Complementarity among plant growth promoting traits in rhizospheric bacterial communities promotes plant growth

Composing a microbial symphony: synthetic communities for promoting plant growth

Plant microbiomes are pivotal for host development, influencing growth, health, fitness, and evolution, and have emerged as promising resources for sustainable agriculture. However, leveraging these microbiomes to improve crop yield and resilience is challenging due to the huge diversity of plant-associated and soil microorganisms and their intricate interactions. Recently, synthetic microbial communities (SynComs) have been exploited as a reductionist approach to harness microbial benefits and to understand multispecies interactions. Additionally, the advanced functionality of SynComs promises to surpass classic single-strain-based biosolutions. Nevertheless, challenges remain in designing customized, robust, and predictable SynComs for agronomic use. Here, we synthesize and discuss the logical and implemented approaches used to design and assemble SynComs, highlighting important principles, challenges, and trends in utilizing SynComs as alternatives to agrochemicals.

Plant growth-promoting microorganisms as natural stimulators of nitrogen uptake in citrus

Improving nitrogen uptake efficiency by citrus in Mediterranean areas, where this crop predominates, is crucial for reducing ground-water pollution and enhancing environmental sustainability. This aligns with the Farm to Fork Strategy (European Green Deal) objectives, which aim to reduce the use of mineral fertilizers by up to 20% and to eliminate soil contamination from nitrogen entirely. In this context, exploring the potential of plant growth-promoting bacteria application to reduce nutrient inputs is a promising opportunity. The objective of the present study was to evaluate the effect of two Bacillus subtilis strains either individually inoculated or in combination with Saccharomyces cerevisiae on 15N-labeled fertilizer uptake efficiency and physiological parameters. Individual inoculations positively affected tree water potential, leaf chlorophyll concentrations (SPAD-values) and photosynthetic performance, enhancing tree growth. Fertilizer-15N use efficiency increased, as did phosphorus and potassium uptakes. Conversely, no response was observed in the trees co-inoculated with S cerevisiae. Therefore, PGPB can be considered an interesting means to reduce reliance on synthetic fertilizers in citrus orchards, minimizing the environmental impact and promoting sustainable production practices.

Implications of bacteria‒bacteria interactions within the plant microbiota for plant health and productivity

Crop production currently relies on the widespread use of agrochemicals to ensure food security. This practice is considered unsustainable, yet has no viable alternative at present. The plant microbiota can fulfil various functions for its host, some of which could be the basis for developing sustainable protection and fertilization strategies for plants without relying on chemicals. To harness such functions, a detailed understanding of plant‒microbe and microbe‒microbe interactions is necessary. Among interactions within the plant microbiota, those between bacteria are the most common ones; they are not only of ecological importance but also essential for maintaining the health and productivity of the host plants. This review focuses on recent literature in this field and highlights various consequences of bacteria‒bacteria interactions under different agricultural settings. In addition, the molecular and genetic backgrounds of bacteria that facilitate such interactions are emphasized. Representative examples of commonly found bacterial metabolites with bioactive properties, as well as their modes of action, are given. Integrating our understanding of various binary interactions into complex models that encompass the entire microbiota will benefit future developments in agriculture and beyond, which could be further facilitated by artificial intelligence-based technologies.

Unique dissolved organic matter molecules and microbial communities in rhizosphere of three typical crop soils and their significant associations based on FT-ICR-MS and high-throughput sequencing analysis

Using cucumber, maize, and ryegrass as model plants, the diversity and uniqueness of the molecular compositions of dissolved organic matter (DOM) and the structures of microbial communities in typical crop rhizosphere soils, as well as their associations, were investigated based on high-resolution mass spectrometry combined with high-throughput sequencing. The results showed that the rhizosphere contained 2200 organic molecules that were not identified in the non-rhizosphere soils, as characterized by FT-ICR-MS. The rhizosphere DOM molecules generally contained more N, S, and P heteroatoms, stronger hydrophilicity, and more refractory organic matter, representing high and complex chemical diversity characteristics. 16SrRNA sequencing results demonstrated that Proteobacteria, Actinomycetes and Firmicutes were the dominant flora in the soils. Plant species could significantly change the composition and relative abundance of rhizosphere microbial populations. The microbial community structures of rhizosphere and non-rhizosphere soils showed significant differences at both the phylum and class levels. Multiple interactions between the microorganisms and DOM compositions formed a complex network of relationships. There were strong and remarkable positive or negative couplings between different sizes and categories of DOM molecules and the specific microbial groups (P < 0.05, |R| ≥ 0.9) in the rhizosphere soils as shown by network profiles. The correlations between DOM molecules and microbial groups in rhizosphere soils had plant species specificity. The results above emphasized the relationship between the heterogeneity of DOM and the diversity of microbial communities, and explored the molecular mechanisms of the biochemical associations in typical plant rhizosphere soils, providing a foundation for in-depth understanding of plant-soil-microbe interactions.

