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Nazina TN, Tourova TP, Grouzdev DS, Bidzhieva SK, Poltaraus AB. A Novel View on the Taxonomy of Sulfate-Reducing Bacterium ' Desulfotomaculum salinum' and a Description of a New Species Desulfofundulus salinus sp. nov. Microorganisms 2024; 12:1115. [PMID: 38930497 PMCID: PMC11206085 DOI: 10.3390/microorganisms12061115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Two thermophilic spore-forming sulfate-reducing strains, 435T and 781, were isolated from oil and gas reservoirs in Western Siberia (Russia) about 50 years ago. Both strains were found to be neutrophilic, chemoorganotrophic, anaerobic bacteria, growing at 45-70 °C (optimum, 55-60 °C) and with 0-4.5% (w/v) NaCl (optimum, 0.5-1% NaCl). The major fatty acids were iso-C15:0, iso-C17:0, C16:0, and C18:0. In sulfate-reducing conditions, the strains utilized H2/CO2, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, and palmitate. In 2005, based on phenotypic characteristics and a 16S rRNA gene sequence analysis, the strains were described as 'Desulfotomaculum salinum' sp. nov. However, this species was not validly published because the type strain was not deposited in two culture collections. In this study, a genomic analysis of strain 435T was carried out to determine its taxonomic affiliation. The genome size of strain 435T was 2.886 Mb with a 55.1% genomic G + C content. The average nucleotide identity and digital DNA-DNA hybridization values were highest between strain 435T and members of the genus Desulfofundulus, 78.7-93.3% and 25.0-52.2%, respectively; these values were below the species delineation cut-offs (<95-96% and <70%). The cumulative phenotypic and phylogenetic data indicate that two strains represent a novel species within the genus Desulfofundulus, for which the name Desulfofundulus salinus sp. nov. is proposed. The type strain is 435T (=VKM B-1492T = DSM 23196T). A genome analysis of strain 435T revealed the genes for dissimilatory sulfate reduction, autotrophic carbon fixation via the Wood-Ljungdahl pathway, hydrogen utilization, methanol and organic acids metabolism, and sporulation, which were confirmed by cultivation studies.
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Affiliation(s)
- Tamara N. Nazina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Tatyana P. Tourova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | | | - Salimat K. Bidzhieva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia; (T.P.T.); (S.K.B.)
| | - Andrey B. Poltaraus
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
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Bährle R, Böhnke S, Englhard J, Bachmann J, Perner M. Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications. BIORESOUR BIOPROCESS 2023; 10:84. [PMID: 38647803 PMCID: PMC10992861 DOI: 10.1186/s40643-023-00705-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/16/2023] [Indexed: 04/25/2024] Open
Abstract
Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.
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Affiliation(s)
- Rebecca Bährle
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Stefanie Böhnke
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Jonas Englhard
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Julien Bachmann
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Mirjam Perner
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany.
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Chen X, Liu J, Zhu XY, Xue CX, Yao P, Fu L, Yang Z, Sun K, Yu M, Wang X, Zhang XH. Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole. ISME COMMUNICATIONS 2023; 3:117. [PMID: 37964026 PMCID: PMC10645885 DOI: 10.1038/s43705-023-00327-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023]
Abstract
The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.
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Affiliation(s)
- Xing Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jiwen Liu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Yu Zhu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Chun-Xu Xue
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Peng Yao
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute, Sansha, 573199, China
| | - Zuosheng Yang
- College of Marine Geosciences, Ocean University of China, Qingdao, 266100, China
| | - Kai Sun
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Min Yu
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiaolei Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Xiao-Hua Zhang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, and College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266237, China.
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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Harahap BM, Ahring BK. Acetate Production from Syngas Produced from Lignocellulosic Biomass Materials along with Gaseous Fermentation of the Syngas: A Review. Microorganisms 2023; 11:microorganisms11040995. [PMID: 37110418 PMCID: PMC10143712 DOI: 10.3390/microorganisms11040995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Biotransformation of lignocellulose-derived synthetic gas (syngas) into acetic acid is a promising way of creating biochemicals from lignocellulosic waste materials. Acetic acid has a growing market with applications within food, plastics and for upgrading into a wide range of biofuels and bio-products. In this paper, we will review the microbial conversion of syngas to acetic acid. This will include the presentation of acetate-producing bacterial strains and their optimal fermentation conditions, such as pH, temperature, media composition, and syngas composition, to enhance acetate production. The influence of syngas impurities generated from lignocellulose gasification will further be covered along with the means to alleviate impurity problems through gas purification. The problem with mass transfer limitation of gaseous fermentation will further be discussed as well as ways to improve gas uptake during the fermentation.
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Affiliation(s)
- Budi Mandra Harahap
- Bioproducts, Science, and Engineering Laboratory, Washington State University Tri-Cities, 2710, Crimson Way, Richland, WA 99354, USA
- Department of Biological System Engineering, Washington State University, L. J. Smith Hall, Pullman, WA 99164, USA
| | - Birgitte K Ahring
- Bioproducts, Science, and Engineering Laboratory, Washington State University Tri-Cities, 2710, Crimson Way, Richland, WA 99354, USA
- Department of Biological System Engineering, Washington State University, L. J. Smith Hall, Pullman, WA 99164, USA
- Voiland School of Chemical Engineering and Bioengineering, Washington State University, Wegner Hall, Pullman, WA 99164, USA
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Sobieraj K, Stegenta-Dąbrowska S, Luo G, Koziel JA, Białowiec A. Biological treatment of biowaste as an innovative source of CO-The role of composting process. Front Bioeng Biotechnol 2023; 11:1126737. [PMID: 36845185 PMCID: PMC9947533 DOI: 10.3389/fbioe.2023.1126737] [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: 12/18/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Carbon monoxide (CO) is an essential "building block" for producing everyday chemicals on industrial scale. Carbon monoxide can also be generated though a lesser-known and sometimes forgotten biorenewable pathways that could be explored to advance biobased production from large and more sustainable sources such as bio-waste treatment. Organic matter decomposition can generate carbon monoxide both under aerobic and anaerobic conditions. While anaerobic carbon monoxide generation is relatively well understood, the aerobic is not. Yet many industrial-scale bioprocesses involve both conditions. This review summarizes the necessary basic biochemistry knowledge needed for realization of initial steps towards biobased carbon monoxide production. We analyzed for the first time, the complex information about carbon monoxide production during aerobic, anaerobic bio-waste treatment and storage, carbon monoxide-metabolizing microorganisms, pathways, and enzymes with bibliometric analysis of trends. The future directions recognizing limitations of combined composting and carbon monoxide production have been discussed in greater detail.
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Affiliation(s)
- Karolina Sobieraj
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Sylwia Stegenta-Dąbrowska
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Gang Luo
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University, Shanghai, China,Shanghai Technical Service Platform for Pollution Control and Resource Utilization of Organic Wastes, Shanghai, China,Shanghai Institute of Pollution Control and Ecological Security, Shanghai, China
| | - Jacek A. Koziel
- USDA-ARS Conservation and Production Research Laboratory, Bushland, TX, United States,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States
| | - Andrzej Białowiec
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, Wrocław, Poland,Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA, United States,*Correspondence: Andrzej Białowiec,
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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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He Y, Lens PNL, Veiga MC, Kennes C. Selective butanol production from carbon monoxide by an enriched anaerobic culture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150579. [PMID: 34582872 DOI: 10.1016/j.scitotenv.2021.150579] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
An anaerobic mixed culture able to grow on pure carbon monoxide (CO) as well as syngas (CO, CO2 and H2), that produced unusual high concentrations of butanol, was enriched in a bioreactor with intermittent CO gas feeding. At pH 6.2, it mainly produced acids, generally acetic and butyric acid. After adaptation, under stress conditions of CO exposure at a partial pressure of 1.8 bar and low pH (e.g., 5.7), the enrichment accumulated ethanol, but also high amounts of butanol, up to 6.8 g/L, never reported before, with a high butanol/butyric acid molar ratio of 12.6, highlighting the high level of acid to alcohol conversion. At the end of the assay, both the acetic acid and ethanol concentrations decreased, with concomitant butyric acid production, suggesting C2 to C4 acid bioconversion, though this was not a dominant bioconversion process. The reverse reaction of ethanol oxidation to acetic acid was observed in the presence of CO2 produced during CO fermentation. Interestingly, butanol oxidation with simultaneous butyric acid production occurred upon production of CO2 from CO, which has to the best of our knowledge never been reported. Although the sludge inoculum contained a few known solventogenic Clostridia, the relative taxonomic abundance of the enriched sludge was diverse in Clostridia and Bacilli classes, containing known solventogens, e.g., Clostridium ljungdhalii, Clostridium ragsdalei and Clostridium coskatii, confirming their efficient enrichment. The relative abundance of unassigned Clostridium species amounted to 27% with presumably novel ethanol/butanol producers.
