2014 (July-September) and six events in 2015 (July-October) contained white shrimp. For any year, the earliest identification of white shrimp was July and the latest was

October, and for each of these years, sampling did occur prior to the first encounter of white shrimp.

60 50 Size Class 1 Size Class 2 Size Class 3 Salinity (psu) 45 50 40 35 40 30 30 25

20 Salinity 20 Abundance Abundance (N) 15 10 10 5

0 0

6/1/2010 7/6/2010 6/2/2014 9/8/2014

2011 - ND - 2011 2013 - ND - 2013

6/30/2014 3/30/2015 8/24/2015 4/28/2010 5/11/2010 4/28/2014 7/29/2014 8/11/2014 11/3/2014 2/16/2015 4/27/2015 6/22/2015 7/27/2015 9/21/2015

10/20/2014 12/15/2014 11/24/2015 12/21/2015 Date Figure 15. Time series of push net sampled white shrimp by size classes compared to salinity.

White shrimp are known to have highly temperature and salinity dependent life cycles, so abundance of white shrimp were depicted in time series graphs against these two physical variables (Appendix I, Figure 39), and a PCA comparing physical variables of push net sampled white shrimp identified dissolved oxygen (-0.59) and temperature (-0.56) to be the most highly explanatory physical variables on PC1 (46.3 %) and salinity on PC2 (-0.93), indicating a higher seasonal influence than inflow.

A MDS (stress = 0.08) ordination plot identified an overall trend of higher abundance when temperatures are higher. Two dates, 11 Aug. 2010 and 8 Sep. 2014, both taken from station

C (Figure 16). Each of these events contained only one white shrimp. They were subject to lower monthly inflows (< 4.5 m3 s-1) and depths (0.15 m) than the average over the study period.

Figure 16. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net-sampled white shrimp collected in

Gear Type: Seine

A total of 506 white shrimp were collected in seine net in 9 sampling events from July to

November 2015 (Table 7). White shrimp were encountered one month later in seine samples than in push net samples. This may be an indication that once shrimp reach a certain size, they are able to escape the push net gear type.

A two-way ANOVA (Appendix II, Table 28) identified significant variation between dates and stations and the interaction of the two. Differences across months were identified in length (p

= 0.0270) and weight (p = 0.0325). Differences at the station level were identified for length (p =

0.0582) and biomass (p = 0.0476). A significant interaction was not identified for any variable.

Comparison of the length and biomass variables across dates of the study identified an increasing trend in lengths and weights over their residency time in the seine sampled white shrimp, where

shrimp collected in November were highest and those collected in July were lowest, and these two months were the greatest distance (Figure 17). Tukey post hoc determined differences between stations were not significant.

Figure 17. Box plots of means of log-transformed white shrimp in seine samples, A. length and B. weight.

A MDS (stress = 0.12) ordination plot of the size classes of white shrimp did not indicated any events with significant dissimilarities, but there is noticeable division of sample with lower numbers of white shrimp. Particularly in samples September-November, where fewer specimen of the larger classes were encountered (Figure 18). This was the last sampling event in which white shrimp were encountered. Nine shrimp were collected at this event, all of which measuring > 60.0 mm, and averaging 82.93 mm.

As with all other shrimp categories, there was an increase in abundance as salinities increased until they reach an extreme, followed by a decline in abundance. Again, salinity was the greatest explanatory variable. The relationship between salinity again supports that salinities ranging between 10 and 20 psu coincide with periods of higher abundance (Appendix I, Figure

40).

Figure 18. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine- sampled white shrimp collected in

Rincon Bayou Blue Crab (Callinectes sapidus) Population

A total of 410 blue crab were collected during the study period accounting for 1.02 percent of the total community abundance and 25.02 percent of the total community biomass

(Table 8). Blue crab were encountered 37 of the 49 events of the study period. Sexual identification of the blue crab population indicated that females only accounted for 13.17 percent of the population, but on average displayed greater lengths and weights than males, the first size class (< 20.0 mm) being the most frequently encountered for both sexes of this species

(Appendix II, Tables 29-31)

Table 8. Summary statistics for blue crab by year and station. Values are the total number of crab encountered (N) and their abundance (N m-2), biomass (g), biomass per tow (g m-2), carapace widths (mm) and individual weights (g). Abundance Biomass Carapace Year Station N Biomass (g) Weight (g) (N m-2) (g m-2) Width (mm) C 20 4.00 40.47 8.09 25.56 2.13 2010 F 1 0.20 9.03 1.81 49.30 9.03 G 5 1.00 2.02 0.40 13.65 0.31 C 26 5.20 16.28 3.26 14.98 0.58 2014 F 7 1.40 1.53 0.31 12.33 0.22 G 9 1.80 1.43 0.29 11.68 0.20 C 62 3.67 512.51 12.24 38.93 15.27 2015 F 72 4.04 563.29 11.10 26.83 9.34 G 208 14.87 821.94 74.68 19.34 3.23

Pearson correlation identified strong positive relationships between abundance and average weights (ρ = 0.50, p = 0.0004), abundance and biomass (ρ = 0.96, p < 0.0001), biomass and average weights (ρ = 0.56, p < 0.0001), and average weights and carapace width (ρ = 0.86, p

< 0.0001). Moderately positive correlations were identified in hydrographic variables dissolved oxygen and abundance (ρ = 0.32, p = 0.0278), as well as biomass (ρ = 0.33, p = 0.0244); pH and abundance (ρ = 0.39, p = 0.0064), as well as biomass (ρ = 0.33, p = 0.0251).

A one-way ANOVA (Appendix II, Table 32) to identify variations in the biotic variables according to gear selection indicated significant differences in all but one variable. Tukey lines indicated that the means of variables carapace width (p < 0.0000), individual weights (p = 0.0007 p < 0.0000), abundance (p = 0.0003), and biomass (p < 0.0001) were higher in specimens captured by seines. The means of density (p = 0.0002) were higher in push nets. No significant difference were identified in biomass per tow. Further analysis were reported on gear types independently of each other.

Gear Type: Push Net

Blue crab collected in push nets totaled 158 (38.54 %) of the collective total (Appendix

II, Table 29). A nested ANOVA (Appendix II, Table 33) with Tukey Least Significant testing

results indicated significant variance across only years of the study was detected in crab weights

(p = 0.0542) and biomass (p = 0.0513), where average crab weights and biomass were highest in

2010, with a decline in 2014, and slight increase in 2015. Means for both variables in year 2010 were significantly higher than 2014 (Appendix I, Figure 41).

35 50 30 S1 S2 S3 Salinity (psu) 40 25 20 30

15 20 Salinity

Abundance 10 10 5

0 0

2/2/2015 6/1/2010 7/6/2010 6/2/2014 9/8/2014

2012 - ND - 2012 ND - 2013

5/19/2010 4/28/2010 5/11/2010 6/16/2010 8/17/2010 4/28/2014 6/17/2014 6/30/2014 7/14/2014 7/29/2014 8/11/2014 8/25/2014 10/6/2014 11/3/2014 3/16/2015 3/30/2015 4/10/2015 4/27/2015 5/11/2015 7/27/2015 8/24/2015 9/21/2015 10/9/2015

11/18/2014 12/15/2014 10/28/2015 11/11/2015 12/21/2015 Date 10/20/2014 Figure 19. Time series for push net sampled crab abundance by size class, compared against salinity and inflow regimes. Inflow is log-transformed for scale purposes.

A time series analysis of the blue crab, according to size class (Appendix I, Figure 42), with respect to salinity showed salinity patterns similar to other studies in Rincon Bayou.

Salinities are reduced when there is increased freshwater during the spring and fall months and there was coinciding peaks in abundance at these times. Another trend identified was the entrance of the first size class of crab, which would be newly entering juvenilles, following the spring freshwater delivery (Figure 19). For each year, this was the period of highest abundance and the 2015 spring recruitment was the largest peak in abundance for the study period.

A MDS ordination plot (stress = 0.05) with significant (30 %) cluster overlay identified 6 events that were different than the majority of the samples (Figure 20). Depth ranged from 0.10 to 0.25 m, temperatures were between 25.50 and 35.62 °C, salinity 0.44 to 18.97 psu, dissolved oxygen 6.94 to 10.89 mg L-1, pH 8.02 to 8.87, and monthly inflows ranging 6.88 to 355.09 m3 s-

1. The June 2010 (stations C and F), July 2014 (station C), and November 2015 (station C) events

experienced relatively low abundance (9, 1, 3, and 1, respectively) and occurred following heavy freshwater influxes, where station C experienced high inflows (> 130.00 m3 s-1), temperatures below 30 °C, and salinities (< 2.50 psu) near freshwater. The July (station G) and August (station

F) 2015 events occurrend in periods of little freshwater (< 8.00 m3 s-1) and temperatures greater than 33 °C. Both events from station F (June 2010, August 2015) were subject to salinities greater than 15.0 psu (Appendix I, Table 33).

Figure 20. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net-sampled blue crab collected in

Gear Type: Seine

A total of 252 specimen were collected in seine nets during the study period. Crabs were present in samples each month seines were deployed. A two-way ANOVA (Appendix II, Table

35) with Tukey post hoc testing identified differences in months for carapace widths (p = 0.0029) and weights (p = 0.0260). Carapace widths were significantly greater in the months of June and

July, and crab weights were highest in June. Differences in the means of crab abundance were determined significant between stations (p = 0.0356), where means were significantly higher at station G (Figure 21).

