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Lindsay MR, D’Angelo T, Munson-McGee JH, Saidi-Mehrabad A, Devlin M, McGonigle J, Goodell E, Herring M, Lubelczyk LC, Mascena C, Brown JM, Gavelis G, Liu J, Yousavich DJ, Hamilton-Brehm SD, Hedlund BP, Lang S, Treude T, Poulton NJ, Stepanauskas R, Moser DP, Emerson D, Orcutt BN. Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem. Proc Natl Acad Sci U S A 2024; 121:e2309636121. [PMID: 38573964 PMCID: PMC11009646 DOI: 10.1073/pnas.2309636121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.
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Affiliation(s)
| | | | | | | | - Molly Devlin
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Elizabeth Goodell
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Geology, Oberlin College, Oberlin, OH44074
| | - Melissa Herring
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA02115
| | | | | | - Julia M. Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Greg Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Jiarui Liu
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | - D. J. Yousavich
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Susan Lang
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC29208
| | - Tina Treude
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
- Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | | | - Duane P. Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
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Akaçin İ, Ersoy Ş, Doluca O, Güngörmüşler M. Using custom-built primers and nanopore sequencing to evaluate CO-utilizer bacterial and archaeal populations linked to bioH 2 production. Sci Rep 2023; 13:17025. [PMID: 37813931 PMCID: PMC10562470 DOI: 10.1038/s41598-023-44357-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023] Open
Abstract
The microbial community composition of five distinct thermophilic hot springs was effectively described in this work, using broad-coverage nanopore sequencing (ONT MinION sequencer). By examining environmental samples from the same source, but from locations with different temperatures, bioinformatic analysis revealed dramatic changes in microbial diversity and archaeal abundance. More specifically, no archaeal presence was reported with universal bacterial primers, whereas a significant archaea presence and also a wider variety of bacterial species were reported. These results revealed the significance of primer preference for microbiomes in extreme environments. Bioinformatic analysis was performed by aligning the reads to 16S microbial databases for identification using three different alignment methods, Epi2Me (Fastq 16S workflow), Kraken, and an in-house BLAST tool, including comparison at the genus and species levels. As a result, this approach to data analysis had a significant impact on the genera identified, and thus, it is recommended that use of multiple analysis tools to support findings on taxonomic identification using the 16S region until more precise bioinformatics tools become available. This study presents the first compilation of the ONT-based inventory of the hydrogen producers in the designated hot springs in Türkiye.
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Affiliation(s)
- İlayda Akaçin
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Şeymanur Ersoy
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Osman Doluca
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
- Department of Biomedical Engineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye
| | - Mine Güngörmüşler
- Division of Bioengineering, Graduate School, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
- Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Sakarya Caddesi No: 156, 35330, Balçova, Izmir, Türkiye.
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Balbay MG, Shlafstein MD, Cockell C, Cady SL, Prescott RD, Lim DSS, Chain PSG, Donachie SP, Decho AW, Saw JH. Metabolic versatility of Caldarchaeales from geothermal features of Hawai'i and Chile as revealed by five metagenome-assembled genomes. Front Microbiol 2023; 14:1216591. [PMID: 37799600 PMCID: PMC10547907 DOI: 10.3389/fmicb.2023.1216591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023] Open
Abstract
Members of the archaeal order Caldarchaeales (previously the phylum Aigarchaeota) are poorly sampled and are represented in public databases by relatively few genomes. Additional representative genomes will help resolve their placement among all known members of Archaea and provide insights into their roles in the environment. In this study, we analyzed 16S rRNA gene amplicons belonging to the Caldarchaeales that are available in public databases, which demonstrated that archaea of the order Caldarchaeales are diverse, widespread, and most abundant in geothermal habitats. We also constructed five metagenome-assembled genomes (MAGs) of Caldarchaeales from two geothermal features to investigate their metabolic potential and phylogenomic position in the domain Archaea. Two of the MAGs were assembled from microbial community DNA extracted from fumarolic lava rocks from Mauna Ulu, Hawai'i, and three were assembled from DNA obtained from hot spring sinters from the El Tatio geothermal field in Chile. MAGs from Hawai'i are high quality bins with completeness >95% and contamination <1%, and one likely belongs to a novel species in a new genus recently discovered at a submarine volcano off New Zealand. MAGs from Chile have lower completeness levels ranging from 27 to 70%. Gene content of the MAGs revealed that these members of Caldarchaeales are likely metabolically versatile and exhibit the potential for both chemoorganotrophic and chemolithotrophic lifestyles. The wide array of metabolic capabilities exhibited by these members of Caldarchaeales might help them thrive under diverse harsh environmental conditions. All the MAGs except one from Chile harbor putative prophage regions encoding several auxiliary metabolic genes (AMGs) that may confer a fitness advantage on their Caldarchaeales hosts by increasing their metabolic potential and make them better adapted to new environmental conditions. Phylogenomic analysis of the five MAGs and over 3,000 representative archaeal genomes showed the order Caldarchaeales forms a monophyletic group that is sister to the clade comprising the orders Geothermarchaeales (previously Candidatus Geothermarchaeota), Conexivisphaerales and Nitrososphaerales (formerly known as Thaumarchaeota), supporting the status of Caldarchaeales members as a clade distinct from the Thaumarchaeota.
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Affiliation(s)
- Manolya Gul Balbay
- Department of Biological Sciences, The George Washington University, Washington, DC, United States
| | | | - Charles Cockell
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Sherry L. Cady
- Department of Geology, Portland State University, Portland, OR, United States
| | - Rebecca D. Prescott
- UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, United States
- Department of Biology, University of Mississippi, Oxford, MS, United States
| | | | | | - Stuart P. Donachie
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alan W. Decho
- Department of Environmental Health Sciences, University of South Carolina, Columbia, SC, United States
| | - Jimmy H. Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, United States
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Nishida S, Omae K, Inoue M, Sako Y, Kamikawa R, Yoshida T. Construction of multiple metagenome assembled genomes containing carbon monoxide dehydrogenases from anaerobic carbon monoxide enrichment cultures. Arch Microbiol 2023; 205:292. [PMID: 37470847 DOI: 10.1007/s00203-023-03635-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
Despite its toxicity to many organisms, including most prokaryotes, carbon monoxide (CO) is utilized by some aerobic and anaerobic prokaryotes. Hydrogenogenic CO utilizers employ carbon monoxide dehydrogenase (CODH) and energy-converting hydrogenase (ECH) to oxidize CO and reduce protons to produce H2. Those prokaryotes constitute a rare biosphere and are difficult to detect even with PCR amplification and with metagenomic analyses. In this study, anaerobic CO-enrichment cultures followed by construction of metagenome assembled genomes (MAGs) detected high-quality MAGs from potential hydrogenogenic CO utilizers. Of 32 MAGs constructed, 5 were potential CO utilizer harboring CODH genes. Of the five MAGs, two were classified into the genus Thermolithobacter on the basis of 16S rRNA sequence identity, related to Carboxydocella tharmautotrophica 41, with an average nucleotide identity (ANI) of approximately 72%. Additionally, two were related to Geoglobus acetivorans with ANI values ranging from 75 to 77% to G. acetivorans SBH6, and one MAG was identified as Desulfotomaculum kuznetsovii with an ANI > 96% to D. kuznetsovii DSM 6115. The two Thermolithobacter MAGs identified in this study contained CODH-ECH gene clusters, and were therefore identified as potential hydrogenogenic CO utilizers. However, these MAGs harbored three CODH gene clusters that showed distinct physiological functions in addition to CODH-ECH gene clusters. In total, the five potential CO utilizer MAGs contained sixteen CODH genes. Among those CODHs, four sets did not cluster with any known CODH protein sequences (with an identity of > 90%), and the CODH database was expanded.
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Affiliation(s)
- Shiho Nishida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kimiho Omae
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Masao Inoue
- R-GIRO, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ryoma Kamikawa
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
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5
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Sobieraj K, Stegenta-Dąbrowska S, Zafiu C, Binner E, Białowiec A. Carbon Monoxide Production during Bio-Waste Composting under Different Temperature and Aeration Regimes. MATERIALS (BASEL, SWITZERLAND) 2023; 16:4551. [PMID: 37444865 DOI: 10.3390/ma16134551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023]
Abstract
Despite the development of biorefinery processes, the possibility of coupling the "conventional" composting process with the production of biochemicals is not taken into account. However, net carbon monoxide (CO) production has been observed during bio-waste composting. So far, O2 concentration and temperature have been identified as the main variables influencing CO formation. This study aimed to investigate CO net production during bio-waste composting under controlled laboratory conditions by varying aeration rates and temperatures. A series of composting processes was carried out in conditions ranging from mesophilic to thermophilic (T = 35, 45, 55, and 65 °C) and an aeration rate of 2.7, 3.4, 4.8, and 7.8 L·h-1. Based on the findings of this study, suggestions for the improvement of CO production throughout the composting process have been developed for the first time. The highest concentrations of CO in each thermal variant was achieved with an O2 deficit (aeration rate 2.7 L·h-1); additionally, CO levels increased with temperature, reaching ~300 ppm at 65 °C. The production of CO in mesophilic and thermophilic conditions draws attention to biological CO formation by microorganisms capable of producing the CODH enzyme. Further research on CO production efficiency in these thermal ranges is necessary with the characterization of the microbial community and analysis of the ability of the identified bacteria to produce the CODH enzyme and convert CO from CO2.
