Transcriptomic Insights into Abies koreana Drought Tolerance Conferred by Aureobasidium pullulans AK10.

The conservation of the endangered Korean fir, Abies koreana, is of critical ecological importance. In our previous study, a yeast-like fungus identified as Aureobasidium pullulans AK10, was isolated and shown to enhance drought tolerance in A. koreana seedlings. In this study, the effectiveness of Au. pullulans AK10 treatment in enhancing drought tolerance in A. koreana was confirmed. Furthermore, using transcriptome analysis, we compared A. koreana seedlings treated with Au. pullulans AK10 to untreated controls under drought conditions to elucidate the molecular responses involved in increased drought tolerance. Our findings revealed a predominance of downregulated genes in the treated seedlings, suggesting a strategic reallocation of resources to enhance stress defense. Further exploration of enriched Kyoto Encyclopedia of Genes and Genomes pathways and protein-protein interaction networks revealed significant alterations in functional systems known to fortify drought tolerance, including the terpenoid backbone biosynthesis, calcium signaling pathway, pyruvate metabolism, brassinosteroid biosynthesis, and, crucially, flavonoid biosynthesis, renowned for enhancing plant drought resistance. These findings deepen our comprehension of how AK10 biostimulation enhances the resilience of A. koreana to drought stress, marking a substantial advancement in the effort to conserve this endangered tree species through environmentally sustainable treatment.

Sulfur metabolism-mediated fungal glutathione biosynthesis is essential for oxidative stress resistance and pathogenicity in the plant pathogenic fungus Fusarium graminearum.

IMPORTANCE: Fusarium graminearum is a destructive fungal pathogen that causes Fusarium head blight (FHB) on a wide range of cereal crops. To control fungal diseases, it is essential to comprehend the pathogenic mechanisms that enable fungi to overcome host defenses during infection. Pathogens require an oxidative stress response to overcome host-derived oxidative stress. Here, we identify the underlying mechanisms of the Fgbzip007-mediated oxidative stress response in F. graminearum. ChIP-seq and subsequent genetic analyses revealed that the role of glutathione in pathogenesis is not dependent on antioxidant functions in F. graminearum. Altogether, this study establishes a comprehensive framework for the Fgbzip007 regulon on pathogenicity and oxidative stress responses, offering a new perspective on the role of glutathione in pathogenicity.

Understanding Burkholderia glumae BGR1 Virulence through the Application of Toxoflavin-Degrading Enzyme, TxeA.

Rice (Oryzae sativa cv. dongjin) is a cornerstone of global food security; however, Burkholderia glumae BGR1, which is responsible for bacterial panicle blight (BPB), threatens its productive output, with dire consequences for rice and other crops. BPB is primarily caused by toxoflavin, a potent phytotoxin that disrupts plant growth at various developmental stages. Therefore, understanding the mechanisms through which toxoflavin and BPB affect rice plants is critical. Toxoflavin biosynthesis in B. glumae BGR1 relies on the toxABCDE operon, with ToxA playing a central role. In response to this threat, our study explores a metagenome-derived toxoflavin-degrading enzyme, TxeA, as a potential defense mechanism against toxoflavin's destructive impact. TxeA-induced degradation of toxoflavin represents a potential strategy to mitigate crop damage. We introduce a groundbreaking approach: engineering transgenic rice plants to produce toxoflavin-degrading enzymes. These genetically modified plants, armed with TxeA, hold significant potential for combating toxoflavin-related crop losses. However, removal of toxoflavin, a major virulence factor in B. glumae BGR1, does not completely inhibit virulence. This innovative perspective offers a new shift from pathogen eradication to leveraging transgenic plants' power, offering a beacon of hope for crop protection and disease management. Our study offers insights into the intricate interplay between toxoflavin, BPB, and TxeA, providing a promising avenue to safeguard rice crops, ensure food security, and potentially enhance the resilience of various agricultural crops to B. glumae BGR1-induced diseases.

Aureobasidium pullulans Treatment Mitigates Drought Stress in Abies koreana via Rhizosphere Microbiome Modulation.