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Affiliation(s)
- Yaxue He
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008 La Coruña, Spain; National University of Ireland Galway, H91 TK33 Galway, Ireland
| | - Piet N L Lens
- National University of Ireland Galway, H91 TK33 Galway, Ireland
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008 La Coruña, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Center for Advanced Scientific Research (CICA), BIOENGIN Group, University of La Coruña (UDC), E-15008 La Coruña, Spain.
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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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Biological conversion of carbon monoxide and hydrogen by anaerobic culture: Prospect of anaerobic digestion and thermochemical processes combination. Biotechnol Adv 2021; 58:107886. [PMID: 34915147 DOI: 10.1016/j.biotechadv.2021.107886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/26/2021] [Accepted: 12/08/2021] [Indexed: 01/04/2023]
Abstract
Waste biomass is considered a promising renewable energy feedstock that can be converted by anaerobic digestion. However, anaerobic digestion application can be challenging due to the structural complexity of several waste biomass kinds. Therefore, coupling anaerobic digestion with thermochemical processes can offset the limitations and convert the hardly biodegradable waste biomass, including digestate residue, into value-added products: syngas and pyrogas (gaseous mixtures consisting mainly of H2, CO, CO2), bio-oil, and biochar for further valorisation. In this review, the utilisation boundaries and benefits of the aforementioned products by anaerobic culture are discussed. First, thermochemical process parameters for an enhanced yield of desired products are summarised. Particularly, the microbiology of CO and H2 mixture biomethanation and fermentation in anaerobic digestion is presented. Finally, the state-of-the-art biological conversion of syngas and pyrogas to CH4 mediated by anaerobic culture is adequately described. Extensive research shows the successful selective biological conversion of CO and H2 to CH4, acetic acid, and alcohols. The main bottleneck is the gas-liquid mass transfer which can be enhanced appropriately by bioreactors' configurations. A few research groups focus on bio-oil and biochar addition into anaerobic digesters. However, according to the literature review, there has been no research for utilising all value-added products at once in anaerobic digestion published so far. Although synergic effects of such can be expected. In summary, the combination of anaerobic digestion and thermochemical processes is a promising alternative for wide-scale waste biomass utilisation in practice.
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Omae K, Oguro T, Inoue M, Fukuyama Y, Yoshida T, Sako Y. Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers. Extremophiles 2021; 25:61-76. [PMID: 33415441 PMCID: PMC7811984 DOI: 10.1007/s00792-020-01211-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/23/2020] [Indexed: 11/16/2022]
Abstract
The microbial H2-producing (hydrogenogenic) carbon monoxide (CO)-oxidizing activity by the membrane-associated CO dehydrogenase (CODH)/energy-converting hydrogenase (ECH) complex is an important metabolic process in the microbial community. However, the studies on hydrogenogenic carboxydotrophs had to rely on inherently cultivation and isolation methods due to their rare abundance, which was a bottleneck in ecological study. Here, we provided gene-targeted sequencing method for the diversity estimation of thermophilic hydrogenogenic carboxydotrophs. We designed six new degenerate primer pairs which effectively amplified the coding regions of CODH genes forming gene clusters with ECH genes (CODHech genes) in Firmicutes which includes major thermophilic hydrogenogenic carboxydotrophs in terrestrial thermal habitats. Amplicon sequencing by these primers using DNAs from terrestrial hydrothermal sediments and CO-gas-incubated samples specifically detected multiple CODH genes which were identical or phylogenetically related to the CODHech genes in Firmictes. Furthermore, we found that phylogenetically distinct CODHech genes were enriched in CO-gas-incubated samples, suggesting that our primers detected uncultured hydrogenogenic carboxydotrophs as well. The new CODH-targeted primers provided us with a fine-grained (~ 97.9% in nucleotide sequence identity) diversity analysis of thermophilic hydrogenogenic carboxydotrophs by amplicon sequencing and will bolster the ecological study of these microorganisms.
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Affiliation(s)
- Kimiho Omae
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Tatsuki Oguro
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masao Inoue
- 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.,Research Center for Bioscience and Nanoscience, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, 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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11
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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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12
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Syngas as Electron Donor for Sulfate and Thiosulfate Reducing Haloalkaliphilic Microorganisms in a Gas-Lift Bioreactor. Microorganisms 2020; 8:microorganisms8091451. [PMID: 32971967 PMCID: PMC7565546 DOI: 10.3390/microorganisms8091451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/17/2020] [Accepted: 09/21/2020] [Indexed: 11/16/2022] Open
Abstract
Biodesulfurization processes remove toxic and corrosive hydrogen sulfide from gas streams (e.g., natural gas, biogas, or syngas). To improve the efficiency of these processes under haloalkaline conditions, a sulfate and thiosulfate reduction step can be included. The use of H2/CO mixtures (as in syngas) instead of pure H2 was tested to investigate the potential cost reduction of the electron donor required. Syngas is produced in the gas-reforming process and consists mainly of H2, carbon monoxide (CO), and carbon dioxide (CO2). Purification of syngas to obtain pure H2 implies higher costs because of additional post-treatment. Therefore, the use of syngas has merit in the biodesulfurization process. Initially, CO inhibited hydrogen-dependent sulfate reduction. However, after 30 days the biomass was adapted and both H2 and CO were used as electron donors. First, formate was produced, followed by sulfate and thiosulfate reduction, and later in the reactor run acetate and methane were detected. Sulfide production rates with sulfate and thiosulfate after adaptation were comparable with previously described rates with only hydrogen. The addition of CO marginally affected the microbial community in which Tindallia sp. was dominant. Over time, acetate production increased and acetogenesis became the dominant process in the bioreactor. Around 50% of H2/CO was converted to acetate. Acetate supported biomass growth and higher biomass concentrations were reached compared to bioreactors without CO feed. Finally, CO addition resulted in the formation of small, compact microbial aggregates. This suggests that CO or syngas can be used to stimulate aggregation in haloalkaline biodesulfurization systems.
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13
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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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14
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Bell E, Sherry A, Pilloni G, Suárez‐Suárez A, Cramm MA, Cueto G, Head IM, Hubert CRJ. Sediment cooling triggers germination and sulfate reduction by heat‐resistant thermophilic spore‐forming bacteria. Environ Microbiol 2019; 22:456-465. [DOI: 10.1111/1462-2920.14866] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Emma Bell
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Angela Sherry
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | | | - Ana Suárez‐Suárez
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Margaret A. Cramm
- Department of Biological SciencesUniversity of Calgary Calgary Alberta Canada
| | - Guillermo Cueto
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Ian M. Head
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
| | - Casey R. J. Hubert
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne UK
- Department of Biological SciencesUniversity of Calgary Calgary Alberta Canada
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15
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Emerging technologies for the pretreatment of lignocellulosic materials for bio-based products. Appl Microbiol Biotechnol 2019; 104:455-473. [DOI: 10.1007/s00253-019-10158-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
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16
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Schoelmerich MC, Müller V. Energy-converting hydrogenases: the link between H 2 metabolism and energy conservation. Cell Mol Life Sci 2019; 77:1461-1481. [PMID: 31630229 DOI: 10.1007/s00018-019-03329-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/17/2019] [Accepted: 10/01/2019] [Indexed: 10/25/2022]
Abstract
The reversible interconversion of molecular hydrogen and protons is one of the most ancient microbial metabolic reactions and catalyzed by hydrogenases. A widespread yet largely enigmatic group comprises multisubunit [NiFe] hydrogenases, that directly couple H2 metabolism to the electrochemical ion gradient across the membranes of bacteria and of archaea. These complexes are collectively referred to as energy-converting hydrogenases (Ech), as they reversibly transform redox energy into physicochemical energy. Redox energy is typically provided by a low potential electron donor such as reduced ferredoxin to fuel H2 evolution and the establishment of a transmembrane electrochemical ion gradient ([Formula: see text]). The [Formula: see text] is then utilized by an ATP synthase for energy conservation by generating ATP. This review describes the modular structure/function of Ech complexes, focuses on insights into the energy-converting mechanisms, describes the evolutionary context and delves into the implications of relying on an Ech complex as respiratory enzyme for microbial metabolism.
