Genome sequence of Stenotrophomonas maltophilia RR-10, isolated as an endophyte from rice root

Stenotrophomonas maltophilia virulence: a current view

Stenotrophomonas maltophilia is an opportunistic pathogen intrinsically resistant to multiple and broad-spectrum antibiotics. Although the bacterium is considered a low-virulence pathogen, it can cause various severe diseases and contributes significantly to the pathogenesis of multibacterial infections. During the COVID-19 pandemic, S. maltophilia has been recognized as one of the most common causative agents of respiratory co-infections and bacteremia in critically ill COVID-19 patients. The high ability to adapt to unfavorable environments and new habitat niches, as well as the sophisticated switching of metabolic pathways, are unique mechanisms that attract the attention of clinical researchers and experts studying the fundamental basis of virulence. In this review, we have summarized the current knowledge on the molecular aspects of S. maltophilia virulence and putative virulence factors, partially touched on interspecific bacterial interactions and iron uptake systems in the context of virulence, and have not addressed antibiotic resistance.

Nanoparticle applications in agriculture: overview and response of plant-associated microorganisms

Globally, food security has become a critical concern due to the rise in human population and the current climate change crisis. Usage of conventional agrochemicals to maximize crop yields has resulted in the degradation of fertile soil, environmental pollution as well as human and agroecosystem health risks. Nanotechnology in agriculture is a fast-emerging and new area of research explored to improve crop productivity and nutrient-use efficiency using nano-sized agrochemicals at lower doses than conventional agrochemicals. Nanoparticles in agriculture are applied as nanofertilizers and/or nanopesticides. Positive results have been observed in terms of plant growth when using nano-based agricultural amendments. However, their continuous application may have adverse effects on plant-associated rhizospheric and endospheric microorganisms which often play a crucial role in plant growth, nutrient uptake, and disease prevention. While research shows that the application of nanoparticles has the potential to improve plant growth and yield, their effect on the diversity and function of plant-associated microorganisms remains under-explored. This review provides an overview of plant-associated microorganisms and their functions. Additionally, it highlights the response of plant-associated microorganisms to nanoparticle application and provides insight into areas of research required to promote sustainable and precision agricultural practices that incorporate nanofertilizers and nanopesticides.

Versatility of Stenotrophomonas maltophilia: Ecological roles of RND efflux pumps

S. maltophilia is a widely distributed bacterium found in natural, anthropized and clinical environments. The genome of this opportunistic pathogen of environmental origin includes a large number of genes encoding RND efflux pumps independently of the clinical or environmental origin of the strains. These pumps have been historically associated with the uptake of antibiotics and clinically relevant molecules because they confer resistance to many antibiotics. However, considering the environmental origin of S. maltophilia, the ecological role of these pumps needs to be clarified. RND efflux systems are highly conserved within bacteria and encountered both in pathogenic and non-pathogenic species. Moreover, their evolutionary origin, conservation and multiple copies in bacterial genomes suggest a primordial role in cellular functions and environmental adaptation. This review is aimed at elucidating the ecological role of S. maltophilia RND efflux pumps in the environmental context and providing an exhaustive description of the environmental niches of S. maltophilia. By looking at the substrates and functions of the pumps, we propose different involvements and roles according to the adaptation of the bacterium to various niches. We highlight that i°) regulatory mechanisms and inducer molecules help to understand the conditions leading to their expression, and ii°) association and functional redundancy of RND pumps and other efflux systems demonstrate their complex role within S. maltophilia cells. These observations emphasize that RND efflux pumps play a role in the versatility of S. maltophilia.

Exploring the diversity and potential interactions of bacterial and fungal endophytes associated with different cultivars of olive (Olea europaea) in Brazil

The olive crop has expanded in the southeastern region of South America, particularly in Brazil. Thus, the objectives of this study were to identify the diversity of endophytic microorganisms associated with olive leaves with culture-dependent and culture-independent methods, to explore which factors influence the composition and abundance of this microbial community, to identify the trophic mode of these fungi by FunGuild and, to verify type associations between bacterial and fungal communities. Leaf samples were collected from 93 plants in nine locations in the Brazilian states of São Paulo and Minas Gerais. Leaves were first superficially disinfected before fungal isolation and next-generation metabarcoding sequencing was completed targeting the 16S rRNA regions for bacteria and ITS1 for fungi. In total, 800 isolates were obtained, which were grouped into 191 morphotypes and molecularly identified, resulting in 38 genera, 32 of which were recorded for the first time in cultivated olive trees in Brazil. For the isolated fungi, the most abundant trophic level was pathotrophic and for the culture-independent method was unidentified followed by symbiotrophic. The metabarcoding results revealed that factors such as plant age, altitudinal gradient, and geographic location can influence the microbial community of commercial olive plants, while the specific cultivar did not.

