Peanut Endophytic Phosphate Solubilizing Bacteria Increase Growth and P Content of Soybean and Maize Plants

Soil phosphorus cycling microbial functional genes of monoculture and mixed plantations of native tree species in subtropical China

Background

Transforming coniferous plantation into broadleaved or mixed broadleaved-coniferous plantations is the tendency of forest management strategies in subtropical China. However, the effects of this conversion on soil phosphorus (P) cycling microbial functional genes are still unknown.

Methods

Soil samples were collected from 0-20, 20-40, and 40-60 cm (topsoil, middle layer, and subsoil, respectively) under coniferous Pinus massoniana (PM), broadleaved Erythrophleum fordii (EF), and their mixed (PM/EF) plantation in subtropical China. Used metagenomic sequencing to examine the alterations of relative abundances and molecular ecological network structure of soil P-cycling functional genes after the conversion of plantations.

Results

The composition of P-cycling genes in the topsoil of PM stand was significantly different from that of PM/EF and EF stands (p < 0.05), and total phosphorus (TP) was the main factor causing this difference. After transforming PM plantation into EF plantation, the relative abundances of P solubilization and mineralization genes significantly increased in the topsoil and middle layer with the decrease of soil TP content. The abundances of P-starvation response regulation genes also significantly increased in the subsoil (p < 0.05), which may have been influenced by soil organic carbon (SOC). The dominant genes in all soil layers under three plantations were phoR, glpP, gcd, ppk, and ppx. Transforming PM into EF plantation apparently increased gcd abundance in the topsoil (p < 0.05), with TP and NO3 --N being the main influencing factors. After transforming PM into PM/EF plantations, the molecular ecological network structure of P-cycling genes was more complex; moreover, the key genes in the network were modified with the transformation of PM plantation.

Conclusion

Transforming PM into EF plantation mainly improved the phosphate solubilizing potential of microorganisms at topsoil, while transforming PM into PM/EF plantation may have enhanced structural stability of microbial P-cycling genes react to environmental changes.

Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture

Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.

Promoting the growth of Sulla flexuosa L. by endophytic root nodule bacteria authors and affiliations

Legume plants rely upon multipartite interactions between rhizobia and bacterial endophytes within root nodules to facilitate plant growth. This study aimed to isolate and identify indigenous endophytic bacteria from root nodules of Sulla aculeolata L. in Northeast Morocco. Based on their tri-calcium phosphate (TCP) solubilization capacity, five endophytes were chosen for further evaluation of their plant growth traits. All isolates were hydrogen cyanide (HCN) and siderophore producers, while only BCH24 tested positive for ACC deaminase activity. Indole-3-acetic acid (IAA) synthesis ranged from 1.27 mgL^- 1 to 2.89 mgL^- 1, while soluble phosphate concentrations was between 7.99 mg L^- 1 and 110.58 mg L^- 1. Additionally, all the endophytes were able to produce more than two lytic enzymes. Based on the analysis of 16 S rRNA gene sequences five isolates were identified as Enterobacter sp (BCH13, BCH2), Pseudomonas sp (BCH16, BCH24), and Serratia sp (BCH10). The strains inhibited the growth of three phytopathogenic fungi, with BCH13 exhibiting the highest rate against Aspergillus ochraceus (45%), followed by BCH24 against Fusarium oxysporum (40%) and Botrytis cinerea (35%), respectively. In vivo inoculation of halotolerant strains Enterobacter hormaechei (BCH13) and Pseudomonas moraviensis (BCH16) under gnotobiotic conditions revealed that co-inoculation with Rhizobium sullae KS6 improved plant development compared to single inoculation, making it a promising eco-friendly bio-inoculant for legume Sulla flexuosa L. production.

Microbial Endophytes: Emerging Trends and Biotechnological Applications

A plethora of knowledge on the role of endophytic microorganisms has been reported in recent years. The cooperative chemistry between the endophytes and the internal host tissue has turned them into a crucial aid for biotechnological applications. Microbial endophytes are ubiquitous among most plant species on earth and contribute to the benefit of host plants by generating a wide range of metabolites that provide the plant with survival value. Endophytes can either directly stimulate plant growth by producing phytohormones or indirectly stimulate plant growth by increasing the availability of soil nutrients to plants. Endophytes may also help suppress diseases in plants directly by neutralizing environmental toxic elements, and by inhibiting plant pathogens by antagonistic action, or indirectly by stimulating induced plant systemic resistance. Several natural compounds produced by endophytes as secondary metabolites are beneficial to both plants and humans. This is why endophytes are regarded as a significant source of novel natural products of value in modern medicine, agriculture, and industry. Endophytes are known for producing pigments, bioactive compounds, and industrially important enzymes, like glucanase, amylase, laccase, etc. Some endophytes can also produce nanoparticles that potentially have numerous applications in a variety of fields. They also play an important role in biodegradation and bioremediation, both of which are beneficial to the environment and ecology. In this review, we highlighted potential biotechnological applications of endophytic microbes, as well as their diverse importance in plant growth and public health.

Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria

This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.

New Insights on Endophytic Microbacterium-Assisted Blast Disease Suppression and Growth Promotion in Rice: Revelation by Polyphasic Functional Characterization and Transcriptomics

Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we report agriculturally beneficial traits of rice-leaf-adapted endophytic Microbacterium testaceum. Our polyphasic taxonomic investigations revealed its identity as M. testaceum. The bacterium displayed typical endophytism in rice leaves, indicated by the green fluorescence of GFP-tagged M. testaceum in confocal laser scanning microscopy. Furthermore, the bacterium showed mineral solubilization and production of IAA, ammonia, and hydrolytic enzymes. Tobacco leaf infiltration assay confirmed its non-pathogenic nature on plants. The bacterium showed antifungal activity on Magnaporthe oryzae, as exemplified by secreted and volatile organic metabolome-mediated mycelial growth inhibition. GC-MS analysis of the volatilome of M. testaceum indicated the abundance of antimicrobial compounds. Bacterization of rice seedlings showed phenotypic traits of MAMP-triggered immunity (MTI), over-expression of OsNPR1 and OsCERK, and the consequent blast suppressive activity. Strikingly, M. testaceum induced the transcriptional tradeoff between physiological growth and host defense pathways as indicated by up- and downregulated DEGs. Coupled with its plant probiotic features and the defense elicitation activity, the present study paves the way for developing Microbacterium testaceum-mediated bioformulation for sustainably managing rice blast disease.

Microbial Inoculation Improves Growth, Nutritional and Physiological Aspects of Glycine max (L.) Merr

Considering a scenario where there is a low availability and increasing costs of fertilizers in the global agricultural market, as well as a finitude of important natural resources, such as phosphorus (P), this study tested the effect of the inoculation of rhizospheric or endophytic microorganisms isolated from Hymenaea courbaril and Butia purpurascens on the growth promotion of Glycine max (L.) Merr. The tests were conducted in a controlled greenhouse system, and the effects of biofertilization were evaluated using the following parameters: dry biomass, nutritional content, and photochemical and photosynthetic performance of plants. Seed biopriming was performed with four bacterial and four fungal isolates, and the results were compared to those of seeds treated with the commercial product Biomaphos^®. Overall, microbial inoculation had a positive effect on biomass accumulation in G. max, especially in strains PA12 (Paenibacillus alvei), SC5 (Bacillus cereus), and SC15 (Penicillium sheari). The non-inoculated control plants accumulated less nutrients, both in the whole plant and aerial part, and had reduced chlorophyll index and low photosynthetic rate (A) and photochemical efficiency. Strains PA12 (P. alvei), SC5 (B. cereus), and 328EF (Codinaeopsis sp.) stood out in the optimization of nutrient concentration, transpiration rate, and stomatal conductance. Plants inoculated with the bacterial strains PA12 (P. alvei) and SC5 (B. cereus) and with the fungal strains 328EF (Codinaeopsis sp.) and SC15 (P. sheari) showed the closest pattern to that observed in plants treated with Biomaphos^®, with the same trend of direction of the means associated with chlorophyll index, (A), dry mass, and concentration of important nutrients such as N, P, and Mg. We recommend the use of these isolates in field tests to validate these strains for the production of biological inoculants as part of the portfolio of bioinputs available for G. max.

Genome analysis uncovers the prolific antagonistic and plant growth-promoting potential of endophyte Bacillus velezensis K1

Insights into the application of endophytic bacilli in sustainable agricultural practices have opened up new avenues for the inhibition of soil-borne pathogens and the improvement of plant health. Bacillus subtilis K1, an endophytic bacterium originally isolated from aerial roots of Ficus benghalensis is a potential biocontrol agent secreting a mixture of surfactins, iturins and fengycins. The current study extends the characterization of this bacterium through genomic and comparative genomics approaches. The sequencing of the bacterial genome at Illumina MiSeq platform revealed that it possessed a 4,103,502-bp circular chromosome with 45.98% GC content and 4325 predicted protein-coding sequences. Based on phylogenomics and whole-genome average nucleotide identity, the B. subtilis K1 was taxonomically classified as Bacillus velezensis. The formerly evaluated phenotypic traits viz. C-source utilization and lipopeptide-mediated fungal antagonism were correlated to their molecular determinants. The genome also harbored several genes associated with induced systemic resistance and plant growth promotion i.e, phytohormone production, nitrogen assimilation and reduction, siderophore production, phosphate solubilization, biofilm formation, swarming motility, acetoin and butanediol synthesis. The production of antifungal volatile organic compounds and plant growth promotion was experimentally demonstrated by volatile compound assay and seed germination assay on cumin and groundnut. The isolate also holds great prospects for application as a soil inoculant as indicated by enhancement in the growth of groundnut via in planta pot studies. Bacterial pan-genome analysis based on a comparison of whole genomes with eighteen other Bacillus strains was also conducted. Comparative examination of biosynthetic gene clusters across all genomes indicated that the largest number of gene clusters were harbored by the K1 genome. Based on the findings, we propose K1 as a model for scrutinizing non-ribosomally synthesized peptide synthetase and polyketide synthetase derived molecules.

