The time response of anaerobic digestion microbiome during an organic loading rate shock

Abstract

Knowledge of connections between operational conditions, process stability, and microbial community dynamics is essential to enhance anaerobic digestion (AD) process efficiency and management. In this study, the detailed temporal effects of a sudden glycerol-based organic overloading on the AD microbial community and process imbalance were investigated in two replicate anaerobic digesters by a time-intensive sampling scheme. The microbial community time response to the overloading event was shorter than the shifts of reactor performance parameters. An increase in bacterial community dynamics and in the abundances of several microbial taxa, mainly within the Firmicutes, Tenericutes, and Chloroflexi phyla and Methanoculleus genera, could be detected prior to any shift on the reactor operational parameters. Reactor acidification already started within the first 24 h of the shock and headed the AD process to total inhibition in 72 h alongside with the largest shifts on microbiome, mostly the increase of Anaerosinus sp. and hydrogenotrophic methanogenic Archaea. In sum, this work proved that AD microbial community reacts very quickly to an organic overloading and some shifts occur prior to alterations on the performance parameters. The latter is very interesting as it can be used to improve AD process management protocols.

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References

  1. Abendroth C, Vilanova C, Günther T, Luschnig O, Porcar M (2015) Eubacteria and Archaea communities in seven mesophile anaerobic digester plants in Germany. Biotechnol Biofuels 8:1–10. https://doi.org/10.1186/s13068-015-0271-6

  2. APHA (1998) Standard methods for the examination of water and wastewater, 20th edn. American Public Health Association, Washington, DC

  3. Astals S, Nolla-Ardèvol V, Mata-Alvarez J (2012) Anaerobic co-digestion of pig manure and crude glycerol at mesophilic conditions: biogas and digestate. Bioresour Technol 110:63–70. https://doi.org/10.1016/j.biortech.2012.01.080

    CAS  Article  PubMed  Google Scholar 

  4. Beale DJ, Karpe AV, McLeod JD, Gondalia SV, Muster TH, Othman MZ, Palombo EA, Joshi D (2016) An “omics” approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge. Water Res 88:346–357. https://doi.org/10.1016/j.watres.2015.10.029

    CAS  Article  PubMed  Google Scholar 

  5. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, Mcdonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high- throughput community sequencing data. Nat Methods 7:335–336. https://doi.org/10.1038/nmeth0510-335

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  6. 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 89:303–314. https://doi.org/10.1007/s00253-010-2858-y

    CAS  Article  PubMed  Google Scholar 

  7. Ciriminna R, Della PC, Rossi M, Pagliaro M (2014) Understanding the glycerol market. Eur J Lipid Sci Technol 116:1432–1439. https://doi.org/10.1002/ejlt.201400229

    CAS  Article  Google Scholar 

  8. Cruaud P, Vigneron A, Lucchetti-Miganeh C, Ciron PE, Godfroy A, Cambon-Bonavita MA (2014) Influence of DNA extraction method, 16S rRNA targeted hypervariable regions, and sample origin on microbial diversity detected by 454 pyrosequencing in marine chemosynthetic ecosystems. Appl Environ Microbiol 80:4626–4639. https://doi.org/10.1128/AEM.00592-14

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. De Vrieze J, Gildemyn S, Vilchez-Vargas R, Jáuregui R, Pieper DH, Verstraete W, Boon N (2014) Inoculum selection is crucial to ensure operational stability in anaerobic digestion. Appl Microbiol Biotechnol 99:189–199. https://doi.org/10.1007/s00253-014-6046-3

    CAS  Article  PubMed  Google Scholar 

  10. De Vrieze J, Raport L, Roume H, Vilchez-Vargas R, Jáuregui R, Pieper DH, Boon N (2016) The full-scale anaerobic digestion microbiome is represented by specific marker populations. Water Res 104:101–110. https://doi.org/10.1016/j.watres.2016.08.008

    CAS  Article  PubMed  Google Scholar 

  11. 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 7:173–190. https://doi.org/10.1007/s11157-008-9131-1

    CAS  Article  Google Scholar 

  12. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072. https://doi.org/10.1128/AEM.03006-05

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  13. Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26:2460–2461. https://doi.org/10.1093/bioinformatics/btq461

    CAS  Article  Google Scholar 

  14. Eren AM, Vineis JH, Morrison HG, Sogin ML (2013) A filtering method to generate high quality short reads using Illumina paired-end technology. PLoS One 8:e66643. https://doi.org/10.1371/journal.pone.0066643

