Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

MSystems
Lauren AlteioTanja Woyke

Abstract

Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this "uncultivated majority" remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted meta...Continue Reading

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Citations

Aug 28, 2020·Applied Microbiology and Biotechnology·Anne-Kristin Kaster, Morgan S Sobol
Oct 10, 2020·Scientific Reports·Leila SatariManuel Porcar
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May 11, 2021·Frontiers in Microbiology·Nicholas J ReichartRoland Hatzenpichler

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Datasets Mentioned

BETA
DIAMOND
PRJNA608716

Methods Mentioned

BETA
amplicon sequencing
fluorescence-activated cell sorting
single-cell sequencing
FACS
MDA
PCR

Software Mentioned

BBTools
FastTree2
DIAMOND
hmmsearch
meta
CheckM
BLOSUM30
BBMap
IQTree
R

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