Transition of microbial communities during the adaption to anaerobic digestion of carrot waste

Bioresource Technology

Volumn 102, Issue 15, 2011, Pages 7249-7256

  Garcia, Sarahi L ^a,b   Jangid, Kamlesh ^b   Whitman, William B ^b   Das, K C ^a  

^a University of Georgia   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

16S rRNA Libraries; Anaerobic digestion; Carrot pomace; Microbial community

Indexed keywords

16S RRNA GENE; 16S RRNA LIBRARIES; ARCHAEAL POPULATION; BACTERIAL POPULATION; CARROT POMACE; INOCULA; METHANOGENIC ARCHAEA; MICROBIAL COMMUNITIES; PYROSEQUENCING;

BACTERIOLOGY; GENES; METHANE; MICROORGANISMS; RNA;

ANAEROBIC DIGESTION;

RIBOSOME RNA; RNA 16S;

ANOXIC CONDITIONS; BACTERIUM; DIGESTION; DOMESTIC WASTE; MICROBIAL COMMUNITY;

AGRICULTURAL WASTE; ANAEROBIC DIGESTION; ARCHAEBACTERIUM; ARTICLE; BACILLI; CARROT; GENE LIBRARY; METHANOGENIC ARCHAEON; METHANOSARCINA MAZEI; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PORPHYROMONADACEAE; PRIORITY JOURNAL; PYROSEQUENCING; SEQUENCE ANALYSIS; SPIROCHETE;

ADAPTATION, PHYSIOLOGICAL; ANAEROBIOSIS; ARCHAEA; BACTERIA; BIODEGRADATION, ENVIRONMENTAL; DAUCUS CAROTA; GENES, ARCHAEAL; GENES, BACTERIAL; METHANE; PHYLOGENY; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S; WASTE PRODUCTS;

ARCHAEA; BACILLI (CLASS); BACTERIA (MICROORGANISMS); DAUCUS CAROTA; METHANOSARCINA MAZEI; PORPHYROMONADACEAE; SPIROCHAETES;

EID: 79958277860     PISSN: 09608524     EISSN: 18732976     Source Type: Journal    
DOI: 10.1016/j.biortech.2011.04.098     Document Type: Article

References (35)

