Biology subjects

Priest, T.

Publications and source records attributed to Priest, T..

11 recordsLinked to original sources

bioRxiv2026

Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome

Microbial diversity is organised into operationally defined species. However, it remains unclear whether these, or finer-scale groups represent biologically meaningful units in natural communities. Here, we implement a scalable, cultivation-independent framework to identify 724 genomically discrete and ecologically cohesive subspecies across 270 species in the global ocean microbiome. Their diversification is underpinned by gene-specific, nucleotide-level selection on the core genomic backbone and by variable restructuring of gene content, both of which proceed in a subspecies-specific manner. In over half of the species tested, subspecies were significantly associated with distinct environmental conditions, most frequently temperature. This coupling of genomic discreteness and ecological cohesiveness positions these subspecies as biologically meaningful units, a fundamental level at which ecological and evolutionary processes jointly drive divergence and structure microbial diversity in the oceans.

ecology↗

bioRxiv2026

The Ocean Microbiomics Database reveals thermal niches and projected pressure on marine microbes in a warming ocean

Temperature is a key driver of ocean microbial community structure, yet its role in shaping global distributions and their response to warming remains unclear due to fragmented studies, inconsistent methods, and limited environmental context. We present the Ocean Microbiomics Database (OMDB) containing 274,282 genomes forming 31,058 species-level clusters, searchable at https://omdb.microbiomics.io. We show surface temperature is predicted from community composition, driven by thermal niche partitioning among congeneric taxa. Using these thermal niches to model present-day distributions globally, we find that projected warming results in microbial richness declining faster than relative abundance, with losses concentrated at high latitudes and among poorly characterized lineages. Resolving 5,891 species into four thermal clusters reveals ecological structure correlated with genome streamlining, protein thermostability, and marker-gene physicochemistry, enabling prediction of a microorganism's abundance-maximizing temperature directly from its coding sequence. This positions OMDB as a platform spanning molecular traits to global ecology, offering a genome-resolved foundation for understanding how temperature, shown to be a primary driver of ocean microbial life, will continue to shape it as the ocean warms.

microbiology↗

bioRxiv2026

Conserved multiheme cytochrome machinery for extracellular electron transfer is widespread and transcriptionally active across deep peat profiles

Northern peatlands store approximately one-third of global soil organic carbon, yet the anaerobic respiratory pathways governing carbon turnover remain unclear. In ombrotrophic bogs, the scarcity of inorganic terminal electron acceptors (TEAs) and high CO2:CH4 ratios indicate that methanogenesis alone cannot account for the observed CO2 production. Peat particulate organic matter (POM) has been proposed as an alternative TEA, but whether resident microorganisms encode and express extracellular electron transfer (EET) machinery required to use such extracellular TEAs remains unknown. Using depth-resolved metagenomics and metatranscriptomics across peat profiles from four ombrotrophic Swedish bogs, we identified conserved EET machinery in dominant yet uncultured Acidobacteriota and Verrucomicrobiota, comprising multiheme cytochromes and outer-membrane porins arranged in syntenic gene clusters. This machinery was transcriptionally active up to several meters depth, alongside broader anaerobic respiratory pathways, while methane-cycling processes were more prominent in the upper layers. These results provide systematic genomic and transcriptomic evidence for EET capacity in peatland microorganisms, establishing a molecular foundation for EET-based respiration and its potential role in suppressing methane formation and emissions.

microbiology↗

bioRxiv2026

Active microbial communities and their extrachromosomal elements link organic matter degradation to methane cycling in anoxic sediments

Anaerobic carbon transformation in freshwater sediments drives substantial methane emissions globally, yet the microbial taxa linking complex carbon degradation to methane production remain poorly characterized. Here, we combined metagenomics with the first metatranscriptomic dataset from the anoxic sediments of meromictic Lake Cadagno (Swiss Alps) to identify the active microbial clades, metabolic pathways, and extrachromosomal elements (ecDNA) across a depth gradient within the upper 56 cm of sediment. We recovered 802 species-level metagenome-assembled genomes (MAGs) spanning 66 phyla and identified a Bacteroidota clade (VadinHA17) as one of the most abundant and transcriptionally active populations in the sediment. This clade encodes and transcribes a broad range of diverse glycoside hydrolases (GH), indicating a central role in complex carbohydrate degradation. Transcriptional profiles suggest that this clade ferments organic substrates to acetate and hydrogen, which are key substrates for methanogenesis. In line with this, the acetoclastic methanogen Methanothrix and hydrogenotrophic Methanoregula were among the most abundant and transcriptionally active archaea in the same depth layers. Beyond microbial genomes, we detected 86,905 viral OTUs (vOTUs) and 2,136 plasmid OTUs (pOTUs), with free viruses and plasmids accounting for 5-10% and 0.2% of all sequencing reads, respectively. Notably, plasmids and viruses associated with Bacteroidota VadinHA17 encode and transcribe GHs that could augment host carbohydrate-degrading capacity. Together, these findings reveal new details on how methane production in anoxic lake sediments emerges from a network spanning primary fermentation, methanogenesis and ecDNA-mediated metabolisms.

