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Microbial Ecology

, Volume 75, Issue 1, pp 113–122 | Cite as

A Combination of Stable Isotope Probing, Illumina Sequencing, and Co-occurrence Network to Investigate Thermophilic Acetate- and Lactate-Utilizing Bacteria

  • Weimin Sun
  • Valdis Krumins
  • Yiran Dong
  • Pin Gao
  • Chunyan Ma
  • Min Hu
  • Baoqin Li
  • Bingqing Xia
  • Zijun He
  • Shangling Xiong
Environmental Microbiology

Abstract

Anaerobic digestion is a complicated microbiological process that involves a wide diversity of microorganisms. Acetate is one of the most important intermediates, and interactions between acetate-oxidizing bacteria and archaea could play an important role in the formation of methane in anoxic environments. Anaerobic digestion at thermophilic temperatures is known to increase methane production, but the effects on the microbial community are largely unknown. In the current study, stable isotope probing was used to characterize acetate- and lactate-oxidizing bacteria in thermophilic anaerobic digestion. In microcosms fed 13C-acetate, bacteria related to members of Clostridium, Hydrogenophaga, Fervidobacterium, Spirochaeta, Limnohabitans, and Rhodococcus demonstrated elevated abundances of 13C-DNA fractions, suggesting their activities in acetate oxidation. In the treatments fed 13C-lactate, Anaeromyxobacter, Desulfobulbus, Syntrophus, Cystobacterineae, and Azospira were found to be the potential thermophilic lactate utilizers. PICRUSt predicted that enzymes related to nitrate and nitrite reduction would be enriched in 13C-DNA fractions, suggesting that the acetate and lactate oxidation may be coupled with nitrate and/or nitrite reduction. Co-occurrence network analysis indicated bacterial taxa not enriched in 13C-DNA fractions that may also play a critical role in thermophilic anaerobic digestion.

Keywords

Acetate oxidizing bacteria Thermophilic anaerobic digestion Stable isotope probing Illumina sequencing 

Notes

Acknowledgements

This research was funded by the High-level Leading Talent Introduction Program of GDAS, SPICC Program (2016GDASPT-0105), Construction of Innovative Talents for Pollution Control and Management of Heavy Metals in Farmland (2016B070701015), Innovation-driven Development Capability Construction Program of GDAS (2017GDASCX-0106), the Natural Science Foundation of Shanghai (17ZR1400400), the Fundamental Research Funds for the Central Universities (Donghua University), the DHU Distinguished Young Professor Program (Donghua University), and the Natural Science Foundation of Zhejiang Province (LY12C01003).

Supplementary material

248_2017_1017_MOESM1_ESM.docx (40 kb)
ESM 1 (DOCX 40 kb).