Fungal community composition predicts forest carbon storage at a continental scale

Forest soils harbor hyper-diverse microbial communities which fundamentally regulate carbon and nutrient cycling across the globe. Directly testing hypotheses on how microbiome diversity is linked to forest carbon storage has been difficult, due to a lack of paired data on microbiome diversity and in situ observations of forest carbon accumulation and storage. Here, we investigated the relationship between soil microbiomes and forest carbon across 238 forest inventory plots spanning 15 European countries. We show that the composition and diversity of fungal, but not bacterial, species is tightly coupled to both forest biotic conditions and a seven-fold variation in tree growth rates and biomass carbon stocks when controlling for the effects of dominant tree type, climate, and other environmental factors. This linkage is particularly strong for symbiotic endophytic and ectomycorrhizal fungi known to directly facilitate tree growth. Since tree growth rates in this system are closely and positively correlated with belowground soil carbon stocks, we conclude that fungal composition is a strong predictor of overall forest carbon storage across the European continent.

Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment

Background

Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community.

Methods

In this study, nine PGPR strains, belonging to the genera Pseudomonas and Buttiauxella, were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson's correlation, Kendall's tau correlation and Spearman's rank correlation analysis methods.

Results

The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community.

Discussion

Plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with the modification of the rhizospheric soil microbial community. These data may help us to better understand the positive effects of PGPR on blueberry growth and the rhizosphere soil microenvironment, as well as provide a research basis for the subsequent development of a rhizosphere-promoting microbial fertilizer.

Heritable differences in abundance of bacterial rhizosphere taxa are correlated with fungal necrotrophic pathogen resistance

Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity and community-scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbours substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co-vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defence in natural and human-altered environments.

Biodiversity of the beneficial soil-borne fungi steered by Trichoderma-amended biofertilizers stimulates plant production

The soil microbiota is critical to plant performance. Improving the ability of plant-associated soil probiotics is thus essential for establishing dependable and sustainable crop yields. Although fertilizer applications may provide an effective way of steering soil microbes, it is still unknown how the positive effects of soil-borne probiotics can be maximized and how their effects are mediated. This work aims to seek the ecological mechanisms involved in cabbage growth using bio-organic fertilizers. We conducted a long-term field experiment in which we amended soil with non-sterilized organic or sterilized organic fertilizer either containing Trichoderma guizhouense NJAU4742 or lacking this inoculum and tracked cabbage plant growth and the soil fungal community. Trichoderma-amended bio-organic fertilizers significantly increased cabbage plant biomass and this effect was attributed to changes in the resident fungal community composition, including an increase in the relative abundance and number of indigenous soil growth-promoting fungal taxa. We specifically highlight the fundamental role of the biodiversity and population density of these plant-beneficial fungal taxa in improving plant growth. Together, our results suggest that the beneficial effects of bio-organic fertilizer seem to be a combination of the biological inoculum within the organic amendment as well as the indirect promotion through effects on the diversity and composition of the soil resident plant-beneficial fungal microbiome.

Enhancing Stevia rebaudiana growth and yield through exploring beneficial plant-microbe interactions and their impact on the underlying mechanisms and crop sustainability

Stevia rebaudiana is an important medicinal plant which represents the most important sugar substitute in many countries. Poor seed germination of this plant is a critical problem that affects the final yield and the availability of the products in the market. Continuous cropping without supplying soil nutrients is also a serious issue as it results in declining soil fertility. This review highlights the important use of beneficial bacteria for the enhancement of Stevia rebaudiana growth and its dynamic interactions in the phyllosphere, rhizosphere, and endosphere. Fertilizers can increase crop yield and preserve and improve soil fertility. There is a rising concern that prolonged usage of chemical fertilizers may have negative impacts on the ecosystem of the soil. On the other hand, soil health and fertility are improved by plant growth-promoting bacteria which could eventually increase plant growth and productivity. Accordingly, a biocompatible strategy involving beneficial microorganisms inoculation is applied to boost plant growth and reduce the negative effects of chemical fertilizers. Plants benefit extensively from endophytic bacteria, which promote growth and induce resistance to pathogens and stresses. Additionally, several plant growth-promoting bacteria are able to produce amino acids, polyamines, and hormones that can be used as alternatives to chemicals. Therefore, understanding the dynamic interactions between bacteria and Stevia can help make the favorable bacterial bio-formulations, use them more effectively, and apply them to Stevia to improve yield and quality.

Diazotrophic bacteria improve Hymenaea courbaril seedlings growth and survival in iron mine tailings

One of the largest accidents with mine tailings happened in Brazil in 2015, with the rupture of the Fundão dam, and the physical characteristics of these tailings make it difficult to recover degraded areas. Hymenaea courbaril is a tree species native to Brazil that has low nutritional and water requirements, besides its capacity for survival in contaminated environments. In this study we hypothesized that inoculation with diazotrophs would improve the growth and physiology of H. courbaril in tailings, favoring the reforestation process aiming the recovery of the accident site. Every 20 days for 60 days, we investigated the morphophysiology of H. courbaril grown in iron mine tailings or soil, with the addition of nitrate (N-positive control), non-inoculation (negative control) or inoculation with native diazotrophic bacteria previously isolated from the tailings (UNIFENAS100-569; UNIFENAS100-654 and UNIFENAS100-638). We found that H. courbaril has survival capacity under mine tailings, with no growth alteration in the tailings, although there were signs of reduced ability for photoprotective responses. Inoculation with diazotrophic bacteria improved physiological aspects of H. courbaril and strain UNIFENAS100-638 was the most effective in favoring total growth of plants, net photosynthetic rate and root morphology under mine tailings. The survival capacity and growth of H. courbaril indicates the possibility of its use for reforestation in areas degraded by mine tailings. Further studies are necessary in field conditions and with a larger experimental period to more thoroughly understand H. courbaril tolerance.

