Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities

Journal of Microbiological Methods

Volumn 79, Issue 3, 2009, Pages 279-288

  Franke Whittle, Ingrid H ^a   Goberna, Marta ^a   Pfister, Vanessa ^a   Insam, Heribert ^a  

^a UNIVERSITY OF INNSBRUCK   (Austria)

Author keywords

16S rRNA; Anaerobic digestion; Biogas; Bioreactor; Methanogens; Microarray

Indexed keywords

RNA 16S;

ANAEROBIC DIGESTION; ARTICLE; BIOFUEL PRODUCTION; COMMUNITY STRUCTURE; CONTROLLED STUDY; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; HYBRIDIZATION; METHANOBACTERIUM; METHANOBREVIBACTER; METHANOCULLEUS; METHANOGEN; METHANOSARCINA; METHANOSPHAERA; METHANOTHERMOBACTER; MICROARRAY ANALYSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGONUCLEOTIDE PROBE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SLUDGE;

ANAEROBIOSIS; GENE LIBRARY; GENES, BACTERIAL; METHANOBACTERIACEAE; METHANOMICROBIACEAE; METHANOSARCINA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; REPRODUCIBILITY OF RESULTS; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEWAGE;

ARCHAEA; METHANOBACTERIUM; METHANOBREVIBACTER; METHANOCULLEUS; METHANOSARCINA; METHANOSPHAERA; METHANOTHERMOBACTER; UNCULTURED ARCHAEON;

EID: 70449532360     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2009.09.017     Document Type: Article

