Real-time PCR detection of Holophagae (Acidobacteria) and Verrucomicrobia subdivision 1 groups in bulk and leek (Allium porrum) rhizosphere soils

Journal of Microbiological Methods

Volumn 83, Issue 2, 2010, Pages 141-148

  da Rocha, Ulisses Nunes ^a,b   van Elsas, Jan Dirk ^b   van Overbeek, Leonard Simon ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Acidobacteria; Allium porrum; Holophagae; QPCR; Rhizosphere; Verrucomicrobia subdivision 1

Indexed keywords

BACTERIAL DNA; BACTERIAL RNA; GENOMIC DNA; RNA 16S;

ACIDOBACTERIA; AMPLICON; ARTICLE; COMPUTER MODEL; GENE AMPLIFICATION; LEEK; LUTEOLIBACTER; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROSTHECOBACTER; REAL TIME POLYMERASE CHAIN REACTION; RHIZOSPHERE; RNA SEQUENCE; SOIL MICROFLORA; VERRUCOMICROBIA;

ALLIUM; BACTERIA; BACTERIOLOGICAL TECHNIQUES; DNA PRIMERS; DNA, BACTERIAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RHIZOSPHERE; RNA, RIBOSOMAL, 16S; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOIL MICROBIOLOGY;

ACIDOBACTERIA; ALLIUM PORRUM; BACTERIA (MICROORGANISMS); PROSTHECOBACTER; VERRUCOMICROBIA; VERRUCOMICROBIACEAE;

EID: 77957863316     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mimet.2010.08.003     Document Type: Article

References (29)

1. Barns S.M., Cain E.C., Sommerville L., Kuske C.R. Acidobacteria phylum sequences in uranium-contaminated subsurface sediments greatly expand the known diversity within the phylum. Appl. Environ. Microbiol. 2007, 73:3113-3116.
2. Barns S.M., Takala S.L., Kuske C.R. Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment. Appl. Environ. Microbiol. 1999, 65:1731-1737.
3. Cardenas E., Tiedje J.M. New tools for discovering and characterizing microbial diversity. Curr. Opin. Biotechnol. 2008, 19:544-549.
4. Chow M.L., Radomski C.C., McDermott J.M., Davies J., Axelrood P.E. Molecular characterization of bacterial diversity in Lodgepole pine (Pinus contorta) rhizosphere soils from British Columbia forest soils differing in disturbance and geographic source. FEMS Microbiol. Ecol. 2002, 42:347-357.
5. Da Rocha U.N., Andreote F.D., de Azevedo J.L., van Elsas J.D., van Overbeek L.S. Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere. J. Soils Sediments 2010, 10:326-339.
6. Edwards K.J. Performing real-time PCR. Real-time PCR: An Essential Guide 2004, 71-83. Horizon Bioscience, Norfolk. K. Edwards, J. Logan, N. Saunders (Eds.).
7. Fierer N., Bradford M.A., Jackson R.B. Towards an ecological classification of soil bacteria. Ecol. 2007, 88:1354-1366.
8. Haichar F.E.Z., Marol C., Berge O., Rangel-Castro J.I., Prosser J.I., Balesdent J., et al. Plant host habitat and root exudates shape soil bacterial community structure. ISME J. 2008, 2:1221-1230.
9. Hall J.R., Mitchell K.R., Jackson-Weaver O., Kooser A.S., Cron B.R., Crossey L.J., et al. Molecular characterization of the diversity and distribution of a thermal spring microbial community by using rRNA and metabolic genes. Appl. Environ. Microbiol. 2008, 74:4910-4922.
10. Hugenholtz P., Goebel B.M., Pace N.R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 1998, 180:4765-4774.
11. Jones R.T., Robeson M.S., Lauber C.L., Hamady M., Knight R., Fierer N. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 2009, 3:442-453.
12. Kielak A., Pijl A.S., Van Veen J.A., Kowalchuk G.A. Differences in vegetation composition and plant species identity lead to only minor changes in soil-borne microbial communities in a former arable field. FEMS Microbiol. Ecol. 2008, 63:372-382.
13. Kielak A., Pijl A.S., Van Veen J.A., Kowalchuk G.A. Phylogenetic diversity of Acidobacteria in a former agricultural soil. ISME J. 2009, 3:378-382.
14. Kumar S., Ne M., Dudley J., Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinform. 2008, 9:299-306.
15. Kuramae E.E., Gamper H.A., Yergeau E., Piceno Y.M., Brodie E.L., DeSantis T.Z., et al. Microbial secondary succession in a chronosequence of chalk grasslands. ISME J. 2010, 4:711-715.
16. Lee S.-H., Cho J.-C. Distribution patterns of the members of phylum Acidobacteria in global soil samples. J. Microbiol. Biotechnol. 2009, 19:1281-1287.
17. Liles M.R., Turkmen O., Manske B.F., Zhang M., Rouillard J.-M., George I., et al. A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction. Soil Biol. Biochem. 2010, 42:739-747.
18. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar A., et al. ARB: a software environment for sequence data. Nucleic Acids Res. 2004, 32:1363-1371.
19. Nunes Da Rocha U., Van Overbeek L., Van Elsas J.D. Exploration of hitherto-uncultured bacteria from the rhizosphere. FEMS Microbiol. Ecol. 2009, 69:313-328.
20. Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007, 35:7188-7196.
21. Ruijter J.M., Ramakers C., Hoogaars W.M.H., Karlen Y., Bakker O., van den Hoff M.J.B., et al. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res. 2009, 37:e45.
22. Sanguin H., Remenant B., Dechesne A., Thioulouse J., Vogel T.M., Nesme X., et al. Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities. Appl. Environ. Microbiol. 2006, 72:4302-4312.
23. Schlesner H., Jenkins C., Staley J.T. The Phylum Verrucomicrobia: a phylogenetically heterogeneous bacterial group. Prokaryotes 2006, 7:881-896.
24. Sipos R., Székely A.J., Palatinszky M., Révész S., Márialigeti K., Nikolausz M. Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol. Ecol. 2007, 60:341-350.
25. Stingl U., Tripp H.J., Giovannoni S.J. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J. 2007, 1:361-371.
26. van Elsas J.D., Costa R., Jansson J., Sjöling S., Bailey M., Nalin R., et al. The metagenomics of disease-suppressive soils-experiences from the METACONTROL project. Trends Biotechnol. 2008, 26:591-601.
27. Yoon J., Matsuo Y., Adachi K., Nozawa M., Matsuda S., Kasai H., et al. Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum 'Verrucomicrobia', and emended descriptions of the class Verrucomicrobiae the order Verrucomicrobiales and the family Verrucomicrobiaceae. Int. J. Syst. Evol. Microbiol. 2008, 58:998-1007.
28. Zengler K. Central role of the cell in microbial ecology. Microbiol. Mol. Biol. Rev. 2009, 73:712-729.
29. Zul D., Denzel S., Kotz A., Overmann J. Effects of plant biomass, plant diversity, and water content on bacterial communities in soil lysimeters: implications for the determinants of bacterial diversity. Appl. Environ. Microbiol. 2007, 73:6916-6926.