Diversity of nitrogen-fixing rhizobacteria associated with sugarcane: a comprehensive study of plant-microbe interactions for growth enhancement in Saccharum spp

Enhancing Agricultural Sustainability Through Rhizomicrobiome: A Review

Sustainable agriculture represents the responsible utilization of natural resources while safeguarding the well-being of the natural environment. It encompasses the objectives of preserving the environment, fostering economic growth, and promoting socioeconomic equality. To achieve sustainable development for humanity, it is imperative to prioritize sustainable agriculture. One significant approach to achieving this transition is the extensive utilization of microbes, which play a crucial role due to the genetic reliance of plants on the beneficial functions provided by symbiotic microbes. This review focuses on the significance of rhizospheric microbial communities, also known as the rhizomicrobiome (RM). It is a complex community of microorganisms that live in the rhizosphere and influence the plant's growth and health. It provides its host plant with various benefits related to plant growth, including biocontrol, biofertilization, phytostimulation, rhizoremediation, stress resistance, and other advantageous properties. Yet, the mechanisms by which the RM contributes to sustainable agriculture remain largely unknown. Investigating this microbial population presents a significant opportunity to advance toward sustainable agriculture. Hence, this study aims to provide an overview of the diversity and applications of RM in sustainable agriculture practices. Lately, there has been growing momentum in various areas related to rhizobiome research and its application in agriculture. This includes rhizosphere engineering, synthetic microbiome application, agent-based modeling of the rhizobiome, and metagenomic studies. So, developing bioformulations of these beneficial microorganisms that support plant growth could serve as a promising solution for future strategies aimed at achieving a new green revolution.

Soil and Mineral Nutrients in Plant Health: A Prospective Study of Iron and Phosphorus in the Growth and Development of Plants

Plants being sessile are exposed to different environmental challenges and consequent stresses associated with them. With the prerequisite of minerals for growth and development, they coordinate their mobilization from the soil through their roots. Phosphorus (P) and iron (Fe) are macro- and micronutrient; P serves as an important component of biological macromolecules, besides driving major cellular processes, including photosynthesis and respiration, and Fe performs the function as a cofactor for enzymes of vital metabolic pathways. These minerals help in maintaining plant vigor via alterations in the pH, nutrient content, release of exudates at the root surface, changing dynamics of root microbial population, and modulation of the activity of redox enzymes. Despite this, their low solubility and relative immobilization in soil make them inaccessible for utilization by plants. Moreover, plants have evolved distinct mechanisms to cope with these stresses and coregulate the levels of minerals (Fe, P, etc.) toward the maintenance of homeostasis. The present study aims at examining the uptake mechanisms of Fe and P, and their translocation, storage, and role in executing different cellular processes in plants. It also summarizes the toxicological aspects of these minerals in terms of their effects on germination, nutrient uptake, plant-water relationship, and overall yield. Considered as an important and indispensable component of sustainable agriculture, a separate section covers the current knowledge on the cross-talk between Fe and P and integrates complete and balanced information of their effect on plant hormone levels.

The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f

BACKGROUND

Bletilla striata (Thunb.) Reichb. f. (B. striata) is a perennial herbaceous plant in the Orchidaceae family known for its diverse pharmacological activities, such as promoting wound healing, hemostasis, anti-inflammatory effects, antioxidant properties, and immune regulation. Nevertheless, the microbe-plant-metabolite regulation patterns for B. striata remain largely undetermined, especially in the field of rhizosphere microbes. To elucidate the interrelationships between soil physics and chemistry and rhizosphere microbes and metabolites, a comprehensive approach combining metagenome analysis and targeted metabolomics was employed to investigate the rhizosphere soil and tubers from four provinces and eight production areas in China.

RESULTS

Our study reveals that the core rhizosphere microbiome of B. striata is predominantly comprised of Paraburkholderia, Methylibium, Bradyrhizobium, Chitinophaga, and Mycobacterium. These microbial species are recognized as potentially beneficial for plants health. Comprehensive analysis revealed a significant association between the accumulation of metabolites, such as militarine and polysaccharides in B. striata and the composition of rhizosphere microbes at the genus level. Furthermore, we found that the soil environment indirectly influenced the metabolite profile of B. striata by affecting the composition of rhizosphere microbes. Notably, our research identifies soil organic carbon as a primary driving factor influencing metabolite accumulation in B. striata.

CONCLUSION

Our fndings contribute to an enhanced understanding of the comprehensive regulatory mechanism involving microbe-plant-metabolite interactions. This research provides a theoretical basis for the cultivation of high-quality traditional Chinese medicine B. striata.

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Nodulation Experiment by Cross-Inoculation of Nitrogen-Fixing Bacteria Isolated from Root Nodules of Several Leguminous Plants

Root-nodule nitrogen-fixing bacteria are known for being specific to particular legumes. This study isolated the endophytic root-nodule bacteria from the nodules of legumes and examined them to determine whether they could be used to promote the formation of nodules in other legumes. Forty-six isolates were collected from five leguminous plants and screened for housekeeping (16S rRNA), nitrogen fixation (nifH), and nodulation (nodC) genes. Based on the 16S rRNA gene sequencing and phylogenetic analysis, the bacterial isolates WC15, WC16, WC24, and GM5 were identified as Rhizobium, Sphingomonas, Methylobacterium, and Bradyrhizobium, respectively. The four isolates were found to have the nifH gene, and the study confirmed that one isolate (GM5) had both the nifH and nodC genes. The Salkowski method was used to measure the isolated bacteria for their capacity to produce phytohormone indole acetic acid (IAA). Additional experiments were performed to examine the effect of the isolated bacteria on root morphology and nodulation. Among the four tested isolates, both WC24 and GM5 induced nodulation in Glycine max. The gene expression studies revealed that GM5 had a higher expression of the nifH gene. The existence and expression of the nitrogen-fixing genes implied that the tested strain had the ability to fix the atmospheric nitrogen. These findings demonstrated that a nitrogen-fixing bacterium, Methylobacterium (WC24), isolated from a Trifolium repens, induced the formation of root nodules in non-host leguminous plants (Glycine max). This suggested the potential application of these rhizobia as biofertilizer. Further studies are required to verify the N2-fixing efficiency of the isolates.

Bacillus species as tools for biocontrol of plant diseases: A meta-analysis of twenty-two years of research, 2000-2021

The traditional way of dealing with plant diseases has been the use of chemical products, but these harm the environment and are incompatible with the global effort for sustainable development. The use of Bacillus and related species in the biological control of plant diseases is a trend in green agriculture. Many studies report the positive effect of these bacteria, but a synthesis is still necessary. So, the objective of this work is to perform a meta-analysis of Bacillus biocontrol potential and identify factors that drive its efficacy. Data were compiled from articles published in journals listed in two of the main scientific databases between 2000 and 2021. Among 6159 articles retrieved, 399 research papers met the inclusion criteria for a systematic review. Overall, Bacilli biocontrol agents reduced disease by 60% compared to control groups. Furthermore, experimental tests with higher concentrations show a strong protective effect, unlike low and single concentration essays. Biocontrol efficacy also increased when used as a protective inoculation rather than therapeutic inoculation. Inoculation directly in the fruit has a greater effect than soil drenching. The size of the effect of Bacillus-based commercial products is lower than the newly tested strains. The findings presented in this study confirm the power of Bacillus-based bioinoculants and provide valuable guidance for practitioners, researchers, and policymakers seeking effective and sustainable solutions in plant disease management.

Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health

Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.

Optimizing foliar N-fertilization in sugarcane depends on plant genotype and nitrogen concentration

Foliar N-fertilization (FNf) has emerged as a promising approach to synchronize plant nitrogen (N) demands and application timing, reducing the N losses to the environment associated with traditional soil-based fertilization methods. However, limited information exists regarding the effectiveness of FNf in sugarcane. This study aimed to optimize FNf in sugarcane by evaluating N-fertilizer recovery by the plant (NRP) and assessing potential toxicity effects. Four sugarcane genotypes were subjected to FNf using 15 N-urea at five nitrogen concentrations. NRP was assessed at five time points for roots, stalk, old leaves, 15 N-urea-fertilized leaves (15 NL), and unexpanded leaves (UEL). Leaf scorching, indicating FNf toxicity, was analyzed using morpho-anatomical and histochemical techniques. The results showed that FNf promoted high NRP, with an average recovery of 62.3%. Surprisingly, the redistribution of 15 N-urea did not follow the nitrogen uptake rate by sugarcane leaves, with an average of 41.3% of the total-NRP. The stalk emerged as the primary sink for 15 N-urea, followed by the UEL. Genotypes differed in the leaf scorching intensity, which increased with higher concentration of 15 N-urea. Genotypes also differed in the 15 N-urea uptake rate, down-regulated by the N content in the 15 NL. These findings emphasize that by carefully choosing the appropriate genotype and nitrogen concentration, FNf can significantly enhance N-fertilizer uptake, resulting in potential environmental and economic benefits.

