Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202

Reduced fertilization supplemented with Bacillus safensis RGM 2450 and Bacillus siamensis RGM 2529 promotes tomato production in a sustainable way

The rising demand for vegetables has driven the adoption of greenhouse cultivation to guarantee high yields and quality of fresh produce year-round. Consequently, this elevates the demand for fertilizers, whose costs are progressively escalating. Bacillus safensis RGM 2450 and Bacillus siamensis RGM 2529 are plant growth-promoting rhizobacteria (PGPR). The combination of these strains exhibited synergistic activity in stimulating the growth and seedling hydration of tomatoes. In this study, the effects of inoculation with a RGM 2450 plus RGM 2529 formulation were evaluated under 66% and 100% fertilization programs in tomato crops under greenhouse conditions. Fertilization programs (66% and 100%) with or without commercial biostimulants were used as control treatments. In this assay, the NPK percentage in the plant tissue, tomato average weight, tomato average weight per harvest, tomato diameter, and changes in the colonization, structure, and diversity of the bacterial rhizosphere were measured. The 100% and 66% fertilization programs supplemented with the RGM 2529 plus RGM 2450 formulation increased the average weight of tomatoes per harvest without statistical difference between them, but with the other treatments. The 66% fertilization with RGM 2450 plus RGM 2529 increased between 1.5 and 2.0 times the average weight of tomatoes per harvest compared to the 66% and 100% fertilizations with and without commercial biostimulant treatments, respectively. This study represents the first report demonstrating that the application of a formulation based on a mixture of B. siamensis and B. safensis in a fertilization program reduced by 33% is equivalent in productivity to a conventional fertilization program for tomato cultivation, achieving an increase in potential plant growth-promoting rizobacteria of the genus Flavobacterium. Therefore, the adoption of a combination of these bacterial strains within the framework of a 66% inorganic fertilization program is a sustainable approach to achieving greater tomato production and reducing the environmental risks associated with the use of inorganic fertilization.

Plant growth-promoting rhizobacteria: Peribacillus frigoritolerans 2RO30 and Pseudomonas sivasensis 2RO45 for their effect on canola growth under controlled as well as natural conditions

Even though canola is one of the most important industrial crops worldwide, it has high nutrient requirements and is susceptible to pests and diseases. Therefore, natural methods are sought to support the development of these plants. One of those methods could be a plant growth-promoting rhizobacteria (PGPR) that have a beneficial effect on plant development. The aim of this study was a genomic comparison of two PGPR strains chosen based on their effect on canola growth: Peribacillus frigoritolerans 2RO30, which stimulated canola growth only in sterile conditions, and Pseudomonas sivasensis 2RO45, which promoted canola growth in both sterile and non-sterile conditions. First of all, six bacterial strains: RO33 (Pseudomonas sp.), RO37 (Pseudomonas poae), RO45 (Pseudomonas kairouanensis), 2RO30 (Peribacillus frigoritolerans), 2RO45 (Pseudomonas sivasensis), and 3RO30 (Pseudomonas migulae), demonstrating best PGP traits in vitro, were studied for their stimulating effect on canola growth under sterile conditions. P. frigoritolerans 2RO30 and P. sivasensis 2RO45 showed the best promoting effect, significantly improving chlorophyll content index (CCI) and roots length compared to the non-inoculated control and to other inoculated seedlings. Under non-sterile conditions, only P. sivasensis 2RO45 promoted the canola growth, significantly increasing CCI compared to the untreated control and to other inoculants. Genome comparison revealed that the genome of P. sivasensis 2RO45 was enriched with additional genes responsible for ACC deaminase (acdA), IAA (trpF, trpG), and siderophores production (fbpA, mbtH, and acrB) compared to 2RO30. Moreover, P. sivasensis 2RO45 showed antifungal effect against all the tested phytopathogens and harbored six more biosynthetic gene clusters (BGC), namely, syringomycin, pyoverdin, viscosin, arylpolyene, lankacidin C, and enterobactin, than P. frigoritolerans 2RO30. These BGCs are well known as antifungal agents; therefore, it can be assumed that these BGCs were responsible for the antifungal activity of P. sivasensis 2RO45 against all plant pathogens. This study is the first report describing P. sivasensis 2RO45 as a canola growth promoter, both under controlled and natural conditions, thus suggesting its application in improving canola yield, by improving nutrient availability, enhancing stress tolerance, and reducing environmental impact of farming practices.

