Bacterial communities involved directly or indirectly in the anaerobic degradation of cellulose

  • Yuanyuan Bao
  • Jan Dolfing
  • Baozhan Wang
  • Ruirui Chen
  • Miansong Huang
  • Zhongpei Li
  • Xiangui Lin
  • Youzhi FengEmail author
Original Paper


To determine bacterial communities involved, directly or indirectly, in the anaerobic degradation of cellulose, we conducted a microcosm experiment with soil treated with 13C-cellulose, 12C-cellulose, or without cellulose with analyses of DNA-based stable isotope probing (DNA-SIP), real-time quantitative PCR, and high-throughput sequencing. Firmicutes, Actinobacteria, Verrucomicrobia, and Fibrobacteres were the dominant bacterial phyla-degrading cellulose. Generally, bacteria possessing gene-encoding enzymes involved in the degradation of cellulose and hemicellulose were stimulated. Phylotypes affiliated to Geobacter were also stimulated by cellulose, probably due to their role in electron transfer. Nitrogen-fixing bacteria were also detected, probably due to the decreased N availability during cellulose degradation. High-throughput sequencing showed the presence of bacteria not incorporating 13C and probably involved in the priming effect caused by the addition of cellulose to soil. Collectively, our findings revealed that a more diverse microbial community than expected directly and indirectly participated in anaerobic cellulose degradation.


Cellulose degradation Paddy soil Cellulolytic bacteria Syntrophic microorganisms Nitrogen-fixing bacteria Priming effect 



The authors thank Ms. Yushan Zhan for her assistance of material preparation before the experiment. Authors also thank Editor-in-Chief Prof. Paolo Nannipieri and three anonymous reviewers for their constructive comments and suggestions, which greatly improved the manuscript.


This work was supported by the National Natural Science Foundation of China (Project Nos. 41430859, 41771294, 41671267, and 41471208), the CAS Strategic Priority Research Program Grant (Project No. XDB15020103), National Key R&D Program (2016YFD0200306), Research Program for Key Technologies of Sponge City Construction and Management in Guyuan City (Grant No. SCHM-2018), and Knowledge Innovation Program of Chinese Academy of Sciences (Grant No. ISSASIP1639).

Supplementary material

374_2019_1342_MOESM1_ESM.docx (200 kb)
ESM 1 (DOCX 199 kb)
374_2019_1342_MOESM2_ESM.xlsx (12 kb)
Supplementary Table S2 (XLSX 11 kb)


