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 unique genomes). 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 environments with higher carbon availability. To test this hypothesis, 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 four independent field studies that each captured putative gradients in soil carbon availability (148 metagenomes). We observed a positive relationship between the prevalence of bacterial flagellar motility and soil carbon availability in all datasets. Since soil carbon availability is often correlated with other factors that could influence the prevalence of flagellar motility, we validated these observations using metagenomic data from a soil incubation experiment where carbon availability was directly manipulated with glucose amendments. This confirmed that the prevalence of bacterial flagellar motility is consistently associated with soil carbon availability over other potential confounding factors. This work highlights the value of combining predictive genomic and metagenomic approaches to expand our understanding of microbial phenotypic traits and reveal their general environmental associations.

Drivers and human impacts on topsoil bacterial and fungal community biogeography across Australia.

Soil microbial diversity mediates a wide range of key processes and ecosystem services influencing planetary health. Our knowledge of microbial biogeography patterns, spatial drivers and human impacts at the continental scale remains limited. Here, we reveal the drivers of bacterial and fungal community distribution in Australian topsoils using 1384 soil samples from diverse bioregions. Our findings highlight that climate factors, particularly precipitation and temperature, along with soil properties, are the primary drivers of topsoil microbial biogeography. Using random forest machine-learning models, we generated high-resolution maps of soil bacteria and fungi across continental Australia. The maps revealed microbial hotspots, for example, the eastern coast, southeastern coast, and west coast were dominated by Proteobacteria and Acidobacteria. Fungal distribution is strongly influenced by precipitation, with Ascomycota dominating the central region. This study also demonstrated the impact of human modification on the underground microbial community at the continental scale, which significantly increased the relative abundance of Proteobacteria and Ascomycota, but decreased Chloroflexi and Basidiomycota. The variations in microbial phyla could be attributed to distinct responses to altered environmental factors after human modifications. This study provides insights into the biogeography of soil microbiota, valuable for regional soil biodiversity assessments and monitoring microbial responses to global changes.

A marine heatwave drives significant shifts in pelagic microbiology.

Marine heatwaves (MHWs) cause disruption to marine ecosystems, deleteriously impacting macroflora and fauna. However, effects on microorganisms are relatively unknown despite ocean temperature being a major determinant of assemblage structure. Using data from thousands of Southern Hemisphere samples, we reveal that during an "unprecedented" 2015/16 Tasman Sea MHW, temperatures approached or surpassed the upper thermal boundary of many endemic taxa. Temperate microbial assemblages underwent a profound transition to niche states aligned with sites over 1000 km equatorward, adapting to higher temperatures and lower nutrient conditions bought on by the MHW. MHW conditions also modulate seasonal patterns of microbial diversity and support novel assemblage compositions. The most significant affects of MHWs on microbial assemblages occurred during warmer months, when temperatures exceeded the upper climatological bounds. Trends in microbial response across several MHWs in different locations suggest these are emergent properties of temperate ocean warming, which may facilitate monitoring, prediction and adaptation efforts.

Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis.

Pollen allergies pose a considerable global public health concern. Allergy risk can vary significantly within plant families, yet some key pollen allergens can only be identified to family level by current optical methods. Pollen information with greater taxonomic resolution is therefore required to best support allergy prevention and self-management. We used environmental DNA (eDNA) metabarcoding to deepen taxonomic insights into the seasonal composition of airborne pollen in cool temperate Australia, a region with high rates of allergic respiratory disease. In Hobart, Tasmania, we collected routine weekly air samples from December 2018 until October 2020 and sequenced the internal transcribed spacer 2 (ITS2) and chloroplastic tRNA-Leucine tRNA-Phenylalanine intergenic spacer (trnL-trnF) regions in order to address the following questions: a) What is the genus-level diversity of known and potential aeroallergens in Hobart, in particular, in the families Poaceae, Cupressaceae and Myrtaceae? b) How do the atmospheric concentrations of these taxa change over time, and c) Does trnL-trnF enhance resolution of biodiversity when used in addition to ITS2? Our results suggest that individuals in the region are exposed to temperate grasses including Poa and Bromus in the peak grass pollen season, however low levels of exposure to the subtropical grass Cynodon may occur in autumn and winter. Within Cupressaceae, both metabarcodes showed that exposure is predominantly to pollen from the introduced genera Cupressus and Juniperus. Only ITS2 detected the native genus, Callitris. Both metabarcodes detected Eucalyptus as the major Myrtaceae genus, with trnL-trnF exhibiting primer bias for this family. These findings help refine our understanding of allergy triggers in Tasmania and highlight the utility of multiple metabarcodes in aerobiome studies.