1. Acosta-Martínez V., Dowd S., Sun Y., Allen V. Tag-encoded pyrosequencing analysis of bacterial diversity in a single soil type as affected by management and land use. Soil Biol. Biochem. 2008, 40:2762-2770.
2. Baker G.C., Cowan D.A. 16S rDNA primers and the unbiased assessment of thermophile diversity. Biochem. Soc. Trans. 2004, 32:218-221.
3. Baker G.C., Smith J.J., Cowan D.A. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 2003, 55:541-555.
4. Balch W.E., Fox C.E., Magrum L.J., Woese C.R., Wolfe R.S. Methanogens: reevaluation of a unique biological group. Microbiol. Rev. 1979, 43:260.
5. Calderon K., Rodelas B., Cabirol N., Gonzalez-Lopez J., Noyola A. Analysis of microbial communities developed on the fouling layers of a membrane-coupled anaerobic bioreactor applied to wastewater treatment. Bioresour. Technol. 2011, 102:4616-4627.
6. Cantrell K.B., Ducey T., Ro K.S., Hunt P.G. Livestock waste-to-bioenergy generation opportunities. Bioresour. Technol. 2008, 99:7941-7953.
7. Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Gonzalez Peña, A., Goodrich, J.K., Gordon, J., Huttley, G.A., Kelley, S.T., Knights, D., Koenig, J.E., Ley, R.E., Lozupone, C.A., McDonald, D., Muegge, B.D., Pirrung, M., Reeder, J., Sevinsky, J.R., Turnbaugh, P.J., Walters, W.A., Widmann, J., Yatsunenko, T., Zaneveld, J., Knight, R., 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods, 335.
8. Dröge S., Fröhlich J., Radek R., König H. Spirochaeta coccoides sp. nov., a novel coccoid spirochete from the hindgut of the termite Neotermes castaneus. Appl. Environ. Microbiol. 2005, 72:392-397.
9. Frank J.A., Reich C.I., Sharma S., Weisbaum J.S., Wilson B.A., Olsen G.J. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl. Environ. Microbiol. 2008, 74:2461-2470.
10. Hamady M., Walker J.J., Harris J.K., Gold N.J., Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat. Methods 2008, 5:235-237.
11. Hsu P.-K., Chien P.-J., Chen C.-H., Chau C.-F. Carrot insoluble fiber-rich fraction lowers lipid and cholesterol absorption in hamsters. LWT Food Sci. Technol. 2006, 39:338-343.
12. Huntington G.B. Uptake and transport of nonprotein nitrogen by the ruminant gut. Fed. Proc. 1986, 45:2272.
13. Huse S.M., Dethlefsen L., Huber J.A., Welch D.M., Relman D.A., Sogin M.L. Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLos Genet. 2008, 4:e1000255.
14. Jennett J.C., Dennis J.N.D. Anaerobic filter treatment of pharmaceutical waste. J. Water Pollut. Contr. 1975, 45:104-121.
15. Kalanetra K.M., Bano N., Hollibaugh J.T. Ammonia-oxidizing Archaea in the Arctic Ocean and Antarctic coastal waters. Environ. Microbiol. 2009, 11:2434-2445.
16. Krause L., Diaz N.N., Edwards R.A., Gartemann K.-H., Krömeke H., Neuweger H., Pühler A., Runte K.J., Schlüter A., Stoye J., Szczepanowski R., Tauch A., Goesmann A. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J. Bacteriol. 2008, 136:91-101.
17. Kristensen N.B. Rumen microbial sequestration of [2-(13)C]acetate in cattle. J. Anim. Sci. 2001, 79:2491.
18. Lasher C., Dyszynski G., Everett K., Edmonds J., Ye W., Sheldon W., Wang S., Joye S.B., Moran M.A., Whitman W.B. The diverse bacterial community in intertidal, anaerobic sediments at Sapelo Island, Georgia. Microb. Ecol. 2009, 58:244-261.
19. Martin-Gonzalez L., Castro R., Pereira M.A., Alves M.M., Font X. Thermophilic co-digestion of organic fraction of municipal solid wastes with FOG wastes from a sewage treatment plant: reactor performance and microbial community monitoring. Bioresour. Technol. 2011, 102:4734-4741.
20. McHugh S., Carton M., Mahony T., O'Flaherty V. Methanogenic population structure in a variety of anaerobic bioreactors. FEMS Microbiol. Lett. 2003, 219:297-304.
21. Nishiyama T., Ueki A., Kaku N., Watanabe K., Ueki K. Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste. Int. J. Syst. Evol. Microb. 2009, 59:1901-1907.
22. Prosser J.I. Replicate or lie. Environ. Microbiol. 2010, 12:1806-1810.
23. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001, 11:3-11.
24. Rudi K., Skulberg O.M., Larsen F., Jfkobsen K.S. Strain characterization and classification of oxyphotobacteria in clone cultures on the basis of 16S rRNA sequences from the variable regions V6, V7, and V8. Appl. Environ. Microbiol. 1997, 63:2593-2599.
25. Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microb. 2009, 75:7537-7541.
26. Sekiguchi Y., Kamagata Y., Nakamura K., Ohashi A., Harada H. Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate. Int. J. Syst. Evol. Microbiol. 2000, 50:771-779.
27. Snell-Castro R., Godon J.J., Delgenes J.P., Dabert P. Characterisation of the microbial diversity in a pig manure storage pit using small subunit rDNA sequence analysis. FEMS Microb. Ecol. 2005, 52:229-242.
28. Song Y., Liu C., Lee J., Bolanos M., Vaisanen M.-L., Finegold S.M. Bacteroides goldsteinii sp. nov. isolated from clinical specimens of human intestinal origin. J. Clin. Microbiol. 2005, 43:4522-4527.
29. Sorensen K.B., Teske A. Stratified communities of active archaea in deep marine subsurface sediments. Appl. Environ. Microbiol. 2006, 72:4596-4603.
30. Svensson B.H., Dubourguier H.-C., Prensier G., Zehnder A.J.B. Clostridium quinii sp. nov., a new saccharolytic anaerobic bacterium isolated from granular sludge. Arch. Microb. 1992, 157:97.
31. Takai K., Horikoshi K. Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl. Environ. Microbiol. 2000, 66:5066-5072.
32. Ward A.J., Hobbs P.J., Holliman P.J., Jones D.L. Optimisation of the anaerobic digestion of agricultural resources. Bioresour. Technol. 2008, 99:7928-7940.
33. Wright A.-D.G., Toovey A.F., Pimm C.L. Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea. Anaerobe 2006, 12:134-139.
34. Zhang D., Li J., Guo P., Li P., Suo Y., Wang X., Cui Z. Dynamic transition of microbial communities in response to acidification in fixed-bed anaerobic baffled reactors (FABR) of two different flow directions. Bioresour. Technol. 2011, 102:4703-4711.
35. Zinder S.H. Physiological Ecology of Methanogens 1993, Chapman and Hall, New York.