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.
Similar content being viewed by others
References
Adessi A, de Carvalho RC, De Philippis R, Branquinho C, da Silva JM (2018) Microbial extracellular polymeric substances improve water retention in dryland biological soil crusts. Soil Biol Biochem 116:67–69
Adriaenssens EM, van Zyl L, de Maayer P, Rubagotti E, Rybicki E, Tuffin M, Cowan DA (2015) Metagenomic analysis of the viral community in Namib Desert hypoliths. Environ Microbiol 17:480–495
Adriaenssens EM, van Zyl LJ, Cowan DA, Trindade M (2016) Metaviromics of Namib Desert salt pans: a novel lineage of haloarchaeal salterproviruses and a rich source of ssDNA viruses. Viruses 8:14
André HM, Noti MI, Jacobson KM (1997) The soil microarthropoda of the Namib Desert: a patchy mosaic. J Afr Zool 111:499–518
Angel R, Matthies D, Conrad R (2011) Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS ONE 6:e20453
Angel R, Claus P, Conrad R (2012) Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J 6:847–862
Armstrong A, Valverde A, RamonD J-B, Makhalanyane TP, Jansson JK, Hopkins DW, Aspray TJ, Seely M, Trindade MI, Cowan DA (2016) Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input. Sci Rep 6:34434
Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N (2011) Examining the global distribution of dominant archaeal populations in soil. ISME J 5:908–917
Belnap J, Welter JR, Grimm NB, Barger N, Ludwig JA (2005) Linkages between microbial and hydrologic processes in arid and semiarid watersheds. Ecology 86:298–307
Brain CK, Koste W (1993) Rotifers of the genus Proales from saline springs in the Namib Desert, with the description of a new species. Hydrobiologia 255(256):449–454
Bratbak G, Thingstad F, Heldal M (1994) Viruses and the microbial loop. Microb Ecol 28:209–221
Breitbart M, Delwart E, Rosario K, Segalés J, Varsani A, Consortium IR (2017) ICTV virus taxonomy profile: Circoviridae. J Gen Virol 98:1997
Cleverly J, Eamus D, Luo Q, Coupe NR, Kljun N, Ma X, Ewenz C, Li L, Yu Q, Huete A (2016) The importance of interacting climate modes on Australia’s contribution to global carbon cycle extremes. Scientif Rep 6:23113
Cloete M (2015) Microbial diversity of the Namib Desert salt pans. MSc Thesis, University of the Western Cape, South Africa
Collins GE, Hogg ID, Baxter JR, Maggs-Kölling G, Cowan DA (2019) High levels of genetic variability and deeply divergent lineages among populations of Namib Desert Collembola. Ecol Evolut. https://doi.org/10.1002/ece3.5103
Conti E, Mulder C, Pappalardo AM, Ferrito V, Costa C (2019) How soil granulometry, temperature, and water predict genetic differentiation in Namibian spiders (Ariadna: Segestriidae) and explain their behaviour. Ecol Evolut. https://doi.org/10.1002/ece3.4929
Cooper-Driver GA, Wagner C, Kolberg H (2000) Patterns of Aspergillus niger var. phoenicis (Corda) Al-Musallam infection in Namibian populations of Welwitschia mirabilis Hook. f. J Arid Environ 46:181–198
Cunningham PL, Jankowitz W (2010) A review of fauna and flora associated with coastal and inland saline flats from Namibia with special reference to the Etosha Pan. In: Sabkha ecosystems. Springer, Dordrecht, pp. 9–17
Day JA (1993) The major ion chemistry of some southern African saline systems. Hydrobiologia 267:37–59
Day JA, Seely MK (1988) Physical and chemical conditions in an hypersaline spring in the Namib Desert. Hydrobiologia 160:141–153
Eckardt FD, Drake N (2011) Introducing the Namib desert playas: in sabkha ecosystems, vol 3. Springer, Dordrecht, pp 19–25
