Genus Erwinia Research Articles

Growth promotion and modulation of the soybean microbiome INTACTA RR PRO with the application of the fungi Trichoderma harzianum and Purpureocillum lilacinum

Soybean is an economically important crop for animal and human nutrition. Currently, there is a lack of information on the effects of Trichoderma harzianum and Purpureocillum lilacinum on INTACTA RR PRO transgenic soybean plants. The present study evaluated the application of T. harzianum and P. lilacinum under field conditions. The results revealed a significant increase in soybean yield at 423 kg ha−1 in response to the application of P. lilacinum compared with the control treatment. In addition, the application of P. lilacinum promoted a significant increase in phosphorus levels in the plant leaves, and there were significant correlations between the increase in taxon abundance for the genus Erwinia and productivity and the average phosphorus and nitrogen content for the plant leaves, for the taxon Bacillus and nitrogen content and productivity, and for the taxon Sphingomonas and nitrogen content. The Bradyrhizobium taxon was identified in the P. lilacinum treatment as a taxon linking two different networks of taxa and is an important taxon in the microbiota. The results show that the application of the fungus P. lilacinum can increase the productivity of soybean INTACTA RR PRO and that this increase in productivity may be a function of the modulation of the microbiota composition of the plant leaves by the P. lilacinum effect.

Diet and the Gut Microbiome as Determinants Modulating Metabolic Outcomes in Young Obese Adults.

Obesity, along with metabolic disorders such as dyslipidemia and insulin resistance, increases the risk of cardiovascular disease, diabetes, various cancers, and other non-communicable diseases, thereby contributing to higher mortality rates. The intestinal microbiome plays a crucial role in maintaining homeostasis and influencing human metabolism. This study enrolled 82 young obese individuals, who were stratified into groups with or without metabolic disturbances. No significant differences in the alpha or beta diversity of the microbiota were observed among the groups. Insulin resistance was characterized by an increase in the number of Adlercreutzia and Dialister as well as a decrease in Collinsella, Coprococcus and Clostridiales. The dyslipidemia and dyslipidemia+insulin resistance groups had no significant differences in the gut microbiota. Dietary patterns also influenced microbial composition, with high protein intake increasing Leuconostoc and Akkermansia, and high fiber intake boosting Lactobacillus and Streptococcus. The genus Erwinia was associated with increases in visceral fat and serum glucose as well as a decrease in high-density lipoprotein cholesterol. Our findings highlight a significant association between gut microbiota composition and metabolic disturbances in young obese individuals, and they suggest that dietary modifications may promote a healthy microbiome and reduce the risk of developing metabolic disorders.

Discovery and characterization of a novel pathogen Erwinia pyri sp. nov. associated with pear dieback: taxonomic insights and genomic analysis.

In 2022, a novel disease similar to pear fire blight was found in a pear orchard in Zhangye City, Gansu Province, China. The disease mainly damages the branches, leaves, and fruits of the plant. To identify the pathogen, tissue isolation and pathogenicity testing (inoculating the potential pathogen on healthy plant tissues) were conducted. Furthermore, a comprehensive analysis encompassing the pathogen's morphological, physiological, and biochemical characteristics and whole-genome sequencing was conducted. The results showed that among the eight isolates, the symptoms on the detached leaves and fruits inoculated with isolate DE2 were identical to those observed in the field. Verifying Koch's postulates confirmed that DE2 was the pathogenic bacterium that causes the disease. Based on a 16S rRNA phylogenetic tree, isolate DE2 belongs to the genus Erwinia. Biolog and API 20E results also indicated that isolate DE2 is an undescribed species of Erwinia. Isolate DE2 was negative for oxidase. Subsequently, the complete genome sequence of isolate DE2 was determined and compared to the complete genome sequences of 29 other Erwinia species based on digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses. The ANI and dDDH values between strain DE2 and Erwinia species were both below the species thresholds (ANI < 95-96%, dDDH<70%), suggesting that isolate DE2 is a new species of Erwinia. We will temporarily name strain DE2 as Erwinia pyri sp. nov. There were 548 predicted virulence factors in the genome of strain DE2, comprising 534 on the chromosome and 5 in the plasmids. The whole genome sequence of strain DE2 has been submitted to the NCBI database (ASM3075845v1) with accession number GCA_030758455.1. The strain DE2 has been preserved at the China Center for Type Culture Collection (CCTCC) under the deposit number CCTCC AB 2024080. This study represents the initial report of a potentially new bacterial species in the genus Erwinia that causes a novel pear dieback disease. The findings provide a valuable strain resource for the study of the genus Erwinia and establish a robust theoretical foundation for the prevention and control of emerging pear dieback diseases.

