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© The Author 2014. Published by Oxford University Press. All rights reserved. The zooplankton community changes that may occur with increases in concentration of allochthonous dissolved organic carbon (DOC) are not well understood in unconstrained lowland rivers. We examined in mesocoms over 8 days the short-term responses of river zooplankton to amendments of DOC from two different sources, glucose and leachates of a common riparian tree (Eucalyptus camaldulensis; river red gum) both alone and with inorganic nutrients added. DOC additions with and without nutrients increased heterotrophic respiration and led to significant increases in bacterial biomass. These responses varied between glucose and leachate addition. In treatments with added DOC, zooplankton density significantly increased relative to controls. Some zooplankton genera only responded to the leachate as a DOC source, and community structures significantly varied between the control and the glucose and leachate amendments. Zooplankton are particularly important in lowland river systems as they are key organisms for the transfer of carbon to higher trophic levels and this study indicates that allochthonous DOC has the potential to be an important basal resource to lowland river food webs. This may be particularly important in lowland sections of unconstrained flood plain rivers during and immediately following floods when allochthonous DOC is more available.

Non-protein amino acids (NPAAs) are a large class of amino acids (AAs) that are not genetically encoded for translation into proteins. The analysis of NPAAs can provide crucial information about cellular uptake and/or function, metabolic pathways, and potential toxicity. β-methylamino-L-alanine (BMAA) is a neurotoxic NPAA produced by various algae species and is associated with an increased risk for neurodegenerative diseases, which has led to significant research interest. There are numerous ways to extract AAs for analysis, with liquid chromatography-tandem mass spectrometry being the most common, requiring protein precipitation followed by acid hydrolysis of the protein pellet. Studies on the presence of BMAA in algal species provide contradictory results, with the use of unvalidated sample preparation/extraction and analysis a primary cause. Like most NPAAs, protein precipitation in 10% aqueous TCA and hydrolysis with fuming HCl is the most appropriate form of extraction for BMAA and its isomers aminoethylglycine (AEG) and 2,4-diaminobutyric acid (2,4-DAB). The present protocol describes the steps in a validated NPAA extraction method commonly used in research and teaching laboratories.

Macrophytes can be crucial for maintaining clear water conditions in temperate shallow lakes. However, their restorative potential and role in regulating phytoplankton remains uncertain in tropical lakes. We investigated the effects of emergent (Ludwigia adscendens and Persicaria barbata) and submerged (Vallisneria spiralis) macrophytes on the phytoplankton community of a turbid tropical reservoir. Through two in situ mesocosm experiments (~ 1000 l capacity) lasting 4 weeks, we (1) determined the effects of macrophyte density on phytoplankton biomass and composition, and (2) compared these effects between emergent and submerged macrophytes. In Experiment 1, macrophyte treatments reduced phytoplankton biomass and increased water clarity in a density-dependent manner. Only the ‘high density’ treatment (300 g/m2 emergent and 650 g/m2 submerged macrophytes) induced a taxonomic and functional shift from an initial community dominated by turbid water-adapted filamentous cyanobacteria to one dominated by clear water-adapted green algae and cryptophytes. In Experiment 2, emergent and submerged macrophytes reduced phytoplankton biomass and distinctly altered taxonomic and functional composition, with submerged macrophytes inhibiting Microcystis and stimulating cryptophyte taxa. Our results indicate that macrophytes can induce substantial phytoplankton community shifts in turbid tropical lakes, demonstrating the potential to assist in the reversal from turbid to clear water states during restoration efforts.

Mass fish kills capture the world’s attention and their frequency is increasing worldwide. The sudden death of many millions of native fish in the Darling–Baaka River in Australia in 2018–19 was a catalyst for the 11 articles in this special issue. Collectively, they advance our understanding of how to manage these events, dealing with: ecological impacts and recovery; technologies and approaches for prediction, preparedness and response; and the role of the public in preparing and responding to these catastrophic events.

Cyanobacterial blooms have major impacts on the ecological integrity and anthropogenic value of freshwater systems. Chrysosporum ovalisporum, a potentially toxic cyanobacteria has been rare in Australian waters until recently when is has bloomed in a number of lake and river systems. The aim of this study was to determine drivers of its growth and growing dominance. We performed regular monitoring of Mannus Lake, a small freshwater reservoir in South-Eastern Australia that has recently undergone extremely dense bloom events. Blooms of the diazotrophic Chrysosporum ovalisporum occurred in both summers of the 19 month study during periods of persistent thermal stratification. Following the C. ovalisporum blooms, non-diazotrophic taxa (Microcystis aeruginosa and Woronichinia sp.) dominated the phytoplankton community under less stratified conditions. Thermal stratification and nitrogen availability appeared to be the primary drivers of changes in cyanobacterial community structure. We propose that the observed transition from C. ovalisporum to M. aeruginosa and/or Woronichinia sp. may be a result of nitrogen limitation in early summer, which combined with persistent thermal stratification led to an ecological advantage for the nitrogen-fixing C. ovalisporum. Mixing events caused the senescence of the C. ovalisporum bloom, likely supplementing the nutrient budget of the lake with atmospherically derived N and alleviating N limitation to non-diazotrophic taxa. Non-diazotrophic cyanobacterial growth then increased, albeit at much lower biovolumes compared to the initial bloom. Overall, the results demonstrate the role of thermal stratification and nutrient cycling in structuring the cyanobacterial community and provide insights into the environmental factors driving the proliferation of the relatively new, potentially toxic cyanobacterium C. ovalisporum in Australian waters.