Pseudomonas aeruginosa Strain 91: A Multifaceted Biocontrol Agent against Banana Fusarium Wilt

Banana Fusarium wilt (BFW), caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc), poses significant threats to banana cultivation. Currently, effective control methods are lacking, and biological control has emerged as a possible strategy to manage BFW outbreaks. In this investigation, 109 bacterial strains were isolated from the rhizospheric soil surrounding banana plants in search of potent biological agents against Foc. Strain 91 exhibited the highest antifungal activity against the causal agent of Foc and was identified as Pseudomonas aeruginosa through 16S rRNA gene sequencing and scanning electron microscopy (SEM). Elucidation of strain 91's inhibitory mechanism against Foc revealed a multifaceted antagonistic approach, encompassing the production of bioactive compounds and the secretion of cell wall hydrolytic enzymes. Furthermore, strain 91 displayed various traits associated with promoting plant growth and showed adaptability to different carbon sources. By genetically tagging with constitutively expressing GFP signals, effective colonization of strain 91 was mainly demonstrated in root followed by leaf and stem tissues. Altogether, our study reveals the potential of P. aeruginosa 91 for biocontrol based on inhibition mechanism, adaptation, and colonization features, thus providing a promising candidate for the control of BFW.

The role of plant growth promoting rhizobacteria in strengthening plant resistance to fluoride toxicity: a review

A wide variety of bacteria are present in soil but in rhizospheric area, the majority of microbes helps plant in defending diseases and facilitate nutrient uptake. These microorganisms are supported by plants and they are known as plant growth-promoting rhizobacteria (PGPR). The PGPRs have the potential to replace chemical fertilizers in a way that is more advantageous for the environment. Fluoride (F) is one of the highly escalating, naturally present contaminants that can be hazardous for PGPRs because of its antibacterial capacity. The interactions of F with different bacterial species in groundwater systems are still not well understood. However, the interaction of PGPR with plants in the rhizosphere region reduces the detrimental effects of pollutants and increases plants' ability to endure abiotic stress. Many studies reveal that PGPRs have developed F defense mechanisms, which include efflux pumps, Intracellular sequestration, enzyme modifications, enhanced DNA repair mechanism, detoxification enzymes, ion transporter/antiporters, F riboswitches, and genetic mutations. These resistance characteristics are frequently discovered by isolating PGPRs from high F-contaminated areas or by exposing cells to fluoride in laboratory conditions. Numerous studies have identified F-resistant microorganisms that possess additional F transporters and duplicates of the well-known targets of F. Plants are prone to F accumulation despite the soil's low F content, which may negatively affect their growth and development. PGPRs can be used as efficient F bioremediators for the soil environment. Environmental biotechnology focuses on creating genetically modified rhizobacteria that can degrade F contaminants over time. The present review focuses on a thorough systemic analysis of contemporary biotechnological techniques, such as gene editing and manipulation methods, for improving plant-microbe interactions for F remediation and suggests the importance of PGPRs in improving soil health and reducing the detrimental effects of F toxicity. The most recent developments in the realm of microbial assistance in the treatment of F-contaminated environments are also highlighted.

Recent Advances in Microbial-Assisted Remediation of Cadmium-Contaminated Soil

Soil contamination with cadmium (Cd) is a severe concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Industries such as mining, manufacturing, building, etc., rapidly produce a substantial amount of Cd, posing environmental risks. Cd toxicity in crop plants decreases nutrient and water uptake and translocation, increases oxidative damage, interferes with plant metabolism and inhibits plant morphology and physiology. However, various conventional physicochemical approaches are available to remove Cd from the soil, including chemical reduction, immobilization, stabilization and electro-remediation. Nevertheless, these processes are costly and unfriendly to the environment because they require much energy, skilled labor and hazardous chemicals. In contrasting, contaminated soils can be restored by using bioremediation techniques, which use plants alone and in association with different beneficial microbes as cutting-edge approaches. This review covers the bioremediation of soils contaminated with Cd in various new ways. The bioremediation capability of bacteria and fungi alone and in combination with plants are studied and analyzed. Microbes, including bacteria, fungi and algae, are reported to have a high tolerance for metals, having a 98% bioremediation capability. The internal structure of microorganisms, their cell surface characteristics and the surrounding environmental circumstances are all discussed concerning how microbes detoxify metals. Moreover, issues affecting the effectiveness of bioremediation are explored, along with potential difficulties, solutions and prospects.

Rhizobacterial mediated interactions in Curcuma longa for plant growth and enhanced crop productivity: a systematic review

Turmeric (Curcuma longa L.), a significant commercial crop of the Indian subcontinent is widely used as a condiment, natural dye, and as a cure for different ailments. Various bioactive compounds such as turmerones and curcuminoids have been isolated from C. longa that have shown remarkable medicinal activity against various ailments. However, reduced soil fertility, climatic variations, rapid urbanization, and enhanced food demand, pose a multifaceted challenge to the current agricultural practices of C. longa. Plant growth-promoting microbes play a vital role in plant growth and development by regulating primary and secondary metabolite production. Rhizospheric associations are complex species-specific interconnections of different microbiota with a plant that sustain soil health and promote plant growth through nutrient acquisition, nitrogen fixation, phosphate availability, phytohormone production, and antimicrobial activities. An elaborative study of microbiota associated with the roots of C. longa is essential for rhizospheric engineering as there is a huge potential to develop novel products based on microbial consortium formulations and elicitors to improve plant health, stress tolerance, and the production of secondary metabolites such as curcumin. Primarily, the purpose of this review is to implicate the rhizospheric microbial flora as probiotics influencing overall C. longa health, development, and survival for an increase in biomass, enhanced yield of secondary metabolites, and sustainable crop production.

Effect of endophytic diazotroph Enterobacter roggenkampii ED5 on nitrogen-metabolism-related microecology in the sugarcane rhizosphere at different nitrogen levels

Sugarcane is an important sugar and energy crop worldwide, requiring a large amount of nitrogen (N). However, excessive application of synthetic N fertilizer causes environmental pollution in farmland. Endophytic nitrogen-fixing bacteria (ENFB) provide N nutrition for plants through biological N fixation, thus reducing the need for chemical fertilizers. The present study investigated the effect of the N-fixing endophytic strain Enterobacter roggenkampii ED5 on phytohormone indole-3-acetic acid (IAA), N-metabolism enzyme activities, microbial community compositions, and N cycle genes in sugarcane rhizosphere soil at different N levels. Three levels of 15N-urea, such as low N (0 kg/ha), medium N (150 kg/ha), and high N (300 kg/ha), were applied. The results showed that, after inoculating strain ED5, the IAA content in sugarcane leaves was significantly increased by 68.82% under low N condition at the seedling stage (60 days). The nitrate reductase (NR) activity showed a downward trend. However, the glutamine synthase (GS) and NADH-glutamate dehydrogenase (NADH-GDH) activities were significantly enhanced compared to the control under the high N condition, and the GS and NR genes had the highest expression at 180 and 120 days, respectively, at the low N level. The total N content in the roots, stems, and leaves of sugarcane was higher than the control. The 15N atom % excess of sugarcane decreased significantly under medium N condition, indicating that the medium N level was conducive to N fixation in strain ED5. Metagenome analysis of sugarcane rhizosphere soil exhibited that the abundance of N-metabolizing microbial richness was increased under low and high N conditions after inoculation of strain ED5 at the genus level, while it was increased at the phylum level only under the low N condition. The LefSe (LDA > 2, p < 0.05) found that the N-metabolism-related differential microorganisms under the high N condition were higher than those under medium and low N conditions. It was also shown that the abundance of nifDHK genes was significantly increased after inoculation of ED5 at the medium N level, and other N cycle genes had high abundance at the high N level after inoculation of strain ED5. The results of this study provided a scientific reference for N fertilization in actual sugarcane production.