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Affiliation(s)
- Marie Charlotte Schoelmerich
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.,Microbiology and Biotechnology, Institute of Plant Sciences and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Volker Müller
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany.
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17
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Annan FJ, Al-Sinawi B, Humphreys CM, Norman R, Winzer K, Köpke M, Simpson SD, Minton NP, Henstra AM. Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum. Appl Microbiol Biotechnol 2019; 103:4633-4648. [PMID: 30972463 PMCID: PMC6505512 DOI: 10.1007/s00253-019-09763-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/19/2019] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
Clostridium autoethanogenum and Clostridium ljungdahlii are physiologically and genetically very similar strict anaerobic acetogens capable of growth on carbon monoxide as sole carbon source. While exact nutritional requirements have not been reported, we observed that for growth, the addition of vitamins to media already containing yeast extract was required, an indication that these are fastidious microorganisms. Elimination of complex components and individual vitamins from the medium revealed that the only organic compounds required for growth were pantothenate, biotin and thiamine. Analysis of the genome sequences revealed that three genes were missing from pantothenate and thiamine biosynthetic pathways, and five genes were absent from the pathway for biotin biosynthesis. Prototrophy in C. autoethanogenum and C. ljungdahlii for pantothenate was obtained by the introduction of plasmids carrying the heterologous gene clusters panBCD from Clostridium acetobutylicum, and for thiamine by the introduction of the thiC-purF operon from Clostridium ragsdalei. Integration of panBCD into the chromosome through allele-coupled exchange also conveyed prototrophy. C. autoethanogenum was converted to biotin prototrophy with gene sets bioBDF and bioHCA from Desulfotomaculum nigrificans strain CO-1-SRB, on plasmid and integrated in the chromosome. The genes could be used as auxotrophic selection markers in recombinant DNA technology. Additionally, transformation with a subset of the genes for pantothenate biosynthesis extended selection options with the pantothenate precursors pantolactone and/or beta-alanine. Similarly, growth was obtained with the biotin precursor pimelate combined with genes bioYDA from C. acetobutylicum. The work raises questions whether alternative steps exist in biotin and thiamine biosynthesis pathways in these acetogens.
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Affiliation(s)
- Florence J Annan
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Bakir Al-Sinawi
- University of New-South Wales (UNSW) Sydney, Kensington, Australia
| | - Christopher M Humphreys
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Rupert Norman
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michael Köpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anne M Henstra
- BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
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18
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Watanabe M, Kojima H, Fukui M. Review of Desulfotomaculum species and proposal of the genera Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov. Int J Syst Evol Microbiol 2018; 68:2891-2899. [PMID: 30028279 DOI: 10.1099/ijsem.0.002915] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Desulfotomaculumis a heterogeneous group of spore-forming sulfate-reducing bacteria. The type species of the genus is Desulfotomaculum nigrificans (Approved Lists 1980) emend. Visser et al. 2014. The results of phylogenetic analysis demonstrated that the genus Desulfotomaculum already has lost the clustering monophyly and was segregated into some distinct groups with low sequence similarity. Major features of the type strains in these groups were compared, and four novel genera, Desulfallas gen. nov., Desulfofundulus gen. nov., Desulfofarcimen gen. nov. and Desulfohalotomaculum gen. nov. were proposed to accommodate species transferred from the genus Desulfotomaculum.
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Affiliation(s)
- Miho Watanabe
- 2Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan.,1The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Hisaya Kojima
- 1The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Manabu Fukui
- 1The Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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19
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Marietou A, Røy H, Jørgensen BB, Kjeldsen KU. Sulfate Transporters in Dissimilatory Sulfate Reducing Microorganisms: A Comparative Genomics Analysis. Front Microbiol 2018; 9:309. [PMID: 29551997 PMCID: PMC5840216 DOI: 10.3389/fmicb.2018.00309] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 02/09/2018] [Indexed: 12/31/2022] Open
Abstract
The first step in the sulfate reduction pathway is the transport of sulfate across the cell membrane. This uptake has a major effect on sulfate reduction rates. Much of the information available on sulfate transport was obtained by studies on assimilatory sulfate reduction, where sulfate transporters were identified among several types of protein families. Despite our growing knowledge on the physiology of dissimilatory sulfate-reducing microorganisms (SRM) there are no studies identifying the proteins involved in sulfate uptake in members of this ecologically important group of anaerobes. We surveyed the complete genomes of 44 sulfate-reducing bacteria and archaea across six phyla and identified putative sulfate transporter encoding genes from four out of the five surveyed protein families based on homology. We did not find evidence that ABC-type transporters (SulT) are involved in the uptake of sulfate in SRM. We speculate that members of the CysP sulfate transporters could play a key role in the uptake of sulfate in thermophilic SRM. Putative CysZ-type sulfate transporters were present in all genomes examined suggesting that this overlooked group of sulfate transporters might play a role in sulfate transport in dissimilatory sulfate reducers alongside SulP. Our in silico analysis highlights several targets for further molecular studies in order to understand this key step in the metabolism of SRMs.
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Affiliation(s)
- Angeliki Marietou
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Hans Røy
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Bo B Jørgensen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Kasper U Kjeldsen
- Center for Geomicrobiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
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20
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Bell E, Blake LI, Sherry A, Head IM, Hubert CRJ. Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities. Environ Microbiol 2018; 20:1134-1147. [PMID: 29393553 PMCID: PMC6849807 DOI: 10.1111/1462-2920.14056] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 01/23/2018] [Indexed: 12/12/2022]
Abstract
Endospores of thermophilic bacteria are found in cold and temperate sediments where they persist in a dormant state. As inactive endospores that cannot grow at the low ambient temperatures, they are akin to tracer particles in cold sediments, unaffected by factors normally governing microbial biogeography (e.g., selection, drift, mutation). This makes thermophilic endospores ideal model organisms for studying microbial biogeography since their spatial distribution can be directly related to their dispersal history. To assess dispersal histories of estuarine bacteria, thermophilic endospores were enriched from sediments along a freshwater‐to‐marine transect of the River Tyne in high temperature incubations (50°C). Dispersal histories for 75 different taxa indicated that the majority of estuarine endospores were of terrestrial origin; most closely related to bacteria from warm habitats associated with industrial activity. A subset of the taxa detected were marine derived, with close relatives from hot deep marine biosphere habitats. These patterns are consistent with the sources of sediment in the River Tyne being predominantly terrestrial in origin. The results point to microbial communities in estuarine and marine sediments being structured by bi‐directional currents, terrestrial run‐off and industrial effluent as vectors of passive dispersal and immigration.
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Affiliation(s)
- Emma Bell
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Lynsay I Blake
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Angela Sherry
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Ian M Head
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Casey R J Hubert
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,Department of Biological Sciences, University of Calgary, Calgary, T2N 1N4, Canada
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21
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Liu ZH, Yin H, Lin Z, Dang Z. Sulfate-reducing bacteria in anaerobic bioprocesses: basic properties of pure isolates, molecular quantification, and controlling strategies. ACTA ACUST UNITED AC 2018. [DOI: 10.1080/21622515.2018.1437783] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Ze-hua Liu
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
- Key Lab Pollution Control and Ecosystem Restoration in Industry Cluster, Ministry of Education, Guangzhou, People’s Republic of China
- Guangdong Environmental Protection Key Laboratory of Solid Waste Treatment and Recycling, Guangzhou, People’s Republic of China
- Guangdong Provincial Engineering and Technology Research Center for Environment Risk Prevention and Emergency Disposal, South China University of Technology, Guangzhou, People’s Republic of China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
| | - Zhang Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, People’s Republic of China
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22
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Reyes-Alvarado LC, Camarillo-Gamboa Á, Rustrian E, Rene ER, Esposito G, Lens PNL, Houbron E. Lignocellulosic biowastes as carrier material and slow release electron donor for sulphidogenesis of wastewater in an inverse fluidized bed bioreactor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2018; 25:5115-5128. [PMID: 28702909 DOI: 10.1007/s11356-017-9334-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
Industrial wastewaters containing high concentrations of sulphate, such as those generated by mining, metallurgical and mineral processing industries, require electron donor for biological sulfidogenesis. In this study, five types of lignocellulosic biowastes were characterized as potential low-cost slow release electron donors for application in a continuously operated sulphidogenic inverse fluidized bed bioreactor (IFBB). Among them, natural scourer and cork were selected due to their high composition of volatile solids (VS), viz. 89.1 and 96.3%, respectively. Experiments were performed in batch (47 days) and in an IFBB (49 days) using synthetic sulphate-rich wastewater. In batch, the scourer gave higher sulphate reduction rates (67.7 mg SO42- L-1 day-1) in comparison to cork (12.1 mg SO42- L-1 day-1), achieving >82% sulphate reduction efficiencies. In the IFBB packed with the natural scourer, the average sulphate reduction efficiency was 24 (±17)%, while the volumetric sulphate reduction rate was 167 (±117) mg SO42- L-1 day-1. The long incubation time in the batch experiments (47 days) allowed higher sulphate reduction efficiencies in comparison to the short hydraulic retention time (24 h) in the IFBB. This suggests the hydrolysis-fermentation was the rate-limiting step and the electron donor supply (through hydrolysis of the lignocellulosic biowaste) was limiting the sulphate reduction. Lignocellulose as carrier material and slow release electron donor for sulphidogenesis.
