Signal binding at both modules of its dCache domain enables the McpA chemoreceptor of Bacillus velezensis to sense different ligands

The effect of combination of root exudates substances on stimulation of Bacillus spores' germination

Root exudates play a crucial role in the rhizosphere by influencing the growth and activity of plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis. Previous studies have shown that most Bacillus spores can germinate in the rhizosphere while remain dormant in the soil. Understanding the relationship between specific components of root exudates and spore germination could provide valuable insights into how plants alter the ratio of spores in the rhizosphere through root exudates. In this study, we observed that Bacillus spore germination was induced by root exudates from maize (Fengtian) and two cucumber varieties (9930 and Jinchun 4). Maize root exudates induced spore germination at a significantly higher rate compared to cucumber exudates. We identified L-valine, β-alanine, xylose, glucose, and asparagine as key germination-inducing compounds in the exudates. Notably, when these compounds were combined, spore germination rates increased to over 80 %. We found that the maize-specific root exudate asparagine significantly enhanced the spore germination inducing ability of other germinants even at low concentrations. Furthermore, our results indicate that the GerA receptor specifically recognizes amino acids, while GerB and GerK work cooperatively to sense sugars and amides. These findings provide new insights into plant-microbe interactions and could inform the development of more effective Bacillus-based biofertilizers, improving their application in sustainable agriculture.

Biofertilizer Industry and Research Developments in China: A Mini-Review

Reliance on chemical fertilizers has significantly boosted food production in China, but it has also led to soil degradation, environmental pollution, and greenhouse gas emissions. To address these pressing issues, the Chinese government has launched various initiatives to reduce chemical fertilizer consumption and promote biofertilizers as effective alternatives to enhance soil fertility and mitigate environmental pollution. Biofertilizers promote crop growth by providing or activating essential nutrients, suppressing plant pathogens, improving soil health, and increasing resilience to abiotic stresses. The growing adoption of biofertilizers in China is reflected in the registration of more than 10,000 products, an annual production exceeding 35 million tons, and a market value of over US$5.5 billion, indicating a significant shift towards sustainable agricultural practices. Despite this progress, challenges such as the dominance of nitrogen fertilizers, inconsistent product performance, and the need for cultivar-specific microbial inoculants remain. Foundational research on the microbial genera utilised in biofertilizers, including nitrogen-fixing genera Rhizobium, Paenibacillus, and Pseudomonas, the widely used genus, Bacillus and Trichoderma, as well as multipurpose synthetic communities, is essential for overcoming these obstacles and enhancing the efficacy of biofertilizers. This review delves into the historical development of the biofertilizer industry and recent advancements in fundamental research on biofertilizers in China, highlighting the essential role of biofertilizers in promoting green agricultural development.

Functional characterization of the methyl-accepting chemotaxis proteins RS10830 and RS10815 in Xanthomonas oryzae pv. oryzicola

Xanthomonas oryzae pv. oryzicola (Xoc) causes the economically important leaf streak disease in rice. Chemotaxis plays a role in the entry and colonization of some phytopathogens within the host. However, the physiological function and ligand specificity of Xoc methyl-accepting chemotaxis proteins (MCPs) are not well defined. In this study, we show that the transmembrane MCP ACU12_RS10830 (RS10830) binds L-malic acid and L-tartaric acid, whereas the transmembrane MCP ACU12_RS10815 (RS10815) binds ethanolamine, methylamine, ethylamine, ethylenediamine, amylamine, and tyramine, to elicit attractant responses. The chemotactic responses mediated by the sensory domains of RS10830 and RS10815 were also observed for the chimeric receptors in Escherichia coli. Furthermore, the RS10830 and RS10815-mediated positive chemotaxis of Xoc RS105 correlated with the promoting effects of their ligands on bacterial growth and virulence in rice. To the best of our knowledge, this is the first report on the function of Xoc MCPs in virulence and signaling molecules of the Xoc chemotaxis system. RS10830 is the first L-tartaric acid-binding MCP reported in bacteria.

