Perspectives and Challenges of Microbial Application for Crop Improvement

Phosphate fertilization affects rhizosphere microbiome of maize and sorghum genotypes

Despite the lower reactivity of natural phosphates compared to soluble fertilizers, their P bioavailability can increase over the cultivation years, due to the physicochemical processes and the activity of soil microbiota. Therefore, this work aimed to evaluate the α and β diversity of the rhizosphere microbiota of maize and sorghum genotypes grown under different sources and doses of phosphate fertilizers. Four commercial maize and four sorghum genotypes were grown under field conditions with three levels of triple superphosphate (TSP) and two types of rock phosphate sources: phosphorite (RockP) and bayóvar (RP) during two seasons. Maize and sorghum presented a significant difference on the genetic β diversity of both rhizosferic bacterial and arbuscular mycorrhizal fungi. Moreover, P doses within each phosphate source formed two distinct groups for maize and sorghum, and six bacterial phyla were identified in both crops with significant difference in the relative abundance of Firmicutes and Proteobacteria. It was observed that RockP fertilization increased Firmicutes population while Proteobacteria was the most abundant phylum after TSP fertilization in maize. In sorghum, a significant impact of fertilization was observed on the Acidobacteria and Proteobacteria phyla. TSP fertilization increased the Acidobacteria population compared to no fertilized (P0) and RockP while Proteobacteria abundance in RockP was reduced compared to P0 and TSP, indicating a shift toward a more copiotrophic community. Our results suggested that the reactivity of P source is the predominant factor in bacterial community' structures in the maize and sorghum rhizosphere from the evaluated genotypes, followed by P source.

Microbiome: A Tool for Plant Stress Management in Future Production Systems

Climate change, due to the altered composition of the global atmosphere from the “greenhouse effect”, is one of the biggest challenges to agricultural production systems [...]

Biocontrol Methods in Avoidance and Downsizing of Mycotoxin Contamination of Food Crops

By increasing the resistance of seeds against abiotic and biotic stress, the possibility of cereal mold contamination and hence the occurrence of secondary mold metabolites mycotoxins decreases. The use of biological methods of seed treatment represents a complementary strategy, which can be implemented as an environmental-friendlier approach to increase the agricultural sustainability. Whereas the use of resistant cultivars helps to reduce mold growth and mycotoxin contamination at the very beginning of the production chain, biological detoxification of cereals provides additional weapons against fungal pathogens in the later stage. Most efficient techniques can be selected and combined on an industrial scale to reduce losses and boost crop yields and agriculture sustainability, increasing at the same time food and feed safety. This paper strives to emphasize the possibility of implementation of biocontrol methods in the production of resistant seeds and the prevention and reduction in cereal mycotoxin contamination.

Evaluation of developing maize microbiomes and associations among nitrogen cyclers and key fungal taxa

More sustainable approaches to agriculture are urgently needed to protect existing resources and optimize crop yields and to provide food for a growing global human population. More sustainable agricultural practices that utilize plant-microbe relationships across cultivation are urgently needed. The main objectives of this study were to track the prokaryotic and fungal microbiomes associated with key growth stages of developing maize to evaluate the relationships among nitrogen cycling bacteria and major fungal genera including those known to contain arbuscular mycorrhizal fungi and other important taxa. Prokaryotic and fungal microbiomes associated with bulk soils, rhizosphere soils and tissues of developing maize were characterized using Illumina MiSeq sequencing. Similarities in microbiome diversity and abundance were compared to sample metadata to explore the influence of external factors on microbiome development. Correlations among target fungal taxa, bulk bacteria and nitrogen cycling bacteria were determined using non-parametric Spearman correlations. Important maize-associated fungal taxa were detected in all samples across growth stages, with Fusarium, Penicillium and Aspergillus fungi comprising up to 4.21, 4.26 and 0.28% of all fungal genera, respectively. Thirteen statistically significant correlations between nitrogen cycling genera and targeted fungal genera were also identified (r _S≥0.70 or r _S≤-0.70; P<0.05). This study is the first to note a strong positive association among several nitrifying bacteria and Fusarium (R=0.71; P=0.0046), Aspergillus (R=0.71; P=0.0055) and Cladosporium spcies (R=0.74; P=0.0038), suggesting the levels of soil nitrate, nitrite or nitrification intermediates may have large roles in the proliferation of important maize-associated fungi.

Microbial Community and Function-Based Synthetic Bioinoculants: A Perspective for Sustainable Agriculture

Interactions among the plant microbiome and its host are dynamic, both spatially and temporally, leading to beneficial or pathogenic relationships in the rhizosphere, phyllosphere, and endosphere. These interactions range from cellular to molecular and genomic levels, exemplified by many complementing and coevolutionary relationships. The host plants acquire many metabolic and developmental traits such as alteration in their exudation pattern, acquisition of systemic tolerance, and coordination of signaling metabolites to interact with the microbial partners including bacteria, fungi, archaea, protists, and viruses. The microbiome responds by gaining or losing its traits to various molecular signals from the host plants and the environment. Such adaptive traits in the host and microbial partners make way for their coexistence, living together on, around, or inside the plants. The beneficial plant microbiome interactions have been exploited using traditional culturable approaches by isolating microbes with target functions, clearly contributing toward the host plants' growth, fitness, and stress resilience. The new knowledge gained on the unculturable members of the plant microbiome using metagenome research has clearly indicated the predominance of particular phyla/genera with presumptive functions. Practically, the culturable approach gives beneficial microbes in hand for direct use, whereas the unculturable approach gives the perfect theoretical information about the taxonomy and metabolic potential of well-colonized major microbial groups associated with the plants. To capitalize on such beneficial, endemic, and functionally diverse microbiome, the strategic approach of concomitant use of culture-dependent and culture-independent techniques would help in designing novel "biologicals" for various crops. The designed biologicals (or bioinoculants) should ensure the community's persistence due to their genomic and functional abilities. Here, we discuss the current paradigm on plant-microbiome-induced adaptive functions for the host and the strategies for synthesizing novel bioinoculants based on functions or phylum predominance of microbial communities using culturable and unculturable approaches. The effective crop-specific inclusive microbial community bioinoculants may lead to reduction in the cost of cultivation and improvement in soil and plant health for sustainable agriculture.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Linking Soil Microbial Diversity to Modern Agriculture Practices: A Review

Agriculture is a multifarious interface between plants and associated microorganisms. In contemporary agriculture, emphasis is being given to environmentally friendly approaches, particularly in developing countries, to enhance sustainability of the system with the least negative effects on produce quality and quantity. Modern agricultural practices such as extensive tillage, the use of harmful agrochemicals, mono-cropping, etc. have been found to influence soil microbial community structure and soil sustainability. On the other hand, the question of feeding the ever-growing global population while ensuring system sustainability largely remains unanswered. Agriculturally important microorganisms are envisaged to play important roles in various measures to raise a healthy and remunerative crop, including integrated nutrient management, as well as disease and pest management to cut down agrochemicals without compromising the agricultural production. These beneficial microorganisms seem to have every potential to provide an alternative opportunity to overcome the ill effects of various components of traditional agriculture being practiced by and large. Despite an increased awareness of the importance of organically produced food, farmers in developing countries still tend to apply inorganic chemical fertilizers and toxic chemical pesticides beyond the recommended doses. Nutrient uptake enhancement, biocontrol of pests and diseases using microbial inoculants may replace/reduce agrochemicals in agricultural production system. The present review aims to examine and discuss the shift in microbial population structure due to current agricultural practices and focuses on the development of a sustainable agricultural system employing the tremendous untapped potential of the microbial world.

