Biology subjects

Bradley, J. A.

Publications and source records attributed to Bradley, J. A..

5 recordsLinked to original sources

bioRxiv2026

Physiological trade-offs drive the archaeal dominance and carbon turnover in deep subsurface

Marine sediments host a vast deep biosphere, yet how microorganisms persist under severe energy limitation and govern long-term organic carbon (OC) preservation remains poorly understood. Here we show that archaea, primarily Bathyarchaeia, systematically displace bacteria with depth and form net growth zones across East China Sea shelf deep sediments. Multi-omics analyses and bioenergetic modelling reveal that this transition is driven by sustained archaeal metabolism of diverse recalcitrant OC compounds, and a physiological trade-off that prioritizes cellular maintenance over growth, minimizing mortality in deep sediments. This strategy triggers a fundamental shift in sedimentary carbon turnover: from rapid bacterial degradation of labile OC near the surface to persistent archaea-driven turnover of recalcitrant OC at depth. We estimate that Bathyarchaeia mediate [~]77% of total OC degradation after 1,000 years of burial, corresponding to [~]18% ([~]11.4 Pg C) of millennial OC degradation in global shelf sediments. These findings identify subsurface archaea as key microbial regulators of long-term OC preservation and reveal how physiological trade-offs sustain life and carbon turnover in the energy-limited deep biosphere.

microbiology↗

bioRxiv2025

Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems

An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in the forelands of a maritime Antarctic and an alpine Swiss retreating glacier, by integrating quantitative ecology, genome-resolved metagenomics, and biogeochemical measurements. Habitat generalists and opportunists rapidly colonize both forelands and persist across soil depth and decadal chronosequences that serve as proxies for temporal community dynamics. These microbes are metabolically flexible chemotrophic aerobes that overcome oligotrophic conditions by using both organic and inorganic compounds, including atmospheric trace gases and sulfur substrates, for energy and carbon acquisition. They co-exist with metabolically flexible early-colonising opportunists and metabolically restricted later-colonising specialists, including photosynthetic Cyanobacteria, ammonia-oxidising archaea, and obligate predatory and symbiotic bacteria, that exhibit narrower habitat distributions. Analysis of 589 species-level metagenome-assembled genomes reveals early colonisation both by generalists and opportunists is strongly associated with metabolic flexibility. Field- and laboratory-based biogeochemical measurements reveal the activity of metabolically flexible microbes rapidly commenced in the forelands. Altogether, these findings suggest primary succession in glacial foreland soils is driven by self-sufficient metabolically flexible bacteria that mediate chemosynthetic primary production and likely provide a more hospitable soil environment for subsequent colonisation.

microbiology↗

bioRxiv2024

A global atlas of subsurface microbiomes reveals phylogenetic novelty, large scale biodiversity gradients, and a marine-terrestrial divide

Subsurface environments constitute one of Earths largest habitats for microbial life, yet differences between surface and subsurface microbiomes and between marine and terrestrial microbiomes remain unclear. We analyzed 478 archaeal and 1054 bacterial amplicon sequence datasets and 147 metagenomes from diverse and globally distributed surface and subsurface environments. Taxonomic analyses show that archaeal and bacterial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between marine and terrestrial microbiomes, suggesting a horizontal phylogenetic divide between sea and land that mirrors patterns in plant and animal diversity. In contrast, community composition overlapped from surface to subsurface environments indicating vertical diversity continua rather than a discrete subsurface biosphere. Diversity of terrestrial microbiomes decreases from surface to subsurface environments. Marine subsurface diversity and phylogenetic novelty rivaled (bacteria) or even exceeded (archaea) that of surface environments, suggesting that the marine subsurface holds a considerable and underestimated fraction of Earths archaeal and bacterial diversity. TeaserSubsurface ecosystems within Earths crust and seafloor harbor diverse and distinct microbiomes featuring many unknown lineages.

microbiology↗

bioRxiv2023

Antimicrobial resistance in Arctic soils is mediated by competition and facilitation

Antimicrobial resistance (AMR) is widespread in terrestrial ecosystems. However, the natural processes shaping the spatial and temporal dissemination of AMR in soils are not well understood. We aimed to determine whether, how, and why AMR varies in recently deglaciated pioneer and developing Arctic soils. We showed that antibiotic-resistant genes (ARGs), mobile genetic elements (MGEs), and antibiotic-resistant bacteria (ARB) are abundant, exhibit a non-uniform distribution, and generally increase with soil age. Our analyses suggest a strong positive relationship between soil age and ARG and ARB, which we attribute to increased competition between microbes in older soils. We also observed a weak negative relationship between soil age and ARG diversity mediated by soil organic matter - suggesting facilitation due to the alleviation of nutrient limitation. The microbial processes regulating the spread of AMR in Arctic soils may be further susceptible to the effects of future climate change and human activities. TeaserThe spatial and temporal spread of antimicrobial resistance in Arctic soils is dependent on microbial interactions for nutrients

microbiology↗

bioRxiv2018

Predicting humoral alloimmunity from differences in donor-recipient HLA surface electrostatic potential

In transplantation, development of humoral alloimmunity against donor HLA is a major cause of organ transplant failure but our ability to assess the immunological risk associated with a potential donor-recipient HLA combination is limited. We hypothesised that the capacity of donor HLA to induce a specific alloantibody response depends on their structural and physicochemical dissimilarity compared to recipient HLA. To test this hypothesis, we first developed a novel computational scoring system that enables quantitative assessment of surface electrostatic potential differences between donor and recipient HLA molecules at the tertiary structure level (electrostatic mismatch score-three dimensional; EMS-3D). We then examined humoral alloimmune responses in healthy females subjected to a standardised injection of donor lymphocytes from their male partner. This analysis showed a strong association between the EMS-3D of donor HLA and donor-specific alloantibody development; this relationship was strongest for HLA-DQ alloantigens. In the clinical transplantation setting, the immunogenic potential of HLA-DRB1 and -DQ mismatches expressed on donor kidneys, as assessed by their EMS-3D, was an independent predictor of development of donor-specific alloantibody after graft failure. Collectively, these findings demonstrate the translational potential of our approach to improve immunological risk assessment and to decrease the burden of humoral alloimmunity in organ transplantation.

immunology↗