Prospecting the Potential of Plant Growth-Promoting Microorganisms for Mitigating Drought Stress in Crop Plants.

Drought is a global phenomenon affecting plant growth and productivity, the severity of which has impacts around the whole world. A number of approaches, such as agronomic, conventional breeding, and genetic engineering, are followed to increase drought resilience; however, they are often time consuming and non-sustainable. Plant growth-promoting microorganisms are used worldwide to mitigate drought stress in crop plants. These microorganisms exhibit multifarious traits, which not only help in improving plant and soil health, but also demonstrate capabilities in ameliorating drought stress. The present review highlights various adaptive strategies shown by these microbes in improving drought resilience, such as modulation of various growth hormones and osmoprotectant levels, modification of root morphology, exopolysaccharide production, and prevention of oxidative damage. Gene expression patterns providing an adaptive edge for further amelioration of drought stress have also been studied in detail. Furthermore, the practical applications of these microorganisms in soil are highlighted, emphasizing their potential to increase crop productivity without compromising long-term soil health. This review provides a comprehensive coverage of plant growth-promoting microorganisms-mediated drought mitigation strategies, insights into gene expression patterns, and practical applications, while also guiding future research directions.

Cyanobacterial myxoxanthophylls: biotechnological interventions and biological implications.

Cyanobacteria safeguard their photosynthetic machinery from oxidative damage caused by adverse environmental factors such as high-intensity light. Together with many photoprotective compounds, they contain myxoxanthophylls, a rare group of glycosidic carotenoids containing a high number of conjugated double bonds. These carotenoids have been shown to: have strong photoprotective effects, contribute to the integrity of the thylakoid membrane, and upregulate in cyanobacteria under a variety of stress conditions. However, their metabolic potential has not been fully utilized in the stress biology of cyanobacteria and the pharmaceutical industry due to a lack of mechanistic understanding and their insufficient biosynthesis. This review summarizes current knowledge on: biological function, genetic regulation, biotechnological production, and pharmaceutical potential of myxoxanthophyll, with a focus on strain engineering and parameter optimization strategies for increasing their cellular content. The summarized knowledge can be utilized in cyanobacterial metabolic engineering to improve the stress tolerance of useful strains and enhance the commercial-scale synthesis of myxoxanthophyll for pharmaceutical uses.

Prospecting potential of endophytes for modulation of biosynthesis of therapeutic bioactive secondary metabolites and plant growth promotion of medicinal and aromatic plants.

Medicinal and aromatic plants possess pharmacological properties (antidiabetes, anticancer, antihypertension, anticardiovascular, antileprosy, etc.) because of their potential to synthesize a wide range of therapeutic bioactive secondary metabolites. The concentration of bioactive secondry metabolites depends on plant species, local environment, soil type and internal microbiome. The internal microbiome of medicinal plants plays the crucial role in the production of bioactive secondary metabolites, namely alkaloids, steroids, terpenoids, peptides, polyketones, flavonoids, quinols and phenols. In this review, the host specific secondry metabolites produced by endophytes, their therapeutic properties and host-endophytes interaction in relation to production of bioactive secondry metaboloites and the role of endophytes in enhancing the production of bioactive secondry metabolites is discussed. How biological nitrogen fixation, phosphorus solubilization, micronutrient uptake, phytohormone production, disease suppression, etc. can play a vital role in enhacing the plant growth and development.The role of endophytes in enhancing the plant growth and content of bioactive secondary metabolites in medicinal and aromatic plants in a sustainable mode is highlighted.

Genetic Diversity and Anti-Oxidative Potential of Streptomyces spp. Isolated from Unexplored Niches of Meghalaya, India.

