Rhizosphere Competence Research Articles

Persistence and Microbiome Modification in Rhizoctonia solani-Inoculated Rhizosphere Following Amendment with a Bacillus Biocontrol Agent

Bacterial biocontrol agents that antagonize soilborne pathogens are increasingly considered alternatives to chemical pesticides, but their in vivo efficacy is often inconsistent, restricting commercial use. The efficacy of a biocontrol agent can depend on rhizosphere competence and its interaction with native microbiomes, which can affect ecosystem functioning. This study investigated the capacity of a Bacillus cereus sensu lato biocontrol strain (S-25) to persist on roots and in the rhizosphere of cucumber and evaluated its impact on bacterial and fungal community composition in the rhizosphere in the absence and presence of Rhizoctonia solani, the causative agent of damping-off disease in young seedlings. Following amendment, S-25 abundance in the cucumber rhizosphere decreased by two orders of magnitude but remained relatively high for the duration of the experiment, in contrast to the root surface, where it was not detected. Amendment with S-25 significantly reduced the incidence of disease caused by R. solani without reducing the relative abundance of the fungal pathogen. Interestingly, R. solani did not substantially alter the rhizosphere microbial community, whereas S-25 reduced bacterial diversity and facilitated a shift in community composition, with increased relative abundance of Acidobacteriota and Actinomycetota, and reduced abundance of Pseudomonadota, Bacteroidota, and Verrucomicrobiota. Collectively, this study provides important insights into the mode of persistence of biocontrol agents and their effect on native microbiomes in the rhizosphere of pathogen-inoculated plants. It demonstrates that amendment can significantly alter local microbiomes and suggests that optimizing amendment regimes or selecting strains with higher rhizosphere competence can enhance future biocontrol agents.

Wheat rhizosphere dynamics of Trichoderma gamsii A5MH and suppression of a Pythium root rot-Fusarium crown rot disease complex over two consecutive cropping seasons.

Determine the wheat rhizosphere competence of Trichoderma gamsii strain A5MH and in planta suppression of the Pythium root and Fusarium crown rot pathogens Globisporangium irregulare and Fusarium pseudograminearum. Wheat was continuously cropped (eight years) at a minimum tillage, low growing season rainfall (GSR≤170mm) site shown as highly conducive to Pythium root and Fusarium crown rots. Root isolation frequency (RIF) and qPCR were used to determine the rhizosphere dynamics of strain A5MH and the target pathogens at tillering, grain harvest, and in postharvest stubble over the final 2 years. Strain A5MH actively colonized the wheat rhizosphere throughout both growing seasons, had high root abundance at harvest [log 4.5 genome copies (GC) g-1] and persisted in standing stubble for at least 293-d postinoculation. Globisporangium irregulare was most abundant in roots at tillering, whereas F. pseudograminearum was only abundant at harvest and up to 9-fold greater in the drier, second year (GSR 105mm). Strain A5MH decreased RIF of both pathogens by up to 40%, root abundance of G. irregulare by 100-fold, and F. pseudogaminearum by 700-fold, but was ineffective against crown rot in the second year when pathogen abundance was>log 6.0 GC g-1 root. Strain A5MH increased crop emergence and tillering biomass by up to 40%. Further trials are required to determine if the A5MH-induced pathogen suppression translates to yield improvements in higher rainfall regions where non-cereal rotations reduce crown rot inoculum.

The conserved iol gene cluster in Pseudomonas is involved in rhizosphere competence

The Pseudomonas genus has shown great potential as a sustainable solution to support agriculture through its plant-growth-promoting and biocontrol activities. However, their efficacy as bioinoculants is limited by unpredictable colonization in natural conditions. Our study identifies the iol locus, a gene cluster in Pseudomonas involved in inositol catabolism, as a feature enriched among superior root colonizers in natural soil. Further characterization revealed that the iol locus increases competitiveness, potentially caused by an observed induction of swimming motility and the production of fluorescent siderophore in response to inositol, a plant-derived compound. Public data analyses indicate that the iol locus is broadly conserved in the Pseudomonas genus and linked to diverse host-microbe interactions. Together, our findings suggest the iol locus as a potential target for developing more effective bioinoculants for sustainable agriculture.

