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2018 | OriginalPaper | Chapter

16. New “Omics” Technologies and Biogas Production

Authors : Gholamreza Salehi Jouzani, Reza Sharafi

Published in: Biogas

Publisher: Springer International Publishing

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Abstract

Biogas production from wastes and residues is classified among the versatile, energy-efficient, and environmentally beneficial strategies considered to gradually replace fossil fuels in the future. Nevertheless, biogas production from different resources is faced with many technical, efficiency, and cost challenges, and therefore, optimization of the various aspects of the process, including feeding, mixing, microbial community, as well as process monitoring and control are vital to enhance process efficiency. The microbial community structure and functions exert vital effects on the process stability and biogas yield. However, due to the lack of optimized culture media and conditions for most of the organisms involved in biogas production, the majority of the participating microbes as well as their genes and metabolic pathways during the process are yet to be well known. Recent developments in culture independent “omics” and next generation sequencing technologies (NGS) have provided excellent opportunities for exploring microbial communities and their factions during the anaerobic digestion process. Therefore, this chapter has focused on recent applications of new “omics”, including NGS-based whole genome sequencing, metagenomics, meta-transcriptomics, meta-proteomics, and met-metabolomics in characterization of microbial flora, their genes and encoded transcripts, proteins, and metabolites, as well as the metabolic pathways contributing to the anaerobic digestion process. Recent findings have confirmed that the revolutionary innovations and developments in these domains will help to enhance the efficiency of biogas production from a diverse range of organic matters with complex structures in the near future.

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Abram F, Enright A-M, O’Reilly J, Botting CH, Collins G, O’Flaherty V (2010) A metaproteomic approach gives functional insights into anaerobic digestion. Appl Microbiol 110:1550–1560CrossRef

Anjum R, Grohmann E, Krakat, N (2017) Anaerobic digestion of nitrogen rich poultry manure: impact of thermophilic biogas process on metal release and microbial resistances. ChemosphereCrossRef

Beale DJ, Karpe AV, McLeod JD, Gondalia SV, Muster TH, Othman MZ, Palombo EA, Joshi D (2016) An ‘omics’ approach towards the characterization of laboratory scale anaerobic digesters treating municipal sewage sludge. Water Res 88:346–357CrossRef

Benato A, Macor A (2017) Biogas engine waste heat recovery using organic Rankine cycle. Energies 10(3):327CrossRef

Bremges A, Maus I, Belmann P, Eikmeyer F, Winkler A, Albersmeier A (2015) Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. GigaScience 4(1):33

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(1):26CrossRef

Carballa M, Smits M, Etchebehere C, Boon N, Verstraete W (2011) Correlations between molecular and operational parameters in continuous lab-scale anaerobic reactors. Appl Microbiol Biotechnol 89:303–314CrossRef

Ciesielski S, Bułkowska K, Dabrowska D, Kaczmarczyk D, Kowal P, Możejko J (2013) Ribosomal intergenic spacer analysis as a tool for monitoring methanogenic archaea changes in an anaerobic digester. Curr Microbiol 67(2):240CrossRef

Connaughton S, Collins G, O’Flaherty V (2006) Development of microbial community structure and activity in a high-rate anaerobic bioreactor at 18 C. Water Res 40:1009–1017CrossRef

Delbès C, Moletta R, Godon JJ (2000) Monitoring of activity dynamics of an anaerobic digester bacterial community using 16S rRNA polymerase chain reaction–single-strand conformation polymorphism analysis. Environ Microbiol 2(5):506–515CrossRef

Delmont TO, Simonet P, vogel TMJ (2012) Describing microbial communities and performing global comparisons in the “omic” era. ISME 6(1625–1628):18

Deng L, Liu Y, Zheng D, Wang L, Pu X, Song L, Wang Z, Lei Y, Chen Z, Long Y (2016) Application and development of biogas technology for the treatment of waste in China. Renew Sustain Energy Rev

Dollhofer V, Callaghan TM, Griffith GW, Lebuhn M, Bauer J (2017) Presence and transcriptional activity of anaerobic fungi in agricultural biogas plants. Biores Technol 235:131–139CrossRef

