Characterization of bacteria associated with pinewood nematode Bursaphelenchus xylophilus

Genomic and phenotypic insights into Serratia interaction with plants from an ecological perspective

We investigated the plant growth-promoting potential of two endophytic strains of Serratia marcescens, namely SmCNPMS2112 and SmUFMG85, which were isolated from the roots of the same maize (Zea mays) plant. The strains were evaluated in vitro for their ability to produce siderophores and indoleacetic acid, form biofilm, solubilize iron phosphate (Fe-P) and Araxá rock phosphate (RP), mineralize phytate, and for their ability to adhere and colonize host roots. Additionally, their plant growth-promoting potential was tested in vivo under greenhouse conditions using millet grown in soil under two fertilization schemes (triple superphosphate, TSP, or commercial rock phosphate, cRP). Both strains improved at least five physiological traits of millet or P content in soil. In order to elucidate the genetic basis of the plant growth-promoting ability of these strains, their genomes were compared. While both genomes exhibited a similar overall functional profile, each strain had unique features. SmCNPMS2112 contained genes related to arsenic and aromatic hydrocarbons degradation, whereas SmUFMG85 harbored genes related to rhamnolipid biosynthesis and chromium bioremediation. Also, we observe a unique repertoire of genes related to plant growth-promotion (PGP) in the SmUFMG85 genome, including oxalate decarboxylase (OxdC), associated with the catabolism of oxalic acid, and aerobactin siderophore (lucD) in the genome of SmCNPMS2112. The alkaline phosphatase was observed on two strains, but acid phosphatase was exclusive to SmUFMG85. Eighteen secondary metabolic gene clusters, such as those involved in the biosynthesis of macrolides and bacillomycin, among others, occur in both strains. Moreover, both genomes contained prophages, suggesting that viral-mediated horizontal gene transfer may be a key mechanism driving genomic variability in the endophytic environment. Indeed, the most genes unique and accessory of SmUFMG85 and SmCNPMS2112 were localized in genomic islands, highlighting genome plasticity and its underlying drivers. To investigate the ecological distribution of plant-interaction traits in the genus Serratia, the genomes of SmUFMG85 and SmCNPMS2112 strains were compared with those of other 19 Serratia strains of different species, which were isolated from different environments. We observe that many features for PGP are present in all genomes, regardless of niche, for instance: formation of flagella, fimbriae and pili, chemotaxis, biosynthesis of siderophores, indole-3-acetic acid (IAA) and volatile organic (VOC) and inorganic (VIC) compounds, such as acetoin and HCN. Also, all the analyzed genomes show an antimicrobial resistance repertoire of genes that confer resistance to several antibiotics belonging to the groups of aminoglycosides and quinolones, for instance. Also, from a niche partitioning perspective, secretion system preference and the ability to produce exopolysaccharides involved in biofilm formation are among the features that vary the most among strains, and most likely influence niche adaptation in Serratia spp., even though only the latter seems to be a feature specifically associated with virulence in the analyzed strains. Our results show that populations of bacteria sharing the same niche can present significant physiological and genomic differences, and reveal the intraspecific metabolic plasticity that underlie plant-bacteria interactions. Also, this study reveals the potential of two Serratia marcescens strains as bioinoculants in agriculture. Considering that Serratia spp. are regarded as low risk biological agents, despite the fact that they can be associated with human disease, we suggest that strain biosafety be evaluated using a combination of genome and phenotypic analyses, as presented herein.

Distinct biogeographic patterns for bacteria and fungi in association with Bursaphelenchus xylophilus nematodes and infested pinewood

Pinewood nematodes (PWN, Bursaphelenchus xylophilus) are destructive plant parasitic nematodes that cause pine wilt disease (PWD) by attacking the vascular systems of pine trees, resulting in widespread tree mortality. Research has shown that there are connections between nematode-associated microbes and PWD. Yet the variations in microbial communities across different geographic regions are not well-understood. In this study, we examined the bacterial and fungal communities associated with nematodes and infested wood collected from 34 sites across three vegetation zones in China, as well as samples from the United States, using 16S rRNA and internal transcribed spacer (ITS) gene amplicon sequencing. The predominant genera Pseudomonas and Rhodococcus were found in nematodes, and Acinetobacter was present in the wood of PWD-infected pine trees across China. Network analysis revealed that core bacterial taxa belonged to the Pseudomonadota and Actinomycetota phyla for the nematodes, whereas the Pseudomonadota and Bacteroidota phyla were dominant in the infested wood. Identification of enriched key microbial taxa in nematodes and infested wood across vegetation zones indicates distinct biogeographic microbial community structures and key bacterial species. Although the nematode-associated bacterial community showed consistency across geographic distances, the similarity of the PWD pine trees' bacterial community decreased with distance, suggesting a spatial correlation with environmental variables. Our findings enhance our understanding of the microbiota associated with pinewood nematode (PWN) and offer valuable insights into PWD management.

IMPORTANCE

Our research uncovered specific bacteria and fungi linked to pinewood nematode (PWN) and infested wood in three different vegetation zones in China, as well as samples from the United States. This sheds light on the critical roles of certain microbial groups, such as Pseudomonas, Acinetobacter, and Stenotrophomonas, in influencing PWN fitness. Understanding these patterns provides valuable insights into the dynamics of PWN-associated microbiomes, offering potential strategies for managing pine wilt disease (PWD). We found significant correlations between geographic distance and similarity in bacterial communities in the infested wood, indicating a spatial influence on wood-associated microbial communities due to limited dispersal and localized environmental conditions. Further investigations of these spatial patterns and driving forces are crucial for understanding the ecological processes that shape microbial communities in complex ecosystems and, ultimately, for mitigating the transmission of PWN in forests.

Effect of Associated Bacteria GD1 on the Low-Temperature Adaptability of Bursaphelenchus xylophilus Based on RNA-Seq and RNAi

To explore the effect of associated bacteria on the low-temperature adaptability of pinewood nematodes (PWNs), transcriptome sequencing (RNA-seq) of PWN AH23 treated with the associated bacterial strain Bacillus cereus GD1 was carried out with reference to the whole PWN genome. Bioinformatic software was utilized to analyze the differentially expressed genes (DEGs). This study was based on the analysis of DEGs to verify the function of daf-11 by RNAi. The results showed that there were 439 DEGs between AH23 treated with GD1 and those treated with ddH₂O at 10 °C. There were 207 pathways annotated in the KEGG database and 48 terms annotated in the GO database. It was found that after RNAi of daf-11, the survival rate of PWNs decreased significantly at 10 °C, and fecundity decreased significantly at 15 °C. It can be concluded that the associated bacteria GD1 can enhance the expression of genes related to PWN low-temperature adaptation and improve their adaptability to low temperatures.

