Abstract
Anaerobic digestion relies on complex microbial communities that closely interact in the anaerobic degradation of biomass and organic waste material to methane and carbon dioxide. The adoption of high-throughput molecular methods and the holistic “omics” approach in applied microbial ecology has greatly extended our view on the manifold metabolic diversity and trophic networks in the microbiomes thriving in anaerobic bioreactors. In this chapter, current concepts in metagenomics and microbial ecology of anaerobic digestion are described. Recent advances in gene-centric and genome-centric approaches and their application on lab-scale and production-scale biogas reactors have paved the way to a knowledge-based microbial resource management in anaerobic bioreactors. The adoption of systems biology principles in systems ecology of reactor microbiomes will open up new perspectives in process control and optimization of biotechnological processes relying on complex open mixed cultures.
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Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KA, Tyson GW, Nielsen PH (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31:533–538
Bremges A, Maus I, Belmann P, Eikmeyer F, Winkler A, Albersmeier A, Pühler A, Schlüter A, Sczyrba A (2015) Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. Gigascience 4:33
Cai M, Wilkins D, Chen J, Ng SK, Lu H, Jia Y, Lee PK (2016) Metagenomic reconstruction of key anaerobic digestion pathways in municipal sludge and industrial wastewater biogas-producing systems. Front Microbiol 7:778
Calusinska M, Marynowska M, Goux X, Lentzen E, Delfosse P (2016) Analysis of dsDNA and RNA viromes in methanogenic digesters reveals novel viral genetic diversity. Environ Microbiol 18:1162–1175
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
Chen Y, Cheng JJ, Creamer KS (2008) Inhibition of anaerobic digestion process: a review. Bioresour Technol 99:4044–4064
Eikmeyer FG, Rademacher A, Hanreich A, Hennig M, Jaenicke S, Maus I, Wibberg D, Zakrzewski M, Pühler A, Klocke M, Schlüter A (2013) Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms. Biotechnol Biofuels 6:49
Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350:434–438
Frank JA, Arntzen MO, Sun L, Hagen LH, McHardy AC, Horn SJ, Eijsink VG, Schnürer A, Pope PB (2016) Novel syntrophic populations dominate an ammonia-tolerant methanogenic microbiome. mSystems 1:e00092-16
Gottstein W, Olivier BG, Bruggeman FJ, Teusink B (2016) Constraint-based stoichiometric modelling from single organisms to microbial communities. J R Soc Interface 13:20160627
Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A, Streit WR (2016) Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies. Biotechnol Biofuels 9:121
Gunnigle E, Siggins A, Botting CH, Fuszard M, O’Flaherty V, Abram F (2015) Low-temperature anaerobic digestion is associated with differential methanogenic protein expression. FEMS Microbiol Lett 362:fnv059
Hagen LH, Frank JA, Zamanzadeh M, Eijsink VG, Pope PB, Horn SJ, Arntzen MO (2017) Quantitative metaproteomics highlight the metabolic contributions of uncultured phylotypes in a thermophilic anaerobic digester. Appl Environ Microbiol 83:e01955-16
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman R (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5:R245–R249
Hanreich A, Schimpf U, Zakrzewski M, Schlüter A, Benndorf D, Heyer R, Rapp E, Pühler A, Reichl U, Klocke M (2013) Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol 36:330–338
Hattori S (2008) Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes Environ 23:118–127
Heyer R, Kohrs F, Reichl U, Benndorf D (2015) Metaproteomics of complex microbial communities in biogas plants. Microb Biotechnol 8:749–763
Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M, Rapp E, Schlüter A, Sczyrba A, Reichl U (2016) Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnol Biofuels 9:155
Jabbour D, Sorger A, Sahm K, Antranikian G (2013) A highly thermoactive and salt-tolerant alpha-amylase isolated from a pilot-plant biogas reactor. Appl Microbiol Biotechnol 97:2971–2978
Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann KH, Jünemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Pühler A, Schlüter A, Goesmann A (2011) Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One 6:e14519
Ju F, Zhang T (2015) Experimental design and bioinformatics analysis for the application of metagenomics in environmental sciences and biotechnology. Environ Sci Technol 49:12628–12640
Konstantinides KT, Rosselló-Móra R (2015) Classifying the uncultivated microbial majority: a place for metagenomic data in the Candidatus proposal. Syst Appl Microbiol 38:223–230
