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Estuarine, Coastal and Shelf Science 93 (2011) 132e141

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Estuarine, Coastal and Shelf Science

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Organic biomarkers to describe the major carbon inputs and cycling of organicmatter in the central Great Barrier Reef region

Kathryn Burns*, Diane BrinkmanAustralian Institute of Marine Science, PM Box 3 Townsville, Qld 4810, Australia

a r t i c l e i n f o

Article history:Received 21 March 2011Accepted 1 April 2011Available online 20 April 2011

Keywords:Great Barrier Reefcarbon cyclinglipidsbiomarkerssediment transport

* Corresponding author.E-mail address: kburns@aims.gov.au (K. Burns).

0272-7714/$ e see front matter Crown Copyright � 2doi:10.1016/j.ecss.2011.04.001

a b s t r a c t

Controversy surrounds the sources and transport of land derived pollutants in the Great Barrier Reefecosystem because there is insufficient knowledge of the mechanism of movement of organic contam-inants and the cycling of organic matter in this dynamic system. Thus a sediment and sediment trapstudy was used to describe the composition of resuspended and surface sediments in the south centralGreat Barrier Reef and its lagoon. This region is characterised by strong tides (6e8 m at Mackay) andtrade winds regularly about 15e20 knots. A series of organic biomarkers detailed the cyclical processes ofsediment resuspension, recolonising with marine algae and bacteria, packaging into zooplankton faecalpellets and resettlement to sediments where the organics undergo further diagenesis. With each cyclethe inshore sediments are diluted with CaCO3 reef sediments and moved further offshore with the strongebb tide currents. This results in transport of land derived materials offshore and little storage of organicmaterials in the lagoon or reef sediments. These processes were detailed by inorganic measurementssuch as %CaCO3 and Al/Ca ratios, and by the compositions of hydrocarbon, sterol, alcohol, and fatty acidlipid fractions. Persistent contaminants such as coal dust from a coastal loading facility can be detected inhigh concentration inshore and decreasing out to the shelf break at 180 m approximately 40 nauticalmiles offshore. The normal processes would likely be amplified during cyclonic and other storms. Thelipids show the sources of carbon to include diatoms and other phytoplankton, creanaerchaeota, sulfatereducing and other bacteria, land plants including mangrove leaves, plus coal dust and other petroleumcontaminants.

Crown Copyright � 2011 Published by Elsevier Ltd. All rights reserved.

1. Introduction

The southern central Great Barrier Reef (GBR) and adjacentlagoon waters are high energy tidally driven mixing zones. Eightmeter tides at Mackay and a normal trade wind of 15e25 knotscontinually resuspends sediments and redistributes land-derivedorganics that make their way to the GBR lagoon from coastalrivers and wetlands. The process of out-flushing land-derivedmaterials to the reefs has been a primary management concern forthe entire Great Barrier Reef ecosystem.

Studies to determine if land-derived materials reach the GBRhave been undertaken in “worst case” conditions such as aftercyclones. For example, comparisonof the d13C ratio of organicmatterin shelf sediments collected immediately before and after cycloneWinifred (1 February 1986) showed that the bulk of terrestrial plantdetritus from the Johnstone River (Far North Queensland) wasdeposited within 2 km of the river mouth and none moved to morethan 15 km offshore. By comparing the magnitude of the Johnstone

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riverflow to themaximumrecordedflowsonother rivers in theGBRprovince, Gagan et al. (1987) concluded that historically, terrestrialrunoff had not reached the outer reef except perhaps during rareBurdekin River floods. These authors further concluded thatterrestrial detritus was initially deposited near shore, and if subse-quently resuspended during storms or strong tidal events, mayeventually be transported to the Reef. This process of sediment re-suspension and transport offshore has been described in estuarineecohydrology models (Wolanski, 2007).

Johns et al. (1994) used molecular biomarkers to trace theorganic fractions from the silty sediments deposited after cycloneWinifred. Their data showed maximum deposition of silty sedi-ment occurred 11 km from the land. Using physical parameters ofsediment and molecular markers they detailed the distribution ofthe terrigenous material within sediment cores. They also foundterrigenous material buried by marine sediments. Their depthprofiles in the sediment cores suggested that biological diagenesiscould be expected to a depth of about 8 cm.

Wolanski and Spagnol (2000) studied the muddy near-shorearea of Cairns during dry season when river runoff was minimal.Wind and wave driven sediment resuspension resulted in fluid

rights reserved.

K. Burns, D. Brinkman / Estuarine, Coastal and Shelf Science 93 (2011) 132e141 133

nepheloid layers that moved with tides and threatened to smotheroffshore reefs.

The organic contaminants that may be absorbed to land-derivedsediments has added another layer of concern to reef conservation.Although Cavanagh et al. (1999) could not detect organo-chlorinepesticide runoff from the low topography catchments draining theBurdekin andHaughton Rivers, others have reported the presence ofpesticides, herbicides, trace metals and other industrial chemicals,in coastal sediments, seagrasses and animals, in higher topographyregions to the north and industrialized areas to the south of theBurdekin/Haughton River study areas (Haynes and Johnson, 2000;Haynes et al., 2000; Muller et al., 2000; Gaus et al., 2001).

In terms of carbon preservation, Alongi (1989) concluded thatthere was very little burial of reactive organic matter in shelf sedi-ments. Benthic standing crops and processes on the central GBRshelf appear to be regulated by a variety of factors, including low andintermittent inputs of detritus, continually warm temperatures inthe tropics, and physical disturbances caused by occasional cyclonesand frequent prawn trawling.

Brunskill et al. (2002) concluded from carbon mass balancecalculations that approximately 1% of combined river and marineorganic carbon production was preserved in across-shelf sedimen-tation, but 3% of total input was preserved in enclosed shelteredcoastal bays. Their mass balance study also predicted respirationrates and concluded that the ratio of organic carbon fixation torespiration (corrected for burial loss) was nearly balanced at 1.06.

In a carbon cycling study of the north central shelf region, Alongi(1990) concluded that benthic nutrient regeneration contributesonlya small portionof thedailynitrogenandphosphorousdemandofcoastal phytoplankton (6 and 9%, respectively), implying supple-mentation from continental runoff and/or high rates of pelagic recy-cling. A mass balance approach for estimating the phosphorousbudget found that upwelling inputs from the Coral Seawould supply

Fig. 1. Map of sampling sites on the south central Great Barrier Reef. Station names have watshelf reefs, PRC are from the inside of the Pompey Reef Complex, OS are from the outside

more P than that contributed by rivers over an average year (Monbetet al., 2007).Upwellingalong theshelf break in frontof thecentral reefhas been noted as a wet seasonal phenomenon (Andrews andGentien,1982;Andrews and Furnas,1986; Furnas andMitchell,1996).

The use of molecular organic biomarkers to describe carbonsources, sinks and cycling has been used in a variety of marineecosystems (Burns et al., 2003, 2004, 2008; Cooke et al., 2008; Lohet al., 2008; Morata et al., 2008; Volkman et al., 2008; and manyothers). In this paper we use a variety of organic biomarkers todescribe the origin and cycling of organicmatter in the south centralGreat Barrier Reef region.

