152 research outputs found
Element and nutrient mass-balances in a large semi-arid riverine lake system (the Lower Lakes, South Australia)
No full textPerran Cook, Kane T. Aldridge, Sébastien
Lamontagne, Justin D. Brookeshttp://trove.nla.gov.au/work/374699
Ambient groundwater flow diminishes nitrate processing in the hyporheic zone of streams
Get PDFModeling and experimental studies demonstrate that ambient groundwater reduces hyporheic exchange, but the implications of this observation for stream N-cycling is not yet clear. Here we utilize a simple process-based model (the Pumping and Streamline Segregation or PASS model) to evaluate N-cycling over two scales of hyporheic exchange (fluvial ripples and riffle-pool sequences), ten ambient groundwater and stream flow scenarios (five gaining and losing conditions and two stream discharges), and three biogeochemical settings (identified based on a principal component analysis of previously published measurements in streams throughout the United States). Model-data comparisons indicate that our model provides realistic estimates for direct denitrification of stream nitrate, but overpredicts nitrification and coupled nitrification-denitrification. Riffle-pool sequences are responsible for most of the N-processing, despite the fact that fluvial ripples generate 3-11 times more hyporheic exchange flux. Across all scenarios, hyporheic exchange flux and the Damköhler Number emerge as primary controls on stream N-cycling; the former regulates trafficking of nutrients and oxygen across the sediment-water interface, while the latter quantifies the relative rates of organic carbon mineralization and advective transport in streambed sediments. Vertical groundwater flux modulates both of these master variables in ways that tend to diminish stream N-cycling. Thus, anthropogenic perturbations of ambient groundwater flows (e.g., by urbanization, agricultural activities, groundwater mining, and/or climate change) may compromise some of the key ecosystem services provided by streams
Factoring stream turbulence into global assessments of nitrogen pollution
Get PDFThe discharge of excess nitrogen to streams and rivers poses an existential threat to both humans and ecosystems. A seminal study of headwater streams across the United States concluded that in-stream removal of nitrate is controlled primarily by stream chemistry and biology. Reanalysis of these data reveals that stream turbulence (in particular, turbulent mass transfer across the concentration boundary layer) imposes a previously unrecognized upper limit on the rate at which nitrate is removed from streams. The upper limit closely approximates measured nitrate removal rates in streams with low concentrations of this pollutant, a discovery that should inform stream restoration designs and efforts to assess the effects of nitrogen pollution on receiving water quality and the global nitrogen cycle
Biogeochemical controls on the relative importance of denitrification and dissimilatory nitrate reduction to ammonium in estuaries
No full textCopyright (2018) American Geophysical Union.Kessler, A. J., Roberts, K. L., Bissett, A. & Cook, P. L. M. (2018) Biogeochemical controls on the relative importance of denitrification and dissimilatory nitrate reduction to ammonium in estuaries. Global Biogeochem. Cycles 32, 1045–1057, doi:10.1029/2018GB005908To view the published open abstract, go to http://dx.doi.org and enter the DOI.</div
Unravelling the nitrogen cycle in a periodically hypoxic estuary
No full textThe incidences of hypoxia (O2 < 100 µmol-O2 L-1) in coastal waters have been increasing in recent decades, largely due anthropogenic induced eutrophication. Hypoxia not only has a detrimental impact on aquatic life it can also lead to a shift in nutrient transformation pathways. To date, several studies have focused on hypoxia in deep coastal waters, such as, Chesapeake Bay (> 10 m) and the Baltic Sea (> 60 m) or oxygen minimum zones (100 - 1000 m). To my knowledge no studies currently exist on the influence of hypoxia on nitrogen cycling in a shallow (3 - 5 m) salt wedge estuary. The Yarra River estuary, Australia, the study site for this research, is a shallow salt wedge estuary prone to periods of hypoxia during low freshwater inflow events. The estuary is a conduit for the transport of nitrogen into Port Phillip Bay; a nitrogen limited system. This research investigated the influence of hypoxia on nitrogen cycling within the Yarra River estuary through two means; 1) an observational survey of in situ nitrogen behaviour in addition to the measurement of nitrate (NO3-) reduction pathways, denitrification and dissimilatory NO3- reduction to ammonium (DNRA) using the 15N isotope pairing technique. 