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Journal articles on the topic 'Carboxydotrophs'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Omae, Kimiho, Tatsuki Oguro, Masao Inoue, Yuto Fukuyama, Takashi Yoshida, and Yoshihiko Sako. "Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers." Extremophiles 25, no. 1 (January 2021): 61–76. http://dx.doi.org/10.1007/s00792-020-01211-y.

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AbstractThe microbial H2-producing (hydrogenogenic) carbon monoxide (CO)-oxidizing activity by the membrane-associated CO dehydrogenase (CODH)/energy-converting hydrogenase (ECH) complex is an important metabolic process in the microbial community. However, the studies on hydrogenogenic carboxydotrophs had to rely on inherently cultivation and isolation methods due to their rare abundance, which was a bottleneck in ecological study. Here, we provided gene-targeted sequencing method for the diversity estimation of thermophilic hydrogenogenic carboxydotrophs. We designed six new degenerate primer pairs which effectively amplified the coding regions of CODH genes forming gene clusters with ECH genes (CODHech genes) in Firmicutes which includes major thermophilic hydrogenogenic carboxydotrophs in terrestrial thermal habitats. Amplicon sequencing by these primers using DNAs from terrestrial hydrothermal sediments and CO-gas-incubated samples specifically detected multiple CODH genes which were identical or phylogenetically related to the CODHech genes in Firmictes. Furthermore, we found that phylogenetically distinct CODHech genes were enriched in CO-gas-incubated samples, suggesting that our primers detected uncultured hydrogenogenic carboxydotrophs as well. The new CODH-targeted primers provided us with a fine-grained (~ 97.9% in nucleotide sequence identity) diversity analysis of thermophilic hydrogenogenic carboxydotrophs by amplicon sequencing and will bolster the ecological study of these microorganisms.

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2

Hardy, Kathleen R., and Gary M. King. "Enrichment of High-Affinity CO Oxidizers in Maine Forest Soil." Applied and Environmental Microbiology 67, no. 8 (August 1, 2001): 3671–76. http://dx.doi.org/10.1128/aem.67.8.3671-3676.2001.

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ABSTRACT Carboxydotrophic activity in forest soils was enriched by incubation in a flowthrough system with elevated concentrations of headspace CO (40 to 400 ppm). CO uptake increased substantially over time, while the apparent Km (app Km ) for uptake remained similar to that of unenriched soils (<10 to 20 ppm). Carboxydotrophic activity was transferred to and further enriched in sterile sand and forest soil. The app Km s for secondary and tertiary enrichments remained similar to values for unenriched soils. CO uptake by enriched soil and freshly collected forest soil was inhibited at headspace CO concentrations greater than about 1%. A novel isolate, COX1, obtained from the enrichments was inhibited similarly. However, in contrast to extant carboxydotrophs, COX1 consumed CO with an app Km of about 15 ppm, a value comparable to that of fresh soils. Phylogenetic analysis based on approximately 1,200 bp of its 16S rRNA gene sequence suggested that the isolate is an α-proteobacterium most closely related to the genera Pseudaminobacter, Aminobacter, andChelatobacter (98.1 to 98.3% sequence identity).

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3

Robb, Frank T., and Stephen M. Techtmann. "Life on the fringe: microbial adaptation to growth on carbon monoxide." F1000Research 7 (December 27, 2018): 1981. http://dx.doi.org/10.12688/f1000research.16059.1.

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Microbial adaptation to extreme conditions takes many forms, including specialized metabolism which may be crucial to survival in adverse conditions. Here, we analyze the diversity and environmental importance of systems allowing microbial carbon monoxide (CO) metabolism. CO is a toxic gas that can poison most organisms because of its tight binding to metalloproteins. Microbial CO uptake was first noted by Kluyver and Schnellen in 1947, and since then many microbes using CO via oxidation have emerged. Many strains use molecular oxygen as the electron acceptor for aerobic oxidation of CO using Mo-containing CO oxidoreductase enzymes named CO dehydrogenase. Anaerobic carboxydotrophs oxidize CO using CooS enzymes that contain Ni/Fe catalytic centers and are unrelated to CO dehydrogenase. Though rare on Earth in free form, CO is an important intermediate compound in anaerobic carbon cycling, as it can be coupled to acetogenesis, methanogenesis, hydrogenogenesis, and metal reduction. Many microbial species—both bacteria and archaea—have been shown to use CO to conserve energy or fix cell carbon or both. Microbial CO formation is also very common. Carboxydotrophs thus glean energy and fix carbon from a “metabolic leftover” that is not consumed by, and is toxic to, most microorganisms. Surprisingly, many species are able to thrive under culture headspaces sometimes exceeding 1 atmosphere of CO. It appears that carboxydotrophs are adapted to provide a metabolic “currency exchange” system in microbial communities in which CO arising either abiotically or biogenically is converted to CO2 and H2 that feed major metabolic pathways for energy conservation or carbon fixation. Solventogenic CO metabolism has been exploited to construct very large gas fermentation plants converting CO-rich industrial flue emissions into biofuels and chemical feedstocks, creating renewable energy while mitigating global warming. The use of thermostable CO dehydrogenase enzymes to construct sensitive CO gas sensors is also in progress.

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4

Nguyen, Sean, Fatime Ala, Cisley Cardwell, Darlene Cai, Katelyn M. McKindles, Aaron Lotvola, Steven Hodges, Yiwei Deng, and Sonia M. Tiquia-Arashiro. "Isolation and screening of carboxydotrophs isolated from composts and their potential for butanol synthesis." Environmental Technology 34, no. 13-14 (July 2013): 1995–2007. http://dx.doi.org/10.1080/09593330.2013.795987.

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5

Omae, Kimiho, Yuto Fukuyama, Hisato Yasuda, Kenta Mise, Takashi Yoshida, and Yoshihiko Sako. "Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan." Archives of Microbiology 201, no. 7 (April 27, 2019): 969–82. http://dx.doi.org/10.1007/s00203-019-01661-9.

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6

King, Gary M., and M. Hungria. "Soil-Atmosphere CO Exchanges and Microbial Biogeochemistry of CO Transformations in a Brazilian Agricultural Ecosystem." Applied and Environmental Microbiology 68, no. 9 (September 2002): 4480–85. http://dx.doi.org/10.1128/aem.68.9.4480-4485.2002.

