Semi-automated genetic analyses of soil microbial communities: comparison of T-RFLP and RISA based on descriptive and discriminative statistical approaches

Journal of Microbiological Methods - Tập 61 - Trang 349-360 - 2005
Martin Hartmann1, Beat Frey2, Roland Kölliker1, Franco Widmer1
1Molecular Ecology, Agroscope FAL Reckenholz, Swiss Federal Research Station for Agroecology and Agriculture, Reckenholzstrasse 191, 8046 Zürich, Switzerland
2Soil Ecology, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), 8903 Birmensdorf, Switzerland

Tài liệu tham khảo

Anderson, 1978, Physiological method for quantitative measurement of microbial biomass in soils, Soil Biology & Biochemistry, 10, 215, 10.1016/0038-0717(78)90099-8 Blackwood, 2003, Terminal restriction fragment length polymorphism data analysis for quantitative comparison of microbial communities, Applied and Environmental Microbiology, 69, 926, 10.1128/AEM.69.2.926-932.2003 Blagodatskaya, 2003, Quantitative isolation of microbial DNA from different types of soils of natural and agricultural ecosystems, Microbiology, 72, 744, 10.1023/B:MICI.0000008379.63620.7b Bochner, 1989, Breathprints at the microbial level, ASM News, 50, 536 Borcard, 1992, Partialling out the spatial component of ecological variation, Ecology, 73, 1045, 10.2307/1940179 Borneman, 1997, Molecular microbial diversity in soils from eastern Amazonia: evidence for unusual microorganisms and microbial population shifts associated with deforestation, Applied and Environmental Microbiology, 63, 2647, 10.1128/AEM.63.7.2647-2653.1997 Braker, 2001, Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes, Applied and Environmental Microbiology, 67, 1893, 10.1128/AEM.67.4.1893-1901.2001 Bruce, 1997, Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent PCR restriction fragment length polymorphism profiling, Applied and Environmental Microbiology, 63, 4914, 10.1128/AEM.63.12.4914-4919.1997 Buckley, 2001, The structure of microbial communities in soil and the lasting impact of cultivation, Microbial Ecology, 42, 11, 10.1007/s002480000108 Bundt, 2001, Preferential flow paths: biological ‘hot spots’ in soils, Soil Biology & Biochemistry, 33, 729, 10.1016/S0038-0717(00)00218-2 Bürgmann, 2001, A strategy for optimizing quality and quantity of DNA extracted from soil, Journal of Microbiological Methods, 45, 7, 10.1016/S0167-7012(01)00213-5 Casamayor, 2002, Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern, Environmental Microbiology, 4, 338, 10.1046/j.1462-2920.2002.00297.x Colwell, 2000 Duarte, 1998, Extraction of ribosomal RNA and genomic DNA from soil for studying the diversity of the indigenous bacterial community, Journal of Microbiological Methods, 32, 21, 10.1016/S0167-7012(98)00004-9 Dunbar, 2000, Assessment of microbial diversity in four southwestern United States soils by 16S rRNA gene terminal restriction fragment analysis, Applied and Environmental Microbiology, 66, 2943, 10.1128/AEM.66.7.2943-2950.2000 Dunbar, 2001, Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities, Applied and Environmental Microbiology, 67, 190, 10.1128/AEM.67.1.190-197.2001 Felske, 2000, Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes, Applied and Environmental Microbiology, 66, 3998, 10.1128/AEM.66.9.3998-4003.2000 Fisher, 1999, Automated approach for ribosomal intergenic spacer analysis of microbial diversity and ITS application to freshwater bacterial communities, Applied and Environmental Microbiology, 65, 4630, 10.1128/AEM.65.10.4630-4636.1999 Fromin, 2002, Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns, Environmental Microbiology, 4, 634, 10.1046/j.1462-2920.2002.00358.x Heuer, 1997, Analysis of actinomycete communities by specific amplification of genes encoding 16S rRNA and gel-electrophoretic separation in denaturing gradients, Applied and Environmental Microbiology, 63, 3233, 10.1128/AEM.63.8.3233-3241.1997 Hofman, 2003, Biochemical analysis of soil organic matter and microbial biomass composition—a pilot study, European Journal of Soil Biology, 39, 217, 10.1016/j.ejsobi.2003.08.002 Jensen, 1993, Rapid identification of bacteria on the basis of polymerase chain reaction-amplified ribosomal DNA spacer polymorphisms, Applied and Environmental Microbiology, 59, 945, 10.1128/AEM.59.4.945-952.1993 Kennedy, 1995, Soil microbial diversity and the sustainability of agricultural soils, Plant and Soil, 170, 75, 10.1007/BF02183056 Kennedy, 2004, Impact of lime, nitrogen and plant species on bacterial community structure in grassland microcosms, Environmental Microbiology, 6, 1070, 10.1111/j.1462-2920.2004.00638.x Kropf, 2004, Significance test for comparing complex microbial community fingerprints using pairwise similarity measures, Journal of Microbiological Methods, 57, 187, 