Community-forming traits play role in effective colonization of plant-growth-promoting bacteria and improved plant growth.

Community-forming traits (CFts) play an important role in the effective colonization of plant-growth-promoting bacterial communities that influence host plants positively by modulating their adaptive functions. In this study, by considering plant-growth-promoting traits (PGPts) and community-forming traits (CFts), three communities were constructed, viz., SM1 (PGPts), SM2 (CFts), and SM3 (PGPts+CFts). Each category isolates were picked up on the basis of their catabolic diversity of different carbon sources. Results revealed a distinctive pattern in the colonization of the communities possessed with CF traits. It was observed that the community with CFts colonized inside the plant in groups or in large aggregations, whereas the community with only PGPts colonized as separate individual and small colonies inside the plant root and leaf. The effect of SM3 in the microcosm experiment was more significant than the uninoculated control by 22.12%, 27.19%, and 9.11% improvement in germination percentage, chlorophyll content, and plant biomass, respectively. The significant difference shown by the microbial community SM3 clearly demonstrates the integrated effect of CFts and PGPts on effective colonization vis-à-vis positive influence on the host plant. Further detailed characterization of the interaction will take this technology ahead in sustainable agriculture.

Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity.

Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heatS (heat susceptible, GW322) and heatT (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heatS variety than in the heatT variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heatS variety, a greater number of isolates from the heatT variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heatT samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.

Characterization of actinobacteria from wheat seeds for plant growth promoting traits and protection against fungal pathogens.

Seeds harbor naturally occurring microbial endophytes that proliferate during seedling development; playing crucial roles in seedling growth, establishment, and protection against fungal pathogens. Resilient actinobacteria of wheat seeds have been explored in this study for their beneficial traits. Ten actinobacteria isolated from the surface-sterilized seeds of wheat variety HD3117 were identified as nine species of Streptomyces and one of Nocardiopsis. Most isolates could grow at 42°C, 5% NaCl, and 10% poly ethylene glycol (PEG); exhibited variable hydrolytic enzyme production for amylase, cellulase, and protease. Few isolates produced indole acetic acid (9.0-18.9 µg ml-1 ) and could solubilize P (11.3-85.2 µg ml-1 ). The isolates were antagonistic against one or more fungal pathogens under test (Fusarium graminearum, Bipolaris sorokiniana, Alternaria sp., and Tilletia indica), of which Streptomyces sampsonii WSA20 inhibited all in dual culture assay. Priming of wheat seeds with the efficient isolate WSA20 led to effective colonization in the root zone and significantly improved germination, shoot and root length in seed germination assay. Significant protection was recorded in microcosm experiment where no symptoms of disease were observed. This study shows the significance of actinobacterial endophytes of wheat seeds in influencing seed germination and seedling growth while protecting from soil-borne pathogens. It is original and suggests that the seed inhabiting efficient actinobacteria may be developed as efficient bioinoculant for sustainable farming system.

Recycling of silicon-rich agro-wastes by their combined application with phosphate solubilizing microbe to solubilize the native soil phosphorus in a sub-tropical Alfisol.

It is imperative to find suitable strategies to utilize the native soil phosphorus (P), as natural rock phosphate deposits are at a verge of depletion. We explored two such cost-effective and eco-friendly strategies for native soil P solubilization: silicon (Si)-rich agro-wastes (as Si source) and phosphate solubilizing microorganism (PSM). An incubation study was conducted in a sub-tropical Alfisol for 90 days at 25 °C under field capacity moisture. A factorial completely randomized design with 3 factors, namely: Si sources (three levels: sugarcane bagasse ash, rice husk ash, and corn cob ash), PSM (two levels: without PSM, and with PSM); and Si doses [three levels: no Si (Si0), 125 (Si125) and 250 (Si250) mg Si kg-1 soil] was followed. The PSM increased solution P and soluble Si level by ∼22.2 and 1.88%, respectively, over no PSM; whereas, Si125 and Si250 increased solution P by ∼60.4 and 77.1%, as well as soluble Si by ∼41.5 and 55.5%, respectively, over Si0. Also, interaction of PSM × Si doses was found significant (P<0.05). Activities of soil enzymes (dehydrogenase, acid phosphatase) and microbial biomass P also increased significantly both with PSM and Si application. Overall, PSM solubilized ∼4.18 mg kg-1 of inorganic P and mineralized ∼5.92 mg kg-1 of organic P; whereas, Si125 and Si250 solubilized ∼3.85 and 5.72 mg kg-1 of inorganic P, and mineralized ∼4.15 and 5.37 mg kg-1 of organic P, respectively. Path analysis revealed that inorganic P majorly contributed to total P solubilization; whereas, soluble and loosely bound, iron bound and aluminium bound P significantly influenced the inorganic P solubilization. Thus, utilization of such wastes as Si sources will not only complement the costly P fertilizers, but also address the waste disposal issue in a sustainable manner.