Microhabitat Governs the Microbiota of the Pinewood Nematode and Its Vector Beetle: Implication for the Prevalence of Pine Wilt Disease

Our understanding of environmental acquisition of microbes and migration-related alteration of microbiota across habitats has rapidly increased. However, in complex life cycles, such as for many parasites, exactly how these microbes are transmitted across multiple environments, such as hosts and habitats, is unknown. Pinewood nematode, the causal agent of the globally devastating pine wilt disease, provides an ideal model to study the role of microbiota in multispecies interactions because its successful host invasion depends on the interactions among its vector insects, pine hosts, and associated microbes. Here, we studied the role of bacterial and fungal communities involved in the nematode’s life cycle across different micro- (pupal chamber, vector beetle, and dispersal nematodes) and macrohabitats (geographical locations). We identified the potential sources, selection processes, and keystone taxa involved in the host pine-nematode-vector beetle microbiota interactions. Nearly 50% of the microbiota in vector beetle tracheae and ~60% that of third-stage dispersal juveniles were derived from the host pine (pupal chambers), whereas 90% of bacteria of fourth-stage dispersal juveniles originated from vector beetle tracheae. Our results also suggest that vector beetles’ tracheae selectively acquire some key taxa from the microbial community of the pupal chambers. These taxa will be then enriched in the dispersal nematodes traveling in the tracheae and hence likely transported to new host trees. Taken together, our findings contribute to the critical information toward a better understanding of the role of microbiota in pine wilt disease, therefore aiding the knowledge for the development of future biological control agents.

IMPORTANCE Our understanding of animal microbiota acquisition and dispersal-mediated variation has rapidly increased. In this study, using the model of host pine-pinewood nematode-vector beetle (Monochamus sp.) complex, we disentangled the routes of microbial community assembly and transmission mechanisms among these different participants responsible for highly destructive pine wilt disease. We provide evidence that the microhabitat is the driving force shaping the microbial community of these participants. The microbiota of third-stage dispersal juveniles (L_III) of the nematodes collected around pupal chambers and of vector beetles were mainly derived from the host pine (pupal chambers), whereas the vector-entering fourth-stage dispersal juveniles (L_IV) of the nematodes had the simplest microbiota community, not influencing vector’s microbiota. These findings enhanced our understanding of the variation in the microbiota of plants and animals and shed light on microbiota acquisition in complex life cycles.

Invasion History of the Pinewood Nematode Bursaphelenchus xylophilus Influences the Abundance of Serratia sp. in Pupal Chambers and Tracheae of Insect-Vector Monochamus alternatus

Pine wilt disease (PWD) has caused extensive mortality in pine forests worldwide. This disease is a result of a multi-species interaction among an invasive pinewood nematode (PWN) Bursaphelenchus xylophilus, its vector Monochamus sp. beetle, and the host pine tree (Pinus sp.). In other systems, microbes have been shown to attenuate negative impacts on invasive species after the invasion has reached a certain time point. Despite that the role of PWD associated microbes involved in the PWD system has been widely studied, it is not known whether similar antagonistic "hidden microbial players" exist in this system due to the lack of knowledge about the potential temporal changes in the composition of associated microbiota. In this study, we investigated the bacteria-to-fungi ratio and isolated culturable bacterial isolates from pupal chambers and vector beetle tracheae across five sampling sites in China differing in the duration of PWN invasion. We also tested the pathogenicity of two candidate bacteria strains against the PWN-vector beetle complex. A total of 118 bacterial species belonging to 4 phyla, 30 families, and 54 genera were classified based on 16S sequencing. The relative abundance of the genus Serratia was lower in pupal chambers and tracheae in newly PWN invaded sites (<10 years) compared to the sites that had been invaded for more than 20 years. Serratia marcescens strain AHPC29 was widely distributed across all sites and showed nematicidal activity against PWN. The insecticidal activity of this strain was dependent on the life stage of the vector beetle Monochamus alternatus: no insecticidal activity was observed against final-instar larvae, whereas S. marcescens was highly virulent against pupae. Our findings improved the understanding of the temporal variation in the microbial community associated with the PWN-vector beetle complex and the progress of PWD and can therefore facilitate the development of biological control agents against PWN and its vector beetle.

Cadmium-Tolerant Plant Growth-Promoting Bacteria Curtobacterium oceanosedimentum Improves Growth Attributes and Strengthens Antioxidant System in Chili (Capsicum frutescens)

The remediation of potentially toxic element-polluted soils can be accomplished through the use of microbial and plant-assisted bioremediation. A total of 32 bacteria were isolated from soil samples contaminated with potentially toxic elements. The isolated bacterial strain DG-20 showed high tolerance to cadmium (up to 18 mM) and also showed bioaccumulative Cd removal properties, as demonstrated by atomic absorption spectroscopy studies. By sequencing the 16S rRNA gene, this strain was identified as Curtobacterium oceanosedimentum. Under stress and normal conditions, isolate DG-20 also produced a wide range of plant growth promoting traits, including ammonia production (51–73 µg/mL) and IAA production (116–183 µg/mL), alongside siderophore production and phosphate solubilization. Additionally, pot experiments were conducted to determine whether the strain could promote Chili growth when Cd salts are present. Over the control, bacterial colonization increased root and shoot lengths significantly up to 58% and 60%, respectively. Following inoculation with the Cd-tolerant strain, the plants also increased in both fresh and dry weight. In both the control and inoculated plants, Cd was accumulated more in roots than in shoots, indicating that Chili was phytostabilizing Cd levels. Besides improving the plant attributes, Cd-tolerant bacteria were also found to increase the amount of total chlorophyll, proline, total phenol, and ascorbic acid in the soil when added to the soil. These results suggest that the inoculant provides protection to plants from negative effects. The results of the present study predict that the combined properties of the tested strain in terms of Cd tolerance and plant growth promotion can be exploited for the purpose of the bioremediation of Cd, and for the improvement of Chili cultivation in soils contaminated with Cd.

Phytochemicals as Biopesticides against the Pinewood Nematode Bursaphelenchus xylophilus: A Review on Essential Oils and Their Volatiles

The impacts of a rapidly changing environment together with the growth in global trade activities has promoted new plant pest pandemic events in forest ecosystems. The pinewood nematode (PWN), Bursaphelenchus xylophilus, causes strong worldwide economic and ecological impacts. Direct control is performed through trunk injection of powerful nematicides, however many of these (hemi)synthetic compounds have raised ecological and human health concerns for affecting non-target species and accumulating in food products. As sustainable alternatives, essential oils (EOs) have shown very promising results. In this work, available literature on the direct activity of EOs against PWN is reviewed, as a contribution to advance the search for safer and greener biopesticides to be used in sustainable PWD pest management strategies. For the first time, important parameters concerning the bioassays performed, the PWNs bioassayed, and the EOs used are summarized and comparatively analyzed. Ultimately, an overview of the chemical composition of the most active EOs allowed to uncover preliminary guidelines for anti-PWN EO efficiency. The analysis of important information on the volatile phytochemicals composing nematicidal EOs provides a solid basis to engineer sustainable biopesticides capable of controlling the PWN under an integrated pest management framework and contributes to improved forest health.

The Threat of Pests and Pathogens and the Potential for Biological Control in Forest Ecosystems

Forests are an essential component of the natural environment, as they support biodiversity, sequester carbon, and play a crucial role in biogeochemical cycles—in addition to producing organic matter that is necessary for the function of terrestrial organisms. Forests today are subject to threats ranging from natural occurrences, such as lightning-ignited fires, storms, and some forms of pollution, to those caused by human beings, such as land-use conversion (deforestation or intensive agriculture). In recent years, threats from pests and pathogens, particularly non-native species, have intensified in forests. The damage, decline, and mortality caused by insects, fungi, pathogens, and combinations of pests can lead to sizable ecological, economic, and social losses. To combat forest pests and pathogens, biocontrol may be an effective alternative to chemical pesticides and fertilizers. This review of forest pests and potential adversaries in the natural world highlights microbial inoculants, as well as research efforts to further develop biological control agents against forest pests and pathogens. Recent studies have shown promising results for the application of microbial inoculants as preventive measures. Other studies suggest that these species have potential as fertilizers.