  1. Akiyama H, Tsuruta H (2003) Effect of organic matter application on N2O, NO, and NO2 fluxes from an Andisol field. Global Biogeochem Cy 17:1100CrossRefGoogle Scholar
  2. Anderson MJ, Walsh DCI (2013) PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: what null hypothesis are you testing? Ecol Monogr 83:557–574CrossRefGoogle Scholar
  3. Bengtsson G, Bengtson P, Mansson KF (2003) Gross nitrogen mineralization-, immobilization-, and nitrification rates as a function of soil C/N ratio and microbial activity. Soil Biol Biochem 35:143–154CrossRefGoogle Scholar
  4. Bernard L, Mougel C, Maron PA, Nowak V, Lévêque J, Henault C, Haichar FZ, Berge O, Marol C, Balesdent J (2007) Dynamics and identification of soil microbial populations actively assimilating carbon from 13C-labelled wheat residue as estimated by DNA- and RNA-SIP techniques. Environ Microbiol 9:752–764CrossRefGoogle Scholar
  5. Bingeman CW, Varner JE, Martin WP (1953) The effect of the addition of organic materials on the decomposition of an organic soil. Soil Sci Soc Am J 17:34–38CrossRefGoogle Scholar
  6. Brune A, Frenzel P, Cypionka H (2000) Life at the oxic-anoxic interface: microbial activities and adaptations. FEMS Microbiol Rev 24:691–710CrossRefGoogle Scholar
  7. Chatzinotas A, Schellenberger S, Glaser K, Kolb S (2013) Assimilation of cellulose-derived carbon by microeukaryotes in oxic and anoxic slurries of an aerated soil. Appl Environ Microb 79:5777–5781CrossRefGoogle Scholar
  8. Choi SY (2003) Distribution of alcohol-tolerant microfungi in paddy field soils. Mycobiology 31:191–195CrossRefGoogle Scholar
  9. Clément JC, Shrestha J, Ehrenfeld JG, Jaffé PR (2005) Ammonium oxidation coupled to dissimilatory reduction of iron under anaerobic conditions in wetland soils. Soil Biol Biochem 37:2323–2328CrossRefGoogle Scholar
  10. Coutinho PM, Andersen MR, Kolenova K, Vankuyk PA, Benoit I, Gruben BS, Trejoaguilar B, Visser H, Van SP, Pakula T (2009) Post-genomic insights into the plant polysaccharide degradation potential of Aspergillus nidulans and and Aspergillus oryzae. Fungal Genet Biol 46:S161–S169CrossRefGoogle Scholar
  11. Dumont MG, Pommerenke B, Casper P, Conrad R (2011) DNA-, rRNA- and mRNA-based stable isotope probing of aerobic methanotrophs in lake sediment. Environ Microbiol 13:1153–1167CrossRefGoogle Scholar
  12. Edgar RC (2013) UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods 10:996–998CrossRefGoogle Scholar
  13. España M, Rasche F, Kandeler E, Brune T, Rodriguez B, Bending GD, Cadisch G (2011) Identification of active bacteria involved in decomposition of complex maize and soybean residues in a tropical Vertisol using 15N-DNA stable isotope probing. Pedobiologia 54:187–193CrossRefGoogle Scholar
  14. Fan F, Yin C, Tang Y, Li Z, Song A, Wakelin SA, Zou J, Liang Y (2014) Probing potential microbial coupling of carbon and nitrogen cycling during decomposition of maize residue by 13C-DNA-SIP. Soil Biol Biochem 70:12–21CrossRefGoogle Scholar
  15. Feng Y, Lin X, Yu Y, Zhang H, Chu H, Zhu J (2013) Elevated ground-level O3 negatively influences paddy methanogenic archaeal community. Sci Rep 3:3193CrossRefGoogle Scholar
  16. Feng YZ, Chen RR, Hu JL, Zhao F, Wang JH, Chu HY, Zhang JB, Dolfing J, Lin XG (2015) Bacillus asahii comes to the fore in organic manure fertilized alkaline soils. Soil Biol Biochem 81:186–194CrossRefGoogle Scholar
  17. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E (2012) Microbial degradation of complex carbohydrates in the gut. Gut Microbes 3:289–306CrossRefGoogle Scholar
  18. Fontaine S, Mariotti A, Abbadie L (2003) The priming effect of organic matter: a question of microbial competition? Soil Biol Biochem 35:837–843CrossRefGoogle Scholar
  19. Fontaine S, Bardoux G, Benest D, Verdier B, Mariotti A, Abbadie L (2004) Mechanisms of the priming effect in a savannah soil amended with cellulose. Soil Sci Soc Am J 68:125–131CrossRefGoogle Scholar
  20. Haichar FEZ, Achouak W, Christen R, Heulin T, Marol C, Marais MF, Mougel C, Ranjard L, Balesdent J, Berge O (2007) Identification of cellulolytic bacteria in soil by stable isotope probing. Environ Microbiol 9:625–634CrossRefGoogle Scholar
  21. Hori T, Muller A, Igarashi Y, Conrad R, Friedrich MW (2010) Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing. ISME J 4:267–278Google Scholar