2. Methods

2.1. Study sites

Inshore to offshore stations across the shelf are indicated inFig. 1. In addition to sediments collected at each site, a mooredsediment trap was deployed for 10 days at 30 m in a 65 m deepwater column, in September 2009 near reef station PRC4. Howeverthe windy turbulent conditions caused the trap to drift approxi-mately 8 nautical miles south toward station PRC5 during deploy-ment. The 2009 traps were 1 m long, 10 cm diameter stainless steelwith 5 traps in an aluminium frame. The traps were filled with 2�salinity brine containing 4 mg of HgCl2 to retard bacterial activity.In February 2010 sediment traps used for lipid analyses weretethered to the anchored research vessel by a 100 m line at stationsPRC4, PCR5, GR1. The tethered traps floated in mid water witha slight tilt in the direction of the currents. Offshore from stationIS9, the trap array was free floating. These traps were made ofpolycarbonate 0.8 m tall and 8 cm in diameter with 12 traps ina frame. The traps were only deployed during daylight hours(w10 h) and no bacterial retardant was added.

er column depth listed below. IS¼ inshore, MS¼mid-shelf, GR and BR are next to mid-of the same reef complex, SB¼ shelf break at 150e180 m.

K. Burns, D. Brinkman / Estuarine, Coastal and Shelf Science 93 (2011) 132e141134

2.2. Sample preparation

Sediment trap samples were filtered though pre-weighed andpre-combusted glass fibre filters. After rinsing with SuperQ waterto remove salt, the filters were folded in half and wrapped inpre-combusted aluminium foil and frozen. Sediments weresub-sampled from the Smith-Mac grab samples described byAlongi et al. (in press). Sub-cores were taken with methanolwashed polycarbonate tubes. Surface sediments (0e1 cm) weretakenwith a clean stainless spoon. Sediments were stored frozen inglass jars. At the lab, samples were freeze-dried to remove water.The trap filters were examined and visible crustacean zooplanktonremoved with tweezers. The remaining material was weighedand then the filters were ground in a cleaned glass motor andpestle. A portion of the ground material was removed for traceelement, CHN, and organic carbon analysis. The remainder wasused for lipid analysis. Sediments were also ground and sub-sampled. Each batch of samples included a complete proceduralblank analysis.

2.3. Sample extraction and preparation for lipid analysis

Dried, ground and weighed samples were poured into 30 mlTeflon screw cap tubes for the filters or into 60 ml Teflon bottles forthe sediments. Pre-combusted Na2SO4 salt was added to bind any

Table 1The organic biomarkers targeted for source estimation and carbon cycling processes in tabout these and other potential source biomarkers. Numbers in Table 7 defined in Jones

Biomarker or diagnostic ratio Source estimate

HydrocarbonsLow molecular weight alkanes (C17, C19, C21);

Low molecular weight alkenes (C17:1, C19:1,C21:5, C21:6)

General phytoplankbiomarkers

Highly branched isoprenoid alkenes (brC30:5,brC25:5 and related isomers)

Diatom biomarkers

Squalene, phytadiene, pristane Zooplankton biomarSpecific sterane and hopanes (C29H, C30H) Petroleum biomarkeUnresolved complex mixture (UCM), Alkane

Carbon Preference Index (odd/even chain lengths),Phytane, Alkylated aromatic hydrocarbons (m-phenanthrene/phenanthrene ratio)

Diploptene: Specific sulfate reducing bacterial andPMI:(polymethyl eicosane) specific Archaea marker.

Hydrocarbon degradmarkers

2-, 3- and 5-ringed aromatic sequiterpenoidaromatic hydrocarbons (cadalene, retene,a-terphenyl, perylene)

Land plant, fungal asoil diagenetic sourc

Benzopyrenes, dibenzanthracenes, benzo(ghi)perylene Combustion productas forest fires

Alcohols and sterolsSpecific sterols General phytoplank

Specific phytoplanktGeneral zooplankton

(campesterol, b-sitosterol, stigmasterol) Vascular plantscoprostanol Sewage biomarkern-alcohols (C12eC23) Zooplanktonn-alcohols (C24eC34) even Land PlantsPhytol Side chain of chloroCrenarchaeols Crenarchaeaota

Fatty acidsHigh content of poly unsaturated (%PUFA, C18:3w6,

C22:6w3)Phytoplankton biom

If C18:0<< C18:1 and C16:0 w C16:1; and there are lowratios of specific phytoplankton markers(C16:1w9/C16:0, C20:5/C16:0), and high ratio ofsum C16/sum C18

Zooplankton pattern

Specific isomer ratios (C18:1w7/C18:1w9)Iso and ante iso C15:0 and C17:0 and other branched or

cyclic fatty acidsBacteria sourced

possible residual water. Extraction solvent was 10% methanol(MeOH) in dichloromethane (DCM). Initial extracts had a surrogatestandard mixture added to track recovery through the procedures.This standard contained orthoterphenyl (OTP), C22:1 n-alkene,b-cholane and C27-n-alcohol. Samples were covered with solvent,15 ml for the tubes and 30 ml for the bottles. These were sealedtightly, shaken well on a vortex mixer and placed in a plastic tray.Water was added to the tray and it was placed in a probe sonicator.Samples were sonicated in groups of 5 for about 1 h. Then theywere placed in the refrigerator overnight. Next day, samples werefiltered through a 10 ml glass syringe containing pre-extractedcotton and about 5 g Na2SO4 into round evaporation flasks usinga vacuum box. Second and third sonication extractions were doneusing DCM. Combined extracts were reduced to about 1 ml usinga chilled rotary evaporator. Extracts were then transferred toa graduated conical glass tube using hexane and DCM rinses andthen reduced by a gentle stream of N2 gas back to 1 ml. Totalextractable organic matter (EOM) weights were done by evapo-rating 10 ml of concentrated extract onto the pan of a 7 decimalplace microbalance.

2.4. Saponification and lipid class separation

Extracts were further reduced to near dry with N2, then 2 ml 10%KOH in MeOH plus 0.5 ml SuperQ water were added. Samples were

he PNG coastal zone. The reference list is not exhaustive as much has been writtenet al., 1989.

References

ton Blumer et al., 1970, 1971; Sinninghe Damstéet al., 1999

Volkman et al., 1994; Belt et al., 2000; Schoutenet al., 2000

kers Avigan and Blumer, 1968; Blumer et al., 1969rs Summarized in Peters and Moldowan, 1993; Peters et al., 2005

er Schouten et al., 1995; Uchida et al., 2004; Elvert andNiemann, 2008

nd/ores

Simoneit, 1986; van Aarssen et al., 1992; Eliaset al., 1996; Jiang et al., 2000

s such Jiang et al., 1998

ton Volkman, 1986on Volkman et al., 1989

Wakeham and Canuel, 1986, 1988Waterson and Canuel, 2008Green and Nichols, 1995Kattner and Krause, 1989Eglinton and Hamilton, 1967

phyll General chlorophyll biomarkerHopmans et al., 2000; SinningheDamsté et al., 2002; Shah et al., 2008; Trommer et al., 2009

arkers Kattner and Krause, 1989;Viso and Marty, 1993; Cripps et al., 1999

Matsuda and Koyma, 1979; Shi et al., 2001Perry et al., 1979

0

20

40

60

80

100

IS

10 IS9

IS9

ST

MS

8

MS

7

B

R1

GR

1

GR

1 S

T

PR

C4

PR

C5

PR

C4

ST

PC

R5

ST

ST

2009

SB

13

SB

14

Stations: Inshore to Offshore

% C

aCO

3

Fig. 2. Percent CaCO3 in sediments and sediment trap samples arranged from inshoreto offshore with sediment traps shown next to corresponding surface sedimentsamples. The 2009 sediment trap dragged its mooring and drifted from deployment atPRC4 to just inshore of PRC5. The traps were set at 25 m depth. The array was deployedand retrieved in 65 m of water.