Genomic Analysis of the 1-Aminocyclopropane-1-Carboxylate Deaminase-Producing Pseudomonas thivervalensis SC5 Reveals Its Multifaceted Roles in Soil and in Beneficial Interactions With Plants

Beneficial 1-aminocyclopropane-1-carboxylate (ACC) deaminase-producing bacteria promote plant growth and stress resistance, constituting a sustainable alternative to the excessive use of chemicals in agriculture. In this work, the increased plant growth promotion activity of the ACC deaminase-producing Pseudomonas thivervalensis SC5, its ability to limit the growth of phytopathogens, and the genomics behind these important properties are described in detail. P. thivervalensis SC5 displayed several active plant growth promotion traits and significantly increased cucumber plant growth and resistance against salt stress (100mmol/L NaCl) under greenhouse conditions. Strain SC5 also limited the in vitro growth of the pathogens Botrytis cinerea and Pseudomonas syringae DC3000 indicating active biological control activities. Comprehensive analysis revealed that P. thivervalensis SC5 genome is rich in genetic elements involved in nutrient acquisition (N, P, S, and Fe); osmotic stress tolerance (e.g., glycine-betaine, trehalose, and ectoine biosynthesis); motility, chemotaxis and attachment to plant tissues; root exudate metabolism including the modulation of plant phenolics (e.g., hydroxycinnamic acids), lignin, and flavonoids (e.g., quercetin); resistance against plant defenses (e.g., reactive oxygens species-ROS); plant hormone modulation (e.g., ethylene, auxins, cytokinins, and salicylic acid), and bacterial and fungal phytopathogen antagonistic traits (e.g., 2,4-diacetylphloroglucinol, HCN, a fragin-like non ribosomal peptide, bacteriocins, a lantipeptide, and quorum-quenching activities), bringing detailed insights into the action of this versatile plant-growth-promoting bacterium. Ultimately, the combination of both increased plant growth promotion/protection and biological control abilities makes P. thivervalensis SC5 a prime candidate for its development as a biofertilizer/biostimulant/biocontrol product. The genomic analysis of this bacterium brings new insights into the functioning of Pseudomonas and their role in beneficial plant-microbe interactions.

The Impact of Pine Wood Nematode Infection on the Host Fungal Community

Pine wilt disease (PWD), caused by pinewood nematode (PWN) Bursaphelenchus xylophilus, is globally one of the most destructive diseases of pine forests, especially in China. However, little is known about the effect of PWD on the host microbiome. In this study, the fungal community and functional structures in the needles, roots, and soil of and around Pinus thunbergii naturally infected by PWN were investigated by using high-throughput sequencing coupled with the functional prediction (FUNGuild). The results showed that fungal richness, diversity, and evenness in the needles of diseased trees were significantly lower than those of healthy ones (p < 0.05), whereas no differences were found in the roots and soil. Principal coordinate analysis (PCoA) showed that the fungal community and functional structures significantly differed only in the needles of diseased and healthy trees, but not in the soil and roots. Functionally, the saprotrophs had a higher abundance in the needles of diseased trees, whereas symbiotrophs abundance was higher in the needles of healthy trees (linear discriminant analysis (LDA) > 2.0, p < 0.05). These results indicated that PWN infection primarily affected the fungal community and functional structures in the needles of P. thunbergii, but not the roots and soil.

Microbial Diversity of Psychrotolerant Bacteria Isolated from Wild Flora of Andes Mountains and Patagonia of Chile towards the Selection of Plant Growth-Promoting Bacterial Consortia to Alleviate Cold Stress in Plants

Cold stress decreases the growth and productivity of agricultural crops. Psychrotolerant plant growth-promoting bacteria (PGPB) may protect and promote plant growth at low temperatures. The aims of this study were to isolate and characterize psychrotolerant PGPB from wild flora of Andes Mountains and Patagonia of Chile and to formulate PGPB consortia. Psychrotolerant strains were isolated from 11 wild plants (rhizosphere and phyllosphere) during winter of 2015. For the first time, bacteria associated with Calycera, Orites, and Chusquea plant genera were reported. More than 50% of the 130 isolates showed ≥33% bacterial cell survival at temperatures below zero. Seventy strains of Pseudomonas, Curtobacterium, Janthinobacterium, Stenotrophomonas, Serratia, Brevundimonas, Xanthomonas, Frondihabitans, Arthrobacter, Pseudarthrobacter, Paenarthrobacter, Brachybacterium, Clavibacter, Sporosarcina, Bacillus, Solibacillus, Flavobacterium, and Pedobacter genera were identified by 16S rRNA gene sequence analyses. Ten strains were selected based on psychrotolerance, auxin production, phosphate solubilization, presence of nifH (nitrogenase reductase) and acdS (1-aminocyclopropane-1-carboxylate (ACC) deaminase) genes, and anti-phytopathogenic activities. Two of the three bacterial consortia formulated promoted tomato plant growth under normal and cold stress conditions. The bacterial consortium composed of Pseudomonas sp. TmR5a & Curtobacterium sp. BmP22c that possesses ACC deaminase and ice recrystallization inhibition activities is a promising candidate for future cold stress studies.

Cd-tolerant SY-2 strain of Stenotrophomonas maltophilia: a potential PGPR, isolated from the Nanjing mining area in China

Microbial and plant assisted bioremediation is an emerging way for the remediation of soils polluted with heavy metals. To screen the cadmium tolerant bacteria, soil samples were collected from Nanjing mining area, China. The average cadmium content of the mine soil reached 45.71 mg/kg, which was indicating serious pollution and potential ecological risk. From the mine soil, six cadmium tolerant plant growth-promoting rhizobacteria (PGPR) were isolated. The isolated bacterial strain "SY-2" showed maximum cadmium tolerance and it was selected for further experimentation. This strain was identified as Stenotrophomonas maltophilia by 16S rRNA gene sequencing (GenBank accession number MG597057). SY-2 was found to tolerate maximum cadmium at 1.0 mM concentration. This strain also exhibited good adsorption capacity (up to 35.7%) of heavy metal at 0.5 mM concentration. The results of this study exhibited organic phosphorus solubilization (37.08 mg/L) and IAA biosynthesis (15.11 mg/L) ability of isolated S. maltophilia. Scanning electron microscopy (SEM) revealed cell shrinkage and the cell wall of S. maltophilia was very rough. Moreover, the energy dispersive X-ray (EDX) analysis endorsed the adsorption of Cd ions on the surface of biomass. FT-IR study described the presence of functional groups and the nature of chemical bonds, before and after cadmium stress. At 0.25 mM cadmium concentration, S. maltophilia treated seeds of Capsicum annuum L. developed 1.46 times longer roots than untreated seeds. The results of this study helped us to conclude that SY-2 strain of S. maltophilia possesses significant metal tolerance and bioremediation potential against cadmium. In the future, this strain can be used as a microbial remediation agent to detoxify heavy metals in contaminated soils.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (10.1007/s13205-020-02524-7s) contains supplementary material, which is available to authorized users.