Engineered Sucrose Metabolism Improves the Smut Disease Suppression Potency of Pseudomonas sp. ST4

Sporisorium scitamineum and Ustilago maydis are two fungal pathogens causing severe sugarcane and maize diseases, respectively. Sexual mating of compatible sporidia is essential for these pathogens to form infections dikaryotic mycelia and cause smut diseases. We showed recently that in the presence of exogenous glucose, the Pseudomonas sp. strain ST4 could block the fungal mating and display a strong disease suppression potency on S. scitamineum. With the aim of conferring strain ST4 the ability to metabolize sucrose in plants for glucose production, we identified a strong native promoter pSsrA in strain ST4 and additional promoter elements to facilitate translation and peptide translocation for the construction of a fusion gene encoding sucrose metabolism. The cscA gene encoding sucrose hydrolase from Pseudomonas protegens Pf-5 was fused to the promoter pSsrA, a translational coupler bicistronic design and a Tat signal peptide, which was then cloned into mini-Tn7 transposon. This synthetic gene cassette was integrated into the chromosome of strain ST4, and the resultant engineered strain ST4E was able to hydrolyze sucrose with high efficiency and displayed elevated inhibitory activity on the mating and virulence of S. scitamineum and U. maydis. The findings from this study provide a valuable device and useful clues for the engineering of sucrose metabolism in non- or weak-sucrose-utilizing bacterial strains and present an improved biocontrol agent against plant smut pathogens. IMPORTANCE Sporisorium scitamineum and Ustilago maydis are typical dimorphic fungi causing severe sugarcane and maize smut diseases, respectively. Sexual mating of compatible sporidia is essential for these pathogens to form infections dikaryotic mycelia and cause smut diseases. We previously demonstrated that the biocontrol strain Pseudomonas sp. ST4 could block the fungal mating and displays a strong suppression potency on smut diseases, while it was unable to utilize the host-sourced sucrose for glucose production critical for antifungus efficiency. In this study, we constructed a high-expression gene cassette for minitransposon-mediated genome integration and sucrose hydrolysis in the bacterial periplasmic space. The resultant engineered strain ST4E was able to hydrolyze sucrose and inhibit the mating and hyphal growth of S. scitamineum and U. maydis. These findings provide a valuable tool and useful clues for the engineering of sucrose metabolism in non- or weak-sucrose-utilizing bacterial strains and present an improved biocontrol agent against plant smut pathogens.

Soil chemistry, metabarcoding, and metabolome analyses reveal that a sugarcane-Dictyophora indusiata intercropping system can enhance soil health by reducing soil nitrogen loss

Introduction

Greater amounts of fertilizer are applied every year to meet the growing demand for food. Sugarcane is one of the important food sources for human beings.

Methods

Here, we evaluated the effects of a sugarcane-Dictyophora indusiata (DI) intercropping system on soil health by conducting an experiment with three different treatments: (1) bagasse application (BAS process), (2) bagasse + DI (DIS process), and (3) the control (CK). We then analyzed soil chemistry, the diversity of soil bacteria and fungi, and the composition of metabolites to clarify the mechanism underlying the effects of this intercropping system on soil properties.

Results and discussion

Soil chemistry analyses revealed that the content of several soil nutrients such as nitrogen (N) and phosphorus (P) was higher in the BAS process than in the CK. In the DIS process, a large amount of soil P was consumed by DI. At the same time, the urease activity was inhibited, thus slowing down the loss of soil in the DI process, while the activity of other enzymes such as β-glucosidase and laccase was increased. It was also noticed that the content of lanthanum and calcium was higher in the BAS process than in the other treatments, and DI did not significantly alter the concentrations of these soil metal ions. Bacterial diversity was higher in the BAS process than in the other treatments, and fungal diversity was lower in the DIS process than in the other treatments. The soil metabolome analysis revealed that the abundance of carbohydrate metabolites was significantly lower in the BAS process than in the CK and the DIS process. The abundance of D(+)-talose was correlated with the content of soil nutrients. Path analysis revealed that the content of soil nutrients in the DIS process was mainly affected by fungi, bacteria, the soil metabolome, and soil enzyme activity. Our findings indicate that the sugarcane-DIS intercropping system can enhance soil health.

The impact of novel azotobacter Bacillus sp. T28 combined sea buckthorn pomace on microbial community structure in paddy soil

Nitrogen (N) fertilizer application is an essential part of agricultural production in order to improve rice yields. However, long-term irrational application and low utilization of N fertilizer have caused a series of environmental problems. Biofertilizer is considered an effective alternative to N fertilizer. In this study, the effect of biofertilizer made of diazotrophic bacteria Bacillus sp. T28 combined with sea buckthorn pomace on the soil N changes and microbial community structure was conducted. Compared to CK, NO₃^--N content decreased 33.1%-43.8% and the rate of N₂O release decreased 8-26 times under different fertilizer treatments during incubation of 0-7 days. On the contrary, NH₄⁺-N in T28 with or without sea buckthorn pomace treatments increased by 56.5-118.8% during incubation of 7-14 days. The results indicated that this biofertilizer reduced the environmental risk associated with the accumulation of NO₃^--N in paddy soil and the release of N₂O to the atmosphere and maintained the soil available N supply capacity. Besides, applying Bacillus T28 with sea buckthorn pomace increased the abundance of soil N functional genes such as nifH, narG, nirS, nirK, and nosZ. The ¹³C-PLFAs results demonstrated that this biofertilizer improves soil microbial community diversity, nutrient turnover rate and ecosystem stability by altering soil pH and total carbon (TC). In conclusion, Bacillus sp. T28 combined with sea buckthorn pomace regulated the indigenous soil microbial community structure and mitigated the environmental risk of conventional N fertilization in agroecosystems.

Inoculation with Plant Growth-Promoting Bacteria and Nitrogen Doses Improves Wheat Productivity and Nitrogen Use Efficiency

Wheat is one of the staple foods of the global population due to its adaptability to a wide range of environments. Nitrogen is one of the crucial limiting factors in wheat production and is considered a challenge to food security. Therefore, sustainable agricultural technologies such as seed inoculation with plant growth-promoting bacteria (PGPBs) can be adopted to promote biological nitrogen fixation (BNF) for higher crop productivity. In this context, the objective of the current study was to evaluate the effects of nitrogen fertilization and seed inoculations with Azospirillum brasilense, Bacillus subtilis and A. brasilense + B. subtilis on agronomic and yield attributes, grain yield, grain N accumulation, N use efficiency and applied N recovery in Brazilian Cerrado, which consists of gramineous woody savanna. The experiment was carried out in two cropping seasons in Rhodic Haplustox soil under a no-tillage system. The experiment was designed in a randomized complete block in a 4 × 5 factorial scheme, with four replications. The treatments consisted of four seed inoculations (control-without inoculation, inoculation with A. brasilense, B. subtilis and A. brasilense + B. subtilis) under five N doses (0, 40, 80, 120 and 160 kg ha^-1, applied from urea) at the wheat tillering stage. Seed co-inoculation with A. brasilense + B. subtilis increased grain N accumulation, number of spikes m^-1, grains spike^-1 and grain yield of wheat in an irrigated no-tillage system of tropical savannah, regardless of the applied N doses. Nitrogen fertilization at a dose of 80 kg ha^-1 significantly increased grain N accumulation and number of grains spikes^-1 and nitrogen use efficiency. Recovery of applied N was increased with inoculation of B. subtilis and co-inoculation of A. brasilense + B. subtilis at increasing N doses. Therefore, N fertilization can be reduced by the inclusion of co-inoculation with A. brasilense + B. subtilis in the cultivation of winter wheat under a no-tillage system of Brazilian Cerrado.