K. Burns, D. Brinkman / Estuarine, Coastal and Shelf Science 93 (2011) 132e141 135

sealed and heated in an oven at 90 �C for 2 h. The neutral lipids wereextracted 4 times with 4:1 DCM/CHCl3, the supernatants combinedandfiltered througha Pasteurpipettefilter containingNa2SO4 to bindwater. The saponification solution was then acidified and the fattyacid fraction extracted as per the neutral lipids. Separation of theneutral lipids was achieved by column chromatography using 3 g ofpre-extracted silica gel, activated and containing 4% H2O. Neutralextracts were reduced to 0.2 ml and the fractions were eluted with10 ml hexaneþ 10 ml 50% DCM/hexane (hydrocarbons), 8 ml DCM(ketones and esters), 10 ml MeOH (alcoholesterolsechrenarchaeol)fractions. The hydrocarbon and ester fractionswere analysed directlyby GC/MS. Themethanol fractionwas halved for HPLC/MS analysis ofchrenarchaeols and GC/MS analysis of sterols and alcohols. Sterolswere converted toTMS ethers by heating the samples for 1 h at 80 �Cwith N,O-bis (trimethylsilyl) trifluoroacetamide (BSTFA, SigmaeAldrich) and. fatty acids were methylated and analysed as theirmethyl ester derivatives.

2.5. Instrumental analysis of lipid fractions

Table 1 gives a list of the compounds targeted and the refer-ences for their use as specific biomarkers. Hydrocarbons wereanalysed in scan/SIM mode (m/z 50e500 scan, m/z 57, 71, 85 SIM)using a 30 m� 0.32 mm� 0.11 mm J&W DB5-MS fused silicacolumn in an Agilent 6890/5975 GCMS system. Alkanes, PMI andunresolved complex mixtures (UCM) were quantified by SIMintegration using ion 57. Mass spectral parameters included ion-isation energy of 70 eV, source temperature of 250 �C, and scanrate of 1.53 scans s�1. A second analysis was conducted in SIMmode to quantify a series of 298 compounds including thearomatic hydrocarbons plus the hopane and sterane series ofpetroleum biomarkers plus the microbial marker diploptene(Burns et al., 2010). In both analyses, the GC temperature programwas 50e320 �C at 4 �Cmin�1 with a 15 min hold time. Helium wasused as carrier gas for GC/MS. Sterols and n-alcohols were analysed

Table 2Percent Calcium Carbonate (CaCO3), Total Carbon (TC), Organic Carbon (OC), TotalNitrogen (TN) plus OC/N, OC/TC, Al/Ca ratios.

Sediment station CaCO3 TC OC TN OC/N OC/TC Al/Ca

% % % % M/M M/M M/M

IS10 0e1 cm* 16.0 2.1 0.16 0.027 5.7 0.08 0.083IS9 0e1 cm 6.6 1.8 0.96 0.081 11.1 0.55 0.883IS9 0e2 cm* 3.6 1.0 0.56 0.047 11.1 0.56IS9 9e11 cm* 6.6 1.2 0.42 0.036 10.9 0.34IS9 sediment trapy 7.0 2.4 1.51 0.187 9.4 0.64MS8 0e1 cm 68.3 8.8 0.56 0.074 7.1 0.06 0.081MS7 0e1 cm 86.4 10.6 0.23 0.042 5.1 0.02 0.020MS7 0e2 cm* 87.5 10.8 0.25 0.043 5.4 0.02MS7 8e10 cm* 86.5 10.7 0.26 0.039 6.2 0.02BR1 0e1 cm 91.0 11.3 0.38 0.061 5.8 0.03 0.008GR1 0e1 cm 91.3 11.4 0.44 0.063 6.6 0.04 0.005GR1 2e10 cm* 92.3 11.6 0.52 0.061 6.6 0.04GR1 sediment trapy 53.4 8.54 2.14 0.225 11.1 0.25PRC4 0e1 cm 62.5 8.2 0.70 0.130 5.0 0.09 0.002PRC5 0e1 cm 86.7 10.8 0.39 0.060 6.1 0.04 0.002PRC4-PRC5 sediment trap 33.4 4.45 0.50 0.070 6.8 0.13 0.005PRC4 sediment trapy 62.2 9.2 1.71 0.251 7.9 0.19PRC5 sediment trapy 53.4 8.54 2.14 0.225 11.1 0.25SB13 0e1 cm 91.6 11.3 0.30 0.048 5.9 0.03 0.009SB14 0e1 cm 92.5 11.4 0.29 0.044 6.1 0.03 0.003SB14 0e5 cm* 92.9 11.5 0.35 0.049 6.6 0.03

* Means samples were collected in April 2009.y Collected in February 2010, others collected in September 2009. CaCO3 was

calculated as (TC-OC)� 8.33. Ratios are molar. ST samples are shaded grey foremphasis. Arranged inshore to offshore.

using full scan GC/MS, over a range ofm/z 50e650 and the same GCprogram. Fatty acids were analysed as their methyl ester derivatesin scan mode using the same GC program. Relevant internal stan-dards were added just before analysis. Quantification was achievedwith five point calibrations of sets of relevant external standardsanalysed with each batch of analyses. Recovery of surrogate stan-dards was used to correct for losses during the procedures.Detailed lists of compounds quantified in each fraction are as givenin Burns et al. (2008).

Crenarchaeol analysis was done by normal phase chromatog-raphy on an Agilent 1100 series HPLC system comprising degasser,binary pump, PDA and Gilson 215 Liquid Handler autosampler/collector. All LC/MS data were collected using Bruker DaltonicsEsquire Control v5.3 and Hystar v3.1 operating on Windows XPProfessional. Normal phase seals were installed on the A pump-head. The LC was run using the following conditions: Column:Prevail� Cyano 3 mm,150� 2.1 mm (Alltech, part no. 99243). A 5 mlinjection loop was used and 10 ml of sample injected. Mobile phase:A¼ hexane, B¼ isopropanol (all solvent were HPLC grade). Flowrate: 0.2 ml/min. Column temperature: 30 �C. Programme: isocratic0e30 min 1% B. After 5 injections the columnwas washed with 10%B for 10 min and then re-equilibrated. MS detectionwas done usinga Bruker Esquire 3000 plus ion trap MS with an APCI source.Crenarchaeols were quantified by response factors derived from anintercalibration extract distributed by the Netherlands Institute ofOceanography (Schouten et al., 2007).

