Freshwater inflows to estuaries : organic carbon and microbial food webs in south-east Australia

University of Technology, Sydney. Faculty of Science.Freshwater inflows (FWI) play a crucial role in maintaining estuarine processes and productivity. River regulation and extraction have greatly reduced FWI to estuaries. Little attention has been paid to the role FWI has in delivering organic carbon to estuaries. The aim of this thesis was to define the relationship between freshwater inflows, organic carbon, bacteria and zooplankton dynamics. To do this, I performed a series of monitoring and experimental studies on the Bega and Clyde River estuaries, Australia. Discharge on both rivers was highly episodic during the study. On the Bega and Clyde Rivers, increasing dissolved organic carbon (DOC) concentrations were closely coupled with increasing discharge. The bioavailability of DOC increased during FWI events, and in turn bacterial growth rates were also higher during and immediately following inflow events. Bacterial growth was carbon limited most of the time, though during high flows, bacteria often became phosphorus limited. Changing availability of DOC and phosphorus during inflow events was the main reason for shifting resource limitation. On both rivers bacterial biomass was positively related to increasing DOC and phosphorus concentrations. Highly episodic discharge during this study had a major structuring role over carbon and bacteria dynamics. On the Bega River I found strong evidence that allochthonous carbon and bacteria can subsidise zooplankton production following the input of DOC during FWI events. Zooplankton density increased following a flooding event on the Bega River and stable isotope analysis indicated allochthonous terrestrial carbon was the dominant source of carbon utilised by zooplankton. Experimental mesocosms confirmed that allochthonous carbon and bacteria can support increased zooplankton in the presence of high subsidies. The individual studies forming this thesis all contribute new insights to their respective sub-disciplines within aquatic ecology. Viewed together, they present a novel conceptualisation of hydrology and freshwater inflows in the coastal carbon cycle and microbial food webs in south-east Australian estuaries. The results provide a strong case to protect freshwater inflows to estuaries

Highs and lows: The effect of differently sized freshwater inflows on estuarine carbon, nitrogen, phosphorus, bacteria and chlorophyll a dynamics

© 2014. Freshwater inflows play a key role in the delivery of organic carbon to estuaries. However, our understanding of the dynamics between discharge and carbon globally is limited. In this study we performed a 30-month monitoring study on the Bega and Clyde River estuaries, Australia, to understand the influence that discharge had on carbon, nitrogen, phosphorus, bacteria and chlorophyll a dynamics. We hypothesised that 1) discharge would be the most important factor influencing carbon and nutrient concentrations, though during low flows chlorophyll a would also be positively related to carbon, 2) bacteria would be related to dissolved organic carbon (DOC), and chlorophyll a to temperature, nitrogen and phosphorus, and 3) that concentrations of carbon, nitrogen, phosphorus, bacterial biomass and chlorophyll a would be significantly different between large 'flood flows', smaller 'fresh flows' and base flow conditions. We found that discharge was always the most important factor influencing carbon and nutrient concentrations, and that primary production appeared to have little influence on the variation in DOC concentration even during base flow conditions. We suggest this relationship is likely due to highly episodic discharge that occurred during the study period. Bacteria were related to DOC in the lower estuary sites, but phosphorus in the upper estuary. We suggest this is likely due to the input of bioavailable carbon in the upper estuary leading bacteria to be P limited, which changes downstream to carbon limitation as DOC becomes more refractory. Chlorophyll a was positively related to temperature but not nutrients, which we suggest may be due to competition with bacteria for phosphorus in the upper estuary. Carbon, nitrogen and phosphorus concentrations were different under flood, fresh and base flow conditions, though these differences sometimes varied between estuary locations for different resources. Overall, the results demonstrate that discharge plays an important structuring role for carbon, nutrient and bacteria dynamics on the Bega and Clyde Rivers, and that the differences observed between flood and fresh inflows suggest that further study into the influence of differently sized inflow events is important

Prediction of Ubiquitination Sites by Using the Composition of k-Spaced Amino Acid Pairs