The effect of seed bacterization with Bacillus paralicheniformis 2R5 on bacterial and fungal communities in the canola rhizosphere

Bacillus sp. is one of the best-studied plant growth-promoting rhizobacteria (PGPR). However, more detailed studies targeting its effect on the rhizosphere microbial community are required for improving management practices regarding its commercial application in the field. Our earlier study showed that PGPR Bacillus paralicheniformis 2R5 stimulated canola growth. Hence, this study aimed to assess the time-course impact of B. paralicheniformis 2R5 on bacterial and fungal community structure and diversity. The results showed that inoculation with B. paralicheniformis 2R5 initially significantly decreased the observed bacterial richness compared to the control, while after 44 days of treatment this alpha diversity metrics increased. A linear discriminant analysis effect size showed that B. paralicheniformis 2R5 altered the soil bacterial and fungal community structure by increasing the abundance of plants' beneficial microorganisms such as Nitrospira, Ramlibacter, Sphingomonas, Massilia, Terrimonas as well as Solicoccozyma, Schizothecium, Cyphellophora, Fusicolla, Humicola. B. paralicheniformis 2R5 seems to be a promising alternative to chemical pesticides and can be considered for practical application in the field. Its ability to alter the rhizosphere microbiome by increasing the diversity and composition of bacterial communities and increasing plants' beneficial groups of fungi, appears to be important in terms of improving canola development. However, further studies on these increased microbial taxa are necessary to confirm their function in promoting canola growth.

Bacillus paralicheniformis 2R5 and its impact on canola growth and N-cycle genes in the rhizosphere

Chemical fertilization has a negative impact on the natural environment. Plant growth-promoting (PGP) rhizobacterial biofertilizers can be a safer alternative to synthetic agrochemicals. In this research, a culture-based method was used to assess the population size of rhizobacteria at the vegetative, flowering, and maturity stages of canola. Rhizobacteria were then isolated from each of the canola growth stages, and their seven PGP traits were determined. The highest abundance of culturable bacteria was found at the vegetative stage of the plants. Furthermore, four out of seven PGP traits were produced by the highest % of isolates at the vegetative stage. In the greenhouse experiment that included six rhizobacterial strains with best PGP traits, the greatest canola growth promotion ability under sterile conditions was observed after the introduction of Bacillus paralicheniformis 2R5. Moreover, under nonsterile conditions, 2R5 significantly increased canola growth. The presence of the trpA, B, C, D, E, F and pstA, and S genes in the 2R5 genome could be associated with canola growth promotion abilities. The chiA and mbtH genes could contribute to 2R5 antifungal activity against fungal pathogens. Moreover, the introduction of 2R5 significantly increased the abundance of the narG, nosZ, nifH, and nirS genes, which can prove that the 2R5 strain may be an important member of the soil bacterial community.

The rhizosphere Microbiome of Malus sieversii (Ldb.) Roem. in the geographic and environmental gradients of China's Xinjiang

Malus sieversii (Ldb.) Roem. is the original species of modern cultivated apple and a key national essential conservation plant in China. In recent years, degradation and death of wild apple has been exacerbated by imbalances in the rhizosphere micro-ecosystems of wild apple forests due to soil nutrient loss, grazing, climate change and pest and disease outbreaks. However, the structure, diversity and response to environmental factors of wild apple rhizosphere microbial communities are so far unclear. In this study, the rhizosphere bacterial and eukaryotic communities of M. sieversii (Ldb.) Roem. in eight regions of the Yili River were analyzed using 16S/18S rDNA high-throughput sequencing technology. The results indicated that the bacterial operational taxonomic units (OTUs), Shannon index, and community composition were significantly lower in regions A, E, and F than in other regions. By contrast, the dominant eukaryotic communities in all regions were relatively similar in composition and differed less than the relative abundance of bacterial communities. Geographical and climatic distance were found to be key factors influencing the composition and diversity of wild apple rhizosphere microbial communities through mantel analysis. Moreover, these factors above were more correlated with bacterial diversity than with eukaryotes. This study identified the structure of wild apple rhizosphere microbial communities in Xinjiang and their interaction mechanisms under geographical and environmental gradients. It provides guidance for the sustainable management and ecological construction of wild apple forests in China.

Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community

Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.

The role of auxins and auxin-producing bacteria in the tolerance and accumulation of cadmium by plants

Cadmium (Cd) is one of the most toxic heavy metals for plant physiology and development. This review discusses Cd effects on auxin biosynthesis and homeostasis, and the strategies for restoring plant growth based on exogenous auxin application. First, the two well-characterized auxin biosynthesis pathways in plants are described, as well as the effect of exogenous auxin application on plant growth. Then, review describes the impacts of Cd on the content, biosynthesis, conjugation, and oxidation of endogenous auxins, which are related to a decrease in root development, photosynthesis, and biomass production. Finally, compelling evidence of the beneficial effects of auxin-producing rhizobacteria in plants exposed to Cd is showed, focusing on photosynthesis, oxidative stress, and production of antioxidant compounds and osmolytes that counteract Cd toxicity, favoring plant growth and improve phytoremediation efficiency. Expanding our understanding of the positive effects of exogenous auxins application and the interactions between bacteria and plants growing in Cd-polluted environments will allow us to propose phytoremediation strategies for restoring environments contaminated with this metal.

A photosynthetic bacterial inoculant exerts beneficial effects on the yield and quality of tomato and affects bacterial community structure in an organic field

Plant growth-promoting rhizobacteria (PGPR) are microorganisms that promote plant health and play a critical role in sustainable agriculture. As a PGPR, Rhodopseudomonas palustris strain PS3, when applied as a microbial inoculant, exhibited beneficial effects on a variety of crops. In this study, we investigated the effects of PS3 on tomato growth, soil properties, and soil microbiota composition in an organic field. The results demonstrated that PS3 inoculation significantly improved the yield of marketable tomato fruit (37%) and the postharvest quality (e.g., sweetness, taste, vitamin C, total phenolic compounds, and lycopene). Additionally, soil nutrient availability (35–56%) and enzymatic activities (13–62%) also increased. We detected that approximately 10⁷ CFU/g soil of R. palustris survived in the PS3-treated soil after harvest. Furthermore, several bacterial genera known to be associated with nutrient cycling (e.g., Dyella, Novosphingobium, Luteimonas, Haliangium, and Thermomonas) had higher relative abundances (log2 fold change >2.0). To validate the results of the field experiment, we further conducted pot experiments with field-collected soil using two different tomato cultivars and obtained consistent results. Notably, the relative abundance of putative PGPRs in the genus Haliangium increased with PS3 inoculation in both cultivars (1.5 and 34.2%, respectively), suggesting that this genus may have synergistic interactions with PS3. Taken together, we further demonstrated the value of PS3 in sustainable agriculture and provided novel knowledge regarding the effects of this PGPR on soil microbiota composition.

Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops

Despite growing evidence that plant growth-promoting bacteria can be used to improve crop vigor, a comparison of the different methods of delivery to determine which is optimal has not been published. An optimal inoculation method ensures that the inoculant colonizes the host plant so that its potential for plant growth-promotion is fully evaluated. The objective of this study was to compare the efficacy of three seed coating methods, seedling priming, and soil drench for delivering three bacterial inoculants to the sorghum rhizosphere and root endosphere. The methods were compared across multiple time points under axenic conditions and colonization efficiency was determined by quantitative polymerase chain reaction (qPCR). Two seed coating methods were also assessed in the field to test the reproducibility of the greenhouse results under non-sterile conditions. In the greenhouse seed coating methods were more successful in delivering the Gram-positive inoculant (Terrabacter sp.) while better colonization from the Gram-negative bacteria (Chitinophaga pinensis and Caulobacter rhizosphaerae) was observed with seedling priming and soil drench. This suggested that Gram-positive bacteria may be more suitable for the seed coating methods possibly because of their thick peptidoglycan cell wall. We also demonstrated that prolonged seed coating for 12 h could effectively enhance the colonization of C. pinensis, an endophytic bacterium, but not the rhizosphere colonizing C. rhizosphaerae. In the field only a small amount of inoculant was detected in the rhizosphere. This comparison demonstrates the importance of using the appropriate inoculation method for testing different types of bacteria for their plant growth-promotion potential.

