Abstract
Plants are symbiotically associated with microorganisms such as bacteria and fungi; and these are known as endophytes. Endophytes have emerged as a valuable sources of novel secondary metabolites; industrially important enzymes and as stress relievers for plants, but there are still many aspects of endophytic biology which remain unknown. One of the major challenges in studying plant microbial interactions is the culturability of a wide range of endophytic communities using culture dependent methods. Advances in next generation sequencing (NGS) have led to the development of omics techniques such as metagenomics which is able to study the diversity and abundance of microbial species including unculturable groups based on their sequence information. This research project aimed at isolating and identifying bacterial endophytes from the roots and leaves associated with Dicoma anomala. D. anomala is a medicinal plant that is known for its excellent ethno-medicinal uses which include treatment of ulcers, coughs and dysentery; using metagenomics during three seasons (autumn, winter and spring). Metagenomics analysis confirmed that D. anomala has a rich diversity of bacterial endophyte communities belonging to 11 phyla, 10 classes, 14 orders, 17 families, 19 genera and 56 species. The results indicated that the winter (leaves) samples collected in August, harbour higher bacterial operational taxonomic units (OTUs), alpha diversity and bacterial community composition in comparison with autumn and spring samples. The taxonomic composition analysis showed that the majority of bacterial endophytes were composed of Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Some endophytic bacteria were found to be tissue specific. Sequences of Cutibacterium, Acinetobacter and Methylobacterium were prevalent in the leaves, whereas Amycolatopsis and Bradyrhizobium were the dominant genera in the root samples. Furthermore, the whole genome DNA of one culturable bacterial endophyte, Stenotrophomonas pavanii strain MHSD12 was sequenced, assembled and annotated. The data contribute to the ongoing research on microbial plant colonisation and the role of microbes in plant growth promotion; and the genomic data adds on to the knowledge about genes involved in endophytic life style.
M.Sc. (Biotechnology)