Straw- and slurry-associated prokaryotic communities differ during co-fermentation of straw and swine manure

Applied Microbiology and Biotechnology

Volumn 98, Issue 10, 2014, Pages 4771-4780

  Li, Jiabao ^a   Rui, Junpeng ^a   Pei, Zhaojun ^b   Sun, Xiaori ^c   Zhang, Shiheng ^a   Yan, Zhiying ^a   Wang, Yuanpeng ^d   Liu, Xiaofeng ^a   Zheng, Tao ^c   Li, Xiangzhen ^a  

^a CHENGDU INSTITUTE OF BIOLOGY   (China)

^b CHENGDU UNIVERSITY OF TECHNOLOGY   (China)

^c NANJING TECH UNIVERSITY   (China)

^d XIAMEN UNIVERSITY   (China)

Author keywords

16S rRNA gene pyrosequencing; Co fermentation; Prokaryotic community; Straw; Swine manure

Indexed keywords

MANURES; MICROORGANISMS; PROCESS CONTROL; PROTEINS; RNA; STRAW; SUBSTRATES; VOLATILE FATTY ACIDS; WASTE TREATMENT;

ANAEROBIC CO FERMENTATIONS; BIOREACTOR PERFORMANCE; COFERMENTATION; COMMUNITY COMPOSITION; PROKARYOTIC COMMUNITY; PYROSEQUENCING; SUBSTRATE HYDROLYSIS; SWINE MANURE;

FERMENTATION;

MICROORGANISM PROTEIN; PROPIONIC ACID; RNA 16S; VOLATILE FATTY ACID; MANURE; PROPIONIC ACID DERIVATIVE; SEWAGE;

ANOXIC CONDITIONS; BACTERIUM; BIOGAS; BIOREACTOR; COMMUNITY COMPOSITION; FERMENTATION; MANURE; MICROBIAL COMMUNITY; PIG; SLURRY; STRAW; SUBSTRATE; WASTE TREATMENT;

ACETIVIBRIO; AGRICULTURAL SLURRY; AMINOBACTERIUM; ANAEROBIC FERMENTATION; ARTICLE; BACTEROIDES; CLOACIBACILLUS; CLOSTRIDIUM III; CONTROLLED STUDY; DNA EXTRACTION; EURYARCHAEOTA; FIBROBACTER; FIBROBACTERES; GENE AMPLIFICATION; GENE SEQUENCE; LUTISPORA; MANURE; METHANOCULLEUS; METHANOSAETA; MICROBIAL COMMUNITY; MICROBIAL GENE; MICROBIAL POPULATION DYNAMICS; MICROORGANISM; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; PAPILLIBACTER; PELOTOMACULUM; PROKARYOTE; PYROSEQUENCING; SEDIMENTIBACTER; SPIROCHETE; STRAW; SWINE; SYNERGISTETES; TREPONEMA; ANAEROBIC GROWTH; ANIMAL; ARCHAEON; BACTERIA; BIOREACTOR; BIOTA; CLASSIFICATION; DNA SEQUENCE; FERMENTATION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; OXIDATION REDUCTION REACTION; PLANT STEM; SEWAGE; WHEAT;

ACETIVIBRIO; AMINOBACTERIUM; BACTEROIDES; CLOSTRIDIUM; EURYARCHAEOTA; FIBROBACTER; FIBROBACTERES; METHANOCULLEUS; METHANOSAETA; PAPILLIBACTER; PELOTOMACULUM; PROKARYOTA; SEDIMENTIBACTER; SPIROCHAETES; SUIDAE; TREPONEMA; TRITICUM AESTIVUM;

ANAEROBIOSIS; ANIMALS; ARCHAEA; BACTERIA; BIOREACTORS; BIOTA; FERMENTATION; MANURE; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PLANT STEMS; PROPIONATES; SEQUENCE ANALYSIS, DNA; SEWAGE; SWINE; TRITICUM;

EID: 84900825977     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-5629-3     Document Type: Article

References (41)

