Involvement of type VI secretion system in secretion of iron chelator pyoverdine in Pseudomonas taiwanensis

A Comparative Transcriptome Analysis Unveils the Mechanisms of Response in Feather Degradation by Pseudomonas aeruginosa Gxun-7

Microbial degradation of feathers offers potential for bioremediation, yet the microbial response mechanisms warrant additional investigation. In prior work, Pseudomonas aeruginosa Gxun-7, which demonstrated robust degradation of feathers at elevated concentrations, was isolated. However, the molecular mechanism of this degradation remains only partially understood. To investigate this, we used RNA sequencing (RNA-seq) to examine the genes that were expressed differentially in P. aeruginosa Gxun-7 when exposed to 25 g/L of feather substrate. The RNA-seq analysis identified 5571 differentially expressed genes; of these, 795 were upregulated and 603 were downregulated. Upregulated genes primarily participated in proteolysis, amino acid, and pyruvate metabolism. Genes encoding proteases, as well as those involved in sulfur metabolism, phenazine synthesis, and type VI secretion systems, were notably elevated, highlighting their crucial function in feather decomposition. Integration of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) taxonomies, combined with a review of the literature, led us to propose that metabolic feather degradation involves environmental activation, reducing agent secretion, protease release, peptide/amino acid uptake, and metabolic processes. Sulfite has emerged as a critical activator of keratinase catalysis, while cysteine serves as a regulatory mediator. qRT-PCR assay results for 11 selected gene subset corroborated the RNA-seq findings. This study enhances our understanding of the transcriptomic responses of P. aeruginosa Gxun-7 to feather degradation and offers insights into potential degradation mechanisms, thereby aiding in the formulation of effective feather waste management strategies in poultry farming.

Secretory molecules from secretion systems fine-tune the host-beneficial bacteria (PGPRs) interaction

Numerous bacterial species associate with plants through commensal, mutualistic, or parasitic association, affecting host physiology and health. The mechanism for such association is intricate and involves the secretion of multiple biochemical substances through dedicated protein systems called secretion systems SS. Eleven SS pathways deliver protein factors and enzymes in their immediate environment or host cells, as well as in competing microbial cells in a contact-dependent or independent fashion. These SS are instrumental in competition, initiation of infection, colonization, and establishment of association (positive or negative) with host organisms. The role of SS in infection and pathogenesis has been demonstrated for several phytopathogens, including Agrobacterium, Xanthomonas, Ralstonia, and Pseudomonas. Since there is overlap in mechanisms of establishing association with host plants, several studies have investigated the role of SSs in the interaction of plant and beneficial bacteria, including symbiotic rhizobia and plant growth bacteria (PGPB). Therefore, the present review updates the role of different SSs required for the colonization of beneficial bacteria such as rhizobia, Burkholderia, Pseudomonas, Herbaspirillum, etc., on or inside plants, which can lead to a long-term association. Most SS like T3SS, T4SS, T5SS, and T6SS are required for the antagonistic activity needed to prevent competing microbes, including phytopathogens, ameliorate biotic stress in plants, and produce substances for successful colonization. Others are required for chemotaxis, adherence, niche formation, and suppression of immune response to establish mutualistic association with host plants.

The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings

Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact-dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed-to-seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB, abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild-type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS-deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomonas genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris.

Characterization of Type VI secretion system in Edwardsiella ictaluri

Edwardsiella ictaluri is a Gram-negative facultative intracellular fish pathogen causing enteric septicemia of catfish (ESC). While various secretion systems contribute to E. ictaluri virulence, the Type VI secretion system (T6SS) remains poorly understood. In this study, we constructed 13 E. ictaluri T6SS mutants using splicing by overlap extension PCR and characterized them, assessing their uptake and survival in channel catfish (Ictalurus punctatus) peritoneal macrophages, attachment and invasion in channel catfish ovary (CCO) cells, in vitro stress resistance, and virulence and efficacy in channel catfish. Among the mutants, EiΔevpA, EiΔevpH, EiΔevpM, EiΔevpN, and EiΔevpO exhibited reduced replication inside peritoneal macrophages. EiΔevpM, EiΔevpN, and EiΔevpO showed significantly decreased attachment to CCO cells, while EiΔevpN and EiΔevpO also displayed reduced invasion of CCO cells (p < 0.05). Overall, T6SS mutants demonstrated enhanced resistance to oxidative and nitrosative stress in the nutrient-rich medium compared to the minimal medium. However, EiΔevpA, EiΔevpH, EiΔevpM, EiΔevpN, and EiΔevpO were susceptible to oxidative stress in both nutrient-rich and minimal medium. In fish challenges, EiΔevpD, EiΔevpE, EiΔevpG, EiΔevpJ, and EiΔevpK exhibited attenuation and provided effective protection against E. ictaluri wild-type (EiWT) infection in catfish fingerlings. However, their attenuation and protective efficacy were lower in catfish fry. These findings shed light on the role of the T6SS in E. ictaluri pathogenesis, highlighting its significance in intracellular survival, host cell attachment and invasion, stress resistance, and virulence. The attenuated T6SS mutants hold promise as potential candidates for protective immunization strategies in catfish fingerlings.

The RND efflux system ParXY affects siderophore secretion in Pseudomonas putida KT2440

IMPORTANCE

Gram-negative bacteria from the Pseudomonas group are survivors in various environmental niches. For example, the bacteria secrete siderophores to capture ferric ions under deficiency conditions. Tripartite efflux systems are involved in the secretion of siderophores, which are also important for antibiotic resistance. For one of these efflux systems, the resistance-nodulation-cell division transporter ParXY from the model organism Pseudomonas putida KT2440, we show that it influences the secretion of the siderophore pyoverdine in addition to its already known involvement in antibiotic resistance. Phenotypically, its role in pyoverdine secretion is only apparent when other pyoverdine secretion systems are inactive. The results confirm that the different tripartite efflux systems have overlapping substrate specificities and can at least partially functionally substitute for each other, especially in important physiological activities such as supplying the cell with iron ions. This fact must be taken into account when developing specific inhibitors for tripartite efflux systems.

T6SS: A Key to Pseudomonas's Success in Biocontrol?

Bacteria from the genus Pseudomonas have been extensively studied for their capacity to act as biological control agents of disease and pests and for their ability to enhance and promote crop production in agricultural systems. While initial research primarily focused on the human pathogenic bacteria Pseudomonas aeruginosa, recent studies indicate the significance of type VI secretion (T6SS) in other Pseudomonas strains for biocontrol purposes. This system possibly plays a pivotal role in restricting the biological activity of target microorganisms and may also contribute to the bolstering of the survival capabilities of the bacteria within their applied environment. The type VI secretion system is a phage-like structure used to translocate effectors into both prokaryotic and eukaryotic target cells. T6SSs are involved in a myriad of interactions, some of which have direct implications in the success of Pseudomonas as biocontrol agents. The prevalence of T6SSs in the genomes of Pseudomonas species is notably greater than the estimated 25% occurrence rate found in Gram-negative bacteria. This observation implies that T6SS likely plays a pivotal role in the survival and fitness of Pseudomonas. This review provides a brief overview of T6SS, its role in Pseudomonas with biocontrol applications, and future avenues of research within this subject matter.

