Seagrass Condition Monitoring: Light and Port Adelaide 2020

Jason E. Tanner

SARDI Publication No. F2020/000252-01 SARDI Research Report Series No. 1062

SARDI Aquatics Sciences PO Box 120 Henley Beach SA 5022

June 2020

Final report prepared for the Adelaide and Mount Lofty Ranges Natural

Resources Management Board

Tanner (2020) 2020 seagrass condition monitoring

Seagrass Condition Monitoring: Light River and Port Adelaide 2020

Final report prepared for the Adelaide and Mount Lofty Ranges Natural Resources Management Board

Jason E. Tanner

SARDI Publication No. F2020/000252-01 SARDI Research Report Series No. 1062

June 2020

II Tanner (2020) 2020 seagrass condition monitoring

This publication may be cited as: Tanner, J.E. (2020). Seagrass Condition Monitoring: Light River and Port Adelaide 2020. South Australian Research and Development Institute (Aquatic Sciences), Adelaide. SARDI Publication No. F2020/000252-01. SARDI Research Report Series No. 1062. 29pp.

South Australian Research and Development Institute SARDI Aquatic Sciences 2 Hamra Avenue West Beach SA 5024 Telephone: (08) 8207 5400 Facsimile: (08) 8207 5415 http://www.pir.sa.gov.au/research

DISCLAIMER The authors warrant that they have taken all reasonable care in producing this report. The report has been through the SARDI internal review process, and has been formally approved for release by the Research Director, Aquatic Sciences. Although all reasonable efforts have been made to ensure quality, SARDI does not warrant that the information in this report is free from errors or omissions. SARDI and its employees do not warrant or make any representation regarding the use, or results of the use, of the information contained herein as regards to its correctness, accuracy, reliability and currency or otherwise. SARDI and its employees expressly disclaim all liability or responsibility to any person using the information or advice. Use of the information and data contained in this report is at the user’s sole risk. If users rely on the information they are responsible for ensuring by independent verification its accuracy, currency or completeness. The SARDI Report Series is an Administrative Report Series which has not been reviewed outside the department and is not considered peer- reviewed literature. Material presented in these Administrative Reports may later be published in formal peer-reviewed scientific literature.

© 2020 SARDI This work is copyright. Apart from any use as permitted under the Copyright Act 1968 (Cth), no part may be reproduced by any process, electronic or otherwise, without the specific written permission of the copyright owner. Neither may information be stored electronically in any form whatsoever without such permission.

SARDI Publication No. F2020/000252-01 SARDI Research Report Series No. 1062

Author(s): Jason E. Tanner

Reviewer(s): Kathryn Wiltshire and Paul van Ruth

Approved by: A/Prof Tim Ward Science Leader, Marine Ecosystems

Signed:

Date: 29 June 2020

Distribution: SAASC Library, Parliamentary Library, State Library and National Library

Circulation: Public Domain

III Tanner (2020) 2020 seagrass condition monitoring

TABLE OF CONTENTS

ACKNOWLEDGEMENTS ...... VI EXECUTIVE SUMMARY ...... 1 1. INTRODUCTION ...... 2 2. ASSESSMENT OF SEAGRASS CONDITION AND EPIPHYTE COVER OFF THE LIGHT RIVER DELTA ...... 4 2.1. Introduction ...... 4 2.2. Methods ...... 5 2.3. Results ...... 9 2.4. Discussion ...... 14 3. ASSESSMENT OF SEAGRASS CONDITION AND EPIPHYTE COVER OFF PORT ADELAIDE ...... 16 3.1. Introduction ...... 16 3.2. Methods ...... 16 3.3. Results ...... 17 3.4. Discussion ...... 23 4. CONCLUSIONS ...... 25 REFERENCES ...... 27

IV Tanner (2020) 2020 seagrass condition monitoring

LIST OF FIGURES

Figure 2-1: Map of the Light River catchment (from Harding et al. 2003)...... 4 Figure 2-2: Map of the Light River delta showing survey lines profiled and videotaped in April 2011 (red) and 2020 (blue)...... 7 Figure 2-3: Habitat along survey lines off the Light River in 2020...... 10 Figure 2-4: H' values for the along-shore data (survey line 520010 running parallel to the shore)...... 12 Figure 2-5: Epiphyte cover on the across-shore transects at Light River in 2011 and 2020...... 13 Figure 2-6: Epiphyte cover for the along-shore data (survey line 520010 running parallel to the shore)...... 14 Figure 3-1: Map of Port Adelaide showing the survey lines videotaped in February/March 2014 (red) and April 2020 (blue)...... 18 Figure 3-2: Cover of major habitat types off the in 2014 and 2020 (note habitats classified as reef/rubble in 2014 are reclassified here as macroalgae for consistency)...... 19 Figure 3-3: Habitat change along survey lines off the Port River mouth between 2014 (wide lines) and 2020 (narrower inner lines). Absence of the inner line indicates no change in habitat classification...... 20 Figure 3-4: Cover of different seagrass genera off the Port River in 2014 and 2020...... 21

LIST OF TABLES

Table 2-1: Cover of different habitat types off the Light River delta in April 2011 and 2020...... 9 Table 2-2: ANOVA results for difference in H’ between years, survey lines and distance from shore...... 11 Table 2-3: ANOVA results for difference in H’ between years, survey lines and distance from shore...... 13 Table 3-1: Habitat Condition Index score (H’) for survey lines off Port Adelaide...... 22 Table 3-2: ANOVA results for difference in H’ between years and survey...... 22 Table 3-3: Epiphyte loads on seagrasses for survey lines off Port Adelaide...... 23 Table 3-4: ANOVA results for difference in epiphyte loads between years and survey...... 23

V Tanner (2020) 2020 seagrass condition monitoring

ACKNOWLEDGEMENTS This work was funded by the Adelaide and Mount Lofty Ranges Natural Resources Management Board, under the direction of Kristian Peters. I thank Ian Moody and Leonardo Mantilla for undertaking the fieldwork, and Mandee Theil for processing the video imagery. Comments on an earlier draft of this report from Kathryn Wiltshire and Paul van Ruth, and the editorial oversight of Tim Ward, were appreciated.

