Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium
            <i>Acidovorax ebreus</i>
            Strain TPSY

Byrne-Bailey, Kathryne G.; Weber, Karrie A.; Bose, Saumyaditya; Knox, Traci R.; Spanbauer, Trisha L.; Chertkov, Olga; Coates, John D.

doi:10.1128/jb.01449-09

Cited by 84 publications

(54 citation statements)

References 21 publications

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“…In this system it was postulated that anaerobic conditions are established inside the cathodic biofilm resulting in the enrichment of denitrifying members, including the Comamonadaceae, which use electrons from the cathode to reduce nitrite, a product of aerobic ammonium oxidation (He et al, 2009). Consistent with their enrichment in cathodic denitrifying systems, members of the Comamonadaceae have been shown to denitrify chemolithotrophically, by oxidizing iron minerals coupled to the reduction of nitrate (Straub et al, 2004;Byrne-Bailey et al, 2010).…”

Section: Identification Of Bacteria Most Active In Denitrifying Biofilmsmentioning

confidence: 82%

Bacterial community structure corresponds to performance during cathodic nitrate reduction

et al. 2010

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Microbial fuel cells (MFCs) have applications other than electricity production, including the capacity to power desirable reactions in the cathode chamber. However, current knowledge of the microbial ecology and physiology of biocathodes is minimal, and as a result more research dedicated to understanding the microbial communities active in cathode biofilms is required. Here we characterize the microbiology of denitrifying bacterial communities stimulated by reducing equivalents generated from the anodic oxidation of acetate. We analyzed biofilms isolated from two types of cathodic denitrification systems: (1) a loop format where the effluent from the carbon oxidation step in the anode is subjected to a nitrifying reactor which is fed to the cathode chamber and (2) an alternative non-loop format where anodic and cathodic feed streams are separated. The results of our study indicate the superior performance of the loop reactor in terms of enhanced current production and nitrate removal rates. We hypothesized that phylogenetic or structural features of the microbial communities could explain the increased performance of the loop reactor. We used PhyloChip with 16S rRNA (cDNA) and fluorescent in situ hybridization to characterize the active bacterial communities. Our study results reveal a greater richness, as well as an increased phylogenetic diversity, active in denitrifying biofilms than was previously identified in cathodic systems. Specifically, we identified Proteobacteria, Firmicutes and Chloroflexi members that were dominant in denitrifying cathodes. In addition, our study results indicate that it is the structural component, in terms of bacterial richness and evenness, rather than the phylogenetic affiliation of dominant bacteria, that best corresponds to cathode performance.

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Section: Identification Of Bacteria Most Active In Denitrifying Biofilmsmentioning

confidence: 82%

Bacterial community structure corresponds to performance during cathodic nitrate reduction

et al. 2010

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“…Anaerobic cultures of A. ebreus strain TPSY, formerly Diaphorobacter sp. strain TPSY (11), and Azospira suillum strain PS were grown organotrophically in anoxic bicarbonate-buffered basal medium (BBM) (27), pH 6.8, at 37°C with 10 mM sodium nitrate and various concentrations of sodium acetate and harvested in late log phase. BBM contained (per liter) 0.25 g NH 4 Cl, 0.6 g NaH 2 PO 4 , 0.1 g KCl, and 2.52 g NaHCO 3 with the addition of vitamins and minerals according to Bruce et al (27) and the appropriate concentration of electron donors and acceptors.…”

Section: Methodsmentioning

confidence: 99%

“…Like several other species in the Acidovorax genus (12)(13)(14), A. ebreus was isolated on the basis of its capacity for NDFO (11). Previous studies have reported a growth advantage from NDFO by Acidovorax species in both batch and continuous-flow cultures (12,14), in addition to the accumulation of nitrite (NO 2 Ϫ ) and periplasmic mineral encrustations (26).…”

mentioning

confidence: 99%

“…Bacterial species that couple the oxidation of Fe(II) to nitrate reduction have been isolated from a wide range of habitats and are phylogenetically diverse, indicating their environmental prevalence and importance (5,9,10). Recently, species of the genus Acidovorax have dominated enrichment cultures and been isolated as proficient nitrate-dependent Fe(II) oxidizers (11)(12)(13)(14); however, even Escherichia coli has been demonstrated to be capable of Fe(II) oxidation coupled to nitrate reduction (15). Although NDFO is based on thermodynamically favorable redox reactions (16,17), only a few studies have suggested growth enhancement from this metabolism (12,18).…”

mentioning

confidence: 99%

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Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

Carlson

Clark²,

Blazewicz³

et al. 2013

Journal of Bacteriology

148

156

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Phylogenetically diverse species of bacteria can catalyze the oxidation of ferrous iron [Fe(II)] coupled to nitrate (NO 3؊ ) reduction, often referred to as nitrate-dependent iron oxidation (NDFO). Very little is known about the biochemistry of NDFO, and though growth benefits have been observed, mineral encrustations and nitrite accumulation likely limit growth. Acidovorax ebreus, like other species in the Acidovorax genus, is proficient at catalyzing NDFO. Our results suggest that the induction of specific Fe(II) oxidoreductase proteins is not required for NDFO. No upregulated periplasmic or outer membrane redox-active proteins, like those involved in Fe(II) oxidation by acidophilic iron oxidizers or anaerobic photoferrotrophs, were observed in proteomic experiments. We demonstrate that while "abiotic" extracellular reactions between Fe(II) and biogenic NO 2 ؊ /NO can be involved in NDFO, intracellular reactions between Fe(II) and periplasmic components are essential to initiate extensive NDFO. We present evidence that an organic cosubstrate inhibits NDFO, likely by keeping periplasmic enzymes in their reduced state, stimulating metal efflux pumping, or both, and that growth during NDFO relies on the capacity of a nitrate-reducing bacterium to overcome the toxicity of Fe(II) and reactive nitrogen species. On the basis of our data and evidence in the literature, we postulate that all respiratory nitrate-reducing bacteria are innately capable of catalyzing NDFO. Our findings have implications for a mechanistic understanding of NDFO, the biogeochemical controls on anaerobic Fe(II) oxidation, and the production of NO 2 ؊ , NO, and N 2 O in the environment.

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“…(ACD23) (Coates et al, 2001;Byrne-Bailey et al, 2010). Organisms closely related to those studied here have been demonstrated to have a role in nitrate, as well as selenium reduction at this and other subsurface sites (Byrne-Bailey et al, 2010).…”

Section: Metabolic Interdependencies In An Aquifer Microbial Communitmentioning

confidence: 99%

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

et al. 2014

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Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via acetate amendment of the groundwater occurring over 2 successive years. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include organisms from a new phylum, Melainabacteria, most closely related to Cyanobacteria, phylogenetically novel members of the Chloroflexi and Bacteroidales, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen metabolism in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate and iron reduction. Thus, fermentation carried out by previously unknown members of sediment microbial communities may be an important driver of nitrogen, hydrogen, sulfur, carbon and iron cycling.

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Completed Genome Sequence of the Anaerobic Iron-Oxidizing Bacterium Acidovorax ebreus Strain TPSY

Cited by 84 publications

References 21 publications

Bacterial community structure corresponds to performance during cathodic nitrate reduction

Bacterial community structure corresponds to performance during cathodic nitrate reduction

Fe(II) Oxidation Is an Innate Capability of Nitrate-Reducing Bacteria That Involves Abiotic and Biotic Reactions

Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer

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