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Fontana A, Campanaro S, Treu L, Kougias PG, Cappa F, Morelli L, Angelidaki I. Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes. WATER RESEARCH 2018; 134:181-191. [PMID: 29427960 DOI: 10.1016/j.watres.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 05/25/2023]
Abstract
The present research is the first comprehensive study regarding the thermophilic anaerobic degradation of cheese wastewater, which combines the evaluation of different reactor configurations (i.e. single and two-stage continuous stirred tank reactors) on the process efficiency and the in-depth characterization of the microbial community structure using genome-centric metagenomics. Both reactor configurations showed acidification problems under the tested organic loading rates (OLRs) of 3.6 and 2.4 g COD/L-reactor day and the hydraulic retention time (HRT) of 15 days. However, the two-stage design reached a methane yield equal to 95% of the theoretical value, in contrast with the single stage configuration, which reached a maximum of 33% of the theoretical methane yield. The metagenomic analysis identified 22 new population genomes and revealed that the microbial compositions between the two configurations were remarkably different, demonstrating a higher methanogenic biodiversity in the two-stage configuration. In fact, the acidogenic reactor of the serial configuration was almost solely composed by the lactose degrader Bifidobacterium crudilactis UC0001. The predictive functional analyses of the main population genomes highlighted specific metabolic pathways responsible for the AD process and the mechanisms of main intermediates production. Particularly, the acetate accumulation experienced by the single stage configuration was mainly correlated to the low abundant syntrophic acetate oxidizer Tepidanaerobacter acetatoxydans UC0018 and to the absence of aceticlastic methanogens.
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Affiliation(s)
- Alessandra Fontana
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy; Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Laura Treu
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Panagiotis G Kougias
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Fabrizio Cappa
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Process - DiSTAS, Catholic University of the Sacred Heart, 29122 Piacenza, Italy
| | - Irini Angelidaki
- Department of Environmental Engineering, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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52
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Schuelke T, Pereira TJ, Hardy SM, Bik HM. Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Mol Ecol 2018; 27:1930-1951. [DOI: 10.1111/mec.14539] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Taruna Schuelke
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Tiago José Pereira
- Department of Nematology; University of California, Riverside; Riverside CA USA
| | - Sarah M. Hardy
- School of Fisheries and Ocean Sciences; University of Alaska; Fairbanks AK USA
| | - Holly M. Bik
- Department of Nematology; University of California, Riverside; Riverside CA USA
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53
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Chiriac CM, Baricz A, Szekeres E, Rudi K, Dragoș N, Coman C. Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania. MICROBIAL ECOLOGY 2018; 75:38-51. [PMID: 28702708 DOI: 10.1007/s00248-017-1031-x] [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: 03/31/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
A limited number of studies have investigated the biodiversity in deep continental hyperthermal aquifers and its influencing factors. Here, we present the first description of microbial communities inhabiting the Pannonian and Triassic hyperthermal aquifers from the Western Plain of Romania, the first one being considered a deposit of "fossilized waters," while the latter is embedded in the hydrological cycle due to natural refilling. The 11 investigated drillings have an open interval between 952 and 3432 m below the surface, with collected water temperatures ranging between 47 and 104 °C, these being the first microbial communities characterized in deep continental water deposits with outflow temperatures exceeding 80 °C. The abundances of bacterial 16S rRNA genes varied from approximately 105-106 mL-1 in the Pannonian to about 102-104 mL-1 in the Triassic aquifer. A 16S rRNA gene metabarcoding analysis revealed distinct microbial communities in the two water deposits, especially in the rare taxa composition. The Pannonian aquifer was dominated by the bacterial genera Hydrogenophilus and Thermodesulfobacterium, together with archaeal methanogens from the Methanosaeta and Methanothermobacter groups. Firmicutes was prevalent in the Triassic deposit with a large number of OTUs affiliated to Thermoanaerobacteriaceae, Thermacetogenium, and Desulfotomaculum. Species richness, evenness, and phylogenetic diversity increased alongside with the abundance of mesophiles, their presence in the Triassic aquifer being most probably caused by the refilling with large quantities of meteoric water in the Carpathian Mountains. Altogether, our results show that the particular physico-cheminal characteristics of each aquifer, together with the water refilling possibilities, seem to determine the microbial community structure.
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Affiliation(s)
- Cecilia M Chiriac
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Andreea Baricz
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Edina Szekeres
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Knut Rudi
- Chemistry, Biotechnology and Food Science Department, Norwegian University of Life Sciences, Aas, Norway
| | - Nicolae Dragoș
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania
- Molecular Biology and Biotechnology Department, Faculty of Biology and Geology, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Cristian Coman
- NIRDBS, Institute of Biological Research, 48 Republicii street, 400015, Cluj-Napoca, Romania.
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54
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Watanabe K, Koyama M, Ueda J, Ban S, Kurosawa N, Toda T. Effect of operating temperature on anaerobic digestion of the Brazilian waterweed Egeria densa and its microbial community. Anaerobe 2017; 47:8-17. [DOI: 10.1016/j.anaerobe.2017.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 10/20/2022]
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55
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Lee JY, Park JH, Park HD. Effects of an applied voltage on direct interspecies electron transfer via conductive materials for methane production. WASTE MANAGEMENT (NEW YORK, N.Y.) 2017; 68:165-172. [PMID: 28743578 DOI: 10.1016/j.wasman.2017.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/13/2017] [Accepted: 07/16/2017] [Indexed: 06/07/2023]
Abstract
Direct interspecies electron transfer (DIET) between exoelectrogenic bacteria and methanogenic archaea via conductive materials is reported as an efficient method to produce methane in anaerobic organic waste digestion. A voltage can be applied to the conductive materials to accelerate the DIET between two groups of microorganisms to produce methane. To evaluate this hypothesis, two sets of anaerobic serum bottles with and without applied voltage were used with a pair of graphite rods as conductive materials to facilitate DIET. Initially, the methane production rate was similar between the two sets of serum bottles, and later the serum bottles with an applied voltage of 0.39V showed a 168% higher methane production rate than serum bottles without an applied voltage. In cyclic voltammograms, the characteristic redox peaks for hydrogen and acetate oxidation were identified in the serum bottles with an applied voltage. In the microbial community analyses, hydrogenotrophic methanogens (e.g. Methanobacterium) were observed to be abundant in serum bottles with an applied voltage, while methanogens utilizing carbon dioxide (e.g., Methanosaeta and Methanosarcina) were dominant in serum bottles without an applied voltage. Taken together, the applied voltage on conductive materials might not be effective to promote DIET in methane production. Instead, it appeared to generate a condition for hydrogenotrophic methanogenesis.
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Affiliation(s)
- Jung-Yeol Lee
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Jeong-Hoon Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul, South Korea; KU-KIST Green School, Graduate School of Energy and Environment, Korea University, Seoul, South Korea.
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56
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Fernandez-Bayo JD, Toniato J, Simmons BA, Simmons CW. Structure and activity of thermophilic methanogenic microbial communities exposed to quaternary ammonium sanitizer. J Environ Sci (China) 2017; 56:164-168. [PMID: 28571852 DOI: 10.1016/j.jes.2016.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/31/2016] [Accepted: 10/08/2016] [Indexed: 06/07/2023]
Abstract
Food processing facilities often use antimicrobial quaternary ammonium compound (QAC) sanitizers to maintain cleanliness. These QACs can end up in wastewaters used as feedstock for anaerobic digestion. The aim of this study was to measure the effect of QAC contamination on biogas production and structure of microbial communities in thermophilic digester sludge. Methane production and biogas quality data were analyzed in batch anaerobic digesters containing QAC at 0, 15, 50, 100 and 150mg/L. Increasing sanitizer concentration in the bioreactors negatively impacted methane production rate and biogas quality. Microbial community composition data was obtained through 16S rRNA gene sequencing from the QAC-contaminated sludges. Sequencing data showed no significant restructuring of the bacterial communities. However, significant restructuring was observed within the archaeal communities as QAC concentration increased. Further studies to confirm these effects on a larger scale and with a longer retention time are necessary.