Figure 21. Box plots of log-transformed blue crabs collected in seine samples, Left: length and Right: weight.

A time series graph of seine samples collected from June-December depict the abundance of blue crab during the summer months of 2015. Because seine samples were only added to the study as of June 2015, there are fewer dates and it is not possible to clearly indicate inflow and salinity regimes outside of this 6-month period. As was seen in the push net sampled crab collections, abundance of crabs is markedly higher following the spring inflows, with a large peak of new recruits in late October (Appendix I, Figure 43).

An MDS ordination plot (stress = 0.09) of seine sampled abundance with cluster overlay identified six events that differed from the majority of samples where crab were collected (Figure

22). Events on the left include 8 Jun. 2015, station C, 6 Jul. 2015 stations C and F, and 11 Aug.

2015, station F. Events on the right include 22 June and 27 July 2015, station C. These dates incurred some of the lowest counts of crabs than others of the study (N ≤ 2).

Events on the left were subject some of the more extreme conditions were evident, where depths for each event were ≤ 0.10 m. Recorded salinities for these samples ranged from 4.56 to

17.02 psu. Dissolved oxygen ranged from 5.93 to 15.97 mg L-1. Temperatures were > 28.50 °C.

Inflows were < 7.50 in each month.

Events 8 and 22 June displayed the greatest distances from other samples. Both events occurred in June, so monthly inflows were the same. However, by the 22 June sampling event, persistent precipitation had ended, depths and temperatures had declined, and salinity, dissolved oxygen, and pH had started to increase. The 8 June dissolved oxygen levels were the lowest recorded during the study (3.90 mg L-1). Salinities were < 1.0 psu and dissolved oxygen ≤ 6.0 mg

L-1. Again, these events followed one the most significant flooding periods in South Texas, which occurred during the months of May and June.

Figure 22. A MDS ordination plot of Bray-Curtis similarity matrix of log-transformed abundance data from the seine-sampled blue crab collected in

Benthic Macrofauna Correlation to Epifauna

A Pearson correlation was utilized to identify relationships between the current research findings in relation to the benthic samples collected. The benthic sampling period included continuous data for station C for 2014 and 2015. Only the dates of epifaunal data that coincide with dates of the benthic data were used. No correlations were identified between diversity variables of the benthic and epibenthic samples (Table 9).

Table 9. Pearson correlation values comparing benthic to epibenthic biotic and diversity variables. Pearson Correlation Coefficients, N = 35 Prob > |r| under H0: Rho=0 Epibenthic Epibenthic Epibenthic Epibenthic Epibenthic Epibenthic Log Density Density (N m-2) Biomass (g m-2) Richness Dominance Evenness (N m-2) Benthic Density -0.17478 -0.09449 -0.11429 0.13106 0.25019 0.25398 (N m-2) 0.3153 0.5893 0.5133 0.453 0.1472 0.1409 Benthic Log -0.06411 0.1722 -0.04886 0.16598 0.06977 -0.10436 Density (N m-2) 0.7144 0.3226 0.7804 0.3406 0.6904 0.5508 Benthic Biomass -0.16851 -0.09193 -0.13375 0.03857 0.09348 0.17534 (g m-2) 0.3332 0.5994 0.4437 0.8259 0.5932 0.3137 -0.19963 -0.06634 -0.18625 0.10511 0.07205 -0.14685 Benthic Richness 0.2503 0.7050 0.2840 0.5479 0.6808 0.3999 Benthic -0.17306 -0.0386 -0.09785 -0.04901 -0.07858 -0.21384 Dominance 0.3201 0.8257 0.5760 0.7798 0.6536 0.2174 Benthic -0.18084 0.00368 -0.07233 0.02095 0.00006 -0.10803 Evenness 0.2985 0.9833 0.6797 0.9049 0.9997 0.5368

DISCUSSION

The epifaunal community of Rincon Bayou did not show significant variation between sites, but seasonal patterns were evident. Especially in the populations of estuarine-dependent crustaceans, continuous pumping may have impacted recruitment events. Most organisms identified would be considered resident species, but disturbance organisms were recognized, particularly following freshwater events (natural and pumped). At this trophic level, organisms exhibited signs of being less susceptible to fluctuations in salinity.

Previous studies in Rincon Bayou have identified the region as an atypical estuarine system that alternates between a hydrologically negative and positive system, where salinities can range from 0 to 89 psu (Montagna et al 2015). Being located in South Texas already implies high summer temperatures and very mild winters. Late spring and early summer are often inundated by heavy rains, and again, with reduced volumes, in the fall. Additionally, there are seasonal tidal fluctuations, where high tides occur in the spring and fall, transporting higher salinity waters that can pool in the lower reaches of the delta (Palmer et al 2002). During the current study, May and June 2015 were subject to record highs of precipitation and subsequent flooding (East 2016).

For each year of the study, average salinities were lower at station C than the other two stations. Because of the proximity of station C to the pump outfall, salinities tend to be lower

(Montagna et al 2015). That salinities are greater at stations in the lower reaches should not be surprising and are explained by these stations’ proximity to the Nueces Bay, and higher marine influence. This represents a restoration of the normal salinity gradient in contrast to the reverse estuary that characterized Rincon Bayou in the 1990’s (Ward et al. 2002). Station G will have

higher salinities, especially during spring and fall high tides, when water from Nueces Bay is driven into the lower reaches of Rincon Bayou (Hill et al 2012).

Salinity has proved to be a driving factor in benthic community structure (Montagna et al

2002, Montagna et al 2015, Palmer et al 2002, Ritter et al 2005, Montagna et al 2013). There is an indication in the epibenthic community that peeks and deficits in biotic variables and diversity occur when there are major fluctuations in salinity. However, the results of this study indicated that salinity and pH were only moderately affecting overall species composition, and dissolved oxygen and depth have more significant influence on the overall epibenthic community.

Dissolved oxygen concentrations tend to be lower when temperatures and salinities are higher (Moorehead et al 2002). Rincon Bayou’s natural vegetation includes several halophytes

(Dunton et al 2001) that can be choked out during freshwater inundation, which produces an abundance of decaying biota, which can also be a source of decreased dissolved oxygen concentrations (Lellis-Dibble et al 2008). Hypoxic conditions are considered those that exist when dissolved oxygen concentrations are below 2.0 mg L-1 (Moorehead et al 2002). The recommended dissolved oxygen to fully support estuarine life is levels greater than 5.0 mg L-1

(Montagna and Applebaum 2006). By this standard, hypoxic conditions did not occur during any sampling event, but dissolved oxygen levels did fall below 6.0 mg L-1 for some events. There is a tidal influence, particularly in the lower reaches of Rincon Bayou, which helps to circulate water and prevent hypoxic conditions (Morehead et al 2002).

Depth was also found to be a significant driving factor in the overall community of

Rincon Bayou, where significant precipitation and overbanking are the cause of deeper water and lowered dissolved oxygen levels. Inflows have a direct effect on water quality where greater amounts of freshwater delivered to the bayou correlate to greater depths, lowered dissolved

oxygen, and lowered salinities. In 2015, the seasonal wet period was the highest in Texas history

(East 2016). In addition to the excessive freshwater, pumps remained on for several months following. This significantly prolongs the duration of freshwater conditions, potentially delaying recruitment events into the marsh (Tolan 2008).

The average rise in pH in the region was less than one standard deviation from the mean, but there was evidence to indicate that the region is experiencing a trend in rising pH, and that this had moderate effects on the overall community. Rincon Bayou is subject to the formation of algal blooms in the warmer months, and because of the release of carbon dioxide, pH will rise as growth continues (Lellis-Dibble et al 2008). During this study, in years 2010 and 2014, sample collections did not begin until the spring, which could have an effect on the average trend because warmer months were sampled every year, but not necessarily cooler months.

When considering the community as a whole, the results indicated that the epibenthic community of Rincon Bayou experienced some enhancement from 2010 to current, where density, richness, and diversity indices were greater each year. Biomass experienced a significant decline in 2014, but was improving in 2015. In the epibenthic community, diversity proved to be the most highly positively correlated variable to richness and evenness. Moderately negative correlations showed that as inflows and pH increase, community diversity decreases.

The results of this study also found significant differences in community structure when comparing sampling methods. This held true for the analyses of fish, shrimp, and crab, as well.

Major differences were found in the sizes of organisms targeted. When considering the trophic level being investigated, varying methods that can target varying size classes is important (Wells

2008). The seines are targeting larger shrimp, crab and fish, which are easily capable of escaping the push nets. Push nets capture newly entering species, where the mesh diameter of

seines is too large to capture many new recruits. This provides a better representation of the overall community size and quality.

It is important to note that samples where no species were observed only occurred in the push net samples, when conditions could be considered extreme, such as when water levels are severely low in Rincon Bayou, and the push net merely disturbs the sediment and surrounding environment and it is difficult to capture organisms. The absence of empty samples in seines supports the idea that even in the most extreme conditions, the seines are better capturing organisms representative of what is present in harsher environments.

Analysis of strictly push net sampled community data still found that density, richness, and diversity increased. Two particular events were identified, 8 and 22 June 2015, as significantly different, where this event was coincident of the date with the highest depth, lowest salinity, lowest dissolved oxygen, and lowest pH of the study. Species composition was low, with freshwater insect larvae and snails being the most abundant organisms, some of which, this was the only encounter during the study period. Furthermore, there was an absence of organisms typically more abundant, such as shrimp and crab.

