Delving into the Aftermath of a Disease-Associated Near-Extinction Event: A Five-Year Study of a Serpentovirus (Nidovirus) in a Critically Endangered Turtle Population.

Bellinger River virus (BRV) is a serpentovirus (nidovirus) that was likely responsible for the catastrophic mortality of the Australian freshwater turtle Myuchelys georgesi in February 2015. From November 2015 to November 2020, swabs were collected from turtles during repeated river surveys to estimate the prevalence of BRV RNA, identify risk factors associated with BRV infection, and refine sample collection. BRV RNA prevalence at first capture was significantly higher in M. georgesi (10.8%) than in a coexisting turtle, Emydura macquarii (1.0%). For M. georgesi, various risk factors were identified depending on the analysis method, but a positive BRV result was consistently associated with a larger body size. All turtles were asymptomatic when sampled and conjunctival swabs were inferred to be optimal for ongoing monitoring. Although the absence of disease and recent BRV detections suggests a reduced ongoing threat, the potential for the virus to persist in an endemic focus or resurge in cyclical epidemics cannot be excluded. Therefore, BRV is an ongoing potential threat to the conservation of M. georgesi, and strict adherence to biosecurity principles is essential to minimise the risk of reintroduction or spread of BRV or other pathogens.

Consequences of hydrological alteration for beta diversity of fish assemblages at multiple spatial scales.

Effects of dam operation and extraction of water from rivers on spatial variation in hydrological regimes, and consequences for freshwater biodiversity, are widely predicted but seldom assessed empirically. Evidence of linkages between hydrology and beta diversity contributes to water-management decisions to support landscape-scale biodiversity and avoid inadvertently contributing to further biodiversity decline. Using six lowland rivers in Australia's Murray - Darling Basin that formed a gradient of hydrological alteration, we examined (1) spatial variation in hydrology under modelled scenarios of low water-resource development and flow modification by dams and extraction, (2) how beta diversity of fish among and within rivers was associated with spatial hydrological variation and whether patterns of overall beta diversity differed between native and non-native species, and (3) the associations of spatial and environmental variables and both recent and long-term hydrology with beta diversity. Spatial variation in hydrology among rivers was higher under the modified scenario than under the low-development scenario yet change in the magnitude of within-river (longitudinal) variation was inconsistent between rivers. Beta diversity among rivers was significantly associated with spatial variation in hydrology only in certain circumstances (native species assemblages in specific years). Within-river beta diversity varied among rivers yet was unrelated to longitudinal variation in modified hydrological regimes. Patterns of beta diversity did not differ appreciably if non-native species were included in or excluded from analyses. These findings contradict predictions adopted in ecohydrological science that water resource development homogenises hydrological regimes, in turn causing biotic homogenisation in lowland rivers.

Limitations of trait-based approaches for stressor assessment: The case of freshwater invertebrates and climate drivers.

The appeal of trait-based approaches for assessing environmental vulnerabilities arises from the potential insight they provide into the mechanisms underlying the changes in populations and community structure. Traits can provide ecologically based explanations for observed responses to environmental changes, along with predictive power gained by developing relationships between traits and environmental variables. Despite these potential benefits, questions remain regarding the utility and limitations of these approaches, which we explore focusing on the following questions: (a) How reliable are predictions of biotic responses to changing conditions based on single trait-environment relationships? (b) What factors constrain detection of single trait-environment relationships, and how can they be addressed? (c) Can we use information on meta-community processes to reveal conditions when assumptions underlying trait-based studies are not met? We address these questions by reviewing published literature on aquatic invertebrate communities from stream ecosystems. Our findings help to define factors that influence the successful application of trait-based approaches in addressing the complex, multifaceted effects of changing climate conditions on hydrologic and thermal regimes in stream ecosystems. Key conclusions are that observed relationships between traits and environmental stressors are often inconsistent with predefined hypotheses derived from current trait-based thinking, particularly related to single trait-environment relationships. Factors that can influence findings of trait-based assessments include intercorrelations of among traits and among environmental variables, spatial scale, strength of biotic interactions, intensity of habitat disturbance, degree of abiotic stress, and methods of trait characterization. Several recommendations are made for practice and further study to address these concerns, including using phylogenetic relatedness to address intercorrelation. With proper consideration of these issues, trait-based assessment of organismal vulnerability to environmental changes can become a useful tool to conserve threatened populations into the future.

Scaling biodiversity responses to hydrological regimes.

