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Inoculum selection is crucial to ensure operational stability in anaerobic digestion

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Abstract

Anaerobic digestion is considered a key technology for the future bio-based economy. The microbial consortium carrying out the anaerobic digestion process is quite complex, and its exact role in terms of “elasticity”, i.e., the ability to rapidly adapt to changing conditions, is still unknown. In this study, the role of the initial microbial community in terms of operational stability and stress tolerance was evaluated during a 175-day experiment. Five different inocula from stable industrial anaerobic digesters were fed a mixture of waste activated sludge and glycerol. Increasing ammonium pulses were applied to evaluate stability and stress tolerance. A different response in terms of start-up and ammonium tolerance was observed among the different inocula. Methanosaetaceae were the dominant acetoclastic methanogens, yet, Methanosarcinaceae increased in abundance at elevated ammonium concentrations. A shift from a Firmicutes to a Proteobacteria dominated bacterial community was observed in failing digesters. Methane production was strongly positively correlated with Methanosaetaceae, but also with Bacteria related to Anaerolinaceae, Clostridiales, and Alphaproteobacteria. Volatile fatty acids were strongly positively correlated with Betaproteobacteria and Bacteroidetes, yet ammonium concentration only with Bacteroidetes. Overall, these results indicate the importance of inoculum selection to ensure stable operation and stress tolerance in anaerobic digestion.

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References

  • Angelidaki I, Ahring BK (1993) Thermophilic anaerobic digestion of livestock waste: the effect of ammonia. Appl Microbiol Biotechnol 38(4):560–564

    Article  CAS  Google Scholar 

  • Angenent LT, Karim K, Al-Dahhan MH, Domiguez-Espinosa R (2004) Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends Biotechnol 22(9):477–485. doi:10.1016/j.tibtech.2004.07.001

    Article  CAS  PubMed  Google Scholar 

  • Anthonisen AC, Loehr RC, Prakasam TBS, Srinath EG (1976) Inhibition of nitrification by ammonia and nitrous acid. J Water Pollut Control Fed 48(5):835–852

    CAS  PubMed  Google Scholar 

  • Bayr S, Pakarinen O, Korppoo A, Liuksia S, Vaisanen A, Kaparaju P, Rintala J (2012) Effect of additives on process stability of mesophilic anaerobic monodigestion of pig slaughterhouse waste. Bioresour Technol 120:106–113. doi:10.1016/j.biortech.2012.06.009

    Article  CAS  PubMed  Google Scholar 

  • Bengelsdorf FR, Gerischer U, Langer S, Zak M, Kazda M (2013) Stability of a biogas-producing bacterial, archaeal and fungal community degrading food residues. FEMS Microbiol Ecol 84(1):201–212. doi:10.1111/1574-6941.12055

    Article  CAS  PubMed  Google Scholar 

  • Bohorquez LC, Delgado-Serrano L, Lopez G, Osorio-Forero C, Klepac-Ceraj V, Kolter R, Junca H, Baena S, Zambrano MM (2012) In-depth characterization via complementing culture-independent approaches of the microbial community in an acidic hot spring of the Colombian Andes. Microb Ecol 63(1):103–115. doi:10.1007/s00248-011-9943-3

    Article  PubMed  Google Scholar 

  • Briones A, Raskin L (2003) Diversity and dynamics of microbial communities in engineered environments and their implications for process stability. Curr Opin Biotechnol 14(3):270–276. doi:10.1016/s0958-1669(03)00065-x

    Article  CAS  PubMed  Google Scholar 

  • Calli B, Mertoglu B, Inanc B, Yenigun O (2005) Community changes during start-up in methanogenic bioreactors exposed to increasing levels of ammonia. Environ Technol 26(1):85–91

    Article  CAS  PubMed  Google Scholar 

  • Camarinha-Silva A, Jáuregui R, Chaves-Moreno D, Oxley APA, Schaumburg F, Becker K, Wos-Oxley ML, Pieper DH (2014) Comparing the anterior nare bacterial community of two discrete human populations using illumina amplicon sequencing. Environ Microbiol. doi:10.1111/1462-2920.12362