Molecular variation among virulent and avirulent strains of the quarantine nematode Bursaphelenchus xylophilus

Bursaphelenchus xylophilus is an emerging pathogenic nematode that is responsible for a devastating epidemic of pine wilt disease worldwide, causing severe ecological damage and economic losses to forestry. Two forms of this nematode have been reported, i.e., with strong and weak virulence, commonly referred as virulent and avirulent strains. However, the pathogenicity-related genes of B. xylophilus are not sufficiently characterized. In this study, to find pathogenesis related genes we re-sequenced and compared genomes of two virulent and two avirulent populations. We identified genes affected by genomic variation, and functional annotation of those genes indicated that some of them might play potential roles in pathogenesis. The performed analysis showed that both avirulent populations differed from the virulent ones by 1576 genes with high impact variants. Demonstration of genetic differences between virulent and avirulent strains will provide effective methods to distinguish these two nematode virulence forms at the molecular level. The reported results provide basic information that can facilitate development of a better diagnosis for B. xylophilus isolates/strains which present different levels of virulence and better understanding of the molecular mechanism involved in the development of the PWD.

Transcriptome Analysis of Bursaphelenchus xylophilus Uncovers the Impact of Stenotrophomonas maltophilia on Nematode and Pine Wilt Disease

Stenotrophomonas maltophilia influences the reproduction, pathogenicity, and gene expression of aseptic Bursaphelenchus xylophilus after inoculation of aseptic Pinus massoniana. Pine wilt disease is a destructive pine forest disease caused by B. xylophilus, and its pathogenesis is unclear. The role of bacteria associated with B. xylophilus in pine wilt disease has attracted widespread attention. S. maltophilia is one of the most dominant bacteria in B. xylophilus, and its effect is ambiguous. This study aims to explore the role of S. maltophilia in pine wilt disease. The reproduction and virulence of aseptic B. xylophilus and B. xylophilus containing S. maltophilia were examined by inoculating aseptic P. massoniana seedlings. The gene expressions of two nematode treatments were identified by transcriptome sequencing. The reproduction and virulence of B. xylophilus containing S. maltophilia were stronger than that of aseptic nematodes. There were 4240 differentially expressed genes between aseptic B. xylophilus and B. xylophilus containing S. maltophilia after inoculation of aseptic P. massoniana, including 1147 upregulated genes and 2763 downregulated genes. These differentially expressed genes were significantly enriched in some immune-related gene ontology (GO) categories, such as membrane, transporter activity, metabolic processes, and many immune-related pathways, such as the wnt, rap1, PI3K-Akt, cAMP, cGMP-PKG, MAPK, ECM-receptor interaction, and calcium signaling pathways. The polyubiquitin-rich gene, leucine-rich repeat serine/threonine-protein kinase gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene, acetyl-CoA carboxylase gene, and heat shock protein genes were the key genes associated with immune resistance. Moreover, there were four cell wall hydrolase genes, thirty-six detoxification- and pathogenesis-related protein genes, one effector gene and ten cathepsin L-like cysteine proteinase genes that were differentially expressed. After inoculation of the host pine, S. maltophilia could affect the virulence and reproduction of B. xylophilus by regulating the expression of parasitic, immune, and pathogenicity genes of B. xylophilus.

Characterization of bacterial communities associated with the pinewood nematode insect vector Monochamus alternatus Hope and the host tree Pinus massoniana

Background

Monochamus alternatus Hope is one of the insect vectors of pinewood nematode (Bursaphelenchus xylophilus), which causes the destructive pine wilt disease. The microorganisms within the ecosystem, comprising plants, their environment, and insect vectors, form complex networks. This study presents a systematic analysis of the bacterial microbiota in the M. alternatus midgut and its habitat niche.

Methods

Total DNA was extracted from 20 types of samples (with three replicates each) from M. alternatus and various tissues of healthy and infected P. massoniana (pines). 16S rDNA amplicon sequencing was conducted to determine the composition and diversity of the bacterial microbiota in each sample. Moreover, the relative abundances of bacteria in the midgut of M. alternatus larvae were verified by counting the colony-forming units.

Results

Pinewood nematode infection increased the microbial diversity in pines. Bradyrhizobium, Burkholderia, Dyella, Mycobacterium, and Mucilaginibacter were the dominant bacterial genera in the soil and infected pines. These results indicate that the bacterial community in infected pines may be associated with the soil microbiota. Interestingly, the abundance of the genus Gryllotalpicola was highest in the bark of infected pines. The genus Cellulomonas was not found in the midgut of M. alternatus, but it peaked in the phloem of infected pines, followed by the phloem of heathy pines. Moreover, the genus Serratia was not only present in the habitat niche, but it was also enriched in the M. alternatus midgut. The colony-forming unit assays showed that the relative abundance of Serratia sp. peaked in the midgut of instar II larvae (81%).

Conclusions

Overall, the results indicate that the bacterial microbiota in the soil and in infected pines are correlated. The Gryllotalpicola sp. and Cellulomonas sp. are potential microbial markers of pine wilt disease. Additionally, Serratia sp. could be an ideal agent for expressing insecticidal protein in the insect midgut by genetic engineering, which represents a new use of microbes to control M. alternatus.

Plant growth-promoting activities and genomic analysis of the stress-resistant Bacillus megaterium STB1, a bacterium of agricultural and biotechnological interest

In this work, the stress-resistant Bacillus megaterium STB1 is characterized and its ability to promote plant growth under normal and stress conditions is demonstrated. The genomic sequence of this bacterium, and a detailed analysis of the genes involved in facilitating its stress resistance and plant growth-promoting activities is also reported. The B. megaterium STB1 genome is rich in genetic elements involved in multiple stress resistance, xenobiotic degradation, pathogen antagonistic activities, and other traits related to soil and rhizosphere colonization. Moreover, genes participating in the biosynthesis of auxins and cytokinins, the modulation of polyamines, GABA, brassinosteroids and ethylene levels were also found. Ultimately, this study brings new insights into the role of B. megaterium as a plant growth-promoting bacterium and opens new opportunities for the development of novel strategies for agriculture and biotechnology.

Bacterial Metabolites Produced Under Iron Limitation Kill Pinewood Nematode and Attract Caenorhabditis elegans

Pine Wilt Disease (PWD) is caused by Bursaphelenchus xylophilus, the pinewood nematode, and affects several species of pine trees worldwide. The ecosystem of the Pinus pinaster trees was investigated as a source of bacteria producing metabolites affecting this ecosystem: P. pinaster trees as target-plant, nematode as disease effector and its insect-vector as shuttle. For example, metals and metal-carrying compounds contribute to the complex tree-ecosystems. This work aimed to detect novel secondary metabolites like metallophores and related molecules produced under iron limitation by PWD-associated bacteria and to test their activity on nematodes. After screening 357 bacterial strains from Portugal and United States, two promising metallophore-producing strains Erwinia sp. A41C3 and Rouxiella sp. Arv20#4.1 were chosen and investigated in more detail. The genomes of these strains were sequenced, analyzed, and used to detect genetic potential for secondary metabolite production. A combinatorial approach of liquid chromatography-coupled tandem mass spectrometry (LC-MS) linked to molecular networking was used to describe these compounds. Two major metabolites were detected by HPLC analyses and described. One HPLC fraction of strain Arv20#4.1 showed to be a hydroxamate-type siderophore with higher affinity for chelation of Cu. The HPLC fraction of strain A41C3 with highest metal affinity showed to be a catecholate-type siderophore with higher affinity for chelation of Fe. LC-MS allowed the identification of several desferrioxamines from strain Arv20#4.1, in special desferrioxamine E, but no hit was obtained in case of strain A41C3 which might indicate that it is something new. Bacteria and their culture supernatants showed ability to attract C. elegans. HPLC fractions of those supernatant-extracts of Erwinia strain A41C3, enriched with secondary metabolites such as siderophores, were able to kill pinewood nematode. These results suggest that metabolites secreted under iron limitation have potential to biocontrol B. xylophilus and for management of Pine Wilt Disease.