Table 3Total Carbon (TC), Organic Carbon (OC), Total Nitrogen (TN), and OC/N, OC/TV, Al/Caratios for sediment traps drifting inside reef September 2009. Averages are given inTable 2 as PRC4-PRC5 Sediment Trap.

Trap number CaCO3 TC OC TN OC/N OC/TC Al/Ca

% % % M/M M/M M/M

6 24.6 3.57 0.62 0.10 6.0 0.17 0.0056 29.0 4.06 0.57 0.08 6.4 0.14 0.0057 36.8 5.00 0.58 0.07 7.3 0.12 0.0047 34.3 4.66 0.53 0.08 6.3 0.11 0.0058 34.7 4.93 0.77 0.12 5.9 0.16 0.0048 31.0 4.35 0.63 0.09 6.3 0.14 0.0059 31.2 4.28 0.53 0.06 7.8 0.12 0.0059 34.7 4.71 0.55 0.06 8.0 0.12 0.00410 39.4 5.29 0.56 0.08 7.0 0.11 0.00510 38.3 5.13 0.53 0.07 7.4 0.10 0.004

Average 33.4 4.45 0.50 0.07 6.8 0.13 0.005STD 4.5 0.53 0.07 0.01 0.8 0.02 0.000%RSD 13.5% 12.0% 14.3% 0.07 11.1% 17.9% 6.4%

CaCO3 was calculated as (TC-OC)� 8.33. Ratios are molar.

K. Burns, D. Brinkman / Estuarine, Coastal and Shelf Science 93 (2011) 132e141136

2.6. Trace element analysis (ICP-AES)

Sediment samples for elemental measurements were freeze-dried and homogenised by grinding. Organic carbon was deter-mined by acidification, combustion, and infra-red detection ona Shimadzu TOC-5000 Analyzer with a solid sample chamber. Totalcarbon (carbonate plus organic carbon) and nitrogen were deter-mined on a Perkin Elmer 2400 CHNS/O Series II Analyzer. Lowconcentrations of N in these sediment samples required additionalmeasurements by chemiluminescence on an ANTEK 720 NitrogenDetector. P, S, Al, Fe, Mn, Ca, Ba, Mg, Sr, Li, B, and Cu were deter-mined by inductively coupled plasma atomic emission spectros-copy (ICP-AES, Varian Liberty 220) after nitric and perchloric aciddigestion of the sediment sample (Loring and Rantala, 1992;Thompson and Walsh, 1993). Pb and Cd were determined by Zee-man graphite furnace atomic absorption spectroscopy (AAS) ona similar digestion. These ICP and AAS measurements representperchloric/nitric acid extracts of the bulk sediment, and do notinclude elements contained in acid resistant minerals. Analyticalprecision was 5% for N and 3% for all other elements.

3. Results and discussion

3.1. Total organic carbon, nitrogen and trace elements

Sediments showed the progression from landward silicatesediments to offshore carbonate dominated sediments. Inshoresediments at IS-9 had 1% of the total carbon (TC) as organic carbon(OC), less than 7% as CaCO3, an OC/N ratio of 11 and an Al/Ca ratio of0.883 (Table 2). IS-10 was intermediate to a marine signal with 0.2%of TC as OC, 16% as CaCO3, an OC/N ratio of 5.7 and an Al/Ca ratio of0.083. Mid shelf and reef stations had 0.2 to 0.7% of TC as OC, 62 to91% as CaCO3, OC/N ratios of 5.0 to 7.1 and Al/Ca ratios 0.002 to 0.08.Offshore shelf break sediments had 0.3% of TC as OC, 92% as CaCO3,

OC/N ratios of 5.9e6.1 and Al/Ca ratios of 0.003e0.009. Fig. 2 showsthe percentage of CaCO3 in sediments and sediment trap samples.

Table 4Summary hydrocarbons in sediments and mid water sediment traps, including markerssamples are shaded grey for emphasis. Arranged inshore to offshore.

Station IS10 IS 9 IS 9 IS 9 wIS 9 MS8

Sediment (cm) layer or sediment trap (ST) 0e1 0e1 2e6 6e10 ST 0e1

EOM (mg g�1) 1.6 0.5 0.6 1.1 45.1 5.9Total hydrocarbons (mg g�1) 1.0 3.5 1.8 1.8 46.9 1.3%UCM* 66 44 49 61 52 60Total n-Alkanes C11eC38 (ng g�1

) 196 1654 758 916 6916 291CPI C25eC38y nc nc nc nc nc ncPhytoplankton markersz (ng g�1) 380 425 423 195 2919 90Zooplankton markersx (n ng g�1) 77 1266 842 587 191 80PMI Archaea markerk (ng g�1) 1.3 2.4 4.8 2.7 7.4 0.4Diploptene SRB marker{ (ng g�1) 146 344 317 290 2473 1.7Sum Oil PAHS (ng g�1)# 111 213 302 304 1771 66.0Sum Combustion PAHs** (ng g�1) 0.7 14.2 22.4 36.2 20.8 1.9Sum Triterpanes (ng g�1)yy nd 1.4 2.9 2.0 12.6 0.03Sum Steranes (ng g�1)zz nd 0.2 0.4 0.3 2.0 nd

* UCM is unresolved complex mixture of hydrocarbons indicative of petroleum residuy CPI is the Carbon Preference Index for the given alkane range with odd over even chai

alkanes were odd carbon chain lengths indicative of biogenics.z Phytoplankton markers include C15, C17, C19, C21 alkanes and their unsaturated comx Zooplankton markers include squalene and pristine.k PMI is polymethyleicosene produced by Archaea.{ Diploptene is a marker for sulfate reducing bacteria (SRB).# Oil PAHs is the sum of the naphthalene/biphenyl, phenanthrene/anthracene, acena

chrysene series of parent and alkylated PAHs.** Sum Combustion PAHs is the sum of the benzofluoranthene, benzopyrene, indenopyyy Sum of triterpanes and steranes are sums of those individual petroleum biomarkerszz nd mean non-detectable or generally less than 0.1 ng g�1.

Note the sediment traps set at the reefs in 2010 have lower values,more like the mid shelf sediments, while the 2009 trap had evenlower values. This shows that the resuspended sediments moveoffshore by resuspension. Table 3 gives the analysis of the 5 tubes ofthe 2009 sediment trap in duplicate to indicate analyticalreproducibility.