The composite microbial agent controls tomato bacterial wilt by colonizing the root surface and regulating the rhizosphere soil microbial community

Introduction

Bacterial wilt caused by Ralstonia solanacearum seriously affects the healthy growth of tomato seedlings. Biocontrol microbes have been used to manage tomato bacterial wilt. Herein, we aim to investigate the behavior of the Enterobacter hormaechei Rs-5 and Bacillus subtilis SL-44 composite microbial agent (EB) in the rhizosphere soil, and assess its impact on both the soil microbial community and tomato plant growth in this study.

Methods

The plate confrontation experiment and the pot experiment were respectively used to explore the control ability of EB against Ralstonia solanacearum and bacterial wilt disease. The absolute quantitative PCR (AQ-PCR) was employed to investigate the migration ability of EB in the rhizosphere of tomatoes, and the chemotactic response of EB to tomato root exudates was analyzed by the swimming plate method. Scanning electron microscopy was utilized to study the biofilm formation of EB during its colonization on the root surface of tomatoes. Finally, high-throughput sequencing was adopted to analyze the impact of EB on the microbial community in the rhizosphere soil of tomatoes after being infected by Ralstonia solanacearum.

Results

The absolute quantitative PCR and scanning electron microscope showed that the EB could migrate and efficiently colonize the elongation zone of tomato roots to form a biofilm. In addition, the EB exhibits a chemotactic response to tomato root exudates like sucrose, leucine, glutamic acid, and aspartic acid. The pot experiment demonstrated that the EB can reduce the incidence of tomato bacterial wilt from 77.78% to 22.22%, and significantly increase the biomass, physicochemical properties, and rhizosphere soil nutrient contents of tomato seedlings. Besides, the relative abundance of beneficial bacteria such as Massilia, Pseudomonas, Bacillus, and Enterobacter increased, and the fungi community diversity was improved.

Conclusion

Overall, the EB can reduce the amount of Ralstonia solanacearum in rhizosphere soil, and then control tomato bacterial wilt directly. Besides, the EB can migrate to the root under the induction of tomato root exudates and colonize on the root surface efficiently, thereby indirectly regulating the soil microbial community structure and controlling tomato bacterial wilt.

Bacillus megaterium NCT-2 agent alters soil nutrients, vegetable quality, and root microecology in secondary salinized soil

Microbial remediation technology has the characteristics of high efficiency and environmental protection, which has attracted attention. However, there is complexity in the microorganism-soil-plant system. The effects of microbial agents on soil nutrients, plant quality, rhizosphere, and endophytic microorganisms are still unclear. Here, we demonstrate the application of Bacillus megaterium NCT-2 as a multifunctional agent that concurrently addresses salinization-driven nutrient imbalances and reshapes keystone microbial taxa to restore soil-plant homeostasis. The results showed that NCT-2 agent improved the soil nutrients, reduced the loss of nitrogen and sulfur, increased the content of available phosphorus, and decreased the electrical conductivity. The agent increased the number of bacteria and fungi in the soil. Meanwhile, NCT-2 agent improved the vegetable quality and yield. Specifically, the NCT-2 agent significantly increased the aboveground fresh weight, underground fresh weight, total flavonoids, antioxidant enzyme activity, ascorbic acid, Cu, Zn, Fe, P, and K in lettuce, while significantly reduced nitrate. The chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll were significantly increased by the agent. Critically, high-throughput sequencing revealed NCT-2-driven enrichment of stress-resilient taxa (e.g., Firmicutes, Acidobacteria) and functional synergists (e.g., Acetobacter), which correlated with soil nutrient fluxes and plant antioxidant capacity. By decoupling the interplay between microbial community restructuring and systemic remediation outcomes, this work establishes a novel framework for leveraging keystone taxa to optimize salinized agroecosystems.

Structural and functional diversity of sensor domains in bacterial transmembrane receptors

The ability of bacteria to adapt to changing environmental conditions largely depends on transmembrane receptors that sense signal molecules and generate responses such as chemotaxis, changes in gene expression, or alterations in second-messenger levels. Although these receptors differ significantly in function, they share a common mode of activation that involves signal molecule interaction with sensor domains. A major challenge in microbiology lies in the limited knowledge of ligands that stimulate receptors. Here, we review recent advances in this field, including the occurrence of multi-modular sensor domains, the identification of co-component signal transduction systems, evidence for sensor domain evolution from transporters, and the use of binding pocket sequence motifs to identify sensor domain ligands.