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ABSTRACT Although anthropogenic land use has major impacts on the exchange of soil and atmosphere gas in general, relatively little is known about its impacts on carbon monoxide. We compared soil-atmosphere CO exchanges as a function of land use, crop type, and tillage treatment on an experimental farm in Parãna, Brazil, that is representative of regionally important agricultural ecosystems. Our results showed that cultivated soils consumed CO at rates between 3 and 6 mg of CO m−2 day−1, with no statistically significant effect of tillage method or crop. However, CO exchange for a pasture soil was near zero, and an unmanaged woodlot emitted CO at a rate of 9 mg of CO m−2 day−1. Neither nitrite, aluminum sulfate, nor methyl fluoride additions affected CO consumption by tilled or untilled soils from soybean plots, indicating that CO oxidation did not depend on ammonia oxidizers and that CO oxidation patterns differed in part from patterns reported for forest soils. The apparent Km for CO uptake, 5 to 11 ppm, was similar to values reported for temperate forest soils; V max values, approximately 1 μg of CO g (dry weight)−1 h−1, were comparable for woodlot and cultivated soils in spite of the fact that the latter consumed CO under ambient conditions. Short-term (24-h) exposure to elevated levels of CO (10% CO) partially inhibited uptake at lower concentrations (i.e., 100 ppm), suggesting that the sensitivity to CO of microbial populations that are active in situ differs from that of known carboxydotrophs. Soil-free soybean and corn roots consumed CO when they were incubated with 100-ppm concentrations and produced CO when they were incubated with ambient concentrations. These results document for the first time a role for cultivated plant roots in the dynamics of CO in an agricultural ecosystem.

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7

Sorokin, Dimitry Yu, Tatjana P. Tourova, Olga L. Kovaleva, J. Gijs Kuenen, and Gerard Muyzer. "Aerobic carboxydotrophy under extremely haloalkaline conditions in Alkalispirillum/Alkalilimnicola strains isolated from soda lakes." Microbiology 156, no. 3 (March 1, 2010): 819–27. http://dx.doi.org/10.1099/mic.0.033712-0.

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Aerobic enrichments from soda lake sediments with CO as the only substrate resulted in the isolation of five bacterial strains capable of autotrophic growth with CO at extremely high pH and salinity. The strains belonged to the Alkalispirillum/Alkalilimnicola cluster in the Gammaproteobacteria, where the ability to oxidize CO, but not growth with CO, has been demonstrated previously. The growth with CO was possible only at an oxygen concentration below 5 % and CO concentration below 20 % in the gas phase. The isolates were also capable of growth with formate but not with H2. The carboxydotrophic growth occurred within a narrow pH range from 8 to 10.5 (optimum at 9.5) and a broad salt concentration from0.3 to 3.5 M total Na+ (optimum at 1.0 M). Cells grown on CO had high respiration activity with CO and formate, while the cells grown on formate actively oxidized formate alone. In CO-grown cells, CO-dehydrogenase (CODH) activity was detectable both in soluble and membrane fractions, while the NAD-independent formate dehydrogenase (FDH) resided solely in membranes. The results of total protein profiling and the failure to detect CODH with conventional primers for the coxL gene indicated that the CO-oxidizing enzyme in haloalkaliphilic isolates might differ from the classical aerobic CODH complex. A single cbbL gene encoding the RuBisCO large subunit was detected in all strains, suggesting the presence of the Calvin cycle of inorganic carbon fixation. Overall, these results demonstrated the possibility of aerobic carboxydotrophy under extremely haloalkaline conditions.

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8

Geelhoed, Jeanine S., Anne M. Henstra, and Alfons J. M. Stams. "Carboxydotrophic growth of Geobacter sulfurreducens." Applied Microbiology and Biotechnology 100, no. 2 (October 19, 2015): 997–1007. http://dx.doi.org/10.1007/s00253-015-7033-z.

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9

Yoneda, Yasuko, Takashi Yoshida, Satoshi Kawaichi, Takashi Daifuku, Keiji Takabe, and Yoshihiko Sako. "Carboxydothermus pertinax sp. nov., a thermophilic, hydrogenogenic, Fe(III)-reducing, sulfur-reducing carboxydotrophic bacterium from an acidic hot spring." International Journal of Systematic and Evolutionary Microbiology 62, Pt_7 (July 1, 2012): 1692–97. http://dx.doi.org/10.1099/ijs.0.031583-0.

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A novel anaerobic, Fe(III)-reducing, hydrogenogenic, carboxydotrophic bacterium, designated strain Ug1T, was isolated from a volcanic acidic hot spring in southern Kyushu Island, Japan. Cells of the isolate were rod-shaped (1.0–3.0 µm long) and motile due to peritrichous flagella. Strain Ug1T grew chemolithoautotrophically on CO (100 % in the gas phase) with reduction of ferric citrate, amorphous iron (III) oxide, 9,10-anthraquinone 2,6-disulfonate, thiosulfate or elemental sulfur. No carboxydotrophic growth occurred with sulfate, sulfite, nitrate or fumarate as electron acceptor. During growth on CO, H2 and CO2 were produced. Growth occurred on molecular hydrogen as an energy source and carbon dioxide as a sole carbon source. Growth was observed on various organic compounds under an N2 atmosphere with the reduction of ferric iron. The temperature range for carboxydotrophic growth was 50–70 °C, with an optimum at 65 °C. The pH25 °C range for growth was 4.6–8.6, with an optimum between 6.0 and 6.5. The doubling time under optimum conditions using CO with ferric citrate was 1.5 h. The DNA G+C content was 42.2 mol%. Analysis of 16S rRNA gene sequences demonstrated that this strain belongs to the thermophilic carboxydotrophic bacterial genus Carboxydothermus , with sequence similarities of 94.1–96.6 % to members of this genus. The isolate can be distinguished from other members of the genus Carboxydothermus by its ability to grow with elemental sulfur or thiosulfate coupled to CO oxidation. On the basis of phylogenetic analysis and unique physiological features, the isolate represents a novel species of the genus Carboxydothermus for which the name Carboxydothermus pertinax sp. nov. is proposed; the type strain of the novel species is Ug1T ( = DSM 23698T = NBRC 107576T).

