ABSTRACT Floodplain wetlands are characterised by dynamic hydrological regimes and seasonal patterns of wetting and drying. They support distinct communities of fish, many of which are adapted to dynamic and variable conditions. Seasonal hydrological variation and the degree of water permanence influence physicochemical conditions and local habitat, which together with the surrounding landscape strongly influence the distribution and persistence of fish within individual wetlands. This study aimed to evaluate how broad‐scale landscape and temporal environmental factors of wetland ecosystems and biological traits of wetland fishes can determine occurrence patterns in floodplain wetland fish assemblages. We analysed inundation and environmental data spanning 37 years (1986–2022) across floodplain wetlands in the southern Murray–Darling Basin (MDB), Australia. Fish occurrence records for 14 species (10 native and 4 introduced) were sourced from public databases and combined with remotely sensed estimates of inundation frequency and land‐cover data to assess species‐environment‐relationships. To better understand the potential influence of biological determinants of habitat use (i.e., biological traits and species interactions), we also incorporated species‐specific traits related to life history, trophic levels and potential population growth, as well as phylogenetic relatedness. We applied Joint Species Distribution Models (JSDMs) to evaluate how environmental and biological factors jointly shape wetland fish community structure. Fish assemblages were primarily structured by environmental conditions, with water temperature, wetland area, and inundation regime identified as influential factors. Species‐specific responses to these environmental filters were heterogeneous. Biological traits, including life history, trophic level and resilience, collectively explained 26% of the variance in species occurrences, highlighting their role in determining habitat use. Spatial effects, accounting for variation among wetland locations and catchments, also contributed significantly to community structure. Phylogenetic relatedness did not influence species co‐occurrence. After accounting for environmental, trait‐based, and spatial factors, residual species associations suggested the potential for biotic interactions such as competition or facilitation acting at different scales. Fish communities in floodplains wetlands of the southern Murray–Darling Basin (MDB) are predominantly shaped by environmental filtering, with hydrology (inundation) the dominant factor, moderated by species traits and spatial context. This underscores that effective conservation and restoration of floodplain fish communities will require management strategies that buffer thermal extremes and enhance wetland permanence, along with maintaining a mosaic of wetland areas and considering landscape connectivity to accommodate both environmental influences and species‐specific habitat requirements.

Microbial communities within biofilms are widely recognised as important contributors to ecological food webs and elemental cycles within stream systems. Yet, little is known about how these biofilm communities respond compositionally to storm-event-driven changes in dissolved organic carbon (DOC) characteristics. Alpine headwater peatland-draining streams offer a unique opportunity to investigate this response as these systems are known to export high loads of DOC during storm events, with little further upstream input. This study investigated how sub-alpine peatland-draining stream biofilm composition changed in response to storm-event-driven pulses of DOC. It was found that during the peak of each DOC pulse, the composition of DOC changed to include increased contributions of organic acids, protein-like substances and microbially derived DOC. Despite this change in DOC composition, the composition of most biofilm microbial communities did not significantly shift following each pulse; rather, differences in biofilm community composition appeared to be more closely linked to peatland stream site. The findings of this study suggest biofilm microbial communities maintain compositional stability following short-term rapid changes in stream water chemistry, and that site-specific environmental factors may be more important in determining biofilm microbial community composition in sub-alpine headwater peatland-draining streams.