References

  1. 1.
    Narihiro T, Sekiguchi Y (2007) Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update Curr. Opin. Biotechnol. 18:273–278CrossRefPubMedGoogle Scholar
  2. 2.
    Talbot G, Topp E, Palin M, Massé D (2008) Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors Water Res. 42:513–537CrossRefPubMedGoogle Scholar
  3. 3.
    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. 72:5138–5141CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Mackie RI, Bryant MP (1981) Metabolic activity of fatty acid-oxidizing bacteria and the contribution of acetate, propionate, butyrate, and CO2 to methanogenesis in cattle waste at 40 and 60 °C Appl. Environ. Microbiol. 41:1363–1373PubMedPubMedCentralGoogle Scholar
  5. 5.
    Mountfort D, Asher R (1978) Changes in proportions of acetate and carbon dioxide used as methane precursors during the anaerobic digestion of bovine waste Appl. Environ. Microbiol. 35:648–654PubMedPubMedCentralGoogle Scholar
  6. 6.
    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:e00159–e00111CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Sasaki D, Hori T, Haruta S, Ueno Y, Ishii M, Igarashi Y (2011) Methanogenic pathway and community structure in a thermophilic anaerobic digestion process of organic solid waste J. Biosci. Bioeng. 111:41–46CrossRefPubMedGoogle Scholar
  8. 8.
    Pfennig N, Biebl H (1976) Desulfuromonas acetoxidans gen. Nov. and sp. nov., a new anaerobic, sulfur-reducing, acetate-oxidizing bacterium Arch. Microbiol. 110:3–12CrossRefPubMedGoogle Scholar
  9. 9.
    Caccavo F, Lonergan DJ, Lovley DR, Davis M, Stolz JF, McInerney MJ (1994) Geobacter sulfurreducens sp. nov., a hydrogen-and acetate-oxidizing dissimilatory metal-reducing microorganism Appl. Environ. Microbiol. 60:3752–3759PubMedPubMedCentralGoogle Scholar
  10. 10.
    Hobson PN, Wheatley AD (1993) Anaerobic digestion: modern theory and practice. Elsevier Applied Science, London, Google Scholar
  11. 11.
    McHugh S, Carton M, Mahony T, O'Flaherty V (2003) Methanogenic population structure in a variety of anaerobic bioreactors FEMS Microbiol. Lett. 219:297–304CrossRefPubMedGoogle Scholar
  12. 12.
    Zinder S, Anguish T, Cardwell S (1984) Effects of temperature on methanogenesis in a thermophilic (58 °C) anaerobic digester Appl. Environ. Microbiol. 47:808–813PubMedPubMedCentralGoogle Scholar
  13. 13.
    De la Rubia M, Riau V, Raposo F, Borja R (2013) Thermophilic anaerobic digestion of sewage sludge: focus on the influence of the start-up. A review Crit. Rev. Biotechnol. 33:448–460CrossRefPubMedGoogle Scholar
  14. 14.
    Khemkhao M, Nuntakumjorn B, Techkarnjanaruk S, Phalakornkule C (2012) UASB performance and microbial adaptation during a transition from mesophilic to thermophilic treatment of palm oil mill effluent J. Environ. Manag. 103:74–82CrossRefGoogle Scholar
  15. 15.
    Hattori S, Kamagata Y, Hanada S, Shoun H (2000) Thermacetogenium phaeum gen. Nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium Int. J. Syst. Evol. Microbiol. 50:1601–1609CrossRefPubMedGoogle Scholar
  16. 16.
    Imachi H, Sekiguchi Y, Kamagata Y, Hanada S, Ohashi A, Harada H (2002) Pelotomaculum thermopropionicum gen. Nov., sp. nov., an anaerobic, thermophilic, syntrophic propionate-oxidizing bacterium Int. J. Syst. Evol. Microbiol. 52:1729–1735PubMedGoogle Scholar
  17. 17.
    Héry M, Rizoulis A, Sanguin H, Cooke DA, Pancost RD, Polya DA, Lloyd JR (2015) Microbial ecology of arsenic—mobilizing Cambodian sediments: lithological controls uncovered by stable isotope probing Environ. Microbiol. 17:1857–1869CrossRefPubMedGoogle Scholar
  18. 18.
    Dumont MG, Murrell JC (2005) Stable isotope probing—linking microbial identity to function Nat. Rev. Microbiol. 3:499–504CrossRefPubMedGoogle Scholar
  19. 19.
    Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology Nature 403:646–649CrossRefPubMedGoogle Scholar
  20. 20.