Assessing rhizosphere Trichoderma asperellum strains for root colonizing and antagonistic competencies against Fusarium wilt through molecular and biochemical responses in castor

The study was aimed at identifying the effective strain(s) of Trichoderma asperellum to colonize castor roots, promote growth and limit pathogen infection. Two castor genotypes; DCS-107 and 48-1 varying for stress tolerance to Fusarium wilt were treated with four Trichoderma asperellum strains; 7316, N13, TV5 and TV2B16 to analyze root colonizing and antagonistic competencies. A significant decline in the colony-forming unit (CFU) counts was observed in Trichoderma-treated bulk and rhizosphere soil compared to controls indicating a high rhizosphere competence of the Trichoderma asperellum strains; 7316 followed by N13. These strains also showed high mycoparasitic propensity against Fusarium oxysporum through dual culture-confrontation and in-planta assays. Bio-priming with Trichoderma strains enhanced plant growth in the tolerant genotype, DCS-107 compared to the susceptible genotype, 48-1 suggesting differential responses of the host genotypes. An increase in shoot length by 46.2, 28.9 and 21.7% was observed upon treatment of DCS-107 genotype with the Trichoderma strains, 7316, N13 and TV5 respectively. Further, a quantitative polymerase chain reactions (qPCRs) of 13 stress and defence response genes revealed gene transcript reprogramming, causing a transient repression of the plant immune responses to enable root colonization. Further, biochemical analysis revealed higher antioxidant enzyme activity of catalase, superoxide dismutase and glutathione peroxidase and total phenol content in co-stressed conditions compared to the controls suggesting that Trichoderma confers protection against oxidative stress damage. Trichoderma strains, 7316, N13 and TV5, either individually or in combination could be utilized as potential biocontrol agents to enhance growth and confer resistance to wilt pathogen, Fusarium oxysporum ricini.

Wheat rhizosphere colonization by Bacillus amyloliquefaciens W10 and Pseudomonas protegens FD6 suppress soil and in planta abundance of the sharp eyespot pathogen Rhizoctonia cerealis.

Develop quantitative assays (qPCR) to determine the wheat rhizosphere competence of inoculant strains Bacillus amyloliquefaciens W10 and Pseudomonas protegens FD6, and their suppressive efficacies against the sharp eyespot pathogen Rhizoctonia cerealis. Antimicrobial metabolites of strains W10 and FD6 decreased in vitro growth of R. cerealis. A qPCR assay for strain W10 was designed from a diagnostic AFLP fragment and the rhizosphere dynamics of both strains in wheat seedlings were compared by culture-dependent (CFU) and qPCR assays. The qPCR minimum detection limits for strains W10 and FD6 were log 3.04 and log 4.03 genome (cell) equivalents g-1 soil, respectively. Inoculant soil and rhizosphere abundance determined by CFU and qPCR were highly correlated (r>0.91). In wheat bioassays, rhizosphere abundance of strain FD6 was up to 80-fold greater (P<0.001) than strain W10 at 14 and 28 days postinoculation. Both inoculants reduced (P<0.05) rhizosphere soil and root abundance of R. cerealis by up to 3-fold. Strain FD6 exhibited greater abundance in wheat roots and rhizosphere soil than strain W10 and both inoculants decreased rhizosphere abundance of R. cerealis.

A 1-aminocyclopropane-1-carboxylate deaminase MrACCD from Metarhizium robertsii is associated with plant growth promotion for Metarhizium spp

