Biology subjects

Veseli, I. A.

Publications and source records attributed to Veseli, I. A..

5 recordsLinked to original sources

bioRxiv2025

Proteobacteria with chemosynthetic potential are highly enriched in the gills of Hypoplectrus reef fishes

A variety of marine invertebrates are known to form associations with chemosynthetic bacteria, but to the best of our knowledge this has not been documented in fishes. Here, we apply genome-resolved metagenomics to the hamlets (Hypoplectrus spp), a model system for the study of speciation in the sea. The analysis of 304 gill samples from 12 hamlet species collected at six locations over 13 years revealed a stark contrast between the gill microbiota and ambient water microbial communities. One novel lineage in the Burkholderiaceae-B family was particularly prevalent across host species, sampling locations and years. Its genome encoded highly complete metabolic modules for carbon fixation and sulfur oxidation, indicating chemosynthetic potential. Its pangenome revealed large-scale geographic structure (western Caribbean, eastern Caribbean and Gulf of Mexico), paralleling the phylogenomic pattern observed in the hamlet radiation. Our survey also identified genomes of multiple novel gill-associated lineages related to known fish gill pathogens, fish gut microbes and free-living seawater taxa. These lineages harbor diverse metabolic modules, involved notably in nitrogen cycling, antibiotic production and biofilm formation, revealing a highly dynamic microbial ecosystem. Overall, our findings suggest complex host-microbe and microbe-microbe eco-evolutionary interactions that may influence fish physiology, homeostasis and immune response.

microbiology↗

bioRxiv2025

Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities

The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and apply this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates in two genome-resolved investigations of the human gut and oral cavity. Our results demonstrate that EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark genome collections.

microbiology↗

bioRxiv2024

Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights

Gene function annotations enable microbial ecologists to make inferences about metabolic potential from genomes and metagenomes. However, even tools that use the same database and general approach can differ markedly in the annotations they recover. We compare three popular methods for identifying KEGG Orthologs, applying them to genomes drawn from a range of bacterial families that occupy different host-associated and free-living biomes. Our results show that by adaptively tuning sequence similarity thresholds, sensitivity can be substantially improved while maintaining accuracy. We observe the largest improvements when few reference sequences exist for a given protein family, and when annotating genomes from non-model organisms (such as gut-dwelling Lachnospiraceae). Our results suggest that straightforward heuristic adjustments can broadly improve microbial metabolic predictions.

bioinformatics↗

bioRxiv2023

A 2-million-year-old microbial and viral communities from the Kap Kobenhavn Formation in North Greenland

Environmental DNA (eDNA) from the 2-million-year-old Kap Kobenhavn Formation of northern Greenland has revealed an ecosystem of plants and animals with no contemporary analogue1. Here, we reconstruct the microbial (bacterial, archaeal, and viral) communities that thrived at the site during this time. By leveraging a novel analytical framework that integrates taxonomic profiling, DNA damage estimates, and functional reconstructions, we identify and distinguish pioneer microbial communities from later permafrost microbial assemblages. We show that at the time of sediment deposition, the terrestrial input at the Kap Kobenhavn site originated from a palustrine wetland, suggesting warmer, non-permafrost conditions. During this period, the detection of methanogenic archaea and signals of their carbon metabolism is consistent with Kap Kobenhavn and similar northern ecosystems contributing moderate methane emissions. Intriguingly, we discover a remarkable nucleotide sequence similarity--exceeding 98%--between pioneer methanogens and present-day analogues in thawing permafrost. This aligns with the concept of "time-traveling" microbes2 surviving across geological time and waiting for conditions to turn favourable rather than evolving to adapt to changing conditions. Importantly, in contrast to the plant and animal communities of the Kap Kobenhavn, a striking similarity in microbial composition to that of a contemporary thawing Arctic suggests that microbial communities may serve as the first indication of broader climate-driven ecosystem disruptions.

microbiology↗

bioRxiv2022

The diversity and functional capacity of microbes associated with coastal phototrophs

Coastal marine phototrophs exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their phototroph hosts through metabolisms that are unique to microbial taxa. Here we characterized the metabolic functions of phototroph-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.) and the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 72 metagenome assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic gene content. All host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis. Additionally, we found a range of nitrogen metabolism genes that transform dissolved inorganic nitrogen into forms that may be more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms, and contributes to the functional capabilities of microbes and their influence on carbon and nitrogen cycling in nearshore ecosystems. ImportanceKelps, seagrasses and surfgrasses are ecosystem engineers on rocky shorelines where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms and the production of B vitamins. In turn, these microbes have the genetic capability to assimilate the dissolved organic compounds released by their phototroph hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal phototrophs is likely due in part to the activities of associated microbes and an increased understanding of these associations is needed.

ecology↗