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Affiliation(s)
- Karolina Sobieraj
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, 37a Chełmońskiego Str., 51-630 Wrocław, Poland
| | - Sylwia Stegenta-Dąbrowska
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, 37a Chełmońskiego Str., 51-630 Wrocław, Poland
| | - Christian Zafiu
- Department of Water-Atmosphere-Environment, Institute of Waste Management and Circularity, University of Natural Resources and Life Sciences, Muthgasse 107, 1190 Vienna, Austria
| | - Erwin Binner
- Department of Water-Atmosphere-Environment, Institute of Waste Management and Circularity, University of Natural Resources and Life Sciences, Muthgasse 107, 1190 Vienna, Austria
| | - Andrzej Białowiec
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, 37a Chełmońskiego Str., 51-630 Wrocław, Poland
- Department of Agricultural and Biosystems Engineering, Iowa State University, 605 Bissell Road, Ames, IA 50011, USA
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6
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Sorokin DY, Merkel AY, Messina E, Tugui C, Pabst M, Golyshin PN, Yakimov MM. Anaerobic carboxydotrophy in sulfur-respiring haloarchaea from hypersaline lakes. THE ISME JOURNAL 2022; 16:1534-1546. [PMID: 35132120 PMCID: PMC9123189 DOI: 10.1038/s41396-022-01206-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/03/2022] [Accepted: 01/27/2022] [Indexed: 05/24/2023]
Abstract
Anaerobic carboxydotrophy is a widespread catabolic trait in bacteria, with two dominant pathways: hydrogenogenic and acetogenic. The marginal mode by direct oxidation to CO2 using an external e-acceptor has only a few examples. Use of sulfidic sediments from two types of hypersaline lakes in anaerobic enrichments with CO as an e-donor and elemental sulfur as an e-acceptor led to isolation of two pure cultures of anaerobic carboxydotrophs belonging to two genera of sulfur-reducing haloarchaea: Halanaeroarchaeum sp. HSR-CO from salt lakes and Halalkaliarchaeum sp. AArc-CO from soda lakes. Anaerobic growth of extremely halophilic archaea with CO was obligatory depended on the presence of elemental sulfur as the electron acceptor and yeast extract as the carbon source. CO served as a direct electron donor and H2 was not generated from CO when cells were incubated with or without sulfur. The genomes of the isolates encode a catalytic Ni,Fe-CODH subunit CooS (distantly related to bacterial homologs) and its Ni-incorporating chaperone CooC (related to methanogenic homologs) within a single genomic locus. Similar loci were also present in a genome of the type species of Halalkaliarchaeum closely related to AArc-CO, and the ability for anaerobic sulfur-dependent carboxydotrophy was confirmed for three different strains of this genus. Moreover, similar proteins are encoded in three of the four genomes of recently described carbohydrate-utilizing sulfur-reducing haloarchaea belonging to the genus Halapricum and in two yet undescribed haloarchaeal species. Overall, this work demonstrated for the first time the potential for anaerobic sulfur-dependent carboxydotrophy in extremely halophilic archaea.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia.
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Enzo Messina
- IRBIM-CNR, Spianata S.Raineri 86, 98122, Messina, Italy
| | - Claudia Tugui
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Gwynedd, LL57 2UW, UK
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Hotta Y, Yagoshi C, Okazaki R, Ikeda M. Studies on the inhibition of methanogenesis and dechlorination by (4-hydroxyphenyl) chloromethanesulfonate. JOURNAL OF PESTICIDE SCIENCE 2022; 47:69-77. [PMID: 35800391 PMCID: PMC9184246 DOI: 10.1584/jpestics.d21-071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
The purpose of this study was to demonstrate the inhibitory effect of chemicals on methane emissions in paddy soil. We found that (4-hydroxyphenyl) chloromethanesulfonate (C-1) has a methanogenic inhibition activity, and we studied its inhibition mechanism using laboratory tests. The study found that C-1 treatment of flooded soil did not significantly affect the bacterial community but rather the archaeal community; particularly, Methanosarcina spp. C-1 strongly inhibited the aceticlastic methanogenesis route. It was suggested that the inhibitory target of C-1 was different from the well-known methanogenic inhibitor 2-bromoethanesulfonate, which targets methyl-coenzyme M reductase of methanogen. In addition, C-1 had a secondary effect of inhibiting the dechlorination of chlorophenols. Although field trials are required as the next development step, C-1 can be used to reduce methane emissions from paddy fields, one of the largest sources in the agricultural sector.
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Affiliation(s)
- Yudai Hotta
- Life Science Research Institute, Kumiai Chemical Industry Co. Ltd., Tamari, Kakegawa, Shizuoka 436–0011, Japan
| | - Chizu Yagoshi
- Life Science Research Institute, Kumiai Chemical Industry Co. Ltd., Tamari, Kakegawa, Shizuoka 436–0011, Japan
| | - Ryo Okazaki
- Life Science Research Institute, Kumiai Chemical Industry Co. Ltd., Tamari, Kakegawa, Shizuoka 436–0011, Japan
| | - Mitsumasa Ikeda
- Life Science Research Institute, Kumiai Chemical Industry Co. Ltd., Tamari, Kakegawa, Shizuoka 436–0011, Japan
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DePoy AN, King GM. Putative Nickel-Dependent Anaerobic Carbon Monoxide Uptake Occurs Commonly in Soils and Sediments at Ambient Temperature and Might Contribute to Atmospheric and Sub-Atmospheric Carbon Monoxide Uptake During Anoxic Conditions. Front Microbiol 2022; 13:736189. [PMID: 35401450 PMCID: PMC8987735 DOI: 10.3389/fmicb.2022.736189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Carbon monoxide (CO) occurs naturally in the atmosphere where it plays a critical role in tropospheric chemistry. Atmospheric CO uptake by soils has been well documented as an important CO sink and has been attributed to a group of aerobic bacteria that possess a molybdenum-dependent CO dehydrogenase (Mo-CODH). CO can also be oxidized by obligate Ni-dependent anaerobes (Ni-COX) that possess nickel-dependent CODHs (Ni-CODH) but relatively little is known about their ecology or their potential to contribute to CO dynamics within soils and sediments or to soil-atmosphere CO exchanges. Results from a series of assays undertaken with diverse soils and sediments and CO concentrations of 10 ppm and 25% with incubation temperatures of 10, 25, and 60°C revealed anaerobic uptake rates with 10 ppm CO that were comparable to those measured under oxic conditions; further, anaerobic CO uptake occurred without a lag and at atmospheric and sub-atmospheric CO concentrations. Assays with 25% CO revealed previously undocumented activity at 10°C and showed extensive activity at 25°C. Results from prior studies with isolates and soils suggest that anaerobic uptake at both 10 ppm and 25% CO concentrations might be attributed to Ni-COX. Collectively the results considerably expand the ecological range for Ni-COX and indicate that they could play previously unsuspected roles in soil CO dynamics.
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10
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Inoue M, Omae K, Nakamoto I, Kamikawa R, Yoshida T, Sako Y. Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases. Extremophiles 2022; 26:9. [PMID: 35059858 PMCID: PMC8776680 DOI: 10.1007/s00792-022-01259-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/04/2022] [Indexed: 11/24/2022]
Abstract
Ni-containing carbon monoxide dehydrogenase (Ni-CODH) plays an important role in the CO/CO2-based carbon and energy metabolism of microbiomes. Ni-CODH is classified into distinct phylogenetic clades, A–G, with possibly distinct cellular roles. However, the types of Ni-CODH clade used by organisms in different microbiomes are unknown. Here, we conducted a metagenomic survey of a protein database to determine the relationship between the phylogeny and biome distribution of Ni-CODHs. Clustering and phylogenetic analyses showed that the metagenome assembly-derived Ni-CODH sequences were distributed in ~ 60% Ni-CODH clusters and in all Ni-CODH clades. We also identified a novel Ni-CODH clade, clade H. Biome mapping on the Ni-CODH phylogenetic tree revealed that Ni-CODHs of almost all the clades were found in natural aquatic environmental and engineered samples, whereas those of specific subclades were found only in host-associated samples. These results are comparable with our finding that the diversity in the phylum-level taxonomy of host-associated Ni-CODH owners is statistically different from those of the other biomes. Our findings suggest that while Ni-CODH is a ubiquitous enzyme produced across diverse microbiomes, its distribution in each clade is biased and mainly affected by the distinct composition of microbiomes.
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Affiliation(s)
- Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
- R-GIRO, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga, 525-8577, Japan.
| | - Kimiho Omae
- Department of Integrated Biosciences, Graduate School of Frontier Science, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Issei Nakamoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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Anaerobic Digestion of the Organic Fraction of Municipal Solid Waste in Plug-Flow Reactors: Focus on Bacterial Community Metabolic Pathways. WATER 2022. [DOI: 10.3390/w14020195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of this study is to investigate the performance of a pilot-scale plug-flow reactor (PFR) as a biorefinery system to recover chemicals (i.e., volatile fatty acids (VFAs)), and biogas during the dry thermophilic anaerobic digestion (AD) of the organic fraction of municipal solid waste (OFMSW). The effects of the hydraulic retention time (HRT) on both outputs were studied, reducing the parameter from 22 to 16 days. In addition, VFA variation along the PFR was also evaluated to identify a section for a further valorization of VFA-rich digestate stream. A particular focus was dedicated for characterizing the community responsible for the production of VFAs during hydrolysis and acidogenesis. The VFA concentration reached 4421.8 mg/L in a section located before the end of the PFR when the HRT was set to 16 days. Meanwhile, biogas production achieved 145 NLbiogas/d, increasing 2.7 times when compared to the lowest HRT tested. Defluviitoga sp. was the most abundant bacterial genus, contributing to 72.7% of the overall bacterial population. The genus is responsible for the hydrolysis of complex polysaccharides at the inlet and outlet sections since a bimodal distribution of the genus was found. The central zone of the reactor was distinctly characterized by protein degradation, following the same trend of propionate production.