Besides killing insects, Metarhizium spp. have shown another ecological role as plant associates. Partial genra and groups of these entomopathogenic fungi act as plant growth promoters during root colonization. Here, we report that Metarhizium robertsii produces a 1-aminocyclopropane-1-carboxylate (ACC) deaminase (ACCD encoded by MracdS, MrACCD), which is involved in promoting early vegetative growth in wheat, while Metarhizium acridum lacks a functional ACCD, although a gene encoding for a putative ACCD has been identified in its genome. MracdS expression was up-regulated by a max 10.7-fold with 3 mM ACC and high ACCD enzymatic activities were induced by either ACC (7.5-fold) or wheat root (3.2-fold). In contrast, no ACCD activity was detected in M. acridum in the presence of both inducers. In pot assay, wheat seeds were treated with wild-type M. robertsii (Mr23), wild-type M. acridum (Mac324), MracdS disruption mutant (ΔMracdS) and M. acridum transformant harboring heterologous MracdS (Mac324-MracdS). Relative to the control seeds treated with heat-killed conidia, Mr23, ΔMracdS and Mac324-MracdS increased root length (by 66.2, 31.8 and 40.2%), and plant biomass (by 56.6, 42.1 and 40.9%). Nevertheless, ΔMracdS deficient in ACCD activity heavily impaired its capability of wheat growth promotion by decrease of 20.7% in root length relative to Mr23. In addition, Mr23 and Mac324-MracdS also increased shoot growth (by 42.3, and 42.7%) while ΔMracdS failed. Mac324 showed no effect on plant growth during the test. These data suggest a role for ACCD in the plant growth promotion effect by M. robertsii, which is irrelevant to Metarhizium colonization of roots since rhizosphere competency of both Mr23 and Mac324 are unaffected by the change of ACCD activity.

Competition in the Phaseolus vulgaris-Rhizobium symbiosis and the role of resident soil rhizobia in determining the outcomes of inoculation

Background and AimsInoculation of legumes with effective N2-fixing rhizobia is a common practice to improve farming profitability and sustainability. To succeed, inoculant rhizobia must overcome competition for nodulation by resident soil rhizobia that fix N2 ineffectively. In Kenya, where Phaseolus vulgaris (common bean) is inoculated with highly effective Rhizobium tropici CIAT899 from Colombia, response to inoculation is low, possibly due to competition from ineffective resident soil rhizobia. Here, we evaluate the competitiveness of CIAT899 against diverse rhizobia isolated from cultivated Kenyan P. vulgaris.MethodsThe ability of 28 Kenyan P. vulgaris strains to nodulate this host when co-inoculated with CIAT899 was assessed. Rhizosphere competence of a subset of strains and the ability of seed inoculated CIAT899 to nodulate P. vulgaris when sown into soil with pre-existing populations of rhizobia was analyzed.ResultsCompetitiveness varied widely, with only 27% of the test strains more competitive than CIAT899 at nodulating P. vulgaris. While competitiveness did not correlate with symbiotic effectiveness, five strains were competitive against CIAT899 and symbiotically effective. In contrast, rhizosphere competence strongly correlated with competitiveness. Soil rhizobia had a position-dependent numerical advantage, outcompeting seed-inoculated CIAT899 for nodulation of P. vulgaris, unless the resident strain was poorly competitive.ConclusionSuboptimally effective rhizobia can outcompete CIAT899 for nodulation of P. vulgaris. If these strains are widespread in Kenyan soils, they may largely explain the poor response to inoculation. The five competitive and effective strains characterized here are candidates for inoculant development and may prove better adapted to Kenyan conditions than CIAT899.

Integrated analysis of potential microbial consortia, soil nutritional status, and agro-climatic datasets to modulate P nutrient uptake and yield effectiveness of wheat under climate change resilience.