Draft genome sequence of Stenotrophomonas maltophilia strain P13 gives insight into its protease production and assessment of sulfur and nitrogen metabolism

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In this study draft genome sequence of Stenotrophomonas maltophilia strain P13 which was isolated from Kanchengayao glacier, North Sikkim, India.

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The genome of P13 strain possesses 2689,565 total reads, with an average G + C content of 69.9%.

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The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase.

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FAME, morphological and biochemical characterization, and scanning electron microscopy (SEM) of Stenotrophomonas maltophilia strain P13 are provided.

Stenotrophomonas maltophilia strain P13 was isolated from the Kanchengayao glacier's accumulation zone. A comprehensive study was done on this strain as it produced protease enzyme and thus having industrial potential. The whole genome sequence, FAME, morphological and biochemical characteristics of the S. maltophilia strain P13 is being presented. The genome of P13 strain possesses 2,689,565 total reads, with an average G + C content of 69.9%. The whole-genome assembly is having 548 contigs (with PEGs). The genome contains 2,985 coding sequences with 55 rRNA predicted genes. More than 88% of the total pre-processed reads from samples were mapped. The identified coding proteins were classified into 27 functional categories based on COG classification. The genome was found to possess genes for ammonium assimilation, galactosylceramide and sulfatide metabolism. The major enzymes present are beta-galactosidase, thiol peroxidase, thiolredoxin reductase, glutamate synthase, and glutamate-ammonia-ligase adenyltransferase. The genome information of Stenotrophomonas maltophilia P13 provides the basis for understanding the functional properties and abilities to act as a potential cold-active enzyme producer and nitrogen-fixing bacteria.

Genomic Analysis of the Endophytic Stenotrophomonas Strain 169 Reveals Features Related to Plant-Growth Promotion and Stress Tolerance

Plant-associated Stenotrophomonas isolates have great potential for plant growth promotion, especially under stress conditions, due to their ability to promote tolerance to abiotic stresses such as salinity or drought. The endophytic strain Stenotrophomonas sp. 169, isolated from a field-grown poplar, increased the growth of inoculated in vitro plants, with a particular effect on root development, and was able to stimulate the rooting of poplar cuttings in the greenhouse. The strain produced high amounts of the plant growth-stimulating hormone auxin under in vitro conditions. The comparison of the 16S rRNA gene sequences and the phylogenetic analysis of the core genomes showed a close relationship to Stenotrophomonas chelatiphaga and a clear separation from Stenotrophomonas maltophilia. Whole genome sequence analysis revealed functional genes potentially associated with attachment and plant colonization, growth promotion, and stress protection. In detail, an extensive set of genes for twitching motility, chemotaxis, flagella biosynthesis, and the ability to form biofilms, which are connected with host plant colonization, could be identified in the genome of strain 169. The production of indole-3-acetic acid and the presence of genes for auxin biosynthesis pathways and the spermidine pathway could explain the ability to promote plant growth. Furthermore, the genome contained genes encoding for features related to the production of different osmoprotective molecules and enzymes mediating the regulation of stress tolerance and the ability of bacteria to quickly adapt to changing environments. Overall, the results of physiological tests and genome analysis demonstrated the capability of endophytic strain 169 to promote plant growth. In contrast to related species, strain 169 can be considered non-pathogenic and suitable for biotechnology applications.

Detection of multidrug resistant environmental isolates of acinetobacter and Stenotrophomonas maltophilia: a possible threat for community acquired infections?

Acinetobacter spp. and Stenotrophomonas maltophilia are bacteria commonly associated with infections at the clinical settings. Reports of infections caused by environmental isolates are rare. Therefore, this study focused on determination of the antibiotic resistance patterns, antibiotic resistance genes, efflux pumps and virulence signatures of Acinetobacter spp. and S. maltophilia recovered from river water, plant rhizosphere and river sediment samples. The isolates were identified and confirmed using biochemical tests and PCR. The antimicrobial resistance profiles of the isolates were determined using Kirby Bauer disk diffusion assay and presence of antibiotic resistance and virulence genes were detected using PCR. S. maltophilia was more frequent in plant rhizosphere and sediment samples than the water samples. Acinetobacter spp. were mostly resistant to trimethoprim-sulfamethoxazole (96% of isolates), followed by polymyxin b (86%), cefixime (54%), colistin (42%), ampicillin (35%) and meropenem (19%). The S. maltophilia isolates displayed total resistance (100%) to trimethoprim- sulfamethoxazole, meropenem, imipenem, ampicillin and cefixime, while 80% of the isolates were resistant to ceftazidime. Acinetobacter spp. contained different antibiotic resistance genes such as sul1 (24% of isolates), sul2 (29%), blaOXA 23/51 (21%) and blaTEM (29%), while S. maltophilia harbored sul1 (8%) and blaTEM (20%). Additionally, efflux pump genes were present in all S. maltophilia isolates. The presence of multidrug resistant Acinetobacter spp. and Stenotrophomonas maltophilia in surface water raises concerns for community-acquired infections as this water is directly been used by the community for various purposes. Therefore, there is the need to institute measures aimed at reducing the risks of these infections and the resulting burden this may have on the health care system within the study area.