An Orphan VrgG Auxiliary Module Related to the Type VI Secretion Systems from Pseudomonas ogarae F113 Mediates Bacterial Killing

The model rhizobacterium Pseudomonas ogarae F113, a relevant plant growth-promoting bacterium, encodes three different Type VI secretion systems (T6SS) in its genome. In silico analysis of its genome revealed the presence of a genetic auxiliary module containing a gene encoding an orphan VgrG protein (VgrG5a) that is not genetically linked to any T6SS structural cluster, but is associated with genes encoding putative T6SS-related proteins: a possible adaptor Tap protein, followed by a putative effector, Tfe8, and its putative cognate immunity protein, Tfi8. The bioinformatic analysis of the VgrG5a auxiliary module has revealed that this cluster is only present in several subgroups of the P. fluorescens complex of species. An analysis of the mutants affecting the vgrG5a and tfe8 genes has shown that the module is involved in bacterial killing. To test whether Tfe8/Tfi8 constitute an effector-immunity pair, the genes encoding Tfe8 and Tfi8 were cloned and expressed in E. coli, showing that the ectopic expression of tfe8 affected growth. The growth defect was suppressed by tfi8 ectopic expression. These results indicate that Tfe8 is a bacterial killing effector, while Tfi8 is its cognate immunity protein. The Tfe8 protein sequence presents homology to the proteins of the MATE family involved in drug extrusion. The Tfe8 effector is a membrane protein with 10 to 12 transmembrane domains that could destabilize the membranes of target cells by the formation of pores, revealing the importance of these effectors for bacterial interaction. Tfe8 represents a novel type of a T6SS effector present in pseudomonads.

Detrimental impact of the Geobacter metallireducens type VI secretion system on direct interspecies electron transfer

Direct interspecies electron transfer (DIET) is important in anaerobic communities of environmental and practical significance. Other than the need for close physical contact for electrical connections, the interactions of DIET partners are poorly understood. Type VI secretion systems (T6SSs) typically kill competitive microbes. Surprisingly, Geobacter metallireducens highly expressed T6SS genes when DIET-based co-cultures were initiated with Geobacter sulfurreducens. T6SS gene expression was lower when the electron shuttle anthraquinone-2,6-disulfonate was added to alleviate the need for interspecies contact. Disruption of hcp, the G. metallireducens gene for the main T6SS needle-tube protein subunit, and the most highly upregulated gene in DIET-grown cells eliminated the long lag periods required for the initiation of DIET. The mutation did not aid DIET in the presence of granular-activated carbon (GAC), consistent with the fact that DIET partners do not make physical contact when electrically connected through conductive materials. The hcp-deficient mutant also established DIET quicker with Methanosarcina barkeri. However, the mutant also reduced Fe(III) oxide faster than the wild-type strain, a phenotype not expected from the loss of the T6SS. Quantitative PCR revealed greater gene transcript abundance for key components of extracellular electron transfer in the hcp-deficient mutant versus the wild-type strain, potentially accounting for the faster Fe(III) oxide reduction and impact on DIET. The results highlight that interspecies interactions beyond electrical connections may influence DIET effectiveness. The unexpected increase in the expression of genes for extracellular electron transport components when hcp was deleted emphasizes the complexities in evaluating the electromicrobiology of highly adaptable Geobacter species. IMPORTANCE Direct interspecies electron transfer is an alternative to the much more intensively studied process of interspecies H2 transfer as a mechanism for microbes to share electrons during the cooperative metabolism of energy sources. DIET is an important process in anaerobic soils and sediments generating methane, a significant greenhouse gas. Facilitating DIET can accelerate and stabilize the conversion of organic wastes to methane biofuel in anaerobic digesters. Therefore, a better understanding of the factors controlling how fast DIET partnerships are established is expected to lead to new strategies for promoting this bioenergy process. The finding that when co-cultured with G. sulfurreducens, G. metallireducens initially expressed a type VI secretion system, a behavior not conducive to interspecies cooperation, illustrates the complexity of establishing syntrophic relationships.

From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants

Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.

Tn5 Transposon-based Mutagenesis for Engineering Phage-resistant Strains of Escherichia coli BL21 (DE3)

Escherichia coli is a preferred strain for recombinant protein production, however, it is often plagued by phage infection during experimental studies and industrial fermentation. While the existing methods of obtaining phage-resistant strains by natural mutation are not efficient enough and time-consuming. Herein, a high-throughput method by combining Tn5 transposon mutation and phage screening was used to produce Escherichia coli BL21 (DE3) phage-resistant strains. Mutant strains PR281-7, PR338-8, PR339-3, PR340-8, and PR347-9 were obtained, and they could effectively resist phage infection. Meanwhile, they had good growth ability, did not contain pseudolysogenic strains, and were controllable. The resultant phage-resistant strains maintained the capabilities of producing recombinant proteins since no difference in mCherry red fluorescent protein expression was found in phage-resistant strains. Comparative genomics showed that PR281-7, PR338-8, PR339-3, and PR340-8 mutated in ecpE, nohD, nrdR, and livM genes, respectively. In this work, a strategy was successfully developed to obtain phage-resistant strains with excellent protein expression characteristics by Tn5 transposon mutation. This study provides a new reference to solve the phage contamination problem.

Bacterial type VI secretion system (T6SS): an evolved molecular weapon with diverse functionality

Bacterial secretion systems are nanomolecular complexes that release a diverse set of virulence factors/or proteins into its surrounding or translocate to their target host cells. Among these systems, type VI secretion system 'T6SS' is a recently discovered molecular secretion system which is widely distributed in Gram-negative (-ve) bacteria, and shares structural similarity with the puncturing device of bacteriophages. The presence of T6SS is an advantage to many bacteria as it delivers toxins to its neighbour pathogens for competitive survival, and also translocates protein effectors to the host cells, leading to disruption of lipid membranes, cell walls, and cytoskeletons etc. Recent studies have characterized both anti-prokaryotic and anti-eukaryotic effectors, where T6SS is involved in diverse cellular functions including favouring colonization, enhancing the survival, adhesive modifications, internalization, and evasion of the immune system. With the evolution of advanced genomics and proteomics tools, there has been an increase in the number of characterized T6SS effector arsenals and also more clear information about the adaptive significance of this complex system. The functions of T6SS are generally regulated at the transcription, post-transcription and post-translational levels through diverse mechanisms. In the present review, we aimed to provide information about the distribution of T6SS in diverse bacteria, any structural similarity/or dissimilarity, effectors proteins, functional significance, and regulatory mechanisms. We also tried to provide information about the diverse roles played by T6SS in its natural environments and hosts, and further any changes in the microbiome.

The ABC transporter family efflux pump PvdRT-OpmQ of Pseudomonas putida KT2440: purification and initial characterization

Tripartite efflux systems of the ABC-type family transport a variety of substrates and contribute to the antimicrobial resistance of Gram-negative bacteria. PvdRT-OpmQ, a member of this family, is thought to be involved in the secretion of the newly synthesized and recycled siderophore pyoverdine in Pseudomonas species. Here, we purified and characterized the inner membrane component PvdT and the periplasmic adapter protein PvdR of the plant growth-promoting soil bacterium Pseudomonas putida KT2440. We show that PvdT possesses an ATPase activity that is stimulated by the addition of PvdR. In addition, we provide the first biochemical evidence for direct interactions between pyoverdine and PvdRT.

Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens

Lettuce is a major vegetable crop worldwide that is affected by numerous bacterial pathogens, including Xanthomonas hortorum pv. vitians, Pseudomonas cichorii, and Pectobacterium carotovorum. Control methods are scarce and not always effective. To develop new and sustainable approaches to contain these pathogens, we screened more than 1,200 plant-associated Pseudomonas strains retrieved from agricultural soils for their in vitro antagonistic capabilities against the three bacterial pathogens under study. Thirty-five Pseudomonas strains significantly inhibited some or all three pathogens. Their genomes were fully sequenced and annotated. These strains belong to the P. fluorescens and P. putida phylogenomic groups and are distributed in at least 27 species, including 15 validly described species. They harbor numerous genes and clusters of genes known to be involved in plant-bacteria interactions, microbial competition, and biocontrol. Strains in the P. putida group displayed on average better inhibition abilities than strains in the P. fluorescens group. They carry genes and biosynthetic clusters mostly absent in the latter strains that are involved in the production of secondary metabolites such as 7-hydroxytropolone, putisolvins, pyochelin, and xantholysin-like and pseudomonine-like compounds. The presence of genes involved in the biosynthesis of type VI secretion systems, tailocins, and hydrogen cyanide also positively correlated with the strains' overall inhibition abilities observed against the three pathogens. These results show promise for the development of biocontrol products against lettuce bacterial pathogens, provide insights on some of the potential biocontrol mechanisms involved, and contribute to public Pseudomonas genome databases, including quality genome sequences on some poorly represented species.

Bacterial Siderophores: Structure, Functions, and Role in the Pathogenesis of Infections

This review systematizes and analyzes the data published over the past decade, devoted to the study of low-molecular-weight high affinity iron chelators – siderophores. Siderophores, which are found in bacteria, fungi and mammals, are able to extract iron from insoluble inorganic compounds, and in the host organism – from complexes with proteins that perform the function of nonspecific protection of mammals from infections. The extracted iron is delivered to cells through surface protein receptors specific for each siderophore, as well as various protein transport systems that make up membranes. Siderophores play an important role in virulence in pathogenic bacteria, performing many functions in the host organism, in addition to providing microbes with iron and other biological metals. They participate in the storage of excess iron, toxic to cells, protect bacteria from reactive oxygen compounds, compete for iron with phagocytes, and have a harmful effect on host cells, acting as secreted bacterial toxin in some cases. Bacterial siderophores perform a signaling function and regulate both, their own synthesis and the synthesis of other virulence factors. Many pathogenic bacteria produce several siderophores that are active under different conditions, against various sources of iron in the host organism and at different stages of infectious process. The review presents the results of the experimental studies aimed at elucidating the structure and diverse functions of bacterial siderophores, the mechanisms of their biosynthesis and regulation of expression, as well as the role of these molecules in the physiology and virulence of pathogenic bacteria. Special emphasis is put on siderophores of bacteria causing particularly dangerous infections.

Bacterial protein secretion systems: Game of types

Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.

Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets

In silico genome mining provides easy access to secondary metabolite biosynthetic gene clusters (BGCs) encoding the biosynthesis of many bioactive compounds, which are the basis for many important drugs used in human medicine. However, the association between BGCs and other functions encoded in the genomes of producers have remained elusive. Here, we present a systems biology workflow that integrates genome mining with a detailed pangenome analysis for detecting genes associated with a particular BGC. We analyzed 3,889 enterobacterial genomes and found 13,266 BGCs, represented by 252 distinct BGC families and 347 additional singletons. A pangenome analysis revealed 88 genes putatively associated with a specific BGC coding for the colon cancer-related colibactin that code for diverse metabolic and regulatory functions. The presented workflow opens up the possibility to discover novel secondary metabolites, better understand their physiological roles, and provides a guide to identify and analyze BGC associated gene sets.

Presence and absence of type VI secretion systems in bacteria

The type VI secretion system (T6SS) is a molecular puncturing device that enables Gram-negative bacteria to kill competitors, manipulate host cells and take up nutrients. Who would want to miss such superpowers? Indeed, many studies show how widespread the secretion apparatus is among microbes. However, it is becoming evident that, on multiple taxonomic levels, from phyla to species and strains, some bacteria lack a T6SS. Here, we review who does and does not have a type VI secretion apparatus and speculate on the dynamic process of gaining and losing the secretion system to better understand its spread and distribution across the microbial world.

Evaluation of the Antifungal Activities of Photorhabdus akhurstii and Its Secondary Metabolites against Phytopathogenic Colletotrichum gloeosporioides

Colletotrichum gloeosporioides is a phytopathogenic fungus that causes devastating losses in strawberries without effective countermeasures. Members of the genus Photorhabdus exhibit antimicrobial capability and have been found to have the potential for use as biocontrol agents against C. gloeosporioides. Photorhabdus species exhibit two phase variations with a differentiated composition of secondary metabolites designated to each phase. In this study, Photorhabdus akhurstii sp. nov. 0813-124 exhibited phase I (PL1) and phase II (PL2); however, only PL1 displayed distinct inhibition of C. gloeosporioides in the confrontation assay. We identified the bioactive ingredients of P. akhurstii sp. nov. 0813-124 to be glidobactin A and cepafungin I, with MIC values lower than 1.5 and 2.0 µg/mL, respectively. Furthermore, we revealed the biosynthetic gene cluster (BGC) of corresponding bioactive molecules through genomics analysis and determined its expression level in PL1 and PL2. The expression of glidobactin BGC in PL1 increased rapidly within 24 h, while PL2 was eventually stimulated after 60 h. In summary, we demonstrated that P. akhurstii sp. nov. 0813-124 could potentially be used as a biocontrol agent or part of a natural product repertoire for combating C. gloeosporioides.

Roles of Type VI Secretion System in Transport of Metal Ions

The type VI secretion system (T6SS) is a transmembrane protein nanomachine employed by many gram-negative bacteria to directly translocate effectors into adjacent cells or the extracellular milieu, showing multiple functions in both interbacterial competition and bacteria-host interactions. Metal ion transport is a newly discovered T6SS function. This review summarizes the identified T6SS functions and highlights the features of metal ion transport mediated by T6SS and discusses its regulation.

Beyond dueling: roles of the type VI secretion system in microbiome modulation, pathogenesis and stress resistance

Bacteria inhabit diverse and dynamic environments, where nutrients may be limited and toxic chemicals can be prevalent. To adapt to these stressful conditions, bacteria have evolved specialized protein secretion systems, such as the type VI secretion system (T6SS) to facilitate their survival. As a molecular syringe, the T6SS expels various effectors into neighboring bacterial cells, eukaryotic cells, or the extracellular environment. These effectors improve the competitive fitness and environmental adaption of bacterial cells. Although primarily recognized as antibacterial weapons, recent studies have demonstrated that T6SSs have functions beyond interspecies competition. Here, we summarize recent research on the role of T6SSs in microbiome modulation, pathogenesis, and stress resistance.

