Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR.

ABSTRACT: Molecular methods to investigate functional groups in microbial communities rely on the specificity and selectivity of the primer set towards the target. Here, using rapid sand filters for drinking water production as model environment, we investigated the consistency of two commonly used quantitative PCR methods to enumerate ammonia-oxidizing bacteria (AOB): one targeting the phylogenetic gene 16S rRNA and the other, the functional gene amoA. Cloning-sequencing with both primer sets on DNA from two waterworks revealed contrasting images of AOB diversity. The amoA-based approach preferentially recovered sequences belonging to Nitrosomonas Cluster 7 over Cluster 6A ones, while the 16S rRNA one yielded more diverse sequences belonging to three AOB clusters, but also a few non-AOB sequences,

SUBMITTER: Dechesne A 

PROVIDER: S-EPMC4919994 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature