Biofilm formation in plant–microbe associations

Rationally designed antimicrobial peptides with high selectivity and efficiency against phytopathogenic Ralstonia solanecearum

Ralstonia solanacearum, the causative agent of bacterial wilt, poses a global threat to agriculture, necessitating urgent and sustainable solutions as traditional methods lose efficacy. This study developed WRF-13, a synthetic antimicrobial peptide (AMP) designed to mimic natural AMPs, exhibiting potent antibacterial and anti-biofilm activity with high specificity against R. solanacearum. Mechanistic studies, including microscopy and computational analyses, demonstrated that WRF-13 disrupts the bacterial membrane. WRF-13 remained stable across a wide pH (5-8) and temperature (25-50 °C) range, essential for field applications, and showed no detectable toxicity to mammalian or plant cells at elevated concentrations. Greenhouse trials confirmed its efficacy in reducing bacterial wilt severity up to 65 %, highlighting its potential to protect crops from R. solanacearum infection. Overall, this study highlights WRF-13 as a targeted solution for managing bacterial wilt and advancing sustainable agriculture.

Isolation and Functional Characterization of Endophytic Bacteria from Muscadine Grape Berries: A Microbial Treasure Trove

Muscadine grapes are renowned for their unique traits, natural disease resistance, and rich bioactive compounds. Despite extensive research on their phytochemical properties, microbial communities, particularly endophytic bacteria, remain largely unexplored. These bacteria play crucial roles in plant health, stress tolerance, and ecological interactions. This study represents the first comprehensive effort to isolate, identify, and functionally characterize the bacterial endophytes inhabiting muscadine grape berries using a culture-dependent approach. We isolated diverse bacterial species spanning six genera-Bacillus, Staphylococcus, Paenibacillus, Calidifontibacillus, Curtobacterium, and Tatumella. Microscopic and physiological analysis revealed variations in bacterial morphology, with isolates demonstrating adaptability to varied temperatures. Cluster-based analysis indicated functional specialization among the isolates, with species from Pseudomonadota and Actinomycetota exhibiting superior plant growth-promoting abilities, whereas Bacillota species displayed potential biocontrol and probiotic properties. Among them, Tatumella ptyseos demonstrated exceptional plant growth-promoting traits, including indole-3-acetic acid production, nitrogen fixation, phosphate solubilization, and carbohydrate fermentation. Additionally, Bacillus spp. showed presumptive biocontrol potential, while Paenibacillus cineris emerged as a potential probiotic candidate. The identification of Calidifontibacillus erzurumensis as a novel endophytic species further expands the known biodiversity of grape-associated microbes. These findings provide insights into the metabolic diversity and functional roles of muscadine grape-associated endophytes, highlighting their potential for agricultural and biotechnological applications.

Arginine kinase McsB and ClpC complex impairs the transition to biofilm formation in Bacillus subtilis

Robust biofilm formation on host niches facilitates beneficial Bacillus to promote plant growth and inhibit plant pathogens. Arginine kinase McsB is involved in bacterial development and stress reaction by phosphorylating proteins for degradation through a ClpC/ClpP protease. Conversely, cognate arginine phosphatase YwlE counteracts the process. Regulatory pathways of biofilm formation have been studied in Bacillus subtilis, of which Spo0A∼P is a master transcriptional regulator, which is transcriptionally activated by itself in biofilm formation. Previous studies have shown that Spo0A∼P transcript regulation controls biofilm formation, where MecA binds ClpC to inhibit Spo0A∼P-dependent transcription without triggering degradation. It remains unclear whether McsB and ClpC regulate biofilm formation together and share a similar non-proteolytic mechanism like MecA/ClpC complex. In this study, we characterized McsB and ClpC as negative regulators of biofilm formation and matrix gene eps expression. Our genetic and morphological evidence further indicates that McsB and ClpC inhibit eps expression by decreasing the spo0A and sinI expression, leading to the release of SinR, a known repressor of eps transcription. Given that the spo0A and sinI expression is transcriptionally activated by Spo0A∼P in biofilm formation, we next demonstrate that McsB interacts with Spo0A directly by bacterial two-hybrid system and Glutathione transferase pull-down experiments. Additionally, we present that McsB forms a complex with ClpC to dampen biofilm formation in vivo. Finally, we show that YwlE acts as a positive regulator of biofilm formation, counteracting the function of McsB. These findings suggest that McsB, ClpC, and YwlE play vital roles in the transition to biofilm formation in Bacillus subtilis, providing new insights into the regulatory mechanisms underlying biofilm development and sharing a similar non-proteolytic mechanism in biofilm formation as MecA/ClpC complex.

In vitro biofilm formation only partially predicts beneficial Pseudomonas fluorescens protection against rhizosphere pathogens

Plant roots form associations with both beneficial and pathogenic soil microorganisms. While members of the rhizosphere microbiome can protect against pathogens, the mechanisms are poorly understood. We hypothesized that the ability to form a robust biofilm on the root surface is necessary for the exclusion of pathogens; however, it is not known if the same biofilm formation components required in vitro are necessary in vivo. Pseudomonas fluorescens WCS365 is a beneficial strain that is phylogenetically closely related to an opportunistic pathogen P. fluorescens N2C3 and confers robust protection against P. fluorescens N2C3 in the rhizosphere. We used this plant-mutualist-pathogen model to screen collections of P. fluorescens WCS365 increased attachment mutants (iam) and surface attachment defective (sad) transposon insertion mutants that form increased or decreased levels of biofilm on an abiotic surface, respectively. We found that while the P. fluorescens WCS365 mutants had altered biofilm formation in vitro, only a subset of these mutants, including those involved in large adhesion protein (Lap) biosynthesis, flagellin biosynthesis and O-antigen biosynthesis, lost protection against P. fluorescens N2C3. We found that the inability of P. fluorescens WCS365 mutants to grow in planta, and the inability to suppress pathogen growth, both partially contributed to loss of plant protection. We did not find a correlation between the extent of biofilm formed in vitro and pathogen protection in planta indicating that biofilm formation on abiotic surfaces may not fully predict pathogen exclusion in planta. Collectively, our work provides insights into mechanisms of biofilm formation and host colonization that shape the outcomes of host-microbe-pathogen interactions.

Holliday junction resolvase RuvC targets biofilm eDNA and confers plant resistance to vascular pathogens

A biofilm lifestyle is critical for bacterial pathogens to colonize and protect themselves from host immunity and antimicrobial chemicals in plants and animals. The formation and regulation mechanisms of phytobacterial biofilm are still obscure. Here we found that the protein Ralstonia solanacearum resistance to ultraviolet C (RuvC) is highly abundant in biofilm and positively regulates pathogenicity by controlling systemic movement in tomato xylem. RuvC protein accumulates at the later stage of biofilm development and specifically targets Holliday junction (HJ)-like structures to disrupt the biofilm extracellular DNA (eDNA) lattice, thus facilitating biofilm dispersal. Recombinant RuvC protein can resolve extracellular HJ to prevent bacterial biofilm formation. Heterologous expression of R. solanacearum or Xanthomonas oryzae pv. oryzae RuvC with plant secretion signal in tomato or rice confers resistance to bacterial wilt or bacterial blight disease, respectively. Plant chloroplast-localized HJ resolvase monokaryotic chloroplast 1 (MOC1), which shares structural similarity with bacterial RuvC, shows a strong inhibitory effect on bacterial biofilm formation. Relocalization of SlMOC1 to apoplast in tomato roots leads to increased resistance to bacterial wilt. Our novel finding reveals a critical pathogenesis mechanism of R. solanacearum and provides an efficient biotechnology strategy to improve plant resistance to bacterial vascular disease.

