Abstract Description

The Cape Floristic Region (CFR) is one of South Africa’s nine distinct biomes, boasting over 8500 endemic plant species. Between the Clanwilliam region in the Western Cape, home to the indigenous Aspalathus linearis (rooibos), and carbon-rich emerging peatlands in the Agulhas Plain, little is known about the actinobacterial diversity (phylum Actinomycetota) associated with these locations. Next-generation sequencing has become an integral tool used to study the biodiversity of microorganisms associated with soil environments. Variations in the methodology used to determine bacterial taxa may be influenced by various factors, including DNA extraction bias, primer bias, and sequencing bias. This baseline study compared the taxonomic assignments from whole metagenome sequencing (WMG) to those of an actinobacterial-specific 16S rRNA gene metabarcoding (MB) dataset, to compare family-level resolution. The whole metagenomes of composite soil samples from each of the rooibos and peat environments were extracted using a Qiagen PowerSoil Pro Kit and sequenced on the Ion Torrent S5 platform. Actinobacterial 16S rRNA gene amplicons were similarly sequenced. Taxonomic assignments of the whole metagenome reads were performed with kaiju, using the NCBI RefSeq non-redundant protein collection as reference. To evenly match the WMG assignments as closely as possible, the SILVA Ref Nr database was used. For the peat environment, the major represented families consisted of Mycobacteriaceae (WMG:9 - 32 %; MB: 5 - 35 %), Pseudonocardiaceae (WMG: 1 - 4 %; MB: 3 - 18 %), Acidimicrobiacea (WMG: 6 - 12 %; MB: 3 - 18 %), and Nocardioidaceae (WMG: 4 - 19 %; MB: 1 - 23 %). For the rooibos environment, the major taxa consisted of Mycobacteriaceae (WMG: 18 - 24 %; MB: 14 - 28 %), Pseudonocardiaceae (WMG: 6 - 9 %; MB: 11 - 29 %), Frankiaceae (WMG: 0.8 - 1 %, MB: 3 - 10 %), and Geodermatophilaceae (WMG: 2 - 4 %; MB: 3 - 21 %). Interestingly, Frankiaceae and Geodermatophila for the rooibos environment are vastly underrepresented in the WMG data. Despite overall consistencies in the majority-represented taxa between the two approaches, the data from the metabarcoding set more discriminately identified the actinobacterial taxa in terms of abundance. WMG can, as such, be a useful tool to gain a snapshot into environmental biodiversity, especially with the advent of increasingly cost-effective sequencing platforms, but phyla-specific primers may still be more suited to grasp insights into a target group of microorganisms.