1. Barber RD, Zhang L, Harnack M, Olson MV, Kaul R, Ingram-Smith C, Smith KS (2011) Complete genome sequence of Methanosaeta concilii, a specialist in aceticlastic methanogenesis. J Bacteriol 193(14):3668-3669
2. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena 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(5):335-336
3. Cheng L, Qiu TL, Li X, Wang WD, Deng Y, Yin XB, Zhang H (2008) Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China. FEMS Microbiol Lett 285(1):65-71 (Pubitemid 352000213)
4. Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Spring S, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP (2010) Complete genome sequence of Aminobacterium colombiense type strain (ALA-1). Stand Genomic Sci 2(3):280-289
5. de Bok FA, Harmsen HJ, Plugge CM, de Vries MC, Akkermans AD, de Vos WM, Stams AJ (2005) The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum. Int J Syst EvolMicrobiol 55(Pt 4):1697-1703 (Pubitemid 41015624)
6. Deng Y, He Z, Xu M, Qin Y, Van Nostrand JD, Wu L, Roe BA, Wiley G, Hobbie SE, Reich PB, Zhou J (2012) Elevated carbon dioxide alters the structure of soil microbial communities. Appl Environ Microbiol 78(8):2991-2995
7. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27(16):2194-2200
8. Ferrer P, Cambra-Lopez M, Cerisuelo A, Penaranda DS, Moset V (2014) The use of agricultural substrates to improve methane yield in anaerobic co-digestion with pig slurry: effect of substrate type and inclusion level. Waste Manag 34(1):196-203
9. Gallert C, Winter J (2008) Propionic acid accumulation and degradation during restart of a full-scale anaerobic biowaste digester. Bioresour Technol 99:170-178 (Pubitemid 47503762)
10. Ganesan A, Chaussonnerie S, Tarrade A, Dauga C, Bouchez T, Pelletier E, Le Paslier D, Sghir A (2008) Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum 'Synergistetes', isolated from an anaerobic sludge digester. Int J Syst Evol Microbiol 58(Pt 9):2003-2012
11. Hanreich A, Schimpf U, Zakrzewski M, Schluter A, Benndorf D, Heyer R, Rapp E, Puhler A, Reichl U, Klocke M (2013) Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol 36(5):330-338
12. Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM (2011) Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331(6016):463-467
13. Hongoh Y, Deevong P, Hattori S, Inoue T, Noda S, Noparatnaraporn N, Kudo T, Ohkuma M (2006) Phylogenetic diversity, localization, and cell morphologies of members of the candidate phylum TG3 and a subphylum in the phylum Fibrobacteres, recently discovered bacterial groups dominant in termite guts. Appl Environ Microbiol 72(10):6780-6788 (Pubitemid 44582922)
14. Hongoh Y, Deevong P, Inoue T, Moriya S, Trakulnaleamsai S, Ohkuma M, Vongkaluang C, Noparatnaraporn N, Kudo T (2005) Intra- and interspecific comparisons of bacterial diversity and community structure support coevolution of gut microbiota and termite host. Appl Environ Microbiol 71(11):6590-6599 (Pubitemid 43194141)
15. Imachi H, Aoi K, Tasumi E, Saito Y, Yamanaka Y, Saito Y, Yamaguchi T, Tomaru H, Takeuchi R, Morono Y, Inagaki F, Takai K (2011) Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor. ISME J 5(12):1913-1925
16. Ishii S, Kosaka T, Hori K, Hotta Y, Watanabe K (2005) Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus. Appl Environ Microbiol 71(12):7838-7845 (Pubitemid 41803903)
17. Jaenicke S, Ander C, Bekel T, Bisdorf R, Dröge M, Gartemann K-H, Jünemann S, Kaiser O, Krause L, Tille F, Zakrzewski M, Pühler A, Schlüter A, Goesmann A (2011) Comparative and joint analysis of twometagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS ONE 6(1):e14519
18. Li A, Chu Y, Wang X, Ren L, Yu J, Liu X, Yan J, Zhang L, Wu S, Li S (2013) A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor. Biotechnol Biofuels 6(1):3
19. Li XZ, Rui JP, Mao YJ, Yannarell A, Mackie R (2014) Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar. Soil Biol Biochem 68:392-401