Diversification of the Type VI Secretion System in Agrobacteria

The type VI secretion system (T6SS) is used by many Gram-negative bacteria to deploy toxic effectors for interbacterial competition. This system provides a competitive advantage in planta to agrobacteria, a diverse group with phytopathogenic members capable of genetically transforming plants. To inform on the ecology and evolution of agrobacteria, we revealed processes that diversify their effector gene collections. From genome sequences of diverse strains, we identified T6SS loci, functionally validated associated effector genes for toxicity, and predicted genes homologous to those that encode proteins known to interact with effectors. The gene loci were analyzed in a phylogenetic framework, and results show that strains of some species-level groups have different patterns of T6SS expression and are enriched in specific sets of T6SS loci. Findings also demonstrate that the modularity of T6SS loci and their associated genes engenders dynamicity, promoting reshuffling of entire loci, fragments therein, and domains to swap toxic effector genes across species. However, diversification is constrained by the need to maintain specific combinations of gene subtypes, congruent with observations that certain genes function together to regulate T6SS loading and activation. Data are consistent with a scenario where species can acquire unique T6SS loci that are then reshuffled across the genus in a restricted manner to generate new combinations of effector genes. IMPORTANCE The T6SS is used by several taxa of Gram-negative bacteria to secrete toxic effector proteins to attack others. Diversification of effector collections shapes bacterial interactions and impacts the health of hosts and ecosystems in which bacteria reside. We uncovered the diversity of T6SS loci across a genus of plant-associated bacteria and show that diversification is driven by the acquisition of new loci and reshuffling among species. However, linkages between specific subtypes of genes need to be maintained to ensure that proteins whose interactions are necessary to activate the T6SS remain together. Results reveal how organization of gene loci and domain structure of genes provides flexibility to diversify under the constraints imposed by the system. Findings inform on the evolution of a mechanism that influences bacterial communities.

Defending against the Type Six Secretion System: beyond Immunity Genes

The bacterial type six secretion system (T6SS) delivers toxic effector proteins into neighboring cells, but bacteria must protect themselves against their own T6SS. Immunity genes are the best-characterized defenses, protecting against specific cognate effectors. However, the prevalence of the T6SS and the coexistence of species with heterologous T6SSs suggest evolutionary pressure selecting for additional defenses against it. Here we review defenses against the T6SS beyond self-associated immunity genes, such as diverse stress responses that can recognize T6SS-inflicted damage and coordinate induction of molecular armor, repair pathways, and overall survival. Some of these stress responses are required for full survival even in the presence of immunity genes. Finally, we propose that immunity gene-independent protection is, mechanistically, bacterial innate immunity and that such defenses and the T6SS have co-evolved and continue to shape one another in polymicrobial communities.

Siderophore mediated mineralization of struvite: A novel greener route of sustainable phosphate management

Efficient and sustainable removal of phosphate ions from an aqueous solution is of great challenge. Herein we demonstrated a greener route for phosphate recovery through struvite formation by using bacterial siderophore. This method was efficient for removal of phosphate as low as 1.3 mM with 99% recovery efficiency. The siderophore produced by Pseudomonas taiwanensis R-12-2 act as template for the nucleation of struvite crystals and was found sustainable for recycling the phosphorous efficiently after twenty cycles. The formation of struvite crystals is driven by surrounding pH (9.0) and presence of Mg²⁺ and NH₄⁺ ions along with PO₄^3- and siderophore which was further validated by computational studies. The morphology of struvite was characterized by scanning electron microscopy, followed by elemental analysis. Furthermore, our results revealed that the siderophore plays an important role in struvite biomineralization. We have successfully demonstrated the phosphate sequestration by using industrial waste samples, as possible application for environmental sustainability and phosphate conservation. For the first time electrochemical super-capacitance performance of the struvite was studied. The specific capacitance value for the struvite was found to be 320 F g^-1 at 1.87 A g^-1 and retained 92 % capacitance after 250 cycles. The study revealed the potential implications of siderophore for the phosphate recycling and the new mechanism for biomineralization by sequestering into struvite.

Hemolysin Co-regulated Family Proteins Hcp1 and Hcp2 Contribute to Edwardsiella ictaluri Pathogenesis

Edwardsiella ictaluri is a Gram-negative facultative intracellular pathogen causing enteric septicemia of catfish (ESC), a devastating disease resulting in significant economic losses in the U.S. catfish industry. Bacterial secretion systems are involved in many bacteria's virulence, and Type VI Secretion System (T6SS) is a critical apparatus utilized by several pathogenic Gram-negative bacteria. E. ictaluri strain 93-146 genome has a complete T6SS operon with 16 genes, but the roles of these genes are still not explored. In this research, we aimed to understand the roles of two hemolysin co-regulated family proteins, Hcp1 (EvpC) and Hcp2. To achieve this goal, single and double E. ictaluri mutants (EiΔevpC, EiΔhcp2, and EiΔevpCΔhcp2) were generated and characterized. Catfish peritoneal macrophages were able to kill EiΔhcp2 better than EiΔevpC, EiΔevpCΔhcp2, and E. ictaluri wild-type (EiWT). The attachment of EiΔhcp2 and EiΔevpCΔhcp2 to ovary cells significantly decreased compared to EiWT whereas the cell invasion rates of these mutants were the same as that of EiWT. Mutants exposed to normal catfish serum in vitro showed serum resistance. The fish challenges demonstrated that EiΔevpC and EiΔevpCΔhcp2 were attenuated completely and provided excellent protection against EiWT infection in catfish fingerlings. Interestingly, EiΔhcp2 caused higher mortality than that of EiWT in catfish fingerlings, and severe clinical signs were observed. Although fry were more susceptible to vaccination with EiΔevpC and EiΔevpCΔhcp2, their attenuation and protection were significantly higher compared to EiWT and sham groups, respectively. Taken together, our data indicated that evpC (hcp1) is involved in E. ictaluri virulence in catfish while hcp2 is involved in adhesion to epithelial cells and survival inside catfish macrophages.

The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482

Pseudomonas donghuensis P482 is a tomato rhizosphere isolate with the ability to inhibit growth of bacterial and fungal plant pathogens. Herein, we analysed the impact of the carbon source on the antibacterial activity of P482 and expression of the selected genes of three genomic regions in the P482 genome. These regions are involved in the synthesis of pyoverdine, 7-hydroxytropolone (7-HT) and an unknown compound ("cluster 17") and are responsible for the antimicrobial activity of P482. We showed that the P482 mutants, defective in these regions, show variations and contrasting patterns of growth inhibition of the target pathogen under given nutritional conditions (with glucose or glycerol as a carbon source). We also selected and validated the reference genes for gene expression studies in P. donghuensis P482. Amongst ten candidate genes, we found gyrB, rpoD and mrdA the most stably expressed. Using selected reference genes in RT-qPCR, we assessed the expression of the genes of interest under minimal medium conditions with glucose or glycerol as carbon sources. Glycerol was shown to negatively affect the expression of genes necessary for 7-HT synthesis. The significance of this finding in the light of the role of nutrient (carbon) availability in biological plant protection is discussed.

Pyoverdines Are Essential for the Antibacterial Activity of Pseudomonas chlororaphis YL-1 under Low-Iron Conditions

Pseudomonas chlororaphis YL-1 has extensive antimicrobial activities against phytopathogens, and its genome harbors a pyoverdine (PVD) biosynthesis gene cluster. The alternative sigma factor PvdS in Pseudomonas aeruginosa PAO1 acts as a critical regulator in response to iron starvation. The assembly of the PVD backbone starts with peptide synthetase enzyme PvdL. PvdF catalyzes formylation of l-OH-Orn to produce l-N ⁵-hydroxyornithine. Here, we describe the characterization of PVD production in YL-1 and its antimicrobial activity in comparison with that of its PVD-deficient ΔpvdS, ΔpvdF, and ΔpvdL mutants, which were obtained using a sacB-based site-specific mutagenesis strategy. Using in vitro methods, we examined the effect of exogenous iron under low-iron conditions and an iron-chelating agent under iron-sufficient conditions on PVD production, antibacterial activity, and the relative expression of the PVD transcription factor gene pvdS in YL-1. We found that strain YL-1, the ΔpvdF mutant, and the ΔpvdS(pUCP26-pvdS) complemented strain produced visible PVDs and demonstrated a wide range of inhibitory effects against Gram-negative and Gram-positive bacteria in vitro under low-iron conditions and that with the increase of iron, its PVD production and antibacterial activity were reduced. The antibacterial compounds produced by strain YL-1 under low-iron conditions were PVDs based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Moreover, the antibacterial activity observed in vitro was correlated with in vivo control efficacies of strain YL-1 against rice bacterial leaf blight (BLB) disease caused by Xanthomonas oryzae pv. oryzae. Collectively, PVDs are responsible for the antibacterial activities of strain YL-1 under both natural and induced low-iron conditions.IMPORTANCE The results demonstrated that PVDs are essential for the broad-spectrum antibacterial activities of strain YL-1 against both Gram-positive and Gram-negative bacteria under low-iron conditions. Our findings also highlight the effect of exogenous iron on the production of PVD and the importance of this bacterial product in bacterial interactions. As a biocontrol agent, PVDs can directly inhibit the proliferation of the tested bacteria in addition to participating in iron competition.