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. Faust K, Lahti L, Gonze D, De VWM, Raes J (2015) Metagenomics meets time series analysis: unraveling microbial community dynamics. Curr Opin Microbiol 25:56–66. https://doi.org/10.1016/j.mib.2015.04.004

    Article  PubMed  Google Scholar 

  16. Ferguson RMW, Coulon F, Villa R (2016) Organic loading rate: a promising microbial management tool in anaerobic digestion. Water Res 100:348–356. https://doi.org/10.1016/j.watres.2016.05.009

    CAS  Article  PubMed  Google Scholar 

  17. Fountoulakis MS, Manios T (2009) Enhanced methane and hydrogen production from municipal solid waste and agro-industrial by-products co-digested with crude glycerol. Bioresour Technol 100:3043–3047. https://doi.org/10.1016/j.biortech.2009.01.016

    CAS  Article  PubMed  Google Scholar 

  18. García-Gen S, Sousbie P, Rangaraj G, Lema JM, Rodríguez J, Steyer JP, Torrijos M (2015) Kinetic modelling of anaerobic hydrolysis of solid wastes, including disintegration processes. Waste Manag 35:96–104. https://doi.org/10.1016/j.wasman.2014.10.012

    Article  PubMed  Google Scholar 

  19. Goux X, Calusinska M, Lemaigre S, Marynowska M, Klocke M, Udelhoven T, Benizri E, Delfosse P (2015) Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery. Biotechnol Biofuels 8:122. https://doi.org/10.1186/s13068-015-0309-9

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Hao L, Bize A, Conteau D, Chapleur O, Courtois S, Kroff P, Desmond-Le Quéméner E, Bouchez T, Mazéas L, Qu ED (2016) New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions. Water Res 102:158–169. https://doi.org/10.1016/j.watres.2016.06.014

    CAS  Article  PubMed  Google Scholar 

  21. de Jonge N, Moset V, Møller HB, Nielsen JL (2017) Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation. Bioresour Technol 232:313–320. https://doi.org/10.1016/j.biortech.2017.02.036

    CAS  Article  PubMed  Google Scholar 

  22. Ju F, Lau F, Zhang T (2017) Linking microbial community, environmental variables, and methanogenesis in anaerobic biogas digesters of chemically enhanced primary treatment sludge. Environ Sci Technol 51:3982–3992. https://doi.org/10.1021/acs.est.6b06344

    CAS  Article  PubMed  Google Scholar 

  23. Kampmann K, Ratering S, Geißler-Plaum R, Schmidt M, Zerr W, Schnell S (2014) Changes of the microbial population structure in an overloaded fed-batch biogas reactor digesting maize silage. Bioresour Technol 174:108–117. https://doi.org/10.1016/j.biortech.2014.09.150

    CAS  Article  PubMed  Google Scholar 

  24. Kim S, Bae J, Choi O, Ju D, Lee J, Sung H, Park S, Sang BI, Um Y (2014) A pilot scale two-stage anaerobic digester treating food waste leachate (FWL): performance and microbial structure analysis using pyrosequencing. Process Biochem 49:301–308. https://doi.org/10.1016/j.procbio.2013.10.022

    CAS  Article  Google Scholar 

  25. Kirkegaard RH, McIlroy SJ, Kristensen JM, Nierychlo M, Karst SM, Dueholm MS, Albertsen M, Nielsen PH (2017) The impact of immigration on microbial community composition in full-scale anaerobic digesters. Sci Rep 7:1–11. https://doi.org/10.1038/s41598-017-09303-0

    CAS  Article  Google Scholar 

  26. Kleyböcker A, Liebrich M, Verstraete W, Kraume M, Würdemann H (2012) Early warning indicators for process failure due to organic overloading by rapeseed oil in one-stage continuously stirred tank reactor, sewage sludge and waste digesters. Bioresour Technol 123:534–541. https://doi.org/10.1016/j.biortech.2012.07.089

    CAS  Article  PubMed  Google Scholar 

  27. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41:1–11. https://doi.org/10.1093/nar/gks808

    CAS  Article  Google Scholar 

  28. Lagkouvardos I, Fischer S, Kumar N, Clavel T (2017) Rhea: a transparent and modular R pipeline for microbial profiling based on 16S rRNA gene amplicons. PeerJ 5:e2836. https://doi.org/10.7717/peerj.2836

    Article  PubMed  PubMed Central  Google Scholar 

  29. Legendre P, Gallagher ED (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129:271–280. https://doi.org/10.1007/s004420100716