Bacterial Communities and Virulence Associated with Pine Wood Nematode Bursaphelenchus xylophilus from Different Pinus spp

Bursaphelenchus xylophilus, the causal agent of pine wilt disease, is a destructive threat to pine forests. The role of bacteria associated with B. xylophilus in pine wilt disease has attracted widespread attention. This study investigated variation in bacterial communities and the virulence of surface-sterilized B. xylophilus from different Pinus spp. The predominant culturable bacteria of nematodes from different pines were Stenotrophomonas and Pseudomonas. Biolog EcoPlate analysis showed that metabolic diversity of bacteria in B. xylophilus from P. massoniana was the highest, followed by P. thunbergii and P. densiflora. High-throughput sequencing analysis indicated that bacterial diversity and community structure in nematodes from the different pine species varied, and the dominant bacteria were Stenotrophomonas and Elizabethkingia. The virulence determination of B. xylophilus showed that the nematodes from P. massoniana had the greatest virulence, followed by the nematodes from P. thunbergii and P. densiflora. After the nematodes were inoculated onto P. thunbergii, the relative abundance of the predominant bacteria changed greatly, and some new bacterial species emerged. Meanwhile, the virulence of all the nematode isolates increased after passage through P. thunbergii. These inferred that some bacteria associated with B. xylophilus isolated from different pine species might be helpful to adjust the PWN’s parasitic adaptability.

The role of bacteria in pine wilt disease: insights from microbiome analysis

Pine Wilt Disease (PWD) has a significant impact on Eurasia pine forests. The microbiome of the nematode (the primary cause of the disease), its insect vector, and the host tree may be relevant for the disease mechanism. The aim of this study was to characterize these microbiomes, from three PWD-affected areas in Portugal, using Denaturing Gradient Gel Electrophoresis, 16S rRNA gene pyrosequencing, and a functional inference-based approach (PICRUSt). The bacterial community structure of the nematode was significantly different from the infected trees but closely related to the insect vector, supporting the hypothesis that the nematode microbiome might be in part inherited from the insect. Sampling location influenced mostly the tree microbiome (P < 0.05). Genes related both with plant growth promotion and phytopathogenicity were predicted for the tree microbiome. Xenobiotic degradation functions were predicted in the nematode and insect microbiomes. Phytotoxin biosynthesis was also predicted for the nematode microbiome, supporting the theory of a direct contribution of the microbiome to tree-wilting. This is the first study that simultaneously characterized the nematode, tree and insect-vector microbiomes from the same affected areas, and overall the results support the hypothesis that the PWD microbiome plays an important role in the disease's development.

From plants to nematodes: Serratia grimesii BXF1 genome reveals an adaptation to the modulation of multi-species interactions

Serratia grimesii BXF1 is a bacterium with the ability to modulate the development of several eukaryotic hosts. Strain BXF1 was isolated from the pinewood nematode, Bursaphelenchus xylophilus, the causative agent of pine wilt disease affecting pine forests worldwide. This bacterium potentiates Bursaphelenchus xylophilus reproduction, acts as a beneficial pine endophyte, and possesses fungal and bacterial antagonistic activities, further indicating a complex role in a wide range of trophic relationships. In this work, we describe and analyse the genome sequence of strain BXF1, and discuss several important aspects of its ecological role. Genome analysis indicates the presence of several genes related to the observed production of antagonistic traits, plant growth regulation and the modulation of nematode development. Moreover, most of the BXF1 genes are involved in environmental and genetic information processing, which is consistent with its ability to sense and colonize several niches. The results obtained in this study provide the basis to a better understanding of the role and evolution of strain BXF1 as a mediator of interactions between organisms involved in a complex disease system. These results may also bring new insights into general Serratia and Enterobacteriaceae evolution towards multitrophic interactions.

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics

Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.

The Microbiome of Endophytic, Wood Colonizing Bacteria from Pine Trees as Affected by Pine Wilt Disease

Pine wilt disease (PWD) is a devastating forest disease present worldwide. In this study we analyzed the effects of the invasion of the pinewood nematode Bursaphelenchus xylophilus, the major pathogen causing PWD, on the endophytic microbiome of adult P. pinaster trees. Wood samples from trees with different degrees of PWD disease were collected at two sites (A and M) in Portugal. Endophytic bacteria were characterized based on directly extracted DNA by fingerprinting and barcoding using the 16S rRNA gene as marker. Furthermore, cultivation-based approaches were used to obtain isolates of the major taxa to study their ecophysiology. The endophytic microbiome from P. pinaster trees differed significantly between the two sampling sites. Main bacterial OTUs belonged to the Proteobacteria (39% (site M) - 97% (site A)), and Firmicutes (0.70% (site A) - 44% (site M)). However, consequences of the invasion with the pathogen were comparable. Interestingly diversity of wood endophytic bacteria increased with the severity of the diseases, with highest diversity levels observed in in the most affected trees. Our results suggest that in the first stages of the disease, the defence mechanisms of plants are repressed by the pathogen, resulting in a colonization of the wood interior by soil microorganisms.

Cu-resistant Kocuria sp. CRB15: a potential PGPR isolated from the dry tailing of Rakha copper mine

Rhizobacteria may enhance biomass production and heavy metal tolerance of plants under stress conditions. The present study was carried out for isolation of metal-resistant bacteria that can be further utilized for phytoremediation process. A potential metal-resistant strain CRB15 was isolated from rhizospheric region of Saccharum spontaneum that was found to be resistant against Cu (6.29 mM), Zn (3.25 mM), Pb (1.5 mM), Ni (1.25 mM), and Cd (0.25 mM). SEM analysis was performed for evaluation of morphological changes on bacterial isolate. FTIR analysis observed the change in wavenumbers after the addition of Cu. 16S rDNA sequence analysis showed that CRB15 isolate matched best with genus of Kocuria and was named as Kocuria sp. CRB15. The isolate Kocuria sp. CRB15 was a potential plant growth-promoting rhizobacterium as it had a high IAA (46 µg ml^-1), P solubilisation (39.37 µg ml^-1), ammonia production (30.46 µmol ml^-1), and hydrogen cyanide production capacity. Root-shoot elongation assay conducted on Brassica nigra under lab conditions with strain CRB15 demonstrated positive effects of strain CRB15 in root and shoot elongation of Cu-treated seedlings. This study proved the Kocuria sp. CRB15 a potential PGPR for bacterial-assisted phytoremediation.

