Molecular community analysis of microbial diversity

Current Opinion in Biotechnology

Volumn 13, Issue 3, 2002, Pages 213-217

  Dahllöf, Ingela ^a  

^a Department of Marine Ecology NERI ^*  (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID;

BIOTECHNOLOGY; DNA MICROARRAY; ECOLOGY; EXTRACTION; GENE AMPLIFICATION; MICROBIAL DIVERSITY; MICROORGANISM; MOLECULAR BIOLOGY; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REVIEW;

EID: 0036624813     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(02)00314-2     Document Type: Review

References (53)

1. Woese C.R. Bacterial evolution. Microbiol Rev. 51:1987;221-271.
2. Amann R. Who is out there? Microbial aspects of biodiversity. Syst Appl Microbiol. 23:2000;1-8.
3. Rossello-Mora R., Amann R. The species concept for prokaryotes. FEMS Microbiol Rev. 25:2001;39-67. A thorough review of the species concept in relation to eukaryotes, with a suggestion for a pragmatic phylophenetic species concept for prokaryotes.
4. Gupta R.S. The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes. FEMS Microbiol Rev. 24:2000;367-402.
5. Klappenbach J.A., Saxman P.R., Cole J.R., Schmidt T.M. rrndb: The ribosomal RNA operon copy number database. Nucleic Acids Res. 29:2001;181-184.
6. Shimizu T., Ohshima S., Ohtani K., Hoshino K., Honjo K., Hayashi H. Sequence heterogeneity of the ten rRNA operons in Clostridium perfringens. Syst Appl Microbiol. 24:2001;149-156.
7. McCaig A.E., Glover L.A., Prosser J.I. Numerical analysis of grassland bacterial community structure under different land management regimens by using 16S ribosomal DNA sequence data and denaturing gradient gel electrophoresis banding patterns. Appl Environ Microbiol. 67:2001;4554-4559.
8. Cocolin L., Manzano M., Cantoni C., Comi G. Denaturing gradient gel electrophoresis analysis of the 16S rRNA gene V1 region to monitor dynamic changes in the bacterial population during fermentation of Italian sausages. Appl Environ Microbiol. 67:2001;5113-5121.
9. Schmalenberger A., Schwieger F., Tebbe C.C. Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Appl Environ Microbiol. 67:2001;3557-3563. This study demonstrates how the choice of universal 16S primers can affect diversity analysis.
10. Petri R., Imhoff J.F. Genetic analysis of sea-ice bacterial communities of the Western Baltic Sea using an improved double gradient method. Polar Biol. 24:2001;252-257.
11. Qi Y.A., Patra G., Liang X.D., Williams L.E., Rose S., Redkar R.J., DelVecchio V.G. Utilization of the rpoB gene as a specific chromosomal marker for real-time PCR detection of Bacillus anthracis. Appl Environ Microbiol. 67:2001;3720-3727.
12. Meusnier I., Olsen J.L., Stam W.T., Destombe C., Valero M. Phylogenetic analyses of Caulerpa taxifolia (Chlorophyta) and of its associated bacterial microflora provide clues to the origin of the Mediterranean introduction. Mol Ecol. 10:2001;931-946.
13. Ranjard L., Poly F., Lata J.C., Mougel C., Thioulouse J., Nazaret S. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol. 67:2001;4479-4487.
14. Tilsala-Timisjarvi A., Alatossava T. Characterization of the 16S-23S and 23S-5S rRNA intergenic spacer regions of dairy propionibacteria and their identification with species-specific primers by PCR. Int J Food Microbiol. 68:2001;45-52.
15. Toth I.K., Avrova A.O., Hyman L.J. Rapid identification and differentiation of the soft rot erwinias by 16S-23S intergenic transcribed spacer-PCR and restriction fragment length polymorphism analyses. Appl Environ Microbiol. 67:2001;4070-4076.
16. Zhou J., Xia B., Treves D.S., Wu L.-Y., Marsh T.L., O'Neill R.V., Palumbo A.V., Tiedje J.M. Spatial and resource factors influencing high microbial diversity in soil. Appl Environ Microbiol. 68:2002;326-334. An excellent example of thoroughness when estimating diversity using 16S.
