Identification and analysis of PCB dechlorinating anaerobic enrichments by amplification: accuracy of community structure based on restriction analysis and partial sequencing of 16S rRNA genes.
The composition of polychlorinated biphenyl (PCB) dechlorinating mixed communities was analysed by restriction fragment length polymorphism of PCR amplified rDNAs (ARDRA) and partial sequencing of 16S rRNA genes amplified from PCB degrading enrichments. Restriction analysis confirms that the 16S rRNA genes amplified from PCB dechlorinating communities vary depending on the PCB congener dechlorinated. Comparison of 16S rRNA sequences to published ribosomal databases indicates that the two most abundant Operational Taxonomic Units (OTUs) appear to be species of the genus Clostridium. The amount that the amplification procedure contributed to this result was determined by varying the amplification procedure and by creating an artificial template mixture. Varying the amount of template by sixfold in the amplification did not affect the distribution of OTUs but the number of OTUs observed decreased with decreasing template concentration. Comparison of products amplified from mixtures of 16S rDNA clones indicates that the more abundant Clostridium OTU did not amplify more efficiently than those of less abundant OTUs. Hybridization to a probe designed to detect the most abundant OTUs indicates that two other OTUs are closely related to this Clostridium species.
LaMontagne
M G
MG
Department of Biology, Howard University, Washington, D.C., USA.
Davenport
G J
GJ
Hou
L H
LH
Dutta
S K
SK
D001421:Bacteria, Anaerobic / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism*; D001673:Biodegradation, Environmental; D003013:Clostridium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D004275:DNA, Ribosomal / Q000032:analysis; D017753:Ecosystem; D011078:Polychlorinated Biphenyls / Q000378:metabolism*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012407:rRNA Operon
D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D011078:Polychlorinated Biphenyls