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Affiliation(s)
- Jesus D Fernandez-Bayo
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA; Department of Biological and Agricultural Engineering, University of California, Davis, CA 95616, USA
| | - Juliano Toniato
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Christopher W Simmons
- Department of Food Science and Technology, University of California, Davis, CA 95616, USA; Energy Efficiency Center, University of California, Davis, CA 95616, USA.
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57
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Kouzuma A, Tsutsumi M, Ishii S, Ueno Y, Abe T, Watanabe K. Non-autotrophic methanogens dominate in anaerobic digesters. Sci Rep 2017; 7:1510. [PMID: 28473726 PMCID: PMC5431450 DOI: 10.1038/s41598-017-01752-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/03/2017] [Indexed: 12/12/2022] Open
Abstract
Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.
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Affiliation(s)
- Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.
| | - Maho Tsutsumi
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Shun'ichi Ishii
- R&D Center for Submarine Resources, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Nankoku, Kochi, 783-8502, Japan
| | - Yoshiyuki Ueno
- Kajima Technical Research Institute, Chofu, Tokyo, 182-0036, Japan
| | - Takashi Abe
- Graduate School of Science and Technology, Niigata University, Niigata, Niigata, 950-2181, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
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58
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Guneratnam AJ, Ahern E, FitzGerald JA, Jackson SA, Xia A, Dobson ADW, Murphy JD. Study of the performance of a thermophilic biological methanation system. BIORESOURCE TECHNOLOGY 2017; 225:308-315. [PMID: 27898322 DOI: 10.1016/j.biortech.2016.11.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/15/2016] [Accepted: 11/16/2016] [Indexed: 05/07/2023]
Abstract
This study investigated the operation of ex-situ biological methanation at two thermophilic temperatures (55°C and 65°C). Methane composition of 85-88% was obtained and volumetric productivities of 0.45 and 0.4LCH4/Lreactor were observed at 55°C and 65°C after 24h respectively. It is postulated that at 55°C the process operated as a mixed culture as the residual organic substrates in the starting inoculum were still available. These were consumed prior to the assessment at 65°C; thus the methanogens were now dependent on gaseous substrates CO2 and H2. The experiment was repeated at 65°C with fresh inoculum (a mixed culture); methane composition and volumetric productivity of 92% and 0.46LCH4/Lreactor were achieved in 24h. Methanothermobacter species represent likely and resilient candidates for thermophilic biogas upgrading.
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Affiliation(s)
| | - Eoin Ahern
- The MaREI Centre, Environmental Research Institute, University College Cork, Ireland
| | - Jamie A FitzGerald
- The MaREI Centre, Environmental Research Institute, University College Cork, Ireland; School of Microbiology, University College Cork, Ireland
| | | | - Ao Xia
- Key Laboratory of Low-grade Energy Utilisation Technologies and Systems, Chongqing University, Chongqing 400044, China
| | | | - Jerry D Murphy
- The MaREI Centre, Environmental Research Institute, University College Cork, Ireland; School of Engineering, University College Cork, Ireland.
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59
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Bharathi M, Chellapandi P. Intergenomic evolution and metabolic cross-talk between rumen and thermophilic autotrophic methanogenic archaea. Mol Phylogenet Evol 2016; 107:293-304. [PMID: 27864137 DOI: 10.1016/j.ympev.2016.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 09/17/2016] [Accepted: 11/13/2016] [Indexed: 02/01/2023]
Abstract
Methanobrevibacter ruminantium M1 (MRU) is a rumen methanogenic archaean that can be able to utilize formate and CO2/H2 as growth substrates. Extensive analysis on the evolutionary genomic contexts considered herein to unravel its intergenomic relationship and metabolic adjustment acquired from the genomic content of Methanothermobacter thermautotrophicus ΔH. We demonstrated its intergenomic distance, genome function, synteny homologs and gene families, origin of replication, and methanogenesis to reveal the evolutionary relationships between Methanobrevibacter and Methanothermobacter. Comparison of the phylogenetic and metabolic markers was suggested for its archaeal metabolic core lineage that might have evolved from Methanothermobacter. Orthologous genes involved in its hydrogenotrophic methanogenesis might be acquired from intergenomic ancestry of Methanothermobacter via Methanobacterium formicicum. Formate dehydrogenase (fdhAB) coding gene cluster and carbon monoxide dehydrogenase (cooF) coding gene might have evolved from duplication events within Methanobrevibacter-Methanothermobacter lineage, and fdhCD gene cluster acquired from bacterial origins. Genome-wide metabolic survey found the existence of four novel pathways viz. l-tyrosine catabolism, mevalonate pathway II, acyl-carrier protein metabolism II and glutathione redox reactions II in MRU. Finding of these pathways suggested that MRU has shown a metabolic potential to tolerate molecular oxygen, antimicrobial metabolite biosynthesis and atypical lipid composition in cell wall, which was acquainted by metabolic cross-talk with mammalian bacterial origins. We conclude that coevolution of genomic contents between Methanobrevibacter and Methanothermobacter provides a clue to understand the metabolic adaptation of MRU in the rumen at different environmental niches.
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Affiliation(s)
- M Bharathi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - P Chellapandi
- Molecular Systems Engineering Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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60
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Robbins SJ, Evans PN, Parks DH, Golding SD, Tyson GW. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well. Front Microbiol 2016; 7:731. [PMID: 27375557 PMCID: PMC4897734 DOI: 10.3389/fmicb.2016.00731] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 05/02/2016] [Indexed: 02/01/2023] Open
Abstract
Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid.
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Affiliation(s)
- Steven J Robbins
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
| | - Suzanne D Golding
- School of Earth Sciences, The University of Queensland Brisbane, QLD, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland Brisbane, QLD, Australia
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61
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Battumur U, Yoon YM, Kim CH. Isolation and Characterization of a New Methanobacterium formicicum KOR-1 from an Anaerobic Digester Using Pig Slurry. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:586-93. [PMID: 26949961 PMCID: PMC4782095 DOI: 10.5713/ajas.15.0507] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/08/2015] [Accepted: 07/17/2015] [Indexed: 11/28/2022]
Abstract
A new methanogen was isolated from an anaerobic digester using pig slurry in South Korea. Only one strain, designated KOR-1, was characterized in detail. Cells of KOR-1 were straight or crooked rods, non-motile, 5 to 15 μm long and 0.7 μm wide. They stained Gram-positive and produced methane from H2+CO2 and formate. Strain KOR-1 grew optimally at 38°C. The optimum pH for growth was 7.0. The strain grew at 0.5% to 3.0% NaCl, with optimum growth at 2.5% NaCl. The G+C content of genomic DNA of strain KOR-1 was 41 mol%. The strain tolerated ampicillin, penicillin G, kanamycin and streptomycin but tetracycline inhibited cell growth. A large fragment of the 16S rRNA gene (~1,350 bp) was obtained from the isolate and sequenced. Comparison of 16S rRNA genes revealed that strain KOR–1 is related to Methanobacterium formicicum (98%, sequence similarity), Methanobacterium bryantii (95%) and Methanobacterium ivanovii (93%). Phylogenetic analysis of the deduced mcrA gene sequences confirmed the closest relative as based on mcrA gene sequence analysis was Methanobacterium formicicum strain (97% nucleic acid sequence identity). On the basis of physiological and phylogenetic characteristics, strain KOR-1 is proposed as a new strain within the genus Methanobacterium, Methanobacterium formicicum KOR-1.
