in

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea

  • 1.

    Luff, R. & Wallmann, K. Fluid flow, methane fluxes, carbonate precipitation and biogeochemical turnover in gas hydrate-bearing sediments at Hydrate Ridge, Cascadia Margin: numerical modeling and mass balances. Geochim. et. Cosmochim. Acta67, 3403–3421 (2003).

    CAS  ADS  Google Scholar 

  • 2.

    Brown, K. et al. Correlated transient fluid pulsing and seismic tremor in the Costa Rica subduction zone. Earth Planet. Sci. Lett.238, 189–203 (2005).

    CAS  ADS  Google Scholar 

  • 3.

    Ruff, S. E. et al. Microbial communities of deep-sea methane seeps at Hikurangi continental margin (New Zealand). PLoS ONE8, e72627 (2013).

    CAS  PubMed  PubMed Central  ADS  Google Scholar 

  • 4.

    Felden, J. et al. Anaerobic methanotrophic community of a 5346-m-deep vesicomyid clam colony in the Japan Trench. Geobiology12, 183–199 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 5.

    Pop Ristova, P. et al. Bacterial diversity and biogeochemistry of different chemosynthetic habitats of the REGAB cold seep (West African margin, 3160 m water depth). Biogeosciences9, 5031–5048 (2012).

    ADS  Google Scholar 

  • 6.

    Knittel, K. & Boetius, A. Anaerobic oxidation of methane: progress with an unknown process. Annu. Rev. Microbiol.63, 311–334 (2009).

    CAS  PubMed  Google Scholar 

  • 7.

    Niemann, H. et al. Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature443, 854–858 (2006).

    CAS  PubMed  ADS  Google Scholar 

  • 8.

    Schreiber, L. et al. Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ. Microbiol.56, 2327–2340 (2010).

    Google Scholar 

  • 9.

    Holler, T. et al. Carbon and sulfur back flux during anaerobic microbial oxidation of methane and coupled sulfate reduction. Proc. Natl Acad. Sci.109, 21170–21170 (2012).

    CAS  Google Scholar 

  • 10.

    Michaelis, W. Microbial reefs in the black sea fueled by anaerobic oxidation of methane. Science297, 1013–1015 (2002).

    CAS  PubMed  ADS  Google Scholar 

  • 11.

    Treude, T. et al. Consumption of methane and CO2 by methanotrophic microbial mats from gas seeps of the anoxic black sea. Appl. Environ. Microbiol.73, 3770–3770 (2007).

    CAS  PubMed Central  Google Scholar 

  • 12.

    Jørgensen, B. B. & Boetius, A. Feast and famine—microbial life in the deep-sea bed. Nat. Rev. Microbiol.5, 770–781 (2007).

    PubMed  Google Scholar 

  • 13.

    Reeburgh, W. S. Oceanic methane biogeochemistry. Chem. Rev.107, 486–513 (2007).

    CAS  PubMed  Google Scholar 

  • 14.

    Lee, J.-W. et al. Microbial community structures of methane hydrate-bearing sediments in the Ulleung Basin, East Sea of Korea. Mar. Pet. Geol.47, 136–146 (2013).

    CAS  Google Scholar 

  • 15.

    Lee, Y. M. et al. Genomic insight into the predominance of candidate phylum atribacteria JS1 lineage in marine sediments. Front. Microbiol.9, 198 (2018).

    Google Scholar 

  • 16.

    Cui, H. et al. Microbial diversity of two cold seep systems in gas hydrate-bearing sediments in the South China Sea. Mar. Environ. Res.144, 230–239 (2019).

    CAS  PubMed  Google Scholar 

  • 17.

    Wang, F.-P. et al. Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways. ISME J.8, 1069–1078 (2013).

    PubMed  PubMed Central  Google Scholar 

  • 18.

    Soo, V. W. C. et al. Reversing methanogenesis to capture methane for liquid biofuel precursors. Microb. Cell Factor.15, 621 (2016).