Antimicrobial activity and comparative metabolomic analysis of Priestia megaterium strains derived from potato and dendrobium

The growth of endophytic bacteria is influenced by the host plants and their secondary metabolites and activities. In this study, P. megaterium P-NA14 and P. megaterium D-HT207 were isolated from potato tuber and dendrobium stem respectively. They were both identified as Priestia megaterium. The antimicrobial activities and metabolites of both strains were explored. For antimicrobial activities, results showed that P. megaterium P-NA14 exhibited a stronger inhibition effect on the pathogen of dendrobium, while P. megaterium D-HT207 exhibited a stronger inhibition effect on the pathogen of potato. The supernatant of P. megaterium P-NA14 showed an inhibition effect only on Staphylococcus aureus, while the sediment of P. megaterium D-HT207 showed an inhibition effect only on Escherichia coli. For metabolomic analysis, the content of L-phenylalanine in P. megaterium P-NA14 was higher than that of P. megaterium D-HT207, and several key downstream metabolites of L-phenylalanine were associated with inhibition of S. aureus including tyrosine, capsaicin, etc. Therefore, we speculated that the different antimicrobial activities between P. megaterium P-NA14 and P. megaterium D-HT207 were possibly related to the content of L-phenylalanine and its metabolites. This study preliminarily explored why the same strains isolated from different hosts exhibit different activities from the perspective of metabolomics.

Impact of intercropping grass on the soil rhizosphere microbial community and soil ecosystem function in a walnut orchard

The intercropping of grass in orchards has beneficial effects on soil properties and soil microbial communities and is an important soil management measure for improving orchard productivity and land-use efficiency. However, few studies have explored the effects of grass intercropping on rhizosphere microorganisms in walnut orchards. In this study, we explored the microbial communities of clear tillage (CT), walnut/ryegrass (Lolium perenne L.) (Lp), and walnut/hairy vetch (Vicia villosa Roth.) (Vv) intercropping system using MiSeq sequencing and metagenomic sequencing. The results revealed that the composition and structure of the soil bacterial community changed significantly with walnut/Vv intercropping compared to CT and walnut/Lp intercropping. Moreover, the walnut/hairy vetch intercropping system had the most complex connections between bacterial taxa. In addition, we found that the soil microorganisms of walnut/Vv intercropping had a higher potential for nitrogen cycling and carbohydrate metabolism, which may be related to the functions of Burkholderia, Rhodopseudomonas, Pseudomonas, Agrobacterium, Paraburkholderia, and Flavobacterium. Overall, this study provided a theoretical basis for understanding the microbial communities associated with grass intercropping in walnut orchards, providing better guidance for the management of walnut orchards.

Biological nitrogen fixation in cereal crops: Progress, strategies, and perspectives

Nitrogen is abundant in the atmosphere but is generally the most limiting nutrient for plants. The inability of many crop plants, such as cereals, to directly utilize freely available atmospheric nitrogen gas means that their growth and production often rely heavily on the application of chemical fertilizers, which leads to greenhouse gas emissions and the eutrophication of water. By contrast, legumes gain access to nitrogen through symbiotic association with rhizobia. These bacteria convert nitrogen gas into biologically available ammonia in nodules through a process termed symbiotic biological nitrogen fixation, which plays a decisive role in ecosystem functioning. Engineering cereal crops that can fix nitrogen like legumes or associate with nitrogen-fixing microbiomes could help to avoid the problems caused by the overuse of synthetic nitrogen fertilizer. With the development of synthetic biology, various efforts have been undertaken with the aim of creating so-called "N-self-fertilizing" crops capable of performing autonomous nitrogen fixation to avoid the need for chemical fertilizers. In this review, we briefly summarize the history and current status of engineering N-self-fertilizing crops. We also propose several potential biotechnological approaches for incorporating biological nitrogen fixation capacity into non-legume plants.

A Metagenomic Based Approach on Abundance and Diversity of Bacterial Communities Across the Life Stages of Culicoides peregrinus (Diptera: Ceratopogonidae) a Vector of Bluetongue Virus

During larval rearing of Culicoides peregrinus Kieffer (Diptera: Ceratopogonidae) it was obligatory to add a small quantity of mud from larval habitat to nutrient broth in culture plates. This initiated microbial growth in rearing plates which facilitated growth and development of immature. The primary aim was to enumerate gut microbial communities across the different life stages of C. peregrinus. Amplicon sequencing of the V3-V4 hypervariable region (16S rDNA) was done on Illumina Miseq platform to detect gut bacterial communities at different life stages, while ITS regions (18S rRNA) were targeted for fungal communities of the 4th instar larvae. The major findings were: 1) Phylum Proteobacteria and Firmicutes were the most abundant throughout the life stages, along with the highest bacterial alpha diversity in the egg, 2) bacterial compositions were similar to laboratory reared and field collected adults, and 3) abundant fungal phyla associated with the larval gut were Ascomycota and Basidiomycota. Furthermore, analyses of the gut microbiome with METAGENassist might be indicative of their likely function in the natural habitat. Abundant gut-associated bacteria and/or fungal genera detected in the present study could be used as dietary supplements to establish laboratory colonies for further vectorial research. While, individual roles of the bacteria or fungi in paratransgenesis are warned for their possible utilization to frame the management strategy in upcoming works.

PGPR: the treasure of multifarious beneficial microorganisms for nutrient mobilization, pest biocontrol and plant growth promotion in field crops

Plant growth-promoting rhizobacteria (PGPR) have multifarious beneficial activities for plant growth promotion; act as source of metabolites, enzymes, nutrient mobilization, biological control of pests, induction of disease resistance vis-a-vis bioremediation potentials by phytoextraction and detoxification of heavy metals, pollutants and pesticides. Agrochemicals and synthetic pesticides are currently being utilized widely in all major field crops, thereby adversely affecting human and animal health, and posing serious threats to the environments. Beneficial microorganisms like PGPR could potentially substitute and supplement the toxic chemicals and pesticides with promising application in organic farming leading to sustainable agriculture practices and bioremediation of heavy metal contaminated sites. Among field crops limited bio-formulations have been prepared till now by utilization of PGPR strains having plant growth promotion, metabolites, enzymes, nutrient mobilization and biocontrol activities. The present review contributes comprehensive description of PGPR applications in field crops including commercial, oilseeds, leguminous and cereal crops to further extend the utilization of these potent groups of beneficial microorganisms so that even higher level of crop productivity and quality produce of field crops could be achieved. PGPR and bacteria based commercialized bio-formulations available worldwide for its application in the field crops have been compiled in this review which can be a substitute for the harmful synthetic chemicals. The current knowledge gap and potential target areas for future research have also been projected.

Enhancing plant growth promoting rhizobacterial activities through consortium exposure: A review

Plant Growth Promoting Rhizobacteria (PGPR) has gained immense importance in the last decade due to its in-depth study and the role of the rhizosphere as an ecological unit in the biosphere. A putative PGPR is considered PGPR only when it may have a positive impact on the plant after inoculation. From the various pieces of literature, it has been found that these bacteria improve the growth of plants and their products through their plant growth-promoting activities. A microbial consortium has a positive effect on plant growth-promoting (PGP) activities evident by the literature. In the natural ecosystem, rhizobacteria interact synergistically and antagonistically with each other in the form of a consortium, but in a natural consortium, there are various oscillating environmental conditions that affect the potential mechanism of the consortium. For the sustainable development of our ecological environment, it is our utmost necessity to maintain the stability of the rhizobacterial consortium in fluctuating environmental conditions. In the last decade, various studies have been conducted to design synthetic rhizobacterial consortium that helps to integrate cross-feeding over microbial strains and reveal their social interactions. In this review, the authors have emphasized covering all the studies on designing synthetic rhizobacterial consortiums, their strategies, mechanism, and their application in the field of environmental ecology and biotechnology.