VI Tanner (2020) 2020 seagrass condition monitoring

EXECUTIVE SUMMARY Video transects were undertaken along a number of survey lines off the Light River in 2011 and Port Adelaide in 2014, primarily to assess seagrass condition in these regions. In addition, epiphyte loads were scored from the video footage as a potential indicator of nutrient stress. Here, we undertake repeat surveys of the same lines in 2020 to assess if there have been any changes over time.

Off the Light River, there were small increases in both seagrass cover (from 95% to 99%) and habitat condition index (from 97.1 to 99.6). These were accompanied by a decrease in epiphyte loads (from 8% to 2.9%). Overall, these changes indicate that the seagrass in this region, which was classified as being in very good condition in 2011, has remained in very good condition and possibly slightly improved.

Off Port Adelaide, seagrass cover increased from 56% to 64%, with increases in both ephemeral Halophila and the long-lived Posidonia. Habitat condition was variable, with two survey lines remaining stable, one improving and one declining. The decline, however, was actually due to Halophila colonizing areas that had been bare sand. In scoring habitat condition, areas of bare sand are ignored. Halophila is scored, although as it is structurally simple it receives a lower score than other seagrass species. Consequently, including areas that have transitioned from bare sand to Halophila can bring the overall score down. Epiphyte loads decreased along three survey lines, but increased on the fourth for unknown reasons.

Keywords: Seagrass, habitat condition, Posidonia, Amphibolis, Halophila

1 Tanner (2020) 2020 seagrass condition monitoring

1. INTRODUCTION Declines in seagrass habitat have been a major concern worldwide, with 29% of known seagrass area lost since 1879 (Waycott et al. 2009). South has not been immune to this loss and its flow on effects. At Bolivar, just north of Adelaide, extensive loss of seagrass has led to a changed wave climate, and contributed to a die-off of mangroves (Mifsud et al. 2004). Similarly, extensive areas of seagrass have been lost off Beachport in the south-east, and this has led to substantial shore-line erosion, with the need for costly remediation works to protect the town (Seddon et al. 2003). Over 7000 ha has been lost off the Adelaide metropolitan (e.g. Westphalen et al. 2004, Bryars and Rowling 2009), contributing to the need for an extensive sand replenishment operation along the metropolitan beaches to mitigate coastal erosion. The largest area of seagrass loss in , however, has been in Spencer Gulf, where declines have exceeded 130 km2, primarily due to dieback in a heatwave (Irving 2014).

In 2009, the Department for Environment and Heritage (DEH, now Department for Environment and Water - DEW) and the South Australian Research and Development Institute (SARDI) undertook a joint program to assess the condition of seagrasses in Yankalilla Bay (Murray-Jones et al. 2009). In that project, a standardised methodology was developed to assess seagrass condition from data that can be collected using a remote video camera. The technique was then applied to a series of video transects running offshore in the vicinity of the Bungala River and Carrickalinga Creek. Seagrasses were found to be in good condition in these areas. Subsequent surveys were undertaken off the Light River delta and off the in Encounter Bay in 2011 (Tanner et al. 2012), and around the in Encounter Bay in 2013/14 and Port Adelaide in 2014 (Tanner et al. 2014b). The Yankalilla Bay and Encounter Bay surveys were repeated in 2019 (Tanner and Theil 2019), showing no change in habitat condition, and a decrease in epiphyte load, at the former, but a regional decline in condition at the latter.

To determine if any changes have occurred since these original surveys, we repeated surveys at the Light River and Port Adelaide sites. The same methodology was utilised, allowing a direct comparison between surveys. We document both seagrass habitat condition, and epiphyte cover, and compare these to the results of the previous surveys in 2009 and 2013/14 respectively.

Understanding and maintaining or improving the condition of marine assets (e.g. seagrasses) remains a legislative requirement under the South Australian Natural Resources Management Act (2004). The Adelaide and Mount Lofty Ranges (AMLR) NRM Plan identifies seagrass as an important component of regional marine ecosystems, and measuring the health and condition

2 Tanner (2020) 2020 seagrass condition monitoring against its regional targets is fundamental to measuring success of the implementation of the Regional Plan. Regional Targets that this work contributes to include:

T9: Improvement in conservation prospects of native species from current levels

T10: Reduced land-based impacts on coastal, estuarine and marine processes

T11: Halt the decline of seagrass, reef and other coast, estuarine and marine habitats and a trend toward restoration.

Seagrass monitoring is an invaluable component to providing information that informs the regional Marine Health conceptual model found within the AMLR NRM Plan. Seagrass monitoring is also underpinned by guiding targets 10, 12 and 13 of the South Australia’s NRM Plan (2007-2017), respective regional NRM plans, the South Australian New Life for our Coastal Environment strategy and the Adelaide coastal waters quality improvement plan (ACWQIP).