Prolonged and persistent freshwater inundation can make species migration into the delta very difficult (Longley 1994). For the first event, flooding within Rincon Bayou made sampling access to other stations impossible, so the distance that organisms may have traveled to escape these conditions is unknown. Freshwater conditions have been identified as more persistent in the upper reaches of the bayou. At the next event (22 June), other stations were still inaccessible, and many of the freshwater species were still present. By the July events, all three stations were accessible, shrimp and resident species were documented, although in small numbers, and some freshwater organisms still persisted.

Different size classes and counts of organisms were being captured depending on gear selection, but the same species were identified as the most abundant in both gear types, with a few exceptions. Push net samples identified insect taxa in high densities and a few larger organisms were identified in seines. The species found in highest abundance for either gear type were those that accounted for greater than one percent of the total abundance. Other species encountered would be considered rare.

Species found at lower trophic levels included S. benedicti, which has been identified as an opportunistic, pioneer species that has been known to dominate in hypoxic conditions and has a wide salinity tolerance as well (Mannino and Montagna 1997, Ritter and Montagna 1999). It has also been recognized to establish itself after major disturbances, including flooding events

(Palmer et al 2002). Trichocorixa sp. (water boatmen) are an aquatic insect found in streams and temporary bodies of water. They are air-breathers, so have a tolerance to fluctuating salinities.

Insect species of the Ephemeroptera family (mayflies) are also an aquatic species that emerge in summer months. High densities of freshwater species such as these can be explained by periods of prolonged freshwater, which are coincidental of a decline in marine species (DeWalt et al

2010).

The dominating crustaceans were Palaemonetes sp. (grass shrimp), A. almyra (mysids),

F. aztecus (brown shrimp), and C. sapidus (blue crab). Palaemonetes species accounted for the highest abundance in push net samples and a considerable percentage of the community biomass.

They are considered euryhaline species that occupy the same marsh habitat for the entirety of their life. Because they do not overwinter, their presence would be expected year-round and only in extreme conditions would they seek refuge in farther reaches of the delta (Kneib 1985).

Mysids emerge in spring and fall, and will typically overwinter by moving to deeper waters

when temperatures drop (Lesutiene 2008). F. aztecus and C. sapidus are addressed in greater depth later in this discussion.

Fish identified in the highest abundance were C. variegatus (sheepshead minnow), A. mitchilli (bay anchovy), F. grandis (gulf killifish), and M. beryllina (inland silverside). Fish found in highest abundance are those common to estuarine habitats, with little susceptibility to fluctuations in water quality. Sheepshead minnow and silversides are an ecologically important forage species (Gosselink 1984, Longley 1994). Bay anchovy and gulf killifish are considered forage species (Longley 1994), but also have a small recreational value as bait fish (Green 2007,

Morton 1989).

C. variagatus is a euryhaline fish species with salinity tolerances from freshwater up to

78 psu and an equally wide range of temperatures and dissolved oxygen (Peterson 1990,

Raimondo et al 2013). Bay anchovy are often seen as a dominating species in estuarine and nursery ground locations for certain seasons, moving towards deeper water in colder months

(Suprenand 2015). They have a broad salinity and temperature tolerance, but are often found after salinities decrease (Longley 1994). Typically never seen in environments where dissolved oxygen falls below 7.0 mg L-1, and for larval fish, hypoxic conditions result in fish kills within

24 hours (Moore et al 1997). Gulf killifish are a common estuarine resident species with a Texas

(Longley 1994), with a wide salinity tolerance (Tolan 2013). Silversides are typically spring and summer spawners, but in warmer waters have been known to spawn from February to August with peaks in late spring and early summer. They are found in fresh and coastal waters

(Chizinski 2007).

For both gear types, organisms found in high densities were typically the greatest contributors to biomass. However, a few fish and white shrimp (discussed later) were identified

to be contributing significantly to the total biomass, even though they occurred in lower numbers. These fish included B. patronus (gulf menhaden), E. saurus (ladyfish, skipjack), M. cephalus (striped mullet), and P. latipinna (sailfin molly).

Gulf menhaden occur March through August, which indicates a distinct seasonal influence. In the Gulf of Mexico they have a spawning season November to February, and increased water temperatures may lead to increased growth rates. Gulf menhaden are estuarine dependent fish, dependent on temperature and salinity cues. Of the 22 fish identified during this study, gulf menhaden are the only commercially important species. In the U. S., gulf menhaden catch was over $120 million (Lowther and Liddel 2014). In the Gulf of Mexico, gulf menhaden accounted for nearly 75 percent of the national total, where they are commonly sold as bait fish and used for production of fish oil (VanderKooy and Smith 2002, VanderKooy and Smith 2015,

Lowther and Liddel 2014). Menhaden were also identified to be a dominant species in a significant series of events evident in the MDS plot of push-net sampled fish assemblage including samples taken in the moths of March, April, May, and June.

Ladyfish are an estuarine-dependent fish species found in waters of the Atlantic, Pacific, and Indian Oceans and the Gulf of Mexico. They are a bony fish typically found in warmer waters that range from brackish to marine. Ladyfish < 60 mm have displayed growth rates > 0.5 mm/day and larger juveniles have shown faster rates around 2 mm day-1. Their tolerance to lowered dissolved oxygen is widely unknown, but there is some evidence that they can withstand ranges as low as 1.0 mg L-1 (Zale 1989). Their broad range of suitable water quality makes them poor indicators as an immediate response organism. However, as was seen in this study, ladyfish occurring as a solitary fish species may be useful in gauging overall physical variables.

The U. S. commercial fishery for ladyfish does account for a little more than $1 million in annual landings (Lowther and Liddel 2014). In the Gulf of Mexico, they have some recreational value, particularly off the coast of Florida as a sportfish. Ladyfish are closely related to tarpon (Megalops atlantius – not encountered in this study), which is a major recreational sportfish. Tarpon and ladyfish occupy the same estuarine larval habitats, which are highly susceptible to eroding and degrading habitat for completion of their lifecycle (Zale 1989).

Additionally, ladyfish were only encountered in push nets in months March, April and May, and cluster overlay identified a series of events in these months ladyfish were found to be the dominant species. Ladyfish were only collected in seine samples June and September.

Striped mullet are shown to have a wide salinity tolerance (Tolan 2013) and display aquatic surface respiration (ASR) in response to reduction in dissolved oxygen (Peterson 1990).

In Texas, they are considered a popular baitfish (Green 2007). As with many other species identified, its suitability to fluctuations in water quality make it a highly adaptable species to the environment in Rincon Bayou. Habitat loss and freshwater reduction are thought to be a contributing factor to declines of this species (Buskey et al 2015.)

Sailfin molly wide is another estuarine-resident species identified to have a wide range of salinity tolerance and can also exhibit ASR in response to variation in water quality (Peterson

1990). It is often found in regions where depths are lower and salinities are higher (Akin 2002), making it another suitable species. Generally speaking, this fish is from the order,

Cyprinodontiformes (this order includes Cyprinodon and Fundulus sp.), which serve as ecologically valuable foraging species.

Analyses on the fish community included Pearson correlations procedures of fish diversity indices, where strong positive correlations were found between Hill’s diversity and

richness, as well as evenness. In the fish community, there was also a correlation between abundance and biomass not seen in the community as a whole. Richness and diversity were also highest in 2015, supporting that the region is experiencing positive changes. Subsequent MDS plots identified several events taken from push nets and seines with significant variation that indicated that a seasonal influence exists for fish assemblages in Rincon Bayou.

Results from analysis of push net sampled fish community identified dates in which only one species was encountered. The 2 June 2014 event returned only one juvenile pinfish at station

C while Rincon was experiencing low salinities. This is an interesting anomaly because they are typically considered a fish that has a higher salinity preference, but they are known to seek refuge in marsh habitat. This particular specimen was a juvenile. They reach adulthood/sexual maturity around 80 mm and migrate into deeper waters in fall, spawning in the fall and winter months. Eggs hatch approximately 48 hours later, and are not considered juveniles until they reach approximately 12 mm. They are considered ecologically important wetland species and forage species for other finish (Longley 1994).

The 27 Apr. 2015 encounter of alligator gar was one occurrence of three from the study, and only at station C, but they are seen throughout Rincon, especially at the pump fallout. Gar are typically considered a freshwater species, but are known for a wide salinity tolerance and have been previous identified in marsh and wetland areas (Akin 2003, Buckmeier 2008).

Additionally, gar are a target sport fish for Lake Corpus Christi and Choke Canyon, so their presence is not overly surprising, especially following large pulses of fresh water from the

Nueces River (overbanking etc.). While numbers of gar were not significant, and the Gulf of

Mexico does not have a commercial fishery, they have become an important recreational and

commercial species for other regions, and are experiencing a population decline (Binion et al

2015). For Rincon Bayou, this may be a species indicative of freshwater conditions.

Blue gill encountered 22 Jun. 2015 are another freshwater species dominant in Lake

Corpus Christi. These specimen were juveniles. This is a spring spawning fish that grows rapidly in warmer conditions. These were found after the June flooding events, so again, freshwater species of Lake Corpus Christi are not surprising during this period.

Rainwater killifish were collected in samples for both events in June 2010. This was the only period where they would be considered the dominant fish species. Rainwater killifish have been documented as being present in reduced abundance when inflows are low (Tolan 2013).

This species low numbers may be indicative of a lack of inflow. This fish is not considered a seasonal fish, and it was only found in samples early summer and late fall.

Seasonal influence on push net sampled fish was indicated by strong relationships between dissolved oxygen, depth, and temperature, with little to no effect from salinity.

