Biology subjects

Bissett, A.

Publications and source records attributed to Bissett, A..

10 recordsLinked to original sources

bioRxiv2026

Population density is a selective driver of urban soil microbiomes: evidence from bacteria, fungi and protozoan communities in a regional city

Urbanisation is widely recognised as a major driver of environmental change, yet its impacts on soil microbiomes remain poorly understood, particularly outside megacities and beyond bacterial taxa. Population density is frequently used as a proxy for urban intensity, but its relevance across different microbial kingdoms and urban contexts is unclear. Here, we investigated how soil microbial communities vary across population density bands in the regional, temperate city of Hobart, Australia. Using a multi-kingdom metabarcoding approach, we analysed bacterial, fungal, and protozoan communities from soils collected in urban green spaces along a population density gradient. Bacterial alpha-diversity differed significantly across population density bands, exhibiting an inverse U-shaped relationship, with the highest diversity at green spaces in intermediate population density areas. In contrast, fungal and protozoan alpha-diversity did not vary with population density. Community composition (beta-diversity) did not differ consistently across density bands for any microbial group, and variation in soil physicochemical properties explained more community variation than population density alone. These results indicate that population density is a selective, rather than universal, driver of urban soil microbiomes and that responses to urbanisation differ markedly among microbial kingdoms. Our findings highlight important limitations of using population density as a sole indicator of urban impact and challenge the generalisability of conclusions drawn from bacteria-focused studies in large cities. By demonstrating kingdom-specific and context-dependent responses in a regional city, this study underscores the need for multi-kingdom, multi-scale approaches to better understand how urbanisation shapes soil microbiomes and their potential implications for urban ecosystem functioning and human health.

ecology↗

bioRxiv2025

Use of the Pacific oyster (Magallana gigas) as a natural sampler for the detection of Neoparamoeba perurans

Amoebic gill disease (AGD), caused by Neoparamoeba perurans, is a challenge for Atlantic salmon aquaculture. Research has, therefore, focused on detecting/monitoring N. perurans loads within/around fish pens. Recently, molecular methods to detect N. perurans have been used to reduce labour-intensive sampling, inconsistency, and stress on stock, while complimenting gill scoring and histology methods for AGD assessment. Molecular detection depends on reliable and simple sample collection, opening the possibility of using natural samplers (organisms that collect/accumulate DNA through feeding/foraging) for aquatic eDNA collection. We evaluated, through aquarium-based experiments, the utility of the Pacific oyster (Magallana gigas) to collect N. perurans DNA from the water column. In aquaria inoculated with N. perurans, total water column amoeba load decreased significantly over time in the presence of oysters. Despite this decrease no correlation between the level of amoeba accumulation within oysters and the decrease in the water column was observed. N. perurans was detected in every oyster organ type tested (mantle, gill, palp and digestive gland), though with high variation. The detection of N. perurans DNA within the digestive gland indicates that oysters ingested amoeba. Oysters were found to be viable eDNA samplers for N. perurans, providing a useful, simplified collection method.

molecular biology↗

bioRxiv2025

Continent-wide assessment of the strain-level diversity of Bradyrhizobium, a dominant soil bacterial genus

Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so dominant across a wide range of soil types and environmental conditions. Here we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. While members of the genus Bradyrhizobium were detected in > 80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework and methodology for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.

microbiology↗

bioRxiv2025

Contrasting dynamics and biotic association networks in estuarine microbenthic communities along an environmental disturbance gradient

Estuarine ecosystems experience a range of anthropogenic pressures. Consequently, robust monitoring tools are essential for their management and protection. Utilising environmental DNA in routine monitoring programs enables the inclusion of benthic microorganisms, which are not only good indicators of environmental condition, but also play critical roles in ecosystem functioning. In this study we collect eDNA from sediment samples across time in six estuaries, from the Basque coast (Spain), under varying degrees of disturbance. To identify potential indicators of biotic integrity (environmental health status), we used time series data to examine the prokaryotic microbial communities and consensus networks associated with different levels of pollution. In general, sediment communities were relatively temporally stable, with the moderately and heavily disturbed sites showing more variation. The consensus networks also differed significantly in their topologies, with more impacted estuaries having fewer nodes, edges and connectance, among others, and higher modularity compared to those less impacted. Moreover, the potential keystone taxa and predicted functional profiles differed between consensus networks. This illustrates how modelled association networks can reveal new insights regarding the state of estuarine ecosystems and their potential functional processes.