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10

Lee, Hyun Sook, Sung Gyun Kang, Seung Seob Bae, Jae Kyu Lim, Yona Cho, Yun Jae Kim, Jeong Ho Jeon, et al. "The Complete Genome Sequence of Thermococcus onnurineus NA1 Reveals a Mixed Heterotrophic and Carboxydotrophic Metabolism." Journal of Bacteriology 190, no. 22 (September 12, 2008): 7491–99. http://dx.doi.org/10.1128/jb.00746-08.

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ABSTRACT Members of the genus Thermococcus, sulfur-reducing hyperthermophilic archaea, are ubiquitously present in various deep-sea hydrothermal vent systems and are considered to play a significant role in the microbial consortia. We present the complete genome sequence and feature analysis of Thermococcus onnurineus NA1 isolated from a deep-sea hydrothermal vent area, which reveal clues to its physiology. Based on results of genomic analysis, T. onnurineus NA1 possesses the metabolic pathways for organotrophic growth on peptides, amino acids, or sugars. More interesting was the discovery that the genome encoded unique proteins that are involved in carboxydotrophy to generate energy by oxidation of CO to CO2, thereby providing a mechanistic basis for growth with CO as a substrate. This lithotrophic feature in combination with carbon fixation via RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) introduces a new strategy with a complementing energy supply for T. onnurineus NA1 potentially allowing it to cope with nutrient stress in the surrounding of hydrothermal vents, providing the first genomic evidence for the carboxydotrophy in Thermococcus.

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11

Sobotta, Jessica, Thomas Geisberger, Carolin Moosmann, Christopher M. Scheidler, Wolfgang Eisenreich, Günter Wächtershäuser, and Claudia Huber. "A Possible Primordial Acetyleno/Carboxydotrophic Core Metabolism." Life 10, no. 4 (April 7, 2020): 35. http://dx.doi.org/10.3390/life10040035.

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Carbon fixation, in addition to the evolution of metabolism, is a main requirement for the evolution of life. Here, we report a one-pot carbon fixation of acetylene (C2H2) and carbon monoxide (CO) by aqueous nickel sulfide (NiS) under hydrothermal (>100 °C) conditions. A slurry of precipitated NiS converts acetylene and carbon monoxide into a set of C2–4-products that are surprisingly representative for C2–4-segments of all four central CO2-fixation cycles of the domains Bacteria and Archaea, whereby some of the products engage in the same interconversions, as seen in the central CO2-fixation cycles. The results suggest a primordial, chemically predetermined, non-cyclic acetyleno/carboxydotrophic core metabolism. This metabolism is based on aqueous organo–metal chemistry, from which the extant central CO2-fixation cycles based on thioester chemistry would have evolved by piecemeal modifications.

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12

O'Donnell, Anthony G., Christine Falconer, Michael Goodfellow, Alan C. Ward, and Edwin Williams. "Biosystematics and diversity amongst novel carboxydotrophic actinomycetes." Antonie van Leeuwenhoek 64, no. 3-4 (1994): 325–40. http://dx.doi.org/10.1007/bf00873091.

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13

Sokolova, Tatyana G., Anne-Meint Henstra, Jan Sipma, Sofiya N. Parshina, Alfons J. M. Stams, and Alexander V. Lebedinsky. "Diversity and ecophysiological features of thermophilic carboxydotrophic anaerobes." FEMS Microbiology Ecology 68, no. 2 (May 2009): 131–41. http://dx.doi.org/10.1111/j.1574-6941.2009.00663.x.

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14

Kraut, Maria, and Ortwin Meyer. "Plasmids in carboxydotrophic bacteria: physical and restriction analysis." Archives of Microbiology 149, no. 6 (April 1988): 540–46. http://dx.doi.org/10.1007/bf00446758.

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15

Carr, Stephanie A., Sean P. Jungbluth, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Tanja Woyke, Michael S. Rappé, and Beth N. Orcutt. "Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere." ISME Journal 13, no. 6 (February 7, 2019): 1457–68. http://dx.doi.org/10.1038/s41396-019-0352-9.

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16

Fukuyama, Yuto, Kimiho Omae, Takashi Yoshida, and Yoshihiko Sako. "Transcriptome analysis of a thermophilic and hydrogenogenic carboxydotroph Carboxydothermus pertinax." Extremophiles 23, no. 4 (April 3, 2019): 389–98. http://dx.doi.org/10.1007/s00792-019-01091-x.

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17

Kim, Min-Sik, Seung Seob Bae, Yun Jae Kim, Tae Wan Kim, Jae Kyu Lim, Seong Hyuk Lee, Ae Ran Choi, et al. "CO-Dependent H2Production by Genetically Engineered Thermococcus onnurineus NA1." Applied and Environmental Microbiology 79, no. 6 (January 18, 2013): 2048–53. http://dx.doi.org/10.1128/aem.03298-12.

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ABSTRACTHydrogenogenic CO oxidation (CO + H2O → CO2+ H2) has the potential for H2production as a clean renewable fuel.Thermococcus onnurineusNA1, which grows on CO and produces H2, has a unique gene cluster encoding the carbon monoxide dehydrogenase (CODH) and the hydrogenase. The gene cluster was identified as essential for carboxydotrophic hydrogenogenic metabolism by gene disruption and transcriptional analysis. To develop a strain producing high levels of H2, the gene cluster was placed under the control of a strong promoter. The resulting mutant, MC01, showed 30-fold-higher transcription of the mRNA encoding CODH, hydrogenase, and Na+/H+antiporter and a 1.8-fold-higher specific activity for CO-dependent H2production than did the wild-type strain. The H2production potential of the MC01 mutant in a bioreactor culture was 3.8-fold higher than that of the wild-type strain. The H2production rate of the engineered strain was severalfold higher than those of any other CO-dependent H2-producing prokaryotes studied to date. The engineered strain also possessed high activity for the bioconversion of industrial waste gases created as a by-product during steel production. This work represents the first demonstration of H2production from steel mill waste gas using a carboxydotrophic hydrogenogenic microbe.

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18

Ramió-Pujol, Sara, Ramon Ganigué, Lluís Bañeras, and Jesús Colprim. "How can alcohol production be improved in carboxydotrophic clostridia?" Process Biochemistry 50, no. 7 (July 2015): 1047–55. http://dx.doi.org/10.1016/j.procbio.2015.03.019.

