Microbial community composition and methanogens’ biodiversity during a temperature shift in a methane fermentation chamber

References

• Yu D, Kurola JM, Lähde K, et al. Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes. J Environ Manag. 2014;143:54–60. doi: 10.1016/j.jenvman.2014.04.025
   PubMed Web of Science ®Google Scholar
• Lozano CJS, Mendoza MV, de Arango MC, et al. Microbiological characterization and specific methanogenic activity of anaerobe sludges used in urban solid waste treatment. Waste Manag. 2009;29:704–711. doi: 10.1016/j.wasman.2008.06.021
   PubMed Web of Science ®Google Scholar
• Leven L, Anders RBE, Schnurer A. Effect of process temperature on bacterial and archaeal communities in two methanogenic bioreactors treating organic household waste. FEMS Microbiol Ecol. 2007;59:683–693. doi: 10.1111/j.1574-6941.2006.00263.x
   PubMed Web of Science ®Google Scholar
• Thian Z, Zhang Y, Li Y, et al. Rapid establishment of thermophilic anaerobic microbial community during the one-step startup of thermophilic anaerobic digestion from a mesophilic digester. Water Res. 2015;69:9–19. doi: 10.1016/j.watres.2014.11.001
   PubMed Web of Science ®Google Scholar
• Watanabe H, Kitamura T, Ochi S, et al. Inactivation of pathogenic bacteria under mesophilic and thermophilic conditions. Water Sci Technol. 1997;36:25–32. doi: 10.2166/wst.1997.0571
   Web of Science ®Google Scholar
• Amani T, Nosrati M, Sreekrishnan TR. A precise experimental study on key dissimilarities between mesophilic and thermophilic anaerobic digestion of waste activated sludge. Int J Environ Res. 2011;5:333–342.
   Web of Science ®Google Scholar
• Sekiguchi Y, Kamagata Y, Ohashi A, et al. Molecular and conventional analyses of microbial diversity in mesophilic and thermophilic upflow anaerobic sludge blanket granular sludges. Water Sci Technol. 2002;45:19–25. doi: 10.2166/wst.2002.0279
   PubMed Web of Science ®Google Scholar
• Hernon F, Forbes C, Colleran E. Identification of mesophilic and thermophilic fermentative species in anaerobic granular sludge. Water Sci Technol. 2006;54:19–24. doi: 10.2166/wst.2006.481
   PubMed Web of Science ®Google Scholar
• Song BYJ, Woo JH, Kwon SJ, et al. Microbial activity and population structure of anaerobic sludge alternately exposed to mesophilic and thermophilic conditions. Environ Eng. 2006;10:319–323.
   Google Scholar
• Morris R, Schauer-Gimenez A, Bhattad U, et al. Methyl coenzyme M reductase (mcrA) gene abundance correlates with activity measurements of methanogenic H2/CO2-enriched anaerobic biomass. Microb Biotechnol. 2014;7(1):77–84. doi: 10.1111/1751-7915.12094
   PubMed Web of Science ®Google Scholar
• Friedrich MW. Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea. Method Enzymol. 2005;397:428–442. doi: 10.1016/S0076-6879(05)97026-2
   PubMed Web of Science ®Google Scholar
• Luton EP, Wayne JM, Sharp RJ, et al. The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 2002;148:3521–3530. doi: 10.1099/00221287-148-11-3521
   PubMed Web of Science ®Google Scholar
• Barns SM, Delwiche CF, Palmer JD, et al. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc Natl Acad Sci USA. 1996;93:9188–9193. doi: 10.1073/pnas.93.17.9188
   PubMed Web of Science ®Google Scholar
• Garcia JL, Patel BKC, Ollivier B. Taxonomic phylogenetic and ecological diversity of methanogenic Archaea. Anaerobe. 2000;6:205–226. doi: 10.1006/anae.2000.0345
   PubMed Web of Science ®Google Scholar
• Siroshi SK, Chaudhary PP, Singh N, et al. The 16S rRNA and mcrA gene based comparative diversity of methanogens in cattle fed on high fibre based diet. Gene. 2013;523:161–166. doi: 10.1016/j.gene.2013.04.002
   PubMed Web of Science ®Google Scholar
• Sheppard SK, McCarthy AJ, Loughnane JP, et al. The impact of sludge amendment on methanogen community structure in an upland soil. Appl Soil Ecol. 2005;28:147–162. doi: 10.1016/j.apsoil.2004.07.004
   Web of Science ®Google Scholar
• Ziembińska-Buczynska A, Banach A, Bacza T, et al. Diversity and variability of methanogens during the shift from mesophilic to thermophilic conditions while biogas production. World J Microbiol Biotechnol. 2014;30:3047–3053. doi: 10.1007/s11274-014-1731-z
   PubMed Web of Science ®Google Scholar
• Klindworth A, Pruesse E, Schweer T, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucl Acid Res. 2013;41:e1. doi: 10.1093/nar/gks808
   PubMed Web of Science ®Google Scholar
• Ondreičková K, Kraic J. Impact of genetically modified stacked maize NK603 × MON810 on the genetic diversity of rhizobacterial communities. Agriculture (Polnohospodárstvo). 2015;61(4):193–148.