Climate change has a devastating effect on wheat production; therefore, crop production might decline by 2030. Phosphorus (P) nutrient deficiency is another main limiting factor of reduced yield. Hence, there is a dire need to judiciously consider wheat yield, so that human requirements and nutrition balance can be sustained efficiently. Despite the great significance of biostimulants in sustainable agriculture, there is still a lack of integrated technology encompassing the successful competitiveness of inoculated phosphate-solubilizing bacteria (PSB) in agricultural systems in the context of climatic conditions/meteorological factors and soil nutritional status. Therefore, the present study reveals the modulation of an integrated P nutrient management approach to develop potential PSB consortia for recommended wheat varieties by considering the respective soil health and agro-climatic conditions. The designed consortia were found to maintain adequate viability for up to 9 months, verified through field emission scanning electron microscopy and viable count. Furthermore, a significant increase in grain yield (5%-8%) and seed P (4%) content was observed in consortia-inoculated wheat plants with 20% reduced Diammonium phosphate (DAP) application under net house conditions. Fluorescence in situ hybridization analysis of roots and amplification of the gcd gene of Ochrobactrum sp. SSR indicated the survival and rhizosphere competency of the inoculated PSB. Categorical principal component analysis (CAT-PCA) showed a positive correlation of inoculated field-grown wheat varieties in native soils to grain yield, soil P content, and precipitation for sites belonging to irrigated plains and seed P content, soil organic matter, and number of tillers for sites belonging to Northern dry mountains. However, the impact of inoculation at sites belonging to the Indus delta was found significantly correlated to soil potassium (K) content, electrical conductivity (EC), and temperature. Additionally, a significant increase in grain yield (15%) and seed P (14%) content was observed in inoculated wheat plants. Thus, the present study demonstrates for the first time the need to integrate soil biological health and agro-climatic conditions for consistent performance of augmented PSB and enhanced P nutrient uptake to curtail soil pollution caused by the extensive use of agrochemicals. This study provides innovative insights and identifies key questions for future research on PSB to promote its successful implementation in agriculture.

The Impact of Trichoderma spp. on Agriculture and Their Identification

Fungi belonging to the genus Trichoderma were discovered in the late 18th century and they have been utilized ever since their biocontrol potential was uncovered. Trichoderma species have greatly assisted the blooming of agricultural industries due to their aggressive characteristics against plant pathogens. Their role as a biocontrol agent is owed to their mode of mechanisms: induction of the plant’s defence system, mycoparasitism, the production of secondary metabolites, and rhizosphere competence. Meanwhile, their role as a biofertilizer became evident when studies conducted hitherto showed that they could increase plant’s nutrient uptake, improve the yield of crops, enhance plant’s tolerance to external stresses, and induce the germination of seeds. Since this genus is hyperdiverse, accurate identification of them is indispensable. In the past, Trichoderma spp. were identified via their morphological characteristics. However, the emergence of molecular technology has made the identification of Trichoderma isolates more precise, explicit and rapid. Hence, this paper briefly reviews the accumulated knowledge in respect of this genus. Nevertheless, an extensive study must be done in order to explore the potential in improving the natural strains of Trichoderma.

The Suppressive Effects of Biochar on Above- and Belowground Plant Pathogens and Pests: A Review.

Soilborne pathogens and pests in agroecosystems are serious problems that limit crop yields. In line with the development of more ecologically sustainable agriculture, the possibility of using biochar to control pests has been increasingly investigated in recent years. This work provides a general overview of disease and pest suppression using biochar. We present an updated view of the literature from 2015 to 2022 based on 61 articles, including 117 experimental case studies. We evaluated how different biochar production feedstocks, pyrolysis temperatures, application rates, and the pathosystems studied affected disease and pest incidence. Fungal pathogens accounted for 55% of the case studies, followed by bacteria (15%), insects and nematodes (8%), oomycetes and viruses (6%), and only 2% parasitic plants. The most commonly studied belowground pathogen species were Fusarium oxysporum f. sp. radicis lycopersici in fungi, Ralstonia solanacearum in bacteria, and Phytophthora capisci in oomycetes, while the most commonly studied pest species were Meloidogyne incognita in nematodes, Epitrix fuscula in insects, and both Phelipanche aegyptiaca and Orobanche crenata in parasitic plants. Biochar showed suppression efficiencies of 86% for fungi, 100% for oomycetes, 100% for viruses, 96% for bacteria, and 50% for nematodes. Biochar was able to potentially control 20 fungal, 8 bacterial, and 2 viral plant pathogens covered by our review. Most studies used an application rate between 1% and 3%, a pyrolysis temperature between 500 °C and 600 °C, and a feedstock based on sawdust and wood waste. Several mechanisms have been proposed to explain disease suppression by biochar, including induction of systemic resistance, enhancement of rhizosphere competence of the microbial community, and sorption of phytotoxic compounds of plant and/or microbial origin. Overall, it is important to standardize biochar feedstock and the rate of application to improve the beneficial effects on plants in terms of disease control.