The Korean fir tree Abies koreana, an endangered species in Korea, faces threats primarily from climate change-induced stress and drought. This study proposed a sustainable method to enhance A. koreana drought tolerance using a black yeast-like fungus identified as Aureobasidium pullulans (AK10). The 16S/ITS metabarcoding analysis assessed the impact of drought and AK10 treatment on the seedlings' rhizosphere microbiome. Results revealed a profound drought influence on the microbiome, particularly affecting fungal mycobiota. Drought-stressed seedlings exhibited elevated Agaricaceae levels, opportunistic fungi generally associated with decomposition. AK10 treatment significantly mitigated this proliferation and increased the relative abundance of beneficial fungi like Cystofilobasidium and Mortierella, known biocontrol agents and phosphate solubilizers. A notable reduction in the phytopathogenic Fusarium levels was observed with AK10, alongside an increase in beneficial bacteria, including Azospirillum and Nitrospirillum. Furthermore, the conducted correlation analysis shed light on microbial interrelationships within the rhizosphere, elucidating potential co-associations and antagonisms. Taken together, the isolated A. pullulans AK10 identified in this study serves as a potential biostimulant, enhancing the drought tolerance in A. koreana through beneficial alterations in the rhizosphere microbiome. This approach presents a promising strategy for the conservation of this endangered species.

Improved and simplified method for aseptic isolation of nematodes and nematode-endosymbiotic bacteria from pine seedlings.

Pine wilt disease (PWD), caused by the pinewood nematode (PWN), Bursaphelenchus xylophilus, significantly impacts pine species and poses a broader ecological concern. An understanding of these nematode-associated microbes is essential for formulating sustainable PWD management strategies. We introduce a streamlined method for the aseptic extraction of B. xylophilus from pine seedlings, evolving beyond traditional Baermann funnel approaches. The method ensures optimal nematode extraction under sterile parameters, with seedling cutting discs processed using a unique sterile syringe assembly setup. The efficiency and simplicity of this method promise to significantly reduce the time and resources required. It also incorporates endosymbiotic bacterial isolation from isolated nematodes. The robustness of this method is affirmed by the successful isolation and identification of nematodes and bacterial strains as endosymbionts. Collectively, this protocol paves the way for more effective studies of nematodes and associated microbes, promoting the understanding of PWD and offering practical implications for better PWD management.•A simplified, aseptic method for extracting B. xylophilus from pine seedlings, offering a modern alternative to traditional Baermann funnel method.•Utilization of a specialized sterile syringe assembly setup, ensuring controlled and optimal nematode isolation.•Method validation achieved through the successful isolation and identification of bacterial strains as nematode endosymbionts.

Taxonomy-guided selection of Paraburkholderia busanensis sp. nov.: a versatile biocontrol agent with mycophagy against Colletotrichum scovillei causing pepper anthracnose.

IMPORTANCE: Traditional control methods for postharvest diseases rely on fungicides, which cause human health and environmental concerns. This study introduces a taxonomy-guided strategy for selecting biocontrol agents. By focusing on Paraburkholderia group, which harbors diverse plant-beneficial strains, the inadvertent selection of harmful strains was circumvented, thereby obviating the need for laborious in vitro screening assays. A highly promising candidate, strain P39, has been identified, exhibiting remarkable biocontrol activity against Colletotrichum scovillei. Through comprehensive genomic, physiological, and biochemical analyses, P39 was characterized as a novel species within the Paraburkholderia genus and designated Paraburkholderia busanensis. Moreover, these findings deepen our understanding of bacterial-fungal interactions, as they elucidate a potential pathway for the utilization of fungal chitin, thereby enhancing our understanding of bacterial mycophagy. P. busanensis is a promising source of antifungal volatiles and putative novel secondary metabolites.

Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities.

Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.

A combined transcriptomic and physiological approach to understanding the adaptive mechanisms to cope with oxidative stress in Fusarium graminearum.