Insight into soil nitrogen and phosphorus availability and agricultural sustainability by plant growth-promoting rhizobacteria

Nitrogen and phosphorus are critical for the vegetation ecosystem and two of the most insufficient nutrients in the soil. In agriculture practice, many chemical fertilizers are being applied to soil to improve soil nutrients and yield. This farming procedure poses considerable environmental risks which affect agricultural sustainability. As robust soil microorganisms, plant growth-promoting rhizobacteria (PGPR) have emerged as an environmentally friendly way of maintaining and improving the soil's available nitrogen and phosphorus. As a special PGPR, rhizospheric diazotrophs can fix nitrogen in the rhizosphere and promote plant growth. However, the mechanisms and influences of rhizospheric nitrogen fixation (NF) are not well researched as symbiotic NF lacks summarizing. Phosphate-solubilizing bacteria (PSB) are important members of PGPR. They can dissolve both insoluble mineral and organic phosphate in soil and enhance the phosphorus uptake of plants. The application of PSB can significantly increase plant biomass and yield. Co-inoculating PSB with other PGPR shows better performance in plant growth promotion, and the mechanisms are more complicated. Here, we provide a comprehensive review of rhizospheric NF and phosphate solubilization by PGPR. Deeper genetic insights would provide a better understanding of the NF mechanisms of PGPR, and co-inoculation with rhizospheric diazotrophs and PSB strains would be a strategy in enhancing the sustainability of soil nutrients.

Synergistic effect of ACC deaminase producing Pseudomonas sp. TR15a and siderophore producing Bacillus aerophilus TR15c for enhanced growth and copper accumulation in Helianthus annuus L

Copper (Cu) is an essential element, however it's excess into the environment causes detrimental effect on plant and risks for public health. Four Cu and drought tolerant 1-aminocyclopropane-1-carboxylate (ACC) deaminase producing rhizobacteria were isolated from the roots of Trifolium repens L. growing on Cu smelter contaminated soils, characterized and identified based on 16S rRNA gene sequencing. A consortium of high ACC deaminase (53.74 μM α-ketobutyrate mg^-1 protein h^-1) producing bacteria Pseudomonas sp. strain TR15a + siderophore producing Bacillus aerophilus strain TR15c significantly (p < 0.05) produced better results for multiple-metal tolerance including Cu (1750 mg kg^-1), antibiotic resistance (ampicillin, kanamycin, chloramphenicol, penicillin, tetracycline, and streptomycin) and plant growth promoting attributes (phosphate solubilization: 315 mg L^-1, indole-3-acetic acid (IAA) production: 8 mg L^-1, ammonia and hydrogen cyanide production) as compared to individual isolates. Pot scale experiment (enriched with 100 mg Cu kg^-1) showed inoculation of Helianthus annuus seeds with consortium of TR15a + TR15c had significantly (p < 0.05) improved seed germination by 32%, total dry biomass by 64%, root Cu by 47% and shoot Cu by 75% as compared to uninoculated control whereas 0.2-7 fold higher results were observed for above stated parameters as compared to four individual isolates studied. The result suggests consortium of ACC deaminase producing Pseudomonas sp. TR15a and siderophore producing B. aerophilus TR15c could play a vital role in enhanced Cu uptake and improvement of biomass and may provide a better alternative for decontamination of Cu contaminated natural ecosystem than individual isolates.

Diversity and function of rhizosphere microorganisms between wild and cultivated medicinal plant Glycyrrhiza uralensis Fisch under different soil conditions

Glycyrrhiza uralensis Fisch is a widely cultivated traditional Chinese medicine plant. In the present study, culture-independent microbial diversity analysis and functional prediction of rhizosphere microbes associated with wild and cultivated G. uralensis Fisch plant (collected from two locations) were carried. Soil physicochemical parameters were tested to assess their impact on microbial communities. A total of 4428 OTUs belonging to 41 bacterial phyla were identified. In general, cultivated sample sites were dominated by Actinobacteria whereas wild sample sites were dominated by Proteobacteria. The alpha diversity analysis showed the observed species number was higher in cultivated soil samples when compared with wild soil samples. In beta diversity analysis, it was noticed that the weighted-unifrac distance of two cultivated samples was closer although the samples were collected from different regions. Functional annotation based on PICRUST and FAPROTAX showed that the nitrogen metabolism pathway such as nitrate reduction, nitrogen fixation, nitrite ammonification, and nitrite respiration were more abundant in rhizosphere microorganisms of wild G. uralensis Fisch. These results also correlate in redundancy analysis results which show correlation between NO^3--N and wild samples, which indicated that nitrogen nutrition conditions might be related to the quality of G. uralensis Fisch.

