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31

Company Document No L384-AW-REP-10047 Revision No 0

Document Title Seagrass Dark Recovery Experiment Report

Contract/Purchase Order No 800429

Equipment Tag No

Contractor Document No EL1112047 Contractors Rev No 0

Contractor shall ensure that documents have been fully checked and approved prior to submittal to INPEX.

Prepared Isabel Jimenez Checked Joanna Lamb Approved Craig Blount

Date 26/03/2013 Date 26/03/2013 Date 26/03/2013

Notes: Contractor Name, Address and Logo

Cardno (NSW/ACT) Pty Ltd

Level 9, 203 Pacific Highway

St Leonards NSW 2065

Cardno WA Pty Ltd

11 Harvest Terrace

West Perth WA 6008

Telephone: 08 9273 3888

Cardno NT Pty Ltd

Level 6 93 Mitchell St

Darwin NT 0800

A 18/03/2013 Issued for review

B 22/03/2013 Issued for review

0 26/03/2013 Issued for use

REV No DATE ISSUE PURPOSE

Revision History to Company’s Document Number

DOCUMENT NUMBER: C067-AG-FRM-0003 REV 2

Seagrass Dark Recovery Experiment

Ichthys Nearshore Environmental Monitoring Program L384-AW-REP-10047

Prepared for INPEX

March 2013

Seagrass Dark Recovery Experiment

Ichthys Nearshore Environmental Monitoring Program L384-AW-REP-10047

Seagrass Dark Recovery Experiment Ichthys Nearshore Environmental Monitoring Program

Prepared for INPEX Cardno ii

Document Information

Prepared for INPEX

Project Name Ichthys Nearshore Environmental Monitoring Program

File Reference L384-AW-REP-10047_0_Seagrass Dark Recovery Experiment Report.docx

Job Reference L384-AW-REP-10047

Date March 2013

Contact Information

Cardno (NSW/ACT) Pty Ltd Cardno (WA) Pty Ltd Cardno (NT) Pty Ltd

Level 9, The Forum 11 Harvest Terrace Level 6, 93 Mitchell Street

203 Pacific Highway West Perth WA 6005 Darwin NT 0800

St Leonards NSW 2065

Telephone: 02 9496 7700 Telephone: 08 9273 3888 Telephone: 08 8942 8200

Facsimile: 02 9499 3902 Facsimile: 08 9486 8664 Facsimile: 08 8942 8211

International: +61 2 9496 7700 International: +61 8 9273 3888 International: +61 8 8942 8211

www.cardno.com.au www.cardno.com.au www.cardno.com.au

Document Control

Version Date Author Author Initials

Reviewer Reviewer Initials

A 18/03/2013

Isabel Jimenez

Andrea Nicastro

Brendan Alderson

IJ

AN

BA

Joanna Lamb

Craig Blount

JL

CB

B 22/03/2013 Isabel Jimenez IJ Joanna Lamb

Craig Blount

JL

CB

0 26/03/2013 Isabel Jimenez IJ Joanna Lamb

Craig Blount

JL

CB

This document is produced by Cardno solely for the benefit and use by the client in accordance with the terms of the engagement for the performance of the Services. Cardno does not and shall not assume any responsibility or liability whatsoever to any third party arising out of any use or reliance by any third party on the content of this document.

http://www.cardno.com.au/

http://www.cardno.com.au/


Prepared for INPEX Cardno iii

Executive Summary

A Seagrass Monitoring Program has been developed to detect potential changes in seagrass health

indicators and infer whether any changes are a result of dredging and/or spoil disposal activities associated

with the Ichthys Project (the Project) in Darwin Harbour. The Dredging and Spoil Disposal Management

Plan – East Arm (DSDMP, INPEX 2012) sets out the framework for the Monitoring Program including a dark

recovery (shading) experiment (the Experiment) to mimic potential effects of dredging and to investigate

what the expected rate of recovery of seagrass may be.

The Experiment involved exposing seagrass plots to continuous darkness (the Shaded treatment) at two

sites (Casuarina and Fannie Bay) for a period of two months (24 September to 24 November 2012), followed

by a three month recovery phase (25 November 2012 to 24 February 2013). For comparison, seagrass was

also monitored in Control (unshaded) plots.

After two months exposure to darkness (Dark phase), quasi-complete mortality was observed in the Shaded

plots at both sites, whereas shoot densities in the Control plots remained similar to initial levels. No recovery

was observed in the Shaded plots in the three months following removal of the shade screens (i.e. in the

Recovery phase). Further, shoot density declined considerably in Control plots and decreased to

approximately 5% of initial levels by the end of the Experiment.

The severe decline of seagrass density in Control plots during the Recovery phase of the Experiment

coincided with widespread natural seasonal declines in seagrass distribution and abundance. Strong

westerly winds and increased wave heights were noted in January 2013 following Tropical Cyclone (TC)

Narelle which formed off the coast of Western Australia, and these were associated with increased sediment

resuspension and turbidity in shallow areas. The subsequent decrease in benthic light availability during this

period most likely accounted for the observed decline within the Control plots and would have prevented

seagrass potentially recovering in Shaded plots. Benthic light availability was reduced to 0% of surface

irradiance for two to three weeks, a level known to impact Halodule and Halophila sp. Hence, the similarity

in the rate and severity of the decline in the Shaded plots (during the Dark phase) to the decline in the

Control plots (during the Recovery phase) illustrated how a simulated dredging impact was comparable to

that of a natural, weather-related impact (i.e. an increase in turbidity during the wet season).