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Affiliation(s)
| | - Young-Man Yoon
- Biogas Research Center, Hankyong National University, Anseong 456-749, Korea
| | - Chang-Hyun Kim
- Biogas Research Center, Hankyong National University, Anseong 456-749, Korea ; Department of Animal Life and Environment Science, Hankyong National University, Anseong 456-749, Korea
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62
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Zhang D, Yuan H, Yu B, Dai X, Huang X, Lou Z, Zhu N. Performance and microbial communities of a batch anaerobic reactor treating liquid and high-solid sludge at thermophilic conditions. RSC Adv 2016. [DOI: 10.1039/c6ra21111a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
HS-AD with TS of 20% achieved similar reactor utilization efficiency as that in L-AD, and enriched hydrogenotrophic methanogensMethanoculleus.
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Affiliation(s)
- Dongling Zhang
- School of Environmental Science and Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- PR China
| | - Haiping Yuan
- School of Environmental Science and Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- PR China
| | - Bao Yu
- School of Environmental Science and Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- PR China
| | - Xiaohu Dai
- School of Environmental Science and Engineering
- Tongji University
- Shanghai 200092
- PR China
| | - Xiaoting Huang
- School of Environmental Science and Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- PR China
| | - Ziyang Lou
- School of Environmental Science and Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- PR China
| | - Nanwen Zhu
- School of Environmental Science and Engineering
- Shanghai Jiao Tong University
- Shanghai 200240
- PR China
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63
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Holmes D, Smith J. Biologically Produced Methane as a Renewable Energy Source. ADVANCES IN APPLIED MICROBIOLOGY 2016; 97:1-61. [PMID: 27926429 DOI: 10.1016/bs.aambs.2016.09.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO2. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane. Their habitats range from the human digestive tract to hydrothermal vents. Although biologically produced methane can negatively impact the environment if released into the atmosphere, when captured, it can serve as a potent fuel source. The anaerobic digestion of wastes such as animal manure, human sewage, or food waste produces biogas which is composed of ∼60% methane. Methane from biogas can be cleaned to yield purified methane (biomethane) that can be readily incorporated into natural gas pipelines making it a promising renewable energy source. Conventional anaerobic digestion is limited by long retention times, low organics removal efficiencies, and low biogas production rates. Therefore, many studies are being conducted to improve the anaerobic digestion process. Researchers have found that addition of conductive materials and/or electrically active cathodes to anaerobic digesters can stimulate the digestion process and increase methane content of biogas. It is hoped that optimization of anaerobic digesters will make biogas more readily accessible to the average person.
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64
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Knappy C, Barillà D, Chong J, Hodgson D, Morgan H, Suleman M, Tan C, Yao P, Keely B. Mono-, di- and trimethylated homologues of isoprenoid tetraether lipid cores in archaea and environmental samples: mass spectrometric identification and significance. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:1420-1432. [PMID: 26634977 DOI: 10.1002/jms.3709] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 08/20/2015] [Accepted: 09/17/2015] [Indexed: 06/05/2023]
Abstract
Higher homologues of widely reported C(86) isoprenoid diglycerol tetraether lipid cores, containing 0-6 cyclopentyl rings, have been identified in (hyper)thermophilic archaea, representing up to 21% of total tetraether lipids in the cells. Liquid chromatography-tandem mass spectrometry confirms that the additional carbon atoms in the C(87-88) homologues are located in the etherified chains. Structures identified include dialkyl and monoalkyl ('H-shaped') tetraethers containing C(40-42) or C(81-82) hydrocarbons, respectively, many representing novel compounds. Gas chromatography-mass spectrometric analysis of hydrocarbons released from the lipid cores by ether cleavage suggests that the C(40) chains are biphytanes and the C(41) chains 13-methylbiphytanes. Multiple isomers, having different chain combinations, were recognised among the dialkyl lipids. Methylated tetraethers are produced by Methanothermobacter thermautotrophicus in varying proportions depending on growth conditions, suggesting that methylation may be an adaptive mechanism to regulate cellular function. The detection of methylated lipids in Pyrobaculum sp. AQ1.S2 and Sulfolobus acidocaldarius represents the first reported occurrences in Crenarchaeota. Soils and aquatic sediments from geographically distinct mesotemperate environments that were screened for homologues contained monomethylated tetraethers, with di- and trimethylated structures being detected occasionally. The structural diversity and range of occurrences of the C(87-89) tetraethers highlight their potential as complementary biomarkers for archaea in natural environments.
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Affiliation(s)
- Chris Knappy
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | - Daniela Barillà
- Department of Biology, University of York, York, YO10 5DD, UK
| | - James Chong
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Dominic Hodgson
- British Antarctic Survey, Madingley Road, Cambridge, CB3 0ET, UK
| | - Hugh Morgan
- Thermophile Research Unit, University of Waikato, Hamilton, New Zealand
| | - Muhammad Suleman
- Department of Chemistry, University of York, York, YO10 5DD, UK
- Department of Agricultural Chemistry, Agricultural University, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Christine Tan
- Thermophile Research Unit, University of Waikato, Hamilton, New Zealand
| | - Peng Yao
- Department of Chemistry, University of York, York, YO10 5DD, UK
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Brendan Keely
- Department of Chemistry, University of York, York, YO10 5DD, UK
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65
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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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66
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You J, Wu G, Ren F, Chang Q, Yu B, Xue Y, Mu B. Microbial community dynamics in Baolige oilfield during MEOR treatment, revealed by Illumina MiSeq sequencing. Appl Microbiol Biotechnol 2015; 100:1469-1478. [PMID: 26496917 DOI: 10.1007/s00253-015-7073-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 10/03/2015] [Accepted: 10/07/2015] [Indexed: 10/22/2022]
Abstract
This study was carried out to understand microbial diversity and function in the microbial enhanced oil recovery (MEOR) process and to assess the impact of MEOR treatment on the microbial community in an oil reservoir. The Illumina MiSeq-based method was used to investigate the structure and dynamics of the microbial community in a MEOR-treated block of the Baolige oilfield, China. The results showed that microbial diversity was high and that 23 phyla occurred in the analyzed samples. Proteobacteria, Firmicutes, Bacteroidetes, Thermotogae, and Euryarchaeota were present in relatively high abundance in all analyzed samples. Injection of bacteria and nutrients resulted in interesting changes in the composition of the microbial community. During MEOR treatment, the community was dominated by the known hydrocarbon-utilizing genera Pseudomonas and Acinetobacter. After the treatment, the two genera decreased in abundance over time while Methanobacteriaceae, as well as known syntrophic genera such as Syntrophomonas, Pelotomaculum, Desulfotomaculum, and Thermacetogenium gradually increased. The change in dominant microbial populations indicated the presence of a succession of microbial communities over time, and the hydrocarbon degradation and syntrophic oxidation of acetate and propionate to methane in the MEOR-treated oilfield. This work contributes to a better understanding of microbial processes in oil reservoirs and helps to optimize MEOR technology.
