Solutions in microbiome engineering: prioritizing barriers to organism establishment

被引：98

作者：

Albright, Michaeline B. N. ^{[1
]}

Louca, Stilianos ^{[2
]}

Winkler, Daniel E. ^{[3
]}

Feeser, Kelli L. ^{[1
]}

Haig, Sarah-Jane ^{[4
]}

Whiteson, Katrine L. ^{[5
]}

Emerson, Joanne B. ^{[6
]}

Dunbar, John ^{[1
]}

机构：

[1] Los Alamos Natl Lab, Biosci Div, Los Alamos, NM 87544 USA

[2] Univ Oregon, Dept Biol, Eugene, OR 97403 USA

[3] US Geol Survey, Southwest Biol Sci Ctr, Moab, UT USA

[4] Univ Pittsburgh, Dept Civil & Environm Engn, Pittsburgh, PA USA

[5] Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92717 USA

[6] Univ Calif Davis, Dept Plant Biol, Davis, CA 95616 USA

来源：

ISME JOURNAL | 2022年 / 16卷 / 02期

基金：

美国国家科学基金会; 美国食品与农业研究所;

关键词：

COMMUNITY; INVASION; RESTORATION; COMPETITION; PROBIOTICS; ECOLOGY; GROWTH; SOIL; BIOREMEDIATION; BIODIVERSITY;

D O I：

10.1038/s41396-021-01088-5

中图分类号：

Q14 [生态学（生物生态学）];

学科分类号：

071012 ; 0713 ;

摘要：

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.

引用

页码：331 / 338

页数：8

共 100 条

[11] Preadaptation and Naturalization of Nonnative Species: Darwin's Two Fundamental Insights into Species Invasion [J].

Cadotte, Marc W. ;

Campbell, Sara E. ;

Li, Shao-peng ;

Sodhi, Darwin S. ;

Mandrak, Nicholas E. .

ANNUAL REVIEW OF PLANT BIOLOGY, VOL 69, 2018, 69 :661-684

[12] Restoration ecology: The state of an emerging field [J].

Cairns, J ;

Heckman, JR .

ANNUAL REVIEW OF ENERGY AND THE ENVIRONMENT, 1996, 21 :167-189

[13] Combination of antibiotic and probiotic treatment is efficacious in prophylaxis of post-operative recurrence of Crohn's disease: A randomized controlled study vs mesalamine. [J].

Campieri, M ;

Rizzello, F ;

Venturi, A ;

Poggioli, G ;

Ugolini, F ;

Helwig, U ;

Amadini, C ;

Romboli, E ;

Gionchetti, P .

GASTROENTEROLOGY, 2000, 118 (04) :A781-A781

[14] Use and abuse of correlation analyses in microbial ecology [J].

Carr, Alex ;

Diener, Christian ;

Baliga, Nitin S. ;

Gibbons, Sean M. .

ISME JOURNAL, 2019, 13 (11) :2647-2655

[15] Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework [J].

Catford, Jane A. ;

Jansson, Roland ;

Nilsson, Christer .

DIVERSITY AND DISTRIBUTIONS, 2009, 15 (01) :22-40

[16] Applications of quorum sensing in biotechnology [J].

Choudhary, Swati ;

Schmidt-Dannert, Claudia .

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 2010, 86 (05) :1267-1279

[17]

COMEAU Y, 1993, APPL MICROBIOL BIOT, V38, P681, DOI 10.1007/BF00182810

[18] Microbiome engineering to improve biocontrol and plant growth-promoting mechanisms [J].

del Carmen Orozco-Mosqueda, Ma ;

del Carmen Rocha-Granados, Ma ;

Glick, Bernard R. ;

Santoyo, Gustavo .

MICROBIOLOGICAL RESEARCH, 2018, 208 :25-31

[19] SELECTION IN CHEMOSTATS [J].

DYKHUIZEN, DE ;

HARTL, DL .

MICROBIOLOGICAL REVIEWS, 1983, 47 (02) :150-168

[20] Niche dimensionality links biodiversity and invasibility of microbial communities [J].

Eisenhauer, Nico ;

Schulz, Wiebke ;

Scheu, Stefan ;

Jousset, Alexandre .

FUNCTIONAL ECOLOGY, 2013, 27 (01) :282-288

← 1 2 3 4 5 6 7 8 9 10 →