Review and re-analysis of domain-specific 16S primers

Baker, 1999, Prototheca richardsi, a pathogen of anuran larvae, is related to a clade of protistan parasites near the animal-fungal divergence, Microbiology, 145, 1777, 10.1099/13500872-145-7-1777 Baker, 2001, Bacterial community analysis of Indonesian hot springs, FEMS Microbiol. Lett., 200, 103, 10.1111/j.1574-6968.2001.tb10700.x Barns, 1994, Remarkable archaeal diversity detected in Yellowstone national Park hot spring environment, Proc. Natl. Acad. Sci. U. S. A., 91, 1609, 10.1073/pnas.91.5.1609 Barns, 1996, Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences, PNAS, 93, 9188, 10.1073/pnas.93.17.9188 Brunk, 1998, Quantitative measure of small subunit rRNA gene sequences of the Kingdom Korarchaeota, Appl. Environ. Microbiol., 64, 5064, 10.1128/AEM.64.12.5064-5066.1998 Burggraf, 1997, A pivotal archaea group, Nature (London), 385, 780, 10.1038/385780a0 Casamayor, 2002, Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparision of genetic fingerprinting methods in a multipond solar saltern scaling plots, Environ. Microbiol., 4, 338, 10.1046/j.1462-2920.2002.00297.x Coloqhoun, J.A., 1997. Discovery of deep-sea actinomycetes. PhD Dissertation. Research School of Biosciences. University of Kent, Canterbury. DasSarma, 1995, 269 DeLong, 1994, High abundance of Archaea in Antarctic marine picoplankton, Nature, 371, 695, 10.1038/371695a0 Elwood, 1985, The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata, Mol. Biol. Evol., 2, 399 Farelly, 1995, Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species, Appl. Environ. Microbiol., 61, 2798, 10.1128/AEM.61.7.2798-2801.1995 Groflkopf, 1998, 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, 960, 10.1128/AEM.64.3.960-969.1998 Hansen, 1998, Biased 16S rDNA PCR amplication caused by interference from DNA flanking template region, FEMS Microbiol. Ecol., 26, 141, 10.1111/j.1574-6941.1998.tb00500.x Hill, 2000, Methods for assessing the composition and diversity of soil microbial communities, Appl. Soil Ecol., 15, 25, 10.1016/S0929-1393(00)00069-X Hohn, 2002, Detection of 16S rDNA sequences representing the novel phylum “Nanoarchaeota”: indication for a wide distribution in high temperature biotopes, Syst. Appl. Microbiol., 25, 551, 10.1078/07232020260517698 Huber, 2002, A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont, Nature, 417, 63, 10.1038/417063a Huber, 2003, The phylum Nanoarchaeota: present knowledge and future perspectives of a unique form of life, Res. Microbiol., 154, 165, 10.1016/S0923-2508(03)00035-4 Hugenholtz, 1998, Novel division level bacterial diversity in a Yellowstone hot spring, J. Bacteriol., 180, 366, 10.1128/JB.180.2.366-376.1998 Jurgens, 1997, Novel group within the kingdom Crenarchaeota from boreal forest soil, Appl. Environ. Microbiol., 63, 803, 10.1128/AEM.63.2.803-805.1997 Jurgens, 2000, Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridisation, FEMS Microbiol. Ecol., 34, 45 Kim, 2000, A deeply branched novel phylotype found in Japanese paddy soils, Microbiology, 146, 2309, 10.1099/00221287-146-9-2309 Kolganova, 2002, Designing and testing oligonucleotide primers for amplification and sequencing of Archaeal 16S rRNA genes, Mikrobiologiya, 71, 283 Lee, 1996, Estimation of the abundance of an uncultured soil bacterial strain by a competitive quantitative PCR method, Appl. Environ. Microbiol., 62, 3787, 10.1128/AEM.62.10.3787-3793.1996 Lopez-Garcia, 2001, A novel haloarchaeal-related lineage is widely distributed in deep oceanic regions, Environ. Microbiol., 3, 72, 10.1046/j.1462-2920.2001.00162.x López-Garcı́a, 2002, Wide bacterial diversity associated with tubes of the vent worm Riftia pachyptila, Environ. Microbiol., 4, 204, 