However, hydrographic variables in relation to only seine-sampled fish were recognized for moderate explanatory relationships between salinity and species richness and diversity. This means that as salinities increased, richness and the number of dominant species decreased. This would indicate that inflow has a greater effect on larger fish than smaller, but it should also be considered that seine-sampled fish were only collected from June to December 2015, following an incredibly wet period. Analysis of seines identified additional clustered events not identified in the pooled fish. One cluster represented a single date in which striped mullet was found in

August.

The second clustering of events included June 2015 sampling events, in which there was higher richness and diversity of fish than most other events. However, fish identified were

comprised mostly of fish species that can exploit freshwater conditions and lowered dissolved oxygen concentrations. Tolan and Newstead’s (2005) study included major precipitation/flooding events in June 2004, where the only period of higher volumes of water in

Texas history is that of June 2015 (East 2016). Findings of this study corroborate their reports that resident and recruiting species remained low, and species that could benefit from prolonged reduced salinities were lizard fish (Synodus foetens – not encountered in this study), striped mullet, silversides, and ladyfish (Tolan and Newstead 2005).

The majority of fish species encountered would be considered year-round residents of the area. However, there are some indicators of disturbance, i.e. over-inundation of freshwater leading to the intrusion of freshwater species. There is evidence that when this happens, mobile organisms may be seeking refuge elsewhere. In general, it does not appear that fish are utilizing

Rincon Bayou as juvenile habitat as greatly as the crustacean community.

This study confirmed that shrimp are definitely exploiting areas of the region, reflecting findings of other studies, in that there is a seasonal influence for brown and white shrimp identified by seasonal cues when each enter and leave the marsh (Baxter 1966). In a typical south

Texas marsh, post-larval brown shrimp would enter nursery and juvenile habitats in late March or early April, leaving approximately three months later (Larson 1989). Time series for push net sampled brown shrimp similar findings of previous studies, in that, that new recruits are entering the region in April and May as long as freshwater delivery is timed accordingly (Tolan and

Newstead 2004, Tolan and Newstead 2005). An interesting finding of this study was that in

2014, there was a second recruitment event in the fall when white shrimp would typically be entering the marsh. Pumping occurred essentially non-stop from April-July 2014.

Several events were identified in an MDS plot, pertaining to push net sampled brown shrimp where abundance of brown shrimp were very low. Half of these events occurred in the fall (October and November). Nearly developed shrimp should be exiting the marsh in this period and low numbers should be expected. Two additional events were identified in seine sampled shrimp, where low counts were identified in July and October and again in the larger size class.

Results of this study identified a decline in brown shrimp abundance from 2010 to 2015.

Each year volumes of inflow increased and salinities remained lower for longer durations.

However, correlation coefficients indicated that salinity was not the driving factor of brown shrimp populations. A study to identify the salinity tolerance of post-larval brown shrimp found that while the brown-shrimp lifecycle is dependent on salinity cues, lowered salinities have only moderate effects on post-larval shrimp. They reported findings of additional studies in which salinity had minimal to no correlation, and in one study a negative correlation to brown shrimp abundance (Saoud and Davis 2003).

Brown shrimp enter the estuary around May as post-larval shrimp, ranging 8 to 14 mm, as spring high tides enter into the marsh region. If freshwater floods the region, larval shrimp cannot tolerate the low salinities (Saoud and Davis 2003). Depending on the duration of lowered salinities, shrimp may escape to areas of higher salinities, but persistent freshwater would result in later recruitment (Tolan and Newstead 2005). They have a residence time of a couple months and move out of the marsh habitats as sub-adults to adult specimen, and into deeper waters, where they ultimately contribute to the commercial fishery (Baxter 1966).

This study found that the lengths and weights of brown shrimp sampled in seines were lowest in August and September and greatest in July and November. This would indicate that

two groups of new recruits entered in the spring and mid-summer of 2015. After the flooding in

2015, brown shrimp were not collected in seines until the end of July. Temperature-dependent growth characteristics have been found to be greatly affected with only minor fluctuations in water temperatures (Baxter 1966).

Brown shrimp begin emigration out of the protected waters of the estuaries and into open water once they have reached a lengths ranging from 70-110 mm. Brown shrimp mate and spawn offshore. More than 75 percent of the U. S. commercial landings of shrimp are caught in the Gulf of Mexico. The national fishery was valued at approximately $690 million in 2000

(TPWD 2002). The Texas shrimp fishery is the most highly valued, where the combined annual value of white and brown shrimp ranges from approximately $110-200 million (Picariello and

Rosenberg 2016).

White shrimp were only identified months July through October, overlapping slightly with brown shrimp. No correlation of the white shrimp population was identified in comparison to hydrographic variables, but salinity was the greatest explanatory variable in PCA results. Time series graphs of white shrimp abundance according to size class depicted changes in salinities and abundance, where there were salinity increases, abundance of white shrimp were shown to decrease.

White shrimp move into estuaries in late spring or early summer. Post-larval growth is quick in warmer months of spring, but will being to slow down as the cooler fall months approach. White shrimp have been known to remain and overwinter in estuaries. White shrimp also have a tendency to move into waters with lower salinities than brown (Longley 1994).

Higher abundance in station C is to be expected. There was an overall decreasing trend in the lengths and biomass of white shrimp. Events where abundance of white shrimp were low

followed periods of low inflows and higher temperatures. The largest recruitment event for white shrimp occurred in 2015, following the spring freshets. Their lifecycle is highly temperature dependent, and decreases in water temperature, which occur during periods of heavy precipitation, can cue early emigration (TPWD 2002).

For the blue crab populations in Rincon Bayou, correlations were identified between biotic variables and hydrographic variables, dissolved oxygen and pH, which implied that abundance and biomass slightly increased with elevated dissolved oxygen and pH levels. Larval stages are highly salinity-dependent, but subsequent stages display broad tolerances to water quality (Ward 2012). Young female crabs are known to seek waters where salinities are < 15 psu until mating occurs in the estuary, and then move to higher salinity water to spawn (Gandy 2011,

Picariello 2015, Ward 2012). In Rincon Bayou, females were found in much fewer numbers, but tended to be larger. They use salinity cues to begin emigration to open water and have the potential to exit the marsh region early if freshwater inundation or drought persists at irregular timing.

Additionally, it has been suggested that smaller female crabs are less fecund which would mean that a trend in decreasing size would ultimately conclude to a reduction in abundance as well (Guillory et al 2001). A decreasing trend in individual crab weights suggests smaller crab are entering the region, but there were no significant differences in carapace width, which may imply that water quality had an effect on development. In the seine samples, crab proved to be largest in early summer months. In general, smaller crabs were more abundant, but this is to be expected as large groups of larval crab enter the estuary, and are highly susceptible to predation and cannibalism (Picariello 2015).

When conditions are extreme, there was evidence of negative effects on crab populations as extreme wet and dry periods showed to have reduced numbers. Results of an MDS plot of blue crab abundance identified six events where there was low abundance of blue crab following heavy precipitation and prolonged drought periods. However, each year of the study identified the highest abundance of blue crab to follow spring freshets.

The Texas blue crab fishery is second only to the shrimp fishery, with 2013 commercial landings valued at $2.3 million (Picariello 2015). Texas contributes approximately 14 percent to the Gulf of Mexico blue crab landings, which accounts for a range of 21-35 percent of national landings (Guillory et al 2001). Corpus Christi Bay, and those further south, only account for 2% of Texas landings (Sutton and Wagner 2007). This fishery has seen dramatic declines since 1989, with the lowest landings in 2005 (Picariello 2015, Sutton and Wagner 2007).

Blue crab are also an important ecological species preyed on by birds and popular finfish, such red drum (Sciaenops ocellatus – not encountered during this study), black drum (Pagonias cromis – not encountered in this study), spotted seatrout (Cynoscion nebulosus), and alligator gar. These predatory species, including blue crab, and several of the estuarine-dependent and resident species identified in this study, are heavily reliant on a healthy benthic community is to support higher trophic levels (Guillory et al 2001, Montagna and Li 2010). However, results of this study did not identify significant correlations when comparing the benthcic community structure to the epibenthic community.

CONCLUSION

This study was designed to identify spatial and seasonal variability within the epibenthic trophic structure of Rincon Bayou with respect to freshwater inflows. While there was little evidence that the epibenthic community is affected by spatial differences, there were very distinct seasonal influences. Additionally, there were consistent positive correlations between diversity indices, which may indicate that the epibenthic community does not exhibit signs of a stressed ecosystem in the same manner that the benthic community has shown.

The majority of organisms identified would all be considered resident species that would be present year-round given hospitable conditions. In the overall community, crustaceans are the dominating taxa in abundance and biomass. Of the identified dominating species, brown shrimp, white shrimp, and blue crab are the only estuarine-dependent species with significant economic value that are utilizing this area for refuge. There was evidence that over-inundation of freshwater may be affecting recruitment of these crustaceans. Additional organisms were identified that were more adapted to freshwater and were present following heavy rains in the spring and fall.

Typically, Rincon Bayou is subject to low inflows and water depths, high salinities and temperatures, and moderate pH and dissolved oxygen levels. Inflows are sometimes limited to monthly inflow volumes < 1 m3 s-1, and salinities that range in freshwater conditions at times.

Recommendations for the water quality of Rincon Bayou have been suggested to increase inflows that could maintain depths between 0.2 and 0.3 m and salinities between 6 and 18 psu

(Montagna et al 2015). From this study, further evidence is provided that Rincon Bayou is not just a salinity-stressed environment, but that there are overall effects due to all water quality parameters.