Eckardt FD, Soderberg K, Coop LJ, Muller AA, Vickery KJ, Grandin RD, Jack C, Kapalanga T, Henschel J (2013) The nature of moisture at Gobabeb, in the Central Namib Desert. J Arid Environ 93:7–19
Foissner W, Agatha S, Berger H (2002) Soil ciliates (Protozoa, Ciliophora) from Namibia (Southwest Africa), with emphasis on two contrasting environments, the Etosha region and the Namib Desert. Biologiezentrum der Oberösterreichischen Landesmuseums. Publ. Denisia 5:1–1459
Frossard A, Ramond J-B, Seely M, Cowan DA (2015) Water regime history drives responses of soil Namib Desert microbial communities to wetting events. Scientif Rep 5:12263
Getzin S, Yizhaq H, Bell B, Erickson TE, Postle AC, Katra I, Tzuk O, Zelnik YR, Wiegand K, Wiegand T, Meron E (2016) Discovery of fairy circles in Australia supports self-organization theory. PNAS USA 113:3551–3556
Gombeer S, Ramond J-B, Eckardt FD, Seely M, Cowan DA (2015) The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert. Geobiology 13:494–505
Graham RC, Hirmas DR, Wood YA, Amrhein C (2008) Large near-surface nitrate pools in soils capped by desert pavement in the Mojave Desert, California. Geology 36:259–262
Gunnigle E, Ramond JB, Frossard A, Seely M, Cowan DA (2014) A sequential co-extraction method for DNA, RNA and protein recovery from soil for future system-based approaches. J Microbiol Meth 103:118–123
Gunnigle E, Frossard A, Ramond J-B, Guerrero L, Seely M, Cowan DA (2017) Diel-scale temporal dynamics recorded for bacterial groups in Namib Desert soil. Sci Rep 7:40189
Henschel JR, Lancaster N (2013) Gobabeb-50 years of Namib Desert research. J Arid Environ 93:1–6
Hu X (2014) Ciliates in extreme environments. J Eukaryot Microbiol 61:410–418
IPCC (2014) Climate Change 2014: Synthesis Report. Contribution of Working Groups I, II and III to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change. In: Pachauri RK, Meyer LA (eds) IPCC, Geneva, Switzerland, p. 151
Jacobson KM (1997) Moisture and substrate stability determine VA-mycorrhizal fungal community distribution and structure in an arid grassland. J Arid Environ 35:59–75
Jacobson KM, Jacobson PJ (1998) Rainfall regulates decomposition of buried cellulose in the Namib Desert. J Arid Environ 38:571–583
Jacobson KM, Jacobson PJ, Miller OK (1993) The mycorrhizal status of Welwitschia mirabilis. Mycorrhiza 3:13–17
Jacobson K, van Diepeningen A, Evans S, Fritts R, Gemmel P, Marsho C, Seely M, Wenndt A, Yang X, Jacobson P (2015) Non-rainfall moisture activates fungal decomposition of surface litter in the Namib Sand Sea. PloS One 10:0126977
Johnson RM, Ramond J-B, Gunnigle E, Seely M, Cowan DA (2017) Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters. Extremophiles 21:381–392
Kaseke KF, Wang L, Seely MK (2017) Non rainfall water origins and formation mechanisms. Science Adv 3:e1603131
Lancaster J, Lancaster N, Seely MK (1984) Climate of the Namib Desert. Madoqua 14:5–61
Lebre P, de Maayer P, Cowan DA (2017) Xerotolerant bacteria: surviving through a dry spell. Nature Rev Microbiol 15:285–296
León-Sobrino C, Ramond J-B, Maggs-Kölling G, Cowan DA (2019) Nutrient acquisition, rather than stress response over diel cycles, drives microbial transcription in a hyper-arid Namib Desert soil. Frontiers Microbiol Accepted for publication
Li B, Wang L, Kaseke KF, Li L, Seely MK (2016) The impact of rainfall on soil moisture dynamics in a foggy desert. PLoS ONE 11:e0164982
Makhalanyane TP, Valverde A, Lacap DC, Pointing SB, Tuffin MI, Cowan DA (2013) Evidence of species recruitment and development of hot desert hypolithic communities. Environ Microbiol Rep 5:219–224