Streptomyces is genetically and functionally diverse genus known to produce a wide array of phenolics and flavonoids with significant biotechnological applications. 52 isolates belonging to 26 species of Streptomyces collected from Meghalaya, India were analyzed for their genetic diversity using BOX-PCR. Significant inter- and intra- generic diversity was observed among the Streptomyces isolates especially those belonging to S. cacaoi, S. lavendulae, S. olivochromogenes, S. aureus, S. flavovirens. During bioactivity screening of the isolates, S. rectiviolaceus MJM72 recorded the highest DPPH activity (77.13 ± 0.91%) whereas S. antimycoticus MSCA162 showed excellent ABTS radical scavenging activity (99.65 ± 0.41%). On the other hand, S. novaecaesareae MJM58 had the highest (756.4 ± 7.38 µg GAE g-1 fresh weight) phenolic content while S. rectiviolaceus MJM72 was recorded with the highest flavonoid content (69.3 ± 0.12 µg QE g-1 fresh weight). As compared to total flavonoid content, total phenolic content had a stronger correlation with antioxidant activities. HPLC analysis of five selected isolates showed presence of gallic acid and pyrocatechol as predominant phenolics. In case of flavonoids, three isolates showed presence of rutin with S. rochei MSCA130 having the highest rutin content (0.95 µg g-1 fresh weight). The results of this study showed high genetic diversity and antioxidant potential among the Streptomyces isolates.

Cyanobacterial secondary metabolites towards improved commercial significance through multiomics approaches.

Cyanobacteria are ubiquitous photosynthetic prokaryotes responsible for the oxygenation of the earth's reducing atmosphere. Apart from oxygen they are producers of a myriad of bioactive metabolites with diverse complex chemical structures and robust biological activities. These secondary metabolites are known to have a variety of medicinal and therapeutic applications ranging from anti-microbial, anti-viral, anti-inflammatory, anti-cancer, and immunomodulating properties. The present review discusses various aspects of secondary metabolites viz. biosynthesis, types and applications, which highlights the repertoire of bioactive constituents they harbor. Majority of these products have been produced from only a handful of genera. Moreover, with the onset of various OMICS approaches, cyanobacteria have become an attractive chassis for improved secondary metabolites production. Also the intervention of synthetic biology tools such as gene editing technologies and a variety of metabolomics and fluxomics approaches, used for engineering cyanobacteria, have significantly enhanced the production of secondary metabolites.

Bacterial chitinases: genetics, engineering and applications.

Chitinases are a group of enzymes that catalyze chitin hydrolysis and are present in all domains of life. Chitinases belong to different glycosyl hydrolase families with great diversity in their sequences. Microorganisms such as bacteria and fungi produce chitinases for nutrition, and energy, and to parasitize the chitinous hosts. But chitinases from bacteria are of special interest due to their ubiquitous nature and ability to perform under extreme conditions. Chitinases produced by bacteria have been explored for their use in agriculture and industry. In agriculture, their main role is to control chitin-containing insect pests, fungal pathogens, and nematodes. In the seafood industry, they found their role in the management of processing wastes which are mainly chitinous substances. Chitinases are also used to synthesize low molecular weight chitooligomers which are proven bioactive compounds with activities such as anti-tumour, antimicrobial, and immunity modulation. Considering their importance in ecology and biotechnological applications, several bacterial chitinases have been studied in the last two decades. Despite their potential, bacterial chitinases have a few limitations such as low production and lack of secretion systems which make the wild-type enzymes unfit for their applications in industries and other allied sectors. This review is an attempt to collate significant works in bacterial chitinases and their application in various industries and the employment of various tools and techniques for improvement to meet industrial requirements.

Interactive effects of Magnaporthe inoculation and nitrogen doses on the plant enzyme machinery and phyllosphere microbiome of resistant and susceptible rice cultivars.