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.

Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster

Pine wilt disease (PWD) results from the interaction of three elements: the pathogenic nematode, Bursaphelenchus xylophilus; the insect-vector, Monochamus sp.; and the host tree, mostly Pinus species. Bacteria isolated from B. xylophilus may be a fourth element in this complex disease. However, the precise role of bacteria in this interaction is unclear as both plant-beneficial and as plant-pathogenic bacteria may be associated with PWD. Using whole genome sequencing and phenotypic characterization, we were able to investigate in more detail the genetic repertoire of Serratia marcescens PWN146, a bacterium associated with B. xylophilus. We show clear evidence that S. marcescens PWN146 is able to withstand and colonize the plant environment, without having any deleterious effects towards a susceptible host (Pinus thunbergii), B. xylophilus nor to the nematode model C. elegans. This bacterium is able to tolerate growth in presence of xenobiotic/organic compounds, and use phenylacetic acid as carbon source. Furthermore, we present a detailed list of S. marcescens PWN146 potentials to interfere with plant metabolism via hormonal pathways and/or nutritional acquisition, and to be competitive against other bacteria and/or fungi in terms of resource acquisition or production of antimicrobial compounds. Further investigation is required to understand the role of bacteria in PWD. We have now reinforced the theory that B. xylophilus-associated bacteria may have a plant origin.

Effects of Endobacterium (Stenotrophomonas maltophilia) on Pathogenesis-Related Gene Expression of Pine Wood Nematode (Bursaphelenchus xylophilus) and Pine Wilt Disease

Pine wilt disease (PWD) caused by the pine wood nematode (PWN), Bursaphelenchus xylophilus, is responsible for devastating epidemics in pine trees in Asia and Europe. Recent studies showed that bacteria carried by the PWN might be involved in PWD. However, the molecular mechanism of the interaction between bacteria and the PWN remained unclear. Now that the whole genome of B. xylophilus (Bursaphelenchus xylophilus) is published, transcriptome analysis is a unique method to study the role played by bacteria in PWN. In this study, the transcriptome of aseptic B. xylophilus, B. xylophilus treated with endobacterium (Stenotrophomonas maltophilia NSPmBx03) and fungus B. xylophilus were sequenced. We found that 61 genes were up-regulated and 830 were down-regulated in B. xylophilus after treatment with the endobacterium; 178 genes were up-regulated and 1122 were down-regulated in fungus B. xylophilus compared with aseptic B. xylophilus. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to study the significantly changed biological functions and pathways for these differentially expressed genes. Many pathogenesis-related genes, including glutathinone S-transferase, pectate lyase, ATP-binding cassette transporter and cytochrome P450, were up-regulated after B. xylophilus were treated with the endobacterium. In addition, we found that bacteria enhanced the virulence of PWN. These findings indicate that endobacteria might play an important role in the development and virulence of PWN and will improve our understanding of the regulatory mechanisms involved in the interaction between bacteria and the PWN.

The genome and genetics of a high oxidative stress tolerant Serratia sp. LCN16 isolated from the plant parasitic nematode Bursaphelenchus xylophilus

BACKGROUND

Pine wilt disease (PWD) is a worldwide threat to pine forests, and is caused by the pine wood nematode (PWN) Bursaphelenchus xylophilus. Bacteria are known to be associated with PWN and may have an important role in PWD. Serratia sp. LCN16 is a PWN-associated bacterium, highly resistant to oxidative stress in vitro, and which beneficially contributes to the PWN survival under these conditions. Oxidative stress is generated as a part of the basal defense mechanism used by plants to combat pathogenic invasion. Here, we studied the biology of Serratia sp. LCN16 through genome analyses, and further investigated, using reverse genetics, the role of two genes directly involved in the neutralization of H2O2, namely the H2O2 transcriptional factor oxyR; and the H2O2-targeting enzyme, catalase katA.

RESULTS

Serratia sp. LCN16 is phylogenetically most closely related to the phytosphere group of Serratia, which includes S. proteamaculans, S. grimessi and S. liquefaciens. Likewise, Serratia sp. LCN16 shares many features with endophytes (plant-associated bacteria), such as genes coding for plant polymer degrading enzymes, iron uptake/transport, siderophore and phytohormone synthesis, aromatic compound degradation and detoxification enzymes. OxyR and KatA are directly involved in the high tolerance to H2O2 of Serratia sp. LCN16. Under oxidative stress, Serratia sp. LCN16 expresses katA independently of OxyR in contrast with katG which is under positive regulation of OxyR. Serratia sp. LCN16 mutants for oxyR (oxyR::int(614)) and katA (katA::int(808)) were sensitive to H2O2 in relation with wild-type, and both failed to protect the PWN from H2O2-stress exposure. Moreover, both mutants showed different phenotypes in terms of biofilm production and swimming/swarming behaviors.

CONCLUSIONS

This study provides new insights into the biology of PWN-associated bacteria Serratia sp. LCN16 and its extreme resistance to oxidative stress conditions, encouraging further research on the potential role of this bacterium in interaction with PWN in planta environment.

Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus

Monochamus beetles are the dispersing vectors of the nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease (PWD). PWD inflicts significant damages in Eurasian pine forests. Symbiotic microorganisms have a large influence in insect survival. The aim of this study was to characterize the bacterial community associated to PWD vectors in Europe and East Asia using a culture-independent approach. Twenty-three Monochamus galloprovincialis were collected in Portugal (two different locations); twelve Monochamus alternatus were collected in Japan. DNA was extracted from the insects’ tracheas for 16S rDNA analysis through denaturing gradient gel electrophoresis and barcoded pyrosequencing. Enterobacteriales, Pseudomonadales, Vibrionales and Oceanospirilales were present in all samples. Enterobacteriaceae was represented by 52.2% of the total number of reads. Twenty-three OTUs were present in all locations. Significant differences existed between the microbiomes of the two insect species while for M. galloprovincialis there were no significant differences between samples from different Portuguese locations. This study presents a detailed description of the bacterial community colonizing the Monochamus insects’ tracheas. Several of the identified bacterial groups were described previously in association with pine trees and B. xylophilus, and their previously described functions suggest that they may play a relevant role in PWD.

Identification and characterization of parasitism genes from the pinewood nematode Bursaphelenchus xylophilus reveals a multilayered detoxification strategy

The migratory endoparasitic nematode Bursaphelenchus xylophilus, which is the causal agent of pine wilt disease, has phytophagous and mycetophagous phases during its life cycle. This highly unusual feature distinguishes it from other plant-parasitic nematodes and requires profound changes in biology between modes. During the phytophagous stage, the nematode migrates within pine trees, feeding on the contents of parenchymal cells. Like other plant pathogens, B. xylophilus secretes effectors from pharyngeal gland cells into the host during infection. We provide the first description of changes in the morphology of these gland cells between juvenile and adult life stages. Using a comparative transcriptomics approach and an effector identification pipeline, we identify numerous novel parasitism genes which may be important for the mediation of interactions of B. xylophilus with its host. In-depth characterization of all parasitism genes using in situ hybridization reveals two major categories of detoxification proteins, those specifically expressed in either the pharyngeal gland cells or the digestive system. These data suggest that B. xylophilus incorporates effectors in a multilayer detoxification strategy in order to protect itself from host defence responses during phytophagy.