Manuka Honey Inhibits Biofilm Formation and Reduces the Expression of the Associated Genes in Pectobacterium brasiliense

Biofilms are major virulence factors formed by pathogenic bacteria to invade their host and maintain their colony. While biofilms usually develop on diverse solid surfaces, floating biofilms, also called pellicles, are formed at the air-liquid interface. To address the problem of biofilm formation by bacterial pathogens, honey has been extensively studied. However, information on the effect of honey on biofilm formation by plant pathogens is scarce. This study aimed to determine the effects of manuka honey on biofilm and pellicle formation by Pectobacterium brasiliense and analyze the expression of genes encoding proteins needed to form biofilm by using semiquantitative PCR and RT-qPCR. Treatment with 5% (w/v) of manuka honey significantly decreased biofilm and pellicle formation by P. brasiliense. RT-qPCR results showed that the expression of bcsA, fis, hrpL, and expI decreased 7.07-fold, 5.71-fold, 13.11-fold, and 6.26-fold, respectively, after exposure to 5% (w/v) manuka honey. Our findings reveal that manuka honey may effectively inhibit biofilm and pellicle formation.

Significance of zinc-solubilizing plant growth-promoting rhizobacterial strains in nutrient acquisition, enhancement of growth, yield, and oil content of canola (Brassica napus L.)

The present study was conducted with the aim to isolate, characterize, and identify the promising zinc-solubilizing rhizobacteria found naturally in the rhizosphere of canola (Brassica napus L.) plants. The study investigated the roles of these strains in nutrient acquisition and assimilation of extracellular molecules such as hormones and secondary metabolites. Ten isolated promising zinc-solubilizing strains (CLS1, CLS2, CLS3, CLS6, CLS8, CLS9, CLS11, CLS12, CLS13, and CLS15) were selected and characterized biochemically. Almost all the tested strains were Gram-positive, could fix nitrogen, and were positive for indole acetic acid, HCN, exopolysaccharides, and siderophore production. These effective zinc-solubilizing strains were identified through 16S rRNA gene sequencing. Based on the amount of solubilized zinc and halo zone diameter, four potent strains (CLS1, CLS2, CLS3, and CLS9) were selected for pot and field evaluation. Among all the identified bacterial genera isolated from the rhizosphere of the same host plant at different sampling sites, Priestia aryabhattai was found most abundant and found at all three sampling sites. The strains Priestia megaterium, Staphylococcus succinus, and Bacillus cereus were found at two different sites. Bacillus subtilis was found at only one site. These strains have a number of plant growth-stimulating characteristics as well as the ability to colonize plant roots successfully. The results indicated that inoculation of all these four zinc-solubilizing tested strains enhanced the plant growth, oil contents, and yield attributes of canola as compared to non-inoculated control with fertilizer levels. Staphylococcus succinus (CLS1) was first reported as a zinc solubilizer and associated with canola. Priestia aryabhattai (CLS2) and Priestia megaterium (CLS9) were found to be the best strains, with the most pronounced beneficial effect on canola growth and yield traits in both pot and field conditions. The site-specific dominance of these strains observed in this study may contribute toward decision-making for the development of specific inocula for canola. Therefore, identification of these strains could help in providing adequate amount of soluble zinc along with enhanced plant growth, yield, and oil content of canola.

Glyphosate effects on growth and biofilm formation in bee gut symbionts and diverse associated bacteria

Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and withstand external pressures. In the context of host-microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate survival within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore in vivo colonization and in vitro biofilm formation abilities of core members of the honey bee (Apis mellifera) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based herbicide formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure elicits variable effects on bacterial growth and biofilm formation. In some instances, the effects correlate with the bacteria's ability to encode a susceptible or tolerant version of the enzyme inhibited by glyphosate in the shikimate pathway. However, in other instances, no such correlation is observed. Testing the herbicide formulation further complicates comparisons, as results often diverge from glyphosate exposure alone, suggesting that co-formulants influence bacterial growth and biofilm formation. These findings highlight the nuanced impacts of environmental stressors on microbial biofilms, with both ecological and host health-related implications.

IMPORTANCE

Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member Snodgrassella alvi forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including Bifidobacterium, Bombilactobacillus, Gilliamella, and Lactobacillus, also form biofilms in vitro. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.

Carbon Source and Substrate Surface Affect Biofilm Formation by the Plant-Associated Bacterium Pseudomonas donghuensis P482

The ability of bacteria to colonize diverse environmental niches is often linked to their competence in biofilm formation. It depends on the individual characteristics of a strain, the nature of the colonized surface (abiotic or biotic), or the availability of certain nutrients. Pseudomonas donghuensis P482 efficiently colonizes the rhizosphere of various plant hosts, but a connection between plant tissue colonization and the biofilm formation ability of this strain has not yet been established. We demonstrate here that the potential of P482 to form biofilms on abiotic surfaces and the structural characteristics of the biofilm are influenced by the carbon source available to the bacterium, with glycerol promoting the process. Also, the type of substratum, polystyrene or glass, impacts the ability of P482 to attach to the surface. Moreover, P482 mutants in genes associated with motility or chemotaxis, the synthesis of polysaccharides, and encoding proteases or regulatory factors, which affect biofilm formation on glass, were fully capable of colonizing the root tissue of both tomato and maize hosts. Investigating the role of cellular factors in biofilm formation using these plant-associated bacteria shows that the ability of bacteria to form biofilm on abiotic surfaces does not necessarily mirror its ability to colonize plant tissues. Our research provides a broader perspective on the adaptation of these bacteria to various environments.

Unlocking the potential of biofilm-forming plant growth-promoting rhizobacteria for growth and yield enhancement in wheat (Triticum aestivum L.)

Plant growth-promoting rhizobacteria (PGPR) boost crop yields and reduce environmental pressures through biofilm formation in natural climates. Recently, biofilm-based root colonization by these microorganisms has emerged as a promising strategy for agricultural enhancement. The current work aims to characterize biofilm-forming rhizobacteria for wheat growth and yield enhancement. For this, native rhizobacteria were isolated from the wheat rhizosphere and ten isolates were characterized for plant growth promoting traits and biofilm production under axenic conditions. Among these ten isolates, five were identified as potential biofilm-producing PGPR based on in vitro assays for plant growth-promoting traits. These were further evaluated under controlled and field conditions for their impact on wheat growth and yield attributes. Surface-enhanced Raman spectroscopy analysis further indicated that the biochemical composition of the biofilm produced by the selected bacterial strains includes proteins, carbohydrates, lipids, amino acids, and nucleic acids (DNA/RNA). Inoculated plants in growth chamber resulted in larger roots, shoots, and increase in fresh biomass than controls. Similarly, significant increases in plant height (13.3, 16.7%), grain yield (29.6, 17.5%), number of tillers (18.7, 34.8%), nitrogen content (58.8, 48.1%), and phosphorus content (63.0, 51.0%) in grains were observed in both pot and field trials, respectively. The two most promising biofilm-producing isolates were identified through 16 s rRNA partial gene sequencing as Brucella sp. (BF10), Lysinibacillus macroides (BF15). Moreover, leaf pigmentation and relative water contents were significantly increased in all treated plants. Taken together, our results revealed that biofilm forming PGPR can boost crop productivity by enhancing growth and physiological responses and thus aid in sustainable agriculture.