    PubMed  Google Scholar 

  • 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(2):303–314. doi:10.1007/s00253-010-2858-y

    Article  CAS  PubMed  Google Scholar 

  • Chen Y, Cheng JJ, Creamer KS (2008) Inhibition of anaerobic digestion process: a review. Bioresour Technol 99(10):4044–4064. doi:10.1016/j.biortech.2007.01.057

    Article  CAS  PubMed  Google Scholar 

  • Conklin A, Stensel HD, Ferguson J (2006) Growth kinetics and competition between Methanosarcina and Methanosaeta in mesophilic anaerobic digestion. Water Environ Res 78(5):486–496. doi:10.2175/106143006x95393

    Article  CAS  PubMed  Google Scholar 

  • De Vrieze J, Hennebel T, Boon N, Verstraete W (2012) Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. Bioresour Technol 112:1–9. doi:10.1016/j.biortech.2012.02.079

    Article  PubMed  Google Scholar 

  • De Vrieze J, Verstraete W, Boon N (2013) Repeated pulse feeding induces functional stability in anaerobic digestion. Microb Biotechnol 6(4):414–424. doi:10.1111/1751-7915.12025

    Article  PubMed Central  PubMed  Google Scholar 

  • Dearman B, Marschner P, Bentham RH (2006) Methane production and microbial community structure in single-stage batch and sequential batch systems anaerobically co-digesting food waste and biosolids. Appl Microbiol Biotechnol 69(5):589–596. doi:10.1007/s00253-005-0076-9

    Article  CAS  PubMed  Google Scholar 

  • Dechrugsa S, Kantachote D, Chaiprapat S (2013) Effects of inoculum to substrate ratio, substrate mix ratio and inoculum source on batch co-digestion of grass and pig manure. Bioresour Technol 146:101–108. doi:10.1016/j.biortech.2013.07.051

    Article  CAS  PubMed  Google Scholar 

  • Delbes C, Moletta R, Godon JJ (2001) Bacterial and archaeal 16S rDNA and 16S rRNA dynamics during an acetate crisis in an anaerobic digestor ecosystem. FEMS Microbiol Ecol 35(1):19–26. doi:10.1111/j.1574-6941.2001.tb00784.x

    Article  CAS  PubMed  Google Scholar 

  • Demirel B, Scherer P (2008) The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review. Rev Environ Sci Biotechnol 7(2):173–190. doi:10.1007/s11157-008-9131-1

    Article  CAS  Google Scholar 

  • Fernandez AS, Hashsham SA, Dollhopf SL, Raskin L, Glagoleva O, Dazzo FB, Hickey RF, Criddle CS, Tiedje JM (2000) Flexible community structure correlates with stable community function in methanogenic bioreactor communities perturbed by glucose. Appl Environ Microbiol 66(9):4058–4067

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Gallert C, Winter J (1997) Mesophilic and thermophilic anaerobic digestion of source-sorted organic wastes: effect of ammonia on glucose degradation and methane production. Appl Microbiol Biotechnol 48(3):405–410

    Article  CAS  Google Scholar 

  • Gallert C, Bauer S, Winter J (1998) Effect of ammonia on the anaerobic degradation of protein by a mesophilic and thermophilic biowaste population. Appl Microbiol Biotechnol 50(4):495–501

    Article  CAS  PubMed  Google Scholar 

  • Greenberg AE, Clesceri LS, Eaton AD (1992) Standard methods for the examination of water and wastewater 18th edn. American Public Health Association Publications, Washington

    Google Scholar 

  • Gujer W, Zehnder AJB (1983) Conversion processes in anaerobic digestion. Water Sci Technol 15(8–9):127–167

    CAS  Google Scholar 

  • Hansen KH, Angelidaki I, Ahring BK (1998) Anaerobic digestion of swine manure: inhibition by ammonia. Water Res 32(1):5–12. doi:10.1016/s0043-1354(97)00201-7

    Article  CAS  Google Scholar 

  • Hao LP, Lu F, He PJ, Li L, Shao LM (2011) Predominant contribution of syntrophic acetate oxidation to thermophilic methane formation at high acetate concentrations. Environ Sci Technol 45(2):508–513. doi:10.1021/es102228v