2) an in depth experimental study on the behaviour of denitrification and DNRA under changing oxygen conditions alongside availability of reductants using microelectrodes combined with diffusive equilibrium in thin layer (DET) gels and slurries. The observational survey of the Yarra River estuary was carried out from September 2009 through to March 2011. The estuary was a source of dissolved organic nitrogen (DON) and ammonium (NH4+) during hypoxic conditions using deviations from conservative mixing (Δ). Dissolved inorganic carbon (DIC) was used as a proxy for mineralisation and comparison of the in situ nutrient measurements (whole system) and DIC and NH4+ fluxes from intact core incubations showed that NH4+ was regenerated more efficiently relative to DIC under hypoxic conditions. For the whole system, mean ∆DIC : ∆NH4+ ratios under oxic (85 ± 33) and hypoxic (20 ± 3) conditions were significantly different. The more efficient NH4+ regeneration during hypoxia was due to a disconnect between mineralisation and nitrogen removal via nitrification-denitrification coupling due the cessation of nitrification; DNRA was not a significant contributor. Unexpectedly, DNRA increased in the presence of oxygen in the water column; the mean DNRA rate under oxic conditions (124 ± 31 µmol m-2 h-1) was significantly higher than rates during hypoxia (0.6 ± 0.1 µmol m-2 h-1). High DNRA rates led to a significant decrease in the denitrification : DNRA ratio under oxic (19 ± 18) conditions compared to the ratio during hypoxia (144 ± 48). In contradiction to the current paradigm, the increased DNRA rates can be explained by the presence of Fe2+ in the sediment supported by data from both intact cores and slurries. The coupling of Fe2+ oxidation and NO3- reduction to NH4+ has been observed in a bacterial study Weber et al. (2006) however to our knowledge this is the first study to observe this process in intact estuarine sediments. The absence of DNRA under hypoxic conditions was explained by the presence of high S2- concentrations and the binding of FeS, removing available Fe2+ for DNRA. This study identified the impact of hypoxia on the nitrogen removal capacity of a shallow estuarine system; the nitrogen removal capacity of the Yarra River estuary was low with < 4 % of the dissolved inorganic nitrogen load removed when compared to 20 - 50 % removal presented for other estuarine systems. During hypoxia the removal of NO3- via denitrification was minimal compared with the efflux of NH4+ from the sediment due to the disconnect between NH4+ removal via nitrification-denitrification coupling and mineralisation. Importantly, this study observed DNRA under conditions not considered to be conducive toward this process; Fe2+ oxidation coupled to NO3- reduction to NH4+. The Yarra River estuary is prone to high inputs of iron both filterable and colloidal, and as such has high concentrations of Fe2+ in the porewaters under oxic conditions. In large rivers such as the Amazon and Mississippi, significant amounts of iron may be deposited on the continental shelf, leading to high rates of iron reduction and Fe2+ accumulation within the porewaters. It is therefore possible that Fe-driven DNRA observed in the Yarra River estuary may occur at globally significant rates within these diagenetic hotspots
Inorganic carbon dynamics in coastal marine systems
No full textCarbon dioxide (CO2) plays a central role in the Earth’s climate and there is presently a great deal of interest in the exchange of this compound between atmospheric, terrestrial and marine realms. The terrestrial-marine interface is particularly dynamic and is attracting increasing interest because there is significant material deposition and recycling at this point. While there have been many studies of carbon cycling and CO2 emissions in this environment, there have been few specific studies on how anthropogenic activities affect carbon emissions and how this affects the balance between export as carbon dioxide and dissolved inorganic carbon (DIC), or carbonate alkalinity. Unlike CO2, DIC in the form of carbonate alkalinity cannot diffuse into the atmosphere, so remains dissolved. For this reason, the production of alkalinity may control the balance of inorganic carbon export to the atmosphere and to the ocean. One major source of alkalinity production in coastal systems is sulfate reduction. In order for a net alkalinity flux to occur, the product of sulfate reduction, sulfide, must be buried as iron sulfide (FeS) so that it is not reoxidised, consuming alkalinity. I therefore expect the burial of reduced solutes to play a key control over the release of inorganic carbon as CO2 (to the atmosphere) and alkalinity (exported to the ocean). This thesis examines the following 3 questions, each of which is on a different spatial scale: 1. Does alkalinity generation within tidal flat sediments control the relative export of inorganic carbon to the atmosphere and to coastal waters? 2. Do differing degrees of terrestrial inputs influence the dominant modes of carbon export from tidal flats? 