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Lynes MM, Krukenberg V, Jay ZJ, Kohtz AJ, Gobrogge CA, Spietz RL, Hatzenpichler R. Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments. ISME COMMUNICATIONS 2023; 3:22. [PMID: 36949220 PMCID: PMC10033731 DOI: 10.1038/s43705-023-00225-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/17/2023] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Abstract
Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.
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Affiliation(s)
- Mackenzie M Lynes
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Viola Krukenberg
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | | | - Rachel L Spietz
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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Wang N, Zhu X, Zuo Y, Liu J, Yuan F, Guo Z, Zhang L, Sun Y, Gong C, Song C, Xu X. Metagenomic evidence of suppressed methanogenic pathways along soil profile after wetland conversion to cropland. Front Microbiol 2022; 13:930694. [PMID: 36204618 PMCID: PMC9530824 DOI: 10.3389/fmicb.2022.930694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Wetland conversion to cropland substantially suppresses methane (CH4) emissions due to the strong suppression of methanogenesis, which consists of various pathways. In this study, we evaluated the cultivation impacts on four predominant CH4 production pathways, including acetate, carbon dioxide (CO2), methylamines, and methanol, in a wetland and cultivated cropland in northeastern China. The results showed significant suppression of CH4 production potential and the abundance of genes for all four methanogenic pathways in cropland. The consistency between CH4 production and methanogenesis genes indicates the robustness of genomic genes in analyzing methanogenesis. The suppression effects varied across seasons and along soil profiles, most evident in spring and 0 to 30 cm layers. The acetate pathway accounted for 55% in wetland vs. 70% in the cropland of all functional genes for CH4 production; while the other three pathways were stronger in response to cultivation, which presented as stronger suppressions in both abundance of functional genes (declines are 52% of CO2 pathway, 68% of methanol pathway, and 62% of methylamines pathway, vs. 19% of acetate pathway) and their percentages in four pathways (from 20 to 15% for CO2, 15 to 9% for methylamines, and 10 to 6% for methanol pathway vs. 55 to 70% for acetate pathway). The structural equation models showed that substrate availability was most correlated with CH4 production potential in the wetland, while the positive correlations of acetate, CO2, and methylamine pathways with CH4 production potential were significant in the cropland. The quantitative responses of four CH4 production pathways to land conversion reported in this study provide benchmark information for validating the CH4 model in simulating CH4 cycling under land use and land cover change.
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Affiliation(s)
- Nannan Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- *Correspondence: Nannan Wang
| | - Xinhao Zhu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yunjiang Zuo
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianzhao Liu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fenghui Yuan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, United States
| | - Ziyu Guo
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lihua Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Ying Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Chao Gong
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Changchun Song
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Xiaofeng Xu
- Biology Department, San Diego State University, San Diego, CA, United States
- Xiaofeng Xu
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Hellal J, Saaidi PL, Bristeau S, Crampon M, Muselet D, Della-Negra O, Mauffret A, Mouvet C, Joulian C. Microbial Transformation of Chlordecone and Two Transformation Products Formed During in situ Chemical Reduction. Front Microbiol 2021; 12:742039. [PMID: 34803959 PMCID: PMC8600967 DOI: 10.3389/fmicb.2021.742039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/30/2021] [Indexed: 01/12/2023] Open
Abstract