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APPENDIX I: FIGURES

20 C F G

) ) 1 - 10

5 DO (mg L (mg DO

Jul-10 Jul-14 Jul-14 Jul-15 Jul-15

Jan-15

Jun-10 Jun-10 Jun-14 Jun-14 Jun-14 Jun-15 Jun-15

Oct-14 Oct-14 Oct-15 Oct-15

Apr-10 Apr-14 Apr-15 Apr-15

Sep-14 Sep-14 Feb-15 Feb-15 Sep-15 Sep-15

Dec-14 Dec-14 Dec-15 Dec-15

Aug-10 Aug-10 Aug-14 Aug-14 Aug-15 Aug-15

Nov-14 Nov-14 Nov-15 Nov-15 Nov-15

Mar-15 Mar-15

May-10 May-10 May-10 May-14 May-15

2011-ND 2011-ND 2012-ND 2012-ND 2013-ND 2013-ND Date 50 C F G 40 30 20

Salinity Salinity (psu) 10

Jul-10 Jul-14 Jul-14 Jul-15 Jul-15

Jan-15

Jun-14 Jun-10 Jun-10 Jun-14 Jun-14 Jun-15 Jun-15

Oct-14 Oct-14 Oct-15 Oct-15

Apr-14 Apr-10 Apr-15 Apr-15

Sep-14 Sep-14 Feb-15 Feb-15 Sep-15 Sep-15

Dec-14 Dec-14 Dec-15 Dec-15

Aug-14 Aug-10 Aug-10 Aug-14 Aug-15 Aug-15

Nov-14 Nov-14 Nov-15 Nov-15 Nov-15

Mar-15 Mar-15

May-10 May-10 May-10 May-14 May-15

2012-ND 2011-ND 2011-ND 2012-ND 2013-ND 2013-ND Date 0.5 C F G 0.4 0.3 0.2 Depth(m) 0.1

Jul-14 Jul-10 Jul-14 Jul-15 Jul-15

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Jun-10 Jun-10 Jun-14 Jun-14 Jun-14 Jun-15 Jun-15

Oct-14 Oct-14 Oct-15 Oct-15

Apr-10 Apr-14 Apr-15 Apr-15

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Dec-14 Dec-14 Dec-15 Dec-15

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Mar-15 Mar-15

May-10 May-10 May-10 May-14 May-15

2011-ND 2011-ND 2012-ND 2012-ND 2013-ND 2013-ND Date 10 C F G Linear (C) Linear (F) Linear (G) 9 8

pH pH 7 6

Jul-10 Jul-14 Jul-14 Jul-15 Jul-15

Jan-15

Jun-10 Jun-10 Jun-14 Jun-14 Jun-14 Jun-15 Jun-15

Oct-14 Oct-14 Oct-15 Oct-15

Apr-10 Apr-14 Apr-15 Apr-15

Sep-14 Sep-14 Feb-15 Feb-15 Sep-15 Sep-15

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Mar-15 Mar-15

May-10 May-10 May-10 May-14 May-15

2011-ND 2011-ND 2012-ND 2012-ND 2013-ND 2013-ND Date

40 C F G Linear (C) Linear (F) Linear (G) C) º 30

Temperature(

Jul-10 Jul-14 Jul-14 Jul-15 Jul-15

Jan-15

Jun-10 Jun-10 Jun-14 Jun-14 Jun-14 Jun-15 Jun-15

Oct-14 Oct-14 Oct-15 Oct-15

Apr-10 Apr-14 Apr-15 Apr-15

Sep-14 Sep-14 Feb-15 Feb-15 Sep-15 Sep-15

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Nov-14 Nov-14 Nov-15 Nov-15 Nov-15

Mar-15 Mar-15

May-10 May-10 May-10 May-14 May-15

2011 ND - 2011 ND - 2012 ND - 2012 ND - 2013 ND - 2013 ND - Date Figure 23. Time series of physical variables recorded at each station, C, F, or G in Rincon Bayou during the study period. From top to bottom: Dissolved oxygen, Salinity, Depth, pH, and Temperature, where the physical variable is plotted on the y-axis and dates of the study are plotted on the x-axis, with trend lines added to variables pH and Temperature.

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Salinity (psu) Abundance (N/m2)

50 450 400 40 350 300 30 250 20 200 Salinity 150

10 100 Abundance 50

0 0

9/8/2014 7/6/2015 9/9/2015

2011 - ND - 2011 2012 - ND - 2012 ND - 2013

10/20/2014 10/28/2015 11/11/2015 11/24/2015 12/21/2015 A Date

Salinity (psu) Biomass (g/m2)

50 25 40 20 30 15

20 10

Salinity Salinity Biomass 10 5

0 0

9/9/2015 9/8/2014 7/6/2015

2011 - ND - 2011 ND - 2012 ND - 2013

8/11/2014 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 5/15/2014 6/17/2014 6/30/2014 7/14/2014 8/25/2014 11/3/2014 12/2/2014 1/16/2015 3/16/2015 3/30/2015 4/10/2015 5/11/2015 7/27/2015 8/24/2015 9/21/2015

10/20/2014 10/28/2015 11/11/2015 11/24/2015 12/21/2015 Date B

Salinity (psu) Hill's N1 Diversity

50 10 40 8 30 6

20 4 Salinity 10 2 Diversity

0 0

9/9/2015 9/8/2014 7/6/2015

2011 - ND - 2011 ND - 2012 ND - 2013

10/20/2014 10/28/2015 11/11/2015 11/24/2015 12/21/2015 C Date

Figure 24. Time series showing changes in recorded physical variable, salinity, over time as it pertains to diversity indices A) Abundance (N m-2), B) Biomass (g m-2), and C) Diversity (Hill’s N1) from pooled samples collected in Rincon Bayou during the study period (2010-2015).

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Figure 25. A MDS of Bray-Curtis similarity matrix of log-transformed total abundance of all samples comparing gear types (Method), push net (PN) and seine (RS). A cluster overlay of significant groupings identifying samples with less than 30 percent similarities between samples.

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Figure 27. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from push net samples with bubble plot overlay displaying the most abundant species found in push net collections from Rincon Bayou. An additional PCA overlay depicting physical variable gradients.

Figure 28. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from seine samples with bubble plot overlay displaying the five most abundant species found in Rincon Bayou, with an additional PCA overlay depicting physical variable gradients.

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Figure 29. Euclidian distance matrix PCA of physical variables recorded in Rincon Bayou during the study period, including Depth (m), Salinity (psu), Temperature (°C), Dissolved Oxygen (DO mg L-1), and pH as they pertain to the total fish assemblage of Rincon Bayou. PC1 is representative of the inflow axis, Left: PCA sample scores, where labels represent months of the study, and Right: Variable loads.

Figure 30. MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from the total fish assemblage in Rincon Bayou with bubble plot overlay displaying fish identified in outliers, with an additional PCA overlay depicting physical variable gradients.

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Figure 31. A MDS ordination plot of Bray-Curtis similarity matrix for log-transformed abundance data from the push net sampled fish assemblage, with bubble plot overlay displaying the four most abundant fish species encountered in Rincon Bayou, with a PCA overlay, where dissolved oxygen, temperature, and depth represent the inflow axis (PC1).

Figure 32. A MDS ordination plot (after removing outliers) of push net sampled fish assemblage data from Rincon Bayou, with trajectory overlay, identifying seasonal influence. Symbols represent stations (C, F, or G), and labels are periods.

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Figure 33. A MDS plot of Bray-Curtis similarity matrix of log-transformed abundance data from the total fish assemblage in Rincon Bayou with bubble plot overlay displaying fish identified in highest abundance, with a PCA overlay depicting physical variable gradients.

Figure 34. Seasonal influence in fish assemblage for Subset of original MDS ordination plot (after removing outliers) of seine sampled fish assemblage data from Rincon Bayou, with trajectory overlay, identifying seasonal influence. Symbols represent stations (C, F, or G), and labels are periods.

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Weight (g) Weight Length (mm) Length

Figure 35. Box plots of distribution of means of log-transformed variables, A. Length and B. Weight, for push net sampled brown shrimp collected in Rincon Bayou.

70 50 Total N Salinity (psu) 60 40 50 40 30 30 20 20 Salinity Abundance 10 10

0 0

6/2/2014 2/2/2015 7/6/2015

2011 - ND - 2011 ND - 2012

4/28/2014 10/9/2015 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 6/17/2014 6/30/2014 7/29/2014 8/11/2014 8/25/2014 9/22/2014 11/3/2014 3/16/2015 3/30/2015 4/27/2015 8/11/2015 9/21/2015 12/7/2015

10/20/2014 12/15/2014 11/11/2015 12/21/2015 Date 70 0.5 Total N Depth (m) 60 0.4 50 40 0.3 30 0.2 20 Depth

Abundance 10 0.1

0 0

6/2/2014 2/2/2015 7/6/2015

2011 - ND - 2011 2012 - ND - 2012

12/7/2015 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 4/28/2014 6/17/2014 6/30/2014 7/29/2014 8/11/2014 8/25/2014 9/22/2014 11/3/2014 3/16/2015 3/30/2015 4/27/2015 8/11/2015 9/21/2015 10/9/2015

10/20/2014 12/15/2014 11/11/2015 12/21/2015 Date

Figure 36. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Depth, over time as they pertain to abundance of brown shrimp collected in push nets from Rincon Bayou during the study period (2010-2015).