In plant-pathogen interactions, oxidative bursts are crucial for plants to defend themselves against pathogen infections. Rapid production and accumulation of reactive oxygen species kill pathogens directly and cause local cell death, preventing pathogens from spreading to adjacent cells. Meanwhile, the pathogens have developed several mechanisms to tolerate oxidative stress and successfully colonize plant tissues. In this study, we investigated the mechanisms responsible for resistance to oxidative stress by analyzing the transcriptomes of six oxidative stress-sensitive strains of the plant pathogenic fungus Fusarium graminearum. Weighted gene co-expression network analysis identified several pathways related to oxidative stress responses, including the DNA repair system, autophagy, and ubiquitin-mediated proteolysis. We also identified hub genes with high intramodular connectivity in key modules and generated deletion or conditional suppression mutants. Phenotypic characterization of those mutants showed that the deletion of FgHGG4, FgHGG10, and FgHGG13 caused sensitivity to oxidative stress, and further investigation on those genes revealed that transcriptional elongation and DNA damage responses play roles in oxidative stress response and pathogenicity. The suppression of FgHGL7 also led to hypersensitivity to oxidative stress, and we demonstrated that FgHGL7 plays a crucial role in heme biosynthesis and is essential for peroxidase activity. This study increases the understanding of the adaptive mechanisms to cope with oxidative stress in plant pathogenic fungi. IMPORTANCE Fungal pathogens have evolved various mechanisms to overcome host-derived stresses for successful infection. Oxidative stress is a representative defense system induced by the host plant, and fungi have complex response systems to cope with it. Fusarium graminearum is one of the devastating plant pathogenic fungi, and understanding its pathosystem is crucial for disease control. In this study, we investigated adaptive mechanisms for coping with oxidative stress at the transcriptome level using oxidative stress-sensitive strains. In addition, by introducing genetic modification technique such as CRISPR-Cas9 and the conditional gene expression system, we identified pathways/genes required for resistance to oxidative stress and also for virulence. Overall, this study advances the understanding of the oxidative stress response and related mechanisms in plant pathogenic fungi.

Transcriptomic analysis of neutrophil apoptosis induced by diffuse large B-cell lymphoma unveils a potential role in neutropenia.

BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoma that arises from malignant transformation of B lymphocytes. Outcome of patients with DLBCL has been significantly improved by rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) therapy, which is regarded "gold standard" of DLBCL therapy. It is unfortunate that febrile neutropenia, a decrease of the neutrophil count in the blood accompanying fever, is one of the most common complications that DLBCL patients receiving R-CHOP regimen experience. Given the critical role of neutrophils against bacterial and fungal infections, neutropenia could be deadly. While the association between R-CHOP therapy and neutropenia has been well-established, the negative effect of DLBCL cells on the survival of neutrophils has not been clearly understood. Our previous study have shown that conditioned medium (CM) derived from Ly1 DLBCL cells induces apoptosis in murine neutrophils ex vivo. Additionally, Ly1 CM and doxorubicin synergize to further enhance apoptotic rate in neutrophils, possibly contributing to neutropenia in DLBCL patients. OBJECTIVE: We investigated the mechanism and genes that regulate neutrophil apoptosis induced by secretome of DLBCL cells, which would give insight into the potential role of DLBCL in neutropenia. METHOD: Murine neutrophils were isolated from bone marrow in C57BL6/J mice using flow cytometry. QuantSeq 3' mRNA-sequencing was conducted on neutrophils following exposure to CM derived from Ly1 DLBCL cells or murine bone marrow cells (control). Quantseq 3'mRNA sequencing data were aligned to identify differentially expressed mRNAs. Next, the expression of genes related to neutrophil apoptosis and proliferation were analyzed and Gene classification and ontology were analyzed. RESULT: We identified 1196 (198 upregulated and 998 downregulated) differentially expressed genes (DEGs) in Ly1 DLBCL co-culture group compared to the control group. The functional enrichment analyses of DEGs in co-culture group revealed significant enriched in apoptosis process, and immune system process in gene ontology and the highly enriched pathway of various bacterial infection, leukocyte transendothelial migration, apoptosis, and cell cycle in KEGG pathway. Importantly, Bcl7b, Bnip3, Bmx, Mcl1, and Pim1 were identified as critical regulators of neutrophil apoptosis, which may be potential drug targets for the treatment of neutropenia. We are currently testing the efficacy of the activators/inhibitors of the proteins encoded by these genes to investigate whether they would block DLBCL-induced neutrophil apoptosis. CONCLUSION: In the present study, bioinformatic analyses of gene expression profiling data revealed the crucial genes involved in neutrophil apoptosis and gave insight into the underlying mechanism. Given our data, it may be likely that novel opportunities for the treatment of neutropenia, and eventually improvement of prognosis of DLBCL patients, might emerge.

Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential.

The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.

Genome-guided comparative in planta transcriptome analyses for identifying cross-species common virulence factors in bacterial phytopathogens.