ecology↗

bioRxiv2024

Characterization of bacteria colonizing the mucosal layer of the gastrointestinal tract of Atlantic salmon farmed in a warm water region

Atlantic salmon (Salmo salar) farmed in seawater in Tasmania (lutruwita) can experience temperatures close to their thermotolerance limit during summer. Gut microbiome data from eight successive annual surveys and a specific survey of GI tract mucosa and digesta bacterial cross-sectional distributions indicated members of the genus Aliivibrio, Vibrio, and an unclassified Mycoplasmoidaceae are the main colonizers of the gut mucosal layer in Tasmanian farmed salmon. Peak abundance levels are reached after 7-8 months, corresponding to the late summer, following the transfer of hatchery smolt to seawater farms. Salmon Aliivibrio isolates comprise three novel non-bioluminescent species distinct from species found in the northern hemisphere growing regions. Along with other Aliivibrio species these species share many genes required for host colonization and biofilm formation and also include species and strain-level dependent features. Two of the novel Aliivibrio species surprisingly possessed genes for cytolethal distending toxin while the more predominant species lacked any known virulence genes. The overall observations suggest a small number of species actively colonize the mucosal layer of Atlantic salmon farmed in Tasmania and that this process is strongly influenced by the environmental temperature.

microbiology↗

bioRxiv2024

The ecological relevance of flagellar motility in soil bacterial communities

Flagellar motility is a key bacterial trait as it allows bacteria to navigate their immediate surroundings. Not all bacteria are capable of flagellar motility, and the distribution of this trait, its ecological associations, and the life history strategies of flagellated taxa remain poorly characterized. We developed and validated a genome-based approach to infer the potential for flagellar motility across 12 bacterial phyla (26,192 genomes in total). The capacity for flagellar motility was associated with a higher prevalence of genes for carbohydrate metabolism and higher maximum potential growth rates, suggesting that flagellar motility is more prevalent in resource-rich environments due to the energetic costs associated with this trait. To test this hypothesis, we focused on soil bacterial communities, where flagellar motility is expected to be particularly important given the heterogeneous nature of the soil environment. We applied a method to infer the prevalence of flagellar motility in whole bacterial communities from metagenomic data, and quantified the prevalence of flagellar motility across 4 independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). As expected, we observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in each of these datasets. Given that soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data acquired from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments, confirming that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. Flagellar motility is a fundamental phenotypic trait for bacterial adaptation to soil, defining life history strategies primarily associated with resource availability. More generally, this work highlights the value of combining genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.

ecology↗

bioRxiv2022

Defining marine bacterioplankton community assembly rules by contrasting the importance of environmental determinants and biotic interactions