Dong M, Wu Y, Li Q, Tian G, Yang B, Li Y, ZhangL Wang Y, Xiao W, Yin F, Zhao X, Zhang W, Cui X (2015) Investigation of methanogenic community structures in rural biogas digesters from different climatic regions in Yunnan, south west China. Curr Microbiol 70(5):679–684CrossRef

Dubey SK, Meena RK, Sao S, Patel J, Shukla P (2014) Isolation and characterization of cellulose degrading bacteria from biogas slurry and their RAPD profiling. Curr Res Microbiol Biotechnol 2(4):416–421

Dudhagara P, Ghelani A, Bhavsar S, Bhatt S (2015) Metagenomic data of fungal internal transcribed Spacer and 18S rRNA gene sequences from Lonar lake sediment, India. Data Brief 4:266–268CrossRef

Gilbert JA, Meyer F, Bailey MJ (2011) The future of microbial metagenomics (or is ignorance bliss?). ISME J 5(5):777CrossRef

Gruninger RJ, Puniya AK, Callaghan TM, Edwards JE, Youssef N, Dagar SS, Fliegerová K, Griffith GW, Forster R, Tsang A, McAllister T, Elshahed MS (2014) Anaerobic fungi (phylum Neocallimastigomycota): advances in understanding their taxonomy, life cycle, ecology, role and biotechnological potential. FEMS Microbiol Ecolo 90:1–17CrossRef

Güllert S, Fischer MA, Turaev D, Noebauer B, Ilmberger N, Wemheuer B, Alawi M, Rattei T, Daniel R, Schmitz RA, Grundhoff A (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(1):121CrossRef

Hahnke S, Maus I, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A (2015) Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor. J Biotechnol 193:34–36CrossRef

Hanreich A, Schimpf U, Zakrzewski M, Schluter A, Benndorf D, Heyer R (2013) Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. System App Microbiol 36(5):330–338CrossRef

Heyer R, Benndorf D, Kohrs F, De Vrieze J, Boon N, Hoffmann M (2016) Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. Biotechnol Biofuels 9(1):155

Heyer R, Kohrs F, Benndorf D, Rapp E, Kausmann R, Heiermann M (2013) Metaproteome analysis of the microbial communities in agricultural biogas plants. New Biotechnol 30(6):614–622. https://doi.org/10.1016/j.nbt.2013.01.002CrossRef

Jaenicke S, Ander C, Bekel T, Bisdorf R, Droge M, Gartemann K-H, Junemann S, Kaiser O, Krause L, Tille F et al (2010) Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS ONE 6:1–15

Koeck DE, Ludwig W, Wanner G, Zverlov VV, Liebl W, Schwarz WH (2015a) Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor. Int J Syst Evol Microbiol 65(8):2365–2371CrossRef

Koeck DE, Maus I, Wibberg D, Winkler A, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A (2015b) Draft genome sequence of Herbinix hemicellulosilytica T3/55 T, a new thermophilic cellulose degrading bacterium isolated from a thermophilic biogas reactor. J Biotechnol 214:59–60CrossRef

Koeck DE, Wibberg D, Maus I, Winkler A, Albersmeier A, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A (2014a) Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant. J Biotechnol 188:136–137CrossRef

Koeck DE, Zverlov VV, Liebl W, Schwarz WH (2014b) Comparative genotyping of Clostridium thermocellum strains isolated from biogas plants: genetic markers and characterization of cellulolytic potential. Syst Appl Microbiol 37(5):311–319CrossRef

Kohrs F, Heyer R, Bissinger T, Kottler R, Schallert K, Püttker S, Behne A, Rapp E, Benndorf D, Reichl U (2017) Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition. Anaerobe

Kohrs F, Heyer R, Magnussen A, Benndorf D, Muth T, Behne A, Rapp E, Kausmann R, Heiermann M, Klocke M, Reichl U (2014) Sample prefractionation with liquid isoelectric focusing enables in depth microbial metaproteome analysis of mesophilic and thermophilic biogas plants. Anaerobe 29:59–67CrossRef

Kohrs F, Wolter S, Benndorf D, Heyer R, Hoffmann M, Rapp E et al. (2015) Fractionation of biogas plant sludge material improves metaproteomic characterization to investigate metabolic activity of microbial communities. Proteomics 15(20):3585–3589. https://doi.org/10.1002/pmic.201400557CrossRef