The results of the Experiment are consistent with expected seasonal growth patterns of ephemeral tropical

seagrasses such as Halodule and Halophila spp. (i.e. a wet season die-off). This is further supported by

results from monitoring and mapping surveys undertaken since June 2012 (Cardno 2012c, Cardno 2012d,

Geo Oceans 2013), which indicated that seagrass distribution in Darwin Harbour reached a seasonal peak

towards the end of the dry season (October), after which severe and widespread decline occurred during the

wet season.

Opportunistic field observations of new seagrass shoots over the shade screens indicate a potential for rapid

recovery should conditions be favourable; however it is unknown whether the shoots grew from seed or

vegetatively from fragments. Seagrass mapping results found a 250% increase in overall seagrass habitat

extent between June and October 2012, including a ten-fold habitat expansion at East Point, further

indicating the potential for rapid growth and recovery from declines potentially associated with dredging. The

Seagrass Monitoring Program will continue to monitor seagrass presence throughout the duration of the

dredging program.


Prepared for INPEX Cardno iv

Glossary

Term or Acromym Definition

Benthic On the seafloor

DSDMP Dredging and Spoil Disposal Management Plan – East Arm

DSV Dive Support Vessel

EIS Environmental Impact Statement

GPS Global Positioning System

HSE Health Safety Environment

Intertidal The portion of shoreline between low and high tide marks, that is intermittently

submerged

LAT Lowest Astronomical Tide

NEMP Nearshore Environmental Monitoring Plan

NTU Nephelometric Turbidity Units

PAR Photosynthetically Available Radiation

Permanova Permutational Analysis of Variance

Photoquadrat Virtual sampling unit of known dimensions within a photograph of the seafloor,

used to quantify seagrass density and percent cover

QA Quality Assurance

SE Standard error of the mean

Subtidal Waters below the low-tide mark

Turbidity An indication of water clarity


Prepared for INPEX Cardno v

Table of Contents

Executive Summary iii

Glossary iv

1 Introduction 7

1.1 Background 7

1.2 Requirement to Monitor Seagrass in Darwin Harbour 7

1.3 Objectives 7

2 Methodology 8

2.1 Vessels, Safety and Environmental Management 8

2.2 Sampling Design 8

2.2.1 Sites, Timing and Frequency of Surveys 8

2.2.2 Experimental Treatments and Plots 10

2.3 Measurement of Shoot Density 11

2.3.1 Image Analysis 11

2.3.2 Statistical Analysis 12

2.4 Water Quality and Light Availability 13

2.5 Quality Control 14

3 Results 15

3.1 Shoot Density 15

3.2 Water Quality and Light Availability 16

3.3 Quality Control 16

4 Discussion 19

5 Conclusions 21

6 Acknowledgements 22

7 References 23

Tables

Table 2-1 Co-ordinates of dark recovery experiment sites 8

Table 2-2 Survey dates for the Experiment and corresponding activities 8

Table 2-3 Explanation of factors used in the statistical analyses 13

Table 2-4 Terms used in describing the outcomes of the statistical analyses 13

Table 3-1 Mean and standard error (SE) of shoot density (Shoots m-2

) for Halodule and Halophila sp. during the Dark and Recovery phases at A) Casuarina Beach and B) Fannie Bay 15

Table 3-2 Summary of Permanova for seagrass shoot density showing the level of significance. * = P(perm) < 0.05; - = redundant term, ns = not significant. 16


Prepared for INPEX Cardno vi

Figures

Figure 2-1 Location of dark recovery experiment sites 9

Figure 2-2 Example of shade screen plot installed at Casuarina Beach showing the reinforced pegs that anchored the shade screen to the seabed and swim line linking each plot 10

Figure 2-3 Diver taking images of seagrasses within plots at Casuarina Beach (quadrat can be seen on the seabed) 11

Figure 2-4 Quadrat set-up showing the individual sub-quadrats within the larger 1 m2 quadrat (the field of

view of the camera was slightly larger than each sub-quadrat) 12

Figure 3-1 Mean seagrass shoot density (±SE) for Shaded and Control plots during two months of dark exposure (grey shaded area) and three months of recovery (clear area) at Casuarina and Fannie Bay 16

Figure 3-2 Time-series of turbidity, PAR (mol photons m-2

s-1

) and water temperature at the Casuarina Water Quality monitoring site from 24 September 2012 to 15 February 2013 17


s-1

) and water temperature at the Fannie Bay Water Quality monitoring site (Site 01) from 24 September 2012 to 15 February 2013 18

Figure 4-1 Field observation of Halodule sp. growing in sediment layer deposited over a shade screen at Casuarina (23 November 2012). Image scale approximately 9 cm x 12 cm 20

Appendices

Appendix A Results of Statistical Analyses 24

Appendix B Water Quality Summary Data 27

Appendix C Quality Control 29


Prepared for INPEX Cardno 7

1 Introduction

1.1 Background

INPEX is the operator of the Ichthys Gas Field Development Project (the Project). The Project comprises the

development of offshore production facilities at the Ichthys Field in the Browse Basin, some 820 km west-

south-west of Darwin, an 889 km long subsea gas export pipeline (GEP) and an onshore processing facility

and product loading jetty at Blaydin Point on Middle Arm Peninsula in Darwin Harbour. To support the

nearshore infrastructure at Blaydin Point, dredging works will be carried out to extend safe shipping access

from near East Arm Wharf to the new product loading facilities at Blaydin Point, these will be supported by

piles driven into the sediment. A trench will also be dredged to seat and protect the GEP for the Darwin

Harbour portion of its total length. Dredged material will be disposed at the spoil ground which is located

approximately 12 km north-west of Lee Point. A detailed description of the dredging and spoil disposal

methodology is provided in Section 2 of the DSDMP (INPEX 2012).