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Jain S, Katsyv A, Basen M, Müller V. The monofunctional CO dehydrogenase CooS is essential for growth of Thermoanaerobacter kivui on carbon monoxide. Extremophiles 2021; 26:4. [PMID: 34919167 PMCID: PMC8683389 DOI: 10.1007/s00792-021-01251-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Abstract
Thermoanaerobacter kivui is a thermophilic acetogen that can grow on carbon monoxide as sole carbon and energy source. To identify the gene(s) involved in CO oxidation, the genome sequence was analyzed. Two genes potentially encoding CO dehydrogenases were identified. One, cooS, potentially encodes a monofunctional CO dehydrogenase, whereas another, acsA, potentially encodes the CODH component of the CODH/ACS complex. Both genes were cloned, a His-tag encoding sequence was added, and the proteins were produced from a plasmid in T. kivui. His-AcsA copurified by affinity chromatography with AcsB, the acetyl-CoA synthase of the CO dehydrogenase/acetyl CoA synthase complex. His-CooS copurified with CooF1, a small iron-sulfur center containing protein likely involved in electron transport. Both protein complexes had CO:ferredoxin oxidoreductase as well as CO:methyl viologen oxidoreductase activity, but the activity of CooSF1 was 15-times and 231-times lower, respectively. To underline the importance of CooS, the gene was deleted in the CO-adapted strain. Interestingly, the ∆cooS deletion mutant did not grow on CO anymore. These experiments clearly demonstrated that CooS is essential for growth of T. kivui on CO. This is in line with the hypothesis that CooS is the CO-oxidizing enzyme in cells growing on CO.
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Affiliation(s)
- Surbhi Jain
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Alexander Katsyv
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
| | - Mirko Basen
- Microbiology, Institute of Biological Sciences, University of Rostock, 18059, Rostock, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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13
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Li C, Zhu X, Angelidaki I. Syngas biomethanation: effect of biomass-gas ratio, syngas composition and pH buffer. BIORESOURCE TECHNOLOGY 2021; 342:125997. [PMID: 34583116 DOI: 10.1016/j.biortech.2021.125997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
The concept of syngas biomethanation is attractive, however, it still needs improvement in optimizing the operational conditions. In the present study, syngas fermentations under different carbon monoxide (CO), carbon dioxide (CO2) and hydrogen (H2) compositions were conducted under two different biomass-gas ratio (BGR) systems. The results showed that high BGR enhanced the CO consumption rate, achieving a 60% enhancement with CO as the sole substrate. Stoichiometric H2 addition could successfully convert all the CO and CO2 to pure methane, however, higher H2 partial pressure might decline the CO consumption due to pH inhibition from consumption of bicarbonate. Microbial analysis showed different syngas composition could affect the bacteria community, while, archaea community was only slightly affected with Methanothermobacter as the dominant methanogen. This study provided strategy for efficient syngas biomethanation and deeper insight into effect of H2 addition on CO conversion under different BGR systems.
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Affiliation(s)
- Chunxing Li
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - Xinyu Zhu
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.
| | - Irini Angelidaki
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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14
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Duan H, He P, Shao L, Lü F. Functional genome-centric view of the CO-driven anaerobic microbiome. THE ISME JOURNAL 2021; 15:2906-2919. [PMID: 33911204 PMCID: PMC8443622 DOI: 10.1038/s41396-021-00983-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 03/17/2021] [Accepted: 04/09/2021] [Indexed: 02/02/2023]
Abstract
CO is a promising substrate for producing biochemicals and biofuels through mixed microbial cultures, where carboxydotrophs play a crucial role. The previous investigations of mixed microbial cultures focused primarily on overall community structures, but under-characterized taxa and intricate microbial interactions have not yet been precisely explicated. Here, we undertook DNA-SIP based metagenomics to profile the anaerobic CO-driven microbiomes under 95 and 35% CO atmospheres. The time-series analysis of the isotope-labeled amplicon sequencing revealed the essential roles of Firmicutes and Proteobacteria under high and low CO pressure, respectively, and Methanobacterium was the predominant archaeal genus. The functional enrichment analysis based on the isotope-labeled metagenomes suggested that the microbial cultures under high CO pressure had greater potential in expressing carboxylate metabolism and citrate cycle pathway. The genome-centric metagenomics reconstructed 24 discovered and 24 under-characterized metagenome-assembled genomes (MAGs), covering more than 94% of the metagenomic reads. The metabolic reconstruction of the MAGs described their potential functions in the CO-driven microbiomes. Some under-characterized taxa might be versatile in multiple processes; for example, under-characterized Rhodoplanes sp. and Desulfitobacterium_A sp. could encode the complete enzymes in CO oxidation and carboxylate production, improving functional redundancy. Finally, we proposed the putative microbial interactions in the conversion of CO to carboxylates and methane.
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Affiliation(s)
- Haowen Duan
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China
| | - Pinjing He
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Liming Shao
- Institute of Waste Treatment and Reclamation, Tongji University, Shanghai, China
| | - Fan Lü
- State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai, China.
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China.
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15
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Abstract
In recent years, the tree of life has expanded substantially. Despite this, many abundant yet uncultivated microbial groups remain to be explored. Sumerlaeota is a mysterious, putative phylum-level lineage distributed globally but rarely reported. As such, their physiology, ecology, and evolutionary history remain unknown. The 16S rRNA gene survey reveals that Sumerlaeota is frequently detected in diverse environments globally, especially cold arid desert soils and deep-sea basin surface sediments, where it is one dominant microbial group. Here, we retrieved four Sumerlaeota metagenome-assembled genomes (MAGs) from two hot springs and one saline lake. Including another 12 publicly available MAGs, they represent six of the nine putative Sumerlaeota subgroups/orders, as indicated by 16S rRNA gene-based phylogeny. These elusive organisms likely obtain carbon mainly through utilization of refractory organics (e.g., chitin and cellulose) and proteinaceous compounds, suggesting that Sumerlaeota act as scavengers in nature. The presence of key bidirectional enzymes involved in acetate and hydrogen metabolisms in these MAGs suggests that they are acetogenic bacteria capable of both the production and consumption of hydrogen. The capabilities of dissimilatory nitrate and sulfate reduction, nitrogen fixation, phosphate solubilization, and organic phosphorus mineralization may confer these heterotrophs great advantages to thrive under diverse harsh conditions. Ancestral state reconstruction indicated that Sumerlaeota originated from chemotrophic and facultatively anaerobic ancestors, and their smaller and variably sized genomes evolved along dynamic pathways from a sizeable common ancestor (2,342 genes), leading to their physiological divergence. Notably, large gene gain and larger loss events occurred at the branch to the last common ancestor of the order subgroup 1, likely due to niche expansion and population size effects.
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16
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DePoy AN, King GM, Ohta H. Anaerobic Carbon Monoxide Uptake by Microbial Communities in Volcanic Deposits at Different Stages of Successional Development on O-yama Volcano, Miyake-jima, Japan. Microorganisms 2020; 9:E12. [PMID: 33375160 PMCID: PMC7822213 DOI: 10.3390/microorganisms9010012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/14/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Research on Kilauea and O-yama Volcanoes has shown that microbial communities and their activities undergo major shifts in response to plant colonization and that molybdenum-dependent CO oxidizers (Mo-COX) and their activities vary with vegetation and deposit age. Results reported here reveal that anaerobic CO oxidation attributed to nickel-dependent CO oxidizers (Ni-COX) also occurs in volcanic deposits that encompass different developmental stages. Ni-COX at three distinct sites responded rapidly to anoxia and oxidized CO from initial concentrations of about 10 ppm to sub-atmospheric levels. CO was also actively consumed at initial 25% concentrations and 25 °C, and during incubations at 60 °C; however, uptake under the latter conditions was largely confined to an 800-year-old forested site. Analyses of microbial communities based on 16S rRNA gene sequences in treatments with and without 25% CO incubated at 25 °C or 60 °C revealed distinct responses to temperature and CO among the sites and evidence for enrichment of known and potentially novel Ni-COX. The results collectively show that CO uptake by volcanic deposits occurs under a wide range of conditions; that CO oxidizers in volcanic deposits may be more diverse than previously imagined; and that Ni-dependent CO oxidizers might play previously unsuspected roles in microbial succession.
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Affiliation(s)
- Amber N. DePoy
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Gary M. King
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Hiroyuki Ohta
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami-machi, Ibaraki 300-0393, Japan;
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17
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Alves JI, Visser M, Arantes AL, Nijsse B, Plugge CM, Alves MM, Stams AJM, Sousa DZ. Effect of Sulfate on Carbon Monoxide Conversion by a Thermophilic Syngas-Fermenting Culture Dominated by a Desulfofundulus Species. Front Microbiol 2020; 11:588468. [PMID: 33304333 PMCID: PMC7701048 DOI: 10.3389/fmicb.2020.588468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
A syngas-degrading enrichment culture, culture T-Syn, was dominated by a bacterium closely related to Desulfofundulus australicus strain AB33T (98% 16S rRNA gene sequence identity). Culture T-Syn could convert high CO concentrations (from pCO ≈ 34 kPa to pCO ≈ 170 kPa), both in the absence and in the presence of sulfate as external electron acceptor. The products formed from CO conversion were H2 and acetate. With sulfate, a lower H2/acetate ratio was observed in the product profile, but CO conversion rates were similar to those in the absence of sulfate. The ability of D. australicus strain AB33T to use CO was also investigated. D. australicus strain AB33T uses up to 40% CO (pCO ≈ 68 kPa) with sulfate and up to 20% CO (pCO ≈ 34 kPa) without sulfate. Comparison of the metagenome-assembled genome (MAG) of the Desulfofundulus sp. from T-Syn culture with the genome of D. australicus strain AB33T revealed high similarity, with an ANI value of 99% and only 32 unique genes in the genome of the Desulfofundulus sp. T-Syn. So far, only Desulfotomaculum nigrificans strain CO-1-SRB had been described to grow with CO with and without sulfate. This work further shows the carboxydotrophic potential of Desulfofundulus genus for CO conversion, both in sulfate-rich and low-sulfate environments.