3. Do differing regimes of anthropogenic land use in river catchments control inorganic carbon and alkalinity production in estuaries? In chapter 2, I investigated dissolved inorganic carbon (DIC), gaseous CO2 and total alkalinity (TA) fluxes from intertidal mudflats during periods of exposure and inundation, using laboratory core incubations, field data and reactive transport model simulations. During periods of alkalinity production, the flux of DIC out of the sediment was 1.8 times greater during inundation than exposure. The observed alkalinity production was attributed to the accumulation of reduced sulfur species within the sediment. This finding was supported by the reactive transport simulations, which showed that large amounts of sulfate reduction and subsequent reduced sulfur burial, as FeS, induced an alkalinity flux from the sediment during high tide conditions. Model simulations also found that the amount of oxidised Fe in the sediment influences the extent of net alkalinity production. Our finding, that CO2 fluxes can be significantly lower than total metabolism during exposure, has implications for studies that aim to measure metabolism on tidal flats. In chapter 3, carbon and TA export from two adjacent intertidal inlets with different terrestrial inputs were investigated. One inlet receives water from a small creek from a highly impacted, agriculturally dominated catchment, leading to the input of terrestrially sourced material; whereas, the other is relatively isolated from terrestrial inputs. The inlet with the greater amount of terrestrial inputs exported much more TA (310 vs. 46 mmol m-2 d-1), indicating that the extent of land-to-sea connectivity influences how carbon is exported from this interface. I hypothesize this is due to the increased input of iron from terrestrial sources, which fosters net TA production through the burial of reduced sulfur species as iron sulfides as found by the previous chapter. A simple mass balance showed the TA fluxes observed over 24 h were higher than could be sustained continuously with iron input from the catchment (0.49 mmol Fe m-2 d-1), indicating that the observed TA fluxes could not be sustained on long times scales by this mechanism. It is likely that there are periods of net reduction and net oxidation in response to wave action and calm conditions, highlighting the importance of long term monitoring over different seasons and weather patterns to obtain representative budgets. Keeling plots of δ13CDIC measurements over the sampling period suggested the source of DIC was from mineralisation of seagrass/microphytobenthos and mangrove organic matter. The carbon budget I produced showed that DIC was the dominant mode of carbon export from mangroves, which is relevant to recent investigations on the missing mangrove carbon sink. The 222Rn data collected during the time series measurements indicated that porewater exchange played an important part in controlling carbon export from the sediment and the residence time of porewater within both inlets was ~6.6–7.4 h, indicating that porewater exchange was driven by tidal pumping. In chapter 4, I used δ13CDIC, DIC, TA and partial pressure of carbon dioxide (pCO2) measurements to determine the dominant carbon cycling processes; aerobic respiration, anaerobic respiration (alkalinity generation) and photosynthesis in eight Southern Australian temperate estuaries. For each estuary, I calculated inorganic carbon and alkalinity budgets, and using δ13CDIC measurements, I employed a mass balance approach to determine the drivers of DIC production or consumption in the estuaries. By comparing the export of carbonate alkalinity from estuaries with varying catchment land uses, I was able to determine the differences in carbon dynamics under different levels of land use impact within the catchment. All but the least impacted estuaries showed clear non-conservative mixing behaviour of DIC, TA and δ13CDIC. The estuaries ranged between large sources and large sinks of atmospheric CO2, with fluxes from -17 – 502 mmol m-2 d-1, and were highly dependent on the sampling period. It was found that in highly impacted estuaries, there were often high rates of DIC production within the estuary (up to 510 mmol m-2 d-1) and this coincided with a high production of alkalinity(up to 273 mmol m-2 d-1). As more impacted catchments will tend to export more organic carbon and Fe, the higher rates of DIC and alkalinity production are expected owing to the burial of reduced solutes as discussed previously. Likewise, in some estuaries, high rates of photosynthesis reflect the higher loadings of inorganic nutrients from more impacted catchments. The export of alkalinity from highly impacted estuaries was highly variable between seasons. I hypothesise this is due to a higher amount of FeS being buried within sediments, which is easily oxidised when conditions permit
The biogeochemistry of phosphorus in a temperate coastal lagoon afflicted by recurring cyanobacterial blooms
No full textEstuaries and coastal waters are highly productive ecosystems that provide critical habitats and nurseries for many marine species in additional to other environmental and economic values. Recent research all points to changes in anthropogenic input of nutrients to estuaries as the primary cause of increasing eutrophication. The role of nitrogen (N) and phosphorus (P) as the primary agents of eutrophication and the link to the formation of harmful algal blooms is increasingly being studied. Studies into P dynamics show that P is not uniformly mixed within an ecosystem, but rather partitioned into ‘pools’ (eg. Dissolved within the water column/pore water, and buried within the solid phase). These pools of P exhibit vastly different dynamics and as such offer differing degrees of bioavailbility/lability with only the highly labile pools observed to be contributing the estuarine eutrophication. It is well known that phosphorus within the sediment is closely associated with