The endophytes are facultative or obligate symbiotic microorganisms, living in apparently healthy internal plant tissues, without causing disease in the host. Bacterial endophytes are found in a diverse group of plants including many horticultural crops, viz. fruits, flowers and medicinal plants. They harbour diverse group of bacterial endophytes including members of Pseudomonads, Bacillus and Streptomyces, which have been found successful against many phytopathogenic fungi and bacteria. Endophytes can suppress diseases through various mechanisms, viz. antibiosis, competion, lysis, siderophore production, enhanced host defense etc. Many Actinobacteria produce metabolites with antimicrobial activity which can be explored as a potential alternative to chemical in plant disease management. Moreover, bacterial endophytes have been reported to play a crucial role in bioremediation of organic and inorganic pollutants and promoting plant growth through nutrient enhanced nutrient uptake.

Phytophthora gummosis, foot rot, and root rot are considered major challenges to the citrus industry worldwide. Little is known about the Phytophthora–microbiome interaction, despite several studies demonstrating changes in the microbial composition of the rhizosphere following challenges by a pathogen. In the present study, we studied the microbial diversity and community structure in healthy rhizospheres and Phytophthora-infected rhizospheres of Khasi mandarin (Citrus reticulata Blanco), a commercial cultivar extensively grown in the northeast of India. An exploratory study was conducted to identify Phytophthora-infected orchards of Khasi mandarin, and the isolated pathogen was confirmed as P. nicotianae based on its morpho-cultural and molecular characteristics coupled with pathogenicity tests. This study on culturable microbes established the dominance of Trichoderma spp. in the healthy rhizosphere, while the diseased rhizosphere showed the presence of Fusarium spp. A metagenomic study further revealed that the rhizospheres of Phytophthora-infected plants were dominated by species such as Bacteroidia spp., Patescibacteria spp., and Pythium spp., while the healthy Khasi mandarin rhizospheres had a more diverse community predominantly represented by Trichoderma, Penicillium, Linnemannia, Mortierella, Talaromyces, Saitozyma, Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Terrabacteria and FCB (Fibrobacterota, Chlorobiota, and Bacteroidota groups) were found to exist in higher relative abundance in disease-free soils than in Phytophthora-infected soils, while phylum Proteobacteria showed identical relative abundance in all soil types. The phyla represented by Pseudomonas, Flavobacteriia, Candidatus, Mycobacterium, Rhizobium, Mesorhizobium, Sphingomonas, and Cytophagia were the most common bacterial phyla in all soil samples, but healthy soil exhibited a greater abundance of Bacteroidetes, Pseudomonas, Cytophagia, Cyanobacteria, Bacteroidia, Sphingobacteriia, Burkholderia, Bacillus, and Bradyrhizobium. Our study suggests that the presence of Phytophthora spp. in the rhizosphere alters microbial community structure, having potentially strong implications for plant health and productivity. These rhizosphere microbiome-derived citrus responses shed light on exploring effective management strategies for Phytophthora gummosis disease ailing Khasi mandarin.

Arbuscular mycorrhizal fungi (AMF) enhance plant disease resistance, while the underlying mechanisms in the molecular levels are not yet known. In this study, five-leaf-old trifoliate orange seedlings were inoculated with Funneliformis mosseae for 14 weeks and subsequently were infected by a citrus root rot pathogen Phytophthora parasitica by 7 days. The transcriptome results by Illumina HiSeq 4000 revealed that the percentage of Q30 bases reached 92.99% or above, and 29696 unigenes were annotated in a total of 63531 unigenes. 654 and 103 differentially expressed genes (DEGs) were respectively annotated in AMF-inoculated versus non-AMF-inoculated plants under non-infection and infection with P. parasitica, respectively, whilst these DEGs were related to defense mechanisms, signal transduction mechanisms and secondary metabolites biosynthesis. Forty-two genes were functionally annotated as the putative 'defense mechanism', whilst AMF inoculation induced 1 gene down-regulated and 3 genes up-regulated under P. parasitica infection. AMF inoculation stimulated more genes linked to signal transduction mechanism down-regulated than non-AMF plants. Eight genes were involved in secondary metabolites biosynthesis in AMF versus non-AMF seedlings under P. parasitica-infection conditions. Such transcriptome database provided total information in the molecular levels regarding mycorrhizal roles in tolerating Phytophthora parasitica infection.