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19

Pomaranski, Eric, and Sonia M. Tiquia-Arashiro. "Butanol tolerance of carboxydotrophic bacteria isolated from manure composts." Environmental Technology 37, no. 15 (February 10, 2016): 1970–82. http://dx.doi.org/10.1080/09593330.2015.1137360.

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20

Svetlichny, V. A., T. G. Sokolova, M. Gerhardt, N. A. Kostrikina, and G. A. Zavarzin. "Anaerobic extremely thermophilic carboxydotrophic bacteria in hydrotherms of Kuril Islands." Microbial Ecology 21, no. 1 (December 1991): 1–10. http://dx.doi.org/10.1007/bf02539140.

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21

Yoneda, Yasuko, Takashi Yoshida, Takashi Daifuku, Takayuki Kitamura, Takahiro Inoue, Sanae Kano, and Yoshihiko Sako. "Quantitative detection of carboxydotrophic bacteria Carboxydothermus in a hot aquatic environment." Fundamental and Applied Limnology / Archiv für Hydrobiologie 182, no. 2 (February 1, 2013): 161–70. http://dx.doi.org/10.1127/1863-9135/2013/0374.

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22

Sinharoy, Arindam, N. Arul Manikandan, and Kannan Pakshirajan. "A novel biological sulfate reduction method using hydrogenogenic carboxydotrophic mesophilic bacteria." Bioresource Technology 192 (September 2015): 494–500. http://dx.doi.org/10.1016/j.biortech.2015.05.085.

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23

Kraut, M., I. Hugendieck, S. Herwig, and O. Meyer. "Homology and distribution of CO dehydrogenase structural genes in carboxydotrophic bacteria." Archives of Microbiology 152, no. 4 (September 1989): 335–41. http://dx.doi.org/10.1007/bf00425170.

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24

Mu, Andre, Brian C. Thomas, Jillian F. Banfield, and John W. Moreau. "Subsurface carbon monoxide oxidation capacity revealed through genome‐resolved metagenomics of a carboxydotroph." Environmental Microbiology Reports 12, no. 5 (July 23, 2020): 525–33. http://dx.doi.org/10.1111/1758-2229.12868.

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25

Alves, J. I., A. H. van Gelder, M. M. Alves, D. Z. Sousa, and C. M. Plugge. "Moorella stamsii sp. nov., a new anaerobic thermophilic hydrogenogenic carboxydotroph isolated from digester sludge." International Journal of Systematic and Evolutionary Microbiology 63, Pt_11 (November 1, 2013): 4072–76. http://dx.doi.org/10.1099/ijs.0.050369-0.

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A novel anaerobic, thermophilic, carbon monoxide-utilizing bacterium, strain E3-OT, was isolated from anaerobic sludge from a municipal solid waste digester. Cells were straight rods, 0.6–1 µm in diameter and 2–3 µm in length and grew as single cells or in pairs. Cells formed round terminal endospores. The temperature range for growth was 50–70 °C, with an optimum at 65 °C. The pH range for growth was 5.7–8.0, with an optimum at 7.5. Strain E3-OT had the ability to ferment various sugars, such as fructose, galactose, glucose, mannose, raffinose, ribose, sucrose and xylose, producing mainly H2 and acetate. In addition, the isolate was able to grow with CO as the sole carbon and energy source. CO oxidation was coupled to H2 and CO2 formation. The G+C content of the genomic DNA was 54.6 mol%. Based on 16S rRNA gene sequence analysis, this bacterium is most closely related to Moorella glycerini (97 % sequence identity). Based on the physiological features and phylogenetic analysis, it is proposed that strain E3-OT should be classified in the genus Moorella as a representative of a novel species, Moorella stamsii. The type strain of Moorella stamsii is E3-OT ( = DSM 26271T = CGMCC 1.5181T).

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26

Kim, S. B. "Streptomyces thermospinisporus sp. nov., a moderately thermophilic carboxydotrophic streptomycete isolated from soil." INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 52, no. 4 (July 1, 2002): 1225–28. http://dx.doi.org/10.1099/ijs.0.02003-0.

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27

Kim, Seung Bum, and Michael Goodfellow. "Streptomyces thermospinisporus sp. nov., a moderately thermophilic carboxydotrophic streptomycete isolated from soil." International Journal of Systematic and Evolutionary Microbiology 52, no. 4 (July 1, 2002): 1225–28. http://dx.doi.org/10.1099/00207713-52-4-1225.

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28

Aliyu, Habibu, Ronnie Kastner, Pieter de Maayer, and Anke Neumann. "Carbon Monoxide Induced Metabolic Shift in the Carboxydotrophic Parageobacillus thermoglucosidasius DSM 6285." Microorganisms 9, no. 5 (May 19, 2021): 1090. http://dx.doi.org/10.3390/microorganisms9051090.

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Parageobacillus thermoglucosidasius is known to catalyse the biological water gas shift (WGS) reaction, a pathway that serves as a source of alternative energy and carbon to a wide variety of bacteria. Despite increasing interest in this bacterium due to its ability to produce biological hydrogen through carbon monoxide (CO) oxidation, there are no data on the effect of toxic CO gas on its physiology. Due to its general requirement of O2, the organism is often grown aerobically to generate biomass. Here, we show that carbon monoxide (CO) induces metabolic changes linked to distortion of redox balance, evidenced by increased accumulation of organic acids such as acetate and lactate. This suggests that P. thermoglucosidasius survives by expressing several alternative pathways, including conversion of pyruvate to lactate, which balances reducing equivalents (oxidation of NADH to NAD+), and acetyl-CoA to acetate, which directly generates energy, while CO is binding terminal oxidases. The data also revealed clearly that P. thermoglucosidasius gained energy and grew during the WGS reaction. Combined, the data provide critical information essential for further development of the biotechnological potential of P. thermoglucosidasius.

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29

Parshina, Sofiya N., Jan Sipma, Anne Meint Henstra, and Alfons J. M. Stams. "Carbon Monoxide as an Electron Donor for the Biological Reduction of Sulphate." International Journal of Microbiology 2010 (2010): 1–9. http://dx.doi.org/10.1155/2010/319527.