Pseudomonas fluorescens F113 type VI secretion systems mediate bacterial killing and adaption to the rhizosphere microbiome

The genome of Pseudomonas fluorescens F113, a model rhizobacterium and a plant growth-promoting agent, encodes three putative type VI secretion systems (T6SSs); F1-, F2- and F3-T6SS. Bioinformatic analysis of the F113 T6SSs has revealed that they belong to group 3, group 1.1, and group 4a, respectively, similar to those previously described in Pseudomonas aeruginosa. In addition, in silico analyses allowed us to identify genes encoding a total of five orphan VgrG proteins and eight putative effectors (Tfe), some with their cognate immunity protein (Tfi) pairs. Genes encoding Tfe and Tfi are found in the proximity of P. fluorescens F113 vgrG, hcp, eagR and tap genes. RNA-Seq analyses in liquid culture and rhizosphere have revealed that F1- and F3-T6SS are expressed under all conditions, indicating that they are active systems, while F2-T6SS did not show any relevant expression under the tested conditions. The analysis of structural mutants in the three T6SSs has shown that the active F1- and F3-T6SSs are involved in interbacterial killing while F2 is not active in these conditions and its role is still unknown.. A rhizosphere colonization analysis of the double mutant affected in the F1- and F3-T6SS clusters showed that the double mutant was severely impaired in persistence in the rhizosphere microbiome, revealing the importance of these two systems for rhizosphere adaption.

Enzymatic and non-enzymatic functional attributes of plant microbiome

Microbiome plays an important role in plant growth and adaptation to various environmental conditions. The cross-talk between host plant and microbes (including microbe-microbe interactions) plays a crucial role in shaping the microbiome. Recent studies have highlighted that plant microbiome is enriched in genes encoding enzymes and natural products. Several novel antimicrobial compounds, bioactive natural products and lytic/degrading enzymes with industrial implications are being identified from the microbiome. Moreover, advancements in metagenomics and culture techniques are facilitating the development of synthetic microbial communities to promote sustainable agriculture. We discuss the recent advancements, opportunities and challenges in harnessing the full potential of plant microbiome.

Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp

Plant growth-promoting rhizobacteria (PGPR) actively colonize the soil portion under the influence of plant roots, called the rhizosphere. Many plant-beneficial Pseudomonas spp. have been characterized as PGPR. They are ubiquitous rod-shaped motile Gram-negative bacteria displaying a high metabolic versatility. Their capacity to protect plants from pathogens and improve plant growth closely depends on their rhizosphere colonization abilities. Various molecular and cellular mechanisms are involved in this complex process, such as chemotaxis, biofilm formation, secondary metabolites biosynthesis, metabolic versatility, and evasion of plant immunity. The burst in Pseudomonas spp. genome sequencing in recent years has been crucial to better understand how they colonize the rhizosphere. In this review, we discuss the recent advances regarding these mechanisms and the underlying bacterial genetic factors required for successful rhizosphere colonization.

Whole Genome Sequencing and Tn5-Insertion Mutagenesis of Pseudomonas taiwanensis CMS to Probe Its Antagonistic Activity Against Rice Bacterial Blight Disease

The Gram-negative bacterium Pseudomonas taiwanensis is a novel bacterium that uses shrimp shell waste as its sole sources of carbon and nitrogen. It is a versatile bacterium with potential for use in biological control, with activities including toxicity toward insects, fungi, and the rice pathogen Xanthomonas oryzae pv.oryzae (Xoo). In this study, the complete 5.08-Mb genome sequence of P. taiwanensis CMS was determined by a combination of NGS/Sanger sequencing and optical mapping. Comparison of optical maps of seven Pseudomonas species showed that P. taiwanensis is most closely related to P. putida KT 2400. We screened a total of 11,646 individual Tn5-transponson tagged strains to identify genes that are involved in the production and regulation of the iron-chelator pyoverdine in P. taiwanensis, which is a key anti-Xoo factor. Our results indicated that the two-component system (TCS) EnvZ/OmpR plays a positive regulatory role in the production of pyoverdine, whereas the sigma factor RpoS functions as a repressor. The knowledge of the molecular basis of the regulation of pyoverdine by P. taiwanensis provided herein will be useful for its development for use in biological control, including as an anti-Xoo agent.

Modes of Action of Microbial Biocontrol in the Phyllosphere

A fast-growing field of research focuses on microbial biocontrol in the phyllosphere. Phyllosphere microorganisms possess a wide range of adaptation and biocontrol factors, which allow them to adapt to the phyllosphere environment and inhibit the growth of microbial pathogens, thus sustaining plant health. These biocontrol factors can be categorized in direct, microbe-microbe, and indirect, host-microbe, interactions. This review gives an overview of the modes of action of microbial adaptation and biocontrol in the phyllosphere, the genetic basis of the mechanisms, and examples of experiments that can detect these mechanisms in laboratory and field experiments. Detailed insights in such mechanisms are key for the rational design of novel microbial biocontrol strategies and increase crop protection and production. Such novel biocontrol strategies are much needed, as ensuring sufficient and consistent food production for a growing world population, while protecting our environment, is one of the biggest challenges of our time.

The Evolution and Ecology of Bacterial Warfare

Bacteria have evolved a wide range of mechanisms to harm and kill their competitors, including chemical, mechanical and biological weapons. Here we review the incredible diversity of bacterial weapon systems, which comprise antibiotics, toxic proteins, mechanical weapons that stab and pierce, viruses, and more. The evolution of bacterial weapons is shaped by many factors, including cell density and nutrient abundance, and how strains are arranged in space. Bacteria also employ a diverse range of combat behaviours, including pre-emptive attacks, suicidal attacks, and reciprocation (tit-for-tat). However, why bacteria carry so many weapons, and why they are so often used, remains poorly understood. By comparison with animals, we argue that the way that bacteria live - often in dense and genetically diverse communities - is likely to be key to their aggression as it encourages them to dig in and fight alongside their clonemates. The intensity of bacterial aggression is such that it can strongly affect communities, via complex coevolutionary and eco-evolutionary dynamics, which influence species over space and time. Bacterial warfare is a fascinating topic for ecology and evolution, as well as one of increasing relevance. Understanding how bacteria win wars is important for the goal of manipulating the human microbiome and other important microbial systems.