3.2. Hydrocarbons

Table 4 summarizes the hydrocarbons found in the sedimentsand sediment traps. Total EOM and hydrocarbons were an order ofmagnitude higher in the sediment traps than the surface sedi-ments. The saturated hydrocarbons inshore sediments werea mixture of “petroleum” plus biogenic zooplankton and phyto-plankton biomarkers. There was a significant content of poly-nuclear aromatic hydrocarbons which could be divided intoa “petroleum” or a “combustion product” pattern. The wIS9 sedi-ment trap drifted offshore approximately 35 to 38 nmiles northeast of a coal loading facility at Hay Point, north of Mackay. Thepattern of PAHs was the same in the offshore sediment traps atwIS9 as in the IS9 sediments taken nearshore at 5 m depth. Theobserved “petroleum” pattern was not characteristic of oil, whichusually consists of a homologous series of n-alkanes with a carbonpreference index (CPI) close to 1, and isoprenoid alkanes set over anunresolved complex mixture of hydrocarbons that includesa significant portion of sterane and triterpane oil biomarkers(Peters and Moldowan, 1993; Peters et al., 2005). Instead, the lowcontent of a homologous series of n-alkanes and petroleumbiomarkers, but a significant concentration of the aromatichydrocarbons, indicated that the PAH pattern was more charac-teristic of coal residue (Yunker and Macdonald, 2003). This PAHpattern was visible in the sediments all the way out to the shelfbreak, but in decreasing concentrations (Table 5). Enhancedconcentration of PAH in the sediment traps set near the reefs againindicates they contain particles originating inshore, resuspendedand moved offshore. The sediment traps set in 2010 contained high

for petroleum, phyto- and zoo-plankton, Archaea and sulfate reducing bacteria. ST

MS7 MS7 GR1 GR1 PRC4 PRC4- PRC4 PRC5 SB13 SB14

0e2 8e10 0e2 ST 0e1 PRC5 ST ST ST 0e1 0e1

2.7 0.8 2.8 8.1 1.2 0.7 10.6 13.1 3.1 4.50.6 1.0 0.9 55.3 2.4 23.2 52.1 54.5 0.6 0.571 60 68 75 69 35 75 74 63 7188 202 109 7455 285 7652 5420 4940 91 94nc nc nc nc nc 1.0 nc nc nc nc83 168 222 18,052 260 117 11,680 11,272 146 138149 174 102 2479 58 0.4 3171 2504 72 680.6 1.0 0.5 21.8 0.5 4.4 nd nd 0.4 0.53.3 2.1 9.1 3071 133 1.5 3562 6701 1.2 4.527.2 27.6 28.7 2387 108 8.1 2182 1841 26.0 28.80.3 0.2 0.15 1.9 nd 15.4 1.2 1.7 0.8 0.70.02 0.01 0.01 68 0.3 1064 14.9 38.1 nd ndnd nd 0.00 8.8 nd 1080 8.9 3.9 nd nd

es.n lengths. CPI close to 1 indicative of petroleum content. Nc means all the detectable

ponents plus Highly Branched Isoprenoid (HBI) hydrocarbons.

phthylene, acenaphthene, fluorene, DBT, fluoranthene/pyrene, benz[a]anthracene/

rene, dibenzanthracene and benzoperylene series of PAHs..

K. Burns, D. Brinkman / Estuarine, Coastal and Shelf Science 93 (2011) 132e141 137

concentrations of the sulfate reducing hydrocarbon degradingbacterial marker, diploptene (Schouten et al., 1995; Uchida et al.,2004; Elvert and Niemann, 2008). The concentration of PMI, thearchaeal hydrocarbon degrading biomarker, was generally low inmost sediments and sediment trap samples. The highest concen-tration of PMI was in the GR1 sediment trap. Within sediments atIS9, the highest concentration of the Archaea biomarker was in the2e6 cm subsurface layer, likely just below the oxygen interface. Theresults indicate that sulfate reducing bacteria arewidely distributedin sediments and the water column, probably in higher numbersthan the Archaea. Thus the bacterial community was there todegrade some of the saturated hydrocarbons associated with thecoal as the particles moved offshore.

The sediment trap that floated for 10 days in September 2009was the only trap with a recognizable oil hydrocarbon pattern,namely n-alkanes with a CPI of 1.0, plus the expected pattern ofisoprenoid, triterpane and sterane petroleum markers. The esti-mate for diploptene biomarkers was very low compared to othertrap samples, yet the PMI was high. The 2009 traps contained HgCl2which was meant to inhibit bacterial growth for the longerdeployment time. This relatively fresh oil input may be from aspassing ship, or it could be oil from the Pacific Adventurer oil spillwhich happened north of Brisbane in March 2009.

The patterns of hydrocarbons in the further offshore sampleschanged to high concentrations of highly branched isoprenoids,

Table 5PAHs in sediments and sediment trap samples. Units are pg g�1. Arranged inshore to offs

Station IS10 IS9 IS9 IS9 wIS9 MS8 MS

Sediment cm depthor ST

0e1 0e1 2e6 6e10 ST 0e1 0e

Naphthalene 387 440 487 304 849 53 48S C1-Naphth 1633 1590 1811 1291 9896 944 594S C2-Naphth 4921 6831 10,236 8516 64,603 3386 214S C3-Naphth 7128 12,335 19,717 17,768 124,950 3219 247S C4-Naphth 22,782 42,937 57,798 52,034 421,148 3855 368Biphenyl 153 275 470 379 2161 83 124S C1-Biphenyls 967 1637 2531 2249 14,882 537 784S C2-Biphenyls 4358 7116 7693 9257 70,435 969 140Fluorene 25 256 530 721 574 3 ndS C1-fluorene 33 78 131 115 648 nd ndS C2-fluorene 587 978 1570 1497 10,501 152 212Phenanthrene 1557 2721 3706 3398 27,227 34 46Anthacene 4535 7962 10,646 9087 73,781 429 745S C1-Phen/Anth 1684 2327 2948 2656 23,084 95 139S C2-Phen/Anth 1684 2424 2960 2613 24,382 175 249S C3-Phen/Anth 5349 6600 10,673 9126 84,031 1101 154S C4-Phen/Anth 3417 5635 6717 5774 67,136 892 115Dibenzothiophene nd nd nd nd nd nd ndS C1-DBTs 25,000 38,475 48,714 44,455 338,309 1439 247S C2-DBTs 1034 1736 2532 2616 13,774 25 25S C3-DBTs 8082 14,471 18,927 16,931 119,089 1130 191Fluoranthene 7803 15,380 20,798 18,995 126,253 2052 398Pyrene 5148 8211 14,161 22,351 46,928 1060 149S C1-Fl/Pyr 766 1265 1843 1640 12,911 427 587S C2-Fl/Pyr 567 4716 6793 11,422 13,668 149 234S C3-Fl/Pyr nd 4340 6399 9631 20,726 264 374Dibenzanthracene 222 2210 3348 5605 6912 77 95Chrysene 209 2013 4267 4787 8489 74 87S C1-BDA/chrys 51 1162 1869 1971 4724 31 27S C2-BDA/chrys 109 2560 3787 7609 3790 22 27S C3-BDA/chrys 91 1795 2773 4669 3878 nd ndS C4-BDA/chrys 99 1772 3238 4316 7824 91 57Benzo(b)fluoranthene 114 2490 3997 5985 3986 50 51Benzo(k)fluoranthene 41 1106 1891 3388 1317 15 16Benzo(e)pyrene 133 2785 4447 6826 5184 58 52Benzo(a)pyrene 121 3121 4543 8788 3678 25 32Perylene 172 9801 19,216 17,104 17,272 37 87Indeno(1,2,3-cd)pyrene 113 2124 3312 5292 2680 65 50Dibenz(a,h)anthracene 18 418 686 1227 580 8.7 6.3Benzo(ghi)perylene 124 2169 3502 4702 3408 58 44

sourced from diatoms (Volkman et al., 1994; Belt et al., 2000;Schouten et al., 2000), and the pristane and squalenezooplankton biomarkers (Avigan and Blumer, 1968; Blumer et al.,1969). These compounds were two orders of magnitude higher inthe 2010 sediment traps than in the sediments. Thus the resus-pended particles sourced from the mid shelf area were recoatedwith marine organics.

