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Microbiomics of Namib Desert habitats

Abstract

The Namib Desert is one of the world’s only truly coastal desert ecosystem. Until the end of the 1st decade of the twenty-first century, very little was known of the microbiology of this southwestern African desert, with the few reported studies being based solely on culture-dependent approaches. However, from 2010, an intense research program was undertaken by researchers from the University of the Western Cape Institute for Microbial Biotechnology and Metagenomics, and subsequently the University of Pretoria Centre for Microbial Ecology and Genomics, and their collaborators, led to a more detailed understanding of the ecology of the indigenous microbial communities in many Namib Desert biotopes. Namib Desert soils and the associated specialized niche communities are inhabited by a wide array of prokaryotic, lower eukaryotic and virus/phage taxa. These communities are highly heterogeneous on both small and large spatial scales, with community composition impacted by a range of macro- and micro-environmental factors, from water regime to soil particle size. Community functionality is also surprisingly non-homogeneous, with some taxa retaining functionality even under hyper-arid soil conditions, and with subtle changes in gene expression and phylotype abundances even on diel timescales. Despite the growing understanding of the structure and function of Namib Desert microbiomes, there remain enormous gaps in our knowledge. We have yet to quantify many of the processes in these soil communities, from regional nutrient cycling to community growth rates. Despite the progress that has been made, we still have little knowledge of either the role of phages in microbial community dynamics or inter-species interactions. Furthermore, the intense research efforts of the past decade have highlighted the immense scope for future microbiological research in this dynamic, enigmatic and charismatic region of Africa.

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Fig. 1

Adapted from Li et al. 2016 and Kaseke et al. 2017

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Acknowledgements

The authors wish to thank the National Research Foundation of South Africa and their Institutions for financial and other support. Thanks are also extended to the research staff, past and present, of the University of Pretoria Centre of Microbial Ecology and Genomics and of the Gobabeb-Namib Research Institute for their invaluable contributions to many of the studies cited in this review.

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This manuscript is part of a special issue of Extremophiles journal for the 12th International Congress of Extremophiles (Extremophiles2018) that was held on 16–20 September 2018 in Ischia, Naples, Italy.

Communicated by S. Albers.

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Cowan, D.A., Hopkins, D.W., Jones, B.E. et al. Microbiomics of Namib Desert habitats. Extremophiles 24, 17–29 (2020). https://doi.org/10.1007/s00792-019-01122-7

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Keywords

  • Namib Desert
  • Microbial diversity
  • Microbiomics
  • Microbial ecology
  • Desert soil