The breakdown of allochthonous organic matter, is a central step in nutrient cycling in stream ecosystems. There is concern that increased temperatures from climate change will alter the breakdown rate of organic matter, with important consequences for the ecosystem functioning of alpine streams. This study investigated the rate of leaf litter breakdown and how temperature and other factors such as microbial and invertebrate activities influenced this over elevational and temporal gradients. Dried leaves of Snow Gum (Eucalyptus pauciflora) and cotton strips were deployed in coarse (6 mm), and fine (50 mu m) mesh size bags along an 820 m elevation gradient. Loss of mass in leaf litter and cotton tensile strength per day (k per day), fungal biomass measured as ergosterol concentration, invertebrate colonization of leaf litter, and benthic organic matter (mass and composition) were determined. Both microbial and macroinvertebrate activities were equally important in leaf litter breakdown with the abundance of shredder invertebrate taxa. The overall leaf litter breakdown rate and loss of tensile strength in cotton strips (both k per day) were greater during warmer deployment periods and at lower elevations, with significant positive relationships between mean water temperature and leaf breakdown and loss of tensile strength rate, but no differences between sites, after accounting for the effects of temperature. Despite considerably lower amounts of benthic organic matter in streams above the tree line relative to those below, shredders were present in coarse mesh bags at all sites. Ergosterol concentration was greater on leaves in coarse mesh bags than in fine mesh bags, implying differences in the microbial communities. The importance of water temperatures on the rate of leaf litter breakdown suggests the potential effects of climate change-induced temperature increases on ecological processes in such streams.

In late 2018 to early 2019, three significant fish death events occurred in the Lower Darling River, Australia, with mortality estimates of millions of fish. We examined the proximate and ultimate causes of these events. We determined that not only were the conditions existing at the time a significant contributing factor, but that antecedent conditions, particularly during the period 2010–17, also contributed. The extreme hot and dry climate during 2018, extending into 2019, shaped the conditions that saw a large fish biomass, which had flourished in the Darling River and Menindee Lakes since favourable spawning conditions in 2016, isolated in weir pools, with no means of escaping upstream or downstream. Strong and persistent weir pool stratification created hypoxic conditions in the hypolimnion. A series of sudden cool changes subsequently initiated rapid and sudden mixing of the stratified waters, causing depletion of oxygen throughout the water column and resulting in the fish deaths. The events were also shaped by broader climatic, hydrological and basin management contexts that placed the Lower Darling River at risk of such fish deaths. Our observations have implications for future river management, and we make several suggestions how policy makers and river operators can minimise fish death risks into the future.

Decaying fish play an important role in delivering nutrients into rivers and lakes but can create water quality issues. The release of cyprinid herpesvirus-3 (CyHV-3) in Australia with an associated mass common carp mortality may have serious effects on water quality in lakes. To evaluate the effect of a virus-induced fish kill, different biomasses of dead common carp (250–6000 kg ha–1) were placed into 2000-L mesocosms within Prospect Reservoir, Australia, for up to 40 days. Decaying carp created anoxic conditions within all treatments except the 250 kg ha–1 treatment, in which oxygen saturation dropped to 30%. A higher biomass of carp led to longer periods of anoxia. Total nitrogen (TN) increased from a baseline of 0.25 to 1.5–30 mg L–1 in the different treatments, whereas total phosphorus (TP) increased from 0.01 to 0.05–5.0 mg L–1. Chlorophyll-a levels increased from

Freshwater inflows are linked to the abundance and catch rates of fish in estuaries. The role of terrestrial carbon resources brought into estuaries after inflows may be important, but this is currently not well understood. Therefore, we performed a study examining the effect of terrestrial dissolved organic matter (tDOM) dietary additions on the growth of food-limited juvenile Australian bass (Macquaria novemculeata). Crustaceous zooplankton Artemia franciscana (Artemia) were reared for two days under control conditions (no addition) or with additions of tDOM leachate at dissolved organic carbon (DOC) concentrations of 5 mg/L or 10 mg/L. Artemia were fed to juvenile bass in their treatment tanks over 42 days at feeding rates reduced by 65–75% of ad libitum. Juvenile fish from the 5 mg/L treatment exhibited no statistical difference in weight or standard, fork and total lengths compared to the control treatment. In contrast, the fish in the 10 mg/L tDOM treatment had significant increases (p < 0.05) in all length parameters after 42 days compared to the other treatments. The greater lengths of fish where tDOM is available indicate that tDOM can contribute to improved growth and development in juvenile Australian bass. While stable isotope analysis of fish tissue showed only minor changes toward terrestrial carbon signatures, increased terrestrial resource availability in the juvenile fish diets may have subsidised energetic needs, facilitating the greater utilisation of endogenous resources. Overall, the results indicate that freshwater inflows that deliver terrestrial resources may be important for the growth and development of estuarine fish.

