Identifying the core microbiome of two South African lichens

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Lichens are a symbiotic relationship formed between fungi (the mycobiont) and algae and/or cyanobacteria (the photobiont). The microbiome (i.e. fungi and bacteria) associated South African lichens have not been investigated. Given the unique South African climate, and the many different lichen taxa found in South Africa, lichens could represent a rich source of novel microorganisms that produce biotechnologically relevant molecules and enzymes and could serve as a tool for environmental and climate change monitoring. The aim of this study was to investigate the microbiomes of two lichens, Parmotrema and Flavopunctelia in three locations in Gauteng, across both the winter and summer seasons, to determine the influence of biotic and abiotic factors on the microbial community structure of these lichens. The total genomic DNA was extracted from the lichens and subjected to 16S ribosomal RNA (16S rRNA) / Internal Transcribed Spacer (ITS) based tag-encoded FLX amplicon pyrosequencing (bTEFAP) at MR DNA (Texas, USA) to identify the bacterial and fungal components of the lichen microbiome, respectively. The core microbiome was identified, and the alpha and beta diversities were calculated to determine the composition of the microbiome and the influence of the lichen mycobiont, lichen sampling location, and seasonal changes on its structure. The core bacteriome was found to be mainly denominated by the phyla Proteobacteria, Acidobacteria and Bacteroidetes. The core mycobiome was largely made up of black meristematic fungi which provide lichens with nutrient sources and protection in nutrient poor environments and was dominated by the phylum Ascomycota. The lichen mycobiont was observed to have little to no influence on the composition and diversity of the lichen microbiome. This finding may be attributed to that fact that both sampled lichens are members of the same family. In contrast, significant differences in the microbial composition and diversity were observed between the sample locations and the seasons, which are characterised by differences in temperature and rainfall. Additionally, the microbial diversity was found to increase with an increase in rainfall. All of this shows that the lichen microbiome may vary with different environmental conditions. This study provides the first look at the South African lichen microbiome and paves the way for more studies to investigate a broader range of lichen taxa over a wider geographical area and over a longer study period.
A research report submitted in fulfilment of the requirements for the degree of Master of Science to the Faculty of Science, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, 2023
Lichens, Microbiome