Specificities of Chemosensory Receptors in the Human Gut Microbiota

The human gut is rich in metabolites and harbors a complex microbial community, yet the sensory repertoire of its commensal bacteria remains largely uncharacterized. Here we systematically mapped ligand specificities of extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. We identified diverse metabolites as specific stimuli for three major functional classes of transmembrane receptors. We further characterized novel subsets of sensors belonging to the Cache superfamily, specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs), respectively, and investigated the evolution of their ligand specificity. Structural and biochemical analysis of the newly described dCache_1UR domain revealed an independent binding of uracil and SCFA at distinct modules. Altogether, we could identify or predict specificities for over a half of the Cache-type chemotactic sensors in the selected gut commensals, with the carboxylic acids representing the largest class of ligands. Among those, the most commonly found specificities were for lactate and formate, indicating particular importance of these metabolites in the human gut microbiome and consistent with their observed beneficial impact on the growth of selected bacterial species.

Bacterial sensor evolved by decreasing complexity

Bacterial receptors feed into multiple signal transduction pathways that regulate a variety of cellular processes including gene expression, second messenger levels, and motility. Receptors are typically activated by signal binding to ligand-binding domains (LBDs). Cache domains are omnipresent LBDs found in bacteria, archaea, and eukaryotes, including humans. They form the predominant family of extracytosolic bacterial LBDs and were identified in all major receptor types. Cache domains are composed of either a single (sCache) or a double (dCache) structural module. The functional relevance of bimodular LBDs remains poorly understood. Here, we identify the PacF chemoreceptor in the phytopathogen Pectobacterium atrosepticum that recognizes formate at the membrane-distal module of its dCache domain, triggering chemoattraction. We further demonstrate that a family of formate-specific sCache domains has evolved from a dCache domain, exemplified by PacF, by losing the membrane-proximal module. By solving high-resolution structures of two family members in complex with formate, we show that the molecular basis for formate binding at sCache and dCache domains is highly similar, despite their low sequence identity. The apparent loss of the membrane-proximal module may be related to the observation that dCache domains bind ligands typically at the membrane-distal module, whereas studies have failed to find ligands bound in the membrane-proximal module. This work advances our understanding of signal sensing in bacterial receptors and suggests that evolution by reducing complexity may be a route for shaping diversity.

Photoimmunologic Therapy of Stubborn Biofilm via Inhibiting Bacteria Revival and Preventing Reinfection

Stubborn biofilm infections pose serious threats to public health. Clinical practices highly rely on mechanical debridement and antibiotics, which often fail and lead to persistent and recurrent infections. The main culprits are 1) persistent bacteria reviving, colonizing, and rejuvenating biofilms, and 2) secondary pathogen exposure, particularly in individuals with chronic diseases. Addressing how to inhibit persistent bacteria revival and prevent reinfection simultaneously is still a major challenge. Herein, an oligo-ethylene glycol-modified lipophilic cationic photosensitizer (PS), TBTCP-PEG7, is developed. It effectively eradicates Methicillin-Resistant Staphylococcus aureus (MRSA) under light irradiation. Furthermore, TBTCP-PEG7-mediated photodynamic therapy (PDT) not only conquers stubborn biofilm infections by downregulating the two-component system (TCS), quorum sensing (QS), and virulence factors, thereby reducing intercellular communication, inhibiting persistent bacterial regrowth and biofilm remodeling but also prevents reinfection by upregulating heat shock protein-related genes to induce immunogenetic cell death (ICD) and establish immune memory. In vivo, TBTCP-PEG7 efficiently eradicates MRSA biofilm adhered to medical catheters, stimulates angiogenesis, reduces inflammatory factor expression, and accelerates wound healing. Furthermore, ICD promotes short-term immune and long-term immunological memory for coping with secondary infections. This two-pronged strategy not only effectively overcomes stubborn, persistent and recurrent biofilm infection, but also provides theoretical guidance for designing the next generation of antibacterial materials.