1.2 Requirement to Monitor Seagrass in Darwin Harbour

Following an Environmental Impact Statement (EIS) (INPEX 2011), the Project was approved subject to

conditions that included monitoring for potential effects of dredging or spoil disposal on local ecosystems

(including seagrasses) and potentially vulnerable populations. Dredging can impact seagrasses directly

through physical removal or smothering and indirectly through the creation of turbid plumes and

sedimentation. As seagrasses are photosynthetic, reduction of light from increased turbidity may affect their

growth and survival. Excessive sedimentation and settlement of suspended material on leaf blades may also

interfere with photosynthesis (McMahon et al. 2011).

The DSDMP sets out a monitoring program to examine the potential impact on seagrasses from dredging

and spoil disposal activities associated with the Project in and around Darwin Harbour, including a seagrass

recovery (shading) experiment to mimic potential effects of dredging and to investigate what the expected

rate of recovery of seagrass may be (see Section 8.3.2 of the DSDMP). The Nearshore Environmental

Management Plan (NEMP) establishes the methodology and indicators for the monitoring program and the

Experiment (Cardno 2012a).

1.3 Objectives

The DSDMP sets out the objectives of the Experiment as follows:

> Gain an understanding of the potential for seagrasses in Darwin Harbour (and surrounds) to recover from

dredging-related impacts; and

> Provide supporting data that may be used in the event of a Level 3 trigger exceedance to determine what

level of response is appropriate and practicable.

The methodology was designed to have sufficient replication to determine whether seagrass can recover

from potential dredging related impacts, accounting for any spatial variation in rates of recovery.

This report describes the results of the Experiment that was undertaken between 24 September 2012 and

24 February 2013.



2 Methodology

2.1 Vessels, Safety and Environmental Management

Field work conducted during the Experiment was carried out from the DSV Josh Sarelle and DSV Bushman

operated by Neptune Diving Services (NDS). All work was completed in accordance with the Project Health

Safety and Environment (HSE) Plan. Diving was conducted using a combination of Self Contained

Underwater Breathing Apparatus (SCUBA) (Australian Diver Accreditation Scheme (ADAS) Level AS

2815.1) and surface supply breathing apparatus (SSBA) (ADAS Level AS 2815.2) in accordance with

Australia/New Zealand Standard Occupational Diving Operations Part 1: Standard Operational Practice

(ASNZS 2299.1:2007). Data were collected by scientific divers and site installation and maintenance was

completed by commercial divers from NDS.

2.2 Sampling Design

2.2.1 Sites, Timing and Frequency of Surveys

The Experiment was undertaken in seagrass beds at Casuarina Beach and Fannie Bay (Table 2-1; Figure

2-1). Consistent with the methodology described in the NEMP, these sites provided information for varying

seagrass density covers as seagrasses at Casuarina Beach tend to be of lower density than those within

Fannie Bay. Both locations lie outside of the Zone of Moderate Impact for turbidity and sedimentation

impacts to seagrass predicted to occur as a result of the Project’s dredging and spoil disposal activities (refer

to Section 6.5 of the DSDMP).

Table 2-1 Co-ordinates of dark recovery experiment sites

Sites Latitude (°S) Longitude (°E)

Casuarina Beach -12.361783° 130.853783°

Fannie Bay -12.431450° 130.830150°

The Experiment involved six surveys undertaken at monthly intervals (Table 2-2), with Survey 1 being the

initial Experiment set up. There were two phases of the Experiment: Dark and Recovery. The ‘Dark’ phase

(two months) simulated conditions of no light (potentially associated with great turbidity). The ‘Recovery’

phase simulated recovery of seagrass from two months of ’dark’ conditions. As stated in the NEMP, plots

were merely inspected for the presence of seagrass after one month Dark exposure (Survey 2), and shoot

density was quantified at the end of the Dark phase and start of the Recovery phase (Survey 3).

Due to poor weather conditions (strong westerly winds and large swell) sampling was unable to be

completed during Survey 5 (i.e. the two month recovery survey).

Table 2-2 Survey dates for the Experiment and corresponding activities

Recovery Experiment Sampling Dates Phase

Survey 1 (Site Set up) 24 to 26 September 2012 Initial set up

Survey 2 24 to 25 October 2012 1 month Dark

Survey 3 20 to 24 November 2012 2 month Dark

Survey 4 20 to 24 December 2012 1 month Recovery

Survey 5 21 to 24 January 2013 2 month Recovery

Survey 6 22 to 24 February 2013 3 month Recovery



Figure 2-1 Location of dark recovery experiment sites



2.2.2 Experimental Treatments and Plots

At each site (Casuarina Beach and Fannie Bay) divers installed five replicate 1 m2 plots on the seabed in two

experimental treatments (‘Shaded’ and ‘Control’) for a total of 20 plots. At each site, plots were placed

approximately 3 m apart and were connected with a swim line to assist the divers in relocation for

subsequent surveys. Each plot was marked out with 6 mm silver rope, pegged down onto the seabed with

steel reinforced pegs and numbered tags were installed on each plot (Figure 2-2). The allocation of plots to

treatments was done alternately to ensure that all plots from a particular treatment were not grouped

together.

Plots in the ‘Shaded’ treatment were covered by a shade screen for the first two months of the Experiment

(Dark phase: Surveys 1 to 3). The shade screen consisted of shade mesh (which was rated to exclude 95%

of light) attached to a reinforced steel reo-bar frame, approximately 1 m2 in size. The frame was secured to

the seabed at each corner and along the edges with steel reinforced pegs. Control plots remained

uncovered for the duration of the Experiment. Two additional shaded indicator plots (i.e. with shade screens

installed) were installed at each site to verify the loss of seagrass leaves and rhizomes throughout the Dark

phase of the Experiment. Seagrass in these indicator plots was monitored without disturbing the actual

Experimental plots prior to the start of the Recovery phase (i.e. when shade screens were removed). To

prevent surrounding seagrasses translocating nutrients into the treatment plots, all plots were ‘gardened’

around the perimeter of the frames at each survey.