Background Non-alcoholic fatty liver disease (NAFLD) has been recognized as a common condition in inflammatory bowel disease (IBD) patients and could contribute to their overall morbidity. Anti-TNFα and anti-integrin agents have been the cornerstones of IBD therapy with proven clinical efficacy, but it΄s effect on liver steatosis is still unclear. Therefore this study aimed to evaluate the impact of anti-TNFα and anti-integrin agents on liver steatosis in IBD patients with proven NAFLD. Methods A total of 32 IBD patients with NAFLD, naive to biologic agents, 21 with an established diagnosis of ulcerative colitis, and 11 with Crohn's disease were prospectively recruited for the study. NAFLD was defined by a baseline attenuation (ATT) coefficient measured by shear-wave (SW) elastometry of 0.63 dB/cm/MHz or higher and a baseline alanine aminotransferase (ALT) of more than 40 IU/L for males and 35 IU/L for females. The exclusion criteria were alcohol use (consuming > 40 g alcohol/day for men and > 20 g/day for women in the preceding 12 months), concomitant chronic viral hepatitis, the presence of hepatic carcinoma, biliary disease, drug use, and hypothyroidism. A total of 11 patients were treated with Adalimumab, 9 patients with Infliximab, and 12 patients with Vedolizumab. The SW elastometry and laboratory exams were performed at the moment of therapy induction and after the 6-month course of therapy. Results The anti-TNFα treatment significantly reduced liver steatosis according to the ATT coefficient dynamic (0.70±0.07 vs 0.66±0.03 dB/cm/MHz, p=0.021) and ALT level dynamic came on the verge of statistical significance (44±7 vs 40±6 IU/L, p=0.058). We did not observe a significant difference between the Infliximab- and Adalimumab-treated patients. The anti-integrin agent, Vedolizumab, had no impact on liver steatosis (0.66±0.03 vs 0.67±0.04 dB/cm/MHz) and ALT level dynamic (47±4 vs 45±5, p=0.29). Both groups of agents had no impact on patients' lipid profile dynamic. We found no correlation between liver steatosis level and CRP and fecal calprotectin dynamic. Conclusion In the short term, we observed potential beneficial effects of anti-TNFα agents on liver steatosis of IBD patients with proven NAFLD.

Micronutrients play key roles in numerous metabolic processes in cyanobacteria. However, our understanding of whether the micronutrient cobalt influences the productivity of freshwater systems or the occurrence of cyanobacterial blooms is limited. This study aimed to quantify the concentration of Co necessary for optimal cyanobacterial growth by exposing Microcystis aeruginosa to a range of Co concentrations under culture conditions. Extended exposure to concentrations below ˜0.06 μg · L-1 resulted in notable inhibition of M. aeruginosa growth. A clear negative relationship was observed between Co concentration in solution and intracellular Fe quota of M. aeruginosa, possibly due to decreased transport of Fe at higher Co concentrations. Cyanocobalamin and any Co within the structure of cyanocobalamin appears to be non-bioavailable to M. aeruginosa, instead they likely rely on the synthesis of a structural variant - pseudocobalamin, which may have implications for the wider algal community as the variants of cobalamin are not necessarily functionally exchangeable. To evaluate the likelihood of Co limitation of cyanobacterial growth under field conditions, a survey of 10 freshwater reservoirs in South-Eastern Australia was conducted. Four of the ten sites had dissolved Co concentrations below the 0.06 μg · L-1 threshold value. All four of these sites rarely undergo cyanobacterial blooms, strengthening evidence of the potential for Co to limit growth, perhaps either alone or in combination with phosphorus.

Assessing and comparing global river ecosystem health in an objective and quantitative way remains a major challenge. In this study the widely-used semi-quantitative methods Rapid Biological assessment Protocols (RBPs) was used to determine the health of rivers. The findings were then compared to the results derived from our new UAV (Unmanned aerial vehicles) orthophotographic imagery method. This method quantitatively and objectively assesses river ecosystem health. As a comparison, our method was used to quantitatively measure distance and areas of a range of hydrological and biological attributes thus improving the accuracy of distance- and area-related indices, consequently avoiding subjective errors in these estimations that is fraught in methods like the RBPs. To strengthen the objectivity of the assessment the weights of these indices were objectively determined using the entropy weighting method. This new method was then tested using 9551 UAV orthophotographs taken over six field campaigns. It performed satisfactorily, showing that in our study area the health status of mountain rivers was the best with the highest score of 0.94 out of 1.0. Temporally, the health of the river was better in summer (0.65) compared with that in autumn (0.40). Changes in river ecosystem health were driven by variations in biology and water quality. In contrast the outputs of RBPs, especially in relation to distance and area indices, had ~ 20% uncertainty due to visual errors and subjectivity in estimations by observers. The UAV orthophotographic imaging method proposed in this study can improve the ability to compare the health of rivers across different periods and regions throughout the globe.

