ArticlemSystems
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- Upwelling periodically disturbs the ecological assembly of microbial communities in Lake Ontario.ISME communications · 2026Article
- Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.Microbiome · 2025Article
- Opsins are Phospholipid Scramblases in All Domains of Life.bioRxiv : the preprint server for biology · 2025Article
- Seed2LP: seed inference in metabolic networks for reverse ecology applications.Bioinformatics (Oxford, England) · 2025Article
- Two decades of bacterial ecology and evolution in a freshwater lake.Nature microbiology · 2025Article
- Metabolites of pathogenic microorganisms database (MPMdb) and its seed metabolite applications.Microbiology spectrum · 2024Article
- TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome.ISME communications · 2022Article
- Ecological modelling approaches for predicting emergent properties in microbial communities.Nature ecology & evolution · 2022Review
- Heme auxotrophy in abundant aquatic microbial lineages.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins.Journal of microbiology and biotechnology · 2020Review
- acI Actinobacteria Assemble a Functional Actinorhodopsin with Natively Synthesized Retinal.Applied and environmental microbiology · 2018Article
- Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments.Nature communications · 2018Article
- Human gut microbe co-cultures have greater potential than monocultures for food waste remediation to commodity chemicals.Scientific reports · 2018Article
- TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.mSphere · 2018Article
- Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.mSphere · 2018Article
- Freshwater carbon and nutrient cycles revealed through reconstructed population genomes.PeerJ · 2018Article
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An explosion in the number of available genome sequences obtained through metagenomics and single-cell genomics has enabled a new view of the diversity of microbial life, yet we know surprisingly little about how microbes interact with each other or their environment. In fact, the majority of microbial species remain uncultivated, while our perception of their ecological niches is based on reconstruction of their metabolic potential. In this work, we demonstrate how the "seed set framework," which computes the set of compounds that an organism must acquire from its environment (E. Borenstein, M. Kupiec, M. W. Feldman, and E. Ruppin, Proc Natl Acad Sci U S A 105:14482-14487, 2008, https://doi.org/10.1073/pnas.0806162105), enables computational analysis of metabolic reconstructions while providing new insights into a microbe's metabolic capabilities, such as nutrient use and auxotrophies. We apply this framework to members of the ubiquitous freshwater actinobacterial lineage acI, confirming and extending previous experimental and genomic observations implying that acI bacteria are heterotrophs reliant on peptides and saccharides. We also present the first metatranscriptomic study of the acI lineage, revealing high expression of transport proteins and the light-harvesting protein actinorhodopsin. Putative transport proteins complement predictions of nutrients and essential metabolites while providing additional support of the hypothesis that members of the acI are photoheterotrophs.
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