3 Tanner (2020) 2020 seagrass condition monitoring

2. ASSESSMENT OF SEAGRASS CONDITION AND EPIPHYTE COVER OFF THE LIGHT RIVER DELTA

2.1. Introduction The Light River enters to the north of Adelaide (Figure 2-1), in an area with extensive shallow-water seagrasses, and has a total catchment of ~200,000 ha. While flows are intermittent, the river catchment is predominantly used for dry-land agriculture (cropping and grazing), and thus there is the potential for negative impacts on the marine fauna and flora in the Light River delta. Descriptions of the sub-catchments can be found in (Harding et al. 2003, 2005) and Henschke et al. (2008). Water level and rainfall is monitored in the lower Light River sub- catchment (https://amlr.waterdata.com.au), however, flow in the river is not, but modelling indicates a mean natural outflow of 22,900 ML yr-1 (http://www.anra.gov.au/topics/water/availability/sa/swma-light-river.html).

Figure 2-1: Map of the Light River catchment (from Harding et al. 2003).

4 Tanner (2020) 2020 seagrass condition monitoring

The seagrasses in northern Gulf St Vincent, including those off the Light River delta, have received very little formal attention, and thus not much is known about their condition, or how it might change with increasing development of the catchment. There has been some broad-scale habitat mapping of the region, using satellite imagery (Edyvane 1999) and aerial imagery ground- truthed with in situ video transects (DEH 2008). The latter work is the most comprehensive, and has resulted in a series of 5 km x 5 km maps of habitat, but only has a resolution of 1:20,000, and seagrass species are not distinguished. Therefore, while providing a useful broad-scale indicator of the status of seagrasses in the region, it does not provide detailed information that can be used to assess the condition of seagrasses in a specific area. As a result, the AMLR NRM Board has identified this region as a priority for establishing a baseline of ecosystem health, focussing on seagrasses.

In April 2011, the then Department of Environment and Natural Resources surveyed a series of transects off the Light River delta, which were then examined by SARDI to assess seagrass condition index and epiphyte loads (Tanner et al. 2012). This study found close to 100% seagrass cover in the survey area, dominated by Posidonia, and with some Amphibolis and Zostera. Epiphyte loads on these transects were low. In the current report, these surveys are repeated, and comparisons made between 2011 and 2020.

2.2. Methods Field work

Sampling of seagrass beds was conducted off the Light River delta, South Australia on April 8 and 9, 2020, following the methods described in Murray-Jones et al. (2009). Six survey lines perpendicular to the shore were sampled (Figure 2-2). Each of the survey lines ran from ~1100- 1600 m offshore towards the inshore region to the shallowest point that the boat could operate (generally ~0.8 – 1 m in depth). In addition, one longer (~5000 m) survey line running parallel to the coastline connecting the offshore end of each transect was run (transect coded 520010, Figure 2-2). These followed the survey lines that were videoed in 2011 as closely as possible while navigating a small vessel. In 2020, tidal conditions and vessel size meant that it was not possible to survey as close inshore as the 2011 surveys achieved.

For each survey line, a video camera was towed over the seagrass meadow just above the canopy (0.5-1m) at ~1.3 ms-1, which recorded continuous video transects of the seafloor. A GPS signal was overlaid on the footage, indicating the location of the camera at all times.

5 Tanner (2020) 2020 seagrass condition monitoring

From the videotape data of each survey line shown in Figure 2-2, subsets of 50 m in length (subsequently referred to as transects) were randomly selected, to provide replication. For each of the perpendicular survey lines, three separate 50 m transects were randomly selected from each of the inshore and offshore halves of the line. This enabled comparisons between inshore and offshore sites. In addition, 12 × 50 m transects were randomly selected from the along-shore survey line (520010), referred to as the along-shore data.

As an initial estimate of seagrass condition, the data required to calculate the habitat structure index, H′, which ranks the sampled seagrass on a scale of 0-100 (100 being excellent, 0 being poor) were recorded (for further description of the rationale and methods for calculating H' see Murray-Jones et al. (2009), Irving et al. (2013)). Five variables (seagrass area, continuity, proximity, percentage cover and species identity) were recorded for 50 sequential ~1 m2 quadrats along each replicate transect from the video, hence covering an entire 50 m transect, and integrated to calculate H'. Information on habitat type (e.g. seagrass, sand, rock, macroalgae) was also collected and epiphyte load determined.

To obtain the above data, for each transect, the video was paused approximately every 1 m, and a transparent grid of 44 squares overlying the screen used to facilitate estimation of both percent seagrass and percent epiphyte cover. As there was some minor variation in boat speed, the time interval equating to 1 m was calculated for each transect based on the GPS records for the distance points closest to the start and end of each transect. Seagrass was scored according to type (note that the difficulty of identification from video meant that seagrass was only identified to genus) and density. Percentage cover was estimated for all seagrass visible. Other substrate types were scored (e.g. areas of sand) and grouped together for analysis. Epiphyte cover on seagrasses was also estimated in the same way, and re-expressed as a percentage of total seagrass cover.

6 Tanner (2020) 2020 seagrass condition monitoring

Figure 2-2: Map of the Light River delta showing survey lines profiled and videotaped in April 2011 (red) and 2020 (blue).

7 Tanner (2020) 2020 seagrass condition monitoring

Analysis of data

Seagrass Condition Index

Following Tanner et al. (2012), the data were divided into two components for analysis. Data from the transects perpendicular to shore were analysed using analysis of variance (ANOVA) in SPSS Statistics (v 26) to examine effects of ‘Distance from shore’ (Inshore vs Offshore) crossed with ‘Survey line’ (52004 vs 52005 etc.) and ‘Year’ (all fixed and orthogonal). With this design, the three 50 m long transects within each ‘Survey line’ × ‘Distance from shore’ × ‘Year’ combination were replicates.

