Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil
Year: 2020
Type: article
Abstract: Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.
Source: mSystems
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
SDG: Life on land
Open Access status: gold
Estimated APC paid: $3,500
Funders: National Science Foundation, U.S. Department of Energy, U.S. Department of Agriculture, Joint Genome Institute, Austrian Science Fund, Universität Wien, Ministry of Science,Technology and Research, National Institute of Food and Agriculture, Office of Science, University of Massachusetts Amherst, National Science Foundation of Sri Lanka, Division of Environmental Biology
Awards: G1117004060, G1286236842, G1416433235, Investigating the function of the ubiquitous Acidobacteria in terrestrial environments, G1863003419, G2071463538, G2536596559, G2890232221, G3083819904, G419881185, G42916606, G4325257263, G4501827968, G498139845, Collaborative Research: LTREB: Soil Warming and Forest Ecosystem Feedbacks to the Climate System, LTER V: New Science, Synthesis, Scholarship, and Strategic Vision for Society, G6652958823, G7205239661, G834277795, G864045717, G876836414, G969889393, G980307288
OpenAlex ID: W3010880267