Coastal marine environments receive large influxes of anthropogenic contaminants from land-based sources such as metal(loid) s and emerging persistent organic pollutants (POPs). These contaminants can accumulate in marine sediments, seagrass and herbivorous marine megafauna such as dugongs, manatees and green turtles. Using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) approach, we evaluated 131 publications on the bioaccumulation and effects of metal(loid)s and organic contaminants in seagrass, dugongs, manatees and green turtles. The global distribution of these publications was mapped, with concentration and effects data extracted to calculate chemical risk quotients (RQ). Metal(loid)s were the most studied contaminant class, while research on other chemicals including per - and polyfluoroalkyl substances (PFAS) and pharmaceuticals and personal care products (PPCP) were under-represented. The link between the concentration of a contaminant measured in tissue and its biological effect was often lacking. New Approach Methods (NAMs), which include in vitro assays and omics approaches, were highlighted as valuable but not widely used. The reported bioaccumulated concentrations of contaminants in the literature varied greatly, with little data on the cumulative risk of mixtures. The calculation of RQ suggest a risk to many wild populations to the adverse effects of some contaminants. This review emphasises the need for standardised methods and data sharing, which will foster a more unified and global approach to better assess the risk contaminants pose to seagrass and the megafauna they support.

Thermal regimes of aquatic ecosystems are predicted to change as climate warming progresses over the next century, with high‐latitude and high‐elevation regions predicted to be particularly impacted. Here, we have modelled alpine stream water temperatures from air temperature data and used future predicted air temperature trajectories (representative concentration pathway [rcp] 4.5 and 8.5) to predict future water temperatures. Modelled stream water temperatures have been used to calculate cumulative degree days (CDDs) under current and future climate conditions. These calculations show that degree days will accumulate more rapidly under the future climate scenarios, and with a stronger effect for higher CDD values (e.g., rcp 4.5: 18–28 days earlier [CDD = 500]; 42–55 days earlier [CDD = 2000]). Changes to the time to achieve specific CDDs may have profound and unexpected consequences for alpine ecosystems. Our calculations show that while the effect of increased CDDs may be relatively small for organisms that emerge in spring–summer, the effects for organisms emerging in late summer–autumn may be substantial. For these organisms, the air temperatures experienced upon emergence could reach 9°C (rcp 4.5) or 12°C (rcp 8.5) higher than under current climate conditions, likely impacting on the metabolism of adults, the availability of resources, including food and suitable oviposition habitat, and reproductive success. Given that the movement of aquatic fauna to the terrestrial environment represents an important flux of energy and nutrients, differential changes in the time periods to achieve CDDs for aquatic and terrestrial fauna may de‐couple existing predator–prey interactions.

The nature of Australia’s high mountains is changing. Recent, repeated landscape-scale fires have burnt much of the subalpine forests dominated by snow gum (Eucalyptus pauciflora). Long-unburnt snow gum forests are important for ecosystem services, have socio-cultural benefits, and conservation values, but they are now exceedingly rare, comprising <1% of snow gum forests in the Victorian Alps. We identify where long-unburnt snow gum stands persist in the Victorian Alps and outline why management intervention is necessary to protect unburnt refuges and, more broadly, to allow mature/adult stands (such as occur on the Baw Baw Plateau) to develop into future old forests.

This review of the status of Australian caddisflies focuses on publications from 1982 to 2022. Information is provided on new species described in that period, new keys, new descriptions of both adults and larvae, and the distribution of families and genera from states/regions and the Northern Territory. Australia’s caddisfly fauna now totals 27 families, 111 genera and 868 species, with 97.9% of species endemic to Australia (only 19 of the 868 species are known from outside Australia, mainly from the nearby island of New Guinea – Papua New Guinea and Papua Province, Indonesia); some species also extend into New Zealand and South-East Asia. The biogeography of the Australian fauna is discussed briefly in terms of “northern” and “southern” faunal elements, faunal provinces, distributional barriers, areas of highest biodiversity and refuge areas. Northern and southern elements in the Australian Trichoptera fauna are indicated. The highest biodiversity is recorded in the following states/regions: New South Wales with 263 species, northern Queensland (N-Qld) with 248 species and Victoria with 247 species. The highest endemicity is in southern Western Australia (S-WA), with 73% endemic species, followed by N-Qld with 58% and Tasmania with 57%. The lowest numbers of species have been recorded from South Australia and S-WA, with 42 and 49 species respectively.