Benthic diatom communities are used widely as indicators of river health due to their rapid response to changes in water quality. The ability for diatom-based indices to detect eutrophication has been well documented; however, an index designed specifically to detect herbicide impacts is yet to be established. This is required as herbicide contamination of rivers is common in agricultural regions and poses a potential threat to aquatic ecosystems. This study developed a new biomonitoring index (SPEARherbicides) using benthic diatom communities to detect the toxic impacts of herbicides in rivers, and tested it across 14 rivers in the Great Barrier Reef catchment area, Australia. The new index uses diatom species traits to classify diatoms as either sensitive or tolerant to herbicides and calculates the fraction of sensitive taxa within a sample. The SPEARherbicides index showed a decline in herbicide sensitive diatoms with increasing herbicide toxicity of the sites. The impacts of herbicide toxicity on the diatom community were only apparent after the wet season when aqueous herbicide concentrations typically peak and diatoms were able to recover during the dry season when herbicide concentrations were lower. SPEARherbicides values had a negative relationship with the percentage of grazing and cropping in catchments but had a positive relationship with the percentage of conservation in catchments. SPEARherbicides also had a negative relationship with co-occurring potential stressors such as nutrients and total suspended solids.

Interactions between macrophytes and phytoplankton have been studied extensively in temperate water bodies, but far less attention has been paid to those for emergent macrophytes in the tropics. We investigated the effects of six emergent macrophyte species (Brachiaria mutica, Ipomoea aquatica, Sphagneticola trilobata, Ludwigia adscendens, Pandanus amaryllifolius and Persicaria barbata) on the phytoplankton community of a tropical reservoir using ex situ experiments with multiple planting densities (Treatment 1: 0.108, Treatment 2: 0.24, Treatment 3: 0.40, Treatment 4: 0.58 g dry weight L−1) in 100-L mesocosms. Chlorophyll a (as a proxy of total phytoplankton biomass) and phytoplankton community structure were examined. The initial phytoplankton community (average chlorophyll a: 20.36 ± 0.69 µg L−1) was dominated by cyanobacteria: Planktolyngybya, Pseudanabaena and Cylindrospermopsis (average relative biovolume 0.68 ± 0.03). Over four weeks, L. adscendens (Treatments 3 and 4) and P. barbata (Treatments 2 to 4) significantly reduced chlorophyll a concentrations by 3.29–6.69 µg L−1 compared to the controls. Comparing species effects over four weeks for Treatment 4, P. barbata significantly lowered chlorophyll a concentrations compared to I. aquatica while there were no significant differences between all other species. All treatments of L. adscendens and P. barbata significantly reduced the relative biovolume of cyanobacteria in the phytoplankton communities by 0.19–0.39 compared to the controls. The highest-density treatments of all six macrophyte species led to significant shifts in the phytoplankton community structure by reducing the relative abundance of filamentous cyanobacteria (Planktolyngbya, Pseudanabaena) and/or increasing the relative abundance of cryptomonads (Chroomonas, Rhodomonas). This study shows the potential of emergent macrophyte species, especially L. adscendens and P. barbata, to reduce total phytoplankton biomass and cyanobacterial dominance in tropical water bodies, and a range of plant densities which were effective.

Widespread wastewater pollution is a major barrier to the sustainable management of freshwater and coastal marine ecosystems worldwide. Integrated multi-disciplinary studies are necessary to improve waterway management and protect ecosystem integrity. This study used the Generalised Likelihood Uncertainty Estimation (GLUE) methodology to link microbial community ecotoxicology laboratory data to a mechanistic aquatic ecosystem response model. The generic model provided good predictive skill for major water quality constituents, including heterotrophic bacteria dynamics (r2 = 0.91). The model was validated against observed data across a gradient of effluent concentrations from community whole effluent toxicity (WET) laboratory tests. GLUE analysis revealed that a combined likelihood measure increased confidence in the predictive capability of the model. This study highlights the importance of calibrating aquatic ecosystem response models with net growth rates (i.e., sum of the growth minus loss rate parameter terms) of biological functional groups. The final calibrated net growth rate value of heterotrophic bacteria determined using the GLUE analysis was selected to be 0.58, which was significantly greater than the average literature value of -0.15. This finding demonstrated that use of literature parameter values without a good understanding of the represented processes could create misleading outputs and result in unsatisfactory conclusions. Further, fixed bulk mineralisation rate literature values are typically higher than realistically required in aquatic ecosystem response models. This indicates that explicitly including bacterial mineralisation is crucial to represent microbial ecosystem functioning more accurately. Our study suggests that improved data collection and modelling efforts in real-world management applications are needed to better address nutrients released into the natural environment. Future studies should aim to better understand the sensitivity of aquatic ecosystem response models to bacterial mineralisation rates.