NTO Sensing by Fluorescence Quenching of a Pyoverdine Siderophore-A Mechanistic Approach

In this study, a siderophore, pyoverdine (PVD), has been isolated from Pseudomonas sp. and used to develop a fluorescence quenching-based sensor for efficient detection of nitrotriazolone (NTO) in aqueous media, in contrast to other explosives such as research department explosive (RDX), picric acid, and trinitrotoulene (TNT). The siderophore PVD exhibited enhanced fluorescence quenching above 50% at 470 nm for a minimal concentration (38 nM) of NTO. The limit of detection estimated from interpolating the graph of fluorescence intensity (at 470 nm) versus NTO concentration is found to be 12 nM corresponding to 18% quenching. The time delay fluorescence spectroscopy of the PVD-NTO solution showed a negligible change of 0.09 ns between the minimum and maximum NTO concentrations. The in silico absorption at the emission peak of static fluorescence remains invariant upon the addition of NTO. The computational studies revealed the formation of inter- and intramolecular hydrogen-bonding interactions between the energetically stable complexes of PVD and NTO. Although the analysis of Stern-Volmer plots and computational studies imply that the quenching mechanism is a combination of both dynamic and static quenching, the latter is dominant over the earlier. The static quenching is attributed to ground-state complex formation, as supported by the computational analysis.

Crosstalk between the Type VI Secretion System and the Expression of Class IV Flagellar Genes in the Pseudomonas fluorescens MFE01 Strain

Type VI secretion systems (T6SSs) are contractile bacterial multiprotein nanomachines that enable the injection of toxic effectors into prey cells. The Pseudomonas fluorescens MFE01 strain has T6SS antibacterial activity and can immobilise competitive bacteria through the T6SS. Hcp1 (hemolysin co-regulated protein 1), a constituent of the T6SS inner tube, is involved in such prey cell inhibition of motility. Paradoxically, disruption of the hcp1 or T6SS contractile tail tssC genes results in the loss of the mucoid and motile phenotypes in MFE01. Here, we focused on the relationship between T6SS and flagella-associated motility. Electron microscopy revealed the absence of flagellar filaments for MFE01Δhcp1 and MFE01ΔtssC mutants. Transcriptomic analysis showed a reduction in the transcription of class IV flagellar genes in these T6SS mutants. However, transcription of fliA, the gene encoding the class IV flagellar sigma factor, was unaffected. Over-expression of fliA restored the motile and mucoid phenotypes in both MFE01Δhcp1+fliA, and MFE01ΔtssC+fliA and a fliA mutant displayed the same phenotypes as MFE01Δhcp1 and MFE01ΔtssC. Moreover, the FliA anti-sigma factor FlgM was not secreted in the T6SS mutants, and flgM over-expression reduced both motility and mucoidy. This study provides arguments to unravel the crosstalk between T6SS and motility.

An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization

Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient. These compounds have highly diverse chemical structures, with various chelating groups. They are released by bacteria into their environment to scavenge iron and bring it back into the cells. The biosynthesis of siderophores requires complex enzymatic processes and expression of the enzymes involved is very finely regulated by iron availability and diverse transcriptional regulators. Recent data have also highlighted the organization of the enzymes involved in siderophore biosynthesis into siderosomes, multi-enzymatic complexes involved in siderophore synthesis. An understanding of siderophore biosynthesis is of great importance, as these compounds have many potential biotechnological applications because of their metal-chelating properties and their key role in bacterial growth and virulence. This review focuses on the biosynthesis of siderophores produced by fluorescent Pseudomonads, bacteria capable of colonizing a large variety of ecological niches. They are characterized by the production of chromopeptide siderophores, called pyoverdines, which give the typical green colour characteristic of fluorescent pseudomonad cultures. Secondary siderophores are also produced by these strains and can have highly diverse structures (such as pyochelins, pseudomonine, yersiniabactin, corrugatin, achromobactin and quinolobactin).

Edwardsiella ictaluri evpP is required for colonisation of channel catfish ovary cells and necrosis in anterior kidney macrophages

Edwardsiella ictaluri is a Gram-negative facultative anaerobe that can survive inside channel catfish phagocytes. E. ictaluri can orchestrate Type VI Secretion System (T6SS) for survival in catfish macrophages. evpP encodes one of the T6SS translocated effector proteins. However, the role of evpP in E. ictaluri is still unexplored. In this work, we constructed an E. ictaluri evpP mutant (EiΔevpP) and assessed its survival under complement and oxidative stress. Persistence of EiΔevpP in catfish as well as attachment and invasion in catfish macrophage and ovary cells were determined. Further, virulence of EiΔevpP in catfish and apoptosis it caused in macrophages were explored. EiΔevpP behaved same as wild type (EiWT) under complement and oxidative stress in complex media, whereas oxidative stress affected mutant's survival significantly in minimal media (p < .05). Persistence of EiΔevpP in live catfish and uptake and survival inside peritoneal macrophages were similar. The attachment and invasion capabilities of EiΔevpP in catfish ovary cells were significantly less than that of EiWT (p < .05). Although EiΔevpP showed reduced attenuation in catfish, causing decreased catfish mortality compared with EiWT (44.73% vs. 67.53%), this difference was not significant. The apoptosis assay using anterior kidney macrophages indicated that the number of live macrophages exposed to EiΔevpP was significantly higher compared with EiWT exposed macrophages at 24-hr post-treatment (p < .05). However, there were no significant differences in the early and late apoptosis. Remarkably, necrosis in EiΔevpP exposed macrophages was significantly less than that of EiWT exposed macrophages at 24 hr (p < .05). Our results demonstrated that evpP is required for colonisation of catfish ovary cells and increased apoptosis and necrosis in anterior kidney macrophages.

A Pseudomonas aeruginosa type VI secretion system regulated by CueR facilitates copper acquisition

The type VI secretion system (T6SS) is widely distributed in Gram-negative bacteria, whose function is known to translocate substrates to eukaryotic and prokaryotic target cells to cause host damage or as a weapon for interbacterial competition. Pseudomonas aeruginosa encodes three distinct T6SS clusters (H1-, H2-, and H3-T6SS). The H1-T6SS-dependent substrates have been identified and well characterized; however, only limited information is available for the H2- and H3-T6SSs since relatively fewer substrates for them have yet been established. Here, we obtained P. aeruginosa H2-T6SS-dependent secretomes and further characterized the H2-T6SS-dependent copper (Cu²⁺)-binding effector azurin (Azu). Our data showed that both azu and H2-T6SS were repressed by CueR and were induced by low concentrations of Cu²⁺. We also identified the Azu-interacting partner OprC, a Cu²⁺-specific TonB-dependent outer membrane transporter. Similar to H2-T6SS genes and azu, expression of oprC was directly regulated by CueR and was induced by low Cu²⁺. In addition, the Azu-OprC-mediated Cu²⁺ transport system is critical for P. aeruginosa cells in bacterial competition and virulence. Our findings provide insights for understanding the diverse functions of T6SSs and the role of metal ions for P. aeruginosa in bacteria-bacteria competition.

The type VI secretion system (T6SS) is a specific macromolecular protein export apparatus, and widely distributed in Gram-negative bacteria. T6SS plays an important role in anti-bacterial competition or delivers effector proteins to both eukaryotic and prokaryotic cells. In the present study, we performed secretomes analysis and identified 21 substrates of P. aeruginosa H2-T6SS-dependent. Specifically, we report a Cu²⁺-scavenging pathway consisting of a copper transporter, OprC, and a type VI secretion system (H2-T6SS)-secreted Cu²⁺-binding protein, Azu. Both of them are under control of the transcriptional regulator CueR. Indeed, the Azu-OprC-mediated Cu²⁺ transport system is critical for P. aeruginosa cells in bacterial competition and virulence. These findings exemplify how P. aeruginosa deploys this metal system to adapt to the complex environment during evolution.