The ams proteins and the amylovoran biosynthetic pathway: an extensive bioinformatic study

The genus Erwinia includes plant-pathogenic, non-pathogenic and even opportunistic human pathogens. Among them, Erwinia amylovora is one of the most studied species, as the etiological agent of the relevant necrotic plant disease fire blight. Its most important pathogenicity factor is amylovoran, an exopolysaccharide essential in the formation of a protective biofilm used by the bacterium to escape the plant protection mechanisms. Amylovoran biosynthesis, regulation and secretion require the concerted action of twelve genes clustered in a region spanning 16 kb, the ams operon. Most of the encoded proteins build and polymerize the repeating oligosaccharide units of galactose, glucose, glucuronic acid and pyruvate, others have signalling, regulation and secretion functions. We compared the ams operon organisation, predicted 3D structure of the encoded proteins of Erwinia amylovora in eighteen Erwinia species. We detected the presence of a paralog (for the amsG gene) and some rearrangements in the EPS biosynthetic operon in specific taxa that could be connected to the species-specific pathogenicity profile. The present study adds fundamental information about the genomic determinants of exopolysaccharide secretion in the Erwinia genus, and clarifies the evolutionary relationships among the genes in the ams operon.

Gut microbiota alterations in critically Ill patients with carbapenem-resistant Enterobacteriaceae colonization: A clinical analysis.

Carbapenem-resistant Enterobacteriaceae (CRE) are an emerging concern for global health and are associated with high morbidity and mortality in critically ill patients. Risk factors for CRE acquisition include broad-spectrum antibiotic use and microbiota dysbiosis in critically ill patients. Therefore, we evaluated the alteration of the intestinal microbiota associated with CRE colonization in critically ill patients. Fecal samples of 41 patients who were diagnosed with septic shock or respiratory failure were collected after their admission to the intensive care unit (ICU). The gut microbiota profile determined using 16S rRNA gene sequencing and quantitative measurement of fecal short-chain fatty acids were evaluated in CRE-positive (n = 9) and CRE negative (n = 32) patients. The analysis of bacterial metabolic abundance to identify an association between CRE acquisition and metabolic pathway was performed. CRE carriers showed a significantly increased proportion of the phyla Proteobacteria and decreased numbers of the phyla Bacteroidetes as compared to the CRE non-carriers. Linear discriminant analysis (LDA) with linear discriminant effect size showed that the genera Erwinia, Citrobacter, Klebsiella, Cronobacter, Kluyvera, Dysgomonas, Pantoea, and Alistipes had an upper 2 LDA score in CRE carriers. The alpha-diversity indices were significantly decreased in CRE carriers, and beta-diversity analysis demonstrated that the two groups were clustered significantly apart. Among short-chain fatty acids, the levels of isobutyric acid and valeric acid were significantly decreased in CRE carriers. Furthermore, the PICRUSt-predicted metabolic pathways revealed significant differences in five features, including ATP-binding cassette transporters, phosphotransferase systems, sphingolipid metabolism, other glycan degradation, and microbial metabolism, in diverse environments between the two groups. Critically ill patients with CRE have a distinctive gut microbiota composition and community structure, altered short-chain fatty acid production and changes in the metabolic pathways. Further studies are needed to determine whether amino acids supplementation improves microbiota dysbiosis in patients with CRE.

A novel phytopathogen Erwinia sorbitola sp. nov., isolated from the feces of ruddy shelducks.

