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ISME J. 2010 May;4(5):633-41. doi: 10.1038/ismej.2009.152. Epub 2010 Jan 21.

Ecological and evolutionary factors underlying global and local assembly of denitrifier communities.

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Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.


The conversion of nitrite to nitric oxide in the denitrification pathway is catalyzed by at least two structurally dissimilar nitrite reductases, NirS and NirK. Although they are functionally equivalent, a genome with genes encoding both reductases has yet to be found. This exclusivity raises questions about the ecological equivalency of denitrifiers with either nirS or nirK, and how different ecological and evolutionary factors influence community assembly of nirS and nirK denitrifiers. Using phylogeny-based methods for analyzing community structure, we analyzed nirS and nirK data sets compiled from sequence repositories. Global patterns of phylogenetic community structure were determined using Unifrac, whereas community assembly processes were inferred using different community relatedness metrics. Similarities between globally distributed communities for both genes corresponded to similarities in habitat salinity. The majority of communities for both genes were phylogenetically clustered; however, nirK marine communities were more phylogenetically overdispersed than nirK soil communities or nirS communities. A more in-depth analysis was performed using three case studies in which a comparison of nirS and nirK community relatedness within the sites could be examined along environmental gradients. From these studies we observed that nirS communities respond differently to environmental gradients than nirK communities. Although it is difficult to attribute nonrandom patterns of phylogenetic diversity to specific niche-based or neutral assembly processes, our results indicate that coexisting nirS and nirK denitrifier communities are not under the same community assembly rules in different environments.

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