Fluorescent pseudomonads harboring type III secretion genes are enriched in the mycorrhizosphere of Medicago truncatula

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.

Genomic and transcriptomic characterization of the Collimonas quorum sensing genes and regulon

Collimonads are well-adapted to nutrient-poor environments. They are known to hydrolyse chitin, produce antifungal metabolites, weather minerals, and are effective biocontrol agents protecting plants from fungal diseases. The production of N-acyl homoserine lactones (AHLs) was suggested to be a conserved trait of collimonads, but little is known about the genes that underlie this production or the genes that are controlled by AHLs. To improve our understanding of the role of AHLs in the ecology of collimonads, we carried out transcriptomic analyses, combined with chemical and functional assays, on strain Collimonas pratensis PMB3(1). The main AHLs produced by this strain were identified as 3-hydroxy-hexa- and octa-noyl-homoserine lactone. Genome analysis permitted to identify putative genes coding for the autoinducer synthase (colI) and cognate transcriptional regulator (colR). The ability to produce AHLs was lost in ΔcolI and ΔcolR mutants. Functional assays revealed that the two mutants metabolized glucose, formate, oxalate, and leucine better than the wild-type (WT) strain. Transcriptome sequencing analyses revealed an up-regulation of different metabolic pathways and of motility in the QS-mutants compared to the WT strain. Overall, our results provide insights into the role of the AHL-dependent regulation system of Collimonas in environment colonization, metabolism readjustment, and microbial interactions.

Bridging the Gap: Type III Secretion Systems in Plant-Beneficial Bacteria

Type III secretion systems (T3SSs) are bacterial membrane-embedded nanomachines translocating effector proteins into the cytoplasm of eukaryotic cells. They have been intensively studied for their important roles in animal and plant bacterial diseases. Over the past two decades, genome sequencing has unveiled their ubiquitous distribution in many taxa of Gram-negative bacteria, including plant-beneficial ones. Here, we discuss the distribution and functions of the T3SS in two agronomically important bacterial groups: the symbiotic nodule-forming nitrogen-fixing rhizobia and the free-living plant-beneficial Pseudomonas spp. In legume-rhizobia symbiosis, T3SSs and their cognate effectors play important roles, including the modulation of the plant immune response and the initiation of the nodulation process in some cases. In plant-beneficial Pseudomonas spp., the roles of T3SSs are not fully understood, but pertain to plant immunity suppression, biocontrol against eukaryotic plant pathogens, mycorrhization facilitation, and possibly resistance against protist predation. The diversity of T3SSs in plant-beneficial bacteria points to their important roles in multifarious interkingdom interactions in the rhizosphere. We argue that the gap in research on T3SSs in plant-beneficial bacteria must be bridged to better understand bacteria/eukaryotes rhizosphere interactions and to support the development of efficient plant-growth promoting microbial inoculants.

"Breeding on Mountains" Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants (Ligusticum chuanxiong Hort.)

"Breeding on mountains, cultivation in dam areas" is a unique propagation method for the vegetatively propagated plant Ligusticum chuanxiong, including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on L. chuanxiong and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in L. chuanxiong increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of L. chuanxiong, while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant Gibberella, Phoma, Pericona, Paraphoma, and Neocosmospora. The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.

Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant - microbiome - soil continuum

Mutualistic relationships of legume plants with, either bacteria (like rhizobia) or fungi (like arbuscular mycorrhizal fungi), have been investigated intensively, usually as bi-partite interactions. However, diverse symbiotic interactions take place simultaneously or sequentially under field conditions. Their collective, but not additive, contribution to plant growth and performance remains hard to predict, and appears to be furthermore affected by crop species and genotype, non-symbiotic microbial interactions and environmental variables. The challenge is: (i) to unravel the complex overlapping mechanisms that operate between the microbial symbionts as well as between them, their hosts and the rhizosphere (ii) to understand the dynamics of the respective mechanisms in evolutionary and ecological terms. The target for agriculture, food security and the environment, is to use this insight as a solid basis for developing new integrated technologies, practices and strategies for the efficient use of beneficial microbes in legumes and other plants. We review recent advances in our understanding of the symbiotic interactions in legumes roots brought about with the aid of molecular and bioinformatics tools. We go through single symbiont-host interactions, proceed to tripartite symbiont-host interactions, appraise interactions of symbiotic and associative microbiomes with plants in the root-rhizoplane-soil continuum of habitats and end up by examining attempts to validate community ecology principles in the legume-microbe-soil biosystem.