    Google Scholar 

  • 19.

    Zhang, Y., Henriet, J.-P., Bursens, J. & Boon, N. Stimulation of in vitro anaerobic oxidation of methane rate in a continuous high-pressure bioreactor. Bioresour. Technol.101, 3132–3138 (2010).

    CAS  PubMed  Google Scholar 

  • 20.

    Ingram-Smith, C., Woods, B. I. & Smith, K. S. Characterization of the acyl substrate binding pocket of acetyl-CoA synthetase. Biochemistry45, 11482–11490 (2006).

    CAS  PubMed  Google Scholar 

  • 21.

    Schmidt, M. & Schönheit, P. Acetate formation in the photoheterotrophic bacterium Chloroflexus aurantiacus involves an archaeal type ADP-forming acetyl-CoA synthetase isoenzyme I. FEMS Microbiol. Lett.349, 171–179 (2013).

    CAS  PubMed  Google Scholar 

  • 22.

    Parizzi, L. P. et al. The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential. BMC Genomics13, 562 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 23.

    Musfeldt, M. & Schonheit, P. Novel type of ADP-forming acetyl coenzyme A synthetase in hyperthermophilic archaea: heterologous expression and characterization of isoenzymes from the sulfate reducer Archaeoglobus fulgidus and the methanogen Methanococcus jannaschii. J. Bacteriol.184, 636–644 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 24.

    Mai, X. & Adams, M. W. Purification and characterization of two reversible and ADP-dependent acetyl coenzyme A synthetases from the hyperthermophilic archaeon Pyrococcus furiosus. J. Bacteriol.178, 5897–5903 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 25.

    Glasemacher, J., Bock, A. K., Schmid, R. & Schonheit, P. Purification and properties of acetyl-CoA synthetase (ADP-forming), an archaeal enzyme of acetate formation and ATP synthesis, from the hyperthermophile Pyrococcus furiosus. Eur. J. Biochem.244, 561–567 (1997).

    CAS  PubMed  Google Scholar 

  • 26.

    Musfeldt, M., Selig, M. & Schonheit, P. Acetyl coenzyme A synthetase (ADP forming) from the hyperthermophilic Archaeon pyrococcus furiosus: identification, cloning, separate expression of the encoding genes, acdAI and acdBI, in Escherichia coli, and in vitro reconstitution of the active heterotetrameric enzyme from its recombinant subunits. J. Bacteriol.181, 5885–5888 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 27.

    Jones, W. J. et al. Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch. Microbiol.136, 254–261 (1983).

    CAS  Google Scholar 

  • 28.

    Bräsen, C. & Schönheit, P. AMP-forming acetyl-CoA synthetase from the extremely halophilic archaeon Haloarcula marismortui: purification, identification and expression of the encoding gene, and phylogenetic affiliation. Extremophiles9, 355–365 (2005).

    PubMed  Google Scholar 

  • 29.

    Bräsen, C., Urbanke, C. & Schönheit, P. A novel octameric AMP-forming acetyl-CoA synthetase from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. FEBS Lett.579, 477–482 (2004).

    Google Scholar 

  • 30.

    Rabus, R. & Heider, J. Initial reactions of anaerobic metabolism of alkylbenzenes in denitrifying and sulfate-reducing bacteria. Arch. Microbiol.170, 377–384 (1998).

    CAS  Google Scholar 

  • 31.

    Ruff, S. E. et al. Global dispersion and local diversification of the methane seep microbiome. Proc. Natl Acad. Sci.112, 4015–4020 (2015).

    CAS  PubMed  ADS  Google Scholar 

  • 32.

    Zhuang, G.-C. et al. Significance of acetate as a microbial carbon and energy source in the water column of Gulf of Mexico: implications for marine carbon cycling. Glob. Biogeochem. Cycles33, 223–235 (2019).