References (52)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1991) 403-410
2. Amann R., Ludwig W., and Schleifer K.H. Identification of uncultured bacteria: a challenging task for molecular taxonomists. ASM News 60 (1994) 360-365
3. Buchholz-Cleven B.E.E., Rattunde B., and Straub K.L. Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst. Appl. Microbiol. 20 (1997) 301-309
4. Byers H.K., Stackebrandt E., Hayward C., and Blackall L.L. Molecular investigation of a microbial mat associated with the Great Artesian basin. FEMS Microbiol. Ecol. 25 (1998) 391-403
5. Chandler D.P., Brockman F.J., and Fredrickson J.K. Use of 16S rDNA clone libraries to study changes in a microbial community resulting from ex situ perturbation of a subsurface sediment. FEMS Microbiol. Rev. 20 (1997) 217-230
6. Chen Y., Cheng J.J., and Creamer K.S. Inhibition of anaerobic digestion process: a review. Bioresour. Technol. 99 (2008) 4044-4064
7. Chouari R., Le Paslier D., Dauga C., Daegelen P., Weissenbach J., and Sghir A. Novel major bacterial candidate division within a municipal anaerobic sludge digester. Appl. Environ. Microbiol. 71 (2005) 2145-2153
8. Demirel B., and Scherer P. The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review. Rev. Environ. Sci. Biotechnol. 7 (2008) 173-190
9. Demirel B., and Yenigün O. Two-phase anaerobic digestion processes: a review. J. Chem. Technol. Biotechnol. 77 (2002) 743-755
10. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17 (1981) 368-376
11. Fernández A., Huang S., Sheston S., Xing J., Hickey R., Criddle C., and Tiedje J. How stable is stable? Function versus community composition. Appl. Environ. Microbiol. 65 (1999) 3697-3704
12. Franke-Whittle I.H., Klammer S., and Insam H. Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J. Microbiol. Methods 62 (2005) 37-56
13. Franke-Whittle I.H., Knapp B., Fuchs J., Kaufmann R., and Insam H. Application of COMPOCHIP microarray to investigate the bacterial communities of different composts. Microb. Ecol. 57 (2009) 510-521
14. Goberna M., Insam H., and Franke-Whittle I.H. Effect of biowaste sludge maturation on the diversity of thermophilic bacteria and archaea in an anaerobic reactor. Appl. Environ. Microbiol. 75 (2009) 2566-2572
15. Godon J.J., Zumstein E., Dabert P., Habouzit F., and Moletta R. Molecular microbial diversity of an anaerobic digestor as determined by small-subunit rDNA sequence analysis. Appl. Environ. Microbiol. 63 (1997) 2802-2813
16. Good I. The population frequencies of species and the estimation of the population parameters. Biometrika 40 (1953) 237-264
17. Grosskopf R., Janssen P.H., and Liesack W. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval. Appl. Environ. Microbiol. 64 (1998) 960-969
18. Guschin D., Mobarry B., Proudnikov D., Stahl D., Rittmann B., and Mirzabekov A. Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63 (1997) 2397-2402
19. Huber T., Faulkner G., and Hugenholtz P. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20 (2004) 2317-2319
20. Insam H., and Wett B. Control of GHG emission at the microbial community level. Waste Manage. 28 (2008) 699-706
21. Kayhanian M. Performance of a high-solids anaerobic digestion process under various ammonia concentrations. J. Chem. Technol. Biotechnol. 59 (1994) 349-352
22. Koizumi Y., Kelly J.J., Nakagawa T., Urakawa H., El-Fantroussi S., Al-Muzaini S., Fukui M., Urushigawa Y., and Stahl D.A. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl. Environ. Microbiol. 68 (2002) 3215-3225
23. Kröber M., Bekel T., Diaz N.N., Goesmann A., Jaenicke S., Krause L., Miller D., Runte K.J., Viehöver P., Pühler A., and Schlüter A. Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing: solar bio-fuels. J. Biotechnol. 142 (2009) 38-49
24. Lane D.J. 16S/23S rRNA sequencing. In: Stackebrandt E., and Goodfellow M. (Eds). Nucleic Acid Techniques in Bacterial Systematics (1991), John Wiley and Sons, Chichester, UK 115-147
25. Lastella G., Testa C., Cornacchia G., Notornicola M., Voltasio F., and Sharma V.K. Anaerobic digestion of semi-solid organic waste: biogas production and its purification. Energy Convers. Manag. 43 (2002) 63-75
26. Leclerc M., Delbes C., Moletta R., and Godon J. Single stand conformation polymorphism monitoring of 16s rDNA Archaea during start-up of an anaerobic digester. FEMS Microbiol. Ecol. 34 (2001) 213-220
27. Liu W.-T., Mirzabekov A.D., and Stahl D.A. Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ. Microbiol. 3 (2001) 619-629
28. Liu F.H., Wang S.B., Zhang J.S., Zhang J., Yan X., Zhou H.K., Zhao G.P., and Zhou Z.H. 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 (2009) 952-966