Plant Symbionts Are Engineers of the Plant-Associated Microbiome

Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.

Unusual extracellular appendages deployed by the model strain Pseudomonas fluorescens C7R12

Pseudomonas fluorescens is considered to be a typical plant-associated saprophytic bacterium with no pathogenic potential. Indeed, some P. fluorescens strains are well-known rhizobacteria that promote plant growth by direct stimulation, by preventing the deleterious effects of pathogens, or both. Pseudomonas fluorescens C7R12 is a rhizosphere-competent strain that is effective as a biocontrol agent and promotes plant growth and arbuscular mycorrhization. This strain has been studied in detail, but no visual evidence has ever been obtained for extracellular structures potentially involved in its remarkable fitness and biocontrol performances. On transmission electron microscopy of negatively stained C7R12 cells, we observed the following appendages: multiple polar flagella, an inducible putative type three secretion system typical of phytopathogenic Pseudomonas syringae strains and densely bundled fimbria-like appendages forming a broad fractal-like dendritic network around single cells and microcolonies. The deployment of one or other of these elements on the bacterial surface depends on the composition and affinity for the water of the microenvironment. The existence, within this single strain, of machineries known to be involved in motility, chemotaxis, hypersensitive response, cellular adhesion and biofilm formation, may partly explain the strong interactions of strain C7R12 with plants and associated microflora in addition to the type three secretion system previously shown to be implied in mycorrhizae promotion.

Type III Secretion System of Beneficial Rhizobacteria Pseudomonas simiae WCS417 and Pseudomonas defensor WCS374

Plants roots host myriads of microbes, some of which enhance the defense potential of plants by activating a broad-spectrum immune response in leaves, known as induced systemic resistance (ISR). Nevertheless, establishment of this mutualistic interaction requires active suppression of local root immune responses to allow successful colonization. To facilitate host colonization, phytopathogenic bacteria secrete immune-suppressive effectors into host cells via the type III secretion system (T3SS). Previously, we searched the genomes of the ISR-inducing rhizobacteria Pseudomonas simiae WCS417 and Pseudomonas defensor WCS374 for the presence of a T3SS and identified the components for a T3SS in the genomes of WCS417 and WCS374. By performing a phylogenetic and gene cluster alignment analysis we show that the T3SS of WCS417 and WCS374 are grouped in a clade that is enriched for beneficial rhizobacteria. We also found sequences of putative novel effectors in their genomes, which may facilitate future research on the role of T3SS effectors in plant-beneficial microbe interactions in the rhizosphere.

Appropriate nonmycorrhizal controls in arbuscular mycorrhiza research: a microbiome perspective

Establishment of nonmycorrhizal controls is a "classic and recurrent theme" in mycorrhizal research. For decades, authors reported mycorrhizal plant growth/nutrition as compared to various nonmycorrhizal controls. In such studies, uncertainties remain about which nonmycorrhizal controls are most appropriate and, in particular, what effects the control inoculations have on substrate and root microbiomes. Here, different types of control and mycorrhizal inoculations were compared with respect to plant growth and nutrition, as well as the structure of root and substrate microbiomes, assessed by next-generation sequencing. We compared uninoculated ("absolute") control to inoculation with blank pot culture lacking arbuscular mycorrhizal fungi, filtrate of that blank inoculum, and filtrate of complex pot-produced mycorrhizal inoculum. Those treatments were compared to a standard mycorrhizal treatment, where the previously sterilized substrate was inoculated with complex pot-produced inoculum containing Rhizophagus irregularis SYM5. Besides this, monoxenically produced inoculum of the same fungus was applied either alone or in combination with blank inoculum. The results indicate that the presence of mycorrhizal fungus always resulted in stimulation of Andropogon gerardii plant biomass as well as in elevated phosphorus content of the plants. The microbial (bacterial and fungal) communities developing in the differently inoculated treatments, however, differed substantially from each other and no control could be obtained comparable with the treatment inoculated with complex mycorrhizal inoculum. Soil microorganisms with significant biological competences that could potentially contribute to the effects of the various inoculants on the plants were detected in roots and in plant cultivation substrate in some of the treatments.

Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom)

Tricholoma matsutake is an ectomycorrhizal fungus usually associated with Pinus densiflora in South Korea. Fruiting bodies (mushrooms) of T. matsutake are economically important due to their attractive aroma; yet, T. matsutake is uncultivatable and its habitat is rapidly being eradicated due to global climate change. Root-associated bacteria can influence the growth of ectomycorrhizal fungi that co-exist in the host rhizosphere and distinctive bacterial communities are associated with T. matsutake. In this study, we investigated how these bacterial communities affect T. matsutake growth by isolating bacteria from the roots of P. densiflora colonized by ectomycorrhizae of T. matsutake and co-culturing rootassociated bacteria with T. matsutake isolates. Thirteen species of bacteria (27 isolates) were found in pine roots, all belonging to the orders Bacillales or Burkholderiales. Two species in the genus Paenibacillus promoted the growth of T. matsutake in glucose poor conditions, likely using soluble metabolites. In contrast, other bacteria suppressed the growth of T. matsutake using both soluble and volatile metabolites. Antifungal activity was more frequent in glucose poor conditions. In general, pine rhizospheres harbored many bacteria that had a negative impact on T. matsutake growth and the few Paenibacillus species that promoted T. matsutake growth. Paenibacillus species, therefore, may represent a promising resource toward successful cultivation of T. matsutake.

The Ecological Role of Type Three Secretion Systems in the Interaction of Bacteria with Fungi in Soil and Related Habitats Is Diverse and Context-Dependent

Bacteria and fungi constitute important organisms in many ecosystems, in particular terrestrial ones. Both organismal groups contribute significantly to biogeochemical cycling processes. Ecological theory postulates that bacteria capable of receiving benefits from host fungi are likely to evolve efficient association strategies. The purpose of this review is to examine the mechanisms that underpin the bacterial interactions with fungi in soil and other systems, with special focus on the type III secretion system (T3SS). Starting with a brief description of the versatility of the T3SS as an interaction system with diverse eukaryotic hosts, we subsequently examine the recent advances made in our understanding of its contribution to interactions with soil fungi. The analysis used data sets ranging from circumstantial evidence to gene-knockout-based experimental data. The initial finding that the abundance of T3SSs in microbiomes is often enhanced in fungal-affected habitats like the mycosphere and the mycorrhizosphere is now substantiated with in-depth knowledge of the specific systems involved. Different fungal–interactive bacteria, in positive or negative associations with partner fungi, harbor and express T3SSs, with different ecological outcomes. In some particular cases, bacterial T3SSs have been shown to modulate the physiology of its fungal partner, affecting its ecological characteristics and consequently shaping its own habitat. Overall, the analyses of the collective data set revealed that diverse T3SSs have assumed diverse roles in the interactions of bacteria with host fungi, as driven by ecological and evolutionary niche requirements.

Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities

Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil

Tricholoma matsutake, the pine mushroom, is a valuable forest product with high economic value in Asia, and plays an important ecological role as an ectomycorrhizal fungus. Around the host tree, T. matsutake hyphae generate a distinctive soil aggregating environment called a fairy ring, where fruiting bodies form. Because T. matsutake hyphae dominate the soil near the fairy ring, this species has the potential to influence the microbial community. To explore the influence of T. matsutake on the microbial communities, we compared the microbial community and predicted bacterial function between two different soil types-T. matsutake dominant and T. matsutake minor. DNA sequence analyses showed that fungal and bacterial diversity were lower in the T. matsutake dominant soil compared to T. matsutake minor soil. Some microbial taxa were significantly more common in the T. matsutake dominant soil across geographic locations, many of which were previously identified as mycophillic or mycorrhiza helper bacteria. Between the two soil types, the predicted bacterial functional profiles (using PICRUSt) had significantly distinct KEGG modules. Modules for amino acid uptake, carbohydrate metabolism, and the type III secretion system were higher in the T. matsutake dominant soil than in the T. matsutake minor soil. Overall, similar microbial diversity, community structure, and bacterial functional profiles of the T. matsutake dominant soil across geographic locations suggest that T. matsutake may generate a dominance effect.

Type III secretion system and virulence markers highlight similarities and differences between human- and plant-associated pseudomonads related to Pseudomonas fluorescens and P. putida

Pseudomonas fluorescens is commonly considered a saprophytic rhizobacterium devoid of pathogenic potential. Nevertheless, the recurrent isolation of strains from clinical human cases could indicate the emergence of novel strains originating from the rhizosphere reservoir, which could be particularly resistant to the immune system and clinical treatment. The importance of type three secretion systems (T3SSs) in the related Pseudomonas aeruginosa nosocomial species and the occurrence of this secretion system in plant-associated P. fluorescens raise the question of whether clinical isolates may also harbor T3SSs. In this study, isolates associated with clinical infections and identified in hospitals as belonging to P. fluorescens were compared with fluorescent pseudomonads harboring T3SSs isolated from plants. Bacterial isolates were tested for (i) their genetic relationships based on their 16S rRNA phylogeny, (ii) the presence of T3SS genes by PCR, and (iii) their infectious potential on animals and plants under environmental or physiological temperature conditions. Two groups of bacteria were delineated among the clinical isolates. The first group encompassed thermotolerant (41°C) isolates from patients suffering from blood infections; these isolates were finally found to not belong to P. fluorescens but were closely related and harbored highly conserved T3SS genes belonging to the Ysc-T3SS family, like the T3SSs from P. aeruginosa. The second group encompassed isolates from patients suffering from cystic fibrosis; these isolates belonged to P. fluorescens and harbored T3SS genes belonging to the Hrp1-T3SS family found commonly in plant-associated P. fluorescens.