Deep modifications of the microbiome of rice roots infected by the parasitic nematode Meloidogyne graminicola in highly infested fields in Vietnam

Meloidogyne graminicola, also known as the rice root-knot nematode, is one of the most damaging plant-parasitic nematode, especially on rice. This obligate soilborne parasite induces the formation of galls that disturb the root morphology and physiology. Its impact on the root microbiome is still not well described. Here, we conducted a survey in Northern Vietnam where we collected infected (with galls) and non-infected root tips from the same plants in three naturally infested fields. Using a metabarcoding approach, we discovered that M. graminicola infection caused modifications of the root bacterial community composition and network structure. Interestingly, we observed in infected roots a higher diversity and species richness (+24% observed ESVs) as well as a denser and more complex co-occurrence network (+44% nodes and +136% links). We identified enriched taxa that include several hubs, which could serve as potential indicators or biocontrol agents of the nematode infection. Moreover, the community of infected roots is more specific suggesting changes in the functional capabilities to survive in the gall environment. We thus describe the signature of the gall microbiome (the 'gallobiome') with shifting abundances and enrichments that lead to a strong restructuration of the root microbiome.

Significance of Plant Growth Promoting Rhizobacteria in Grain Legumes: Growth Promotion and Crop Production

Grain legumes are an important component of sustainable agri-food systems. They establish symbiotic association with rhizobia and arbuscular mycorrhizal fungi, thus reducing the use of chemical fertilizers. Several other free-living microbial communities (PGPR—plant growth promoting rhizobacteria) residing in the soil-root interface are also known to influence biogeochemical cycles and improve legume productivity. The growth and function of these microorganisms are affected by root exudate molecules secreted in the rhizosphere region. PGPRs produce the chemicals which stimulate growth and functions of leguminous crops at different growth stages. They promote plant growth by nitrogen fixation, solubilization as well as mineralization of phosphorus, and production of phytohormone(s). The co-inoculation of PGPRs along with rhizobia has shown to enhance nodulation and symbiotic interaction. The recent molecular tools are helpful to understand and predict the establishment and function of PGPRs and plant response. In this review, we provide an overview of various growth promoting mechanisms of PGPR inoculations in the production of leguminous crops.

Complete Genome Sequence of Stenotrophomonas maltophilia Strain CF13, Recovered from Sputum from an Australian Cystic Fibrosis Patient

Stenotrophomonas maltophilia isolate CF13 is a multidrug-resistant isolate that was recovered in Sydney, Australia, in 2011, from a sputum sample from an individual with cystic fibrosis. The genome sequence of CF13 was completed using long- and short-read technologies.

Species Interaction and Selective Carbon Addition During Antibiotic Exposure Enhances Bacterial Survival

Biofilms are multifaceted and robust microbiological systems that enable microorganisms to withstand a multitude of environmental stresses and expand their habitat range. We have shown previously that nutritional status alters antibiotic susceptibility in a mixed-species biofilm. To further elucidate the effects of nutrient addition on inter-species dynamics and whole-biofilm susceptibility to high-dose streptomycin exposures, a CO₂ Evolution Measurement System was used to monitor the metabolic activity of early steady state pure-culture and mixed-species biofilms containing Pseudomonas aeruginosa and Stenotrophomonas maltophilia, with and without added carbon. Carbon supplementation was needed for biofilm recovery from high-dose streptomycin exposures when P. aeruginosa was either the dominant community member in a mixed-species biofilm (containing predominantly P. aeruginosa and S. maltophilia) or as a pure culture. By contrast, S. maltophilia biofilms could recover from high-dose streptomycin exposures without the need for carbon addition during antibiotic exposure. Metagenomic analysis revealed that even when inocula were dominated by Pseudomonas, the relative abundance of Stenotrophomonas increased upon biofilm development to ultimately become the dominant species post-streptomycin exposure. The combined metabolic and metagenomic results demonstrated the relevance of inter-species influence on survival and that nutritional status has a strong influence on the survival of P. aeruginosa dominated biofilms.