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Several strains of Gram-negative and Gram-positive sulphate-reducing bacteria (SRB) are able to use carbon monoxide (CO) as a carbon source and electron donor for biological sulphate reduction. These strains exhibit variable resistance to CO toxicity. The most resistant SRB can grow and use CO as an electron donor at concentrations up to 100%, whereas others are already severely inhibited at CO concentrations as low as 1-2%. Here, the utilization, inhibition characteristics, and enzymology of CO metabolism as well as the current state of genomics of CO-oxidizing SRB are reviewed. Carboxydotrophic sulphate-reducing bacteria can be applied for biological sulphate reduction with synthesis gas (a mixture of hydrogen and carbon monoxide) as an electron donor.

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30

Novikov, Andrey A., Tatyana G. Sokolova, Alexander V. Lebedinsky, Tatyana V. Kolganova, and Elizaveta A. Bonch-Osmolovskaya. "Carboxydothermus islandicus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic bacterium isolated from a hot spring." International Journal of Systematic and Evolutionary Microbiology 61, no. 10 (October 1, 2011): 2532–37. http://dx.doi.org/10.1099/ijs.0.030288-0.

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An anaerobic, thermophilic bacterium, strain SET IS-9T, was isolated from an Icelandic hot spring. Cells of strain SET IS-9T are short, slightly curved, motile rods. The strain grows chemolithotrophically on CO, producing equimolar quantities of H2 and CO2. It also grows fermentatively on lactate or pyruvate in the presence of yeast extract (0.2 g l−1). Products of pyruvate fermentation are acetate, CO2 and H2. Growth occurs at 50–70 °C, with an optimum at 65 °C, and at pH 5.0–8.0, with an optimum at pH 5.5–6.0. The generation time during chemolithotrophic growth on CO under optimal conditions is 2.0 h. 16S rRNA gene sequence analysis suggested that the organism belongs to the genus Carboxydothermus. On the basis of phenotypic features and phylogenetic analysis, Carboxydothermus islandicus sp. nov. is proposed, with the type strain SET IS-9T ( = DSM 21830T = VKM B-2561T). An emended description of the genus Carboxydothermus is also given.

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31

Vannier, P., V. T. Marteinsson, O. H. Fridjonsson, P. Oger, and M. Jebbar. "Complete Genome Sequence of the Hyperthermophilic, Piezophilic, Heterotrophic, and Carboxydotrophic Archaeon Thermococcus barophilus MP." Journal of Bacteriology 193, no. 6 (January 7, 2011): 1481–82. http://dx.doi.org/10.1128/jb.01490-10.

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32

Kita, Akihisa, Yuki Iwasaki, Shinsuke Sakai, Shinya Okuto, Kazue Takaoka, Tohru Suzuki, Shinichi Yano, et al. "Development of genetic transformation and heterologous expression system in carboxydotrophic thermophilic acetogen Moorella thermoacetica." Journal of Bioscience and Bioengineering 115, no. 4 (April 2013): 347–52. http://dx.doi.org/10.1016/j.jbiosc.2012.10.013.

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33

Ganigué, Ramon, Sara Ramió-Pujol, Patricia Sánchez, Lluís Bañeras, and Jesús Colprim. "Conversion of sewage sludge to commodity chemicals via syngas fermentation." Water Science and Technology 72, no. 3 (May 12, 2015): 415–20. http://dx.doi.org/10.2166/wst.2015.222.

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Gasification of sewage sludge allows the recovery of energy, and produces a mix of CO, CO2 and H2 called synthesis gas (or syngas), which can be fermented by acetogenic bacteria to added-value products. This work presents the conversion of syngas to organic acids and alcohols using both pure and mixed cultures. Pure culture kinetic experiments with Clostridium carboxidivorans P7 resulted in the production of high concentrations of acetate (454 mgC/L) and ethanol (167 mgC/L). The pH was the main factor driving solventogenesis, with about 50% of the products in the form of alcohols at pH 5. Conversely, laboratory-scale experiments using a carboxydotrophic mixed culture of the genus Clostridium enriched from anaerobic digester sludge of a municipal wastewater treatment plant was capable of producing mainly butyrate, with maximum concentration of 1,184 mgC/L.

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Chinnasamy Perumal, Rajadurai, Ashok Selvaraj, and Gopal Ramesh Kumar. "Elementary Flux Mode Analysis of Acetyl-CoA Pathway in Carboxydothermus hydrogenoformans Z-2901." Advances in Bioinformatics 2014 (April 16, 2014): 1–10. http://dx.doi.org/10.1155/2014/928038.

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Carboxydothermus hydrogenoformans is a carboxydotrophic hydrogenogenic bacterium species that produces hydrogen molecule by utilizing carbon monoxide (CO) or pyruvate as a carbon source. To investigate the underlying biochemical mechanism of hydrogen production, an elementary mode analysis of acetyl-CoA pathway was performed to determine the intermediate fluxes by combining linear programming (LP) method available in CellNetAnalyzer software. We hypothesized that addition of enzymes necessary for carbon monoxide fixation and pyruvate dissimilation would enhance the theoretical yield of hydrogen. An in silico gene knockout of pyk, pykC, and mdh genes of modeled acetyl-CoA pathway allows the maximum theoretical hydrogen yield of 47.62 mmol/gCDW/h for 1 mole of carbon monoxide (CO) uptake. The obtained hydrogen yield is comparatively two times greater than the previous experimental data. Therefore, it could be concluded that this elementary flux mode analysis is a crucial way to achieve efficient hydrogen production through acetyl-CoA pathway and act as a model for strain improvement.

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Yun, Sung-Ho, Sang Oh Kwon, Gun Wook Park, Jin Young Kim, Sung Gyun Kang, Jung-Hyun Lee, Young-Ho Chung, Soohyun Kim, Jong-Soon Choi, and Seung Il Kim. "Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth." Journal of Proteomics 74, no. 10 (September 2011): 1926–33. http://dx.doi.org/10.1016/j.jprot.2011.05.010.

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Kim, S. B., C. Falconer, E. Williams, and M. Goodfellow. "Streptomyces thermocarboxydovorans sp. nov. and Streptomyces thermocarboxydus sp. nov., two moderately thermophilic carboxydotrophic species from soil." International Journal of Systematic Bacteriology 48, no. 1 (January 1, 1998): 59–68. http://dx.doi.org/10.1099/00207713-48-1-59.