    Article  CAS  PubMed  Google Scholar 

  • Hashimoto AG (1986) Ammonia inhibition of methanogenesis from cattle wastes. Agric Wastes 17(4):241–261. doi:10.1016/0141-4607(86)90133-2

    Article  CAS  Google Scholar 

  • Hattori S (2008) Syntrophic acetate-oxidizing microbes in methanogenic environments. Microbes Environ 23(2):118–127. doi:10.1264/jsme2.23.118

    Article  PubMed  Google Scholar 

  • Holm-Nielsen JB, Al Seadi T, Oleskowicz-Popiel P (2009) The future of anaerobic digestion and biogas utilization. Bioresour Technol 100(22):5478–5484. doi:10.1016/j.biortech.2008.12.046

    Article  CAS  PubMed  Google Scholar 

  • Hurlbert SH (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology 52(4):577–586. doi:10.2307/1934145

    Article  Google Scholar 

  • Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academy Press, New York

    Google Scholar 

  • Karakashev D, Batstone DJ, Trably E, Angelidaki I (2006) Acetate oxidation is the dominant methanogenic pathway from acetate in the absence of Methanosaetaceae. Appl Environ Microbiol 72(7):5138–5141. doi:10.1128/aem.00489-06

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kato S, Watanabe K (2010) Ecological and evolutionary interactions in syntrophic methanogenic consortia. Microbes Environ 25(3):145–151. doi:10.1264/jsme2.ME10122

    Article  PubMed  Google Scholar 

  • Krakat N, Schmidt S, Scherer P (2011) Potential impact of process parameters upon the bacterial diversity in the mesophilic anaerobic digestion of beet silage. Bioresour Technol 102(10):5692–5701. doi:10.1016/j.biortech.2011.02.108

    Article  CAS  PubMed  Google Scholar 

  • Krober M, Bekel T, Diaz NN, Goesmann A, Jaenicke S, Krause L, Miller D, Runte KJ, Viehover P, Puhler A, Schluter 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):38–49. doi:10.1016/j.jbiotec.2009.02.010

    Article  PubMed  Google Scholar 

  • Lee S-H, Kang H-J, Lee YH, Lee TJ, Han K, Choi Y, Park H-D (2012) Monitoring bacterial community structure and variability in time scale in full-scale anaerobic digesters. J Environ Monit 14(7):1893–1905. doi:10.1039/c2em10958a

    Article  CAS  PubMed  Google Scholar 

  • Letunic I, Bork P (2011) Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39:W475–W478. doi:10.1093/nar/gkr201

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li Q, Wang C, Tang C, Li N, Li J (2012) Molecular-Phylogenetic Characterization of the Microbiota in Ulcerated and Non-Ulcerated Regions in the Patients with Crohn's Disease. PLoS One 7(4) doi:10.1371/journal.pone.0034939

  • 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):952–966. doi:10.1111/j.1365-2672.2008.04064.x

    Article  CAS  PubMed  Google Scholar 

  • Lu F, Hao LP, Guan DX, Qi YJ, Shao LM, He PJ (2013) Synergetic stress of acids and ammonium on the shift in the methanogenic pathways during thermophilic anaerobic digestion of organics. Water Res 47(7):2297–2306. doi:10.1016/j.watres.2013.01.049

    Article  CAS  PubMed  Google Scholar 

  • Marzorati M, Wittebolle L, Boon N, Daffonchio D, Verstraete W (2008) How to get more out of molecular fingerprints: practical tools for microbial ecology. Environ Microbiol 10(6):1571–1581. doi:10.1111/j.1462-2920.2008.01572.x

    Article  CAS  PubMed  Google Scholar 

  • Mata-Alvarez J, Mace S, Llabres P (2000) Anaerobic digestion of organic solid wastes. An Overview of Res Achievements and Perspect Bioresour Technol 74(1):3–16. doi:10.1016/s0960-8524(00)00023-7

