Year: 2023
Type: article
Abstract: Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.
Source: Nature Microbiology
Authors: Cale O. Seymour, Marike Palmer, Eric D. Becraft, Ramunas Stepanauskas, Ariel D. Friel, Frederik Schulz, Tanja Woyke, Emiley Eloe-Fadrosh, Dengxun Lai, Jian-Yu Jiao, Zheng-Shuang Hua, Lan Liu, Zheng-Han Lian, Wen-Jun Li, Maria Chuvochina, Brianna K. Finley, Benjamin J. Koch, Egbert Schwartz, Paul Dijkstra, Duane P. Moser, Bruce A. Hungate, Brian P. Hedlund
Institutions: University of Nevada, Las Vegas, University of North Alabama, Bigelow Laboratory for Ocean Sciences, Lawrence Berkeley National Laboratory, Joint Genome Institute, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), University of Science and Technology of China, Chinese Academy of Sciences, Xinjiang Institute of Ecology and Geography, State Key Laboratory of Desert and Oasis Ecology, The University of Queensland, Northern Arizona University, University of California, Irvine, Desert Research Institute
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $11,690
Funders: National Science Foundation, U.S. Department of Energy, National Aeronautics and Space Administration, U.S. Department of Agriculture, Joint Genome Institute, National Natural Science Foundation of China, Nuclear Safety and Security Commission, Department of Education and Training, U.S. Fish and Wildlife Service, Office of Science, U.S. Forest Service, U.S. Bureau of Land Management, National Park Service, Australian Research Council
Awards: G1058167406, G1117004060, G1286236842, G1414775356, G1632040200, G1816284028, G1863003419, G2277153758, RII Track-2 FEC: Single Cell Genome-to-Phenome: Integrating Genome and Phenome Analyses of Individual Microbial Cells in Complex Microbiomes, G3083819904, G365575497, Collaborative Research: Tectonic and climatic forcing of hydrological systems in the southern Great Basin: Implications for ancient and future aquatic system resilience, Engagement of early-career and diverse scientists in international science on Archaea at the International Conference on Geo-Omics of Archaea; October 25-27, 2019; Shenzhen, China, G419881185, G4206956643, G42916606, G4501827968, G498139845, Collaborative research: Untangling the Deep Genealogy of Microbial Dark Matter, RECENT ADVANCEMENTS IN METAGENOMICS AND SINGLE-CELL GENOMICS HAVE ENABLED UNPRECEDENTED ACCESS TO GENOMES FROM CANDIDATE (YET-UNCULTIVATED) PHYLA OF BACTERIA AND ARCHAEA INCLUDING THOSE INHABITING EXTREME AND EARLY EARTH-LIKE SYSTEMS. THESE DATA HAVE ENABLED INSIGHTS INTO THE BIOLOGY OF THESE ORGANISMS INCLUDING THEIR CATABOLIC AND ANABOLIC POTENTIAL MOLECULAR ADAPTATIONS TO LIFE IN EXTREME ENVIRONMENTS AND INSIGHTS INTO THE EARLY DIVERSIFICATION OF MICROBIAL LINEAGES. HOWEVER THE PREDICTED METABOLIC FUNCTIONS OF THESE ORGANISMS AND THEIR GENES REMAIN LARGELY UNTESTED. THE CENTRAL GOAL OF THIS PROPOSAL IS TO LEVERAGE A FOUNDATION OF GENOMIC EXPLORATION IN GREAT BOILING SPRING (GBS) NV TO ASSESS METABOLIC FUNCTIONS OF THERMOPHILES REPRESENTING CANDIDATE PHYLA OF BACTERIA AND ARCHAEA AND THEIR ROLES IN MAJOR BIOGEOCHEMICAL CYCLES. WE HAVE RECENTLY DESCRIBED THE FIRST SUBSTANTIAL GENOMIC DATA FOR THE CANDIDATE BACTERIAL PHYLA ATRIBACTERIA (OP9) CALESCAMANTES (EM19) AND FERVIDIBACTERIA (OCTSPA1-106) AND KRYPTONIA. TO ADDRESS THE METABOLIC FUNCTIONS OF THESE AND OTHER YET-UNCULTIVATED MAJOR LINEAGES WE WILL USE A COMBINATION OF TARGETED AND BROADBASED APPROACHES. OBJECTIVE 1: ASSESS C AND N ASSIMILATORY METABOLISMS IN SPECIFIC TARGETED TAXA IN MICROCOSMS AND ENRICHMENT CULTURES USING (A) STABLE-ISOTOPE PROBING (SIP) FLUORESCENCE IN SITU HYBRIDIZATION AND NANOSIMS IMAGING (FISH-SIMS) AND (B) IN SITU TRANSCRIPTION OF GENES PREDICTED TO BE INVOLVED IN H C N AND S CYCLING BY QUANTITATIVE REVERSE-TRANSCRIPTASE PCR. OBJECTIVE 2: DETERMINE METABOLIC FUNCTION OF ABUNDANT COMMUNITY MEMBERS USING BROAD-BASED APPROACHES SUCH AS (A) 16S RRNA SIP WITH A CUSTOM PHYLOGENETIC MICROARRAY (CHIP-SIP) TO ASSESS C AND N ASSIMILATION IN MICROCOSMS AND ENRICHMENT CULTURES (B) WHOLECOMMUNITY TRANSCRIPTOMICS AND (C) WHOLE-COMMUNITY PROTEOMICS. ULTIMATELY THE COMBINATION OF BOTH TARGETED AND UNTARGETED APPROACHES WILL PROVIDE ROBUST EVIDENCE OF THE ECOLOGICAL ROLES OF SEVERAL YET-UNCULTIVATED MICROBIAL PHYLA IN GBS AND BEYOND., G6519249983, Reconstructing the universal tree and network of life, G704498496, G7205239661, G805243471, G834277795, G969889393
OpenAlex ID: W4327568911