29. Loy A., Lehner A., Lee N., Adamczyk J., Meier H., Ernst J., Schleifer K.-H., and Wagner M. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68 (2002) 5064-5081
30. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S., Jobb G., Forster W., Brettske I., Gerber S., Ginhart A.W., Gross O., Grumann S., Hermann S., Jost R., Konig A., Liss T., Lussmann R., May M., Nonhoff B., Reichel B., Strehlow R., Stamatakis A., Stuckmann N., Vilbig A., Lenke M., Ludwig T., Bode A., and Schleifer K.-H. ARB: a software environment for sequence data. Nucleic Acids Res. 32 (2004) 1363-1371
31. Malin C., and Illmer P. Ability of DNA content and DGGE analysis to reflect the performance condition of an anaerobic biowaste fermenter. Microbiol. Res. 163 (2008) 503-511
32. Maskos U., and Southern E.M. Oligonucleotide hybridizations on glass supports-a novel linker for oligonucleotide synthesis and hybridization properties of oligonucleotides synthesized in situ. Nucleic Acids Res. 20 (1992) 1679-1684
33. Mladenovska Z., Dabrowski S., and Ahring B.K. Anaerobic digestion of manure and mixture of manure with lipids: biogas reactor performance and microbial community analysis. Water Sci. Technol. 48 (2003) 271-278
34. Peplies J., Glockner F.O., and Amann R. Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl. Environ. Microbiol. 69 (2003) 1397-1407
35. Pohlan F.G., and Ghosh S. Developments in anaerobic treatment process. Biotechnol. Bioeng. 2 (1971) 85-106
36. Raskin L., Zheng D.D., Griffin M.E., Stroot P.G., and Misra P. Characterization of microbial communities in anaerobic bioreactors using molecular probes. A. Van. Leeuw. 68 (1995) 297-308
37. Rastogi G., Ranade D.R., Yeole T.Y., Patole M.S., and Shouche Y.S. Investigation of methanogen population structure in biogas reactor by molecular characterization of methyl-coenzyme M reductase A (mcrA) genes. Bioresour. Technol. 99 (2008) 5317-5326
38. Rudi K., Flateland S.L., Hanssen J.F., Bengtsson G., and Nissen H. Development and evaluation of a 16S ribosomal DNA array-based approach for describing complex microbial communities in ready-to-eat vegetable salads packed in a modified atmosphere. Appl. Environ. Microbiol. 68 (2002) 1146-1156
39. Sanguin H., Herrera A., Oger-Desfeux C., Dechesne A., Simonet P., Navarro E., Vogel T., Moenne-Loccoz Y., Xavier N., and Grundmann G.L. Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ. Microbiol. 8 (2006) 289-307
40. Schmidt J.E., Mladenovska Z., Lange M., and Ahring B.K. Acetate conversion in anaerobic biogas reactors: traditional and molecular tools for studying this important group of anaerobic microorganisms. Biodegradation 11 (2000) 359-364
41. Schnürer A., Zellner G., and Svensson B.H. Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors. FEMS Microbiol. Ecol. 29 (1999) 249-261
42. Small J., Call D.R., Brockman F.J., Straub T.M., and Chandler D.P. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl. Environ. Microbiol. 67 (2001) 4708-4716
43. Southern E., Mir K., and Shchepinov M. Molecular interactions on microarrays. Nat. Genet. supplement 21 (1999) 5-9
44. Stahl D.A., and Amann R. Development and application of nucleic acid probes in bacterial systematics. In: Stackebrandt E., and Goodfellow M. (Eds). Nucleic Acid Techniques in Bacterial Systematics (1991), John Wiley & Sons, Chichester, England 205-248
45. Stralis-Pavese N., Sessitsch A., Weilharter A., Reichenauer T., Riesing J., Csontos J., Murrell J.C., and Bodrossy L. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ. Microbiol. 6 (2004) 347-363
46. Suzuki M.T., and Giovannoni S.J. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62 (1996) 625-630
47. Tang Y., Shigematsu T., Ikbal, Morimura S., and Kida K. The effects of micro-aeration on the phylogenetic diversity of microorganisms in a thermophilic anaerobic municipal solid-waste digester. Water Res. 38 (2004) 2537-2550
48. Thummes K., Kampfer P., and Jackel U. Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material. Syst. Appl. Microbiol. 30 (2007) 418-429
49. Wang R.-F., Beggs M.L., Robertson L.H., and Cerniglia C.E. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples. FEMS Microbiol. Lett. 213 (2002) 175-182
50. Weiss A., Jérôme V., Freitag R., and Mayer H. Diversity of the resident microbiota in a thermophilic municipal biogas plant. Appl. Microbiol. Biotechnol. 81 (2008) 163-173
51. Whitehead T.T., and Cotta M.A. Phylogenetic diversity of methanogenic archaea in swine waste storage pits. FEMS Microbiol. Lett. 179 (1999) 223-226
52. Yadvika S., Sreekrishnan T.R., Kohli S., and Rana V. Enhancement of biogas production from solid substrates using different techniques-a review. Bioresour. Technol. 95 (2004) 1-10