In agriculture, these challenges have major implications on the yield, health and quality of harvested crops. Therefore, the agricultural sector of any country strives to minimize the impact of stress on domestic crops in order to meet the food demand of its population and for profitable trade. These targets have been particularly difficult to achieve for countries in Sub-Saharan Africa, where semi-arid conditions, plant diseases and under-developed farming techniques prove to be major hindrances in sustainable production of good quality crops. As a result, this region is burdened with issues including food shortage, poverty and malnutrition, and these have a far-reaching impact on other socio-economic aspects such as disease management (e.g. HIV/AIDS and diabetes) and the overall economic growth.

As a result, intensified research efforts seek to develop effective strategies for management of crop health and growth. Increased use of chemical fertilizers and pesticides has been effective in the short term; however, this has led to deposition of toxic compounds in natural ecosystems and deterioration of soil quality on arable land. Developments in plant genetics and genetic engineering have brought forth fortified cultivars of important crops including maize, sugarcane and rice with increased nutrient content and stress-tolerant qualities.

Bacteria are found in distinctive plant-created microhabitats including the rhizosphere (soil surrounding the roots), the perisphere (the plant surface) and the endosphere (the habitat within plant tissues), where they continuously interact with the host plant. These bacteria play an important role in the plant’s development. Some species have shown to increase nutrient availability by metabolising complex molecules and liberating soluble nutrients (e.g. phosphate solubilising bacteria), whereas some convert atmospheric nitrogen to accessible nitrogen compounds (diazotrophic bacteria). Other bacteria produce plant growth promoting hormones and/or anti-microbial compounds that kill plant pathogens, thus reducing the chance for plant diseases. These beneficial bacteria are thus aptly named plant growth promoting bacteria (PGPBs). However, not all bacteria are beneficial. In fact, pathogenic and parasitic bacteria cause plant disease and stress, thus reducing plant fitness.

The extent of plant-microbe interactions is not fully understood. This is largely due to the researchers’ inability to recreate optimal growth conditions for culturing and isolation of all endophytic bacterial species in the laboratory. Some endophytes cannot grow independently of the plant host. As a result, previous culture-based studies of endophytic bacteria have significantly undermined the true diversity of these bacterial communities. Therefore, molecular techniques that bypass the culturing process promise better insight into this complex liaison.

Research at the University of the Western Cape’s Institute for Microbial Biotechnology and Metagenomics (IMBM) explored the exploitation of the crop's endophytic bacterial symbionts to improve plant health and yield. Modern molecular and genomic techniques (terminal restriction fragment length polymorphism (t-RFLP) and Next Generation Sequencing (NGS)) were employed to study the diversity of endophytic bacteria associated with two important South African crops: sorghum and pearl millet. With both techniques, metagenomic DNA (mDNA) was extracted from surface-sterilised sorghum and millet root and stem tissues. Metagenomic DNA represents the genomic material from the plant and all its associated endophytic organisms, and is an important tool used to evaluate the total microbial population, including the majority of the organisms which cannot be cultured in a laboratory. By analysing the nucleotide sequence of a gene which is highly conserved in all bacteria (16S rRNA) we were able to identify individual bacterial species and analyse the diversity of the bacterial community associated with each plant tissue.


Over 300 different bacteria were identified to be associated with these plant tissues. Furthermore the tissues harboured significantly different endophytic communities. The bacterial communities were dominated by agriculturally important organisms and include a broad range of species with plant growth promoting properties. A very exciting aspect was the identification of previously unidentified bacteria, representing bacteria which have never been seen and studied before. This provides many opportunities to enhance our understanding of microbiology, plant microbe interactions and ecology, and additionally has the potential for discovery of new bioactivities for biotechnological application.

From an agricultural perspective, this study shows that endophytic bacteria associated with South African crops can, and should, be further explored to tap into their potential in plant growth promotion. In future, sorghum and pearl millet plant growth promoting bacteria (PGPBs) can be specifically targeted for a wide range of agricultural applications. For instance, PGPBs can be isolated to develop biofertilizers, live inocula that are applied to plant tissues or soils to enhance plant growth and health; or as biocontrol agents for plant disease management. Bacteria found in sorghum and pearl millet can also be considered for other non-agricultural applications such as soil remediation and the source of bioactive compounds and enzymes which can be applied in the medical sector and many other industries in South Africa.

Journal Reference: Maropola, M. K. A., Ramond, J. B., & Trindade, M. (2015). Impact of metagenomic DNA extraction procedures on the identifiable endophytic bacterial diversity in Sorghum bicolor (L. Moench). Journal of Microbiological Methods, 112, 104-117.

Authors: Mapula Maropola, Marla Trindade (Tuffin)
Institute for Microbial Biotechnology and Metagenomics (IMBM)
University of the Western Cape