    Article  PubMed  Google Scholar 

  30. Lerm S, Kleyböcker A, Miethling-Graff R, Alawi M, Kasina M, Liebrich M, Würdemann H (2012) Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload. Waste Manag 32:389–399. https://doi.org/10.1016/j.wasman.2011.11.013

    CAS  Article  PubMed  Google Scholar 

  31. Li J, Ban Q, Zhang L, Jha AK (2012) Syntrophic propionate degradation in anaerobic digestion: a review. Int J Agric Biol 14:843–850

    CAS  Google Scholar 

  32. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:1–21. https://doi.org/10.1186/s13059-014-0550-8

    CAS  Article  Google Scholar 

  33. Mao C, Feng Y, Wang X, Ren G (2015) Review on research achievements of biogas from anaerobic digestion. Renew Sust Energ Rev 45:540–555. https://doi.org/10.1016/j.rser.2015.02.032

    CAS  Article  Google Scholar 

  34. 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 10:1571–1581. https://doi.org/10.1111/j.1462-2920.2008.01572.x

    CAS  Article  PubMed  Google Scholar 

  35. Mata-Alvarez J, Macé S, Llabrés P (2000) Anaerobic digestion of organic solid wastes. An overview of research achievements and perspectives. Bioresour Technol 74:3–16

    CAS  Article  Google Scholar 

  36. McMurdie PJ, Holmes S (2013) Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217. https://doi.org/10.1371/journal.pone.0061217

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H (2018) Vegan: community ecology package. R package version 2.4–6

  38. Orwin KH, Wardle DA (2004) New indices for quantifying the resistance and resilience of soil biota to exogenous disturbances. Soil Biol Biochem 36:1907–1912. https://doi.org/10.1016/j.soilbio.2004.04.036

    CAS  Article  Google Scholar 

  39. R Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, Austria

  40. Razaviarani V, Buchanan ID (2014) Reactor performance and microbial community dynamics during anaerobic co-digestion of municipal wastewater sludge with restaurant grease waste at steady state and overloading stages. Bioresour Technol 172:232–240. https://doi.org/10.1016/j.biortech.2014.09.046

    CAS  Article  PubMed  Google Scholar 

  41. Read S, Marzorati M, Guimarães BCM, Boon N (2011) Microbial Resource Management revisited: successful parameters and new concepts. Appl Microbiol Biotechnol 90:861–871. https://doi.org/10.1007/s00253-011-3223-5

    CAS  Article  PubMed  Google Scholar 

  42. Regueiro L, Veiga P, Figueroa M, Alonso-Gutierrez J, Stams AJM, Lema JM, Carballa M (2012) Relationship between microbial activity and microbial community structure in six full-scale anaerobic digesters. Microbiol Res 167:581–589. https://doi.org/10.1016/j.micres.2012.06.002

    CAS  Article  PubMed  Google Scholar 

  43. Regueiro L, Lema JM, Carballa M (2015) Key microbial communities steering the functioning of anaerobic digesters during hydraulic and organic overloading shocks. Bioresour Technol 197:208–216. https://doi.org/10.1016/j.biortech.2015.08.076

    CAS  Article  PubMed  Google Scholar 

  44. Rétfalvi T, Tukacs-Hájos A, Albert L, Marosvölgyi B (2011) Laboratory scale examination of the effects of overloading on the anaerobic digestion by glycerol. Bioresour Technol 102:5270–5275. https://doi.org/10.1016/j.biortech.2011.02.020

    CAS  Article  PubMed  Google Scholar 

  45. Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584. https://doi.org/10.7717/peerj.2584

    Article  PubMed  PubMed Central  Google Scholar 

  46. Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (2014) The Prokaryotes: Firmicutes and Tenericutes. Springer-Verlag, Heidelberg.

  47. Saito Y, Aoki M, Hatamoto M, Yamaguchi T (2015) Presence of a novel methanogenic archaeal lineage in anaerobic digesters inferred from mcrA and 16S rRNA gene phylogenetic analyses. J Water Environ Technol 13:279–289

    Article  Google Scholar 

  48. Shade A, Gilbert JA (2015) Temporal patterns of rarity provide a more complete view of microbial diversity. Trends Microbiol 23:335–340. https://doi.org/10.1016/j.tim.2015.01.007

    CAS  Article  PubMed  Google Scholar 

  49. Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, Huber DH, Langenheder S, Lennon JT, Martiny JBH, Matulich KL, Schmidt TM, Handelsman J (2012) Fundamentals of microbial community resistance and resilience. Front Microbiol 3:417. https://doi.org/10.3389/fmicb.2012.00417