Linking niche size and phylogenetic signals to predict future soil microbial relative abundances.

Bacteria provide ecosystem services (e.g., biogeochemical cycling) that regulate climate, purify water, and produce food and other commodities, yet their distribution and likely responses to change or intervention are difficult to predict. Using bacterial 16S rRNA gene surveys of 1,381 soil samples from the Biomes of Australian Soil Environment (BASE) dataset, we were able to model relative abundances of soil bacterial taxonomic groups and describe bacterial niche space and optima. Hold out sample validated hypothetical causal networks (structural equation models; SEM) were able to predict the relative abundances of bacterial taxa from environmental data and elucidate soil bacterial niche space. By using explanatory SEM properties as indicators of microbial traits, we successfully predicted soil bacterial response, and in turn potential ecosystem service response, to near-term expected changes in the Australian climate. The methods developed enable prediction of continental-scale changes in bacterial relative abundances, and demonstrate their utility in predicting changes in bacterial function and thereby ecosystem services. These capabilities will be strengthened in the future with growing genome-level data.

Symbiotic status alters fungal eco-evolutionary offspring trajectories.

Despite host-fungal symbiotic interactions being ubiquitous in all ecosystems, understanding how symbiosis has shaped the ecology and evolution of fungal spores that are involved in dispersal and colonization of their hosts has been ignored in life-history studies. We assembled a spore morphology database covering over 26,000 species of free-living to symbiotic fungi of plants, insects and humans and found more than eight orders of variation in spore size. Evolutionary transitions in symbiotic status correlated with shifts in spore size, but the strength of this effect varied widely among phyla. Symbiotic status explained more variation than climatic variables in the current distribution of spore sizes of plant-associated fungi at a global scale while the dispersal potential of their spores is more restricted compared to free-living fungi. Our work advances life-history theory by highlighting how the interaction between symbiosis and offspring morphology shapes the reproductive and dispersal strategies among living forms.

Fungal genome size and composition reflect ecological strategies along soil fertility gradients.

Genomic traits reflect the evolutionary processes that have led to ecological variation among extant organisms, including variation in how they acquire and use resources. Soil fungi have diverse nutritional strategies and exhibit extensive variation in fitness along resource gradients. We tested for trade-offs in genomic traits with mycelial nutritional traits and hypothesize that such trade-offs differ among fungal guilds as they reflect contrasting resource exploitation and habitat preferences. We found species with large genomes exhibited nutrient-poor mycelium and low GC content. These patterns were observed across fungal guilds but with varying explanatory power. We then matched trait data to fungal species observed in 463 Australian grassland, woodland and forest soil samples. Fungi with large genomes and lower GC content dominated in nutrient-poor soils, associated with shifts in guild composition and with species turnover within guilds. These findings highlight fundamental mechanisms that underpin successful ecological strategies for soil fungi.

Multi-omics eco-surveillance of complex legacy contamination with a locally adapted estuarine invertebrate.

Complex legacy contamination from human use is a major issue for estuaries globally. In particular, contamination of water and sediments with bioavailable metals/metalloids, in addition to other industrial contaminants, such as hydrocarbons. Yet, understanding of complex toxicity and local adaptation in field exposed, non-model, invertebrate communities is limited. Herein, we apply multi-omics (metabolomics, lipidomics, proteomics) coupled to traditional sediment quality analyses, to better characterise molecular and cellular responses necessary for application to monitoring, as an eco-surveillance tool. Using these approaches, we characterise functional phenotypes of a sediment associated invertebrate (sipunculid), from an estuary exposed to complex legacy contamination (metals: Zn, Hg, Cd, Pb, Cu, As; and polycyclic aromatic hydrocarbons, PAHs). We sampled individuals at a range of exposure sites, highly (NTB5), moderately (NTB13), and lesser-influenced reference sites. Size differences were observed in sampled individuals between sites, with smaller individuals collected from NTB13. Analysis of environmental variables that correlated with change in the metabolite data revealed that the metabolism of smaller individuals at medium exposure NTB13 was highly differentiated by sediment concentrations of Hg, despite higher concentrations at more exposed NTB5. Functional phenotypes of these smaller individuals were characterised by sulphur and aromatic amino acid metabolism, increases in oxidised intermediates, upregulation of protein responses to oxidative stress, and melanin synthesis, and saturation of membrane and storage of lipids; in addition to the metabolism of naphthalene (PAH). Such widespread change was not observed in the metabolite and lipid profiles of larger individuals at high exposure NTB5, suggesting possible differences in effects between sites may also be associated with size (developmental stage, or age) and/or PAH exposure. This study serves to further understanding of differing modes of toxicity and local adaptation to multiple contaminants, and drivers of functional change in a complex estuary environment.