  22. Huang Y, Zou J, Zheng X, Wang Y, Xu X (2004) Nitrous oxide emissions as influenced by amendment of plant residues with different C:N ratios. Soil Biol Biochem 36:973–981CrossRefGoogle Scholar
  23. Jia ZJ, Conrad R (2009) Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11:1658–1671CrossRefGoogle Scholar
  24. Kato S, Hashimoto K, Watanabe K (2012) Methanogenesis facilitated by electric syntrophy via (semi)conductive iron-oxide minerals. Environ Microbiol 14:1646–1654CrossRefGoogle Scholar
  25. Li Y, Lee CG, Watanabe T, Murase J, Asakawa S, Kimura M (2011) Identification of microbial communities that assimilate substrate from root cap cells in an aerobic soil using a DNA-SIP approach. Soil Biol Biochem 43:1928–1935CrossRefGoogle Scholar
  26. Li Y, Yu S, Strong J, Wang H (2012a) Are the biogeochemical cycles of carbon, nitrogen, sulfur, and phosphorus driven by the “FeIII-FeII redox wheel” in dynamic redox environments? J Soils Sediments 12:683–693CrossRefGoogle Scholar
  27. Li Y, Watanabe T, Asakawa S, Kimura M (2012b) Bacterial communities that decompose root cap cells in an anaerobic soil: estimation by DNA-SIP method using rice plant callus cells. Soil Sci Plant Nutr 58:297–308CrossRefGoogle Scholar
  28. Li JB, Rui JP, Pei ZJ, Sun XR, Zhang SH, Yan ZY, Wang YP, Liu XF, Zheng T, Li XZ (2014) Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure. Appl Microbiol Biotechnol 98:4771–4780CrossRefGoogle Scholar
  29. Li HJ, Chang JL, Liu PF, Fu L, Ding DW, Lu YH (2015) Direct interspecies electron transfer accelerates syntrophic oxidation of butyrate in paddy soil enrichments. Environ Microbiol 17:1533–1547CrossRefGoogle Scholar
  30. Liesack W, Schnell S, Revsbech NP (2000) Microbiology of flooded rice paddies. FEMS Microbiol Rev 24:625–645CrossRefGoogle Scholar
  31. Luo F, Devine CE, Edwards EA (2016) Cultivating microbial dark matter in benzene-degrading methanogenic consortia. Environ Microbiol 18:2923–2936CrossRefGoogle Scholar
  32. Magoc T, Salzberg SL (2011) FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963CrossRefGoogle Scholar
  33. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12CrossRefGoogle Scholar
  34. Millar N, Baggs EM (2005) Relationships between N2O emissions and water-soluble C and N contents of agroforestry residues after their addition to soil. Soil Biol Biochem 37:605–608CrossRefGoogle Scholar
  35. Miron J, Ben-Ghedalia D (1992) The degradation and utilization of wheat-straw cell-wall monosaccharide components by defined ruminal cellulolytic bacteria. Appl Microbiol Biot 38:432–437CrossRefGoogle Scholar
  36. Moon YH, Iakiviak M, Bauer S, Mackie RI, Cann IKO (2011) Biochemical analyses of multiple endoxylanases from the rumen bacterium Ruminococcus albus 8 and their synergistic activities with accessory hemicellulose-degrading enzymes. Appl Environ Microb 77:5157–5169CrossRefGoogle Scholar
  37. Neufeld JD, Dumont MG, Vorha J, Murrell JC (2007) Methodological considerations for the use of stable isotope probing in microbial ecology. Microb Ecol 53:435–442CrossRefGoogle Scholar
  38. Nottingham AT, Hicks LC, Ccahuana AJ, Salinas N, Bååth E, Meir P (2018) Nutrient limitations to bacterial and fungal growth during cellulose decomposition in tropical forest soils. Biol Fertil Soils 54:219–228Google Scholar
  39. Ozbayram EG, Kleinsteuber S, Nikolausz M, Ince B, Ince O (2017) Effect of bioaugmentation by cellulolytic bacteria enriched from sheep rumen on methane production from wheat straw. Anaerobe 46:122–130CrossRefGoogle Scholar
  40. Paul EA, Clark FE (1989) Soil microbiology and biochemistry. Academic Press, London, pp 93–97Google Scholar
  41. Pérez J, Muñozdorado J, De lRT, Martínez J (2002) Biodegradation and biological treatments of cellulose, hemicellulose and lignin: an overview. Int Microbiol 5:53–63CrossRefGoogle Scholar
  42. Reichenbach H, Lang E, Schumann P, Spröer C (2006) Byssovorax cruenta gen. nov., sp. nov., nom. rev., a cellulose-degrading myxobacterium: rediscovery of ‘Myxococcus cruentus’ Thaxter 1897. Int J Syst Evol Microbiol 56:2357–2363CrossRefGoogle Scholar
  43. Richmond PA (1991) Occurrence and functions of native cellulose. In: Haigler CH, Weimer JP (eds) Biosynthesis and biodegradation of cellulose. Dekker, New York, pp 5–23Google Scholar