The role of trace metal micronutrients in limiting cyanobacterial growth and structuring the phytoplankton community is becoming more evident. However, little is known regarding the extent of micronutrient limitation in freshwaters or which micronutrient conditions favour potentially-toxic cyanobacteria. To assess how freshwater phytoplankton respond to micronutrient and macronutrient additions, we conducted nutrient amendment bioassays at seven sites across South Eastern-Australia. Sites were variable in cyanobacterial cell densities and phytoplankton community compositions. At two sites, Mannus Lake and Burrendong Dam, micronutrient additions (iron, cobalt, copper, manganese, molybdenum and zinc) increased cyanobacterial growth, indicating micronutrient limitation. Both sites had cyanobacterial blooms present at the onset of the experiment, dominated by Chrysosporum ovalisporum at Mannus Lake and Microcystis aeruginosa at Burrendong Dam. This suggests that micronutrients may be an important regulator of the severity of cyanobacterial blooms and may become limiting when there is high competition for nutrient resources. The addition of the micronutrient mixture resulted in a higher proportion of cyanobacteria compared to the control and a lower diversity community compared to phosphorus additions, indicating that micronutrients can not only influence cyanobacterial biovolume but also their ability to dominate the phytoplankton community. This reinforces that micronutrient requirements of phytoplankton are often species specific. As micronutrient enrichment is often overlooked when assessing nutrient-constraints on cyanobacterial growth, this study provides valuable insight into the conditions that may influence cyanobacterial blooms and the potential contribution of micronutrients to eutrophication.

Temperature is essential to the maintenance of optimal physiological functioning in aquatic organisms. Fish can manage natural fluctuations in temperature; however, in freshwater ecosystems acute and rapid temperature changes can originate from sources such as large dams and industrial effluents. These rapid temperature changes may induce several physiological and behavioural responses that can result in lethal and sub-lethal consequences. The present study assessed immediate sub-lethal and short-term (10 days) lethal responses of three species of Australian freshwater fish larvae and early-stage juveniles to a range of different 'field-relevant' cold shocks (-4, -6, -8 and -10°C). Murray cod (

Temperature is a key determinant that governs fish survival, reproduction, growth and metabolism. In freshwater ecosystems, anthropogenic influences have resulted in acute and prolonged temperature changes which lead to lethal and sub-lethal impacts on the biota that occupy these environments. We assessed the effects of temperature on somatic and otolith growth and development of three species of native Australian freshwater fish (silver perch Bidyanus bidyanus, trout cod Maccullochella macquariensis and golden perch Macquaria ambigua) to simulate how thermal pollution from the release of unseasonably cold water from thermally stratified dams in Australian freshwater ecosystems may impact fish at critical life-history stages. Fish (31 days post-hatch) were exposed to four temperature treatments (13, 16, 20, 24 °C) for 30 days. Low temperatures resulted in reduced somatic growth, with no growth observed in silver perch and golden perch held at 13 °C over 30 days. Somatic growth was highest at the upper temperature of 24 °C. Morphological assessment of fish size reiterated that low water temperatures resulted in reduced body size, particularly in terms of body width and head size. Low temperatures were associated with reduced otolith growth in all species, however a somatic-otolith size relationship was maintained for all species in measures of otolith weight, area, length and perimeter. The sub-lethal impacts observed in our study are likely to manifest at the population level through a reduced capacity of larvae and juveniles to avoid size-dependent predation, a narrower range of prey sources due to extended gape-limited feeding and, ultimately, poorer survival and recruitment.

Rapid reductions in water temperature can originate in freshwater ecosystems from the operation of dams. We demonstrate that these ‘cold shocks’ can cause mortality and reduce swimming ability in three species of Australian freshwater fish larvae and early-stage juveniles, with younger fish being more sensitive to cold shock., Temperature is essential to the maintenance of optimal physiological functioning in aquatic organisms. Fish can manage natural fluctuations in temperature; however, in freshwater ecosystems acute and rapid temperature changes can originate from sources such as large dams and industrial effluents. These rapid temperature changes may induce several physiological and behavioural responses that can result in lethal and sub-lethal consequences. The present study assessed immediate sub-lethal and short-term (10 days) lethal responses of three species of Australian freshwater fish larvae and early-stage juveniles to a range of different ‘field-relevant’ cold shocks (−4, −6, −8 and −10°C). Murray cod (Maccullochella peelii), silver perch (Bidyanus bidyanus) and golden perch (Macquaria ambigua) were tested at two age groups to elucidate the interaction between ontogeny and sensitivity to cold shock. Cold shock caused mortality and reductions in swimming ability (time to exhaustion and lines crossed) in all species of fish at both age groups. Sensitivity was correlated to the magnitude of cold shock; a 10°C drop in temperature caused the highest mortalities. Ontogeny interacted with the severity of cold shock; the younger fish experienced higher mortalities and greater impairment to swimming ability. This study demonstrates the potential lethal and sub-lethal impacts of cold shock on freshwater fish at a critical life-history stage. Understanding the impacts of cold shock will aid management of freshwater ecosystems for the benefit of fish populations, with the current study identifying critical life stages to be considered in remediation and guiding thresholds necessary to reduce the impact of cold shock on native fish populations.