Diversity of endosymbiont bacteria associated with a non-filarial nematode group

There is a significant knowledge gap with regard to non-filarial nematodes and their relationships, if any, with intracellular bacteria, with only sporadic reports in the literature. An intracellular bacteriaXiphinematobacter, belonging to subdivision 2 of the Verrucomicrobia, was previously reported in the ovaries of three species of the non-filarialXiphinema americanum-group of nematodes. We explored the diversity ofXiphinematobacterin 22 populations ofX. americanumsourced from six continents and conservatively have identified nine phylotypes, six of which have not previously been reported. A geographic basis to the phylotypes was noted with phylotypes A and B only found in Europe, whereas phylotypes F, G, H and I were mainly found in North America. Phylotypes C, D and E showed greater geographical variation. Sequences ofXiphinematobacterfrom this study help to inform the taxonomy of Verrucomicrobia such that the status and composition of Verrucomicrobia subdivision 2 potentially requires reflection.

Community and functional diversity of bacteria associated with propagative and dispersal forms of Bursaphelenchus xylophilus

The pine wood nematode (PWN),Bursaphelenchus xylophilus, the pathogen of pine wilt disease, has propagative and dispersal forms in its life cycle, which is associated with the insect vectorMonochamus alternatus. Pine wood nematode-associated bacteria could play important roles in pine wilt disease. In this study, the diversity and population dynamics of bacteria in propagative and dispersal stages of PWN were analysed using cultural and Biolog Eco™ methods coupled with high-throughput sequencing. The results revealed that culturableStenotrophomonasin PWN from diseased pine was not found fromM. alternatus. Bacteria in dispersal PWN carried byM. alternatusshowed the highest total carbon utilisation. The high-throughput analysis showed thatStenotrophomonas,AchromobacterandSphingobacteriumwere more abundant in propagative PWN than in dispersal PWN, whereasCitrobacter,Vibrioand Enterobacteriaceae were more abundant in dispersal PWN. The results showed that bacteria of PWN in different developmental forms differed. This change of bacteria might help PWN to adapt to the changing environment.

Bacterial Diversity and Community Structure in the Pine Wood Nematode Bursaphelenchus xylophilus and B. mucronatus with Different Virulence by High-Throughput Sequencing of the 16S rDNA

Bursaphelenchus xylophilus is the pathogen of pine wilt disease. Bursaphelenchus mucronatus is similar to B. xylophilus in morphology. Both species share a common niche, but they are quite different in pathogenicity. Presently, the role of bacteria in pine wilt disease development has been widely speculated. The diversity of bacteria associated with B. xylophilus and B. mucronatus with different virulence remains unclear. In this study, virulence of four B. xylophilus and four B. mucronatus strains were evaluated by inoculating Pinus thunbergii. High-throughput sequencing targeted 16S rDNA of different virulence nematode strains was carried out. The associated bacterial community structures of the eight strains were analyzed. The results showed that 634,051 high-quality sequences were obtained from the eight nematode strains. The number of OTUs of bacteria associated with B. mucronatus was generally greater than those of B. xylophilus. The richness of the community of bacteria associated with high virulent B. xylophilus ZL1 and AmA3 was higher than moderately virulent B. xylophilus AA3, HE2, and all B. mucronatus strains. While the diversity of bacteria associated with B. mucronatus was higher than B. xylophilus. Stenotrophomonas, Pseudomonadaceae_Unclassified or Rhizobiaceae_Unclassified were predominant in the nematode strains with different virulence. Oxalobacteraceae and Achromobacter were found more abundant in the low virulent B. xylophilus and non-virulent B. mucronatus strains.

In vitro co-cultures of Pinus pinaster with Bursaphelenchus xylophilus: a biotechnological approach to study pine wilt disease

Co-cultures of Pinus pinaster with Bursaphelenchus xylophilus were established as a biotechnological tool to evaluate the effect of nematotoxics addition in a host/parasite culture system. The pinewood nematode (PWN), Bursaphelenchus xylophilus, the causal agent of pine wilt disease (PWD), was detected for the first time in Europe in 1999 spreading throughout the pine forests in Portugal and recently in Spain. Plant in vitro cultures may be a useful experimental system to investigate the plant/nematode relationships in loco, thus avoiding the difficulties of field assays. In this study, Pinus pinaster in vitro cultures were established and compared to in vivo 1 year-old plantlets by analyzing shoot structure and volatiles production. In vitro co-cultures were established with the PWN and the effect of the phytoparasite on in vitro shoot structure, water content and volatiles production was evaluated. In vitro shoots showed similar structure and volatiles production to in vivo maritime pine plantlets. The first macroscopic symptoms of PWD were observed about 4 weeks after in vitro co-culture establishment. Nematode population in the culture medium increased and PWNs were detected in gaps of the callus tissue and in cavities developed from the degradation of cambial cells. In terms of volatiles main components, plantlets, P. pinaster cultures, and P. pinaster with B. xylophilus co-cultures were all β- and α-pinene rich. Co-cultures may be an easy-to-handle biotechnological approach to study this pathology, envisioning the understanding of and finding ways to restrain this highly devastating nematode.

Associated bacteria of different life stages of Meloidogyne incognita using pyrosequencing-based analysis

The root knot nematode (RKN), Meloidogyne incognita, belongs to the most damaging plant pathogens worldwide, and is able to infect almost all cultivated plants, like tomato. Recent research supports the hypothesis that bacteria often associated with plant-parasitic nematodes, function as nematode parasites, symbionts, or commensal organisms etc. In this study, we explored the bacterial consortia associated with M. incognita at different developmental stages, including egg mass, adult female and second-stage juvenile using the pyrosequencing approach. The results showed that Proteobacteria, with a proportion of 71-84%, is the most abundant phylum associated with M. incognita in infected tomato roots, followed by Actinobacteria, Bacteroidetes, Firmicutes etc. Egg mass, female and second-stage juvenile of M. incognita harbored a core microbiome with minor difference in communities and diversities. Several bacteria genera identified in M. incognita are recognized cellulosic microorganisms, pathogenic bacteria, nitrogen-fixing bacteria and antagonists to M. incognita. Some genera previously identified in other plant-parasitic nematodes were also found in tomato RKNs. The potential biological control microorganisms, including the known bacterial pathogens and nematode antagonists, such as Actinomycetes and Pseudomonas, showed the largest diversity and proportion in egg mass, and dramatically decreased in second-stage juvenile and female of M. incognita. This is the first comprehensive report of bacterial flora associated with the RKN identified by pyrosequencing-based analysis. The results provide valuable information for understanding nematode-microbiota interactions and may be helpful in the development of novel nematode-control strategies.

Bacterial role in pine wilt disease development - review and future perspectives

Mutualistic and beneficial relationships between nematodes and bacteria are highly present in nature, mostly occurring because of nutritional dependence and pathogen protection, and intrinsically related with the environment, the ecological conditions and the nematode life stages. Thirty-four years have passed since the first hypothesis suggesting a bacterial role in pine wilt disease (PWD), associated with the pinewood nematode (PWN), Bursaphelenchus xylophilus. In 1980, researchers reported that bacteria associated with the PWN could produce toxins that lead to PWD development in pine seedlings. It was also suggested a double vector system for PWD, where bacteria were vectored by the PWN and the PWN vectored by an insect from the Monochamus genus. Presently, the specific involvement of bacteria in such complex disease is still controversial, even though the increased number of studies focused on the potential bacteria role has increased considerably. This review is an up-to-date comprehensive perspective and brings new insights on the role of PWN-associated bacteria in PWD.