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Affiliation(s)
- Jing You
- Petroleum Production Engineering Institute of Huabei Oilfield Ltd, Renqiu, 062552, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Gang Wu
- Petroleum Production Engineering Institute of Huabei Oilfield Ltd, Renqiu, 062552, China
| | - Fuping Ren
- Petroleum Production Engineering Institute of Huabei Oilfield Ltd, Renqiu, 062552, China
| | - Qi Chang
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bo Yu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yanfen Xue
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bozhong Mu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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67
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Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:170571. [PMID: 26494982 PMCID: PMC4606414 DOI: 10.1155/2015/170571] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022]
Abstract
With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information on in vitro activities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments). We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase from Pyrococcus furiosus and the RNA ligase from Methanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.
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68
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Niu Q, Takemura Y, Kubota K, Li YY. Comparing mesophilic and thermophilic anaerobic digestion of chicken manure: Microbial community dynamics and process resilience. WASTE MANAGEMENT (NEW YORK, N.Y.) 2015; 43:114-22. [PMID: 26054964 DOI: 10.1016/j.wasman.2015.05.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 05/10/2015] [Accepted: 05/12/2015] [Indexed: 05/19/2023]
Abstract
While methane fermentation is considered as the most successful bioenergy treatment for chicken manure, the relationship between operational performance and the dynamic transition of archaeal and bacterial communities remains poorly understood. Two continuous stirred-tank reactors were investigated under thermophilic and mesophilic conditions feeding with 10%TS. The tolerance of thermophilic reactor on total ammonia nitrogen (TAN) was found to be 8000mg/L with free ammonia (FA) 2000mg/L compared to 16,000mg/L (FA1500mg/L) of mesophilic reactor. Biomethane production was 0.29 L/gVSin in the steady stage and decreased following TAN increase. After serious inhibition, the mesophilic reactor was recovered successfully by dilution and washing stratagem compared to the unrecoverable of thermophilic reactor. The relationship between the microbial community structure, the bioreactor performance and inhibitors such as TAN, FA, and volatile fatty acid was evaluated by canonical correspondence analysis. The performance of methanogenic activity and substrate removal efficiency were changed significantly correlating with the community evenness and phylogenetic structure. The resilient archaeal community was found even after serious inhibition in both reactors. Obvious dynamics of bacterial communities were observed in acidogenic and hydrolytic functional bacteria following TAN variation in the different stages.
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Affiliation(s)
- Qigui Niu
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yasuyuki Takemura
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering Tohoku University, 6-6-06 Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Key Lab of Northwest Water Resource, Environment and Ecology, MOE, Xi'an University of Architecture and Technology, Xi'an, PR China.
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69
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From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples. Appl Microbiol Biotechnol 2015; 99:10271-82. [DOI: 10.1007/s00253-015-6866-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/16/2015] [Accepted: 07/18/2015] [Indexed: 11/25/2022]
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70
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Kern T, Linge M, Rother M. Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester. Int J Syst Evol Microbiol 2015; 65:1975-1980. [PMID: 25807978 DOI: 10.1099/ijs.0.000210] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.
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Affiliation(s)
- Tobias Kern
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
| | - Mary Linge
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
| | - Michael Rother
- Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany
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71
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A novel cytosolic NADH:quinone oxidoreductase from Methanothermobacter marburgensis. Biosci Rep 2014; 34:e00167. [PMID: 25372605 PMCID: PMC4274662 DOI: 10.1042/bsr20140143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Methanothermobacter marburgensis is a strictly anaerobic, thermophilic methanogenic archaeon that uses methanogenesis to convert H2 and CO2 to energy. M. marburgensis is one of the best-studied methanogens, and all genes required for methanogenic metabolism have been identified. Nonetheless, the present study describes a gene (Gene ID 9704440) coding for a putative NAD(P)H:quinone oxidoreductase that has not yet been identified as part of the metabolic machinery. The gene product, MmNQO, was successfully expressed, purified and characterized biochemically, as well as structurally. MmNQO was identified as a flavin-dependent NADH:quinone oxidoreductase with the capacity to oxidize NADH in the presence of a wide range of electron acceptors, whereas NADPH was oxidized with only three acceptors. The 1.50 Å crystal structure of MmNQO features a homodimeric enzyme where each monomer comprises 196 residues folding into flavodoxin-like α/β domains with non-covalently bound FMN (flavin mononucleotide). The closest structural homologue is the modulator of drug activity B from Streptococcus mutans with 1.6 Å root-mean-square deviation on 161 Cα atoms and 28% amino-acid sequence identity. The low similarity at sequence and structural level suggests that MmNQO is unique among NADH:quinone oxidoreductases characterized to date. Based on preliminary bioreactor experiments, MmNQO could provide a useful tool to prevent overflow metabolism in applications that require cells with high energy demand. A novel NADH:quinone oxidoreductase, MmNQO, from Methanothermobacter marburgensis was identified. MmNQO oxidizes NADH with several electron acceptors and is structurally similar to bacterial MdaB. It is localized in the cytosol and may provide a useful tool to prevent overflow metabolism.
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72
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One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia. J Bacteriol 2014; 197:717-26. [PMID: 25448816 DOI: 10.1128/jb.02365-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In cells, N(10)-formyltetrahydrofolate (N(10)-fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis of N(10)-fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We used Escherichia coli, which naturally lacks fhs, as our model. We show that in E. coli, the essential function of folD could be replaced by Clostridium perfringens fhs when it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. The fhs-supported folD deletion (ΔfolD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N(10)-fTHF in the ΔfolD strain (supported by plasmid-borne fhs) were limiting despite the high capacity of the available Fhs to synthesize N(10)-fTHF in vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The ΔfolD strain (harboring fhs on the chromosome) showed a high NADP(+)-to-NADPH ratio and hypersensitivity to trimethoprim. The presence of fhs in E. coli was disadvantageous for its aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. The computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria.
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73
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Kallistova AY, Goel G, Nozhevnikova AN. Microbial diversity of methanogenic communities in the systems for anaerobic treatment of organic waste. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714050142] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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74
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Comparison of the microbial communities in solid-state anaerobic digestion (SS-AD) reactors operated at mesophilic and thermophilic temperatures. Appl Microbiol Biotechnol 2014; 99:969-80. [DOI: 10.1007/s00253-014-6036-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/11/2014] [Accepted: 08/15/2014] [Indexed: 10/24/2022]
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75
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Lee J, Hwang B, Koo T, Shin SG, Kim W, Hwang S. Temporal variation in methanogen communities of four different full-scale anaerobic digesters treating food waste-recycling wastewater. BIORESOURCE TECHNOLOGY 2014; 168:59-63. [PMID: 24767792 DOI: 10.1016/j.biortech.2014.03.161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/28/2014] [Accepted: 03/29/2014] [Indexed: 06/03/2023]
Abstract
Methanogen communities were investigated using 454 pyrosequencing in four different full-scale anaerobic digesters treating food waste-recycling wastewater. Seasonal samples were collected for 2 years, and 24 samples were available for microbial analysis from a plug flow thermophilic (PT) digester, a continuously-stirred tank thermophilic (CT) digester, an upflow anerobic sludge blanket mesophilic (UM) digester, and a continuously-stirred tank mesophilic (CM) digester. Methanoculleus, Methanobacterium, Methanothermobacter, and Methanosaeta were revealed to be key methanogens in full-scale anaerobic digestion process treating food waste-recycling wastewater. In the PT digester, Methanoculleus was dominant (96.8%). In the CT digester, Methanoculleus was dominant (95.4%) during the first year of operation, but the dominant genus was shifted to Methanothermobacter (98.5%) due to pH increase. In the UM digester, Methanosaeta was dominant (87.2%). In the CM digester, Methanoculleus was constantly dominant (74.8%) except during CM5 when Methanosaeta was dominant (62.6%) due to the low residual acetate concentration (0.1 g/L).