Bioaugmentation with copper tolerant endophyte Pseudomonas lurida strain EOO26 for improved plant growth and copper phytoremediation by Helianthus annuus

Organic fertilizers became a better alternative to chemical fertilizers in modern agricultural practices however, contamination of copper (Cu) from organic fertilizer is still a major concern for the globe. Plant growth promoting (PGP) microorganisms showed their efficiency to combat with this problem and thus Cu tolerant PGP endophytes from roots of Odontarrhena obovata (Alyssum obovatum) growing on Cu smelter contaminated serpentine soil were explored in present study. Out of twenty-four isolates, Pseudomonas lurida strain EOO26 identified by 16s rRNA gene sequencing was selected to check its efficacy for Cu-remediation. The strain EOO26 showed multi-metal tolerance, drought resistance and exhibited PGP attributes such as 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, siderophore and ammonia production. Significant production of indole-3-acetic acid and phosphate-solubilization under different Cu concentration (0-100 mg L^-1) at varying pH (5.0-8.0) suggests potentiality of this strain to work effectively under wide range of abiotic stress conditions. Plant growth experiment (pH 6.8 ± 0.3) in copper spiked soil suggested a significant increase in length and dry weight of root and shoot of sunflower (Helianthus annuus) after inoculation with strain EOO26. Plants inoculated with strain EOO26 resulted in increase in Cu uptake by 8.6-fold for roots and 1.9-fold for leaves than uninoculated plants. The total plant uptake in inoculated Cu treatment was 2.6-fold higher than uninoculated one, which is much higher than the previously reported Cu accumulating plants. The excellent adaptation abilities and promising metal removal efficiency strongly indicate superiority of strain EOO26 for phytoremediation of Cu-contamination and may work effectively for Cu removal from contaminated soils.

Rhizobacterial species richness improves sorghum growth and soil nutrient synergism in a nutrient-poor greenhouse soil

Although microbes influence plant growth, little is known about the impact of microbial diversity on plant fitness trade-offs, intraspecific-interactions, and soil nutrient dynamics in the context of biodiversity-ecosystem functioning (BEF) research. The BEF theory states that higher species richness can enhance ecosystem functioning. Thus, we hypothesize that rhizobacterial species richness will alter sorghum (Sorghum bicolor L.) growth, soil nutrient dynamics and interactions (antagonism or synergism) in a nutrient-poor greenhouse soil. Using six rhizobacterial species in a BEF experiment, we tested the impact of a species richness gradient (0, 1, 3, 5 or 6 species per community) on plant growth, nutrient assimilation, and soil nutrient dynamics via seed-inoculation. Our experiment included, one un-inoculated control, six rhizobacterial monoculture (Pseudomonas poae, Pseudomonas sp., Bacillus pumilus., Pantoea agglomerance., Microbacterium sp., and Serratia marcescens), and their nine mixture treatments in triplicate (48). Rhizobacterial species richness enhanced per pot above- or below-ground dry mass. However, the per plant growth and plant nutrient assimilation declined, most likely, due to microbial-driven competitive interactions among sorghum plants. But nevertheless, some rhizobacterial monoculture and mixture treatments improved per plant (shoot and root) growth and nutrient assimilation as well. Soil nutrient contents were mostly lower at higher plant-associated rhizobacterial diversity; among these, the soil Zn contents decreased significantly across the rhizobacterial diversity gradient. Rhizobacterial diversity promoted synergistic interactions among soil nutrients and improved root–soil interactions. Overall, our results suggest that a higher rhizobacterial diversity may enhance soil–plant interactions and total productivity under resource limited conditions.

Bacillus subtilis strain GOT9 confers enhanced tolerance to drought and salt stresses in Arabidopsis thaliana and Brassica campestris

Soil is a primary source of water and inorganic nutrients vital for plant growth. In particular, the rhizosphere, a microecological region around the plant roots, is enriched with root exudates that enable beneficial microbial communities to form. Plant growth-promoting rhizobacteria (PGPR) are rhizosphere bacteria that contribute to the improvement of plant growth through diverse physiological mechanisms. Identifying PGPR is beneficial for agriculture because their use can effectively increase the productivity of plants without the harmful side effects of chemical fertilizers. To further enrich the pool of PGPR that contribute to abiotic stress resistance in plants, we screened roughly 491 bacteria that had previously been isolated in soil from Gotjawal in Jeju island, South Korea. Among several candidates, the application of Bacillus subtilis strain GOT9, led to the enhancement of drought and salt stress tolerance in Arabidopsis. In agreement with the increased stress tolerance phenotypes, its application resulted in increases in the transcripts of various drought stress- and salt stress-inducible genes in the absence or presence of the stresses. Furthermore, the treatment resulted in improved lateral root growth and development in Arabidopsis. GOT9 also led to enhanced tolerance against drought and salt stresses and to upregulation of drought-inducible genes in Brassica, a closely related crop to Arabidopsis. Taken together, these results show that GOT9 could be utilized as a biotic resource that effectively minimizes damage to plants from environmental stresses.