3.3. n-Alcohols

Most of the n-alcohols were derived from phytoplankton andzooplankton (Table 6) (Kattner and Krause, 1989). Phytol concen-tration was highest in the sediment traps, which correlates wellwith the high content of phytoplankton biomarkers in hydrocarbonand fatty acid fractions. The reef and midshelf sediments containedmuch less phytol, and its concentration decreased from surface todepth as expected with degradation. Zooplankton biomarkers inthe C16, C18 etc range were also higher in the reef and midshelfsediment trap samples than in the sediments, although no changewas observed with increasing sediment depth. The coastal sedi-ments at station IS9 had high values of buried phytoplanktonmarkers indicating sedimentation rate is much faster than offshore.Land plant biomarkers represented by C24 to C32 even chainlengths, were highest in the inshore stations, constituting 55% and74% of total n-alcohols (Eglinton and Hamilton, 1967). Mid shelf

hore. ST samples are shaded grey for emphasis.

7 GR1 GR1 PRC4 PRC4-PRC5 PRC4 PRC5 SB13 SB14

2 0e2 ST 0e1 ST ST ST 0e1 0e1

3617 855 8 nd 330 432 nd 563360 724 390 2303 279 65 475 1472

0 6182 9451 1674 17,205 6982 3508 2471 58317 89 32,829 4648 19,701 25,069 14,472 2769 58045 564 245,444 19,057 28,042 223,552 97,223 4022 6258

1034 702 48 360 409 477 38 13017 7397 594 3394 6335 3760 385 866

9 nd 52,123 3603 5242 65,131 112,551 892 1778175 nd 8 nd nd nd 16 nd39 nd 11 nd nd nd nd 32563 6527 457 732 5965 3593 114 283166 22,406 1518 786 22,557 14,328 49 72272 106,367 4619 2370 93,939 66,328 955 12061395 35,627 1603 nd 34,177 28,561 310 3491040 43,163 1838 746 38,523 36,230 472 585

5 nd 142,320 5488 4120 121,813 136,185 1805 28046 1935 112,150 4795 3028 96,788 104,127 1087 1867

27 nd nd nd nd 5646 nd nd4 1526 749,578 25,433 5313 740,395 637,698 2484 3562

2724 37,475 1173 187 34,356 25,905 35 655 1231 212,831 9047 4648 186,052 186,311 2193 29474 418 226,246 10,438 8338 209,120 216,312 2989 47312 153 248,259 8223 5570 188,350 56,405 1217 1946

308 16,519 955 1054 13,655 16,759 546 88174 22,294 589 522 20,376 22,911 194 231109 42,895 1020 935 38,506 44,198 332 53414 4955 279 163 3272 5531 151 8413 2994 81 252 2128 3188 339 111nd 204 42 67 745 633 153 1035 730 20 93 369 432 83 1174 974 24 199 217 284 99 nd66 473 64 169 537 728 803 35392 229 nd nd 127 162 67 2228 67 nd 36 36 98 19 78 415 nd 174 226 322 318 2832 nd nd 75 nd nd 67 1418 nd nd nd nd nd 28 ndnd 123 5 102 47 55 49 2832 82 nd 55 57 124 39.2 4.64.7 966 9 nd 743 929 96.8 24

K. Burns, D. Brinkman / Estuarine, Coastal and Shelf Science 93 (2011) 132e141138

sediments contained 31% and 52%, the GR1 sediments and trapscontained 23% and 48%, while sediment traps set near the mid shelfreefs contained 13%e14% n-alcohols indicative of land pants. Thesediments at the shelf break stations, while having low concen-trations of all n-alcohols, still showed 48% and 52% of those as theland plant biomarkers.

3.4. Sterols

The sediment trapwIS9 contained an order of magnitude higherconcentration of phytoplankton (13,600 ng g�1) and zooplankton(11,160 ng g�1) sterols than the inshore surface sediments of IS9(1279 and 546 respectively) (Table 7) (Volkman, 1986; Volkmanet al., 1989). The ratio of sterol to stanols was 5.2 in the wIS9sediment traps, indicating the sterols were undegraded; whereasthe ratio in sediments was 1.7e2.0, indicating significant degra-dation. The amount of taraxerol, the mangrove biomarker(Versteegh et al., 2004), was similar in the wIS9 traps and IS9sediments. This indicated the particles in the sediment traps wereresuspended sediments that had been coated by marine phyto andzooplankton markers. The ratio of phyto/zooplankton markers waslower in the traps indicating that a significant portion of the sterolswere in zooplankton faecal pellets. The traps also contained higherconcentrations of sterols sourced to land plants than the sediments(Waterson and Canuel, 2008).

Mid shelf sediments had 399 and 996 ng g�1 phyto-, 327 to504 ng g�1 zooplankton biomarkers that decreased an order ofmagnitude in deeper sediments at MS7. Ratios of sterols to stanolswere 4.8 and 6.2 in surface sediments. Concentrations were too lowin deeper sediments to calculate this ratio. Land plant markersdecreased an order of magnitude in deeper sediments. Thisdecrease in sterols with sediment depth indicates diagenesis in themid shelf sediments.

Table 6N-alcohols in sediments and sediment trap samples. Units are mg g�1. Samples arranged

Station IS10 IS9 IS9 IS9 wIS9 MS8 MS7 M

cm sediment orsediment trap (ST)

0e1 0e1 2e6 6e10 ST 0e15 0e2 8e

Undecanol 0.6 nd 1.2 6.4 nd 0.6 0.1 48Dodecanol 8.9 7.7 16.3 101 2.6 8.6 1.5 0.Tridecanol 1.9 2.3 3.3 24.5 0.7 1.9 0.4 1.Tetradecanol 11.7 19.9 46.0 191 4.0 11.7 2.7 0.Pentadecanol 10.9 11.4 14.3 67.9 2.3 10.9 1.8 2.Hexadecanol 44.2 56.1 59.1 333 10.6 44.2 9.1 1.Heptadecanol 10.7 11.2 12.9 45.4 1.3 10.7 1.3 9.Octadecanol nd 24.6 nd 134 8.1 nd 5.3 1.Nonadecanol nd 2.9 3.1 15.8 1.0 nd 0.5 5.Eicosanol nd nd nd 121 12.1 nd 5.6 0.Heneicosanol 2.4 6.3 7.1 31.1 4.0 2.4 1.4 5.Docosanol 26.1 84.4 103 377 38.1 26.1 14.5 1.Tricosanol 4.1 14.9 20.3 54.9 5.4 4.1 2.2 14Tetracosanol 36.0 157 216 386 28.7 36.0 11.7 2.Pentacosanol 4.12 19.6 27.8 51.9 2.5 4.1 0.8 11Hexacosanol 34.2 194 265 413 16.6 34.2 6.8 0.Octacosanol 51.1 319 341 796 26.3 51.1 18.7 6.Nonacosanol 6.2 24.9 29.9 83.9 2.5 6.2 0.9 18Triacontanol 44.3 162 174 579 18.3 44.3 11.8 0.Hentriacontanol 12.2 15.1 15.2 59.0 1.7 12.2 0.5 11Dotriacontanol 26.1 101 99.5 537 13.3 26.1 5.7 0.Tritriacontanol 5.4 5.4 6.8 34.1 0.5 5.4 0.2 5.Tetratriacontanol 6.1 18.7 25.5 117 2.0 6.1 0.7 0.