Innovative Rhizosphere-Based Enrichment under P-Limitation Selects for Bacterial Isolates with High-Performance P-Solubilizing Traits.

The use of phosphate solubilizing bacteria (PSB) as inoculants for the rhizosphere is a well-known strategy to mitigate P-deficiency in plants. However, despite the multiple modes of action to render P available for plants, PSB often fail to deliver in the field as their selection is often based on a single P-solubilizing trait assessed in vitro. Anticipating these shortcomings, we screened 250 isolates originating from rhizosphere-based enriched consortia for the main in vitro P-solubilizing traits, and subsequently grouped the isolates through trait-based HCPC (hierarchical clustering on principal components). Representative isolates of each cluster were tested in an in planta experiment to compare their in vitro P-solubilizing traits with their in planta performance under conditions of P-deprivation. Our data convincingly show that bacterial consortia capable to mitigate P-deficiency in planta were enriched in bacterial isolates that had multiple P-solubilizing traits in vitro and that had the capacity to mitigate plant P-stress in planta under P-deprived conditions. Furthermore, although it was assumed that bacteria that looked promising in vitro would also have a positive effect in planta, our data show that this was not always the case. Opposite, lack of performance in vitro did not automatically result in a lack of performance in planta. These results corroborate the strength of the previously described in planta-based enrichment and selection technique for the isolation of highly efficient rhizosphere competent PSB. IMPORTANCE With the growing awareness on the ecological impact of chemical phosphate fertilizers, research concerning the use of phosphate solubilizing bacteria (PSB) as a sustainable alternative for, or addition to these fertilizers is of paramount importance. In previous research, we successfully implemented a plant-based enrichment technique for PSB, which simultaneously selected for the rhizosphere competence and phosphate solubilizing characteristics of bacterial suspensions. Current research follows up on our previous findings, whereas we screened 250 rhizobacteria for their P-solubilizing traits and were able to substantiate the results obtained from the enriched suspensions at a single-isolate level. With this research, we aim for a paradigm shift toward the plant-based selection of PSB, which is a more holistic approach compared to the plate-based methods. We emphasize the strength of the previously described plant-based enrichment and selection technique for the isolation of highly efficient and diverse PSB.

Improvement of fitness and biocontrol properties of Pseudomonas putida via an extracellular heme peroxidase.

The extracellular 373‐kDa PehA heme peroxidase of Pseudomonas putida KT2440 has two enzymatic domains which depend on heme cofactor for their peroxidase activity. A null pehA mutant was generated to examine the impact of PehA in rhizosphere colonization competence and the induction of plant systemic resistance (ISR). This mutant was not markedly hampered in colonization efficiency. However, increase in pehA dosage enhanced colonization fitness about 30 fold in the root and 900 fold in the root apex. In vitro assays with purified His‐tagged enzymatic domains of PehA indicated that heme‐dependent peroxidase activity was required for the enhancement of root tip colonization. Evaluation of live/dead cells confirmed that overexpression of pehA had a positive effect on bacterial cell viability. Following root colonization of rice plants by KT2440 strain, the incidence of rice blast caused by Magnaporthe oryzae was reduced by 65% and the severity of this disease was also diminished in comparison to non‐treated plants. An increase in the pehA dosage was also beneficial for the control of rice blast as compared with gene inactivation. The results suggest that PehA helps P. putida to cope with the plant‐imposed oxidative stress leading to enhanced colonization ability and concomitant ISR‐elicitation.

Microbe Related Chemical Signalling and Its Application in Agriculture.

The agriculture sector has been put under tremendous strain by the world’s growing population. The use of fertilizers and pesticides in conventional farming has had a negative impact on the environment and human health. Sustainable agriculture attempts to maintain productivity, while protecting the environment and feeding the global population. The importance of soil-dwelling microbial populations in overcoming these issues cannot be overstated. Various processes such as rhizospheric competence, antibiosis, release of enzymes, and induction of systemic resistance in host plants are all used by microbes to influence plant-microbe interactions. These processes are largely founded on chemical signalling. Producing, releasing, detecting, and responding to chemicals are all part of chemical signalling. Different microbes released distinct sorts of chemical signal molecules which interacts with the environment and hosts. Microbial chemicals affect symbiosis, virulence, competence, conjugation, antibiotic production, motility, sporulation, and biofilm growth, to name a few. We present an in-depth overview of chemical signalling between bacteria-bacteria, bacteria-fungi, and plant-microbe and the diverse roles played by these compounds in plant microbe interactions. These compounds’ current and potential uses and significance in agriculture have been highlighted.

