Re-vitalizing of endophytic microbes for soil health management and plant protection

Unearthing the power of microbes as plant microbiome for sustainable agriculture

In recent years, research into the complex interactions and crosstalk between plants and their associated microbiota, collectively known as the plant microbiome has revealed the pivotal role of microbial communities for promoting plant growth and health. Plants have evolved intricate relationships with a diverse array of microorganisms inhabiting their roots, leaves, and other plant tissues. This microbiota mainly includes bacteria, archaea, fungi, protozoans, and viruses, forming a dynamic and interconnected network within and around the plant. Through mutualistic or cooperative interactions, these microbes contribute to various aspects of plant health and development. The direct mechanisms of the plant microbiome include the enhancement of plant growth and development through nutrient acquisition. Microbes have the ability to solubilize essential minerals, fix atmospheric nitrogen, and convert organic matter into accessible forms, thereby augmenting the nutrient pool available to the plant. Additionally, the microbiome helps plants to withstand biotic and abiotic stresses, such as pathogen attacks and adverse environmental conditions, by priming the plant's immune responses, antagonizing phytopathogens, and improving stress tolerance. Furthermore, the plant microbiome plays a vital role in phytohormone regulation, facilitating hormonal balance within the plant. This regulation influences various growth processes, including root development, flowering, and fruiting. Microbial communities can also produce secondary metabolites, which directly or indirectly promote plant growth, development, and health. Understanding the functional potential of the plant microbiome has led to innovative agricultural practices, such as microbiome-based biofertilizers and biopesticides, which harness the power of beneficial microorganisms to enhance crop yields while reducing the dependency on chemical inputs. In the present review, we discuss and highlight research gaps regarding the plant microbiome and how the plant microbiome can be used as a source of single and synthetic bioinoculants for plant growth and health.

Co-application of biochars and Piriformospora indica improved the quality of coastal saline soil and promoted the growth of forage

Soil quality is defined as the ability of soil to maintain the soil environment and the biosphere. Due to the limitation of salt and alkali stress, soil quality can be reduced, which in turn affects agricultural production. Biochar is widely used in saline-alkali land improvement because of its special pore structure and strong ion exchange ability, while Piriformospora indica is widely used in saline-alkali land improvement because it can symbiose with plants and improve plant stress resistance. However, the synergistic effect of combined biochar application and inoculation of P. indica on the quality of saline-alkali soil and plant development is uncertain. Hence, we investigated the combined influences of biochar and P. indica on the soil physicochemical characteristics, as well as the growth and chlorophyll florescence of sorghum-sudangrass hybrids (Sorghum bicolor × Sorghum sudane) in our study. The results indicated that after applying biochar and P. indica together, there was a considerable drop in soil pH, conductivity, Na+, and Cl- concentrations. Meanwhile, the soil organic matter (SOM), available phosphorus (AP), and alkaline hydrolyzable nitrogen (AN) increased by 151.81%, 50.84%, and 103.50%, respectively, when the Bamboo biochar was combined with 120 ml/pot of P. indica. Eventually, sorghum-sudangrass hybrid biomass, transpiration rate, and chlorophyll content increased by 111.69%, 204.98%, and 118.54%, respectively. According to our findings, using P. indica and biochar together can enhance soil quality and plant growth. The results also provide insights to enhance the quality of saline-alkali soils and the role of microorganisms in nutrient cycling.

Harnessing chickpea bacterial endophytes for improved plant health and fitness

Endophytic bacteria live asymptomatically inside the tissues of host plants without inflicting any damage. Endophytes can confer several beneficial traits to plants, which can contribute to their growth, development, and overall health. They have been found to stimulate plant growth by enhancing nutrient uptake and availability. They can produce plant growth-promoting substances such as auxins, cytokinins, and gibberellins, which regulate various aspects of plant growth and development. Endophytes can also improve root system architecture, leading to increased nutrient and water absorption. Some endophytes possess the ability to solubilize nutrients, such as phosphorus and potassium, making them more available for plant uptake, and fixing atmospheric nitrogen. Chickpea (Cicer arietinum) is a major legume crop that has mutualistic interactions with endophytes. These endophytes can benefit the chickpea plant in various ways, including higher growth, improved nutrient uptake, increased tolerance to abiotic and biotic stressors, and disease suppression. They can produce enzymes and metabolites that scavenge harmful reactive oxygen species, thus reducing oxidative stress. Moreover, several studies reported that endophytes produce antimicrobial compounds, lytic enzymes, and volatile organic compounds that inhibit the growth of fungal pathogens and trigger systemic defense responses in plants, leading to increased resistance against a broad range of pathogens. They can activate plant defense pathways, including the production of defense-related enzymes, phytoalexins, and pathogenesis-related proteins, thereby providing long-lasting protection. It is important to note that the diversity and function of chickpea-associated endophytes can vary depending on factors such as variety, geographical location, and environmental conditions. The mechanisms behind the plant-beneficial interactions are still being intensively explored. In this review, new biotechnologies in agricultural production and ecosystem stability were presented. Thus, harnessing chickpea endophytes could be exploited in developing drought-resistant cultivars that can maintain productivity in arid and semi-arid environments, crucial for meeting the global demand for chickpeas.