    CAS  Google Scholar 

  • McMahon KD, Zheng DD, Stams AJM, Mackie RI, Raskin L (2004) Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge. Biotechnol Bioeng 87(7):823–834. doi:10.1002/bit.20192

    Article  CAS  PubMed  Google Scholar 

  • Michail S, Durbin M, Turner D, Griffiths AM, Mack DR, Hyams J, Leleiko N, Kenche H, Stolfi A, Wine E (2012) Alterations in the gut microbiome of children with severe ulcerative colitis. Inflamm Bowel Dis 18(10):1799–1808. doi:10.1002/ibd.22860

    Article  PubMed Central  PubMed  Google Scholar 

  • Mondot S, Kang S, Furet JP, de Carcer DA, McSweeney C, Morrison M, Marteau P, Dore J, Leclerc M (2011) Highlighting new phylogenetic specificities of Crohn’s disease microbiota. Inflamm Bowel Dis 17(1):185–192. doi:10.1002/ibd.21436

    Article  CAS  PubMed  Google Scholar 

  • Nettmann E, Bergmann I, Pramschufer 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):2540–2548. doi:10.1128/aem.01423-09

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Oksanen, J, Blanchet, G, Kindt, R, Legendre, P, Minchin, PR, O’Hara, RB, Simpson, GL, Solymos, P, Henry, M., Stevens, H, Wagner, H (2012) Vegan: Community ecology package. R package version 2.0-1. http://CRAN.R-project.org/package=vegan

  • Peterson G, Allen CR, Holling CS (1998) Ecological resilience, biodiversity, and scale. Ecosystems 1(1):6–18. doi:10.1007/s100219900002

    Article  Google Scholar 

  • Pitk P, Kaparaju P, Palatsi J, Affes R, Vilu R (2013) Co-digestion of sewage sludge and sterilized solid slaughterhouse waste: methane production efficiency and process limitations. Bioresour Technol 134:227–232. doi:10.1016/j.biortech.2013.02.029

    Article  CAS  PubMed  Google Scholar 

  • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Gloeckner FO (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35(21):7188–7196. doi:10.1093/nar/gkm864

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Qu X, Vavilin VA, Mazeas L, Lemunier M, Duquennoi C, He PJ, Bouchez T (2009) Anaerobic biodegradation of cellulosic material: batch experiments and modelling based on isotopic data and focusing on aceticlastic and non-aceticlastic methanogenesis. Waste Manage 29(6):1828–1837. doi:10.1016/j.wasman.2008.12.008

    Article  CAS  Google Scholar 

  • R Development Core Team (2013) R: A Language and Environment for Statistical Computing. 3.0 ed. Vienna, Austria: R Foundation for Statistical Computing

  • Rajagopal R, Masse DI, Singh G (2013) A critical review on inhibition of anaerobic digestion process by excess ammonia. Bioresour Technol 143:632–641. doi:10.1016/j.biortech.2013.06.030

    Article  CAS  PubMed  Google Scholar 

  • 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(6):700–714. doi:10.1038/ismej.2009.2

    Article  PubMed  Google Scholar 

  • Sanders HL (1968) Marine benthic diversity: a comparative study. Am Nat 102(925):243–282. doi:10.1086/282541

    Article  Google Scholar 

  • Sawayama S, Tada C, Tsukahara K, Yagishita T (2004) Effect of ammonium addition on methanogenic community in a fluidized bed anaerobic digestion. J Biosci Bioeng 97(1):65–70

    Article  CAS  PubMed  Google Scholar 

  • Schink B (1997) Energetics of syntrophic cooperation in methanogenic degradation. Microbiol Mol Biol Rev 61(2):262

    CAS  PubMed Central  PubMed  Google Scholar 

  • Schnurer A, Nordberg A (2008) Ammonia, a selective agent for methane production by syntrophic acetate oxidation at mesophilic temperature. Water Sci Technol 57(5):735–740. doi:10.2166/wst.2008.097

    Article  CAS  PubMed  Google Scholar 

  • Steinberg LM, Regan JM (2011) Response of lab-scale methanogenic reactors inoculated from different sources to organic loading rate shocks. Bioresour Technol 102(19):8790–8798. doi:10.1016/j.biortech.2011.07.017