Impact of carbendazim on cellular growth, defence system and plant growth promoting traits of Priestia megaterium ANCB-12 isolated from sugarcane rhizosphere

Agrochemicals are consistently used in agricultural practices to protect plants from pathogens and ensure high crop production. However, their overconsumption and irregular use cause adverse impacts on soil flora and non-target beneficial microorganisms, ultimately causing a hazard to the ecosystem. Taking this into account, the present study was conducted to determine the high dosage of fungicide (carbendazim: CBZM) effects on the rhizobacteria survival, plant growth promoting trait and reactive oxygen species (ROS) scavenging antioxidant enzyme system. Thus, a multifarious plant growth promoting rhizobacteria (PGPR) isolate, ANCB-12, was obtained from the sugarcane rhizosphere through an enrichment technique. The taxonomic position of the isolated rhizobacteria was confirmed through 16S rRNA gene sequencing analysis as Priestia megaterium ANCB-12 (accession no. ON878101). Results showed that increasing concentrations of fungicide showed adverse effects on rhizobacterial cell growth and survival. In addition, cell visualization under a confocal laser scanning microscope (CLSM) revealed more oxidative stress damage in the form of ROS generation and cell membrane permeability. Furthermore, the increasing dose of CBZM gradually decreased the plant growth promoting activities of the rhizobacteria ANCB-12. For example, CBZM at a maximum 3,000 μg/ml concentration decreases the indole acetic acid (IAA) production by 91.6%, ACC deaminase by 92.3%, and siderophore production by 94.1%, respectively. Similarly, higher dose of fungicide enhanced the ROS toxicity by significantly (p < 0.05) modulating the stress-related antioxidant enzymatic biomarkers in P. megaterium ANCB-12. At a maximum 3,000 μg/ml CBZM concentration, the activity of superoxide dismutase (SOD) declined by 82.3%, catalase (CAT) by 61.4%, glutathione peroxidase (GPX) by 76.1%, and glutathione reductase (GR) by 84.8%, respectively. The results of this study showed that higher doses of the fungicide carbendazim are toxic to the cells of plant-beneficial rhizobacteria. This suggests that a recommended dose of fungicide should be made to lessen its harmful effects.

Endophytic nitrogen-fixing bacteria DX120E inoculation altered the carbon and nitrogen metabolism in sugarcane

Endophytic nitrogen-fixing bacteria are versatile and widely distributed in plants. Numerous strains of endophytic nitrogen-fixing bacteria are used as biofertilizers to minimize the utilization of chemical fertilizers, improve nutrient use efficiency, increase crop productivity, and reduce environmental pollution. However, the mechanism underlying the interaction between nitrogen-fixing bacteria and plants is still unclear. So, the present study was planned to assess the effects of endophytic nitrogen-fixing bacteria on sugarcane by analyzing the changes in physiological and biochemical activities. In the current study, Klebsiella variicola DX120E, an endophytic nitrogen-fixing bacterium, was inoculated on sugarcane varieties B8 and ROC22 to evaluate the effects on nitrogen and carbon metabolism-related enzymatic activity and biomass. Results showed that DX120E inoculation improved the enzymatic activities related to gluconeogenesis and nitrogen metabolism increased the sugarcane plant’s height, cane juice Brix, biomass, chlorophyll, and soluble sugar content in sugarcane. Metabolomics analysis revealed that the metabolome modules were highly enriched in carbon and nitrogen metabolic pathways of strain-affected sugarcane than uninoculated control. The identified carbohydrates were associated with the glycolysis or gluconeogenesis and tricarboxylic acid (TCA) cycle in plants. Metabolomic profiling in the present investigation showed that carbohydrate metabolism is coordinated with nitrogen metabolism to provide carbon skeletons and energy to amino acid synthesis, and amino acid degradation results in several metabolites used by the citric acid cycle as an energy source. Moreover, differentially expressed metabolites of non-proteinogenic amino acids have a further complementary role to the action of endophytic nitrogen-fixing bacteria. Meanwhile, a significant difference in metabolites and metabolic pathways present in stems and leaves of B8 and ROC22 varieties was found. This study discovered the potential benefits of DX120E in sugarcane and suggested candidate regulatory elements to enhance interactions between nitrogen-fixing microbes and sugarcane.

Mechanistic Insights and Potential Use of Siderophores Producing Microbes in Rhizosphere for Mitigation of Stress in Plants Grown in Degraded Land

Plant growth performance under a stressful environment, notably in the agriculture field, is directly correlated with the rapid growth of the human population, which triggers the pressure on crop productivity. Plants perceived many stresses owing to degraded land, which induces low plant productivity and, therefore, becomes a foremost concern for the future to face a situation of food scarcity. Land degradation is a very notable environmental issue at the local, regional, and global levels for agriculture. Land degradation generates global problems such as drought desertification, heavy metal contamination, and soil salinity, which pose challenges to achieving many UN Sustainable Development goals. The plant itself has a varied algorithm for the mitigation of stresses arising due to degraded land; the rhizospheric system of the plant has diverse modes and efficient mechanisms to cope with stress by numerous root-associated microbes. The suitable root-associated microbes and components of root exudate interplay against stress and build adaptation against stress-mediated mechanisms. The problem of iron-deficient soil is rising owing to increasing degraded land across the globe, which hampers plant growth productivity. Therefore, in the context to tackle these issues, the present review aims to identify plant-stress status owing to iron-deficient soil and its probable eco-friendly solution. Siderophores are well-recognized iron-chelating agents produced by numerous microbes and are associated with the rhizosphere. These siderophore-producing microbes are eco-friendly and sustainable agents, which may be managing plant stresses in the degraded land. The review also focuses on the molecular mechanisms of siderophores and their chemistry, cross-talk between plant root and siderophores-producing microbes to combat plant stress, and the utilization of siderophores in plant growth on degraded land.

Unraveling Nitrogen Fixing Potential of Endophytic Diazotrophs of Different Saccharum Species for Sustainable Sugarcane Growth

Sugarcane (Saccharum officinarum L.) is one of the world’s highly significant commercial crops. The amounts of synthetic nitrogen (N₂) fertilizer required to grow the sugarcane plant at its initial growth stages are higher, which increases the production costs and adverse environmental consequences globally. To combat this issue, sustainable environmental and economic concerns among researchers are necessary. The endophytic diazotrophs can offer significant amounts of nitrogen to crops through the biological nitrogen fixation mediated nif gene. The nifH gene is the most extensively utilized molecular marker in nature for studying N₂ fixing microbiomes. The present research intended to determine the existence of novel endophytic diazotrophs through culturable and unculturable bacterial communities (EDBCs). The EDBCs of different tissues (root, stem, and leaf) of five sugarcane cultivars (Saccharum officinarum L. cv. Badila, S. barberi Jesw.cv Pansahi, S. robustum, S. spontaneum, and S. sinense Roxb.cv Uba) were isolated and molecularly characterized to evaluate N₂ fixation ability. The diversity of EDBCs was observed based on nifH gene Illumina MiSeq sequencing and a culturable approach. In this study, 319766 operational taxonomic units (OTUs) were identified from 15 samples. The minimum number of OTUs was recorded in leaf tissues of S. robustum and maximum reads in root tissues of S. spontaneum. These data were assessed to ascertain the structure, diversity, abundance, and relationship between the microbial community. A total of 40 bacterial families with 58 genera were detected in different sugarcane species. Bacterial communities exhibited substantially different alpha and beta diversity. In total, 16 out of 20 genera showed potent N₂-fixation in sugarcane and other crops. According to principal component analysis (PCA) and hierarchical clustering (Bray–Curtis dis) evaluation of OTUs, bacterial microbiomes associated with root tissues differed significantly from stem and leaf tissues of sugarcane. Significant differences often were observed in EDBCs among the sugarcane tissues. We tracked and validated the plethora of individual phylum strains and assessed their nitrogenase activity with a culture-dependent technique. The current work illustrated the significant and novel results of many uncharted endophytic microbial communities in different tissues of sugarcane species, which provides an experimental system to evaluate the biological nitrogen fixation (BNF) mechanism in sugarcane. The novel endophytic microbial communities with N₂-fixation ability play a remarkable and promising role in sustainable agriculture production.

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.

