DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples.
A small scale DNA microarray containing a set of oligonucleotide probes targeting the 16S rRNAs of several groups of nitrifying bacteria was developed for the monitoring of wastewater treatment plant samples. The microarray was tested using reference rRNAs from pure cultures of nitrifying bacteria. Characterization of samples collected from an industrial wastewater treatment facility demonstrated that nitrifying bacteria could be detected directly by microarray hybridization without the need for PCR amplification. Specifically, the microarray detected Nitrosomonas spp. but did not detect Nitrobacter. The specificity and sensitivity of direct detection was evaluated using on-chip dissociation analysis, and by two independent analyses--an established membrane hybridization format and terminal restriction fragment length polymorphism fingerprinting (T-RFLP). The latter two analyses also revealed Nitrospira and Nitrobacter to be contributing populations in the treatment plant samples. The application of DNA microarrays to wastewater treatment systems, which has been demonstrated in the current work, should offer improved monitoring capabilities and process control for treatment systems, which are susceptible to periodic failures.
Kelly
John J
JJ
Department of Biology, Loyola University Chicago, 6525 N. Sheridan Rd, Chicago, IL 60626, USA. jkelly7@luc.edu
Siripong
Slil
S
McCormack
John
J
Janus
Lori R
LR
Urakawa
Hidetoshi
H
El Fantroussi
Said
S
Noble
Peter A
PA
Sappelsa
Laura
L
Rittmann
Bruce E
BE
Stahl
David A
DA
D016172:DNA Fingerprinting; D009573:Nitrites / Q000737:chemistry / Q000378:metabolism*; D009576:Nitrobacter / Q000235:genetics / Q000302:isolation & purification; D009606:Nitrosomonas / Q000235:genetics / Q000302:isolation & purification; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000032:analysis*; D012680:Sensitivity and Specificity; D013696:Temperature; D014865:Waste Disposal, Fluid / Q000379:methods*
D009573:Nitrites; D012336:RNA, Ribosomal, 16S