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Affiliation(s)
- Luis C Reyes-Alvarado
- UNESCO-IHE Institute for Water Education, P.O. Box 3015, 2601 DA, Delft, The Netherlands.
| | | | - Elena Rustrian
- Facultad de Ciencias Químicas, Universidad Veracruzana, 94340, Orizaba, VER, Mexico
| | - Eldon R Rene
- UNESCO-IHE Institute for Water Education, P.O. Box 3015, 2601 DA, Delft, The Netherlands
| | - Giovanni Esposito
- Department of Mechanics, Structures and Environmental Engineering, University of Cassino, via Di Biasio 43, 03043, Cassino, FR, Italy
| | - Piet N L Lens
- UNESCO-IHE Institute for Water Education, P.O. Box 3015, 2601 DA, Delft, The Netherlands
| | - Eric Houbron
- Facultad de Ciencias Químicas, Universidad Veracruzana, 94340, Orizaba, VER, Mexico
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23
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Arantes AL, Alves JI, Stams AJM, Alves MM, Sousa DZ. Enrichment of syngas-converting communities from a multi-orifice baffled bioreactor. Microb Biotechnol 2017; 11:639-646. [PMID: 29160026 PMCID: PMC6011948 DOI: 10.1111/1751-7915.12864] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 08/31/2017] [Accepted: 09/03/2017] [Indexed: 12/04/2022] Open
Abstract
The substitution of natural gas by renewable biomethane is an interesting option to reduce global carbon footprint. Syngas fermentation has potential in this context, as a diverse range of low‐biodegradable materials that can be used. In this study, anaerobic sludge acclimatized to syngas in a multi‐orifice baffled bioreactor (MOBB) was used to start enrichments with CO. The main goals were to identify the key players in CO conversion and evaluate potential interspecies metabolic interactions conferring robustness to the process. Anaerobic sludge incubated with 0.7 × 105 Pa CO produced methane and acetate. When the antibiotics vancomycin and/or erythromycin were added, no methane was produced, indicating that direct methanogenesis from CO did not occur. Acetobacterium and Sporomusa were the predominant bacterial species in CO‐converting enrichments, together with methanogens from the genera Methanobacterium and Methanospirillum. Subsequently, a highly enriched culture mainly composed of a Sporomusa sp. was obtained that could convert up to 1.7 × 105 Pa CO to hydrogen and acetate. These results attest the role of Sporomusa species in the enrichment as primary CO utilizers and show their importance for methane production as conveyers of hydrogen to methanogens present in the culture.
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Affiliation(s)
- Ana L Arantes
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Joana I Alves
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Alfons J M Stams
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - M Madalena Alves
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Diana Z Sousa
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.,Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
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24
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Nakazawa MM, Gavazza S, Kato MT, Florencio L. Evaluation of rhamnolipid addition on the natural attenuation of estuarine sediments contaminated with diesel oil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:25522-25533. [PMID: 27388594 DOI: 10.1007/s11356-016-7152-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 06/26/2016] [Indexed: 06/06/2023]
Abstract
The aim of the present study was to assess the bioremediation of estuarine sediments contaminated with diesel oil. The following two experiments were performed: natural attenuation (NA) and stimulated natural attenuation (SNA), using rhamnolipid as biosurfactant. Sediment samples were accommodated into glass columns and then contaminated with diesel oil on the top. The column profiles were separated into surface, middle, and bottom for the analyses. The 16 polycyclic aromatic hydrocarbons (PAHs) prioritized by US Environmental Protection Agency (EPA) were monitored for 349 days. Those with three and four rings showed increasing concentrations through the operation period in the middle and bottom samples, particularly between days 111 and 338, and in the SNA experiment. Those with five and six rings were also detected in the deeper portions of the columns, suggesting the percolation of PAHs with a high molecular weight. Total organic carbon was reduced by 91 and 89 % in the NA and SNA samples, respectively, although no statistically significant differences (p > 0.05) were found between the two treatments. The analyses by denaturing gradient gel electrophoresis indicated a slight shift in the microbial community structure over the experiments. Microorganisms belonging to the γ-Proteobacteria phylum were the main bacteria involved. The archaeal community exhibited dominance of hydrogenotrophic methanogens, indicating the obligate anaerobic biodegradation of intermediate compounds from hydrocarbon degradation.
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Affiliation(s)
- Mitsue M Nakazawa
- Laboratory of Environmental Sanitation, Department of Civil and Environmental Engineering, Federal University of Pernambuco, Av. Acadêmico Hélio Ramos, s/n. Cidade Universitária, CEP, Recife, PE, 50740-530, Brazil
| | - Sávia Gavazza
- Laboratory of Environmental Sanitation, Department of Civil and Environmental Engineering, Federal University of Pernambuco, Av. Acadêmico Hélio Ramos, s/n. Cidade Universitária, CEP, Recife, PE, 50740-530, Brazil.
| | - Mario T Kato
- Laboratory of Environmental Sanitation, Department of Civil and Environmental Engineering, Federal University of Pernambuco, Av. Acadêmico Hélio Ramos, s/n. Cidade Universitária, CEP, Recife, PE, 50740-530, Brazil
| | - Lourdinha Florencio
- Laboratory of Environmental Sanitation, Department of Civil and Environmental Engineering, Federal University of Pernambuco, Av. Acadêmico Hélio Ramos, s/n. Cidade Universitária, CEP, Recife, PE, 50740-530, Brazil
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25
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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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Shen Y, Jarboe L, Brown R, Wen Z. A thermochemical–biochemical hybrid processing of lignocellulosic biomass for producing fuels and chemicals. Biotechnol Adv 2015; 33:1799-813. [DOI: 10.1016/j.biotechadv.2015.10.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 10/16/2015] [Accepted: 10/16/2015] [Indexed: 12/28/2022]
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Visser M, Stams AJM, Frutschi M, Bernier-Latmani R. Phylogenetic comparison of Desulfotomaculum species of subgroup 1a and description of Desulfotomaculum reducens sp. nov. Int J Syst Evol Microbiol 2015; 66:762-767. [PMID: 26597812 DOI: 10.1099/ijsem.0.000786] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A genome and physiological comparison was made of the type strains of Desulfotomaculum species belonging to subgroup 1a and of 'Desulfotomaculum reducens' strain MI-1. Phenotypically, 'Desulfotomaculum reducens' strain MI-1 can be distinguished from the other described Desulfotomaculum species of subgroup 1a by its ability to grow with propionate and butyrate. In addition, the strain is able to use a variety of metals as electron acceptors. Metal reduction has not been tested in the other species, but seems likely based on our genome analysis. Phylogenetic 16S rRNA gene sequence analysis and the average nucleotide identity between the genomes of the species of subgroup 1a show that strain MI-1 represents a novel species within the Desulfotomaculum 1a subgroup, Desulfotomaculum reducens sp. nov. The type strain is MI-1T.
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Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands.,CEB-Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Manon Frutschi
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, CH A1 375 Station 6, Lausanne CH-1015, Switzerland
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne, CH A1 375 Station 6, Lausanne CH-1015, Switzerland
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Diender M, Stams AJM, Sousa DZ. Pathways and Bioenergetics of Anaerobic Carbon Monoxide Fermentation. Front Microbiol 2015; 6:1275. [PMID: 26635746 PMCID: PMC4652020 DOI: 10.3389/fmicb.2015.01275] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/31/2015] [Indexed: 11/29/2022] Open
Abstract
Carbon monoxide can act as a substrate for different modes of fermentative anaerobic metabolism. The trait of utilizing CO is spread among a diverse group of microorganisms, including members of bacteria as well as archaea. Over the last decade this metabolism has gained interest due to the potential of converting CO-rich gas, such as synthesis gas, into bio-based products. Three main types of fermentative CO metabolism can be distinguished: hydrogenogenesis, methanogenesis, and acetogenesis, generating hydrogen, methane and acetate, respectively. Here, we review the current knowledge on these three variants of microbial CO metabolism with an emphasis on the potential enzymatic routes and bio-energetics involved.
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Affiliation(s)
- Martijn Diender
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands ; Centre of Biological Engineering, University of Minho Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
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29
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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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Magnabosco C, Ryan K, Lau MCY, Kuloyo O, Sherwood Lollar B, Kieft TL, van Heerden E, Onstott TC. A metagenomic window into carbon metabolism at 3 km depth in Precambrian continental crust. ISME JOURNAL 2015; 10:730-41. [PMID: 26325359 DOI: 10.1038/ismej.2015.150] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 07/04/2015] [Accepted: 07/20/2015] [Indexed: 11/09/2022]
Abstract
Subsurface microbial communities comprise a significant fraction of the global prokaryotic biomass; however, the carbon metabolisms that support the deep biosphere have been relatively unexplored. In order to determine the predominant carbon metabolisms within a 3-km deep fracture fluid system accessed via the Tau Tona gold mine (Witwatersrand Basin, South Africa), metagenomic and thermodynamic analyses were combined. Within our system of study, the energy-conserving reductive acetyl-CoA (Wood-Ljungdahl) pathway was found to be the most abundant carbon fixation pathway identified in the metagenome. Carbon monoxide dehydrogenase genes that have the potential to participate in (1) both autotrophic and heterotrophic metabolisms through the reversible oxidization of CO and subsequent transfer of electrons for sulfate reduction, (2) direct utilization of H2 and (3) methanogenesis were identified. The most abundant members of the metagenome belonged to Euryarchaeota (22%) and Firmicutes (57%)-by far, the highest relative abundance of Euryarchaeota yet reported from deep fracture fluids in South Africa and one of only five Firmicutes-dominated deep fracture fluids identified in the region. Importantly, by combining the metagenomics data and thermodynamic modeling of this study with previously published isotopic and community composition data from the South African subsurface, we are able to demonstrate that Firmicutes-dominated communities are associated with a particular hydrogeologic environment, specifically the older, more saline and more reducing waters.
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Affiliation(s)
- Cara Magnabosco
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA
| | - Kathleen Ryan
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA
| | - Maggie C Y Lau
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, USA
| | - Olukayode Kuloyo
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | | | - Thomas L Kieft
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Esta van Heerden
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Tullis C Onstott
- Department of Geosciences, Guyot Hall, Princeton University, Princeton, NJ, 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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Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:235384. [PMID: 26345487 PMCID: PMC4543118 DOI: 10.1155/2015/235384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/09/2015] [Accepted: 06/14/2015] [Indexed: 11/23/2022]
Abstract
The hyperthermophilic, sulfate-reducing archaeon, Archaeoglobus fulgidus, utilizes CO as an energy source and it is resistant to the toxic effects of high CO concentrations. Herein, transcription profiles were obtained from A. fulgidus during growth with CO and sulfate or thiosulfate, or without an electron acceptor. This provided a basis for a model of the CO metabolism of A. fulgidus. The model suggests proton translocation by “Mitchell-type” loops facilitated by Fqo catalyzing a Fdred:menaquinone oxidoreductase reaction, as the major mode of energy conservation, rather than formate or H2 cycling during respiratory growth. The bifunctional CODH (cdhAB-2) is predicted to play an ubiquitous role in the metabolism of CO, and a novel nitrate reductase-associated respiratory complex was induced specifically in the presence of sulfate. A potential role of this complex in relation to Fdred and APS reduction is discussed. Multiple membrane-bound heterodisulfide reductase (DsrMK) could promote both energy-conserving and non-energy-conserving menaquinol oxidation. Finally, the FqoF subunit may catalyze a Fdred:F420 oxidoreductase reaction. In the absence of electron acceptor, downregulation of F420H2 dependent steps of the acetyl-CoA pathway is linked to transient formate generation. Overall, carboxidotrophic growth seems as an intrinsic capacity of A. fulgidus with little need for novel resistance or respiratory complexes.
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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Chan CS, Chan KG, Tay YL, Chua YH, Goh KM. Diversity of thermophiles in a Malaysian hot spring determined using 16S rRNA and shotgun metagenome sequencing. Front Microbiol 2015; 6:177. [PMID: 25798135 PMCID: PMC4350410 DOI: 10.3389/fmicb.2015.00177] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/17/2015] [Indexed: 02/04/2023] Open
Abstract
The Sungai Klah (SK) hot spring is the second hottest geothermal spring in Malaysia. This hot spring is a shallow, 150-m-long, fast-flowing stream, with temperatures varying from 50 to 110°C and a pH range of 7.0–9.0. Hidden within a wooded area, the SK hot spring is continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). In this study, a sample taken from the middle of the stream was analyzed at the 16S rRNA V3-V4 region by amplicon metagenome sequencing. Over 35 phyla were detected by analyzing the 16S rRNA data. Firmicutes and Proteobacteria represented approximately 57% of the microbiome. Approximately 70% of the detected thermophiles were strict anaerobes; however, Hydrogenobacter spp., obligate chemolithotrophic thermophiles, represented one of the major taxa. Several thermophilic photosynthetic microorganisms and acidothermophiles were also detected. Most of the phyla identified by 16S rRNA were also found using the shotgun metagenome approaches. The carbon, sulfur, and nitrogen metabolism within the SK hot spring community were evaluated by shotgun metagenome sequencing, and the data revealed diversity in terms of metabolic activity and dynamics. This hot spring has a rich diversified phylogenetic community partly due to its natural environment (plant litter, high TOC, and a shallow stream) and geochemical parameters (broad temperature and pH range). It is speculated that symbiotic relationships occur between the members of the community.
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Affiliation(s)
- Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | | | | | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia Skudai, Malaysia
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Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A. Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:14. [PMID: 25688290 PMCID: PMC4329661 DOI: 10.1186/s13068-014-0193-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/22/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Decomposition of biomass for biogas production can be practiced under wet and dry fermentation conditions. In contrast to the dry fermentation technology, wet fermentation is characterized by a high liquid content and a relatively low total solid content. In this study, the composition and functional potential of a biogas-producing microbial community in an agricultural biogas reactor operating under wet fermentation conditions was analyzed by a metagenomic approach applying 454-pyrosequencing. The obtained metagenomic dataset and corresponding 16S rRNA gene amplicon sequences were compared to the previously sequenced comparable metagenome from a dry fermentation process, meeting explicitly identical boundary conditions regarding sample and community DNA preparation, sequencing technology, processing of sequence reads and data analyses by bioinformatics tools. RESULTS High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total. Taxonomic comparison of the communities from wet and dry fermentation revealed similar microbial profiles with Bacteria being the predominant superkingdom, while the superkingdom Archaea was less abundant. In both biogas plants, the bacterial phyla Firmicutes, Bacteroidetes, Spirochaetes and Proteobacteria were identified with descending frequencies. Within the archaeal superkingdom, the phylum Euryarchaeota was most abundant with the dominant class Methanomicrobia. Functional profiles of the communities revealed that environmental gene tags representing methanogenesis enzymes were present in both biogas plants in comparable frequencies. 16S rRNA gene amplicon high-throughput sequencing disclosed differences in the sub-communities comprising methanogenic Archaea between both processes. Fragment recruitments of metagenomic reads to the reference genome of the archaeon Methanoculleus bourgensis MS2(T) revealed that dominant methanogens within the dry fermentation process were highly related to the reference. CONCLUSIONS Although process parameters, substrates and technology differ between the wet and dry biogas fermentations analyzed in this study, community profiles are very similar at least at higher taxonomic ranks, illustrating that core community taxa perform key functions in biomass decomposition and methane synthesis. Regarding methanogenesis, Archaea highly related to the type strain M. bourgensis MS2(T) dominate the dry fermentation process, suggesting the adaptation of members belonging to this species to specific fermentation process parameters.
