3 research outputs found
Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes
Soil microorganisms provide key ecological functions that often rely on metabolic interactions between individual populations of the soil microbiome. To better understand these interactions and community processes, we used chitin, a major carbon and nitrogen source in soil, as a test substrate to investigate microbial interactions during its decomposition. Chitin was applied to a model soil consortium that we developed, “model soil consortium-2” (MSC-2), consisting of eight members of diverse phyla and including both chitin degraders and nondegraders. A multiomics approach revealed how MSC-2 community-level processes during chitin decomposition differ from monocultures of the constituent species. Emergent properties of both species and the community were found, including changes in the chitin degradation potential of Streptomyces species and organization of all species into distinct roles in the chitin degradation process. The members of MSC-2 were further evaluated via metatranscriptomics and community metabolomics. Intriguingly, the most abundant members of MSC-2 were not those that were able to metabolize chitin itself, but rather those that were able to take full advantage of interspecies interactions to grow on chitin decomposition products. Using a model soil consortium greatly increased our knowledge of how carbon is decomposed and metabolized in a community setting, showing that niche size, rather than species metabolic capacity, can drive success and that certain species become active carbon degraders only in the context of their surrounding community. These conclusions fill important knowledge gaps that are key to our understanding of community interactions that support carbon and nitrogen cycling in soi
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Thousands of small, novel genes predicted in global phage genomes.
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families in ∼2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000 families encode predicted anti-CRISPR proteins, and more than 500 families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions
Thousands of small, novel genes predicted in global phage genomes
Fremin BJ, Bhatt AS, Kyrpides NC, et al. Thousands of small, novel genes predicted in global phage genomes. Cell Reports. 2022;39(12): 110984