The species in the genus Erwinia are Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped. Most species in the genus Erwinia are phytopathogens. Also, Erwinia persicina was involved in several human infections. Based on the reverse microbial etiology principles, it is worth analyzing the pathogenicity of species in this genus. In this study, we isolated and sequenced two species of Erwinia. Phylogenetic, phenotypic, biochemical, and chemotaxonomic analyses were performed to identify its taxonomy position. The virulence tests on plant leaves and pear fruits were used to identify the plant pathogenicity of two species of Erwinia. Bioinformatic methods predicted the possible pathogenic determinants based on the genome sequence. Meanwhile, adhesion, invasion, and cytotoxicity assays on RAW 264.7 cells were applied to identify animal pathogenicity. We isolated two Gram-stain-negative, facultatively anaerobic, motile, and rod-shaped strains from the feces of ruddy shelducks in the Tibet Plateau of China, designated J780T and J316. Distinct phylogenetic, genomic, phenotypic, biochemical, and chemotaxonomic characters of J780T and J316 identified they were novel species and belonged to the genus Erwinia, for which the name Erwinia sorbitola sp. nov. was proposed, the type strain was J780T (= CGMCC 1.17334T = GDMCC 1.1666T = JCM 33839T). Virulence tests showed blight and rot on the leaves and pear fruits confirmed Erwinia sorbitola sp. nov. was a phytopathogen. Predicted gene clusters of motility, biofilm formation, exopolysaccharides, stress survival, siderophores, and Type VI secretion system might be the causes of pathogenicity. In addition, predicted polysaccharide biosynthesis gene clusters on the genome sequence, and the high capacity for adhesion, invasion, and cytotoxicity to animal cells confirmed it has pathogenicity on animals. In conclusion, we isolated and identified a novel phytopathogen Erwinia sorbitola sp. nov. in ruddy shelducks. A predefined pathogen is beneficial for preventing from suffering potential economic losses caused by this new pathogen.

Three novel Erwinia billingiae phages isolated from organic waste represent three new genera.

Despite the ecological significance of viral communities, phages remain insufficiently studied. Current genomic databases lack high-quality phage genome sequences linked to specific bacteria. Bacteria of the genus Erwinia are known to colonize the phyllosphere of plants, both as commensals and as pathogens. We isolated three Erwinia billingiae phages-Zoomie, Pecta, and Snitter-from organic household waste. Based on sequence similarity to their closest relatives, we propose that they represent three new genera: "Pectavirus" within the family Zobellviridae, "Snittervirus" in the subfamily Tempevirinae, family Drexlerviridae, and "Zoomievirus" within the family Autographiviridae, which, together with the genus Limelightvirus, may constitute a new subfamily.

The management of microbiological regime of the irrigated light chestnut soils in the Nizhnee Povolzhye under drip irrigation

There is a certain relation between soil fertility and its microorganism content. The article considers the microbiological characteristics of irrigated light chestnut soils in the Nizhnee Povolzhye on various media. The soil samples were taken in the plow horizon (0-20 cm) in five replications for each experimental variant. To determine and account for the microorganism groups in the studied soil, the following nutrient media were used: MPA (meat-and-peptone agar), Wort – Agar and Czapek’s, Waksman’s. The studies also included the determination of the nutrient content in the soil in order to adjust the fertilizer application system for drip irrigation, since the soil arable layer on the experimental plot was poorly provided with easily hydrolyzed nitrogen and exchangeable potassium, and in medium way with mobile phosphorus. On the irrigated area one selected the plots with onion and cucumber crops with different mineral nutrition and the levels of maintaining pre-irrigation soil moisture, as well as a variant with a virgin (nonirrigated) plot. The development features of microbial communities on irrigated and non-irrigated lands were revealed. In the arable layer of the irrigated light chestnut soil of the Volgograd region, a fungus of the genus Fusarium, bacteria Bacillus subtilis, bacteria of the genus Erwinia were found, which can make it difficult to grow and store agricultural products. The options for maintaining pre-irrigation soil moisture during drip irrigation of vegetable crops did not have any significant effect on the quantitative and qualitative composition of microorganisms. The studied soil, according to agro-chemical analysis, is fertile and can be used for crop growing. Crop cultivation on non-irrigated areas should be carried out with the application of appropriate fertilizers.

Species-Specific Detection and Quantification of Erwinia pyrifoliae in Plants by a Direct SYBR Green Quantitative Real-Time PCR Assay

The present study describes a SYBR Green real-time quantitative (q) PCR assay to detect Erwinia pyrifoliae in plants. E. pyrifoliae, first described in South Korea, is a phytopathogenic bacterial species in the genus Erwinia. In particular, specific detection, quantitation, and identification of E. pyrifoliae is still challenging, as symptoms resulting from its colonization of Asian pear blossoms are very similar to those caused by E. amylovora. E. pyrifoliae has biochemical, phenotypic, and genetic properties similar to those of E. amylovora. Moreover, other Erwinia species, including E. tasmaniensis and E. billingiae, are also detected by currently available molecular methods and with traditional methods as well. Therefore, in this study, previously published genome sequences of the genera Erwinia and Pantoea were compared to exploit species-specific genes for use as improved qPCR targets to detect E. pyrifoliae. In silico analyses of the selected gene and designed primer sequences, in conjunction with bio-SYBR Green real-time qPCR, confirmed the robustness of this newly developed assay. Consequently, the bio-SYBR Green real-time qPCR-based protocols developed here can be used for rapid and specific detection of E. pyrifoliae. They will potentially simplify and facilitate diagnosis and monitoring of this pathogen and guide plant disease management. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Transfer of Erwinia toletana and Erwinia iniecta to a novel genus Winslowiella gen. nov. as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov. and description of Winslowiella arboricola sp. nov., isolated from bleeding cankers on broadleaf hosts.