Drought-tolerant Bacillus megaterium isolated from semi-arid conditions induces systemic tolerance of wheat under drought conditions

A detailed study of the response of wheat plants, inoculated with drought-tolerant PGPR is studied which would be beneficial to achieve genetic improvement of wheat for drought tolerance. Drought stress, a major challenge under current climatic conditions, adversely affects wheat productivity. In the current study, we observed the response of wheat plants, inoculated with drought-tolerant plant growth-promoting rhizobacteria (PGPR) Bacillus megaterium (MU2) and Bacillus licheniformis (MU8) under induced drought stress. In vitro study of 90 rhizobacteria exhibited 38 isolates showed one or more plant growth-promoting properties, such as solubilization of phosphorus, potassium, and exopolysaccharide production. Four strains revealing the best activities were tested for their drought-tolerance ability by growing them on varying water potentials (- 0.05 to - 0.73 MPa). Among them, two bacterial strains Bacillus megaterium and Bacillus licheniformis showed the best drought-tolerance potential, ACC deaminase activities, IAA production, and antagonistic activities against plant pathogens. Additionally, these strains when exposed to drought stress (- 0.73 MPa) revealed the induction of three new polypeptides (18 kDa, 35 kDa, 30 kDa) in Bacillus megaterium. We determined that 10⁶ cells/mL of Bacillus megaterium and Bacillus licheniformis were enough to induce drought tolerance in wheat under drought stress. These drought-tolerant strains increased the germination index (11-46%), promptness index (16-50%), seedling vigor index (11-151%), fresh weight (35-192%), and dry weight (58-226%) of wheat under irrigated and drought stress. Moreover, these strains efficiently colonized the wheat roots and increased plant biomass, relative water content, photosynthetic pigments, and osmolytes. Upon exposure to drought stress, Bacillus megaterium inoculated wheat plants exhibited improved tolerance by enhancing 59% relative water content, 260, 174 and 70% chlorophyll a, b and carotenoid, 136% protein content, 117% proline content and 57% decline in MDA content. Further, activities of defense-related antioxidant enzymes were also upregulated. Our results revealed that drought tolerance was more evident in Bacillus megaterium as compared to Bacillus licheniformis. These strains could be effective bioenhancer and biofertilizer for wheat cultivation in arid and semi-arid regions. However, a detailed study at the molecular level to deduce the mechanism by which these strains alleviate drought stress in wheat plants needs to be explored.

Green molybdenum nanoparticles-mediated bio-stimulation of Bacillus sp. strain ZH16 improved the wheat growth by managing in planta nutrients supply, ionic homeostasis and arsenic accumulation

The present work mechanistically addressed the problem of arsenic (As) contamination in agricultural soils by using locally isolated Bacillus sp. strain ZH16 and biogenic molybdenum nanoparticles (MoNPs) simultaneously for the first time. The interactions of MoNPs with strain ZH16 and ZH16-inoculated wheat plants were examined under As non-spiked and spiked conditions. The biogenic MoNPs showed efficient biocompatibility with strain ZH16 by promoting indole-3-acetic acid synthesis, phosphate solubilization and ACC deaminase activity without and with As stress. The results from greenhouse experiment revealed that co-application of biogenic MoNPs and bacterial strain ZH16 significantly promoted the morphological parameters, nutrients content and ionic balance of wheat plants under normal and As spiked conditions. Furthermore, combining the bacterial strain ZH16 with biogenic MoNPs dramatically reduced As translocation in plants (30.3%) as compared to ZH16-inoculated wheat plants. Conclusively, our results elucidate the importance of synergistic application of plant growth promoting rhizobacteria (PGPR) and biogenic MoNPs to counteract global food safety issues in a sustainable manner. The biogenic NPs could serve as stabilizing agent for PGPR by facilitating their colonization in plant holobiont regardless of environmental conditions. These novel advancements will provide new insights into nano-oriented PGPR research in the agricultural sector.

Role of Rhizospheric Bacillus megaterium HGS7 in Maintaining Mulberry Growth Under Extremely Abiotic Stress in Hydro-Fluctuation Belt of Three Gorges Reservoir

Plant growth-promoting rhizobacteria have been shown to play important roles in maintaining host fitness under periods of abiotic stress, and yet their effect on mulberry trees which regularly suffer drought after flooding in the hydro-fluctuation belt of the Three Gorges Reservoir Region in China remains largely uncharacterized. In the present study, 74 bacterial isolates were obtained from the rhizosphere soil of mulberry after drought stress, including 12 phosphate-solubilizing and 10 indole-3-acetic-acid-producing isolates. Bacillus megaterium HGS7 was selected for further study due to the abundance of traits that might benefit plants. Genomic analysis revealed that strain HGS7 possessed multiple genes that contributed to plant growth promotion, stress tolerance enhancement, and antimicrobial compound production. B. megaterium HGS7 consistently exhibited antagonistic activity against phytopathogens and strong tolerance to abiotic stress in vitro. Moreover, this strain stimulated mulberry seed germination and seedling growth. It may also induce the production of proline and antioxidant enzymes in mulberry trees to enhance drought tolerance and accelerate growth recovery after drought stress. The knowledge of the interactions between rhizobacteria HGS7 and its host plant might provide a potential strategy to enhance the drought tolerance of mulberry trees in a hydro-fluctuation belt.

Plant growth-promoting properties of bacterial endophytes isolated from roots of Thymus vulgaris L. and investigate their role as biofertilizers to enhance the essential oil contents

The main objective of the current study was to improve the essential oil contents of Thymus vulgaris L. using bio-inoculation with bacterial endophytes. Therefore, out of fourteen endophytic bacterial isolates obtained from roots of T. vulgaris, five isolates were selected based on the highest nitrogen-fixation and phosphate solubilization activity and identified as: Bacillus haynesii T9r, Citrobacter farmeri T10r, Bacillus licheniformis T11r, Bacillus velezensis T12r, and Bacillus velezensis T13r. These five strains have been recorded as ammonia, hydrogen cyanide (HCN), siderophores, and indole-3-acetic acid (IAA) producers. These strains have the efficacy to fix-nitrogen by reduction of acetylene with values of 82.133±1.4-346.6±1.4 n-mole-C₂H₄/ml/24 h. The IAA, gibberellic acid, abscisic acid, benzyl, kinten, and ziaten production were confirmed using HPLC. Two strains of T11r and T13r showed the highest plant growth-promoting properties and were selected for bio-inoculation of T. vulgaris individually or in a consortium with different mineral fertilization doses (0, 50, 75, and 100%) under field conditions. The highest growth performance was attained with the endophytic consortium (T11r+T13r) in the presence of 100% mineral fertilization. The GC-MS analysis of thyme oil contents showed the presence of 23 various compounds with varying percentages and the thymol fraction represented the highest percentages (39.1%) in the presence of the bacterial consortium.

Impact of seed-applied fungicide and insecticide on Azospirillum brasilense survival and wheat growth-promoting ability

The use of Azospirillum brasilense as a crop inoculant has increased in recent years. Thus, the compatibility of the inoculation technology with seed treatments using pesticides needs to be evaluated. In this study, we evaluated the effect of an insecticide and fungicide formulation on Azospirillum brasilense strain FP2 population by culturing and culture-independent approaches. In addition, we evaluated the impact of these pesticides on the ability of A. brasilense to promote plant growth by monitoring biometric traits (root and shoot dry mass and length) of wheat grown in Greenhouse conditions. Seed pesticide dressings, mainly fungicide, led to a significant mortality of A. brasilense over time. The ability of A. brasilense to promote wheat growth also decreased due to pesticide treatments combined with sowing delay. Considering that pesticides confer fitness advantages to the wheat in field condition, our results suggest that sowing within the first 4 h after inoculation maintain the beneficial effects of A. brasilense on wheat growth promotion. Furthermore, we conclude that inoculation and treatment of seeds with pesticides may be compatible techniques when carried out immediately before sowing.

