Biodiversity and Conservation

, Volume 23, Issue 7, pp 1709–1733 | Cite as

Niche partitioning of bacterial communities in biological crusts and soils under grasses, shrubs and trees in the Kalahari

  • David R. Elliott
  • Andrew D. Thomas
  • Stephen R. Hoon
  • Robin Sen
Original Paper


The Kalahari of southern Africa is characterised by sparse vegetation interspersed with microbe-dominated biological soil crusts (BSC) which deliver a range of ecosystem services including soil stabilisation and carbon fixation. We characterised the bacterial communities of BSCs (0–1 cm depth) and the subsurface soil (1–2 cm depth) in an area typical of lightly grazed Kalahari rangelands, composed of grasses, shrubs, and trees. Our data add substantially to the limited amount of existing knowledge concerning BSC microbial community structure, by providing the first bacterial community analyses of both BSCs and subsurface soils of the Kalahari region based on a high throughput 16S ribosomal RNA gene sequencing approach. BSC bacterial communities were distinct with respect to vegetation type and soil depth, and varied in relation to soil carbon, nitrogen, and surface temperature. Cyanobacteria were predominant in the grass interspaces at the soil surface (0–1 cm) but rare in subsurface soils (1–2 cm depth) and under the shrubs and trees. Bacteroidetes were significantly more abundant in surface soils of all areas even in the absence of a consolidated crust, whilst subsurface soils yielded more sequences affiliated to Acidobacteria, Actinobacteria, Chloroflexi, and Firmicutes. The common detection of vertical stratification, even in disturbed sites, suggests a strong potential for BSC recovery after physical disruption, however severe depletion of Cyanobacteria near trees and shrubs may limit the potential for natural BSC regeneration in heavily shrub-encroached areas.


Biological soil crust 454 Pyrosequencing Bacterial community Kalahari Sand Carbon Vegetation 



Financial support was provided by the Leverhulme Trust (F/00 426/H) and Manchester Metropolitan University. Research in Botswana was conducted with the Republic of Botswana Research Permit No. EWT8/36/4 VIII(4). We would like to thank Jill Thomas of Berrybush farm for her considerable support and access to her land. We also thank Peter Harding for assistance with computer resources and configuration. The constructive feedback of an anonymous reviewer and Matthew Bowker is greatly appreciated.

Supplementary material

10531_2014_684_MOESM1_ESM.txt (11 kb)
OR1. Sample metadata and summary statistics, including pyrosequencing barcodes, number of sequences obtained, richness estimates, and diversity measures. This is a tab separated text file based on the sample map used in the QIIME pipeline and other downstream analyses. (TXT 11 kb)
10531_2014_684_MOESM2_ESM.png (429 kb)
OR2: Constrained and unconstrained correspondence analyses of the microbial community including scree plots. (PNG 429 kb)
10531_2014_684_MOESM3_ESM.txt (7 kb)
OR3. Text file containing results from the ADONIS test comparing community structure with respect to vegetation, depth, and month. The test was performed at all taxonomic ranks from phylum to species. (TXT 8 kb) (500 kb)
OR4. Zip file containing plots, statistical tests, and result tables of OTU abundances for the top 9 OTUs in each phylum, and the proteobacterial classes. Files are descriptively named and include for each group of OTUs a zone plot and a carbon plot similar to those shown in Figure 4a and 4b respectively. Boxes represent the interquartile range (IQR), and error bars extend to the most extreme values within 1.5 * IQR of the box (n=6). Median values are shown as a line within the box and outliers are shown as black spots. Sample coding: AG=annual grass, PG=perennial grass, S=shrub, T=tree. Significance and direction of correlation between OTU abundance and soil carbon is indicated by + or – (determined by Spearman test). Significance codes for positive correlation: +++ < 0.001; ++ < 0.01; + <0.05. (ZIP 500 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • David R. Elliott
    • 1
  • Andrew D. Thomas
    • 2
  • Stephen R. Hoon
    • 1
  • Robin Sen
    • 1
  1. 1.School of Science & the EnvironmentManchester Metropolitan UniversityManchesterUK
  2. 2.Department of Geography and Earth ScienceAberystwyth UniversityAberystwythUK

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