    Sun W, Yu G, Louie T, Liu T, Zhu C, Xue G, Gao P (2015) From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples Appl. Microbiol. Biotechnol. 99:10271–10282CrossRefPubMedGoogle Scholar
  21. 21.
    Lovley DR, Holmes DE, Nevin KP (2004) Dissimilatory Fe(III) and Mn (IV) reduction Adv. Microb. Physiol. 49:219–286CrossRefPubMedGoogle Scholar
  22. 22.
    Liu T, Ahn H, Sun W, McGuinness LR, Kerkhof LJ, Häggblom MM (2016) Identification of a Ruminococcaceae species as the methyl tert-butyl ether (MTBE) degrading bacterium in a methanogenic consortium Environ. Sci. Technol. 50:1455–1464CrossRefPubMedGoogle Scholar
  23. 23.
    Sun W, Li Y, McGuinness LR, Luo S, Huang W, Kerkhof LJ, Mack EE, Häggblom MM, Fennell DE (2015) Identification of anaerobic aniline-degrading bacteria at a contaminated industrial site Environ. Sci. Technol. 49:11079–11088CrossRefPubMedGoogle Scholar
  24. 24.
    Seyler LM, McGuinness LM, Kerkhof LJ (2014) Crenarchaeal heterotrophy in salt marsh sediments ISME J. 8:1534–1543CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Tuorto SJ, Darias P, McGuinness LR, Panikov N, Zhang T, Häggblom MM, Kerkhof LJ (2013) Bacterial genome replication at subzero temperatures in permafrost ISME J. 8:139–149CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R (2011) Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample Proc. Natl. Acad. Sci. U.S.A. 108:4516–4522CrossRefPubMedGoogle Scholar
  27. 27.
    Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E (2011) Chimeric 16S rRNA sequence formation and detection in sanger and 454-pyrosequenced PCR amplicons Genome Res. 21:494–504CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    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. 72:5069–5072CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Thurber RLV, Knight R (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences Nat. Biotechnol. 31:814–821CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Blankenberg D, Kuster GV, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 19.10. 1–19.10. 21Google Scholar
  31. 31.
    Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J (2005) Galaxy: a platform for interactive large-scale genome analysis Genome Res. 15:1451–1455CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    Goecks J, Nekrutenko A, Taylor J (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Genome Biol. 11:R86CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Cleary DF, Becking LE, Voogd NJ, Pires AC, Polónia AR, Egas C, Gomes N (2013) Habitat-and host-related variation in sponge bacterial symbiont communities in Indonesian waters FEMS Microbiol. Ecol. 85:465–482CrossRefPubMedGoogle Scholar
  34. 34.
    Newman ME (2006) Modularity and community structure in networks Proc. Natl. Acad. Sci. U.S.A. 103:8577–8582CrossRefPubMedPubMedCentralGoogle Scholar
  35. 35.
    Newman ME (2003) The structure and function of complex networks SIAM Rev. 45:167–256CrossRefGoogle Scholar
  36. 36.
    Csardi G, Nepusz T (2006) The igraph software package for complex network research Int J Complex Syst. 1695:1–9Google Scholar
  37. 37.
    Barberan A, Bates ST, Casamayor EO, Fierer N (2012) Using network analysis to explore co-occurrence patterns in soil microbial communities ISME J. 6:343–351CrossRefPubMedGoogle Scholar
  38. 38.
    Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof F-M, Boon N, Bodelier PL (2016) Biotic interactions in microbial communities as modulators of biogeochemical processes: methanotrophy as a model system Front. Microbiol. 7:1285CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Li B, Yang Y, Ma L, Ju F, Guo F, Tiedje JM, Zhang T (2015) Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes ISME J. 9:2490–2502CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Montoya JM, Pimm SL, Solé RV (2006) Ecological networks and their fragility Nature 442:259–264CrossRefPubMedGoogle Scholar
  41. 41.