Bacterioplankton communities play major roles in governing marine productivity and biogeochemical cycling, yet what drives the relative influence of the types of deterministic ecological processes which result in diversity patterns remains unclear. Here we examine how differing deterministic processes (environmental factors and biotic interactions) drive temporal dynamics of bacterioplankton diversity at three different oceanographic time-series locations, spanning 15 degrees of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples, collected over a period of 5.5 years, were analyzed using 16S rRNA amplicon sequencing. The high and mid-latitude sites of Maria Island and Port Hacking were characterized by high and intermediate levels of environmental heterogeneity respectively, with both alpha (local) diversity (72 % and 24 % of total variation) and beta diversity (32 % and 30 %) patterns within bacterioplankton assemblages primarily explained by environmental determinants, including day length, ammonium, and mixed layer depth. In contrast, at North Stradbroke Island, a sub-tropical location where environmental conditions are less seasonally variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha diversity: 33 %; beta diversity: 26 %) with environment only contributing 11 and 13 % to predicting diversity, respectively. Our results demonstrate that bacterioplankton diversity is the result of both deterministic environmental and biotic processes and that the importance of these different deterministic processes varies, potential in response to environmental heterogeneity. ImportanceMarine bacterioplankton drives important biological processes, including the cycling of key nutrients or fixing atmospheric carbon. Therefore, to predict future climate scenarios its critical to model these communities accurately. Processes that drive bacterioplankton diversity patterns in the oceans however remain unresolved, with most studies focusing on deterministic environmental drivers, ie temperature or available inorganic nutrients. Biotic deterministic processes including interactions among individuals are also important for structuring diversity patterns, however, this is rarely included to predict bacterioplankton communities. We develop an approach for determining the relative contribution of environmental and potential biotic interactions that structure marine bacterioplankton at three series at different latitudes. Environmental factors best predicted temporal trends in bacterioplankton diversity at the two high latitude time series, while biotic influence was most apparent at the low latitude time series. Our results suggest environmental heterogeneity is an important attribute driving the contribution of varying deterministic influence of bacterioplankton diversity.

ecology↗

bioRxiv2022

The importance of environmental parameters and mixing zone in shaping estuarine microbial communities along a freshwater-marine gradient.

Microbial communities are important elements in the marine environment, contributing to nutrient cycling and biogeochemical processes. Estuaries comprise environments exhibiting characteristics from freshwater to marine, leading to distinct microbial communities across this environmental gradient. Here, we examine the spatial dynamics of microbial communities in Macquarie Harbour, an estuarine system on the West coast of Tasmania, Australia. Water was sampled along the estuary to explore the structure and composition of the microbial communities using 16S/18S rRNA gene amplicon sequencing. Multivariate analyses showed environmental variables and community compositions varying along a longitudinal (river to adjacent ocean) gradient at the surface. In the harbour, differences in the microbial community were observed between surface (0-1 m) and intermediate depths (4.5-11 m depth). The results of differential abundance, network and Partial Least Square analyses suggest that Macquarie Harbour is a mixing zone, where the distributions of archaeal, bacterial and eukaryotic communities are influenced by oceanic and riverine inputs. Coupled with the natural characteristics of the Harbour, the heterotrophic component of this microbial communities inhabiting the surface and intermediate waters may play important roles in the nutrient cycle in the studied area. These results provide critical insights into the Macquarie Harbour environment and the importance of understanding the role of microbial communities for similar systems elsewhere.

microbiology↗

bioRxiv2021

An ecological perspective on microbial genes of unknown function in soil

Genes that remain hypothetical, uncharacterized, and unannotated comprise a substantial portion of metagenomic datasets and are likely to be particularly prevalent in soils where poorly characterized taxa predominate. Documenting the prevalence, distribution, and potential roles of these genes of unknown function is an important first step to understanding their functional contributions in soil communities. We identified genes of unknown function from 50 soil metagenomes and analyzed their environmental distributions and ecological associations. We found that genes of unknown function are prevalent in soils, particularly fine-textured, higher pH soils that harbor greater abundances of Crenarchaeota, Gemmatimonadota, Nitrospirota, and Methylomirabilota. We identified 43 dominant (abundant and ubiquitous) gene clusters of unknown function and determined their associations with soil microbial phyla and other "known" genes. We found that these dominant unknown genes were commonly associated with microbial phyla that are relatively uncharacterized, with the majority of these dominant unknown genes associated with mobile genetic elements. This work demonstrates a strategy for investigating genes of unknown function in soils, emphasizes the biological insights that can be learned by adopting this strategy, and highlights specific hypotheses that warrant further investigation regarding the functional roles of abundant and ubiquitous genes of unknown function in soil metagenomes.

microbiology↗

bioRxiv2021

Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets

In post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (> 25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that many alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states.

ecology↗