Changes in Protein Expression Across Laboratory and Field Experiments in Geobacter bemidjiensis

Abstract

Bacterial extracellular metal respiration, as carried out by members of the genus Geobacter, is of interest for applications including microbial fuel cells and bioremediation. Geobacter bemidjiensis is the major species whose growth is stimulated during groundwater amendment with acetate. We have carried out label-free proteomics studies of G. bemidjiensis grown with acetate as the electron donor and either fumarate, ferric citrate, or one of two hydrous ferric oxide mineral types as electron acceptor. The major class of proteins whose expression changes across these conditions is c-type cytochromes, many of which are known to be involved in extracellular metal reduction in other, better-characterized Geobacter species. Some proteins with multiple homologues in G. bemidjiensis (OmcS, OmcB) had different expression patterns than observed for their G. sulfurreducens homologues under similar growth conditions. We also compared the proteome from our study to a prior proteomics study of biomass recovered from an aquifer in Colorado, where the microbial community was dominated by strains closely related to G. bemidjiensis. We detected an increased number of proteins with functions related to motility and chemotaxis in the Colorado field samples compared to the laboratory samples, suggesting the importance of motility for in situ extracellular metal respiration.

Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium

“…A greater number of proteins were observed while D. reducens was either reducing sulfate (with lactate as electron donor) or fermenting pyruvate compared with Fe(III)-reducing conditions. The soluble and insoluble Fe(III)-reducing proteomes, analyzed for the first time in a Gram-positive organism, were distinctive from one another, a result consistent with findings in the Gram-negative metal-reducing organisms Geobacter sulfurreducens and Geobacter bemidjiensis (Ding et al, 2008 ; Merkley et al, 2015 ). Peptides for the sole MHC annotated in the genome (Dred_0700-1) were detected only on the insoluble Fe(III) condition, and an enzyme involved in heme biosynthesis was upregulated >100-fold on Fe(III)-oxide relative to pyruvate.…”

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea

“…There is no known physiological function for the homologs of these cytochromes in cultured organisms, and so the significance of these clades cannot be determined. Proteomic and transcriptomic experiments in Anaeromyxobacter dehalogenans 2CP-C ( 47 ), Geobacter sulfurreducens ( 48 ), Geobacter bemidjiensis ( 49 ), and Desulfuromonas acetoxidans ( 50 ) showed that these cytochromes are not expressed during metal respiration. However, metal respiration donates electrons to the extracellular environment rather than accepting them from external sources.…”

Iron oxidation by a fused cytochrome-porin common to diverse iron-oxidizing bacteria

“…Homologs of cyc2 are also found in Geobacter spp. , specifically G. bemidjiensis, G. uraniireducens , and Geobacter M18, M21, and Rf64, members of a clade that predominates in aquifers (Holmes et al , 2007; Merkley et al , 2015). These organisms reduce Fe(III), though it is thought that this happens via the Omc system.…”

“…These organisms reduce Fe(III), though it is thought that this happens via the Omc system. A study on the G. bemidjiensis proteome showed that the Cyc2 homolog Gbem_3353 was expressed at same levels during Fe(III) and fumarate reduction (Merkley et al , 2015), so function remained unclear, but could involve a more general EET role.…”