Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community
Authors: Hemme Christopher L. , Green Stefan J. , Rishishwar Lavanya , Prakash Om , Pettenato Angelica , Chakraborty Romy , Deutschbauer Adam M. , Van Nostrand Joy D. , Wu Liyou , He Zhili , Jordan I. King , Hazen Terry C. , Arkin Adam P. , Kostka Joel E. , Zhou Jizhong 
Published: April 2016

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
c
553
, 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.