Enhanced nitrogen fixation and Cd passivation in rhizosphere soil by biochar-loaded nitrogen-fixing bacteria: Chemisorption and microbial mechanism

This study developed a biochar-loaded Ac material and clarified its chemical and microbial mechanisms for cadmium (Cd) immobilization and plant growth promotion. Results showed that biochar-loaded nitrogen-fixing bacteria (Azotobacter chroococcum; BAc) enhanced Cd adsorption by forming stable complexes with bacterial secretions and activating biochar functional groups. Compared with BC and Ac, after BAc application, Ac successfully colonized the lettuce rhizosphere, tagged with green fluorescent protein. It improved plant nitrogen by 47.39-72.47 % and increased root and shoot biomass by 50.35-107.32 % through nitrogen fixation and amino acid release. BAc reduced soil Cd bioavailability by 16.67-46.42 % and Cd accumulation in root and shoot by 14.28-69.74 %. This occurred through increasing soil pH and converting exchangeable Cd to carbonate-bound and Fe/Mn oxide-bound fractions. Importantly, BAc improved the rhizosphere nutrient environment and promoted the deterministic assembly of the rhizosphere microbial community. It also increased microbial diversity and attracted taxa like Actinomycetales (7.59 %), Solirubrobacteriales (5.17 %), Rhizobiales (5.17 %), and Sphingomonadales (5.17 %), all associated with nitrogen fixation, plant growth promotion, and Cd immobilization. Structural equation modeling (SEM) confirmed that BAc increased nitrogen utilization efficiency in lettuce and facilitated biotic immobilization of soil Cd by optimizing the microbial structure. This study provides insights into how biochar-loaded Ac improve plant growth and control soil Cd pollution.

Harnessing biosynthesized selenium nanoparticles for recruitment of beneficial soil microbes to plant roots

Root exudates can benefit plant growth and health by reshaping the rhizosphere microbiome. Whether nanoparticles biosynthesized by rhizosphere microbes play a similar role in plant microbiome manipulation remains enigmatic. Herein, we collect elemental selenium nanoparticles (SeNPs) from selenobacteria associated with maize roots. In vitro and soil assays show that the SeNPs enhanced plant performance by recruiting plant growth-promoting bacteria (e.g., Bacillus) in a dose-dependent manner. Multiomic profilings unravel a cross-kingdom-signaling cascade that mediates efficient biosynthesis of SeNPs by selenobacteria. Specifically, maize roots perceive histamine signaling from Bacillus spp., which stimulates the plant to produce p-coumarate via root exudation. The rpoS gene in selenobacteria (e.g., Pseudomonas sp. ZY71) responds to p-coumarate signaling and positively regulates the biosynthesis of SeNPs. This study demonstrates a novel mechanism for recruiting host-beneficial soil microbes by microbially synthesized nanoparticles and unlocks promising possibilities for plant microbiome manipulation.

Bridging the Gap: Biofilm-mediated establishment of Bacillus velezensis on Trichoderma guizhouense mycelia

Bacterial-fungal interactions (BFIs) are important in ecosystem dynamics, especially within the soil rhizosphere. The bacterium Bacillus velezensis SQR9 and the fungus Trichoderma guizhouense NJAU 4742 have gathered considerable attention due to their roles in promoting plant growth and protecting their host against pathogens. In this study, we utilized these two model microorganisms to investigate BFIs. We firstly demonstrate that while co-inoculation of B. velezensis and T. guizhouense could promote tomato growth, these two microorganisms display mutual antagonism on agar solidified medium. To resolve this contradiction, we developed an inoculation method, that allows B. velezensis colonization of T. guizhouense hyphae and performed a transcriptome analysis. During colonization of the fungal hyphae, B. velezensis SQR9 upregulates expression of biofilm related genes (e.g. eps, tasA, and bslA) that is distinct from free-living cells. This result suggested an intricate association between extracellular matrix expression and hyphae colonization. In accordance, deletion epsD, tasA, or both epsD and tasA genes of B. velezensis diminished colonization of the T. guizhouense hyphae. The insights from our study demonstrate that soil BFIs are more complex than we understood, potentially involving both competition and cooperation. These intricate biofilm-mediated BFI dynamics might contribute to the remarkable diversity observed within soil microbiota, providing a fresh perspective for further exploration of BFIs in the plant rhizosphere.