Although the aboveground biomass of seagrass within the shaded indicator plots was greatly reduced

following the first month of the Experiment, it was decided that the shade screens be left in place for an

additional month to ensure all sub-surface seagrass biomass (i.e. rhizomes) underneath the shade screen

had disappeared. During Survey 3, the indicator plots exhibited the complete loss of aboveground biomass

and no presence of live rhizome material was apparent; the screens were then removed for the recovery

phase (Surveys 4 to 6).

Figure 2-2 Example of shade screen plot installed at Casuarina Beach showing the reinforced pegs that anchored the shade screen to the seabed and swim line linking each plot



2.3 Measurement of Shoot Density

2.3.1 Image Analysis

In Survey 1, immediately prior to the installation of the shade screens, plots were surveyed to assess initial

seagrass conditions and to estimate seagrass shoot density. Sampling was undertaken using photography.

A 1 m2 quadrat was placed over the plot and images were taken using a Canon G12 digital camera with

underwater housing mounted to a camera frame (Figure 2-3).

Figure 2-3 Diver taking images of seagrasses within plots at Casuarina Beach (quadrat can be seen on the seabed)

To ensure sufficient image quality for analysis, the 1 m2 quadrats were divided into eight smaller adjoining

frames (sub-quadrats) each covering 0.075 m2 (Figure 2-4). The frame held the camera approximately

43 cm from the seabed, ensuring that each sub-quadrat was captured in the camera’s field of view and

resulting in eight images of each plot. The total area covered by the eight sub-quadrats (i.e. the area

surveyed within the larger 1 m2 quadrat) was 0.6 m

2. Initially, still images were captured by taking

photographs of each sub-quadrat; however, this was often difficult due to the presence of wave surges

(especially at Casuarina Beach), which at times prevented the diver from taking suitable quality still images.

This problem was overcome by taking video footage and extracting still images of each sub-quadrat from the

video footage prior to processing. In the event that water clarity was poor and no suitable images of plots

could be captured, in situ diver counts of seagrass shoots in each sub-quadrat were also conducted to

ensure that data was collected for that particular plot/site.

Each image was colour corrected prior to processing to enhance image quality and allow for a more accurate

estimation of seagrass shoot density within each sub-quadrat.



The number of shoots for each seagrass species within eight sub-quadrats within plots was counted and

recorded for all replicates within both treatments and then added together to provide a count for the entire

quadrat. Shoot counts for individual species were converted to a density measurement by dividing the

recorded shoot count for each replicate plot by 0.6 m2 (i.e. the survey area of the larger quadrat).

Figure 2-4 Quadrat set-up showing the individual sub-quadrats within the larger 1 m2 quadrat (the

field of view of the camera was slightly larger than each sub-quadrat)

2.3.2 Statistical Analysis

Statistical analyses were undertaken on total seagrass shoot density.

Repeated Measures Analysis of Variance was undertaken using PERMANOVA+ software in PRIMER v6 to

examine the rate of seagrass recovery from shading-induced disturbance. The analyses focused on testing

the null hypothesis that there were no differences in seagrass shoot density among surveys, treatments or

sites and, in effect, examining the rate of recovery of seagrass from a disturbance where light had been

reduced. Factors in the analysis were:

> Survey (fixed, orthogonal) – 4 levels (Surveys 1, 3, 4 and 6);

> Site (random, orthogonal) – 2 levels (Fannie Bay and Casuarina Beach);

> Treatment (fixed, orthogonal) – 2 levels (Shaded and Control); and

> Plots (nested within Site and Treatment, random) – repeated measures term.

Statistical analyses were based on dissimilarity matrices created using Euclidian distance measures.

Results of the statistical analyses (i.e. rejection of null hypotheses) were interpreted through a series of

statistically significant main factors and interactions (Table 2-3 and Table 2-4). Where significant

interactions or main factor effects were detected, post hoc permutational t-tests using PERMANOVA+

software were carried out to identify the levels of factors in which differences occurred. No multiple test

corrections were applied to t-test results, consistent with a conservative statistical approach and in line with

the Precautionary Principle.

Sub-quadrat 1

Sub-quadrat 2

Sub-quadrat 3

Sub-quadrat 4

Sub-quadrat 5

Sub-quadrat 6

Sub-quadrat 7

Sub-quadrat 8



Table 2-3 Explanation of factors used in the statistical analyses

Component of Variation Interpretation

Survey Indicates a significant difference between Surveys (Survey 1 to Survey 6)

independent of Site and Treatment.

Site Indicates larger-scale significant variability between Sites (Fannie Bay and

Casuarina Beach) independent of Survey and Treatment.

Treatment Indicates a significant difference between Treatments (Shaded and Control)

independent of Surveys and Sites.

Plot (Site x Treatment) Indicates smaller-scale significant variability among Plots within Sites and

Treatments independent of Survey.

Survey x Site Indicates differences between Surveys are dependent on the Site and vice

versa.

Survey x Treatment

Indicates differences between Surveys are dependent on the Treatment and

vice versa. Indicative of a shading effect and recovery of seagrasses

consistent for both Sites.

Site x Treatment Indicates the variability among Sites is dependent on the Treatment and vice

versa.

Survey x Site x Treatment

Indicates differences among Surveys are dependent on both Sites and

Treatment and vice versa. Indicative of a shading effect and recovery of

seagrasses, although dependant on the Site.

Residual

This term is a measure of the variation in the data not explained by the

variation attributed to the main factors in the experimental model (i.e. Survey,

Sites, Treatment, Plots and their associated interactions).