Biofertilizers: An ecofriendly technology for nutrient recycling and environmental sustainability

Modern intensive agricultural practices face numerous challenges that pose major threats to global food security. In order to address the nutritional requirements of the ever-increasing world population, chemical fertilizers and pesticides are applied on large scale to increase crop production. However, the injudicious use of agrochemicals has resulted in environmental pollution leading to public health hazards. Moreover, agriculture soils are continuously losing their quality and physical properties as well as their chemical (imbalance of nutrients) and biological health. Plant-associated microbes with their plant growth- promoting traits have enormous potential to solve these challenges and play a crucial role in enhancing plant biomass and crop yield. The beneficial mechanisms of plant growth improvement include enhanced nutrient availability, phytohormone modulation, biocontrol of phytopathogens and amelioration of biotic and abiotic stresses. Solid-based or liquid bioinoculant formulation comprises inoculum preparation, addition of cell protectants such as glycerol, lactose, starch, a good carrier material, proper packaging and best delivery methods. Recent developments of formulation include entrapment/microencapsulation, nano-immobilization of microbial bioinoculants and biofilm-based biofertilizers. This review critically examines the current state-of-art on use of microbial strains as biofertilizers and the important roles performed by these beneficial microbes in maintaining soil fertility and enhancing crop productivity.

Enhancement of drought tolerance in diverse Vicia faba cultivars by inoculation with plant growth-promoting rhizobacteria under newly reclaimed soil conditions

Water deficit has devastating impacts on legume production, particularly with the current abrupt climate changes in arid environments. The application of plant growth-promoting rhizobacteria (PGPR) is an effective approach for producing natural nitrogen and attenuating the detrimental effects of drought stress. This study investigated the influence of inoculation with the PGPR Rhizobium leguminosarum biovar viciae (USDA 2435) and Pseudomonas putida (RA MTCC5279) solely or in combination on the physio-biochemical and agronomic traits of five diverse Vicia faba cultivars under well-watered (100% crop evapotranspiration [ETc]), moderate drought (75% ETc), and severe drought (50% ETc) conditions in newly reclaimed poor-fertility sandy soil. Drought stress substantially reduced the expression of photosynthetic pigments and water relation parameters. In contrast, antioxidant enzyme activities and osmoprotectants were considerably increased in plants under drought stress compared with those in well-watered plants. These adverse effects of drought stress reduced crop water productivity (CWP) and seed yield‐related traits. However, the application of PGPR, particularly a consortium of both strains, improved these parameters and increased seed yield and CWP. The evaluated cultivars displayed varied tolerance to drought stress: Giza-843 and Giza-716 had the highest tolerance under well-watered and moderate drought conditions, whereas Giza-843 and Sakha-4 were more tolerant under severe drought conditions. Thus, co-inoculation of drought-tolerant cultivars with R. leguminosarum and P. putida enhanced their tolerance and increased their yield and CWP under water-deficit stress conditions. This study showed for the first time that the combined use of R. leguminosarum and P. putida is a promising and ecofriendly strategy for increasing drought tolerance in legume crops.

From Lab to Farm: Elucidating the Beneficial Roles of Photosynthetic Bacteria in Sustainable Agriculture

Photosynthetic bacteria (PSB) possess versatile metabolic abilities and are widely applied in environmental bioremediation, bioenergy production and agriculture. In this review, we summarize examples of purple non-sulfur bacteria (PNSB) through biofertilization, biostimulation and biocontrol mechanisms to promote plant growth. They include improvement of nutrient acquisition, production of phytohormones, induction of immune system responses, interaction with resident microbial community. It has also been reported that PNSB can produce an endogenous 5-aminolevulinic acid (5-ALA) to alleviate abiotic stress in plants. Under biotic stress, these bacteria can trigger induced systemic resistance (ISR) of plants against pathogens. The nutrient elements in soil are significantly increased by PNSB inoculation, thus improving fertility. We share experiences of researching and developing an elite PNSB inoculant (Rhodopseudomonas palustris PS3), including strategies for screening and verifying beneficial bacteria as well as the establishment of optimal fermentation and formulation processes for commercialization. The effectiveness of PS3 inoculants for various crops under field conditions, including conventional and organic farming, is presented. We also discuss the underlying plant growth-promoting mechanisms of this bacterium from both microbial and plant viewpoints. This review improves our understanding of the application of PNSB in sustainable crop production and could inspire the development of diverse inoculants to overcome the changes in agricultural environments created by climate change.

Integrated Nutrient Management Enhances Productivity and Nitrogen Use Efficiency of Crops in Acidic and Charland Soils

Integrated Plant Nutrient System (IPNS) is practiced worldwide to maintain soil quality. Two field experiments were conducted in 2019 and 2020 in acidic and charland soils to assess the impact of different manures, viz., poultry manure (PM), vermicompost (VC), compost (OF), rice husk biochar (RHB), poultry manure biochar (PMB)-based IPNS, and dolomite over control on productivity and nitrogen use efficiency (NUE) of the Mustard-Boro-Transplanted Aman and Maize-Jute-Transplanted Aman cropping patterns, and on soil properties. The experiments were laid out in a randomized complete block design with four replications. The results showed that IPNS treatments significantly improved soil aggregate properties and total nitrogen in acidic soil, and bulk density in charland soil. In both years, IPNS treatments increased system productivity from 55.4 to 82.8% in acidic soil and from 43.3 to 115.4% in charland soil over that of control. IPNS and dolomite treatments increased nitrogen uptake from 35.5 to 105.7% over that of control and NUE in both soils in 2019 and 2020. PMB- and OF-based INPS treatments exhibited superior performances in both soils, and the impact was more prominent in 2020. Therefore, PMB- and OF-based IPNS can be recommended for maximizing system productivity and NUE with concurrent improvement of physicochemical properties of acidic and charland soils.

Plant Growth-Promoting Rhizobacteria Modulate the Concentration of Bioactive Compounds in Tomato Fruits

Background: The application of microorganisms as bioestimulants in order to increase the yield and/or quality of agricultural products is becoming a widely used practice in many countries. In this work, five plant growth-promoting rhizobacteria (PGPR), isolated from cultivated rice paddy soils, were selected for their plant growth-promoting capacities (e.g., auxin synthesis, chitinase activity, phosphate solubilisation and siderophores production). Two different tomato cultivars were inoculated, Tres Cantos and cherry. Plants were grown under greenhouse conditions and different phenotypic characteristics were analysed at the time of harvesting. Results: Tres Cantos plants inoculated with PGPR produced less biomass but larger fruits. However, the photosynthetic rate was barely affected. Several antioxidant activities were upregulated in these plants, and no oxidative damage in terms of lipid peroxidation was observed. Finally, ripe fruits accumulated less sugar but, interestingly, more lycopene. By contrast, inoculation of cherry plants with PGPR had no effect on biomass, although photosynthesis was slightly affected, and the productivity was similar to the control plants. In addition, antioxidant activities were downregulated and a higher lipid peroxidation was detected. However, neither sugar nor lycopene accumulation was altered. Conclusion: These results support the use of microorganisms isolated from agricultural soils as interesting tools to manipulate the level of important bioactive molecules in plants. However, this effect seems to be very specific, even at the variety level, and deeper analyses are necessary to assess their use for specific applications.