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Affiliation(s)
- Joonyeob Lee
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Byungchul Hwang
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Taewoan Koo
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea
| | - Seung Gu Shin
- Infrastructure and Environment Division, School of Engineering, University of Glasgow, Glasgow G12 8LT, UK
| | - Woong Kim
- Department of Chemical and Biomolecular Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Seokhwan Hwang
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, Republic of Korea.
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76
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Yamada C, Kato S, Kimura S, Ishii M, Igarashi Y. Reduction of Fe(III) oxides by phylogenetically and physiologically diverse thermophilic methanogens. FEMS Microbiol Ecol 2014; 89:637-45. [PMID: 24920412 DOI: 10.1111/1574-6941.12365] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/27/2014] [Accepted: 06/04/2014] [Indexed: 11/29/2022] Open
Abstract
Three thermophilic methanogens (Methanothermobacter thermautotrophicus, Methanosaeta thermophila, and Methanosarcina thermophila) were investigated for their ability to reduce poorly crystalline Fe(III) oxides (ferrihydrite) and the inhibitory effects of ferrihydrite on their methanogenesis. This study demonstrated that Fe(II) generation from ferrihydrite occurs in the cultures of the three thermophilic methanogens only when H2 was supplied as the source of reducing equivalents, even in the cultures of Mst. thermophila that do not grow on and produce CH4 from H2/CO2. While supplementation of ferrihydrite resulted in complete inhibition or suppression of methanogenesis by the thermophilic methanogens, ferrihydrite reduction by the methanogens at least partially alleviates the inhibitory effects. Microscopic and crystallographic analyses on the ferrihydrite-reducing Msr. thermophila cultures exhibited generation of magnetite on its cell surfaces through partial reduction of ferrihydrite. These findings suggest that at least certain thermophilic methanogens have the ability to extracellularly transfer electrons to insoluble Fe(III) compounds, affecting their methanogenic activities, which would in turn have significant impacts on materials and energy cycles in thermophilic anoxic environments.
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Affiliation(s)
- Chihaya Yamada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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77
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Hidese R, Inoue T, Imanaka T, Fujiwara S. Cysteine desulphurase plays an important role in environmental adaptation of the hyperthermophilic archaeon Thermococcus kodakarensis. Mol Microbiol 2014; 93:331-45. [PMID: 24893566 DOI: 10.1111/mmi.12662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2014] [Indexed: 11/29/2022]
Abstract
The sulphur atoms of sulphur-containing cofactors that are essential for numerous cellular functions in living organisms originate from L-cysteine via cysteine desulphurase (CSD) activity. However, many (hyper)thermophilic archaea, which thrive in solfataric fields and are positioned near the root of the evolutionary tree of life, lack CSD orthologues. The existence of CSD orthologues in a subset of (hyper)thermophilic archaea is of interest with respect to the evolution of sulphur-trafficking systems for the cofactors. This study demonstrates that the disruption of the csd gene of Thermococcus kodakarensis, a facultative elemental sulphur (S(0))-reducing hyperthermophilic archaeon, encoding Tk-CSD, conferred a growth defect evident only in the absence of S(0), and that growth can be restored by the addition of S(0), but not sulphide. We show that the csd gene is not required for biosynthesis of thiamine pyrophosphate or molybdopterin, irrespective of the presence or absence of S(0), but is necessary for iron-sulphur cluster biosynthesis in the absence of S(0). Recombinant form of Tk-CSD expressed in Escherichia coli was obtained and it was found to catalyse the desulphuration of L-cysteine. The obtained data suggest that hyperthermophiles might benefit from a capacity for CSD-dependent iron-sulphur cluster biogenesis, which allows them to thrive outside solfataric environments.
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Affiliation(s)
- Ryota Hidese
- Research Center for Environmental Bioscience, Graduate School of Science and Technology, Kwansei-Gakuin University, Sanda, Hyogo, 669-1337, Japan
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78
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Kosaka T, Toh H, Fujiyama A, Sakaki Y, Watanabe K, Meng XY, Hanada S, Toyoda A. Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:268-277. [PMID: 24983531 DOI: 10.1111/1758-2229.12128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/05/2013] [Indexed: 06/03/2023]
Abstract
Several thermophilic hydrogenotrophic methanogens naturally aggregate in their habitats in association with hydrogen-producing bacteria for efficient transfer of the methane fermentation intermediates to produce methane. However, physiology of aggregation and the identity of aggregation-specific genes remain to be elucidated. Here, we isolated and characterized a hydrogen and formate-utilizing Methanothermobacter sp. CaT2 that is capable of self-aggregation and utilizing formate. CaT2 produced methane from propionate oxidation in association with a syntrophic propionate-oxidizing bacterium faster than other methanogens, including Methanothermobacter thermautotrophicus ΔH and Methanothermobacter thermautotrophicus Z-245. CaT2 also aggregated throughout the culture period and was coated with polysaccharides, which was not found on the ΔH and Z-245 cells. Sugar content (particularly of rhamnose and mannose) was also higher in the CaT2 cells than the ΔH and Z-245 cells. Comparative genomic analysis of CaT2 indicated that four candidate genes, all of which encode glycosyltransferase, were involved in aggregation of CaT2. Transcriptional analysis showed that one glycosyltransferase gene was expressed at relatively high levels under normal growth conditions. The polysaccharide layer on the CaT2 cell surface, which is probably assembled by these glycosyltransferases, may be involved in cell aggregation.
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Affiliation(s)
- Tomoyuki Kosaka
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan; PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, 332-0012, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
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79
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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81
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Zamanzadeh M, Parker WJ, Verastegui Y, Neufeld JD. Biokinetic and molecular studies of methanogens in phased anaerobic digestion systems. BIORESOURCE TECHNOLOGY 2013; 149:318-326. [PMID: 24125797 DOI: 10.1016/j.biortech.2013.09.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/09/2013] [Accepted: 09/13/2013] [Indexed: 06/02/2023]
Abstract
The influence of differing operational conditions of two-stage digesters on biokinetic characteristics and communities of methanogenic archaea was evaluated. Operating temperature of each phase influenced the archaeal communities significantly. Also, a strong correlation was observed between community composition and temperature and pH. The maximum specific substrate utilization rates (k max) of acetoclastic methanogens in the mesophilic and thermophilic 1st phases were 11.4 and 22.0 mgCOD mgCOD(-1)d(-1), respectively, whereas significantly lower k max values were estimated for the mesophilic and thermophilic 2nd-phase digesters which were 7.6 and 16.6 mgCOD mgCOD(-1)d(-1), respectively. It appeared that the biokinetic characteristics of the acetoclastic methanogen communities were reliant on digester loading rates. Also, higher temperature dependency coefficients (θ) were observed for the long retention time digesters when compared to the values computed for the 1st-phase digesters. Accordingly, the implementation of two sets of biokinetic parameters for acetoclastic methanogen will improve modeling of phased anaerobic digesters.
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Affiliation(s)
- Mirzaman Zamanzadeh
- Department of Civil and Environmental Engineering, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.