  44. Rotaru AE, Shrestha PM, Liu F, Markovaite B, Chen S, Nevin KP, Lovley DR (2014) Direct interspecies electron transfer between Geobacter metallireducens and Methanosarcina barkeri. Appl Environ Microb 80:4599–4605CrossRefGoogle Scholar
  45. Rui JP, Peng JJ, Lu YH (2009) Succession of bacterial populations during plant residue decomposition in rice field soil. Appl Environ Microb 75:4879–4886CrossRefGoogle Scholar
  46. Ruppel S, Torsvik V, Daae FL, Øvreås L, Rühlmann J (2007) Nitrogen availability decreases prokaryotic diversity in sandy soils. Biol Fertil Soils 43:449–459CrossRefGoogle Scholar
  47. Saiz-Jimenez C (1996) The chemical structure of humic substances: recent advances. In: Piccolo A (ed) Humic substances in terrestrial ecosystems. Elsevier, Amsterdam, pp 1–45Google Scholar
  48. Schöler A, Jacquiod S, Vestergaard G, Schulz S, Schloter M (2017) Analysis of soil microbial communities based on amplicon sequencing of marker genes. Biol Fertil Soils 53:485–489CrossRefGoogle Scholar
  49. Seneviratne G (2000) Litter quality and nitrogen release in tropical agriculture: a synthesis. Biol Fertil Soils 31:60–64CrossRefGoogle Scholar
  50. Shan J, Yan XY (2013) Effects of crop residue returning on nitrous oxide emissions in agricultural soils. Atmos Environ 71:170–175CrossRefGoogle Scholar
  51. Shaw AK, Halpern AL, Beeson K, Tran B, Venter JC, Martiny JBH (2008) It’s all relative: ranking the diversity of aquatic bacterial communities. Environ Microbiol 10:2200–2210CrossRefGoogle Scholar
  52. Shrestha PM, Rotaru AE, Summers ZM, Shrestha M, Liu F, Lovley DR (2013) Transcriptomic and genetic analysis of direct interspecies electron transfer. Appl Environ Microbiol 79:2397–2404CrossRefGoogle Scholar
  53. Smith SA, Hughes E, Coats ER, Brinkman CK, McDonald AG, Harper JR, Feris K, Newby D (2016) Toward sustainable dairy waste utilization: enhanced VFA and biogas synthesis via upcycling algal biomass cultured on waste effluent. J Chem Technol Biot 91:113–121CrossRefGoogle Scholar
  54. Sun W, Krumins V, Dong Y, Gao P, Ma C, Hu M, Li B, Xia B, He Z, Xiong S (2017) A combination of stable isotope probing, illumina sequencing, and co-occurrence network to investigate thermophilic acetate- and lactate-utilizing bacteria. Microb Ecol 75:113–122CrossRefGoogle Scholar
  55. Vestergaard G, Schulz S, Schöler A, Schloter M (2017) Making big data smart—how to use metagenomics to understand soil quality. Biol Fertil Soils 53:479–484CrossRefGoogle Scholar
  56. Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microb 73:5261–5267CrossRefGoogle Scholar
  57. Wartiainen I, Eriksson T, Zheng W, Rasmussen U (2008) Variation in the active diazotrophic community in rice paddy-nifH PCR-DGGE analysis of rhizosphere and bulk soil. Appl Soil Ecol 39:65–75CrossRefGoogle Scholar
  58. Wegner CE, Liesack W (2016) Microbial community dynamics during the early stages of plant polymer breakdown in paddy soil. Environ Microbiol 18:2825–2842CrossRefGoogle Scholar
  59. Xiang X, Huang Y, Madey G, Cabaniss S, Arthurs L, Maurice P (2010) Modeling the evolution of natural organic matter in the environment with an agent-based stochastic approach. Nat Resour Model 19:67–90CrossRefGoogle Scholar
  60. Yi W, You J, Zhu C, Wang B, Qu D (2013) Diversity, dynamic and abundance of Geobacteraceae species in paddy soil following slurry incubation. Eur J Soil Biol 56:11–18CrossRefGoogle Scholar
  61. Zgadzaj R, Garrido-Oter R, Jensen DB, Koprivova A, Schulze-Lefert P, Radutoiu S (2016) Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities. Proc Natl Acad Sci U S A 113:E7996–E8005CrossRefGoogle Scholar
  62. Zhuang L, Tang J, Wang YQ, Hu M, Zhou SG (2015) Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation. J Hazard Mater 293:37–45CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Yuanyuan Bao
    • 1
    • 2
  • Jan Dolfing
    • 3
  • Baozhan Wang
    • 1
  • Ruirui Chen
    • 1
  • Miansong Huang
    • 4
  • Zhongpei Li
    • 1
  • Xiangui Lin
    • 1
  • Youzhi Feng
    • 1
    Email author
  1. 1.State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingPeople’s Republic of China
  2. 2.University of Chinese Academy of SciencesBeijingPeople’s Republic of China
  3. 3.School of Engineering, Newcastle UniversityNewcastle-upon-TyneUK
  4. 4.Beijing Capital Co., LTDBeijingPeople’s Republic of China

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