Kougias PG, Treu L, Campanaro S, Zhu X, Angelidaki I (2016) Dynamic functional characterization and phylogenetic changes due to long chain fatty acids pulses in biogas reactors. Sci Rep 6:28810
Kovács E, Wirth R, Maroti G, Bagi Z, Rakhely G, Kovács KL (2013) Biogas production from protein-rich biomass: fed-batch anaerobic fermentation of casein and of pig blood and associated changes in microbial community composition. PLoS One 8:e77265
Krause L, Diaz NN, Edwards RA, Gartemann KH, Kromeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A (2008) Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J Biotechnol 136:91–101
Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehover P, Pühler A, Schlüter A (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. J Biotechnol 142:38–49
Kumar S, Krishnani KK, Bhushan B, Brahmane MP (2015) Metagenomics: retrospect and prospects in high throughput age. Biotechnol Res Int 2015:121735
Kunin V, Copeland A, Lapidus A, Mavromatis K, Hugenholtz P (2008) A bioinformatician’s guide to metagenomics. Microbiol Mol Biol Rev 72:557–578
Lebuhn M, Hanreich A, Klocke M, Schlüter A, Bauer C, Perez CM (2014) Towards molecular biomarkers for biogas production from lignocellulose-rich substrates. Anaerobe 29:10–21
Lu F, Bize A, Guillot A, Monnet V, Madigou C, Chapleur O, Mazeas L, He P, Bouchez T (2014) Metaproteomics of cellulose methanisation under thermophilic conditions reveals a surprisingly high proteolytic activity. ISME J 8:88–102
Luo G, Fotidis IA, Angelidaki I (2016) Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis. Biotechnol Biofuels 9:51
Luo G, Li B, Li LG, Zhang T, Angelidaki I (2017) Antibiotic resistance genes and correlations with microbial community and metal resistance genes in full-scale biogas reactors as revealed by metagenomic analysis. Environ Sci Technol 51:4069–4080
Luton PE, Wayne JM, Sharp RJ, Riley PW (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen population in landfill. Microbiology 148:3521–3530
Lykidis A, Chen CL, Tringe SG, McHardy AC, Copeland A, Kyrpides NC, Hugenholtz P, Macarie H, Olmos A, Monroy O, Liu WT (2011) Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium. ISME J 5:122–130
Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9:386
Mori K, Yamaguchi K, Sakiyama Y, Urabe T, Suzuki K (2009) Caldisericum exile gen. Nov., sp. nov., an anaerobic, thermophilic, filamentous bacterium of a novel bacterial phylum, Caldiserica phyl. Nov., originally called the candidate phylum OP5, and description of Caldisericaceae fam. Nov., Caldisericales Ord. Nov. and Caldisericia classis nov. Int J Syst Evol Microbiol 59:2894–2898
Mosbæk F, Kjeldal H, Mulat DG, Albertsen M, Ward AJ, Feilberg A, Nielsen JL (2016) Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics. ISME J 10:2405–2418
Nolla-Ardevol V, Peces M, Strous M, Tegetmeyer HE (2015a) Metagenome from a Spirulina digesting biogas reactor: analysis via binning of contigs and classification of short reads. BMC Microbiol 15:277
Nolla-Ardevol V, Strous M, Tegetmeyer HE (2015b) Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome. Front Microbiol 6:597
Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum SP, Jaenicke S, Fracowiak J, Pühler A, Schlüter A (2016) An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant. J Biotechnol 231:268–279
Pandit PD, Gulhane MK, Khardenavis AA, Purohit HJ (2016) Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community. Bioresour Technol 216:923–930
Pap B, Gyorkei A, Boboescu IZ, Nagy IK, Biro T, Kondorosi E, Maroti G (2015) Temperature-dependent transformation of biogas-producing microbial communities points to the increased importance of hydrogenotrophic methanogenesis under thermophilic operation. Bioresour Technol 177:375–380
Pelletier E, Kreimeyer A, Bocs S, Rouy Z, Gyapay G, Chouari R, Riviere D, Ganesan A, Daegelen P, Sghir A, Cohen GN, Medigue C, Weissenbach J, Le Paslier D (2008) “Candidatus Cloacamonas acidaminovorans”: genome sequence reconstruction provides a first glimpse of a new bacterial division. J Bacteriol 190:2572–2579
Perez-Garcia O, Lear G, Singhal N (2016) Metabolic network modeling of microbial interactions in natural and engineered environmental systems. Front Microbiol 7:673
Prosser JI (2015) Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology. Nat Rev Microbiol 13:439–446
Rademacher A, Zakrzewski M, Schlüter A, Schönberg M, Szczepanowski R, Goesmann A, Pühler A, Klocke M (2012) Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiol Ecol 79:785–799
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides NC, Stepanauskas R, Rubin EM, Hugenholtz P, Woyke T (2013) Insights into the phylogeny and coding potential of microbial dark matter. Nature 499:431–437