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Affiliation(s)
- Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Michael Visser
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Ana L Arantes
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Bart Nijsse
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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18
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Influence of Liquid-to-Gas Ratio on the Syngas Fermentation Efficiency: An Experimental Approach. Bioengineering (Basel) 2020; 7:bioengineering7040138. [PMID: 33142703 PMCID: PMC7712742 DOI: 10.3390/bioengineering7040138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 11/17/2022] Open
Abstract
Syngas fermentation by methanogens is a novel process to purify biogas. Methanogens are able to ferment non-desirable CO2, H2, and CO to methane. However, to use methanogens on an industrial scale, more research has to be done. There are studies that discuss the growth of methanogens on syngas in combination with acetate. In this research, growth of methanogens on syngas as sole carbon source is discussed. Effluent of an anaerobic fed-batch was selectively cultivated with syngas in 400 mL Eppendorf© bioreactors. After a period of 7 days, fifteen 120 mL flasks were filled with three different liquid-to-gas ratios (1:1, 1:3, 1:5). Results showed that different liquid-to-gas ratios change the metabolic preference of the anaerobic microbial community. Moreover, complete conversion in a four-to-eight-day period, via the carboxidotrophic pathway, was observed in all three liquid-to-gas ratios.
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19
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Zhou Z, Tran PQ, Kieft K, Anantharaman K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME JOURNAL 2020; 14:2060-2077. [PMID: 32393808 PMCID: PMC7367891 DOI: 10.1038/s41396-020-0669-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/15/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Proteobacteria constitute one of the most diverse and abundant groups of microbes on Earth. In productive marine environments like deep-sea hydrothermal systems, Proteobacteria are implicated in autotrophy coupled to sulfur, methane, and hydrogen oxidation, sulfate reduction, and denitrification. Beyond chemoautotrophy, little is known about the ecological significance of poorly studied Proteobacteria lineages that are globally distributed and active in hydrothermal systems. Here we apply multi-omics to characterize 51 metagenome-assembled genomes from three hydrothermal vent plumes in the Pacific and Atlantic Oceans that are affiliated with nine Proteobacteria lineages. Metabolic analyses revealed these organisms to contain a diverse functional repertoire including chemolithotrophic ability to utilize sulfur and C1 compounds, and chemoorganotrophic ability to utilize environment-derived fatty acids, aromatics, carbohydrates, and peptides. Comparative genomics with marine and terrestrial microbiomes suggests that lineage-associated functional traits could explain niche specificity. Our results shed light on the ecological functions and metabolic strategies of novel Proteobacteria in hydrothermal systems and beyond, and highlight the relationship between genome diversification and environmental adaptation.
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Affiliation(s)
- Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Patricia Q Tran
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Kristopher Kieft
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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20
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Inoue M, Izumihara H, Fukuyama Y, Omae K, Yoshida T, Sako Y. Carbon monoxide-dependent transcriptional changes in a thermophilic, carbon monoxide-utilizing, hydrogen-evolving bacterium Calderihabitans maritimus KKC1 revealed by transcriptomic analysis. Extremophiles 2020; 24:551-564. [PMID: 32388815 PMCID: PMC7306483 DOI: 10.1007/s00792-020-01175-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/27/2020] [Indexed: 11/30/2022]
Abstract
Calderihabitans maritimus KKC1 is a thermophilic, carbon monoxide (CO)-utilizing, hydrogen-evolving bacterium that harbors seven cooS genes for anaerobic CO dehydrogenases and six hyd genes for [NiFe] hydrogenases and capable of using a variety of electron acceptors coupled to CO oxidation. To understand the relationships among these unique features and the transcriptional adaptation of the organism to CO, we performed a transcriptome analysis of C. maritimus KKC1 grown under 100% CO and N2 conditions. Of its 3114 genes, 58 and 32 genes were significantly upregulated and downregulated in the presence of CO, respectively. A cooS–ech gene cluster, an “orphan” cooS gene, and bidirectional hyd genes were upregulated under CO, whereas hydrogen-uptake hyd genes were downregulated. Transcriptional changes in anaerobic respiratory genes supported the broad usage of electron acceptors in C. maritimus KKC1 under CO metabolism. Overall, the majority of the differentially expressed genes were oxidoreductase-like genes, suggesting metabolic adaptation to the cellular redox change upon CO oxidation. Moreover, our results suggest a transcriptional response mechanism to CO that involves multiple transcription factors, as well as a CO-responsive transcriptional activator (CooA). Our findings shed light on the diverse mechanisms for transcriptional and metabolic adaptations to CO in CO-utilizing and hydrogen-evolving bacteria.
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Affiliation(s)
- Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hikaru Izumihara
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuto Fukuyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kimiho Omae
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.
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21
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Kochetkova TV, Mardanov AV, Sokolova TG, Bonch-Osmolovskaya EA, Kublanov IV, Kevbrin VV, Beletsky AV, Ravin NV, Lebedinsky AV. The first crenarchaeon capable of growth by anaerobic carbon monoxide oxidation coupled with H2 production. Syst Appl Microbiol 2020; 43:126064. [DOI: 10.1016/j.syapm.2020.126064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 12/01/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022]
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22
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Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. mSystems 2020; 5:5/1/e00795-19. [PMID: 31911466 PMCID: PMC6946796 DOI: 10.1128/msystems.00795-19] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.
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Fukuyama Y, Inoue M, Omae K, Yoshida T, Sako Y. Anaerobic and hydrogenogenic carbon monoxide-oxidizing prokaryotes: Versatile microbial conversion of a toxic gas into an available energy. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:99-148. [PMID: 32386607 DOI: 10.1016/bs.aambs.2019.12.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbon monoxide (CO) is a gas that is toxic to various organisms including humans and even microbes; however, it has low redox potential, which can fuel certain microbes, namely, CO oxidizers. Hydrogenogenic CO oxidizers utilize an energy conservation system via a CO dehydrogenase/energy-converting hydrogenase complex to produce hydrogen gas, a zero emission fuel, by CO oxidation coupled with proton reduction. Biochemical and molecular biological studies using a few model organisms have revealed their enzymatic reactions and transcriptional response mechanisms using CO. Biotechnological studies for CO-dependent hydrogen production have also been carried out with these model organisms. In this chapter, we review recent advances in the studies of these microbes, which reveal their unique and versatile metabolic profiles and provides future perspectives on ecological roles and biotechnological applications. Over the past decade, the number of isolates has doubled (37 isolates in 5 phyla, 20 genera, and 32 species). Some of the recently isolated ones show broad specificity to electron acceptors. Moreover, accumulating genomic information predicts their unique physiologies and reveals their phylogenomic relationships with novel potential hydrogenogenic CO oxidizers. Combined with genomic database surveys, a molecular ecological study has unveiled the wide distribution and low abundance of these microbes. Finally, recent biotechnological applications of hydrogenogenic CO oxidizers have been achieved via diverse approaches (e.g., metabolic engineering and co-cultivation), and the identification of thermophilic facultative anaerobic CO oxidizers will promote industrial applications as oxygen-tolerant biocatalysts for efficient hydrogen production by genomic engineering.
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Affiliation(s)
- Yuto Fukuyama
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Masao Inoue
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kimiho Omae
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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Mohr T, Aliyu H, Biebinger L, Gödert R, Hornberger A, Cowan D, de Maayer P, Neumann A. Effects of different operating parameters on hydrogen production by Parageobacillus thermoglucosidasius DSM 6285. AMB Express 2019; 9:207. [PMID: 31872380 PMCID: PMC6928187 DOI: 10.1186/s13568-019-0931-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/11/2019] [Indexed: 11/28/2022] Open
Abstract
Hydrogen gas represents a promising alternative energy source to dwindling fossil fuel reserves, as it carries the highest energy per unit mass and its combustion results in the release of water vapour as only byproduct. The facultatively anaerobic thermophile Parageobacillus thermoglucosidasius is able to produce hydrogen via the water–gas shift reaction catalyzed by a carbon monoxide dehydrogenase–hydrogenase enzyme complex. Here we have evaluated the effects of several operating parameters on hydrogen production, including different growth temperatures, pre-culture ages and inoculum sizes, as well as different pHs and concentrations of nickel and iron in the fermentation medium. All of the tested parameters were observed to have a substantive effect on both hydrogen yield and (specific) production rates. A final experiment incorporating the best scenario for each tested parameter showed a marked increase in the H2 production rate compared to each individual parameter. The optimised parameters serve as a strong basis for improved hydrogen production with a view of commercialisation of this process.
