Sampling Design

At both locations, a transect consisting of 3 sites from east to west was set up to study benthic respiration and nutrient cycling (Figure 1-3). At the upper location, the sites were called upper east, upper centre and upper west and will be referred to as UE, UC and UW respectively throughout the rest of the thesis. Likewise, the sites at the lower location were called lower east, lower centre and lower west and will be referred to as LE, LC and LW respectively throughout the rest of this thesis.

At each site triplicate cores were taken to measure sediment-water exchange of nutrients and respiration, duplicate cores were taken to measure oxygen and nutrient micro-profiles while sediment samples were also obtained for bulk carbon and

nitrogen analysis, sediment porosity and grain size as well as stable isotopes δ13C and δ15N and lipid molecular biomarkers. Water samples were also taken to measure basic water quality parameters and background nutrient concentrations

The study locations were visited three times in 2004, including March, July and November, using a small research vessel. The two locations were sampled on separate occasions, generally 3 days to a week apart, due to resource and labour limitations. Data from an additional sampling trip in April 2005 from Hideaway bay (P3) and Garden Island (P4) (Figure 1-3) have also been used in this thesis and will serve as a comparative study of the benthic processes with the upper and lower locations of the main study.

The rationale behind selecting the upper and lower locations was to elucidate the impact of different sources of organic carbon on benthic respiration and nutrient cycling and to examine the spatial variability within a sampling location (i.e. variation between cores at site UW), between sites within the same location (i.e. UW v. UE) and between sampling locations (i.e. Upper estuary v. Lower estuary). Samples from both locations were also taken at different times during the year to determine if there was any temporal variability associated with the sources of organic matter, benthic respiration and nutrient cycling. Measuring algal sedimentation was not undertaken during this study due to time and technical constraints of the fieldwork. It is noted

however that such measurements would have being desirable and would have added valuable information to the thesis.

A separate study (chapter 5) was also done to assess the impact of organic enrichment on sediment biogeochemical processes. A detailed description of the methodology and experimental design can be found in chapter 5. Briefly however, sediment core samples were collected in June 2005, homogenised, reconstituted into cores and then loaded with different concentrations of organic carbon after a re-equilibrium period. To test the efficacy of using re-homogenised cores, sediment exchange of oxygen and nutrients were measured prior to carbon loading and compared with results from the 2004 field study.

Figure 1-3 The sampling sites for the Huon Estuary Study. The sampling locations include the upper estuary stations UE, UC & UW, the lower estuary stations LE, LC & LW, and additional sampling stations at Hideaway bay (P4) and Garden island (P3). Also included is sampling station at Stingers cove, which was used in a different study, but is referred to in this study for comparative purposes.

LE LC LW P3 P4 UE UC UW Stringers Cove

Chapter Two

Sources of Organic matter in the

Huon Estuary

Chapter 2. Sources of Organic Matter

2.1 Introduction

Sediments play a vital role in the ecological functioning of an estuary by retaining much of the organic matter and minerals supplied naturally by rivers, catchment run- off and inputs from the water column. Much of the organic matter is remineralised by the microbial and faunal populations present, liberating nutrients and consuming oxygen, but more refractory material is buried in the sediments (Herbert, 1999).

The quality of the organic matter reaching the seafloor will heavily influence the rates and recycling pathways of carbon and nitrogen in sediments (Herbert, 1999). The carbon to nitrogen (C/N) ratio can be used as a proxy to measure the quality of the organic matter. A C/N ratio close to that of the Redfield ratio (6.625) is indicative of organic matter derived from microalgae while organic matter derived from terrestrial sources can have a C/N ratio of 20 or more (Bordovskiy, 1965).

Where the original organic matter undergoing decomposition has a high C/N ratio, much of the nitrogen remineralised may be reassimilated into microbial biomass (Schlesinger, 1997). Organic matter that is more labile and has a lower C/N ratio will stimulate rapid remineralisation rates and a release of nitrogen from the sediment (Hansen and Blackburn, 1992). Note, however, that as degradation proceeds the C/N ratio usually increases as nitrogen-rich labile organic matter is consumed (Thornton and McManus, 1994).

Ratios of 12C/13C stable isotopes provide a good estimate of the relative contribution of terrestrial and marine sources to sedimentary organic matter (Fry and Sherr, 1984). Terrestrial organic matter will generally have a δ13C value of -26 to -30‰ and organic matter with a marine origin will generally have a δ13C of -19‰ to -23‰ depending on the particular organisms present (Heip et al., 1995). As a first approximation, the relative proportion of marine and terrestrial carbon in a sample can be estimated by linear additions of these end-members. While this approach is relatively simple and gives an integrated estimate of sources for the total carbon in the sample, it will only provide useful information when there are two well-defined end-members.

Furthermore, this technique gives little information about the type of marine or terrestrial organic matter in question.

Various other proxies have been used to estimate the sources of organic matter in sediments and from this inferences about the amount of labile organic matter present can be made. For example, biochemical’s such as carbohydrates, proteins and lipids are rapidly degraded in sediments and so measures of their abundance provide an estimate of the labile organic matter present (Misic and Fabiano, 1996; Fabiano and Pusceddu, 1998; Pusceddu et al., 1999; Danovaro et al., 2001). Alternatively, lipid and pigment biomarkers can allow the various sources of various sub-fractions of organic matter to be identified.

Fatty acids provide a range of useful markers for microalgae, macroalgae, bacteria, seagrasses and terrestrial plants (Volkman et al., 1980; Meziane et al., 1997; Volkman et al., 1998; Kharlamenko et al., 2001). Sterols have also been used to identify

sources of organic matter including that derived from faeces, diatoms and terrestrial sources (Volkman, 1986; Barrett et al., 1995). Triterpenoid alcohols such as α- and β- amyrins, lupeol, taraxasterol, betulin etc. are widely used as markers for higher plants (e.g. Volkman et al., 1987; Volkman, 2000), even though some of these have

additional minor sources (Volkman, 2005). Hopanoid alcohols are excellent markers for cyanobacteria and other prokaryotes (Summons et al., 1999).

The aim of the work described in this chapter was to determine the source and quality of sedimentary organic matter at the two study locations to help understand how organic carbon and nitrogen is recycled in the Huon estuary. Furthermore, very few sediment ecological studies have been undertaken in cold temperate Southern hemisphere estuaries and thus these data provide a good comparison with more heavily degraded Northern hemisphere estuaries. In order to get a comprehensive picture of sedimentary organic matter a variety of organic geochemical techniques were employed including analysing the sediments for total organic carbon and nitrogen contents, δ13C and δ15N isotopes and lipid biomarkers.