Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 94, Issue 3, 2008, Pages 439-453

  Kyselková, Martina ^a,b,c,d   Kopecký, Jan ^e   Felföldi, Tamás ^f   Čermák, Ladislav ^g   Omelka, Marek ^h   Grundmann, Geneviève L ^a,b,c,d   Moënne Loccoz, Yvan ^a,b,c,d   Ságová Marečková, Markéta ^e  

^a UNIVERSITÉ DE LYON   (France)

^b UNIVERSITÉ LYON 1   (France)

^c University of Lyon   (France)

^d IFR 41   (France)

^e CROP RESEARCH INSTITUTE   (Czech Republic)

^f EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^g INSTITUTE OF MICROBIOLOGY   (Czech Republic)

^h CHARLES UNIVERSITY   (Czech Republic)

Author keywords

Actinomycete diversity; Cloning; Soil communities; Taxonomic microarray

Indexed keywords

GENOMIC DNA; RNA 16S;

ACCURACY; ACTINOBACTERIA; ALPHAPROTEOBACTERIA; ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIUM DETECTION; BACTEROIDETES; BETAPROTEOBACTERIA; CONTROLLED STUDY; DNA EXTRACTION; ECOSYSTEM; FOREST SOIL; GENE SEQUENCE; GENETIC POLYMORPHISM; GENUS; GRAM POSITIVE BACTERIUM; HYBRIDIZATION; MICROARRAY ANALYSIS; MOLECULAR CLONING; MOLECULAR PROBE; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SIGNAL PROCESSING; SOIL MICROFLORA; TAXONOMY;

ACTINOBACTERIA; BASE SEQUENCE; CLONING, MOLECULAR; DATABASES, GENETIC; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; ECOSYSTEM; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; SPECIES SPECIFICITY;

ACTINOBACTERIA (CLASS); POSIBACTERIA;

EID: 50949116865     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10482-008-9261-z     Document Type: Article