Identification and profiling of silicate-solubilizing bacteria for plant growth-promoting traits and rhizosphere competence

Excessive use of synthetic fertilizers may negatively affect overall soil health and the environment. There is a need to come up with alternative strategies to ensure competitive yields of crops and at the same time maintain soil ecological balance. The use of soil microorganisms as microbial inoculants in agriculture is considered an alternative approach to enhance crop growth. Soil is a good source of microorganisms that are capable of producing different beneficial enzymes such as silicase, phosphatase and other growth-promoting enzymes which are important in crop growth. Soil beneficial microorganisms such as silicate-solubilizing bacteria play an important role in solubilizing insoluble forms of silicates that are important in crop growth. This study was conducted to identify and profile silicate-solubilizing bacteria (SSB) in Louisiana soils and to document the colonization potential of SSB in rice (Oryza sativa) plants. Bacterial isolates were spot-inoculated on silica agar medium and incubated at 37 °C for 48 h. The clearing zone around colonies was measured and used to compute for solubilization index (SI), i.e., halo diameter (mm)/colony diameter (mm). Despite of the abundance of microorganisms found in these soils only 20 bacterial isolates are capable of solubilizing silicates; 16 were with low (SI < 2.0) and 4 with intermediate (2.00 < SI < 4.00) solubilization capacities. Further analysis also revealed that three of the isolates with intermediate silicate solubilization capacities also produced plant growth-promoting enzymes: phosphatase, 1-aminocyclopropane-1-carboxylic acid deaminase and indole-3-acetic acid enzyme. Based on the sequencing information and the phylogenetic tree, the putative SSB were identified into four genera: Aeromonas, Bacillus, Enterobacter and Pseudomonas. The fluorescent microscopy analysis revealed that the GFP-tagged SSB can colonize roots of young rice seedlings, a good indicator of SSB potential as seed treatment for scaling up its application in production field. Furthermore, information on the survival of SSB inoculates in different soil-plant systems in Louisiana and impact of management practices on SSB activity and population are needed to fully develop this bio-based approach to improve Si nutrition in soil and plants.

The Type VI Secretion Systems in Plant-Beneficial Bacteria Modulate Prokaryotic and Eukaryotic Interactions in the Rhizosphere.

Rhizosphere colonizing plant growth promoting bacteria (PGPB) increase their competitiveness by producing diffusible toxic secondary metabolites, which inhibit competitors and deter predators. Many PGPB also have one or more Type VI Secretion System (T6SS), for the delivery of weapons directly into prokaryotic and eukaryotic cells. Studied predominantly in human and plant pathogens as a virulence mechanism for the delivery of effector proteins, the function of T6SS for PGPB in the rhizosphere niche is poorly understood. We utilized a collection of Pseudomonas chlororaphis 30–84 mutants deficient in one or both of its two T6SS and/or secondary metabolite production to examine the relative importance of each T6SS in rhizosphere competence, bacterial competition, and protection from bacterivores. A mutant deficient in both T6SS was less persistent than wild type in the rhizosphere. Both T6SS contributed to competitiveness against other PGPB or plant pathogenic strains not affected by secondary metabolite production, but only T6SS-2 was effective against strains lacking their own T6SS. Having at least one T6SS was also essential for protection from predation by several eukaryotic bacterivores. In contrast to diffusible weapons that may not be produced at low cell density, T6SS afford rhizobacteria an additional, more immediate line of defense against competitors and predators.

The Sugar Transporter MST1 Is Involved in Colonization of Rhizosphere and Rhizoplane by Metarhizium robertsii.