Microplastics (MPs) of varying sizes are widespread pollutants in our environment. The general opinion is that the smaller the size, the more dangerous the MPs are due to enhanced uptake possibilities. It would be of considerably ecological significance to understand the response of biota to microplastic contamination both physically and physiologically. Here, we report on an area choice experiment (avoidance test) using Enchytraeus crypticus, in which we mixed different amounts of high-density polyethylene microplastic particles into the soil. In all experimental scenarios, more Enchytraeids moved to the unspiked sections or chose a lower MP-concentration. Worms in contact with MP exhibited an enhanced oxidative stress status, measured as the induced activity of the antioxidative enzymes catalase and glutathione S-transferase. As plastic polymers per se are nontoxic, the exposure time employed was too short for chemicals to leach from the microplastic, and as the microplastic particles used in these experiments were too large (4 mm) to be consumed by the Enchytraeids, the likely cause for the avoidance and oxidative stress could be linked to altered soil properties.

Real-world observational datasets that record and quantify pressure-stressor-response linkages between effluent discharges and natural aquatic systems are rare. With global wastewater volumes increasing at unprecedented rates, it is urgent that the present dataset is available to provide the necessary information about microbial community structure and functioning. Field studies were performed at two time-points in the Austral summer. Single-species and microbial community whole effluent toxicity (WET) testing was performed at a complete range of effluent concentrations and two salinities, with accompanying environmental data to provide new insights into nutrient and organic matter cycling, and to identify ecotoxicological tipping points. The two salinity regimes were chosen to investigate future scenarios based on a predicted salinity increase at the study site, typical of coastal regions with rising sea levels globally. Flow cytometry, amplicon sequencing of 16S and 18S rRNA genes and micro-fluidic quantitative polymerase-chain reactions (MFQPCR) were used to determine chlorophyll-a and total bacterial cell numbers and size, as well as taxonomic and functional diversity of pelagic microbial communities. This strong pilot dataset could be replicated in other regions globally and would be of high value to scientists and engineers to support the next advances in microbial ecotoxicology, environmental biomonitoring and estuarine water quality modelling., Measurement(s)water composition • total dissolved solids • conductivity of water • pH • concentration of oxygen in water • Total Organic Carbon • dinitrogen • phosphorus atom • ammonia • nitrate • nitrite • biological oxygen demand • chlorophyll a • Cell Density • Algae • Bacteria • hydrogen sulfide • Toxicity • rRNA_16S • rRNA_18S • abundance of nutrient cycling genes • abundance of antibiotic resistance genesTechnology Type(s)water quality unit • water testing suite • dilution method • autofluorescence • flow cytometry method • whole effluent toxicity testing • DNA sequencing • microfluidic quantitative polymerase chain reactionFactor Type(s)effluent concentration • salinity levelsSample Characteristic - OrganismBacteria • algaeSample Characteristic - Environmentwaste water • estuary • sea coast • saline water • fresh water bodySample Characteristic - LocationHunter River Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12221738

Cyanobacteria and other microbes are important moderators of biogeochemical processes in semi-arid floodplain wetlands with varying inundation regimes. Inundation is a key environmental driver for floodplain biological communities. Little is known about the effect of historical inundation frequency on the spatial abundance of floodplain–wetland Cyanobacteria and other microbes. In this study, soil samples were collected at two locations with a gradient of low-to-high inundation frequency in the Macquarie Marshes, south-east Australia. We used high-throughput sequencing to estimate the proportional abundance of the soil Cyanobacteria and other dominant microbes, targeting the bacterial 16S rRNA gene. Of the microbes recovered, Cyanobacteria constituted proportionally a minor component, relative to other dominant phyla like Proteobacteria and Actinobacteria. Linear regression (generalised least-squares) models accounting for spatial autocorrelation showed that historical inundation frequency had no significant effect on the proportional abundance of Cyanobacteria at both wetlands studied. However, inundation frequency had a significant positive effect on the proportional abundance of Proteobacteria and a significant negative effect on the proportional abundance of Actinobacteria. Cyanobacteria seem to occupy a different hydrological niche from Proteobacteria and Actinobacteria in semi-arid floodplain wetlands, suggesting taxon-dependent response of floodplain microbial communities to varying inundation regimes and associated soil conditions in those environments.