Forest tree associated bacteria for potential biological control of Fusarium solani and of Fusarium kuroshium, causal agent of Fusarium dieback

Although the use of crop-associated bacteria as biological control agents of fungal diseases has gained increasing interest, the biotechnological potential of forest tree-associated microbes and their natural products has scarcely been investigated. The objective of this study was to identify bacteria or bacterial products with antagonistic activity against Fusarium solani and Fusarium kuroshium, causal agent of Fusarium dieback, by screening the rhizosphere and phyllosphere of three Lauraceae species. From 195 bacterial isolates, we identified 32 isolates that significantly reduced the growth of F. solani in vitro, which mostly belonged to bacterial taxa Bacillus, Pseudomonas and Actinobacteria. The antifungal activity of their volatile organic compounds (VOCs) was also evaluated. Bacterial strain Bacillus sp. CCeRi1-002, recovered from the rhizosphere of Aiouea effusa, showed the highest percentage of direct inhibition (62.5 %) of F. solani and produced diffusible compounds that significantly reduced its mycelial growth. HPLC-MS analyses on this strain allowed to tentatively identify bioactive compounds from three lipopeptide groups (iturin, surfactin and fengycin). Bacillus sp. CCeRi1-002 and another strain identified as Pseudomonas sp. significantly inhibited F. solani mycelial growth through the emission of VOCs. Chemical analysis of their volatile profiles indicated the likely presence of 2-nonanone, 2-undecanone, disulfide dimethyl and 1-butanol 3-methyl-, which had been previously reported with antifungal activity. In antagonism assays against F. kuroshium, Bacillus sp. CCeRi1-002 and its diffusible compounds exhibited significant antifungal activity and induced hyphal deformations. Our findings highlight the importance of considering bacteria associated with forest species and the need to include bacterial products in the search for potential antagonists of Fusarium dieback.

More Than the Sum of Its Parts: Microbiome Biodiversity as a Driver of Plant Growth and Soil Health

Microorganisms drive several processes needed for robust plant growth and health. Harnessing microbial functions is thus key to productive and sustainable food production. Molecular methods have led to a greater understanding of the soil microbiome composition. However, translating species or gene composition into microbiome functionality remains a challenge. Community ecology concepts such as the biodiversity–ecosystem functioning framework may help predict the assembly and function of plant-associated soil microbiomes. Higher diversity can increase the number and resilience of plant-beneficial functions that can be coexpressed and unlock the expression of plant-beneficial traits that are hard to obtain from any species in isolation. We combine well-established community ecology concepts with molecular microbiology into a workable framework that may enable us to predict and enhance soil microbiome functionality to promote robust plant growth in a global change context.

Phytobiome metabolism: beneficial soil microbes steer crop plants' secondary metabolism

Crops are negatively affected by abiotic and biotic stresses, however, plant-microbe cooperation allows prompt buffering of these environmental changes. Microorganisms exhibit an extensive metabolic capability to assist plants in reducing these burdens. Interestingly, beneficial microbes may also trigger, at the host side, a sequence of events from signal perception to metabolic responses leading to stress tolerance or protection against biotic threats. Although plants are well known for their vast chemical diversity, plant-microbial interactions often stimulate the production of a rich and different repertoire of metabolites in plants. The targeted microbial-plant interactions reprogramming plant metabolism represent potential means to foster various pest managements. However, the molecular mechanisms of microbial modulation of plant metabolic plasticity are still poorly understood. Here, we review an increasing amount of reports providing evidence for alterations to plant metabolism caused by beneficial microbial colonization. In addition, we highlight the vital importance of these metabolic reprograms for plants under stress erratic conditions. © 2019 Society of Chemical Industry.

Field-Specific Microbial Consortia Are Feasible: A Response to Kaminsky et al

Kaminsky et al. (Trends Biotechnol. 2019:37;140-151) discuss the conflicts in developing microbial inoculants for agriculture. The authors affirm that microbial inoculants should perform across a wide range of environments but rule out the feasibility of personalized inoculants for individual fields. Here, I propose customized microbial consortia for specific field environments.

Colonization and Competition Dynamics of Plant Growth-Promoting/Inhibiting Bacteria in the Phytosphere of the Duckweed Lemna minor

Despite the considerable role of aquatic plant-associated bacteria in host plant growth and nutrient cycling in aquatic environments, the mode of their plant colonization has hardly been understood. This study examined the colonization and competition dynamics of a plant growth-promoting bacterium (PGPB) and two plant growth-inhibiting bacteria (PGIB) in the aquatic plant Lemna minor (common duckweed). When inoculated separately to L. minor, each bacterial strain quickly colonized at approximately 10⁶ cells per milligram (plant fresh weight) and kept similar populations throughout the 7-day cultivation time. The results of two-membered co-inoculation assays revealed that the PGPB strain Aquitalea magnusonii H3 consistently competitively excluded the PGIB strain Acinetobacter ursingii M3, and strain H3 co-existed at almost 1:1 proportion with another PGIB strain, Asticcacaulis excentricus M6, regardless of the inoculation ratios (99:1-1:99) and inoculation order. We also found that A. magnusonii H3 exerted its growth-promoting effect over the negative effects of the two PGIB strains even when only a small amount was inoculated, probably due to its excellent competitive colonization ability. These experimental results demonstrate that there is a constant ecological equilibrium state involved in the bacterial colonization of aquatic plants.