Abstract Animals must invest some portion of their metabolism to activities related to physiological maintenance and the remainder to processes related to the production of new biomass for growth and reproduction. Animal metabolism is fuelled by food, and the quality and quantity of food, along with the effort invested to obtain it, are fundamental to supporting populations. Biofilms are a primary basal food resource within riverine food webs, and it is thought that their nutritional value for animals decreases with age due to dynamic changes in community composition. We sought to test assumptions of spatiotemporal changes to biofilm nutritional value by assessing variations in biofilm mass and fatty acid composition in three rivers for 73 days. We also used a multi‐prong eDNA approach to characterize changes to biofilm fungal (ITS1–4), bacterial (16S), and algal (23S) community compositions. We anticipated biofilm food value to decrease with biofilm age due to shifts in composition from high‐quality green algae and diatoms to low‐quality cyanobacteria and filamentous algae. Our results partially support this contention; biofilm food value, assessed as a combination of fatty acid mass per unit area (in grams per square meter) and concentration of fatty acids (in milligrams per gram), was dynamic and peaked between 24 and 43 days following submersion. After 43 days, biofilm food value decreased. However, despite significant temporal changes in biofilm community composition and a decrease in overall lipid concentration, the proportions of different fatty acid classes among total lipids did not vary. Instead, the observed increase in the abundance of cyanobacteria and filamentous algae compared with diatoms and green algae, along with higher quantities of lipid‐poor extracellular polymeric substances (EPS), likely contributed to the reduction in overall lipid concentration relative to the biofilm dry mass. Here we present a novel approach to balance consumer energetic costs with food quality within aquatic food webs. Our results have important implications for river management and provide valuable information for the use of environmental water to support lotic ecosystems.

Alteration of riverine flows can modify the structure and function of ecosystems, changing energy pathways and patterns of micronutrient transfer between trophic levels. Fatty acids (FAs) commonly are used to evaluate food quality, since some FAs required for somatic growth and physiological functions in animals must be obtained from their diet. FAs also are used in food-web studies as biotracers as a consequence of their constrained metabolic biosynthesis by animals. However, their utility may be confounded by selective retention or modification of dietary FAs by consumers. We conducted a 70-day feeding trial to compare growth and survival of an abundant and widespread mesoconsumer (Cherax destructor, the common yabby or crayfish) fed three contrasting diets: a poor-quality detritus-based diet; a high protein invertebrate diet; and a high-quality commercial aquaculture pellet. Fatty acid profiles were obtained for each dietary treatment and contrasted with crayfish FA profiles at the end of the experiment to examine patterns of FA retention and integration. We also collected wild crayfish from floodplain wetland and river habitats, and obtained FA profiles from their stomach contents and body tissue to compare with experimental crayfish. Experimental crayfish fed high-quality commercial pellets doubled in mass during the 70-day assay, invertebrate fed crayfish growth was intermediate, and growth of crayfish fed detritus was negligible. Fatty acid profiles of crayfish fed our three contrasting diets differed significantly at the end of the experiment. Proportions of the polyunsaturated omega-6 FA linoleic acid (LIN, 18:2 omega 6) in crayfish followed the same inequality observed in growth and diets: pellets > invertebrates > detritus. Pellet-fed crayfish preferentially assimilated greater proportions of FAs 20:4 omega 6 (ARA), 20:5 omega 3 (EPA) 18:1 omega 9 (OA) and 16:1 omega 7 (POA) into their tissue. Fatty acid profiles of floodplain crayfish differed to profiles of riverine crayfish, and floodplain crayfish had higher proportions of essential FAs ARA and LIN in their tissues. Fatty acid biosynthesis by crayfish was best described by a hypothesis of FA allostasis rather than homeostasis; in this, FA profiles of crayfish were shaped by their diet, and selective integration and modification of high-quality FAs from basal resources rich in these micronutrients led to higher proportions in crayfish tissues. Here we present evidence for the conversion of shorter-chain essential FAs by freshwater crayfish to compensate for a lack of long-chain FAs in their diet. We provide a necessary step for improving our understanding of micronutrient dynamics and the transfer of essential molecules between trophic levels in lowland river food webs. Floodplain habitats are known to provide higher-quality basal food resources for mesoconsumers than riverine habitats, and here we identify one mechanism by which that may be extended to subsequent trophic levels.