Plant Growth-promoting and Bio-control Activity of Micrococcus luteus Strain AKAD 3-5 Isolated from the Soybean (Glycine max (L.) Merr.) Rhizosphere

Background:

Applications of bioinoculants for improving crop productivity may be an eco-friendly alternative to chemical fertilizers. Rhizosphere or soil-inhabiting beneficial microbes can enhance plant growth and productivity through direct and indirect mechanisms, i.e., phosphate solubilization, nutrient acquisition, phytohormone production, etc.

Objective:

This study is based on the hypothesis that diseases resistant plants can act as a source of potential microbes that can have good plant growth-promoting traits and bio-control potential.

Methods:

In this study, we have isolated the rhizobacterial strains (AKAD 2-1, AKAD 2-10, AKAD 3-5, AKAD 3-9) from the rhizosphere of a disease-resistant variety of soybean (JS-20-34) (Glycine max (L.) Merr.). These bacterial strains were further screened for various plant growth-promoting traits (phosphate solubilization, indole acetic acid (IAA), ammonia, biofilm, HCN, Exopolysaccharide (EPS), and enzyme production activity (catalase, cellulase, and chitinase)).

Results:

Among four, only bacterial strain AKAD 3-5 has shown plant-growth-promoting and biocontrol (98%) activity against Fusarium oxysporum. Morphological, biochemical, and molecular characterization (16S rRNA) revealed that this rhizobacterial isolate AKAD 3-5 closely resembles Micrococcus luteus (Gene bank accession: MH304279).

Conclusion:

Here, we conclude that this strain can be utilized to promote soybean growth under varied soil stress conditions.

Changes in Bacterial Diversity and Composition in Response to Co-inoculation of Arbuscular Mycorrhizae and Zinc-Solubilizing Bacteria in Turmeric Rhizosphere

In the present study, the impact of co-inoculation of arbuscular mycorrhizal fungi (AM Rhizophagus sp., NCBI-MN710507) and Zinc solubilizing bacteria (ZSB2- Bacillus megaterium, NCBI-KY687496) on plant growth, soil dehydrogenase activity, soil respiration and the changes in bacterial diversity in rhizosphere of turmeric (Curcuma longa) were examined. Our results showed that higher plant height and dry biomass were observed in treatments co-inoculated with AM and ZSB2. Likewise, dehydrogenase activity and soil respiration were more significant in the co-inoculation treatment, indicating abundance of introduced as well as inherent microflora. Bacterial community analysis using 16S rRNA revealed changes in the structure and diversity of various taxa due to co-inoculation of AM and ZSB2. Alpha diversity indexes (Shannon and Chao1) and beta diversity indexes obtained through unweighted unifrac approach also showed variation among the treated samples. Chloroflexi was the dominant phylum followed by Proteobacteria, Actinobacteria and Acidobacteria which accounted for 80% of all treated samples. The composition of bacterial communities at genus level revealed that co-inoculation caused distinct bacterial profiles. The Linear discriminant analysis effect size revealed the dominance of ecologically significant genera such as Bradyrhizobium, Candidatus, Pedomicrbium, Thermoporothrix, Acinetobacter and Nitrospira in treatments co-inoculated with AM and ZSB2. On the whole, co-inoculated treatments revealed enhanced microbial activities and caused significant positive shifts in the bacterial diversity and abundance compared to treatments with sole application of ZSB2 or AM.