Engineering the Plant Microenvironment To Facilitate Plant-Growth-Promoting Microbe Association

New technologies that enhance soil biodiversity and minimize the use of scarce resources while boosting crop production are highly sought to mitigate the increasing threats that climate change, population growth, and desertification pose on the food infrastructure. In particular, solutions based on plant-growth-promoting bacteria (PGPB) bring merits of self-replication, low environmental impact, tolerance to biotic and abiotic stressors, and reduction of inputs, such as fertilizers. However, challenges in facilitating PGPB delivery in the soil still persist and include survival to desiccation, precise delivery, programmable resuscitation, competition with the indigenous rhizosphere, and soil structure. These factors play a critical role in microbial root association and development of a beneficial plant microbiome. Engineering the seed microenvironment with protein and polysaccharides is one proposed way to deliver PGPB precisely and effectively in the seed spermosphere. In this review, we will cover new advancements in the precise and scalable delivery of microbial inoculants, also highlighting the latest development of multifunctional rhizobacteria solutions that have beneficial impact on not only legumes but also cereals. To conclude, we will discuss the role that legislators and policymakers play in promoting the adoption of new technologies that can enhance the sustainability of crop production.

Impact of nanophos in agriculture to improve functional bacterial community and crop productivity

BACKGROUND

Since the World's population is increasing, it's critical to boost agricultural productivity to meet the rising demand for food and reduce poverty. Fertilizers are widely used in traditional agricultural methods to improve crop yield, but they have a number of negative environmental consequences such as nutrient losses, decrease fertility and polluted water and air. Researchers have been focusing on alternative crop fertilizers mechanisms to address these issues in recent years and nanobiofertilizers have frequently been suggested. "Nanophos" is a biofertilizer and contains phosphate-solubilising bacteria that solubilises insoluble phosphate and makes it available to the plants for improved growth and productivity as well as maintain soil health. This study evaluated the impact of nanophos on the growth and development of maize plants and its rhizospheric microbial community such as NPK solubilising microbes, soil enzyme activities and soil protein under field condition after 20, 40 and 60 days in randomized block design.

RESULTS

Maize seeds treated with nanophos showed improvement in germination of seeds, plant height, number of leaves, photosynthetic pigments, total sugar and protein level over control. A higher activity of phenol, flavonoid, antioxidant activities and yield were noticed in nanophos treated plants over control. Positive shift in total bacterial count, nitrogen fixing bacteria, phosphate and potassium solubilizers were observed in the presence of nanophos as compared to control. Soil enzyme activities were significantly (P < 0.05) improved in treated soil and showed moderately correlation between treatments estimated using Spearman rank correlation test. Real time PCR and total soil protein content analysis showed enhanced microbial population in nanophos treated soil. Obtained results showed that nanophos improved the soil microbial population and thus improved the plant growth and productivity.

CONCLUSION

The study concluded a stimulating effect of nanophos on Zea mays health and productivity and indicates good response towards total bacterial, NPK solubilising bacteria, soil enzymes, soil protein which equally showed positive response towards soil nutrient status. It can be a potential way to boost soil nutrient use efficiency and can be a better alternative to fertilizers used in the agriculture.

Prospect and Challenges for Sustainable Management of Climate Change-Associated Stresses to Soil and Plant Health by Beneficial Rhizobacteria

Climate change imposes biotic and abiotic stresses on soil and plant health all across the planet. Beneficial rhizobacterial genera, such as Bacillus, Pseudomonas, Paraburkholderia, Rhizobium, Serratia, and others, are gaining popularity due to their ability to provide simultaneous nutrition and protection of plants in adverse climatic conditions. Plant growth-promoting rhizobacteria are known to boost soil and plant health through a variety of direct and indirect mechanisms. However, various issues limit the wider commercialization of bacterial biostimulants, such as variable performance in different environmental conditions, poor shelf-life, application challenges, and our poor understanding on complex mechanisms of their interactions with plants and environment. This study focused on detecting the most recent findings on the improvement of plant and soil health under a stressful environment by the application of beneficial rhizobacteria. For a critical and systematic review story, we conducted a non-exhaustive but rigorous literature survey to assemble the most relevant literature (sorting of a total of 236 out of 300 articles produced from the search). In addition, a critical discussion deciphering the major challenges for the commercialization of these bioagents as biofertilizer, biostimulants, and biopesticides was undertaken to unlock the prospective research avenues and wider application of these natural resources. The advancement of biotechnological tools may help to enhance the sustainable use of bacterial biostimulants in agriculture. The perspective of biostimulants is also systematically evaluated for a better understanding of the molecular crosstalk between plants and beneficial bacteria in the changing climate towards sustainable soil and plant health.

Plant Tolerance to Drought Stress in the Presence of Supporting Bacteria and Fungi: An Efficient Strategy in Horticulture

Increasing temperature leads to intensive water evaporation, contributing to global warming and consequently leading to drought stress. These events are likely to trigger modifications in plant physiology and microbial functioning due to the altered availability of nutrients. Plants exposed to drought have developed different strategies to cope with stress by morphological, physiological, anatomical, and biochemical responses. First, visible changes influence plant biomass and consequently limit the yield of crops. The presented review was undertaken to discuss the impact of climate change with respect to drought stress and its impact on the performance of plants inoculated with plant growth-promoting microorganisms (PGPM). The main challenge for optimal performance of horticultural plants is the application of selected, beneficial microorganisms which actively support plants during drought stress. The most frequently described biochemical mechanisms for plant protection against drought by microorganisms are the production of phytohormones, antioxidants and xeroprotectants, and the induction of plant resistance. Rhizospheric or plant surface-colonizing (rhizoplane) and interior (endophytic) bacteria and fungi appear to be a suitable alternative for drought-stress management. Application of various biopreparations containing PGPM seems to provide hope for a relatively cheap, easy to apply and efficient way of alleviating drought stress in plants, with implications in productivity and food condition.

Interactions Between Bacillus Spp., Pseudomonas Spp. and Cannabis sativa Promote Plant Growth

Plant growth-promoting rhizobacteria (PGPR) deploy several mechanisms to improve plant health, growth and yield. The aim of this study was to evaluate the efficacy of two Pseudomonas spp. strains and three Bacillus spp. strains used as single treatments and in consortia to improve the yield of Cannabis sativa and characterize the impact of these treatments on the diversity, structure and functions of the rhizosphere microbiome. Herein, we demonstrate a significant C. sativa yield increase up to 70% when inoculated with three different Pseudomonas spp./Bacillus spp. consortia but not with single inoculation treatments. This growth-promoting effect was observed in two different commercial soil substrates commonly used to grow cannabis: Promix and Canna coco. Marker-based genomic analysis highlighted Bacillus spp. as the main modulator of the rhizosphere microbiome diversity and Pseudomonas spp. as being strongly associated with plant growth promotion. We describe an increase abundance of predicted PGPR metabolic pathways linked with growth-promoting interactions in C. sativa.

Harnessing Chemical Ecology for Environment-Friendly Crop Protection

Heavy reliance on synthetic pesticides for crop protection has become increasingly unsustainable, calling for robust alternative strategies that do not degrade the environment and vital ecosystem services. There are numerous reports of successful disease control by various microbes used in small-scale trials. However, inconsistent efficacy has hampered their large-scale application. A better understanding of how beneficial microbes interact with plants, other microbes, and the environment and which factors affect disease control efficacy is crucial to deploy microbial agents as effective and reliable pesticide alternatives. Diverse metabolites produced by plants and microbes participate in pathogenesis and defense, regulate the growth and development of themselves and neighboring organisms, help maintain cellular homeostasis under various environmental conditions, and affect the assembly and activity of plant and soil microbiomes. However, research on the metabolites associated with plant health-related processes, except antibiotics, has not received adequate attention. This review highlights several classes of metabolites known or suspected to affect plant health, focusing on those associated with biocontrol and belowground plant-microbe and microbe-microbe interactions. The review also describes how new insights from systematic explorations of the diversity and mechanism of action of bioactive metabolites can be harnessed to develop novel crop protection strategies.