Molecular and Phenotypic Investigation on Antibacterial Activities of Limonene Isomers and Its Oxidation Derivative against Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) causes a devastating bacterial leaf blight in rice. Here, the antimicrobial effects of D-limonene, L-limonene, and its oxidative derivative carveol against Xoo were investigated. We revealed that carveol treatment at ≥ 0.1 mM in liquid culture resulted in significant decrease in Xoo growth rate (> 40%) in a concentration-dependent manner, and over 1 mM, no growth was observed. The treatment with D-limonene and L-limonene also inhibited the Xoo growth but to a lesser extent compared to carveol. These results were further elaborated with the assays of motility, biofilm formation and xanthomonadin production. The carveol treatment over 1 mM caused no motilities, basal level of biofilm formation (< 10%), and significantly reduced xanthomonadin production. The biofilm formation after the treatment with two limonene isomers was decreased in a concentration-dependent manner, but the degree of the effect was not comparable to carveol. In addition, there was negligible effect on the xanthomonadin production mediated by the treatment of two limonene isomers. Field emission-scanning electron microscope (FE-SEM) unveiled that all three compounds used in this study cause severe ultrastructural morphological changes in Xoo cells, showing shrinking, shriveling, and holes on their surface. Moreover, quantitative real-time PCR revealed that carveol and D-limonene treatment significantly down-regulated the expression levels of genes involved in virulence and biofilm formation of Xoo, but not with L-limonene. Together, we suggest that limonenes and carveol will be the candidates of interest in the development of biological pesticides.

Oxygen-dependent biofilm dynamics in leaf decay: an in vitro analysis

Biofilms are important in the natural process of plant tissue degradation. However, fundamental knowledge of biofilm community structure and succession on decaying leaves under different oxygen conditions is limited. Here, we used 16S rRNA and ITS gene amplicon sequencing to investigate the composition, temporal dynamics, and community assembly processes of bacterial and fungal biofilms on decaying leaves in vitro. Leaves harvested from three plant species were immersed in lake water under aerobic and anaerobic conditions in vitro for three weeks. Biofilm-covered leaf samples were collected weekly and investigated by scanning electron microscopy. The results showed that community composition differed significantly between biofilm samples under aerobic and anaerobic conditions, though not among plant species. Over three weeks, a clear compositional shift of the bacterial and fungal biofilm communities was observed. The alpha diversity of prokaryotes increased over time in aerobic assays and decreased under anaerobic conditions. Oxygen availability and incubation time were found to be primary factors influencing the microbial diversity of biofilms on different decaying plant species in vitro. Null models suggest that stochastic processes governed the assembly of biofilm communities of decaying leaves in vitro in the early stages of biofilm formation and were further shaped by niche-associated factors.

Investigation of the antibacterial activity of benziothiazolinone against Xanthomonas oryzae pv. oryzae

Plant pathogenic bacteria can cause numerous diseases for higher plants and result in severe reduction of crop yield. Introduction of new bactericides can always effectively control these plant diseases. Benziothiazolinone (BIT) is a novel fungicide registered in China for the control of plant fungal diseases, however, its anti-bacterial activity is not well studied. The results of activity tests showed that BIT exhibited stronger inhibitory activity against bacteria, particularly for Xanthomonas oryzae pv. oryzae (Xoo) (EC50 = 0.17 μg/mL), which was superior than that of the tested fungi in vitro. BIT also exhibited excellent protective and curative activity against rice bacterial leaf blight (BLB) caused by Xoo with the control efficacies of 71.37% and 91.64% at 600 μg/mL, respectively. After treatment with BIT, Xoo cell surface became wrinkled and the cell shape was distorted with extruding cellular content. It was also found that BIT decreased DNA synthesis and affected the biofilm formation and motility of Xoo cells. However, no significant change in the protein content was observed. Moreover, the results of quantitative real-time PCR also showed that expressions of several genes related to DNA synthesis, biofilm formation and motility of Xoo cells were down- or up-regulated, which further proved the anti-bacterial activity of BIT in influencing the biological properties of Xoo. Additionally, BIT also enhanced the activity of phenylalanine ammonia lyase (PAL), a plant defense enzyme. Taken together, benziothiazolinone might be served as an alternative candidate for the control of BLB.

Residual cells and nutrient availability guide wound healing in bacterial biofilms

Biofilms are multicellular heterogeneous bacterial communities characterized by social-like division of labor, and remarkable robustness with respect to external stresses. Increasingly often an analogy between biofilms and arguably more complex eukaryotic tissues is being drawn. One illustrative example of where this analogy can be practically useful is the process of wound healing. While it has been extensively studied in eukaryotic tissues, the mechanism of wound healing in biofilms is virtually unexplored. Combining experiments in Bacillus subtilis bacteria, a model organism for biofilm formation, and a lattice-based theoretical model of biofilm growth, we studied how biofilms recover after macroscopic damage. We suggest that nutrient gradients and the abundance of proliferating cells are key factors augmenting wound closure. Accordingly, in the model, cell quiescence, nutrient fluxes, and biomass represented by cells and self-secreted extracellular matrix are necessary to qualitatively recapitulate the experimental results for damage repair. One of the surprising experimental findings is that residual cells, persisting in a damaged area after removal of a part of the biofilm, prominently affect the healing process. Taken together, our results outline the important roles of nutrient gradients and residual cells on biomass regrowth on macroscopic scales of the whole biofilm. The proposed combined experiment-simulation framework opens the way to further investigate the possible relation between wound healing, cell signaling and cell phenotype alternation in the local microenvironment of the wound.

Quantification of Mixed-Linkage β-Glucan (MLG) in Bacteria

Prokaryotes are known to produce and secrete a broad range of biopolymers with a high functional and structural heterogeneity, often with critical duties in the bacterial physiology and ecology. Among these, exopolysaccharides (EPS) play relevant roles in the interaction of bacteria with eukaryotic hosts. EPS can help to colonize the host and assist in bacterial survival, making this interaction more robust by facilitating the formation of structured biofilms. In addition, they are often key molecules in the specific recognition mechanisms involved in both beneficial and pathogenic bacteria-host interactions. A novel EPS known as MLG (Mixed-Linkage β-Glucan) was recently discovered in rhizobia, where it participates in bacterial aggregation and biofilm formation and is required for efficient attachment to the roots of their legume host plants. MLG is the first and, so far, the only reported linear Mixed-Linkage β-glucan in bacteria, containing a perfect alternation of β (1 → 3) and β (1 → 4) bonds. A phylogenetic study of MLG biosynthetic genes suggests that far from being exclusive of rhizobia, different soil and plant-associated bacteria likely produce MLG, adding this novel polymer to the plethora of surface polysaccharides that help bacteria thrive in the changing environment and to establish successful interactions with their hosts.In this work, a quantification method for MLG is proposed. It relays on the hydrolysis of MLG by a specific enzyme (lichenase), and the subsequent quantification of the released disaccharide (laminaribiose) by the phenol-sulfuric acid method. The protocol has been set up and optimized for its use in 96-well plates, which makes it suitable for high-throughput screening (HTS) approaches. This method stands out by its fast processing, technical simplicity, and capability to handle multiple samples and biological replicates at a time.

Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming beneficial biofilms

Hydroponic cultivation of Solanum lycopersicum (tomato) is important, and high tomato production depends on the use of nitrogen and phosphate fertilizers. We had developed a microbial fertilizer (MF), which is mainly composed of nitrate. To investigate the effect of MF on plant growth, hydroponic tomato was grown with MF or commercial inorganic fertilizer (IF), and the microbiomes of the rhizosphere and the liquid phase were analyzed by confocal microscopy and high-throughput sequencing. Plant biomass and biofilm formation were increased by growth in MF compared to IF. The microbial community structures of tomato roots and hydroponic water differed between the two conditions, and three operational taxonomic units (OTUs) dominated in plants grown with MF. The three OTUs were related to Rudaea spp., Chitinophaga spp., and Stenotrophobacter terrae, which are reported to be disease-suppressive epiphytic or endophytic microbes of plant roots. Because these three OTUs also predominated in the MF itself, they were likely provided to the rhizosphere or endophytic environments of tomato roots via hydroponic water. KEY POINTS: • Microbial fertilizer for hydroponic growth enhanced biofilm formation on tomato root. • Microbial fertilizer contains tomato-root epiphytic or endophytic microbes. • Microbial fertilizer provided beneficial microbes to the rhizosphere and endophytic environments of tomato roots via hydroponic water.

Origins of symbiosis: shared mechanisms underlying microbial pathogenesis, commensalism and mutualism of plants and animals

Regardless of the outcome of symbiosis, whether it is pathogenic, mutualistic or commensal, bacteria must first colonize their hosts. Intriguingly, closely related bacteria that colonize diverse hosts with diverse outcomes of symbiosis have conserved host-association and virulence factors. This review describes commonalities in the process of becoming host associated amongst bacteria with diverse lifestyles. Whether a pathogen, commensal or mutualist, bacteria must sense the presence of and migrate towards a host, compete for space and nutrients with other microbes, evade the host immune system, and change their physiology to enable long-term host association. We primarily focus on well-studied taxa, such as Pseudomonas, that associate with diverse model plant and animal hosts, with far-ranging symbiotic outcomes. Given the importance of opportunistic pathogens and chronic infections in both human health and agriculture, understanding the mechanisms that facilitate symbiotic relationships between bacteria and their hosts will help inform the development of disease treatments for both humans, and the plants we eat.

Unveiling the Secrets of Calcium-Dependent Proteins in Plant Growth-Promoting Rhizobacteria: An Abundance of Discoveries Awaits

The role of Calcium ions (Ca2+) is extensively documented and comprehensively understood in eukaryotic organisms. Nevertheless, emerging insights, primarily derived from studies on human pathogenic bacteria, suggest that this ion also plays a pivotal role in prokaryotes. In this review, our primary focus will be on unraveling the intricate Ca2+ toolkit within prokaryotic organisms, with particular emphasis on its implications for plant growth-promoting rhizobacteria (PGPR). We undertook an in silico exploration to pinpoint and identify some of the proteins described in the existing literature, including prokaryotic Ca2+ channels, pumps, and exchangers that are responsible for regulating intracellular Calcium concentration ([Ca2+]i), along with the Calcium-binding proteins (CaBPs) that play a pivotal role in sensing and transducing this essential cation. These investigations were conducted in four distinct PGPR strains: Pseudomonas chlororaphis subsp. aurantiaca SMMP3, P. donghuensis SVBP6, Pseudomonas sp. BP01, and Methylobacterium sp. 2A, which have been isolated and characterized within our research laboratories. We also present preliminary experimental data to evaluate the influence of exogenous Ca2+ concentrations ([Ca2+]ex) on the growth dynamics of these strains.

Plant myo-inositol transport influences bacterial colonization phenotypes

Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host metabolites are consistently identified as important mediators of microbial interactions. We combine information from a large-scale metatranscriptomic dataset from natural poplar trees and experimental genetic manipulation assays in seedlings of the model plant Arabidopsis thaliana to converge on a conserved role for transport of the plant metabolite myo-inositol in mediating host-microbe interactions. While microbial catabolism of this compound has been linked to increased host colonization, we identify bacterial phenotypes that occur in both catabolism-dependent and -independent manners, suggesting that myo-inositol may additionally serve as a eukaryotic-derived signaling molecule to modulate microbial activities. Our data suggest host control of this compound and resulting microbial behavior are important mechanisms at play surrounding the host metabolite myo-inositol.

Effects of vermicompost leachate on nitrogen, phosphorus, and microbiome in a food waste bioponic system

Food waste is rich in nutrients, such as nitrogen and phosphorus, and can be integrated with bioponics, a closed-loop agricultural system that combines hydroponics with biological nutrient recovery. Vermicompost leachate (VCL) supplementation has been shown to improve the co-composting of organic waste (i.e., compost quality) and the biodegradation of organic compounds. Thus, VCL has high potential for enhancing nutrient availability in bioponics from food waste. However, the understanding of nitrogen and phosphorus availability in food waste-based bioponics is limited, both with and without VCL. In this study, food waste derived from cafeteria vegetable waste was used as the substrate (500 g dry wt./system) in bioponics to grow lettuce (Lactuca sativa L.) for two consecutive cycles (35 days/cycle) without substrate replacement. VCL was applied weekly (1-5% v/v) and compared to the control without VCL. The results showed that the food waste in bioponics provided nitrogen and phosphorus for plant growth (15.5-65.8 g/lettuce head). Organic-degrading and nutrient-transforming bacteria (Hydrogenispora, Clostridium_sensu_stricto_1, Ruminiclostridium_1, Cellvibrio, Thauera, Hydrogenophaga, and Bacillus) were predominantly found in plant roots and residual food waste. VCL addition significantly increased nitrate, phosphate, and chemical oxygen demand levels in bioponics, owing to the nutrients in VCL and the enhancement of keystone microorganisms responsible for organic degradation and nutrient cycling (e.g., Ellin6067, Actinomyces, and Pirellula). These findings suggest that nitrogen, phosphorus, and organic carbon concentrations in an ecosystem of nutrient-transforming and organic-degrading microbes are key in managing nutrient recovery from food waste in bioponics.

Acinetobacter oleivorans IRS14 alleviates cold stress in wheat by regulating physiological and biochemical factors

AIMS

Climate change is responsible for extreme cold winters, causing a significant loss in crop yield and productivity due to chilling stress. This study aims to investigate the potential of psychrotrophic plant growth-promoting rhizobacteria (PGPR) strain to promote wheat growth under cold stress and explore the adaptive responses of wheat.

METHODS AND RESULTS

Wheat seeds and seedlings were inoculated with the psychrotrophic strain IRS14 and the plants were cultivated for five weeks at 6°C ± 2°C. The genetic, biochemical, physiological, and molecular analysis of the bacterium and plant was done to evaluate the effect of the PGPR strain in alleviating chilling stress. IRS14 possesses antioxidant activity and produced multiple phytohormones, which enhanced seed germination (∼50%) and plant growth (∼50%) during chilling stress.

CONCLUSIONS

Here, we reported that the application of IRS14 helps to regulate the biochemical and metabolic pathways in wheat plants. It alleviates chilling stress and increases plant growth rate and biomass. Strain IRS14 in wheat effectively increased chlorophyll content, antioxidants, carotenoid, proline, and endogenous phytohormones compared with untreated wheat.