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Slepova, T. V., T. G. Sokolova, T. V. Kolganova, T. P. Tourova, and E. A. Bonch-Osmolovskaya. "Carboxydothermus siderophilus sp. nov., a thermophilic, hydrogenogenic, carboxydotrophic, dissimilatory Fe(III)-reducing bacterium from a Kamchatka hot spring." INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 59, no. 2 (February 1, 2009): 213–17. http://dx.doi.org/10.1099/ijs.0.000620-0.

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Yoneda, Yasuko, Takashi Yoshida, Hisato Yasuda, Chiaki Imada, and Yoshihiko Sako. "A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera." International Journal of Systematic and Evolutionary Microbiology 63, Pt_10 (October 1, 2013): 3602–8. http://dx.doi.org/10.1099/ijs.0.050468-0.

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A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1T, was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0–3.0 µm straight rods, often observed with round endospores. Strain KKC1T grew at 55–68 °C, pH 5.2–9.2 and 0.8–14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0–7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1T grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1T was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1T ( = DSM 26464T = NBRC 109353T).

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Kim, Min-Sik, Ae Ran Choi, Seong Hyuk Lee, Hae-Chang Jung, Seung Seob Bae, Tae-Jun Yang, Jeong Ho Jeon, et al. "A Novel CO-Responsive Transcriptional Regulator and Enhanced H2Production by an Engineered Thermococcus onnurineus NA1 Strain." Applied and Environmental Microbiology 81, no. 5 (December 29, 2014): 1708–14. http://dx.doi.org/10.1128/aem.03019-14.

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ABSTRACTGenome analysis revealed the existence of a putative transcriptional regulatory system governing CO metabolism inThermococcus onnurineusNA1, a carboxydotrophic hydrogenogenic archaeon. The regulatory system is composed of CorQ with a 4-vinyl reductase domain and CorR with a DNA-binding domain of the LysR-type transcriptional regulator family in close proximity to the CO dehydrogenase (CODH) gene cluster. Homologous genes of the CorQR pair were also found in the genomes ofThermococcusspecies and “CandidatusKorarchaeum cryptofilum” OPF8. In-frame deletion of eithercorQorcorRcaused a severe impairment in CO-dependent growth and H2production. WhencorQandcorRdeletion mutants were complemented by introducing thecorQRgenes under the control of a strong promoter, the mRNA and protein levels of the CODH gene were significantly increased in a ΔCorR strain complemented with integratedcorQR(ΔCorR/corQR↑) compared with those in the wild-type strain. In addition, the ΔCorR/corQR↑strain exhibited a much higher H2production rate (5.8-fold) than the wild-type strain in a bioreactor culture. The H2production rate (191.9 mmol liter−1h−1) and the specific H2production rate (249.6 mmol g−1h−1) of this strain were extremely high compared with those of CO-dependent H2-producing prokaryotes reported so far. These results suggest that thecorQRgenes encode a positive regulatory protein pair for the expression of a CODH gene cluster. The study also illustrates that manipulation of the transcriptional regulatory system can improve biological H2production.

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Sokolova, Tatyana G., Nadezhda A. Kostrikina, Nikolai A. Chernyh, Tatjana V. Kolganova, Tatjana P. Tourova, and Elizaveta A. Bonch-Osmolovskaya. "Thermincola carboxydiphila gen. nov., sp. nov., a novel anaerobic, carboxydotrophic, hydrogenogenic bacterium from a hot spring of the Lake Baikal area." International Journal of Systematic and Evolutionary Microbiology 55, no. 5 (September 1, 2005): 2069–73. http://dx.doi.org/10.1099/ijs.0.63299-0.

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A novel anaerobic, thermophilic, alkalitolerant bacterium, strain 2204T, was isolated from a hot spring of the Baikal Lake region. The cells of strain 2204T were straight rods of variable length, Gram-positive with an S-layer, motile with one to two lateral flagella, and often formed aggregates of 3–15 cells. The isolate was shown to be an obligate anaerobe oxidizing CO and producing equimolar quantities of H2 and CO2 according to the equation CO+H2O→CO2+H2. No organic substrates were used as energy sources. For lithotrophic growth on CO, 0·2 g acetate or yeast extract l−1 was required but did not support growth in the absence of CO. Growth was observed in the temperature range 37–68 °C, the optimum being 55 °C. The pH range for growth was 6·7–9·5, the optimum pH being 8·0. The generation time under optimal conditions was 1·3 h. The DNA G+C content was 45 mol%. Penicillin, erythromycin, streptomycin, rifampicin, vancomycin and tetracycline completely inhibited both growth and CO utilization by strain 2204T. Thus, isolate 2204T was found to be the first known moderately thermophilic and alkalitolerant H2-producing anaerobic carboxydotroph. The novel bacterium fell within the cluster of the family Peptococcaceae within the low-G+C-content Gram-positive bacteria, where it formed a separate branch. On the basis of morphological, physiological and phylogenetic features, strain 2204T should be assigned to a novel genus and species, for which the name Thermincola carboxydiphila gen. nov., sp. nov. is proposed. The type strain is strain 2204T (=DSM 17129T=VKM B-2283T=JCM 13258T).

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Visser, Michael, Sofiya N. Parshina, Joana I. Alves, Diana Z. Sousa, Inês A. C. Pereira, Gerard Muyzer, Jan Kuever, et al. "Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans." Standards in Genomic Sciences 9, no. 3 (March 1, 2014): 655–75. http://dx.doi.org/10.4056/sigs.4718645.

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Hugendieck, Iris, and Ortwin Meyer. "The structural genes encoding CO dehydrogenase subunits (cox L, M and S) in Pseudomonas carboxydovorans OM5 reside on plasmid pHCG3 and are, with the exception of Streptomyces thermoautotrophicus, conserved in carboxydotrophic bacteria." Archives of Microbiology 157, no. 3 (February 1992): 301–4. http://dx.doi.org/10.1007/bf00245166.

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Sokolova, Tatyana G., Juan M. González, Nadezhda A. Kostrikina, Nikolai A. Chernyh, Tatiana V. Slepova, Elizaveta A. Bonch-Osmolovskaya, and Frank T. Robb. "Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park." International Journal of Systematic and Evolutionary Microbiology 54, no. 6 (November 1, 2004): 2353–59. http://dx.doi.org/10.1099/ijs.0.63186-0.

