Enterobacter asburiae and Pantoea ananatis Causing Rice Bacterial Blight in China

Current status of molecular rice breeding for durable and broad-spectrum resistance to major diseases and insect pests

In the past century, there have been great achievements in identifying resistance (R) genes and quantitative trait loci (QTLs) as well as revealing the corresponding molecular mechanisms for resistance in rice to major diseases and insect pests. The introgression of R genes to develop resistant rice cultivars has become the most effective and eco-friendly method to control pathogens/insects at present. However, little attention has been paid to durable and broad-spectrum resistance, which determines the real applicability of R genes. Here, we summarize all the R genes and QTLs conferring durable and broad-spectrum resistance in rice to fungal blast, bacterial leaf blight (BLB), and the brown planthopper (BPH) in molecular breeding. We discuss the molecular mechanisms and feasible methods of improving durable and broad-spectrum resistance to blast, BLB, and BPH. We will particularly focus on pyramiding multiple R genes or QTLs as the most useful method to improve durability and broaden the disease/insect spectrum in practical breeding regardless of its uncertainty. We believe that this review provides useful information for scientists and breeders in rice breeding for multiple stress resistance in the future.

Advancements in Green Nanoparticle Technology: Focusing on the Treatment of Clinical Phytopathogens

Opportunistic pathogenic microbial infections pose a significant danger to human health, which forces people to use riskier, more expensive, and less effective drugs compared to traditional treatments. These may be attributed to several factors, such as overusing antibiotics in medicine and lack of sanitization in hospital settings. In this context, researchers are looking for new options to combat this worrying condition and find a solution. Nanoparticles are currently being utilized in the pharmaceutical sector; however, there is a persistent worry regarding their potential danger to human health due to the usage of toxic chemicals, which makes the utilization of nanoparticles highly hazardous to eukaryotic cells. Multiple nanoparticle-based techniques are now being developed, offering essential understanding regarding the synthesis of components that play a crucial role in producing anti-microbial nanotherapeutic pharmaceuticals. In this regard, green nanoparticles are considered less hazardous than other forms, providing potential options for avoiding the extensive harm to the human microbiome that is prevalent with existing procedures. This review article aims to comprehensively assess the current state of knowledge on green nanoparticles related to antibiotic activity as well as their potential to assist antibiotics in treating opportunistic clinical phytopathogenic illnesses.

Enterobacter asburiae ST229: an emerging carbapenemases producer

Enterobacter asburiae, member of the Enterobacter cloacae complex (ECC) group, shows an increasing clinical relevance being responsible for infections like pneumonia, urinary tract infections and septicemia. The aim of the present study was the investigation of the genomic features of two XDR E. asburiae ST229 clinical strains co-carrying blaNDM-1 and blaVIM-1 determinants, collected in October 2021 and in June 2022, respectively. Two E. asburiae strains were collected from rectal swabs of as many patients admitted to the cardiopulmonary intensive care unit of Fondazione I.R.C.C.S. "Policlinico San Matteo" in Pavia, Italy. Based on the antibiotic susceptibility profile results, both isolates showed an XDR phenotype, retaining susceptibility only to fluoroquinolones. Both isolates shared identical resistome, virulome, plasmid content, and belonged to ST229, a rarely reported sequence type. They co-harbored blaNDM-1 and blaVIM-1 genes, that resulted located on transferable plasmids by conjugation and transformation. Moreover, both strains differed in 24 SNPs and showed genetic relatedness with E. asburiae ST709 and ST27. We described the first case of ST229 E. asburiae co-harboring blaNDM-1 and blaVIM-1 in Italy. This study points out the emergence of carbapenemases in low-risk pathogens, representing a novel challenge for public health, that should include such types of strains in dedicated surveillance programs. Antimicrobial susceptibility testing was carried out using Thermo Scientific™ Sensititre™ Gram Negative MIC Plates DKMGN. Both strains underwent whole-genome sequencing (WGS) using Illumina Miseq platform. Resistome, plasmidome, virulome, MLST, plasmid MLST and a SNPs-based phylogenetic tree were in silico determined.