ABSTRACTIt is widely recognized that plant-symbiotic fungi are supported by photosynthates; however, little is known about the molecular mechanisms underlying the utilization of plant-derived sugars by rhizospheric fungi. In the insect-pathogenic and plant-symbiotic fungus Metarhizium robertsii, we previously showed that the utilization of oligosaccharides by the transporter MRT (Metarhizium raffinose transporter) is important for rhizosphere competency. In this study, we identified a novel monosaccharide transporter (MST1) that is involved in the colonization of the rhizoplane and acts additively with MRT to colonize the rhizosphere. MST1 is not involved in infection of insects by M. robertsii. MST1 is an H+ symporter and is able to transport a broad spectrum of monosaccharides, including glucose, sorbose, mannose, rhamnose, and fructose. Deletion of the Mst1 gene impaired germination and mycelial growth in medium containing the sugars that it can transport. Homologs of MST1 were widely found in many fungi, including plant symbionts such as Trichoderma spp. and mycorrhizal fungi and plant pathogens such as Fusarium spp. This work significantly advances insights into the development of symbiotic relationships between plants and fungi.IMPORTANCE Over 90% of all vascular plant species develop an intimate symbiosis with fungi, which has an enormous impact on terrestrial ecosystems. It is widely recognized that plant-symbiotic fungi are supported by photosynthates, but little is known about the mechanisms for fungi to utilize plant-derived carbon sources. In the fungus Metarhizium robertsii, we identified a novel monosaccharide transporter (MST1) that is an H+ symporter and can transport a broad spectrum of monosaccharides, including glucose, sorbose, mannose, rhamnose, and fructose. MST1 is involved in the colonization of the rhizoplane and acts additively with the previously characterized oligosaccharide transporter MRT to colonize the rhizosphere. Homologs of MST1 were found in many fungi, including plant symbionts and plant pathogens, suggesting that the utilization of plant-derived sugars by MST1 homologs could also be important for other fungi to develop a symbiotic or parasitic relationship with their respective plant hosts.

The Perception of Rhizosphere Bacterial Communication Signals Leads to Transcriptome Reprogramming in Lysobacter capsici AZ78, a Plant Beneficial Bacterium.

The rhizosphere is a dynamic region governed by complex microbial interactions where diffusible communication signals produced by bacteria continuously shape the gene expression patterns of individual species and regulate fundamental traits for adaptation to the rhizosphere environment. Lysobacter spp. are common bacterial inhabitants of the rhizosphere and have been frequently associated with soil disease suppressiveness. However, little is known about their ecology and how diffusible communication signals might affect their behavior in the rhizosphere. To shed light on the aspects determining rhizosphere competence and functioning of Lysobacter spp., we carried out a functional and transcriptome analysis on the plant beneficial bacterium Lysobacter capsici AZ78 (AZ78) grown in the presence of the most common diffusible communication signals released by rhizosphere bacteria. Mining the genome of AZ78 and other Lysobacter spp. showed that Lysobacter spp. share genes involved in the production and perception of diffusible signal factors, indole, diffusible factors, and N-acyl-homoserine lactones. Most of the tested diffusible communication signals (i.e., indole and glyoxylic acid) influenced the ability of AZ78 to inhibit the growth of the phytopathogenic oomycete Pythium ultimum and the Gram-positive bacterium Rhodococcus fascians. Moreover, RNA-Seq analysis revealed that nearly 21% of all genes in AZ78 genome were modulated by diffusible communication signals. 13-Methyltetradecanoic acid, glyoxylic acid, and 2,3-butanedione positively influenced the expression of genes related to type IV pilus, which might enable AZ78 to rapidly colonize the rhizosphere. Moreover, glyoxylic acid and 2,3-butanedione downregulated tRNA genes, possibly as a result of the elicitation of biological stress responses. On its behalf, indole downregulated genes related to type IV pilus and the heat-stable antifungal factor, which might result in impairment of twitching motility and antibiotic production in AZ78. These results show that diffusible communication signals may affect the ecology of Lysobacter spp. in the rhizosphere and suggest that diffusible communication signals might be used to foster rhizosphere colonization and functioning of plant beneficial bacteria belonging to the genus Lysobacter.

