Current Microbiology

, Volume 75, Issue 5, pp 541–549 | Cite as

PCR–DGGE Analysis on Microbial Community Structure of Rural Household Biogas Digesters in Qinghai Plateau

  • Rui Han
  • Yongze Yuan
  • Qianwen Cao
  • Quanhui Li
  • Laisheng Chen
  • Derui Zhu
  • Deli Liu


To investigate contribution of environmental factor(s) to microbial community structure(s) involved in rural household biogas fermentation at Qinghai Plateau, we collected slurry samples from 15 digesters, with low-temperature working conditions (11.1–15.7 °C) and evenly distributed at three counties (Datong, Huangyuan, and Ledu) with cold plateau climate, to perform polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) and further sequencing. The bacterial communities in the total 15 digesters were classified into 38 genera with Mangroviflexus (12.1%) as the first dominant, and the archaeal communities into ten genera with Methanogenium (38.5%) as the most dominant. For each county, the digesters with higher biogas production, designated as HP digesters, exclusively had 1.6–3.1 °C higher fermentation temperature and the unique bacterial structure composition related, i.e., unclassified Clostridiales for all the HP digesters and unclassified Marinilabiliaceae and Proteiniclasticum for Ledu HP digesters. Regarding archaeal structure composition, Methanogenium exhibited significantly higher abundances at all the HP digesters and Thermogymnomonas was the unique species only identified at Ledu HP digesters with higher-temperature conditions. Redundancy analysis also confirmed the most important contribution of temperature to the microbial community structures investigated. This report emphasized the correlation between temperature and specific microbial community structure(s) that would benefit biogas production of rural household digesters at Qinghai Plateau.



This work was supported by the National Natural Science Foundation of China (31560039), the Applied Basic Research Program of Qinghai Province (2015-ZJ-730), the Natural Science Foundation of Qinghai Province (2015-ZJ-929Q), and Qinghai Special Project for Key Science and Technology (2016-NK-A8).

Compliance with Ethical Standards

Conflict of interest

All authors declare that they have no conflict of interest.

Supplementary material

284_2017_1414_MOESM1_ESM.doc (195 kb)
Supplementary material 1 (DOC 195 KB)