    Lupatini M, Suleiman AK, Jacques RJ, Antoniolli ZI, de Siqueira FA, Kuramae EE, Roesch LF (2014) Network topology reveals high connectance levels and few key microbial genera within soils Front. Environ. Sci. 2:10CrossRefGoogle Scholar
  42. 42.
    Schnürer A, Schink B, Svensson BH (1996) Clostridium ultunense sp. nov., a mesophilic bacterium oxidizing acetate in syntrophic association with a hydrogenotrophic methanogenic bacterium Int. J. Syst. Evol. Microbiol. 46:1145–1152Google Scholar
  43. 43.
    Schnürer A, Svensson BH, Schink B (1997) Enzyme activities in and energetics of acetate metabolism by the mesophilic syntrophically acetate-oxidizing anaerobe Clostridium ultunense FEMS Microbiol. Lett. 154:331–336CrossRefGoogle Scholar
  44. 44.
    Ng TK, Ben-Bassat A, Zeikus J (1981) Ethanol production by thermophilic bacteria: fermentation of cellulosic substrates by cocultures of Clostridium thermocellum and Clostridium thermohydrosulfuricum Appl. Environ. Microbiol. 41:1337–1343PubMedPubMedCentralGoogle Scholar
  45. 45.
    Bouanane-Darenfed A, Fardeau M-L, Grégoire P, Joseph M, Kebbouche-Gana S, Benayad T, Hacene H, Cayol J-L, Ollivier B (2011) Caldicoprobacter algeriensis sp. nov. a new thermophilic anaerobic, xylanolytic bacterium isolated from an Algerian hot spring Curr. Microbiol. 62:826–832CrossRefPubMedGoogle Scholar
  46. 46.
    Friedrich AB, Antranikian G (1996) Keratin degradation by Fervidobacterium pennavorans, a novel thermophilic anaerobic species of the order thermotogales Appl. Environ. Microbiol. 62:2875–2882PubMedPubMedCentralGoogle Scholar
  47. 47.
    Willems A, Busse J, Goor M, Pot B, Falsen E, Jantzen E, Hoste B, Gillis M, Kersters K, Auling G (1989) Hydrogenophaga, a new genus of hydrogen-oxidizing bacteria that includes Hydrogenophaga flava comb. nov. (formerly Pseudomonas flava), Hydrogenophaga palleronii (formerly Pseudomonas palleronii), Hydrogenophaga pseudoflava (formerly Pseudomonas pseudoflava and “Pseudomonas carboxydoflava”), and Hydrogenophaga taeniospiralis (formerly Pseudomonas taeniospiralis) Int. J. Syst. Evol. Microbiol. 39:319–333Google Scholar
  48. 48.
    Kimura Z-I, Okabe S (2013) Acetate oxidation by syntrophic association between Geobacter sulfurreducens and a hydrogen-utilizing exoelectrogen ISME J. 7:1472–1482CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Plugge CM, Zoetendal EG, Stams A (2000) Caloramator coolhaasii sp. nov., a glutamate-degrading, moderately thermophilic anaerobe Int. J. Syst. Evol. Microbiol. 50:1155–1162CrossRefPubMedGoogle Scholar
  50. 50.
    Seyfried M, Lyon D, Rainey FA, Wiegel J (2002) Caloramator viterbensis sp. nov., a novel thermophilic, glycerol-fermenting bacterium isolated from a hot spring in Italy Int. J. Syst. Evol. Microbiol. 52:1177–1184PubMedGoogle Scholar
  51. 51.
    Tarlera S, Muxí L, Soubes M, Stams AJ (1997) Caloramator proteoclasticus sp. nov., a new moderately thermophilic anaerobic proteolytic bacterium Int. J. Syst. Evol. Microbiol. 47:651–656Google Scholar
  52. 52.
    Zhilina T, Zavarzina D, Kolganova T, Tourova T, Zavarzin G (2005) “Candidatus Contubernalis alkalaceticum,” an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum Microbiology 74:695–703CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2017

Authors and Affiliations

  1. 1.Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and ManagementGuangdong Institute of Eco-environment Science and TechnologyGuangzhouChina
  2. 2.Department of Environmental SciencesRutgers UniversityNew BrunswickUSA
  3. 3.Carl R. Woese Institute for Genomic BiologyUniversity of Illinois, Urbana-ChampaignUrbanaUSA
  4. 4.College of Environmental Science and Engineering, State Environmental Protection Engineering Center for Pollution Treatment and Control in Textile IndustryDonghua UniversityShanghaiChina
  5. 5.Biological and Environmental CollegeZhejiang Wanli UniversityNingboChina

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