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Volumn 1, Issue 5, 2016, Pages

Novel syntrophic populations dominate an ammonia-tolerant methanogenic microbiome

Author keywords

Anaerobic digestion; Biogas; Metagenomics; Metaproteomics; Syntrophic acetate oxidation

Indexed keywords


EID: 85009983667     PISSN: None     EISSN: 23795077     Source Type: Journal    
DOI: 10.1128/mSystems.00092-16     Document Type: Article
Times cited : (28)

References (46)
  • 1
    • 84880702454 scopus 로고    scopus 로고
    • A critical review on inhibition of anaerobic digestion process by excess ammonia
    • Rajagopal R, Massé DI, Singh G. 2013. A critical review on inhibition of anaerobic digestion process by excess ammonia. Bioresour Technol 143:632-641. http://dx.doi.org/10.1016/j.biortech.2013.06.030.
    • (2013) Bioresour Technol , vol.143 , pp. 632-641
    • Rajagopal, R.1    Massé, D.I.2    Singh, G.3
  • 2
    • 40749156248 scopus 로고    scopus 로고
    • Inhibition of anaerobic digestion process: A review
    • Chen Y, Cheng JJ, Creamer KS. 2008. Inhibition of anaerobic digestion process: a review. Bioresour Technol 99:4044-4064. http://dx.doi.org/10.1016/j.biortech.2007.01.057.
    • (2008) Bioresour Technol , vol.99 , pp. 4044-4064
    • Chen, Y.1    Cheng, J.J.2    Creamer, K.S.3
  • 4
    • 84977561073 scopus 로고    scopus 로고
    • Biogas production through syntrophic acetate oxidation and deliberate operating strategies for improved digester performance
    • Westerholm M, Moestedt J, Schnürer A. 2016. Biogas production through syntrophic acetate oxidation and deliberate operating strategies for improved digester performance. Appl Energy 179:124-135. http://dx.doi.org/10.1016/j.apenergy.2016.06.061.
    • (2016) Appl Energy , vol.179 , pp. 124-135
    • Westerholm, M.1    Moestedt, J.2    Schnürer, A.3
  • 5
    • 84890938542 scopus 로고    scopus 로고
    • Syntrophic acetate oxidation in industrial CSTR biogas digesters
    • Sun L, Müller B, Westerholm M, Schnürer A. 2014. Syntrophic acetate oxidation in industrial CSTR biogas digesters. J Biotechnol 171:39-44. http://dx.doi.org/10.1016/j.jbiotec.2013.11.016.
    • (2014) J Biotechnol , vol.171 , pp. 39-44
    • Sun, L.1    Müller, B.2    Westerholm, M.3    Schnürer, A.4
  • 6
    • 58549119451 scopus 로고    scopus 로고
    • Syntrophic acetate-oxidizing microbes in methanogenic environments
    • Hattori S. 2008. Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes Environ 23:118-127. http://dx.doi.org/10.1264/jsme2.23.118.
    • (2008) Microbes Environ , vol.23 , pp. 118-127
    • Hattori, S.1
  • 7
    • 80051927166 scopus 로고    scopus 로고
    • Quantification of syntrophic acetate-oxidizing microbial communities in biogas processes
    • Westerholm M, Dolfing J, Sherry A, Gray ND, Head IM, Schnürer A. 2011. Quantification of syntrophic acetate-oxidizing microbial communities in biogas processes. Environ Microbiol Rep 3:500-505. http://dx.doi.org/10.1111/j.1758-2229.2011.00249.x.
    • (2011) Environ Microbiol Rep , vol.3 , pp. 500-505
    • Westerholm, M.1    Dolfing, J.2    Sherry, A.3    Gray, N.D.4    Head, I.M.5    Schnürer, A.6
  • 8
    • 79959969124 scopus 로고    scopus 로고
    • Detection of active, potentially acetate-oxidizing syntrophs in an anaerobic digester by flux measurement and formyltetrahydrofolate synthetase (FTHFS) expression profiling
    • Hori T, Sasaki D, Haruta S, Shigematsu T, Ueno Y, Ishii M, Igarashi Y. 2011. Detection of active, potentially acetate-oxidizing syntrophs in an anaerobic digester by flux measurement and formyltetrahydrofolate synthetase (FTHFS) expression profiling. Microbiology 157:1980-1989. http://dx.doi.org/10.1099/mic.0.049189-0.
    • (2011) Microbiology , vol.157 , pp. 1980-1989
    • Hori, T.1    Sasaki, D.2    Haruta, S.3    Shigematsu, T.4    Ueno, Y.5    Ishii, M.6    Igarashi, Y.7
  • 9
    • 81855185536 scopus 로고    scopus 로고
    • Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge
    • Ito T, Yoshiguchi K, Ariesyady HD, Okabe S. 2011. Identification of a novel acetate-utilizing bacterium belonging to Synergistes group 4 in anaerobic digester sludge. ISME J 5:1844-1856. http://dx.doi.org/10.1038/ismej.2011.59.
    • (2011) ISME J , vol.5 , pp. 1844-1856
    • Ito, T.1    Yoshiguchi, K.2    Ariesyady, H.D.3    Okabe, S.4
  • 10
    • 84964618064 scopus 로고    scopus 로고
    • Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics
    • 29 April
    • Mosbæk F, Kjeldal H, Mulat DG, Albertsen M, Ward AJ, Feilberg A, Nielsen JL. 29 April 2016. Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics. ISME J http://dx.doi.org/10.1038/ismej.2016.39.
    • (2016) ISME J
    • Mosbæk, F.1    Kjeldal, H.2    Mulat, D.G.3    Albertsen, M.4    Ward, A.J.5    Feilberg, A.6    Nielsen, J.L.7
  • 12
    • 84975794217 scopus 로고    scopus 로고
    • The microbial community structure in industrial biogas plants influences the degradation rate of straw and cellulose in batch tests
    • Sun L, Liu T, Müller B, Schnürer A. 2016. The microbial community structure in industrial biogas plants influences the degradation rate of straw and cellulose in batch tests. Biotechnol Biofuels 9:128. http://dx.doi.org/10.1186/s13068-016-0543-9.
    • (2016) Biotechnol Biofuels , vol.9 , pp. 128
    • Sun, L.1    Liu, T.2    Müller, B.3    Schnürer, A.4
  • 13
    • 84969172659 scopus 로고    scopus 로고
    • Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data
    • Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VG, McHardy AC, Nederbragt AJ, Pope PB. 2016. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Sci Rep 6:25373. http://dx.doi.org/10.1038/srep25373.
    • (2016) Sci Rep , vol.6 , pp. 25373
    • Frank, J.A.1    Pan, Y.2    Tooming-Klunderud, A.3    Eijsink, V.G.4    McHardy, A.C.5    Nederbragt, A.J.6    Pope, P.B.7
  • 15
    • 43049156579 scopus 로고    scopus 로고
    • Dethiobacter alkaliphilus gen. Nov. Sp. Nov., and Desulfurivibrio alkaliphilus gen. Nov. Sp. Nov.: Two novel representatives of reductive sulfur cycle from soda lakes
    • Sorokin DY, Tourova TP, Mußmann M, Muyzer G. 2008. Dethiobacter alkaliphilus gen. Nov. Sp. Nov., and Desulfurivibrio alkaliphilus gen. Nov. Sp. Nov.: two novel representatives of reductive sulfur cycle from soda lakes. Extremophiles 12:431-439. http://dx.doi.org/10.1007/s00792-008-0148-8.
    • (2008) Extremophiles , vol.12 , pp. 431-439
    • Sorokin, D.Y.1    Tourova, T.P.2    Mußmann, M.3    Muyzer, G.4
  • 16
    • 84911440829 scopus 로고    scopus 로고
    • Autotrophy at the thermodynamic limit of life: A model for energy conservation in acetogenic bacteria
    • Schuchmann K, Müller V. 2014. Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. Nat Rev Microbiol 12:809-821. http://dx.doi.org/10.1038/nrmicro3365.
    • (2014) Nat Rev Microbiol , vol.12 , pp. 809-821
    • Schuchmann, K.1    Müller, V.2
  • 18
    • 84872654948 scopus 로고    scopus 로고
    • Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermoacetogenium phaeum
    • Oehler D, Poehlein A, Leimbach A, Müller N, Daniel R, Gottschalk G, Schink B. 2012. Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermoacetogenium phaeum. BMC Genomics 13:723. http://dx.doi.org/10.1186/1471-2164-13-723.
    • (2012) BMC Genomics , vol.13 , pp. 723
    • Oehler, D.1    Poehlein, A.2    Leimbach, A.3    Müller, N.4    Daniel, R.5    Gottschalk, G.6    Schink, B.7
  • 19
    • 84924328742 scopus 로고    scopus 로고
    • A genomeguided analysis of energy conservation in the thermophilic, cytochromefree acetogenic bacterium Thermoanaerobacter kivui
    • Hess V, Poehlein A, Weghoff MC, Daniel R, Müller V. 2014. A genomeguided analysis of energy conservation in the thermophilic, cytochromefree acetogenic bacterium Thermoanaerobacter kivui. BMC Genomics 15:1139. http://dx.doi.org/10.1186/1471-2164-15-1139.