Metal oxide nanoparticles inhibit nitrogen fixation and rhizosphere colonization by inducing ROS in associative nitrogen-fixing bacteria Pseudomonas stutzeri A1501

The potential effects of engineered metal oxide nanoparticles (MONPs) on bacterial nitrogen fixation are of great concern. Herein, the impact and mechanism of the increasing-used MONPs, including TiO₂, Al₂O₃, and ZnO nanoparticles (TiO₂NP, Al₂O₃NP, and ZnONP, respectively), on nitrogenase activity was studied at the concentrations ranging from 0 to 10 mg L^-1 using associative rhizosphere nitrogen-fixing bacteria Pseudomonas stutzeri A1501. Nitrogen fixation capacity was inhibited by MONPs in an increasing degree of TiO₂NP < Al₂O₃NP < ZnONP. Realtime qPCR analysis showed that the expressions of nitrogenase synthesis-related genes, including nifA and nifH, were inhibited significantly when MONPs were added. MONPs could cause the explosion of intracellular ROS, and ROS not only changed the permeability of the membrane but also inhibited the expression of nifA and biofilm formation on the root surface. The repressed nifA gene could inhibit transcriptional activation of nif-specific genes, and ROS reduced the biofilm formation on the root surface which had a negative effect on resisting environmental stress. This study demonstrated that MONPs, including TiO₂NP, Al₂O₃NP, and ZnONP, inhibited bacterial biofilm formation and nitrogen fixation in the rice rhizosphere, which might have a negative effect on the nitrogen cycle in bacteria-rice system.

Colonization Mechanism of Endophytic Enterobacter cloacae TMX-6 on Rice Seedlings Mediated by Organic Acids Exudated from Roots

Small molecular organic acids (SMOAs) in root exudates are critical for plant-microbe interaction, especially under environmental stresses. However, the dominant organic acids driving the process and promoting the colonization are unclear. Here, using a target metabolomics, 20 main SMOAs of rice root exudates were identified and analyzed in control and 10 mg/L thiamethoxam-treated groups. The composition of these SMOAs differed significantly between the two treatments. Among which, malic acid, citric acid, succinic acid, and proline induced a chemotactic response, swimming ability, and biofilm formation of Enterobacter cloacae TMX-6 in a dose-dependent manner. The maximal chemotactic response of TMX-6 was induced by proline at 10 mg/L, and a strong chemotactic response was even observed at 0.01 mg/L. The recruitment assay confirmed that the addition of these four compounds promoted the colonization of TMX-6. The results provide insight for directional regulation of plant-microbe interactions for beneficial outcomes.

Evaluating the adhesive potential of the newly isolated bacterial strains in research exploitation of plant microbial interaction

Bacterial adhesion potential constitutes the transition of bacteria from the planktonic to the static phase by promoting biofilm formation, which plays a significant role in plant-microbial interaction in the agriculture industry. In present study, the adhesion potential of five soil-borne bacterial strains belonging to different genera was studied. All bacterial strains were capable of forming colonies and biofilms of different levels of firmness on polystyrene. Significant variation was observed in hydrophobicity and motility assays. Among the five bacterial strains (SH-6, SH-8, SH-9, SH-10, and SH-19), SH-19 had a strong hydrophobic force, while SH-10 showed the most hydrophilic property. SH-6 showed great variability in motility; SH-8 had a swimming diffusion diameter of 70 mm, which was three times higher than that of SH-19. In the motility assay, SH-9 and SH-10 showed diffusion diameters of approximately 22 mm and 55 mm, respectively. Furthermore, among the five strains, four are predominately electron donors and one is electron acceptors. Overall, positive correlation was observed among Lewis acid base properties, hydrophobicity, and biofilm forming ability. However, no correlation of motility with bacterial adhesion could be found in present experimental work. Scanning electron microscopy images confirmed the adhesion potential and biofilm ability within extra polymeric substances. Research on the role of adhesion in biofilm formation of bacteria isolated from plants is potentially conducive for developing strategies such as plant-microbial interaction to mitigate the abiotic stress.

Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt

Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.

Biofilm Formation and Structure in the Filamentous Fungus Fusarium graminearum, a Plant Pathogen

Biofilms are protective structures for pathogens of plants and animals, in which cells are shielded from host defense responses and antimicrobial treatments. Although biofilms are well studied in bacterial pathogens, their development and structure in filamentous fungi, as well as their role in pathogenicity, are poorly understood. We show that the economically important plant pathogen Fusarium graminearum, a filamentous fungus, forms biofilms in vitro, which adhere to polystyrene, a hydrophobic surface. The biofilms have complex hyphal structures surrounded by a polymeric matrix that consists primarily of polysaccharides and extracellular nucleic acids, and lack lipids. Pellicles are formed in liquid cultures, floating biofilm masses that are common in bacterial biofilms, and noted but undescribed in filamentous fungal biofilms. Commonly, F. graminearum grows as hyphal colonies; however, on media which lack electron acceptors, an altered morphology is formed with predominantly short, bulbous hyphae embedded in the matrix. Supplementation of the biofilm-inducing medium with an electron acceptor restores the filamentous hyphal morphology, demonstrating that the formation of bulbous hyphae is due, at least in part, to oxidative stress. Plant hosts infected with pathogens generally respond by producing reactive oxygen species, commonly produced as a defense response. Thus, the formation of biofilms strongly suggests a role in protecting cells from host responses during the course of plant disease. IMPORTANCE Fusarium graminearum is a filamentous fungal pathogen that causes Fusarium head blight (FHB) in cereal crops, leading to devastating crop losses. We have demonstrated the ability of this pathogen to form biofilms. Biofilms are likely to be important in the disease cycle of F. graminearum and other plant pathogens, protecting cells from plant defenses and environmental conditions. Towards this end, we have characterized the formation of biofilms in F. graminearum in vitro, which, together with ongoing characterization of their association with host plants, provides a basis for understanding the functionality of biofilms in the pathogen disease cycle.

Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes

Root exudates are important for shaping root-associated microbiomes. However, studies on a wider range of metabolites in exudates are required for a comprehensive understanding about their influence on microbial communities. We identified maize inbred lines that differ in exudate concentrations of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA) and γ-aminobutyric acid (GABA) using a semi-hydroponic system. These lines were grown in the field to determine the changes in microbial diversity and gene expression due to varying concentrations of DIMBOA and GABA in exudates using 16S rRNA amplicon sequencing and metatranscriptomics. Results showed individual and interaction effects of DIMBOA and GABA on the rhizosphere and root endosphere β-diversity, most strongly at the V10 growth stage. The main bacterial families affected by both compounds were Ktedonobacteraceae and Xanthomonadaceae. Higher concentrations of DIMBOA in exudates affected the rhizosphere metatranscriptome, enriching for metabolic pathways associated with plant disease. This study validated the use of natural variation within plant species as a powerful approach for understanding the role of root exudates on microbiome selection. We also showed that a semi-hydroponic system can be used to identify maize genotypes that differ in GABA and DIMBOA exudate concentrations under field conditions. The impact of GABA exudation on root-associated microbiomes is shown for the first time.

