Relationship between soil parameters and phylotype richness, phylogenetic diversity and phylotype diversity for the whole community and Thaumarchaeota.

<p>We tested three models (linear-l, quadratic-q, and cubic-c) to describe the relatioships; model selection was carried out based on adjusted R² and RMSE (root mean square error; value not shown). Significance level was shown with***P<0.001;</p>**<p>P<0.01; and P<0.05; only relationships which were significant are shown in table.</p

Neighbor joining tree based on the alignment of 16S rRNA gene sequences (∼400 bp long) showing the relationship between archaeal phylotypes (DFT: Dominant Fuji Thaumarchaeota and DFE: Dominant Fuji Euryarchaeota) recovered from Mt. Fuji by pyrosequencing.

<p>The dominant soil thaumarchaeote DFT1 is indicated along representative archaeal isolates and clone 54d9. The tree is rooted with an AOB from bacterial phylum Proteobacteria.</p

Relationship between elevation and phylotype richness (left), phylogenetic diversity (middle), phylotype diversity (right) in the whole community (first row) and Thaumarchaeota (second row).

<p>We tested three models (linear, quadratic, and cubic) to describe the relationships and model selection was carried out based on adjusted R² and RMSE (root mean square error; value not shown). Significance level is shown with ***P<0.001; **P<0.01; and P<0.05.</p

Rarefaction analysis of one example from each elevational set of samples calculated for the 0.3 OTU definition (defined at ≥97% sequence similarity level) based on pairwise distance.

<p>Each line type denotes the elevation (meters above sea level) from which the samples were collected.</p

Elevational Patterns in Archaeal Diversity on Mt. Fuji

<div><p>Little is known of how archaeal diversity and community ecology behaves along elevational gradients. We chose to study Mount Fuji of Japan as a geologically and topographically uniform mountain system, with a wide range of elevational zones. PCR-amplified soil DNA for the archaeal 16 S rRNA gene was pyrosequenced and taxonomically classified against EzTaxon-e archaeal database. At a bootstrap cut-off of 80%, most of the archaeal sequences were classified into phylum Thaumarchaeota (96%) and Euryarchaeota (3.9%), with no sequences classified into other phyla. Archaeal OTU richness and diversity on Fuji showed a pronounced ‘peak’ in the mid-elevations, around 1500 masl, within the boreal forest zone, compared to the temperate forest zone below and the alpine fell-field and desert zones above. Diversity decreased towards higher elevations followed by a subtle increase at the summit, mainly due to an increase in the relative abundance of the group I.1b of Thaumarchaeota. Archaeal diversity showed a strong positive correlation with soil NH₄⁺, K and NO₃⁻_. Archaeal diversity does not parallel plant diversity, although it does roughly parallel bacterial diversity. Ecological hypotheses to explain the mid diversity bulge on Fuji include intermediate disturbance effects, and the result of mid elevations combining a mosaic of upper and lower slope environments. Our findings show clearly that archaeal soil communities are highly responsive to soil environmental gradients, in terms of both their diversity and community composition. Distinct communities of archaea specific to each elevational zone suggest that many archaea may be quite finely niche-adapted within the range of soil environments. A further interesting finding is the presence of a mesophilic component of archaea at high altitudes on a mountain that is not volcanically active. This emphasizes the importance of microclimate – in this case solar heating of the black volcanic ash surface – for the ecology of soil archaea.</p> </div

Heat map showing the percent relative abundance of the 10 most abundant phylotypes at different elevational sampling points with a color legend and scale provided.

<p>DFT here abbreviates for Dominant Fuji Thaumarchaeota and DFE for Dominant Fuji Euryarchaeota. The number written against them denotes their abundance e.g., DFT1 stands for the most abundant thaumarchaeotal phylotype present on Mt. Fuji.</p

Diversity indices of the fungal community across different land uses in Sabah, Malaysian Borneo.

<p>(a) OTU richness and (b) Chao1 index. Pairwise comparisons are shown; different letters denote significant differences between groups at P<0.05.</p

Comparison of relative abundance of the dominant fungal orders within the phyla Ascomycota and Basidiomycota among land uses^a.

a<p>Only orders for which significant differences were found are shown.</p>b<p>Effect of land use on relative abundance evaluated by linear or generalized linear model or by the Kruskal-Wallis test (*).</p>c<p>Pairwise comparisons by <i>post hoc</i> Tukey test for linear/generalized linear models or <i>P</i> values Bonferroni-corrected for Kruskal-Wallis. Differences were considered significant at a P value of <0.05.</p><p>Comparison of relative abundance of the dominant fungal orders within the phyla Ascomycota and Basidiomycota among land uses^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111525#nt101" target="_blank">a</a>}.</p

Relative abundance of dominant fungal phyla among different land uses in Sabah, Malaysian Borneo.

<p>Relative abundance of dominant fungal phyla among different land uses in Sabah, Malaysian Borneo.</p

Fungal community true β-diversity (i.e.

<p><b>) among the four land uses in Sabah, Malaysian Borneo.</b> Boxes show the lower quartile, the median and the upper quartile. Pairwise comparisons are shown; different letters denote significant differences between groups at P<0.05.</p