Makhalanyane TP, Valverde A, Gunningle E, Frossard A, Ramond J-B, Cowan DA (2015) Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev 39:203–221
Marasco R, Mosqueira MJ, Fusi M, Ramond J-B, Merlino G, Booth JM, Maggs-Kölling G, Cowan DA, Daffonchio D (2018) Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host. Microbiome 6:215
Marsh B (1987) Micro-arthropods associated with Welwitschia mirabilis in the Namib Desert. S Afr J Zool 22:89–96
Noy-Meir I (1973) Desert ecosystems: environment and producers. Ann Rev Ecol System 4:25–51
Pinseel E, Kulichová J, Scharfen V, Urbánková P, Van de Vijver B, Vyverman W (2019) Extensive cryptic diversity in the terrestrial diatom Pinnularia borealis (Bacillariophyceae). Protist 170:121–140
Pointing SB (2016) Hypolithic communities. An organizing principle in Drylands. Springer International Publishing, In Biological Soil Crusts, pp 199–213
Pointing SB, Belnap J (2012) Microbial colonization and controls in dryland systems. Nat Rev Microbiol 10:551–562
Prestel E, Salamitou S, DuBow MS (2008) An examination of the bacteriophages and bacteria of the Namib desert. J Microbiol 46:364–372
Ramond J-B, Pienaar A, Armstrong A, Seely M, Cowan DA (2014) Niche-partitioning of edaphic microbial communities in the Namib Desert gravel plain fairy circles. PLoS ONE 9:e109539
Ramond J-B, Woodborne S, Hall G, Seely M, Cowan DA (2018) Namib Desert primary productivity is driven by cryptic microbial community N-fixation. Scientif Rep 8:6921
Rao B, Hatzinger PB, Bohlke JK, Sturchio NC, Andraski BJ, Eckardt FD, Jackson WA (2010) Natural chlorate in the environment: application of a new IC-ESI/MS/MS method with a Cl(18)O(3)(-) internal standard. Environ Science Technol 44:8429–8434
Rohwer F, Thurber R-V (2009) Viruses manipulate the marine environment. Nature 459:207–212
Ronca S, Ramond J-B, Jones BE, Seely M, Cowan DA (2015) Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities. Front Microbiol 6:845–845
Rumrich U, Rumrich M, Lange-Bertalot H (1989) Diatomeen als „Fensteralgen“ in der Namib-Wüste und anderen ariden Gebieten von SWA/Namibia. Dinteria (Windhoek S.W.A.) 21:9–16
Rumrich U, Rumrich M, Lange-Bertalot H (1991) Diatomeen aus Pflanzen in der Namib. Dinteria (Windhoek S.W.A.) 20:23–29
Rumrich U, Rumrich M, Lange-Bertalot H (1992) Diatomeen unter Steinen in der Namib-Wüste und angrenzenden Savannen. Acta Biol Benrodis 4:53–66
Scola V, Ramond J-B, Frossard A, Zablocki O, Adriaenssens EM, Johnson RM, Seely M, Cowan DA (2018) Namib desert soil microbial community diversity, assembly and function along a natural xeric stress gradient. Microb Ecol 75:193–203
Seely MK (1990) Namib ecology: 25 years of Namib research. Transvaal Museum Monographs 7:223
Seely M, Pallett J (2008) Namib: secrets of a desert uncovered. Venture Publications, Windhoek, Namibia, p 197
Seo JH (2011) Solving the Mystery of the Atacama Nitrate Deposits: the use of stable oxygen isotope analysis and geochemistry. J Purdue Undergrad Res 1:7
Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N (2013) A meta-analysis of changes in bacterial and archaeal communities with time. ISME J 7:1493–1506
Stomeo F, Valverde A, Pointing SB, McKay CP, Warren-Rhodes KA, Tuffin MI, Seely M, Cowan DA (2013) Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert. Extremophiles 17:329–337
Stutz JC, Copeman R, Martin CA, Morton JB (2000) Patterns of species composition and distribution of arbuscular mycorrhizal fungi in arid regions of southwestern North America and Namibia, Africa. Can J Botany 78:237–245