Chlordecone (CLD) is a very persistent synthetic organochlorine pesticide found in the French West Indies. Recently published work has demonstrated the potential of zero-valent iron to dechlorinate CLD by in situ chemical reduction (ISCR) in soils under water-saturated conditions, forming mono- to penta-dechlorinated CLD transformation products. These transformation products are more mobile than CLD and less toxic; however, nothing is known about their further degradation, although increasing evidence of CLD biodegradation by bacteria is being found. The present study began with the enrichment from wastewater sludge of a CLD-transforming community which was then inoculated into fresh media in the presence of either CLD or two of the main ISCR transformation products, 10-monohydroCLD (-1Cl-CLD) and tri-hydroCLD (-3Cl-CLD). Carried out in triplicate batches and incubated at 38°C under anoxic conditions and in the dark, the cultures were sampled regularly during 3 months and analyzed for CLD, -1Cl-CLD, -3Cl-CLD, and possible transformation products by gas chromatography coupled to mass spectrometry. All batches showed a decrease in the amended substrates (CLD or hydroCLD). CLD degradation occurred with concomitant formation of a nine-carbon compound (pentachloroindene) and two sulfur-containing transformation products (chlordecthiol, CLD-SH; methyl chlordecsulfide, CLD-SCH3), demonstrating competing transformation pathways. In contrast, -1Cl-CLD and -3Cl-CLD only underwent a sequential reductive sulfidation/S-methylation process resulting in -1Cl-CLD-SH and -1Cl-CLD-SCH3 on the one hand, and -3Cl-CLD-SH, -3Cl-CLD-SCH3 on the other hand. Some sulfur-containing transformation products have been reported previously with single bacterial strains, but never in the presence of a complex microbial community. At the end of the experiment, bacterial and archaeal populations were investigated by 16S rRNA gene amplicon sequencing. The observed diversity was mostly similar in the CLD and -1Cl-CLD conditions to the inoculum with a dominant archaea genus, Methanobacterium, and four OTU affiliated to bacteria, identified at the family (Spirochaetaceae) or genus level (Desulfovibrio, Aminobacterium, and Soehngenia). On the other hand, in the -3Cl-CLD condition, although the same OTU were found, Clostridium sensu stricto 7, Candidatus Cloacimonas, and Proteiniphilum were also present at > 2% sequences. Presence of methanogens and sulfate-reducing bacteria could contribute to sulfidation and S-methylation biotransformations. Overall, these results contribute to increasing our knowledge on the biodegradability of CLD and its transformation products, helping to progress toward effective remediation solutions.
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Affiliation(s)
| | - Pierre-Loïc Saaidi
- UMR 8030 Génomique Métabolique, CEA, Institut de Biologie François Jacob, Genoscope, Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France
| | | | | | - Delphine Muselet
- UMR 8030 Génomique Métabolique, CEA, Institut de Biologie François Jacob, Genoscope, Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France
| | - Oriane Della-Negra
- UMR 8030 Génomique Métabolique, CEA, Institut de Biologie François Jacob, Genoscope, Université d'Evry Val d'Essonne, Université Paris-Saclay, Evry, France
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Gelsinger DR, Dallon E, Reddy R, Mohammad F, Buskirk A, DiRuggiero J. Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution. Nucleic Acids Res 2020; 48:5201-5216. [PMID: 32382758 PMCID: PMC7261190 DOI: 10.1093/nar/gkaa304] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/09/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022] Open
Abstract
High-throughput methods, such as ribosome profiling, have revealed the complexity of translation regulation in Bacteria and Eukarya with large-scale effects on cellular functions. In contrast, the translational landscape in Archaea remains mostly unexplored. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii, elucidating, for the first time, the translational landscape of a representative of the third domain of life. We determined the ribosome footprint of H. volcanii to be comparable in size to that of the Eukarya. We linked footprint lengths to initiating and elongating states of the ribosome on leadered transcripts, operons, and on leaderless transcripts, the latter representing 70% of H. volcanii transcriptome. We manipulated ribosome activity with translation inhibitors to reveal ribosome pausing at specific codons. Lastly, we found that the drug harringtonine arrested ribosomes at initiation sites in this archaeon. This drug treatment allowed us to confirm known translation initiation sites and also reveal putative novel initiation sites in intergenic regions and within genes. Ribosome profiling revealed an uncharacterized complexity of translation in this archaeon with bacteria-like, eukarya-like, and potentially novel translation mechanisms. These mechanisms are likely to be functionally essential and to contribute to an expanded proteome with regulatory roles in gene expression.