Table 2-4 Terms used in describing the outcomes of the statistical analyses

Outcome (code) Interpretation

Redundant term (-) A term becomes redundant if a lower order interaction including that term is

significant.

Non-significant (ns)

Non-significant describes the convention by which a statistical comparison is

deemed not to be an actual effect (i.e. accept the null hypothesis that there is

no effect). Here the cut-off point was set at P > 0.05.

Significant (asterisks)

The statistical comparison indicating the presence of an actual effect. These

signify the probability (P) of an effect being considered to actually occur.

Here, * = P < 0.05, ** = P < 0.01, *** = P < 0.001. These indicate that the

likelihood of an effect occurring by chance alone (and therefore not explained

by the factor being considered) would be 5 in 100, 1 in 100, or 1 in 1000

respectively. By convention, significant terms are indicated in tables in bold

typeface.

2.4 Water Quality and Light Availability

Time series measurements of temperature (oC), turbidity (NTU) and underwater light (PAR, (mol photons

m-2

s-1

) taken at 15 minute intervals were used to assist the interpretation of temporal changes in seagrass

density in the Control plots throughout the Experiment and in the Shaded plots during the Recovery Phase.

Data were recorded at Water Quality Monitoring sites at Fannie Bay and Casuarina (Figure 2-1) for the

duration of the Experiment (Appendix B). The monitoring stations, established as part of the Water Quality

and Subtidal Sedimentation Monitoring Program (Cardno 2012b), were installed at approximately -3m LAT

offshore from the Experimental sites and at a height of approximately 1.5 m above the seabed. Telemetered

data were used for the period 13 to 24 February 2013 at Casuarina as the logged data had not been

recovered from the loggers at the time of reporting.



2.5 Quality Control

The Quality Control processes followed in the field and in the office by all Project personnel (i.e. field and

office staff) in order to complete the scope of work to a consistent and high quality are described in detail in

the Method Statement and in the Work Instructions (Cardno 2012c). Results of Quality Control procedures

are given in Appendix C.



3 Results

3.1 Shoot Density

Most of the seagrass recorded in plots was Halodule sp. (Table 3-1). Halophila sp. was recorded at both

sites at the start of the Experiment but only at low densities and it accounted for less than 5% of total

seagrass density at that time. Halophila sp. had disappeared from both Control and Shaded plots by the end

of the Dark phase; therefore, results described hereafter pertain mostly to Halodule sp. Changes in total

seagrass (both species combined) shoot density in Shaded and Control plots during the Dark and the

Recovery phases are illustrated in Figure 3-1.

Significant differences in seagrass shoot density between Control and Shaded treatments depended on the

Survey and Site (p<0.05, Table 3-2). Two months after the start of the Experiment, the Shaded plots were

almost completely unvegetated (Figure 3-1 and Table 3-1) and differed significantly from the Control plots,

where seagrass shoot density remained similar to initial levels (pairwise comparisons, Appendix A).

Seagrass in the Shaded plots showed no sign of recovery in the three months following removal of the shade

screens. During this time, seagrass density in the Control plots declined steadily and reached values of

approximately 3 to 5% of initial levels by the end of the Experiment. The timing of the decline in the Control

plots differed slightly among the two sites, occurring in the first month of the recovery phase at Fannie Bay

and within the last two months at Casuarina Beach (Figure 3-1).

Table 3-1 Mean and standard error (SE) of shoot density (Shoots m-2

) for Halodule and Halophila sp. during the Dark and Recovery phases at A) Casuarina Beach and B) Fannie Bay

A. Casuarina Beach

Species Treatment

Start

September 2012

2 Months Dark

November 2012

1 Month Recovery

December 2013

3 Month Recovery

February 2013

Halodule sp. Control 414 ± 105

272 ± 33

374 ± 50

12 ± 4

Shaded 573 ± 84

2 ± 2

6 ± 2

0 ± 0

Halophila sp. Control 10 ± 7

0 ± 0

0 ± 0

0 ± 0

Shaded 29 ± 15 0 ± 0 0 ± 0 0 ± 0

B. Fannie Bay

Species Treatment Start 2 Months Dark

1 Month Recovery

3 Month Recovery

Halodule sp. Control 649 ± 182

581 ± 203

154 ± 44

30 ± 13

Shaded 479 ± 117

0 ± 0

0 ± 0

0 ± 0

Halophila sp. Control 4 ± 4

0 ± 0

0 ± 0

0 ± 0

Shaded 1 ± 1 0 ± 0 0 ± 0 0 ± 0



Figure 3-1 Mean seagrass shoot density (±SE) for Shaded and Control plots during two months of dark exposure (grey shaded area) and three months of recovery (clear area) at Casuarina and Fannie Bay

Table 3-2 Summary of Permanova for seagrass shoot density showing the level of significance. * = P(perm) < 0.05; - = redundant term, ns = not significant.

Source of Variation Seagrass Shoot Density

Survey −

Site −

Treatment −

Survey x Site ns

Survey x Treatment ns

Site x Treatment ns

Plot (Site x Treatment) ns

Survey x Site x Treatment *

3.2 Water Quality and Light Availability

Time series of turbidity (NTU), light (PAR) and water temperature measured at Water Quality monitoring

stations at Casuarina Beach and Fannie Bay are shown in Figure 3-2 and Figure 3-3, respectively.

Turbidity levels before January 2013 were generally below 10 NTU at both sites. This increased

considerably from 10 January 2013, coinciding with strong westerly winds and increased wave heights

associated with TC Narelle. As a result, PAR was greatly reduced for two to three weeks in late January

2013, approximately two months into the recovery phase.

3.3 Quality Control

The Quality Control results for data checking are presented in Appendix C.