Chickpea seed endophyte Enterobacter sp. mediated yield and nutritional enrichment of chickpea for improving human and livestock health

Chickpeas (Cicer arietinum L.) are used as a good source of proteins and energy in the diets of various organisms including humans and animals. Chickpea straws can serve as an alternative option for forage for different ruminants. This research mainly focussed on screening the effects of adding beneficial chickpea seed endophytes on increasing the nutritional properties of the different edible parts of chickpea plants. Two efficient chickpea seed endophytes (Enterobacter sp. strain BHUJPCS-2 and BHUJPCS-8) were selected and applied to the chickpea seeds before sowing in the experiment conducted on clay pots. Chickpea seeds treated with both endophytes showed improved plant growth and biomass accumulation. Notably, improvements in the uptake of mineral nutrients were found in the foliage, pericarp, and seed of the chickpea plants. Additionally, nutritional properties such as total phenolics (0.47, 0.25, and 0.55 folds), total protein (0.04, 0.21, and 0.18 folds), carbohydrate content (0.31, 0.32, and 0.31 folds), and total flavonoid content (0.45, 027, and 0.8 folds) were increased in different parts (foliage, pericarp, and seed) of the chickpea plants compared to the control plants. The seed endophyte-treated plants showed a significant increase in mineral accumulation and improvement in nutrition in the different edible parts of chickpea plants. The results showed that the seed endophyte-mediated increase in dietary and nutrient value of the different parts (pericarp, foliage, and seeds) of chickpea are consumed by humans, whereas the other parts (pericarp and foliage) are used as alternative options for forage and chaff in livestock diets and may have direct effects on their nutritional conditions.

Plant Growth-Promoting Endophytic Bacteria Isolated from Miscanthus giganteus and Their Antifungal Activity

Modern technologies can satisfy human needs only with the use of large quantities of fertilizers and pesticides that are harmful to the environment. For this reason, it is possible to develop new technologies for sustainable agriculture. The process could be carried out by using endophytic microorganisms with a (possible) positive effect on plant vitality. Bacterial endophytes have been reported as plant growth promoters in several kinds of plants under normal and stressful conditions. In this study, isolates of bacterial endophytes from the roots and leaves of Miscanthus giganteus plants were tested for the presence of plant growth-promoting properties and their ability to inhibit pathogens of fungal origin. Selected bacterial isolates were able to solubilize inorganic phosphorus, fix nitrogen, and produce phytohormones, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, and siderophore. Leaf bacterial isolate Pantoea ananat is 50 OL 2 had high production of siderophores (zone ≥ 5 mm), and limited phytohormone production, and was the only one to show ACC deaminase activity. The root bacterial isolate of Pseudomonas libanensis 5 OK 7A showed the best results in phytohormone production (N6-(Δ2-isopentenyl)adenine and indole-3-acetic acid, 11.7 and 12.6 ng·mL-1, respectively). Four fungal cultures-Fusarium sporotrichioides DBM 4330, Sclerotinia sclerotiorum SS-1, Botrytis cinerea DS 90 and Sphaerodes fimicola DS 93-were used to test the antifungal activity of selected bacterial isolates. These fungal cultures represent pathogenic families, especially for crops. All selected root endophyte isolates inhibited the pathogenic growth of all tested fungi with inhibition percentages ranging from 30 to 60%. Antifungal activity was also tested in two forms of immobilization of selected bacterial isolates: one in agar and the other on dextrin-coated cellulose carriers. These results demonstrated that the endophytic Pseudomonas sp. could be used as biofertilizers for crops.

The effect of shrubs admixture in pine forest stands on soil bacterial and fungal communities and accumulation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are a group of persistent toxic pollutants. The species composition of the stand is important in shaping the quality of soil organic matter and, consequently, the PAH content. The main purpose of the research was to determine the role of shrubs in shaping PAH accumulation in forest soils. The study covered the soils of the pine stands of the Rybnik Forest District, which experiences some of the highest deposition of industrial emissions in Europe. Pine stands with admixture of shrubs (alder buckthorn Frangula alnus and European hazelnut Coryllus avellana) growing in the same soil conditions were selected for the study. Samples for analyses were collected from the organic horizon (O) (from a depth of 0-7 cm) and humus mineral horizon (A) (from a depth of 7-15 cm). The organic C and total N concentrations, pH, alkaline cation content, soil enzyme activity and PAH content were determined. Additionally, the taxonomic composition of soil bacterial and fungal communities was determined. The highest activity of enzymes was noted in soils under influence of shrubs. The enzymatic activity was positively correlated with the content of total N, organic C, pH H2O and KCl and negatively with the C/N ratio. The highest PAH content was recorded in the soils of pine stands without the admixture of shrubs. Our research indicates the importance of shrubs in shaping the properties of surface horizons of forest soil and, consequently on the accumulation of PAHs. Shrubs stimulate biochemical activity of soils which results in lower PAHs accumulation by providing more easily decomposable organic matter.