Minerals solubilizing and mobilizing microbiomes: A sustainable approach for managing minerals' deficiency in agricultural soil.

Agriculture faces challenges to fulfil the rising food demand due to shortage of arable land and various environmental stressors. Traditional farming technologies help in fulfilling food demand but they are harmful to humans and environmental sustainability. The food production along with agro-environmental sustainability could be achieved by encouraging farmers to use agro-environmental sustainable products such as biofertilizers and biopesticides consisting of live microbes or plant extract instead of chemical-based inputs. The eco-friendly formulations play a significant role in plant growth promotion, crop yield and repairing degraded soil texture and fertility sustainably. Mineral solubilizing microbes that provide vital nutrients like phosphorus, potassium, zinc and selenium are essential for plant growth and development and could be developed as biofertilizers. These microbes could be plant associated (rhizospheric, endophytic and phyllospheric) or inhabit the bulk soil and diverse extreme habitats. Mineral solubilizing microbes from soil, extreme environments, surface and internal parts of the plant belong to diverse phyla such as Ascomycota, Actinobacteria, Basidiomycota, Bacteroidetes, Chlorobi, Cyanobacteria, Chlorophyta, Euryarchaeota, Firmicutes, Gemmatimonadetes, Mucoromycota, Proteobacteria and Tenericutes. Mineral solubilizing microbes (MSMs) directly or indirectly stimulate plant growth and development either by releasing plant growth regulators; solubilizing phosphorus, potassium, zinc, selenium and silicon; biological nitrogen fixation and production of siderophores, ammonia, hydrogen cyanide, hydrolytic enzymes and bioactive compound/secondary metabolites. Biofertilizer developed using mineral solubilizing microbes is an eco-friendly solution to the sustainable food production system in many countries worldwide. The present review deals with the biodiversity of mineral solubilizing microbes, and potential roles in crop improvement and soil well-being for agricultural sustainability.

Radiochemical Evidence for the Contribution of Chemotyped Siderophore Producing Bacteria Towards Plant Iron Nutrition.

Fe deficiency is a major challenge that limits agricultural productivity and is a serious human health concern worldwide. Under iron-limiting conditions soil microorganisms produce siderophores, that chelates Fe3+ (ferric) and make it available to the plants. Selection of efficient siderophore producing bacteria and establishing their role in enhancing iron uptake is a strategic approach for improving plant nutrition. Hence 3 efficient isolates Pantoea agglomerans, Pseudomonas plecoglossida and Lactococcus lactis, selected from a repository of 154 bacteria, producing catecholate, hydroxamate and carboxylate siderophores, respectively, were assessed for Fe chelation efficiency using 59Fe and their role in plant biometric parameters, Fe uptake and antioxidant enzymes with tomato (Strategy I) and wheat (Strategy II) test plants under hydroponic system. Cell-free siderophore preparation (Sid) improved plant parameters and iron nutrition more efficiently than bacterial inoculants. Pantoea agglomerans was proven best as its 59Fe-bound siderophore complex showed the highest uptake of 4.25 and 1.59 Bq plant-1 in wheat and tomato, respectively. Further, the Fe-starved plants (1 µm Fe-EDTA) showed around two-fold higher 59Fe uptake than those raised under Fe-sufficient condition (100 µm Fe-EDTA). Results indicated that probably the bacterial mediated iron translocation in plants is Strategy III, complementing both Strategy I and II by facilitating higher availability of chelated Fe to plant reductases directly and/or through ligand exchange with phytosiderophores, respectively. This study highlights the need for integration of siderophore based formulations in INM strategies for enhancing plant iron content to address the Fe deficiency challenge of the soil and human nutrition.

Soil type influence nutrient availability, microbial metabolic diversity, eubacterial and diazotroph abundance in chickpea rhizosphere.

