Biology subjects

Gios, E.

Publications and source records attributed to Gios, E..

3 recordsLinked to original sources

bioRxiv2025

Adaptations of DNA viruses are influenced by host and environment with proliferations constrained by environmental niche

Viruses are ubiquitous albeit individually constrained by host-range. Less well understood are environmental limitations on virus proliferation. To investigate estuarine viral diversity, niche constraints, and genomic traits of environmental adaptation, we analysed metagenomic and metatranscriptomic data from across an estuarine salinity gradient, including water and sediment habitats. We then expanded our analysis to globally distributed viral genomes. Viral distributions varied by estuary habitat, reflecting prokaryote community patterns, and highlighting that virus-host interactions are strongly influenced by environment. Viral lineages, up until approximately the rank of genus, were largely partitioned by ecological niche based on factors such as salinity and the aquatic-terrestrial divide. Across habitat boundaries, we identified variations in genomic GC content, and genomic signatures of salinity adaptation, particularly in virus major tail and capsid proteins. These included elevated ratios of acidic to basic amino acids and decreased protein isoelectric points at higher salinities which did not solely reflect biases inherited due to reliance on host machinery. Salinity is a well-described physiological stressor for prokaryotes. Results suggest that viruses employ some of the same osmoadaptive strategies independent of adaptation based on host machinery. Our findings indicate that, in addition to host range limitations, successful proliferation of viruses into distinct biomes (e.g. freshwater, saline, terrestrial) is constrained by adaptation to specific ecological niches.

microbiology↗

bioRxiv2022

Genetic exchange shapes ultra-small Patescibacteria metabolic capacities in the terrestrial subsurface

Bacterial genomes are highly dynamic entities, mostly due to the extent of horizontal gene transfer (HGT) occurring in these organisms. HGT is thought to be the main driver of genetic variation and adaptation to local environment in bacteria. However, little is known about the modalities of HGT within natural microbial communities, especially the implications of genetic exchange for streamlined microorganisms such as Patescibacteria (Candidate Phyla Radiation). We searched for evidence of genetic exchange in 125 Patescibacteria genomes recovered from aquifer environments and detected the presence of hundreds of genomic islands, individually transferred genes and prophage combined, with up to 29% of genome length attributed to HGT. Results show that most individual gene transfer events occurred between Patescibacteria, but donors were also phylogenetically diverse groundwater microorganisms. Using gene donor-recipient information, we identified one potential host (Omnitrophota) of the ultra-small bacteria, and confirmed this by matching relative abundance patterns across 16 groundwater samples. A wide variety of metabolic functions were introduced in Patescibacteria genomes by HGT including transcription, translation and DNA replication, recombination and repair. This study illustrates the evolutionarily dynamic nature of Patescibacteria genomes despite the constraints of streamlining, and that HGT in these organisms is also mediated via viral infection.

evolutionary biology↗

bioRxiv2021

Metabolic diversity and aero-tolerance in anammox bacteria from geochemically distinct aquifers

BackgroundAnaerobic ammonium oxidation (anammox) is important for converting bioavailable nitrogen into dinitrogen gas, particularly in carbon poor environments. Yet, the diversity and prevalence of anammox bacteria in the terrestrial subsurface - a typically oligotrophic environment - is little understood across different geochemical conditions. To determine the distribution and activity of anammox bacteria across a range of aquifer lithologies and physicochemistries, we analysed 16S rRNA genes, metagenomes and metatranscriptomes, and quantified hydrazine synthase genes and transcripts sampled from 59 groundwater wells distributed over 1 240 km2. ResultsData indicate that anammox-associated bacteria (class Brocadiae) and the anammox process are prevalent in aquifers (identified in aquifers with sandy-gravel, sand-silt and volcanic lithologies). While Brocadiae diversity decreased with increasing DO, Brocadiae 16S rRNA genes and hydrazine synthase genes and transcripts (hydrazine synthase, hzsB) were detected across a wide range of bulk groundwater dissolved oxygen (DO) concentrations (0 - 10 mg/L). Anammox genes and transcripts (hzsB) correlated significantly with those involved in bacterial and archaeal ammonia oxidation (ammonia monooxygenase, amoA), which could represent a major source of nitrite for anammox. Differences in anammox community composition were strongly associated with DO and bore depth (and to a lesser extent pH and phosphate), revealing niche differentiation among anammox bacteria in groundwater that was largely driven by water oxygen contents, and not ammonium/nitrite. Eight Brocadiae genomes (63-95% estimated completeness) reconstructed from a subset of groundwater sites belong to 2 uncharacterized families and 6 novel species (based on average nucleotide identity). Distinct groups of these genomes dominated the anammox-associated community at dysoxic and oxic sites, further reflecting the influence of DO on Brocadiae composition. Six of the genomes (dominating dysoxic or oxic sites) have genes characteristic of anammox (hydrazine synthase and/or dehydrogenase). These genes, in addition to aerotolerance genes, belonging to four Brocadiae genomes, were transcriptionally active, although transcript numbers clearly highest in dyoxic groundwater. ConclusionsOur findings indicate anammox bacteria contribute to loss of fixed N across diverse anoxic-to-oxic aquifer conditions, and that this is likely supported by nitrite from aerobic ammonia oxidation. Results provide an insight into the distribution and activity of anammox bacteria across distinct aquifer physicochemisties.

microbiology↗