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25
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Fukuyama Y, Omae K, Yoshida T, Sako Y. Transcriptome analysis of a thermophilic and hydrogenogenic carboxydotroph Carboxydothermus pertinax. Extremophiles 2019; 23:389-398. [PMID: 30941583 PMCID: PMC6557876 DOI: 10.1007/s00792-019-01091-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022]
Abstract
A thermophilic and hydrogenogenic carboxydotroph, Carboxydothermus pertinax, performs hydrogenogenic CO metabolism in which CODH-II couples with distally encoded ECH. To enhance our knowledge of its hydrogenogenic CO metabolism, we performed whole transcriptome analysis of C. pertinax grown under 100% CO or 100% N2 using RNA sequencing. Of the 2577 genes, 36 and 64 genes were differentially expressed genes (DEGs) with false discovery rate adjusted P value < 0.05 when grown under 100% CO or 100% N2, respectively. Most of the DEGs were components of 23 gene clusters, suggesting switch between metabolisms via intensive expression changes in a relatively low number of gene clusters. Of the 9 significantly expressed gene clusters under 100% CO, CODH-II and ECH gene clusters were found. Only the ECH gene cluster was regulated by the CO-responsive transcriptional factor CooA, suggesting that others were separately regulated in the same transcriptional cascade as the ECH gene cluster. Of the 14 significantly expressed gene clusters under 100% N2, ferrous iron transport gene cluster involved in anaerobic respiration and prophage region were found. Considering that the expression of the temperate phage was strictly repressed under 100% CO, hydrogenogenic CO metabolism might be stable for C. pertinax.
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Affiliation(s)
- Yuto Fukuyama
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kimiho Omae
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yoshihiko Sako
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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Omae K, Fukuyama Y, Yasuda H, Mise K, Yoshida T, Sako Y. Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan. Arch Microbiol 2019; 201:969-982. [PMID: 31030239 PMCID: PMC6687684 DOI: 10.1007/s00203-019-01661-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/15/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022]
Abstract
In hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H2 for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)–energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH–ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing > 98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus, Carboxydocella, Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low.
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Affiliation(s)
- Kimiho Omae
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Yuto Fukuyama
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Hisato Yasuda
- Center for Advanced Marine Core Research, Kochi University, B200 Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Kenta Mise
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8503, Japan.
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Inoue M, Nakamoto I, Omae K, Oguro T, Ogata H, Yoshida T, Sako Y. Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases. Front Microbiol 2019; 9:3353. [PMID: 30705673 PMCID: PMC6344411 DOI: 10.3389/fmicb.2018.03353] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/31/2018] [Indexed: 11/30/2022] Open
Abstract
Anaerobic Ni-containing carbon-monoxide dehydrogenases (Ni-CODHs) catalyze the reversible conversion between carbon monoxide and carbon dioxide as multi-enzyme complexes responsible for carbon fixation and energy conservation in anaerobic microbes. However, few biochemically characterized model enzymes exist, with most Ni-CODHs remaining functionally unknown. Here, we performed phylogenetic and structure-based Ni-CODH classification using an expanded dataset comprised of 1942 non-redundant Ni-CODHs from 1375 Ni-CODH-encoding genomes across 36 phyla. Ni-CODHs were divided into seven clades, including a novel clade. Further classification into 24 structural groups based on sequence analysis combined with structural prediction revealed diverse structural motifs for metal cluster formation and catalysis, including novel structural motifs potentially capable of forming metal clusters or binding metal ions, indicating Ni-CODH diversity and plasticity. Phylogenetic analysis illustrated that the metal clusters responsible for intermolecular electron transfer were drastically altered during evolution. Additionally, we identified novel putative Ni-CODH-associated proteins from genomic contexts other than the Wood–Ljungdahl pathway and energy converting hydrogenase system proteins. Network analysis among the structural groups of Ni-CODHs, their associated proteins and taxonomies revealed previously unrecognized gene clusters for Ni-CODHs, including uncharacterized structural groups with putative metal transporters, oxidoreductases, or transcription factors. These results suggested diversification of Ni-CODH structures adapting to their associated proteins across microbial genomes.
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Affiliation(s)
- Masao Inoue
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Issei Nakamoto
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kimiho Omae
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tatsuki Oguro
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hiroyuki Ogata
- Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Takashi Yoshida
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiko Sako
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Abstract
Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of CO with water to CO2, two electrons, and two protons. Two classes of CODHs exist, having evolved from different scaffolds featuring active sites built from different transition metals. The basic properties of both classes are described in this overview chapter.
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Affiliation(s)
- Jae-Hun Jeoung
- Institute of Biology, Structural Biology and Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Berta M Martins
- Institute of Biology, Structural Biology and Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Holger Dobbek
- Institute of Biology, Structural Biology and Biochemistry, Humboldt-Universität zu Berlin, Berlin, Germany.
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Abstract
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 CO
2 and H
2 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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Affiliation(s)
- Frank T Robb
- Department of Microbiology and Immunology, and Inst of Marine and Environmental Technology, University of Maryland, Baltimore, Baltimore, MD, 21202, USA
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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Xavier JC, Preiner M, Martin WF. Something special about CO-dependent CO 2 fixation. FEBS J 2018; 285:4181-4195. [PMID: 30240136 PMCID: PMC6282760 DOI: 10.1111/febs.14664] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/08/2018] [Accepted: 09/19/2018] [Indexed: 01/02/2023]
Abstract
Carbon dioxide enters metabolism via six known CO2 fixation pathways, of which only one is linear, exergonic in the direction of CO2‐assimilation, and present in both bacterial and archaeal anaerobes – the Wood‐Ljungdahl (WL) or reductive acetyl‐CoA pathway. Carbon monoxide (CO) plays a central role in the WL pathway as an energy rich intermediate. Here, we scan the major biochemical reaction databases for reactions involving CO and CO2. We identified 415 reactions corresponding to enzyme commission (EC) numbers involving CO2, which are non‐randomly distributed across different biochemical pathways. Their taxonomic distribution, reversibility under physiological conditions, cofactors and prosthetic groups are summarized. In contrast to CO2, only 15 reaction classes involving CO were detected. Closer inspection reveals that CO interfaces with metabolism and the carbon cycle at only two enzymes: anaerobic carbon monoxide dehydrogenase (CODH), a Ni‐ and Fe‐containing enzyme that generates CO for CO2 fixation in the WL pathway, and aerobic CODH, a Mo‐ and Cu‐containing enzyme that oxidizes environmental CO as an electron source. The CO‐dependent reaction of the WL pathway involves carbonyl insertion into a methyl carbon‐nickel at the Ni‐Fe‐S A‐cluster of acetyl‐CoA synthase (ACS). It appears that no alternative mechanisms to the CO‐dependent reaction of ACS have evolved in nearly 4 billion years, indicating an ancient and mechanistically essential role for CO at the onset of metabolism.
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Affiliation(s)
- Joana C Xavier
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - Martina Preiner
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany
| | - William F Martin
- Institut für Molekulare Evolution, Heinrich Heine Universität Düsseldorf, Germany.,Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
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St John E, Liu Y, Podar M, Stott MB, Meneghin J, Chen Z, Lagutin K, Mitchell K, Reysenbach AL. A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring. Syst Appl Microbiol 2018; 42:94-106. [PMID: 30195930 DOI: 10.1016/j.syapm.2018.08.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/08/2018] [Accepted: 08/08/2018] [Indexed: 01/22/2023]
Abstract
Three thermophilic Nanoarchaeota-Crenarchaeota symbiotic systems have been described. We obtained another stable anaerobic enrichment culture at 80°C, pH 6.0 from a New Zealand hot spring. The nanoarchaeote (Ncl-1) and its host (NZ3T) were isolated in co-culture and their genomes assembled. The small (∼200nm) flagellated cocci were often attached to larger cocci. Based on 16S rRNA gene similarity (88.4%) and average amino acid identity (52%), Ncl-1 is closely related to Candidatus Nanopusillus acidilobi. Their genomes both encode for archaeal flagella and partial glycolysis and gluconeogenesis pathways, but lack ATP synthase genes. Like Nanoarchaeum equitans, Ncl-1 has a CRISPR-Cas system. Ncl-1 also relies on its crenarchaeotal host for most of its biosynthetic needs. The host NZ3T was isolated and grows on proteinaceous substrates but not on sugars, alcohols, or fatty acids. NZ3T requires thiosulfate and grows best at 82°C, pH 6.0. NZ3T is most closely related to the Desulfurococcaceae, Ignisphaera aggregans (∼92% 16S rRNA gene sequence similarity, 45% AAI). Based on phylogenetic, physiological and genomic data, Ncl-1 and NZ3T represent novel genera in the Nanoarchaeota and the Desulfurococcaceae, respectively, with the proposed names Candidatus Nanoclepta minutus and Zestosphaera tikiterensis gen. nov., sp. nov., type strain NZ3T (=DSMZ 107634T=OCM 1213T).