Background Inflammatory bowel disease (IBD) is often associated with ophatlmological complications, such as blepharitis, conjunctivitis, episcleritis and iridociclitis. Although present in approximately quarter of all IBD patients, ophthalmological posterior segment findings are often overseen and possibly related to disease activity. Methods A total of, 136 patients, with previous IBD, underwent a complete ophthalmological examination, including fundus photography and optical coherence tomography/angiography (OCT/OCTA) using Optovue Avanti XR HD-OCT. The retinal foveolar avascular zone (FAZ) and choroidal thickness was measured using AngioPlex OCTA software. IBD activity was evaluated using adapted Mayo score and Crohn’s disease activity index (CDAI), for ulcerative colitis (UC) and Crohn’s disease (CD), respectively, as well as faecal calprotectin and serum C-reactive protein levels. UC remission based on the modified Mayo score was defined as stool frequency sub-score, 0 to, 1, rectal bleeding sub-score of, 0, and endoscopy sub-score, 0 to, 1. CD remission was defined with CDAI score bellow, 150. Patients with recent ophthalmological surgery, refractive errors greater than +3 or -3, as well as patients with retinopathies were excluded from analysis. Results We performed a cross-sectional study of, 272 eyes of, 136 IBD patients (91 UC and, 45 CD) average age, 45 years, of which, 87 females. A total of, 37 patients (27.2%), of which, 18 UC and, 19 CD patients, were defined as having an active disease. The most prevalent fundoscopic finding was vascular tortuosity, observed in, 47 eyes (17.2%). The difference between choroidal thickness between UC and CD patients was not observed (308±35µm vs, 314±29µm, p=0.32), as well as the FAZ difference (0.32 vs, 0.33 mm2, p=0.21). On the other hand, if we take in count only patients with active disease, the FAZ area of CD patients was significantly greater in comparison to UC patients (0.31 vs, 0.34 mm2, p=0.028). Correlation study showed significant correlation between choroidal thickness and CDAI (Rho, 0.448, p=0.036). Conclusion The choroidal thickness and FAZ area are ophthalmological parameters that could be easily obtained using OCTA and may be taken in count as possible non-invasive markers of disease severity, especially in CD patients.

© 2018, Springer International Publishing AG, part of Springer Nature. This study explored biofilm metabolism as a functional indicator of ecological responses to dissolved organic carbon and inorganic nutrients from managed dam releases. We hypothesised that the dam releases would stimulate epilithic biofilm community respiration (CR), and trigger a larger increase in biofilm CR relative to gross primary production (GPP). We predicted that biofilm respiration would be related to water column dissolved carbon and nutrient concentrations. Tiles colonised with epilithic biofilm were exposed to dam release waters in a stream-side mesocosm system that separated out the physical effects of flow velocity. Biofilm CR increased during two of three releases, and increases in CR were larger relative to GPP during all three releases. Biofilm CR was not linearly related to dissolved resources or abiotic environmental variables. These results show that managed dam releases can influence biofilm metabolism via a mechanism independent from the direct physical effects of increased flow velocity. This study provides new insights into the complex pathways through which managed dam releases may influence ecological processes. The stimulation of benthic CR through physical and chemical variations in dam water is a potential mechanism through which dam releases may influence biogeochemical processing and energy flow through the riverine food web.

The emerging toxin β-methylamino-l-alanine (BMAA) has been linked to the development of a number of neurodegenerative diseases in humans including amyotrophic lateral sclerosis (ALS), Alzheimer's disease, and Parkinson's disease. BMAA has been found to be produced by a range of cyanobacteria, diatoms, and dinoflagellates worldwide, and is present in freshwater, saltwater, and terrestrial ecosystems. Surface scum samples were collected from waterways in rural and urban New South Wales, Australia and algal species identified. Reverse phase liquid chromatography-tandem mass spectrometry was used to analyse sixteen cyanobacterial scum for the presence of BMAA as well as its toxic structural isomer 2,4-diaminobutyric acid (2,4-DAB). BMAA was detected in ten of the samples analysed, and 2,4-DAB in all sixteen. The presence of these toxins in water used for agriculture raises concerns for public health and food security in Australia.

