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As an increasing number of ecosystems face departures from long standing environmental conditions under climate change, our understanding of the capacity of species to adapt will become important for directing conservation and management of biodiversity. Insights into the potential for genetic adaptation might be gained by assessing genomic signatures of adaptation to historic or prevailing environmental conditions. The river red gum (Eucalyptus camaldulensis Dehnh.) is a widespread Australian eucalypt inhabiting riverine and floodplain habitats which spans strong environmental gradients. We investigated the effects of adaptation to environment on population level genetic diversity of E. camaldulensis, examining SNP variation in candidate gene loci sampled across 20 climatically diverse populations approximating the species natural distribution. Genetic differentiation among populations was high (F(ST) = 17%), exceeding previous estimates based on neutral markers. Complementary statistical approaches identified 6 SNP loci in four genes (COMT, Dehydrin, ERECTA and PIP2) which, after accounting for demographic effects, exhibited higher than expected levels of genetic differentiation among populations and whose allelic variation was associated with local environment. While this study employs but a small proportion of available diversity in the eucalyptus genome, it draws our attention to the potential for application of wide spread eucalypt species to test adaptive hypotheses.

In nutritional ecology the intake target is the diet that maximises consumer fitness. A key hypothesis of nutritional ecology is that natural selection has acted upon the behavioural and physiological traits of consumers to result in them Selectively Consuming prey to match the Intake Target (SCIT). SCIT has been documented in some herbivores and omnivores, which experience strong heterogeneity in the nutritional quality of available foods. Although carnivores experience a prey community with a much more homogeneous nutrient composition, SCIT by carnivores has nevertheless been deemed highly likely by some researchers. Here we test for SCIT for micronutrients (amino acids) in two freshwater carnivores: the river blackfish and the two-spined blackfish. Although both blackfishes exhibited non-random consumption of prey from the environment, this resulted in non-random consumption of amino acids in only one species, the river blackfish. Non-random consumption of amino acids by river blackfish was not SCIT, but instead an artefact of habitat-specific foraging. We present hypotheses to explain why wild populations of freshwater carnivores may not exhibit SCIT for amino acids. Our work highlights the need for careful, critical tests of the hypotheses and assumptions of nutritional ecology and its application to wild populations.

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.

Nonnative riparian plants can affect stream microbial dynamics by altering the quality, quantity, and timing of allochthonous inputs, but little consideration has been given to the potential influence of co-invading mutualists associated with nonnative riparian invaders. We used a high-resolution ecogenomic approach to examine the effects of riparian invasion by nonnative willows on microbial composition in associated small temperate streams. Willow infestation led to significant differences in fungal and bacterial communities between willow-infested and reference reaches. Fungal taxon richness was lower and phototrophic bacteria were less common in willow-infested reaches. Aquatic hyphomycetes contributed less to community composition of fungal communities in willow-infested reaches. Nonnative ectomycorrhizal fungi Inocybe spp. and Tormentella spp., known willow mutualists in their home ranges, were primary drivers of microbial community differences among infested and reference reaches. Nonnative obligate-mutualistic plant invaders can avoid symbiont limitation in their new territories by invading with co-evolved symbionts. We showed how co-invading, nonnative ectomycorrhizal fungi associated with invasive willows can modify microbial dynamics within streams. Our results provide new insights to the effects of riparian invaders, and our methods can be applied to test co-invasion hypotheses in streams and riverine habitats globally.

Dissolved organic nitrogen (DON) can comprise up to 80% of the dissolved N pool in riverine ecosystems, but concentration and compositional responses to catchment conditions has received limited attention. We examined the suite of nitrogenous nutrients along the length of the Ovens River, Victoria, Australia, a river with identifiable regions of native vegetation, agricultural activity and floodplain forest connection, carrying out longitudinal surveys in winter during a period of high flow and in summer during a period of stable base flow. We examined: the concentrations of DON, the proportion of DON that occurs as dissolved combined amino acids (DCAAs), whether concentration and DCAA composition varied between flow and whether land-use and tributaries have an impact upon nutrient concentration and DON composition. DON concentrations were greater than dissolved inorganic nitrogen under both base flow and high flow conditions. Under base flow DON exhibited a continuous increase in concentration downstream (ranging from 50 to 300 μg/L), compared to a much larger increase under high flow (150–600 μg/L) coupled with a major discrete increase of ~ 350 μg/L at a tributary input (King River). Concentrations of NOₓ (oxides of nitrogen) species were much higher under high flow conditions (range 50–250 μg/L) compared to 0–50 μg/L at base flow, and showed a significant increase in concentration with distance downstream. A discrete change in NOₓ concentrations was also observed at the King River confluence under high flow, although in this case causing a decrease in concentration of ~ 100 μg/L. DCAA concentrations varied little along the length of the river at base flow but increased with distance downstream at high flow. The DCAA concentrations were of the same order of magnitude as ammonium at both base and high flows and nitrate concentrations at base flow. The proportion of DON that was in the form of DCAA was reasonably uniform during high flow (3–6%), but highly variable at base flow (5–44%). The amino acid (AA) composition of the DCAA varied along the river and differed between flow regimes (except below the confluence with the King River where AA composition under the two flow conditions converged) suggesting a strong influence of land use. We show that DON is potentially a large component (4–81%) of the total N budget and given that 5–23% is in the form of peptide/protein, represents an important source of N. DON and more specifically DCAAs should therefore be considered both when constructing N budgets and monitoring levels of in-stream nitrogen.