Plant growth promoting bacteria: role in soil improvement, abiotic and biotic stress management of crops

Agricultural production-a major contributing factor towards global food supply-is highly reliant on field crops which are under severe threats ranging from poor soil quality, biotic, abiotic stresses and changing climatic conditions. To overcome these challenges, larger exertions are required to boost production of agricultural crops in a defensible mode. Since the evolution of fertilizers and pesticides, global crop productivity has experienced an unprecedented elevation, but at the cost of environmental and ecological unsustainability. To enhance the agricultural outputs in a sustainable way, the novel and eco-friendly strategies must be employed in agriculture, which would lead to reduced use of hazardous chemicals. Thus, the utilization of our knowledge about natural growth stimulators can lead to decrease reliance on fertilizers and pesticide which are widely used for increasing crop productivity. Among beneficial microbes, plant growth promoting bacteria offers excellent opportunities for their wide utilization in agriculture to manage soil quality and other factors which correspond to limited growth and yield output of major field crops. The aim of this review is to examine the potential role of plant growth stimulating bacteria in soil fertility and enabling crops to cope with biotic and abiotic challenges.

Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress

The modification of rhizosphere microbial diversity and ecological processes are of rising interest as shifting in microbial community structure impacts the mutual role of host-microbe interactions. Nevertheless, the connection between host-microbial community diversity, their function under biotic stress in addition to their impact on plant performances is poorly understood. The study was designed with the aim to analyze the tripartite interactions among Chitiniphilus sp., Streptomyces sp. and their combination with indigenous rhizospheric microbial population of Bacopa monnieri for enhancing the plant growth and bacoside A content under Meloidogyne incognita stress. Overall, plants treated with the microbial combination recorded enhanced growth as illustrated by significantly higher biomass (2.0 fold), nitrogen uptake (1.8 fold) and bacoside A content (1.3 fold) along with biocontrol efficacy (58.5%) under nematode infected field. The denaturing gradient gel electrophoresis (DGGE) fingerprints of 16S-rDNA revealed that microbial inoculations are major initiators of bacterial community structure in the plant rhizosphere. Additionally, the plants treated with microbial combination showed maximum diversity viz., Shannon's (3.29), Margalef's (4.21), and Simpson's (0.96) indices. Likewise the metabolic profiling data also showed a significant variation among the diversity and evenness indices upon microbial application on the native microflora. We surmise that the application of beneficial microbes in combinational mode not only helped in improving the microbial community structure but also successfully enhanced plant and soil health under biotic stress.

Potentially toxic elements to maize in agricultural soils-microbial approach of rhizospheric and bulk soils and phytoaccumulation

Maize fields near Mae Tao Creek in Pha Te Village, Tak Province, Thailand are contaminated with Zn, Cd, and Pb. This research studied the interaction between levels of the metals contaminating the soil and maize development, heavy metal accumulation in the seeds, and the soil bacterial community structure. Our field experiment was carried out in five plots with metal contents that gradually decreased from a high level near the creek to a lower level further into the land: Zn 380-4883 mg kg^-1, Cd 6-85 mg kg^-1, and Pb 34-154 mg kg^-1. Cultivation and isolation on nutrient agar (NA) was utilized to study the culturable bacterial community, and polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was utilized for the unculturable bacterial communities. All statistical analyses clearly indicated that rainfall and irrigation were the main factors affecting total Zn concentration and bioavailable Zn, Cd, and Pb in the field. The variation in the contents of the heavy metals was weakly correlated with the culturable bacterial community indices (Shannon-Wiener, evenness and richness), but the contents resulted in a difference in the overall diversity of the bacteria in the soil. The richness, numbers of culturable rhizobacteria, and maize growth stage significantly affected the amount of Zn and Cd that accumulated in the roots. In addition, maize accumulated a high level of Zn in the seeds, while the low contents of Cd and Pb in the seeds were below our limit of detection. The results obtained could be informative for the management of maize cultivation in the area.

Synergistic and antagonistic effects of mixing monospecific soils on plant-soil feedbacks

BACKGROUND AND AIMS

Plants influence the soil they grow in, and this can alter the performance of other, later growing plants in the same soil. This is called plant-soil feedback and is usually tested with monospecific soils, i.e. soils that are conditioned by one plant species. Here, we test if plant-soil feedbacks of inocula consisting of mixtures of monospecific soils can be predicted from the effects of the component inocula.

METHODS

Chrysanthemum plants were grown in sterile soil inoculated with eight monospecific conditioned soils and with mixtures consisting of all pairwise combinations. Plant biomass and leaf yellowness were measured and the additivity was calculated.