10.1016/j.mimet.2004.01.002 Lee, 1996, Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism, Applied and Environmental Microbiology, 62, 3112, 10.1128/AEM.62.9.3112-3120.1996 Leps, 2003 Liu, 1997, Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA, Applied and Environmental Microbiology, 63, 4516, 10.1128/AEM.63.11.4516-4522.1997 Ludwig, 2004, ARB: a software environment for sequence data, Nucleic Acids Research, 32, 1363, 10.1093/nar/gkh293 Lueders, 2001, Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage, Environmental Microbiology, 3, 194, 10.1046/j.1462-2920.2001.00179.x Lukow, 2000, Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants, FEMS Microbiology Ecology, 32, 241, 10.1111/j.1574-6941.2000.tb00717.x Maidak, 2001, The RDP-II (ribosomal database project), Nucleic Acids Research, 29, 173, 10.1093/nar/29.1.173 Mantel, 1967, Detection of disease clustering and a generalized regression approach, Cancer Research, 27, 209 Marsh, 1999, Terminal restriction fragment length polymorphism (T-RFLP): an emerging method for characterizing diversity among homologous populations of amplification products, Current Opinion in Microbiology, 2, 323, 10.1016/S1369-5274(99)80056-3 Marstorp, 2000, Relationship between dsDNA, chloroform labile C and ergosterol in soils of different organic matter contents and pH, Soil Biology & Biochemistry, 32, 879, 10.1016/S0038-0717(99)00210-2 Moeseneder, 1999, Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis, Applied and Environmental Microbiology, 65, 3518, 10.1128/AEM.65.8.3518-3525.1999 Moyer, 1994, Estimation of diversity and community structure through restriction-fragment-length-polymorphism distribution analysis of bacterial 16S ribosomal-RNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii, Applied and Environmental Microbiology, 60, 871, 10.1128/AEM.60.3.871-879.1994 Muyzer, 1998, Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology, Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 73, 127, 10.1023/A:1000669317571 Muyzer, 1993, Profiling of complex microbial-populations by denaturing gradient gel-electrophoresis analysis of polymerase chain reaction-amplified genes-coding for 16S ribosomal RNA, Applied and Environmental Microbiology, 59, 695, 10.1128/AEM.59.3.695-700.1993 Nicolaisen, 2002, Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria, Journal of Microbiological Methods, 50, 189, 10.1016/S0167-7012(02)00026-X Normand, 1996, ITS analysis of prokaryotes, 1 Pesaro, 2002, Soil DNA content—a novel quantitative bulk parameter for description of microbiological soil characteristics Pesaro, 2003, Effects of freeze–thaw stress during soil storage on microbial communities and methidathion degradation, Soil Biology & Biochemistry, 35, 1049, 10.1016/S0038-0717(03)00147-0 Pesaro, 2004, Impact of soil drying–rewetting stress on microbial communities and activities and on degradation of two crop protection products, Applied Environmental Microbiology, 70, 2577, 10.1128/AEM.70.5.2577-2587.2004 Ranjard, 2001, Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability, Applied and Environmental Microbiology, 67, 4479, 10.1128/AEM.67.10.4479-4487.2001 Rohlf, 2000 Rosenblum, 1997, Improved single-strand DNA sizing accuracy in capillary electrophoresis, Nuclear Acids Research, 25, 3925, 10.1093/nar/25.19.3925 Schwieger, 1998, A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis, Applied and Environmental Microbiology, 64, 4870, 10.1128/AEM.64.12.4870-4876.1998 Shaffer, 2000, Temporal and spatial distribution of the nifH gene of N-2 fixing bacteria in forests and clearcuts in western Oregon, Microbial Ecology, 39, 12, 10.1007/s002489900183 Sigler, 2002, Microbial diversity and activity along the forefields of two receding glaciers, Microbial Ecology, 43, 397, 10.1007/s00248-001-0045-5 ter Braak, 2002 Tiedje, 1995, Approaches to the comprehensive evaluation of prokaryote diversity of a habitat, 73 Tiedje, 1999, Opening the black box of soil microbial diversity, Applied Soil Ecology, 13, 109, 10.1016/S0929-1393(99)00026-8 Torsvik, 2002, Microbial diversity and function in soil: from genes to ecosystems, Current Opinion in Microbiology, 5, 240, 10.1016/S1369-5274(02)00324-7 Vance, 1987, An extraction method for measuring soil microbial biomass C, Soil Biology & Biochemistry, 19, 703, 10.1016/0038-0717(87)90052-6 Widmer, 2001, Assessing soil biological characteristics: a comparison of bulk soil community DNA-, PLFA-, and BiologTM-analyses, Soil Biology & Biochemistry, 33, 1029, 10.1016/S0038-0717(01)00006-2 Zhang, 2004, Optimized sequence retrieval from single bands of temperature gradient gel electrophoresis profiles of the amplified 16S rDNA fragments from an activated sludge system, Journal of Microbiological Methods, 60, 1, 10.1016/j.mimet.2004.08.015