Solutions in microbiome engineering: prioritizing barriers to organism establishment

Michaeline B N Albright; Stilianos Louca; Daniel E Winkler; Kelli L Feeser; Sarah-Jane Haig; Katrine L Whiteson; Joanne B Emerson; John Dunbar

doi:10.1038/s41396-021-01088-5

Solutions in microbiome engineering: prioritizing barriers to organism establishment

ISME J. 2022 Feb;16(2):331-338. doi: 10.1038/s41396-021-01088-5. Epub 2021 Aug 21.

Authors

Michaeline B N Albright¹, Stilianos Louca², Daniel E Winkler³, Kelli L Feeser⁴, Sarah-Jane Haig⁵, Katrine L Whiteson⁶, Joanne B Emerson⁷, John Dunbar⁴

Affiliations

¹ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA. malbright@lanl.gov.
² Department of Biology, University of Oregon, Eugene, OR, USA.
³ United States Geological Survey, Southwest Biological Science Center, Moab, UT, USA.
⁴ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
⁵ Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, PA, USA.
⁶ Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA.
⁷ Department of Plant Pathology, University of California, Davis, CA, USA.

Abstract

Microbiome engineering is increasingly being employed as a solution to challenges in health, agriculture, and climate. Often manipulation involves inoculation of new microbes designed to improve function into a preexisting microbial community. Despite, increased efforts in microbiome engineering inoculants frequently fail to establish and/or confer long-lasting modifications on ecosystem function. We posit that one underlying cause of these shortfalls is the failure to consider barriers to organism establishment. This is a key challenge and focus of macroecology research, specifically invasion biology and restoration ecology. We adopt a framework from invasion biology that summarizes establishment barriers in three categories: (1) propagule pressure, (2) environmental filtering, and (3) biotic interactions factors. We suggest that biotic interactions is the most neglected factor in microbiome engineering research, and we recommend a number of actions to accelerate engineering solutions.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Agriculture
Ecology
Microbiota*