Bactericidal Efficacy of Oxidized Silver against Biofilms Formed by Curtobacterium flaccumfaciens pv. flaccumfaciens

Bacterial wilt is a re-emerging disease on dry bean and can affect many other crop species within the Fabaceae. The causal agent, Curtobacterium flaccumfaciens pv. flaccumfaciens (CFF), is a small, Gram-positive, rodshaped bacterium that is seed-transmitted. Infections in the host become systemic, leading to wilting and economic loss. Clean seed programs and bactericidal seed treatments are two critical management tools. This study characterizes the efficacies of five bactericidal chemicals against CFF. It was hypothesized that this bacterium was capable of forming biofilms, and that the cells within biofilms would be more tolerant to bactericidal treatments. The minimum biocide eradication concentration assay protocol was used to grow CFF biofilms, expose the biofilms to bactericides, and enumerate survivors compared to a non-treated control (water). Streptomycin and oxysilver bisulfate had EC95 values at the lowest concentrations and are likely the best candidates for seed treatment products for controlling seed-borne bacterial wilt of bean. The results showed that CFF formed biofilms during at least two phases of the bacterial wilt disease cycle, and the biofilms were much more difficult to eradicate than their planktonic counterparts. Overall, biofilm formation by CFF is an important part of the bacterial wilt disease cycle in dry edible bean and antibiofilm bactericides such as streptomycin and oxysilver bisulfate may be best suited for use in disease management.

Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism

Background

Paris polyphylla is a herb widely used in traditional Chinese medicine to treat various diseases. Stem rot diseases seriously affected the yield of P. polyphylla in subtropical areas of China. Therefore, cost-effective, chemical-free, eco-friendly strategies to control stem rot on P. polyphylla are valuable and urgently needed.

Results

In this paper, we reported the biocontrol efficiency of Paenibacillus peoriae HJ-2 and its complete genome sequence. Strain HJ-2 could serve as a potential biocontrol agent against stem rot on P. polyphylla in the greenhouse and field. The genome of HJ-2 consists of a single 6,001,192 bp chromosome with an average GC content of 45% and 5,237 predicted protein coding genes, 39 rRNAs and 108 tRNAs. The phylogenetic tree indicated that HJ-2 is most closely related to P. peoriae IBSD35. Functional analysis of genome revealed numerous genes/gene clusters involved in plant colonization, biofilm formation, plant growth promotion, antibiotic and resistance inducers synthesis. Moreover, metabolic pathways that potentially contribute to biocontrol mechanisms were identified.

Conclusions

This study revealed that P. peoriae HJ-2 could serve as a potential BCA against stem rot on P. polyphylla. Based on genome analysis, the genome of HJ-2 contains more than 70 genes and 12 putative gene clusters related to secondary metabolites, which have previously been described as being involved in chemotaxis motility, biofilm formation, growth promotion, antifungal activity and resistance inducers biosynthesis. Compared with other strains, variation in the genes/gene clusters may lead to different antimicrobial spectra and biocontrol efficacies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08330-0.

Root-Associated Microbiota Response to Ecological Factors: Role of Soil Acidity in Enhancing Citrus Tolerance to Huanglongbing

The citrus orchards in southern China are widely threatened by low soil pH and Huanglongbing (HLB) prevalence. Notably, the lime application has been used to optimize soil pH, which is propitious to maintain root health and enhance HLB tolerance of citrus; however, little is known about the interactive effects of soil acidity on the soil properties and root-associated (rhizoplane and endosphere) microbial community of HLB-infected citrus orchard. In this study, the differences in microbial community structures and functions between the acidified and amended soils in the Gannan citrus orchard were investigated, which may represent the response of the host-associated microbiome in diseased roots and rhizoplane to dynamic soil acidity. Our findings demonstrated that the severity of soil acidification and aluminum toxicity was mitigated after soil improvement, accompanied by the increase in root activity and the decrease of HLB pathogen concentration in citrus roots. Additionally, the Illumina sequencing-based community analysis showed that the application of soil amendment enriched functional categories involved in host-microbe interactions and nitrogen and sulfur metabolisms in the HLB-infected citrus rhizoplane; and it also strongly altered root endophytic microbial community diversity and structure, which represented by the enrichment of beneficial microorganisms in diseased roots. These changes in rhizoplane-enriched functional properties and microbial composition may subsequently benefit the plant's health and tolerance to HLB disease. Overall, this study advances our understanding of the important role of root-associated microbiota changes and ecological factors, such as soil acidity, in delaying and alleviating HLB disease.

Identification of Adhesins in Plant Beneficial Rhizobacteria Bacillus velezensis SQR9 and Their Effect on Root Colonization

Probiotic Bacillus colonization of plant root surfaces has been reported to improve its beneficial effect. Chemotaxis, adhesion, aggregation, and biofilm formation are the four steps of root colonization by plant growth-promoting rhizobacteria (PGPRs). Compared with the other three well-studied processes, adhesion of PGPRs is less known. In this study, using mutant strains deleted for potential adhesin genes in PGPR strain Bacillus velezensis SQR9, adherence to both cucumber root surface and abiotic surface by those strains was evaluated. Results showed that deletion mutations ΔlytB, ΔV529_10500, ΔfliD, ΔyhaN, and ΔsacB reduced the adhesion to root surfaces, while, among them, only ΔfliD had significant defects in adhesion to abiotic surfaces (glass and polystyrene). In addition, B. velevzensis SQR9 mutants defective in adhesion to root surfaces showed a deficiency in rhizosphere colonization. Among the encoded proteins, FliD and YhaN played vital roles in root adhesion. This research systematically explored the potential adhesins in a well-studied PGPR strain and also indicated that adhesion progress was required for root colonization, which will help to enhance rhizosphere colonization and beneficial function of PGPRs in agricultural production.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Regulatory network controls microbial biofilm development, with Candida albicans as a representative: from adhesion to dispersal

Microorganisms mainly exist in the form of biofilm in nature. Biofilm can contaminate food and drinking water system, as well as cause chronic wound infections, thereby posing a potential threat to public health safety. In the last two decades, researchers have made efforts to investigate the genetic contributors control different stages of biofilm development (adherence, initiation, maturation, and dispersal). As an opportunistic pathogen, C. albicans causes severe superficial or systemic infections with high morbidity and mortality under conditions of immune dysfunction. It has been reported that 80% of C. albicans infections are directly or indirectly associated with biofilm formation on host or abiotic surfaces including indwelling medical devices, resulting in high morbidity and mortality. Significantly, the outcome of C. albicans biofilm development includes enhanced invasion, exacerbated inflammatory responses and intrinsic resistance to antimicrobial chemotherapy. Thus, this review aimed at providing a comprehensive overview of the regulatory network controls microbial biofilm development, with C. albicans as a representative, served as reference for therapeutic targets.

Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15

Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g^–1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92–43.16 and 41.36–51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.

Insulin Regulation of Escherichia coli Abiotic Biofilm Formation: Effect of Nutrients and Growth Conditions

Escherichia coli plays an important role in biofilm formation across a wide array of disease and ecological settings. Insulin can function as an adjuvant in the regulation of biofilm levels. The modulation of insulin-regulated biofilm formation by environmental conditions has not been previously described. In the present study, the effects that various environmental growth conditions and nutrients have on insulin-modulated levels of biofilm production were measured. Micropipette tips were incubated with E. coli ATCC^® 25922™ in a Mueller Hinton broth (MH), or a yeast nitrogen base with 1% peptone (YNBP), which was supplemented with glucose, lactose, galactose and/or insulin (Humulin^®-R). The incubation conditions included a shaking or static culture, at 23 °C or 37 °C. After incubation, the biofilm production was calculated per CFU. At 23 °C, the presence of insulin increased biofilm formation. The amount of biofilm formation was highest in glucose > galactose >> lactose, while the biofilm levels decreased in shaking cultures, except for galactose (3-fold increase; 0.1% galactose and 20 μU insulin). At 37 °C, regardless of condition, there was more biofilm formation/CFU under static conditions in YNBP than in MH, except for the MH containing galactose. E. coli biofilm formation is influenced by aeration, temperature, and insulin concentration in combination with the available sugars.