ecology↗

bioRxiv2025

Variations in the latitudinal diversity gradients of the ocean microbiome

Latitudinal diversity gradients (LDGs), typically declining from equator to poles, are a pervasive macroecological pattern, yet their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed layer microbiomes exhibited diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) showed no latitudinal diversity structuring. Taxonomic resolution revealed that the mixed layer LDG was underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibited distinct or contrasting LDGs. Diversity structuring also varied by seasons and regions, governed by temperature and nutrient availability. Together, these findings highlight that within the ocean microbiome, LDGs are not universal, but lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.

microbiology↗

bioRxiv2025

The JEDI marker as a universal measure of planetary biodiversity

Despite its critical importance in the formation and maintenance of ecosystems and homeostasis on Earth, biodiversity remains a complex and non-unified concept. Consequently, standards for measuring global biodiversity are lacking, hindering our capacity to document Earths biota and track its change. Here, we propose the Joint, cellular life-Encompassing DIversity (JEDI) marker as a simple, effective and quantitative measure to assess and monitor biodiversity. The JEDI marker is a ribosomal RNA gene fragment that can be amplified from all domains of life using a single pair of PCR primers. We demonstrate the applicability and effectiveness of this approach for assessing biodiversity across ecological and biological scales, from holobionts to diverse ecosystems. In addition, we provide an automated bioinformatic workflow to support the standardised and reproducible analysis of the JEDI marker in future studies. While this approach is not free from trade-offs, we argue that its advantages outweigh its limitations by providing a unique, operational and scalable solution that builds on established infrastructure to integrate the microbial majority into biodiversity assessments and provide fundamental insights into organismal dynamics and associations across domains of life. Thus, the JEDI marker approach addresses the urgent need for a universal and standardised framework to effectively measure and monitor biodiversity at planetary scales in an era of profound global change.

ecology↗

bioRxiv2024

Arctic Ocean virus communities: seasonality, bipolarity, and prokaryotic interactions

Viruses play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemical processes. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. To address this, we studied dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction. Among 5,662 vOTUs, 69%, 30% and 1.4% were bacteriophages (Myoviridae, Podoviridae, and Siphoviridae), Unassigned, and Phycodnaviridae, respectively. Viral coverage was, on average, 5-fold higher than prokaryotic coverage, and 8-fold higher in summer. Viral community composition showed annual peaks in similarity and was strongly correlated with prokaryotic community composition. Using a Convergent Cross Mapping network, we identified putative virus-host interactions and six ecological modules, each associated with distinct environmental conditions. The network also revealed putative novel cyanophages with time-lagged correlations to their hosts (late summer) as well as diverse viruses correlated with Nitrososphaerales (winter). By comparison with global metagenomes, we found that 42% of Fram Strait vOTUs peaked in abundance in high latitude regions of both hemispheres (average 61{degrees}N and 51{degrees}S), and encoded proteins with biochemical signatures of cold adaptation. Our study reveals a rich diversity of polar viruses with pronounced seasonality, providing a foundation for understanding how they regulate and impact ecosystem functionality in changing polar oceans.