As one of the most important reversible protein post-translation modifications, ubiquitination has been reported to be involved in lots of biological processes and closely implicated with various diseases. To fully decipher the molecular mechanisms of ubiquitination-related biological processes, an initial but crucial step is the recognition of ubiquitylated substrates and the corresponding ubiquitination sites. Here, a new bioinformatics tool named CKSAAP_UbSite was developed to predict ubiquitination sites from protein sequences. With the assistance of Support Vector Machine (SVM), the highlight of CKSAAP_UbSite is to employ the composition of k-spaced amino acid pairs surrounding a query site (i.e. any lysine in a query sequence) as input. When trained and tested in the dataset of yeast ubiquitination sites (Radivojac et al, Proteins, 2010, 78: 365–380), a 100-fold cross-validation on a 1∶1 ratio of positive and negative samples revealed that the accuracy and MCC of CKSAAP_UbSite reached 73.40% and 0.4694, respectively. The proposed CKSAAP_UbSite has also been intensively benchmarked to exhibit better performance than some existing predictors, suggesting that it can be served as a useful tool to the community. Currently, CKSAAP_UbSite is freely accessible at http://protein.cau.edu.cn/cksaap_ubsite/. Moreover, we also found that the sequence patterns around ubiquitination sites are not conserved across different species. To ensure a reasonable prediction performance, the application of the current CKSAAP_UbSite should be limited to the proteome of yeast

Environmental controls, oceanography and population dynamics of pathogens and harmful algal blooms: connecting sources to human exposure

© 2008 Author et al. This is an open access article distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Health 7 (2008): S5, doi:10.1186/1476-069X-7-S2-S5.Coupled physical-biological models are capable of linking the complex interactions between environmental factors and physical hydrodynamics to simulate the growth, toxicity and transport of infectious pathogens and harmful algal blooms (HABs). Such simulations can be used to assess and predict the impact of pathogens and HABs on human health. Given the widespread and increasing reliance of coastal communities on aquatic systems for drinking water, seafood and recreation, such predictions are critical for making informed resource management decisions. Here we identify three challenges to making this connection between pathogens/HABs and human health: predicting concentrations and toxicity; identifying the spatial and temporal scales of population and ecosystem interactions; and applying the understanding of population dynamics of pathogens/HABs to management strategies. We elaborate on the need to meet each of these challenges, describe how modeling approaches can be used and discuss strategies for moving forward in addressing these challenges.The authors acknowledge the financial support for the NSF/NIEHS and NOAA Centers for Oceans and Human Healt

Five Nuclear Loci Resolve the Polyploid History of Switchgrass (Panicum virgatum L.) and Relatives

Polyploidy poses challenges for phylogenetic reconstruction because of the need to identify and distinguish between homoeologous loci. This can be addressed by use of low copy nuclear markers. Panicum s.s. is a genus of about 100 species in the grass tribe Paniceae, subfamily Panicoideae, and is divided into five sections. Many of the species are known to be polyploids. The most well-known of the Panicum polyploids are switchgrass (Panicum virgatum) and common or Proso millet (P. miliaceum). Switchgrass is in section Virgata, along with P. tricholaenoides, P. amarum, and P. amarulum, whereas P. miliaceum is in sect. Panicum. We have generated sequence data from five low copy nuclear loci and two chloroplast loci and have clarified the origin of P. virgatum. We find that all members of sects. Virgata and Urvilleana are the result of diversification after a single allopolyploidy event. The closest diploid relatives of switchgrass are in sect. Rudgeana, native to Central and South America. Within sections Virgata and Urvilleana, P. tricholaenoides is sister to the remaining species. Panicum racemosum and P. urvilleanum form a clade, which may be sister to P. chloroleucum. Panicum amarum, P. amarulum, and the lowland and upland ecotypes of P. virgatum together form a clade, within which relationships are complex. Hexaploid and octoploid plants are likely allopolyploids, with P. amarum and P. amarulum sharing genomes with P. virgatum. Octoploid P. virgatum plants are formed via hybridization between disparate tetraploids. We show that polyploidy precedes diversification in a complex set of polyploids; our data thus suggest that polyploidy could provide the raw material for diversification. In addition, we show two rounds of allopolyploidization in the ancestry of switchgrass, and identify additional species that may be part of its broader gene pool. This may be relevant for development of the crop for biofuels

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

Storm events as key moments of microplastic contamination in aquatic ecosystems.