Bacterial amino acid chemotaxis: a widespread strategy with multiple physiological and ecological roles

Chemotaxis is the directed, flagellum-based movement of bacteria in chemoeffector gradients. Bacteria respond chemotactically to a wide range of chemoeffectors, including amino, organic, and fatty acids, sugars, polyamines, quaternary amines, purines, pyrimidines, aromatic hydrocarbons, oxygen, inorganic ions, or polysaccharides. Most frequent are chemotactic responses to amino acids (AAs), which were observed in numerous bacteria regardless of their phylogeny and lifestyle. Mostly chemoattraction responses are observed, although a number of bacteria are repelled from certain AAs. Chemoattraction is associated with the important metabolic value of AAs as growth substrates or building blocks of proteins. However, additional studies revealed that AAs are also sensed as environmental cues. Many chemoreceptors are specific for AAs, and signaling is typically initiated by direct ligand binding to their four-helix bundle or dCache ligand-binding domains. Frequently, bacteria possess multiple AA-responsive chemoreceptors that at times possess complementary AA ligand spectra. The identification of sequence motifs in the binding sites at dCache_1 domains has permitted to define an AA-specific family of dCache_1AA chemoreceptors. In addition, AAs are among the ligands recognized by broad ligand range chemoreceptors, and evidence was obtained for chemoreceptor activation by the binding of AA-loaded solute-binding proteins. The biological significance of AA chemotaxis is very ample including in biofilm formation, root and seed colonization by beneficial bacteria, plant entry of phytopathogens, colonization of the intestine, or different virulence-related features in human/animal pathogens. This review provides insights that may be helpful for the study of AA chemotaxis in other uncharacterized bacteria.

Hydrolysis products of agricultural waste can serve as microbial fertilizer enhancers to promote the growth of maize crops

Efficient utilization of agricultural wastes and reduction of chemical fertilizer inputs are crucial for sustainable development of agriculture. Plant growth promoting rhizobacteria (PGPR) are widely used as biofertilizers to partially replace chemical fertilizers in agricultural production. The functional performance of PGPR strains is closely related to their root colonization capacity. Some organic acids from root exudates can recruit PGPR to colonize the root. In this study, agricultural organic wastes such as mushroom bran and tobacco waste materials were used to produce organic acids through the hypoxic hydrolysis process. The hydrolysis conditions were optimized to maximize the production of a mixture of complex organic acids from the hypoxic hydrolysis of these materials, employing both single-factor and orthogonal experimental methods. The diluted hydrolysates were tested for their effects on the rhizosphere colonization of the PGPR strain Bacillus amyloliquefaciens SQR9 using fluorogenic quantitative PCR in greenhouse pot experiments. The results demonstrated that hypoxic hydrolysates from tobacco waste and mushroom bran significantly enhanced the colonization of SQR9 in the maize rhizosphere. Specifically, a 2000-fold dilution of tobacco waste hydrolysate yielded the most effective result, while a 5000-fold dilution of mushroom bran hydrolysate provided the best outcome. All treatments combining these hydrolysates with SQR9 significantly increased maize stem dry weight, indicating that with appropriate treatment, such as anaerobic fermentation, these agricultural organic wastes can serve as synergistic agents of microbial fertilizers, contributing to agricultural sustainability.

