Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman

Abstract

Biological soil crusts (biocrusts) occur within drylands throughout the world, covering ~12% of the global terrestrial soil surface. Their occurrence in the deserts of the Arabian Peninsula has rarely been reported and their spatial distribution, diversity, and microbial composition remained largely unexplored. We investigated biocrusts at six different locations in the coastal and central deserts of Oman. The biocrust types were characterized, and the bacterial and fungal community compositions of biocrusts and uncrusted soils were analysed by amplicon sequencing. The results were interpreted based on the environmental parameters of the different sites. Whereas at lowland sites, mainly cyanobacteria-dominated biocrusts were observed, both cyanobacteria- and lichen-dominated biocrusts occurred at mountain sites. The majority of bacterial sequences (32-83% of total sequences) belonged to Actinobacteria, Cyanobacteria, Alphaproteobacteria, and Bacteroidetes, whereas fungal sequences belonged to Ascomycota, Basidiomycota, and Chytridiomycota (>95%). With biocrust development, a notable increase in cyanobacterial and decrease in actinobacterial proportions was observed for cyanobacteria-dominated crusts. In coastal areas, where salinity is high, biocrusts were replaced by a unique marine mat-like microbial community, dominated by halotolerant taxa. Redundancy analysis revealed a significant contribution of soil texture, cover type, carbon content, and elevation to the variations in bacterial and fungal communities. Multivariate analysis placed microbial communities in significantly separated clusters based on their carbon content, elevation and electrical conductivity. We conclude that Oman hosts a variety of cyanobacteria- and lichen-dominated crusts with their bacterial and fungal communities being largely dictated by soil properties and environmental parameters.

Figure 1

Map composition presenting the sampling locations and sample types in the Sultanate of Oman. Framed and serially numbered pictures show the different sampling locations. On the right hand side close-up pictures of different biocrust types and bare soil samples are shown (A) bare soil; (B) cyanobacteria-dominated biocrust; (C) cyanobacteria-dominated biocrust with cyanolichen; (D) chlorolichen-dominated biocrust with Placidium sp.; (E) chlorolichen-dominated biocrust with Psora sp. and cyanolichens; (F) salt crust with microbial communities growing inside the crust; (G) soft, marine microbial mats (cross section)). Topographic information obtained from the NASA Shuttle Radar Topography Mission (SRTM). All maps were created using ArcGIS Desktop 10.3 (Copyright(©) 1995–2015 ESRI; License acquired by the university of Almeria thought the agreement between University and Centro Informático Científico de Andalucía, CICA). Country boundaries were obtained from the FGGD coastal and country boundaries of the world 1.0 (2007; http://ref.data.fao.org/map?entryId = 18329470-472d-11db-88e0-000d939bc5d8&tab = metadata).

Figure 2

PCA plot of environmental parameters. Color, shape, and size of points indicate sampling location, surface cover type, and soil texture, respectively. Based on their environmental characteristics, samples group into 3 distinct categories, shown as shaded hulls: disturbed (red), marine (blue), and elevated (green) sites. TC and TN refer to total carbon and total nitrogen, respectively.

Figure 3

Bacterial and fungal richness (number of OTUs). Color, shape, and size of points indicate sampling location, surface cover type, and soil texture, respectively. The sample color codes are as in Fig. 2.

Figure 4

Non-metric multidimensional scaling (NMDS) plot based on Bray-Curtis dissimilarity of bacterial and fungal communities. Color, shape, and size of points indicate sampling location, surface cover type, and soil texture, respectively. Dotted lines show clusters with a maximum intra-group dissimilarity of 0.7. Solid lines group samples with similar elevation. Shaded hulls indicate organic carbon content (TC in %).

Figure 5

Bacterial community composition on phylum and genus level. Order of plots from top to bottom: hierarchical cluster diagram based on Bray-Curtis dissimilarity, bar plot of relative sequence proportions of dominant bacterial phyla (class-level taxonomy for Proteobacteria), heatmap of dominant genera (white: no sequences), total sequence proportion of genera displayed in heatmap.

Figure 6

Fungal community composition on phylum and genus level. Order of plots from top to bottom: hierarchical cluster diagram based on Bray-Curtis dissimilarity, bar plot of relative sequence proportions of dominant bacterial phyla, heatmap of dominant genera (white: no sequences), total sequence proportion of genera displayed in heatmap.