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

Bacterioplankton communities govern marine productivity and biogeochemical cycling, yet drivers of bacterioplankton assembly remain unclear. Here, we contrast the relative contribution of deterministic processes (environmental factors and biotic interactions) in driving temporal dynamics of bacterioplankton diversity at three different oceanographic time series locations, spanning 15° of latitude, which are each characterized by different environmental conditions and varying degrees of seasonality. Monthly surface samples (5.5 years) were analysed 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 diversity (72%; 24% of total variation) and beta diversity (32%; 30%) patterns within bacterioplankton assemblages explained by day length, ammonium, and mixed layer depth. In contrast, North Stradbroke Island, a sub-tropical location where environmental conditions are less variable, interspecific interactions were of increased importance in structuring bacterioplankton diversity (alpha: 33%; beta: 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.

Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments.

Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO2 fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.

Which soil microbiome? Bacteria, fungi, and protozoa communities show different relationships with urban green space type and use-intensity.

Exposure to diverse microbial communities early in life can help support healthy human immune function. Soil microbiomes in public and private urban green spaces are potentially important sources of contact with diverse microbiomes for much of the global population. However, we lack understanding of how soil microbial communities vary across and within urban green spaces, and whether these patterns vary across microbial kingdoms; closing this knowledge gap may help us optimise green spaces' capacities to provide this ecosystem service. Here we explore the diversity and community compositions of soil microbiomes across urban green space types in Tasmania, Australia. Specifically, we analysed soil bacterial, fungal, and protozoan diversity and composition across private backyards and public parks. Within parks, we conducted separate sampling for areas of high and low intensity use. We found that: (i) bacteria, fungi, and protozoa showed different patterns of variation, (ii) bacterial alpha-diversity was lowest in low-intensity use areas of parks, (iii) there was relatively little variation in the community composition across backyards, and high and low intensity-use park areas and (iv) neither human-associated bacteria, nor potential microbial community function of bacteria and fungi differed significantly across green space types. To our knowledge, this is the first urban soil microbiome analysis which analyses these three soil microbial kingdoms simultaneously across public and private green space types and within public spaces according to intensity of use. These findings demonstrate how green space type and use intensity may impact on soil microbial diversity and composition, and thus may influence our opportunity to gain healthy exposure to diverse environmental microbiomes.

Host-Gut Microbiome Metabolic Interactions in PFAS-Impacted Freshwater Turtles (Emydura macquarii macquarii).

Per-and polyfluoroalkyl substances (PFAS) are a growing concern for humans, wildlife, and more broadly, ecosystem health. Previously, we characterised the microbial and biochemical impact of elevated PFAS on the gut microbiome of freshwater turtles (Emydura macquarii macquarii) within a contaminated catchment in Queensland, Australia. However, the understanding of PFAS impacts on this species and other aquatic organisms is still very limited, especially at the host-gut microbiome molecular interaction level. To this end, the present study aimed to apply these leading-edge omics technologies within an integrated framework that provides biological insight into the host turtle-turtle gut microbiome interactions of PFAS-impacted wild-caught freshwater turtles. For this purpose, faecal samples from PFAS-impacted turtles (n = 5) and suitable PFAS-free reference turtles (n = 5) were collected and analysed. Data from 16S rRNA gene amplicon sequencing and metabolomic profiling of the turtle faeces were integrated using MetOrigin to assign host, microbiome, and co-metabolism activities. Significant variation in microbial composition was observed between the two turtle groups. The PFAS-impacted turtles showed a higher relative abundance of Firmicutes and a lower relative abundance of Bacteroidota than the reference turtles. The faecal metabolome showed several metabolites and pathways significantly affected by PFAS exposure. Turtles exposed to PFAS displayed altered amino acid and butanoate metabolisms, as well as altered purine and pyrimidine metabolism. It is predicted from this study that PFAS-impacted both the metabolism of the host turtle and its gut microbiota which in turn has the potential to influence the host's physiology and health.

Perturbation of the gut microbiome in wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels.

Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent and pervasive. Understanding the toxicity of PFAS to wildlife is difficult, both due to the complexity of biotic and abiotic perturbations in the taxa under study and the practical and ethical problems associated with studying the impacts of environmental pollutants on free living wildlife. One avenue of inquiry into the effects of environmental pollutants, such as PFAS, is assessing the impact on the host gut microbiome. Here we show the microbial composition and biochemical functional outputs from the gut microbiome of sampled faeces from euthanised and necropsied wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels. The microbial community composition was profiled by 16S rRNA gene sequencing using a Nanopore MinION and the biochemical functional outputs of the gut microbiome were profiled using a combination of targeted central carbon metabolism metabolomics using liquid chromatography coupled to a triple quadrupole mass spectrometer (LC-QqQ-MS) and untargeted metabolomics using liquid chromatography coupled to a quadrupole time of flight mass spectrometer (LC-QToF-MS). Total PFAS was measured in the turtle serum using standard methods. These preliminary data demonstrated a 60-fold PFAS increase in impacted turtles compared to the sampled aquatic environment. The microbiome community was also impacted in the PFAS exposed turtles, with the ratio of Firmicutes-to-Bacteroidetes rising from 1.4 at the reference site to 5.5 at the PFAS impacted site. This ratio increase is indicative of host stress and dysfunction of the gut microbiome that was correlated with the biochemical metabolic function data, metabolites observed that are indications of stress and inflammation in the gut microbiome. Utilising the gut microbiome of sampled faeces collected from freshwater turtles provides a non-destructive avenue for investigating the impacts of PFAS in native wildlife, and provides an avenue to explore other contaminants in higher-order taxa within the environment.

Omics-based ecosurveillance for the assessment of ecosystem function, health, and resilience.

Current environmental monitoring efforts often focus on known, regulated contaminants ignoring the potential effects of unmeasured compounds and/or environmental factors. These specific, targeted approaches lack broader environmental information and understanding, hindering effective environmental management and policy. Switching to comprehensive, untargeted monitoring of contaminants, organism health, and environmental factors, such as nutrients, temperature, and pH, would provide more effective monitoring with a likely concomitant increase in environmental health. However, even this method would not capture subtle biochemical changes in organisms induced by chronic toxicant exposure. Ecosurveillance is the systematic collection, analysis, and interpretation of ecosystem health-related data that can address this knowledge gap and provide much-needed additional lines of evidence to environmental monitoring programs. Its use would therefore be of great benefit to environmental management and assessment. Unfortunately, the science of 'ecosurveillance', especially omics-based ecosurveillance is not well known. Here, we give an overview of this emerging area and show how it has been beneficially applied in a range of systems. We anticipate this review to be a starting point for further efforts to improve environmental monitoring via the integration of comprehensive chemical assessments and molecular biology-based approaches. Bringing multiple levels of omics technology-based assessment together into a systems-wide ecosurveillance approach will bring a greater understanding of the environment, particularly the microbial communities upon which we ultimately rely to remediate perturbed ecosystems.

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 numerous 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.

Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors.

We investigated the Southern Ocean (SO) prokaryote community structure via zero-radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71-99°E, summer) and Pacific (170-174°W, autumn-winter) sectors of the SO. At higher taxonomic levels (phylum-family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus-zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi- and bathy-abyssopelagic water masses. Common surface bacteria were abundant in several deep-water masses and vice-versa suggesting connectivity between surface and deep-water microbial assemblages. Bacteria from same-sector Antarctic Bottom Water samples showed patchy, high beta-diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep-water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide-scale SO ecosystem microbial modelling.

Metabolomics as a tool for in situ study of chronic metal exposure in estuarine invertebrates.

