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Title: Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture


To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helping to solve these challenges. However, the results of their use in agriculture have been variable, probably because of poor colonization. Phytomicrobiome engineering is an emerging field of synthetic biology that may offer ways to alleviate this limitation. This review highlights recent advances in both bottom-up and top-down approaches to engineering non-model bacteria and microbiomes to promote beneficial plant-microbe interactions, as well as advances in strategies to evaluate these interactions. Biosafety, biosecurity, and biocontainment strategies to address the environmental concerns associated with field use of synthetic microbes are also discussed.

; ;
Publication Date:
Research Org.:
Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Urbana, IL (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
Alternate Identifier(s):
OSTI ID: 1807576; OSTI ID: 1813363
Grant/Contract Number:  
SC0018420; AC02-05CH11231; SC0018260; SC0020390
Resource Type:
Published Article
Journal Name:
Trends in Biotechnology
Additional Journal Information:
Journal Name: Trends in Biotechnology Journal Volume: 39 Journal Issue: 3; Journal ID: ISSN 0167-7799
Country of Publication:
59 BASIC BIOLOGICAL SCIENCES; phytomicrobiome engineering; genome engineering; sustainable agriculture; synthetic microbial community; plant growth promotion; safe genes strategies

Citation Formats

Ke, Jing, Wang, Bing, and Yoshikuni, Yasuo. Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture. Netherlands: N. p., 2021. Web.
Ke, Jing, Wang, Bing, & Yoshikuni, Yasuo. Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture. Netherlands.
Ke, Jing, Wang, Bing, and Yoshikuni, Yasuo. Mon . "Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture". Netherlands.
title = {Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture},
author = {Ke, Jing and Wang, Bing and Yoshikuni, Yasuo},
abstractNote = {To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helping to solve these challenges. However, the results of their use in agriculture have been variable, probably because of poor colonization. Phytomicrobiome engineering is an emerging field of synthetic biology that may offer ways to alleviate this limitation. This review highlights recent advances in both bottom-up and top-down approaches to engineering non-model bacteria and microbiomes to promote beneficial plant-microbe interactions, as well as advances in strategies to evaluate these interactions. Biosafety, biosecurity, and biocontainment strategies to address the environmental concerns associated with field use of synthetic microbes are also discussed.},
doi = {10.1016/j.tibtech.2020.07.008},
journal = {Trends in Biotechnology},
number = 3,
volume = 39,
place = {Netherlands},
year = {2021},
month = {3}

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  • Wenzel, Walter W.; Wieshammer, Gottfried; Fitz, Walter J.
  • Plant and Soil, Vol. 237, Issue 1, p. 37-45
  • DOI: 10.1023/A:1013395122730

Metagenomic mining of regulatory elements enables programmable species-selective gene expression
journal, March 2018

  • Johns, Nathan I.; Gomes, Antonio L. C.; Yim, Sung Sun
  • Nature Methods, Vol. 15, Issue 5
  • DOI: 10.1038/nmeth.4633

Antibiotic resistance in Pseudomonas aeruginosa – Mechanisms, epidemiology and evolution
journal, May 2019

Single-copy chromosomal integration systems for Francisella tularensis
journal, April 2009

  • LoVullo, Eric D.; Molins-Schneekloth, Claudia R.; Schweizer, Herbert P.
  • Microbiology, Vol. 155, Issue 4
  • DOI: 10.1099/mic.0.022491-0

Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases
journal, January 2017

Characterization of a Bacteroides Mobilizable Transposon, NBU2, Which Carries a Functional Lincomycin Resistance Gene
journal, June 2000

Plant-microbe partnerships in 2020
journal, July 2016

  • Mitter, Birgit; Pfaffenbichler, Nikolaus; Sessitsch, Angela
  • Microbial Biotechnology, Vol. 9, Issue 5
  • DOI: 10.1111/1751-7915.12382

Uncoupling virulence and biocontrol
journal, May 2019

Genome-wide identification of bacterial plant colonization genes
journal, September 2017

3D printing of microscopic bacterial communities
journal, October 2013

  • Connell, J. L.; Ritschdorff, E. T.; Whiteley, M.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 46
  • DOI: 10.1073/pnas.1309729110

Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms
journal, September 2009

  • van Opijnen, Tim; Bodi, Kip L.; Camilli, Andrew
  • Nature Methods, Vol. 6, Issue 10
  • DOI: 10.1038/nmeth.1377

Anti-CRISPR-Associated Proteins Are Crucial Repressors of Anti-CRISPR Transcription
journal, September 2019

Evaluation of a novel tool for sampling root exudates from soil-grown plants compared to conventional techniques
journal, March 2013

Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla
journal, February 2019

Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota
journal, August 2019

Microfluidic platforms for plant cells studies
journal, January 2014

Manipulating Bacterial Communities by in situ Microbiome Engineering
journal, April 2016