Platypuses ( Ornithorhynchus anatinus ) forage for macroinvertebrate prey exclusively in freshwater habitats. Because food material in their faeces is well digested and mostly unidentifiable, previous dietary studies have relied on cheek pouch assessments and stable isotope analysis. Given DNA metabarcoding can identify species composition from only fragments of genetic material, we investigated its effectiveness in analysing the diet of platypuses, and to assess variation across seasons and sexes. Of the 18 orders and 60 families identified, Ephemeroptera and Diptera were the most prevalent orders, detected in 100% of samples, followed by Trichoptera, Pulmonata, and Odonata (86.21% of samples). Caenidae and Chironomidae were the most common families. Diptera had a high average DNA read, suggesting it is an important dietary component that may have been underestimated in previous studies. We found no variation in diet between sexes and only minimal changes between seasons. DNA metabarcoding proved to be a highly useful tool for assessing platypus diet, improving prey identification compared to cheek pouch analysis, which can underestimate soft-bodied organisms, and stable isotope analysis which cannot distinguish all taxa isotopically. This will be a useful tool for investigating how platypus prey diversity is impacted by habitat degradation as a result of anthropogenic stressors.

Groundwater ecosystems have a diverse and unique fauna, often dominated by Crustacea and generally characterised by short range endemics confined to single aquifers. Much of this knowledge has come from studies conducted either in fractured rock aquifers or alluvial aquifers. Karstic subterranean environments are present in the Cambrian Limestone Aquifer (CLA) in the Northern Territory, Australia, a freshwater aquifer which spans an area of ~28,000 km2. The presence of underground caverns and channels potentially allows extensive connectivity within this groundwater system. The emerging shale gas industry in the Beetaloo region, which underlies the CLA, provided the impetus to undertake the first survey of the potential existence of a stygofaunal community. Twenty-six groundwater wells (bores) and two springs were sampled in August and October 2019, across a distance of ~500 km, from the sub-tropical Mataranka region in the north to the semi-arid Barkly Tablelands in the south. Plankton nets and motorised pumps were used to collect water samples and conventional microscope-based morphological examinations in conjunction with environmental DNA (eDNA) were used to determine the presence of stygofauna. COI barcoding and 16S rRNA regions were also used for phylogenetic analysis. All stygofaunal communities were dominated by crustaceans, namely shrimps, amphipods, ostracods, copepods and syncarids. This fauna showed little affinity with the stygofauna recorded from more extensively sampled aquifers in north-western Australia, with new genera and species present in the CLA. eDNA analysis showed the presence of diverse biota at sites where direct water sampling for intact animals was difficult. COI and 16S analysis confirmed that a species of blind shrimp, Parisia unguis, occurred extensively throughout the aquifer, over a distance of at least ~300 km. The presence of Pa. unguis at widely separated sites across the CLA is consistent with substantial connectivity within the aquifer. This connectivity indicates that the risk of groundwater contamination from fracking chemicals needs to be adequately mitigated to prevent widespread effects.