Theron GK (1979) Die verskynsel van kaal kolle in Kaokoland, Suidwes-Afrika. J S Afr Biol Soc 20:43–53
Tschinkel WR (2015) Experiments testing the causes of Namibian fairy circles. PLoS ONE 10:e0140099
Uhlmann E, Görke C, Petersen A, Oberwinkler F (2006) Arbuscular mycorrhizae from arid parts of Namibia. J Arid Environ 64:221–237
Unc A, Maggs-Kölling G, Marais E, Sherman C, Doniger T, Steinberger Y (2019) Soil bacterial community associated with the dioecious Acanthosicyos horridus in the Namib Desert. Biol Fert Soils. https://doi.org/10.1007/s00374-019-01358-7
Valverde A, Makhalanyane TP, Seely M, Cowan DA (2015) Cyanobacteria drive community composition and functionality in rock–soil interface communities. Molec Ecol 24:812–821
Valverde A, De Maayer P, Oberholster T, Henschel J, Louw MK, Cowan DA (2016) Specific microbial communities associate with the rhizosphere of Welwitschia mirabilis, a living fossil. PLoS ONE 11:e0153353
Van der Walt AJ, Johnson RM, Cowan DA, Seely M, Ramond J-B (2016) Unique microbial phylotypes in Namib Desert dune and gravel plain fairy circle soils. Appl Environ Microbiol 82:4592–4601
Van Goethem MW, Makhalanyane TP, Cowan DA, Valverde A (2017) Cyanobacteria and Alphaproteobacteria may facilitate cooperative interactions in niche communities. Front Microbiol 8:2099
Van Rooyen MW, Theron GK, Van Rooyen N, Jankowitz WJ, Matthews WS (2004) Mysterious circles in the Namib Desert: Review of hypotheses on their origin. J Arid Environ 57:467–485
Ventosa A, Oren A, Ma Y (2011) Halophiles and hypersaline environments: current research and future trends. Springer, Heidelberg, p 401
Vikram S, Guerrero LD, Makhalanyane TP, Le PT, Seely M, Cowan DA (2015) Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community. Environ Microbiol 18:1875–1888
Walvoord MA, Phillips FM, Stonestrom DA, Evans RD, Hartsough PC, Newman BD, Striegl RG (2003) A reservoir of nitrate beneath desert soils. Science 302:1021–1102
Warren-Rhodes KA, McKay CP, Boyle LN, Wing MR, Cowan DA, Stomeo F, Pointing SB, Kaseke KF, Eckardt F, Henschel JR, Anisfeld H, Seely M, Rhodes KL (2013) Physical ecology of hypolithic communities in the central Namib Desert: the role of fog, rain, rock habitat and light. J Geophys Res 118:1451–1460
Xu R, Prentice IC (2008) Terrestrial nitrogen cycle simulation with a dynamic global vegetation model. Glob Change Biol 14:1745–1764
Zaady E (2005) Seasonal change and nitrogen cycling in a patchy Negev Desert: a review. Arid Land Res Manag 19:111–124
Zablocki ODJ, Rybicki EP, Cowan DA (2014) First report of a potyvirus infecting Albuca rautanenii in the Namib Desert. Plant Dis 98:1749–1749
Zablocki O, Adriaenssens EM, Cowan DA (2016) Diversity and ecology of viruses in hyperarid desert soils. Appl Environ Microbiol 82:770–777
Zablocki O, Adriaenssens EM, Frossard A, Seely M, Ramond J-B, Cowan DA (2017) Metaviromes of extracellular soil viruses along a Namib Desert aridity gradient. Genome Ann 5:e01470–e1516
Zerbini FM, Briddon RW, Idris A, Martin DP, Moriones E, Navas-Castillo J, Rivera-Bustamante R, Roumagnac P, Varsani A, Consortium IR (2017) ICTV virus taxonomy profile: Geminiviridae. J Gen Virol 98:131
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.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by S. Albers.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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.
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00792-019-01122-7