    CAS  ADS  Google Scholar 

  • 33.

    Zhuang, G.-C., Montgomery, A. & Joye, S. B. Heterotrophic metabolism of C1 and C2 low molecular weight compounds in northern Gulf of Mexico sediments: controlling factors and implications for organic carbon degradation. Geochim. et. Cosmochim. Acta247, 243–260 (2019).

    CAS  ADS  Google Scholar 

  • 34.

    Bräsen, C., Schmidt, M., Grötzinger, J. & Schönheit, P. Reaction mechanism and structural model of ADP-forming acetyl-CoA synthetase from the hyperthermophilic archaeon Pyrococcus furiosus. J. Biol. Chem.283, 15409–15418 (2008).

    PubMed  PubMed Central  Google Scholar 

  • 35.

    Haroon, M. F. et al. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature500, 567–570 (2013).

    CAS  PubMed  ADS  Google Scholar 

  • 36.

    Ino, K. et al. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. ISME J.12, 31–47 (2017).

    PubMed  PubMed Central  Google Scholar 

  • 37.

    Wegener, G. et al. Metabolic capabilities of microorganisms involved in and associated with the anaerobic oxidation of methane. Front. Microbiol.7, 869 (2016).

    Google Scholar 

  • 38.

    Cai, C. et al. Acetate production from anaerobic oxidation of methane via intracellular storage compounds. Environ. Sci. Technol.53, 7371–7379 (2019).

    CAS  PubMed  ADS  Google Scholar 

  • 39.

    Valentine, D. L. & Reeburgh, W. S. New perspectives on anaerobic methane oxidation. Environ. Microbiol.2, 477–484 (2000).

    CAS  PubMed  Google Scholar 

  • 40.

    Stams, A. J. M. & Plugge, C. M. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat. Rev. Microbiol.7, 568–577 (2009).

    CAS  PubMed  Google Scholar 

  • 41.

    Deusner, C., Meyer, V. & Ferdelman, T. G. High-pressure systems for gas-phase free continuous incubation of enriched marine microbial communities performing anaerobic oxidation of methane. Biotechnol. Bioeng.105, 524–533 (2010).

    CAS  PubMed  Google Scholar 

  • 42.

    Timmers, P. H. A. et al. Growth of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a high-pressure membrane capsule bioreactor. Appl. Environ. Microbiol.81, 1286–1296 (2015).

    PubMed  PubMed Central  Google Scholar 

  • 43.

    Weber, T., Wiseman, N. A. & Kock, A. Global ocean methane emissions dominated by shallow coastal waters. Nat. Commun.10, 4584–4510 (2019).

    PubMed  PubMed Central  ADS  Google Scholar 

  • 44.

    Zhang, Y. et al. Enrichment of a microbial community performing anaerobic oxidation of methane in a continuous high-pressure bioreactor. BMC Microbiol.11, 137 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 45.

    Zhang, Y., Li, X., Bartlett, D. H. & Xiao, X. Current developments in marine microbiology: high-pressure biotechnology and the genetic engineering of piezophiles. Curr. Opin. Biotechnol.33, 157–164 (2015).

    PubMed  Google Scholar 

  • 46.

    Widdel, F. & Bak, F. Gram-negative mesophilic sulfate-reducing bacteria. Prokaryotes4, 3352–3378 (1992).

    Google Scholar 

  • 47.

    Natarajan, V. P. et al. A modified SDS-based DNA extraction method for high quality environmental DNA from seafloor environments. Front. Microbiol.07, 1281 (2016).

    Google Scholar 

  • 48.

    Klindworth, A. et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res.41, e1–e1 (2012).

    PubMed  PubMed Central  Google Scholar 

  • 49.

    Magoc, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics27, 2957–2963 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 50.

    Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nat. Publ. Group7, 335–336 (2010).

    CAS  Google Scholar 

  • 51.

