Abstract
Although much work has explored how microbes can benefit plant growth, the mechanisms underlying this intriguing process remain largely unknown, especially considering the diversity of bacteria that surrounds plants. The objective of the present study was to identify bacterial genes contributing to plant–microbe associations, beneficial effects, and host specificities. For this purpose, comparative genomics investigation of 151 plant-associated bacteria was performed. A principal component analysis of seven key genomic features revealed patterns in the specific properties of these bacteria: N2-fixing bacteria were more closely related to pathogenic ones than to beneficial bacteria. A common set of genes over-represented in these plant-associated bacteria were found to be remarkably similar in terms of (1) genetic information processing, (2) amino acid metabolism, (3) metabolism of cofactors and vitamins, (4) nucleotide metabolism, (5) human diseases, and (6) metabolism of terpenoids and polyketides. Although we did not detect a common genetic basis for these beneficial effects, further in-depth analysis revealed that each of five beneficial bacterial groups shared specific gene sets. Functional annotation showed that environmental information processing, genetic information processing and cellular processes predominated in these beneficial groups. Hypothesizing that plant-associated bacteria may have overlapping strategies to colonize their plant hosts, we successfully identified many putative genes that determine host specificities. Most of these genes were classified as transcription factors, enzymes, transporters, and chemotaxis regulators. Comparative genomics provides a powerful tool for helping to identify genes that are common among species. Genome-based views of plant-associated bacteria reveal specific interactions between bacteria and plant hosts.
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Acknowledgements
This study was supported by the National Key Research and Development Program of China (2017YFD0101303), Youth Foundation of Harbin Normal University (KGB201217), and the National Natural Science Foundation of China (31770575, 31470571).
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Hongsheng Cai declares that he has no conflict of interest. Yan Bai declares that he has no conflict of interest. Changhong Guo declares that she has no conflict of interest.
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Supplementary material 3 Neighbor-joining phylogenetic tree based on the 16S rRNA gene sequences showing the classical relationships among the selected 151 plant-associated bacteria. (PDF 39 KB)
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Cai, H., Bai, Y. & Guo, C. Comparative genomics of 151 plant-associated bacteria reveal putative mechanisms underlying specific interactions between bacteria and plant hosts. Genes Genom 40, 857–864 (2018). https://doi.org/10.1007/s13258-018-0693-1
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DOI: https://doi.org/10.1007/s13258-018-0693-1