Martins Samuel J, Pasche Josephine, Silva Hiago Antonio O, Selten Gijs, Savastano Noah, Abreu Lucas Magalhães, Bais Harsh P, Garrett Karen A, Kraisitudomsook Nattapol, Pieterse Corné M J, Cernava Tomislav
Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A.
Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
Phytopathology. 2023 Aug;113(8):1369-1379. doi: 10.1094/PHYTO-01-23-0016-IA. Epub 2023 Sep 20.
Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.
尽管植物从益生菌中获得了诸多益处，但在不同应用中保持一致的效果仍是一项挑战。与测序成本降低相关的非培养方法极大地增进了人们对植物环境中微生物生态学的整体理解。因此，现在有可能构建一个旨在改善植物健康的微生物联合体。这种合成微生物群落（SynComs）包含经过精心挑选的微生物物种，以产生所需的微生物组功能。微生物生物膜形成、次级代谢产物的产生以及诱导植物抗性的能力是设计SynComs时需要考虑的一些微生物特性。与植物相关的微生物群落并非随机组装。生态学理论表明，这些群落具有由一般群落组装规则构建的明确系统发育组织。利用机器学习，我们可以研究这些规则并靶向产生所需植物表型的微生物功能。与经典的单一微生物活性或分类学选择相比，结构良好的组合更有可能产生一个在环境压力下茁壮成长的稳定SynCom。然而，确保微生物定殖和植物表型的长期稳定性仍然是SynComs需要克服的挑战之一，因为合成群落可能会随着微生物水平基因转移和保留的突变而随时间变化。在这里，我们探讨了SynCom研究在植物健康方面取得的进展，重点关注细菌，因为与微生物组的其他成员相比，细菌是最主要的微生物形式，也是SynCom研究中最常见的。
