Legacy Metal Contaminants and Excess Nutrients in Low Flow Estuarine Embayments Alter Composition and Function of Benthic Bacterial Communities

Riverine bacterial communities are more shaped by species sorting in intensive urban and agricultural watersheds

Bacterial communities play a crucial role in maintaining the stability of river ecosystems and driving biogeochemical cycling, exhibiting high sensitivity to environmental change. However, understanding the spatial scale effects and assembly mechanisms of riverine bacterial communities under distinct anthropogenic disturbances remains a challenge. Here, we investigated bacterial communities across three distinct watersheds [i.e., intensive urban (UW), intensive agricultural (AW), and natural (NW)] in both dry and wet seasons. We explored biogeographic patterns of bacterial communities and the influence of landscape patterns at multi-spatial scales and water chemistry on bacterial communities. Results showed that α diversity was significantly lower in UW and AW compared to NW, particularly in the dry season. A gradient of β diversity with NW > UW > AW was observed across both seasons (p < 0.05). Pseudomonadota, Bacteroidota, and Actinobacteriota were the most abundant phyla across all watersheds, with specific taxa enriched in each watershed (i.e., the class Actinobacteria was significant enrichment in UW and AW, and Clostridia in NW). The influence of landscape patterns on bacterial communities was significantly lower in human-disturbed watersheds, particularly in UW, where this influence also varied slightly from near riparian buffers to sub-watershed. Homogeneous selection and drift jointly dominated the bacterial community assembly across all watersheds, with homogeneous selection exhibiting a greater influence in UW and AW. Landscape patterns explained less variance in bacterial communities in UW and AW than in NW, and more variance was explained by water chemistry (particularly in UW). These suggest that the stronger influence of species sorting in UW and AW was driven by more allochthonous inputs of water chemistry (greater environmental stress). These findings provide a theoretical foundation for a deeper understanding of riverine bacterial community structure, spatial scale effects, and ecological management under different anthropogenic activities.

Tree of life metabarcoding can serve as a biotic benchmark for shifting baselines in urbanized estuaries

Urbanization of estuaries drastically changed existing shorelines and bathymetric contours, in turn modifying habitat for marine foundational species that host critical biodiversity. And yet we lack approaches to characterize a significant fraction of the biota that inhabit these ecosystems on time scales that align with rates of urbanization. Environmental DNA (or eDNA) metabarcoding that combines multiple assays targeting a broad range of taxonomic groups can provide a solution, but we need to determine whether the biological communities it detects ally with different habitats in these changing aquatic environments. In this study, we tested whether tree of life metabarcoding (ToL-metabarcoding) data extracted from filtered seawater samples correlated with four known geomorphic habitat zones across a heavily urbanized estuary (Sydney Harbour, Australia). Using this method, we substantially expanded our knowledge on the composition and spatial distribution of marine biodiversity across the tree of life in Sydney Harbour, particularly for organisms where existing records are sparse. Excluding terrestrial DNA inputs, we identified significant effects of both distance from the mouth of Sydney Harbour and geomorphic zone on biological community structure in the ToL-metabarcoding dataset (entire community), as well as in each of the taxonomic subgroups that we considered (fish, macroinvertebrates, algae and aquatic plants, bacteria). This effect appeared to be driven by taxa as a collective versus a few individual taxa, with each taxon explaining no more than 0.62% of the variation between geomorphic zones. Similarly, taxonomic richness was significantly higher within geomorphic zones with large sample sizes, but also decreased by 1% with each additional kilometer from the estuary mouth, a result consistent with a reduction in tidal inputs and available habitat in upper catchments. Based on these results, we suggest that ToL-metabarcoding can be used to benchmark biological monitoring in other urbanized estuaries globally, and in Sydney Harbour at future time points based on detection of bioindicators across the tree of life. We also suggest that robust biotic snapshots can be archived following extensive curation of taxonomic assignments that incorporates ecological affinities, supported by records from relevant and regional biodiversity repositories.

Response of planktonic microbial assemblages to disturbance in an urban sub-tropical estuary