Stenotrophomonas maltophilia Encodes a VirB/VirD4 Type IV Secretion System That Modulates Apoptosis in Human Cells and Promotes Competition against Heterologous Bacteria, Including Pseudomonas aeruginosa

Stenotrophomonas maltophilia is an emerging opportunistic and nosocomial pathogen. S. maltophilia is also a risk factor for lung exacerbations in cystic fibrosis patients. S. maltophilia attaches to various mammalian cells, and we recently documented that the bacterium encodes a type II secretion system which triggers detachment-induced apoptosis in lung epithelial cells. We have now confirmed that S. maltophilia also encodes a type IVA secretion system (VirB/VirD4 [VirB/D4] T4SS) that is highly conserved among S. maltophilia strains and, looking beyond the Stenotrophomonas genus, is most similar to the T4SS of Xanthomonas To define the role(s) of this T4SS, we constructed a mutant of strain K279a that is devoid of secretion activity due to loss of the VirB10 component. The mutant induced a higher level of apoptosis upon infection of human lung epithelial cells, indicating that a T4SS effector(s) has antiapoptotic activity. However, when we infected human macrophages, the mutant triggered a lower level of apoptosis, implying that the T4SS also elaborates a proapoptotic factor(s). Moreover, when we cocultured K279a with strains of Pseudomonas aeruginosa, the T4SS promoted the growth of S. maltophilia and reduced the numbers of heterologous bacteria, signaling that another effector(s) has antibacterial activity. In all cases, the effect of the T4SS required S. maltophilia contact with its target. Thus, S. maltophilia VirB/D4 T4SS appears to secrete multiple effectors capable of modulating death pathways. That a T4SS can have anti- and prokilling effects on different targets, including both human and bacterial cells, has, to our knowledge, not been seen before.

Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity

Chitin is the second most abundant organic compound in nature and represents a rich carbon and nitrogen source that is primarily transformed by bacterial communities. Bacteria capable of gradually hydrolyzing chitin into N-acetylglucosamine monomers can have applications in the transformation of residues from shrimp and other crustaceans. The objective of the present study was to isolate, characterize and identify microorganisms with high chitinolytic activity. These microorganisms were isolated and characterized based on macro- and microscopic morphological traits. Strains were selected on colloidal chitin agar medium primarily based on a hydrolysis halo larger than 2 mm and a growing phase no longer than 6 days. Secondary selection consisted of semi-quantitative evaluation of chitinolytic activity with a drop dilution assay. From the above, ten strains were selected. Then, strain-specific activity was evaluated. The B4 strain showed the highest specific activity, which was 6,677.07 U/mg protein. Molecular identification indicated that the isolated strains belong to the species Stenotrophomonas maltophilia.

The Endophytic Strain Klebsiella michiganensis Kd70 Lacks Pathogenic Island-Like Regions in Its Genome and Is Incapable of Infecting the Urinary Tract in Mice

Klebsiella spp. have been isolated from many different environmental habitats but have mainly been associated with nosocomial acquired diseases in humans. Although there are many recently published sequenced genomes of members of this genus, there are very few studies on whole genome comparisons between clinical and non-clinical isolates, and it is therefore still an open question if a strain found in nature is capable of infecting humans/animals. Klebsiella michiganensis Kd70 was isolated from the intestine of larvae of Diatraea saccharalis but genome analysis revealed multiple genes associated with colonization and growth promotion in plants suggesting an endophytic lifestyle. Kd70 cells labeled with gfp confirmed capability of root colonization and soil application of Kd70 promoted growth in greenhouse grown sugarcane. Further genomic analysis showed that the Kd70 genome harbored fewer mammalian virulence factors and no pathogen island-like regions when compared to clinical isolates of this species, suggesting attenuated animal/human pathogenicity. This postulation was corroborated by in vivo experiments in which it was demonstrated that Kd70 was unable to infect the mouse urinary tract. This is to the best of our knowledge the first experimental example of a member of a pathogenic Klebsiella spp. unable to infect a mammalian organism. A proteomic comparison deduced from the genomic sequence between Kd70 and several other K. michiganensis strains showed a high similarity with isolates from many different environments including clinical strains, and demonstrated the existence of conserved genetic lineages within this species harboring members from different ecological niches and geographical locations. Furthermore, most genetic differences were found to be associated with genomic islands of clinical isolates, suggesting that evolutionary adaptation of animal pathogenicity to a large extent has depended on horizontal gene transfer. In conclusion our results demonstrate the importance of conducting thorough in vivo pathogenicity studies before presupposing animal/human virulence of non-clinical bacterial isolates.

