Title: Strategies to improve reference databases for soil microbiomes

Abstract

A database of curated genomes is needed to better assess soil microbial communities and their processes associated with differing land management and environmental impacts. Interpreting soil metagenomic datasets with existing sequence databases is challenging because these datasets are biased towards medical and biotechnology research and can result in misleading annotations. We have curated a database of 928 genomes of soil-associated organisms (888 bacteria, 34 archaea, and 6 fungi). Using this database as a representation of the current state of knowledge of soil microbes that are well-characterized, we evaluated its composition and compared it to broader microbial databases, specifically NCBI’s RefSeq, as well as 3,035 publicly available soil amplicon datasets. These comparisons identified phyla and functions that are enriched in soils as well as those that may be underrepresented in RefSoil. For example, RefSoil was observed to have increased representation of Firmicutes despite its low abundance in soil environments and also lacked representation of Acidobacteria and Verrucomicrobia, which are abundant in soils. Our comparison of RefSoil to soil amplicon datasets allowed us to identify targets that if cultured or sequenced would significantly increase the biodiversity represented within RefSoil. To demonstrate the opportunities to access these underrepresented targets, we employed single cellmore » genomics in a pilot experiment to recover 14 genomes from the "most wanted" list, which improved RefSoil's representation of EMP sequences by 7% by abundance. This effort demonstrates the value of RefSoil in the guidance of future research efforts and the capability of single cell genomics as a practical means to fill the existing genomic data gaps.« less

Authors:

Choi, Jinlyung  ^[1];

• Search DOE PAGES for author "Choi, Jinlyung"
• Search DOE PAGES for ORCID "0000-0003-4546-2789"

Yang, Fan ^[1]; Stepanauskas, Ramunas  ^[2];

• Search DOE PAGES for author "Stepanauskas, Ramunas"
• Search DOE PAGES for ORCID "0000-0003-4458-3108"

Cardenas, Erick  ^[3];

• Search DOE PAGES for author "Cardenas, Erick"
• Search DOE PAGES for ORCID "0000-0002-5456-013X"

Garoutte, Aaron ^[4]; Williams, Ryan ^[1]; Flater, Jared ^[1]; Tiedje, James M. ^[4]; Hofmockel, Kirsten S.  ^[5];

• Search DOE PAGES for author "Hofmockel, Kirsten S."
• Search DOE PAGES for ORCID "0000-0003-1586-2167"

Gelder, Brian ^[1]; Howe, Adina ^[1]

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+ Show Author Affiliations

1. Iowa State Univ., Ames, IA (United States). Dept. of Agricultural and Biosystems Engineering
2. Bigelow Lab. for Ocean Sciences, East Boothbay, ME (United States)
3. Univ. of British Columbia, Vancouver, BC (Canada). Dept. of Microbiology & Immunology
4. Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology
5. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL); Iowa State Univ., Ames, IA (United States). Dept. of Ecology, Evolution and Organismal Biology

Publication Date:

Fri Dec 09 00:00:00 EST 2016

Research Org.:

Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Org.:

USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)

OSTI Identifier:

1353315

Report Number(s):

PNNL-SA-122172
Journal ID: ISSN 1751-7362

Grant/Contract Number:  

AC05-76RL01830; SC0010775

Resource Type:

Accepted Manuscript

Journal Name:

The ISME Journal

Additional Journal Information:

Journal Volume: 11; Journal Issue: 4; Journal ID: ISSN 1751-7362

Publisher:

Nature Publishing Group

Country of Publication:

United States

Language:

English

Subject:

96 KNOWLEDGE MANAGEMENT AND PRESERVATION; 59 BASIC BIOLOGICAL SCIENCES