Willows (Salix spp.) are listed as a weed of national significance in Australia. Despite this recognition, functional effects of willows on streams compared to native species are largely unknown. Leaves supply carbon to instream food webs, but may also act as surfaces for biofilm, and thus can contribute in different ways to stream metabolism. Salix fragilis L. and Eucalyptus camaldulensis Dehnh. leaves that had been colonised by biofilms were placed into chambers in laboratory conditions, and metabolic rates were measured. Gross Primary Production (GPP) of biofilms on E. camaldulensis leaves after 10 days of incubation were significantly greater than biofilms on S. fragilis leaves. S. fragilis leaves displayed greater rates of microbial decomposition per leaf mass. Autotrophic biomass was one hundred fold greater on E. camaldulensis leaves. The biofilm on E. camaldulensis leaves is likely to support a greater population of grazers, compared to S. fragilis. The alien S. fragilis leaves, therefore, are fuelling a different component of the food web to endemic E. camaldulensis leaves. Endemic Eucalyptus spp. leaves play an important role in temperate Australian streams as a substrate for autotrophic growth and provide a year round pathway for carbon to reach secondary invertebrate consumers.

Organic carbon is a critical component of aquatic systems, providing energy storage and transfer between organisms. Fungi are a major decomposer group in the aquatic carbon cycle, and are one of few groups thought to be capable of breaking down woody (lignified) tissue. In this work we have used high spatial resolution (synchrotron light source) infrared micro-spectroscopy to study the interaction between aquatic fungi and lignified leaf vein material (xylem) from River Redgum trees (E. camaldulensis) endemic to the lowland rivers of South-Eastern Australia. The work provides spatially explicit evidence that fungal colonisation of leaf litter involves the oxidative breakdown of lignin immediately adjacent to the fungal tissue and depletion of the lignin-bound cellulose. Cellulose depletion occurs over relatively short length scales (5-15 µm) and highlights the likely importance of mechanical breakdown in accessing the carbohydrate content of this resource. Low bioavailability compounds (oxidized lignin and polyphenols of plant origin) remain in colonised leaves, even after fungal activity diminishes, and suggests a possible pathway for the sequestration of carbon in wetlands. The work shows that fungi likely have a critical role in the partitioning of lignified material into a biodegradable fraction that can re-enter the aquatic carbon cycle, and a recalcitrant fraction that enters long-term storage in sediments or contribute to the formation of dissolved organic carbon in the water column.

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.

Invasive riparian plants are a significant threat to riverine environments and are thought to alter the structure and function of stream ecosystems. Salix spp. are a genus of highly invasive northern hemisphere trees and shrubs that have invaded substantial areas of southern hemisphere riparian corridors. We set out to review the existing peer reviewed literature surrounding the impacts of Salix spp. infestation to streams by rigorously testing a suite of cause–effect hypotheses using a causal criteria analysis. Our analysis found evidence in the literature that infestation by exotic Salix spp. can cause a decrease in incidental illumination and benthic periphyton density, increased rates of allochthonous litter leaching and decomposition and changes to secondary consumer assemblage and trophic organisation. The review also highlighted a number of aspects of Salix spp. invasion for which there are significant knowledge gaps in the literature. Our results emphasise the importance site specificity, seasonal variation, physical properties of supplanted vegetation, stream size and magnitude of infestation when predicting putative cause–effect relationships between Salix spp. invasion and stream structure and function. We show that, by possessing incongruent biological and physical characteristics to native plants, invasive terrestrial trees have the capacity to influence adjacent aquatic ecosystems.

Terminal restriction fragment length polymorphism (T-RFLP) is increasingly being used to examine microbial community structure and accordingly, a range of approaches have been used to analyze data sets. A number of published reports have included data and results that were statistically flawed or lacked rigorous statistical testing. A range of simple, yet powerful techniques are available to examine community data, however their use is seldom, if ever, discussed in microbial literature. We describe an approach that overcomes some of the problems associated with analyzing community datasets and offer an approach that makes data interpretation simple and effective. The Bray-Curtis coefficient is suggested as an ideal coefficient to be used for the construction of similarity matrices. Its strengths include its ability to deal with data sets containing multiple blocks of zeros in a meaningful manner. Non-metric multi-dimensional scaling is described as a powerful, yet easily interpreted method to examine community patterns based on T-RFLP data. Importantly, we describe the use of significance testing of data sets to allow quantitative assessment of similarity, removing subjectivity in comparing complex data sets. Finally, we introduce a quantitative measure of sample dispersion and suggest its usefulness in describing site heterogeneity.