20. 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
21. Looft T, Levine UY, Stanton TB (2013) Cloacibacillus porcorum sp. nov., a mucin-degrading bacterium from the swine intestinal tract and emended description of the genus Cloacibacillus. Int J Syst Evol Microbiol 63(Pt 6):1960-1966
22. 2: process performance and microbial insights. Appl Microbiol Biotechnol 97(3):1373-1381
23. McInerney MJ, Sieber JR, Gunsalus RP (2009) Syntrophy in anaerobic global carbon cycles. Curr Opin Biotechnol 20(6):623-632
24. Muller N, Worm P, Schink B, Stams AJ, Plugge CM (2010) Syntrophic butyrate and propionate oxidation processes: from genomes to reaction mechanisms. Environ Microbiol Rep 2(4):489-499
25. Nelson MC, Morrison M, Schanbacher F, Yu Z (2012) Shifts inmicrobial community structure of granular and liquid biomass in response to changes to infeed and digester design in anaerobic digesters receiving food-processing wastes. Bioresour Technol 107:135-143
26. Nelson MC, Morrison M, Yu Z (2011) A meta-analysis of the microbial diversity observed in anaerobic digesters. Bioresour Technol 102(4):3730-3739
27. O'Sullivan CA, Burrell PC, ClarkeWP, Blackall LL (2005) Structure of a cellulose degrading bacterial community during anaerobic digestion. Biotechnol Bioeng 92(7):871-878
28. Rademacher A, Zakrzewski M, Schluter A, Schonberg M, Szczepanowski R, Goesmann A, Puhler A, Klocke M (2012) Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiol Ecol 79(3):785-799
29. Sieber JR, McInerney MJ, Gunsalus RP (2012) Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation. Annu Rev Microbiol 66:429-452
30. Stams AJ, Plugge CM (2009) Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nat Rev Microbiol 7(8):568-577
31. Sundberg C, Al-Soud WA, Larsson M, Alm E, Shakeri Yekta S, Svensson BH, Sorensen 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
32. Supaphol S, Jenkins SN, Intomo P, Waite IS, O'Donnell AG (2011) Microbial community dynamics in mesophilic anaerobic codigestion of mixed waste. Bioresour Technol 102(5):4021-4027
33. Syutsubo K, Nagaya Y, Sakai S, Miya A (2005) Behavior of cellulose-degrading bacteria in thermophilic anaerobic digestion process. Water Sci Technol 52(1-2):79-84 (Pubitemid 41350251)
34. Tamaki H, Wright CL, Li X, Lin Q, Hwang C, Wang S, Thimmapuram J, Kamagata Y, Liu WT (2011) Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform. PLoS ONE 6(9):e25263
35. Tang YQ, Shigematsu T, Morimura S, Kida K (2005) Microbial community analysis of mesophilic anaerobic protein degradation process using bovine serum albumin (BSA)-fed continuous cultivation. J Biosci Bioeng 99(2):150-164
36. Town JR, Links MG, Fonstad TA, Dumonceaux TJ (2014) Molecular characterization of anaerobic digester microbial communities identifies microorganisms that correlate to reactor performance. Bioresour Technol 151:249-257
37. Tzollas NM, Zachariadis GA, Anthemidis AN, Stratis JA (2010) A new approach to indophenol blue method for determination of ammonium in geothermal waters with high mineral content. Int J Environ Anal Chem 90(2):115-126
38. Werner JJ, Knights D, Garcia ML, Scalfone NB, Smith S, Yarasheski K, Cummings TA, Beers AR, Knight R, Angenent LT (2011) Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci USA 108(10):4158-4163
39. Wu CG, Dong XZ, Liu XL (2007) Syntrophomonas wolfei subsp. methylbutyratica subsp. nov., and assignment of Syntrophomonas wolfei subsp. saponavida to Syntrophomonas saponavida sp. nov. comb. nov. Syst Appl Microbiol 30(5):376-380
40. Ye J, Li D, Sun Y, Wang G, Yuan Z, Zhen F, Wang Y (2013) Improved biogas production from rice straw by co-digestion with kitchen waste and pig manure. Waste Manag 33(12):2653-2658
41. Zakrzewski M, Goesmann A, Jaenicke S, Junemann S, Eikmeyer F, Szczepanowski R, Al-Soud WA, Sorensen S, Puhler A, Schluter A (2012) Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. J Biotechnol 158(4):248-258