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Affiliation(s)
| | - Emma Dallon
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
| | - Rahul Reddy
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
| | - Fuad Mohammad
- Department of Molecular Biology and Genetics, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, the Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jocelyne DiRuggiero
- Department of Biology, the Johns Hopkins University, Baltimore, MD, USA
- Department of Earth and Planetary Sciences, the Johns Hopkins University, Baltimore, MD, USA
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5
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Guan Y, Ngugi DK, Vinu M, Blom J, Alam I, Guillot S, Ferry JG, Stingl U. Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea. Front Microbiol 2019; 10:839. [PMID: 31068917 PMCID: PMC6491703 DOI: 10.3389/fmicb.2019.00839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/02/2019] [Indexed: 01/25/2023] Open
Abstract
Halophilic methanogens play an important role in the carbon cycle in hypersaline environments, but are under-represented in culture collections. In this study, we describe a novel Methanohalophilus strain that was isolated from the sulfide-rich brine-seawater interface of Kebrit Deep in the Red Sea. Based on physiological and phylogenomic features, strain RSK, which is the first methanogenic archaeon to be isolated from a deep hypersaline anoxic brine lake of the Red Sea, represents a novel species of this genus. In order to compare the genetic traits underpinning the adaptations of this genus in diverse hypersaline environments, we sequenced the genome of strain RSK and compared it with genomes of previously isolated and well characterized species in this genus (Methanohalophilus mahii, Methanohalophilus halophilus, Methanohalophilus portucalensis, and Methanohalophilus euhalobius). These analyses revealed a highly conserved genomic core of greater than 93% of annotated genes (1490 genes) containing pathways for methylotrophic methanogenesis, osmoprotection through salt-out strategy, and oxidative stress response, among others. Despite the high degree of genomic conservation, species-specific differences in sulfur and glycogen metabolisms, viral resistance, amino acid, and peptide uptake machineries were also evident. Thus, while Methanohalophilus species are found in diverse extreme environments, each genotype also possesses adaptive traits that are likely relevant in their respective hypersaline habitats.
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Affiliation(s)
- Yue Guan
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David K. Ngugi
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Manikandan Vinu
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jochen Blom
- Bioinformatik und Systembiologie, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sylvain Guillot
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - James G. Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Microbiology and Cell Science, UF/IFAS Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
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6
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da Silva-Marques RP, Zervoudakis JT, Nakazato L, Hatamoto-Zervoudakis LK, da Silva Cabral L, do Nascimento Matos NB, da Silva MIL, Feliciano AL. Ruminal Microbial Populations and Fermentation Characteristics in Beef Cattle Grazing Tropical Forage in Dry Season and Supplemented with Different Protein Levels. Curr Microbiol 2019; 76:270-278. [PMID: 30721320 DOI: 10.1007/s00284-019-01631-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 01/17/2019] [Indexed: 11/30/2022]
Abstract
We tested the hypothesis that supplementation with protein improves fermentation parameters without damaging the rumen microbial populations of beef cattle grazing Urochloa brizantha cv. Marandu during the dry season. Four rumen-cannulated Nellore bulls (571 ± 31 kg of body weight) were used in a 4 × 4 Latin square design. The treatments were not supplemented with concentrate (only free-choice mineral salt ad libitum) and supplemented (supplements with low-LPSU, medium-MPS, and high protein supplement-HPS), supplying 155, 515, and 875 g/animal/day of crude protein (CP), respectively. The abundance of each target taxon was calculated as a fraction of the total 16S rRNA gene copies in the samples, using taxon-specific and domain bacteria primers. There was no difference (P > 0.05) across treatments for intakes of dry matter (DM), forage and neutral detergent fiber (NDF), digestibility of DM and NDF, and ruminal pH. Animals supplemented with concentrate had greater (P < 0.05) intakes and digestibility of CP, ether extract and non-fibrous carbohydrate contents of the substrates (EE + NFC), and ruminal ammonia nitrogen (RAN) compared to control. Bulls that received only mineral salt had lower proportions of Butyrivibrio fibrisolvens and had greater (P < 0.05) proportions of Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, Methanogen archaea than bulls supplemented with concentrate. The MPS animals had greater (P < 0.05) intake and digestibility of CP, RAN concentration, and had lower (P < 0.05) proportions of Fibrobacter succinogenes, Ruminococcus flavefaciens, and Selenomonas ruminantium than LPSU animals. The HPS provided higher (P < 0.05) intake of CP, RAN and proportion of Ruminococcus albus when compared with MPS. In conclusion, supply of 515 g/animal/day of protein via supplement provides better ruminal conditions for the growth of cellulolytic bacteria of bulls on pasture during dry season.