High-Throughput Sequencing-Based Analysis of Rhizosphere and Diazotrophic Bacterial Diversity Among Wild Progenitor and Closely Related Species of Sugarcane (Saccharum spp. Inter-Specific Hybrids)

Considering the significant role of genetic background in plant-microbe interactions and that most crop rhizospheric microbial research was focused on cultivars, understanding the diversity of root-associated microbiomes in wild progenitors and closely related crossable species may help to breed better cultivars. This study is aimed to fill a critical knowledge gap on rhizosphere and diazotroph bacterial diversity in the wild progenitors of sugarcane, the essential sugar and the second largest bioenergy crop globally. Using a high-throughput sequencing (HTS) platform, we studied the rhizosphere and diazotroph bacterial community of Saccharum officinarum L. cv. Badila (BRS), Saccharum barberi (S. barberi) Jesw. cv Pansahi (PRS), Saccharum robustum [S. robustum; (RRS), Saccharum spontaneum (S. spontaneum); SRS], and Saccharum sinense (S. sinense) Roxb. cv Uba (URS) by sequencing their 16S rRNA and nifH genes. HTS results revealed that a total of 6,202 bacteria-specific operational taxonomic units (OTUs) were identified, that were distributed as 107 bacterial groups. Out of that, 31 rhizobacterial families are commonly spread in all five species. With respect to nifH gene, S. barberi and S. spontaneum recorded the highest and lowest number of OTUs, respectively. These results were validated by quantitative PCR analysis of both genes. A total of 1,099 OTUs were identified for diazotrophs with a core microbiome of 9 families distributed among all the sugarcane species. The core microbiomes were spread across 20 genera. The increased microbial diversity in the rhizosphere was mainly due to soil physiochemical properties. Most of the genera of rhizobacteria and diazotrophs showed a positive correlation, and few genera negatively correlated with the soil properties. The results showed that sizeable rhizospheric diversity exists across progenitors and close relatives. Still, incidentally, the rhizosphere microbial abundance of progenitors of modern sugarcane was at the lower end of the spectrum, indicating the prospect of Saccharum species introgression breeding may further improve nutrient use and disease and stress tolerance of commercial sugarcane. The considerable variation for rhizosphere microbiome seen in Saccharum species also provides a knowledge base and an experimental system for studying the evolution of rhizobacteria-host plant association during crop domestication.

Root-Derived Endophytic Diazotrophic Bacteria Pantoea cypripedii AF1 and Kosakonia arachidis EF1 Promote Nitrogen Assimilation and Growth in Sugarcane

Excessive, long-term application of chemical fertilizers in sugarcane crops disrupts soil microbial flora and causes environmental pollution and yield decline. The role of endophytic bacteria in improving crop production is now well-documented. In this study, we have isolated and identified several endophytic bacterial strains from the root tissues of five sugarcane species. Among them, eleven Gram-negative isolates were selected and screened for plant growth-promoting characteristics, i.e., production of siderophores, indole-3-acetic acid (IAA), ammonia, hydrogen cyanide (HCN), and hydrolytic enzymes, phosphorus solubilization, antifungal activity against plant pathogens, nitrogen-fixation, 1-aminocyclopropane-1-carboxylic acid deaminase activity, and improving tolerance to different abiotic stresses. These isolates had nifH (11 isolates), acdS (8 isolates), and HCN (11 isolates) genes involved in N-fixation, stress tolerance, and pathogen biocontrol, respectively. Two isolates Pantoea cypripedii AF1and Kosakonia arachidis EF1 were the most potent strains and they colonized and grew in sugarcane plants. Both strains readily colonized the leading Chinese sugarcane variety GT42 and significantly increased the activity of nitrogen assimilation enzymes (glutamine synthetase, NADH glutamate dehydrogenase, and nitrate reductase), chitinase, and endo-glucanase and the content of phytohormones gibberellic acid, indole-3-acetic acid, and abscisic acid. The gene expression analysis of GT42 inoculated with isolates of P. cypripedii AF1 or K. arachidis EF1 showed increased activity of nifH and nitrogen assimilation genes. Also, the inoculated diazotrophs significantly increased plant nitrogen content, which was corroborated by the 15N isotope dilution analysis. Collectively, these findings suggest that P. cypripedii and K. arachidis are beneficial endophytes that could be used as a biofertilizer to improve plant nitrogen nutrition and growth of sugarcane. To the best of our knowledge, this is the first report of sugarcane growth enhancement and nitrogen fixation by Gram-negative sugarcane root-associated endophytic bacteria P. cypripedii and K. arachidis. These strains have the potential to be utilized as sugarcane biofertilizers, thus reducing nitrogen fertilizer use and improving disease management.

Insights into the Bacterial and Nitric Oxide-Induced Salt Tolerance in Sugarcane and Their Growth-Promoting Abilities

Soil salinity causes severe environmental stress that affects agriculture production and food security throughout the world. Salt-tolerant plant-growth-promoting rhizobacteria (PGPR) and nitric oxide (NO), a distinctive signaling molecule, can synergistically assist in the alleviation of abiotic stresses and plant growth promotion, but the mechanism by which this happens is still not well known. In the present study, in a potential salt-tolerant rhizobacteria strain, ASN-1, growth up to 15% NaCl concentration was achieved with sugarcane rhizosphere soil. Based on 16S-rRNA gene sequencing analysis, the strain ASN-1 was identified as a Bacillus xiamenensis. Strain ASN-1 exhibits multiple plant-growth-promoting attributes, such as the production of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, siderophores, HCN, ammonia, and exopolysaccharides as well as solubilized phosphate solubilization. Biofilm formation showed that NO enhanced the biofilm and root colonization capacity of the PGPR strain ASN-1 with host plants, evidenced by scanning electron microscopy. The greenhouse study showed that, among the different treatments, the combined application of PGPR and sodium nitroprusside (SNP) as an NO donor significantly (p ≤ 0.05) enhanced sugarcane plant growth by maintaining the relative water content, electrolyte leakage, gas exchange parameters, osmolytes, and Na⁺/K⁺ ratio. Furthermore, PGPR and SNP fertilization reduced the salinity-induced oxidative stress in plants by modulating the antioxidant enzyme activities and stress-related gene expression. Thus, it is believed that the acquisition of advanced information about the synergistic effect of salt-tolerant PGPR and NO fertilization will reduce the use of harmful chemicals and aid in eco-friendly sustainable agricultural production under salt stress conditions.

Different Amounts of Nitrogen Fertilizer Applications Alter the Bacterial Diversity and Community Structure in the Rhizosphere Soil of Sugarcane

Sugarcane cropping systems receive elevated application of nitrogen (N) fertilizer for higher production, which may affect production costs and cause environmental pollution. Therefore, it is critical to elucidate the response of soil microbial to N fertilizer inputs in sugarcane soil. A field experiment was carried out to investigate the effects of optimum (N375, 375 kg N/ha) and excessive (N563, 563 kg N/ha) amounts of N fertilizer on soil bacterial diversity and community structure in a sugarcane cropping system by MiSeq high-throughput sequencing; 50,007 operational taxonomic units (OTUs) were obtained by sequencing the 16S rRNA gene amplicons. Results showed that the most abundant phyla in the sugarcane rhizosphere soil were Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, whose ensemble mean accounted for 74.29%. Different amounts of N application indeed change the bacterial diversity and community structures. Excessive application of N fertilizers significantly decreased the pH and increased the available N in soils and unexpectedly obtained a lower yield. Excessive N resulted in a relatively lower bacterial species richness and significantly increased the relative abundance of phyla Proteobacteria, Acidobacteria, and Bacteroidetes and the genera Sphingomonas and Gemmatimonas, while optimum N treatment significantly increased the phylum Actinobacteria and the genera Bacillus and Nitrospira (P < 0.05). N application shifted the N cycle in nitrification, mainly on the Nitrospira, but showed no significant effect on the genera related to nitrogen fixation, methane oxidation, sulfate reduction, and sulfur oxidation (P > 0.05). Overall, the optimum amount of N application might be conducive to beneficial microorganisms, such as Actinobacteria, Nitrospira, and Bacillus and, thus, result in a healthier ecosystem and higher sustainable crop production.