Microbes are sensitive indicators of estuarine processes because they respond rapidly to dynamic disturbance events. As most of the world's population lives in urban areas and climate change-related disturbance events are becoming more frequent, estuaries bounded by cities are experiencing increasing stressors, at the same time that their ecosystem services are required more than ever. Here, using a multidisciplinary approach, we determined the response of planktonic microbial assemblages in response to seasonality and a rainfall disturbance in an urban estuary bounded by Australia's largest city, Sydney. We used molecular barcoding (16S, 18S V4 rRNA) and microscopy-based identification to compare microbial assemblages at locations with differing characteristics and urbanisation histories. Across 142 samples, we identified 8,496 unique free-living bacterial zOTUs, 8,175 unique particle associated bacterial zOTUs, and 1,920 unique microbial eukaryotic zOTUs. Using microscopy, we identified only the top <10% abundant, larger eukaryotic taxa (>10 µm), however quantification was possible. The site with the greater history of anthropogenic impact showed a more even community of associated bacteria and eukaryotes, and a significant increase in dissolved inorganic nitrogen following rainfall, when compared to the more buffered site. This coincided with a reduced proportional abundance of Actinomarina and Synechococcus spp., a change in SAR 11 clades, and an increase in the eukaryotic microbial groups Dinophyceae, Mediophyceae and Bathyoccocaceae, including a temporary dominance of the harmful algal bloom dinoflagellate Prorocentrum cordatum (syn. P. minimum). Finally, a validated hydrodynamic model of the estuary supported these results, showing that the more highly urbanised and upstream location consistently experienced a higher magnitude of salinity reduction in response to rainfall events during the study period. The best abiotic variables to explain community dissimilarities between locations were TDP, PN, modelled temperature and salinity (r = 0.73) for the free living bacteria, TP for the associated bacteria (r = 0.43), and modelled temperature (r = 0.28) for the microbial eukaryotic communities. Overall, these results show that a minor disturbance such as a brief rainfall event can significantly shift the microbial assemblage of an anthropogenically impacted area within an urban estuary to a greater degree than a seasonal change, but may result in a lesser response to the same disturbance at a buffered, more oceanic influenced location. Fine scale research into the factors driving the response of microbial communities in urban estuaries to climate related disturbances will be necessary to understand and implement changes to maintain future estuarine ecosystem services.

Exotic asphyxiation: interactions between invasive species and hypoxia

Non-indigenous species (NIS) and hypoxia (<2 mg O2 l-1 ) can disturb and restructure aquatic communities. Both are heavily influenced by human activities and are intensifying with global change. As these disturbances increase, understanding how they interact to affect native species and systems is essential. To expose patterns, outcomes, and generalizations, we thoroughly reviewed the biological invasion literature and compiled 100 studies that examine the interaction of hypoxia and NIS. We found that 64% of studies showed that NIS are tolerant of hypoxia, and 62% showed that NIS perform better than native species under hypoxia. Only one-quarter of studies examined NIS as creators of hypoxia; thus, NIS are more often considered passengers associated with hypoxia, rather than drivers of it. Paradoxically, the NIS that most commonly create hypoxia are primary producers. Taxa like molluscs are typically more hypoxia tolerant than mobile taxa like fish and crustaceans. Most studies examine individual-level or localized responses to hypoxia; however, the most extensive impacts occur when hypoxia associated with NIS affects communities and ecosystems. We discuss how these influences of hypoxia at higher levels of organization better inform net outcomes of the biological invasion process, i.e. establishment, spread, and impact, and are thus most useful to management. Our review identifies wide variation in the way in which the interaction between hypoxia and NIS is studied in the literature, and suggests ways to address the number of variables that affect their interaction and refine insight gleaned from future studies. We also identify a clear need for resource management to consider the interactive effects of these two global stressors which are almost exclusively managed independently.

Linking freshwater ecotoxicity to damage on ecosystem services in life cycle assessment

Freshwater ecosystems provide major benefits to human wellbeing-so-called ecosystem services (ES)-but are currently threatened among others by ecotoxicological pressure from chemicals reaching the environment. There is an increased motivation to incorporate ES in quantification tools that support decision-making, such as life cycle assessment (LCA). However, mechanistic models and frameworks that can systematically translate ecotoxicity effect data from chemical tests into eventual damage on species diversity, functional diversity, and ES in the field are still missing. While current approaches focus on translating predicted ecotoxicity impacts to damage in terms of species loss, no approaches are available in LCA and other comparative assessment frameworks for linking ecotoxicity to damage on ecosystem functioning or ES. To overcome this challenge, we propose a way forward based on evaluating available approaches to characterize damage of chemical pollution on freshwater ES. We first outline an overall framework for linking freshwater ecotoxicity effects to damage on related ES in compliance with the boundary conditions of quantitative, comparative assessments. Second, within the proposed framework, we present possible approaches for stepwise linking ecotoxicity effects to species loss, functional diversity loss, and damage on ES. Finally, we discuss strengths, limitations, and data availability of possible approaches for each step. Although most approaches for directly deriving damage on ES from either species loss or damage to functional diversity have not been operationalized, there are some promising ways forward. The Threshold Indicator Taxa ANalysis (TITAN) seems suitable to translate predicted ecotoxicity effects to a metric of quantitative damage on species diversity. A Trait Probability Density Framework (TPD) approach that incorporates various functional diversity components and functional groups could be adapted to link species loss to functional diversity loss. An Ecological Production Function (EPF) approach seems most promising for further linking functional diversity loss to damage on ES flows for human wellbeing. However, in order to integrate the entire pathway from predicted freshwater ecotoxicity to damage on ES into LCA and other comparative frameworks, the approaches adopted for each step need to be harmonized in terms of assumptions, boundary conditions and consistent interfaces with each other.