Plant bacterial disease is a complex outcome achieved through a combination of virulence factors that are activated during infection. However, the common virulence factors across diverse plant pathogens are largely uncharacterized. Here, we established a pan-genome shared across the following plant pathogens: Burkholderia glumae, Ralstonia solanacearum, and Xanthomonas oryzae pv. oryzae. By overlaying in planta transcriptomes onto the pan-genome, we investigated the expression profiles of common genes during infection. We found over 70% of identical patterns for genes commonly expressed by the pathogens in different plant hosts or infection sites. Co-expression patterns revealed the activation of a signal transduction cascade to recognize and respond to external changes within hosts. Using mutagenesis, we uncovered a relationship between bacterial virulence and functions highly conserved and shared in the studied genomes of the bacterial phytopathogens, including flagellar biosynthesis protein, C4-dicarboxylate ABC transporter, 2-methylisocitrate lyase, and protocatechuate 3,4-dioxygenase (PCD). In particular, the disruption of PCD gene led to attenuated virulence in all pathogens and significantly affected phytotoxin production in B. glumae. This PCD gene was ubiquitously distributed in most plant pathogens with high homology. In conclusion, our results provide cross-species in planta models for identifying common virulence factors, which can be useful for the protection of crops against diverse pathogens.

Versatile Roles of Microbes and Small RNAs in Rice and Planthopper Interactions.

Planthopper infestation in rice causes direct and indirect damage through feeding and viral transmission. Host microbes and small RNAs (sRNAs) play essential roles in regulating biological processes, such as metabolism, development, immunity, and stress responses in eukaryotic organisms, including plants and insects. Recently, advanced metagenomic approaches have facilitated investigations on microbial diversity and its function in insects and plants, highlighting the significance of microbiota in sustaining host life and regulating their interactions with the environment. Recent research has also suggested significant roles for sRNA-regulated genes during rice-planthopper interactions. The response and behavior of the rice plant to planthopper feeding are determined by changes in the host transcriptome, which might be regulated by sRNAs. In addition, the roles of microbial symbionts and sRNAs in the host response to viral infection are complex and involve defense-related changes in the host transcriptomic profile. This review reviews the structure and potential functions of microbes and sRNAs in rice and the associated planthopper species. In addition, the involvement of the microbiota and sRNAs in the rice-planthopper-virus interactions during planthopper infestation and viral infection are discussed.

Intron turnover is essential to the development and pathogenicity of the plant pathogenic fungus Fusarium graminearum.

Intron lariats excised during the splicing process are rapidly degraded by RNA lariat debranching enzyme (Dbr1) and several exonucleases. Rapid turnover of lariat RNA is essential to cellular RNA homeostasis. However, the functions of Dbr1 have not been investigated in filamentous fungi. Here, we characterized the molecular functions of Dbr1 in Fusarium graminearum, a major fungal plant pathogen. Deletion of FgDBR1 resulted in pleiotropic defects in hyphal growth, conidiation, sexual reproduction, and virulence. Through transcriptome analysis, we revealed that the deletion mutant exhibited global accumulation of intron lariats and upregulation of ribosome-related genes. Excessive accumulation of lariat RNA led to reduced overall protein synthesis, causing various phenotypic defects in the absence of FgDBR1. The results of this study demonstrate that a compromised intron turnover process affects development and pathogenesis in this fungus and that Dbr1 function is critical to plant pathogenic fungi.

Comparative Analyses of Four Complete Genomes in Pseudomonas amygdali Revealed Differential Adaptation to Hostile Environments and Secretion Systems.

Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.

Dysbiosis in the Rhizosphere Microbiome of Standing Dead Korean Fir (Abies koreana).

The Korean fir (Abies koreana), a native coniferous tree species mainly found on Mt. Halla in Jeju, South Korea, is suffering from continuous population decline and has been declared an endangered species. Research efforts have focused on the possible abiotic causes behind this worrying decline. However, the potential link between tree vitality and the rhizosphere microbiome remains unclear. In this study, a comparative metagenomic 16S rRNA sequence analysis was used to investigate the composition of the rhizosphere microbiota of samples collected from healthy and die-back-affected trees on Mt. Halla. The results indicated a significant reduction in the richness and diversity of microbiota in the rhizosphere of die-back-affected trees. Moreover, the relative abundance of Proteobacteria, Actinobacteria, and Bacteroidetes were significantly higher in healthy trees than in standing dead trees. Many bacterial genera were significantly more abundant in the rhizosphere of healthy trees, including those known for promoting plant growth and tolerance to biotic and abiotic stresses (e.g., Bradyrhizobium, Rhizomicrobium, Caulobacter, Nitrosospira, Rhizobacter, Paraburkholderia, Rhizobium, Devosia, Caballeronia, Niveispirillum, Dyella, Herbaspirillum, Frankia, Streptomyces, Actinoallomurus, Lysobacter, Luteibacter, Mucilaginibacter, and Variovorax). To our knowledge, this is the first report on rhizosphere bacterial microbiome dysbiosis in die-back-affected Korean fir trees, suggesting that the influence of rhizosphere microbiota should be considered to save this endangered species by investigating possible intervention strategies in future work.

