Horizontal gene transfer in an acid mine drainage microbial community.

Jiangtao Guo,Jinxian Yao,Fumeng Wang,Qi Wang,Huaiqiu Zhu,Xiaoqi Wang

doi:10.1186/s12864-015-1720-0

Abstract

BackgroundHorizontal 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.ResultsUsing 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1720-0) contains supplementary material, which is available to authorized users.

Highlights

Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes
HGT identification and overview of HGTs among acid mine drainage (AMD) microbial genomes We first reported our identification of the genes that were horizontally transferred among the genomes including eight organisms in AMD and nine previously isolated organisms
Using the method of strict reciprocal best basic local alignment search tool (BLAST) hit [20, 21] based on the accurate gene reannotation by the current computational tools [22] or annotation from the National Center for Biotechnology Information (NCBI) [23], we obtained 251 orthologous gene families that were present in more than seven genomes in which at least one genome was from AMD, while 185 of them showed phylogenetic tree incongruities using an approximately unbiased test (AU test) [24]

Summary

Introduction

Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. 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. Horizontal gene transfer (HGT), known as lateral gene transfer, is defined as the movement of genetic material between phylogenetically unrelated organisms by mechanisms other than parent-to-progeny inheritance. This horizontal flow of genetic material utilizes three routes: conjugation, transduction, or transformation. Many microorganisms live as communities and interact with each other They exhibit complex social relationships and co-evolve to continuously adapt to the specific environment. As an important driving force of evolution, HGT is thought to significantly influence the dynamics of microbial communities [10, 11]

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