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Affiliation(s)
| | | | - Luciano Nakazato
- Graduate Program in Veterinary Science, Universidade Federal de Mato Grosso - UFMT, Cuiabá, MT, 78060-900, Brazil
| | | | - Luciano da Silva Cabral
- Graduate Program in Animal Science, Universidade Federal de Mato Grosso - UFMT, Cuiabá, MT, 78060-900, Brazil
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Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN, Galinski EA, Ciordia S, Mena MC, Merkel AY, Wolf YI, van Loosdrecht MCM, Koonin EV. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat Microbiol 2017; 2:17081. [PMID: 28555626 PMCID: PMC5494993 DOI: 10.1038/nmicrobiol.2017.81] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/18/2017] [Indexed: 01/24/2023]
Abstract
Methanogenic archaea are major players in the global carbon cycle and in the biotechnology of anaerobic digestion. The phylum Euryarchaeota includes diverse groups of methanogens that are interspersed with non-methanogenic lineages. So far, methanogens inhabiting hypersaline environments have been identified only within the order Methanosarcinales. We report the discovery of a deep phylogenetic lineage of extremophilic methanogens in hypersaline lakes and present analysis of two nearly complete genomes from this group. Within the phylum Euryarchaeota, these isolates form a separate, class-level lineage 'Methanonatronarchaeia' that is most closely related to the class Halobacteria. Similar to the Halobacteria, 'Methanonatronarchaeia' are extremely halophilic and do not accumulate organic osmoprotectants. The high intracellular concentration of potassium implies that 'Methanonatronarchaeia' employ the 'salt-in' osmoprotection strategy. These methanogens are heterotrophic methyl-reducers that use C1-methylated compounds as electron acceptors and formate or hydrogen as electron donors. The genomes contain an incomplete and apparently inactivated set of genes encoding the upper branch of methyl group oxidation to CO2 as well as membrane-bound heterodisulfide reductase and cytochromes. These features differentiate 'Methanonatronarchaeia' from all known methyl-reducing methanogens. The discovery of extremely halophilic, methyl-reducing methanogens related to haloarchaea provides insights into the origin of methanogenesis and shows that the strategies employed by methanogens to thrive in salt-saturating conditions are not limited to the classical methylotrophic pathway.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Centre for Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd LL57 2UW, UK
| | - Erwin A Galinski
- Institute of Microbiology and Biotechnology, Rheinische Friedrich-Wilhelms University, Bonn, Germany
| | - Sergio Ciordia
- Proteomics Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - María Carmen Mena
- Proteomics Facility, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Centre for Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | | | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Pramanik P, Kim PJ. Contrasting effects of EDTA applications on the fluxes of methane and nitrous oxide emissions from straw-treated rice paddy soils. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:278-283. [PMID: 27010126 DOI: 10.1002/jsfa.7727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 03/15/2016] [Accepted: 03/17/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Submerged rice paddy soils are the major anthropogenic source of methane (CH4 ) emission to the atmosphere. Straw incorporation for sustaining soil organic C pool increases CH4 emission flux from rice paddy soils. Though the rate of nitrous oxide (N2 O) emission is much less than CH4 , the former has 298 times higher global warming potential (GWP) than equivalent quantity of carbon dioxide. The effect of chelating agents, such as EDTA, on N2 O emission and on GWP due to CH4 and N2 O emissions has not been evaluated before. RESULTS The emission of CH4 gas from submerged soil may be mitigated by EDTA application; however, it also increases concentration of nitrate-N in soil, the precursor of N2 O gas formation under anaerobic condition. In this experiment, irrespective of straw application, EDTA-treated soils emitted less CH4 to the atmosphere than the corresponding control. Though N2 O emission was increased from soil due to EDTA applications, total GWP was at least 15% reduced in EDTA treated soils during rice cultivation. The plant growth and rice grain yield was not affected by EDTA application. CONCLUSION EDTA application at 5.0 ppm might be used to reduce total global warming potential during rice cultivation. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Prabhat Pramanik
- Soils Department, Tocklai Experimental Station, Tea Research Association, Jorhat, 785008, Assam, India
| | - Pil Joo Kim
- Division of Applied Life Science (BK 21 Program), Gyeongsang National University, Jinju, 660701, South Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, 660701, South Korea
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9
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Graças DA, Miranda PR, Baraúna RA, McCulloch JA, Ghilardi R, Schneider MPC, Silva A. Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia. MICROBIAL ECOLOGY 2011; 62:853-861. [PMID: 21755290 DOI: 10.1007/s00248-011-9906-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 06/10/2011] [Indexed: 05/31/2023]
Abstract
Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.