Following a screening campaign of bleeding cankers of broadleaf hosts in Great Britain, numerous bacterial strains were isolated, identified by 16S rRNA and protein-coding gene sequencing and ultimately classified. During the course of the study, several Gram-negative, facultatively anaerobic strains were isolated from bleeding Platanus x acerifolia (London plane) and Tilia x europaea (common lime) cankers that could not be assigned to an existing species. Partial 16S rRNA gene sequencing placed these strains in the genus Erwinia, as a close phylogenetic relative of Erwinia toletana. In an effort to determine the taxonomic position of the strains, a polyphasic approach was followed including genotypic, genomic, phenotypic, and chemotaxonomic assays. Multilocus sequence analysis based on four protein-coding genes (gyrB, rpoB, infB, and atpD) confirmed the phylogenetic position of the strains as a novel taxon of subgroup 3 of the genus Erwinia, along with E. toletana and E. iniecta, and furthermore, provided support for their reclassification in a novel genus. Whole genome comparisons allowed the delimitation of the novel species and also supported the proposed transfer of subgroup 3 species to a novel genus in the Erwiniaeae. Phenotypically the novel species could be differentiated from E. toletana and E. iniecta, and the novel genus could be differentiated from the closely related genera Erwinia and Mixta. Therefore, we propose (1) the reclassification of E. toletana and E. iniecta in a novel genus, Winslowiella gen. nov., as Winslowiella toletana comb. nov. and Winslowiella iniecta comb. nov., with W. toletana comb. nov. as the type species (type strain A37T = CFBP 6631T = ATCC 700880T = CECT 5263T), and (2) classification of the novel strains as Winslowiella arboricola sp. nov. (type strain BAC 15a-03bT = LMG 32576T = NCPPB 4696T).

PM 7/20 (3) Erwinia amylovora

PM 7/20 (3) <i>Erwinia amylovora</i>

Draft Genomes of Six Philippine Erwinia mallotivora Isolates: Comparative Genomics and Genome-Wide Analysis of Candidate Secreted Proteins.

Erwinia mallotivora is one of the most important bacterial pathogens of papaya and causes bacterial crown rot disease in the Philippines. In this paper, we present the draft genome sequences of six Philippine E. mallotivora isolates to provide insights into the genes involved in host-pathogen interactions and compare their genomes to other Erwinia species. The genomes were sequenced using Illumina Miseq platform. The draft whole-genome assemblies of the E. mallotivora isolates are composed of 36-64 contigs with N50 value ranging from 285 to 332 kbp and cover 96.2-100% of the estimated genome size. Structural genome annotation of these assemblies has predicted 4489-4749 protein-coding genes. Comparative genomic analysis using orthologous gene sets led to the identification of conserved genes within the genus and species-specific gene orthologous groups, which collectively provide a baseline for functional genomic studies to determine genes affecting virulence and host specificity. Secreted proteins of E. mallotivora were also predicted and characterized to unravel putative genes involved in plant-pathogen interactions. This study provides the first draft whole-genome sequences of Philippine isolates of E. mallotivora, thus expanding the genomic knowledge for this species in comparison with other members of the genus Erwinia.

First Report of Stalk Rot of Celery Caused by Erwinia rhapontici in China.