Profiles of Bacillus spp. Isolated from the Rhizosphere of Suaeda glauca and Their Potential to Promote Plant Growth and Suppress Fungal Phytopathogens

Members of the genus Bacillus are known to play an important role in promoting plant growth and protecting plants against phytopathogenic microorganisms. In this study, 21 isolates of Bacillus spp. were obtained from the root micro-ecosystem of Suaeda glauca. Analysis of the 16S rRNA genes indicated that the isolates belong to the species Bacillus amyloliquefaciens, Bacillus velezensis, Bacillus subtilis, Bacillus pumilus, Bacillus aryabhattai and Brevibacterium frigoritolerans. One of the interesting findings of this study is that the four strains B1, B5, B16 and B21 are dominant in rhizosphere soil. Based on gyrA, gyrB, and rpoB gene analyses, B1, B5, and B21 were identified as B. amyloliquefaciens and B16 was identified as B. velezensis. Estimation of antifungal activity showed that the isolate B1 had a significant inhibitory effect on Fusarium verticillioides, B5 and B16 on Colletotrichum capsici (syd.) Butl, and B21 on Rhizoctonia cerealis van der Hoeven. The four strains grew well in medium with 1-10% NaCl, a pH value of 5-8, and promoted the growth of Arabidopsis thaliana. Our results indicate that these strains may be promising agents for the biocontrol and promotion of plant growth and further study of the relevant bacteria will provide a useful reference for the development of microbial resources.

A Thermotolerant Marine Bacillus amyloliquefaciens S185 Producing Iturin A5 for Antifungal Activity against Fusarium oxysporum f. sp. cubense

Fusarium wilt of banana (also known as Panama disease), is a severe fungal disease caused by soil-borne Fusarium oxysporum f. sp. cubense (Foc). In recent years, biocontrol strategies using antifungal microorganisms from various niches and their related bioactive compounds have been used to prevent and control Panama disease. Here, a thermotolerant marine strain S185 was identified as Bacillus amyloliquefaciens, displaying strong antifungal activity against Foc. The strain S185 possesses multiple plant growth-promoting (PGP) and biocontrol utility properties, such as producing indole acetic acid (IAA) and ammonia, assimilating various carbon sources, tolerating pH of 4 to 9, temperature of 20 to 50 °C, and salt stress of 1 to 5%. Inoculation of S185 colonized the banana plants effectively and was mainly located in leaf and root tissues. To further investigate the antifungal components, compounds were extracted, fractionated, and purified. One compound, inhibiting Foc with minimum inhibitory concentrations (MICs) of 25 μg/disk, was identified as iturin A5 by high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) and nuclear magnetic resonance (NMR). The isolated iturin, A5, resulted in severe morphological changes during spore germination and hyphae growth of Foc. These results specify that B. amyloliquefaciens S185 plays a key role in preventing the Foc pathogen by producing the antifungal compound iturin A5, and possesses potential as a cost-effective and sustainable biocontrol strain for Panama disease in the future. This is the first report of isolation of the antifungal compound iturin A5 from thermotolerant marine B. amyloliquefaciens S185.

Deciphering distinct biological control and growth promoting potential of multi-stress tolerant Bacillus subtilis PM32 for potato stem canker

Plant growth-promoting rhizobacteria (PGPR) represent a set of microorganisms that play significant role in improving plant growth and controlling the phytopathogens. Unpredictable performance after the application of PGPR has been observed when these were shifted from in-vitro to in-vivo conditions due to the prevalence of various abiotic stress conditions. During growing period, the potato crop is subjected to a combination of biotic and abiotic stresses. Rhizoctonia solani, a soil-borne plant pathogen, causes reduced vigor and yield of potato crop worldwide. In the current study, multi-stress-tolerant rhizobacterial strain, Bacillus subtilis PM32, was isolated from field-grown potato with various plant growth promoting (PGP) traits including zinc and potassium solubilization, biological nitrogen fixation, ammonia and siderophore, as well as extracellular enzyme productions (cellulase, catalase, amylase, protease, pectinase, and chitinase). The strain PM32 exhibited a distinct potential to support plant growth by demonstrating production of indole-3-acetic acid (102.6 μM/mL), ACC-deaminase activity (1.63 μM of α-ketobutyrate/h/mg protein), and exopolysaccharides (2.27 mg/mL). By retarding mycelial growth of R. solani the strain PM32 drastically reduced pathogenicity of R. solani. The strain PM32 also suppressed the pathogenic activity significantly by impeding mycelial expansion of R. solani with inhibition co-efficient of 49.87. The B. subtilis PM32 also depicted significant tolerance towards salt, heavy metal (Pb), heat and drought stress. PCR based amplification of ituC and acds genes coding for iturin and ACC-deaminase activity respectively indicated potential of strain PM32 for lipopeptides production and ACC deaminase enzyme activity. Results of both in-vitro and pot experiments under greenhouse conditions depicted the efficiency of B. subtilis PM32 as a promising bio-control agent for R. solani infection together with enhanced growth of potato plants as deciphered from biomass accumulation, chlorophyll a, b, and carotenoid contents. Therefore, it was envisioned that application of indigenous multi-stress tolerant PGPR may serve to induce biotic and abiotic stress tolerance in crops/plants for pathogen control and sustainable global food supply.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01067-2.

The "beauty in the beast"-the multiple uses of Priestia megaterium in biotechnology

Abstract

Over 30 years, the Gram-positive bacterium Priestia megaterium (previously known as Bacillus megaterium) was systematically developed for biotechnological applications ranging from the production of small molecules like vitamin B₁₂, over polymers like polyhydroxybutyrate (PHB) up to the in vivo and in vitro synthesis of multiple proteins and finally whole-cell applications. Here we describe the use of the natural vitamin B₁₂ (cobalamin) producer P. megaterium for the elucidation of the biosynthetic pathway and the subsequent systematic knowledge-based development for production purposes. The formation of PHB, a natural product of P. megaterium and potential petro-plastic substitute, is covered and discussed. Further important biotechnological characteristics of P. megaterium for recombinant protein production including high protein secretion capacity and simple cultivation on value-added carbon sources are outlined. This includes the advanced system with almost 30 commercially available expression vectors for the intracellular and extracellular production of recombinant proteins at the g/L scale. We also revealed a novel P. megaterium transcription-translation system as a complementary and versatile biotechnological tool kit. As an impressive biotechnology application, the formation of various cytochrome P450 is also critically highlighted. Finally, whole cellular applications in plant protection are completing the overall picture of P. megaterium as a versatile giant cell factory.

Key points

• The use of Priestia megaterium for the biosynthesis of small molecules and recombinant proteins through to whole-cell applications is reviewed.

• P. megaterium can act as a promising alternative host in biotechnological production processes.

Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community

The continuous cropping of plants can result in the disruption of the soil microbial community and caused significant declines in yields. However, there are few reports on the effects of continuous cropping of sugarcane on the microbial community structure and functional pathway. In the current study, we analyzed the structural and functional changes of microbial community structure in the rhizospheric soil of sugarcane in different continuous cropping years using Illumina Miseq high-throughput sequencing and metagenomics analysis. We collected rhizosphere soils from fields of no continuous cropping history (NCC), 10 years of continuous cropping (CC10), and 30 years of continuous cropping (CC30) periods in the Fujian province. The results demonstrated that continuous sugarcane cropping resulted in significant changes in the physicochemical properties of soil and the composition of soil bacterial and fungal communities. With the continuous cropping, the crop yield dramatically declined from NCC to CC30. Besides, the redundancy analysis (RDA) of the dominant bacterial and fungal phyla and soil physicochemical properties revealed that the structures of the bacterial and fungal communities were mainly driven by pH and TS. Analysis of potential functional pathways during the continuous cropping suggests that different KEGG pathways were enriched in different continuous cropping periods. The significant reduction of bacteria associated with rhizospheric soil nitrogen and sulfur cycling functions and enrichment of pathogenic bacteria may be responsible for the reduction of effective nitrogen and total sulfur content in rhizospheric soil of continuous sugarcane as well as the reduction of sugarcane yield and sugar content. Additionally, genes related to nitrogen and sulfur cycling were identified in our study, and the decreased abundance of nitrogen translocation genes and AprAB and DsrAB in the dissimilatory sulfate reduction pathway could be the cause of declined biomass. The findings of this study may provide a theoretical basis for uncovering the mechanism of obstacles in continuous sugarcane cropping and provide better guidance for sustainable development of the sugarcane.