Isolation and Identification of Endophytic Bacteria with Plant Growth Promoting Activity and Biocontrol Potential from Wild Pistachio Trees

In this study, samples were collected from the leaves and stems of healthy wild Pistachio trees (Pistacia atlantica L.) from various locations of Baneh and Marivan regions, Iran. In total, 61 endophytic bacteria were isolated and grouped according to phenotypic properties. Ten selected isolates from each group were further identified by partial sequencing of the 16S rRNA gene. Based on the results, isolates were identified as bacteria belonging to Pseudomonas, Stenotrophomonas, Bacillus, Pantoea and Serratia genus. The ability of these isolates was evaluated to phytohormone production such as auxin and gibberellin, siderophore production, phosphate solubilization, atmospheric nitrogen fixation, protease and hydrogen cyanide production. All strains were able to produce the plant growth hormone auxin and gibberellin in different amounts. The majority of strains were able to solubilize phosphate. The results of atmospheric nitrogen fixation ability, protease and siderophore production were varied among strains. Only Ba66 could produce a low amount of hydrogen cyanide. The results of biocontrol assay showed that Pb78 and Sp15 strains had the highest and lowest inhibition effects on bacterial plant pathogens, Pseudomonas syringae pv. syringae Pss20 and Pseudomonas tolaasii Pt18 under in vitro condition. Pb3, Pb24 and Pb71 strains significantly promote root formation on carrot slices. To our knowledge this is the first report of the isolation of endophytic bacterial strains belonging to Pantoea, Bacillus, Pseudomonas, Serratia and Stenotrophomonas genus from wild pistachio trees with plant growth promoting potential and biocontrol activity.

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

Chemical signaling involved in plant-microbe interactions

Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

Stenotrophomonas maltophilia as an Emerging Ubiquitous Pathogen: Looking Beyond Contemporary Antibiotic Therapy

Stenotrophomonas maltophilia is a commensal and an emerging pathogen earlier noted in broad-spectrum life threatening infections among the vulnerable, but more recently as a pathogen in immunocompetent individuals. The bacteria are consistently being implicated in necrotizing otitis, cutaneous infections including soft tissue infection and keratitis, endocarditis, meningitis, acute respiratory tract infection (RTI), bacteraemia (with/without hematological malignancies), tropical pyomyositis, cystic fibrosis, septic arthritis, among others. S. maltophilia is also an environmental bacteria occurring in water, rhizospheres, as part of the animals' microflora, in foods, and several other microbiota. This review highlights clinical reports on S. maltophilia both as an opportunistic and as true pathogen. Also, biofilm formation as well as quorum sensing, extracellular enzymes, flagella, pili/fimbriae, small colony variant, other virulence or virulence-associated factors, the antibiotic resistance factors, and their implications are considered. Low outer membrane permeability, natural MDR efflux systems, and/or resistance genes, resistance mechanisms like the production of two inducible chromosomally encoded β-lactamases, and lack of carefully compiled patient history are factors that pose great challenges to the S. maltophilia control arsenals. The fluoroquinolone, some tetracycline derivatives and trimethoprim-sulphamethaxole (TMP-SMX) were reported as effective antibiotics with good therapeutic outcome. However, TMP-SMX resistance and allergies to sulfa together with high toxicity of fluoroquinolone are notable setbacks. S. maltophilia's production and sustenance of biofilm by quorum sensing enhance their virulence, resistance to antibiotics and gene transfer, making quorum quenching an imperative step in Stenotrophomonas control. Incorporating several other proven approaches like bioengineered bacteriophage therapy, Epigallocatechin-3-gallate (EGCG), essential oil, nanoemulsions, and use of cationic compounds are promising alternatives which can be incorporated in Stenotrophomonas control arsenal.

Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

The genus Stenotrophomonas (Gammaproteobacteria) has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR), opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc). Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs). The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They were significantly more susceptible to antibiotics than S. maltophilia. We demonstrate that the sympatric lineages recovered display significantly differentiated habitat preferences, antibiotic resistance profiles and β-lactamase expression phenotypes, as shown by diverse multivariate analyses and robust univariate statistical tests. We discuss our data in light of current models of bacterial speciation, which fit these data well, stressing the implications of species delimitation in ecological, evolutionary and clinical research.

