Microarrays Research Today is a free monthly online journal that collates and summarizes the latest research about Microarrays, including details on experiments, designs, statistics, analysis, software.

Application of a nifH oligonucleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats.

Moisander PH, Shiue L, Steward GF, Jenkins BD, Bebout BM, Zehr JP

Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA. pmoisander@pmc.ucsc.edu

Diazotrophic community structure in microbial mats from Guerrero Negro (GN), Baja California, Mexico, was studied using polymerase chain reaction amplification of the nifH gene and a newly developed nifH oligonucleotide microarray. Ninety-six oligonucleotide probes designed for nifH sequences from cultivated isolates and the environment were printed on glass microarrays. Phylogenetic analysis showed that the probes represented all of the main nifH clusters. Specificity was tested by (i) evaluation of cross hybridization using individual targets, and (ii) comparison of the observed hybridization signals and those predicted from the sequences cloned from microbial mats. Signal intensity had a positive relationship with target concentration and the percentage identity between probe and target. Under moderate stringency and high target concentration, specificity of the probes varied from 77% to 100% with the individual targets tested. At the end of a 7-month long nutrient manipulation experiment in GN microbial mats, no expression of nitrogen fixation under nitrogen loading was detected, although a diverse community of diazotrophs was detected. The diversity in diazotrophic population present was higher than in the population expressing the nifH gene, and there were taxa specific differences in response to nutrients. The nifH microarray is a powerful tool for diazotroph community analysis in the marine environment.

Published 8 September 2006 in Environ Microbiol, 8(10): 1721-35.
Full-text of this article is available online (may require subscription).

© 2004-2008 Microarrays Research Today. All Rights Reserved.