Synthesis and Characterization of Mesoporous Silica Nanoparticles Loaded with P-Cymene against Rice Bacterial Blight

Mesoporous silica nanoparticles (MSNs) can be used as carrier materials for the controlled release of pesticides while reducing their negative environmental impact. In this study, we screened an active ingredient, p-cymene (PC), with an excellent inhibitory effect on rice bacterial blight. Subsequently, the PC was successfully loaded onto MSNs via physisorption (PC@MSNs). PC@MSNs, characterized by a regular spherical shape, smooth surface, and an MSN average size of 262.9 nm, achieved an 8.6% drug loading capacity. The release kinetics of the PC from the PC@MSNs demonstrated a sustained release (288 h) pattern influenced by drug diffusion. The efficacy of the PC@MSNs against Xanthomonas oryzae pv. Oryzae paralleled those of PC. Acute toxicity assays revealed that the PC@MSNs were less toxic to aquatic life (LC50 = 257.867 mg/L) and that the formulation showed no adverse effects on rice seedling growth. In summary, these results suggest that PC@MSNs can broaden PC's scope of application in managing rice diseases.

Molecular epidemiology and genomic characterization of a plasmid-mediated mcr-10 and blaNDM-1 co-harboring multidrug-resistant Enterobacter asburiae

Colistin is considered as one of the last-resort antimicrobial agents for treating multidrug-resistant bacterial infections. Multidrug-resistant E. asburiae has been increasingly isolated from clinical patients, which posed a great challenge for antibacterial treatment. This study aimed to report a mcr-10 and blaNDM-1 co-carrying E. asburiae clinical isolate 5549 conferred a high-level resistance against colistin. Antibiotic susceptibility testing was performed using the microdilution broth method. Transferability of mcr-10 and blaNDM-1-carrying plasmids were investigated by conjugation experiments. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to identify modifications in lipid A. Whole genome sequencing and phylogenetic analysis between strain 5549 and a total of 301 E. asburiae genomes retrieved from NCBI database were performed. The genetic characteristics of mcr-10 and blaNDM-1-bearing plasmids were also analyzed. Our study indicated that strain 5549 showed extensively antibiotic-resistant trait, including colistin and carbapenem resistance. The mcr-10 and blaNDM-1 were carried by IncFIB/IncFII type p5549_mcr-10 (159417 bp) and IncN type p5549_NDM-1 (63489 bp), respectively. Conjugation assays identified that only the blaNDM-1-carrying plasmid could be successfully transferred to E. coli J53. Interestingly, mcr-10 did not mediate colistin resistance when it was cloned into E. coli DH5α. Mass spectrometry analysis showed the lipid A palmitoylation of the C-lacyl-oxo-acyl chain to the chemical structure of lipid A at m/z 2063 in strain 5549. In summary, this study is the first to report a mcr-10 and blaNDM-1 co-occurrence E. asburiae recovered from China. Our investigation revealed the distribution of different clonal lineage of E. asburiae with epidemiology perspective and the underlying mechanisms of colistin resistance. Active surveillance is necessary to control the further dissemination of multidrug-resistant E. asburiae.

Bulk segregant analysis coupled with transcriptomics and metabolomics revealed key regulators of bacterial leaf blight resistance in rice

BACKGROUND

Bacterial leaf blight (BLB) is a highly destructive disease, causing significant yield losses in rice (Oryza sativa). Genetic variation is contemplated as the most effective measure for inducing resistance in plants. The mutant line T1247 derived from R3550 (BLB susceptible) was highly resistant to BLB. Therefore, by utilizing this valuable source, we employed bulk segregant analysis (BSA) and transcriptome profiling to identify the genetic basis of BLB resistance in T1247.

RESULTS

The differential subtraction method in BSA identified a quantitative trait locus (QTL) on chromosome 11 spanning a 27-27.45 Mb region with 33 genes and 4 differentially expressed genes (DEGs). Four DEGs (P < 0.01) with three putative candidate genes, OsR498G1120557200, OsR498G1120555700, and OsR498G1120563600,0.01 in the QTL region were identified with specific regulation as a response to BLB inoculation. Moreover, transcriptome profiling identified 37 resistance analogs genes displaying differential regulation.

CONCLUSIONS

Our study provides a substantial addition to the available information regarding QTLs associated with BLB, and further functional verification of identified candidate genes can broaden the scope of understanding the BLB resistance mechanism in rice.