Understanding pine wilt disease: roles of the pine endophytic bacteria and of the bacteria carried by the disease-causing pinewood nematode

Pine wilt disease (PWD) is one of the most destructive diseases in trees of the genus Pinus and is responsible for environmental and economic losses around the world. The only known causal agent of the disease is the pinewood nematode (PWN) Bursaphelenchus xylophilus. Despite that, bacteria belonging to several different genera have been found associated with PWN and their roles in the development of PWD have been suggested. Molecular methodologies and the new era of genomics have revealed different perspectives to the problem, recognizing the manifold interactions between different organisms involved in the disease. Here, we reviewed the possible roles of nematode-carried bacteria in PWD, what could be the definition of this group of microorganisms and questioned their origin as possible endophytes, discussing their relation within the endophytic community of pine trees. The diversity of the nematode-carried bacteria and the diversity of pine tree endophytes, reported until now, is revised in detail in this review. What could signify a synergetic effect with PWN harming the plant, or what could equip bacteria with functions to control the presence of nematodes inside the tree, is outlined as two possible roles of the microbial community in the etiology of this disease. An emphasis is put on the potential revealed by the genomic data of isolated organisms in their potential activities as effective tools in PWD management.

The outer membrane proteins of Stenotrophomonas maltophilia are potential vaccine candidates for channel catfish (Ictalurus punctatus)

Channel catfish (Ictalurus punctatus) is an important agricultural fish that has been plagued by Stenotrophomonas maltophilia (S. maltophilia) infections in recent years, some of them severe. The outer membrane proteins (OMPs) of S. maltophilia are one of the most immunogenic and highly conserved candidates for vaccine development in aquaculture. The present study investigated OMPs of S. maltophilia as vaccine on immune response and disease resistance against S. maltophilia of channel catfish and investigated the enhancement effect of natural adjuvants Propolis (Pro), FIG polysaccharide (Fcps), Glycyrrhizine (Gly) to OMPs of S. maltophilia for further study. The results indicated that channel catfish injected intraperitoneally with OMPs showed better immune response including leukocytes phagocytosis activity, serum bactericidal activity, complement C3, IgM level and an increasement of resistance against S. maltophilia compared to the control group. Moreover, Pro, Fcps and Gly could enhance the immune response of OMPs. The relative percent of survival (RPS) was 73.33%, 66.67%, 63.33%, 60%, 0% in fish injected OMPs + Pro, OMPs + Fcps, OMPs + Gly, OMPs and 0.65% normal saline, respectively. These results suggested that OMPs used as vaccine could induce and stimulate immune response and enhance disease resistance in channel catfish, especially for Pro as immunoenhancer. Results revealed that OMPs were an effective vaccine against S. maltophilia in channel catfish.

Probiotic Lactobacillus casei expressing porcine antimicrobial peptide PR39 elevates antibacterial activity in the gastrointestinal tract

PR39, a 4.7 kDa proline-rich antimicrobial peptide, acts as a cationic host defense peptide. In addition to killing bacteria, PR39 mediates inflammatory reactions, including cell proliferation, migration, wound healing, and angiogenesis. Here, we examined the antibacterial effects of this peptide. The synthetic gene fragment PR39 was inserted into the secretory expression vector plasmid pPG:612 of Lactobacillus casei, yielding the recombinant strain pPG:612-PR39/L. casei 393. In vitro antibacterial tests showed that expression of the PR39 peptide in recombinant L. casei resulted in antibacterial activity against Escherichia coli and Salmonella but had only minor antibacterial effects in Staphylococcus aureus. In addition, BALB/c mice fed the recombinant pPG:612-PR39/L. casei 393 grew better and had increased peripheral blood lymphocyte percentages, white blood cell numbers, and spleen indices than mice in the control group. Scanning electron microscopy showed that jejunum and duodenum villus height, crypt depth, and the ratio of villus height/crypt depth in the intestinal villi also increased. Moreover, mice fed the recombinant strain showed significantly lower mortality rates than the control group mice when challenged with the enterotoxigenic E. coli K88⁺. Thus, this recombinant expression system had the beneficial characteristics of both L. casei and PR39, supporting its potential as an animal feed additive.