Harnessing the action mechanisms of microbial endophytes for enhancing plant performance and stress tolerance: current understanding and future perspectives

Microbial endophytes are microorganisms that reside within plant tissues without causing any harm to their hosts. These microorganisms have been found to confer a range of benefits to plants, including increased growth and stress tolerance. In this review, we summarize the recent advances in our understanding of the mechanisms by which microbial endophytes confer abiotic and biotic stress tolerance to their host plants. Specifically, we focus on the roles of endophytes in enhancing nutrient uptake, modulating plant hormones, producing secondary metabolites, and activating plant defence responses. We also discuss the challenges associated with developing microbial endophyte-based products for commercial use, including product refinement, toxicology analysis, and prototype formulation. Despite these challenges, there is growing interest in the potential applications of microbial endophytes in agriculture and environmental remediation. With further research and development, microbial endophyte-based products have the potential to play a significant role in sustainable agriculture and environmental management.

Abiotic factors and endophytes co-regulate flavone and terpenoid glycoside metabolism in Glycyrrhiza uralensis

Recently, endorhizospheric microbiota is realized to be able to promote the secondary metabolism in medicinal plants, but the detailed metabolic regulation metabolisms and whether the promotion is influenced by environmental factors are unclear yet. Here, the major flavonoids and endophytic bacterial communities in various Glycyrrhiza uralensis Fisch. roots collected from seven distinct places in northwest China, as well as the edaphic conditions, were characterized and analyzed. It was found that the soil moisture and temperature might modulate the secondary metabolism in G. uralensis roots partially through some endophytes. One rationally isolated endophyte Rhizobium rhizolycopersici GUH21 was proved to promote the accumulation of isoliquiritin and glycyrrhizic acid significantly in roots of the potted G. uralensis under the relatively high-level watering and low temperature. Furthermore, we did the comparative transcriptome analysis of G. uralensis seedling roots in different treatments to investigate the detailed mechanisms of the environment-endophyte-plant interactions and found that the low temperature went hand in hand with the high-level watering to activate the aglycone biosynthesis in G. uralensis, while GUH21 and the high-level watering cooperatively promoted the in planta glucosyl unit production. Our study is of significance for the development of methods to rationally promote the medicinal plant quality. KEY POINTS: • Soil temperature and moisture related to isoliquiritin contents in Glycyrrhiza uralensis Fisch. • Soil temperature and moisture related to the hosts' endophytic bacterial community structures. • The causal relation among abiotic factors-endophytes-host was proved through the pot experiment.

The Role of Endophytes in Combating Fungal- and Bacterial-Induced Stress in Plants

Plants are subjected to multifaceted stresses that significantly jeopardize crop production. Pathogenic microbes influence biotic stress in plants, which ultimately causes annual crop loss worldwide. Although the use of pesticides and fungicides can curb the proliferation of pathogens in plants and enhance crop production, they pollute the environment and cause several health issues in humans and animals. Hence, there is a need for alternative biocontrol agents that offer an eco-friendly mode of controlling plant diseases. This review discusses fungal- and bacterial-induced stress in plants, which causes various plant diseases, and the role of biocontrol defense mechanisms, for example, the production of hydrolytic enzymes, secondary metabolites, and siderophores by stress-tolerant fungi and bacteria to combat plant pathogens. It is observed that beneficial endophytes could sustain crop production and resolve the issues regarding crop yield caused by bacterial and fungal pathogens. The collated literature review indicates that future research is necessary to identify potential biocontrol agents that can minimize the utility of synthetic pesticides and increase the tenable agricultural production.

Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis

The development of artificial biocrust using cyanobacterium Phormidium tenue has been suggested as an effective strategy to prevent soil degradation. Here, a combination of in silico approaches with growth rate, photosynthetic pigment, morphology, and transcript analysis was used to identify specific genes and their protein products in response to 500 mM NaCl in P. tenue. The results show that 500 mM NaCl induces the expression of genes encoding glycerol-3-phosphate dehydrogenase (glpD) as a Flavoprotein, ribosomal protein S12 methylthiotransferase (rimO), and a hypothetical protein (sll0939). The constructed co-expression network revealed a group of abiotic stress-responsive genes. Using the Basic Local Alignment Search Tool (BLAST), the homologous proteins of rimO, glpD, and sll0939 were identified in the P. tenue genome. Encoded proteins of glpD, rimO, and DUF1622 genes, respectively, contain (DAO and DAO C), (UPF0004, Radical SAM and TRAM 2), and (DUF1622) domains. The predicted ligand included 22B and MG for DUF1622, FS5 for rimO, and FAD for glpD protein. There was no direct disruption in ligand-binding sites of these proteins by Na+, Cl-, or NaCl. The growth rate, photosynthetic pigment, and morphology of P. tenue were investigated, and the result showed an acceptable tolerance rate of this microorganism under salt stress. The quantitative real-time polymerase chain reaction (qRT-PCR) results revealed the up-regulation of glpD, rimO, and DUF1622 genes under salt stress. This is the first report on computational and experimental analyses of the glpD, rimO, and DUF1622 genes in P. tenue under salt stress to the best of our knowledge.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-03050-w.