Immobilization-Based Bio-formulation of Aspergillus awamori S29 and Evaluation of Its Shelf Life and Re-usability in the Soil-Plant Experiment

The present study was an attempt to evaluate the bio-formulations of phosphate-solubilizing fungus Aspergillus awamori S29 using two economically viable carriers (calcium alginate and agar) in repeated batch fermentation. Further, the viable cell count under storage and response of these stored bio-formulations on the growth of wheat plants were studied at the end of 2, 4, and 6 months of incubation. Also, the response of these formulations in next season on pearl millet (bajra) was studied without further inoculation. In repeated batch fermentation assay, immobilized form performed significantly better than free form. The viability of fungal inoculant was 88.2% in calcium alginate-based bio-formulation after six months of storage. These bio-formulations showed not only a statistically significant increase in the growth of wheat crop in first season but also of pearl millet in next season. This work strengthens the re-usability potential of immobilized bio-formulations for next season crop.

Effect of Rhizobacteria Inoculation via Soil and Seeds on Glycine max L. Plants Grown on Soils with Different Cropping History

Field experiments testing the effect of phosphate-solubilizing rhizobacteria (PSRB) should consider the cropping history and the method used to inoculate the strains. We evaluated the hypothesis that PSRB previously isolated from soybean seedlings could be effective in promoting growth in this oilseed crop in soils with different cultivation periods. We also evaluated whether this growth promotion could be influenced by cultivation histories or the inoculation method (via seeds or soil). Thus, we conducted an experiment in five fields cultivating Glycine max during two seasons (2019/2020 and 2020/2021), to test the effectiveness of PSRB (SAF9-Brevibacillus sp., SAF11-Brevibacillus sp., and SAC36-Bacillus velezensis) compared with results observed for the inoculant BiomaPhos (mix of Bacillus subtilis and Bacillus megaterium). The present study was based on the evaluation of vegetative growth, nutritional and yield parameters, and microbial biomass carbon (MBC). PSRB were more effective than, or showed similar effectiveness to, BiomaPhos for most of the evaluated vegetative, nutritional, and yield characteristics. In the fields tested in the summer 2019/2020 crop, SAC36 and SAF9 strains stood out as growth promoters, whereas in the 2020/2021 crop, SAF11, SAC36, and BiomaPhos were notable. There did not seem to be a direct relationship between long histories of soybean cultivation as a monoculture and low yield in the field. However, yield seems to be associated with soil nutritional characters such as Ca, Mg, K, P, cation exchange capacity, and organic matter levels. PSRB inoculation positively affected nodulation (NN) and nodule dry mass (NDM) in the evaluated fields in the 2019/2020 crop, and the aerial part dry mass (APDM), NN, NDM, yield, and MBC of the evaluated fields in the 2020/2021 crop. In contrast, the inoculation method was observed to have a strong effect on APDM, NN, root dry mass, and MBC, as the plants inoculated via seed showed higher mean values than those in the plants inoculated via soil. This study demonstrated the growth-promoting potential of new phosphate-solubilizing strains, which may eventually be incorporated by the biostimulants market to freely compete with BiomaPhos.

Characterization of Phosphate Solubilizing Bacterial Endophytes and Plant Growth Promotion In Vitro and in Greenhouse

Phosphate is one of the most important nutrients for plant growth and development, and only 0.1% of the phosphate in soils is available to plants. Currently, the use of excess phosphate fertilizer has caused surface and ground water pollution and water eutrophication, resulting in algal blooms in lakes and oceans. Therefore, it is imperative to explore alternative ways to solve these problems for sustainable agricultural production and improvement of soil fertility, while protecting the environment. Microorganisms from the rhizosphere and within plants are able to solubilize insoluble soil phosphate, making it available to plants. Five high phosphate solubilizing bacteria from our bacterial endophyte library were chosen for this study and identified as Pantoea vagans IALR611, Pseudomonas psychrotolerans IALR632, Bacillus subtilis IALR1033, Bacillus&nbsp;safensis IALR1035 and Pantoea agglomerans IALR1325. All five bacteria significantly promoted tall fescue growth in vitro. Greenhouse experiments showed that IALR1325 significantly promoted pepper and tomato growth, and IALR632 was the best in promoting tomato growth. In addition, all these bacteria had extracellular acid phosphatase and phytase activities. One of the mechanisms for phosphate solubilization by bacteria is pH reduction caused by gluconic acid production. Our results indicate that P. agglomerans IALR1325 is a promising bacterium for future applications.