References (43)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Amann RI, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919-1925
3. Ashelford KE, Weightman AJ, Fry JC (2002) PRIMROSE: A computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 30:3481-3489. doi: 10.1093/nar/gkf450
4. Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566-582. doi: 10.1046/ j.1462-2920.2003.00450.x
5. Brant JB, Myrold DD, Sulzman EW (2006) Root controls on soil microbial community structure in forest soils. Oecologia 148:650-659. doi: 10.1007/ s00442-006-0402-7
6. Bredholdt H, Galatenko OA, Engelhardt K, Fjaervik E, Terekhova LP, Zotchev SB (2007) Rare actinomycete bacteria from the shallow water sediments of the Trondheim fjord, Norway: Isolation, diversity and biological activity. Environ Microbiol 9:2756-2764. doi: 10.1111/ j.1462-2920.2007.01387.x
7. Brodie EL, DeSantis TZ, Joyner DC, Baek SM, Larsen JT, Andersen GL et al (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72:6288-6298. doi: 10.1128/ AEM.00246-06
8. Bruce KD, Hiorns WD, Hobman JL, Osborn AM, Strike P, Ritchie DA (1992) Amplification of DNA from native populations of soil bacteria by using the polymerase chain reaction. Appl Environ Microbiol 58:3413-3416
9. Carlsohn MR, Groth I, Tan GYA, Schutze B, Saluz HP, Munder T et al (2007) Amycolatopsis saalfeldensis sp nov., a novel actinomycete isolated from a medieval alum slate mine. Int J Syst Evol Microbiol 57:1640-1646. doi: 10.1099/ijs.0.64903-0
10. Diehl F, Grahlmann S, Beier M, Hoheisel JD (2001) Manufacturing DNA-microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Res 29:e38
11. Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792-1797. doi: 10.1093/nar/ gkh340
12. Felsenstein J (1989) PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164-166
13. Fenical W, Jensen PR (2006) Developing a new resource for drug discovery: Marine actinomycete bacteria. Nat Chem Biol 2:666-673. doi: 10.1038/nchembio841
14. Franke-Whittle IH, Klammer SH, Insam H (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J Microbiol Methods 62:37-56. doi: 10.1016/ j.mimet.2005.01.008
15. Fritze H, Pietikaeinen J, Pennanen T (2000) Distribution of microbial biomass and phospholipid fatty acids in Podzol profiles under coniferous forest. Eur J Soil Sci 51:565-573. doi: 10.1046/j.1365-2389.2000.00346.x
16. Heuer H, Krsek M, Baker P, Smalla K, Wellington EM (1997) Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients. Appl Environ Microbiol 63:3233-3241
17. Kurtböke DI, Neller RJ, Bellgard SE (2007) Mesophilic actinomycetes in the natural and reconstructed sand dune vegetation zones of Fraser Island, Australia. Microb Ecol 54:332-340. doi: 10.1007/s00248-007-9207-4
18. Legendre P, Legendre L (1998) Numerical ecology, 2nd edn. Elsevier Science, Amsterdam
19. Lipson DA, Schmidt SK (2004) Seasonal changes in an alpine soil bacterial community in the Colorado Rocky Mountains. Appl Environ Microbiol 70:2867-2879. doi: 10.1128/AEM.70.5.2867-2879.2004
20. Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J et al (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064-5081. doi: 10.1128/ AEM.68.10.5064-5081.2002
21. Loy A, Schulz C, Lucker S, Schopfer-Wendels A, Stoecker K, Baranyi C et al (2005) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the beta proteobacterial order "Rhodocyclales". Appl Environ Microbiol 71:1373-1386. doi: 10.1128/AEM.71.3.1373-1386.2005
22. 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 AW, 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, Schleifer KH (2004) ARB: A software environment for sequence data. Nucleic Acids Res 32:1363-1371. doi: 10.1093/nar/gkh293
23. Markham NR, Zuker M (2005) DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res 33:W577-W581. doi: 10.1093/nar/gki591
24. Miller DN, Bryant JE, Madsen EL, Ghiorse WC (1999) Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl Environ Microbiol 65:4715-4724
25. Nelson BP, Liles MR, Frederick KB, Corn RM, Goodman RM (2002) Label-free detection of 16S ribosomal RNA hybridization on reusable DNA arrays using surface plasmon resonance imaging. Environ Microbiol 4:735-743. doi: 10.1046/j.1462-2920.2002.00350.x
26. Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK et al (2006) Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 34:e5. doi: 10.1093/nar/gnj007
27. Peplies J, Lau SCK, Pernthaler J, Amann R, Glockner FO (2004) Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ Microbiol 6:638-645. doi: 10.1111/j.1462-2920.2004.00588.x
28. Pozhitkov A, Noble PA, Domazet-Loso T, Nolte AW, Sonnenberg R, Staehler P et al (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res 34:e66. doi: 10.1093/nar/gkl133
29. Sanguin H, Remenant B, Dechesne A, Thioulouse J, Vogel TM, Nesme X et al (2006a) Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Appl Environ Microbiol 72:4302-4312. doi: 10.1128/ AEM.02686-05
30. Sanguin H, Herrera A, Oger-Desfeux C, Dechesne A, Simonet P, Navarro E et al (2006b) Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ Microbiol 8:289-307. doi: 10.1111/j.1462-2920.2005.00895.x
31. Sanguin H, Kroneisen L, Gazengel K, Kyselková M, Remenant B, Prigent-Combaret C et al (2008) Development of a 16S rRNA microarray approach for the monitoring of rhizosphere Pseudomonas populations associated with the decline of take-all disease of wheat. Soil Biol Biochem 40:1028-1039. doi: 10.1016/j.soilbio.2007.11.023
32. Selyanin VV, Oborotov GE, Zenova GM, Zvyagintsev DG (2005) Alkaliphilic soil actinomycetes. Microbiology 74:729-734. doi: 10.1007/ s11021-005-0131-7
33. Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E (2001) Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl Environ Microbiol 67:4215-4224. doi: 10.1128/AEM.67.9.4215-4224.2001
34. Singleton DR, Furlong MA, Rathbun SL, Whitman WB (2001) Quantitative comparisons of 16S rDNA sequence libraries from environmental samples. Appl Environ Microbiol 67:4373-4376. doi: 10.1128/AEM.67.9.4374-4376.2001
35. Spiess AN, Mueller N, Ivell R (2003) Amplified RNA degradation in T7-amplication methods results in biased microarray hybridizations. BMC Genomics 4:44
36. Stach JE, Bathe S, Clapp JP, Burns RG (2001) PCR-SSCP comparison of 16S rRNA sequence diversity in soil DNA obtained using different isolation and purification methods. FEMS Microbiol Ecol 36:139-151. doi: 10.1111/ j.1574-6941.2001.tb00834.x
37. Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J et al (2004) Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 6:347-363. doi: 10.1111/ j.1462-2920.2004.00582.x
38. Wang Y, Zhang ZS, Ruan JS, Wang YM, Ali SM (1999) Investigation of actinomycete diversity in the tropical rainforests of Singapore. J Ind Microbiol Biotechnol 23:178-187
39. Wawrik B, Kudiev D, Abdivasievna UA, Kukor JJ, Zystra GJ, Kerkhof L (2007) Biogeography of actinomycete communities and type II polyketide synthase genes in soils collected in New Jersey and Central Asia. Appl Environ Microbiol 73:2982-2989. doi: 10.1128/AEM.02611-06
40. Wohl DL, McArthur JV (1998) Actinomycete-flora associated with submersed freshwater macrophytes. FEMS Microbiol Ecol 26:135-140. doi: 10.1111/ j.1574-6941.1998.tb00499.x
41. Zakalyukina YV, Zenova GM, Zvyagintsev DG (2002) Acidophilic soil actinomycetes. Microbiology 71:342-345. doi: 10.1023/A:1015819131117
42. Zhang QC, Wang GH, Yao HY (2007) Phospholipid fatty acid patterns of microbial communities in paddy soil under different fertilizer treatments. J Environ Sci (China) 19:55-59. doi: 10.1016/ S1001-0742(07)60009-6
43. Zhou J, Xia B, Treves DS, Wu LY, Marsh TL, O'Neill RV et al (2002) Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol 68:326-334. doi: 10.1128/ AEM.68.1.326-334.2002