Co-existence of Leclercia adecarboxylata (LSE-1) and Bradyrhizobium sp. (LSBR-3) in nodule niche for multifaceted effects and profitability in soybean production

Enhancing Pisum sativum growth and symbiosis under heat stress: the synergistic impact of co-inoculated bacterial consortia and ACC deaminase-lacking Rhizobium

The 1-aminocyclopropane-1-carboxylate (ACC) deaminase is a crucial bacterial trait, yet it is not widely distributed among rhizobia. Hence, employing a co-inoculation approach that combines selected plant growth-promoting bacteria with compatible rhizobial strains, especially those lacking ACC deaminase, presents a practical solution to alleviate the negative effects of diverse abiotic stresses on legume nodulation. Our objective was to explore the efficacy of three non-rhizobial endophytes, Phyllobacterium salinisoli (PH), Starkeya sp. (ST) and Pseudomonas turukhanskensis (PS), isolated from native legumes grown in Tunisian arid regions, in improving the growth of cool-season legume and fostering symbiosis with an ACC deaminase-lacking rhizobial strain under heat stress. Various combinations of these endophytes (ST + PS, ST + PH, PS + PH, and ST + PS + PH) were co-inoculated with Rhizobium leguminosarum 128C53 or its ΔacdS mutant derivative on Pisum sativum plants exposed to a two-week heat stress period.Our findings revealed that the absence of ACC deaminase activity negatively impacted both pea growth and symbiosis under heat stress. Nevertheless, these detrimental effects were successfully mitigated in plants co-inoculated with ΔacdS mutant strain and specific non-rhizobial endophytes consortia. Our results indicated that heat stress significantly altered the phenolic content of pea root exudates. Despite this, there was no impact on IAA production. Interestingly, these changes positively influenced biofilm formation in consortia containing the mutant strain, indicating synergistic bacteria-bacteria interactions. Additionally, no positive effects were observed when these endophytic consortia were combined with the wild-type strain. This study highlights the potential of non-rhizobial endophytes to improve symbiotic performance of rhizobial strains lacking genetic mechanisms to mitigate stress effects on their legume host, holding promising potential to enhance the growth and yield of targeted legumes by boosting symbiosis.

Co-existence of halo-tolerant Pseudomonas fluorescens and Enterococcus hirae with multifunctional growth promoting traits to ameliorate salinity stress in Vigna radiata

Soil salinization has become a prominent obstacle in diverse arid and semi-arid region damaging agricultural productivity globally. From this perspective, present investigation was aimed to compare the potential compatible consortium of bio-inoculants for improving Plant Growth Promoting (PGP) attributes, anti-oxidative enzymes, grain yield and profitability of Vigna radiata in saline soil conditions. A total of 101 rhizobacterium isolated from salt affected regions of Punjab, India were screened for their ability to induce salt tolerance, multifunctional PGP traits and antagonistic activities. The 16S rRNA sequencing identified the strains LSMR-29 and LSMRS-7 as Pseudomonas flourescens and Enterococcus hirae, respectively. In-vitro compatible halo-tolerant dual inoculant (LSMR-29 + LSMRS-7) as bio-inoculants mitigated salt stress in Vigna radiata (spring mungbean) seedling with improved seed germination, biomass and salt tolerance index together with the presence of nifH, acds, pqq and ipdc gene under salinity stress as compared to single inoculants. Further, the potential of single and dual bio-inoculants were also exploited for PGP attributes in pot and field experiments. Results indicated that a significant improvement in chlorophyll content (2.03 fold), nodulation (1.24 fold), nodule biomass (1.23 fold) and leghemoglobin content (1.13 fold) with dual inoculant of LSMR-29 + LSMRS-7 over the LSMR-29 alone. The concentrations of macro & micronutrients, proline, soil enzyme activities i.e. soil dehydrogenase, acid & alkaline phosphatases and antioxidant enzymes such as superoxide dismutase, catalase and peroxidase also found to be high for LSMR-29 + LSMRS-7 as compared to un-inoculated control. The high grain yield thereby leading to Benefit: Cost (B: C) ratio at field scale was indicative of the commercial use bio-inoculants under salt affected Vigna radiata (spring mungbean) to improvement of productivity and soil health. The current finding reveals a co-inoculation of halo-tolerating Pseudomonas fluorescens and Enterococcus hirae containing ACC deaminase could prove to be novel approach for inducing salt tolerance and improving productivity of Vigna radiata (spring mungbean).