The second analysis component tested for ‘along-shore’ differences in H'. Here, data from the single long survey line (520010) that ran parallel to the shore were used. A single factor ANOVA was used to examine differences between years. In both cases Levene’s test of homogeneity of variances and quantile-quantile (QQ) plots showed no major departures from the assumptions of ANOVA.

Epiphytes

The analysis was performed as described above on percent of seagrass area covered by epiphytes for each transect. Levene’s test of homogeneity of variances and QQ plots showed no major departures from the assumptions of ANOVA.

8 Tanner (2020) 2020 seagrass condition monitoring

2.3. Results

General habitat description

Seagrass cover in April 2020 was >99% across the seven survey lines, a slight increase on the 94.9% in 2011 (Table 2-1, Figure 2-3). Posidonia was by far the most dominant taxon in both years, increasing from 81% to 85%, followed by Amphibolis, which increased from 6% to 12%. No Zostera was found in 2020, although it comprised 7.5% cover in 2011.

Table 2-1: Cover of different habitat types off the Light River delta in April 2011 and 2020.

Habitat 2011 2020 Amphibolis 5.9 12 Posidonia 81.4 85.4 Mixed Amphibolis/Posidonia 0 2.1 Zostera 7.5 0 Sand 5.1 0.4

9 Tanner (2020) 2020 seagrass condition monitoring

Figure 2-3: Habitat along survey lines off the Light River in 2020.

10 Tanner (2020) 2020 seagrass condition monitoring

Seagrass Condition Index

‘Across-shore’ patterns

The calculated values of H' were very high across the area of study (mean 97.1 ± 0.6 (se) and 99.6 ± 0.001 in 2011 and 2020 respectively), indicating very good structure of seagrass meadows in the region overall (i.e. extensive and continuous meadows with species of high value). There was significant variation in H’ between years, but not with either survey line or distance from shore, or any interactions (Table 2-2).

Table 2-2: ANOVA results for difference in H’ between years, survey lines and distance from shore.

df MS F P Year 1 107.8 14.2 <0.001 Survey Line 5 5.83 0.77 0.58 Distance 1 15.2 1.99 0.17 Year x Survey Line 5 5.8 0.76 0.58 Year x Distance 1 15.3 2.01 0.16 Survey Line x Distance 5 5.0 0.65 0.66 Year x Survey Line x Distance 5 5.0 0.65 0.66 Error 48 7.6

‘Along-shore’ patterns

Overall, H’ on the along-shore transect showed similar patterns to the cross-shore transects, although it was slightly lower than cross-shore transect H’ values in both years (92.2 ± 4.0 and 97.7 ± 1.1 in 2011 and 2020 respectively). Variability was higher in 2011 than in 2020, and lower values tended to occur towards the southern end of the transect in both years (Figure 2-4). There

was no significant difference in along-shore H’ values between years (ANOVA: F1,22=1.70, p=0.21).

11 Tanner (2020) 2020 seagrass condition monitoring

Figure 2-4: H' values for the along-shore data (survey line 520010 running parallel to the shore).

Epiphytes

Mean epiphyte cover over the entire study area was 8.0% (± 1.6 se) in 2011 and 2.9% (± 0.6) in 2020.

‘Across-shore’ patterns

Epiphyte cover was highly variable between survey lines, and between years, but there was no effect of distance from shore or any of the interactions (Table 2-3). In 2011, epiphytes peaked in the middle of the survey area, as well as at the southern end, while in 2020 only the southernmost survey line had high cover (Figure 2-5).

12 Tanner (2020) 2020 seagrass condition monitoring

Table 2-3: ANOVA results for difference in epiphyte cover between years, survey lines and distance from shore.

df MS F P Year 1 922 15.86 <0.001 Survey Line 5 152 2.62 0.036 Distance 1 75 1.29 0.26 Year x Survey Line 5 107 1.84 0.12 Year x Distance 1 28 0.47 0.50 Survey Line x Distance 5 121 2.08 0.085 Year x Survey Line x Distance 5 100 1.71 0.15 Error 48 58

Figure 2-5: Epiphyte cover on the across-shore transects at Light River in 2011 and 2020.

‘Along-shore’ patterns

For the along-shore survey line, epiphyte cover peaked at either end in 2011, whereas it generally increased from north to south in 2020 (Figure 2-6). There were no significant differences between years in cover on this line (ANOVA: F1,22=0.21, P=0.65).

13 Tanner (2020) 2020 seagrass condition monitoring

Figure 2-6: Epiphyte cover for the along-shore data (survey line 520010 running parallel to the shore).

2.4. Discussion

Seagrass cover was very high over most of the study area, comprising mostly Posidonia, with a small amount of Amphibolis, and some Zostera in shallower water in 2011. While Zostera was not found in 2020, this is likely to be because it was not possible to survey as far inshore as was surveyed in 2011, with this genus being more commonly found in very shallow subtidal and intertidal waters. It should be noted that Tanner et al. (2012) talk about Zostera/Heterozostera, but subsequent taxonomic revisions have merged the two genera into Zostera.