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Weight (g) Weight Length (mm) Length

Figure 38. Box plots of distribution of means of log-transformed variables, A. Length and B. Weight, for push net sampled white shrimp collected in Rincon Bayou.

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70 50 Total N Salinity (psu) 60 40 50 40 30 30 20

20 Salinity Abundance 10 10

0 0

9/8/2014 7/6/2015

2011 - ND - 2011 2012 - ND - 2012 ND - 2013

6/30/2014 3/30/2015 8/24/2015 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 5/15/2014 6/17/2014 7/14/2014 8/11/2014 8/25/2014 11/3/2014 12/2/2014 1/16/2015 3/16/2015 4/10/2015 5/11/2015 8/11/2015 9/21/2015 12/7/2015

10/20/2014 11/23/2015 12/21/2015 Date 70 50 Total N Temperature (°C) 60 40 50 40 30 30 20 20 Abundance 10 10 Temperature

0 0

9/8/2014 7/6/2015

2011 - ND - 2011 2012 - ND - 2012 ND - 2013

10/20/2014 11/23/2015 12/21/2015 Date Figure 39. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Temperature, over time as they pertain to abundance of white shrimp collected in push nets from Rincon Bayou during the study period (2010-2015).

80 Total N Salinity (psu) 30 60 20 40

10 Salinity

20 Abundance 0 0 Jun-15 Jul-15 Aug-15 Sep-15 Oct-15 Nov-15 Dec-15 Date

80 Total N Temperature (°C) 50 60 40 30 40 20 20

Abundance 10 Temperature 0 0 Jun-15 Jul-15 Aug-15 Sep-15 Oct-15 Nov-15 Dec-15 Date Figure 40. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Temperature, over time as they pertain to abundance of white shrimp collected in in seine nets from Rincon Bayou during 2015.

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(mm)

ht (g) ht

Weig

Carapace Width

Figure 41. Boxplot of log-transformed variable, carapace width and weights, as they pertain to push net sampled blue crab.

50 50 45 Total N Salinity (psu) 45 40 40 35 35 30 30 25 25

20 20 Salinity

Abundance 15 15 10 10 5 5

0 0

9/8/2014 9/9/2015

2011 - ND - 2011

2013 - ND - 2013

11/3/2014 10/9/2015 4/28/2010 5/11/2010 5/19/2010 6/16/2010 8/11/2010 5/15/2014 6/17/2014 6/30/2014 7/14/2014 8/11/2014 8/25/2014 12/2/2014 1/16/2015 3/16/2015 3/30/2015 4/10/2015 5/11/2015 8/11/2015 12/7/2015 11/11/2015 Date 10/20/2014 50 16 Total N DO (mg L-1) 45 14 40 12 35 30 10 25 8 20 6

Abundance 15 4

10 Oxygen Dissolved 5 2

0 0

2/2/2015 6/1/2010 7/6/2010 6/2/2014 9/8/2014

2012 - ND - 2012 ND - 2013

10/20/2014 11/18/2014 12/15/2014 10/28/2015 11/11/2015 12/21/2015 Date Figure 42. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Dissolved Oxygen, over time as they pertain to abundance of blue crab collected in push nets from Rincon Bayou during the study period (2010-2015).

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45 Total N Salinity (psu) 30 40 25 35 30 20 25 15 20 15 10 Salinity

Abundance Abundance (N) 10 5 5 0 0 6/8/2015 7/27/2015 8/24/2015 9/9/2015 10/9/2015 11/11/2015 12/7/2015 Date

45 Total N DO (mg L-1) 18 40 16 35 14 30 12 25 10 20 8 15 6

Abundance Abundance (N) 10 4 Dissolved Oxygen Dissolved 5 2 0 0 6/8/2015 7/27/2015 8/24/2015 9/9/2015 10/9/2015 11/11/2015 12/7/2015 Date Figure 43. Time series showing changes in recorded physical variables, Top: Salinity, and Bottom: Temperature, over time as they pertain to abundance of blue crab collected in in seine nets from Rincon Bayou during 2015.

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APPENDIX II: TABLES

Table 10. Species composition for collective community (combined gears) displaying percent abundance and biomass. Table for collective data showing % contribution of abundance and biomass for push nets and seines, as well as the total contribution of each taxonomic category. Major Taxa/Species % Abundance % Biomass Chordata Push net Seine Push net Seine A. hepsetus 0.01 0.00 0.01 0.00 A. mitchilli 0.20 6.09 0.84 1.82 A. spatula 0.01 0.02 0.00 0.06 A. xenica 0.00 0.34 0.02 0.10 B. patronus 0.26 0.21 1.10 0.35 C. nebulosus 0.04 0.11 0.01 0.35 C. variegatus 1.63 25.93 9.77 15.66 Carpiodes carpio 0.00 0.02 0.00 0.01 D. petenense 0.00 0.12 0.00 0.69 E. saurus 0.08 0.19 0.14 4.07 F. grandis 0.05 5.45 1.05 18.90 F. pulvereus 0.00 0.32 0.00 0.27 G. bosc 0.13 0.07 0.12 0.02 I. furcatus 0.00 0.02 0.33 0.04 L. macrochirus 0.01 0.00 0.00 0.00 L. parva 0.02 0.07 0.09 0.03 L. rhomboides 0.00 0.00 0.03 0.00 L. xanthurus 0.01 0.02 0.20 0.39 M. beryllina 0.54 1.19 1.84 2.02 M. cephalus 0.00 0.18 0.00 3.87 P. latipinna 0.00 0.73 0.06 1.01 S. scovelli 0.00 0.00 0.06 0.00 Total 3.35 25.35 Arthropoda - Crustaceans F. aztecus 1.96 7.46 24.93 7.03 F. setiferus 0.93 4.98 6.86 10.95 C. sapidus 0.38 2.78 6.39 27.01 Palaemonetes sp. (unidentified) 24.25 37.31 39.00 5.26 Decopod larvae sp. (unidentified) 0.02 0.04 0.02 0.02 A. almyra 62.42 0.23 6.59 0.00 A. bahia 0.05 0.05 0.00 0.00 C. louisianae 0.01 0.66 0.00 0.00 T. bowmani 0.06 0.00 0.01 0.00 T. louisianae 0.07 0.00 0.00 0.00 Gammaridae sp. (unidentified) 0.35 0.64 0.05 0.00 Melitidae sp. (unidentified) 0.01 0.00 0.00 0.00 Talitridae sp. (unidentified) 0.01 0.00 0.00 0.00 Amphipoda sp. (unidentified) 0.00 0.00 0.00 0.00 L. rapax 0.00 0.02 0.00 0.00 Tanaidae sp. (unidentified) 0.00 0.44 0.00 0.00 Total 90.19 74.29 Arthropoda - Other Calanoida sp. (unidentified) 0.83 0.05 0.00 0.00 Cyclopoida sp. (unidentified) 0.01 0.02 0.00 0.00 Harpacticoida sp. (unidentified) 0.03 0.05 0.00 0.00 Ostracoda sp. (unidentified) 0.25 0.07 0.00 0.00 Conchastraca sp. (unidentified) 0.10 0.00 0.00 0.00 Halacaridae sp. (unidentified) 0.22 0.00 0.00 0.00

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Diplostraca sp. (unidentified) 0.00 0.02 0.00 0.00 Daphniidae sp. (unidentified) 0.00 0.00 0.00 0.00 Aegidae sp. (unidentified) 0.04 0.04 0.03 0.00 Argulus sp. (unidentified) 0.04 0.11 0.00 0.00 Probopyrus sp. (unidentified) 0.00 0.04 0.00 0.00 Arachnida sp. (unidentified) 0.01 0.00 0.00 0.00 Total 1.52 0.03 Arthropoda - Insecta Ceratopogonidae sp. (unidentified) 0.19 0.30 0.00 0.00 Chironomid larvae sp. (unidentified) 0.11 0.23 0.00 0.00 Chironomid pupae sp. (unidentified) 0.00 0.00 0.00 0.00 Coleoptera sp. (unidentified) 0.01 0.02 0.01 0.00 Culicidae sp. (unidentified) 0.01 0.00 0.00 0.00 Diptera sp. (unidentified) 0.02 0.02 0.00 0.00 Dolichopodidae sp. (unidentified) 0.00 0.00 0.00 0.00 Dragonfly nymphs sp. (unidentified) 0.00 0.02 0.00 0.00 Ephemeroptera sp. (unidentified) 1.00 0.02 0.21 0.00 Hemiptera (adult) sp. (unidentified) 0.00 0.04 0.00 0.00 Hemiptera (nymph) sp. (unidentified) 0.00 0.02 0.00 0.00 Hydrophilidae sp. (unidentified) 0.01 0.04 0.00 0.00 Hymenoptera sp. (unidentified) 0.02 0.02 0.00 0.00 Odonata sp. (unidentified) 0.10 0.02 0.01 0.00 Psychodidae (larvae) sp. (unidentified) 0.00 0.02 0.00 0.00 Trichocorixa sp. (unidentified) 1.12 0.00 0.15 0.00 Insecta sp. (unidentified) 0.02 0.00 0.01 0.00 Total 2.59 0.29 Mollusca Hydrobiidae sp. (unidentified) 0.02 0.00 0.00 0.00 Lymnaeidae sp. (unidentified) 0.18 0.00 0.00 0.00 M. lateralis 0.11 0.55 0.01 0.01 M. leucophaeta 0.00 0.00 0.00 0.00 Physidae sp. (unidentified) 0.14 0.00 0.00 0.00 Planorbidae sp. (unidentified) 0.04 0.00 0.00 0.00 Pulmonata sp. (unidentified) 0.00 0.02 0.00 0.00 R. cuneata 0.00 0.04 0.00 0.01 Total 0.50 0.02 Annelida H. florida 0.00 0.02 0.00 0.00 Hirudinea sp. (unidentified) 0.05 0.46 0.02 0.00 L. culveri 0.06 0.05 0.01 0.00 M. ambiseta 0.06 0.11 0.00 0.00 Neredidae sp. (unidentified) 0.00 0.02 0.00 0.00 Oligochaeta sp. (unidentified) 0.01 0.04 0.00 0.00 Onuphidae sp. (unidentified) 0.00 0.02 0.00 0.00 Polychaeta sp. (unidentified) 0.00 0.02 0.00 0.00 Polydora sp. (unidentified) 0.00 0.00 0.00 0.00 S. benedicti 1.61 1.49 0.01 0.01 Total 1.80 0.03 Cnidaria + Nematoda Other Anthozoa sp. (unidentified) 0.01 0.02 0.00 0.00 Nematoda sp. (unidentified) 0.04 0.37 0.00 0.00 Total 0.05 0.00

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Table 11. Nested ANOVA output for factors year, month, and station comparing biotic and diversity variables as they pertain to the collective epifaunal community of Rincon Bayou.