Acinetobacter nematophilus sp. nov., Alcaligenes nematophilus sp. nov., Enterobacter nematophilus sp. nov., and Kaistia nematophila sp. nov., Isolated from Soil-Borne Nematodes and Proposal for the Elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the Species Level

Four bacterial strains, A-IN1T, A-TC2T, E-TC7T, and K-TC2T, isolated from soil-borne nematodes of the species Oscheius tipulae and Acrobeloides bodenheimeri, were found to represent new species of the genera Acinetobacter, Alcaligenes, Enterobacter, and Kaistia, respectively. In this study, we described these new species using a polyphasic taxonomic approach that included whole-genome and whole-proteome phylogenomic reconstructions, core genome sequence comparisons, and phenotypic characterization. Phylogenomic reconstructions using whole-genome and whole-proteome sequences show that A-IN1T is closely related to Acinetobacter guillouiae DSM 590T and to Acinetobacter bereziniae LMG 1003T. The dDDH values between A-IN1T and these latest strains are 25.1 and 39.6%, respectively, which are below the 70% divergence threshold for prokaryotic species delineation. A-TC2T is closely related to Alcaligenes faecalis subsp. faecalis DSM 30030T and to Alcaligenes faecalis subsp. phenolicus DSM 16503T. The dDDH values between A-TC2T and these latest strains are 47.0 and 66.3%, respectively. In addition, the dDDH values between Alcaligenes faecalis subsp. faecalis DSM 30030T, Alcaligenes faecalis subsp. phenolicus DSM 16503T, and Alcaligenes faecalis subsp. parafaecalis are always lower than 70%, demonstrating that the three strains represent species within the genus Alcaligenes rather than subspecies within Alcaligenes faecalis. E-TC7T is closely related to Enterobacter kobei DSM 13645T, Enterobacter chuandaensis 090028T, and to Enterobacter bugandensis STN0717-56T. The dDDH values between E-TC7T and these strains are 43.5, 42.9, and 63.7%, respectively. K-TC2T is closely related to Kaistia terrae DSM 21341T and to Kaistia defluvii JCM 18034T. The dDDH values between these strains are 29.2 and 30.7%, respectively. Several biochemical tests allow to differentiate the type strains of the newly described species from the type strains of their more closely related species. Based on the results of this polyphasic taxonomic approach, the following new species are proposed: Acinetobacter nematophilus sp. nov. with A-IN1T (=CCM 9231T =CCOS 2018T) as the type strain, Alcaligenes nematophilus sp. nov. with A-TC2T (=CCM 9230T =CCOS 2017T) as the type strain, Enterobacter nematophilus sp. nov. with E-TC7T (=CCM 9232T =CCOS 2020T) as the type strain, and Kaistia nematophila sp. nov. with K-TC2T (=CCM 9239T =CCOS 2022T) as the type strain. In addition, we propose the elevation of Alcaligenes faecalis subsp. faecalis, Alcaligenes faecalis subsp. parafaecalis, and Alcaligenes faecalis subsp. phenolicus to the species level. Therefore, we propose the creation of Alcaligenes parafaecalis sp. nov. with DSM 13975T as the type strain, and Alcaligenes phenolicus sp. nov. with DSM 16503T as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of bacteria associated with soil-borne nematodes.

Pest categorisation of Pantoea ananatis

The EFSA Plant Health Panel performed a pest categorisation of Pantoea ananatis, a Gram-negative bacterium belonging to the Erwiniaceae family. P. ananatis is a well-defined taxonomic unit; nonetheless, its pathogenic nature is not well defined and non-pathogenic populations are known to occupy several, very different environmental niches as saprophytes, or as plant growth promoting bacteria or biocontrol agents. It is also described as a clinical pathogen causing bacteraemia and sepsis or as a member of the gut microbiota of several insects. P. ananatis is the causal agent of different diseases affecting numerous crops: in particular, centre rot of onion, bacterial leaf blight and grain discoloration of rice, leaf spot disease of maize and eucalyptus blight/dieback. A few insect species have been described as vectors of P. ananatis, among them, Frankliniella fusca and Diabrotica virgifera virgifera. This bacterium is present in several countries in Europe, Africa, Asia, North and South America, and Oceania from tropical and subtropical regions to temperate areas worldwide. P. ananatis has been reported from the EU territory, both as pathogen on rice and maize and as an environmental, non-pathogenic bacterium in rice marshes and poplar rhizosoil. It is not included in EU Commission Implementing Regulation 2019/2072. The pathogen can be detected on its host plants using direct isolation, or PCR-based methods. The main pathway for the entry of the pathogen into the EU territory is host plants for planting, including seeds. In the EU, there is a large availability of host plants, with onion, maize, rice and strawberry being the most important ones. Therefore, disease outbreaks are possible almost at any latitude, except in the most northern regions. P. ananatis is not expected to have frequent or consistent impact on crop production and is not expected to have any environmental impact. Phytosanitary measures are available to mitigate the further introduction and spread of the pathogen into the EU on some hosts. The pest does not satisfy the criteria, which are within the remit for EFSA to evaluate whether the pest meets the definition of a Union quarantine pest. P. ananatis is probably widely distributed in different ecosystems in the EU. It may impact some specific hosts such as onions while on other hosts such as rice it has been reported as a seed microbiota without causing any impact and can even be beneficial to plant growth. Hence, the pathogenic nature of P. ananatis is not fully established.

