Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.

Endophytic microbes are present in nearly all of the plant species known to date but how they enter and flourish inside a host plant and display multiple benefits like plant growth promotion (PGP), biodegradation, and stress alleviation are still unexplored. Until now, the majority of the research has been conducted assuming that the host–endophyte interaction is analogous to the PGP microbes, although, studies related to the mechanisms of their infection, colonization as well as conferring important traits to the plants are limited. It would be fascinating to explore the role of these endophytic microbes in host gene expression, metabolism, and the modulation of phenotypic traits, under abiotic and biotic stress conditions. In this review, we critically focused on the following areas: (i) endophytic lifestyle and the mechanism of their entry into plant tissues, (ii) how endophytes modulate the immune system of plants and affect the genotypic and phenotypic expression of host plants under abiotic and biotic stress condition, and (iii) the role of omics and other integrated genomic approaches in unraveling complex host–endophyte signaling crosstalk. Furthermore, we discussed their role in phytoremediation of heavy metal stress and whole genomic analysis based on an understanding of different metabolic pathways these endophytes utilize to combat stress.

Recently, the application of endophytes in the alleviation of different types of stresses has received considerable attention, but their role in drought stress alleviation and growth promotion in soybean is not well-stated. In this study, twenty bacterial endophytes were isolated from soybean root tissues and screened for plant growth-promoting (PGP) traits, biocontrol potential, and drought stress alleviation. Out of them, 80% showed PGP traits, and 20% showed antagonistic activity against Fusarium oxysporum (ITCC 2389), Macrophomina phaseolina (ITCC 1800), and Alternaria alternata (ITCC 3467), and only three of them showed drought tolerance up to 15% (−0.3 MPa). Results indicated that drought-tolerant PGP endophytic bacteria enhanced soybean seedling growth under drought stress conditions. Morphological, biochemical, and molecular characterization (16S rRNA) revealed that these three bacterial isolates, AKAD A1-1, AKAD A1-2, and AKAD A1-16, closely resemble Bacillus cereus (GenBank accession No. MN079048), Pseudomonas otitidis (MW301101), and Pseudomonas sp. (MN079074), respectively. We observed that the soybean seedlings were grown in well-watered and drought-stressed soil showed the adverse effect of drought stress on morphological (stem length, root length, plant fresh and dry weight) as well as on biochemical parameters (a decline of photosynthetic pigments, membrane damage, etc.). However, soybean seedlings inoculated with these endophytes have improved the biomass significantly (p ≤ 0.05) under normal as well as in drought stress conditions over control treatments by influencing several biochemical changes. Among these three endophytes, AKAD A1-16 performed better than AKAD A1-2 and AKAD A1-1, which was further validated by the ability to produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase in the following order: AKAD A1-16 > AKAD A1-2 > AKAD A1-1. Scanning electron microscopy images also showed a bacterial presence inside the roots of soybean seedlings. These findings supported the application of bacterial root endophytes as a potential tool to mitigate the effect of drought as well as of fungal diseases on the early seedling growth of soybean.

Water hyacinth is a rapidly growing troublesome aquatic weed plant, which causes eutrophication in water bodies and irreversible damage to the ecological system. In this work, we have investigated the water hyacinth biomass (WHB) hydrolysis efficacy of dilute alkaline (DA) pretreatment followed by biological pretreatment with white-rot fungus Alternaria alternata strain AKJK-2. The effectiveness of the dilute alkaline (DA) and biological pretreatment process on WHB was confirmed by using X-ray Diffraction (XRD) and Fourier Transform Infrared Spectrophotometer (FTIR), and was further visualized by Scanning Electron Microscope (SEM) and Confocal Laser Scanning Microscopy (CLSM). XRD spectra showed the increase in the crystallinity of pretreated samples, attributed to the elimination of amorphous components as lignin and hemicellulose. FTIR peak analysis of pre-treated WHB showed substantial changes in the absorption of cellulose functional groups and the elimination of lignin signals. Scanning electron microscopy (SEM) images showed firm, compact, highly ordered, and rigid fibril structures without degradation in the untreated WHB sample, while the pretreated samples exhibited loose, dispersed, and distorted structures. XRD indices (Segal, Landis, and Faneite), and FTIR indices [Hydrogen bond intensity (HBI); Total crystallinity index (TCI); and Lateral order crystallinity (LOI)] results were similar to the aforementioned results, and also showed an increase in the crystallinity both in alkaline and biological pretreatments. Alkaline pretreated WHB, with these indices, also showed the highest crystallinity and a crystalline allomorphs mixture of cellulose I (native) and cellulose II. These results were further validated by the CLSM, wherein fluorescent signals were lost after the pretreatment of WHB over control. Overall, these findings showed the significant potential of integrated assessment tools with chemical and biological pretreatment for large-scale utilization and bioconversion of this potential aquatic weed for bioenergy production.

Maize, along with rice and wheat, is a popular staple food crop worldwide, and the most widely produced cereal crop. It is a versatile crop that may be utilized as a source of raw materials for human and animal fodders. Low agricultural yield and rapid population expansion significantly threaten future food security. Maize production is hampered by biotic and abiotic causes, with abiotic factors being the most critical limitation to agricultural output worldwide. Soil salinity is a key abiotic factor that reduces agricultural production by imposing negative impacts at several life cycle phases, including germination, seedling, vegetative, and reproductive development. Maize plants experience many physiological changes due to osmotic stress, toxicity of particular ions, and nutritional imbalance induced by salt stress. The degree and duration of stress, crop growth phases, genetic characteristics, and soil conditions influence yield reduction. Maize plants can tolerate salt stress involving a complex mechanism by changing their physiological, biochemical, and metabolic activities like stomatal functioning, photosynthesis, respiration, transpiration, hormone regulation, enzymes, metabolite generation, etc. After studying the salt tolerance mechanisms of maize plants under stress, integrated management techniques should be developed for maize agriculture in saline settings. Therefore, the study of plant responses to salt stress, stress tolerance mechanisms, and management strategies is one of the most imperative research fields in plant biology, and the study will focus on the effects of salt stress in different growth stages, plant tolerance mechanisms, and agronomic management practices for successful maize production all over the world.