RESULTS

On average, plant biomass in the mixed inocula was slightly but significantly (6%) lower than predicted. In contrast, when growing in mixed inocula, plants showed 38% less disease symptoms than predicted. Moreover, the larger the difference between the effects of the two monospecific soils on plant growth, the higher the observed effect in the mixture exceeded the predicted effects.

CONCLUSIONS

We show that mixed monospecific soils interact antagonistically in terms of plant growth, but synergistically for disease symptoms. Our study further advances our understanding of plant-soil feedbacks, and suggests that mixing soils can be a powerful tool to steer soil microbiomes to improve plant-soil feedback effects.

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions

Rhizobacteria associated with crops constitute an important source of potentially beneficial microorganisms with plant growth promoting activity or antagonistic effects against phytopathogens. In this study, we evaluated the plant growth promoting activity of 11 bacterial isolates that were obtained from the rhizosphere of healthy avocado trees and from that of avocado trees having survived root rot infestations. Seven bacterial isolates, belonging to the genera Bacillus, Pseudomonas and Arthrobacter, promoted in vitro growth of Arabidopsis thaliana. These isolates were then tested for antagonistic activity against Phytophthora cinnamomi, in direct dual culture assays. Two of those rhizobacterial isolates, obtained from symptomatic-declining trees, displayed antagonistic activity. Isolate A8a, which is closely related to Bacillus acidiceler, was also able to inhibit P. cinnamomi growth in vitro by 76% through the production of volatile compounds. Solid phase microextraction (SPME) and analysis by gas chromatography coupled with mass spectrometry (GC-MS) allowed to tentatively identify the main volatiles emitted by isolate A8a as 2,3,5-trimethylpyrazine, 6,10-dimethyl-5,9-undecadien-2-one and 3-amino-1,3-oxazolidin-2-one. These volatile compounds have been reported to show antifungal activity when produced by other bacterial isolates. These results confirm the significance of rhizobacteria and suggest that these bacteria could be used for biocontrol of soil borne oomycetes through their volatiles emissions.

Interplay between r- and K-strategists leads to phytoplankton underyielding under pulsed resource supply

Fluctuations in nutrient ratios over seasonal scales in aquatic ecosystems can result in overyielding, a condition arising when complementary life-history traits of coexisting phytoplankton species enables more complete use of resources. However, when nutrient concentrations fluctuate under short-period pulsed resource supply, the role of complementarity is less understood. We explore this using the framework of Resource Saturation Limitation Theory (r-strategists vs. K-strategists) to interpret findings from laboratory experiments. For these experiments, we isolated dominant species from a natural assemblage, stabilized to a state of coexistence in the laboratory and determined life-history traits for each species, important to categorize its competition strategy. Then, using monocultures we determined maximum biomass density under pulsed resource supply. These same conditions of resource supply were used with polycultures comprised of combinations of the isolated species. Our focal species were consistent of either r- or K-strategies and the biomass production achieved in monocultures depended on their efficiency to convert resources to biomass. For these species, the K-strategists were less efficient resource users. This affected biomass production in polycultures, which were characteristic of underyielding. In polycultures, K-strategists sequestered more resources than the r-strategists. This likely occurred because the intermittent periods of nutrient limitation that would have occurred just prior to the next nutrient supply pulse would have favored the K-strategists, leading to overall less efficient use of resources by the polyculture. This study provides evidence that fluctuation in resource concentrations resulting from pulsed resource supplies in aquatic ecosystems can result in phytoplankton assemblages' underyielding.

Defining the functional traits that drive bacterial decomposer community productivity

Microbial communities are essential to a wide range of ecologically and industrially important processes. To control or predict how these communities function, we require a better understanding of the factors which influence microbial community productivity. Here, we combine functional resource use assays with a biodiversity–ecosystem functioning (BEF) experiment to determine whether the functional traits of constituent species can be used to predict community productivity. We quantified the abilities of 12 bacterial species to metabolise components of lignocellulose and then assembled these species into communities of varying diversity and composition to measure their productivity growing on lignocellulose, a complex natural substrate. A positive relationship between diversity and community productivity was caused by a selection effect whereby more diverse communities were more likely to contain two species that significantly improved community productivity. Analysis of functional traits revealed that the observed selection effect was primarily driven by the abilities of these species to degrade β-glucan. Our results indicate that by identifying the key functional traits underlying microbial community productivity we could improve industrial bioprocessing of complex natural substrates.

Evaluation of environmental bacterial communities as a factor affecting the growth of duckweed Lemna minor

BACKGROUND

Duckweed (family Lemnaceae) has recently been recognized as an ideal biomass feedstock for biofuel production due to its rapid growth and high starch content, which inspired interest in improving their productivity. Since microbes that co-exist with plants are known to have significant effects on their growth according to the previous studies for terrestrial plants, this study has attempted to understand the plant-microbial interactions of a duckweed, Lemna minor, focusing on the growth promotion/inhibition effects so as to assess the possibility of accelerated duckweed production by modifying co-existing bacterial community.