Genomic analysis of siderophore β-hydroxylases reveals divergent stereocontrol and expands the condensation domain family

Genome mining of biosynthetic pathways streamlines discovery of secondary metabolites but can leave ambiguities in the predicted structures, which must be rectified experimentally. Through coupling the reactivity predicted by biosynthetic gene clusters with verified structures, the origin of the β-hydroxyaspartic acid diastereomers in siderophores is reported herein. Two functional subtypes of nonheme Fe(II)/α-ketoglutarate-dependent aspartyl β-hydroxylases are identified in siderophore biosynthetic gene clusters, which differ in genomic organization-existing either as fused domains (IβH_Asp) at the carboxyl terminus of a nonribosomal peptide synthetase (NRPS) or as stand-alone enzymes (TβH_Asp)-and each directs opposite stereoselectivity of Asp β-hydroxylation. The predictive power of this subtype delineation is confirmed by the stereochemical characterization of β-OHAsp residues in pyoverdine GB-1, delftibactin, histicorrugatin, and cupriachelin. The l-threo (2S, 3S) β-OHAsp residues of alterobactin arise from hydroxylation by the β-hydroxylase domain integrated into NRPS AltH, while l-erythro (2S, 3R) β-OHAsp in delftibactin arises from the stand-alone β-hydroxylase DelD. Cupriachelin contains both l-threo and l-erythro β-OHAsp, consistent with the presence of both types of β-hydroxylases in the biosynthetic gene cluster. A third subtype of nonheme Fe(II)/α-ketoglutarate-dependent enzymes (IβH_His) hydroxylates histidyl residues with l-threo stereospecificity. A previously undescribed, noncanonical member of the NRPS condensation domain superfamily is identified, named the interface domain, which is proposed to position the β-hydroxylase and the NRPS-bound amino acid prior to hydroxylation. Through mapping characterized β-OHAsp diastereomers to the phylogenetic tree of siderophore β-hydroxylases, methods to predict β-OHAsp stereochemistry in silico are realized.

Plant-Pathogenic Agrobacterium tumefaciens Strains Have Diverse Type VI Effector-Immunity Pairs and Vary in In-Planta Competitiveness

The type VI secretion system (T6SS) is used by gram-negative bacteria to translocate effectors that can antagonize other bacterial cells. Models predict the variation in collections of effector and cognate immunity genes determine competitiveness and can affect the dynamics of populations and communities of bacteria. However, the outcomes of competition cannot be entirely explained by compatibility of effector-immunity (EI) pairs. Here, we characterized the diversity of T6SS loci of plant-pathogenic Agrobacterium tumefaciens and showed that factors other than EI pairs can impact interbacterial competition. All examined strains encode T6SS active in secretion and antagonism against Escherichia coli. The spectra of EI pairs as well as compositions of gene neighborhoods are diverse. Almost 30 in-planta competitions were tested between different genotypes of A. tumefaciens. Fifteen competitions between members of different species-level groups resulted in T6SS-dependent suppression in in-planta growth of prey genotypes. In contrast, ten competitions between members within species-level groups resulted in no significant effect on the growth of prey genotypes. One strain was an exceptional case and, despite encoding a functional T6SS and toxic effector protein, could not compromise the growth of the four tested prey genotypes. The data suggest T6SS-associated EI pairs can influence the competitiveness of strains of A. tumefaciens, but genetic features have a significant role on the efficacy of interbacterial antagonism.

PvdRT-OpmQ and MdtABC-OpmB efflux systems are involved in pyoverdine secretion in Pseudomonas putida KT2440

Fluorescent pseudomonads produce and secrete a siderophore termed pyoverdine to capture iron when it becomes scarce. The molecular basis of pyoverdine secretion is only partially understood. Here, we investigate the role of the putative PvdRT-OpmQ and MdtABC-OpmB efflux systems in pyoverdine secretion in the soil bacterium Pseudomonas putida KT2440. Expression from the respective promoters is stimulated by iron limitation albeit to varying degrees. Deletion of pvdRT-opmQ leads to reduced amounts of pyoverdine in the medium and decreased growth under iron limitation. Deletion of mdtABC-opmB does not affect growth. However, when both systems are deleted, strong effects on growth and pyoverdine secretion (yellow colony phenotype, less pyoverdine in medium, more pyoverdine in the periplasm) are observed. Overexpression of pvdRT-opmQ causes the opposite effect. These results provide first evidence for an involvement of the multidrug efflux system MdtABC-OpmB in pyoverdine secretion. In addition, the PvdRT-OpmQ system was shown to contribute to pyoverdine secretion in P. putida KT2440, extending previous investigations on its role in Pseudomonas species. Since the double deletion mutant still secrets pyoverdine, at least one additional efflux system participates in the transport of the siderophore. Furthermore, our results suggest a contribution of both efflux systems to ampicillin resistance.

Green Technology: Bacteria-Based Approach Could Lead to Unsuspected Microbe⁻Plant⁻Animal Interactions

The recent and massive revival of green strategies to control plant diseases, mainly as a consequence of the Integrated Pest Management (IPM) rules issued in 2009 by the European Community and the increased consumer awareness of organic products, poses new challenges for human health and food security that need to be addressed in the near future. One of the most important green technologies is biocontrol. This approach is based on living organisms and how these biocontrol agents (BCAs) directly or indirectly interact as a community to control plant pathogens and pest. Although most BCAs have been isolated from plant microbiomes, they share some genomic features, virulence factors, and trans-kingdom infection abilities with human pathogenic microorganisms, thus, their potential impact on human health should be addressed. This evidence, in combination with the outbreaks of human infections associated with consumption of raw fruits and vegetables, opens new questions regarding the role of plants in the human pathogen infection cycle. Moreover, whether BCAs could alter the endophytic bacterial community, thereby leading to the development of new potential human pathogens, is still unclear. In this review, all these issues are debated, highlighting that the research on BCAs and their formulation should include these possible long-lasting consequences of their massive spread in the environment.

Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp

Plant-beneficial Pseudomonas spp. competitively colonize the rhizosphere and display plant-growth promotion and/or disease-suppression activities. Some strains within the P. fluorescens species complex produce phenazine derivatives, such as phenazine-1-carboxylic acid. These antimicrobial compounds are broadly inhibitory to numerous soil-dwelling plant pathogens and play a role in the ecological competence of phenazine-producing Pseudomonas spp. We assembled a collection encompassing 63 strains representative of the worldwide diversity of plant-beneficial phenazine-producing Pseudomonas spp. In this study, we report the sequencing of 58 complete genomes using PacBio RS II sequencing technology. Distributed among four subgroups within the P. fluorescens species complex, the diversity of our collection is reflected by the large pangenome which accounts for 25 413 protein-coding genes. We identified genes and clusters encoding for numerous phytobeneficial traits, including antibiotics, siderophores and cyclic lipopeptides biosynthesis, some of which were previously unknown in these microorganisms. Finally, we gained insight into the evolutionary history of the phenazine biosynthetic operon. Given its diverse genomic context, it is likely that this operon was relocated several times during Pseudomonas evolution. Our findings acknowledge the tremendous diversity of plant-beneficial phenazine-producing Pseudomonas spp., paving the way for comparative analyses to identify new genetic determinants involved in biocontrol, plant-growth promotion and rhizosphere competence.