    • (2014) BMC Genomics , vol.15 , pp. 1139
    • Hess, V.1    Poehlein, A.2    Weghoff, M.C.3    Daniel, R.4    Müller, V.5
  • 20
    • 0037955289 scopus 로고    scopus 로고
    • ATP synthases: Structure, function and evolution of unique energy converters
    • Müller V, Grüber G. 2003. ATP synthases: structure, function and evolution of unique energy converters. Cell Mol Life Sci 60:474-494. http://dx.doi.org/10.1007/s000180300040.
    • (2003) Cell Mol Life Sci , vol.60 , pp. 474-494
    • Müller, V.1    Grüber, G.2
  • 21
    • 77951112274 scopus 로고    scopus 로고
    • Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme
    • Say RF, Fuchs G. 2010. Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature 464:1077-1081. http://dx.doi.org/10.1038/nature08884.
    • (2010) Nature , vol.464 , pp. 1077-1081
    • Say, R.F.1    Fuchs, G.2
  • 22
    • 10744223111 scopus 로고    scopus 로고
    • Energy conservation in acetogenic bacteria
    • Müller V. 2003. Energy conservation in acetogenic bacteria. Appl Environ Microbiol 69:6345-6353. http://dx.doi.org/10.1128/AEM.69.11.6345-6353.2003.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 6345-6353
    • Müller, V.1
  • 23
    • 84926175534 scopus 로고    scopus 로고
    • Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation
    • Müller B, Manzoor S, Niazi A, Bongcam-Rudloff E, Schnürer A. 2015. Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation. PLoS One 10:e0121237. http://dx.doi.org/10.1371/journal.pone.0121237.
    • (2015) PLoS One , vol.10 , pp. e0121237
    • Müller, B.1    Manzoor, S.2    Niazi, A.3    Bongcam-Rudloff, E.4    Schnürer, A.5
  • 25
    • 84959344956 scopus 로고    scopus 로고
    • Trace element and temperature effects on microbial communities and links to biogas digester performance at high ammonia levels
    • Westerholm M, Müller B, Isaksson S, Schnürer A. 2015. Trace element and temperature effects on microbial communities and links to biogas digester performance at high ammonia levels. Biotechnol Biofuels 8:154. http://dx.doi.org/10.1186/s13068-015-0328-6.
    • (2015) Biotechnol Biofuels , vol.8 , pp. 154
    • Westerholm, M.1    Müller, B.2    Isaksson, S.3    Schnürer, A.4
  • 26
    • 84979539115 scopus 로고    scopus 로고
    • Bacterial community composition and fhs profiles of low-and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria
    • Müller B, Sun L, Westerholm M, Schnürer A. 2016. Bacterial community composition and fhs profiles of low-and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria. Biotechnol Biofuels 9:48. http://dx.doi.org/10.1186/s13068-016-0454-9.
    • (2016) Biotechnol Biofuels , vol.9 , pp. 48
    • Müller, B.1    Sun, L.2    Westerholm, M.3    Schnürer, A.4
  • 27
    • 84957001273 scopus 로고    scopus 로고
    • Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy
    • Campanaro S, Treu L, Kougias PG, De Francisci D, Valle G, Angelidaki I. 2016. Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. Biotechnol Biofuels 9:26. http://dx.doi.org/10.1186/s13068-016-0441-1.
    • (2016) Biotechnol Biofuels , vol.9 , pp. 26
    • Campanaro, S.1    Treu, L.2    Kougias, P.G.3    De Francisci, D.4    Valle, G.5    Angelidaki, I.6
  • 28
    • 84969188196 scopus 로고    scopus 로고
    • Ph.D. dissertation. Swedish University of Agricultural Sciences, Uppsala, Sweded.
    • Sun L. 2015. Biogas production from lignocellulosic materials. Ph.D. dissertation. Swedish University of Agricultural Sciences, Uppsala, Sweded. http://pub.epsilon.slu.se/12494/7/Sun-L-150810.pdf.
    • (2015) Biogas Production from Lignocellulosic Materials
    • Sun, L.1
  • 29
    • 0031986087 scopus 로고    scopus 로고
    • Anaerobic digestion of swine manure: Inhibition by ammonia
    • Hansen KH, Angelidaki I, Ahring BK. 1998. Anaerobic digestion of swine manure: inhibition by ammonia. Water Res 32:5-12. http://dx.doi.org/10.1016/S0043-1354(97)00201-7.