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82
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Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter. Appl Microbiol Biotechnol 2013; 98:2321-34. [PMID: 23989973 DOI: 10.1007/s00253-013-5144-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m(3) digester produced biogas with 57% methane, and chemical oxygen demand removal of 54%. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93% of the clones and 76% of the pyrotags. Of the Firmicutes, class Clostridia (52% pyrotags) was most abundant followed by class Bacilli (13% pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97% minimum similarity level. Fifteen OTUs were dominant (≥2% abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (<0.5% abundance), 75% were Firmicutes. The dominant methanogen was Methanothermobacter which has hydrogenotrophic metabolism, and accounted for >99% of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels.
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83
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Complete Genome Sequence of a Thermophilic Hydrogenotrophic Methanogen, Methanothermobacter sp. Strain CaT2. GENOME ANNOUNCEMENTS 2013; 1:1/4/e00672-13. [PMID: 23990577 PMCID: PMC3757452 DOI: 10.1128/genomea.00672-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We isolated a thermophilic hydrogenotrophic methanogen, Methanothermobacter sp. strain CaT2, which is able to aggregate and utilize formate. Here, we report the complete genome sequence of this organism.
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84
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Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
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85
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Extremophilic SHMTs: from structure to biotechnology. BIOMED RESEARCH INTERNATIONAL 2013; 2013:851428. [PMID: 23841096 PMCID: PMC3697235 DOI: 10.1155/2013/851428] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Accepted: 05/30/2013] [Indexed: 01/23/2023]
Abstract
Recent advances in molecular and structural biology have improved the availability of virtually any biocatalyst in large quantity and have also provided an insight into the detailed structure-function relationships of many of them. These results allowed the rational exploitation of biocatalysts for use in organic synthesis. In this context, extremophilic enzymes are extensively studied for their potential interest for many biotechnological and industrial applications, as they offer increased rates of reactions, higher substrate solubility, and/or longer enzyme half-lives at the conditions of industrial processes. Serine hydroxymethyltransferase (SHMT), for its ubiquitous nature, represents a suitable model for analyzing enzyme adaptation to extreme environments. In fact, many SHMT sequences from Eukarya, Eubacteria and Archaea are available in data banks as well as several crystal structures. In addition, SHMT is structurally conserved because of its critical metabolic role; consequently, very few structural changes have occurred during evolution. Our research group analyzed the molecular basis of SHMT adaptation to high and low temperatures, using experimental and comparative in silico approaches. These structural and functional studies of SHMTs purified from extremophilic organisms can help to understand the peculiarities of the enzyme activity at extreme temperatures, indicating possible strategies for rational enzyme engineering.
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86
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Zhou Y, Dorchak AE, Ragsdale SW. In vivo activation of methyl-coenzyme M reductase by carbon monoxide. Front Microbiol 2013; 4:69. [PMID: 23554601 PMCID: PMC3612591 DOI: 10.3389/fmicb.2013.00069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/11/2013] [Indexed: 12/21/2022] Open
Abstract
Methyl-coenzyme M reductase (MCR) from methanogenic archaea catalyzes the rate-limiting and final step in methane biosynthesis. Using coenzyme B as the two-electron donor, MCR reduces methyl-coenzyme M (CH3-SCoM) to methane and the mixed disulfide, CoBS-SCoM. MCR contains an essential redox-active nickel tetrahydrocorphinoid cofactor, Coenzyme F430, at its active site. The active form of the enzyme (MCRred1) contains Ni(I)-F430. Rapid and efficient conversion of MCR to MCRred1 is important for elucidating the enzymatic mechanism, yet this reduction is difficult because the Ni(I) state is subject to oxidative inactivation. Furthermore, no in vitro methods have yet been described to convert Ni(II) forms into MCRred1. Since 1991, it has been known that MCRred1 from Methanothermobacter marburgensis can be generated in vivo when cells are purged with 100% H2. Here we show that purging cells or cell extracts with CO can also activate MCR. The rate of in vivo activation by CO is about 15 times faster than by H2 (130 and 8 min-1, respectively) and CO leads to twofold higher MCRred1 than H2. Unlike H2-dependent activation, which exhibits a 10-h lag time, there is no lag for CO-dependent activation. Based on cyanide inhibition experiments, carbon monoxide dehydrogenase is required for the CO-dependent activation. Formate, which also is a strong reductant, cannot activate MCR in M. marburgensis in vivo.
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Affiliation(s)
- Yuzhen Zhou
- Department of Biological Chemistry, University of Michigan Medical School, University of Michigan Ann Arbor, MI, USA
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87
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Sasaki D, Sasaki K, Watanabe A, Morita M, Igarashi Y, Ohmura N. Efficient production of methane from artificial garbage waste by a cylindrical bioelectrochemical reactor containing carbon fiber textiles. AMB Express 2013; 3:17. [PMID: 23497472 PMCID: PMC3608157 DOI: 10.1186/2191-0855-3-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 03/01/2013] [Indexed: 11/30/2022] Open
Abstract
A cylindrical bioelectrochemical reactor (BER) containing carbon fiber textiles (CFT; BER + CFT) has characteristics of bioelectrochemical and packed-bed systems. In this study, utility of a cylindrical BER + CFT for degradation of a garbage slurry and recovery of biogas was investigated by applying 10% dog food slurry. The working electrode potential was electrochemically regulated at −0.8 V (vs. Ag/AgCl). Stable methane production of 9.37 L-CH4 · L−1 · day−1 and dichromate chemical oxygen demand (CODcr) removal of 62.5% were observed, even at a high organic loading rate (OLR) of 89.3 g-CODcr · L−1 · day−1. Given energy as methane (372.6 kJ · L−1 · day−1) was much higher than input electric energy to the working electrode (0.6 kJ · L−1 · day−1) at this OLR. Methanogens were highly retained in CFT by direct attachment to the cathodic working electrodes (52.3%; ratio of methanogens to prokaryotes), compared with the suspended fraction (31.2%), probably contributing to the acceleration of organic material degradation and removal of organic acids. These results provide insight into the application of cylindrical BER + CFT in efficient methane production from garbage waste including a high percentage of solid fraction.
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88
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Nakamura K, Takahashi A, Mori C, Tamaki H, Mochimaru H, Nakamura K, Takamizawa K, Kamagata Y. Methanothermobacter
tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field. Int J Syst Evol Microbiol 2013; 63:715-722. [DOI: 10.1099/ijs.0.041681-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic and hydrogenotrophic methanogen, strain RMAST, was isolated from gas-associated formation water of a gas-producing well in a natural gas field in Japan. Strain RMAST grew solely on H2/CO2 but required Casamino acids, tryptone, yeast extract or vitamins for growth. Growth of strain RMAST was stimulated by acetate. Cells were non-motile, straight rods (0.5×3.5–10.5 µm) and occurred singly or in pairs. Bundles of fimbriae occurred at both poles of cells and the cell wall was thick (approximately 21 nm, as revealed by ultrathin section electron microscopy). Strain RMAST grew at 45–80 °C (optimum, 70 °C), at pH 5.8–8.7 (optimum, pH 6.9–7.7) and with 0.001–20 g NaCl l−1 (optimum, 2.5 g NaCl l−1). Phylogenetic analysis revealed that
Methanothermobacter thermautotrophicus
ΔHT was most closely related to the isolate (95.7 % 16S rRNA gene sequence similarity). On the basis of morphological, phenotypic and phylogenetic characteristics, it is clear that strain RMAST represents a novel species of the genus
Methanothermobacter
, for which we propose the name
Methanothermobacter
tenebrarum sp. nov. The type strain is RMAST ( = DSM 23052T = JCM 16532T = NBRC 106236T).