Severity of plant diseases is often influenced by the availability of nutrients, particularly N; however, its effect on the phyllosphere microbiome in foliar pathogen challenged plants is less investigated in rice. The tripartite interaction among the fungal pathogen (Magnaporthe oryzae), rice cultivars (basmati and non-basmati, blast resistant or susceptible) and nitrogen (N) fertilization (0, 120 and 180 N) was investigated. Plant growth, elicitation of defense responses and abundance of microbial members in the rice phyllosphere were monitored using biochemical and molecular methods. In general, photosynthetic pigments were distinct for each cultivar, and optimal N doses led to higher values. The susceptible var. CO-39 and resistant CO-39I exhibited higher contents of photosynthetic pigments and micronutrients such as zinc in leaves in response to N doses. Elicitation of defense and hydrolytic enzymes was significantly influenced by pathogen inoculation and modulated by N doses, but varietal effects were distinct. Scoring indices emphasized the pathogen susceptibility of var. CO-39 and PB-1, which showed almost 40-60% higher values than the resistant cultivars; the interactions of cultivars and N doses was also significant. Characteristic changes were recorded in the abundances of the gene copies, particularly, with an overall increase in the number of cyanobacterial 16S rRNA, and bacterial amoA in pathogen-challenged treatments, while nifH gene copies exhibited a reducing trend with increasing N doses, in the presence or absence of pathogen. The varietal differences in the cause and effect relationships can be valuable in crop protection for more effective foliar application of pesticides or biocontrol agents.

Influence of fertilizers and rice cultivation methods on the abundance and diversity of phyllosphere microbiome.

Rice paddies are man-made, cross-over ecologies of aquatic and terrestrial systems, which favor the proliferation of characteristic microbial communities. Moisture regimes under flooded and different levels of irrigation such as in direct seeded rice (DSR) and system of rice intensification (SRI) lead to modulation in crop physiology, soil nutrient availability, and the soil microbiome. However, the diversity of the rice phyllosphere microbiome is less investigated in terms of the influence of fertilizer application and the method of rice cultivation (conventional-flooded, DSR and SRI). Scanning electron micrographs revealed the presence of bacteria as aggregates at microsites of the leaves. Phylogenetic analysis of the dominant culturable bacterial isolates using 16S rDNA sequences revealed that they belonged to the genera - Bacillus, Brevibacillus, Pantoea, Enterobacter, Pseudomonas, Erwinia, and Streptomyces. Fertilizer application brought about a distinct modulation in the communities belonging to phyla such as Bacteriodetes, Firmicutes, and Planctomyces, besides Proteobacteria. The cyanobacterial population was much influenced by the cultivation methods, particularly the SRI. Principal component analysis (PCA), involving the culturable phyllospheric microbial groups and leaf attributes (nutrients and pigments), illustrated the importance of leaf nitrogen and zinc. Also, the communities of the phylum Firmicutes exhibited marked changes in terms of the diversity, not only due to the cultivation method, but also the application of fertilizers. Thus, the cultivation methods and fertilizer application played important roles in modulating both the structural (taxonomical) and functional attributes of the phyllosphere microbiome.

Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria.

Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.

Detection of endophytic association between Aeschynomene nodulating Bradyrhizobium sp. and traditional Desariya rice roots under rice-Aeschynomene ecosystem of chaur land, Bihar, India.

Engineering diazotrophic rice having either an integral component of diazotrophic microbes or placing microbial origin nif gene to the rice plant is the dream of biotechnologist. Rice-Aeschynomene ecosystem of pristine chaur land provides a suitable niche to search Rhizobium endophytes in rice. Accordingly, the work was initiated to search suitable endophytic Rhizobium strain for artificial symbiosis within the roots of Desariya rice and its source through morphological, biochemical and molecular approaches. Detection of Acetylene reduction assay (ARA) activity in sterilized Desariya rice root confirmed the presence of putative diazotrophic endophytes in rice root. Isolates from Aeschynomene aspera L. nodulating and Desariya rice endophytic Rhizobium were evaluated for growth, IAA, morphological and biochemical features. Carbon profiling pattern of both these isolates indicated that Desariya rice endophytic Rhizobium has its similarity with Aeschynomene aspera L. nodulating Rhizobium. 16S rRNA gene sequencing confirmed the presence of endophytic Bradyrhizobium sp. in Desariya rice roots and its similarity with Aeschynomene aspera L. nodulating Bradyrhizobium. Desariya rice Bradyrhizobium may be an ideal candidate in the future for creating artificial symbiosis in rice due to its similarity with Aeschynomene aspera L. Bradyrhizobium.