Investigation of soil microbiome under the influence of different mulching treatments in northern highbush blueberry

Microbial communities on soil are fundamental for the long-term sustainability of agriculture ecosystems. Microbiota in soil would impact the yield and quality of blueberries since microbial communities in soil can interact with the rhizosphere of plant. This study was conducted to determine how different mulching treatments induce changes in soil microbial composition, diversity, and functional properties. A total of 150 soil samples were collected from 5 different mulch treatments (sawdust, green weed mat, sawdust topped with green weed mat, black weed mat, and sawdust topped with black weed mat) at 3 different depths (bottom, middle, and top region of 20 cm soil depth) from 2 different months (June and July 2018). A total of 8,583,839 sequencing reads and 480 operational taxonomic units (OTUs) of bacteria were identified at genus level. Eight different plant growth promoting rhizobacteria (PGPR) were detected, and the relative abundances of Bradyrhizobium, Bacillus, and Paenibacillus were more than 0.1% among all soil samples. Sampling depth and month of soil samples impacted the amount of PGPR, while there were no significant differences based on mulch type. Functional properties of bacteria were identified through PICRUSt2, which found that there is no significant difference between mulch treatment, depth, and month. The results indicated that sampling month and depth of soil impacted the relative abundance of PGPR in soil samples, but there were no significant differences of functional properties and beneficial microbial communities based on mulch type.

Microbe-assisted phytoremediation of environmental pollutants and energy recycling in sustainable agriculture

The perception of phytoremediation is efficiently utilized as an eco-friendly practice of green plants combating and cleaning up the stressed environment without harming it. The industrial revolution was followed by the green revolution which fulfilled the food demands of the growing population caused an increase in yield per unit area in crop production, but it also increased the use of synthetic fertilizers in agriculture. Globally, the intensive use of inorganic fertilizers in agriculture has led to serious health problems and irreversible environmental damage. Biofertilizers improve the growth of the plant and can be applied as an alternative to chemical/synthetic fertilizers. Cyanobacteria, bacteria, and fungi are known as some of the principal microbe groups used to produce biofertilizers that form symbiotic associations with plants. Microorganisms perform a key role in phosphate solubilization and mobilization, nitrogen fixation, nutrient management, biotic elicitors and probiotics, and pollution management (biodegradation agents), specifically bacteria which also help in atmospheric nitrogen fixation and are thus available for the growth of the plant. Management or biodegradation of hazardous chemical residues and heavy metals produced by a huge number of large-scale industries should be given primary importance to be transformed by various bacterial strains, fungi, algae. Currently, modern omics technologies such as metagenomic, transcriptomic, and proteomic are being used to develop strategies for studying the ecology of microorganisms, as well as their use in environmental monitoring and bioremediation. This review briefly discusses some of the major groups of microorganisms that can perform different functions responsible for plant health, crop production, phytoremediation and also focus on the omics techniques reportedly used in environmental monitoring to tackle the pollution load.

Biofertilizer Activity of Azospirillum sp. B510 on the Rice Productivity in Ghana

Rice production in Ghana has become unsustainable due to the extremely nutrient-poor soils. It is caused by inadequate soil fertility management, including the inefficient application of fertilizers. A practical solution could be the biofertilizers, Azospirillum sp. B510. We performed field trials in Ghana and Japan to compare the effects of B510 colonization on selected Ghanaian rice varieties grown. The B510 inoculation significantly enhanced the rice cultivars’ growth and yield. The phenotypic characteristics observed in rice varieties Exbaika, Ex-Boako, AgraRice, and Amankwatia were mainly short length and high tillering capacity. These features are attributed to the host plant (cv. Nipponbare), from which the strain B510 was isolated. Furthermore, Azospirillum species has been identified as the dominant colonizing bacterium of rice rhizosphere across a diverse range of agroecologies in all major rice-growing regions in Ghana. Our results suggest that the utilization of B510 as a bio-fertilizer presents a promising way to improve rice growth, enhance soil fertility, and sustain rice productivity in Ghana.

Towards sustainable agriculture: rhizosphere microbiome engineering

Soil microbiomes are extremely complex, with dense networks of interconnected microbial species underpinning vital functions for the ecosystem. In advanced agricultural research, rhizosphere microbiome engineering is gaining much attention, as the microbial community has been acknowledged to be a crucial partner of associated plants for their health fitness and yield. However, single or combined effects of a wide range of soil biotic and abiotic factors impact the success of engineered microbiomes, as these microbial communities exhibit uneven structural and functional networks in diverse soil conditions. Therefore, once a deep understanding of major influential factors and corresponding microbial responses is developed, the microbiome can be more effectively manipulated and optimized for cropping benefits. In this mini-review, we propose the concept of a microbiome-mediated smart agriculture system (MiMSAS). We summarize some of the advanced strategies for engineering the rhizosphere microbiome to withstand the stresses imposed by dominant abiotic and biotic factors. This work will help the scientific community gain more clarity about engineered microbiome technologies for increasing crop productivity and environmental sustainability.Key points• Individual or combined effects of soil biotic and abiotic variables hamper the implementation of engineered microbiome technologies in the field.• As a traditional approach, reduced-tillage practices coinciding with biofertilization can promote a relatively stable functional microbiome.• Increasing the complexity and efficiency of the synthetic microbiome is one way to improve its field-application success rate.• Plant genome editing/engineering is a promising approach for recruiting desired microbiomes for agricultural benefit.

Elucidating key plant growth-promoting (PGPR) traits in Burkholderia sp. Nafp2/4-1b (=SARCC-3049) using gnotobiotic assays and whole-genome-sequence analysis

Burkholderia sp. Nafp2/4-1b (=SARCC-3049) is a plant growth-promoting rhizobacteria (PGPR) initially isolated from the rhizosphere of pristine grassland in South Africa, and its ability to enhance growth was previously evaluated on maize (Zea mays L.). Here, the bacterium was tested with the aim of investigating its role in improving the nodulation and growth of the forage legume lucerne (Medicago sativa L.) when it is co-inoculated with the rhizobial symbionts of this legume in the glasshouse. When the co-inoculation resulted in a statistically significant (P = 0·05) increase in the number of nodules and improved plant biomass compared with single inoculation, we sequenced and analysed its genome to gain a better understanding of the genetic determinants responsible for the observed PGPR traits. The Illumina HiSeq 2500-sequenced genome resulted in 92 scaffolds, with an N50 of 322 407 bp, a total draft genome size of 7 788 045 bp and GC content of 66·2%. Analysis of the genome sequence confirmed the presence of a number of essential genes that code for various PGPR traits. The main plant beneficial genes associated with PGPR traits in Burkholderia sp. Nafp2/4-1b include pyoverdine siderophores biosynthesis gene (PvdF); acdS that codes for 1-aminocyclopropane-1-carboxylate (ACC) deaminase; the tryptophan synthase genes involved in auxin biosynthesis (TSA1, TSB1) and the pqqABCDE operon related to phosphate solubilization. This study generated valuable information on the potential of the PGPR Burkholderia sp. strain Nafp2/4-1b as an effective commercial inoculant, which warrants further formulation and field application studies before developing it into a low cost, environmentally safe and effective biofertilizer.