Deciphering Bacterial Chemorepulsion: The Complex Response of Microbes to Environmental Stimuli

Bacterial motility relying on flagella is characterized by several modes, including swimming, swarming, twitching, and gliding. This motility allows bacteria to adapt remarkably well to hostile environments. More than 50% of bacteria naturally contain flagella, which are crucial for bacterial chemotaxis motility. Chemotaxis can be either positive, where bacteria move towards a chemical source, or negative, known as chemorepulsion, where bacteria move away from the source. Although much is known about the mechanisms driving chemotaxis towards attractants, the molecular mechanisms underlying chemorepulsion remain elusive. Chemotaxis plays an important role in the colonization of the rhizosphere by rhizobacteria. Recently, researchers have systematically studied the identification and recognition mechanisms of chemoattractants. However, the mechanisms underlying chemorepellents remain unclear. Systematically sorting and analyzing research on chemorepellents could significantly enhance our understanding of how these compounds help probiotics evade harmful environments or drive away pathogens.

Selenium-Mediated Shaping of Citrus Rhizobiome for Promotion in Root Growth and Soil Phosphorus Activation

Selenium (Se) has been widely reported to affect plant growth, nutrient cycling, and the rhizobiome. However, how Se shapes the rhizobiome and interacts with plants remains largely elusive. Pot and hydroponic experiments were employed to elucidate the regulatory mechanism of Se in the citrus rhizobiome. Compared to the control, soil Se application significantly increased the root biomass (34.7%) and markedly reduced rhizosphere HCl-P, H2O-P, NaHCO3-IP, and residual-P of citrus, which were related to the variation of citrus rhizobiome. Se primarily enriched Proteobacteria and Actinobacteria as well as the phosphorus (P) functional genes phod and pqqc. Further study revealed that Se altered the metabolite profile of root exudate, particularly enhancing the abundance of l-cyclopentylglycine, cycloleucine, l-proline, l-pipecolic acid, and inositol, which played a key role in reshaping the citrus rhizobiome. These metabolites could serve as both nutrient sources and signaling molecules, thus supporting the growth or chemotaxis of the functional microbes. These bacterial taxa have the potential to solubilize P or stimulate plant growth. These findings provide a novel mechanistic understanding of the intriguing interactions between Se, root exudate, and rhizosphere microbiomes, and demonstrate the potential for utilizing Se to regulate rhizobiome function and enhance soil P utilization in citrus cultivation.

Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture

The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant-beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment-dominated and plant genetic-dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment-dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic-dominated rhizosphere microbiome for breeding microbiome-assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome.

Bacterial sensor evolved by decreasing complexity

Bacterial receptors feed into multiple signal transduction pathways that regulate a variety of cellular processes including gene expression, second messenger levels and motility. Receptors are typically activated by signal binding to ligand binding domains (LBD). Cache domains are omnipresent LBDs found in bacteria, archaea, and eukaryotes, including humans. They form the predominant family of extracytosolic bacterial LBDs and were identified in all major receptor types. Cache domains are composed of either a single (sCache) or a double (dCache) structural module. The functional relevance of bimodular LBDs remains poorly understood. Here, we identify the PacF chemoreceptor in the phytopathogen Pectobacterium atrosepticum that recognizes formate at the membrane distal module of its dCache domain, triggering chemoattraction. We further demonstrate that a family of formate-specific sCache domains has evolved from a dCache domain, exemplified by PacF, by losing the membrane proximal module. By solving high-resolution structures of two family members in complex with formate, we show that the molecular basis for formate binding at sCache and dCache domains is highly similar, despite their low sequence identity. The apparent loss of the membrane proximal module may be related to the observation that dCache domains bind ligands typically at the membrane distal module, whereas the membrane proximal module is not involved in signal sensing. This work advances our understanding of signal sensing in bacterial receptors and suggests that evolution by reducing complexity may be a common trend shaping their diversity.

Significance

Many bacterial receptors contain multi-modular sensing domains indicative of complex sensory processes. The presence of more than one sensing module likely permits the integration of multiple signals, although, the molecular detail and functional relevance for these complex sensors remain poorly understood. Bimodular sensory domains are likely to have arisen from the fusion or duplication of monomodular domains. Evolution by increasing complexity is generally believed to be a dominant force. Here we reveal the opposite - how a monomodular sensing domain has evolved from a bimodular one. Our findings will thus motivate research to establish whether evolution by decreasing complexity is typical of other sensory domains.