Supramolecular Structure and Functional Analysis of the Type III Secretion System in Pseudomonas fluorescens 2P24

The type III secretion system (T3SS) of plant and animal bacterial pathogens directs the secretion and injection of proteins into host cells. Some homologous genes of T3SS were found also in non-pathogenic bacteria, but the organization of its machinery and basic function are still unknown. In this study, we identified a T3SS gene cluster from the plant growth-promoting Pseudomonas fluorescens 2P24 and isolated the corresponding T3SS apparatus. The T3SS gene cluster of strain 2P24 is similar organizationally to that of pathogenic P. syringae, except that it lacks the regulator hrpR and the hrpK1 and hrpH genes, which are involved in translocation of proteins. Electron microscopy revealed that the T3SS supramolecular structure of strain 2P24 was comprised of two distinctive substructures: a long extracellular, filamentous pilus, and a membrane-embedded base. We show that strain 2P24 deploys a harpin homolog protein, RspZ1, to elicit a hypersensitive response when infiltrated into Nicotiana tabacum cv. xanthi leaves with protein that is partially purified, and by complementing the hrpZ1 mutation of pHIR11. The T3SS of strain 2P24 retained ability to secrete effectors, whereas its effector translocation activity appeared to be excessively lost. Mutation of the rscC gene from 2P24 T3SS abolished the secretion of effectors, but the general biocontrol properties were unaffected. Remarkably, strain 2P24 induced functional MAMP-triggered immunity that included a burst of reactive oxygen species, strong suppression of challenge cell death, and disease expansion, while it was not associated with the secretion functional T3SS.

Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut

Coconut, cocoa and arecanut are commercial plantation crops that play a vital role in the Indian economy while sustaining the livelihood of more than 10 million Indians. According to 2012 Food and Agricultural organization's report, India is the third largest producer of coconut and it dominates the production of arecanut worldwide. In this study, three Plant Growth Promoting Rhizobacteria (PGPR) from coconut (CPCRI-1), cocoa (CPCRI-2) and arecanut (CPCRI-3) characterized for the PGP activities have been sequenced. The draft genome sizes were 4.7 Mb (56% GC), 5.9 Mb (63.6% GC) and 5.1 Mb (54.8% GB) for CPCRI-1, CPCRI-2, CPCRI-3, respectively. These genomes encoded 4056 (CPCRI-1), 4637 (CPCRI-2) and 4286 (CPCRI-3) protein-coding genes. Phylogenetic analysis revealed that both CPCRI-1 and CPCRI-3 belonged to Enterobacteriaceae family, while, CPCRI-2 was a Pseudomonadaceae family member. Functional annotation of the genes predicted that all three bacteria encoded genes needed for mineral phosphate solubilization, siderophores, acetoin, butanediol, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, chitinase, phenazine, 4-hydroxybenzoate, trehalose and quorum sensing molecules supportive of the plant growth promoting traits observed in the course of their isolation and characterization. Additionally, in all the three CPCRI PGPRs, we identified genes involved in synthesis of hydrogen sulfide (H2S), which recently has been proposed to aid plant growth. The PGPRs also carried genes for central carbohydrate metabolism indicating that the bacteria can efficiently utilize the root exudates and other organic materials as energy source. Genes for production of peroxidases, catalases and superoxide dismutases that confer resistance to oxidative stresses in plants were identified. Besides these, genes for heat shock tolerance, cold shock tolerance and glycine-betaine production that enable bacteria to survive abiotic stress were also identified.

