Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs

Nature Communications
Emiley A Eloe-FadroshNatalia Ivanova

Abstract

Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum ('Candidatus Kryptonia') found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic 'blind spot' because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery.

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Datasets Mentioned

BETA
AP011715
PRJEB11785
PRJEB11788
PRJEB11711
PRJEB11728

Methods Mentioned

BETA
PCR
mathFISH

Software Mentioned

hmmsearch
ProDeGe
SPAdes
blast
CRISPRmap
cmalign
mathFISH
MAFFT
DECIPHER ProbeMelt
hmmalign

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