Riviere D, Desvignes V, Pelletier E, Chaussonnerie S, Guermazi S, Weissenbach J, Li T, Camacho P, Sghir A (2009) Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J 3:700–714
Sales CM, Lee PK (2015) Resource recovery from wastewater: application of meta-omics to phosphorus and carbon management. Curr Opin Biotechnol 33:260–267
Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann K-H, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A (2008) The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J Biotechnol 136:77–90
Solli L, Havelsrud OE, Horn SJ, Rike AG (2014) A metagenomic study of the microbial communities in four paralel biogas reactors. Biotechnol Biofuels 7:146
Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Pühler A, Schlüter A (2015) Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnol Biofuels 8:14
Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Pühler A, Sczyrba A, Schlüter A (2016) Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants. Biotechnol Biofuels 9:156
Thanh PM, Ketheesan B, Yan Z, Stuckey D (2016) Trace metal speciation and bioavailability in anaerobic digestion: a review. Biotechnol Adv 34:122–136
Thomas T, Gilbert J, Meyer F (2012) Metagenomics – a guide from sampling to data analysis. Microb Inform Exp 2:3
Treu L, Campanaro S, Kougias PG, Zhu X, Angelidaki I (2016a) Untangling the effect of fatty acid addition at species level revealed different transcriptional responses of the biogas microbial community members. Environ Sci Technol 50:6079–6090
Treu L, Kougias PG, Campanaro S, Bassani I, Angelidaki I (2016b) Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes. Bioresour Technol 216:260–266
Tukacs-Hájos A, Pap B, Maróti G, Szendefy J, Szabó P, Rétfalvi T (2014) Monitoring of thermophilic adaptation of mesophilic anaerobe fermentation of sugar beet pressed pulp. Bioresour Technol 166:288–294
Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ranm RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43
Vanwonterghem I, Jensen PD, Ho DP, Batstone DJ, Tyson GW (2014) Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Curr Opin Biotechnol 27:55–64
Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ, Hugenholtz P, Tyson GW (2016a) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol 1:16170
Vanwonterghem I, Jensen PD, Rabaey K, Tyson GW (2016b) Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environ Microbiol 18:3144–3158
Wang M, Lai GL, Nie Y, Geng S, Liu L, Zhu B, Shi Z, Wu XL (2015) Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester. Front Microbiol 6:509
Wei Y, Zhou H, Zhang J, Zhang L, Geng A, Liu F, Zhao G, Wang S, Zhou Z, Yan X (2015) Insight into dominant cellulolytic bacteria from two biogas digesters and their glycoside hydrolase genes. PLoS One 10:e0129921
Wirth R, Kovács E, Maróti G, Bagi Z, Rakhely G, Kovács KL (2012) Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing. Biotechnol Biofuels 5:41
Wirth R, Lakatos G, Bojti T, Maróti G, Bagi Z, Kis M, Kovács A, Acs N, Rakhely G, Kovács KL (2015) Metagenome changes in the mesophilic biogas-producing community during fermentation of the green alga Scenedesmus obliquus. J Biotechnol 215:52–61
Wong MT, Zhang D, Li J, Hui RK, Tun HM, Brar MS, Park TJ, Chen Y, Leung FC (2013) Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment. Biotechnol Biofuels 6:38
Xia Y, Ju F, Fang HH, Zhang T (2013) Mining of novel thermo-stable cellulolytic genes from a thermophilic cellulose-degrading consortium by metagenomics. PLoS One 8:e53779
Yan X, Geng A, Zhang J, Wei Y, Zhang L, Qian C, Wang Q, Wang S, Zhou Z (2013) Discovery of (hemi-) cellulase genes in a metagenomic library from a biogas digester using 454 pyrosequencing. Appl Microbiol Biotechnol 97:8173–8182
Yang Y, Yu K, Xia Y, Lau FT, Tang DT, Fung WC, Fang HH, Zhang T (2014) Metagenomic analysis of sludge from full-scale anaerobic digesters operated in municipal wastewater treatment plants. Appl Microbiol Biotechnol 98:5709–5718
Yang C, Xia Y, Qu H, Li AD, Liu R, Wang Y, Zhang T (2016) Discovery of new cellulases from the metagenome by a metagenomics-guided strategy. Biotechnol Biofuels 9:138
Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sørensen S, Pühler A, Schlüter A (2012) Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol 158:248–258
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Kleinsteuber, S. (2018). Metagenomics of Methanogenic Communities in Anaerobic Digesters. In: Stams, A., Sousa, D. (eds) Biogenesis of Hydrocarbons. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-53114-4_16-1
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