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Abstract

Sediment biogeochemistry was studied in the Huon estuary, which is located in
Southern Tasmania, Australia. The sources of organic matter and rates of
decomposition were investigated as well as fluxes of nutrients, which are liberated
during organic matter decomposition. The study aimed to develop a conceptual
understanding of benthic respiration and nutrient cycling in the Huon estuary and the
influence of organic carbon on these processes. This study also sought to evaluate the
ecological significance of nutrient inputs from sediments compared with other
nutrient sources to the estuary.
Sediments were studied over one year, including sampling in March, July and
November in 2004 and then in April 2005. To represent the terrestrial and marine end
members of the estuary, locations were situated in the upper and lower reaches
respectively.
Employing a variety of organic – geochemical approaches, this study showed that
sediments were dominated (i.e. >50%) by allochthonous, river-supplied terrestrial
organic matter. Spatial differences were observed between the upper and lower
locations with the upper estuary receiving most of its source of organic matter from
terrestrial sources (approx. 75%). In contrast, the lower location had a greater variety
of organic matter sources, with approximately 50% coming from terrestrial sources,
approximately 20% from phytoplankton and about 15% from bacteria. No discernable
differences were found between sampling stations within each location.
Organic matter source markers for some inputs, in particular markers for terrestrial
organic matter, were higher in winter, most likely due to an increase in input from
catchment runoff. Increased river flows were observed in July during this study,
carrying higher concentrations of particulate organic matter from catchment runoff,
which is likely to increase the terrestrial detritus load at the seafloor as indicated by
the increase in terrestrial biomarkers during this period.
Oxygen and CO2 fluxes indicated that aerobic respiration was one of the main
pathway for carbon degradation in Huon estuary sediments, although anaerobic respiration was also present. The low CO2:O2 and Alkalinity:O2 flux ratios was
evidence of aerobic respiration. Additionally modelled oxygen consumption profiles
showed that the majority of oxygen was consumed near the surface, most likely due
to aerobic heterotrophic bacteria. A small oxygen consumption peak was also
observed at the anoxic/oxic interface most likely due to sulphide oxidation.
Spatial and temporal differences in respiration occurred with carbon contents and
temperature considered the main drivers respectively for this variability. Differences
also occurred between total versus diffusive oxygen uptake rates, and was likely due
to the presence of benthic fauna. Respiration in Huon estuary sediments compared
well with other deep coastal sediments whereby rates of TCO2 and O2 fluxes were
very similar to Monterey Bay in California and the Southern Kattergat in the Baltic
Sea
Benthic fluxes of nutrients were low in the Huon estuary. Average fluxes of
ammonia, nitrate, phosphate and silicate were 1.3, 10.1, 1.6 and 32.5 μmol m-2 h-1
respectively. An extrapolation of these measurements to the whole estuary revealed
that the sediments were only a minor source of nutrients, providing approximately 96
tonnes of inorganic nitrogen, 32 tonnes of phosphate and 586 tonnes of silicate.
On all occasions, the DIN flux was dominated by nitrate, which was always released
from the sediment to the overlying water. The effluxes of nitrate and influxes of
nitrite and ammonium are most likely associated with intensive nitrification,
stimulated by the presence of relatively deep oxygenated zones. Peaks of nitrate in the
oxic zone observed from nitrate pore water profiles also provided additional evidence
of nitrification. The net efflux of nitrate from the sediments, suggests that they act as
net regenerators of nitrogen as opposed to nitrogen assimilators.
The benthic effluxes of nitrogen however were smaller then expected from carbon
oxidation rates. The low N:P ratio of benthic fluxes (approx. 3:1) indicates that
processes such as denitrification and anaerobic ammonium oxidation (ANAMMOX)
may be important nitrogen elimination process. However another potential pathway
for nitrogen released during organic matter remineralisation is for the decomposing bacteria to reassimilate some of the ammonium due to the low nitrogen content of the
organic matter been decomposed.
Due to increasing levels of chlorophyll a, largely due to the growing aquaculture
industry, a laboratory experiment was conducted to observe the response of Huon
estuary sediments to increasing loads of labile organic carbon. The addition of
Spirulina, produced a dramatic increase in the flux rates of all analytes. The change in
fluxes for most analytes correlated well with increasing carbon loading however the
rate change occurred in two distinct stages for some of the analytes, including oxygen
and ammonium. Results showed rapid change in oxygen and ammonium flux rates
and oxygen penetration with increasing carbon load size. However when the carbon
load became >20.2 g C m-2 the change in flux rates and decrease in oxygen
penetration slowed significantly for these analytes.
The point at which the rate change of fluxes slowed possibly indicates that the
biogeochemical system was switching from one that was dominated by aerobic
respiration to one dominated by anaerobic respiration. A number of trends in the data
indicate this including increasing CO2:O2 ratio, increasing alkalinity fluxes out of the
sediments, most likely due to sulphate reduction: an anaerobic metabolic process, and
declining oxygen penetration depths. DIN fluxes also became dominated by
ammonium rather then nitrate as sediments became more anaerobic. Nitrate effluxes,
evidence of nitrification, rapidly became nitrate fluxes into the sediment, suggesting
denitrifiers could no longer obtain nitrate in situ due to the reduction in nitrification,
and thus the breakdown of coupled nitrification/denitrification. As the sediments
became anaerobic, denitrification became dominated by direct denitrification whereby
denitrifiers obtain their nitrate requirements from the water column, as evidenced by
uptake of nitrate by the sediments. Dissimilatory nitrate reduction to ammonium
(DNRA) may also have contributed to the large efflux of ammonium as sediments
became more anaerobic.
This study has provided insights into how sediments function in relatively pristine
coastal environments, in particular what the sediments are not doing at the moment
(such as releasing large amounts of ammonium), but what they could be doing if
labile organic carbon is increased. The findings have provided a good contrast to sediments that exist in environments exposed to increasing anthropogenic influence
and provide a snapshot of how heavily polluted systems may once have functioned.
This study has therefore added to the growing literature of how coastal sediments
recycle carbon and nitrogen and their importance to local and global carbon and
nitrogen cycles.
Finally this thesis has shown that it is difficult to interpret specific processes such as
nitrification and denitrification from core incubations and the inferred stoichiometric
relationships of the carbon, nitrogen and phosphate fluxes due to the complex nature
of biogeochemical processes occurring in the sediments at any time. To build on the
foundations laid by this study, the next step would be to carry out a set of carefully
designed experiments in regards to both benthic respiration and nutrient cycling. In
particular, an experiment that simultaneously measures bacterial nitrogen
assimilation, ANAMMOX, denitrification and nitrification would be useful to gain a
better understanding of the nitrogen cycle. These experiments should be carried out
under both unimpacted and impacted sediments as while I have shown that organic
carbon loading alters sediment metabolism which is consistent with the literature, at
this stage it is still unknown as to exactly how benthic metabolism would be
controlled if farming does greatly increase. Furthermore, how these individual
processes (i.e. nitrification, ANAMMOX, denitrification and DNRA) collectively
influence nutrient fluxes from the sediment under unimpacted and impacted
conditions needs to be elucidated.

Item Type:	Thesis - PhD
Authors/Creators:	Thomson, DC
Additional Information:	Copyright © the Author
Item Statistics:	View statistics for this item

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