Identification of a dCache-type chemoreceptor in Campylobacter jejuni that specifically mediates chemotaxis towards methyl pyruvate

The foodborne pathogenic bacterium Campylobacter jejuni utilizes chemotaxis to assist in the colonization of host niches. A key to revealing the relationship among chemotaxis and pathogenicity is the discovery of signaling molecules perceived by the chemoreceptors. The C. jejuni chemoreceptor Tlp11 is encoded by the highly infective C. jejuni strains. In the present study, we report that the dCache-type ligand-binding domain (LBD) of C. jejuni ATCC 33560 Tlp11 binds directly to novel ligands methyl pyruvate, toluene, and quinoline using the same pocket. Methyl pyruvate elicits a strong chemoattractant response, while toluene and quinoline function as the antagonists without triggering chemotaxis. The sensory LBD was used to control heterologous proteins by constructing chimeras, indicating that the signal induced by methyl pyruvate is transmitted across the membrane. In addition, bioinformatics and experiments revealed that the dCache domains with methyl pyruvate-binding sites and ability are widely distributed in the order Campylobacterales. This is the first report to identify the class of dCache chemoreceptors that bind to attractant methyl pyruvate and antagonists toluene and quinoline. Our research provides a foundation for understanding the chemotaxis and virulence of C. jejuni and lays a basis for the control of this foodborne pathogen.

The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria

Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.

Root colonization by beneficial rhizobacteria

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

Accessing nutrients as the primary benefit arising from chemotaxis

About half of the known bacterial species perform chemotaxis that gains them access to sites that are optimal for growth and survival. The motility apparatus and chemotaxis signaling pathway impose a large energetic and metabolic burden on the cell. There is almost no limit to the type of chemoeffectors that are recognized by bacterial chemoreceptors. For example, they include hormones, neurotransmitters, quorum-sensing molecules, and inorganic ions. However, the vast majority of chemoeffectors appear to be of metabolic value. We review here the experimental evidence indicating that accessing nutrients is the main selective force that led to the evolution of chemotaxis.

Negative chemotaxis of Ligilactobacillus agilis BKN88 against gut-derived substances

Ligilactobacillus agilis is a motile lactic acid bacterium found in the gastrointestinal tracts of animals. The findings of our previous study suggest that the motility of L. agilis BKN88 enables gut colonization in murine models. However, the chemotactic abilities of motile lactobacilli remain unknown. This study aimed to identify the gut-derived chemoeffectors and their corresponding chemoreceptors in L. agilis BKN88. Chemotaxis assays with chemotactic and non-chemotactic (ΔcheA) L. agilis strains revealed that low pH, organic acids, and bile salts served as repellents. L. agilis BKN88 was more sensitive to bile and acid than the gut-derived non-motile lactobacilli, implying that L. agilis might utilize motility and chemotaxis instead of exhibiting stress tolerance/resistance. L. agilis BKN88 contains five putative chemoreceptor genes (mcp1-mcp5). Chemotaxis assays using a series of chemoreceptor mutants revealed that each of the five chemoreceptors could sense multiple chemoeffectors and that these chemoreceptors were functionally redundant. Mcp2 and Mcp3 sensed all tested chemoeffectors. This study provides further insights into the interactions between chemoreceptors and ligands of motile lactobacilli and the unique ecological and evolutionary features of motile lactobacilli, which may be distinct from those of non-motile lactobacilli.

Sensing preferences for prokaryotic solute binding protein families

Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three-dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron-chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.

Listening to plant's Esperanto via root exudates: reprogramming the functional expression of plant growth-promoting rhizobacteria

Rhizomicrobiome plays important roles in plant growth and health, contributing to the sustainable development of agriculture. Plants recruit and assemble the rhizomicrobiome to satisfy their functional requirements, which is widely recognized as the 'cry for help' theory, but the intrinsic mechanisms are still limited. In this study, we revealed a novel mechanism by which plants reprogram the functional expression of inhabited rhizobacteria, in addition to the de novo recruitment of soil microbes, to satisfy different functional requirements as plants grow. This might be an efficient and low-cost strategy and a substantial extension to the rhizomicrobiome recruitment theory. We found that the plant regulated the sequential expression of genes related to biocontrol and plant growth promotion in two well-studied rhizobacteria Bacillus velezensis SQR9 and Pseudomonas protegens CHA0 through root exudate succession across the plant developmental stages. Sixteen key chemicals in root exudates were identified to significantly regulate the rhizobacterial functional gene expression by high-throughput qPCR. This study not only deepens our understanding of the interaction between the plant-rhizosphere microbiome, but also provides a novel strategy to regulate and balance the different functional expression of the rhizomicrobiome to improve plant health and growth.