0

200

400

600

800

1000

24-Sep-12 24-Oct-12 24-Nov-12 24-Dec-12 24-Jan-13 23-Feb-13

Sh

oo

ts m

-2

Casuarina Control

Casuarina Shaded

Fannie Bay Control

Fannie Bay Shaded




s-1

) and water temperature at the Casuarina Water Quality monitoring site from 24 September 2012 to 15 February 2013




s-1

) and water temperature at the Fannie Bay Water Quality monitoring site (Site 01) from 24 September 2012 to 15 February 2013



4 Discussion

The aim of the Experiment was to investigate the rate of recovery of seagrass in Darwin Harbour by

simulating losses potentially related to dredging-induced increases in turbidity. The Experiment involved

exposing seagrass plots to continuous darkness (the Shaded treatment) at two sites (Casuarina and Fannie

Bay) for a period of two months (The Dark phase - 24 September to 24 November 2012), followed by a three

month period of monitoring (the Recovery phase - 25 November 2012 to 24 February 2013).

In the Dark phase of the Experiment, seagrass shoot density declined to zero after two months of continued

darkness, with no significant change at the Control plots. However, there was virtually no recovery of

seagrass in the Shaded plots in the following three months of the Recovery phase.

As seagrass shoot density in the Control plots also gradually declined to zero in the Recovery phase of the

Experiment, it is likely that seagrass at the sites was:

> in a natural phase of decline; or

> affected by a natural disturbance.

Possible reasons for natural declines in seagrass distribution and abundance can be inferred from data

collected in the Recovery Phase on turbidity, benthic light availability and weather conditions. Turbidity

increased substantially in January 2013 associated with TC Narelle and this resulted in complete light

attenuation at both Casuarina and Fannie Bay for approximately three weeks. Analogous shading

experiments have demonstrated that, should extreme turbidity levels reduce light below the requirements of

seagrass for more than approximately three weeks, deleterious effects on seagrass condition may occur.

Results of shading studies in Gladstone Harbour (Chartrand et al. 2010) indicate that changes in morphology

can be seen from two weeks (Halophila spp.) to one month (Halodule spp.) following exposure to low light.

Different species respond differently to declines in benthic light availability as a result of increased turbidity

and sedimentation (McMahon et al. 2011, Duarte et al. 2006, Erftemeijer and Lewis 2006, Larkum et al.

2006, Vermaat et al. 1997). Halophila spp. have been found to tolerate light levels as low as 3 to 8 % of

surface irradiance (SI), compared to 5 to 30 % SI for Halodule spp. (Erftemeijer et al. 2006).

In shading experiments in the Gulf of Carpentaria (Longstaff and Dennison 1999), plant death in Halophila

ovalis occurred after 38 days exposure to darkness, while Halodule pinifolia survived 100 days. Therefore,

the reduction in benthic light availability during the Recovery phase (to 0% SI for approximately three weeks)

would be expected to impact on seagrass growth within the Control plots, and would most certainly have

prevented recovery in the treatment plots. Hence, the similarity in the rate and severity of the decline in the

Shaded plots (during the Dark phase) to the decline in the Control plots (during the Recovery phase)

illustrated how a simulated dredging impact was comparable to that of a natural, weather related impact

(i.e. an increase in turbidity during the wet season).

Light and turbidity measurements from the Water Quality monitoring stations provided contextual information

on temporal changes in light availability near the experimental sites. It should be noted that the sites were

located within intertidal seagrass beds further inshore from the monitoring stations. Wave action at these

shallower sites may cause further sediment resuspension, which could result in greater inshore turbidity.

The differing rates of seagrass decline observed at Casuarina Beach and Fannie Bay may have been

associated with localised differences in turbidity, potentially not evident at the offshore stations. Other

factors that may have impacted on the condition of seagrass during the Recovery phase included physical

impact from wave action and sedimentation from wind and wave driven resuspension associated with strong

westerly winds, as recorded during that period (Cardno 2013).

Results from monitoring and mapping surveys undertaken since June 2012 (Cardno 2012c, Cardno 2012d,

Geo Oceans 2013) indicate that a seasonal peak in seagrass distribution in Darwin Harbour is reached

towards the end of the dry season in October/November. In particular, results from towed video mapping

surveys completed in February 2013 indicate that seagrass distribution and abundance across the foreshore

of Darwin Harbour has declined by approximately 75% since October 2012 (Geo Oceans 2013). Results are

consistent with expected seasonal growth patterns of ephemeral tropical seagrasses such as Halodule and



Halophila spp. (Coles et al. 2011), likely characterised by wet season die-offs followed by recovery in the dry

season.

Some evidence of recovery occurred at the end of the Dark phase (Survey 3), where divers observed shoots

of Halodule sp. growing in an estimated 2 to 3 cm of sediment deposited on shade screens (Figure 4-1).

Upon removal of the shade screens for the start of the recovery phase, no below ground biomass was

visible, indicating that growth had most likely occurred in the overlaying sediment rather than from surviving

seagrass below. Considering that the sediment layer would have deposited over a period of a month since

the previous survey, the observed new growth would have occurred within a timeframe of one week to one

month. While it is unknown whether the shoots grew from seed or vegetatively from fragments, these

observations indicate a potential for rapid growth and recovery should conditions be favourable. Seagrass

mapping results found a 250% increase in overall seagrass habitat extent between June and October 2012,

including a ten-fold habitat expansion at East Point, further indicating rapid growth and recovery potential

during the dry season.