There was a small improvement in habitat condition between 2011 and 2020, with higher overall seagrass cover in the later. This is not attributable to the inability to survey close inshore in 2020, as 50 m transects with relatively low cover in 2011 occurred both in areas that were and weren’t surveyed in 2020. In addition, there was a substantial decline in epiphyte loads between the two surveys. With only two survey times, it is not possible to determine if these results indicate a long- term improvement in seagrass condition in this region, or if the changes simply fall within the natural year-to-year variation experienced at the site. In 2020, there was a consistent spatial pattern of increasing epiphyte load from north to south on the along-shore transect, which was not present in 2011. This could be an early indication of increased nutrient supply coming from the southern end of the study area, and warrants further attention to ascertain if this is the case,

14 Tanner (2020) 2020 seagrass condition monitoring

or if it is simply interannual variability. The Light River enters the gulf just south of the study area, and so could be a source of elevated nutrients. Persistent increases in epiphyte load are a precursor to most nutrient induced losses of seagrasses, as heavy epiphyte loads reduce light availability to the seagrass, reducing its capacity to photosynthesise and maintain a source of energy (Bryars et al. 2011).

Overall, the data presented show the seagrasses off the Light River delta to be in very good (possibly improving) condition, and they do not appear to be degraded due to discharges from the Light River. There were no losses of seagrasses observed around the mouth of the river, as has been seen around drain discharges in the south-east of South Australia (Wear et al. 2006). This may be due to the intermittent and low flows experienced by the Light River. Additionally, the Light River discharges through a mangrove delta and across intertidal mudflats (see Figure 2-2), and thus does not present a concentrated point source like many other and drains in South Australia, but rather is a more diffuse source of freshwater and any accompanying pollutants. Thus it may simply be that inputs are sufficiently diluted before they reach the seagrass as to not cause any detectable impacts.

15 Tanner (2020) 2020 seagrass condition monitoring

3. ASSESSMENT OF SEAGRASS CONDITION AND EPIPHYTE COVER OFF PORT ADELAIDE

3.1. Introduction The Port River is a major pathway for industrial effluents to enter Gulf St Vincent, although since the construction of Breakout Creek in the 1930s, and the closure of the Port Adelaide Wastewater Treatment plant in 2005, freshwater inputs have been limited to locally derived stormwater (Fox et al. 2007). One of the major water quality concerns with the Port River has previously been the Penrice soda-ash plant, which discharged up to 1000 tonnes of nitrogen in the form of ammonia to the river each year. This accounted for up to half of the total anthropogenic nitrogen entering the coastal zone (Fox et al. 2007). These nitrogen inputs have been identified as a major cause of the extensive seagrass loss that has been documented off the Adelaide metropolitan coast (> 7000 ha Neverauskas 1987, Hart 1997, Cameron 1999). With the closure of the soda-ash plant in 2013, this source of nitrogen has been eliminated, and in 2014 a baseline of seagrass condition was obtained in the region to determine if this has positive environmental benefits (Tanner et al. 2014b). Subsequently, in 2019, Flinders Ports undertook a major capital dredging program in the Outer Harbour approach channel to widen it from 130 m to 170 m. EPA resurveyed the lines surveyed by Tanner et al. (2014b) prior to the dredging, although this data has yet to be analysed.

In this chapter, we document the changes in seagrass that have occurred between 2014 and 2020, capturing both any recovery due to the cessation of the nitrogen inputs from the soda ash plant, and any impacts of the Outer Harbour dredging operation.

3.2. Methods Field work

Sampling of seagrass beds was conducted off Port Adelaide, South Australia on April 8 and 9, 2020, following the methods described in Murray-Jones et al. (2009). Four survey lines perpendicular to the shore were sampled (Figure 3-1). Each of the survey lines ran from approximately 3500-4200 m offshore towards the inshore region to the shallowest point that the vessel could operate (generally ~0.8 – 1 m in depth). Survey protocols and data analysis followed those described in Chapter 2.

From the videotape data of each survey line shown in Figure 2-2, subsets of 50 m in length (subsequently referred to as transects) were randomly selected, to provide replication. For each

16 Tanner (2020) 2020 seagrass condition monitoring

of the perpendicular survey lines, 50 m transects were randomly selected without overlap from seagrass habitat, with 1 transect from every segment 50 - 350 m in length, 2 for segments 350- 650 m, and an additional transect for every additional 300 m.

Analysis of data

Seagrass Condition Index

A two factor ANOVA was used to examine differences between years, with Transect and Year as fixed factors. Levene’s test of homogeneity of variances and QQ plots showed no major departures from the assumptions of ANOVA.

Epiphytes

The analysis was performed as described above on percent of seagrass area covered by epiphytes for each transect.

3.3. Results

General habitat description

Seagrass cover in April 2020 averaged 64% (± 13 se), compared to 56% (± 22) in 2014, which was also accompanied by an increase in mixed seagrass/macroalgae from 0.1% (± 0.1) to 7.5% (± 4.5). This increase was primarily on the two survey lines either side of the Port River mouth, and came primarily at the expense of decreased bare sand (Figure 3-2, Figure 3-3). The increase in seagrass was almost entirely driven by the small ephemeral Halophila (Figure 3-4), which increased in cover from ~4% to ~12%, and Posidonia (from 44% to 53%) (note these figures include mixed seagrass/macroalgae habitat).

17 Tanner (2020) 2020 seagrass condition monitoring

Figure 3-1: Map of Port Adelaide showing the survey lines videotaped in February/March 2014 (red) and April 2020 (blue).

18 Tanner (2020) 2020 seagrass condition monitoring

Figure 3-2: Cover of major habitat types off the Port River in 2014 and 2020 (note habitats classified as reef/rubble in 2014 are reclassified here as macroalgae for consistency).