Evidence for foliar endophytic nitrogen fixation in a widely distributed subalpine conifer

Coniferous forest nitrogen (N) budgets indicate unknown sources of N. A consistent association between limber pine (Pinus flexilis) and potential N2 -fixing acetic acid bacteria (AAB) indicates that native foliar endophytes may supply subalpine forests with N. To assess whether the P. flexilis-AAB association is consistent across years, we re-sampled P. flexilis twigs at Niwot Ridge, CO and characterized needle endophyte communities via 16S rRNA Illumina sequencing. To investigate whether endophytes have access to foliar N2 , we incubated twigs with (13) N2 -enriched air and imaged radioisotope distribution in needles, the first experiment of its kind using (13) N. We used the acetylene reduction assay to test for nitrogenase activity within P. flexilis twigs four times from June to September. We found evidence for N2 fixation in P. flexilis foliage. N2 diffused readily into needles and nitrogenase activity was positive across sampling dates. We estimate that this association could provide 6.8-13.6 μg N m(-2)  d(-1) to P. flexilis stands. AAB dominated the P. flexilis needle endophyte community. We propose that foliar endophytes represent a low-cost, evolutionarily stable N2 -fixing strategy for long-lived conifers. This novel source of biological N2 fixation has fundamental implications for understanding forest N budgets.

Dhar M. "Omics" Tools for Better Understanding the Plant-Endophyte Interactions

Endophytes, which mostly include bacteria, fungi and actinomycetes, are the endosymbionts that reside asymptomatically in plants for at least a part of their life cycle. They have emerged as a valuable source of novel metabolites, industrially important enzymes and as stress relievers of host plant, but still many aspects of endophytic biology are unknown. Functions of individual endophytes are the result of their continuous and complex interactions with the host plant as well as other members of the host microbiome. Understanding plant microbiomes as a system allows analysis and integration of these complex interactions. Modern genomic studies involving metaomics and comparative studies can prove to be helpful in unraveling the gray areas of endophytism. A deeper knowledge of the mechanism of host infestation and role of endophytes could be exploited to improve the agricultural management in terms of plant growth promotion, biocontrol and bioremediation. Genome sequencing, comparative genomics, microarray, next gen sequencing, metagenomics, metatranscriptomics are some of the techniques that are being used or can be used to unravel plant-endophyte relationship. The modern techniques and approaches need to be explored to study endophytes and their putative role in host plant ecology. This review highlights "omics" tools that can be explored for understanding the role of endophytes in the plant microbiome.

Comparative Genomics of Environmental and Clinical Stenotrophomonas maltophilia Strains with Different Antibiotic Resistance Profiles

Stenotrophomonas maltophilia, a ubiquitous Gram-negative γ-proteobacterium, has emerged as an important opportunistic pathogen responsible for nosocomial infections. A major characteristic of clinical isolates is their high intrinsic or acquired antibiotic resistance level. The aim of this study was to decipher the genetic determinism of antibiotic resistance among strains from different origins (i.e., natural environment and clinical origin) showing various antibiotic resistance profiles. To this purpose, we selected three strains isolated from soil collected in France or Burkina Faso that showed contrasting antibiotic resistance profiles. After whole-genome sequencing, the phylogenetic relationships of these 3 strains and 11 strains with available genome sequences were determined. Results showed that a strain's phylogeny did not match their origin or antibiotic resistance profiles. Numerous antibiotic resistance coding genes and efflux pump operons were revealed by the genome analysis, with 57% of the identified genes not previously described. No major variation in the antibiotic resistance gene content was observed between strains irrespective of their origin and antibiotic resistance profiles. Although environmental strains generally carry as many multidrug resistant (MDR) efflux pumps as clinical strains, the absence of resistance-nodulation-division (RND) pumps (i.e., SmeABC) previously described to be specific to S. maltophilia was revealed in two environmental strains (BurA1 and PierC1). Furthermore the genome analysis of the environmental MDR strain BurA1 showed the absence of SmeABC but the presence of another putative MDR RND efflux pump, named EbyCAB on a genomic island probably acquired through horizontal gene transfer.

A function of SmeDEF, the major quinolone resistance determinant of Stenotrophomonas maltophilia, is the colonization of plant roots

Quinolones are synthetic antibiotics, and the main cause of resistance to these antimicrobials is mutation of the genes encoding their targets. However, in contrast to the case for other organisms, such mutations have not been found in quinolone-resistant Stenotrophomonas maltophilia isolates, in which overproduction of the SmeDEF efflux pump is a major cause of quinolone resistance. SmeDEF is chromosomally encoded and highly conserved in all studied S. maltophilia strains; it is an ancient element that evolved over millions of years in this species. It thus seems unlikely that its main function would be resistance to quinolones, a family of synthetic antibiotics not present in natural environments until the last few decades. Expression of SmeDEF is tightly controlled by the transcriptional repressor SmeT. Our work shows that plant-produced flavonoids can bind to SmeT, releasing it from smeDEF and smeT operators. Antibiotics extruded by SmeDEF do not impede the binding of SmeT to DNA. The fact that plant-produced flavonoids specifically induce smeDEF expression indicates that they are bona fide effectors regulating expression of this resistance determinant. Expression of efflux pumps is usually downregulated unless their activity is needed. Since smeDEF expression is triggered by plant-produced flavonoids, we reasoned that this efflux pump may have a role in the colonization of plants by S. maltophilia. Our results showed that, indeed, deletion of smeE impairs S. maltophilia colonization of plant roots. Altogether, our results indicate that quinolone resistance is a recent function of SmeDEF and that colonization of plant roots is likely one original function of this efflux pump.