Kröber M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehöver 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(1):38–49CrossRef

Kučera L, Kurka O, Barták P, Bednář P (2017) Liquid chromatography/high resolution tandem mass spectrometry–tool for the study of polyphenol profile changes during micro-scale biogas digestion of grape marcs. Chemosphere 166:463–472CrossRef

Langley SR, Dwyer J, Drozdov I, Yin X, Mayr M (2013) Proteomics: from single molecules to biological pathways. Cardiovasc Res 97:612–622CrossRef

Leclerc M, Delbes C, Moletta R, Godon JJ (2001) Single strand conformation polymorphism monitoring of 16S rDNA Archaea during start-up of an anaerobic digester. FEMS Microbiol Ecol 34(3):213–220CrossRef

Li JM (2013) Biogas production in China: current status and future development. www.epa.gov/agstar/documents/conf13/Biogas Production in China—current status. Accessed June 2017

Li X, Liu YH, Zhang X, Ge CM, Piao RZ, Wang WD, Cui ZJ, Zhao HY (2017) Evaluation of biogas production performance and dynamics of the microbial community in different straws. J Microbiol Biotechnol 27:524–534CrossRef

Lin YW, Tuan NN, Huang SL (2016) Metaproteomic analysis of the microbial community present in a thermophilic swine manure digester to allow functional characterization: A case study. Int Biodeterior Biodegradation 115:64–73CrossRef

Liu F, Rotaru AE, Shrestha PM, Malvankar NS, Nevin KP, Lovley DR (2012) Promoting direct interspecies electron transfer with activated carbon. Energy Environ Sci 5(10):8982–8989CrossRef

Liu Y, Balkwill DL, Aldrich HC, Drake GR, Boone DR (1999) Characterization of the anaerobic propionate-degrading syntrophs Smithella propionica gen. nov., sp. nov. and Syntrophobacter wolinii. Int J Sys Bacteriol 49:545–556CrossRef

Liu FH, Wang SB, Zhang JS, Zhang J, Yan X, Zhou HK, Zhao GP, Zhou ZH (2009) The structure of the bacterial and archaeal community in a biogas digester as revealed by denaturing gradient gel electrophoresis and 16S rDNA sequencing analysis. J Appl Microbiol 106(3):952–966CrossRef

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(1):51CrossRef

Manzoor S, Müller B, Niazi A, Bongcam-Rudloff E, Schnürer A (2013) Draft genome sequence of Clostridium ultunense strain Esp, a syntrophic acetate-oxidizing bacterium. Genome announcements 1(2):e00107–e00113

Mao C, Feng Y, Wang X, Ren G (2015) Review on research achievements of biogas from anaerobic digestion. Renew Sustain Energy Rev 45:540–555CrossRef

Maus I, Stantscheff R, Wibberg D, Stolze Y, Winkler A, Pühler A, König H, Schlüter A (2014) Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MFT. J Biotechnol 192:40–41CrossRef

Maus I, Wibberg D, Winkler A, Pühler A, Schnürer A (2016) Complete genome sequence of the methanogen Methanoculleus bourgensis BA1 isolated from a biogas reactor, 4(3):3–4

Montag D, Schink B (2016) Biogas process parameters—energetics and kinetics of secondary fermentations in methanogenic biomass degradation. Appl Microbiol Biotechnol 100(2):1019–1026CrossRef

Morita M, Malvankar NS, Franks AE, Summers ZM, Giloteaux L, Rotaru AE, Rotaru C, Lovley DR (2011) Potential for direct interspecies electron transfer in methanogenic wastewater digester aggregates. MBio 2(4):e00159–11CrossRef

Nettmann E, Bergmann I, Pramschüfer S, Mundt K, Plogsties V, Herrmann C, Klocke M (2010) Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants. Appl Environ Microbiol 76(8):2540–2548CrossRef

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 231:268–279CrossRef

Raupach MJ, Amann R, Wheeler QD, Roos C (2016) The application of “-omics” technologies for the classification and identification of animals. Organisms Diversity Evol 16(1):1–12CrossRef

Sasaki D, Sasaki K, Tsuge Y, Morita M, Kondo A (2014) Comparison of metabolomic profiles of microbial communities between stable and deteriorated methanogenic processes. Biores Technol 172:83–90CrossRef