Insight Into the Role of PGPR in Sustainable Agriculture and Environment

A multitude of roles is played by microbes in food and agriculture that include nutrient cycling and management, organic matter decomposition and fermentation. Plant growth promoting rhizobacteria (PGPR), representing microbial groups and with ability of colonizing plant roots, influence plant growth through various indirect and direct modes in order to promote its growth and/or protect it from diseases or damage due to insect attack. Thus, PGPR research has received renewed interest worldwide. Increasing number of crop-specific PGPR are being commercialized these days. Approaches like seed-inoculation and soil application either alone or in combination with bacterial culture/product for increased nutrient availability through phosphate solubilisation, potassium solubilisation, sulfur oxidation, nitrogen fixation, iron, and copper chelation are gaining popularity. Arbuscular mycorrhizal fungi (AMF) are root fungal symbiont that improve management of abiotic stress such as phosphorus deficiency. PGPR involves roles like production of indole acetic acid (IAA), ammonia (NH3), hydrogen cyanide (HCN), catalase, etc. PGPR also improve nutrient uptake by altering the level of plant hormone that enhances root surface area by increasing its girth and shape, thereby helping in absorbing more nutrients. PGPR facilitate seed germination, seedling growth and crop yield. An array of microbes includingPseudomonas, Azospirillum, Azotobacter, Klebsiella, Enterobacter, Alcaligenes, Arthrobacter, Burkholderia, Bacillus, andSerratiaenhance plant growth. VariousPseudomonassp. have demonstrated significant increase in germination, seedling growth and yield in different agricultural crops, including wheat. Hence, developing a successful crop-specific PGPR formulation, the candidate should possess characteristics like high rhizosphere competence, extensive competitive saprophytic ability, growth enhancing ability, ease of mass production, broad-spectrum action, safety toward the environment and compatibility with other partnering organisms.

Shifts in the rhizobiome during consecutive inplanta enrichment for phosphate-solubilizing bacteria differentially affect maize P status.

SummaryPhosphorus (P) is despite its omnipresence in soils often unavailable for plants. Rhizobacteria able to solubilize P are therefore crucial to avoid P deficiency. Selection for phosphate‐solubilizing bacteria (PSB) is frequently done in vitro; however, rhizosphere competence is herein overlooked. Therefore, we developed an in planta enrichment concept enabling simultaneous microbial selection for P‐solubilization and rhizosphere competence. We used an ecologically relevant combination of iron‐ and aluminium phosphate to select for PSB in maize (Zea mays L.). In each consecutive enrichment, plant roots were inoculated with rhizobacterial suspensions from plants that had grown in substrate with insoluble P. To assess the plants’ P statuses, non‐destructive multispectral imaging was used for quantifying anthocyanins, a proxy for maize’s P status. After the third consecutive enrichment, plants supplied with insoluble P and inoculated with rhizobacterial suspensions showed a P status similar to plants supplied with soluble P. A parallel metabarcoding approach uncovered that the improved P status in the third enrichment coincided with a shift in the rhizobiome towards bacteria with plant growth‐promoting and P‐solubilizing capacities. Finally, further consecutive enrichment led to a functional relapse hallmarked by plants with a low P status and a second shift in the rhizobiome at the level of Azospirillaceae and Rhizobiaceae.

An Overview of Metabolic Activity, Beneficial and Pathogenic Aspects of Burkholderia Spp.

Burkholderia is an important bacterial species which has different beneficial effects, such as promoting the plant growth, including rhizosphere competence for the secretion of allelochemicals, production of antibiotics, and siderophores. In addition, most of Burkholderia species have demonstrated promising biocontrol action against different phytopathogens for diverse crops. In particular, Burkholderia demonstrates significant biotechnological potential as a source of novel antibiotics and bioactive secondary metabolites. The current review is concerned with Burkholderia spp. covering the following aspects: discovering, classification, distribution, plant growth promoting effect, and antimicrobial activity of different species of Burkholderia, shedding light on the most important secondary metabolites, their pathogenic effects, and biochemical characterization of some important species of Burkholderia, such as B. cepacia, B. andropogonis, B. plantarii, B. rhizoxinica, B. glumae, B. caryophylli and B. gladioli.