The effect of endobacteria on the development and virulence of the pine wood nematode, Bursaphelenchus xylophilus

Pine wilt disease (PWD) caused by the pine wood nematode (PWN), Bursaphelenchus xylophilus, is a destructive forest disease. Recent studies showed that bacteria associated with PWN might play important roles in PWD. In this study, the effects of endobacteria isolated from PWN on the development and virulence of PWN were evaluated. The results revealed that endobacteria isolated from high virulence PWN could partially promote the development of the nematode, while endobacteria from PWN with low virulence could inhibit the development of nematode. Both bacteria-free and non-sterilised nematodes were able to infect microcuttings of Pinus densiflora. The endobacterial isolates, Stenotrophomonas maltophilia NSBx.14 and Achromobacter xylosoxidans ssp. xylosoxidans NSBx.22, enhanced the virulence of low virulence PWN but reduced the virulence of high virulence PWN. The results suggest the pathogenicity of PWN is not affected by loss of bacteria and endobacteria might play a role in the development and virulence of PWN.

Diversity of bacteria carried by pinewood nematode in USA and phylogenetic comparison with isolates from other countries

Pine wilt disease (PWD) is native to North America and has spread to Asia and Europe. Lately, mutualistic relationship has been suggested between the pinewood nematode (PWN), Bursaphelenchus xylophilus the causal nematode agent of PWD, and bacteria. In countries where PWN occurs, nematodes from diseased trees were reported to carry bacteria from several genera. However no data exists for the United States. The objective of this study was to evaluate the diversity of the bacterial community carried by B. xylophilus, isolated from different Pinus spp. with PWD in Nebraska, United States. The bacteria carried by PWN belonged to Gammaproteobacteria (79.9%), Betaproteobacteria (11.7%), Bacilli (5.0%), Alphaproteobacteria (1.7%) and Flavobacteriia (1.7%). Strains from the genera Chryseobacterium and Pigmentiphaga were found associated with the nematode for the first time. These results were compared to results from similar studies conducted from other countries of three continents in order to assess the diversity of bacteria with associated with PWN. The isolates from the United States, Portugal and China belonged to 25 different genera and only strains from the genus Pseudomonas were found in nematodes from all countries. The strains from China were closely related to P. fluorescens and the strains isolated from Portugal and USA were phylogenetically related to P. mohnii and P. lutea. Nematodes from the different countries are associated with bacteria of different species, not supporting a relationship between PWN with a particular bacterial species. Moreover, the diversity of the bacteria carried by the pinewood nematode seems to be related to the geographic area and the Pinus species. The roles these bacteria play within the pine trees or when associated with the nematodes, might be independent of the presence of the nematode in the tree and only related on the bacteria's relationship with the tree.

Pinewood nematode-associated bacteria contribute to oxidative stress resistance of Bursaphelenchus xylophilus

Background

Pine wilt disease (PWD) caused by the pinewood nematode Bursaphelenchus xylophilus is one of the most serious forest diseases in the world. The role of B. xylophilus-associated bacteria in PWD and their interaction with the nematode, have recently been under substantial investigation. Several studies report a potential contribution of the bacteria for the PWD development, either as a helper to enhance the pathogenicity of the nematode or as a pathogenic agent expressing interesting traits related to lifestyle host-adaptation.

Results

We investigated the nematode-bacteria interaction under a severe oxidative stress (OS) condition using a pro-oxidant hydrogen peroxide and explored the adhesion ability of these bacteria to the cuticle surface of the nematodes. Our results clearly demonstrated a beneficial effect of the Serratia spp. (isolates LCN-4, LCN-16 and PWN-146) to B. xylophilus under the OS condition. Serratia spp. was found to be extremely OS-resistant, and promote survival of B. xylophilus and down-regulate two B. xylophilus catalase genes (Bxy-ctl-1 and Bxy-ctl-2). In addition, we show that the virulent isolate (Ka4) of B. xylophilus survives better than the avirulent (C14-5) isolate under the OS condition. The bacterial effect was transverse for both B. xylophilus isolates. We could not observe a strong and specific adhesion of these bacteria on the B. xylophilus cuticle surface.

Conclusions

We report, for the first time, that B. xylophilus associated bacteria may assist the nematode opportunistically in the disease, and that a virulent B. xylophilus isolate displayed a higher tolerance towards the OS conditions than an avirulent isolate.

Nematicidal bacteria associated to pinewood nematode produce extracellular proteases

Bacteria associated with the nematode Bursaphelenchus xylophilus, a pathogen of trees and the causal agent of pine wilt disease (PWD) may play a role in the disease. In order to evaluate their role (positive or negative to the tree), strains isolated from the track of nematodes from infected Pinus pinaster trees were screened, in vitro, for their nematicidal potential. The bacterial products, from strains more active in killing nematodes, were screened in order to identify and characterize the nematicidal agent. Forty-seven strains were tested and, of these, 21 strains showed capacity to produce extracellular products with nematicidal activity. All Burkholderia strains were non-toxic. In contrast, all Serratia strains except one exhibited high toxicity. Nematodes incubated with Serratia strains showed, by SEM observation, deposits of bacteria on the nematode cuticle. The most nematicidal strain, Serratia sp. A88copa13, produced proteases in the supernatant. The use of selective inhibitors revealed that a serine protease with 70 kDa was majorly responsible for the toxicity of the supernatant. This extracellular serine protease is different phylogenetically, in size and biochemically from previously described proteases. Nematicidal assays revealed differences in nematicidal activity of the proteases to different species of Bursaphelenchus, suggesting its usefulness in a primary screen of the nematodes. This study offers the basis for further investigation of PWD and brings new insights on the role bacteria play in the defense of pine trees against B. xylophilus. Understanding all the factors involved is important in order to develop strategies to control B. xylophilus dispersion.

Characterization of bacterial communities associated with the pine sawyer beetle Monochamus galloprovincialis, the insect vector of the pinewood nematode Bursaphelenchus xylophilus

Pine wilt disease (PWD) has a tremendous impact on worldwide forestlands, both from the environmental and economical viewpoints. Monochamus sp., a xylophagous insect from the Cerambycidae family, plays an important role in dissemination of the pinewood nematode, Bursaphelenchus xylophilus, the primary pathogenic agent of PWD. This study investigates, for the first time, the bacterial communities of Monochamus galloprovincialis collected from Portuguese Pinus pinaster trees and B. xylophilus free, using a metagenomics approach. Overall, our results show that natural bacterial communities of M. galloprovincialis are mainly composed by γ-proteobacteria, Firmicutes and Bacteroidetes, which may be a reflection of insects' feeding diet and habitat characteristics. We also report different bacterial communities' composition in the thorax and abdomen of M. galloprovincialis, with high abundance of Serratia sp. in both. Our results encourage further studies in the possible relationship between bacteria from the insect vector and B. xylophilus.