Stark L, Giersch T, Wünschiers R (2014) Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics. Anaerobe 29:85–90CrossRef

Stevenson BS, Eichorst SA, Wertz JT, Schmidt TM, Breznak JA (2004) New strategies for cultivation and detection of previously uncultured microbes. Appl Environ Microbiol 70:4748–4755CrossRef

Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N et al. (2015) Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions. Biotechnol Biofuels 8(1):14CrossRef

Su C, Lei L, Duan Y, Zhang K-Q, Yang J (2012) Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol 93:993–1003CrossRef

Suksong W, Kongjan P, Prasertsan P, Imai T, Sompong O (2016) Optimization and microbial community analysis for production of biogas from solid waste residues of palm oil mill industry by solid-state anaerobic digestion. Biores Technol 214:166–174CrossRef

Sun L, Schnürer A (2016) Draft genome sequence of the cellulolytic strain Clostridium sp. Bc-iso-3 isolated from an industrial-scale anaerobic digester. Genome Announcements, 4(5):e01188–16

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(1):128CrossRef

Sundberg C, Al-Soud WA, Larsson M, Alm E, Yekta SS, Scvensson BH, Sorenson SJ, Karlsson A (2013) 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. FEMS Microbiol Ecol 85:612–626CrossRef

Tian G, Li Q, Dong M, Wu Y, Yang B, Zhang L et al. (2016) Spatiotemporal dynamics of bacterial and archaeal communities in household biogas digesters from tropical and subtropical regions of Yunnan Province, China. Environ Sci Poll Res 23(11):11137–11148CrossRef

Tomazetto G, Hahnke S, Koeck DE, Wibberg D, Maus I, Pühler A, Klocke M, Schlüter A (2016) Complete genome analysis of Clostridium bornimense strain M2/40 T: A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor. J Biotechnol 232:38–49CrossRef

Tomazetto G, Hahnke S, Maus I, Wibberg D, Pühler A, Schlüter A, Klocke M (2014) Complete genome sequence of Peptoniphilus sp. strain ing2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation. J Biotechnol 192:59–61CrossRef

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(11):6079–6090CrossRef

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. Biores Technol 216:260–266CrossRef

Tsapekos P, Kougias PG, Frison A, Raga R, Angelidaki I (2016) Improving methane production from digested manure biofibers by mechanical and thermal alkaline pretreatment. Biores Technol 216:545–552CrossRef

Tsapekos P, Kougias PG, Vasileiou SA, Treu L, Campanaro S, Lyberatos G, Angelidaki I (2017) Bioaugmentation with hydrolytic microbes to improve the anaerobic biodegradability of lignocellulosic agricultural residues. Biores Technol 234:350–359CrossRef

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 27:55–64CrossRef

Wirth R, Kovács E, Maróti G, Bagi Z, Rákhely G, Kovács KL (2012) Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing. Biotechnol Biofuels 5(1):41CrossRef

Yang D, Fan X, Shi X, Lian S, Qiao J, Guo R (2014) Metabolomics reveals stage-specific metabolic pathways of microbial communities in two-stage anaerobic fermentation of corn-stalk. Biotech Lett 36(7):1461–1468CrossRef

Zakrzewski M, Goesmann A, Jaenicke S, Junemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sorensen S, Puhler A, Schluter A (2012) Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol 158:248–258CrossRef

Zhao C, Ai C, Li Q, Yang C, Zhou G, Liu B (2016) Diversity of archaea and bacteria in a biogas reactor fed with Pennisetum sinese Roxb by 16S rRNA sequence analysis. Tropic J Pharmaceutical Res 15(12):2659–2667CrossRef

Ziganshin AM, Liebetrau J, Pröter J, Kleinsteuber S (2013) Microbial community structure and dynamics during anaerobic digestion of various agricultural waste materials. Appl Microbiol Biotechnol 97:5161–5174CrossRef

Title: New “Omics” Technologies and Biogas Production
Authors: Gholamreza Salehi Jouzani
Reza Sharafi
Publisher: Springer International Publishing
Book: Biogas
Print ISBN: 978-3-319-77334-6

Electronic ISBN: 978-3-319-77335-3

Copyright Year: 2018
DOI: https://doi.org/10.1007/978-3-319-77335-3_16