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Affiliation(s)
- Emily St John
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Yitai Liu
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Mircea Podar
- Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA; Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Jennifer Meneghin
- Biology Department, Portland State University, Portland, OR 97201, USA
| | - Zhiqiang Chen
- Center for Electron Microscopy and Nanofabrication, Portland State University, Portland, OR 97201, USA
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Toshchakov SV, Lebedinsky AV, Sokolova TG, Zavarzina DG, Korzhenkov AA, Teplyuk AV, Chistyakova NI, Rusakov VS, Bonch-Osmolovskaya EA, Kublanov IV, Gavrilov SN. Genomic Insights Into Energy Metabolism of Carboxydocella thermautotrophica Coupling Hydrogenogenic CO Oxidation With the Reduction of Fe(III) Minerals. Front Microbiol 2018; 9:1759. [PMID: 30123201 PMCID: PMC6085454 DOI: 10.3389/fmicb.2018.01759] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/13/2018] [Indexed: 01/17/2023] Open
Abstract
The genus Carboxydocella forms a deeply branching family in the class Clostridia and is currently represented by three physiologically diverse species of thermophilic prokaryotes. The type strain of the type species, Carboxydocella thermautotrophica 41T, is an obligate chemolithoautotroph growing exclusively by hydrogenogenic CO oxidation. Another strain, isolated from a hot spring at Uzon caldera, Kamchatka in the course of this work, is capable of coupling carboxydotrophy and dissimilatory reduction of Fe(III) from oxic and phyllosilicate minerals. The processes of carboxydotrophy and Fe(III) reduction appeared to be interdependent in this strain. The genomes of both isolates were sequenced, assembled into single chromosome sequences (for strain 41T a plasmid sequence was also assembled) and analyzed. Genome analysis revealed that each of the two strains possessed six genes encoding diverse Ni,Fe-containing CO dehydrogenases (maximum reported in complete prokaryotic genomes), indicating crucial role of carbon monoxide in C. thermautotrophica metabolism. Both strains possessed a set of 30 multiheme c-type cytochromes, but only the newly isolated Fe-reducing strain 019 had one extra gene of a 17-heme cytochrome, which is proposed to represent a novel determinant of dissimilatory iron reduction in prokaryotes. Mössbauer studies revealed that strain 019 induced reductive transformation of the abundant ferric/ferrous-mica mineral glauconite to siderite during carboxydotrophic growth. Reconstruction of the C. thermautotrophica strains energy metabolism is the first comprehensive genome analysis of a representative of the deep phylogenetic branch Clostridia Incertae Sedis, family V. Our data provide insights into energy metabolism of C. thermautotrophica with an emphasis on its ecological implications.
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Affiliation(s)
- Stepan V. Toshchakov
- Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander V. Lebedinsky
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana G. Sokolova
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Daria G. Zavarzina
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Alexei A. Korzhenkov
- Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina V. Teplyuk
- Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | | | | | | | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey N. Gavrilov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russia
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Mohr T, Aliyu H, Küchlin R, Polliack S, Zwick M, Neumann A, Cowan D, de Maayer P. CO-dependent hydrogen production by the facultative anaerobe Parageobacillus thermoglucosidasius. Microb Cell Fact 2018; 17:108. [PMID: 29986719 PMCID: PMC6036681 DOI: 10.1186/s12934-018-0954-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/02/2018] [Indexed: 01/03/2023] Open
Abstract
Background The overreliance on dwindling fossil fuel reserves and the negative climatic effects of using such fuels are driving the development of new clean energy sources. One such alternative source is hydrogen (H2), which can be generated from renewable sources. Parageobacillus thermoglucosidasius is a facultative anaerobic thermophilic bacterium which is frequently isolated from high temperature environments including hot springs and compost. Results Comparative genomics performed in the present study showed that P. thermoglucosidasius encodes two evolutionary distinct H2-uptake [Ni-Fe]-hydrogenases and one H2-evolving hydrogenases. In addition, genes encoding an anaerobic CO dehydrogenase (CODH) are co-localized with genes encoding a putative H2-evolving hydrogenase. The co-localized of CODH and uptake hydrogenase form an enzyme complex that might potentially be involved in catalyzing the water-gas shift reaction (CO + H2O → CO2 + H2) in P. thermoglucosidasius. Cultivation of P. thermoglucosidasius DSM 2542T with an initial gas atmosphere of 50% CO and 50% air showed it to be capable of growth at elevated CO concentrations (50%). Furthermore, GC analyses showed that it was capable of producing hydrogen at an equimolar conversion with a final yield of 1.08 H2/CO. Conclusions This study highlights the potential of the facultative anaerobic P. thermoglucosidasius DSM 2542T for developing new strategies for the biohydrogen production. Electronic supplementary material The online version of this article (10.1186/s12934-018-0954-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Teresa Mohr
- Section II: Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany. .,Section II: Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institut für Technologie (KIT), Kaiserstrasse 12, 76131, Karlsruhe, Germany.
| | - Habibu Aliyu
- Section II: Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Raphael Küchlin
- Section II: Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Shamara Polliack
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield 0028 Pretoria, South Africa
| | - Michaela Zwick
- Section II: Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Anke Neumann
- Section II: Technical Biology, Institute of Process Engineering in Life Science, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Don Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Hatfield 0028 Pretoria, South Africa
| | - Pieter de Maayer
- School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, WITS 2050 Johannesburg, South Africa
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Insight into Energy Conservation via Alternative Carbon Monoxide Metabolism in Carboxydothermus pertinax Revealed by Comparative Genome Analysis. Appl Environ Microbiol 2018; 84:AEM.00458-18. [PMID: 29728389 DOI: 10.1128/aem.00458-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/28/2018] [Indexed: 11/20/2022] Open
Abstract
Carboxydothermus species 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 genus Carboxydothermus to show variations in the CO dehydrogenase-energy-converting hydrogenase gene cluster, which is responsible for CO metabolism with H2 production (hydrogenogenic CO metabolism). Indeed, the ability or inability to produce H2 with CO oxidation is explained by the presence or absence of this gene cluster in Carboxydothermus hydrogenoformans, Carboxydothermus islandicus, and Carboxydothermus ferrireducens Interestingly, despite its hydrogenogenic CO metabolism, Carboxydothermus pertinax lacks the Ni-CO dehydrogenase catalytic subunit (CooS-I) and its transcriptional regulator-encoding genes in this gene cluster, probably due to inversion. Transcriptional analysis in C. pertinax showed 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 of C. pertinax were 3.1-fold and 1.5-fold higher, respectively, than when thiosulfate was absent. The amount of H2 produced was only 62% of the amount of CO consumed, less than expected according to hydrogenogenic CO oxidation (CO + H2O → CO2 + H2). Accordingly, C. pertinax would couple CO oxidation by Ni-CO dehydrogenase II with simultaneous reduction of not only H2O but also thiosulfate when grown in 100% CO.IMPORTANCE Anaerobic hydrogenogenic carboxydotrophs are thought to fill a vital niche by scavenging potentially toxic CO and producing H2 as 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 carboxydotroph Carboxydothermus pertinax lacks the gene for the Ni-CO dehydrogenase catalytic subunit encoded in the gene cluster. Here, we performed a comparative genome analysis of the genus Carboxydothermus, a transcriptional analysis, and a cultivation study in 100% CO to prove the hydrogenogenic CO metabolism. Results revealed that C. pertinax could couple Ni-CO dehydrogenase II alternatively to the distal energy-converting hydrogenase. Furthermore, C. pertinax represents 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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Esquivel-Elizondo S, Maldonado J, Krajmalnik-Brown R. Anaerobic carbon monoxide metabolism by Pleomorphomonas carboxyditropha sp. nov., a new mesophilic hydrogenogenic carboxydotroph. FEMS Microbiol Ecol 2018; 94:4980905. [DOI: 10.1093/femsec/fiy056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sofia Esquivel-Elizondo
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287- 5701, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-5701, USA
| | - Juan Maldonado
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287- 5701, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287–6101, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, P.O. Box 875701, Tempe, AZ 85287- 5701, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ 85287-5701, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, AZ 85287–6101, USA
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Sokolova TG, Yakimov MM, Chernyh NA, Lun’kova EY, Kostrikina NA, Taranov EA, Lebedinskii AV, Bonch-Osmolovskaya EA. Aerobic carbon monoxide oxidation in the course of growth of a hyperthermophilic archaeon, Sulfolobus sp. ETSY. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717050174] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Genomic Analysis of Calderihabitans maritimus KKC1, a Thermophilic, Hydrogenogenic, Carboxydotrophic Bacterium Isolated from Marine Sediment. Appl Environ Microbiol 2017; 83:AEM.00832-17. [PMID: 28526793 DOI: 10.1128/aem.00832-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/13/2017] [Indexed: 11/20/2022] Open
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.IMPORTANCECalderihabitans 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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Draft Genome Sequences of Two Hydrogenogenic Carboxydotrophic Bacteria, Carboxydocella sp. Strains JDF658 and ULO1, Isolated from Two Distinct Volcanic Fronts in Japan. GENOME ANNOUNCEMENTS 2017; 5:5/16/e00242-17. [PMID: 28428313 PMCID: PMC5399272 DOI: 10.1128/genomea.00242-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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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Dalmasso C, Oger P, Selva G, Courtine D, L’Haridon S, Garlaschelli A, Roussel E, Miyazaki J, Reveillaud J, Jebbar M, Takai K, Maignien L, Alain K. Thermococcus piezophilus sp. nov., a novel hyperthermophilic and piezophilic archaeon with a broad pressure range for growth, isolated from a deepest hydrothermal vent at the Mid-Cayman Rise. Syst Appl Microbiol 2016; 39:440-444. [DOI: 10.1016/j.syapm.2016.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/26/2016] [Accepted: 08/11/2016] [Indexed: 10/21/2022]
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Kozhevnikova DA, Taranov EA, Lebedinsky AV, Bonch-Osmolovskaya EA, Sokolova TG. Hydrogenogenic and sulfidogenic growth of Thermococcus archaea on carbon monoxide and formate. Microbiology (Reading) 2016. [DOI: 10.1134/s0026261716040135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Gavrilov SN, Stracke C, Jensen K, Menzel P, Kallnik V, Slesarev A, Sokolova T, Zayulina K, Bräsen C, Bonch-Osmolovskaya EA, Peng X, Kublanov IV, Siebers B. Isolation and Characterization of the First Xylanolytic Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1 and Its Unusual Multidomain Glycosidase. Front Microbiol 2016; 7:552. [PMID: 27199905 PMCID: PMC4853606 DOI: 10.3389/fmicb.2016.00552] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 04/04/2016] [Indexed: 12/12/2022] Open
Abstract
Enzymes from (hyper)thermophiles “Thermozymes” offer a great potential for biotechnological applications. Thermophilic adaptation does not only provide stability toward high temperature but is also often accompanied by a higher resistance to other harsh physicochemical conditions, which are also frequently employed in industrial processes, such as the presence of, e.g., denaturing agents as well as low or high pH of the medium. In order to find new thermostable, xylan degrading hydrolases with potential for biotechnological application we used an in situ enrichment strategy incubating Hungate tubes with xylan as the energy substrate in a hot vent located in the tidal zone of Kunashir Island (Kuril archipelago). Using this approach a hyperthermophilic euryarchaeon, designated Thermococcus sp. strain 2319x1, growing on xylan as sole energy and carbon source was isolated. The organism grows optimally at 85°C and pH 7.0 on a variety of natural polysaccharides including xylan, carboxymethyl cellulose (CMC), amorphous cellulose (AMC), xyloglucan, and chitin. The protein fraction extracted from the cells surface with Tween 80 exhibited endoxylanase, endoglucanase and xyloglucanase activities. The genome of Thermococcus sp. strain 2319x1 was sequenced and assembled into one circular chromosome. Within the newly sequenced genome, a gene, encoding a novel type of glycosidase (143 kDa) with a unique five-domain structure, was identified. It consists of three glycoside hydrolase (GH) domains and two carbohydrate-binding modules (CBM) with the domain order GH5-12-12-CBM2-2 (N- to C-terminal direction). The full length protein, as well as truncated versions, were heterologously expressed in Escherichia coli and their activity was analyzed. The full length multidomain glycosidase (MDG) was able to hydrolyze various polysaccharides, with the highest activity for barley β-glucan (β- 1,3/1,4-glucoside), followed by that for CMC (β-1,4-glucoside), cellooligosaccharides and galactomannan. The results reported here indicate that the modular MDG structure with multiple glycosidase and carbohydrate-binding domains not only extends the substrate spectrum, but also seems to allow the degradation of partially soluble and insoluble polymers in a processive manner. This report highlights the great potential in a multi-pronged approach consisting of a combined in situ enrichment, (comparative) genomics, and biochemistry strategy for the screening for novel enzymes of biotechnological relevance.
