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Dynamic consortium of microbial communities (bacteria, fungi, protists, viruses, and nematodes) colonizing multiple tissue types and coevolving conclusively with the host plant is designated as a plant microbiome. The interplay between plant and its microbial mutualists supports several agronomic functions, establishing its crucial role in plant beneficial activities. Deeper functional and mechanistic understanding of plant-microbial ecosystems will render many “ecosystem services” by emulating symbiotic interactions between plants, soil, and microbes for enhanced productivity and sustainability. Therefore, microbiome engineering represents an emerging biotechnological tool to directly add, remove, or modify properties of microbial communities for higher specificity and efficacy. The main goal of microbiome engineering is enhancement of plant functions such as biotic/abiotic stresses, plant fitness and productivities, etc. Various ecological-, biochemical-, and molecular-based approaches have come up as a new paradigm for disentangling many microbiome-based agromanagement hurdles. Furthermore, multidisciplinary approaches provide a predictive framework in achieving a reliable and sustainably engineered plant-microbiome for stress physiology, nutrient recycling, and high-yielding disease-resistant genotypes.

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Endophytes from medicinal plants represent a potential source of bioactive compounds. During the present investigation, fungal endophytes were isolated from turmeric (Curcuma longa), an important medicinal plant. A total of 207 endophytic fungal isolates were obtained from the rhizome of C. longa L. They were grouped into seven genera based on morphological and molecular data. The fungal endophytes of C. longa were evaluated for antifungal activity against Colletotrichum gloeosporioides, the causal organism of leaf spot of turmeric. The disease is a major cause for economic loss in turmeric cultivation. Endophytic Phoma herbarum showed significant activity against C. gloeosporioides and was therefore selected for further studies. A compound gentisyl alcohol was isolated from P. herbarum which showed effective antagonism against C. gloeosporioides. The organism could therefore be used as a biocontrol agent against C. gloeosporioides.

Codon usage bias influences the genetic features prevalent in genomes of all the organisms. It also plays a crucial role in establishing the host-pathogen relationship. The present study elucidates the role of codon usage pattern regarding the predilection of fungal pathogens Aspergillus flavus, Aspergillus niger, Fusarium oxysporum and Colletotrichum gloeosporioides towards host plant Zingiber officinale. We found a similar trend of codon usage pattern operative in plant and fungal pathogens. This concurrence might be attributed for the colonization of fungal pathogens in Z. officinale. The transcriptome of both plant and pathogens showed bias towards GC-ending codons. Natural selection and mutational pressure seem to be accountable for shaping the codon usage pattern of host and pathogen. We also identified some distinctive preferred codons in A. flavus, F. oxysporum and Z. officinale that could be regarded as signature codons for the identification of these organisms. Knowledge of favored, avoided and unique codons will help to devise strategies for reducing spice losses due to fungal pathogens.