Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

Christopher L Hemme; Stefan J Green; Lavanya Rishishwar; Om Prakash; Angelica Pettenato; Romy Chakraborty; Adam M Deutschbauer; Joy D Van Nostrand; Liyou Wu; Zhili He; I King Jordan; Terry C Hazen; Adam P Arkin; Joel E Kostka; Jizhong Zhou

doi:10.1128/mBio.02234-15

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

mBio. 2016 Apr 5;7(2):e02234-15. doi: 10.1128/mBio.02234-15.

Authors

Affiliations

¹ Institute for Environmental Genomics, Department of Microbiology and Plant Sciences, University of Oklahoma, Norman, Oklahoma, USA Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA.
² Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA DNA Services Facility, University of Illinois at Chicago, Chicago, Illinois, USA.
³ School of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
⁴ National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India.
⁵ Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁶ Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
⁷ Institute for Environmental Genomics, Department of Microbiology and Plant Sciences, University of Oklahoma, Norman, Oklahoma, USA.
⁸ School of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia.
⁹ Department of Civil & Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
¹⁰ Department of Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
¹¹ Institute for Environmental Genomics, Department of Microbiology and Plant Sciences, University of Oklahoma, Norman, Oklahoma, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China jzhou@ou.edu.

Abstract

Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

Importance: Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear. Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Gammaproteobacteria / genetics*
Gammaproteobacteria / metabolism
Gene Transfer, Horizontal*
Groundwater / analysis
Groundwater / microbiology*
Metals, Heavy / analysis*
Metals, Heavy / metabolism
Microbiota
Water Pollutants, Chemical / analysis*
Water Pollutants, Chemical / metabolism

Substances

Metals, Heavy
Water Pollutants, Chemical