Selected indigenous drought tolerant rhizobium strains as promising biostimulants for common bean in Northern Spain

Drought is the most detrimental abiotic stress in agriculture, limiting crop growth and yield and, currently, its risk is increasing due to climate change. Thereby, ensuring food security will be one of the greatest challenges of the agriculture in the nearest future, accordingly it is essential to look for sustainable strategies to cope the negative impact of drought on crops. Inoculation of pulses with biostimulants such as rhizobium strains with high nitrogen fixation efficiency and drought-tolerance, has emerged as a promising and sustainable production strategy. However, some commercial inoculums are not effective under field conditions due to its lower effectiveness against indigenous rhizobium strains in the establishment of the symbiosis. Thus, in the present study, we evaluated the ability to improve drought tolerance in common bean plants of different indigenous rhizobia strains isolated from nearby crop fields in the Basque Country either affected by drought or salinity. The plants in this trial were grown in a climatic chamber under controlled conditions and exposed to values of 30% relative soil water content at the time of harvest, which is considered a severe drought. From the nine bacteria strains evaluated, three were found to be highly efficient under drought (namely 353, A12 and A13). These strains sustained high infectiveness (nodulation capacity) and effectiveness (shoot biomass production) under drought, even surpassing the plants inoculated with the CIAT899 reference strain, as well as the chemically N-fertilized plants. The tolerance mechanisms developed by plants inoculated with 353, A12 and A13 strains were a better adjustment of the cell wall elasticity that prevents mechanical damages in the plasma membrane, a higher WUE and an avoidance of the phenological delay caused by drought, developing a greater number of flowers. These results provide the basis for the development of efficient common bean inoculants able to increase the yield of this crop under drought conditions in the Northern Spain and, thus, to be used as biostimulants. In addition, the use of these efficient nitrogen fixation bacteria strains is a sustainable alternative to chemical fertilization, reducing cost and minimizing its negative impact on environment.

Construction and carbon source optimization of a microbial-plant coupled reactor for treating acid mine drainage

Acid mine drainage (AMD) is recognized as one of the most serious contamination sources in the nonferrous metal mining industry. In this study, aerobic strains VCZ02 and VCZ09, which were identified as Leclercia adecarboxylata and Klebsiella aerogenes, were screened from 11 strains of copper-zinc-resistant bacteria in the soil of the Dexing copper mine with Cu²⁺/Zn²⁺ removal rates of 46.32%/41.03% and 57.96%/67.05%, respectively. The composition of extracellular polymers plays an important role in the removal of heavy metals by these two strains. A mixed community consisting of VCZ02 and VCZ09 was coupled with Sagittaria trifolia L.var.sinensis (Sims) Mak to construct a microbial-plant coupled reactor to remediate AMD. Under the optimal condition of sodium acetate as carbon source, the pH of AMD increased from less than 5 to above 6.5, showing Cu²⁺/Zn²⁺ removal rates of 70-80% and above 30%, respectively. SEM-EDS results showed that VZC02 and VZC09 in the coupled reactor also helped with resisting the toxicity of heavy metals to plants by forming biofilms on the root surface and increasing the content of heavy metals on the surface of roots, thus improving the treatment effect of plants. This study provides a theoretical basis for the bioremediation of AMD and its application.

Plant organ- and growth stage-diversity of endophytic bacteria with potential as biofertilisers isolated from wheat (Triticum aestivum L.)

BACKGROUND

Chemical fertilisers are extensively used for crop production, which may cause soil deterioration and water pollution. Endophytic bacteria with plant-growth-promoting (PGP) activities may provide a solution to sustainably improve crop yields, including in-demand staples such as wheat. However, the diversity of the PGP endophytic bacteria in wheat across plant organs and growth stages has not been thoroughly characterised.

RESULTS

Here, we report the isolation of endophytic bacteria from root, stem, leaf and seed of three winter wheat varieties at tillering, jointing, heading and seed-filling growth stages that were identified via 16S rRNA gene sequence analysis. Strains were screened for indole-3-acetic acid (IAA) production, potassium and phosphate solubilisation and the ability to grow on a nitrogen-free medium. Strain's capacity to stimulate various plant growth parameters, such as dry root weight, dry above-ground parts weight and plant height, was evaluated in pot trials. A total of 127 strains were randomly selected from 610 isolated endophytic bacterial cultures, representing ten genera and 22 taxa. Some taxa were organ-specific; others were growth-stage-specific. Bacillus aryabhattai, B. stratosphericus, Leclercia adecarboxylata and Pseudomonas oryzihabitans were detected as wheat endophytes for the first time. The IAA production, inorganic phosphorous solubilisation, organic phosphorus solubilisation, potassium solubilisation and growth on N-free medium were detected in 45%, 29%, 37%, 2.4% and 37.8% of the 127 strains, respectively. In pot trials, each strain showed variable effects on inoculated wheat plants regarding the evaluated growth parameters.