19 Tanner (2020) 2020 seagrass condition monitoring

Figure 3-3: Habitat change along survey lines off the Port River mouth between 2014 (wide lines) and 2020 (narrower inner lines). Absence of the inner line indicates no change in habitat classification.

20 Tanner (2020) 2020 seagrass condition monitoring

Figure 3-4: Cover of different seagrass genera off the Port River in 2014 and 2020.

21 Tanner (2020) 2020 seagrass condition monitoring

Seagrass Condition Index

The calculated values of H' were variable across and within survey lines in both years, ranging from 78 to 95 in 2014 and 77 to 98 in 2020 (Table 3-1). There was a significant interaction between year and survey line in the ANOVA (Table 3-2), with 200001 showing a substantial decrease in habitat condition while 200152 increased.

Table 3-1: Habitat Condition Index score (H’) for survey lines off Port Adelaide.

Survey Line 2014 2020 200001 95.6 (1.6) 76.9 (4.7) 200005 93.5 (3.2) 94.8 (2.1) 200151 77.8 (8.9) 77 (5.9) 200152 91.6 (3.1) 97.6 (1.1)

Table 3-2: ANOVA results for difference in H’ between years and survey.

df MS F P Year 1 205 1.25 0.27 Survey Line 3 1118 6.80 <0.001 Year x Survey Line 3 689 4.20 0.008 Error 84 164

Epiphytes

Epiphyte loads were variable across and within survey lines in both years, especially 2020, ranging from 8% to 17% in 2014 and 0.1% to 24% in 2020 (Table 3-3). There was a significant interaction between year and survey line in the ANOVA (Table 3-4), with 200001 showing a substantial increase in epiphyte load while the other three survey lines decreased.

22 Tanner (2020) 2020 seagrass condition monitoring

Table 3-3: Epiphyte loads on seagrasses (%) for survey lines off Port Adelaide.

Survey Line 2014 2020 200001 7.6 (2.9) 23.9 (6.1) 200005 17 (5.4) 2 (0.8) 200151 12.6 (4.7) 0.1 (0.1) 200152 15.3 (3.7) 0.1 (0.1)

Table 3-4: ANOVA results for difference in epiphyte loads between years and survey.

df MS F P Year 1 110 34.2 <0.001 Survey Line 3 9.4 2.9 0.039 Year x Survey Line 3 27.8 8.6 <0.001 Error 84 3.2

3.4. Discussion

Tanner et al. (2014b) documented relatively low seagrass cover on the survey lines either side of the Port River mouth (200151 and 200001), with higher cover on the two more distant lines (200152 and 200005). In 2020, cover had increased on these inner two lines, although was still low compared to the outer lines. This increase was due to both small ephemeral species (Halophila), as well as larger structural species (Posidonia). However, despite the increase in cover, the habitat condition index for these two lines either remained stable (200151 to the north of the river mouth) or decreased (200001 to the south). Epiphyte cover also increased substantially on 200001, although decreased on the other three survey lines.

While the decrease in habitat condition index scores on 200001 initially appears concerning, looking in more detail, this transect experienced a very small increase in Posidonia cover over the study period, but a substantial increase in Halophila. As the condition index score primarily assesses habitat structure, it assigns a lower value to areas of Halophila as opposed to Posidonia as the former is much smaller in stature. Thus, with an increase in Halophila and little change in

23 Tanner (2020) 2020 seagrass condition monitoring

Posidonia, the low scores for Halophila bring the overall average down. We can conclude from this that the overall condition of seagrasses along this survey line is thus not actually declining. The increased epiphyte loads on this survey line, however, are a potential issue. Unusually, the high epiphyte loads occur primarily on Halophila, although the two innermost transects, which were dominated by Posidonia, also had high loads. Halophila being fast-growing and relatively ephemeral tends to have relatively low epiphyte loads. We may find an explanation here in that April would be approaching the end of the growing season for Halophila, and so the leaves would be relatively old and potentially senescing, making them more susceptible to fouling by epiphytes. This does not, however, explain the relatively high epiphyte loads on the Posidonia on the two innermost transects, suggesting that there may also be elevated nutrient loads in the area. Any elevated nutrient levels do not seem to be present at the offshore end of the survey line, as the four outermost transects were devoid of epiphytes. With only two survey times, it is not possible to determine if this increase is sustained, or is just an idiosyncratic response to naturally varying environmental conditions.

24 Tanner (2020) 2020 seagrass condition monitoring

4. CONCLUSIONS Seagrasses off the Light River delta appear to be in very good, and possibly improving, condition. There was a small increase in seagrass cover between 2011 and 2020 (95% to 99%), and a substantial decrease in epiphyte loads (8% to 2.9%). While surveys were not able to extend as far inshore in 2020 as in 2011, these improvements are not related to a contraction in the spatial cover, as they were still present when only data from the offshore areas surveyed in both years were considered.

Seagrass cover also increased at Port Adelaide on the two survey lines that had low cover in 2014. While there was an overall decrease in epiphyte loads here as well, there was a substantial increase on the survey line immediately south of the Port River mouth. This occurred primarily on Halophila, but some areas of Posidonia were also affected. Typically, high epiphyte loads are related to increased nutrient levels. With only two surveys to compare, it is also possible that this increase is just a chance occurrence.

