Sedova, V. V. | bioRxiv Science

bioRxiv2025

Oligotrophy and organic carbon dissipation as trophic strategy in chernozem rare and uncultured taxa

Soil microbial communities harbor vast phylogenetic diversity, yet the functional ecology of rare and uncultured taxa remains poorly understood. These low-abundance microorganisms may employ specialized trophic strategies enabling their persistence in resource-limited environments. This study examined whether established oligotrophy markers could effectively characterize and differentiate the ecophysiology of rare and uncultured bacteria recovered from diverse Russian soil metagenomes. A total of 31 soil samples (chernozems, fluvisols, solonetz, solonchak, kastanozems, and leptosols) were collected from protected natural areas in the Rostov Region, Russia. Shotgun metagenomic sequencing was performed, and 246 metagenome-assembled genomes (MAGs) were recovered through assembly and binning. Genomic and functional traits associated with oligotrophy - including genome size, predicted generation time, ribosomal RNA operon copy number, two-component signaling systems, chemotaxis proteins, and carbohydrate-active enzymes - were analyzed. Metabolic capabilities for C1-compound oxidation, benzoyl-CoA pathway utilization, organosulfonate metabolism, and atmospheric trace gas scavenging were annotated. Principal component analysis was employed to cluster MAGs based on ecological strategy. MAGs spanned 18 bacterial phyla, with genome sizes ranging from 0.58-11.6 Mb and predicted doubling times from 0.6-15.6 hours. Six statistically significant clusters were identified, corresponding to distinct life-history strategies: fast-growing generalists, hydrogenotrophs, C1-compound specialists, polysaccharide degraders, aromatic compound degraders, and minimal-genome specialists. Oligotrophic lifestyles were confidently inferred for Methylomirabilota, Krumholzibacteriota, and Eisenbacteria MAGs, characterized by slow growth, reliance on low-molecular-weight carbon dissipation, and reduced regulatory complexity. Copiotrophic strategies were associated with Myxococcota, Bacteroidota, Gammaproteobacteria, and Verrucomicrobiota, which exhibited large genomes, rapid doubling times, extensive two-component systems, and high carbohydrate-active enzyme abundances. Combined analysis of genome size, generation time, regulatory system complexity, chemotaxis capacity, and substrate utilization pathways provides a robust framework for inferring trophic strategies of uncultured soil bacteria. Oligotrophy among rare taxa is characterized by adaptation to low-molecular-weight carbon dissipation, atmospheric trace gas oxidation, representing ecological strategies that enable persistence in nutrient-limited soil microhabitats.

microbiology↗

bioRxiv2024

Urban microbial communities shift towards carotenoid-producing species under constant anthropogenic stress

During years of investigating soil microbial communities, our research group consistently observed a predominance of carotenoid-producing microbes - characteristically pigmented in hues typical of carotenoids - in urban soil samples, as compared to those from recreational, rural, or non-urban areas. To validate this observation as non-random and to explore the ecological role of carotenoid-producing microorganisms in urban soils, we conducted a series of experiments. Additionally, we extended our study to other components of the urban ecosystem that may harbor and transfer microbial communities, including dust and snow samples. Through ecological monitoring, we assessed the proportion of culturable carotenoid-producing bacteria in those samples. It was found that in urban soils >60% of the isolates are pigmented, and in natural soils only about 30% exhibit carotenoid pigmentation. For snow and dust samples, all sites have shown pigmented bacteria predominance. Further, we analyzed both the physiological traits of individual isolates and the broader characteristics of entire culturomes (comprising all isolates from a single aliquot plated onto Petri dishes). Metagenomic analysis of the culturome washes was also performed to provide deeper insights into the microbial communities present. Metagenome of urban isolates clearly show elevated biodiversity of carotenoid biosynthesis genes and carotenoid-producing taxa, as compared to metagenome of natural habitat. In this study, Flavobacterium was identified as the most abundant pigmented genus of urban settings. Based on data obtained in this work, and similar literature data on urban microbial communities, we propose that the unique combination of environmental factors in urban settings fosters the selective enrichment of carotenoid-producing microorganisms. Finally, we offer a model to explain this selective process.

microbiology↗