Macroinvertebrate surveys are commonly used for assessing the health of freshwater systems around the world. Traditionally, surveying involves morphologically identifying the families, and sometimes genera, present in samples. Biological indices, derived from taxonomic lists, provide convenient ways to summarise community data and may be fairly insensitive to species-level changes in community compositions. In recent years, molecular techniques for identifying taxa have become increasingly popular and metabarcoding approaches that offer the ability to identify species from mixtures of whole animals (bulk-samples) or from environmental samples have gained much attention. However, generating accurate species lists from metabarcode data is challenging and can be impacted by sample type, choice of primers, community composition within samples, and the availability of reference sequences. This study compares the performance of molecular data extracted from bulk-samples against morphological data in calculating two biological indices (the Stream Invertebrate Grade Number Average Level 2 (SIGNAL2), which is calculated from family-level data, and a genus-level equivalent of this index, SIGNAL_SG) and one biological metric (taxon richness). Further, molecular indices and metrics derived from global, local or mixed reference DNA libraries and with varying degrees of filtering processes applied to them, are compared with respect to the strength of their relationships with morphological indices and metrics. Molecularly derived SIGNAL2 and SIGNAL_SG scores correlated strongly with morphologically derived scores, and were strongest when using a reference library containing a mix of local and global data. Molecularly derived richness metrics were moderately correlated with morphological taxa richness; however, the strongest correlations were observed when taxa that could not be assigned SIGNAL grades were omitted from analyses. This study highlights the utility of using molecular data as an objective and sensitive alternative to traditional freshwater biological assessment using macroinvertebrates.

A problem for fisheries ecologists who carry out dietary analysis on their specimens is dealing with contents that are difficult to identify, particularly when the contents comprise digested prey. We used a DNA metabarcoding approach to determine the diets of two co-occurring black fish species (Gadopsis bispinosus and Gadopsis marmoratus) to circumvent any issues with trying to apply microscopic methods to identify diets. We examined the frequency of occurrence of taxa across all specimens and the proportion that taxa contributed to total diet. In this way we hoped to demonstrate that a DNA-based method could resolve dietary differences of coexisting taxa. We showed that 10 macroinvertebrate taxa dominated the diets of both species and, of these, 7 occurred in all specimens of both taxa, indicating they were an important component of the diet of both species. Twelve taxa were present only in the G. bispinosus diet and four of those were terrestrial invertebrates; six taxa were found only in G. marmoratus. Our DNA-based approach to examine the taxa in the guts of two co-existing Gadopsis species provided sufficient resolution to show a significant degree of dietary partitioning.

Macroinvertebrates are commonly sampled for bioassessment of freshwater ecosystems. However, current bioassessment protocols involve laborious sorting of the animals from the debris (sample matrix) and morphological identification, where species level identifications are often difficult. DNA metabarcoding has the potential to improve bioassessment by reducing the time taken to process samples and improve the accuracy and speed of macroinvertebrate species identification. In this study, we evaluated DNA metabarcoding of macroinvertebrate samples, which include macroinvertebrates and the debris collected in the sample nets, to test if bulk, unsorted samples can be used to assess macroinvertebrate diversity. First, we tested if the sample matrix prevented the detection of six target macroinvertebrate taxa when DNA metabarcoding. Second, we tested if sample storage influenced the detection of the same six target macroinvertebrates. We also explored different levels of replication at the sample, sub‐sample, and polymerase chain reaction levels and compared the overall macroinvertebrate families detected using DNA metabarcoding to those identified morphologically. We found that the presence of the sample matrix did not interfere with or inhibit the detection of the six target macroinvertebrate taxa. Furthermore, we found that the various sample storage methods did not affect target macroinvertebrate detection. The reliability of detection of the target macroinvertebrates improved as hierarchical levels of replication were combined. We found strong overlap between the detection of overall macroinvertebrate family diversity when comparing DNA metabarcoding to morphological identification. Extracting DNA from the bulk macroinvertebrate samples that included the sample matrix and using this for DNA metabarcoding could improve bioassessment by removing the need for laborious sorting of samples. Furthermore, DNA metabarcoding detection of the six target taxa was not dependent on sample storage of up to 1 year in 95% ethanol, at room temperature or after heating. DNA metabarcoding had the advantage of identifying macroinvertebrate species, but good DNA barcode libraries are needed for widespread species identifications. Further investigation should focus on including multiple samples with different macroinvertebrate composition and densities to refine and standardise bulk sample processing protocols, and on building comprehensive DNA barcode libraries for aquatic macroinvertebrates.