Efficacy of rhizobacterial exopolysaccharides in improving plant growth, physiology, and soil properties

The current study investigated the influence of exopolysaccharides (EPSs) producing plant growth-promoting rhizobacteria (PGPR) on the growth, physiology, and soil properties. The pre-isolated and compatible EPS producing PGPR strains were first screened based on improvement in soil aggregates in an incubation study. The screened strains (Rhizobium phaseoli strain Mn-6, Pseudomonas bathysetes strain LB₅, and unidentified strain R₂) were then employed in pot study for assessing improvements in maize growth, physiology, and soil properties. Eight treatments including T₁ = control, T₂ = Mn-6, T₃ = R₂, T₄ = LB₅, T₅ = Mn-6 + R₂, T₆ = Mn-6 + LB₅, T₇ = R₂ + LB₅, and T₈ = Mn-6 + R₂ + LB₅ were applied in completely randomized design (CRD) hexa replicated (half for root and half for soil, and yield attributes). The results depicted that among various treatments, the application of PGPR strain Mn-6 increased plant height, root length, root fresh and dry weight, root length density, SPAD value, leaf areas index, photosynthesis rate, transpiration, and stomatal conductance by 24, 79, 72, 90, 49, 35, 23, 21, 75, and 77%, respectively, compared with non-inoculated treatment. Similarly, significant improvement in maize yield and soil physical properties was also observed in response to the application of EPS-producing PGPR. Therefore, it is concluded that the application of EPS producing PGPR is an effective strategy to improve plant growth, physiology, yield, and soil physical properties. Moreover, EPS-producing PGPR should be exploited in field studies for their potential in improving plant growth and soil properties.

Plant Growth Promoting Rhizobacteria, Arbuscular Mycorrhizal Fungi and Their Synergistic Interactions to Counteract the Negative Effects of Saline Soil on Agriculture: Key Macromolecules and Mechanisms

Soil saltiness is a noteworthy issue as it results in loss of profitability and development of agrarian harvests and decline in soil health. Microorganisms associated with plants contribute to their growth promotion and salinity tolerance by employing a multitude of macromolecules and pathways. Plant growth promoting rhizobacteria (PGPR) have an immediate impact on improving profitability based on higher crop yield. Some PGPR produce 1-aminocyclopropane-1-carboxylic (ACC) deaminase (EC 4.1.99.4), which controls ethylene production by diverting ACC into α-ketobutyrate and ammonia. ACC deaminase enhances germination rate and growth parameters of root and shoot in different harvests with and without salt stress. Arbuscular mycorrhizal fungi (AMF) show a symbiotic relationship with plants, which helps in efficient uptake of mineral nutrients and water by the plants and also provide protection to the plants against pathogens and various abiotic stresses. The dual inoculation of PGPR and AMF enhances nutrient uptake and productivity of several crops compared to a single inoculation in both normal and stressed environments. Positively interacting PGPR + AMF combination is an efficient and cost-effective recipe for improving plant tolerance against salinity stress, which can be an extremely useful approach for sustainable agriculture.

The potential of nanomaterials associated with plant growth-promoting bacteria in agriculture

The impacts of chemical fertilizers and pesticides have raised public concerns regarding the sustainability and security of food supplies, prompting the investigation of alternative methods that have combinations of both agricultural and environmental benefits, such as the use of biofertilizers involving microbes. These types of microbial inoculants are living microorganisms that colonize the soil or plant tissues when applied to the soil, seeds, or plant surfaces, facilitating plant nutrient acquisition. They can enhance plant growth by transforming nutrients into a form assimilable by plants and by acting as biological control agents, known as plant growth-promoting bacteria. The potential use of bacteria as biofertilizers in agriculture constitutes an economical and eco-friendly way to reduce the use of chemical fertilizers and pesticides. In this context, nanotechnology has emerged as a new source of quality enrichment for the agricultural sector. The use of nanoparticles can be an effective method to meet the challenges regarding the effectiveness of biofertilizers in natural environments. Given the novel sustainable strategies applied in agricultural systems, this review addresses the effects of nanoparticles on beneficial plant bacteria for promoting plant growth.

Microbial Phosphorus Mobilization Strategies Across a Natural Nutrient Limitation Gradient and Evidence for Linkage With Iron Solubilization Traits

Microorganisms have evolved several mechanisms to mobilize and mineralize occluded and insoluble phosphorus (P), thereby promoting plant growth in terrestrial ecosystems. However, the linkages between microbial P-solubilization traits and the preponderance of insoluble P in natural ecosystems are not well known. We tested the P solubilization traits of hundreds of culturable bacteria representative of the rhizosphere from a natural gradient where P concentration and bioavailability decline as soil becomes progressively more weathered. Aluminum, iron phosphate and organic P (phytate) were expected to dominate in more weathered soils. A defined cultivation medium with these chemical forms of P was used for isolation. A combination of soil chemical, spectroscopic analyses and 16S rRNA gene sequencing were used to understand the in situ ability for solubilization of these predominant forms of P. Locations with more occluded and organic P harbored the greatest abundance of P-mobilizing microorganisms, especially Burkholderiaceae (Caballeronia and Paraburkholderia spp.). Nearly all bacteria utilized aluminum phosphate, however fewer could subsist on iron phosphate (FePO₄) or phytate. Microorganisms isolated from phytic acid were also most effective at solubilizing FePO₄, suggesting that phytate solubilization may be linked to the ability to solubilize Fe. Significantly, we observed Fe to be co-located with P in organic patches in soil. Siderophore addition in lab experiments reinstated phytase mediated P-solubilization from Fe-phytate complexes. Taken together, these results indicate that metal-organic-P complex formation may limit enzymatic P solubilization from phytate in soil. Additionally, the linked traits of phytase and siderophore production were mostly restricted to specific clades within the Burkholderiaceae. We propose that Fe complexation of organic P (e.g., phytate) represents a major constraint on P turnover and availability in acidic soils, as only a limited subset of bacteria appear to possess the traits required to access this persistent pool of soil P.

Bacterial Inoculants Mitigating Water Scarcity in Tomato: The Importance of Long-Term in vivo Experiments

Global population growth and climate change raise a challenge to agriculture, which, combined with the issues concerning the use of chemical fertilizers, have generated increasing attention in the use of plant-associated bacteria as a sustainable strategy in agri-food systems. The objective of this study is to evaluate the ability of five bacterial strains, previously isolated from the rhizosphere or endosphere of plants adapted to harsh environmental conditions, to act as potential plant biofertilizers in different conditions of water availability. The strain biosafety for a deliberate environmental release was investigated through a literature survey and antibiotic resistance testing. The selected strains were first characterized for their plant growth–promoting (PGP) and rhizocompetence-related traits through in vitro assays and then on short-term in vivo experiments on tomato plants. A long-term greenhouse experiment was further conducted to monitor the PGP effect of the bacteria during the entire life cycle of tomato plants subjected to full irrigation or to severe water deficit conditions, aiming to assess their actual effect on plant productivity, which is the ultimate target of the agricultural sector. Some of the strains showed a potential in improving water use efficiency and mitigating plant water stress. Under severe irrigation deficit, four of the tested strains, Micrococcus yunnanensis M1, Bacillus simplex RP-26, Pseudomonas stutzeri SR7-77, and Paenarthrobacter nitroguajacolicus 2–50, significantly increased the number of productive plants in comparison to non-bacterized control ones. Two of them, Bacillus simplex RP-26 and Paenarthrobacter nitroguajacolicus 2–50, demonstrated also, under full irrigation, to significantly improve the water productivity in comparison with non-bacterized plants. Despite all the strains showed promising PGP potential in short-term assays, the positive effect of the bacterial inoculants on plant physiology and fruit yield was observed in some cases but never corroborated by statistical significance. These results highlight the importance of performing long-term in vivo experiments to define the real PGP ability of a bacterial inoculant to positively impact plant production.