   Google Scholar
• Keylock C J. Simpson diversity and the Shannon–Wiener index as special cases of a generalized entropy. Oikos 2005;109(1):203–207. doi: 10.1111/j.0030-1299.2005.13735.x
   Web of Science ®Google Scholar
• Vanwonterghem I, Jensen PD, Ho DP, et al. Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Curr Opin Biotechnol. 2014;27:55–64. doi: 10.1016/j.copbio.2013.11.004
   PubMed Web of Science ®Google Scholar
• Nakano M, Zuber P. Strict and facultative anaerobes: medical and environmental aspects, horizon bioscience. British Library Cataloguing in Publication Data; 2004. p. 365–374.
   Google Scholar
• Moset V, Poulsen M, Wahid R, et al. Mesophilic versus thermophilic anaerobic digestion of cattle manure: methane productivity and microbial ecology. Microbiol Biotechnol. 2015;8(5):787–800. doi: 10.1111/1751-7915.12271
   Google Scholar
• Kim M, Morrison M, Yu Z. Status of the phylogenetic diversity census of ruminal microbiomes. FEMS Microbiol Ecol. 2011;76:49–63. doi: 10.1111/j.1574-6941.2010.01029.x
   PubMed Web of Science ®Google Scholar
• Klocke M, Mähnert P, Mundt K, et al. Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate. Syst Appl Microbiol. 2007;30:139–151. doi: 10.1016/j.syapm.2006.03.007
   PubMed Web of Science ®Google Scholar
• Kampmann K, Ratering S, Kramer I, et al. Unexpected stability of bacteroidetes and firmicutes communities in laboratory biogas reactors fed with different defined substrates. Appl Environ Microbiol. 2012;78:2106–2119. doi: 10.1128/AEM.06394-11
   PubMed Web of Science ®Google Scholar
• Gagliano M, Braguglia A, Gallipoli, GA, et al. Microbial diversity in innovative mesophilic/thermophilic temperature-phased anaerobic digestion of sludge. Environ Sci Pollut Res. 2015;22:7339–7348. doi: 10.1007/s11356-014-3061-y
   PubMed Web of Science ®Google Scholar
• Wilén BM, Onuki M, Hermansson M. Microbial community structure in activated sludge floc analysed by fluorescence in situ hybridization and its relation to floc stability. Water Res. 2008;42:2300–2308. doi: 10.1016/j.watres.2007.12.013
   PubMed Web of Science ®Google Scholar
• Ariesyady HD, Ito T, Okabe S. Functional bacterial and archaeal community structures of major trophic groups in a full-scale anaerobic sludge digester. Water Res. 2007;41:1554–1568. doi: 10.1016/j.watres.2006.12.036
   PubMed Web of Science ®Google Scholar
• Guo J, Peng Y, Ni BJ, et al. Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing. Microb Cell Fact. 2015;14:1. doi: 10.1186/s12934-014-0183-3
   PubMed Web of Science ®Google Scholar
• Narihiro, T, Sekiguchi Y. Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update. Curr Opin Biotechnol. 2007;18(3):273–278. doi: 10.1016/j.copbio.2007.04.003
   PubMed Web of Science ®Google Scholar
• Sekiguchi Y, Kamagata Y, Syutsubo K, et al. Phylogenetic diversity of mesophilic and thermophilic granular sludges determined by 16S rRNA gene analysis. Microbiology. 1998;144:2655–2665. doi: 10.1099/00221287-144-9-2655
   PubMed Web of Science ®Google Scholar
• De Vrieze JD, Saunders AM, He Y, et al. Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome. Water Res. 2015;75:312–323. doi: 10.1016/j.watres.2015.02.025
   PubMed Web of Science ®Google Scholar
• Shnurer A. Biogas production: microbiology and technology. Adv Biochem Eng Biotechnol. 2016;156:195–234.