Commonalities and differences of T3SSs in rhizobia and plant pathogenic bacteria

Plant pathogenic bacteria and rhizobia infect higher plants albeit the interactions with their hosts are principally distinct and lead to completely different phenotypic outcomes, either pathogenic or mutualistic, respectively. Bacterial protein delivery to plant host plays an essential role in determining the phenotypic outcome of plant-bacteria interactions. The involvement of type III secretion systems (T3SSs) in mediating animal- and plant-pathogen interactions was discovered in the mid-80's and is now recognized as a multiprotein nanomachine dedicated to trans-kingdom movement of effector proteins. The discovery of T3SS in bacteria with symbiotic lifestyles broadened its role beyond virulence. In most T3SS-positive bacterial pathogens, virulence is largely dependent on functional T3SSs, while in rhizobia the system is dispensable for nodulation and can affect positively or negatively the mutualistic associations with their hosts. This review focuses on recent comparative genome analyses in plant pathogens and rhizobia that uncovered similarities and variations among T3SSs in their genetic organization, regulatory networks and type III secreted proteins and discusses the evolutionary adaptations of T3SSs and type III secreted proteins that might account for the distinguishable phenotypes and host range characteristics of plant pathogens and symbionts.

Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots

Several bacterial strains of the Pseudomonas genus provide plant growth stimulation, plant protection against pests or bioremediation. Among these bacteria, P. fluorescens Pf29Arp reduces the severity of take-all, a disease caused by the pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) on wheat roots. In this study, we obtained a draft genome of Pf29Arp and subsequent comparative genomic analyses have revealed that this bacterial strain is closely related to strains of the 'P. brassicacearum-like' subgroup including P. brassicacearum ssp. brassicacearum NFM421 and P. fluorescens F113. Despite an overall chromosomal organization similar to these strains, a number of features including antibiotic synthesis gene clusters from secondary metabolism are not found in the Pf29Arp genome. But Pf29Arp possesses different protein secretion systems including type III (T3SS) and type VI (T6SS) secretion systems. Pf29Arp is the first Pseudomonas sp. strain described with four T6SS clusters (cluster I, II, III and IV). In addition, some protein-coding genes involved in the assembly of these secretion systems are basally expressed during Pf29Arp colonization of healthy wheat roots and display different expression patterns on necrotized roots caused by Ggt. These data suggest a role of T3SS and T6SS in the Pf29Arp adaptation to different root environments.

Characterization of the SPI-1 and Rsp type three secretion systems in Pseudomonas fluorescens F113

Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar beet rhizosphere. The recent annotation of the F113 genome sequence has revealed that this strain encodes a wide array of secretion systems, including two complete type three secretion systems (T3SSs) belonging to the Hrp1 and SPI-1 families. While Hrp1 T3SSs are frequently encoded in other P. fluorescens strains, the presence of a SPI-1 T3SS in a plant-beneficial bacterial strain was unexpected. In this work, the genetic organization and expression of these two T3SS loci have been analysed by a combination of transcriptional reporter fusions and transcriptome analyses. Overexpression of two transcriptional activators has shown a number of genes encoding putative T3 effectors. In addition, the influence of these two T3SSs during the interaction of P. fluorescens F113 with some bacterial predators was also assessed. Our data revealed that the transcriptional activator hilA is induced by amoeba and that the SPI-1 T3SS could potentially be involved in resistance to amoeboid grazing.

The complete genome sequence of the plant growth-promoting bacterium Pseudomonas sp. UW4

The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.

Distribution and diversity of bacterial secretion systems across metagenomic datasets

Bacteria can manipulate their surrounding environment through the secretion of proteins into other living organisms and into the extracellular milieu. In Gram stain negative bacteria this process is mediated by different types of secretion systems from type I through type VI secretion system (T1SS-T6SS). In this study the prevalence of these secretion systems in 312 publicly available microbiomes derived from a wide range of ecosystems was investigated by a gene-centric approach. Our analysis demonstrates that some secretion systems are over-represented in some specific samples. In addition, some T3SS and T6SS phylogenetic clusters were specifically enriched in particular ecological niches, which could indicate specific bacterial adaptation to these environments.

Distinct ectomycorrhizospheres share similar bacterial communities as revealed by pyrosequencing-based analysis of 16S rRNA genes

Analysis of the 16S rRNA gene sequences generated from Xerocomus pruinatus and Scleroderma citrinum ectomycorrhizospheres revealed that similar bacterial communities inhabited the two ectomycorrhizospheres in terms of phyla and genera, with an enrichment of the Burkholderia genus. Compared to the bulk soil habitat, ectomycorrhizospheres hosted significantly more Alpha-, Beta-, and Gammaproteobacteria.

Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR

Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen® method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1 / FF390. This in silico analysis of the specificity of FR1 / FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1 / FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C∶N ratio and land use in determining fungal abundance in soils.