Abstract
Different lifestyles, ranging from a saprophyte to a pathogen, have been reported in bacteria of one species. Here, we performed genome-wide survey of the ecological adaptation in four Burkholderia seminalis strains, distinguished by their origin as part of the saprophytic microbial community of soil or water but also including human and plant pathogens. The results indicated that each strain is separated from the others by increased fitness in medium simulating its original niche corresponding to the difference between strains in metabolic capacities. Furthermore, strain-specific metabolism and niche survival was generally linked with genomic variants and niche-dependent differential expression of the corresponding genes. In particular, the importance of iron, trehalose and d-arabitol utilization was highlighted by the involvement of DNA-methylation and horizontal gene transfer in niche-adapted regulation of the corresponding operons based on the integrated analysis of our multi-omics data. Overall, our results provided insights of niche-specific adaptation in bacteria.
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Acknowledgements
This work was supported by the Zhejiang Provincial Natural Science Foundation of China (R13C140001), the National Natural Science Foundation of China (31571971, 31371904 and 31200003), the Zhejiang Provincial Project (2014C32010), the Fundamental Research Funds for the Central Universities, the Agricultural Ministry of China (nyhyzx 201303015, 201003029 and 201003066) and the Key Subject Construction Program of Zhejiang for Modern Agricultural Biotechnology and Crop Disease Control (2010DS700124-KF1101, -KF1203, -KF1309 and -KF1410). We acknowledge the Hangzhou Woosen Biotechnology Co., Ltd, Zhejiang, China for the genome and transcriptome sequencing.
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Zhu, B., Ibrahim, M., Cui, Z. et al. Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria. ISME J 10, 2072–2075 (2016). https://doi.org/10.1038/ismej.2015.251
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DOI: https://doi.org/10.1038/ismej.2015.251
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