Figure 4-1 Field observation of Halodule sp. growing in sediment layer deposited over a shade screen at Casuarina (23 November 2012). Image scale approximately 9 cm x 12 cm



5 Conclusions

No seagrass recovery was observed at the conclusion of the Recovery Experiment undertaken between

September 2012 and February 2013. The Recovery phase of the Experiment coincided with a natural

weather-related reduction of light to the seabed, which most likely accounted for declines in seagrass density

in Control plots and the absence of recovery in the Shaded plots. The period of elevated turbidity and

reduced benthic light associated with the passage of TC Narelle off the northwest coast of Australia was

comparable both in intensity and duration with potential dredging impacts mimicked in the Experiment.

Recent habitat mapping results indicate that rapid seagrass growth and habitat expansion occurs in the dry

season between June and October, after which severe and widespread declines occur during the wet

season. This is consistent with expected seasonal growth patterns of ephemeral tropical seagrasses such

as Halodule and Halophila spp. This, together with opportunistic field observations of new seagrass shoots

over the shade screens, indicates a potential for rapid recovery should conditions be favourable.



6 Acknowledgements

This report was written by Isabel Jimenez, Andrea Nicastro, and Brendan Alderson; Yesmin Chikhani

assisted with table production. Fieldwork was carried out by Brendan Alderson, Hamish Maitland, Kane

Organ, and Daniel Pygas. Image analysis was carried out by Yesmin Chikhani and Blaise Bratter. The

report was reviewed by Joanna Lamb and Craig Blount.



7 References

Cardno (2012a). Ichthys Project – Nearshore Environmental Monitoring Plan. Report for INPEX, Cardno (NSW/ACT) Pty Ltd, Sydney.

Cardno (2012b). Bimontly Water Quality & Subtidal Sedimentation Report: Dredging Report 1 - Ichthys Nearshore Environmental Monitoring Program. Report for INPEX, Cardno (NSW/ACT) Pty Ltd, Sydney.

Cardno (2012c). Seagrass Monitoring Program Baseline Report – Ichthys Nearshore Environmental Monitoring Program. Report for INPEX, Cardno Ecology Lab Pty Ltd, Sydney.

Cardno (2012d). Bimonthly Seagrass Monitoring Report- Dredging Report 1 - Ichthys Nearshore Environmental Monitoring Program. Report for INPEX, Cardno Ecology Lab Pty Ltd, Sydney.

Cardno (2013). Fortnightly Water Quality Report - Weeks 20/21: 7 to 20 January 2013 - Ichthys Nearshore Environmental Monitoring Program. Report for INPEX, Cardno (NSW/ACT) Pty Ltd, Sydney.

Chartrand, K.M, McKenna, S.A, Petrou, K, Jimenez-Denness, I, Franklin, J, Sankey, T.L, Hedge, S.A, Rasheed, M.A and Ralph, P.J (2010). Port Curtis Benthic Primary Producer Habitat Assessment and Health Studies Update: Interim Report December 2010. DEEDI Publication. Fisheries Queensland, Cairns.

Coles, R and Mackenzie, L (2004). Trigger points and achieving targets for managers. Paper presented at workshop session on management issues during the ISBW-6 workshop, Seagrass 2004 Conference, Townsville, 24 September – 1 October 2004.

Coles, R., Grech, A., Rasheed, M., McKenzie, L., Unsworth, R., & Short, F. (2011). Seagrass ecology and threats in the tropical Indo-Pacific bioregion.

Duarte, C.M, Fourqurean, J.W, Krause-Jensen, D and Olesen, B (2006). Dynamics of seagrass stability and change, in: Larkum, A.W.D. et al. (Ed.) (2006). Seagrasses: biology, ecology and conservation. pp. 271-294

Erftmeijer, P.L.A and Lewis, R.R.R (2006). Environmental impacts of dredging on seagrasses: A review. Marine Pollution Bulletin 52: 1553-1572.

Geo Oceans (2013). Seagrass Habitat Monitoring Survey 3 February 2013 - Ichthys Nearshore Environmental Monitoring Program. Draft Technical Report for Cardno Ecology Lab on behalf of INPEX.

INPEX (2011). Ichthys Gas Field Development Project, Supplement to the Draft Environmental Impact Statement.

INPEX (2012). Dredging and Spoil Disposal Management Plan – East Arm.

Larkum, W.D, Orth, R and Duarte, C.M (2006). Seagrasses: Biology, Ecology and Conservation. Springer, Dordrecht, The Netherlands.

Longstaff, B.J and Denison, W.C (1999). Seagrass survival during pulsed turbidity events: the effects of light deprivation on the seagrasses Halodule pinifolia and Halophila ovalis. Aquatic Botany 65: 105-121.

McMahon, K, Lavery, P.S and Mulligan, M (2011). Recovery from the impact of light reduction on the seagrass Amphibolis griffithii, insights for dredging management. Marine Pollution Bulletin 62: 270-283.

Vermaat, J.E, Agawin, N.S.R, Fortes, M.D and Uri, J.S (1997). The capacity of seagrasses to survive increased turbidity and siltation: the significance of growth form and light use. Ambio 25 (2) 499-504.



Ichthys Nearshore Environmental Monitoring Program

APPENDIX A RESULTS OF STATISTICAL ANALYSES



Appendix A-1 Results of PERMANOVA testing for differences in total seagrass shoot density. Significant (P(perm) < 0.05) terms in bold. Monte Carlo (MC) simulation was used to calculate P values where unique permutations < 100

Source df SS MS Pseudo-F P(perm) Unique perms P(MC)

Su 3 3072400 1024100 16.803 0.0412 840 0.0205

Si 1 13347 13347 0.26299 0.613 9810 0.6215

Tr 1 620110 620110 9.0599 0.3345 6 0.2078

SuxSi 3 182850 60951 2.0199 0.123 9947 0.1217

SuxTr 3 627520 209170 2.3676 0.2532 9964 0.2433

SixTr 1 68445 68445 1.3486 0.2741 9816 0.2533

Pl(SIxTr) 16 812030 50752 1.6819 0.0866 9931 0.0847

SuxSixTr 3 265050 88350 2.9278 0.0436 9952 0.0435

Res 48 1448400 30176

Total 79 7110200

Pairwise Comparison

Term 'SuxLoxTr' for pairs of levels of factor 'Treatment'