Of all ecosystems, freshwaters support the most dynamic and highly concentrated biodiversity on Earth. These attributes of freshwater biodiversity along with increasing demand for water mean that these systems serve as significant models to understand drivers of global biodiversity change. Freshwater biodiversity changes are often attributed to hydrological alteration by water-resource development and climate change owing to the role of the hydrological regime of rivers, wetlands and floodplains affecting patterns of biodiversity. However, a major gap remains in conceptualising how the hydrological regime determines patterns in biodiversity's multiple spatial components and facets (taxonomic, functional and phylogenetic). We synthesised primary evidence of freshwater biodiversity responses to natural hydrological regimes to determine how distinct ecohydrological mechanisms affect freshwater biodiversity at local, landscape and regional spatial scales. Hydrological connectivity influences local and landscape biodiversity, yet responses vary depending on spatial scale. Biodiversity at local scales is generally positively associated with increasing connectivity whereas landscape-scale biodiversity is greater with increasing fragmentation among locations. The effects of hydrological disturbance on freshwater biodiversity are variable at separate spatial scales and depend on disturbance frequency and history and organism characteristics. The role of hydrology in determining habitat for freshwater biodiversity also depends on spatial scaling. At local scales, persistence, stability and size of habitat each contribute to patterns of freshwater biodiversity yet the responses are variable across the organism groups that constitute overall freshwater biodiversity. We present a conceptual model to unite the effects of different ecohydrological mechanisms on freshwater biodiversity across spatial scales, and develop four principles for applying a multi-scaled understanding of freshwater biodiversity responses to hydrological regimes. The protection and restoration of freshwater biodiversity is both a fundamental justification and a central goal of environmental water allocation worldwide. Clearer integration of concepts of spatial scaling in the context of understanding impacts of hydrological regimes on biodiversity will increase uptake of evidence into environmental flow implementation, identify suitable biodiversity targets responsive to hydrological change or restoration, and identify and manage risks of environmental flows contributing to biodiversity decline.

Regime shifts, thresholds and multiple stable states in freshwater ecosystems; a critical appraisal of the evidence.

The concepts of ecosystem regime shifts, thresholds and alternative or multiple stable states are used extensively in the ecological and environmental management literature. When applied to aquatic ecosystems, these terms are used inconsistently reflecting differing levels of supporting evidence among ecosystem types. Although many aquatic ecosystems around the world have become degraded, the magnitude and causes of changes, relative to the range of historical variability, are poorly known. A working group supported by the Australian Centre for Ecological Analysis and Synthesis (ACEAS) reviewed 135 papers on freshwater ecosystems to assess the evidence for pressure-induced non-linear changes in freshwater ecosystems; these papers used terms indicating sudden and non-linear change in their titles and key words, and so was a positively biased sample. We scrutinized papers for study context and methods, ecosystem characteristics and focus, types of pressures and ecological responses considered, and the type of change reported (i.e., gradual, non-linear, hysteretic or irreversible change). There was little empirical evidence for regime shifts and changes between multiple or alternative stable states in these studies although some shifts between turbid phytoplankton-dominated states and clear-water, macrophyte-dominated states were reported in shallow lakes in temperate climates. We found limited understanding of the subtleties of the relevant theoretical concepts and encountered few mechanistic studies that investigated or identified cause-and-effect relationships between ecological responses and nominal pressures. Our results mirror those of reviews for estuarine, nearshore and marine aquatic ecosystems, demonstrating that although the concepts of regime shifts and alternative stable states have become prominent in the scientific and management literature, their empirical underpinning is weak outside of a specific environmental setting. The application of these concepts in future research and management applications should include evidence on the mechanistic links between pressures and consequent ecological change. Explicit consideration should also be given to whether observed temporal dynamics represent variation along a continuum rather than categorically different states.

Bioassessment in a harsh environment: a comparison of macroinvertebrate assemblages at reference and assessment sites in an Australian inland river system.

The Lachlan River system of inland New South Wales, which extends into semi-arid areas, is prone to natural extremes of climate and water quality and has been almost entirely modified since European settlement in Australia. We used this system as a proving ground for the mainly qualitative bioassessment metrics for river macroinvertebrates that are used widely in Australia--the EPT (Ephemeroptera, Plecoptera and Trichoptera) index, the SIGNAL (Stream Invertebrate Grade Number Average Level) biotic index and the AUSRIVAS O/E (Australian River Assessment System Observed over Expected) index--plus a recently developed qualitative index, the observed proportion of potential taxa (OPP). We tested these metrics on their ability to discriminate between sites judged to be less disturbed by human activities (reference sites) and sites selected by a semi-random process and therefore expected to have a higher average level of human disturbance (assessment sites). All metrics except the AUSRIVAS O/E index differed significantly between the two types of sites at higher altitudes, with SIGNAL showing the greatest discrimination. Assessment at these altitudes was more effective if based on composite data from multiple mesohabitats rather than data from single mesohabitats. No metric differentiated the two types of sites in the more arid, lowland, floodplain region of the river system. We suggest that Australia relies too heavily on bioassessment concepts developed to assess water pollution in well-watered regions of the Northern Hemisphere. Effective assessment of human impacts on macroinvertebrates in the rivers of inland Australia requires a better understanding of the roles of flow regimes, including flood and drought sequences, and of microhabitat structure and invasive alien species. Quantitative approaches may also be required.