Microplastic (MP) pollution is an emerging issue in aquatic sciences. Rain and storm events are responsible for the mobilization and transport of a range of pollutants in aquatic systems, yet to date no study has examined how microplastic abundance changes in waterways during such events. The aim of this study was to determine how microplastic concentrations changed over the course of the storm event in an urban estuary. Sampling was conducted at high frequency before, during, and after a storm event that caused flooding in the Cooks River estuary, Australia. Microplastic abundance increased during two days of heavy rain from 400 particles m3 before storm event to up to 17,383 particles m3 after the event. Variation in microplastic abundance was positively related to five-day average antecedent rainfall. The results highlight the importance of rain and storm events as key moments of microplastic contamination in aquatic systems. The results have implications for considering the maximum number of microplastics that aquatic life may be exposed to and the importance of strategies to manage stormwater to minimize the input of microplastics to aquatic ecosystems

Microplastic pollution in estuaries across a gradient of human impact

© 2019 Elsevier Ltd Microplastic (MP) pollution is an emerging issue in aquatic sciences. Little comparative information currently exists about the problem in coastal systems exposed to different levels of human impact. Here we report a year-long study on the abundance of MP in the water column of three estuaries on the east-coast of Australia. The estuaries are subject to different scales of human impact; the Clyde estuary has little human modification, the Bega estuary has a small township and single wastewater treatment works discharging to its waters, and the Hunter estuary which has multiple townships, multiple wastewater treatment plants, and heavy industry. MP abundance followed an expected pattern with the lowest abundance in the low-impact Clyde estuary (98 part. m3), moderate levels of MP in the moderately impacted Bega estuary (246 part. m3), and high MP abundance in the highly impacted Hunter estuary (1032 part. m3). The majority of particles were <200 μm and fragment-like rather than fiber-like. MP abundance was positively related to maximum antecedent rainfall in the Bega estuary, however there are no clear environmental factors that could explain MP variation in the other systems. MP were generally higher in summer and following freshwater inflow events. On the Hunter estuary MP abundance was at times as high as zooplankton abundance, and within the range of numbers reported in other highly impacted systems globally. The results confirm that higher levels of human impact lead to greater plastic pollution and highlight the need to examine aquatic ecosystems under a range of conditions in order to adequately characterize the extent of MP pollution in rivers and coastal systems

Different resource limitation by carbon, nitrogen and phosphorus between base flow and high flow conditions for estuarine bacteria and phytoplankton

Freshwater inflows can deliver substantial inputs of allochthonous organic carbon to estuaries. The role that allochthonous DOC has on structuring bacterial and phytoplankton communities is still not well understood. We performed a series of 1.25L bioassay limitation experiments on the Bega and Clyde River estuaries in NSW, Australia, examining what resources limit bacteria and phytoplankton growth. We hypothesized that during base flow conditions bacteria would be carbon limited, and after high flow conditions they would be nutrient limited. A full factorial design was used with additions of carbon (glucose), nitrogen (KNO3) and phosphorus (KH2PO4). During the experiments that took place during base flow conditions bacteria were always primarily C-limited. After high flow conditions, bacteria were P-limited on the Clyde River, and remained C-limited on the Bega River. Phytoplankton growth was limited at all times in each estuary, tending toward N-limitation on the Bega River and P-limitation on the Clyde river. During high flow conditions on the Clyde River, when bacteria and phytoplankton were both primarily P-limited, it appeared that bacteria was able to outcompete phytoplankton for nutrients. These results suggest that freshwater inflows and allochthonous DOC maybe important in structuring estuarine microbial ecosystems and individual estuaries may behave differently in terms of their limiting resources. © 2013 Elsevier Ltd