title: Horizontal gene transfer in an acid mine drainage microbial community.
abstract: BACKGROUND
  Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance.
  
  
  RESULTS
  Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT.
  
  
  CONCLUSIONS
  Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.
authors.affiliation: State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. jtguo@ctb.pku.edu.cn.|Center for Quantitative Biology, Peking University, Beijing, 100871, China. jtguo@ctb.pku.edu.cn.
authors.forename: Jiangtao
authors.initials: J
authors.lastname: Guo
authors.affiliation: State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. qiwangbme@gmail.com.|Center for Quantitative Biology, Peking University, Beijing, 100871, China. qiwangbme@gmail.com.
authors.forename: Qi
authors.initials: Q
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. xiaoqiwang@pku.edu.cn.|Center for Quantitative Biology, Peking University, Beijing, 100871, China. xiaoqiwang@pku.edu.cn.
authors.forename: Xiaoqi
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. wang_fumeng@126.com.|Center for Quantitative Biology, Peking University, Beijing, 100871, China. wang_fumeng@126.com.
authors.forename: Fumeng
authors.initials: F
authors.lastname: Wang
authors.affiliation: School of Life Sciences, Peking University, Beijing, 100871, China. jxyao@pku.edu.cn.
authors.forename: Jinxian
authors.initials: J
authors.lastname: Yao
authors.affiliation: State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China. hqzhu@pku.edu.cn.|Center for Quantitative Biology, Peking University, Beijing, 100871, China. hqzhu@pku.edu.cn.
authors.forename: Huaiqiu
authors.initials: H
authors.lastname: Zhu
mesh_terms: D000143:Acids / Q000737:chemistry*; D001419:Bacteria / Q000235:genetics*; D004323:Drainage, Sanitary; D004777:Environment; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics; D054892:Metagenome / Q000235:genetics*; D056186:Metagenomics / Q000379:methods; D008906:Mining / Q000379:methods; D010802:Phylogeny
chemical_list: D000143:Acids