The decrease in habitat condition along survey line 200001 at Port Adelaide indicates an unforeseen issue with the habitat condition index score. This decrease occurred because areas transitioned from bare sand to Halophila. These areas were not included in the 2014 analysis, as they had no seagrass, and obtained a relatively low score in 2020 due to the simpler structural characteristics of Halophila compared to the other seagrass species present. If the exact same 50m transects had been scored in both years, then the Halophila transects in 2020 which had a condition index score of 60-75 would have received a score of 0 in 2014 (being bare sand), leading to an increase in habitat condition. In effect, not scoring those transects in 2014 means that the zeroes were left out of the calculation. This needs to be kept in mind when comparisons between sites or over time are made.

EPA conduct ~5 yearly aquatic ecosystem condition reporting for the nearshore waters of Gulf St Vincent, which includes an assessment of seagrass habitats (https://www.epa.sa.gov.au/data_and_publications/water_quality_monitoring/aquatic_ecosyste m_monitoring_evaluation_and_reporting). They have a site in the vicinity of our southern-most Port Adelaide survey line, which was recorded as having declining seagrass cover in 2017 compared to 2010/11, whereas their site in between the two northernmost lines increased. This contrasts to our findings for the southern line, which we found to be stable, but accords with increases we found on the line immediately north of the Port River. At sites either side of Light River, EPA documented a substantial decline in seagrass cover, in comparison to our slight

25 Tanner (2020) 2020 seagrass condition monitoring

increase. Further work is required to put the results of these two separate programs into mutual context.

Seagrasses are an integral component of nearshore marine ecosystems in South Australia. Gulf St Vincent and Spencer Gulf are home to some of the most extensive seagrass meadows globally (Edyvane 1999), and they provide foundational ecosystem services including habitat provision (Connolly 1994, Scott et al. 2000, Tanner 2005), nutrient cycling (Fernandes et al. 2009), carbon sequestration (Lavery et al. 2019) and wave attenuation limiting coastal erosion (Reidenbach and Thomas 2018). With increased urbanisation of Adelaide’s metropolitan , continued assessments of seagrass meadow condition and its biota should remain a priority in order to identify further habitat degradation, loss or ecological change, and to assess whether management actions are effective in assisting recovery. The techniques used here allow declines in condition to be detected before full-scale loss occurs, after which eliminating the disturbance(s) that caused the loss may not be sufficient to reverse it (Tanner et al. 2014a, Connell et al. 2017).

26 Tanner (2020) 2020 seagrass condition monitoring

REFERENCES Bryars, S., G. Collings, and D. Miller. 2011. Nutrient exposure causes epiphytic changes and coincident declines in two temperate Australian seagrasses. Marine Ecology Progress Series 441:89-103. Bryars, S., and K. Rowling. 2009. Benthic habitats of eastern Gulf St Vincent: Major changes in benthic cover and composition following European settlement of Adelaide. Transactions of the Royal Society of South Australia 133:318-338. Cameron, J. 1999. Near shore seagrass change between 1989/90 and 1997/98 mapped using Landsat TM satellite imagery, Gulf St Vincent South Australia. Department for Environment, Heritage and Aboriginal Affairs, Adelaide. Connell, S. D., M. Fernandes, O. W. Burnell, Z. A. Doubleday, K. J. Griffin, A. D. Irving, J. Y. S. Leung, S. Owen, B. D. Russell, and L. J. Falkenberg. 2017. Testing for thresholds of ecosystem collapse in seagrass meadows. Conservation Biology 31:1196-1201. Connolly, R. M. 1994. The role of seagrass as preferred habitat for juvenile Sillaginodes punctata (Cuv. & Val.) (Sillaginidae, Pisces): habitat selection or feeding? Journal of Experimental Marine Biology and Ecology 180:39-47. DEH. 2008. Marine Habitats in the Adelaide and Mount Lofty Ranges NRM Region. Final Report to the Adelaide and Mount Lofty Ranges Natural Resources Management Board for the program: Facilitate Coast, Marine and Estuarine Planning and Management by Establishing Regional Baselines. Prepared by the Department for Environment and Heritage, Coast and Marine Conservation Branch. Edyvane, K. 1999. Conserving marine Biodiversity in South Australia. Part 2 - Identification of areas of high conservation value in South Australia. SARDI, Adelaide. Fernandes, M., S. Bryars, G. Mount, and D. Miller. 2009. Seagrasses as a sink for wastewater nitrogen: The case of the Adelaide metropolitan coast. Marine Pollution Bulletin 58:303- 308. Fox, D. R., G. E. Batley, D. Blackburn, Y. Bone, S. Bryars, A. Cheshire, G. Collings, D. Ellis, P. Fairweather, H. Fallowfield, G. Harris, B. Henderson, J. Kampf, S. Nayar, C. Pattiaratchi, P. Petrusevics, M. Townsend, G. Westphalen, and J. Wilkinson. 2007. Adelaide Coastal Waters Study, Final Report, Volume 1, Summary of Study Findings, November 2007. CSIRO, Adelaide. Harding, A., C. Henschke, P. Ciganovic, and T. Dooley. 2003. Upper Light River Salinity Management Plan. Prepared for the Northern and Yorke Agricultural District Integrated Natural Resource Management Committee. Rural Solutions SA, Adelaide. Harding, A., C. Henschke, P. Ciganovic, and T. Dooley. 2005. Gilbert River Salinity Management Plan. Prepared for the Northern and Yorke Agricultural District Integrated Natural Resource Management Committee. Rural Solutions SA, Adelaide. Hart, D. 1997. Near-shore seagrass change between 1949 and 1995 mapped using digital aerial orthophotography. Southern Adelaide area Glenelg-Marino South Australia. Department of Environment and Natural Resources, Adelaide. Henschke, C., A. Harding, and S. Wright. 2008. Mid to Lower Light River Salinity Management Plan. Report to N&Y NRM Board. Rural Solutions SA, Adelaide. Irving, A. D. 2014. Seagrasses of Spencer Gulf. Pages 121-135 in S. A. Shepherd, S. M. Madigan, B. M. Gillanders, S. Murray-Jones, and D. J. Wiltshire, editors. Natural history of Spencer Gulf. Royal Society of South Australia Inc., Adelaide. Irving, A. D., J. E. Tanner, and S. G. Gaylard. 2013. An integrative method for the evaluation, monitoring, and comparison of seagrass habitat structure. Marine Pollution Bulletin 66:176-184. Lavery, P. S., A. Lafratta, O. Serrano, P. Masque, A. Jones, M. Fernandes, S. Gaylard, and B. Gillanders. 2019. Coastal carbon opportunities: technical report on carbon storage and