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Affiliation(s)
- Kohei Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Azumi Takahashi
- Graduate School of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Chikahiro Mori
- Graduate School of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Hanako Mochimaru
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Kazunori Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Kazuhiro Takamizawa
- Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu 501-1193, Japan
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido 062-8517, Japan
- Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
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89
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Draft Genome Sequence of Methanobacterium sp. Maddingley, Reconstructed from Metagenomic Sequencing of a Methanogenic Microbial Consortium Enriched from Coal-Seam Gas Formation Water. GENOME ANNOUNCEMENTS 2013; 1:genomeA00082-12. [PMID: 23405289 PMCID: PMC3569273 DOI: 10.1128/genomea.00082-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 11/07/2012] [Indexed: 11/20/2022]
Abstract
The draft genome of Methanobacterium sp. Maddingley was reconstructed from metagenomic sequencing of a methanogenic microbial consortium enriched from coal-seam gas formation water. It is a hydrogenotrophic methanogen predicted to grow using hydrogen and carbon dioxide.
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90
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Lins P, Schwarzenauer T, Reitschuler C, Wagner AO, Illmer P. Methanogenic potential of formate in thermophilic anaerobic digestion. WASTE MANAGEMENT & RESEARCH : THE JOURNAL OF THE INTERNATIONAL SOLID WASTES AND PUBLIC CLEANSING ASSOCIATION, ISWA 2012; 30:1031-40. [PMID: 22588113 DOI: 10.1177/0734242x12445655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In the present study the methanogenic potential of formate (HCOO(-)) during thermophilic anaerobic digestion was investigated. After appropriate conditions for methanogenesis (HCOO(-) and inoculum concentration, pH and duration of incubation) were assessed, an experiment with initial 31 replicates was run. Diluted fermenter sludge was used as inoculum, and process parameters including the pH, quality and quantity of the produced biogas and the concentrations of volatile fatty acids and HCO(3) (-) were determined. Remarkably, after 5 days of incubation the highest CH(4) production was calculated for a HCOO(-) concentration of 200 mmol L(-1), a concentration, however, which might not occur in situ. During the phase of high CH(4) production HCOO(-) was degraded with a rate of 1.5 mmol L(-1) h(-1), and distinct changes of Gibbs free energy for several reactions were observed. Based on denaturing high-performance liquid chromatography, denaturing gradient gel electrophoresis, and additional subsequent sequencing approaches the hydrogenotrophic Methanothermobacter wolfeii was the dominant methanogen responsible for CH(4) production. Further confirmation was achieved due to the detection of autofluorescing rods with a size of up to ~3 µm, which were often arranged in pairs and chains. It was shown that even high concentrations of HCOO(-) are readily degraded, which might lead to an underestimation of both, the concentration and thus, the importance of HCOO(-) in anaerobic digestion.
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Affiliation(s)
- Philipp Lins
- University of Innsbruck, Institute of Microbiology, Innsbruck, Austria.
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91
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Rademacher A, Nolte C, Schönberg M, Klocke M. Temperature increases from 55 to 75 °C in a two-phase biogas reactor result in fundamental alterations within the bacterial and archaeal community structure. Appl Microbiol Biotechnol 2012; 96:565-76. [PMID: 22899497 DOI: 10.1007/s00253-012-4348-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 11/28/2022]
Abstract
Agricultural biogas plants were operated in most cases below their optimal performance. An increase in the fermentation temperature and a spatial separation of hydrolysis/acetogenesis and methanogenesis are known strategies in improving and stabilizing biogas production. In this study, the dynamic variability of the bacterial and archaeal community was monitored within a two-phase leach bed biogas reactor supplied with rye silage and straw during a stepwise temperature increase from 55 to 75 °C within the leach bed reactor (LBR), using TRFLP analyses. To identify the terminal restriction fragments that were obtained, bacterial and archaeal 16S rRNA gene libraries were constructed. Above 65 °C, the bacterial community structure changed from being Clostridiales-dominated toward being dominated by members of the Bacteroidales, Clostridiales, and Thermotogales orders. Simultaneously, several changes occurred, including a decrease in the total cell count, degradation rate, and biogas yield along with alterations in the intermediate production. A bioaugmentation with compost at 70 °C led to slight improvements in the reactor performance; these did not persist at 75 °C. However, the archaeal community within the downstream anaerobic filter reactor (AF), operated constantly at 55 °C, altered by the temperature increase in the LBR. At an LBR temperature of 55 °C, members of the Methanobacteriales order were prevalent in the AF, whereas at higher LBR temperatures Methanosarcinales prevailed. Altogether, the best performance of this two-phase reactor was achieved at an LBR temperature of below 65 °C, which indicates that this temperature range has a favorable effect on the microbial community responsible for the production of biogas.
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Affiliation(s)
- Antje Rademacher
- Abteilung Bioverfahrenstechnik, Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V. (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
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92
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The performance of a thermophilic microbial fuel cell fed with synthesis gas. Enzyme Microb Technol 2012; 51:163-70. [DOI: 10.1016/j.enzmictec.2012.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/18/2012] [Accepted: 05/21/2012] [Indexed: 11/19/2022]
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93
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Kundu K, Sharma S, Sreekrishnan TR. Effect of operating temperatures on the microbial community profiles in a high cell density hybrid anaerobic bioreactor. BIORESOURCE TECHNOLOGY 2012; 118:502-511. [PMID: 22717570 DOI: 10.1016/j.biortech.2012.05.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/07/2012] [Accepted: 05/11/2012] [Indexed: 06/01/2023]
Abstract
Lack of knowledge about the microbial consortia involved in wastewater treatment at different operating temperatures, is a major reason for failure of anaerobic reactors in field applications. Present study was undertaken to correlate performance of hybrid anaerobic reactors operating at different temperatures (37, 45 and 55 °C) to structures of archaeal and bacterial communities involved. Self-immobilized granules were developed in the reactors continuously fed with synthetic wastewater (10,000 mg COD l(-1)) and operated at an organic loading rate of 2.22 kg COD m(-3) day(-1) and hydraulic retention time of 5 days. The reactor operated at 37 °C showed the best performance as well as the most diverse microbial community revealed by PCR-denaturing gradient gel electrophoresis analysis using 16S rRNA gene amplicons. Sequences derived from reactors operating at higher temperatures revealed presence of different methanogens, but lesser diversity caused a drop in COD degradation capability of the system indicating successful operation at low loading conditions.
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Affiliation(s)
- Kankana Kundu
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110 016, India
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94
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Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. J Mol Biol 2012; 418:145-60. [PMID: 22306461 DOI: 10.1016/j.jmb.2012.01.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 01/05/2012] [Accepted: 01/13/2012] [Indexed: 11/20/2022]
Abstract
Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea.
