Effects of primary microenvironments on archaeal community composition in a semi-arid ecosystem

Background/Question/Methods

A large portion of the enormous biodiversity of soil microbial communities is likely caused by a similar diversity of soil microenvironments.  Recently, the ubiquity of archaea was established, however their niches in soil environments are not well characterized.  Nitrifying microbes play a key role transforming bioavailable nitrogen and ammonia-oxidizing archaea (AOA) often dominate ammonia-oxidizing bacteria (AOB) in soil communities.  In our study ecosystem, the Colorado shortgrass steppe, a plant-interspace spatial structure affects soil microenvironments dramatically, creating the principal patterns in soil resources and environmental properties.  We investigated the composition of AOA communities across this structure and related gradients of inorganic nitrogen to determine how small-scale environmental variation affects microbial diversity.   We sampled vegetated hummocks and bare interspace soil and measured soil properties (pH, moisture) and inorganic nitrogen concentrations (NH₄+ and NO₃-).  We built clone libraries (n=203) of AOA communities using the ammonia mono-oxygenase gene (amoA) and analyzed their compositions phylogenetically and with multivariate statistics.   

Results/Conclusions

The vegetated soils contained 23% higher NH₄+ (p<0.0001) than interspace, while the interspace soils contained 11% higher NO₃- (p=0.0002).  Vegetated soils contained greater total inorganic nitrogen (p<0.0001) and 13% greater moisture (p<0.0001) but there was no difference in pH. While diversity of recovered archaeal amoA sequences did not vary between vegetated and interspace soils, a maximum likelihood phylogeny of amoA sequences separated them into seven subclusters all of which fall into established Nitrososphaera subclusters.  One group, containing 10% of our sequences, is highly correlated with very low NH₄+ concentrations while another group, containing 6% of sequences, is highly correlated with high NH₄+ soils.  These relationships are also strongly supported by principal components analyses.  Thus we conclude that these lineages may have clearly defined ecotypes related to NH₄+ levels. 

This work has important implications for our understanding of microbial niches and their potential effects on nutrient cycling.  It shows that archaeal communities can be structured by environmental properties and resource availability at small-scale.