27 Tanner (2020) 2020 seagrass condition monitoring

accumulation rates at three case study sites. Goyder Institute for Water Research Technical Report Series No. 19/21., Adelaide. Mifsud, J., D. Wiltshire, D. Blackburn, and P. Petrusevics. 2004. Section Bank, Outer Harbor, South Australia. Baseline monitoring program to assess the potential impacts on seagrass and mangrove communities from the proposed sand dredging. Report prepared by Natural Resource Services Pty Ltd. for the Coast Protection Board, DEH. Murray-Jones, S., A. Irving, and J. Dupavillon. 2009. Seagrass Condition Monitoring: A report to the Adelaide and Mount Lofty Ranges Natural Resources Management Board. Department for Environment and Heritage, Coastal Management Branch. . Neverauskas, V. P. 1987. Monitoring seagrass beds around a sewage sludge outfall in South Australia. Marine Pollution Bulletin 18:158-164. Reidenbach, M. A., and E. L. Thomas. 2018. Influence of the Seagrass, Zostera marina, on Wave Attenuation and Bed Shear Stress Within a Shallow Coastal Bay. Frontiers in Marine Science 5:397. Scott, L. C., J. W. Boland, K. S. Edyvane, and G. K. Jones. 2000. Development of a seagrass- fish habitat model - I: A seagrass residency index for economically important species. Environmetrics 11:541-552. Seddon, S., K. A. Moore, D. Fotheringham, S. Burgess, and J. McKechnie. 2003. Beachport seagrass loss and links with Drain M in the Wattle Range Catchment. South Australian Research and Development Institute (Aquatic Sciences), Adelaide. Tanner, J. E. 2005. Edge effects on fauna in fragmented seagrass meadows. Austral Ecology 30:210-218. Tanner, J. E., A. D. Irving, M. Fernandes, D. Fotheringham, A. McArdle, and S. Murray-Jones. 2014a. Seagrass rehabilitation off metropolitan Adelaide: a case study of loss, action, failure and success. Ecological Management & Restoration 15:168-179. Tanner, J. E., and M. Theil. 2019. Seagrass Condition Monitoring: . Final report prepared for the Adelaide and Mount Lofty Ranges Natural Resources Management Board. South Australian Research and Development Institute (Aquatic Sciences), Adelaide. SARDI Publication No. F2019/000198-1. SARDI Research Report Series No.1024. . SARDI, Adelaide. Tanner, J. E., M. Theil, and D. Fotheringham. 2012. Seagrass Condition Monitoring: Yankalilla Bay, Light River and Encounter Bay. Final report prepared for the Adelaide and Mount Lofty Ranges Natural Resources Management Board., South Australian Research and Development Institute (Aquatic Sciences), Adelaide. Tanner, J. E., M. Theil, and D. Fotheringham. 2014b. Seagrass Condition Monitoring: Encounter Bay and Port Adelaide. Final report prepared for the Adelaide and Mount Lofty Ranges Natural Resources Management Board. South Australian Research and Development Institute (Aquatic Sciences), Adelaide. SARDI Publication No. F2012/000139-2. SARDI Research Report Series No. 799. Waycott, M., C. M. Duarte, T. J. B. Carruthers, R. J. Orth, W. C. Dennison, S. Olyarnik, A. Calladine, J. W. Fourqurean, K. L. Heck, A. R. Hughes, G. A. Kendrick, W. J. Kenworthy, F. T. Short, and S. L. Williams. 2009. Accelerating loss of seagrasses across the globe threatens coastal ecosystems. Proceedings of the National Academy of Sciences of the United States of America 106:12377-12381. Wear, R. J., A. Eaton, J. E. Tanner, and S. Murray-Jones. 2006. The impact of drain discharges on seagrass beds in the South East of South Australia. Final Report Prepared for the South East Natural Resource Consultative Committee and the South East Catchment Water Management Board. South Australian Research and Development Institute (Aquatic Sciences) and the Department for Environment and Heritage, Coast Protection Branch, Adelaide. RD04/0229-3. . South Australian Research and Development Institute (Aquatic Sciences), Adelaide.

28 Tanner (2020) 2020 seagrass condition monitoring

Westphalen, G., G. Collings, R. Wear, M. Fernandes, S. Bryars, and A. Cheshire. 2004. A review of seagrass loss on the Adelaide metropolitan coastline. ACWS Technical Report No. 2 prepared for the Adelaide Coastal Waters Study Steering Committee. South Australian Research and Development Institute (Aquatic Sciences) Publication No. RD04/0073, Adelaide.

29