Fe oxides of aquatic systems and that this Fe associated pool can be released with the onset of anoxic conditions and increased organic matter loading. Very few studies have, however, quantified this pool size and dynamic in estuarine systems and how this relates to cyanobacterial bloom dynamics, which are typically P limited. This research investigated the biogeochemical processes fuel the significant cyanobacterial blooms that occur within the Gippsland Lakes, Australia, a coastal lagoonal system prone to extended periods of anoxia and recurrent diazotrophic cyanobacterial blooms (Nodularia spumigena) through two means: (1) a whole system nutrient budget model that incorporates seasonal effects of nutrient inputs and the resultant impacts on the development of summer time cyanobacterial blooms, and (2) an in-depth investigation into the large fluxes of P released from sediments during summer anoxia, through a series of intact sediment core experiments aimed at identifying the highly labile and bioavailable components of the sedimentary Fe and P cycle. The whole system nutrient budget model (LOICZ) of the Gippsland Lakes was carried out from the 1st June 2010 through to 28th March 2012. The LOICZ budget model (LBM) highlighted a number of key features in the cycling of nutrients within the Gippsland Lakes leading up to and during a significant cyanobacterial bloom. These include a flood event (21st July 2011 – 18th August 2011) during which large loads of both Total Nitrogen (TN - 76.1 Mmol) and Total Phosphorus (TP - 3.4 Mmol) were input into the Gippsland Lakes. In the post flood period (19th August 2011 – 20th November 2011) increased nutrient concentrations, surface water temperatures and light availability favoured phytoplankton growth and both diatom and dinoflagellate species began to bloom, lowering the dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) concentrations within the surface waters. Following the mixed diatom-dinoflagellate bloom, water column stratification increased and respiration in the bottom waters caused dissolved oxygen concentrations to decline, creating hypoxic/anoxic bottom waters. Upwelling of DIP (0.83 Mmol) across the pycnocline from the nutrient rich bottom waters to the surface waters, occurred late in the post flood period. This upwelling further drove the development of conditions within the surface waters that were favourable to significant diazotrophic cyanobacterial growth (1:1.3 DIN:DIP). During the initial cyanobacterial bloom period (21st November 2011 – 14th December 2011) N-fixation rates of 8.6 Mmol were calculated for the initial growth period and accounted for 23% of the annual (yearly) input and 196 % of the summer riverine TN input into Lake King. Overall, the Gippsland Lakes were found to be a sink of nutrients across the entire study period, with a calculated annual net retention of both TN 8 % (230 tonnes) and TP 5 % (18 tonnes). The budget model also revealed a large gap in the P budget owing to a significant internal source of P (P released from the sediments ~2.5 Mmol). The internal P flux represented 20 % of the calculated annual riverine input of P from the catchment. The storage and release of P from the sediments was further investigated using a sequential extraction scheme that used ascorbate to extract P and Fe associated with the reactive Fe oxide phase. The ascorbate extraction revealed deep pools of the Fe-bound P within the sediment of up to ~5 mol-P g-1 dry sediment down to ~20 cm depth. This pool of P rapidly decreased with the onset of bottom water anoxia, leading to a release of 2.80 mmol P m-2 d-1 for a period of 105 days. Integrated over the periodically anoxic portion (>7 m depth contour, equating to a surface area of 5 km2) of the lake, this equated to a total P release of 1.4 Mmol. Upon re-oxygenation of the bottom waters, a rapid partial regeneration (14-27%) of the deep Fe-bound P pool was observed in intact core experiments. Extraction analysis performed on suspended sediment entering the Gippsland Lakes indicated that ~60 % of the P associated with particulate material could be considered bioavailable to primary producers (extracted by MgCl2 and ascorbate). Combining the extraction analysis from the suspended sediment with the loads of TP calculated by the LBM, the Gippsland Lakes could receive up to ~11.5 Mmol yr-1 (~6.9 Mmol bioavailable P yr 1), approximately twice the amount of P released from the sediment. We speculate however, that most of this catchment derived P transits the lakes, as it is delivered during flood events. A re-oxidation experiment was undertaken using intact sediment cores collected during bottom water anoxia. The water column was subsequently re-oxygenated and cores were extracted using the modified extraction scheme to identify Fe and P concentrations for a period of 40 days. The re-oxidation experiment revealed the presence of the common polychaete worm Capitella capitata within the sediments at the Lake King North study site in densities of 2900 ± 600 individuals m-2. This experiment confirmed the regeneration of the Fe-bound P observed in previously in-situ and suggested a link between the bioirrigating behaviour of C. capitata and the formation of deep sediment pools of P. A further