17. Dahllof I., Baillie H., Kjelleberg S. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol. 66:2000;3376-3380.
18. Allen A.E., Booth M.G., Frischer M.E., Verity P.G., Zehr J.P., Zani S. Diversity and detection of nitrate assimilation genes in marine bacteria. Appl Environ Microbiol. 67:2001;5343-5348.
19. Zézé A., Mutch L.A., Young J.P.W. Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soil. Environ Microbiol. 3:2001;363-370. The use of a specific gene to exclude all but the group of interest is successfully shown.
20. Aagot N., Nybroe O., Nielsen P., Johnsen K. An altered Pseudomonas diversity is recovered from soil by using nutrient-poor Pseudomonas-selective soil extract media. Appl Environ Microbiol. 67:2001;5233-5239.
21. Fjellbirkeland A., Torsvik V., Ovreas L. Methanotrophic diversity in an agricultural soil as evaluated by denaturing gradient gel electrophoresis profiles of pmoA, mxaF and 16S rDNA sequences. Antonie Van Leeuwenhoek. 79:2001;209-217.
22. Horz H.P., Yimga M.T., Liesack W. Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling. Appl Environ Microbiol. 67:2001;4177-4185.
23. Purkhold U., Pommerening-Roser A., Juretschko S., Schmid M.C., Koops H.P., Wagner M. Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol. 66:2000;5368-5382. An important comparison of genes for phylogenetic studies.
24. Smit E., Leeflang P., Gommans S., van den Broek J., van Mil S., Wernars K. Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol. 67:2001;2284-2291.
25. Amann R., Fuchs B.M., Behrens S. The identification of microorganisms by fluorescence in situ hybridisation. Curr Opin Biotechnol. 12:2001;231-236.
26. Hoshino T., Noda N., Tsuneda S., Hirata A., Inamori Y. Direct detection by in situ PCR of the amoA gene in biofilm resulting from a nitrogen removal process. Appl Environ Microbiol. 67:2001;5261-5266. An exciting alternative to FISH that can be used for all genes, active or not. This method opens the way to detection of functional gene expression.
27. Ravenschlag K., Sahm K., Amann R. Quantitative molecular analysis of the microbial community in marine Arctic sediments (Svalbard). Appl Environ Microbiol. 67:2001;387-395.
28. Martin-Laurent F., Philippot L., Hallet S., Chaussod R., Germon J.C., Soulas G., Catroux G. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol. 67:2001;2354-2359. A thorough study demonstrating the importance of the extraction step.
29. Stach J.E.M., Bathe S., Clapp J.P., Burns R.G. PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods. FEMS Microbiol Ecol. 36:2001;139-151.
30. Bachoon D.S., Otero E., Hodson R.E. Effects of humic substances on fluorometric DNA quantification and DNA hybridization. J Microbiol Methods. 47:2001;73-82.
31. Small J., Call D.R., Brockman F.J., Straub T.M., Chandler D.P. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol. 67:2001;4708-4716. Introduces a sensitive microarray analysis avoiding the PCR step.
32. Bavykin S.G., Akowski J.P., Zakhariev V.M., Barsky V.E., Perov A.N., Mirzabekov A.D. Portable system for microbial sample preparation and oligonucleotide microarray analysis. Appl Environ Microbiol. 67:2001;922-928. An example of an easy to use, rapid technology that is needed within microbial ecology.
33. Wu L., Thompson D.K., Li G., Hurt R.A., Tiedje J.M., Zhou J. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl Environ Microbiol. 67:2001;5780-5790.
34. Becker S., Boger P., Oehlmann R., Ernst A. PCR bias in ecological analysis: a case study for quantitative Taq nuclease assays in analyses of microbial communities. Appl Environ Microbiol. 66:2000;4945-4953.
35. Kurata S, Kanagawa T, Kamagata Y, Yamada K, Yokumako T, Torimura M, Kurane R: T-RFLP analysis using a new real-time quantitative PCR method with a quenching primer (QP-PCR). In Ninth International Symposium on Microbial Ecology (ISME-9): 2001 August 26-31; Amsterdam.