microbiology↗

bioRxiv2024

Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome

Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. Thus far, we know little about the structuring of community functionality and the coupling between taxonomy and function over seasonal environmental gradients. To address this, we employed autonomous sampling devices and in situ sensors to investigate the taxonomic and functional dynamics of a pelagic Arctic Ocean microbiome over a four-year period. We demonstrate that the dominant prokaryotic and microeukaryotic populations exhibit recurrent, unimodal fluctuations each year, with community gene content following the same trend. The recurrent dynamics within the prokaryotic microbiome are structured into five temporal modules that represent distinct ecological states, characterised by unique taxonomic and metabolic signatures and connections to specific microeukaryotic populations and oceanographic conditions. For instance, Cand. Nitrosopumilus and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, along with Radiolarians. In contrast, late summer is characterised by Amylibacter, sulfur compound metabolism and diverse Haptophyta lineages. Exploring the composition of modules further along with their degree of functional redundancy and the structuring of genetic diversity within functions over time revealed seasonal heterogeneity in environmental selection processes. In particular, we observe strong selection pressure on a functional level in spring while late polar night features weaker selection pressure that likely acts on an organismal level. By integrating taxonomic, functional, and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced environmental variability in understudied, yet rapidly changing polar marine ecosystems.

microbiology↗

bioRxiv2023

Spatial heterogeneity in carbohydrates and their utilisation by microbial communities in the high North Atlantic

Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and their utilisation by microbes in Atlantic waters of the Arctic during late summer. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, suggesting limited degradation by microbes. In contrast, the more labile {beta}-1,3-glucan exhibited a patchy distribution, indicating local variations in primary productivity and rapid utilisation. Metatranscriptomics showed active and dynamic microbial populations that targeted specific glycans. Gene transcription of carbohydrate-active enzymes revealed narrow substrate niches for specialists, involving compounds such as -mannans and alginate, along with the targeting of communal substrates, such as laminarin, by multiple populations. The observed spatial heterogeneity indicates that local biological and physical processes continue to shape the carbohydrate pool during late summer in high latitude waters and microbial populations are active and responsive to such changes.

microbiology↗

bioRxiv2022

Variations in Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities

The Arctic Ocean is experiencing unprecedented changes as a result of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here we show the pronounced impact that variations in Atlantic water influx and sea-ice cover have on bacterial communities in the East Greenland Current (Fram Strait) using two, 2-year high-resolution amplicon datasets and an annual cycle of long-read metagenomes. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. In contrast, low-ice cover and Atlantic water influx shifted community dominance to seasonally fluctuating populations enriched in genes for phytoplankton-derived organic matter degradation. We identified signature populations associated with distinct oceanographic conditions and predicted their ecological niches. Our study indicates progressing "Biological Atlantification" in the Arctic Ocean, where the niche space of Arctic bacterial populations will diminish, while communities that taxonomically and functionally resemble those in temperate oceans will become more widespread.

microbiology↗

bioRxiv2022

Not digested: algal glycans move carbon dioxide into the deep-sea

Marine algae annually synthesize gigatons of glycans from carbon dioxide, exporting it within sinking particles into the deep-sea and underlying sea floor, unless those glycans are digested before by bacteria. Identifying algal glycans in the ocean remains challenging with the molecular resolution of conventional analytic techniques. Whether algal glycans are digested by heterotrophic bacteria during downward transport, before they can transfer carbon dioxide from the ocean surface into the deep-sea or the sea floor, remains unknown. In the Red Sea Shaban Deep, where at 1500 m water depth a brine basin acts as a natural sediment trap, we found its high salt and low oxygen concentration accumulated and preserved exported algal glycans for the past 2500 years. By using monoclonal antibodies specific for glycan structures, we detected fucose-containing sulfated polysaccharide, {beta}-glucan, {beta}-mannan and arabinogalactan glycans, synthesized by diatoms, coccolithophores, dinoflagellates and other algae living in the sunlit ocean. Their presence in deep-sea sediment demonstrates these algal glycans were not digested by bacteria. Instead they moved carbon dioxide from the surface ocean into the deep-sea, where it will be locked away from the atmosphere at least for the next 1000 years. Considering their global synthesis, quantity and stability against degradation during transport through the water column, algal glycans are agents for carbon sequestration. Significance statementAlgae and plants use the greenhouse gas carbon dioxide to synthesize polymeric carbohydrates, or glycans, for energy storage, structural support and as protection against invasion by microbes. Glycans provide protection, are carbon sinks and enable carbon sequestration for as long as they are not digested by bacteria or other organisms, which releases the carbon dioxide back in to the atmosphere. In this study, we show that non-digested algal glycans sink into the deep ocean and into marine sediment. Thus, glycans are more than food for animals and prebiotics for bacteria, they are also molecules that remove carbon dioxide from the atmosphere and transfer it to the deep-sea, where it can be stored for 1000 years and longer.

biochemistry↗