F value Probability

Abunadance Abunadance Biomass Biomass Richness Hill's Pielou's (N) (N m-2) (g) (g m-2) (R) Diversity (N1) Eveness (J') 9.67 1.27 4.28 0.49 12.66 8.01 0.79 Year 2 <.0001 0.2832 0.0159 0.6166 <.0001 0.0005 0.454 Month 1.72 1.15 1.2 1.58 2.36 1.83 1.48 23 (Year) 0.0309 0.3062 0.2579 0.0582 0.0013 0.0184 0.0895 1.19 2.1 2.9 9.14 0.43 0.11 0.45 Station 2 0.3064 0.1265 0.0585 0.0002 0.6504 0.8977 0.6382

Table 12.Summary of mean values of biotic and diversity variables for the overall community composition according to each year and station of the study. N. Obs. is the number of samples taken, determined from 1231 total species observations. Abundance Hill's Diversity Pielou's Year STA N. Obs. Biomass (g m-2) Richness (R) (N m-2) (N1) Evenness (J') 2010 C 6 21.10 3.85 6.00 2.25 0.49 F 8 3.63 1.51 2.50 1.53 0.44 G 5 6.84 4.32 3.80 2.28 0.60 2014 C 16 41.94 2.36 5.63 2.34 0.46 F 13 6.43 0.60 2.77 2.00 0.62 G 14 10.20 2.35 3.43 2.45 0.63 2015 C 33 10.54 1.71 8.64 3.77 0.59 F 30 24.35 1.34 8.47 3.34 0.56 G 30 35.67 3.15 8.87 3.10 0.47

Table 13. One-way ANOVA output comparing gear type for the pooled community data sampled from Rincon Bayou. F value Probability Abundance Abundance Biomass Biomass Richness Hill's Diversity Pielou's Source df (N) (N m-2) (g) (g m-2) (R) (N1) Evenness (J') Gear 81.23 10.36 403.09 23.15 64.02 50.97 2.52 1 Type <0.0001 0.0016 <0.0001 <0.0001 <0.0001 <0.0001 0.1139

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Table 14. Nested ANOVA output for factors year, month, and station comparing biotic and diversity variables as they pertain to push net samples only for the epifaunal community of Rincon Bayou. F value Probability Abundance Abundance Biomass Biomass Richness Hill's Pielou's Source df (N) (N m-2) (g) (g m-2) (R) Diversity (N1) Evenness (J') 9.67 1.27 4.28 0.49 12.66 8.01 0.79 Year 3 0.0001 0.2832 0.0159 0.6166 <.0001 0.0005 0.454 Month 1.72 1.15 1.2 1.58 2.36 1.83 1.48 12 (Year) 0.0309 0.3062 0.2579 0.0582 0.0013 0.0184 0.0895 1.19 2.1 2.9 9.14 0.43 0.11 0.45 Station 3 0.3064 0.1265 0.0585 0.0002 0.6504 0.8977 0.6382

Table 15. Values for physical variables depth, temperature, salinity, dissolved oxygen, and pH as recorded in Rincon Bayou for sampling events where no specimen were found in push net collections. Event Temperature Dissolved Station Depth (m) Salinity (psu) pH Date (ºC) Oxygen (mg L-1) 4/28/2010 F 0.04 28.65 36.19 14.04 9.36 8/11/2010 F 0.1 35.74 14.08 9.37 8.47 11/18/2014 C 0.03 17.33 13.64 11.37 8.27 8/11/2015 C 0.05 36.14 16.57 11.16 8.13

Table 16. Two-way ANOVA output for factors month and station, comparing biotic and diversity variables as they pertain to the seine sampled epifaunal community of Rincon Bayou.

F value Probability Abundance Abundance Biomass Biomass Richness Hill's Pielou's Source df (N) (N m-2) (g) (g m-2) (R) Diversity (N1) Evenness (J') Month 1.26 1.06 12.87 8.07 2.16 2.23 0.82 6 0.3198 0.4203 <.0001 0.0002 0.093 0.0851 0.5656 Station 3.1 1.05 15.56 7.13 1.36 0.04 0.02 2 0.0684 0.3684 <.0001 0.0049 0.2808 0.958 0.9801 Month* 1.11 0.28 3.16 2.37 1 1.1 0.48 10 Station 0.4044 0.9771 0.0149 0.0508 0.4775 0.4074 0.8814

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Table 17. Means of hydrographic variables as they pertain to the pooled fish community of Rincon Bayou, displayed by year and site selection. Study Monthly Inflow Depth Temperature Salinity Dissolved Oxygen Station pH Year (m3 s-1) (m) (°C) (psu) (mg L-1) C 284.99 0.13 26.56 8.85 7.30 8.68 2010 F 234.91 0.19 28.76 18.06 7.60 8.59 G 162.28 0.30 31.03 17.68 7.93 8.58 C 118.89 0.16 27.98 9.26 8.40 8.41 2014 F 48.66 0.19 27.12 21.60 8.44 8.34 G 99.31 0.24 25.56 21.50 8.99 8.40 C 278.18 0.19 26.57 6.80 9.07 8.24 2015 F 115.88 0.17 25.65 13.73 9.54 8.22 G 95.90 0.27 26.09 14.76 9.21 8.34

Table 18. Nested ANOVA output for factors year, month, and station, comparing biotic and diversity variables as they pertain to the pooled fish community of Rincon Bayou.

F value Probability Abundance Abundance Biomass Biomass Richness Hill's Pielou's Source df (N) (N m-2) (g) (g m-2) (R) Diversity (N1) Evenness (J') 2.38 1.88 4.28 0.79 4.34 3.41 1.89 Year 3 0.0981 0.159 0.0167 0.456 0.0158 0.0373 0.1575 Month 1.13 1.8 1.56 1.78 1.28 1.45 1.44 12 (Year) 0.3359 0.0293 0.0773 0.032 0.2076 0.1143 0.1208 1.81 4.68 0.98 1.9 2.16 2.48 2.89 Station 3 0.1698 0.0116 0.3775 0.1547 0.1211 0.0892 0.0605

Table 19. One-way ANOVA output comparing gear type for the pooled fish community data sampled from Rincon Bayou.

F value Probability Abundance Abundance Biomass Biomass Richness Hill's Pielou's Source df (N) (N m-2) (g) (g m-2) (R) Diversity (N1) Evenness (J') 189.43 2.51 221.42 34.73 125.21 42.44 9.24 Method 1 < 0.0001 0.1166 < 0.001 < 0.0001 < 0.0001 < 0.0001 0.0029

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Table 20. Nested ANOVA output for factors year, month, and station, comparing biotic and diversity variables as they pertain to the of push net sampled fish community of Rincon Bayou.

F value Probability Pielou's Abundance Abundance Biomass Biomass Richness Hill's Source df Evenness (N) (N m-2) (g) (g m-2) (R) Diversity (N1) (J') 1.17 2.7 0.74 1.52 0.46 0.62 0.3 Year 3 0.3177 0.0765 0.4813 0.2275 0.6339 0.5424 0.7411 Month 1.24 1.2 0.96 1.14 1.5 1.66 1.56 12 (Year) 0.257 0.2851 0.5194 0.3421 0.1155 0.0701 0.0947 4.86 3.64 2.43 2.36 4.23 4.51 4.27 Station 3 0.0114 0.0329 0.0972 0.104 0.0196 0.0154 0.019

Table 21. Two-way ANOVA output for factors month and station, comparing biotic and diversity variables as they pertain to the seine sampled fish community. F value Probability Pielou's Abundance Abundance Biomass Biomass Richness Hill's Source df Evenness (N) (N m-2) (g) (g m-2) (R) Diversity (N1) (J') 2.72 3.58 10.37 11.41 1.9 1.66 1.79 Month 3 0.0446 0.0152 <.0001 <.0001 0.1332 0.1847 0.1553 3.85 2.17 8.29 5.13 2.5 1.11 0.32 Station 12 0.0395 0.1415 0.0026 0.0166 0.109 0.3503 0.7307 Month* 0.96 0.48 1.89 4.4 0.72 0.3 0.74 3 Station 0.5086 0.885 0.1107 0.0027 0.6946 0.9721 0.6777

Table 22. Two-way ANOVA output for factors gear selection and shrimp species, comparing lengths and weights of all brown and white shrimp collected in Rincon Bayou. F value Probability Source df Length (mm) Individual Weights (g) 198.83 157.31 Gear 1 <.0001 <.0001 55.68 49.76 Shrimp 1 <.0001 <.0001 185.24 131.19 Gear*Shrimp 1 <.0001 <.0001

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Table 23. One-way ANOVA output for factor gear selection, comparing biotic variables as they pertain to the collective total of brown shrimp collected in Rincon Bayou.