    Article  CAS  PubMed  Google Scholar 

  • Sundberg C, Al-Soud WA, Larsson M, Alm E, Yekta SS, Svensson BH, Sørensen SJ, Karlsson A (2013) 454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters. FEMS Microbiol Ecol 85(3):612–626. doi:10.1111/1574-6941.12148

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731–2739. doi:10.1093/molbev/msr121

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tyagi VK, Lo SL (2013) Sludge: a waste or renewable source for energy and resources recovery? Renewable Sustainable Energy Rev 25:708–728. doi:10.1016/j.rser.2013.05.029

    Article  CAS  Google Scholar 

  • 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. doi:10.1016/j.copbio.2013.11.004

    Article  CAS  PubMed  Google Scholar 

  • Venables WN, Ripley BD (2002) Modern applied statistics with S, 4th edn. Springer, New York

    Book  Google Scholar 

  • Verstraete W, Morgan-Sagastume F, Aiyuk S, Waweru M, Rabaey K, Lissens G (2005) Anaerobic digestion as a core technology in sustainable management of organic matter. Water Sci Technol 52(1–2):59–66

    CAS  PubMed  Google Scholar 

  • Westerholm M, Roos S, Schnurer A (2010) Syntrophaceticus schinkii gen. nov., sp nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter. FEMS Microbiol Lett 309(1):100–104. doi:10.1111/j.1574-6968.2010.02023.x

    CAS  PubMed  Google Scholar 

  • Williams J, Williams H, Dinsdale R, Guwy A, Esteves S (2013) Monitoring methanogenic population dynamics in a full-scale anaerobic digester to facilitate operational management. Bioresour Technol 140:234–242. doi:10.1016/j.biortech.2013.04.089

    Article  CAS  PubMed  Google Scholar 

  • Wittebolle L, Verstraete W, Boon N (2009) The inoculum effect on the ammonia-oxidizing bacterial communities in parallel sequential batch reactors. Water Res 43(17):4149–4158. doi:10.1016/j.watres.2009.06.034

    Article  CAS  PubMed  Google Scholar 

  • Yu Y, Lee C, Kim J, Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89(6):670–679. doi:10.1002/bit.20347

    Article  CAS  PubMed  Google Scholar 

  • Yu Y, Kim J, Hwang S (2006) Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures. Biotechnol Bioeng 93(3):424–433. doi:10.1002/bit.20724

    Article  CAS  PubMed  Google Scholar 

  • Zinder SH, Koch M (1984) Non-acetoclastic methanogenesis from acetate: acetate oxidation by a thermophilic syntrophic coculture. Arch Microbiol 138(3):263–272. doi:10.1007/bf00402133

    Article  CAS  Google Scholar 

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Acknowledgments

This work was supported by the Ghent University Multidisciplinary Research Partnership (MRP) “Biotechnology for a Sustainable Economy” (01 MRA 510 W). S.G. is funded by the Special Research Fund (BOF) of the University of Ghent (Belgium). R.V.V. is supported by the Inter-University Attraction Pole (IUAP) “μ-manager” funded by the Belgian Science Policy (BELSPO, P7/25). The authors would like to thank Tim Lacoere for his assistance during the molecular work and Jan Arends, Hugo Roume, Eline Vanlancker, and Jana Wijnsouw for the useful suggestions and critically reading the manuscript. The authors declare no conflict of interest.

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ESM 1

Specific details concerning the waste activated sludge characterization, experimental set-up, qPCR quality control, and biogas and VFA analyses can be found in SI, together with total VFA, TAN, and pH profiles in the reactors. A heatmap at family level, the rarefaction curves, and a detailed overview of correlations between the microbial community and the main operational conditions are also presented. (PDF 1511 kb)

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De Vrieze, J., Gildemyn, S., Vilchez-Vargas, R. et al. Inoculum selection is crucial to ensure operational stability in anaerobic digestion. Appl Microbiol Biotechnol 99, 189–199 (2015). https://doi.org/10.1007/s00253-014-6046-3

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