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Affiliation(s)
- Sergey N Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Christina Stracke
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, University Duisburg-Essen Essen, Germany
| | | | - Peter Menzel
- Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Verena Kallnik
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, University Duisburg-Essen Essen, Germany
| | - Alexei Slesarev
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia; Fidelity Systems, Inc., GaithersburgMD, USA
| | - Tatyana Sokolova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Kseniya Zayulina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, University Duisburg-Essen Essen, Germany
| | | | - Xu Peng
- Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences Moscow, Russia
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry, Biofilm Centre, Centre for Water and Environmental Research, University Duisburg-Essen Essen, Germany
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CO Metabolism in the Thermophilic Acetogen Thermoanaerobacter kivui. Appl Environ Microbiol 2016; 82:2312-2319. [PMID: 26850300 DOI: 10.1128/aem.00122-16] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 01/31/2016] [Indexed: 12/14/2022] Open
Abstract
The thermophilic acetogenic bacterium Thermoanaerobacter kivui, previously described not to use carbon monoxide as a carbon and energy source, was adapted to grow on CO. This was achieved by using a preculture grown on H2 plus CO2 and by increasing the CO concentration in small, 10% increments.T. kivui was finally able to grow within a 100% CO atmosphere. Growth on CO was found in complex and mineral media, and vitamins were not required. Carbon monoxide consumption was accompanied by acetate and hydrogen production. Cells also grew on synthesis gas (syngas) with the simultaneous use of CO and H2 coupled to acetate production. CO oxidation in resting cells was coupled to hydrogen and acetate production and accompanied by the synthesis of ATP. A protonophore abolished ATP synthesis but stimulated H2 production, which is consistent with a chemiosmotic mechanism of ATP synthesis. Hydrogenase activity was highest in crude extracts of CO-grown cells, and carbon monoxide dehydrogenase (CODH) activity was highest in H2-plus-CO2- or CO-grown cells. The genome of T. kivui harbors two CODH gene clusters, and both CODH proteins were present in crude extracts, but one CODH was more prevalent in crude extracts from CO-grown cells.
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Baker BJ, Saw JH, Lind AE, Lazar CS, Hinrichs KU, Teske AP, Ettema TJG. Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea. Nat Microbiol 2016; 1:16002. [PMID: 27572167 DOI: 10.1038/nmicrobiol.2016.2] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 01/08/2016] [Indexed: 11/09/2022]
Abstract
The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H2 oxidation (or H2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.
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Affiliation(s)
- Brett J Baker
- Department of Marine Science, University of Texas Austin, Marine Science Institute, Port Aransas, Texas 78373, USA
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Anders E Lind
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Cassandre Sara Lazar
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P Teske
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
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Liu Y, Wan J, Han S, Zhang S, Luo G. Selective conversion of carbon monoxide to hydrogen by anaerobic mixed culture. BIORESOURCE TECHNOLOGY 2016; 202:1-7. [PMID: 26692523 DOI: 10.1016/j.biortech.2015.11.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/22/2015] [Accepted: 11/24/2015] [Indexed: 05/28/2023]
Abstract
A new method for the conversion of CO to H2 was developed by anaerobic mixed culture in the current study. Higher CO consumption rate was obtained by anaerobic granular sludge (AGS) compared to waste activated sludge (WAS) at 55 °C and pH 7.5. However, H2 was the intermediate and CH4 was the final product. Fermentation at pH 5.5 by AGS inhibited CH4 production, while the lower CO consumption rate (50% of that at pH 7.5) and the production of acetate were found. Fermentation at pH 7.5 with the addition of chloroform achieved efficient and selective conversion of CO to H2. Stable and efficient H2 production was achieved in a continuous reactor inoculated with AGS, and gas recirculation was crucial to increase the CO conversion efficiency. Microbial community analysis showed that high abundance (44%) of unclassified sequences and low relative abundance (1%) of known CO-utilizing bacteria Desulfotomaculum were enriched in the reactor.
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Affiliation(s)
- Yafeng Liu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China; School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 201418 Shanghai, China
| | - Jingjing Wan
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China
| | - Sheng Han
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, 201418 Shanghai, China
| | - Shicheng Zhang
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP(3)), Department of Environmental Science and Engineering, Fudan University, 200433 Shanghai, China.
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Schut GJ, Lipscomb GL, Nguyen DMN, Kelly RM, Adams MWW. Heterologous Production of an Energy-Conserving Carbon Monoxide Dehydrogenase Complex in the Hyperthermophile Pyrococcus furiosus. Front Microbiol 2016; 7:29. [PMID: 26858706 PMCID: PMC4731540 DOI: 10.3389/fmicb.2016.00029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
Carbon monoxide (CO) is an important intermediate in anaerobic carbon fixation pathways in acetogenesis and methanogenesis. In addition, some anaerobes can utilize CO as an energy source. In the hyperthermophilic archaeon Thermococcus onnurineus, which grows optimally at 80°C, CO oxidation and energy conservation is accomplished by a respiratory complex encoded by a 16-gene cluster containing a CO dehydrogenase, a membrane-bound [NiFe]-hydrogenase and a Na+/H+ antiporter module. This complex oxidizes CO, evolves CO2 and H2, and generates a Na+ motive force that is used to conserve energy by a Na+-dependent ATP synthase. Herein we used a bacterial artificial chromosome to insert the 13.2 kb gene cluster encoding the CO-oxidizing respiratory complex of T. onnurineus into the genome of the heterotrophic archaeon, Pyrococcus furiosus, which grows optimally at 100°C. P. furiosus is normally unable to utilize CO, however, the recombinant strain readily oxidized CO and generated H2 at 80°C. Moreover, CO also served as an energy source and allowed the P. furiosus strain to grow with a limiting concentration of sugar or with peptides as the carbon source. Moreover, CO oxidation by P. furiosus was also coupled to the re-utilization, presumably for biosynthesis, of acetate generated by fermentation. The functional transfer of CO utilization between Thermococcus and Pyrococcus species demonstrated herein is representative of the horizontal gene transfer of an environmentally relevant metabolic capability. The transfer of CO utilizing, hydrogen-producing genetic modules also has applications for biohydrogen production and a CO-based industrial platform for various thermophilic organisms.
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Affiliation(s)
- Gerrit J Schut
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens GA, USA
| | - Gina L Lipscomb
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens GA, USA
| | - Diep M N Nguyen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens GA, USA
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh NC, USA
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens GA, USA
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Geelhoed JS, Henstra AM, Stams AJM. Carboxydotrophic growth of Geobacter sulfurreducens. Appl Microbiol Biotechnol 2015; 100:997-1007. [PMID: 26481622 PMCID: PMC4703632 DOI: 10.1007/s00253-015-7033-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/14/2015] [Accepted: 09/21/2015] [Indexed: 12/16/2022]
Abstract
This study shows that Geobacter sulfurreducens grows on carbon monoxide (CO) as electron donor with fumarate as electron acceptor. Geobacter sulfurreducens was tolerant to high CO levels, with up to 150 kPa in the headspace tested. During growth, hydrogen was detected in very slight amounts (∼5 Pa). In assays with cell-free extract of cells grown with CO and fumarate, production of hydrogen from CO was not observed, and hydrogenase activity with benzyl viologen as electron acceptor was very low. Taken together, this suggested that CO is not utilized via hydrogen as intermediate. In the presence of CO, reduction of NADP+ was observed at a rate comparable to CO oxidation coupled to fumarate reduction in vivo. The G. sulfurreducens genome contains a single putative carbon monoxide dehydrogenase-encoding gene. The gene is part of a predicted operon also comprising a putative Fe–S cluster-binding subunit (CooF) and a FAD–NAD(P) oxidoreductase and is preceded by a putative CO-sensing transcription factor. This cluster may be involved in a novel pathway for CO oxidation, but further studies are necessary to ascertain this. Similar gene clusters are present in several other species belonging to the Deltaproteobacteria and Firmicutes, for which CO utilization is currently not known.