experiment using a two dimensional oxygen sensor (planar optode) showed flushing events by C. capitata could deliver dissolved oxygen concentrations to a sediment depth of up to 4 cm. An inert tracer experiment was used to quantify C. capitata bioirrigation rates (5.9 38.3 L m 2 d-1) and indicated that irrigation could extent to depths greater than observed oxygen (O2) penetration (potentially 5-10cm). I speculate that the production of Nitrate (NO3-) in the presence of O2 and the subsequent transport to depths greater than observed O2 penetration (via bioirrigation) can mediate the regeneration of the reactive iron oxides and subsequent Fe-bound P through the microbial driven Fe(II) oxidation by NO3-. Multiplying the bioirrigation rates and the average pore water P concentrations in the top 5 cm of sediment (98 µmol L-1, based on data from sediment core 16th February 2012), yields fluxes of P ranging from 0.58 – 3.78 mmol m-2 d-1, which encompasses the flux of 2.80 mmol m-2 d-1 calculated via the mass balance. Overall, C. capitata appear to play a significant role in the Gippsland Lake sediments by acting as biogeochemical amplifiers, mediating the enhancement of both the release of the bioavailable Fe-bound P during anoxia and the subsequent rapid regeneration during oxygenated conditions. This study underscores the importance of internal P cycling in sediments colonised by deep irrigating fauna. It allows highlights the potential negative feedback of P released during water column anoxia due to the cessation of bioirrigation, resulting in optimum nutrient conditions in the water column for diazotrophic cyanobacterial growth
Understanding denitrification in permeable sands
No full textSandy sediments cover the majority of the continental shelf, and yet are poorly understood compared with the cohesive, muddy sediments often observed in rivers, lakes and estuaries. A major difference between the two types of benthos lies in solute transport – slow, homogenous diffusion in muds, compared with rapid, two-dimensional advection through sands. This difference massively affects the biogeochemistry of permeable sediments, but its effects on denitrification – the major process for N removal from most systems – are poorly understood. In this thesis, denitrification in permeable sediments is investigated under a variety of scenarios. First, a combined laboratory and modelling approach is used to demonstrate that the rapid transport in permeable sediments limits the effectiveness of coupled nitrification-denitrification, significantly limiting overall denitrification rates in permeable sediments. Second, the effect of these transport phenomena on 15N isotope fractionation during denitrification is investigated. The apparent effect observed is consistent with low denitrification rates and supports the low isotope fractionation observed in global oceans. Third, a modelling investigation seeks to test a hypothesis that carbonate sands are capable of higher denitrification rates compared with quartz sands, due to pores within the grains themselves facilitating high rates of coupled nitrification-denitrification. The models indicate that this sort of intragranular reaction is plausible, and could indeed lead to higher denitrification rates in a real system. Finally, a further computational study investigates the effect that migrating ripples may have on denitrification in permeable sediments. While moving ripples drive very different transport and solute distribution, the rates of denitrification in sediments with moving ripples is similar to those with stationary ripples
Root effects on the spatial and temporal dynamics of oxygen in sand-based laboratory-scale constructed biofilters
No full textIt is now well known that roots introduce oxygen into the soil environment through radial oxygen loss. The oxygen dynamics surrounding roots in periodically flushed environments, however, remains unstudied. We investigated the impact of roots of the macrophyte Carex appressa (Cyperaceae), on the small (rhizosphere) scale spatiotemporal dynamics of sediment oxygen consumption in a periodically flushed soil mimicking natural percolation events. Oxygen dynamics around the roots of C. appressa were studied using a planar optode installed in a rhizobox containing sand. A sand-based culture medium was used to simulate conditions in constructed biofiltration wetlands. The use of planar optodes allowed the generation of two dimensional images of sediment oxygen dynamics, that were used to quantify the patterns and kinetics of oxygen consumption. In addition to greatly increasing the spatial heterogeneity of oxygen in the substrate, the area immediately surrounding the roots became sites of both enhanced oxygen consumption, likely due to increased microbial activity associated with the input of carbon-rich rhizodeposits, and radial oxygen loss. This study highlights the profound impact of roots upon sub-surface oxygen dynamics in the rhizosphere. © 2013 Elsevier B.V.David A. Minett, Perran L.M. Cook, Adam J. Kessler, Timothy R. Cavagnar
Testing assumptions of the eukaryotic inhibitor method for investigating interactions between aquatic protozoa and bacteria, applied to marine sediment
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