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Affiliation(s)
- Yvonne Stolze
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Martha Zakrzewski
- />QIMR Berghofer Medical Research Institute Herston, 300 Herston Road, Brisbane, QLD 4006 Australia
| | - Irena Maus
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Felix Eikmeyer
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Sebastian Jaenicke
- />Bioinformatics Resource Facility, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Nils Rottmann
- />NORTH-TEC Maschinenbau GmbH, Oldenhörn 1, 25821 Bredstedt, Germany
| | - Clemens Siebner
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andreas Schlüter
- />Institute for Genome Research and Systems Biology, CeBiTec, Bielefeld University, Universitätsstraße 25, D-33615 Bielefeld, Germany
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Rittmann SKM, Lee HS, Lim JK, Kim TW, Lee JH, Kang SG. One-carbon substrate-based biohydrogen production: Microbes, mechanism, and productivity. Biotechnol Adv 2015; 33:165-177. [DOI: 10.1016/j.biotechadv.2014.11.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 10/10/2014] [Accepted: 11/11/2014] [Indexed: 11/28/2022]
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Purcell AM, Mikucki JA, Achberger AM, Alekhina IA, Barbante C, Christner BC, Ghosh D, Michaud AB, Mitchell AC, Priscu JC, Scherer R, Skidmore ML, Vick-Majors TJ, the WISSARD Science Team. Microbial sulfur transformations in sediments from Subglacial Lake Whillans. Front Microbiol 2014; 5:594. [PMID: 25477865 PMCID: PMC4237127 DOI: 10.3389/fmicb.2014.00594] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/21/2014] [Indexed: 11/13/2022] Open
Abstract
Diverse microbial assemblages inhabit subglacial aquatic environments. While few of these environments have been sampled, data reveal that subglacial organisms gain energy for growth from reduced minerals containing nitrogen, iron, and sulfur. Here we investigate the role of microbially mediated sulfur transformations in sediments from Subglacial Lake Whillans (SLW), Antarctica, by examining key genes involved in dissimilatory sulfur oxidation and reduction. The presence of sulfur transformation genes throughout the top 34 cm of SLW sediments changes with depth. SLW surficial sediments were dominated by genes related to known sulfur-oxidizing chemoautotrophs. Sequences encoding the adenosine-5'-phosphosulfate (APS) reductase gene, involved in both dissimilatory sulfate reduction and sulfur oxidation, were present in all samples and clustered into 16 distinct operational taxonomic units. The majority of APS reductase sequences (74%) clustered with known sulfur oxidizers including those within the "Sideroxydans" and Thiobacillus genera. Reverse-acting dissimilatory sulfite reductase (rDSR) and 16S rRNA gene sequences further support dominance of "Sideroxydans" and Thiobacillus phylotypes in the top 2 cm of SLW sediments. The SLW microbial community has the genetic potential for sulfate reduction which is supported by experimentally measured low rates (1.4 pmol cm(-3)d(-1)) of biologically mediated sulfate reduction and the presence of APS reductase and DSR gene sequences related to Desulfobacteraceae and Desulfotomaculum. Our results also infer the presence of sulfur oxidation, which can be a significant energetic pathway for chemosynthetic biosynthesis in SLW sediments. The water in SLW ultimately flows into the Ross Sea where intermediates from subglacial sulfur transformations can influence the flux of solutes to the Southern Ocean.
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Affiliation(s)
- Alicia M. Purcell
- Department of Microbiology, University of TennesseeKnoxville, TN, USA
| | - Jill A. Mikucki
- Department of Microbiology, University of TennesseeKnoxville, TN, USA
| | - Amanda M. Achberger
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
| | - Irina A. Alekhina
- Climate and Environmental Research Laboratory, Arctic and Antarctic Research Institute, St.Petersburg, Russia
| | - Carlo Barbante
- Institute for the Dynamics of Environmental Processes – Consiglio Nazionale delle Ricerche and Department of Environmental Sciences, Informatics and Statistics, Ca’ Foscari University of VeniceVenice, Italy
| | - Brent C. Christner
- Department of Biological Sciences, Louisiana State UniversityBaton Rouge, LA, USA
| | - Dhritiman Ghosh
- Department of Microbiology, University of TennesseeKnoxville, TN, USA
| | - Alexander B. Michaud
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | | | - John C. Priscu
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
| | - Reed Scherer
- Department of Geological and Environmental Sciences, Northern Illinois UniversityDeKalb, IL, USA
| | - Mark L. Skidmore
- Department of Earth Sciences, Montana State UniversityBozeman, MT, USA
| | - Trista J. Vick-Majors
- Department of Land Resources and Environmental Sciences, Montana State UniversityBozeman, MT, USA
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Hao TW, Xiang PY, Mackey HR, Chi K, Lu H, Chui HK, van Loosdrecht MCM, Chen GH. A review of biological sulfate conversions in wastewater treatment. WATER RESEARCH 2014; 65:1-21. [PMID: 25086411 DOI: 10.1016/j.watres.2014.06.043] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/26/2014] [Accepted: 06/30/2014] [Indexed: 06/03/2023]
Abstract
Treatment of waters contaminated with sulfur containing compounds (S) resulting from seawater intrusion, the use of seawater (e.g. seawater flushing, cooling) and industrial processes has become a challenging issue since around two thirds of the world's population live within 150 km of the coast. In the past, research has produced a number of bioengineered systems for remediation of industrial sulfate containing sewage and sulfur contaminated groundwater utilizing sulfate reducing bacteria (SRB). The majority of these studies are specific with SRB only or focusing on the microbiology rather than the engineered application. In this review, existing sulfate based biotechnologies and new approaches for sulfate contaminated waters treatment are discussed. The sulfur cycle connects with carbon, nitrogen and phosphorus cycles, thus a new platform of sulfur based biotechnologies incorporating sulfur cycle with other cycles can be developed, for the removal of sulfate and other pollutants (e.g. carbon, nitrogen, phosphorus and metal) from wastewaters. All possible electron donors for sulfate reduction are summarized for further understanding of the S related biotechnologies including rates and benefits/drawbacks of each electron donor. A review of known SRB and their environmental preferences with regard to bioreactor operational parameters (e.g. pH, temperature, salinity etc.) shed light on the optimization of sulfur conversion-based biotechnologies. This review not only summarizes information from the current sulfur conversion-based biotechnologies for further optimization and understanding, but also offers new directions for sulfur related biotechnology development.
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Affiliation(s)
- Tian-wei Hao
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Peng-yu Xiang
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hamish R Mackey
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Kun Chi
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hui Lu
- SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China
| | - Ho-kwong Chui
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC, Delft, The Netherlands
| | - Guang-Hao Chen
- Department of Civil & Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong; SYSU-HKUST Joint Research Centre for Innovative Environmental Technology, Sun Yat-sen University, Guangzhou, China.
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Cha IT, Roh SW, Kim SJ, Hong HJ, Lee HW, Lim WT, Rhee SK. Desulfotomaculum tongense sp. nov., a moderately thermophilic sulfate-reducing bacterium isolated from a hydrothermal vent sediment collected from the Tofua Arc in the Tonga Trench. Antonie van Leeuwenhoek 2014; 104:1185-92. [PMID: 24078017 DOI: 10.1007/s10482-013-0040-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/18/2013] [Indexed: 11/28/2022]
Abstract
A novel, strictly anaerobic, moderately thermophilic, endospore-forming, sulfate-reducing bacterium, designated TGB60-1T, was isolated from a hydrothermal sediment vent collected from the Tofua Arc in the Tonga Trench. The strain was characterized phenotypically and phylogenetically. The isolated strain was observed to be Gram-positive, with slightly curved rod-shaped cells and a polar flagellum. Strain TGB60-1T was found to grow anaerobically at 37–60 °C (optimum, 50 °C), at pH 6.0–8.5 (optimum, pH 7.0) and with 1.0–4.0 % (w/v) NaCl (optimum, 3.0 %). The electron acceptors utilised were determined to be sulfate, sulfite, and thiosulfate. Strain TGB60-1T was found to utilise pyruvate and H2 as electron donors. Strain TGB60-1T was determined to be related to representatives of the genus Desulfotomaculum and the closest relatives within this genus were identified as Desulfotomaculum halophilum SEBR 3139T, Desulfotomaculum alkaliphilum S1T and Desulfotomaculum peckii LINDBHT1T (92.7, 92.1, and 91.8 % 16S rRNA gene sequence similarity, respectively). The major fatty acids (>20 %) were identified as C16:0 and C18:1 ω7c. The G+C content of the genomic DNA of this novel bacterium was determined to be 53.9 mol%. Based on this polyphasic taxonomic study, strain TGB60-1T is considered to represent a novel species in the genus Desulfotomaculum, for which the name Desulfotomaculum tongense sp. nov. is proposed. The type strain of D. tongense is strain TGB60-1T (= KTCT 4534T = JCM 18733T).