Phytol 1110 311 122 8691* 178 1110 18.0 0.Sum all n-alcohols 347 1258 1486 4561 203 177 347 10SUM (C7-C23) 117 227 266 1448 85 97 117 44% C24-C32 even 55 74 74 59 51 40 55 52

nd was non detectable (<0.1 mg g�1).* This is a minimum value as it was over the calibration for the GC/MS. Sediment trap

Sediment trap samples from reef sites GR1, PRC4, and PRC5 allhad one to two orders of magnitude higher phyto and zooplanktonsterols compared to surface sediments. The sterol to stanol ratiosdid not vary significantly between the sediment traps and thesediments. The ratio of phyto to zooplankton markers ranged from0.6 to 1.0 in the traps and 1.6e2.5 in the sediments. This againshowed a significant portion of the sterols in the traps were likely inzooplankton faecal pellets. The only trap sample to show traces oftaraxerol was the 2009 trap, PRC4-PRC5 (Table 7). Land plant sterolswere an order of the magnitude higher in traps than sediments.This supports the interpretation that the resuspended sedimentscontained some material from the mid shelf sediments.

Offshore sediments had very low concentrations of sterols,which were mostly marine, with minor traces of land plant andmangrove markers. Ratios were not useful in the low sterol contentsamples as many compounds were below detection.

The presence of the sulfate reducer marker diplopterol wassporadic in sediments and sediment trap samples. The marker forCrenarchaeota was high in the offshore sediments and highest inthe sediment traps set near the reefs with decreasing amount seenin mid shelf and inshore samples.

3.5. Fatty acids

Inshore sediment traps had two orders of magnitude higherfatty acid content than sediments (Table 8). The pattern of fattyacids also indicated that a higher phytoplankton than zooplanktoncomponent was present in the wIS9 traps samples than in sedi-ments (Kattner and Krause, 1989; Viso and Marty, 1993; Crippset al., 1999). Branched fatty acids content was higher in the wIS9trap compared with sediments indicating a higher content ofbacterial markers (Matsuda and Koyma, 1979; Perry et al., 1979; Shiet al., 2001). However the % PUFA and the specific phytoplankton

inshore to offshore. ST samples are shaded grey for emphasis.

S7 GR1 GR1 PRC4 PRC4- PRC4 PRC5 SB13 SB14

10 0e2 ST 0e1 PCR5 ST ST ST 0e1 0e1

.1 0.1 13.0 nd nd 38.2 35.4 nd 0.11 2.9 433 8.5 nd 728 652 1.6 2.75 1.2 115 1.8 3.8 205 142 0.5 0.64 17.2 620 7.6 98.2 892 773 2.6 4.17 11.0 201 3.1 18.6 324 268 1.3 3.48 36.9 3138 21.5 284 4762 4536 7.0 10.61 8.3 88.7 0.9 69.9 123 113 0.7 1.33 10.0 1054 nd 151 2620 1508 4.2 4.53 0.9 62.7 nd 10.2 62.4 64.1 0.5 0.65 6.5 552 nd 53.2 648 502 6.8 7.46 1.9 106 nd 16.8 121 102 2.0 1.84 20.4 874 22.7 110 928 643 20.3 17.7.5 3.1 141 nd 17.6 145 104 2.9 2.72 17.8 679 19.3 75.6 745 449 15.8 14.4.7 1.2 56.3 nd 6.1 56.3 46.4 1.3 1.38 9.2 260 7.8 37.5 246 164 8.4 7.98 15.7 662 nd nd 453 513 16.9 17.4.7 1.1 45.4 1.3 5.8 44.3 35.4 1.1 1.29 10.5 467 nd nd 382 3604 11.2 11.1.8 0.8 23.8 0.6 2.8 28.2 70.8 0.8 0.65 5.4 182 3.2 19.2 1590 1194 6.0 4.97 0.2 17.3 nd nd 16.1 24.3 0.3 nd2 0.8 28.1 0.1 2.8 26.2 17.7 0.7 0.6

7 177 25,268 221 1467 21,153 24,054 87 634 183 9818 99 983 13,751 11,241 113 117

117 7257 66 816 11,451 9337 48 5532 23 31 13 14 14 52 48

samples were analyzed at higher dilutions.

Table 7Sterols summary including total sterols, phytoplankton, zooplankton and crenarchaeota biomarkers, mangrove leaf and land plant markers plus useful ratios to determine dominance and degradation stage. Samples arrangedinshore to offshore. ST samples are shaded grey for emphasis.

Station IS10 IS9 IS9 IS9 wIS9 MS8 MS7 MS7 GR1 GR1 PRC4 PCR4- PRC4 PRC5 SB13 SB14

Sediments (cm) or mid water sediment trap (ST) 0e1 0e1 2e6 6e10 ST 0e1 0e2 8e10 0e2 ST 0e1 PRC5 ST ST ST 0e1 0e1

Total Sterols (mg g�1) 1.8 5.1 5.2 4.4 32.2 1.9 1.2 0.13 0.74 111 2.4 14.34 280 167 1.3 0.60Phytoplankton biomarkers (19þ 30þ 37þ 41þ 50þ 62þ 66) (ng g�1) 951 1279 1801 915 13,605 996 399 66 333 42,678 1213 4524 74,289 57,218 89 263Zooplankton (12þ 9) (ng g�1) 363 564 641 313 11,160 504 327 11 215 44,804 495 5427 115,823 60,278 301 195Ratio of Phyto/Zooplankton markers 2.6 2.3 2.8 2.9 1.2 2.0 1.2 1.6 1.0 2.5 0.92 0.6 0.9 0.3 1.4Mangroves (taraxerol) (ng g�1) 93 1222 1348 1420 1332 2.7 0.4Freshwater and land plant marker (33) (ng g�1) 76.6 85.5 147.7 54.7 1713 22.4 16.1 1.3 10.2 2490 61.3 134 5314 2481 7.5Sulfate reducer marker (diplopterol) (ng g�1) 8.60 3.76 2.88 1.62 12.7 5.45 1.03Sterols (ng g�1) (1,12,19,23,30,41,50,55,62,67) 1137 2070 2094 1512 20,565 1328 655 72 495 77,861 1631 9004 171,861 102,507 277 411Stanols (ng g�1) (2,14,20,22,33,43,51,54,66,68) 426 1240 1062 833 3940 215 138 40 119 16,406 445 1878 28,644 16,059 220 89Ratio of sterol/stanol pairs 2.7 1.7 2.0 1.8 5.2 6.2 4.8 4.1 4.7 3.7 5.3 6.4 6.3Crenarchaeol (mg g�1) 134 76 129 88 180 373 118 172 256 1908 267 1422 574 874 414 466

Sterol numbers refer to those assigned by Johns et al. (1989).