Dissolved organic matter (DOM) within freshwaters is essential for broad ecosystem function. The concentration and type of DOM within rivers depends on the relative contributions of allochthonous sources and the production and consumption of DOM by microbes. In this work we have examined the temporal patterns in DOM quality and productivity in three lowland rivers in dryland Australia using fluorescence excitation emission scans. We assessed the production and consumption of DOM within light and dark bottle assays to quantify the relative contribution of bacteria and algae to the DOM pool and simultaneously assessed whether the systems were autotrophic or heterotrophic. DOM varied temporally within the three river systems over the course of the study period. Characterisation of DOM within light and dark bottles following a 6-hour incubation revealed microbial consumption of a humic-like component and production of protein-like components similar in nature to the amino acids tryptophan and tyrosine. The lack of a significant difference in DOM quality between the light and dark bottles indicated that the protein-like DOM is likely derived from bacterial activity. Respiration was shown to be higher than gross primary production in both whole river and bottle assays, yielding negative net production values and demonstrating that these rivers were predominately heterotrophic. Our work suggests that bacterial metabolism of DOM may be a significant contributor to the production of protein-like components within heterotrophic freshwater systems.

Globally, floodplain wetlands have been dramatically impacted by changes in water regimes. A key indicator of change in wetland state is riparian and aquatic plant community composition. Plant communities are traditionally assessed by visual monitoring programs that assess community composition. However, results from these monitoring programs may be effected by antecedent conditions that govern plant growth, such as season. In this study we used environmental DNA (eDNA) to assess the spatial composition of wetland vegetation communities from six floodplain complexes along the Murray River, Australia and compared results to those derived from tradition plant surveys. Our analyses of eDNA were conducted targeting two gene regions: 18S RNA and trnL at the species and operational taxonomic unit (OTU) levels. Analysis revealed significant similarity between the spatial patterns derived from the eDNA data and those derived from the traditional monitoring data. Moreover, using the eDNA data, analysis of endemicity revealed the majority of OTUs and species occurred only at a single wetland or wetland complex. Few genera were shared between the traditional survey data set and the molecular data sets. But for those that were shared, detectability varied between gene fragments and among genera, ranging from 11 to 100% in the trnL data to 14.3–100% in the18S data. Our results show that landscape patterns in plant communities can be reliably derived from eDNA analysis, thus providing a cost-effective way of undertaking vegetation surveys.

The Siamese Crocodile (Crocodylus siamensis) is a critically endangered medium-size crocodilian endemic to Southeast Asia. Extirpated from much of its natural range, conservation efforts in the Cardamom Mountains of Cambodia include the release of captive-reared juveniles and sub-adults into river reaches known to support adult C. siamensis populations. Despite conservation concerns, the biology of wild C. siamensis is not well studied and the ecology of ecosystems at release locations is poorly understood. Fish are thought to comprise a major component of the diet of C. siamensis. Here, the aim was to characterize fish communities within three potential C. siamensis release locations, focusing on community composition, density, size class structure and food web dynamics. The survey sites varied in both C. siamensis density and human fishing pressure, and the results are interpreted in light of these drivers. Genomic interrogation of fishes of the Cardamom Mountains distinguished 13 distinct fish species, contributing to genetic databases and adding to the documented taxon list for the region. The presence of two previously unconfirmed fish genera in the region is confirmed. The first estimates of fish density, biomass and size class distribution for three rivers in the Cardamom Mountains are provided. The three potential C. siamensis release reaches that were sampled showed clear differences in fish community composition, structural and trophic dynamics. Fish density and biomass were highest in the high-density C. siamensis survey reach and lowest in the high human fishing pressure reach. Survey reaches with food webs that were more reliant on autochonously driven food webs supported higher densities and biomass of fish. These results have important implications for future C. siamensis conservation efforts in Cambodia and contribute valuable ecological information on a relatively unexplored region.