CONCLUSIONS

Wheat endophytic bacteria showed organ- and growth-stage diversity, which may reflect their adaptations to different plant tissues and seasonal variations, and differed in their PGP abilities. Bacillus was the most predominant bacterial taxa isolated from winter wheat plants. Our study confirmed wheat root as the best reservoir for screening endophytic bacteria with potential as biofertilisers.

Enhanced Soybean Productivity by Inoculation With Indigenous Bradyrhizobium Strains in Agroecological Conditions of Northeast Germany

Commercial inoculants are often used to inoculate field-grown soybean in Europe. However, nodulation efficiencies in these areas are often low. To enhance biological nitrogen (N) fixation and increase domestic legume production, indigenous strains that are adapted to local conditions could be used to develop more effective inoculants. The objective of this study was to assess the ability of locally isolated Bradyrhizobium strains to enhance soybean productivity in different growing conditions of Northeast Germany. Three indigenous Bradyrhizobium isolates (GMF14, GMM36, and GEM96) were tested in combination with different soybean cultivars of different maturity groups and quality characteristics in one field trial and two greenhouse studies. The results showed a highly significant strain × cultivar interactions on nodulation response. Independent of the Bradyrhizobium strain, inoculated plants in the greenhouse showed higher nodulation, which corresponded with an increased N uptake than that in field conditions. There were significantly higher nodule numbers and nodule dry weights following GMF14 and GMM36 inoculation in well-watered soil, but only minor differences under drought conditions. Inoculation of the soybean cultivar Merlin with the strain GEM96 enhanced nodulation but did not correspond to an increased grain yield under field conditions. USDA110 was consistent in improving the grain yield of soybean cultivars Sultana and Siroca. On the other hand, GMM36 inoculation to Sultana and GEM96 inoculation to Siroca resulted in similar yields. Our results demonstrate that inoculation of locally adapted soybean cultivars with the indigenous isolates improves nodulation and yield attributes. Thus, to attain optimal symbiotic performance, the strains need to be matched with specific cultivars.

Halotolerant Rhizobacteria for Salinity-Stress Mitigation: Diversity, Mechanisms and Molecular Approaches

Agriculture is the best foundation for human livelihoods, and, in this respect, crop production has been forced to adopt sustainable farming practices. However, soil salinity severely affects crop growth, the degradation of soil quality, and fertility in many countries of the world. This results in the loss of profitability, the growth of agricultural yields, and the step-by-step decline of the soil nutrient content. Thus, researchers have focused on searching for halotolerant and plant growth-promoting bacteria (PGPB) to increase soil fertility and productivity. The beneficial bacteria are frequently connected with the plant rhizosphere and can alleviate plant growth under salinity stress through direct or indirect mechanisms. In this context, PGPB have attained a unique position. The responses include an increased rate of photosynthesis, high production of antioxidants, osmolyte accumulation, decreased Na+ ions, maintenance of the water balance, a high germination rate, and well-developed root and shoot elongation under salt-stress conditions. Therefore, the use of PGPB as bioformulations under salinity stress has been an emerging research avenue for the last few years, and applications of biopesticides and biofertilizers are being considered as alternative tools for sustainable agriculture, as they are ecofriendly and minimize all kinds of stresses. Halotolerant PGPB possess greater potential for use in salinity-affected soil as sustainable bioinoculants and for the bioremediation of salt-affected soil.

Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives

In the light of intensification of cropping practices and changing climatic conditions, nourishing a growing global population requires optimizing environmental sustainability and reducing ecosystem impacts of food production. The use of microbiological systems to ameliorate the agricultural production in a sustainable and eco-friendly way is widespread accepted as a future key-technology. However, the multitude of interaction possibilities between the numerous beneficial microbes and plants in their habitat calls for systematic analysis and management of the rhizospheric microbiome. This review exploits present and future strategies for rhizospheric microbiome management with the aim to generate a comprehensive understanding of the known tools and techniques. Significant information on the structure and dynamics of rhizospheric microbiota of isolated microbial communities is now available. These microbial communities have beneficial effects including increased plant growth, essential nutrient acquisition, pathogens tolerance, and increased abiotic as well as biotic stress tolerance such as drought, temperature, salinity and antagonistic activities against the phyto-pathogens. A better and comprehensive understanding of the various effects and microbial interactions can be gained by application of molecular approaches as extraction of DNA/RNA and other biochemical markers to analyze microbial soil diversity. Novel techniques like interactome network analysis and split-ubiquitin system framework will enable to gain more insight into communication and interactions between the proteins from microbes and plants. The aim of the analysis tasks leads to the novel approach of Rhizosphere microbiome engineering. The capability of forming the rhizospheric microbiome in a defined way will allow combining several microbes (e.g. bacteria and fungi) for a given environment (soil type and climatic zone) in order to exert beneficial influences on specific plants. This integration will require a large-scale effort among academic researchers, industry researchers and farmers to understand and manage interactions of plant-microbiomes within modern farming systems, and is clearly a multi-domain approach and can be mastered only jointly by microbiology, mathematics and information technology. These innovations will open up a new avenue for designing and implementing intensive farming microbiome management approaches to maximize resource productivity and stress tolerance of agro-ecosystems, which in return will create value to the increasing worldwide population, for both food production and consumption.

Rice Blast Lesions: an Unexplored Phyllosphere Microhabitat for Novel Antagonistic Bacterial Species Against Magnaporthe oryzae

Dark brown necrotic lesions caused by Magnaporthe oryzae on rice foliage is a contrasting microhabitat for leaf-colonizing microbiome as compared with the surrounding healthy chlorophyll-rich tissues. We explored culturable bacterial communities of blast lesions by adopting microbiological tools for isolating effective biocontrol bacterial strains against M. oryzae. 16S rRNA gene sequencing-based molecular identification revealed a total of 17 bacterial species belonging to Achromobacter (2), Comamonas (1), Curtobacterium (1), Enterobacter (1), Leclercia (2), Microbacterium (1), Pantoea (3), Sphingobacterium (1), and Stenotrophomonas (5) found colonizing the lesion. Over 50% of the bacterial isolates were able to suppress the mycelial growth of M. oryzae either by secretory or volatile metabolites. Volatiles released by Achromobacter sp., Curtobacterium luteum, Microbacterium oleivorans, Pantoea ananatis, Stenotrophomonas maltophilia, and Stenotrophomonas sp., and were found to be fungicidal while others showed fungistatic action. In planta pathogen challenged evaluation trial revealed the biocontrol potential of Stenotrophomonas sp. and Microbacterium oleivorans that showed over 60% blast severity suppression on the rice leaf. The lesion-associated bacterial isolates were found to trigger expression of defense genes such as OsCEBiP, OsCERK1, OsEDS1, and OsPAD4 indicating their capability to elicit innate defense in rice against blast disease. The investigation culminated in the identification of potential biocontrol agents for the management of rice blast disease.

Dual Microbial Inoculation, a Game Changer? - Bacterial Biostimulants With Multifunctional Growth Promoting Traits to Mitigate Salinity Stress in Spring Mungbean

Soil microbes play a vital role in improving plant growth, soil health, ameliorate biotic/abiotic stress and enhance crop productivity. The present study was aimed to investigate a coordinated effect of compatible consortium [salt tolerating Rhizobium and rhizobacterium with 1-aminocyclopropane-1-carboxylate (ACC) deaminase] in enhancing plant growth promoting (PGP) traits, symbiotic efficiency, nutrient acquisition, anti-oxidative enzymes, grain yield and associated profitability in spring mungbean. We identified a non-pathogenic compatible Rhizobium sp. LSMR-32 (MH644039.1) and Enterococcus mundtii LSMRS-3 (MH644178.1) from salt affected areas of Punjab, India and the same were assessed to develop consortium biofertilizer based on salt tolerance, multifarious PGP traits, antagonistic defense activities and presence of nifH, acds, pqq, and ipdc genes. Indole Acetic acid (IAA), P-solubilization, biofilm formation, exo-polysaccharides, siderophore, salt tolerance, ACC deaminase activities were all found highly significant in dual inoculant (LSMR-32 + LSMRS-3) treatment compared to LSMR-32 alone. Under saline soil conditions, dual inoculant showed a higher seed germination, plant height, biomass, chlorophyll content and macro and micro-nutrient uptake, than un-inoculated control. However, symbiotic (nodulation, nodule biomass and leghaemoglobin content) and soil quality parameters (phosphatase and soil dehydrogenase enzymes) increased numerically with LSMR-32 + LSMRS-3 over Rhizobium sp. LSMR-32 alone. Dual bacterial inoculation (LSMR-32 + LSMRS-3) increased the proline content (2.05 fold), anti-oxidative enzymes viz., superoxide dismutase (1.50 fold), catalase (1.43 fold) and peroxidase (3.88 folds) in contrast to control treatment. Decreased Na⁺ accumulation and increased K⁺ uptake resulted in favorable K⁺/Na⁺ ratio through ion homeostasis. Co-inoculation of Rhizobium sp. LSMR-32 and Enterococcus mundtii LSMRS-3 significantly improved the grain yield by 8.92% and led to superior B: C ratio over Rhizobium sp. alone under salt stress. To best of our knowledge this is perhaps the first field report from Indian soils that largely describes dual inoculation of Rhizobium sp. LSMR-32 and Enterococcus mundtii LSMRS-3 and the same can be considered as a game-changer approach to simultaneously induce salt tolerance and improve productivity in spring mungbean under saline stress conditions.