Cloacaenodin, an Antimicrobial Lasso Peptide with Activity against Enterobacter

Using genome mining and heterologous expression, we report the discovery and production of a new antimicrobial lasso peptide from species related to the Enterobacter cloacae complex. Using NMR and mass spectrometric analysis, we show that this lasso peptide, named cloacaenodin, employs a threaded lasso fold which imparts proteolytic resistance that its unthreaded counterpart lacks. Cloacaenodin has selective, low micromolar, antimicrobial activity against species related to the E. cloacae complex, including species implicated in nosocomial infections and against clinical isolates of carbapenem-resistant Enterobacterales. We further used site-directed mutagenesis to probe the importance of specific residues to the peptide's biosynthesis, stability, and bioactivity.

Characterization of Pantoea ananatis from rice planthoppers reveals a clade of rice-associated P. ananatis undergoing genome reduction

Pantoea ananatis is a bacterium that is found in many agronomic crops and agricultural pests. Here, we isolated a P. ananatis strain (Lstr) from the rice planthopper Laodelphax striatellus, a notorious pest that feeds on rice plant sap and transmits rice viruses, in order to examine its genome and biology. P. ananatis Lstr is an insect symbiont that is pathogenic to the host insect and appears to mostly inhabit the gut. Its pathogenicity thus raises the possibility of using the Lstr strain as a biological agent. To this end, we analysed the genome of the Lstr strain and compared it with the genomes of other Pantoea species. Our analysis of these genomes shows that P. ananatis can be divided into two mono-phylogenetic clades (clades one and two). The Lstr strain belongs to clade two and is grouped with P. ananatis strains that were isolated from rice or rice-associated samples. A comparative genomic analysis shows that clade two differs from clade one in many genomic characteristics including genome structures, mobile elements, and categories of coding proteins. The genomes of clade two P. ananatis are significantly smaller, have much fewer coding sequences but more pseudogenes than those of clade one, suggesting that clade two species are at the early stage of genome reduction. On the other hand, P. ananatis has a type VI secretion system that is highly variable but cannot be separated by clades. These results clarify our understanding of P. ananatis' phylogenetic diversity and provide clues to the interactions between P. ananatis, host insect, and plant that may lead to advances in rice protection and pest control.

Beneficial Effect and Potential Risk of Pantoea on Rice Production

Bacteria from the genus Pantoea have been reported to be widely distributed in rice paddy environments with contradictory roles. Some strains promoted rice growth and protected rice from pathogen infection or abiotic stress, but other strain exhibited virulence to rice, even causing severe rice disease. In order to effectively utilize Pantoea in rice production, this paper analyzed the mechanisms underlying beneficial and harmful effects of Pantoea on rice growth. The beneficial effect of Pantoea on rice plants includes growth promotion, abiotic alleviation and disease inhibition. The growth promotion may be mainly attributed to nitrogen-fixation, phosphate solubilization, plant physiological change, the biosynthesis of siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylic acid deaminase and phytohormones, including cytokinin, indole-3-acetic acid (IAA), auxins, abscisic acid and gibberellic acid, while the disease inhibition may be mainly due to the induced resistance, nutrient and spatial competition, as well as the production of a variety of antibiotics. The pathogenic mechanism of Pantoea can be mainly attributed to bacterial motility, production of phytohormones such as IAA, quorum sensing-related signal molecules and a series of cell wall-degrading enzymes, while the pathogenicity-related genes of Pantoea include genes encoding plasmids, such as the pPATH plasmid, the hypersensitive response and pathogenicity system, as well as various types of secretion systems, such as T3SS and T6SS. In addition, the existing scientific problems in this field were discussed and future research prospects were proposed.