Stigmasterol root exudation arising from Pseudomonas inoculation of the duckweed rhizosphere enhances nitrogen removal from polluted waters

Rhizospheric microorganisms such as denitrifying bacteria are able to affect 'rhizobioaugmention' in aquatic plants and can help boost wastewater purification by benefiting plant growth, but little is known about their effects on the production of plant root exudates, and how such exudates may affect microorganismal nitrogen removal. Here, we assess the effects of the rhizospheric Pseudomonas inoculant strain RWX31 on the root exudate profile of the duckweed Spirodela polyrrhiza, using gas chromatography/mass spectrometry. Compared to untreated plants, inoculation with RWX31 specifically induced the exudation of two sterols, stigmasterol and β-sitosterol. An authentic standard assay revealed that stigmasterol significantly promoted nitrogen removal and biofilm formation by the denitrifying bacterial strain RWX31, whereas β-sitosterol had no effect. Assays for denitrifying enzyme activity were conducted to show that stigmasterol stimulated nitrogen removal by targeting nitrite reductase in bacteria. Enhanced N removal from water by stigmasterol, and a synergistic stimulatory effect with RWX31, was observed in open duckweed cultivation systems. We suggest that this is linked to a modulation of community composition of nirS- and nirK-type denitrifying bacteria in the rhizosphere, with a higher abundance of Bosea, Rhizobium, and Brucella, and a lower abundance of Rubrivivax. Our findings provide important new insights into the interaction of duckweed with the rhizospheric bacterial strain RWX31 and their involvement in the aquatic N cycle and offer a new path toward more effective bio-formulations for the purification of N-polluted waters.

Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

Draft genome sequencing and functional annotation and characterization of biofilm-producing bacterium Bacillus novalis PD1 isolated from rhizospheric soil

Biofilm forming bacterium Bacillus novalis PD1 was isolated from the rhizospheric soil of a paddy field. B. novalis PD1 is a Gram-positive, facultatively anaerobic, motile, slightly curved, round-ended, and spore-forming bacteria. The isolate B. novalis PD1 shares 98.45% similarity with B. novalis KB27B. B. vireti LMG21834 and B. drentensis NBRC 102,427 are the closest phylogenetic neighbours for B. novalis PD1. The draft genome RAST annotation showed a linear chromosome with 4,569,088 bp, encoding 6139 coding sequences, 70 transfer RNA (tRNA), and 11 ribosomal RNA (rRNA) genes. The genomic annotation of biofilm forming B. novalis PD1(> 3.6@OD_595nm) showed the presence of exopolysaccharide-forming genes (ALG, PSL, and PEL) as well as other biofilm-related genes (comER, Spo0A, codY, sinR, TasA, sipW, degS, and degU). Antibiotic inactivation gene clusters (ANT (6)-I, APH (3')-I, CatA15/A16 family), efflux pumps conferring antibiotic resistance genes (BceA, BceB, MdtABC-OMF, MdtABC-TolC, and MexCD-OprJ), and secondary metabolites linked to phenazine, terpene, and beta lactone gene clusters are part of the genome.

Differentiation of Closely Related Oak-Associated Gram-Negative Bacteria by Label-Free Surface Enhanced Raman Spectroscopy (SERS)

Due to the harmful effects of chemical fertilizers and pesticides, the need for an eco-friendly solution to improve soil fertility has become a necessity, thus microbial biofertilizer research is on the rise. Plant endophytic bacteria inhabiting internal tissues represent a novel niche for research into new biofertilizer strains. However, the number of species and strains that need to be differentiated and identified to facilitate faster screening in future plant-bacteria interaction studies, is enormous. Surface enhanced Raman spectroscopy (SERS) may provide a platform for bacterial discrimination and identification, which, compared with the traditional methods, is relatively rapid, uncomplicated and ensures high specificity. In this study, we attempted to differentiate 18 bacterial isolates from two oaks via morphological, physiological, biochemical tests and SERS spectra analysis. Previous 16S rRNA gene fragment sequencing showed that three isolates belong to Paenibacillus, 3-to Pantoea and 12-to Pseudomonas genera. Additional tests were not able to further sort these bacteria into strain-specific groups. However, the obtained label-free SERS bacterial spectra along with the high-accuracy principal component (PCA) and discriminant function analyses (DFA) demonstrated the possibility to differentiate these bacteria into variant strains. Furthermore, we collected information about the biochemical characteristics of selected isolates. The results of this study suggest a promising application of SERS in combination with PCA/DFA as a rapid, non-expensive and sensitive method for the detection and identification of plant-associated bacteria.

Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system

Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: • Microbiomes of hydrophytes and their surrounding environments were investigated. • Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. • Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

PREMISE

Within a broader study on leaf fossilization in freshwater environments, a long-term study on the development and microbiome composition of biofilms on the foliage of aquatic plants has been initiated to understand how microbes and biofilms contribute to leaf decay and preservation. Here, water lily leaves are employed as a study model to investigate the relationship between bacterial microbiomes, biodegradation, and fossilization. We compare four DNA extraction kits to reduce biases in interpretation and to identify the most suitable kit for the extraction of DNA from bacteria associated with biofilms on decaying water lily leaves for 16S rRNA amplicon analysis.

METHODS

We extracted surface-associated DNA from Nymphaea leaves in early stages of decay at two water depth levels using four commercially available kits to identify the most suitable protocol for bacterial extraction, applying a mock microbial community standard to enable a reliable comparison of the kits.

RESULTS

Kit 4, the FastDNA Spin Kit for Soil, resulted in high DNA concentrations with better quality and yielded the most accurate depiction of the mock community. Comparison of the leaves at two water depths showed no significant differences in community composition.

DISCUSSION

The success of Kit 4 may be attributed to its use of bead beating with a homogenizer, which was more efficient in the lysis of Gram-positive bacteria than the manual vortexing protocols used by the other kits. Our results show that microbial composition on leaves during early decay remains comparable and may change only in later stages of decomposition.

Deciphering bacterial mechanisms of root colonization

Bacterial colonization of the rhizosphere is critical for the establishment of plant-bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria-bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration.

Identification of a diguanylate cyclase expressed in the presence of plants and its application for discovering candidate gene products involved in plant colonization by Pantoea sp. YR343

Microbial colonization of plant roots is a highly complex process that requires the coordination and regulation of many gene networks, yet the identities and functions of many of these gene products have yet to be discovered. Pantoea sp. YR343, a gamma-proteobacterium isolated from the rhizosphere of Populus deltoides, forms robust biofilms along the root surfaces of Populus and possesses plant growth-promoting characteristics. In this work, we identified three diguanylate cyclases in the plant-associated microbe Pantoea sp. YR343 that are expressed in the presence of plant roots. One of these diguanylate cyclases, DGC2884, localizes to discrete sites in the cells and its overexpression results in reduced motility and increased EPS production and biofilm formation. We performed a genetic screen by expressing this diguanylate cyclase from an inducible promoter in order to identify candidate gene products that may be involved in root colonization by Pantoea sp. YR343. Further, we demonstrate the importance of other domains in DGC2884 to its activity, which in combination with the genes identified by transposon mutagenesis, may yield insights into the mechanisms of plant association as well as the activity and regulation of homologous enzymes in medically and agriculturally relevant microbes.

Rapid evolution of bacterial mutualism in the plant rhizosphere

While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.