Pseudomonas aeruginosa glutathione biosynthesis genes play multiple roles in stress protection, bacterial virulence and biofilm formation

Pseudomonas aeruginosa PAO1 contains gshA and gshB genes, which encode enzymes involved in glutathione (GSH) biosynthesis. Challenging P. aeruginosa with hydrogen peroxide, cumene hydroperoxide, and t-butyl hydroperoxide increased the expression of gshA and gshB. The physiological roles of these genes in P. aeruginosa oxidative stress, bacterial virulence, and biofilm formation were examined using P. aeruginosa ΔgshA, ΔgshB, and double ΔgshAΔgshB mutant strains. These mutants exhibited significantly increased susceptibility to methyl viologen, thiol-depleting agent, and methylglyoxal compared to PAO1. Expression of functional gshA, gshB or exogenous supplementation with GSH complemented these phenotypes, which indicates that the observed mutant phenotypes arose from their inability to produce GSH. Virulence assays using a Drosophila melanogaster model revealed that the ΔgshA, ΔgshB and double ΔgshAΔgshB mutants exhibited attenuated virulence phenotypes. An analysis of virulence factors, including pyocyanin, pyoverdine, and cell motility (swimming and twitching), showed that these levels were reduced in these gsh mutants compared to PAO1. In contrast, biofilm formation increased in mutants. These data indicate that the GSH product and the genes responsible for GSH synthesis play multiple crucial roles in oxidative stress protection, bacterial virulence and biofilm formation in P. aeruginosa.

The biosynthesis of pyoverdines

Pyoverdines are fluorescent siderophores of pseudomonads that play important roles for growth under iron-limiting conditions. The production of pyoverdines by fluorescent pseudomonads permits their colonization of hosts ranging from humans to plants. Prominent examples include pathogenic or non-pathogenic species such as Pseudomonas aeruginosa, P. putida, P. syringae, or P. fluorescens. Many distinct pyoverdines have been identified, all of which have a dihydroxyquinoline fluorophore in common, derived from oxidative cyclizations of non-ribosomal peptides. These serve as precursor of pyoverdines and are commonly known as ferribactins. Ferribactins of distinct species or even strains often differ in their sequence, resulting in a large variety of pyoverdines. However, synthesis of all ferribactins begins with an L-Glu/D-Tyr/L-Dab sequence, and the fluorophore is generated from the D-Tyr/L-Dab residues. In addition, the initial L-Glu residue is modified to various acids and amides that are responsible for the range of distinguishable pyoverdines in individual strains. While ferribactin synthesis is a cytoplasmic process, the maturation to the fluorescent pyoverdine as well as the tailoring of the initial glutamate are exclusively periplasmic processes that have been a mystery until recently. Here we review the current knowledge of pyoverdine biosynthesis with a focus on the recent advancements regarding the periplasmic maturation and tailoring reactions.

Transcriptome analysis of Porphyromonas gingivalis and Acinetobacter baumannii in polymicrobial communities

Acinetobacter baumannii is a nosocomial, opportunistic pathogen that causes several serious conditions including meningitis, septicemia, endocarditis, and pneumonia. It can be found in the oral biofilm, which may be a reservoir for pneumonia and chronic obstructive pulmonary disease. Subgingival colonization by A. baumannii is associated with chronic and aggressive periodontitis as well as refractory periodontal disease. Porphyromonas gingivalis, a keystone periodontal pathogen localized to subgingival plaque, is also implicated in several chronic conditions including aspiration pneumonia. Although both bacteria are found together in subgingival plaque and can cause multiple polymicrobial infections, nothing is known about the interactions between these two important human pathogens. In this study, we used RNA sequencing to understand the transcriptional response of both species as they adapt to heterotypic communities. Among the differentially regulated genes were those encoding a number of important virulence factors for both species including adhesion, biofilm formation, and protein secretion. Additionally, the presence of A. baumannii increased the abundance of P. gingivalis in model dual-species communities. Collectively these results suggest that both P. gingivalis and A. baumannii adapt to each other and have synergistic potential for increased pathogenicity. In identifying the mechanisms that promote pathogenicity and refractory disease, novel approaches to mitigate polymicrobial synergistic interactions may be developed to treat or prevent associated diseases.

The Agrobacterium Type VI Secretion System: A Contractile Nanomachine for Interbacterial Competition

The bacterial type VI secretion system (T6SS) is a contractile nanomachine dedicated to delivering molecules out of bacterial cells. T6SS-encoding loci are in the genome sequences of many Gram-negative bacteria, and T6SS has been implicated in a plethora of roles. In the majority of cases, the T6SSs deliver effector proteins in a contact-dependent manner to antagonize other bacteria. Current models suggest that the effectors are deployed to influence social interactions in microbial communities. In this chapter, we describe the structure, function, and regulation of the T6SS and its effectors. We provide focus on the T6SS of Agrobacterium tumefaciens, the causative agent of crown gall disease, and relate the role of the T6SS to the ecology of A. tumefaciens.

Type VI secretion systems in plant-associated bacteria

The type VI secretion system (T6SS) is a bacterial nanomachine used to inject effectors into prokaryotic or eukaryotic cells and is thus involved in both host manipulation and interbacterial competition. The T6SS is widespread among Gram‐negative bacteria, mostly within the Proteobacterium Phylum. This secretion system is commonly found in commensal and pathogenic plant‐associated bacteria. Phylogenetic analysis of phytobacterial T6SS clusters shows that they are distributed in the five main clades previously described (group 1–5). The even distribution of the system among commensal and pathogenic phytobacteria suggests that the T6SS provides fitness and colonization advantages in planta and that the role of the T6SS is not restricted to virulence. This manuscript reviews the phylogeny and biological roles of the T6SS in plant‐associated bacteria, highlighting a remarkable diversity both in terms of mechanism and function.

Cutaneous Microflora from Geographically Isolated Groups of Bradysia agrestis, an Insect Vector of Diverse Plant Pathogens

Larvae of Bradysia agrestis, an insect vector that transports plant pathogens, were sampled from geographically isolated regions in Korea to identify their cutaneous fungal and bacterial flora. Sampled areas were chosen within the distribution range of B. agrestis; each site was more than 91 km apart to ensure geographical segregation. We isolated 76 microbial (fungi and bacteria) strains (site 1, 29; site 2, 29; site 3, 18 strains) that were identified on the basis of morphological differences. Species identification was molecularly confirmed by determination of universal fungal internal transcribed spacer and bacterial 16S rRNA gene sequences in comparison to sequences in the EzTaxon database and the NCBI GenBank database, and their phylogenetic relationships were determined. The fungal isolates belonged to 2 phyla, 5 classes, and 7 genera; bacterial species belonged to 23 genera and 32 species. Microbial diversity differed significantly among the geographical groups with respect to Margalef's richness (3.9, 3.6, and 4.5), Menhinick's index (2.65, 2.46, and 3.30), Simpson's index (0.06, 0.12, and 0.01), and Shannon's index (2.50, 2.17, and 2.58). Although the microbial genera distribution or diversity values clearly varied among geographical groups, common genera were identified in all groups, including the fungal genus Cladosporium, and the bacterial genera Bacillus and Rhodococcus. According to classic principles of co-evolutionary relationship, these genera might have a closer association with their host insect vector B. agrestis than other genera identified. Some cutaneous bacterial genera (e.g., Pseudomonas) displaying weak interdependency with insect vectors may be hazardous to agricultural environments via mechanical transmission via B. agrestis. This study provides comprehensive information regarding the cutaneous microflora of B. agrestis, which can help in the control of such pests for crop management.