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95
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Isolation and characterization of Methanothermobacter crinale sp. nov., a novel hydrogenotrophic methanogen from the Shengli oil field. Appl Environ Microbiol 2011; 77:5212-9. [PMID: 21705537 DOI: 10.1128/aem.00210-11] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis is an alternative methanogenic pathway in certain thermophilic anaerobic environments such as high-temperature oil reservoirs and thermophilic biogas reactors. In these environments, the dominant thermophilic methanogens were generally related to uncultured organisms of the genus Methanothermobacter. Here we isolated two representative strains, Tm2(T) and HMD, from the oil sands and oil production water in the Shengli oil field in the People's Republic of China. The type strain, Tm2(T), was nonmotile and stained Gram positive. The cells were straight to slightly curved rods (0.3 μm in width and 2.2 to 5.9 μm in length), but some of them possessed a coccal shape connecting with the rods at the ends. Strain Tm2(T) grew with H(2)-CO(2), but acetate is required. Optimum growth of strain Tm2(T) occurred in the presence of 0.025 g/liter NaCl at pH 6.9 and a temperature of 65°C. The G+C content of the genomic DNA was 40.1 mol% ± 1.3 mol% (by the thermal denaturation method) or 41.1 mol% (by high-performance liquid chromatography). Analysis of the 16S rRNA gene sequence indicated that Tm2(T) was most closely related to Methanothermobacter thermautotrophicus ΔH(T) and Methanothermobacter wolfeii VKM B-1829(T) (both with a sequence similarity of 96.4%). Based on these phenotypic and phylogenic characteristics, a novel species was proposed and named Methanothermobacter crinale sp. nov. The type strain is Tm2(T) (ACCC 00699(T) = JCM 17393(T)).
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96
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More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:973848. [PMID: 21559116 PMCID: PMC3087415 DOI: 10.1155/2011/973848] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 12/07/2010] [Accepted: 02/18/2011] [Indexed: 12/19/2022]
Abstract
The hydrogenotrophic methanogens Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus can easily be mass cultured. They have therefore been used almost exclusively to study the biochemistry of methanogenesis from H2 and CO2, and the genomes of these two model organisms have been sequenced. The close relationship of the two organisms is reflected in their genomic architecture and coding potential. Within the 1,607 protein coding sequences (CDS) in common, we identified approximately 200 CDS required for the synthesis of the enzymes, coenzymes, and prosthetic groups involved in CO2 reduction to methane and in coupling this process with the phosphorylation of ADP. Approximately 20 additional genes, such as those for the biosynthesis of F430 and methanofuran and for the posttranslational modifications of the two methyl-coenzyme M reductases, remain to be identified.
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97
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Wagner AO, Malin C, Lins P, Illmer P. Effects of various fatty acid amendments on a microbial digester community in batch culture. WASTE MANAGEMENT (NEW YORK, N.Y.) 2011; 31:431-7. [PMID: 21071199 DOI: 10.1016/j.wasman.2010.10.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Revised: 10/22/2010] [Accepted: 10/22/2010] [Indexed: 05/24/2023]
Abstract
Since biogas production is becoming increasingly important the understanding of anaerobic digestion processes is fundamental. However, large-scale digesters often lack online sensor equipment to monitor key parameters. Furthermore the possibility to selectively change fermenting parameter settings in order to investigate methane output or microbial changes is limited. In the present study we examined the possibility to investigate the microbial community of a large scale (750,000 L) digester within a laboratory small-scale approach. We studied the short-term response of the downscaled communities on various fatty acids and its effects on gas production and compared it with data from the original digester sludge. Even high loads of formic acid led to distinct methane formation, whereas high concentrations of other acids (acetic, butyric, propionic acid) caused a marked inhibition of methanogenesis coupled with an increase in hydrogen concentration. Molecular microbial techniques (DGGE/quantitative real-time-PCR) were used to monitor the microbial community changes which were related to data from GC and HPLC analysis. DGGE band patterns showed that the same microorganisms which were already dominant in the original digester re-established again in the lab-scale experiment. Very few microorganisms dominated the whole fermenting process and species diversity was not easily influenced by moderate varying fatty acid amendments--Methanoculleus thermophilus being the most abundant species throughout the variants. MCR-copy number determined via quantitative real-time-PCR--turned out to be a reliable parameter for quantification of methanogens, even in a very complex matrix like fermenter sludge. Generally the downscaled batch approach was shown to be appropriate to investigate microbial communities from large-scale digesters.
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Affiliation(s)
- Andreas O Wagner
- University of Innsbruck, Institute of Microbiology, Technikerstr. 25, A-6020 Innsbruck, Austria.
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98
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Bioelectrochemical system accelerates microbial growth and degradation of filter paper. Appl Microbiol Biotechnol 2010; 89:449-55. [PMID: 21104243 DOI: 10.1007/s00253-010-2972-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2010] [Revised: 10/18/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]
Abstract
Bioelectrochemical reactors (BERs) with a cathodic working potential of -0.6 or -0.8 V more efficiently degraded cellulosic material, i.e., filter paper (57.4-74.1% in 3 days and 95.9-96.3% in 7 days) than did control reactors without giving exogenous potential (15.4% in 3 days and 64.2% in 7 days). At the same time, resultant conversions to methane and carbon dioxide in cathodic working chamber of BERs by application of electrochemical reduction in 3 days of operation were larger than control reactors. However, cumulative methane production in cathodic BERs was similar to those in control reactors after 7 days of operation. Microscopic observation and 16S rRNA gene analysis showed that microbial growth in the entire consortium was higher after 2 days of operation of cathodic BERs as compared with the control reactors. In addition, the number of methanogenic 16S rRNA gene copies in cathodic BERs was higher than in control reactors. Moreover, archaeal community structures constructed in cathodic BERs consisted of hydrogenotrophic methanogen-related organisms and differed from those in control reactors after 2 days of operation. Specifically, the amount of Methanothermobacter species in cathodic BERs was higher within archaeal communities than in those control reactors after 2 days of operation. Electrochemical reduction may be effective for accelerating microbial growth in the start-up period and thereby increasing microbial treatment of cellulosic waste and methane production.
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99
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Complete genome sequence of Methanothermobacter marburgensis, a methanoarchaeon model organism. J Bacteriol 2010; 192:5850-1. [PMID: 20802048 DOI: 10.1128/jb.00844-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The circular genome sequence of the chemolithoautotrophic euryarchaeon Methanothermobacter marburgensis, with 1,639,135 bp, was determined and compared with that of Methanothermobacter thermautotrophicus. The genomes of the two model methanogens differ substantially in protein coding sequences, in insertion sequence (IS)-like elements, and in clustered regularly interspaced short palindromic repeats (CRISPR) loci.
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100
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Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. Proc Natl Acad Sci U S A 2010; 107:11050-5. [PMID: 20534465 DOI: 10.1073/pnas.1003653107] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). Reduction of this heterodisulfide by heterodisulfide reductase to regenerate HS-CoM and HS-CoB is an exergonic process. Thauer et al. [Thauer, et al. 2008 Nat Rev Microbiol 6:579-591] recently suggested that in hydrogenotrophic methanogens the energy of heterodisulfide reduction powers the most endergonic reaction in the pathway, catalyzed by the formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F(420)-nonreducing hydrogenase, and formate dehydrogenase. In addition to establishing a physical basis for the electron-bifurcation model of energy conservation, the composition of the complex also suggests that either H(2) or formate (two alternative electron donors for methanogenesis) can donate electrons to the heterodisulfide-H(2) via F(420)-nonreducing hydrogenase or formate via formate dehydrogenase. Electron flow from formate to the heterodisulfide rather than the use of H(2) as an intermediate represents a previously unknown path of electron flow in methanogenesis. We further tested whether this path occurs by constructing a mutant lacking F(420)-nonreducing hydrogenase. The mutant displayed growth equal to wild-type with formate but markedly slower growth with hydrogen. The results support the model of electron bifurcation and suggest that formate, like H(2), is closely integrated into the methanogenic pathway.
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