Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils


Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and ‘resistance to antibiotics and toxic compounds’ related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.

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Availability of Data and Material

The metagenome sequence data and 16S amplicon sequence data are available on NCBI (http://www.ncbi.nlm.nih.gov/PRJNA592367).

Code Availability

There are no unreported custom computer code or algorithms used to generate results in this paper.


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The authors are grateful for the funding provided by the National Research Foundation of South Africa for this project.


YN was supported through a Free standing and Research and Development Programme Grant funded by the National Research Foundation (NRF) of South Africa. AV was supported by the project ‘CLU-2019–05 – IRNASA/CSIC Unit of Excellence’, funded by the Junta de Castilla y León and co-financed by the European Union (ERDF ‘Europe drives our growth’).

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Yashini Naidoo, conceptualization, investigation, writing (original draft); Angel Valverde Portal, writing (review and editing), supervision, funding acquisition; Rian Pierneef, software, validation, writing (review and editing); Don Cowan, supervision, funding acquisition, writing (review and editing).

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Correspondence to Yashini Naidoo.

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Naidoo, Y., Valverde, A., Pierneef, R.E. et al. Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils. Microb Ecol (2021). https://doi.org/10.1007/s00248-021-01785-w

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  • 16S rRNA
  • Shotgun metagenomics
  • Precipitation regime
  • Namib Desert
  • Functional potential