Exploiting the antibacterial mechanism of phenazine substances from Lysobacter antibioticus 13-6 against Xanthomonas oryzae pv. oryzicola

Bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most destructive diseases affecting rice production worldwide. In this study, we extracted and purified phenazine substances from the secondary metabolites of Lysobacter antibioticus 13-6. The bacteriostatic mechanism of phenazine substances against Xoc was investigated through physiological response and transcriptomic analysis. Results showed that phenazine substances affects the cell membrane permeability of Xoc, which causes cell swelling and deformation, blockage of flagellum synthesis, and imbalance of intracellular environment. The changes in intracellular environment affect the physiological and metabolic functions of Xoc, which reduces the formation of pathogenic factors and pathogenicity. Through transcriptomic analysis, we found that among differentially expressed genes, the expression of 595 genes was induced significantly (275 up-regulated and 320 down-regulated). In addition, we observed that phenazine substances affects three main functions of Xoc, i.e., transmembrane transporter activity, DNA-mediated transposition, and structural molecular activity. Phenazine substances also inhibits the potassium ion transport system that reduces Xoc resistance and induces the phosphate ion transport system to maintain the stability of the internal environment. Finally, we conclude that phenazine substances could retard cell growth and reduce the pathogenicity of Xoc by affecting cell structure and physiological metabolism. Altogether, our study highlights latest insights into the antibacterial mechanism of phenazine substances against Xoc and provides basic guidance to manage the incidence of bacterial leaf streak of rice.

Isolation and Genome Analysis of Pectobacterium colocasium sp. nov. and Pectobacterium aroidearum, Two New Pathogens of Taro

Bacterial soft rot is one of the most destructive diseases of taro (Colocasia esculenta) worldwide. In recent years, frequent outbreaks of soft rot disease have seriously affected taro production and became a major constraint to the development of taro planting in China. However, little is known about the causal agents of this disease, and the only reported pathogens are two Dickeya species and P. carotovorum. In this study, we report taro soft rot caused by two novel Pectobacterium strains, LJ1 and LJ2, isolated from taro corms in Ruyuan County, Shaoguan City, Guangdong Province, China. We showed that LJ1 and LJ2 fulfill Koch's postulates for taro soft rot. The two pathogens can infect taro both individually and simultaneously, and neither synergistic nor antagonistic interaction was observed between the two pathogens. Genome sequencing of the two strains indicated that LJ1 represents a novel species of the genus Pectobacterium, for which the name "Pectobacterium colocasium sp. nov." is proposed, while LJ2 belongs to Pectobacterium aroidearum. Pan-genome analysis revealed multiple pathogenicity-related differences between LJ1, LJ2, and other Pectobacterium species, including unique virulence factors, variation in the copy number and organization of Type III, IV, and VI secretion systems, and differential production of plant cell wall degrading enzymes. This study identifies two new soft rot Pectobacteriaceae (SRP) pathogens causing taro soft rot in China, reports a new case of co-infection of plant pathogens, and provides valuable resources for further investigation of the pathogenic mechanisms of SRP.

Complete Genomic Data of Pantoea ananatis Strain TZ39 Associated with New Bacterial Blight of Rice in China

Pantoea ananatis is a phytopathogen infecting many economically important crops, including rice worldwide. Here, we report the complete genome of P. ananatis strain TZ39 identified as causative agent of a new bacterial blight of rice that emerged in China in 2020. The assembled genome consists of one circular chromosome of 4,483,976 bp and two plasmids of 135,135 and 276,579 bp. This complete genome of the first Chinese pathogenic P. ananatis strain will provide new insights into the traits of pathogenicity on genomic level from China and worldwide.

Microbial Diversity Analysis and Genome Sequencing Identify Xanthomonas perforans as the Pathogen of Bacterial Leaf Canker of Water Spinach (Ipomoea aquatic)

Ipomoea aquatica is a leafy vegetable widely cultivated in tropical Asia, Africa, and Oceania. Bacterial leaf canker disease has been attacking the planting fields and seriously affecting the quality of I. aquatica in epidemic areas in China. This study examined the microbial composition of I. aquatica leaves with classical symptoms of spot disease. The results showed that Xanthomonas was overwhelmingly dominant in all four diseased leaf samples but rarely present in rhizospheric soil or irrigation water samples. In addition, Pantoea was also detected in two of the diseased leaf samples. Pathogen isolation, identification, and inoculation revealed that both Xanthomonas sp. TC2-1 and P. ananatis were pathogenic to the leaves of I. aquatic, causing crater-shaped ulcerative spots and yellowing with big brown rot lesions on leaves, respectively. We further sequenced the whole genome of strain TC2-1 and showed that it is a member of X. perforans. Overall, this study identified X. perforans as the causal pathogen of I. aquatica bacterial leaf canker, and P. ananatis as a companion pathogen causing yellowing and brown rot on leaves. The correct identification of the pathogens will provide important basis for future efforts to formulate targeted application strategy for bacterial disease control.