Whole Genome Analysis of Sugarcane Root-Associated Endophyte Pseudomonas aeruginosa B18-A Plant Growth-Promoting Bacterium With Antagonistic Potential Against Sporisorium scitamineum

Sugarcane smut is a significant fungal disease that causes a major loss in sugar yield and quality. In this study, we isolated an endophytic strain B18 from a sugarcane root, which showed plant growth-promotion, hydrolytic enzyme production, antifungal activity against sugarcane pathogens (Sporisorium scitamineum, Ceratocystis paradoxa, Fusarium verticillioides), and the presence of nifH, acdS, and antibiotic genes (hcn, prn, and phCA) under in vitro conditions. BIOLOG^(R) phenotypic profiling of B18 established its ability to use various carbon and nitrogen sources and tolerate a range of pH and osmotic and temperature stresses. Whole-genome analysis of B18, identified as Pseudomonas aeruginosa, showed that it consists of a single circular chromosome of 6,490,014 bp with 66.33% GC content. Genome annotation has identified 5,919 protein-coding genes, and 65 tRNA, and 12 rRNA genes. The P. aeruginosa B18 genome encodes genes related to ethylene, nitrogen (nifU, norBCDERQ, gltBDPS, and aatJMPQ), and phosphate (pstABCS and phoBDHRU) metabolism and produce indole-3-acetic acid and siderophores. This also includes genes encoding hydrolases and oxidoreductases, those associated with biocontrol mechanisms (hcnABC, phzA_B, phzDEFGMS, and pchA), colonization (minCDE and lysC), and biofilm formation (efp, hfq, flgBCDEFGHI, and motAB), and those associated with metabolism of secondary metabolites. Collectively, these results suggest a role for P. aeruginosa B18 in plant growth enhancement and biocontrol mechanisms. The P. aeruginosa B18 strain was found to be an efficient colonizer in sugarcane; it can improve growth through modulation of plant hormone production and enhanced host-plant resistance to smut pathogen S. scitamineum in a smut-susceptible sugarcane variety (Yacheng71-374). These biocontrol and plant growth promotion properties of P. aeruginosa B18 area are discussed in this report.

Diazotrophic Bacteria Pantoea dispersa and Enterobacter asburiae Promote Sugarcane Growth by Inducing Nitrogen Uptake and Defense-Related Gene Expression

Sugarcane is a major crop in tropical and subtropical regions of the world. In China, the application of large amounts of nitrogen (N) fertilizer to boost sugarcane yield is commonplace, but it causes substantial environmental damages, particularly soil, and water pollution. Certain rhizosphere microbes are known to be beneficial for sugarcane production, but much of the sugarcane rhizosphere microflora remains unknown. We have isolated several sugarcane rhizosphere bacteria, and 27 of them were examined for N-fixation, plant growth promotion, and antifungal activity. 16S rRNA gene sequencing was used to identify these strains. Among the isolates, several strains were found to have a relatively high activity of nitrogenase and ACC deaminase, the enzyme that reduces ethylene production in plants. These strains were found to possess nifH and acdS genes associated with N-fixation and ethylene production, respectively. Two of these strains, Pantoea dispersa-AA7 and Enterobacter asburiae-BY4 showed maximum plant growth promotion (PGP) and nitrogenase activity, and thus they were selected for detailed analysis. The results show that they colonize different sugarcane tissues, use various growth substrates (carbon and nitrogen), and tolerate various stress conditions (pH and osmotic stress). The positive effect of AA7 and BY4 strains on nifH and stress-related gene (SuCAT, SuSOD, SuPAL, SuCHI, and SuGLU) expression and the induction of defense-related processes in two sugarcane varieties, GT11 and GXB9, showed their potential for stress amelioration and PGP. Both bacterial strains increased several sugarcane physiological parameters. i.e., plant height, shoot weight, root weight, leaf area, chlorophyll content, and photosynthesis, in plants grown under greenhouse conditions. The ability of rhizobacteria on N-fixing in sugarcane was also confirmed by a ¹⁵N isotope-dilution study, and the estimate indicates a contribution of 21-35% of plant nitrogen by rhizobacterial biological N fixation (BNF). This is the first report of sugarcane growth promotion by N-fixing rhizobacteria P. dispersa and E. asburiae strains. Both strains could be used as biofertilizer for sugarcane to minimize nitrogen fertilizer use and better disease management.

Nodule and Root Zone Microbiota of Salt-Tolerant Wild Soybean in Coastal Sand and Saline-Alkali Soil

Soil salinization limits crop growth and yield in agro-ecosystems worldwide by reducing soil health and altering the structure of microbial communities. Salt-tolerant plant growth-promoting rhizobacteria (PGPR) alleviate plant salinity stress. Wild soybean (Glycine soja Sieb. and Zucc.) is unique in agricultural ecosystems owing to its ability to grow in saline-alkali soils and fix atmospheric nitrogen via symbiotic interactions with diverse soil microbes. However, this rhizosphere microbiome and the nodule endosymbionts have not been investigated to identify PGPR. In this study, we investigated the structural and functional rhizosphere microbial communities in saline-alkali soil from the Yellow River Delta and coastal soil in China, as well as wild soybean root nodule endosymbionts. To reveal the composition of the microbial ecosystem, we performed 16S rRNA and nifH gene amplicon sequencing on root nodules and root zones under different environmental conditions. In addition, we used culture-independent methods to examine the root bacterial microbiome of wild soybean. For functional characterization of individual members of the microbiome and their impact on plant growth, we inoculated isolates from the root microbiome with wild soybean and observed nodulation. Sinorhizobium/Ensifer accounted for 97% of the root nodule microbiome, with other enriched members belonging to the phyla Actinobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, and Gemmatimonadetes; the genera Sphingomonas, Microbacterium, Arthrobacter, Nocardioides, Streptomyces, Flavobacterium, Flavisolibacter, and Pseudomonas; and the family Enterobacteriaceae. Compared to saline-alkali soil from the Yellow River Delta, coastal soil was highly enriched for soybean nodules and displayed significant differences in the abundance and diversity of β-proteobacteria, δ-proteobacteria, Actinobacteria, and Bacteroidetes. Overall, the wild soybean root nodule microbiome was dominated by nutrient-providing Sinorhizobium/Ensifer and was enriched for bacterial genera that may provide salt resistance. Thus, this reductionist experimental approach provides an avenue for future systematic and functional studies of the plant root microbiome.

Complete Genome Sequence of Enterobacter roggenkampii ED5, a Nitrogen Fixing Plant Growth Promoting Endophytic Bacterium With Biocontrol and Stress Tolerance Properties, Isolated From Sugarcane Root

Sugarcane is the leading economic crop in China, requires huge quantities of nitrogen in the preliminary plant growth stages. However, the use of an enormous amount of nitrogen fertilizer increases the production price, and have detrimental results on the environment, causes severe soil and water pollution. In this study, a total of 175 endophytic strains were obtained from the sugarcane roots, belonging to five different species, i.e., Saccharum officinarum, Saccharum barberi, Saccharum robustum, Saccharum spontaneum, and Saccharum sinense. Among these, only 23 Enterobacter strains were chosen based on nitrogen fixation, PGP traits, hydrolytic enzymes production, and antifungal activities. Also, all selected strains were showed diverse growth range under different stress conditions, i.e., pH (5–10), temperature (20–45°C), and NaCl (7–12%) and 14 strains confirmed positive nifH, and 12 strains for acdS gene amplification, suggested that these strains could fix nitrogen along with stress tolerance properties. Out of 23 selected strains, Enterobacter roggenkampii ED5 was the most potent strain. Hence, this strain was further selected for comprehensive genome analysis, which includes a genome size of 4,702,851 bp and 56.05% of the average G + C content. Genome annotations estimated 4349 protein-coding with 83 tRNA and 25 rRNA genes. The CDSs number allocated to the KEGG, COG, and GO database were 2839, 4028, and 2949. We recognized a total set of genes that are possibly concerned with ACC deaminase activity, siderophores and plant hormones production, nitrogen and phosphate metabolism, symbiosis, root colonization, biofilm formation, sulfur assimilation and metabolism, along with resistance response toward a range of biotic and abiotic stresses. E. roggenkampii ED5 strain was also a proficient colonizer in sugarcane (variety GT11) and enhanced growth of sugarcane under the greenhouse. To the best of our knowledge, this is the first information on the whole-genome sequence study of endophytic E. roggenkampii ED5 bacterium associated with sugarcane root. And, our findings proposed that identification of predicted genes and metabolic pathways might describe this strain an eco-friendly bioresource to promote sugarcane growth by several mechanisms of actions under multi-stresses.