From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Winston E Anthony; Steven D Allison; Caitlin M Broderick; Luciana Chavez Rodriguez; Alicia Clum; Hugh Cross; Emiley Eloe-Fadrosh; Sarah Evans; Dawson Fairbanks; Rachel Gallery; Júlia Brandão Gontijo; Jennifer Jones; Jason McDermott; Jennifer Pett-Ridge; Sydne Record; Jorge Luiz Mazza Rodrigues; William Rodriguez-Reillo; Katherine L Shek; Tina Takacs-Vesbach; Jeffrey L Blanchard

doi:10.1186/s40793-024-00599-w

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Environ Microbiome. 2024 Aug 2;19(1):56. doi: 10.1186/s40793-024-00599-w.

Authors

Winston E Anthony¹, Steven D Allison^{2

3}, Caitlin M Broderick⁴, Luciana Chavez Rodriguez², Alicia Clum⁵, Hugh Cross⁶, Emiley Eloe-Fadrosh⁵, Sarah Evans⁴, Dawson Fairbanks^{7

8}, Rachel Gallery⁸, Júlia Brandão Gontijo⁹, Jennifer Jones⁴, Jason McDermott¹⁰, Jennifer Pett-Ridge^{11

12}, Sydne Record¹³, Jorge Luiz Mazza Rodrigues^{5

9}, William Rodriguez-Reillo¹⁴, Katherine L Shek¹⁵, Tina Takacs-Vesbach¹⁶, Jeffrey L Blanchard¹⁷

Affiliations

¹ Pacific Northwest National Laboratory, Richland, WA, 99354, USA. [email protected].
² University of California Irvine, Irvine, CA, USA.
³ Department of Earth System Science, University of California, Irvine, CA, USA.
⁴ W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA.
⁵ Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
⁶ National Ecological Observatory Network - Battelle, Boulder, CO, USA.
⁷ University of California Riverside, Riverside, CA, USA.
⁸ The University of Arizona, Tucson, AZ, USA.
⁹ University of California Davis, Davis, CA, USA.
¹⁰ Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
¹¹ Lawrence Livermore National Laboratory, Livermore, CA, USA.
¹² Life & Environmental Sciences Department, University of California Merced, Merced, CA, 95343, USA.
¹³ University of Maine, Orono, ME, USA.
¹⁴ Harvard Medical School, Boston, MA, USA.
¹⁵ University of New Hampshire, Durham, NH, USA.
¹⁶ University of New Mexico, Albuquerque, NM, USA.
¹⁷ University of Massachusetts Amherst, Amherst, MA, USA. [email protected].

Abstract

Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

Keywords: FAIR Data Principles; Genome Resolved Metagenomics; Hybrid Assembly; Microbiome Assembled Genomes; Soil Microbiome.

Publication types

Letter

Abstract

Publication types

Grants and funding