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40
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Liu Y, Qiao JT, Yuan XZ, Guo RB, Qiu YL. Hydrogenispora ethanolica gen. nov., sp. nov., an anaerobic carbohydrate-fermenting bacterium from anaerobic sludge. Int J Syst Evol Microbiol 2014; 64:1756-1762. [DOI: 10.1099/ijs.0.060186-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
An anaerobic, spore-forming, ethanol-hydrogen-coproducing bacterium, designated LX-BT, was isolated from an anaerobic sludge treating herbicide wastewater. Cells of strain LX-BT were non-motile rods (0.3–0.5×3.0–18.0 µm). Spores were terminal with a bulged sporangium. Growth occurred at 20–50 °C (optimum 37–45 °C), pH 5.0–8.0 (optimum pH 6.0–7.7) and 0–2.5 % (w/v) NaCl. The strain could grow fermentatively on glucose, maltose, arabinose, fructose, xylose, ribose, galactose, mannose, raffinose, sucrose, pectin, starch, glycerol, fumarate, tryptone and yeast extract. The major end-products of glucose fermentation were acetate, ethanol and hydrogen. Yeast extract was not required but stimulated growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, anthraquinone-2,6-disulfonate, fumarate and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The G+C content of the genomic DNA was 56.1 mol%. The major cellular fatty acids were anteiso-C15 : 0, iso-C14 : 0 and C16 : 0. The most abundant polar lipids of strain LX-BT were diphosphatidylglycerol and phosphatidylglycerol. 16S rRNA gene sequence analysis revealed that it belongs to an as-yet-unidentified taxon at the order- or class-level (OPB54) within the phylum
Firmicutes
, showing 86.5 % sequence similarity to previously described species of the
Desulfotomaculum
cluster. The name Hydrogenispora ethanolica gen. nov., sp. nov. is proposed to accommodate strain LX-BT ( = DSM 25471T = JCM 18117T = CGMCC 1.5175T) as the type strain.
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Affiliation(s)
- Yi Liu
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Jiang-Tao Qiao
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Xian-Zheng Yuan
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Rong-Bo Guo
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
| | - Yan-Ling Qiu
- Shandong Industrial Engineering Laboratory of Biogas Production & Utilization, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong Province 266101, PR China
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Visser M, Parshina SN, Alves JI, Sousa DZ, Pereira IAC, Muyzer G, Kuever J, Lebedinsky AV, Koehorst JJ, Worm P, Plugge CM, Schaap PJ, Goodwin LA, Lapidus A, Kyrpides NC, Detter JC, Woyke T, Chain P, Davenport KW, Spring S, Rohde M, Klenk HP, Stams AJM. Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans. Stand Genomic Sci 2014; 9:655-75. [PMID: 25197452 PMCID: PMC4149029 DOI: 10.4056/sigs.4718645] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Desulfotomaculum nigrificans and D. carboxydivorans are moderately thermophilic members of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. They are phylogenetically very closely related and belong to ‘subgroup a’ of the Desulfotomaculum cluster 1. D. nigrificans and D. carboxydivorans have a similar growth substrate spectrum; they can grow with glucose and fructose as electron donors in the presence of sulfate. Additionally, both species are able to ferment fructose, although fermentation of glucose is only reported for D. carboxydivorans. D. nigrificans is able to grow with 20% carbon monoxide (CO) coupled to sulfate reduction, while D. carboxydivorans can grow at 100% CO with and without sulfate. Hydrogen is produced during growth with CO by D. carboxydivorans. Here we present a summary of the features of D. nigrificans and D. carboxydivorans together with the description of the complete genome sequencing and annotation of both strains. Moreover, we compared the genomes of both strains to reveal their differences. This comparison led us to propose a reclassification of D. carboxydivorans as a later heterotypic synonym of D. nigrificans.
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Affiliation(s)
- Michael Visser
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Sofiya N Parshina
- Wingradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Joana I Alves
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Diana Z Sousa
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands ; Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Gerard Muyzer
- Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | | | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Petra Worm
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Alla Lapidus
- Theodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia
| | | | - Janine C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hans Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands ; Centre of Biological Engineering, University of Minho, Braga, Portugal
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42
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Aüllo T, Ranchou-Peyruse A, Ollivier B, Magot M. Desulfotomaculum spp. and related gram-positive sulfate-reducing bacteria in deep subsurface environments. Front Microbiol 2013; 4:362. [PMID: 24348471 PMCID: PMC3844878 DOI: 10.3389/fmicb.2013.00362] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 11/14/2013] [Indexed: 11/25/2022] Open
Abstract
Gram-positive spore-forming sulfate reducers and particularly members of the genus Desulfotomaculum are commonly found in the subsurface biosphere by culture based and molecular approaches. Due to their metabolic versatility and their ability to persist as endospores. Desulfotomaculum spp. are well-adapted for colonizing environments through a slow sedimentation process. Because of their ability to grow autotrophically (H2/CO2) and produce sulfide or acetate, these microorganisms may play key roles in deep lithoautotrophic microbial communities. Available data about Desulfotomaculum spp. and related species from studies carried out from deep freshwater lakes, marine sediments, oligotrophic and organic rich deep geological settings are discussed in this review.
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Affiliation(s)
- Thomas Aüllo
- Equipe Environnement et Microbiologie, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM UMR 5254), Université de Pau et des Pays de l'AdourPau, France
| | - Anthony Ranchou-Peyruse
- Equipe Environnement et Microbiologie, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM UMR 5254), Université de Pau et des Pays de l'AdourPau, France
| | - Bernard Ollivier
- Mediterranean Institute of Oceanology (MIO), Aix-Marseille Université, Université du Sud Toulon-Var, CNRS/INSU, IRD, UM 110Marseille, France
| | - Michel Magot
- Equipe Environnement et Microbiologie, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM UMR 5254), Université de Pau et des Pays de l'AdourPau, France
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43
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Population Analysis of Mesophilic Microbial Fuel Cells Fed with Carbon Monoxide. Appl Biochem Biotechnol 2013; 172:713-26. [DOI: 10.1007/s12010-013-0556-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 09/26/2013] [Indexed: 11/25/2022]
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44
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Alves JI, Stams AJ, Plugge CM, Madalena Alves M, Sousa DZ. Enrichment of anaerobic syngas-converting bacteria from thermophilic bioreactor sludge. FEMS Microbiol Ecol 2013; 86:590-7. [DOI: 10.1111/1574-6941.12185] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 07/09/2013] [Accepted: 07/23/2013] [Indexed: 11/26/2022] Open
Affiliation(s)
- Joana I. Alves
- IBB-Institute for Biotechnology and Bioengineering; Centre of Biological Engineering; University of Minho; Braga Portugal
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
| | - Alfons J.M. Stams
- IBB-Institute for Biotechnology and Bioengineering; Centre of Biological Engineering; University of Minho; Braga Portugal
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
| | - Caroline M. Plugge
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
| | - M. Madalena Alves
- IBB-Institute for Biotechnology and Bioengineering; Centre of Biological Engineering; University of Minho; Braga Portugal
| | - Diana Z. Sousa
- IBB-Institute for Biotechnology and Bioengineering; Centre of Biological Engineering; University of Minho; Braga Portugal
- Laboratory of Microbiology; Wageningen University; Wageningen The Netherlands
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45
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Krishnamurthi S, Spring S, Kumar PA, Mayilraj S, Klenk HP, Suresh K. Desulfotomaculum defluvii sp. nov., a sulfate-reducing bacterium isolated from the subsurface environment of a landfill. Int J Syst Evol Microbiol 2013; 63:2290-2295. [DOI: 10.1099/ijs.0.047662-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel sulfate-reducing, strictly anaerobic and endospore-forming bacterium, designated strain A5LFS102T, was isolated from a subsurface landfill sample. The strain was characterized using a polyphasic approach. Optimal growth was observed at 37 °C and pH 7.5 with sulfate as an electron acceptor. Sulfite and thiosulfate were utilized as electron acceptors. The respiratory isoprenoid quinone was menaquinone MK-7. 16S rRNA gene sequence analysis assigned strain A5LFS102T to the genus
Desulfotomaculum
. Both 16S rRNA and dissimilatory sulfate reductase (dsr) genes were compared with those of representative members of the genus
Desulfotomaculum
. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain A5LFS102T was closely related to
Desulfotomaculum aeronauticum
DSM 10349T (94.6 % sequence similarity). The G+C content of the DNA was 45.4 mol%. The total cellular fatty acid profile was dominated by C16 fatty acids. These phenotypic and genotypic data showed that strain A5LFS102T should be recognized as representative of a novel species of the genus
Desulfotomaculum
, for which the name Desulfotomaculum defluvii sp. nov. is proposed. The type strain is A5LFS102T ( = DSM 23699T = JCM 14036T = MTCC 7767T).