Colorimetric loop-mediated isothermal amplification assay for detection and ecological monitoring of Sarocladium oryzae, an important seed-borne pathogen of rice.

Accurate and timely disease detection plays a critical role in achieving sustainable crop protection. Globally, rice has been a staple crop for centuries plagued by the diseases that greatly hamper its productivity. Sheath rot, an emerging disease of rice caused by the seed-borne pathogen Sarocladium oryzae, has reportedly caused heavy losses to agricultural produce in recent years. Our study has led to the development and validation of a LAMP assay for early detection of S. oryzae, the causal agent of sheath rot from the live-infected tissues, seeds, weeds, and environmental samples. The assay could detect as low as 1.6 fg/µl of the pathogen in 15 min. The assay was implemented to bio-surveil the presence of this pathogen by testing it on three weed species (Echinochloa colona, Echinochloa crus-galli, and Cyperus teneriffae) growing around the rice fields. The results showed the presence of the pathogen in two of the weed species viz. E. colona and E. crus-galli. The assay was used to test 13 different rice varieties for the presence of S. oryzae in seeds. In total, three of the varieties did not show the presence of S. oryzae in their seeds while the rest were found to harbor the pathogen. The developed assay can effectively be used to detect and screen the presence of S. oryzae in live samples including seeds and field soil.

Elucidating the impact of boron fertilization on soil physico-chemical and biological entities under cauliflower-cowpea-okra cropping system in an Eastern Himalayan acidic Inceptisol.

Information on the role of boron (B) on soil physico-chemical and biological entities is scarce, and the precise mechanism in soil is still obscure. Present field investigation aimed to assessing the implication of direct and residual effect of graded levels of applied-B on soil biological entities and its concomitant impact on crop productivity. The treatments comprised of five graded levels of B with four replications. To assess the direct effect of B-fertilization, cauliflower was grown as a test crop wherein, B-fertilization was done every year. For assessment of succeeding residual effects of B-fertilization, cowpea and okra were grown as test crops and, B-fertilization was phased out in both crops. The 100% recommended dose of NPK (RDF) along with FYM was uniformly applied to all crops under CCOCS. Results indicated that the direct effect of B had the edge over residual effect of B in affecting soil physico-chemical and biological entities under CCOCS. Amongst the graded levels of B, application of the highest B level (2 kg ha-1) was most prominent in augmenting microbiological pools in soil at different crop growth stages. The order of B treatments in respect of MBC, MBN, and soil respiration at different crop growth stages was 2.0 kg B ha-1 > 1.5 kg B ha-1 > 1.0 kg B ha-1 > 0.5 kg B ha-1 > 0 kg B ha-1, respectively. Moreover, maximum recoveries of potentially mineralizable-C (PMC) and potentially mineralizable-N (PMN) were noticed under 2 kg B ha-1. Analogous trend was recorded in soil microbial populations at different crop growth stages. Similarly, escalating B levels up to 2 kg B ha-1 exhibited significantly greater soil enzymatic activities viz., arylsulphatase (AS), dehydrogenase (DH), fluorescein diacetate (FDA) and phosphomonoesterase (PMA), except urease enzyme (UE) which showed an antagonistic effect of applied-B in soil. Greater geometric mean enzyme activity (GMEA) and soil functional diversity index were recorded under 2 kg B ha-1 in CCOCS, at all crop growth stages over control. The inclusive results indicated that different soil physico-chemical and biological properties CCOCS can be invariably improved by the application of graded levels of B up to 2 kg B ha-1 in an acid Inceptisol.

Transcriptome profiling provides insights into regulatory factors involved in Trichoderma viride-Azotobacter chroococcum biofilm formation.

