Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat

Abstract

Intertidal microbial mats are comprised of distinctly colored millimeter-thick layers whose communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We used molecular techniques to determine how the mat’s layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer. The SSU-rRNA reads were dominated by Cyanobacteria and Chromatiales, but contained a high taxonomic diversity. The composition of each mat core was significantly different for developmental stage, year, and layer. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria below the surface layer, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as oxygenic phototrophs, was measured. Overall, trait diversity measured by orthologous genes was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can impact our ability to test hypotheses pertaining to community assembly. Our results demonstrate that given the appropriate physiochemical conditions, strong phylogenetic, and trait variation, as well as habitat filtering, can occur at the millimeter-scale.

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

“…Following previous notions of scale dependency in plant communities (Levin, 1992;Cavender-Bares et al, 2006Swenson et al, 2006Swenson et al, , 2007 and the idea of beta-versus alpha-niche (Silvertown et al, 2006a, b), we might postulate that large-scale processes such as climatic tolerances (beta-niche) may be better evidenced by broadly resolved community profiles ( Figures 1a and b); whereas, small-scale processes such as biotic interactions and microhabitat differentiation (alpha-niche) may only be evident with fine-level classification data (Figure 1c). With respect to prokaryotes with small cell size and short generation time (as considered in this study), a typical sampling setup probably emphasizes the effect of β-niche (evidenced by broadly resolved taxonomic data), whereas the effect of α-niche may be underestimated because of measurement limitations for biotic properties and microhabitat conditions (Ranjard and Richaume, 2001;Armitage et al, 2012).…”

Disturbance opens recruitment sites for bacterial colonization in activated sludge

“…Based on the taxa.labels algorithm with presence/absence option, mean MPDSES values of the activated sludge increased significantly as the disturbance progressed: 0.89 ± 0.62 (pre-disturbance) to a maximum of 3.23 ± 0.48 during the 3-day SRT and recovery period followed by a return to pre-disturbance levels, 1.50 ± 0.80. The inability of the independent swap algorithm to detect niche-based community assembly is likely a result of its known conservatism (Kembel, 2009;Armitage et al, 2012), but does not change our interpretation of phylogenetic structure. limiting similarity) (MPDSES = 2.95 ± 0.57, P < 0.005) and indicate that co-occurring species are significantly less related than expected by chance.…”

Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities

“…The millimetre scale vertically stratified communities and steep physicochemical gradients give ample opportunities for niche differentiation and the co‐existence of competing microorganisms, but few studies actually considered aspects of phylogenetic clustering and trait diversity along these physicochemical gradients. Armitage and colleagues () observed remarkable differences in microbial diversity when analysing different layers of a salt marsh microbial mat. They concluded that habitat filtering was an important factor for the assembly of these mat layers, except for the top layer of cyanobacteria where the phylogenetic diversity was high and trait richness relatively low.…”