Relevant bibliographies by topics / Carboxydotrophs

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Academic literature on the topic 'Carboxydotrophs'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Carboxydotrophs"

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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Dissertations / Theses on the topic "Carboxydotrophs"

1

Omae, Kimiho. "Genomic and molecular ecological studies on thermophilic hydrogenogenic carboxydotrophs." Kyoto University, 2020. http://hdl.handle.net/2433/253321.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第22485号
農博第2389号
新制||農||1075(附属図書館)
学位論文||R2||N5265(農学部図書室)
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 吉田 天士, 教授 澤山 茂樹, 教授 菅原 達也
学位規則第4条第1項該当
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2

Yoneda, Yasuko. "Physiological and ecological studies on novel carboxydotrophic thermophiles." Kyoto University, 2014. http://hdl.handle.net/2433/188785.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第18347号
農博第2072号
新制||農||1024(附属図書館)
学位論文||H26||N4854(農学部図書室)
31205
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 左子 芳彦, 教授 澤山 茂樹, 准教授 吉田 天士
学位規則第4条第1項該当
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3

Falconer, Christine. "The isolation, physiology and taxonomy of carboxydotrophic actinomycetes." Thesis, University of Newcastle Upon Tyne, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244861.

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4

Fukuyama, Yuto. "Genomic and transcriptional studies on hydrogenogenic carboxydotrophic bacteria." Kyoto University, 2019. http://hdl.handle.net/2433/242689.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第21812号
農博第2325号
新制||農||1066(附属図書館)
学位論文||H31||N5184(農学部図書室)
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 左子 芳彦, 教授 澤山 茂樹, 准教授 吉田 天士
学位規則第4条第1項該当
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5

Inoue, Takahiro. "Genetic engineering studies of Ni-carbon monoxide dehydrogenase from a thermophilic carboxydotrophic bacterium." Kyoto University, 2014. http://hdl.handle.net/2433/188777.

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Kyoto University (京都大学)
0048
新制・課程博士
博士(農学)
甲第18339号
農博第2064号
新制||農||1023(附属図書館)
学位論文||H26||N4846(農学部図書室)
31197
京都大学大学院農学研究科応用生物科学専攻
(主査)教授 左子 芳彦, 教授 澤山 茂樹, 教授 菅原 達也
学位規則第4条第1項該当
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6

Ramió, Pujol Sara. "Insights into key parameters for bio-alcohol production in syngas fermentation using model carboxydotrophic bacteria." Doctoral thesis, Universitat de Girona, 2016. http://hdl.handle.net/10803/388041.

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This doctoral thesis deals with the synthesis of two biofuels (bioethanol and biobuthanol) by bacteria. Concretely, the thesis is focused on a group of bacteria able to grow in a simple substrate such as synthesis gas or syngas. Syngas is a mixture of hydrogen, carbon monoxide, and carbon dioxide obtained through the gasification of urban and forestry wastes. The use of syngas as a substrate requires a good knowledge of bacterial metabolism to successfully control acid production and promote alcohol synthesis. To acquire this knowledge, the researcher carried out a set of experiments at lab scale, always using syngas. Among the most significant results, there is the relevance of both the temperature and the bacteria state at the start of the experiments. Additionally, new insights into bacterial metabolism which are applicable at industrial scale were gathered.
Aquesta tesi doctoral tracta la producció de dos biocombustibles – el bioetanol i el bioalcohol - per mitjà de microorganismes. En concret, la tesi s'ha centrat en un grup de bacteris capaços de sintetitzar bioalcohols a partir del gas de síntesis o syngas. El syngas és una mescla d’hidrogen, diòxid de carboni i monòxid de carboni que s’obté mitjançant la gasificació de diferents tipus de residus. L’ús d’aquest gas com a substrat requereix un bon coneixement del metabolisme dels bacteris involucrats a fi de controlar amb èxit la producció d'àcids i afavorir la d'alcohols. Aquest coneixement s'ha adquirit amb una sèrie d'experiments avançats a escala de laboratori. Entre els resultats més significatius destaca la rellevància que ha demostrat tenir la temperatura en què creixen els bacteris i l’estat del bacteri en el moment d’inici dels experiments. També s’han aportat nous coneixements sobre el metabolisme bacterià que són aplicables a escala industrial.
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Books on the topic "Carboxydotrophs"

1

Tiquia-Arashiro, Sonia M. Thermophilic Carboxydotrophs and their Applications in Biotechnology. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11873-4.

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2

Tiquia-Arashiro, Sonia M. Thermophilic Carboxydotrophs and their Applications in Biotechnology. Springer, 2014.

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Book chapters on the topic "Carboxydotrophs"

1

Tiquia-Arashiro, Sonia M. "Biotechnological Applications of Thermophilic Carboxydotrophs." In Thermophilic Carboxydotrophs and their Applications in Biotechnology, 29–101. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11873-4_4.

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Tiquia-Arashiro, Sonia M. "Introduction." In Thermophilic Carboxydotrophs and their Applications in Biotechnology, 1–3. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11873-4_1.

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Tiquia-Arashiro, Sonia M. "Microbial CO Metabolism." In Thermophilic Carboxydotrophs and their Applications in Biotechnology, 5–9. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11873-4_2.

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Tiquia-Arashiro, Sonia M. "CO-oxidizing Microorganisms." In Thermophilic Carboxydotrophs and their Applications in Biotechnology, 11–28. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11873-4_3.

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Tiquia-Arashiro, Sonia M. "Conclusions." In Thermophilic Carboxydotrophs and their Applications in Biotechnology, 103–4. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-11873-4_5.

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