Molecular Evidence for the Evolution of Metal Homeostasis Genes by Lateral Gene Transfer in Bacteria from the Deep Terrestrial Subsurface

Abstract

Lateral gene transfer (LGT) plays a vital role in increasing the genetic diversity of microorganisms and promoting the spread of fitness-enhancing phenotypes throughout microbial communities. To date, LGT has been investigated in surface soils, natural waters, and biofilm communities but not in the deep terrestrial subsurface. Here we used a combination of molecular analyses to investigate the role of LGT in the evolution of metal homeostasis in lead-resistant subsurface bacteria. A nested PCR approach was employed to obtain DNA sequences encoding P IB -type ATPases, which are proteins that transport toxic or essential soft metals such as Zn(II), Cd(II), and Pb(II) through the cell wall. Phylogenetic incongruencies between a 16S rRNA gene tree and a tree based on 48 P IB -type ATPase amplicons and sequences available for complete bacterial genomes revealed an ancient transfer from a member of the ␤ subclass of the Proteobacteria (␤-proteobacterium) that may have predated the diversification of the genus Pseudomonas. Four additional phylogenetic incongruencies indicate that LGT has occurred among groups of ␤-and ␥-proteobacteria. Two of these transfers appeared to be recent, as indicated by an unusual G؉C content of the P IB -type ATPase amplicons. This finding provides evidence that LGT plays a distinct role in the evolution of metal homeostasis in deep subsurface bacteria, and it shows that molecular evolutionary approaches may be used for investigation of this process in microbial communities in specific environments.The role of lateral gene transfer (LGT) in the evolution of microorganisms becomes more and more apparent with every new microbial genome that is sequenced and annotated (54, 58), which has led many workers to question our basic concepts of microbial speciation (18, 23). The prevalence of laterally transferred genes clearly suggests that this mode of evolution is advantageous to microbial life, possibly by providing the means for genetic innovation in the absence of frequent sexual recombination (37). This variation is likely to increase metabolic diversity, and consequently competence, in environments subject to frequent change (13, 61). The possibility that LGT is an important force in shaping the structure and function of microbial communities in their natural habitats is suggested by (i) the fact that abundant and diverse plasmids (12, 73), viruses (8, 89), insertion sequences (70), transposons (59, 78), integrons (49), and other elements that contribute to genomic plasticity are commonly isolated from environmental samples and strains; (ii) the fact that natural competence is common among microbes (11) and occurs in soils (17, 50) and natural water (88); (iii) the fact that LGT has been demonstrated in model ecosystems (i.e., microcosms) (52, 62, 75, 80) and in intact environmental samples (19); and (iv) the fact that seeding soils with bacteria carrying conjugal catabolic plasmids results in transfer of the plasmids to indigenous soil microbes and the stimulation of plasmid-specified activit...

MrdH, a Novel Metal Resistance Determinant of Pseudomonas putida KT2440, Is Flanked by Metal-Inducible Mobile Genetic Elements

“…The reported DUF156 proteins include NreA from Legionella pneumophila (NreABC), NcrB from Serratia marcescens (NcrABC), NirB from Klebsiella oxytoca (NirABCD), and NcrB from Leptospirillum ferriphilum (NcrABCY) (15,32,33,39,54 The phenomenon of HGT driven by mobile genetic elements, such as plasmids, insertion sequences, integrons, transposons, and phages, has been shown to provide microbes with a wide variety of adaptive traits such as antibiotic resistance, heavy metal resistance, and xenobiotic compound degradation for microbial survival and proliferation (38). Recently, detectable HGT of heavy metal translocating P IB -type ATPases (zntA/cadA/copA-like genes) has been reported in bacterial isolates from pristine, as well as heavy metal-contaminated subsurface environments (8,9). In fact, most of the novel genes in gammaproteobacteria were found to be distributed in GIs, indicating their acquisition through HGT from distant sources (19).…”

“…Recent studies provided support for the prominent role of horizontal gene transfer (HGT) in the evolution of metal homeostasis in proteobacteria and also identified putative genomic islands (GIs) containing metal resistance genes in environmental bacteria like C. metallidurans and Pseudomonas putida KT2440 (8,9,34,56). GIs are defined as horizontally acquired genetic elements that share the same structural features of pathogenicity islands (PAIs) and contribute to a microorganism's fitness, metabolic versatility, and adaptability.…”

Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

“…For example, extensive gene sharing has been observed throughout the commensal human microbiome, including sharing of genes that enable nutrient acquisition from novel food sources (Hehemann et al, 2010;Smillie et al, 2011), and pathogenicity islands and antibiotic resistance genes in pathogenic microbes Hiramatsu et al, 2001;Forsberg et al, 2012). There is evidence of extensive HGT in other natural habitats, such as soil (Coombs and Barkay, 2004;Heuer and Smalla, 2012) and aquatic environments (McDaniel et al, 2010;Frischer et al, 1994). Although these studies offer valuable insights into the frequency and potential impact of genes that can be transferred in microbial communities, the complexity of these systems makes difficult any further examination of the effects of these HGT events on their evolution and ecology.…”

Expression of copA and cusA in Shewanella during copper stress

“…Therefore, transport of copper ions across the cell membrane and subsequent incorporation into metallo-proteins is tightly controlled (Rae et al, 1999;Nies, 1999). Two types of proteins involved in bacterial heavy metal efflux (HME) are CPxtype ATPases and HME RND proteins (from the Resistance, Nodulation and cell Division protein family) (Paulsen et al, 1996;Coombs & Barkay, 2004, 2005Saier, 2003). CopA in Escherichia coli was among the first heavymetal-transporting ATPases to be fully characterized; it showed transport of Cu(I) out of the cytoplasm at the expense of ATP hydrolysis (Rensing et al, 2000).…”