Biology subjects

Thomas, D. N.

Publications and source records attributed to Thomas, D. N..

3 recordsLinked to original sources

bioRxiv2026

Ultra-small bacteria and their phages discovered through metagenomics in a sub-arctic degrading permafrost ecosystem

Patescibacteriota is a diverse bacterial phylum characterized by ultra-small cell size, streamlined genome, incomplete metabolism and episymbiotic lifestyle. While Patescibacteriota have been detected across a wide range of ecosystem types, their phages are not widely described. We utilized metagenomics to explore these less characterized parts of the microbiome in a sporadic permafrost ecosystem, with samples from palsa and peat soils, small ponds and streams. We retrieved 33 high-quality metagenome assembled genomes (MAGs) of Patescibacteriota, mainly from the classes Minisyncoccia and Saccharimonadia. Minisyncoccia was a dominant class in the thawing soils and thaw ponds, whereas the Saccharimonadia was more abundant in the frozen palsa soil layers. The distribution of the Patescibacteria classes was also reflected in their metabolic potential. For example, gluconeogenesis pathway was complete only in MAGs from the class Minisyncoccia, whereas cytochrome o ubiquinol oxidase was mainly found from the MAGs of the class Saccharimondia. The viral community analysis yielded 16 354 viral operational taxonomic units (vOTUs), which represented mainly tailed dsDNA viruses from the class Caudoviricetes. Based on genome size, 16 vOTUs were qualified as jumbophages and one as a megaphage. Similar to the bacterial community, the viral community composition differed across sample types. The most common hosts for bacterial viruses were phyla Pseudomonadota, Acidobacteriota and Actinomycetota. A further 196 vOTUs were in silico linked to Patescibacteriota hosts. The Patescibacteriota phages were diverse, with only two vOTUs representing the same genus. The relative abundance of Patescibacteriota-associated phages was especially high in frozen palsa soils, largely following the same pattern of abundance as Patescibacteriota.

microbiology↗

bioRxiv2026

Northern palsa and peat ecosystem microbiomes are potentially supported by hydrogen and carbon monoxide metabolism

Northern peatland and permafrost ecosystems are facing rapid changes, with increasing temperatures, permafrost thaw and shifts in hydrology. Characterizing microbial communities and metabolic potential from the soils and associated water bodies is crucial to understanding the changes in biogeochemical cycling in these ecosystems. For this, samples were collected and sequenced from subarctic palsa and peat soils, along with samples from associated thaw ponds and streams. Metagenomics was utilized in describing the microbiome and its metabolic potential in these environments. Palsa soils hosted microbial communities that were distinct from the peatland soils, ponds and stream waters. Soils and their adjacent ponds shared taxa, and peat soils and ponds also shared taxa with the streams, unlike palsa soils which were likely more hydrologically isolated. Based on metabolic marker gene ratio for denitrification [(nirS+nirK)/nosZ], palsa soils had the strongest potential to be a source of nitrous oxide (N2O) out of all the sample types. Marker genes for hydrogen gas (H2) and carbon monoxide (CO) utilization were abundant across soil environments and metagenome assembled genomes, suggesting that trace gas oxidation is likely one of the key energy sources for microbiomes. In the palsa ponds and peat soils pmoA, marker gene for methanotrophy, was the most abundant compared to the other sample types.

microbiology↗

bioRxiv2025

Biodegradation of different bioplastics by specialised microbial communities in a coastal brackish environment

Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterised the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss to CO2 after four weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting a link with the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term bioplastisphere to denote the distinctive microbial communities associated with biodegradable plastics.

microbiology↗