Formyl peptide receptor 2 determines sex-specific differences in the progression of nonalcoholic fatty liver disease and steatohepatitis.

Nonalcoholic fatty liver disease (NAFLD) is an important health concern worldwide and progresses into nonalcoholic steatohepatitis (NASH). Although prevalence and severity of NAFLD/NASH are higher in men than premenopausal women, it remains unclear how sex affects NAFLD/NASH pathophysiology. Formyl peptide receptor 2 (FPR2) modulates inflammatory responses in several organs; however, its role in the liver is unknown. Here we show that FPR2 mediates sex-specific responses to diet-induced NAFLD/NASH. NASH-like liver injury was induced in both sexes during choline-deficient, L-amino acid-defined, high-fat diet (CDAHFD) feeding, but compared with females, male mice had more severe hepatic damage. Fpr2 was more highly expressed in hepatocytes and healthy livers from females than males, and FPR2 deletion exacerbated liver damage in CDAHFD-fed female mice. Estradiol induced Fpr2 expression, which protected hepatocytes and the liver from damage. In conclusion, our results demonstrate that FPR2 mediates sex-specific responses to diet-induced NAFLD/NASH, suggesting a novel therapeutic target for NAFLD/NASH.

Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota.

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

Complete Genome Sequence Data of Four Burkholderia glumae Strains Isolated from Rice Fields in the United States.

Bacterial panicle blight caused by Burkholderia glumae is a major disease in rice production worldwide. Currently, only a few whole-genome sequences of B. glumae strains isolated in the United States are available. Here, we report the complete genome sequence of four B. glumae strains, including three virulent strains (336gr-1, 411gr-6, and 957856-41-c) and the nonpathogenic strain B. glumae 257sh-1, which were isolated from rice fields in Louisiana (336gr-1, 957856-41-c, and 257sh-1) and Arkansas (411gr-6). The whole-genome sequence data of B. glumae strains will contribute to investigations of the molecular mechanism underlying bacterial pathogenicity and virulence to rice plants.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli.

Burkholderia gladioli has high versatility and adaptability to various ecological niches. Here, we constructed a pan-genome using 14 genome sequences of B. gladioli, which originate from different niches, including gladiolus, rice, humans, and nature. Functional roles of core and niche-associated genomes were investigated by pathway enrichment analyses. Consequently, we inferred the uniquely important role of niche-associated genomes in (1) selenium availability during competition with gladiolus host; (2) aromatic compound degradation in seed-borne and crude oil-accumulated environments, and (3) stress-induced DNA repair system/recombination in the cystic fibrosis-niche. We also identified the conservation of the rhizomide biosynthetic gene cluster in all the B. gladioli strains and the concentrated distribution of this cluster in human isolates. It was confirmed the absence of complete CRISPR/Cas system in both plant and human pathogenic B. gladioli and the presence of the system in B. gladioli living in nature, possibly reflecting the inverse relationship between CRISPR/Cas system and virulence.

Response of Pine Rhizosphere Microbiota to Foliar Treatment with Resistance-Inducing Bacteria against Pine Wilt Disease.

In this study, two bacterial strains, IRP7 and IRP8, were selected to induce resistance against pine wilt disease (PWD). Foliar application with these strains to nematode-inoculated pine seedlings significantly reduced PWD severity. The effect of nematode inoculation and bacterial treatment on the rhizosphere bacterial community was investigated. The results indicated that the rhizosphere of nematode-inoculated seedlings contained a lower relative abundance of beneficial microbes such as Paraburkholderia, Bradyrhizobium, Rhizobacter, Lysobacter, and Caballeronia. Bacterial treatment resulted in significant changes in the microbes that were represented in relatively low relative abundance. Treatment with IRP7 resulted in an increase in the relative abundance of Nitrospirillum, Bacillus, and Luteibacter, which might be useful for protection against infection. Treatment with IRP8 resulted in an increase in the relative abundance of obligate bacterial predators of the Bdellovibrio genus that were previously shown to control several bacterial phytopathogens and may have a role in the management of nematode-carried bacteria. The selected bacteria were identified as Pseudomonas koreensis IRP7 and Lysobacter enzymogenes IRP8 and are suggested as a potential treatment for induced resistance against PWD. To our knowledge, this is the first report on the effect of foliar treatment with resistance-inducing bacteria on the rhizosphere microbiota.