Silica Particles Trigger the Exopolysaccharide Production of Harsh Environment Isolates of Growth-Promoting Rhizobacteria and Increase Their Ability to Enhance Wheat Biomass in Drought-Stressed Soils

In coming decades, drought is expected to expand globally owing to increased evaporation and reduced rainfall. Understanding, predicting, and controlling crop plants’ rhizosphere has the potential to manipulate its responses to environmental stress. Our plant growth-promoting rhizobacteria (PGPR) are isolated from a natural laboratory, ‘The Evolution Canyon’, Israel, (EC), from the wild progenitors of cereals, where they have been co-habituating with their hosts for long periods of time. The study revealed that commercial TM50 silica particles (SN) triggered the PGPR production of exopolysaccharides (EPS) containing D-glucuronate (D-GA). The increased EPS content increased the PGPR water-holding capacity (WHC) and osmotic pressure of the biofilm matrix, which led to enhanced plant biomass in drought-stressed growth environments. Light- and cryo-electron- microscopic studies showed that, in the presence of silica (SN) particles, bacterial morphology is changed, indicating that SNs are associated with significant reprogramming in bacteria. The findings encourage the development of large-scale methods for isolate formulation with natural silicas that ensure higher WHC and hyperosmolarity under field conditions. Osmotic pressure involvement of holobiont cohabitation is also discussed.

Encapsulation of Pseudomonas libanensis in alginate beads to sustain bacterial viability and inoculation of Vigna unguiculata under drought stress

Conventional agricultural practices based on the application of synthetic fertilizers are increasingly considered as unsustainable. Under a forecasted scenario of drought for the next decades, there is a global demand for innovative and sustainable approaches to ameliorate plant performance. Here, encapsulating beneficial microbes (BMs) to promote plant growth is gaining attention. This study evaluates bacterial encapsulation using polymeric beads of alginate, testing the survival of Pseudomonas libanensis TR1 stored up to 90 days. Produced beads were subjected to different treatments (fresh, air-dried and pulverized), which resulted in a variable size range (1200-860 µm). After storage, bacterial viability was maintained, and air-dried beads displayed a higher number of colony-forming units (2 × 107). Then, a glasshouse experiment investigated the drought resistance (plant growth, biomass, and photosynthetic responses) of Vigna unguiculata plants inoculated with these alginate beads. After 10 days of complete water restriction, turgidity and relative water content of V. unguiculata were still high under drought stress (> 80%). Leaf and root growth and biomass did not evidence significant changes after water restriction even after P. libanensis inoculation. Plant photosynthetic parameters (stomatal conductance, net photosynthetic rate, leaf CO2 concentration, or F v'/F m') were slightly affected due to inoculation but the level of stress-induced minimal plant responses. In our experiment, water restriction might have been insufficient to downregulate photosynthetic efficiency and reduce plant growth, limiting our understanding of the role of P. libanensis inoculation in alleviating drought stress in V. unguiculata, but highlighting the important relationship between the stress level and agricultural benefits of using encapsulated BMs.

Comprehensive characterization of stress tolerant bacteria with plant growth-promoting potential isolated from glyphosate-treated environment

The application of plant growth-promoting bacteria in agricultural systems is an efficient and environment-friendly strategy to improve crop yields and maintain soil quality. However, as different soils have diverse and specific ecological characteristics and may represent adverse abiotic conditions, in vivo application requires the careful selection of the desired beneficial microorganisms. In this study we report Ensifer adhaerens SZMC 25856 and Pseudomonas resinovorans SZMC 25875 isolates recovered from glyphosate-treated soil to possess yet undiscovered plant growth-enhancing potential. The strains were found to promote the growth of tomato seedlings significantly, to have the ability of synthesizing indole-3-acetic acid and siderophores, to tolerate pH in the range of 6.59-7.96, salinity up to 12.5 g L-1 NaCl and drought up to 125 g L-1 polyethylene glycol 6000, as well as to survive in the presence of various pesticides including glyphosate, diuron, chlorotoluron, carbendazim and thiabendazole, and heavy metals such as Al, Fe, Mn, Zn, Pb and Cu. The plant growth-promoting traits of the examined E. adhaerens and P. resinovorans isolates and their tolerance to numerous abiotic stress factors make them promising candidates for application in different agricultural environments, including soils polluted with glyphosate.

Can dispersal be leveraged to improve microbial inoculant success?

Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.

Culturable Yeasts as Biofertilizers and Biopesticides for a Sustainable Agriculture: A Comprehensive Review

The extensive use of synthetic fertilizers and pesticides has negative consequences in terms of soil microbial biodiversity and environmental contamination. Faced with this growing concern, a proposed alternative agricultural method is the use of microorganisms as biofertilizers. Many works have been focused on bacteria, but the limited literature on yeasts and their potential ability to safely promote plant growth is gaining particular attention in recent years. Thus, the objective of this review is to highlight the application of yeasts as biological agents in different sectors of sustainable agricultural practices through direct or indirect mechanisms of action. Direct mechanisms include the ability of yeasts to provide soluble nutrients to plants, produce organic acids and phytohormones (indole-3-acetic acid). Indirect mechanisms involve the ability for yeasts to act as biocontrol agents through their high antifungal activity and lower insecticidal and herbicidal activity, and as soil bioremediating agents. They also act as protective agents against extreme environmental factors by activating defense mechanisms. It is evident that all the aspects that yeasts offer could be useful in the creation of quality biofertilizers and biopesticides. Hence, extensive research on yeasts could be promising and potentially provide an environmentally friendly solution to the increased crop production that will be required with a growing population.

Microbiota, pathogens, and parasites as mediators of tritrophic interactions between insect herbivores, plants, and pollinators

Insect-associated microbes, including pathogens, parasites, and symbionts, influence the interactions of herbivorous insects and pollinators with their host plants. Moreover, herbivory-induced changes in plant resource allocation and defensive chemistry can influence pollinator behavior. This suggests that the outcomes of interactions between herbivores, their microbes and host plants could have implications for pollinators. As epizootic diseases occur at high population densities, pathogen and parasite-mediated effects on plants could have landscape-level impacts on foraging pollinators. The goal of this minireview is to highlight the potential for an herbivore's multitrophic interactions to trigger plant-mediated effects on the immunity and health of pollinators. We highlight the importance of plant quality and gut microbiomes in bee health, and how caterpillars as model herbivores interact with pathogens, parasites, and symbionts to affect plant quality, which forms the centerpiece of multitrophic interactions between herbivores and pollinators. We also discuss the impacts of other herbivore-associated factors, such as agricultural inputs aimed at decreasing herbivorous pests, on pollinator microbiomes.

Tailoring Next Generation Plant Growth Promoting Microorganisms as Versatile Tools beyond Soil Desalinization: A Road Map towards Field Application

Plant growth promoting bacteria (PGPB) have been the target of intensive research studies toward their efficient use in the field as biofertilizers, biocontrol, and bioremediation agents among numerous other applications. Recent trends in the field of PGPB research led to the development of versatile multifaceted PGPB that can be used in different field conditions such as biocontrol of plant pathogens in metal contaminated soils. Unfortunately, all these research efforts lead to the development of PGPB that failed to perform in salty environments. Therefore, it is urgently needed to address this drawback of these PGPB toward their efficient performance in salinity context. In this paper we provide a review of state-of-the-art research in the field of PGPB and propose a road map for the development of next generation versatile and multifaceted PGPB that can perform in salinity. Beyond soil desalinization, our study paves the way towards the development of PGPB able to provide services in diverse salty environments such as heavy metal contaminated, or pathogen threatened. Smart development of salinity adapted next generation biofertilizers will inevitably allow for mitigation and alleviation of biotic and abiotic threats to plant productivity in salty environments.