Widespread wastewater pollution is one of the greatest challenges threatening the sustainable management of rivers globally. Understanding microbial responses to gradients in environmental stressors, such as wastewater pollution, is crucial to identify thresholds of community change and to develop management strategies that protect ecosystem integrity. This study used multiple lines of empirical evidence, including a novel combination of microbial ecotoxicology methods in the laboratory and field to link pressure-stressor-response relationships. Specifically, community-based whole effluent toxicity (WET) testing and environmental genomics were integrated to determine real-world community interactions, shifts and functional change in response to wastewater pollution. Here we show that wastewater effluents above moderate (>10%) concentrations caused consistent significant shifts in bacterial community structure and function. These thresholds of community shifts were also linked to changes in the trophic state of receiving waters in terms of nutrient concentrations. Differences in the community responses along the effluent concentration gradient were primarily driven by two globally relevant bacterial indicator taxa, namely Malikia spp. (Burkholderiales) and hgcI_clade (Frankiales). Species replacement occurred above moderate effluent concentrations with abundances of Malikia spp. increasing, while abundances of hgcI_clade decreased. The responses of Malikia spp. and hgcI_clade matched gene patterns associated with globally important nitrogen cycling pathways, such as denitrification and nitrogen fixation, which linked the core individual taxa to putative function and ecosystem processes, rarely achieved in previous studies. This study has identified potential indicators of change in trophic status and the functional consequences of wastewater pollution. These findings have immediate implications for both the management of environmental stressors and protection of aquatic ecosystems.

© 2019 Author(s). Cyanobacterial blooms are becoming more common in freshwater systems, causing ecological degradation and human health risks through exposure to cyanotoxins. The role of phosphorus and nitrogen in cyanobacterial bloom formation is well documented and these are regularly the focus of management plans. There is also strong evidence that trace metals are required for a wide range of cellular processes, however their importance as a limiting factor of cyanobacterial growth in ecological systems is unclear. Furthermore, some studies have suggested a direct link between cyanotoxin production and some trace metals. This review synthesises current knowledge on the following: (1) the biochemical role of trace metals (particularly iron, cobalt, copper, manganese, molybdenum and zinc), (2) the growth limitation of cyanobacteria by trace metals, (3) the trace metal regulation of the phytoplankton community structure and (4) the role of trace metals in cyanotoxin production. Iron dominated the literature and regularly influenced bloom formation, with 15 of 18 studies indicating limitation or colimitation of cyanobacterial growth. A range of other trace metals were found to have a demonstrated capacity to limit cyanobacterial growth, and these metals require further study. The effect of trace metals on cyanotoxin production is equivocal and highly variable. Better understanding the role of trace metals in cyanobacterial growth and bloom formation is an essential component of freshwater management and a direction for future research.

© 2019 Elsevier Ltd To reveal the occurrence and mechanisms for dispersal of antibiotic resistance (AbR) among the microbial assemblages inhabiting impacted coastal environments, we performed a weekly, two-year duration time-series study at two urban beaches between 2014 and 2016. We combined quantitative PCR and multiplex PCR/reverse line blot techniques to track patterns in the occurrence of 31 AbR genes, including genes that confer resistance to antibiotics that are critically important antimicrobials for human medicine. Patterns in the abundance of these genes were linked to specific microbial groups and environmental parameters by coupling qPCR and 16S rRNA amplicon sequencing data with network analysis. Up to 100-fold increases in the abundance of several AbR genes, including genes conferring resistance to quinolones, trimethoprim, sulfonamides, tetracycline, vancomycin and carbapenems, occurred following storm-water and modelled wet-weather sewer overflow events. The abundance of AbR genes strongly and significantly correlated with several potentially pathogenic bacterial OTUs regularly associated with wastewater infrastructure, such as Arcobacter, Acinetobacter, Aeromonas and Cloacibacterium. These high-resolution observations provide clear links between storm-water discharge and sewer overflow events and the occurrence of AbR in the coastal microbial assemblages inhabiting urban beaches, highlighting a direct mechanism for potentially significant AbR exposure risks to humans.

&beta, methylamino-L-alanine (BMAA) is a non-protein amino acid that has been implicated as a risk factor for motor neurone disease (MND). BMAA is produced by a wide range of cyanobacteria globally and by a small number of marine diatoms. BMAA is commonly found with two of its constitutional isomers: 2,4-diaminobutyric acid (2,4-DAB), and N-(2-aminoethyl)glycine (AEG). The isomer 2,4-DAB, like BMAA, has neurotoxic properties. While many studies have shown BMAA production by cyanobacteria, few studies have looked at other algal groups. Several studies have shown BMAA production by marine diatoms, however, there are no studies examining freshwater diatoms. This study aimed to determine if some freshwater diatoms produced BMAA, and which diatom taxa are capable of BMAA, 2,4-DAB and AEG production. Five axenic diatom cultures were established from river and lake sites across eastern Australia. Cultures were harvested during the stationary growth phase and intracellular amino acids were extracted. Using liquid chromatography triple quadrupole mass spectrometry (LC-MS/MS), diatom extracts were analysed for the presence of both free and protein-associated BMAA, 2,4-DAB and AEG. Of the five diatom cultures analysed, four were found to have detectable BMAA and AEG, while 2,4-DAB was found in all cultures. These results show that BMAA production by diatoms is not confined to marine genera and that the prevalence of these non-protein amino acids in Australian freshwater environments cannot be solely attributed to cyanobacteria.