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Genotypic and Phenotypic Diversity of Cyanobacteria in Biological Soil Crusts of the Succulent Karoo and Nama Karoo of Southern Africa

  • Environmental Microbiology
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Abstract

Biological soil crusts (BSCs) are communities of cryptogamic organisms, occurring in arid and semiarid regions all over the world. Based on both morphological identification and genetic analyses, we established a first cyanobacterial inventory using the biphasic approach for BSCs within two major biomes of southern Africa. The samples were collected at two different sites in the Succulent Karoo and one in the Nama Karoo. After cultivation and morphological identification, the 16S rRNA gene was sequenced from the cyanobacterial cultures. From the soil samples, the DNA was extracted, and the 16S rRNA gene sequenced. All the sequences of the clone libraries from soil and cultures were compared with those of the public databases. Forty-five different species were morphologically identified in the samples of the Succulent Karoo (observatories of Soebatsfontein and Goedehoop). Based on the genetic analyses, 60 operational taxonomic units (OTUs) were identified for the Succulent Karoo and 43 for the Nama Karoo (based on 95 % sequence similarity). The cloned sequences corresponded well with the morphologically described taxa in cultures and sequences in the public databases. Besides known species of typical crust-forming cyanobacterial genera (Microcoleus, Phormidium, Tolypothrix and Scytonema), we found sequences of so far undescribed species of the genera Leptolyngbya, Pseudanabaena, Phormidium, Oscillatoria, Schizothrix and Microcoleus. Most OTUs were restricted to distinct sites. Grazed soils showed lower taxa numbers than undisturbed soils, implying the presence of early successional crust types and reduced soil surface protection. Our combined approach of morphological identification and genetic analyses allowed both a taxa inventory and the analysis of species occurring under specific habitat conditions.

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Acknowledgments

We thank the German Ministry of Education and Research for sponsoring the BIOTA Africa project (Biodiversity Monitoring Transect Analysis in Southern Africa) and our German, South African and Namibian partners for the valuable contributions to the development, design and implementation of the BIOTA biodiversity observatories. Thomas Friedl (University of Göttingen, Germany) and Kathrin Mohr are thanked for the field support and assistance during laboratory work and data management. We also thank Antje Donner (University of Kaiserslautern, Germany) for assistance with the alignment.

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  1. Department of Biology, Plant Ecology and Systematics, University of Kaiserslautern, Erwin-Schrödinger Str. 13, 67663, Kaiserslautern, Germany

    Stephanie Dojani, Frank Kauff, Bettina Weber & Burkhard Büdel

  2. Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, Mainz, 55128, Germany

    Bettina Weber

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  1. Stephanie Dojani
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Correspondence to Stephanie Dojani.

Electronic supplementary material

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Online Resource 1

(File: ESM_1) Abbreviations, accessions numbers and sequence length of own cultures. Compiled sequences are marked with *. All other sequences are based on sequencing with primer PCR 1 (after Wilmotte et al. 1993). (PDF 87.8 kb)

Online Resource 2

(File: ESM_2) Accession numbers of reference strains from GenBank. (PDF 93.2 kb)

Online Resource 3

(File ESM_3) Neighbour-joining tree including all sequences used for the study, bootstrap values are given above the lines. Taxa are coded by site and origin of the sequence as follows: Soebatsfontein: clones: dark blue, pure cultures: light blue; Goedehoop: clones violet, pure cultures: pink; Duruchaus: ungrazed: dark green, grazed: yellow-green; pure cultures originating from different sites: black; reference sequences (GenBank): red. The sequences can be found in GenBank under the accession numbers KC463059 to KC463696. (PDF 2.85 mb)

Online Resource 4

(File ESM_4) List of all OTUs and the corresponding sequences. (PDF 71.7 kb)

Online Resource 5

(File ESM_5) Detailed description and comparison of the results of the neighbour-joining tree and the OTUs composition. (PDF 98.1 kb)

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Dojani, S., Kauff, F., Weber, B. et al. Genotypic and Phenotypic Diversity of Cyanobacteria in Biological Soil Crusts of the Succulent Karoo and Nama Karoo of Southern Africa. Microb Ecol 67, 286–301 (2014). https://doi.org/10.1007/s00248-013-0301-5

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