    • (1998) Water Res , vol.32 , pp. 5-12
    • Hansen, K.H.1    Angelidaki, I.2    Ahring, B.K.3
  • 30
    • 84929508812 scopus 로고    scopus 로고
    • Development of a prokaryotic universal primer for simultaneous analysis of bacteria and archaea using next-generation sequencing
    • Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M. 2014. Development of a prokaryotic universal primer for simultaneous analysis of bacteria and archaea using next-generation sequencing. PLoS One 9:e105592. http://dx.doi.org/10.1371/journal.pone.0105592.
    • (2014) PLoS One , vol.9 , pp. e105592
    • Takahashi, S.1    Tomita, J.2    Nishioka, K.3    Hisada, T.4    Nishijima, M.5
  • 31
    • 84963969179 scopus 로고    scopus 로고
    • PhyloPythiaS: A self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes
    • Gregor I, Dröge J, Schirmer M, Quince C, McHardy AC. 2016. PhyloPythiaS: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes. PeerJ 4:e1603. http://dx.doi.org/10.7717/peerj.1603.
    • (2016) PeerJ , vol.4 , pp. e1603
    • Gregor, I.1    Dröge, J.2    Schirmer, M.3    Quince, C.4    McHardy, A.C.5
  • 33
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460-2461. http://dx.doi.org/10.1093/bioinformatics/btq461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 34
    • 79961181125 scopus 로고    scopus 로고
    • UCHIME improves sensitivity and speed of chimera detection
    • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200. http://dx.doi.org/10.1093/bioinformatics/btr381.
    • (2011) Bioinformatics , vol.27 , pp. 2194-2200
    • Edgar, R.C.1    Haas, B.J.2    Clemente, J.C.3    Quince, C.4    Knight, R.5
  • 37
    • 77955902981 scopus 로고    scopus 로고
    • Ab initio gene identification in metagenomic sequences
    • Zhu W, Lomsadze A, Borodovsky M. 2010. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 38:e132. http://dx.doi.org/10.1093/nar/gkq275.
    • (2010) Nucleic Acids Res , vol.38 , pp. e132
    • Zhu, W.1    Lomsadze, A.2    Borodovsky, M.3
  • 39
    • 84976907502 scopus 로고    scopus 로고
    • KEGG as a reference resource for gene and protein annotation
    • Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:-D457-D462. http://dx.doi.org/10.1093/nar/gkv1070.
    • (2016) Nucleic Acids Res , vol.44 , pp. D457-D462
    • Kanehisa, M.1    Sato, Y.2    Kawashima, M.3    Furumichi, M.4    Tanabe, M.5
  • 42
    • 84928568439 scopus 로고    scopus 로고
    • Proteomic investigation of the response of Enterococcus faecalis V583 when cultivated in urine
    • Arntzen MØ, Karlskås IL, Skaugen M, Eijsink VG, Mathiesen G. 2015. Proteomic investigation of the response of Enterococcus faecalis V583 when cultivated in urine. PLoS One 10:e0126694. http://dx.doi.org/10.1371/journal.pone.0126694.
    • (2015) PLoS One , vol.10 , pp. e0126694
    • Arntzen, M.Ø.1    Karlskås, I.L.2    Skaugen, M.3    Eijsink, V.G.4    Mathiesen, G.5
  • 43
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wiśniewski JR, Zougman A, Nagaraj N, Mann M. 2009. Universal sample preparation method for proteome analysis. Nat Methods 6:359-362. http://dx.doi.org/10.1038/nmeth.1322.
    • (2009) Nat Methods , vol.6 , pp. 359-362
    • Wiśniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 44
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26:1367-1372. http://dx.doi.org/10.1038/nbt.1511.
    • (2008) Nat Biotechnol , vol.26 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 45
    • 84907197082 scopus 로고    scopus 로고
    • Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ
    • Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. 2014. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics 13:2513-2526. http://dx.doi.org/10.1074/mcp.M113.031591.
    • (2014) Mol Cell Proteomics , vol.13 , pp. 2513-2526
    • Cox, J.1    Hein, M.Y.2    Luber, C.A.3    Paron, I.4    Nagaraj, N.5    Mann, M.6


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