The rhizosphere is a dynamic environment in which multiple microbial activities elicit phenotypical, physiological, and molecular crop responses. For a better understanding of the rhizosphere microbiome, researchers are utilizing next-generation sequencing to focus on microbiome regulations with an emphasis on multi-functional microbes. There are two main concepts currently being focused on: identifying microbial antagonists (between beneficial microbes and plant pathogens) from predominant stocks of plant-growth-promoting microbes, preferably with an aim towards bioprospecting soil-plant health; and secondly, developing a more microbially active rhizosphere through a process called rhizosphere hybridization (RH). The present review is focused on some recent studies on the outcome of RH in citrus cultivars, showing renewed functional corridors of the rhizosphere characterized by secondary metabolites providing a load-supporting functional dichotomy through elevated nutrient-supply, activated soil enzyme profiles, and improvements in root- shoot systems and plant defense enzymes. These response trade-offs collectively contributed to higher quality yield coupled with possibly a better shelf life of fruits. The rhizobiome of heritage trees viz., Azadirachta, Ficus, Dendrocalamus, Populus, Sasa, Acer, Alnus, Quercus, and Phyllostachys, could be effectively used in exercising RH. These observations on RH mean the concept could be expanded in other fruit crops, with an emphasis on developing a robust holobiont (climate-smart suppressive soils and engineering rhizosphere microbiomes for microbially engineered plants) as a part of regenerative agriculture.

Fruit rot is one of the most destructive diseases of Capsicum chinense Jacq., popularly known as Bhoot jolokia or King Chilli an export oriented crop in North East India. Morpho-cultural characterization of the isolated fungal pathogen from diseased fruit identified the pathogen as Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. Pathogenicity test further confirmed its association with the disease. A few bacterial and fungal microbial biocontrol agents (MBCAs) were screened in vitro against C. gloeosporioides as a potential solution in organic and integrated crop management practices. Among all the MBCAs Bacillus subtilis LB22 showed highest inhibition (85.00%) on mycelial growth of the pathogen followed by P. fluorescens (84.33%) and B. vallismortis (83.22%). Trichoderma pseudokoningii were recorded the lowest inhibition (53.22%). Our study put forth further exploration B. subtilis LB22 (NCBI accession no. ON386193 and NBAIM accession no. NAIMCC-B-03226) in planta and their response in disease suppression as well growth promotion in Bhut jolokia as a component of sustainable crop health management program.

Growing brinjal (Solanum melongena L.) in a soil polluted with organophosphorus pesticide (OP) residues coupled with an additional threat of wilt disease caused by Ralstonia solanacearum (Rs), pose a formidable management challenge for residue free crop production . Our study aimed at identifying efficient OP-degrading bacteria (OPDB) and their compatibility with microbial bio-control agents (MBCA) for twin objective of microbial degradation of OP -residues and reduction in incidence of bacterial wilt of brinjal in OP- contaminated soil. As many, ten bacterial isolates showing OP- degrading potential were recovered through colony growth in mineral salt (MS) -medium treated with 25 ppm chlorpyriphos. Efficient isolates displaying growth up to 700ppm chlorpyriphos were further screened for OP-degradation, leading to identification of two most efficient OPDB, Acromobacter marplatensis [MW397524] (Am) and Pseudomonas azotoformans [MW397525] (Pa). These two isolates having in vitro compatibility with each other, showed further compatibility with two most widely used MBCA, viz., Pseudomonas flourescens [KT258013] (Pf) and Trichoderma harzianum [ON364138] (Th), facilitating the development of consortium having extended functional corridor. The response of combination of OPDB + MBCA(Am +Pa + Pf + Th) showed 80% lower percent wilt incidence (PWI), 2.8 times higher fruit yield ofbrinjal, and 15-25% lower OP-residues over un-inoculated control treatment. Our studies, hence, put forward a strong unified delivery mechanism of OPDB and MBCA as a part of green technology for chemical residue -free vegetable production in contaminated soils.