  1. 1.
    Akyol Ç, Aydin S, Ince O, Ince B (2016) A comprehensive microbial insight into single-stage and two-stage anaerobic digestion of oxytetracycline-medicated cattle manure. Chem Eng J 303:675–684CrossRefGoogle Scholar
  2. 2.
    Alvarez R, Villca S, Lidén G (2006) Biogas production from llama and cow manure at high altitude. Biomass Bioenergy 30:66–75CrossRefGoogle Scholar
  3. 3.
    Aydin S (2016) Enhanced biodegradation of antibiotic combinations via the sequential treatment of the sludge resulting from pharmaceutical wastewater treatment using white-rot fungi Trametes versicolor and Bjerkandera adusta. Appl Microbiol Biotechnol 100:1–9CrossRefGoogle Scholar
  4. 4.
    Aydin S, Shahi A, Ozbayram EG, Ince B, Ince O (2015) Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations. Bioresour Technol 192:735–740CrossRefPubMedGoogle Scholar
  5. 5.
    Budzianowski WM, Postawa K (2017) Renewable energy from biogas with reduced carbon dioxide footprint: implications of applying different plant configurations and operating pressures. Renew Sustain Energy Rev 68:852–868CrossRefGoogle Scholar
  6. 6.
    Cahyani VR, Murase J, Ishibashi E, Asakawa S, Kimura M (2007) Bacterial communities in manganese nodules in rice field subsoils: estimation using PCR-DGGE and sequencing analyses. Soil Sci Plant Nutr 53:575–584CrossRefGoogle Scholar
  7. 7.
    Chen Y, Hu W, Feng YZ, Sweeney S (2014) Status and prospects of rural biogas development in China. Renew Sustain Energy Rev 39:679–685CrossRefGoogle Scholar
  8. 8.
    Chen Z, Wang YP, Xia D, Jiang XL, Fu D, Shen L, Wang HT, Li QB (2016) Enhanced bioreduction of iron and arsenic in sediment by biochar amendment influencing microbial community composition and dissolved organic matter content and composition. J Hazard Mater 311:20–29CrossRefPubMedGoogle Scholar
  9. 9.
    Collins DS, Avdis A, Allison PA, Johnson HD, Hill J, Piggott MD, Hassan MHA, Damit AR (2017) Tidal dynamics and mangrove carbon sequestration during the Oligo–Miocene in the South China Sea. Nat Commun 8:1–12CrossRefGoogle Scholar
  10. 10.
    Dias MF, Colturato LF, de Oliveira JP, Leite LR, Oliveira G, Chernicharo CA, de Araújo JC (2016) Metagenomic analysis of a desulphurisation system used to treat biogas from vinasse methanisation. Bioresour Technol 205:58–66CrossRefPubMedGoogle Scholar
  11. 11.
    Ding WX, Stewart DI, Humphreys PN, Rout SP, Burke I (2016) Role of an organic carbon-rich soil and Fe(III) reduction in reducing the toxicity and environmental mobility of chromium (VI) at a COPR disposal site. Sci Total Environ 541:1191–1199CrossRefPubMedGoogle Scholar
  12. 12.
    Dong MH, Wu Y, Li QM, Tian GL, Yang B, Li YJ, Zhang LJ, Wang YX, Xiao W, Yin F, Zhao XL, Zhang WD, Cui XL (2015) Investigation of methanogenic community structures in rural biogas digesters from different climatic regions in Yunnan, southwest China. Curr Microbiol 70:679–684CrossRefPubMedGoogle Scholar
  13. 13.
    Feng Y, Guo Y, Yang G, Qin X, Song Z (2012) Household biogas development in rural China: on policy support and other macro sustainable conditions. Renew Sustain Energy Rev 16:5617–5624CrossRefGoogle Scholar
  14. 14.
    Fliegerova K, Tapio I, Bonin A, Mrazek J, Callegari ML, Bani P, Bayat A, Vilkki J, Kopečný J, Shingfield KJ, Boyer F, Coissac E, Taberlet P, Wallace RJ (2014) Effect of DNA extraction and sample preservation method on rumen bacterial population. Anaerobe 29:80–84CrossRefPubMedGoogle Scholar
  15. 15.
    Franke-whittle IH, Goberna M, Insam H (2009) Design and testing of real-time PCR primers for the quantification of Methanoculleus, Methanosarcina, Methanothermobacter, and a group of uncultured methanogens. Can J Microbiol 55:611–616CrossRefPubMedGoogle Scholar
  16. 16.
    Franzmann PD, Liu Y, Balkwill DL, Aldrich HC, Conway de Macario E, Boone DR (1997) Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica. Int J Syst Bacteriol 47:1068–1072CrossRefPubMedGoogle Scholar
  17. 17.
    Friha I, Karray F, Feki F, Jlaiel L, Sayadi S (2014) Treatment of cosmetic industry wastewater by submerged membrane bioreactor with consideration of microbial community dynamics. Int Biodeterior Biodegradation 88:125–133CrossRefGoogle Scholar
  18. 18.
    Gao YM, Yang AY, Bao J, Ma RX, Yan L, Wang YJ, Wang WD (2017) Bioreactor performance and microbial community dynamics in a production-scale biogas plant in northeastern China. Int J Agric Biol Eng 10:191–201Google Scholar
  19. 19.