F value Probability Source DF Length (mm) Weight (g) Abundance (N) Abundance (N m-2) Biomass (g) Biomass (g m-2) 1.44 1.99 9.98 13.39 14.48 8.61 Gear 1 0.2339 0.1617 0.0022 0.0004 0.0003 0.0043

Table 24. Nested ANOVA output for factors year, month, and station, comparing biotic variables as they pertain to push net-sampled brown shrimp collected in Rincon Bayou.

F value Probability Length Weight Abundance Abundance Biomass Biomass Source DF (mm) (g) (N) (N m-2) (g) (g m-2) 0 0.22 17.36 14.56 9.83 8.64 Year 2 0.9988 0.8062 <.0001 <.0001 0.0003 0.0008 Month 2.42 2.65 2.03 1.68 1.26 0.96 14 (Year) 0.0151 0.0082 0.0416 0.1004 0.2775 0.5076 0.21 0.44 2.51 2.77 3.23 3.67 Station 2 0.8099 0.6469 0.0945 0.0753 0.0505 0.0347

Table 25. Two-way ANOVA output for factors month and station, comparing biotic variables as they pertain to the seine sampled brown shrimp community of Rincon Bayou.

F value Probability Length Weight Abundance Abundance Biomass Biomass Source DF (mm) (g) (N) (N m-2) (g) (g m-2) 11.93 18.86 4.34 6.54 3.55 3.18 Month 4 0.0005 <.0001 0.0238 0.006 0.0429 0.0577 3.98 6.51 1.77 2.55 0.25 0.61 Station 2 0.0501 0.0137 0.2156 0.1231 0.7806 0.5618 Month* 0.64 1.83 1.04 2.16 0.82 0.94 7 Station 0.7185 0.1788 0.4588 0.1218 0.5891 0.5116

Table 26. One-way ANOVA output for factor gear selection, comparing biotic variables as they pertain to the collective total of white shrimp collected in Rincon Bayou. F value Probability Source DF Length (mm) Weight (g) Abundance (N) Abundance (N m-2) Biomass (g) Biomass (g m-2) 27.62 24.41 8.66 7.5 32.63 0.05 Gear 1 <0.0001 <0.0001 0.0053 0.0091 <.0001 0.8166

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Table 27. Nested ANOVA output for factors year, month, and station, comparing biotic variables as they pertain to the push net sampled white shrimp community of Rincon Bayou.

F value Probability Length Weight Abundance Abundance Biomass Biomass Source DF (mm) (g) (N) (N m-2) (g) (g m-2) 3.53 3.13 0.99 1.28 4.06 4.81 Year 2 0.0655 0.0839 0.4037 0.3174 0.0477 0.0315 Month 1.16 0.33 1.91 1.87 1.03 0.85 4 (Year) 0.3869 0.883 0.1716 0.1788 0.4447 0.5439 0.15 0.11 3.12 2.83 3.56 3.48 Station 3 0.8604 0.8944 0.0843 0.1018 0.0643 0.0674

Table 28. Two-way ANOVA output for factors month and station, comparing biotic variables for seine sampled white shrimp collected in Rincon Bayou.

F value Probability Source DF Length (mm) Weight (g) Abundance Biomass (g Abundance (N) Biomass (g) (N m-2) m-2) Month 4 4.91 4.57 2.53 1.68 1.19 1.35 0.027 0.0325 0.1228 0.2471 0.3868 0.3322 Sta 2 4.14 1.65 1.72 3.16 4.57 3.46 0.0582 0.2519 0.2388 0.0974 0.0476 0.0825 Mont 7 0.96 0.73 1.07 1.16 1.39 2.42 *Sta 0.516 0.6546 0.4589 0.4148 0.326 0.1198

Table 29. Summary of total blue crab, selected by gear type and size class, encountered in Rincon Bayou. Values are the total number of crab encountered (N) and their abundance (N m-2), biomass (g), biomass per tow (g m-2), carapace widths (mm) and individual weights (g). Size Gear N Abundance (N m-2) Biomass (g) Biomass (g m-2) Carapace Width (mm) Weight (g) Class 1 127 25.40 30.39 6.08 12.04 0.24 Push 2 28 5.60 213.15 42.63 39.61 7.61 net 3 3 0.60 176.54 35.31 96.67 58.85 1 186 3.38 49.01 0.89 13.07 0.26 Seine 2 52 0.95 374.46 6.81 38.12 7.20 3 14 0.25 1125.00 20.45 107.41 80.35

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Table 30. Summary of total blue crab, selected by sex and size class, encountered in Rincon Bayou. Values are the total number of crab encountered (N) and their relative abundance (Nm-2), the total biomass (B) and relative biomass (gm-2), average carapace widths (CW) and individual weights (Wt.) Size Sex N Abundance (N m-2) Biomass (g) Biomass (g m-2) Carapace Width (mm) Weight (g) Class 1 32 4.218 10.96 1.404 14.06 0.342 F 2 21 1.473 248.3 11.14 48.8 11.82 3 1 0.018 70.29 1.278 110 70.29 1 281 24.56 68.44 5.564 12.49 0.244 M 2 59 5.073 339.3 38.3 35.03 5.751 3 16 0.836 1231 54.48 105.2 76.95

Table 31. Summary of physical variables for overall crab population of Rincon Bayou, selected by year and station of the study. Values are the total number of crab encountered (N) and their abundance (N m-2), biomass (g), biomass per tow (g m-2), carapace widths (mm) and individual weights (g). Dissolved Year Station Inflow (m3s-1) Depth (m) Temp. (°C) Salinity (psu) pH Oxygen (mg L-1) C 249.94 0.25 27.97 0.63 7.95 8.69 2010 F 355.09 0.20 30.55 15.17 7.10 8.66 G 74.62 0.28 32.10 22.81 8.04 8.42 C 96.92 0.18 28.03 8.06 8.38 8.40 2014 F 61.37 0.19 26.21 22.08 7.12 8.24 G 62.36 0.30 26.91 22.38 7.24 8.28 C 363.69 0.20 27.08 6.56 8.68 8.18 2015 F 169.57 0.16 27.87 15.00 9.52 8.23 G 40.80 0.27 27.49 15.05 8.84 8.36

Table 32. One-way ANOVA output for log-transformed variables abundance, carapace width, and weight, comparing gear selection for pooled crab data from Rincon Bayou.

F value Probability Source DF Carapace Weight (g) Abundance Abundance Biomass (g Biomass (g) width (mm) (N) (N m-2) m-2) Gear 1 20.01 24.11 14.6 15.29 36.75 0.93 <.0001 <.0001 0.0003 0.0002 <.0001 0.3382

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Table 33. Nested ANOVA output of factors year, month, and station, comparing biotic variables for push net sampled blue crab collected in Rincon Bayou.

F value Probability Carapace width Abundance Abundance Biomass Source DF Weight (g) Biomass (g) (mm) (N) (N m-2) (g m-2) 1.59 3.3 1.07 0.86 3.37 1.91 Year 2 0.2246 0.0542 0.3573 0.4352 0.0513 0.1703 Month 18 0.4 0.75 0.87 0.72 0.65 0.66 (Year) 0.9763 0.7294 0.6149 0.7558 0.8224 0.8127 2.55 1.27 0.49 0.52 1.49 0.89 Station 2 0.0991 0.2999 0.6183 0.6037 0.2456 0.4249

Table 34. Complete summary of physical variables as they pertain to clustered events identified in the MDS ordination plot (Figure 20) of push net sampled crab population of Rincon Bayou. Temperature Salinity Dissolved Date STA N Depth (m) pH Inflow (m3 s-1) (ºC) (psu) Oxygen (mg L-1) 6/1/2010 C 9 0.20 29.08 0.58 7.70 8.87 355.09 6/16/2010 F 1 0.20 30.55 15.17 7.10 8.66 355.09 7/14/2014 C 3 0.25 29.45 0.44 6.94 8.31 234.45 7/27/2015 G 44 0.20 33.74 9.83 10.89 8.87 6.88 8/24/2015 F 1 0.10 35.62 18.97 9.50 8.12 7.45 11/11/2015 C 1 0.25 25.50 2.34 8.52 8.02 132.23

Table 35. Two-way ANOVA output of factors date and station, comparing means of biotic variables as they pertain to seine sampled blue crab collected in Rincon Bayou.

F value Probability Abundance Abundance Biomass Source DF Length (mm) Weight (g) Biomass (g) (N) (N m-2) (g m-2) 6.23 3.56 1.62 1.17 2.23 1.14 Month 6 0.0029 0.026 0.2179 0.3792 0.1064 0.3954 0.17 0.03 4.36 3.3 0.89 0.11 Station 2 0.8439 0.9752 0.0356 0.0695 0.4359 0.9009 Month* 1.87 1.06 1.32 1.03 0.68 0.89 10 Station 0.1446 0.4539 0.3152 0.473 0.7239 0.5623

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