Groups t P(perm) Unique perms P(MC)

Control, Shaded 1.3036 0.2001 114 0.2291

Within level 'RE01' of factor 'Survey'

Within level 'Casuarina' of factor 'Site'

Control, Shaded 0.80 0.4469 113 0.4411


Within level 'Fannie Bay' of factor 'Site'

Control, Shaded 8.04 0.01 53 0.0003



Control, Shaded 2.87 0.0081 16 0.0216



Control, Shaded 7.33 0.0087 72 0.0004



Control, Shaded 3.50 0.0088 16 0.0085



Control, Shaded 3.0697 0.0073 10 0.0159



Control, Shaded 2.2953 0.1719 3 0.0498





Pairwise Comparison

Term 'SuxSixTr' for pairs of levels of factor 'Survey'

Groups t P(perm) Unique perms P(MC)

RE01, RE03 1.80 0.1611 7117 0.1541

RE01, RE04 0.41 0.6989 7092 0.7072

RE01, RE06 4.0111 0.0078 5491 0.0154

RE03, RE04 1.4254 0.2482 5302 0.2268

RE03, RE06 7.0475 0.0076 5384 0.002

RE04, RE06 7.2394 0.0019 5414 0.0023


Within level 'Control' of factor 'Treatment'

RE01, RE03 6.5163 0.0028 2239 0.0036

RE01, RE04 6.4514 0.0054 5012 0.0052

RE01, RE06 6.5166 0.0087 154 0.0045

RE03, RE04 1.1083 0.333 71 0.3304

RE03, RE06 1.4289 0.4379 3 0.2315

RE04, RE06 2.2953 0.0434 20 0.083


Within level 'Shaded' of factor 'Treatment'

RE01, RE03 0.32384 0.7662 7180 0.7661

RE01, RE04 2.7417 0.0569 7293 0.053

RE01, RE06 3.3268 0.0255 3431 0.0299

RE03, RE04 2.6658 0.0372 7193 0.0566

RE03, RE06 2.8556 0.0018 3534 0.0408

RE04, RE06 3.7375 0.0073 3453 0.0207


Within level 'Control' of factor 'Treatment'

RE01, RE03 4.1065 0.0088 155 0.0148

RE01, RE04 4.1065 0.006 155 0.0141

RE01, RE06 4.1065 0.0081 155 0.0162

RE03, RE04 Denominator is 0




Within level 'Shaded' of factor 'Treatment'




APPENDIX B WATER QUALITY SUMMARY DATA



Appendix B-1 Summary of daily average turbidity (NTU), water temperature (°C) and PAR (mol photons m

-2 s

-1) (mean; min; maximum and percentile of occurrence) at Fannie Bay and Casuarina

monitoring stations from 24 September 2012 to 24 February 2013

A. Turbidity Mean Min 5pct 10pct 20pct 50pct 80pct 90pct 95pct Max From To

Fannie Bay 9.1 0.9 1.6 2 2.7 5.6 13.4 20.7 29.4 55.5 24/09/12 24/02/13

Casuarina 7.4 0.7 1.2 1.3 1.6 2.4 5.6 23.2 39.1 71.9 24/09/12 24/02/13

B. Temperature Mean Min 5pct 10pct 20pct 50pct 80pct 90pct 95pct Max From To

Fannie Bay 30.9 28.8 29.1 29.5 30.1 31 31.8 32 32.1 32.2 24/09/12 24/02/13

Casuarina 30.9 28.7 29.2 29.6 30.1 31 31.8 32.1 32.2 32.3 24/09/12 24/02/13

C. PAR Mean Min 5pct 10pct 20pct 50pct 80pct 90pct 95pct Max From To

Fannie Bay 84.5 3.2 13.7 25.4 36.9 79 126.3 154.9 173.4 221.1 24/09/12 24/02/13

Casuarina 98.1 1.9 5.7 33 57.4 96 143.4 170.7 182.6 232.9 24/09/12 24/02/13




APPENDIX C QUALITY CONTROL



Appendix C-1 Quality Control results for data checking of seagrass shoot density determined from diver counts and still images, against video footage of experimental plots at Casuarina and Fannie Bay

Site Survey Plot

No

Shoot Density

(Shoots m-2

)

QA Shoot Density

(Shoots m-2

)

Difference (Shoots m-

2)

Relative Error

(% Original Count) Correction

Fannie Bay 3 1 0 0 0 0%

3 2 52 40 -12 -23% Replaced with video counts

3 4 0 0 0 0%

3 6 0 4 4 0%

3 8 0 0 0 0%

3 10 0 0 0 0%

3 11 0 0 0 0%

3 13 25 20 -5 -20%

3 15 0 0 0 0%

3 17 18 25 7 39% Replaced with video counts

Casuarina 1 82 86 98 12 14%

1 84 76 80 4 5%

1 88 186 190 4 2%

1 90 99 96 -3 -3%




3 82 190 184 -6 -3%


3 86 167 186 19 11%

3 88 2 2 0 0%

3 90 217 236 19 9%



4 76 0 0 0 0%



4 86 5 6 1 20%

4 88 0 0 0 0%

4 90 43 50 7 16%

4 92 0 0 0 0%

6 76 0 0 0 0%


6 80 0 2 2 0%

6 82 2 2 0 0%


6 86 10 11 1 10%


6 90 1 1 0 0%

6 92 0 0 0 0%

6 94 12 10 -2 -17%

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