    Garcia SL (2016) Mixed cultures as model communities: hunting for ubiquitous microorganisms, their partners, and interactions. Aquat Microb Ecol 77:79–85CrossRefGoogle Scholar
  20. 20.
    Garfí M, Ferrer-Martí L, Velo E, Ferrer I (2012) Evaluating benefits of low-cost household digesters for rural Andean communities. Renew Sustain Energy Rev 16:575–581CrossRefGoogle Scholar
  21. 21.
    Hampl V, Pavlicek A, Flegr J (2001) Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with freeware program FreeTree: application to trichomonad parasites. Int J Syst Evol Microbiol 51:731e5CrossRefGoogle Scholar
  22. 22.
    Hao XD, Liang YL, Yin HQ, Liu HW, Zeng WM, Liu XD (2017) Thin-layer heap bioleaching of copper flotation tailings containing high levels of fine grains and microbial community succession analysis. Int J Miner Metall Mater 24:360–368CrossRefGoogle Scholar
  23. 23.
    Kushkevych I, Vítězová M, Vítěz T, Bartoš M (2017) Production of biogas: relationship between methanogenic and sulfate-reducing microorganisms. Open Life Sci 12:82–91Google Scholar
  24. 24.
    Lai Q, Shao Z (2008) Pseudomonas xiamenensis sp. nov., a denitrifying bacterium isolated from activated sludge. Int J Syst Evol Micr 58:1911–1915CrossRefGoogle Scholar
  25. 25.
    Li J, Zhang L, Ban Q, Jha AK, Xu Y (2013) Diversity and distribution of methanogenic archaea in an anaerobic baffled reactor (ABR) treating sugar refinery wastewater. J Microbiol Biotechnol 23:137–143CrossRefPubMedGoogle Scholar
  26. 26.
    Li L, He Q, Ma Y, Wang XM, Peng XY (2016) A mesophilic anaerobic digester for treating food waste: process stability and microbial community analysis using pyrosequencing. Microb Cell Fact 15:65CrossRefPubMedPubMedCentralGoogle Scholar
  27. 27.
    Liu WZ, He ZW, Yang CX, Zhou AJ, Guo ZC, Liang B, Varrone C, Wang AJ (2016) Microbial network for waste activated sludge cascade utilization in an integrated system of microbial electrolysis and anaerobic fermentation. Biotechnol Biofuels 9:83CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann NY Acad Sci 1125:171–189CrossRefPubMedGoogle Scholar
  29. 29.
    Maus I, Bremges A, Stolze Y, Hahnke S, Cibis KG, Koeck DE, Kim YS, Kreubel J, Hassa J, Wibberg D, Weimann A, Off S, Stantscheff R, Zverlov VV, Schwarz WH, König H, Liebl W, Scherer P, McHardy AC, Sczyrba A, Klocke M, Pühler A, Schlüter A (2017) Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes. Biotechnol Biofuels 10:264. CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Narihiro T, Terada T, Kikuchi K, Iguchi A, Ikeda M, Yamauchi T, Shiraishi K, Kamagata Y, Nakamura K, Sekiguchi Y (2009) Comparative analysis of bacterial and archaeal communities in methanogenic sludge granules from upflow anaerobic sludge blanket reactors treating various food-processing, high-strength organic wastewaters. Microbes Environ 24:88–96CrossRefPubMedGoogle Scholar
  31. 31.
    Plumb JJ, Haddad CM, Gibson JAE, Franzmann PD (2007) Acidianus sulfidivorans sp. Nov., an extremely acidophilic, thermophilic archaeon isolated from a solfatara on Lihir Island, Papua New Guinea, and emendation of the genus description. Int J Syst Evol Microbiol 57:1418–1423CrossRefPubMedGoogle Scholar
  32. 32.
    Qin HB, Lang HH, Yang HJ (2013) Characterization of the methanogen community in a household anaerobic digester fed with swine manure in China. Appl Microbiol Biotechnol 97:8163–8171CrossRefPubMedGoogle Scholar
  33. 33.
    Rachbauer L, Beyer R, Bochmann G, Fuchs W (2017) Characteristics of adapted hydrogenotrophic community during biomethanation. Sci Total Environ 595:912–919CrossRefPubMedGoogle Scholar
  34. 34.
    Ratanatamskul C, Wattanayommanaporn O, Yamamoto K (2015) An on-site prototype two-stage anaerobic digester for co-digestion of food waste and sewage sludge for biogas production from high-rise building. Int Biodeterior Biodegradation 102:143–148CrossRefGoogle Scholar
  35. 35.
    Resende JA, Godon JJ, Bonnafous A, Arcuri PB, Silva VL, Otenio MH, Diniz CG (2016) Seasonal variation on microbial community and methane production during anaerobic digestion of cattle manure in Brazil. Microb Ecol 71:735–746CrossRefPubMedGoogle Scholar
  36. 36.
    Roest K, Heilig HG, Smidt H, de Vos WM, Stams AJ, Akkermans AD (2005) Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater. Syst Appl Microbiol 28:175–185CrossRefPubMedGoogle Scholar
  37. 37.
    Sara P, Michele P, Maurizio C, Luca C, Fabrizio A (2013) Effect of veterinary antibiotics on biogas and bio-methane production. Int Biodeterior Biodegradation 85:205–209CrossRefGoogle Scholar