The dCache Domain of the Chemoreceptor Tlp1 in Campylobacter jejuni Binds and Triggers Chemotaxis toward Formate

Chemotaxis is an important virulence factor in some enteric pathogens, and it is involved in the pathogenesis and colonization of the host. However, there is limited knowledge regarding the environmental signals that promote chemotactic behavior and the sensing of these signals by chemoreceptors. To date, there is no information on the ligand molecule that directly binds to and is sensed by Campylobacter jejuni Tlp1, which is a chemoreceptor with a dCache-type ligand-binding domain (LBD). dCache (double Calcium channels and chemotaxis receptor) is the largest group of sensory domains in bacteria, but the dCache-type chemoreceptor that directly binds to formate has not yet been discovered. In this study, formate was identified as a direct-binding ligand of C. jejuni Tlp1 with high sensing specificity. We used the strategy of constructing a functional hybrid receptor of C. jejuni Tlp1 and the Escherichia coli chemoreceptor Tar to screen for the potential ligand of Tlp1, with the binding of formate to Tlp1-LBD being verified using isothermal titration calorimetry. Molecular docking and experimental analyses indicated that formate binds to the membrane-proximal pocket of the dCache subdomain. Chemotaxis assays demonstrated that formate elicits robust attractant responses of the C. jejuni strain NCTC 11168, specifically via Tlp1. The chemoattraction effect of formate via Tlp1 promoted the growth of C. jejuni, especially when competing with Tlp1- or CheY-knockout strains. Our study reveals the molecular mechanisms by which C. jejuni mediates chemotaxis toward formate, and, to our knowledge, is the first report on the high-specificity binding of the dCache-type chemoreceptor to formate as well as the physiological role of chemotaxis toward formate. IMPORTANCE Chemotaxis is important for Campylobacter jejuni to colonize favorable niches in the gastrointestinal tract of its host. However, there is still a lack of knowledge about the ligand molecules for C. jejuni chemoreceptors. The dCache-type chemoreceptor, namely, Tlp1, is the most conserved chemoreceptor in C. jejuni strains; however, the direct-binding ligand(s) triggering chemotaxis has not yet been discovered. In the present study, we found that the ligand that binds directly to Tlp1-LBD with high specificity is formate. C. jejuni exhibits robust chemoattraction toward formate, primarily via Tlp1. Tlp1 is the first reported dCache-type chemoreceptor that specifically binds formate and triggers strong chemotaxis. We further demonstrated that the formate-mediated promotion of C. jejuni growth is correlated with Tlp1-mediated chemotaxis toward formate. Our work provides important insights into the mechanism and physiological function of chemotaxis toward formate and will facilitate further investigations into the involvement of microbial chemotaxis in pathogen-host interactions.

Chemical communication in plant-microbe beneficial interactions: a toolbox for precise management of beneficial microbes

Harnessing the power of beneficial microbes in the rhizosphere to improve crop performance is a key goal of sustainable agriculture. However, the precise management of rhizosphere microbes for crop growth and health remains challenging because we lack a comprehensive understanding of the plant-rhizomicrobiome relationship. In this review, we discuss the latest research progress on root colonisation by representative beneficial microbes (e.g. Bacillus spp. and Pseudomonas spp.). We also highlight the bidirectional chemical communication between microbes and plant roots for precise functional control of beneficial microbes in the rhizosphere, as well as advances in understanding how beneficial microbes overcome the immune system of plants. Finally, we propose future research objectives that will help us better understand the complex network of plant-microbe interactions.