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Affiliation(s)
- Diego A Graças
- Universidade Federal do Pará. Instituto de Ciências Biológicas, 66075-900 Belém, Pará, Brazil
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10
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Abstract
Methane produced in the biosphere is derived from two major pathways. Conversion of the methyl group of acetate to CH(4) in the aceticlastic pathway accounts for at least two-thirds, and reduction of CO(2) with electrons derived from H(2), formate, or CO accounts for approximately one-third. Although both pathways have terminal steps in common, they diverge considerably in the initial steps and energy conservation mechanisms. Steps and enzymes unique to the CO(2) reduction pathway are confined to methanogens and the domain Archaea. On the other hand, steps and enzymes unique to the aceticlastic pathway are widely distributed in the domain Bacteria, the understanding of which has contributed to a broader understanding of prokaryotic biology.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16801, USA.
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De Francisci D, Campanaro S, Kornfeld G, Siddiqui KS, Williams TJ, Ertan H, Treu L, Pilak O, Lauro FM, Harrop SJ, Curmi PMG, Cavicchioli R. The RNA polymerase subunits E/F from the Antarctic archaeon Methanococcoides burtonii bind to specific species of mRNA. Environ Microbiol 2010; 13:2039-55. [DOI: 10.1111/j.1462-2920.2010.02385.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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13
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Williams TJ, Burg DW, Ertan H, Raftery MJ, Poljak A, Guilhaus M, Cavicchioli R. Global Proteomic Analysis of the Insoluble, Soluble, and Supernatant Fractions of the Psychrophilic Archaeon Methanococcoides burtonii Part II: The Effect of Different Methylated Growth Substrates. J Proteome Res 2009; 9:653-63. [DOI: 10.1021/pr9005102] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Dominic W. Burg
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Haluk Ertan
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Mark J. Raftery
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Anne Poljak
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Michael Guilhaus
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, 2052, NSW, Australia, Department of Molecular Biology and Genetics, Science Faculty, Istanbul University, Vezneciler, Istanbul, Turkey, Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, 2052, NSW, Australia, and School of Medical Sciences, The University of New South Wales, Sydney, 2052, Australia
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Abstract
The anaerobic conversion of complex organic matter to CH(4) is an essential link in the global carbon cycle. In freshwater anaerobic environments, the organic matter is decomposed to CH(4) and CO(2) by a microbial food chain that terminates with methanogens that produce methane primarily by reduction of the methyl group of acetate and also reduction of CO(2). The process also occurs in marine environments, particularly those receiving large loads of organic matter, such as coastal sediments. The great majority of research on methanogens has focused on marine and freshwater CO(2)-reducing species, and freshwater acetate-utilizing species. Recent molecular, biochemical, bioinformatic, proteomic, and microarray analyses of the marine isolate Methanosarcina acetivorans has revealed that the pathway for acetate conversion to methane differs significantly from that in freshwater methanogens. Similar experimental approaches have also revealed striking contrasts with freshwater species for the pathway of CO-dependent CO(2) reduction to methane by M. acetivorans. The differences in both pathways reflect an adaptation by M. acetivorans to the marine environment.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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16
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Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat Rev Microbiol 2008; 6:579-91. [PMID: 18587410 DOI: 10.1038/nrmicro1931] [Citation(s) in RCA: 1103] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Most methanogenic archaea can reduce CO(2) with H(2) to methane, and it is generally assumed that the reactions and mechanisms of energy conservation that are involved are largely the same in all methanogens. However, this does not take into account the fact that methanogens with cytochromes have considerably higher growth yields and threshold concentrations for H(2) than methanogens without cytochromes. These and other differences can be explained by the proposal outlined in this Review that in methanogens with cytochromes, the first and last steps in methanogenesis from CO(2) are coupled chemiosmotically, whereas in methanogens without cytochromes, these steps are energetically coupled by a cytoplasmic enzyme complex that mediates flavin-based electron bifurcation.
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Affiliation(s)
- Rudolf K Thauer
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germany.
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