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A new anaerobic, thermophilic, facultatively carboxydotrophic bacterium, strain Nor1T, was isolated from a hot spring at Norris Basin, Yellowstone National Park. Cells of strain Nor1T were curved motile rods with a length of 2·6–3 μm, a width of about 0·5 μm and lateral flagellation. The cell wall structure was of the Gram-negative type. Strain Nor1T was thermophilic (temperature range for growth was 40–68 °C, with an optimum at 60 °C) and neutrophilic (pH range for growth was 6·5–7·6, with an optimum at 6·8–7·0). It grew chemolithotrophically on CO (generation time, 1·15 h), producing equimolar quantities of H2 and CO2 according to the equation CO+H2O→CO2+H2. During growth on CO in the presence of ferric citrate or amorphous ferric iron oxide, strain Nor1T reduced ferric iron but produced H2 and CO2 at a ratio close to 1 : 1, and growth stimulation was slight. Growth on CO in the presence of sodium selenite was accompanied by precipitation of elemental selenium. Elemental sulfur, thiosulfate, sulfate and nitrate did not stimulate growth of strain Nor1T on CO and none of these chemicals was reduced. Strain Nor1T was able to grow on glucose, sucrose, lactose, arabinose, maltose, fructose, xylose and pyruvate, but not on cellobiose, galactose, peptone, yeast extract, lactate, acetate, formate, ethanol, methanol or sodium citrate. During glucose fermentation, acetate, H2 and CO2 were produced. Thiosulfate was found to enhance the growth rate and cell yield of strain Nor1T when it was grown on glucose, sucrose or lactose; in this case, acetate, H2S and CO2 were produced. In the presence of thiosulfate or ferric iron, strain Nor1T was also able to grow on yeast extract. Lactate, acetate, formate and H2 were not utilized either in the absence or in the presence of ferric iron, thiosulfate, sulfate, sulfite, elemental sulfur or nitrate. Growth was completely inhibited by penicillin, ampicillin, streptomycin, kanamycin and neomycin. The DNA G+C content of the strain was 51·7±1 mol%. Analysis of the 16S rRNA gene sequence revealed that strain Nor1T belongs to the Bacillus–Clostridium phylum of the Gram-positive bacteria. On the basis of the studied phenotypic and phylogenetic features, we propose that strain Nor1T be assigned to a new genus, Thermosinus gen. nov. The type species is Thermosinus carboxydivorans sp. nov. (type strain, Nor1T=DSM 14886T=VKM B-2281T).

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Fukuyama, Yuto, Kimiho Omae, Yasuko Yoneda, Takashi Yoshida, and Yoshihiko Sako. "Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism inCarboxydothermus pertinaxRevealed by Comparative Genome Analysis." Applied and Environmental Microbiology 84, no. 14 (May 4, 2018). http://dx.doi.org/10.1128/aem.00458-18.

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ABSTRACTCarboxydothermusspecies are some of the most studied thermophilic carboxydotrophs. Their varied carboxydotrophic growth properties suggest distinct strategies for energy conservation via carbon monoxide (CO) metabolism. In this study, we used comparative genome analysis of the genusCarboxydothermusto show variations in the CO dehydrogenase-energy-converting hydrogenase gene cluster, which is responsible for CO metabolism with H2production (hydrogenogenic CO metabolism). Indeed, the ability or inability to produce H2with CO oxidation is explained by the presence or absence of this gene cluster inCarboxydothermus hydrogenoformans,Carboxydothermus islandicus, andCarboxydothermus ferrireducens. Interestingly, despite its hydrogenogenic CO metabolism,Carboxydothermus pertinaxlacks the Ni-CO dehydrogenase catalytic subunit (CooS-I) and its transcriptional regulator-encoding genes in this gene cluster, probably due to inversion. Transcriptional analysis inC. pertinaxshowed that the Ni-CO dehydrogenase gene (cooS-II) and distantly encoded energy-converting-hydrogenase-related genes were remarkably upregulated with 100% CO. In addition, when thiosulfate was available as a terminal electron acceptor in 100% CO, the maximum cell density and maximum specific growth rate ofC. pertinaxwere 3.1-fold and 1.5-fold higher, respectively, than when thiosulfate was absent. The amount of H2produced was only 62% of the amount of CO consumed, less than expected according to hydrogenogenic CO oxidation (CO + H2O → CO2+ H2). Accordingly,C. pertinaxwould couple CO oxidation by Ni-CO dehydrogenase II with simultaneous reduction of not only H2O but also thiosulfate when grown in 100% CO.IMPORTANCEAnaerobic hydrogenogenic carboxydotrophs are thought to fill a vital niche by scavenging potentially toxic CO and producing H2as an available energy source for thermophilic microbes. This hydrogenogenic carboxydotrophy relies on a Ni-CO dehydrogenase-energy-converting hydrogenase gene cluster. This feature is thought to be common to these organisms. However, the hydrogenogenic carboxydotrophCarboxydothermus pertinaxlacks the gene for the Ni-CO dehydrogenase catalytic subunit encoded in the gene cluster. Here, we performed a comparative genome analysis of the genusCarboxydothermus, a transcriptional analysis, and a cultivation study in 100% CO to prove the hydrogenogenic CO metabolism. Results revealed thatC. pertinaxcould couple Ni-CO dehydrogenase II alternatively to the distal energy-converting hydrogenase. Furthermore,C. pertinaxrepresents an example of the functioning of Ni-CO dehydrogenase that does not always correspond to its genomic context, owing to the versatility of CO metabolism and the low redox potential of CO.

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Omae, Kimiho, Tatsuki Oguro, Masao Inoue, Yuto Fukuyama, Takashi Yoshida, and Yoshihiko Sako. "Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers." Extremophiles, January 7, 2021. http://dx.doi.org/10.1007/s00792-020-01211-y.