  38. 38.
    Sohn SY, Häggblom MM (2016) Reductive dehalogenation activity of indigenous microorganism in sediments of the Hackensack River, New Jersey. Environ Pollut 214:374–383CrossRefPubMedGoogle Scholar
  39. 39.
    Venkatakrishnan H, Tan Y, Majid MB, Pathak S, Sendjaja AY, Li D, Liu JJL, Zhou Y, Ng WJ (2014) Effect of a high strength chemical industry wastewater on microbial community dynamics and mesophilic methane generation. J Environ Sci 26:875–884CrossRefGoogle Scholar
  40. 40.
    Volant A, Desoeuvre A, Casiot C, Lauga B, Delpoux S, Morin G, Personne´ JC. He´ry M, Elbaz-Poulichet F, Bertin PN, Bruneel O (2012) Archaeal diversity: temporal variation in the arsenic-rich creek sediments of Carnoulès Mine, France. Extremophiles 16:645–657CrossRefPubMedGoogle Scholar
  41. 41.
    Watling HR, Collinson DM, Fjastad S, Kaksonen AH, Li J, Morris C, Perrot FA, Rea SM, Shiers DW (2014) Column bioleaching of a polymetallic ore: effects of pH and temperature on metal extraction and microbial community structure. Miner Eng 58:90–99CrossRefGoogle Scholar
  42. 42.
    Wei SZ, Zhang HF, Cai XB, Xu J, Fang JP, Liu HM (2014) Psychrophilic anaerobic co-digestion of highland barley straw with two animal manures at high altitude for enhancing biogas production. Energy Convers Manage 88:40–48CrossRefGoogle Scholar
  43. 43.
    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 5:41CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Wu WJ, Liu QQ, Chen GJ, Du ZJ (2015) Roseimarinus sediminis gen. nov. sp. nov. a facultatively anaerobic bacterium isolated from coastal sediment. Int J Syst Evol Microbiol 65:2260–2264CrossRefPubMedGoogle Scholar
  45. 45.
    Yang Y, LI Y, Sun QY (2014) Archaeal and bacterial communities in acid mine drainage from metal-rich abandoned tailing ponds, Tongling, China. Trans Nonferrous Met Soc China 24:3332–3342CrossRefGoogle Scholar
  46. 46.
    Yilmaz V, Ince-yilmaz E, Yilmazel YD, Duran M (2014) Is aceticlastic methanogen composition in full-scale anaerobic processes related to acetate utilization capacity? Appl Microbiol Biotechnol 98:5217–5226CrossRefPubMedGoogle Scholar
  47. 47.
    Yoshie S, Noda N, Miyano T, Tsuneda S, Hirata A, Inamori Y (2001) Microbial community analysis in the denitrification process of saline-wastewater by denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA and the cultivation method. Int Biodeterior Biodegradation 92:346–353Google Scholar
  48. 48.
    Yu YQ, Lu XW, Wu YF (2014) Performance of an anaerobic baffled filter reactor in the treatment of algae-laden water and the contribution of granular sludge. Water 6:122–138CrossRefGoogle Scholar
  49. 49.
    Zanardini E, May E, Inkpen R, Cappitelli F, Murrell JC, Purdy KJ (2016) Diversity of archaeal and bacterial communities on exfoliated sandstone from Portchester Castle (UK). Int Biodeterior Biodegradation 109:78–87CrossRefGoogle Scholar
  50. 50.
    Zhang J, Ma G, Deng Y, Dong J, Stappen GV, Sui L (2016) Bacterial diversity in Bohai Bay solar saltworks, China. Curr Microbiol 72:55–63CrossRefPubMedGoogle Scholar
  51. 51.
    Zhang SY, Wang QF, Xie SG (2012) Molecular characterization of phenanthrene-degrading methanogenic communities in leachate-contaminated aquifer sediment. Int J Environ Sci Technol 9:705–712CrossRefGoogle Scholar
  52. 52.
    Zhang LL, Mu CL, He XY, Su Y, Mao SY, Zhang J, Smidt H, Zhu WY (2016) Effects of dietary fibre source on microbiota composition in the large intestine of suckling piglets. FEMS Microbiol Lett 363:1–6Google Scholar
  53. 53.
    Zhao C, Gao ZM, Qin QW, Ruan LW (2012) Mangroviflexus xiamenensis gen. nov. sp. nov. a member of the family Marinilabiliaceae isolated from mangrove sediment. Int J Syst Evol Microbiol 62:1819–1824CrossRefPubMedGoogle Scholar
  54. 54.
    Zhou AJ, Zhang JG, Wen KL, Liu ZH, Wang GY, Liu WZ, Wang AJ, Yue XP (2016) What could the entire cornstover contribute to the enhancement of waste activated sludge acidification? Performance assessment and microbial community analysis. Biotechnol Biofuels 9:241CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life SciencesCentral China Normal UniversityWuhanChina
  2. 2.Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and ForestryQinghai UniversityXiningChina
  3. 3.Research Center of Basic Medical SciencesQinghai University Medical CollegeXiningChina

Personalised recommendations