title: Multi-omics analysis of niche specificity provides new insights into ecological adaptation in bacteria.
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.
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: Bo
authors: B
authors: Zhu
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: Muhammad
authors: M
authors: Ibrahim
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: Zhouqi
authors: Z
authors: Cui
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: Guanlin
authors: G
authors: Xie
authors: Hangzhou Guhe Info Co., Ltd, Hangzhou, China.
authors: Gulei
authors: G
authors: Jin
authors: Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany.
authors: Michael
authors: M
authors: Kube
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors: Bin
authors: B
authors: Li
authors: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.|State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
authors: Xueping
authors: X
authors: Zhou
mesh_terms: D000222:Adaptation, Physiological; D019117:Burkholderia / Q000235:genetics / Q000502:physiology*; D004463:Ecology; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D006801:Humans; D010944:Plants / Q000382:microbiology; D012987:Soil; D012988:Soil Microbiology; D013045:Species Specificity
chemical_list: D012987:Soil