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Phylogenetically novel uncultured microbial cells dominate Earth microbiomes

Karen G. Lloyd, Joshua Ladau, Andrew D. Steen, Junqi Yin, Lonnie Crosby
doi: https://doi.org/10.1101/303602
Karen G. Lloyd
1Department of Microbiology, University of Tennessee, Knoxville, TN 37996
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  • For correspondence: klloyd@utk.edu
Joshua Ladau
2Department of Earth and Planetary Sciences, University of Tennessee, Knoxville TN 37996
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Andrew D. Steen
3Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158
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Junqi Yin
4Joint Institute for Computational Sciences, University of Tennessee, Knoxville, TN 37996
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Lonnie Crosby
4Joint Institute for Computational Sciences, University of Tennessee, Knoxville, TN 37996
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Abstract

To unequivocally determine a microbe’s physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 × 1029 (81%) and 2.2 × 1029 (25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 18, 2018.
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Phylogenetically novel uncultured microbial cells dominate Earth microbiomes
Karen G. Lloyd, Joshua Ladau, Andrew D. Steen, Junqi Yin, Lonnie Crosby
bioRxiv 303602; doi: https://doi.org/10.1101/303602
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Phylogenetically novel uncultured microbial cells dominate Earth microbiomes
Karen G. Lloyd, Joshua Ladau, Andrew D. Steen, Junqi Yin, Lonnie Crosby
bioRxiv 303602; doi: https://doi.org/10.1101/303602

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