An efficient direct screening system for microorganisms that activate plant immune responses based on plant-microbe interactions using cultured plant cells

Microorganisms that activate plant immune responses have attracted considerable attention as potential biocontrol agents in agriculture because they could reduce agrochemical use. However, conventional methods to screen for such microorganisms using whole plants and pathogens are generally laborious and time consuming. Here, we describe a general strategy using cultured plant cells to identify microorganisms that activate plant defense responses based on plant-microbe interactions. Microbial cells were incubated with tobacco BY-2 cells, followed by treatment with cryptogein, a proteinaceous elicitor of tobacco immune responses secreted by an oomycete. Cryptogein-induced production of reactive oxygen species (ROS) in BY-2 cells served as a marker to evaluate the potential of microorganisms to activate plant defense responses. Twenty-nine bacterial strains isolated from the interior of Brassica rapa var. perviridis plants were screened, and 8 strains that enhanced cryptogein-induced ROS production in BY-2 cells were selected. Following application of these strains to the root tip of Arabidopsis seedlings, two strains, Delftia sp. BR1R-2 and Arthrobacter sp. BR2S-6, were found to induce whole-plant resistance to bacterial pathogens (Pseudomonas syringae pv. tomato DC3000 and Pectobacterium carotovora subsp. carotovora NBRC 14082). Pathogen-induced expression of plant defense-related genes (PR-1, PR-5, and PDF1.2) was enhanced by the pretreatment with strain BR1R-2. This cell-cell interaction-based platform is readily applicable to large-scale screening for microorganisms that enhance plant defense responses under various environmental conditions.

Engineering rhizobacteria for sustainable agriculture

Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.

Predominant Microbial Colonizers in the Root Endosphere and Rhizosphere of Turfgrass Systems: Pseudomonas veronii, Janthinobacterium lividum, and Pseudogymnoascus spp

Microbes can colonize plant roots to modulate plant health and environmental fitness. Thus, using microbes to improve plant adaptation to biotic and abiotic stresses will be promising to abate the heavy reliance of management systems on synthetic chemicals and limited resource. This is particularly important for turfgrass systems because intensive management for plant available nutrients (e.g., nitrogen), water, and pest control is necessary to maintain a healthy and aesthetic landscape. However, little is known on microbial species and host compatibility in turfgrass root endosphere and rhizosphere. Here, by using marker gene high throughput sequencing approaches we demonstrated that a few bacterial and fungal species prevailed the root endosphere and rhizosphere and were of a broad host spectrum. Irrespective of turfgrass species (bermudagrass, ultradwarf bermudagrass, creeping bentgrass, and tall fescue), defoliation intensities (i.e., mowing height and frequency), turfgrass sites, and sampling time, Pseudomonas veronii was predominant in the root endosphere, constituting ∼38% of the total bacterial community, which was much higher than its presence in the bulk soil (∼0.5%) and rhizosphere (∼4.6%). By contrast, Janthinobacterium lividum and fungal species of the genus Pseudogymnoascus were more abundant in the rhizosphere, constituting ∼15 and ∼ 39% of the total bacterial and fungal community, respectively, compared to their respective presence in the bulk soil (∼ 0.1 and 5%) and root endosphere (∼ 0.8 and 0.3%). Such stark contrasts in the microbiome composition between the root endosphere, rhizosphere, and bulk soil were little influenced by turfgrass species, suggesting the broad turfgrass host compatibility of these bacterial and fungal species. Further, their dominance in respective niches were mutually unaffected, implying the possibility of developing a multiple species formula for coping turfgrass with environmental stresses. These species were likely involved in controlling pests, such as infectious nematodes and fungi, decomposing root debris, and helping turfgrass water and nutrient uptake; yet these possibilities need to be further examined.

Field evaluation of PGP Bacillus sp. strain D5 native to Crocus sativus, in traditional and non traditional areas, and mining of PGP genes from its genome

Native Bacillus sp. strain D5 coded as (Bar D5) has been isolated from the saffron corm that showed plant growth promotion (PGP) properties and also inhibits the growth of corm rot causing Fusarium oxysporum R1 (Fox R1) in-vitro. Bar D5 was more efficient PGP bacterium in comparison to earlier reported native bio-formulations by our group. Pot assays and field evaluation of Bar D5 confirmed its in-vivo efficacy for PGP traits and biocontrol activity as well. Pot trials were followed by field trials at traditional (Kishtwar) and non-traditional (R.S Pura) saffron cultivation areas in Jammu and Kashmir. At both places, Bar D5 bio-formulation treatment led to the increase in root number & length, shoot number & length, flower number and number & weight of daughter corms. Additionally, it also decreased the corm rot disease incidence significantly. Priming of corms with bio-formulation resulted in the reduction of pathogenic fungal load by three fold at the depth of corm sowing from ground level. The shelf life/viability of Bar D5 based bio-formulation was found to be 52% (viable spores) for one year at room temperature. Draft genome sequence of Bar D5 revealed the presence of genes necessary for PGP and biocontrol activity. Further, confirmation of gene sequences and annotation was done by amplification, re-sequencing and mapping of PGP and biocontrol genes on draft genome. Bar D5 based bio-formulation can be provided to companies/researchers interested in saffron cultivation or bio-formulation production for commercial exploitation, since saffron is grown as revenue crop across continents. The present study bridges the gap between genomics and its field application.

Nitrogen Fixing Azotobacter Species as Potential Soil Biological Enhancers for Crop Nutrition and Yield Stability

Biological nitrogen fixation (BNF) refers to a microbial mediated process based upon an enzymatic "Nitrogenase" conversion of atmospheric nitrogen (N₂) into ammonium readily absorbable by roots. N₂-fixing microorganisms collectively termed as "diazotrophs" are able to fix biologically N₂ in association with plant roots. Specifically, the symbiotic rhizobacteria induce structural and physiological modifications of bacterial cells and plant roots into specialized structures called nodules. Other N₂-fixing bacteria are free-living fixers that are highly diverse and globally widespread in cropland. They represent key natural source of nitrogen (N) in natural and agricultural ecosystems lacking symbiotic N fixation (SNF). In this review, the importance of Azotobacter species was highlighted as both important free-living N₂-fixing bacteria and potential bacterial biofertilizer with proven efficacy for plant nutrition and biological soil fertility. In addition, we described Azotobacter beneficial plant promoting traits (e.g., nutrient use efficiency, protection against phytopathogens, phytohormone biosynthesis, etc.). We shed light also on the agronomic features of Azotobacter that are likely an effective component of integrated plant nutrition strategy, which contributes positively to sustainable agricultural production. We pointed out Azotobacter based-biofertilizers, which possess unique characteristics such as cyst formation conferring resistance to environmental stresses. Such beneficial traits can be explored profoundly for the utmost aim to research and develop specific formulations based on inoculant Azotobacter cysts. Furthermore, Azotobacter species still need to be wisely exploited in order to address specific agricultural challenges (e.g., nutrient deficiencies, biotic and abiotic constraints) taking into consideration several variables including their biological functions, synergies and multi-trophic interactions, and biogeography and abundance distribution.

Identification of Beneficial Microbial Consortia and Bioactive Compounds with Potential as Plant Biostimulants for a Sustainable Agriculture

A growing body of evidence demonstrates the potential of various microbes to enhance plant productivity in cropping systems although their successful field application may be impaired by several biotic and abiotic constraints. In the present work, we aimed at developing multifunctional synthetic microbial consortia to be used in combination with suitable bioactive compounds for improving crop yield and quality. Plant growth-promoting microorganisms (PGPMs) with different functional attributes were identified by a bottom-up approach. A comprehensive literature survey on PGPMs associated with maize, wheat, potato and tomato, and on commercial formulations, was conducted by examining peer-reviewed scientific publications and results from relevant European projects. Metagenome fragment recruitments on genomes of potential PGPMs represented in databases were also performed to help identify plant growth-promoting (PGP) strains. Following evidence of their ability to coexist, isolated PGPMs were synthetically assembled into three different microbial consortia. Additionally, the effects of bioactive compounds on the growth of individually PGPMs were tested in starvation conditions. The different combination products based on microbial and non-microbial biostimulants (BS) appear worth considering for greenhouse and open field trials to select those potentially adoptable in sustainable agriculture.