Rapid evolution of bacterial mutualism in the plant rhizosphere

While beneficial plant-microbe interactions are common in nature, direct evidence for the evolution of bacterial mutualism is scarce. Here we use experimental evolution to causally show that initially plant-antagonistic Pseudomonas protegens bacteria evolve into mutualists in the rhizosphere of Arabidopsis thaliana within six plant growth cycles (6 months). This evolutionary transition is accompanied with increased mutualist fitness via two mechanisms: (i) improved competitiveness for root exudates and (ii) enhanced tolerance to the plant-secreted antimicrobial scopoletin whose production is regulated by transcription factor MYB72. Crucially, these mutualistic adaptations are coupled with reduced phytotoxicity, enhanced transcription of MYB72 in roots, and a positive effect on plant growth. Genetically, mutualism is associated with diverse mutations in the GacS/GacA two-component regulator system, which confers high fitness benefits only in the presence of plants. Together, our results show that rhizosphere bacteria can rapidly evolve along the parasitism-mutualism continuum at an agriculturally relevant evolutionary timescale.

CONTROL DE Aedes aegypti (DIPTERA: CULICIDAE) MEDIANTE ACTINOBACTERIAS FORMADORAS DE BIOPELÍCULAS

El phylum Actinobacteria incluye miembros productores de compuestos bioinsecticidas. No obstante, la sobreexplotacion de metabolitos derivados de Streptomyces ha conllevado a explorar nuevas moléculas provenientes de bacterias no estreptomicetos para contrarrestar la resistencia a insecticidas químicos en Aedes aegypti. Concordantes con el uso de bioagentes ecológicos, esta investigación caracterizó actinobacterias formadoras de biopelículas con el fin de evaluar su dinámica de crecimiento, actividad larvicida y efectos subletales. La identificación, crecimiento de biopelículas y bioactividades se realizaron por cultivos, análisis de imágenes por fotomicrografía y bioensayos. Los resultados mostraron que las biopelículas pertenecen a Pseudonocardiaceae (PsA1TA) y Corynebacteriaceae (CoA2CA) característicamente dependientes del revestimiento cuticular. PsA1TA coloniza estructuras membranosas de tórax y abdomen con microcolonias aleatoriamente distribuidas que desarrollan a extensas biopelículas mono y biestratificadas, al cubrir cuatro veces la amplitud toracoabdominal (envergadura infectiva entre 1010 µm a 1036 µm). En contraste, CoA2CA envuelve radialmente estructuras esclerotizadas cefálica y anal al triplicar la amplitud de tales órganos (1820 a 2030 µm y 1650 a 1860 µm, respectivamente). Las biopelículas ejercieron mortalidad diferenciada a todos los estadios larvales, no obstante, PsA1TA resultó más mortal y virulento en el segundo estadio larval (58 %-96 horas, TL50: 3,4 días), mientras que CoA2CA lo fue en el cuarto estadio larval (85 %-96 horas, TL50: 2,5 días). CoA2CA indujo emergencia incompleta de adultos farados y despliegue de tarsos curvos en emergentes, además de revestir con robustas biopelículas cadáveres larvarios. Las biopelículas actinobacterianas revelaron ejercer función larvicida y respuestas subletales en A. aegypti.

Plant-associated fungal biofilms-knowns and unknowns

Nearly all microbes, including fungi, grow firmly attached to surfaces as a biofilm. Yet, attention toward fungal interactions with plants and the environment is dedicated to free-floating (planktonic) cells. Fungal biofilms are generally thought to configure interactions across and among plant populations. Despite this, plant fungal biofilm research lags far behind the research on biofilms of medically important fungi. The deficit in noticing and exploring this research avenue could limit disease management and plant improvement programs. Here, we provide the current state of knowledge of fungal biofilms and the different pivotal ecological roles they impart in the context of disease, through leveraging evidence across medically important fungi, secondary metabolite production, plant beneficial functions and climate change. We also provide views on several important information gaps potentially hampering plant fungal biofilm research, and propose a way forward to address these gaps.

Absence of 4-Formylaminooxyvinylglycine Production by Pseudomonas fluorescens WH6 Results in Resource Reallocation from Secondary Metabolite Production to Rhizocompetence

Pseudomonas fluorescens WH6 produces the non-proteinogenic amino acid 4-formylaminooxyvinylglycine (FVG), a secondary metabolite with antibacterial and pre-emergent herbicidal activities. The gvg operon necessary for FVG production encodes eight required genes: one regulatory (gvgR), two of unknown functional potential (gvgA and C), three with putative biosynthetic function (gvgF, H, and I), and two small ORFs (gvgB and G). To gain insight into the role of GvgA and C in FVG production, we compared the transcriptome of knockout (KO) mutants of gvgR, A, and C to wild type (WT) to test two hypotheses: (1) GvgA and GvgC play a regulatory role in FVG production and (2) non-gvg cluster genes are regulated by GvgA and GvgC. Our analyses show that, collectively, 687 genes, including the gvg operon, are differentially expressed in all KO strains versus WT, representing >10% of the genome. Fifty-one percent of these genes were similarly regulated in all KO strains with GvgC having the greatest number of uniquely regulated genes. Additional transcriptome data suggest cluster regulation through feedback of a cluster product. We also discovered that FVG biosynthesis is regulated by L-glu, L-asp, L-gln, and L-asn and that resources are reallocated in KO strains to increase phenotypes involved in rhizocompetence including motility, biofilm formation, and denitrification. Altogether, differential transcriptome analyses of mutants suggest that regulation of the cluster is multifaceted and the absence of FVG production or its downregulation can dramatically shift the lifestyle of WH6.

Endophytic Bacteria From the Roots of the Medicinal Plant Alkanna tinctoria Tausch (Boraginaceae): Exploration of Plant Growth Promoting Properties and Potential Role in the Production of Plant Secondary Metabolites

Alkannin and shikonin (A/S) are enantiomeric naphthoquinones produced in the roots of certain plants from the Boraginaceae family such as Lithospermum spp. and Alkanna spp. They possess antimicrobial, anti-tumoral and wound healing properties. The production of secondary metabolites by Alkanna tinctoria might be influenced by its endomicrobiome. To study the interaction between this medicinal plant and its bacterial endophytes, we isolated bacteria from the roots of wild growing Alkanna tinctoria collected near to Athens and Thessaloniki in Greece. Representative strains selected by MALDI-TOF mass spectrometry were identified by partial 16S rRNA gene sequence analysis. In total, 197 distinct phylotypes of endophytic bacteria were detected. The most abundant genera recovered were Pseudomonas, Xanthomonas, Variovorax, Bacillus, Inquilinus, Pantoea, and Stenotrophomonas. Several bacteria were then tested in vitro for their plant growth promoting activity and the production of cell-wall degrading enzymes. Strains of Pseudomonas, Pantoea, Bacillus and Inquilinus showed positive plant growth properties whereas those of Bacteroidetes and Rhizobiaceae showed pectinase and cellulase activity in vitro. In addition, bacterial responses to alkannin and shikonin were investigated through resistance assays. Gram negative bacteria were found to be resistant to the antimicrobial properties of A/S, whereas the Gram positives were sensitive. A selection of bacteria was then tested for the ability to induce A/S production in hairy roots culture of A. tinctoria. Four strains belonging to Chitinophaga sp., Allorhizobium sp., Duganella sp., and Micromonospora sp., resulted in significantly more A/S in the hairy roots than the uninoculated control. As these bacteria can produce cell-wall degrading enzymes, we hypothesize that the A/S induction may be related with the plant-bacteria interaction during colonization.