    Article  PubMed  PubMed Central  Google Scholar 

  50. Shade A, Gregory Caporaso J, Handelsman J, Knight R, Fierer N, Caporaso JG, Handelsman J, Knight R, Fierer N (2013) A meta-analysis of changes in bacterial and archaeal communities with time. ISME J 7:1493–1506. https://doi.org/10.1038/ismej.2013.54

    Article  PubMed  PubMed Central  Google Scholar 

  51. Shin SG, Han G, Lim J, Lee C, Hwang S (2010) A comprehensive microbial insight into two-stage anaerobic digestion of food waste-recycling wastewater. Water Res 44:4838–4849. https://doi.org/10.1016/j.watres.2010.07.019

    CAS  Article  PubMed  Google Scholar 

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

    CAS  Article  PubMed  Google Scholar 

  53. Strömp C, Tindall BJ, Jarvis GN, Lünsdorf H, Moore ERB, Hippe H (1999) A re-evaluation of the taxonomy of the genus Anaerovibrio, with the reclassification of Anaerovibrio glycerini as Anaerosinus glycerini gen. nov., comb. nov., and Anaerovibrio burkinabensis as Anaeroarcus burkinensis [corrig.] gen. nov., comb. nov. Int J Syst Bacteriol 49: 1861–1872. https://doi.org/10.1099/00207713-49-4-1861

    CAS  Article  Google Scholar 

  54. Tian JH, Pourcher AM, Bureau C, Peu P (2017) Cellulose accessibility and microbial community in solid state anaerobic digestion of rape straw. Bioresour Technol 223:192–201. https://doi.org/10.1016/j.biortech.2016.10.009

    CAS  Article  PubMed  Google Scholar 

  55. Viana MB, Freitas AV, Leitão RC, Pinto GAS, Santaella ST (2012) Anaerobic digestion of crude glycerol: a review. Environ Technol Rev 1:81–92. https://doi.org/10.1080/09593330.2012.692723

    CAS  Article  Google Scholar 

  56. Wang Z, Yang ST (2013) Propionic acid production in glycerol/glucose co-fermentation by Propionibacterium freudenreichii subsp. shermanii. Bioresour Technol 137:116–123. https://doi.org/10.1016/j.biortech.2013.03.012

    CAS  Article  Google Scholar 

  57. 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 5:41. https://doi.org/10.1186/1754-6834-5-41

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  58. Zhou J, Liu W, Deng Y, Jiang Y-H, Xue K, He Z, Van Nostrand JD, Wu L, Yang Y, Wang A (2013) Stochastic assembly leads to alternative communities with distinct functions in a bioreactor microbial community. MBio 4:e00584–12-e00584–12. https://doi.org/10.1128/mBio.00584-12

  59. Ziganshina EE, Belostotskiy DE, Ilinskaya ON, Boulygina EA, Grigoryeva TV, Ziganshin AM (2015) Effect of the organic loading rate increase and the presence of zeolite on microbial community composition and process stability during anaerobic digestion of chicken wastes. Microb Ecol 70:948–960. https://doi.org/10.1007/s00248-015-0635-2

    CAS  Article  PubMed  Google Scholar 

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Acknowledgments

Computational resources were kindly provided and supported by Fundacion Pública Galega Centro Tecnolóxico de Supercomputación de Galicia (CESGA).

Funding

This research was supported by the Spanish Government (AEI) through CDTI (SmartGreenGas project, 2014-CE224). The authors belong to the Galician Competitive Research Group GRC (ED431C 2017/29) and to the CRETUS Strategic Partnership (AGUP2015/02). All these programs are co-funded by FEDER (UE). GHRB PhD fellowship is supported by CAPES (BEX-2160/2015-03) Foundation, Ministry of Education of Brazil, Brasília – DF 70040-020, Brazil.

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Correspondence to N. Fernandez-Gonzalez.

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Braz, G.H.R., Fernandez-Gonzalez, N., Lema, J.M. et al. The time response of anaerobic digestion microbiome during an organic loading rate shock. Appl Microbiol Biotechnol 102, 10285–10297 (2018). https://doi.org/10.1007/s00253-018-9383-9

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Keywords

  • 16S rRNA gene
  • Firmicutes
  • High-throughput sequencing
  • Methanoculleus
  • Microbial community
  • Organic overloading
  • Tenericutes
  • Turnover