Evidence for Horizontal and Vertical Transmission of Mtr-Mediated Extracellular Electron Transfer among the Bacteria

Abstract

Some bacteria and archaea have evolved the means to use extracellular electron donors and acceptors for energy metabolism, a phenomenon broadly known as extracellular electron transfer (EET). One such EET mechanism is the transmembrane electron conduit MtrCAB, which has been shown to transfer electrons derived from metabolic substrates to electron acceptors, like Fe(III) and Mn(IV) oxides, outside the cell. Although most studies of MtrCAB-mediated EET have been conducted in Shewanella oneidensis MR-1, recent investigations in Vibrio and Aeromonas species have revealed that the electron-donating proteins that support MtrCAB in Shewanella are not as representative as previously thought. This begs the question of how widespread the capacity for MtrCAB-mediated EET is, the changes it has accrued in different lineages, and where these lineages persist today. Here, we employed a phylogenetic and comparative genomics approach to identify the MtrCAB system across all domains of life. We found mtrCAB in the genomes of numerous diverse Bacteria from a wide range of environments, and the patterns therein strongly suggest that mtrCAB was distributed through both horizontal and subsequent vertical transmission, and with some cases indicating downstream modular diversification of both its core and accessory components. Our data point to an emerging evolutionary story about metal-oxidizing and -reducing metabolism, demonstrates that this capacity for EET has broad relevance to a diversity of taxa and the biogeochemical cycles they drive, and lays the foundation for further studies to shed light on how this mechanism may have coevolved with Earth's redox landscape. IMPORTANCE While many metabolisms make use of soluble, cell-permeable substrates like oxygen or hydrogen, there are other substrates, like iron or manganese, that cannot be brought into the cell. Some bacteria and archaea have evolved the means to directly "plug in" to such environmental electron reservoirs in a process known as extracellular electron transfer (EET), making them powerful agents of biogeochemical change and promising vehicles for bioremediation and alternative energy. Yet the diversity, distribution, and evolution of EET mechanisms are poorly constrained. Here, we present findings showing that the genes encoding one such EET system (mtrCAB) are present in a broad diversity of bacteria found in a wide range of environments, emphasizing the ubiquity and potential impact of EET in our biosphere. Our results suggest that these genes have been disseminated largely through horizontal transfer, and the changes they have accrued in these lineages potentially reflect adaptations to changing environments.

Keywords: Shewanella; electron transport; evolution; gene transfer; iron oxidizers; iron reduction; lithoautotrophic metabolism; phylogenetic analysis.

FIG 1

Geographic locales of microorganisms encoding elements of the MtrCAB system. The geographic location of isolation was unavailable for some sequences, and geographical sampling biases are apparent. Large red circles represent the South Pacific, North Atlantic, and Indian Ocean (Eastern Africa Coastal Province) regions described by Tully et al. (146). For more details, see Table S1. The map was created using the Positron base map available in QGIS (https://cartodb.com/basemaps/) (map tiles by CartoDB, under CC BY 3.0. Data by OpenStreetMap, under ODbL).

FIG 2

Phylogenomic relationships among MtrCAB coding sequences. This maximum likelihood tree contains 177 concatenated MtrA(D), MtrB(E), and MtrC(F) amino acid sequences encoded in the genomes of 148 species. Each node represents a single concatenated MtrCAB(MtrDEF) sequence. Color codes were assigned by taxonomic order. Bootstrap values are indicated along branch points. Bold numbers 1 to 7 indicate MtrCAB groups referenced throughout this paper. Groups 1a and 1b represent MtrCAB and MtrDEF, respectively, in the Shewanella spp. and Ferrimonadaceae. Sequences derived from species with previous evidence of MtrCAB/DEF-dependent EET are noted in the “Investigations of Mtr” section in Table S1. Genetic, in vivo evidence is denoted with a bacterium symbol, and biochemical, in vitro evidence is denoted with a test tube symbol.

FIG 3

Genomic comparisons of mtrCAB loci in MtrCAB-encoding organisms and syntenic regions in MtrCAB-lacking relatives highlights the mobility of mtrCAB.

FIG 4

Genomic comparisons of mtrCAB loci in MtrCAB-encoding organisms and syntenic regions in MtrCAB-lacking relatives reveal putative mtrCAB passenger genes and provide further evidence for mtrCAB’s mobility and distribution through HGT.

FIG 5

Hypothetical models of MtrCAB and accessory components encoded in mtrCAB gene clusters show group-specific diversifications. Protein localization along the cell envelope was predicted with PSORTb (78). Proteins outlined with a solid line are found in every species in the MtrCAB group, while dotted lines indicate that the protein is encoded in at least one but not all members of the MtrCAB group. White circles with a question mark indicate that a putative protein in that cellular location was not encoded in the mtrCAB cluster in all or most members of that MtrCAB group. Bar plots show the percentage of members in a given group that encode each MtrCAB component. CymA*, FccA*, and CctA* are not encoded adjacent to the mtrCAB cluster in Shewanella species nor most Ferrimonadaceae species but are included here due to their well-established role in MtrCAB-mediated EET in members of these species. We did not search the genome beyond the identified mtrCAB loci for cymA or the other depicted accessory cytochromes in other organisms.

FIG 6

Tracking mtrC homologs reveals finer-scale gene flow between MtrCAB-encoding species. Arrows filled with color represent mtrC sequences. Colors correspond to the numbered circles (I to VII) in Fig. S1. Arrows with bold outlines indicate the core mtrC whose translated coding sequence was incorporated into the concatenated MtrCAB tree (Fig. 2). Unlabeled white arrows in panel C represent a conserved HhH encoded in some mtrCAB clusters.

FIG 7

A hypothetical model representing two possible modes of mtrCAB’s dissemination to the species identified in our study.