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Affiliation(s)
- Srinivasan Krishnamurthi
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, India
| | - Stefan Spring
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Pinnaka Anil Kumar
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, India
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, India
| | - Hans-Peter Klenk
- DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Korpole Suresh
- Microbial Type Culture Collection and Gene bank (MTCC), CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh – 160 036, India
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Yoneda Y, Yoshida T, Yasuda H, Imada C, Sako Y. A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera. Int J Syst Evol Microbiol 2013; 63:3602-3608. [PMID: 23606483 DOI: 10.1099/ijs.0.050468-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1(T), was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0-3.0 µm straight rods, often observed with round endospores. Strain KKC1(T) grew at 55-68 °C, pH 5.2-9.2 and 0.8-14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1(T) ( = DSM 26464(T) = NBRC 109353(T)).
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Affiliation(s)
- Yasuko Yoneda
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takashi Yoshida
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hisato Yasuda
- Center for Advance Marine Core Research, Kochi University, Kochi 783-8502, Japan
| | - Chiaki Imada
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Yoshihiko Sako
- Laboratory of Marine Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Carbon monoxide as an electron donor for the biological reduction of sulphate. Int J Microbiol 2010; 2010:319527. [PMID: 20628586 PMCID: PMC2901600 DOI: 10.1155/2010/319527] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 03/10/2010] [Accepted: 03/31/2010] [Indexed: 11/17/2022] Open
Abstract
Several strains of Gram-negative and Gram-positive sulphate-reducing bacteria (SRB) are able to use carbon monoxide (CO) as a carbon source and electron donor for biological sulphate reduction. These strains exhibit variable resistance to CO toxicity. The most resistant SRB can grow and use CO as an electron donor at concentrations up to 100%, whereas others are already severely inhibited at CO concentrations as low as 1-2%. Here, the utilization, inhibition characteristics, and enzymology of CO metabolism as well as the current state of genomics of CO-oxidizing SRB are reviewed. Carboxydotrophic sulphate-reducing bacteria can be applied for biological sulphate reduction with synthesis gas (a mixture of hydrogen and carbon monoxide) as an electron donor.
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48
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Carbon monoxide in biology and microbiology: surprising roles for the "Detroit perfume". Adv Microb Physiol 2009; 56:85-167. [PMID: 20943125 DOI: 10.1016/s0065-2911(09)05603-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Carbon monoxide (CO) is a colorless, odorless gas with a reputation for being an anthropogenic poison; there is extensive documentation of the modes of human exposure, toxicokinetics, and health effects. However, CO is also generated endogenously by heme oxygenases (HOs) in mammals and microbes, and its extraordinary biological activities are now recognized and increasingly utilized in medicine and physiology. This review introduces recent advances in CO biology and chemistry and illustrates the exciting possibilities that exist for a deeper understanding of its biological consequences. However, the microbiological literature is scant and is currently restricted to: 1) CO-metabolizing bacteria, CO oxidation by CO dehydrogenase (CODH) and the CO-sensing mechanisms that enable CO oxidation; 2) the use of CO as a heme ligand in microbial biochemistry; and 3) very limited information on how microbes respond to CO toxicity. We demonstrate how our horizons in CO biology have been extended by intense research activity in recent years in mammalian and human physiology and biochemistry. CO is one of several "new" small gas molecules that are increasingly recognized for their profound and often beneficial biological activities, the others being nitric oxide (NO) and hydrogen sulfide (H2S). The chemistry of CO and other heme ligands (oxygen, NO, H2S and cyanide) and the implications for biological interactions are briefly presented. An important advance in recent years has been the development of CO-releasing molecules (CO-RMs) for aiding experimental administration of CO as an alternative to the use of CO gas. The chemical principles of CO-RM design and mechanisms of CO release from CO-RMs (dissociation, association, reduction and oxidation, photolysis, and acidification) are reviewed and we present a survey of the most commonly used CO-RMs. Amongst the most important new applications of CO in mammalian physiology and medicine are its vasoactive properties and the therapeutic potentials of CO-RMs in vascular disease, anti-inflammatory effects, CO-mediated cell signaling in apoptosis, applications in organ preservation, and the effects of CO on mitochondrial function. The very limited literature on microbial growth responses to CO and CO-RMs in vitro, and the transcriptomic and physiological consequences of microbial exposure to CO and CO-RMs are reviewed. There is current interest in CO and CO-RMs as antimicrobial agents, particularly in the control of bacterial infections. Future prospects are suggested and unanswered questions posed.
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Sokolova TG, Henstra AM, Sipma J, Parshina SN, Stams AJM, Lebedinsky AV. Diversity and ecophysiological features of thermophilic carboxydotrophic anaerobes. FEMS Microbiol Ecol 2009; 68:131-41. [PMID: 19573196 DOI: 10.1111/j.1574-6941.2009.00663.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Both natural and anthropogenic hot environments contain appreciable levels of carbon monoxide (CO). Anaerobic microbial communities play an important role in CO conversion in such environments. CO is involved in a number of redox reactions. It is biotransformed by thermophilic methanogens, acetogens, hydrogenogens, sulfate reducers, and ferric iron reducers. Most thermophilic CO-oxidizing anaerobes have diverse metabolic capacities, but two hydrogenogenic species are obligate carboxydotrophs. Among known thermophilic carboxydotrophic anaerobes, hydrogenogens are most numerous, and based on available data they are most important in CO biotransformation in hot environments.
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Affiliation(s)
- Tatyana G Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60 Let Oktyabrya 7/2, Moscow, Russia.
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50
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Techtmann SM, Colman AS, Robb FT. 'That which does not kill us only makes us stronger': the role of carbon monoxide in thermophilic microbial consortia. Environ Microbiol 2009; 11:1027-37. [PMID: 19239487 DOI: 10.1111/j.1462-2920.2009.01865.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon monoxide (CO), while a potent toxin, is also a key intermediate in major autotrophic pathways such as methanogenesis and acetogenesis. The ability of purple sulfur bacteria to use CO as an energy source was first described by Uffen in 1976. The prototype extremely thermophilic carboxydotroph Carboxydothermus hydrogenoformans was described in 1991. Eight bacteria and one archaeon that utilize CO have since been isolated and described from diverse geothermal environments. They derive energy from the oxidation of CO with water to form CO(2) and H(2). Most of these isolates thrive with headspace CO partial pressures around 1 atm, which is grossly elevated relative to CO concentrations in geothermal effluents. To account for this, we suggest that under consortial growth conditions the carboxydotrophs occupy microniches in which biogenic CO accumulates locally to high concentrations. CO oxidizers dissipate these potentially toxic CO hot spots with the production of H(2), CO(2) and acetate whose subsequent oxidation fuels other thermophiles. The identification of genes related to anaerobic CO oxidation in many metagenomic databases attests to widespread distribution of carboxydotrophs. Current evidence suggests that CO-oxidizing bacteria and archaea hold a vital niche in thermophilic ecosystems.
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Affiliation(s)
- Stephen M Techtmann
- Center of Marine Biotechnology, University of Maryland Biotechnology Institute, Baltimore, MD 21202, USA
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