RESULTS

Co-cultivation of aseptic L. minor and bacterial communities collected from various aquatic environments resulted in changes in duckweed growth ranging from -24 to +14% compared to aseptic control. A number of bacterial strains were isolated from both growth-promoting and growth-inhibitory communities, and examined for their co-existing effects on duckweed growth. Irrespective of the source, each strain showed promotive, inhibitory, or neutral effects when individually co-cultured with L. minor. To further analyze the interactions among these bacterial strains in a community, binary combinations of promotive and inhibitory strains were co-cultured with aseptic L. minor, resulting in that combinations of promotive-promotive or inhibitory-inhibitory strains generally showed effects similar to those of individual strains. However, combinations of promotive-inhibitory strains tended to show inhibitory effects while only Aquitalea magnusonii H3 exerted its plant growth-promoting effect in all combinations tested.

CONCLUSION

Significant change in biomass production was observed when duckweed was co-cultivated with environmental bacterial communities. Promotive, neutral, and inhibitory bacteria in the community would synergistically determine the effects. The results indicate the possibility of improving duckweed biomass production via regulation of co-existing bacterial communities.

Probiotic Diversity Enhances Rhizosphere Microbiome Function and Plant Disease Suppression

Bacterial communities associated with plant roots play an important role in the suppression of soil-borne pathogens, and multispecies probiotic consortia may enhance disease suppression efficacy. Here we introduced defined Pseudomonas species consortia into naturally complex microbial communities and measured the importance of Pseudomonas community diversity for their survival and the suppression of the bacterial plant pathogen Ralstonia solanacearum in the tomato rhizosphere microbiome. The survival of introduced Pseudomonas consortia increased with increasing diversity. Further, high Pseudomonas diversity reduced pathogen density in the rhizosphere and decreased the disease incidence due to both intensified resource competition and interference with the pathogen. These results provide novel mechanistic insights into elevated pathogen suppression by diverse probiotic consortia in naturally diverse plant rhizospheres. Ecologically based community assembly rules could thus play a key role in engineering functionally reliable microbiome applications.

The increasing demand for food supply requires more-efficient control of plant diseases. The use of probiotics, i.e., naturally occurring bacterial antagonists and competitors that suppress pathogens, has recently reemerged as a promising alternative to agrochemical use. It is, however, still unclear how many and which strains we should choose for constructing effective probiotic consortia. Here we present a general ecological framework for assembling effective probiotic communities based on in vitro characterization of community functioning. Specifically, we show that increasing the diversity of probiotic consortia enhances community survival in the naturally diverse rhizosphere microbiome, leading to increased pathogen suppression via intensified resource competition and interference with the pathogen. We propose that these ecological guidelines can be put to the test in microbiome engineering more widely in the future.

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture

Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions.

Bacteria as growth-promoting agents for citrus rootstocks

The microbial community plays an essential role in maintaining the ecological balance of soils. Interactions between microorganisms and plants have a major influence on the nutrition and health of the latter, and growth-promoting rhizobacteria can be used to improve plant development through a wide range of mechanisms. Therefore, the objective of the present study was to evaluate bacteria as growth-promoting agents for citrus rootstocks. A total of 30 bacterial isolates (11 of Bacillus spp., 11 actinobacteria, and 8 lactic acid bacteria) were evaluated in vitro for indoleacetic acid production, phosphate solubilization, and nitrogen (N) fixation. In vivo testing consisted of growth promotion trials of the bacterial isolates that yielded the best results on in vitro tests with three rootstocks: Swingle citrumelo [Citrus×paradisi Macfad cv. Duncan×Poncirus trifoliata (L.) Raf.], Sunki mandarin (Citrus sunki Hort. ex Tan), and rangpur (Citrus×limonia Osbeck). The parameters of interest were height, number of leaves, stem diameter, shoot and root dry mass, and total dry mass at 150days after germination. The results showed that most bacterial isolates were capable of IAA production. Only one lactic acid bacterium isolate (BL06) solubilized phosphate, with a high solubilization index (PSI>3). In the actinobacteria group, isolates ACT01 (PSI=2.09) and ACT07 (PSI=2.01) exhibited moderate phosphate-solubilizing properties. Of the Bacillus spp. isolates, only CPMO6 and BM17 solubilized phosphate. The bacterial isolates that most fixated nitrogen were BM17, ACT11, and BL24. In the present study, some bacteria were able to promote growth of citrus rootstocks; however, this response was dependent on plant genotype and isolate. Bacillus spp. BM16 and CPMO4 were able to promote growth of Swingle citrumelo. In Sunki mandarin plants, the best treatment results were obtained with BM17 (Bacillus sp.) and ACT11 (actinobacteria). For Rangpur lime rootstock, only BM05 (Bacillus sp.) was able to promote increase in two parameters assessed, height and number of leaves. When the bacterial isolates were used in mixture there was not promoted growth of plants on rootstocks. This fact may be associated with the different mechanisms of action of each bacteria involved or with the presence of competition among the microorganisms of the mixture.