RRNA genes

Inagaki F et al. (2004) Characterization of Cl-metabolizing prokaryotic communities in methane seep habitat at the Kurishima Knoll, Southern Tyuku Arc, by analysing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 70 7445-7455. 

A stable mixed cnltnre that could degrade benzene was established, and the specihc role of sulfate-redncing bacteria was inferred from the inhibition of degradation in the presence of molybdate. The consortium was characterized from the sequence of small snbnnit rRNA genes, some of which could be assigned to the family Desulfobacteriaceae (Phelps et al. 1998). 

El Fantroussi S, L Verschuere, W Verstraete, EM Top (1999) Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. Appl Environ Microbiol 65 982-988. 

Padmanabhan P, S Padmanabhan, C DeRito, A Gray, D Gannon, JR Snape, DC Tsai, W Park, C Jeon, EL Madsen (2003) Respiration of C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of C-labeled soil DNA. Appl Environ Microbiol 69 1614-1622. 

Briglia M, RIL Eggen, WM de Vos et al. (1996) Rapid and sensitive method for the detection of Mycobacterium chlorophenolicum PCP-1 in soil based on 16S rRNA gene-targeted PCR. Appl Environ Microbiol 62 1478-1480. 

Shrimp Primer for shrimp detechon, FASMAC Co., Ltd. 16S rRNA gene of mitochondrial DNA 187... 

A. Willems, and M. D. Collins, Phylogenetic analysis of rhiz.obia and agrobacteria based on 16S rRNA gene sequences. Int. J. Syst. Bacteriol. 43 305-313 (1993). 

The larger 16S rRNA gene (—1600 nucleotides) allows a broader phylogenetic analysis and a range of methods using 16S rRNA are available for the study of diversity within natural microbial populations. Four of these are addressed below. 

G. C.-Y. Wang and Y. Wang, The frequency of chimeric molecules as a consequence of PCR co-amplification of 16S rRNA genes from different bacterial species, Microbiology 142 107 (1996). 

Patel, J. B. 16S rRNA gene sequencing for bacterial pathogen identification in the clinical laboratory. Mol. Diagn. 2001, 6, 313-321. 

Small subunit rRNA gene sequences have been determined for a large number of nematode taxa distributed across the phylum (Ellis et al., 1986 Zarlenga et al, 1994a,b Fitch et al., 1995 Fitch and Thomas, 1997 Aleshin et al, 1998 Blaxter et al., 1998 Kampfer et al, 1998 Dorris et al., 1999). These can thus be used to examine the relationships of the different nematode orders. The pattern of nematode evolution that emerges is... 

Fig. 1.1. The phylogenetic structure of the Nematoda revealed by small subunit ribosomal RNA analysis. (A) Neighbour-joining (NJ) analysis of aligned ssu rRNA genes from nematodes. The alignment is based on that of Blaxter etal. (1998), with the addition of sequences from Aleshin etal. (1998), Nadler (1998)...

Aleshin, V.V., Kedrova, O.S., Milyutina, LA, Vladychenskaya, N.S. and Petrov, N.B. (1998) Relationships among nematodes based on the analysis of 18S rRNA gene sequences molecular evidence for a monophyly of chromadorian and secernentean nematodes. Russian Journal of Nematology 6, 175-184. 

Evaluation of P. nitroreducens with quinoline as the sole source of nitrogen showed a reduction of the total nitrogen content by 85%. The partial sequence of the 16S-rRNA gene of this Gram-negative, rod-shaped bacterium was determined and shown to be close to P. alcaligenes and P. stutzeri. 

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