New globally distributed bacteria with high proportions of novel protein families involved in sulfur and nitrogen cycling

Gong, Xianzhe; Río, Álvaro Rodríguez del; Xu, Le; Langwig, Marguerite V.; Su, Lei; Sun, Mingxue; Huerta-Cepas, Jaime; Anda, Valerie De; Baker, Brett J.

doi:10.21203/rs.3.rs-1620321/v1

Cited by 3 publications

(3 citation statements)

References 15 publications

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“…Backgrounds of GB and the sampling details were described previously 34 . Details of the procedure of obtaining hydrothermal vent mat and oxide samples from the Indian Ocean and cold seep sediment samples from the SCS were described by Gong et al 105 .…”

Section: Sampling Proceduresmentioning

confidence: 99%

Section: Dna Extraction Metagenomic Sequencing Assembly and Binningmentioning

confidence: 99%

“…Total DNA was extracted from each sample and sequenced after quality control as described in the corresponding references 15,34,104,105 . The sequences were assembled and binned with different protocols based on the batch of the samples 34,105 . In total, 495 MAGs with completeness greater than 50% and contamination less than 10% with CheckM lineage_wf v1.0.5 24 were identi ed as Gemmatimondota based on the taxonomy assigned using GTDB-Tk v1.5.1 106 with release 202.…”

Section: Dna Extraction Metagenomic Sequencing Assembly and Binningmentioning

confidence: 99%

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Globally distributed marine Gemmatimonadota have unique genomic potentials

Baker,

Gong,

et al. 2024

Preprint

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Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments is poorly understood. Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition, and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Lineages associated with coral reefs are enriched in genes encoding secondary metabolites, which are likely utilized for ecological interactions there. Furthermore, viruses associated with Gemmatimonadota have the potential to ‘hijack’ and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts. This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities.

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Section: Sampling Proceduresmentioning

confidence: 99%

Section: Dna Extraction Metagenomic Sequencing Assembly and Binningmentioning

confidence: 99%

Section: Dna Extraction Metagenomic Sequencing Assembly and Binningmentioning

confidence: 99%

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Globally distributed marine Gemmatimonadota have unique genomic potentials

Baker,

Gong,

et al. 2024

Preprint

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Occurrence, Diversity, and Genomes of “ Candidatus Patescibacteria” along the Early Diagenesis of Marine Sediments

Zhao

Farag

Jørgensen

et al. 2022

Appl Environ Microbiol

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Ultrasmall-celled “ Ca. Patescibacteria” have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized.

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Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling

et al. 2023

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Background Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB’s can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. Results Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. Conclusions Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.

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New globally distributed bacteria with high proportions of novel protein families involved in sulfur and nitrogen cycling

Cited by 3 publications

References 15 publications

Globally distributed marine Gemmatimonadota have unique genomic potentials

Globally distributed marine Gemmatimonadota have unique genomic potentials

Occurrence, Diversity, and Genomes of “ Candidatus Patescibacteria” along the Early Diagenesis of Marine Sediments

Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling

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