   PubMed Web of Science ®Google Scholar
• Walter A, Knapp B, Farbmacher A, et al. Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants. Microbiol Biotechnol. 2012;5:717–730. doi: 10.1111/j.1751-7915.2012.00361.x
   Google Scholar
• Elsden SR, Hilton MG, Waller JM. The end products of the metabolism of aromatic amino acids by Clostridia. Arch Microbiol. 1976;107:283–288. doi: 10.1007/BF00425340
   PubMed Web of Science ®Google Scholar
• Rydzak T, McQueen PD, Krokhin OV, et al. Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression. BMC Microbiol. 2012;12:214. doi: 10.1186/1471-2180-12-214
   PubMed Web of Science ®Google Scholar
• Shiratori H, Sasaya K, Ohiwa H, et al. Clostridium clariflavum sp nov and Clostridium caenicola sp nov., moderately thermophilic, cellulose-/cellobiose-digesting bacteria isolated from methanogenic sludge. Int J Syst Evol Micr. 2009;59:1764–1770. doi: 10.1099/ijs.0.003483-0
   PubMed Web of Science ®Google Scholar
• Niu Q, Hojo T, Qiao W, et al. Characterization of methanogenesis, acidogenesis and hydrolysis in thermophilic methane fermentation of chicken manure. Chem Eng J. 2014;244:587–596. doi: 10.1016/j.cej.2013.11.074
   Web of Science ®Google Scholar
• Traversi D, Villa S, Lorenzi E, et al. Application of a real-time qPCR method to measure the methanogen concentration during anaerobic digestion as an indicator of biogas production capacity. J Environ Manag. 2012;111:173–177. doi: 10.1016/j.jenvman.2012.07.021
   PubMed Web of Science ®Google Scholar
• Lin YW, Tuan NN, Huang SL. Metaproteomic analysis of the microbial community present in a thermophilic swine manure digester to allow functional characterization: a case study. Int Biodeter Biodegrad. 2016;115:64–73. doi: 10.1016/j.ibiod.2016.06.013
   Web of Science ®Google Scholar
• Yamada T, Imachi H, Ohashi A, et al. Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int J Syst Evol Microbiol. 2007;57:2299–2306. doi: 10.1099/ijs.0.65098-0
   PubMed Web of Science ®Google Scholar
• Boone DR, Bryant MP. Propionate-degrading bacterium, Syntrophobacter wolinii sp. nov. gen. nov., from methanogenic ecosystems. Appl Environ Microbiol. 1980;40:626–632.
   PubMed Web of Science ®Google Scholar
• Stams AJM, Plugge CM. Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol. 2009;7:568–577. doi: 10.1038/nrmicro2166
   PubMed Web of Science ®Google Scholar
• Zeikus G. Thermophilic bacteria: ecology, physiology and technology. Enzyme Microb Technol. 1979;1(4):243–252. doi: 10.1016/0141-0229(79)90043-7
   Web of Science ®Google Scholar
• Bouskova A, Dohanyos M, Schmidt JE, et al. Strategies for changing temperature from mesophilic to thermophilic conditions in anaerobic CSTR reactors treating sewage sludge. Water Res. 2005;39(8):1481–1488. doi: 10.1016/j.watres.2004.12.042
   PubMed Web of Science ®Google Scholar
• Zhou J, Zhang R, Liu F, et al. Biogas production and microbial community shift through neutral pH control during the anaerobic digestion of pig manure. Bioresour Technol. 2016;217:44–49. doi: 10.1016/j.biortech.2016.02.077
   PubMed Web of Science ®Google Scholar