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Endophytic microorganisms play crucial roles in plant growth and development. They are involved in plant protection against pest and diseases, production of growth regulators, biological nitrogen fixation, organic acid production and phosphate solubilization, and increase plant fitness to overcome extreme conditions. Endophytes colonize the soil-plant system following entry into the interior plant tissues, while the host genetic factors decide which microbes to enter by performing a gating role in particular. In this book chapter, we review the current knowledge of endophytic colonization in host plants, their functions, and underlying mechanisms of these performances and applications in agroecosystems. This also summarizes the setback of their applications in field conditions reported to date. Finally the importance of endophytes being associated with a life partner to overcome these hindrance and future research directions toward for the innovative use of endophytic microbes are summarized.

Microorganisms inhabiting soil/plant systems produce antimicrobial compounds including secondary metabolites (SMs). They are low-molecular-weight structurally diverse and complex compounds that are not essential in their life unless they meet undesirable conditions. SMs such as antibiotics, toxins, ribosomal peptides (RPs), low-molecular-weight volatile organic compounds (VOCs), polyketides (PKs), non-ribosomal peptides (NRPs) and hybrids between PKs and NRPs have shown a diverse performance in antagonistic activity against plant pathogens. These compounds are involved immensely with combatting pathogens following interactions with pathogens inhabiting in soil/plant systems, particularly by developing a disease-suppressive soil. SMs produced by certain microorganisms induce plant defence reactions leading to a systemic resistance to pathogen infection. Bacterial endophytes, particularly inhabiting inside plant tissues, are also source of SMs, which may act as elicitors of plant defences. Biochemical techniques and genomic-based studies have uncovered that several genes encoding SMs associated with biocontrol activity are located in gene clusters. Despite the fact that metabolites have been developed as biopesticides, bio-weedicides, the in-cooperation of new techniques is important for finding new resources from disease suppressive soil, which do not represent when the cultures are tested in vitro. However, this review finds isolation of active compounds is one of the major challenges in biotechnology as many biosynthetic genes are not expressed under standard culture conditions, thus proposing a possible solution to overcome the issue.

Phytoplasmas that infect gramineous plants, including Napier grass stunt, sugarcane whiteleaf, sugarcane grassy shoot, and Bermuda grass whiteleaf, have been classified into two closely related groups, 16SrXI and 16SrXIV, based on the 16S ribosomal RNA (rRNA) gene. Subsequently, phytoplasmas associated with coconut and Areca palm in southern India and Sri Lanka have been added into the 16SrXI group. However, the 16S rRNA gene gives relatively poor resolution between these phytoplasmas. In this study, a new set of universal phytoplasma primers that amplify approximately 1 kb of the leucyl transfer RNA synthetase (leuS) gene have been validated on a broad range of phytoplasma taxonomic groups. These have been used along with partial sequences of the secA gene to clarify the taxonomic classification of 16SrXI and 16SrXIV phytoplasmas. Based on this data, the sugarcane whiteleaf and grassy shoot phytoplasmas appear to be the same phytoplasma. The Napier grass stunt phytoplasma forms a distinct group from the Bermuda grass whiteleaf and sugarcane phytoplasmas, suggesting that Napier grass stunt should be in its own ‘Candidatus Phytoplasma sp.’. The phytoplasmas associated with coconut and arecanut in southern India and Sri Lanka, which are in the same 16SrXI group, appear in different groups based on secA analysis.

Sri Lanka is a tropical country equally having rich diversity of arthropods including natural enemies, economic pests, and indigenous plants majority with unique chemical properties. Because of the substantial losses due to pests and diseases, plant protection remains an essential issue in agriculture production in the country. There is increasing concern over synthetic pesticide usage due to their adverse long-term effects on human health, environment, and natural pest management systems. As an eco-friendly alternate, the importance of biopesticides in raising agricultural productivity is well recognized in Sri Lanka. Biopesticides are quiet popular among farming community due to their unique features, viz., safety, limited host range or target specificity, the absence of toxic residues, eco-friendly nature, and ease of application. Biopesticides have diverse modes of action and hence resistance development in pests is slower/negligible. Currently, plant powders, nonvolatile and volatile oils, and plant crude extracts are commercially available for management of insect pests and nematodes. Further, several bacterial and fungal biopesticides have shown promising results for the efficient management of plant pathogens in Sri Lanka.

Sclerotium rolfsii Sacc. the causal agent of collar and root rot of chili (Capsicum annuum L.), is one of the most important soil-borne pathogens in Sri Lanka. Bacillus subtilis CA32r, a stable spontaneous kanamycin resistant isolate, showing antagonism in a Petri plate assay, was selected for greenhouse pot experiments to control S. rolfsii. An ethyl acetate extract of the culture filtrate of B. subtilis CA32r inhibited radial colony growth as well as germination of sclerotia of the pathogen in vitro, indicating the presence of antifungal compound(s) in the culture extract. B. subtilis CA32r was investigated for its effectiveness as a biological control agent against S. rolfsii infecting transplanted chilli seedlings in greenhouse pot experiments. CA32r significantly decreased the disease incidence in terms of lesion development on stem base and roots depending on the mode of the bacterial application. Seed bacterization and soil application alone did not protect chilli plants, but root bacteriz...

Rhizobacteria Pseudomonas fluorescens CA05, Pseudomonas putida CA28 and Bacillus subtillis CA32 which showed antagonism in a Petri plate assay were tested singly and in combination for their biological control efficacy against Rhizoctonia solani and Sclerotium rolfsii under greenhouse conditions. The bacteria were applied to the seeds before seeding and to the root system prior to transplanting. Two disease assessment criteria were used in this study. All bacterial treatments significantly decreased the disease severity of C. annuum observed up to 30 days after transplanting and the magnitude of the protection was similar when assessed in terms of number of plants which remained healthy during the experimental period. Combining B. subtillis with either Pseudomonads strains gave enhanced control. However, the combined application of two Pseudomondas strains did not improve the plant protection. When the plants were assessed by using a stem-lesion index, none of the Pseudomonads strains either alon...

In this study, only non-antagonistic, root-colonizing bacterial isolates and non-pathogenic F. oxysporum isolates were evaluated either alone or in combination as biological control agents. Two non-pathogenic F. oxysporum isolates significantly reduced the Fusarium root and stem rot severity compared to the pathogen inoculated controls plants. Although the bacterial isolates did not protect cucumber plants from Fusarium rot when they were applied alone, the bacterial isolates significantly enhanced (p

Papaya ( Carica papaya) is a very popular fruit crop in Sri Lanka, grown as a home garden and commercial crop for local and export markets. Papaya is commercially cultivated in Sri Lanka in about 8,000 ha with production of about 32,000 …

Trichoderma spp. are effective biocontrol agents for a number of soil-borne plant pathogens. Some isolates are also known for their ability to induce systemic resistance in plants against different foliar pathogens. Induction of systemic resistance against Uromyces appendiculatus , the causal agent of bean rust, by Trichoderma spp. has not been reported. T. harzianum RU01 consistently triggered a significant (P = 0.05) degree of protection against rust in bean ( Phaseolus vulgaris cv. Keppetipola Nill) under greenhouse conditions. Control efficacy was similar to that of rhizobacterium, Pseudomonas aeruginosa KMPCH, a test strain included in this study, which previously demonstrated induction of systemic resistance in bean. Given the spatial separation of challenging pathogen and biocontrol agent, this effect can be attributed to the induction of systemic resistance by T. harzianum RU01.