36. Schäfer H., Bernard L., Courties C., Lebaron P., Servais P., Pukall R., Stackebrandt E., Troussellier M., Guindulain T., Vives-Rego J., Muyzer G. Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEMS Microbiol Ecol. 34:2001;243-253.
37. Ishii K., Fukui M. Optimization of annealing temperature to reduce bias caused by a primer mismatch in multitemplate PCR. Appl Environ Microbiol. 67:2001;3753-3755. Highlights the importance of annealing temperature for diversity estimates.
38. Marsh T.L. Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products. Curr Opin Microbiol. 2:1999;323-327.
39. Sekiguchi H., Tomioka N., Nakahara T., Uchiyama H. A single band does not always represent single bacterial strains in denaturing gradient gel electrophoresis analysis. Biotechnol Lett. 23:2001;1205-1208.
40. Call D.R., Brockman F.J., Chandler D.P. Detecting and genotyping Escherichia coli O157: H7 using multiplexed PCR and nucleic acid microarrays. Int J Food Microbiol. 67:2001;71-80.
41. Spiro A., Lowe M., Brown D. A bead-based method for multiplexed identification and quantitation of DNA sequences using flow cytometry. Appl Environ Microbiol. 66:2000;4258-4265.
42. Hughes J.B., Hellmann J.J., Ricketts T.H., Bohannan B.J.M. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol. 67:2001;4399-4406. Gives insight and recommendations on how to estimate diversity.
43. Dees P.M., Ghiorse W.C. Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol. 35:2001;207-216.
44. Kaiser O., Puhler A., Selbitschka W. Phylogenetic analysis of microbial diversity in the rhizoplane of oilseed rape (Brassica napus cv. Westar) employing cultivation-dependent and cultivation-independent approaches. Microb Ecol. 42:2001;136-149. Comprehensive comparison of diversity estimated by culturing and cloning of 16S.
45. De Fede K.L., Panaccione D.G., Sexstone A.J. Characterization of dilution enrichment cultures obtained from size-fractionated soil bacteria by BIOLOG((R)) community-level physiological profiles and restriction analysis of 16S rRNA genes. Soil Biol Biochem. 33:2001;1555-1562.
46. Eder W., Jahnke L.L., Schmidt M., Huber R. Microbial diversity of the brine-seawater interface of the Kebrit Deep, Red Sea, studied via 16S rRNA gene sequences and cultivation methods. Appl Environ Microbiol. 67:2001;3077-3085. An advanced culturing technique with high environmental relevance is used together with a polyphasic approach.
47. Bollmann A., Laanbroek H.J. High prokaryote diversity and analysis of community structure in mobile mud deposits off French Guiana: identification of two new bacterial candidate divisions. FEMS Microbiol Ecol. 37:2001;211-221.
48. Purdy K.J., Nedwell D.B., Embley T.M., Takii S. Use of 16S rRNA-targeted oligonucleotide probes to investigate the distribution of sulphate-reducing bacteria in estuarine sediments. FEMS Microbiol Ecol. 36:2001;165-168.
49. Kirby R.R., Reid P.C. PCR from the CPR offers a historical perspective marine population ecology. J Mar Biol Ass UK. 81:2001;539-540.
50. Smalla K., Wieland G., Buchner A., Zock A., Parzy J., Kaiser S., Roskot N., Heuer H., Berg G. Bulk and rhizosphere soil bacterial communities studied by denaturing gradient gel electrophoresis: plant-dependent enrichment and seasonal shifts revealed. Appl Environ Microbiol. 67:2001;4742-4751.
51. Ibekwe A.M., Papiernik S.K., Gan J., Yates S.R., Yang C.H., Crowley D.E. Impact of fumigants on soil microbial communities. Appl Environ Microbiol. 67:2001;3245-3257.
52. Hurt R.A., Qiu X.Y., Wu L.Y., Roh Y., Palumbo A.V., Tiedje J.M., Zhou J.H. Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol. 67:2001;4495-4503.
53. Bachoon D.S., Hodson R.E., Araujo R. Microbial community assessment in oil-impacted salt marsh sediment microcosms by traditional and nucleic acid-based indices. J Microbiol Methods. 46:2001;37-49.