Rhizosphere microbial communities are dynamic and play a crucial role in diverse biochemical processes and nutrient cycling. Soil type and cultivar modulate the composition of rhizosphere microbial communities. Changes in the community composition significantly alter microbial function and ecological process. We examined the influence of soil type on eubacterial and diazotrophic community abundance and microbial metabolic potential in chickpea (cv. BG 372 and cv. BG 256) rhizosphere. The total eubacterial and diazotrophic community as estimated through 16 S rDNA and nifH gene copy numbers using qPCR showed the soil type influence with clear rhizosphere effect on gene abundance. PLFA study has shown the variation in microbial community structure with different soil types. Differential influence of soil types and cultivar on the ratio of Gram positive to Gram negative bacteria was observed with most rhizosphere soils corresponding to higher ratios than bulk soil. The rhizosphere microbial activities (urease, dehydrogenase, alkaline phosphatase and beta-glucosidase) were also assessed as an indicator of microbial metabolic diversity. Principal component analysis and K-means non-hierarchical cluster mapping grouped soils into three categories, each having different soil enzyme activity or edaphic drivers. Soil type and cultivar influence on average substrate utilization pattern analyzed through community level physiological profiling (CLPP) was higher for rhizosphere soils than bulk soils. The soil nutrient studies revealed that both soil type and cultivar influenced the available N, P, K and organic carbon content of rhizosphere soil. Our study signifies that soil type and cultivar jointly influenced soil microbial community abundance and their metabolic potential in chickpea rhizosphere.

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.

Appraisal of diversity and functional attributes of thermotolerant wheat associated bacteria from the peninsular zone of India.

The biodiversity of wheat associated bacteria was deciphered from the peninsular zone of India. A total of 264 isolated bacteria were analyzed through amplified ribosomal DNA restriction analysis (ARDRA, using three restriction enzymes Alu I, Msp I and Hae III, which led to the clustering of these isolates into 12-16 groups for the different sites at >75% similarity index, adding up to 70 groups). 16S rRNA gene based phylogenetic analysis, revealed that all the bacteria belonged to three phyla Proteobacteria, Firmicutes, and Actinobacteria of 32 distinct species of 15 genera namely: Achromobacter, Alcaligenes, Arthrobacter, Bacillus, Delftia, Enterobacter, Exiguobacterium, Klebsiella, Methylobacterium, Micrococcus, Paenibacillus, Pseudomonas, Rhodobacter, Salmonella and Staphylococcus. Representative strains from each cluster were screened in vitro for plant growth promoting traits. Among plant growth promoting activities, siderophore producers were highest (15%), when compared to indole acetic acid producers (13%), Zn-solubilizers (11%), P-solubilizers (11%), ammonia (10%), hydrogen cyanide producers (9%), biocontrol (8%), N2-fixers (7%), 1-aminocyclopropane-1-carboxylate deaminase (6%), GA producers (6%) and K-solubilizers (5%). Among 32 representative strains, Alcaligenes faecalis, Arthrobacter sp., Bacillus siamensis, Bacillus subtilis, Delftia acidovorans, Methylobacterium mesophilicum, Methylobacterium sp., Pseudomonas poae, Pseudomonas putida, and Pseudomonas stutzeri exhibited more than six different plant growth promoting activities at high temperature. Thermotolerant bacterial isolates may have application as inoculants for plant growth promotion and biocontrol agents for crops growing at high temperature conditions.

Growth stage and tissue specific colonization of endophytic bacteria having plant growth promoting traits in hybrid and composite maize (Zea mays L.).

Maize, a crop cultivated worldwide, was investigated for plant tissue and crop stage specific colonization of endophytic bacteria. Such bacterial interactions have high potential to enhance maize grain yield by means of biological nitrogen fixation and/or plant growth promoting activities. In this study endophytic bacteria were isolated from a hybrid PEEHM-5 and composite PC-4 maize varieties using root, stem and leaf tissues of plants at vegetative, flowering and maturity stages of growth. PEEHM-5 harbored higher endophytic bacterial population than PC-4 at all growth stages, with highest in roots and at flowering stage. Morphologically 188 different endophytic isolates (82 from PEEHM-5, 106 from PC-4) were screened for plant growth promoting attributes viz. P, K, Zn solubilization, production of hormones, siderophore, ACC deaminase, HCN, biological nitrogen fixation and biocontrol of two maize fungal pathogens. Thirty one potential PGP isolates on RFLP analysis of their amplified 16S rRNA gene, were clustered in 13 phylogenetic groups. On sequencing and blasting of amplified 16S rRNA gene of representative isolates from each group identified PC-4 endophytic bacterial isolates as Bacillus aryabhattai, Pantoea cypripedii, Bacillus licheniformis, Klebsiella sp., Pantoea dispersa, Klebsiella variicola, Pantoea sp., Agrobacterium larrymoorei and PEEHM-5 endophytic bacterial isolates as Bacillus sp., Bacillus amyloliquefaciens, Lactococcus lactis, Bacillus cereus and Staphylococcus hominis. In planta evaluation of potential isolates at variable chemical fertilizer input indicated their potential in compensating nearly 25% of the fertilizer input as observed on their improvement of shoot and root parameters. Lactococcus lactis inoculation influenced maximum followed by Pantoea and Klebsiella isolates.