Azotobacter chroococcum (Az) and Trichoderma viride (Tv) represent agriculturally important and beneficial plant growth promoting options which contribute towards nutrient management and biocontrol, respectively. When Az and Tv are co-cultured, they form a biofilm, which has proved promising as an inoculant in several crops; however, the basic aspects related to regulation of biofilm formation were not investigated. Therefore, whole transcriptome sequencing (Illumina NextSeq500) and gene expression analyses were undertaken, related to biofilm formation vis a vis Tv and Az growing individually. Significant changes in the transcriptome profiles of biofilm were recorded and validated through qPCR analyses. In-depth evaluation also identified several genes (phoA, phoB, glgP, alg8, sipW, purB, pssA, fadD) specifically involved in biofilm formation in Az, Tv and Tv-Az. Genes coding for RNA-dependent RNA polymerase, ABC transporters, translation elongation factor EF-1, molecular chaperones and double homeobox 4 were either up-regulated or down-regulated during biofilm formation. To our knowledge, this is the first report on the modulation of gene expression in an agriculturally beneficial association, as a biofilm. Our results provide insights into the regulatory factors involved during biofilm formation, which can help to improve the beneficial effects and develop more effective and promising plant- microbe associations.

Nutrients and host attributes modulate the abundance and functional traits of phyllosphere microbiome in rice.

The abundance of phyllosphere bacterial communities of seven genotypes of rice ADT- 38, ADT-43, CR-1009, PB-1, PS-5, P-44, and PB-1509 was investigated, in relation to nutrient dynamics of rhizosphere and leaves. P-44 genotype recorded highest pigment accumulation, while genotypes CR-1009 and P-44 exhibited most number of different bacterial morphotypes, Colony forming units in two media (Nutrient agar and R2A) varied significantly and ranged from 106-107 per g plant tissues. Among the selected 60 distinct morphotypes, IAA and siderophore producers were the dominant functional types. Biocontrol activity against Drechslera oryzae was shown by 38 isolates, while 17 and 9 isolates were potent against Rhizoctonia solani and Magnaporthe oryzae respectively. Principal Component Analysis (PCA) illustrated the significant effects of selected soil and leaf nutrients of seven rice varieties on the culturable phyllospheric population (log CFU), particularly in the R2A medium. Eigen values revealed that 83% of the variance observed could be assigned to Leaf-Fe, Leaf-Mn, chlorophyll b and soil organic carbon (OC). Quantitative PCR analyses of abundance of bacteria, cyanobacteria and archaebacteria revealed a host-specific response, with CR-1009 showing highest number of 16S rRNA copies of bacterial members, while both P-44 and PS-5 had higher cyanobacterial abundance, but lowest number of those belonging to archaebacteria. Nutritional aspects of leaf and soil influenced the abundance of bacteria and their functional attributes; this is of interest for enhancing the efficacy of foliar inoculants, thereby, improving plant growth and disease tolerance.

Influence of cyanobacterial inoculation on the culturable microbiome and growth of rice.

Rice plants are selective with their associations with bacteria that are beneficial for growth, nutrient uptake, exhibit induced resistance or antagonism towards pathogens. Cyanobacteria as bioinoculants are known to promote the growth and health of rice plants. The present investigation was aimed at understanding whether and how cyanobacterial (Calothrix elenkinii) inoculation influenced the rice plant growth and the culturable bacterial populations and identifying the dominant culturable "microbiome" members. The plant tissue extracts were used to enumerate populations of the culturable microbiome members using selected enrichment media with different nutrient levels. About 10-fold increases in population densities of culturable microbiome members in different media were recorded, with some isolates having metabolic potential for nitrogen fixation and phosphorus solubilization. Fatty acid methyl ester (FAME) analysis and 16S rRNA sequencing of selected microbial morphotypes suggested the predominance of the members of Bacillaceae. Significant increases in plant growth attributes, nitrogenase activity and indole acetic acid production, and activities of hydrolytic and defense enzymes were recorded in the Calothrix inoculated plants. The PCR-based analysis and scanning electron microscopic (SEM) observations confirmed the presence of inoculated cyanobacterium inside the plant tissues. This investigation illustrated that cyanobacterial inoculation can play significant roles in improving growth and metabolism of rice directly and interact with the beneficial members from the endophytic microbiome of rice seedlings synergistically.