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AbstractThe microbial H2-producing (hydrogenogenic) carbon monoxide (CO)-oxidizing activity by the membrane-associated CO dehydrogenase (CODH)/energy-converting hydrogenase (ECH) complex is an important metabolic process in the microbial community. However, the studies on hydrogenogenic carboxydotrophs had to rely on inherently cultivation and isolation methods due to their rare abundance, which was a bottleneck in ecological study. Here, we provided gene-targeted sequencing method for the diversity estimation of thermophilic hydrogenogenic carboxydotrophs. We designed six new degenerate primer pairs which effectively amplified the coding regions of CODH genes forming gene clusters with ECH genes (CODHech genes) in Firmicutes which includes major thermophilic hydrogenogenic carboxydotrophs in terrestrial thermal habitats. Amplicon sequencing by these primers using DNAs from terrestrial hydrothermal sediments and CO-gas-incubated samples specifically detected multiple CODH genes which were identical or phylogenetically related to the CODHech genes in Firmictes. Furthermore, we found that phylogenetically distinct CODHech genes were enriched in CO-gas-incubated samples, suggesting that our primers detected uncultured hydrogenogenic carboxydotrophs as well. The new CODH-targeted primers provided us with a fine-grained (~ 97.9% in nucleotide sequence identity) diversity analysis of thermophilic hydrogenogenic carboxydotrophs by amplicon sequencing and will bolster the ecological study of these microorganisms.

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Fukuyama, Yuto, Tatsuki Oguro, Kimiho Omae, Yasuko Yoneda, Takashi Yoshida, and Yoshihiko Sako. "Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic Fronts in Japan." Genome Announcements 5, no. 16 (April 20, 2017). http://dx.doi.org/10.1128/genomea.00242-17.

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ABSTRACT Hydrogenogenic carboxydotrophs may provide hydrogen as primary energy for the microbial community via carbon monoxide oxidation. To investigate the genetics of carbon monoxide metabolism, we report here the draft genome sequences of the hydrogenogenic carboxydotrophs Carboxydocella sp. strains JDF658 (2.60 Mbp; G+C content, 49.2%) and ULO1 (2.70 Mbp; G+C content, 48.8%).

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Fukuyama, Yuto, Kimiho Omae, Yasuko Yoneda, Takashi Yoshida, and Yoshihiko Sako. "Draft Genome Sequences of Carboxydothermus pertinax and C. islandicus, Hydrogenogenic Carboxydotrophic Bacteria." Genome Announcements 5, no. 8 (February 23, 2017). http://dx.doi.org/10.1128/genomea.01648-16.

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ABSTRACT Carboxydothermus spp. are some of the most studied carbon monoxide–oxidizing anaerobic thermophiles. For further investigation into the carbon monoxide metabolism of Carboxydothermus spp., we report here the draft genome sequences of the hydrogenogenic carboxydotrophs Carboxydothermus pertinax (2.47 Mb; G+C content, 40.7%) and C. islandicus (2.39 Mb; G+C content, 42.0%).

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Omae, Kimiho, Yasuko Yoneda, Yuto Fukuyama, Takashi Yoshida, and Yoshihiko Sako. "Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment." Applied and Environmental Microbiology 83, no. 15 (May 19, 2017). http://dx.doi.org/10.1128/aem.00832-17.

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ABSTRACT Calderihabitans maritimus KKC1 is a thermophilic, hydrogenogenic carboxydotroph isolated from a submerged marine caldera. Here, we describe the de novo sequencing and feature analysis of the C. maritimus KKC1 genome. Genome-based phylogenetic analysis confirmed that C. maritimus KKC1 was most closely related to the genus Moorella, which includes well-studied acetogenic members. Comparative genomic analysis revealed that, like Moorella, C. maritimus KKC1 retained both the CO2-reducing Wood-Ljungdahl pathway and energy-converting hydrogenase-based module activated by reduced ferredoxin, but it lacked the HydABC and NfnAB electron-bifurcating enzymes and pyruvate:ferredoxin oxidoreductase required for ferredoxin reduction for acetogenic growth. Furthermore, C. maritimus KKC1 harbored six genes encoding CooS, a catalytic subunit of the anaerobic CO dehydrogenase that can reduce ferredoxin via CO oxidation, whereas Moorella possessed only two CooS genes. Our analysis revealed that three cooS genes formed known gene clusters in other microorganisms, i.e., cooS-acetyl coenzyme A (acetyl-CoA) synthase (which contained a frameshift mutation), cooS–energy-converting hydrogenase, and cooF-cooS-FAD-NAD oxidoreductase, while the other three had novel genomic contexts. Sequence composition analysis indicated that these cooS genes likely evolved from a common ancestor. Collectively, these data suggest that C. maritimus KKC1 may be highly dependent on CO as a low-potential electron donor to directly reduce ferredoxin and may be more suited to carboxydotrophic growth compared to the acetogenic growth observed in Moorella, which show adaptation at a thermodynamic limit. IMPORTANCE Calderihabitans maritimus KKC1 and members of the genus Moorella are phylogenetically related but physiologically distinct. The former is a hydrogenogenic carboxydotroph that can grow on carbon monoxide (CO) with H2 production, whereas the latter include acetogenic bacteria that grow on H2 plus CO2 with acetate production. Both species may require reduced ferredoxin as an actual “energy equivalent,” but ferredoxin is a low-potential electron carrier and requires a high-energy substrate as an electron donor for reduction. Comparative genomic analysis revealed that C. maritimus KKC1 lacked specific electron-bifurcating enzymes and possessed six CO dehydrogenases, unlike Moorella species. This suggests that C. maritimus KKC1 may be more dependent on CO, a strong electron donor that can directly reduce ferredoxin via CO dehydrogenase, and may exhibit a survival strategy different from that of acetogenic Moorella, which solves the energetic barrier associated with endergonic reduction of ferredoxin with hydrogen.

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Poehlein, Anja, Tim Böer, Kerrin Steensen, and Rolf Daniel. "Draft Genome Sequence of the Hydrogenogenic Carboxydotroph Moorella stamsii DSM 26271." Genome Announcements 6, no. 18 (May 3, 2018). http://dx.doi.org/10.1128/genomea.00345-18.

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ABSTRACT The spore-forming, thermophilic, and obligate anaerobic bacterium Moorella stamsii was isolated from digester sludge. Apart from its ability to use carbon monoxide for growth, M. stamsii harbors several enzymes for the use of different sugars. The draft genome has a size of 3,329 Mb and contains 3,306 predicted protein-encoding genes.

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Brady, Allyson L., Christine E. Sharp, Stephen E. Grasby, and Peter F. Dunfield. "Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing." Frontiers in Microbiology 6 (September 1, 2015). http://dx.doi.org/10.3389/fmicb.2015.00897.

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