Molecular diversity and multifarious plant growth promoting attributes of Bacilli associated with wheat (Triticum aestivum L.) rhizosphere from six diverse agro-ecological zones of India.

The diversity of culturable Bacilli was investigated in six wheat cultivating agro-ecological zones of India viz: northern hills, north western plains, north eastern plains, central, peninsular, and southern hills. These agro-ecological regions are based on the climatic conditions such as pH, salinity, drought, and temperature. A total of 395 Bacilli were isolated by heat enrichment and different growth media. Amplified ribosomal DNA restriction analysis using three restriction enzymes AluI, MspI, and HaeIII led to the clustering of these isolates into 19-27 clusters in the different zones at >70% similarity index, adding up to 137 groups. Phylogenetic analysis based on 16S rRNA gene sequencing led to the identification of 55 distinct Bacilli that could be grouped in five families, Bacillaceae (68%), Paenibacillaceae (15%), Planococcaceae (8%), Staphylococcaceae (7%), and Bacillales incertae sedis (2%), which included eight genera namely Bacillus, Exiguobacterium, Lysinibacillus, Paenibacillus, Planococcus, Planomicrobium, Sporosarcina, and Staphylococcus. All 395 isolated Bacilli were screened for their plant growth promoting attributes, which included direct-plant growth promoting (solubilization of phosphorus, potassium, and zinc; production of phytohormones; 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation), and indirect-plant growth promotion (antagonistic, production of lytic enzymes, siderophore, hydrogen cyanide, and ammonia). To our knowledge, this is the first report for the presence of Bacillus endophyticus, Paenibacillus xylanexedens, Planococcus citreus, Planomicrobium okeanokoites, Sporosarcina sp., and Staphylococcus succinus in wheat rhizosphere and exhibit multifunctional PGP attributes. These niche-specific and multifarious PGP Bacilli may serve as inoculants for crops growing in respective climatic conditions.

Modulation of low-temperature-induced biochemical changes in bud and root band zones of sugar cane sets by potassium, zinc, and Ethrel for improving sprouting.

Low-temperature-induced biochemical changes in bud and root band zone of the sugar cane set suppress sprouting, which is responsible for drastic yield decline in ratoon crops. This study was undertaken to modulate these low-temperature-induced biochemical changes using potassium, zinc, and Ethrel to enhance the sprouting of buds at 5 and 10 degrees C. Potassium, zinc, and Ethrel led to 80, 50, and 40% improvement in bud sprouting at 5 degrees C, respectively. An increase in reducing sugars and a decrease in sucrose contents were recorded with treatment of potassium, zinc, and Ethrel. Acid invertase, adenosine triphosphatase, indoleacetic acid oxidase, and nitrate reductase in vivo activities were also enhanced. However, treatments led to a significant decline in indoleacetic acid, total phenols, and superoxide dismutase activity, which rendered the in situ toxicity buildup in sets at low temperatures.

Use of glutaraldehyde and benzalkonium chloride for minimizing post-harvest physio-chemical and microbial changes responsible for sucrose losses in sugar cane.

Sugar cane is sensitive to enormous sucrose losses induced by physio-chemical and microbial changes, the severity being increased during the time lag between harvest and crushing in the mills. Minimization of the sucrose losses in the field is essential for better sugar recovery and prevention of sucrose losses. An experiment was conducted to evaluate the efficacy of glutaraldehyde and benzalkonium chloride for their effects on the microbial counts and physio-chemical changes responsible for sucrose losses. Glutaraldehyde and benzalkonium chloride (1000 + 250 ppm) reduced the losses in sucrose content to 7.1% as compared to the 30.8% loss in the control, thus improving the performance by 76.9%. The application of chemicals reduced the acid invertase activity (by 60%), lowered weight loss, titrable acidity, reducing sugars content, dextran, ethanol, and ethylene production and respiration rates. The application led to the reduction in the total bacterial, fungal, Leuconostoc, and yeast counts by 67.92, 51.3%, 26.08, and 51.2%, respectively.