Effectsof growth-promoting rhizobacteria on maize growth and rhizosphere microbial community under conservation tillage in Northeast China

Conservation tillage in conjunction with straw mulching is a sustainable agricultural approach. However, straw mulching reduces the soil temperature, inhibits early maize growth and reduces grain yield in cold regions. To address this problem, we investigated the effects of inoculation of plant growth‐promoting rhizobacteria (PGPR) on maize growth and rhizosphere microbial communities under conservation tillage in Northeast China. The PGPR strains Sinorhizobium sp. A15, Bacillus sp. A28, Sphingomonas sp. A55 and Enterobacter sp. P24 were isolated from the maize rhizosphere in the same area and inoculated separately. Inoculation of these strains significantly enhanced maize growth, and the strains A15, A28 and A55 significantly increased grain yield by as much as 22%–29%. Real‐time quantitative PCR and high‐throughput sequencing showed that separate inoculation with the four strains increased the abundance and species richness of bacteria in the maize rhizosphere. Notably, the relative abundance of Acidobacteria_Subgroup_6, Chloroflexi_KD4‐96, and Verrucomicrobiae at the class level and Mucilaginibacter at the genus level were positively correlated with maize biomass and yield. Inoculation with PGPR shows potential for improvement of maize production under conservation tillage in cold regions by regulating the rhizosphere bacterial community structure and by direct stimulation of plant growth.

Mechanistic insights into host adaptation, virulence and epidemiology of the phytopathogen Xanthomonas

Xanthomonas is a well-studied genus of bacterial plant pathogens whose members cause a variety of diseases in economically important crops worldwide. Genomic and functional studies of these phytopathogens have provided significant understanding of microbial-host interactions, bacterial virulence and host adaptation mechanisms including microbial ecology and epidemiology. In addition, several strains of Xanthomonas are important as producers of the extracellular polysaccharide, xanthan, used in the food and pharmaceutical industries. This polymer has also been implicated in several phases of the bacterial disease cycle. In this review, we summarise the current knowledge on the infection strategies and regulatory networks controlling virulence and adaptation mechanisms from Xanthomonas species and discuss the novel opportunities that this body of work has provided for disease control and plant health.

Seasonal Variation in the Rhizosphere and Non-Rhizosphere Microbial Community Structures and Functions of Camellia yuhsienensis Hu

Camellia yuhsienensis Hu, endemic to China, is a predominant oilseed crop, due to its high yield and pathogen resistance. Past studies have focused on the aboveground parts of C. yuhsienensis, whereas the microbial community of the rhizosphere has not been reported yet. This study is the first time to explore the influence of seasonal variation on the microbial community in the rhizosphere of C. yuhsienensis using high-throughput sequencing. The results showed that the dominant bacteria in the rhizosphere of C. yuhsienensis were Chloroflexi, Proteobacteria, Acidobacteria, Actinobacteria, and Planctomycetes, and the dominant fungi were Ascomycota, Basidiomycota, and Mucoromycota. Seasonal variation has significant effects on the abundance of the bacterial and fungal groups in the rhizosphere. A significant increase in bacterial abundance and diversity in the rhizosphere reflected the root activity of C. yuhsienensis in winter. Over the entire year, there were weak correlations between microorganisms and soil physiochemical properties in the rhizosphere. In this study, we found that the bacterial biomarkers in the rhizosphere were chemoorganotrophic Gram-negative bacteria that grow under aerobic conditions, and fungal biomarkers, such as Trichoderma, Mortierella, and Lecanicillium, exhibited protection against pathogens in the rhizosphere. In the rhizosphere of C. yuhsienensis, the dominant functions of the bacteria included nitrogen metabolism, oxidative phosphorylation, glycine, serine and threonine metabolism, glutathione metabolism, and sulfur metabolism. The dominant fungal functional groups were endophytes and ectomycorrhizal fungi of a symbiotroph trophic type. In conclusion, seasonal variation had a remarkable influence on the microbial communities and functions, which were also significantly different in the rhizosphere and non-rhizosphere of C. yuhsienensis. The rhizosphere of C. yuhsienensis provides suitable conditions with good air permeability that allows beneficial bacteria and fungi to dominate the soil microbial community, which can improve the growth and pathogen resistance of C. yuhsienensis.