Table 8Summary fatty acid content and composition of sediments and sediment trap samples. ST samples are shaded grey for emphasis. Arranged inshore to offshore.

Station IS10 IS9 IS9 IS9 wIS9 MS8 MS7 MS7 GR1 GR1 PRC4 PRC4- PRC4 PRC5 SB13 SB14 SB14

Sediment layer or sediment trap (ST) 0e1 0e1 2e6 6e10 ST 0e1 0e2 8e10 0e2 ST 0e1 PCR5 ST ST ST 0e1 0e1 0e5

Total Fatty Acids* (mg g�1) 33.7 23.4 24.5 20.5 3794 34.0 10.3 12.6 112 1489 12.0 56.8 944 1250 16.1 9.3 9.4Branched FAy (mg g�1) 0.8 0.7 1.0 0.8 48.2 2.3 1.3 1.7 2.9 12.9 1.2 3.0 7.7 14.5 1.5 1.0 1.5Sum PUFAz (mg g�1) 17.1 4.1 2.5 1.0 2576 13.2 3.0 0.8 69.2 1016 6.0 26.1 664 936 7.0 3.4 2.2SumC16/sumC18

x 2.26 2.86 2.83 2.16 0.94 1.9 1.17 1.00 1.29 2.05 1.22 2.46 3.18 2.03 0.93 0.80 0.86C16:1u9/C16:0k 1.50 0.85 0.62 0.38 2.09 0.75 0.50 0.21 0.93 1.22 0.65 0.55 1.39 1.14 0.54 0.56 0.52C18:0/C18:1 0.36 0.34 0.45 0.50 0.16 0.36 0.41 0.90 0.34 0.60 0.37 0.91 0.56 0.48 0.30 0.30 0.30C18:1u7/C18:1u9þ C18:1u7{ 0.41 0.30 0.33 0.42 0.39 0.24 0.30 0.41 0.29 0.60 0.28 0.53 0.46 0.52 0.34 0.29 0.28%PUFA 51 17 10 5 65 39 29 6 62 68 50 43 70 75 44 37 24%Branched 2.4 3.2 4.2 3.8 1.3 6.7 12.2 13.7 2.6 0.9 10.2 6.2 0.8 1.2 9.1 11.0 15.7C18:3u6 (ng g�1)z 622 47 28 12 11,9859 209 53 33 1857 20,963 54 317 13,080 20,766 45.7 31.4 27.8C22:6u3 (ng g�1)z 2047 867 467 230 960,821 3029 539 85 15,924 407,297 1490 38,4179 265,550 384,179 2498 895 529

* Total fatty acids quantified as their methyl esters from C8 to C30 chain length including saturated, unsaturated and branched isomers.y Branched fatty acids derived from bacteria.z Poly unsaturated fatty acids (PUFA) and some specific biomarkers derived from phytoplankton.x Sum of C16 divided by the sum of C18 fatty acids indicates a zooplankton component.k A low ratio of the C16:1 to C16:0 fatty acids indicates a zooplankton component.{ A high ratio of the C18:1u7/C18:1u9þ C18:1u7 indicates a bacterial component.

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139

0.0

0.5

1.0

1.5

2.0

2.5

3.0

IS10 IS

9

MS8

MS7

BR1

GR

1

PRC

4

PRC

5

PRC

6

OS1

OS2

SB13

SB14

Chl

or A

µg

L-1

Stations: Inshore to Offshore

Fig. 3. Integrated water column chlorophyll A values (mg L�1) for stations arrangedinshore to offshore. Open diamonds and circles are wet season values from April 2009and February 2010. Solid җ are dry season values from September 2009.

K. Burns, D. Brinkman / Estuarine, Coastal and Shelf Science 93 (2011) 132e141140

biomarkers decreased with depth of sediments, while the %branched increased, indicating bacterial degradation.

Mid shelf surface sediments contained from 10 and 34 mg g�1

total fatty acids with the pattern generally showing phytoplankton,zooplankton and bacterial markers higher in surface sediments.Phytoplankton markers decreased while bacterial markersincreased with depth, again indicating degradation.

Sediment trap samples from reef sites GR1, PRC4, PRC5 all hadone to two orders of magnitude higher phytoplankton markersthan surrounding sediments. The % PUFA ranged from 68 to 75% inthe 2010 traps. The % branched ranged from 0.8% to 1.2%. TheSeptember 2009 trap had an order of magnitude less fatty acidcontent than the 2010 traps. Its pattern had a strong phytoplanktoncomponent, but over all, the pattern was more degraded and moresimilar to the sediments. As will be discussed below, this is likelydue to the higher overall production rate in the wet seasoncompared to the dry season.

The shelf break sediments had low concentrations (9.3e16.1mg g�1) of fatty acids. The patterns showed a mixture of phyto-,zooplankton and bacterial markers.

4. Conclusions

The GBR lagoon and reef ecosystem is shallow and subject tostrong currents from tides andwind. The currents are so strong thatit is nearly impossible to anchor fixed sediment traps or to deter-mine surface to sediment fluxes. Drifting and/or suspended trapstethered to the research vessel were used to assess the process ofsediment re-suspension.

The biomarkers show that as sediments are resuspended in thisvery high tidal and trade wind dynamic area, the particles arerecoated with marine organics and probably packaged intozooplankton faeces. Presumably these fall to thesedimentsas the tidepushes thewatermasses offshore and the cycle repeats. Thus there islittle storage of organic matter in the sediments and this is a mecha-nism for the movement offshore of residual terrestrial markers.

The near shore signal from land plants is visible all theway to theshelf break. The n-alcohols, sterols and fatty acids show that thesediment traps contain resuspended sediments that are quicklyrecolonised by marine plankton and bacteria. The fine silicate sandthat is resuspended from the land derived sediment is diluted withthe carbonate reef sediments off shore. This process is shown by thelipid biomarkers, the % CaCO3 and the Al/Ca ratios. Also the presenceof coal residues in decreasing concentrations from the inshore tooffshore show that land derived contaminants that, travel on parti-cles, getdistributedall theway to the shelf breakandperhapsbeyond.

Comparison of the organic carbon and the lipid contents of the2009 and 2010 sediment traps, would indicate that primaryproduction rates were higher in thewet season than the dry season.Fig. 3 is a graph of water column chlorophyll versus station for thewet seasons in April, 2009 and February 2010 and the dry season inSeptember 2009. The graph shows that chlorophyll concentrationswere two to 5 times higher during the twowet seasons than duringthe dry season. This corroborates the lipid data which showedmuch higher lipid values in February 2010 (wet season) comparedwith September 2009 (dry season) in the sediment trap samples.The biomarkers presented here suggested a few of the contributingsource of carbon to the ecosystem such as the diatoms, otherphytoplankton, the Creanarcheaota, the sulfate reducing bacteriaand the Archaea in the microbes plus zooplankton, land plants, coaland oil contaminants.

Acknowledgements

We thank our colleagues at AIMS: Steve Boyle and Cassie Paynefor TE, HCN, and TOC analyses; Samantha Talbot for chlorophyllanalyses; Cherie Motti for HPLC/MS analysis of crenarchaeol, DanAlongi for Fig. 1, and the Captain and crew of RV Cape Ferguson.

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