Biology subjects

Woods, L. C.

Publications and source records attributed to Woods, L. C..

4 recordsLinked to original sources

bioRxiv2025

Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils

Terrestrial Antarctica harbors compositionally diverse and functionally distinct microbial life. Yet the ecological and evolutionary processes enabling these communities to adapt to the polyextreme conditions of the continent remain largely unknown. Here, we address how horizontal gene transfer (HGT) and de novo mutations influence adaptation of microbial communities in 16 proglacial and mountainous Antarctic soils, from a combination of short- and long-read datasets. Phylogenetic reconciliation and mobile genetic element analysis of 676 metagenome-assembled genomes show that HGT events occur frequently within these microbial communities. While the transferred genes are distributed across diverse functional categories, those involved in energy metabolism are exchanged at relatively higher frequency. The genes for aerotrophy, i.e. the consumption of atmospheric trace gases to provide energy, carbon, and hydration, are among the most frequently and widely disseminated. Approximately a quarter of all carbon monoxide (CO) dehydrogenases and [NiFe]-hydrogenases that catalyze atmospheric CO and hydrogen (H2) oxidation are predicted to be horizontally acquired and are often closely associated with mobile genetic elements. In parallel, analysis of polymorphisms in protein-encoding genes suggests widespread purifying selection, demonstrated by a predominance of synonymous mutations. This selection is particularly intense for aerotrophy genes, providing further evidence that this process is critical for microbial survival in Antarctica. The genetic variation of hydrogenases is tightly associated with their predicted protein structures, with intense selection acting on critical sites that preserve their stability and function in Antarctic environments. Together, these findings show that previously unrecognised eco-evolutionary dynamics shape the composition and function of Antarctic desert microbial communities, and confirm aerotrophy is a strongly selected and horizontally disseminated trait.

microbiology↗

bioRxiv2025

Integrated cross-sectoral surveillance of antimicrobial resistance genotypes and phenotypes across disparate reservoirs

Antimicrobial-resistant (AMR) bacteria and genes are continually exchanged among humans, animals, and environmental reservoirs. Disparate and siloed surveillance methods present a major challenge for tracing and disrupting AMR transmission, with clinical monitoring focusing on detecting specific pathogens or specific genes of interest, and environmental surveys often relying on inferences drawn from indicator organisms. Here, we demonstrate that, following sample-specific pre-processing, common surveillance approaches can be applied consistently to profile AMR abundance, distribution, and phenotypes across diverse reservoirs, including soil, sediment, water, wastewater, and faecal samples from both urban and agricultural settings. Across all sample types, three core methods provided complementary insights: (i) quantitative PCR (qPCR) arrays to measure multiple AMR genes, (ii) gene- and genome-centric metagenomics for comprehensive resistome profiling, and (iii) culture-based genomics with susceptibility testing to link genotypes to phenotypes. We applied this approach to profile 1,032 metagenome-assembled genomes, 66 bacterial isolate genomes, and 78 and 6,442 AMR genes/reference sequences via qPCR and metagenomics, respectively. This integrated framework revealed a moderate prevalence but high diversity of resistance mechanisms in both pathogens and non-pathogenic bacteria with potentially transmissible genes, with wastewater especially enriched in AMR genes. We detected mismatches between genotype and phenotype predictions and a prevalence of intermediate resistance phenotypes, highlighting how many mechanisms of environmental resistance remain poorly understood. Overall, this study demonstrates that unified field-leading surveillance methods can be extended beyond clinical contexts into diverse environmental and animal samples, while highlighting that multiple methods are needed to capture the diverse AMR genotypes and phenotypes in these settings to enable comprehensive monitoring and adaptive solutions to restrict transmission.

microbiology↗

bioRxiv2021

Bacteriophage adaptation to a mammalian mucosa reveals a trans-domain evolutionary axis

The majority of viruses within the human gut are obligate bacterial viruses known as bacteriophages (phages)1. Their bacteriotropism underscores the study of phage ecology in the gut, where they sustain top-down control2-4 and co-evolve5 with gut bacterial communities. Traditionally, these were investigated empirically via in vitro experimental evolution6-8 and more recently, in vivo models were adopted to account for gut niche effects4,9. Here, we probed beyond conventional phage-bacteria co-evolution to investigate the potential evolutionary interactions between phages and the mammalian "host". To capture the role of the mammalian host, we recapitulated a life-like mammalian gut mucosa using in vitro lab-on-a-chip devices (to wit, the gut-on-a-chip) and showed that the mucosal environment supports stable phage-bacteria co-existence. Next, we experimentally evolved phage populations within the gut-on-a-chip devices and discovered that phages adapt by de novo mutations and genetic recombination. We found that a single mutation in the phage capsid protein Hoc - known to facilitate phage adherence to mucus10 - caused altered phage binding to fucosylated mucin glycans. We demonstrated that the altered glycan-binding phenotype provided the evolved mutant phage a competitive fitness advantage over their ancestral wildtype phage in the gut-on-a-chip mucosal environment. Collectively, our findings revealed that phages - in addition to their evolutionary relationship with bacteria - are also able to engage in evolution with the mammalian host.

microbiology↗

bioRxiv2018

Alternative hydrogen uptake pathways suppress methane production in ruminants

Farmed ruminants are the largest source of anthropogenic methane emissions globally. The methanogenic archaea responsible for these emissions use molecular hydrogen (H2), produced during bacterial and eukaryotic carbohydrate fermentation, as their primary energy source. In this work, we used comparative genomic, metatranscriptomic, and co-culture-based approaches to gain a system-wide understanding of the organisms and pathways responsible for ruminal H2 metabolism. Two thirds of sequenced rumen bacterial and archaeal genomes encode enzymes that catalyze H2 production or consumption, including 26 distinct hydrogenase subgroups. Metatranscriptomic analysis confirmed that these hydrogenases are differentially expressed in sheep rumen. Electron-bifurcating [FeFe]-hydrogenases from carbohydrate-fermenting Clostridia (e.g. Ruminococcus) accounted for half of all hydrogenase transcripts. Various H2 uptake pathways were also expressed, including methanogenesis (Methanobrevibacter), fumarate reduction and nitrate ammonification (Selenomonas), and acetogenesis (Blautia). Whereas methanogenesis predominated in high methane yield sheep, alternative uptake pathways were significantly upregulated in low methane yield sheep. Complementing these findings, we observed significant differential expression and activity of the hydrogenases of the hydrogenogenic cellulose fermenter Ruminococcus albus and the hydrogenotrophic fumarate reducer Wolinella succinogenes in co-culture compared to pure culture. We conclude that H2 metabolism is a more complex and widespread trait among rumen microorganisms than previously recognized. There is evidence that alternative hydrogenotrophs, including acetogens and selenomonads, can prosper in the rumen and effectively compete with methanogens for H2 in low methane yield ruminants. Strategies to increase flux through alternative H2 uptake pathways, including animal selection, dietary supplementation, and methanogenesis inhibitors, may lead to sustained methane mitigation.

microbiology↗