10.1046/j.1462-2920.2002.00286.x MacGregor, 1997, Crenarchaeota in Lake Michigan sediment, Appl. Environ. Microbiol., 63, 1178, 10.1128/AEM.63.3.1178-1181.1997 Marteinsson, 2001, Discovery and description of giant submarine smectite submarine cones on the seafloor, Eyjafjordur, Northern Iceland, a novel thermal microbial habitat, App. Environ. Microbiol., 67, 827, 10.1128/AEM.67.2.827-833.2001 Martinez-Murcia, 1995, Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments, FEMS Microbiol. Ecol., 17, 247, 10.1016/0168-6496(95)00029-A McInnery, 1995, Recovery and phylogenetic analysis of novel archaeal rRNA sequences from deep-sea deposit feeder, Appl. Environ. Microbiol., 61, 1646, 10.1128/AEM.61.4.1646-1648.1995 McPherson, 1995 Nielsen, 1999, Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorous removal reactor, Appl. Environ. Microbiol., 65, 1251, 10.1128/AEM.65.3.1251-1258.1999 Polz, 1998, Bias in template-to-product ratios in multi-template PCR, Appl. Environ. Microbiol., 64, 3724, 10.1128/AEM.64.10.3724-3730.1998 Reysenbach, 1995, 101 Reysenbach, 1992, Differential amplification of rRNA genes by polymerase chain reaction, Appl. Environ. Microbiol., 58, 3417, 10.1128/AEM.58.10.3417-3418.1992 Reysenbach, 1994, Phylogenetic analysis of the hyperthermophilic pink filament community in Octopus Spring, Yellowstone National Park, Appl. Environ. Microbiol., 60, 2113, 10.1128/AEM.60.6.2113-2119.1994 Rudi, 1997, Strain classification of oxyphotobacteria in clone cultures on the basis of 16S rRNA sequences from variable regions V6, V7 and V8, Appl. Environ. Microbiol., 63, 2593, 10.1128/AEM.63.7.2593-2599.1997 Schleper, 1998, Genomic analysis reveals chromosomal variation in natural populations of the uncultured psychrophilicarchaeon cenarchaeum symbiosum, J. Bacteriol., 180, 5003, 10.1128/JB.180.19.5003-5009.1998 Stach, 2001, PCR-SSCP comparison of 16S rDNA sequence diversity in soil obtained using different isolation and purification methods, FEMS Microbiol. Ecol., 36, 139, 10.1111/j.1574-6941.2001.tb00834.x Stern, 1993 Suzuki, 1996, Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR, Appl. Environ. Microbiol., 62, 625, 10.1128/AEM.62.2.625-630.1996 Tajima, 2001, Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens, FEMS Microbiol. Lett., 200, 67, 10.1111/j.1574-6968.2001.tb10694.x Theron, 2000, Molecular techniques for determining microbial diversity and community structure in natural environments, Crit. Rev. Microbiol., 26, 37, 10.1080/10408410091154174 Van de Peer, 1996, A quantitative map of nucleotide substitution rates in bacterial rRNA, Nucleic Acids Res., 24, 3381, 10.1093/nar/24.17.3381 van Waasbergen, 2000, Genetic diversity among Arthrobacter species collected across a heterogeneous series of terrestrial deep-subsurface sediments as determined on the basis of 16S rRNA and recA gene sequences, Appl. Environ. Microbiol., 66, 3454, 10.1128/AEM.66.8.3454-3463.2000 Vetriani, 1999, Population structure and phylogenetic characterisation of marine benthic Archaea in deep-sea sediments, Appl. Environ. Microbiol., 65, 4375, 10.1128/AEM.65.10.4375-4384.1999 Ward, 1990, 16S rRNA sequences reveal numerous uncultured micro-organisms in a natural community, Nature, 345, 63, 10.1038/345063a0 Watanabe, 2001, Design and evaluation of PCR primers to amplify 16S ribosomal DNA fragments used for community fingerprinting, J. Microbiol. Methods, 44, 253, 10.1016/S0167-7012(01)00220-2 Whitehead, 1999, Phylogenetic diversity of methanogenic Archaea in swine waste storage pits, FEMS Microbiol. Lett., 179, 223, 10.1111/j.1574-6968.1999.tb08731.x Wintzingerode, 1997, Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis, FEMS Microbiol. Rev., 21, 213, 10.1111/j.1574-6976.1997.tb00351.x