Draft Genome Sequence of Stenotrophomonas maltophilia Strain B418, a Promising Agent for Biocontrol of Plant Pathogens and Root-Knot Nematode

Stenotrophomonas maltophilia strain B418 was isolated from a barley rhizosphere in China. This bacterium exhibits broad-spectrum inhibitory activities against plant pathogens and root-knot nematode along with growth-promoting effects. Here, we present the draft genome sequence of S. maltophilia B418.

Laboratory culture and maintenance of Stenotrophomonas maltophilia

Stenotrophomonas maltophilia is a ubiquitous soil bacterium that is increasingly recognized as an emerging nosocomial pathogen. This unit includes protocols for the in vitro growth and maintenance of S. maltophilia.

Draft Genome Sequence of Ralstonia pickettii AU12-08, Isolated from an Intravascular Catheter in Australia

Ralstonia pickettii is a nonfermenting Gram-negative bacillus that creates a significant problem in clinical settings, as it is a widespread cause of nosocomial infections. Here, we report the draft genome sequence of R. pickettii AU12-08, isolated from an intravascular catheter tip.

Genome Sequence of Stenotrophomonas maltophilia Strain AU12-09, Isolated from an Intravascular Catheter

Stenotrophomonas maltophilia is an opportunistic nosocomial pathogen that is characterized by its high-level intrinsic resistance to a variety of antibiotics and its ability to form biofilms. Here, we report the draft genome sequence of Stenotrophomonas maltophilia AU12-09, isolated from an intravascular catheter tip.

Twenty-one genome sequences from Pseudomonas species and 19 genome sequences from diverse bacteria isolated from the rhizosphere and endosphere of Populus deltoides

To aid in the investigation of the Populus deltoides microbiome, we generated draft genome sequences for 21 Pseudomonas strains and 19 other diverse bacteria isolated from Populus deltoides roots. Genome sequences for isolates similar to Acidovorax, Bradyrhizobium, Brevibacillus, Caulobacter, Chryseobacterium, Flavobacterium, Herbaspirillum, Novosphingobium, Pantoea, Phyllobacterium, Polaromonas, Rhizobium, Sphingobium, and Variovorax were generated.

An inducible fusaric acid tripartite efflux pump contributes to the fusaric acid resistance in Stenotrophomonas maltophilia

BACKGROUND

Fusaric acid (5-butylpicolinic acid), a mycotoxin, is noxious to some microorganisms. Stenotrophomonas maltophilia displays an intrinsic resistance to fusaric acid. This study aims to elucidate the mechanism responsible for the intrinsic fusaric acid resistance in S. maltophilia.

METHODOLOGY

A putative fusaric acid resistance-involved regulon fuaR-fuaABC was identified by the survey of the whole genome sequence of S. maltophilia K279a. The fuaABC operon was verified by reverse transcriptase-PCR. The contribution of the fuaABC operon to the antimicrobial resistance was evaluated by comparing the antimicrobials susceptibility between the wild-type strain and fuaABC knock-out mutant. The regulatory role of fuaR in the expression of the fuaABC operon was assessed by promoter transcription fusion assay.

RESULTS

The fuaABC operon was inducibly expressed by fusaric acid and the inducibility was fuaR dependent. FuaR functioned as a repressor of the fuaABC operon in absence of a fusaric acid inducer and as an activator in its presence. Overexpression of the fuaABC operon contributed to the fusaric acid resistance.

SIGNIFICANCE

A novel tripartite fusaric acid efflux pump, FuaABC, was identified in this study. Distinct from the formally classification, the FuaABC may constitute a new type of subfamily of the tripartite efflux pump.

Whole-genome sequence of Stenotrophomonas maltophilia D457, a clinical isolate and a model strain

Stenotrophomonas maltophilia is an opportunistic pathogen with an environmental origin, and it is an increasingly relevant cause of nosocomial infections. Here we present the whole-genome sequence of S. maltophilia strain D457, a clinical isolate that is being used as a model for studying antibiotic resistance in this bacterial species.