    Edgar, R. C. et al. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics27, 2194–2200 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 52.

    Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res.41, D590–D596 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 53.

    Jorgensen, S. L. et al. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc. Natl Acad. Sci.109, 2846–2855 (2012).

    Google Scholar 

  • 54.

    Langille, M. G. I. et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol.31, 814–821 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 55.

    Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics28, 1420–1428 (2012).

    CAS  PubMed  Google Scholar 

  • 56.

    Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods12, 59–60 (2014).

    PubMed  Google Scholar 

  • 57.

    Li, H. et al. The sequence Alignment/Map format and SAMtools. Bioinformatics25, 2078–2079 (2009).

    PubMed  PubMed Central  Google Scholar 

  • 58.

    Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ7, e7359 (2019).

    PubMed  PubMed Central  Google Scholar 

  • 59.

    Lin, H.-H. & Liao, Y.-C. Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes. Sci. Rep.6, 463 (2016).

    Google Scholar 

  • 60.

    Parks, D. H. et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res.25, 1043–1055 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 61.

    Karst, S. M., Kirkegaard, R. H. & Albertsen, M. mmgenome: a toolbox for reproducible genome extraction from metagenomes. bioRxiv https://doi.org/10.1101/059121 (2016).

  • 62.

    Hyatt, D., Locascio, P. F., Hauser, L. J. & Uberbacher, E. C. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics28, 2223–2230 (2012).

    CAS  PubMed  Google Scholar 

  • 63.

    Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res.28, 27–30 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 64.

    Galperin, M. Y., Makarova, K. S., Wolf, Y. I. & Koonin, E. V. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res.43, D261–D269 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 65.

    Srere, P. A., Brazil, H. & Gonen, L. The citrate condensing enzyme of Pigeon breast muscle and moth flight muscle. Acta Chem. Scand.17, 129–134 (1963).

    Google Scholar 

  • 66.

    Castaño-Cerezo, S., Bernal, V. & Cánovas, M. Acetyl-coenzyme A synthetase (Acs) assay. Bio-Protocol2, e256 (2012).

    Google Scholar 

  • 67.

    Sánchez, L. B., Galperin, M. Y. & Müller, M. Acetyl-CoA synthetase from the Amitochondriate eukaryote giardia lamblia belongs to the newly recognized superfamily of Acyl-CoA synthetases (Nucleoside Diphosphate-forming). J. Biol. Chem.275, 5794–5803 (2000).

    PubMed  Google Scholar 

  • 68.

    Katoh, K., Misawa, K., Kuma, K. I. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res.30, 3059–3066 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 69.

    Capella-Gutierrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics25, 1972–1973 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 70.

    Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol.32, 268–274 (2014).

    PubMed  PubMed Central  Google Scholar 

  • 71.

    Bushnell, B. BBMap: A Fast, Accurate, Splice-Aware Aligner. (Lawrence Berkeley National Lab (LBNL), Berkeley, CA, 2014).

    Google Scholar 

  • 72.

    Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol. Biol. Evol.34, 2115–2122 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 73.

    Li, D. et al. MEGAHIT v1.0: a fast and scalable metagenome assembler driven by advanced methodologies and community practices. Methods102, 3–11 (2016).

    CAS  PubMed  Google Scholar 

  • 74.

    Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics30, 923–930 (2014).

    CAS  PubMed  Google Scholar 

  • 75.

    Wu, Y.-W. et al. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome2, 26–18 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 76.

    Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods11, 1144–1146 (2014).

    CAS  PubMed  Google Scholar 

  • 77.

    Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol.3, 836–843 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  • 78.

    Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics36, 1925–1927 (2019).

    Google Scholar 

  • 79.

    Parks, D. H. et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat. Biotechnol.36, 996–1004 (2018).

    CAS  PubMed  Google Scholar 


  • Source: Ecology - nature.com

    When the chemical industry met modern architecture

    MIT Energy Conference goes virtual