Chickpea (Cicer arietinum L.) as model legume for decoding the co-existence of Pseudomonas fluorescens and Mesorhizobium sp. as bio-fertilizer under diverse agro-climatic zones

Microbial co-inoculation strategy utilizes a combination of microbes to stimulate plant growth concomitant with an increased phytopathogen tolerance. In the present study, 15 endophytic bacterial isolates from rhizosphere and roots of wild chickpea accessions (Cicer pinnatifidum, C. judiacum, C. bijugum and C. reticulatum) were characterized for morphological, biochemical and physiological traits. Two promising isolates were identified as Pseudomonas fluorescens strain LRE-2 (KR303708.1) and Pseudomonas argentinensis LPGPR-1 (JX239745.1) based on 16S rRNA gene sequencing. Biocompatibility of selected endophytes with Mesorhizobium sp. CH1233, a standard isolate used as a national check in All India Coordinated Research Project (AICRP) was assessed to develop functional combinations capable of producing Indole acetic acid, gibberellins, siderophores and improving seed vigour (in vitro). In vivo synergistic effect of promising combinations was further evaluated under national AICRP, (Chickpea) at two different agro-climatic zones [North-West plain (Ludhiana and Hisar) and Central zones (Sehore)] for three consecutive Rabi seasons (2015-18) to elucidate their effect on symbiotic, soil quality and yield parameters. On the pooled mean basis across locations over the years, combination of Mrh+LRE-2 significantly enhanced symbiotic, soil quality traits and grain yield over Mrh alone and highly positive correlation was obtained between the nodulation traits and grain yield. Superior B: C ratio (1.12) and additional income of Rs 6,505.18 ha^-1 was obtained by application of Mrh+LRE-2 over Mrh alone and un-inoculated control. The results demonstrate that dual combination of Mrh and Pseudomonas sp. from wild Cicer relatives can be exploited as a potential bio-fertilizer for increasing soil fertility and improving chickpea productivity under sustainable agriculture.

Mechanistic Insights of the Interaction of Plant Growth-Promoting Rhizobacteria (PGPR) With Plant Roots Toward Enhancing Plant Productivity by Alleviating Salinity Stress

Agriculture plays an important role in a country's economy. The sector is challenged by many stresses, which led to huge loss in plant productivity worldwide. The ever-increasing population, rapid urbanization with shrinking agricultural lands, dramatic change in climatic conditions, and extensive use of agrochemicals in agricultural practices that caused environmental disturbances confront mankind of escalating problems of food security and sustainability in agriculture. Escalating environmental problems and global hunger have led to the development and adoption of genetic engineering and other conventional plant breeding approaches in developing stress-tolerant varieties of crops. However, these approaches have drawn flaws in their adoption as the process of generating tolerant varieties takes months to years in bringing the technology from the lab to the field. Under such scenario, sustainable and climate-smart agricultural practices that avail bacterial usage open the avenues in fulfilling the incessant demand for food for the global population. Ensuring stability on economic fronts, bacteria minimizes plant salt uptake by trapping ions in their exopolysaccharide matrix besides checking the expression of Na+/H+ and high-affinity potassium transporters. Herein we describe information on salinity stress and its effect on plant health as well as strategies adopted by plant growth-promoting rhizobacteria (PGPR) in helping plants to overcome salinity stress and in mitigating loss in overall plant productivity. It is believed that acquisition of advanced knowledge of plant-beneficial PGPR will help in devising strategies for sustainable, environment-friendly, and climate-smart agricultural technologies for adoption in agriculture to overcome the constrained environmental conditions.