Distribution, diversity and ecology of aerobic CO-oxidizing bacteria

King, Gary M.; Weber, Carolyn F.

doi:10.1038/nrmicro1595

Cited by 377 publications

(431 citation statements)

References 125 publications

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“…5). The form II protein appears to function as a CODH but may have a reduced capacity for CO oxidation and use an alternate substrate preferentially (15). CO utilization by S. aggregata conforms to a simple Michaelis-Menten kinetic model for low to moderate concentrations, but relatively high concentrations result in inhibition ( Fig.…”

Section: Discussionmentioning

confidence: 99%

Physiological, Ecological, and Phylogenetic Characterization of Stappia , a Marine CO-Oxidizing Bacterial Genus

Weber

King

2007

Appl Environ Microbiol

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Bacteria play a major role in marine CO cycling, yet very little is known about the microbes involved. Thirteen CO-oxidizing Stappia isolates obtained from existing cultures, macroalgae, or surf samples representing geographically and ecologically diverse habitats were characterized using biochemical, physiological, and phylogenetic approaches. All isolates were aerobic chemoorganotrophs that oxidized CO at elevated (1,000 ppm) and ambient-to-subambient concentrations (<0.3 ppm). All contained the form I (OMP) coxL gene for aerobic CO dehydrogenase and also the form II (BMS) putative coxL gene. In addition, some strains possessed cbbL, the large subunit gene for ribulose-1,5-bisphosphate carboxylase/oxygenase, suggesting the possibility of lithotrophic or mixotrophic metabolism. All isolates used a wide range of sugars, organic acids, amino acids, and aromatics for growth and grew at salinities from 5 to 45 ppt. All but one isolate denitrified or respired nitrate. Phylogenetic analyses based on 16S rRNA gene sequences indicated that several isolates could not be distinguished from Stappia aggregata and contributed to a widely distributed species complex. Four isolates (of strains GA15, HI, MIO, and M4) were phylogenetically distinct from validly described Stappia species and closely related genera (e.g., Ahrensia, Pannonibacter, Pseudovibrio, and Roseibium). Substrate utilization profiles, enzymatic activity, and membrane lipid composition further distinguished these isolates and supported their designations as new Stappia species. The observed metabolic versatility of Stappia likely accounts for its cosmopolitan distribution and its ability to contribute to CO cycling as well as other important biogeochemical cycles.

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Section: Discussionmentioning

confidence: 99%

Physiological, Ecological, and Phylogenetic Characterization of Stappia , a Marine CO-Oxidizing Bacterial Genus

Weber

King

2007

Appl Environ Microbiol

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“…This is reflected in differences in the classes of transport systems found in the two data sets, with COG 1462 (permease component of an ABC-transporter), COG 3090 (TRAP-type C4-dicarboxylate transport system, small permease component), COG 0025 (NhaP-type Na þ /H þ and K þ / H þ antiporters) and COG 2223 (Nitrate/nitrite transporter) being overrepresented and COG0659 (Sulphate permease and related transporters, major facilitator superfamily) being underrepresented in the sponge's bacterial community (Figure 3). Fourth, the large (COG1529) and middle (COG1319) subunits of the aerobic-type carbon monoxide dehydrogenase were overrepresented by a factor of greater than three in the sponge metagenome ( Figure 3; the small subunit (COG2080) is more abundant by a factor of 2.2, t-test, P ¼ 0.047), indicating that a portion of the sponge bacterial community can generate reductive energy from the oxidation of CO. Further analysis revealed that both form I and putative form II carbon monoxide dehydrogenase are present (King and Weber, 2007), with no apparent preference in the sponge or plankton data set (Supplementary Figure S4). Lithoheterotrophy based on CO has only been recently recognized in marine bacterioplankton (Moran and Miller, 2007), and in this study, we present evidence for a presence of this process in sponge bacteria.…”

Section: Mobile Genetic Elements and Genetic Transfermentioning

confidence: 99%

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

et al. 2010

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Sponges form close relationships with bacteria, and a remarkable phylogenetic diversity of yet-uncultured bacteria has been identified from sponges using molecular methods. In this study, we use a comparative metagenomic analysis of the bacterial community in the model sponge Cymbastela concentrica and in the surrounding seawater to identify previously unrecognized genomic signatures and functions for sponge bacteria. We observed a surprisingly large number of transposable insertion elements, a feature also observed in other symbiotic bacteria, as well as a set of predicted mechanisms that may defend the sponge community against the introduction of foreign DNA and hence contribute to its genetic resilience. Moreover, several shared metabolic interactions between bacteria and host include vitamin production, nutrient transport and utilization, and redox sensing and response. Finally, an abundance of protein-protein interactions mediated through ankyrin and tetratricopeptide repeat proteins could represent a mechanism for the sponge to discriminate between food and resident bacteria. These data provide new insight into the evolution of symbiotic diversity, microbial metabolism and host-microbe interactions in sponges.

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“…Genes coding for chemolithotrophic pathways known to be associated with extreme environments (Inskeep et al, 2010;Kozubal et al, 2011), including the oxidation of ferrous iron, hydrogen, arsenic, sulfur, ammonium or methane, were not found in the NAG1 assemblies. However, the NAG1 populations have two separate loci that encode aerobic carbon monoxide (CO) dehydrogenases and associated maturases (Dobbek et al, 2002;King and Weber, 2007). One locus encodes a 'Form I' CO dehydrogenase along with coxFSM and the other contains three coxL 'Form II' CO dehydrogenase sequences along with coxDEFG (Supplementary Figures S5, S6).…”

Section: Functional Analysis Of Nag1 Genome Sequencementioning

confidence: 99%

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

et al. 2012

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Geothermal systems in Yellowstone National Park (YNP) provide an outstanding opportunity to understand the origin and evolution of metabolic processes necessary for life in extreme environments including low pH, high temperature, low oxygen and elevated concentrations of reduced iron. Previous phylogenetic studies of acidic ferric iron mats from YNP have revealed considerable diversity of uncultivated and undescribed archaea. The goal of this study was to obtain replicate de novo genome assemblies for a dominant archaeal population inhabiting acidic ironoxide mats in YNP. Detailed analysis of conserved ribosomal and informational processing genes indicates that the replicate assemblies represent a new candidate phylum within the domain Archaea referred to here as 'Geoarchaeota' or 'novel archaeal group 1 (NAG1)'. The NAG1 organisms contain pathways necessary for the catabolism of peptides and complex carbohydrates as well as a bacterial-like Form I carbon monoxide dehydrogenase complex likely used for energy conservation. Moreover, this novel population contains genes involved in the metabolism of oxygen including a Type A heme copper oxidase, a bd-type terminal oxidase and a putative oxygen-sensing protoglobin. NAG1 has a variety of unique bacterial-like cofactor biosynthesis and transport genes and a Type3-like CRISPR system. Discovery of NAG1 is critical to our understanding of microbial community structure and function in extant thermophilic iron-oxide mats of YNP, and will provide insight regarding the evolution of Archaea in early Earth environments that may have important analogs active in YNP today.

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Distribution, diversity and ecology of aerobic CO-oxidizing bacteria

Cited by 377 publications

References 125 publications

Physiological, Ecological, and Phylogenetic Characterization of Stappia , a Marine CO-Oxidizing Bacterial Genus

Physiological, Ecological, and Phylogenetic Characterization of Stappia , a Marine CO-Oxidizing Bacterial Genus

Functional genomic signatures of sponge bacteria reveal unique and shared features of symbiosis

Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park

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