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Affiliation(s)
- Jeanine S Geelhoed
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands.
- NIOZ Royal Netherlands Institute for Sea Research, Korringaweg 7, 4401 NT, Yerseke, The Netherlands.
| | - Anne M Henstra
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
- Centre for Biomolecular Sciences, University of Nottingham, University Park, NG7 2EF, Nottingham, UK
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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Sant'Anna FH, Lebedinsky AV, Sokolova TG, Robb FT, Gonzalez JM. Analysis of three genomes within the thermophilic bacterial species Caldanaerobacter subterraneus with a focus on carbon monoxide dehydrogenase evolution and hydrolase diversity. BMC Genomics 2015; 16:757. [PMID: 26446804 PMCID: PMC4596419 DOI: 10.1186/s12864-015-1955-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/19/2015] [Indexed: 11/22/2022] Open
Abstract
Background The Caldanaerobacter subterraneus species includes thermophilic fermentative bacteria able to grow on carbohydrates substrates with acetate and L-alanine as the main products. In this study, comprehensive analysis of three genomes of C. subterraneus subspecies was carried in order to identify genes encoding key metabolic enzymes and to document the genomic basis for the evolution of these organisms. Methods Average nucleotide identity and in silico DNA relatedness were estimated for the studied C. subterraneus genomes. Genome synteny was evaluated using R2CAT software. Protein conservation was analyzed using mGenome Subtractor. Horizontal gene transfer was predicted through the GOHTAM pipeline (using tetranucleotide composition) and phylogenetic analyses (by maximum likelihood). Hydrolases were identified through the MEROPS and CAZy platforms. Results The three genomes of C. subterraneus showed high similarity, although there are substantial differences in their gene composition and organization. Each subspecies possesses a gene cluster encoding a carbon monoxide dehydrogenase (CODH) and an energy converting hydrogenase (ECH). The CODH gene is associated with an operon that resembles the Escherichia coli hydrogenase hyc/hyf operons, a novel genetic context distinct from that found in archetypical hydrogenogenic carboxydotrophs. Apart from the CODH-associated hydrogenase, these bacteria also contain other hydrogenases, encoded by ech and hyd genes. An Mbx ferredoxin:NADP oxidoreductase homolog similar to that originally described in the archaeon Pyrococcus furiosus was uniquely encoded in the C. subterraneus subsp. yonseiensis genome. Compositional analysis demonstrated that some genes of the CODH-ECH and mbx operons present distinct sequence patterns in relation to the majority of the other genes of each genome. Phylogenetic reconstructions of the genes from these operons and those from the ech operon are incongruent to the species tree. Notably, the cooS gene of C. subterraneus subsp. pacificus and its homologs in C. subterraneus subsp. tengcongensis and C. subterraneus subsp. yonseiensis form distinct clades. The strains have diverse hydrolytic enzymes and they appear to be proteolytic and glycolytic. Divergent glycosidases from 14 families, among them amylases, chitinases, alpha-glucosidases, beta-glucosidases, and cellulases, were identified. Each of the three genomes also contains around 100 proteases from 50 subfamilies, as well about ten different esterases. Conclusions Genomic information suggests that multiple horizontal gene transfers conferred the adaptation of C. subterraneus subspecies to extreme niches throughout the carbon monoxide utilization and hydrogen production. The variety of hydrolases found in their genomes indicate the versatility of the species in obtaining energy and carbon from diverse substrates, therefore these organisms constitute a remarkable resource of enzymes with biotechnological potential. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1955-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- F H Sant'Anna
- Institute of Natural Resources and Agrobiology, Spanish Council for Research, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012, Sevilla, Spain. .,CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, 70040-020, Brazil.
| | - A V Lebedinsky
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia.
| | - T G Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia.
| | - F T Robb
- Department of Microbiology and Immunology, University of Maryland and Institute of Marine and Environmental Technology, 701 E Pratt Street, Baltimore, MD, 21202, USA.
| | - J M Gonzalez
- Institute of Natural Resources and Agrobiology, Spanish Council for Research, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012, Sevilla, Spain.
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Price MT, Fullerton H, Moyer CL. Biogeography and evolution of Thermococcus isolates from hydrothermal vent systems of the Pacific. Front Microbiol 2015; 6:968. [PMID: 26441901 PMCID: PMC4585236 DOI: 10.3389/fmicb.2015.00968] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/01/2015] [Indexed: 11/13/2022] Open
Abstract
Thermococcus is a genus of hyperthermophilic archaea that is ubiquitous in marine hydrothermal environments growing in anaerobic subsurface habitats but able to survive in cold oxygenated seawater. DNA analyses of Thermococcus isolates were applied to determine the relationship between geographic distribution and relatedness focusing primarily on isolates from the Juan de Fuca Ridge and South East Pacific Rise. Amplified fragment length polymorphism (AFLP) analysis and multilocus sequence typing (MLST) were used to resolve genomic differences in 90 isolates of Thermococcus, making biogeographic patterns and evolutionary relationships apparent. Isolates were differentiated into regionally endemic populations however there was also evidence in some lineages of cosmopolitan distribution. The biodiversity identified in Thermococcus isolates and presence of distinct lineages within the same vent site suggests the utilization of varying ecological niches in this genus. In addition to resolving biogeographic patterns in Thermococcus, this study has raised new questions about the closely related Pyrococcus genus. The phylogenetic placement of Pyrococcus type strains shows the close relationship between Thermococcus and Pyrococcus and the unresolved divergence of these two genera.
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Affiliation(s)
- Mark T Price
- Department of Biology, Western Washington University Bellingham, WA, USA
| | - Heather Fullerton
- Department of Biology, Western Washington University Bellingham, WA, USA
| | - Craig L Moyer
- Department of Biology, Western Washington University Bellingham, WA, USA
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Brady AL, Sharp CE, Grasby SE, Dunfield PF. Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing. Front Microbiol 2015; 6:897. [PMID: 26388850 PMCID: PMC4555085 DOI: 10.3389/fmicb.2015.00897] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 08/17/2015] [Indexed: 12/25/2022] Open
Abstract
Carbon monoxide (CO) is a potential energy and carbon source for thermophilic bacteria in geothermal environments. Geothermal sites ranging in temperature from 45 to 65°C were investigated for the presence and activity of anaerobic CO-oxidizing bacteria. Anaerobic CO oxidation potentials were measured at up to 48.9 μmoles CO g−1 (wet weight) day−1 within five selected sites. Active anaerobic carboxydotrophic bacteria were identified using 13CO DNA stable isotope probing (SIP) combined with pyrosequencing of 16S rRNA genes amplified from labeled DNA. Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in 13CO incubations. The predominant bacteria that assimilated 13C derived from CO were closely related (>98% 16S rRNA gene sequence identity) to genera of known carboxydotrophs including Thermincola, Desulfotomaculum, Thermolithobacter, and Carboxydocella, although a few species with lower similarity to known bacteria were also found that may represent previously unconfirmed CO-oxidizers. While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes. These results show that bacteria capable of using CO as a carbon source are common in geothermal springs, and that thermophilic carboxydotrophs are probably already quite well known from cultivation studies.
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Affiliation(s)
- Allyson L Brady
- Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Christine E Sharp
- Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | | | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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Yoneda Y, Kano SI, Yoshida T, Ikeda E, Fukuyama Y, Omae K, Kimura-Sakai S, Daifuku T, Watanabe T, Sako Y. Detection of anaerobic carbon monoxide-oxidizing thermophiles in hydrothermal environments. FEMS Microbiol Ecol 2015. [PMID: 26223231 DOI: 10.1093/femsec/fiv093] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carboxydotrophic anaerobic thermophiles have been isolated from various hydrothermal environments and are considered to be important carbon monoxide (CO) scavengers or primary producers. However, the ecological factors that influence the distribution, abundance and CO-oxidizing activities of these bacteria are poorly understood. A previous study detected the carboxydotrophic bacteria Carboxydothermus spp. in a hot spring sample and found that they constituted up to 10% of the total bacterial cells. In this study, we investigated environmental features, potential microbial CO-oxidation activities and the abundance of Carboxydothermus spp. in various hot springs to determine environmental factors that affect CO oxidizers and to see whether Carboxydothermus spp. are common in these environments. We detected potential microbial CO-oxidation activities in samples that showed relatively high values of total organic carbon, total nitrogen, oxidation-reduction potential and soil-water content. The abundance of Carboxydothermus spp. did not correlate with the presence of potential microbial CO-oxidation activities; however, Carboxydothermus spp. were detected in a wide range of environments, suggesting that these bacteria are widely distributed in spite of the relatively low population size. This study implies that thermophilic CO oxidizers occur in a wide range of environments and oxidize CO in somewhat oxidative environments rich in organic matter.
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Affiliation(s)
- Yasuko Yoneda
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sanae I Kano
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Eitaro Ikeda
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuto Fukuyama
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kimiho Omae
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigeko Kimura-Sakai
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takashi Daifuku
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tetsuhiro Watanabe
- Laboratory of Soil Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
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