Estuaries are subject to intense human use globally, with impacts from multiple stressors, such as metal contaminants. A key challenge is extending beyond traditional monitoring approaches to understand effects to biota and system function. To explore the metabolic effects of complex metal contaminants to sediment dwelling (benthic) fauna, we apply a multiple-lines-of-evidence approach, coupling environmental monitoring, benthic sampling, total metals analysis and targeted metabolomics. We characterise metabolic signatures of metal exposure in three benthic invertebrate taxa, which differed in distribution across sites and severity of metal exposure: sipunculid (very high), amphipod (high), maldanid polychaete (moderate). We observed sediment and tissue metal loads far exceeding sediment guidelines where toxicity-related adverse effects may be expected, for metals including, As, Cd, Pb, Zn and Hg. Change in site- and taxa-specific metabolite profiles was highly correlated with natural environmental drivers (sediment total organic carbon and water temperature). At the most metal influenced sites, metabolite variation was also correlated with sediment metal loads. Using supervised multivariate regression, taxa-specific metabolic signatures of increased exposure and possibility of toxic effects were characterised against multiple reference sites. Metabolic signatures varied according to each taxon and degree of metal exposure, but primarily indicated altered cysteine and methionine metabolism, metal-binding and elimination (lysosomal) activity, coupled to change in complex biosynthesis pathways, responses to oxidative stress, and cellular damage. This novel multiple-lines-of-evidence approach combining metabolomics with traditional environmental monitoring, enabled detection and characterisation of chronic metal exposure effects in situ in multiple invertebrate taxa. With capacity for application to rapid and effective monitoring of non-model species in complex environments, these approaches are critical for improved assessment and management of systems that are increasingly subject to anthropogenic drivers of change.

Omics-based ecosurveillance uncovers the influence of estuarine macrophytes on sediment microbial function and metabolic redundancy in a tropical ecosystem.

Vertical zonation within estuarine ecosystems can strongly influence microbial diversity and function by regulating competition, predation, and environmental stability. The degree to which microbial communities exhibit horizontal patterns through an estuary has received comparatively less attention. Here, we take a multi-omics ecosurveillance approach to study environmental gradients created by the transition between dominant vegetation types along a near pristine tropical river system (Wenlock River, Far North Queensland, Australia). The study sites included intertidal mudflats fringed by saltmarsh, mangrove or mixed soft substrata habitats. Collected sediments were analyzed for eukaryotes and prokaryotes using small sub-unit (SSU) rRNA gene amplicons to profile the relative taxonomic composition. Central carbon metabolism metabolites and other associated organic polar metabolites were analyzed using established metabolomics-based approaches, coupled with total heavy metals analysis. Eukaryotic taxonomic information was found to be more informative of habitat type. Bacterial taxonomy and community composition also showed habitat-specificity, with phyla Proteobacteria and Cyanobacteria strongly linked to mangroves and saltmarshes, respectively. In contrast, metabolite profiling was critical for understanding the biochemical pathways and expressed functional outputs in these systems that were tied to predicted microbial gene function (16S rRNA). A high degree of metabolic redundancy was observed in the bacterial communities, with the metabolomics data suggesting varying degrees of metabolic criticality based on habitat type. The predicted functions of the bacterial taxa combined with annotated metabolites accounted for the conservative perspective of microbial community redundancy against the putative metabolic pathway impacts in the metabolomics data. Coupling these data demonstrates that habitat-mediated estuarine gradients drive patterns of community diversity and metabolic function and highlights the real redundancy potential of habitat microbiomes. This information is useful as a point of comparison for these sensitive ecosystems and provides a framework for identifying potentially vulnerable or at-risk systems before they are significantly degraded.

Disturbance alters the forest soil microbiome.

Billions of microorganisms perform critical below-ground functions in all terrestrial ecosystems. While largely invisible to the naked eye, they support all higher lifeforms, form symbiotic relationships with ~90% of terrestrial plant species, stabilize soils, and facilitate biogeochemical cycles. Global increases in the frequency of disturbances are driving major changes in the structure and function of forests. However, despite their functional significance, the disturbance responses of forest microbial communities are poorly understood. Here, we explore the influence of disturbance on the soil microbiome (archaea, fungi and bacteria) of some of the world's tallest and most carbon-dense forests, the Mountain Ash forests of south-eastern Australia. From 80 sites, we identified 23,277 and 19,056 microbial operational taxonomic units from the 0-10 cm and 20-30 cm depths of soil respectively. From this extensive data set, we found the diversity and composition of these often cryptic communities has been altered by human and natural disturbance events. For instance, the diversity of ectomycorrhizal fungi declined with clearcut logging, the diversity of archaea declined with salvage logging, and bacterial diversity and overall microbial diversity declined with the number of fires. Moreover, we identified key associations between edaphic (soil properties), environmental (slope, elevation) and spatial variables and the composition of all microbial communities. Specifically, we found that soil pH, manganese, magnesium, phosphorus, iron and nitrate were associated with the composition of all microbial communities. In a period of widespread degradation of global forest ecosystems, our findings provide an important and timely insight into the disturbance responses of soil microbial communities, which may influence key ecological functions.

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds.

Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.