Species belonging to the genus Erwinia cause diseases in many economically important plants (Mansfield et al. 2012). In May 2021, celery plants (Apium graveolens var. dulce) showing soft rot symptoms were observed in greenhouses (cv. Queen of France) in Boye County, Baoding, Hebei Province (North China). Disease symptoms began with pinkish water-soaked lesions on the midrib of celery stalks, but at the same time the leaves and root did not show symptoms. The infected celery plants rapidly developed brownish rotten stalks and leaves turned dry and yellow, but root remained asymptomatic. The disease incidence in two greenhouses (0.15 ha in size) was more than 50%. Affected celery stalk tissues were cut into 0.5 cm pieces, followed by surface sterilization using 75% ethanol for 60 sec and then three successive rinses with sterile distilled water. Then, the tissues were immersed in 200 µl 0.9% saline for 15 min. Aliquots of two tenfold dilutions of the tissue specimen soaking solution were plated onto Luria-Bertani (LB) agar plates and incubated at 28°C for 24 h. Single colonies were picked and restreaked onto LB agar three times for purity. The bacterial gDNA was extracted using the EasyPure Bacteria Genomic DNA Kit (TransGen Biotech). The 16S rDNA region was amplified by PCR using the universal primers 27F/1492R and sequenced. Result of blastn analysis of the 16S rDNA amplicons (MZ489246-MZ489247) indicated that the bacterial isolates (BY21311 and BY21312) belonged to the genus Erwinia. Biolog analysis (GEN III Microplate) identified the two isolates BY21311 (SIM=0.668) and BY21312 (SIM=0.638) as E. rhapontici. Housekeeping genes including acnA, gapA, icdA, mdh and rpoS were also amplified using a set of PCR primers (Ma et al. 2007; Waleron et al. 2008) followed by sequencing (MZ463029-MZ463038). To determine the species of the Erwinia isolates BY21311 and BY21312, multi-locus sequence analysis (MLSA) was performed with five housekeeping genes, and phylogenetic tree was reconstructed using RAxML v8.2.12 (Stamatakis et al. 2005). No sequence variation was observed at any MLSA locus between BY21311 and BY21312. The result of phylogenetic analysis showed that the celery stalk rot isolates BY21311 and BY21312 were clustered with E. rhapontici isolates. These celery isolates are closely related to the cabbage (Brassica rapa) isolate MAFF311153 (AP024329.1) in Japan. When celery plants have eight to nine true leaves, plants (cv. Queen of France) were inoculated with the isolate BY21311 by injecting 20 µl of bacterial suspensions (106 CFU·mL-1) into the celery stalks, or injected with 20 µl of 0.9% saline as control. The seedlings were grown at 25 °C and 50% relative humidity. Three days after inoculation, only infected seedling showed disease symptoms resembled to those observed in greenhouses. Bacterial colonies were obtained from the infected stalks and were identified using the same PCR primers of housekeeping genes as described above, fulfill Koch's postulates. E. rhapontici has been reported to cause pink seed, crown and stem rot, soft rot or leaf spot on many plant hosts including pea (Pisum sativum), chickpea (Cicer arietinum), lentil (Lens culinaris), common bean (Phaseolus vulgaris), lucerne (Medicago sativa), wheat (Triticum aestivum), hyacinth (Hyacinthus orientalis), onion (Allium cepa), kiwifruit (Actinidia chinensis) and peach (Prunus persica) (Huang et al. 2003; Wang et al. 2017; Zhang et al. 2018; Kovács et al. 2020). To our knowledge, this is the first report of E. rhapontici causing stalk rot in celery. Stalk rot of celery has increased in prevalence over recent years in the Baoding region, it can cause significant yield loss and no cultivar has been found to be resistant to this disease so far. The stalk rot poses significant threat to local celery production, and further research on epidemiology and disease management options is needed.

First Report of Erwinia persicina Causing Stalk Rot of Celery in China.

Species belonging to the genus Erwinia cause diseases in many economically important plants. In May 2021, celery (Apium graveolens var. dulce) plants (cv. Queen of France) showing soft rot symptoms were observed in greenhouses in Boye County, Baoding, Hebei Province (North China). Disease symptoms began with pinkish water-soaked lesions on the midrib of celery stalks, but at the same time the leaves and root were asymptomatic; and the infected celery plants rapidly developed brownish rotten stalks. The disease incidence in two greenhouses (0.15 ha in size) was more than 50%. Affected celery stalk pieces ca. 0.5 cm in length were surface-sterilized by dipping them in 75% ethanol for one min and then three successive rinses with sterile distilled water. Then, the tissues were immersed in 200 µl 0.9% saline for 15 min. Aliquots (20 μl) of two tenfold dilutions of the tissue specimen soaking solution were plated onto Luria-Bertani (LB) medium and incubated at 28°C for 24 h. Single colonies were picked and restreaked onto LB agar three times for purity. The bacterial gDNA was extracted using the EasyPure Bacteria Genomic DNA Kit (TransGen Biotech, Beijing, China). The 16S rDNA region was amplified by PCR using the universal primers 27F/1492R and sequenced. Result of blastn analysis of the 16S rDNA amplicons (MZ614654, MZ614655) indicated that the bacterial isolates (BY21211 and BY21212) belonged to the genus Erwinia. Housekeeping genes including mdh, gapA, icdA, rpoS, acnA and proA were also amplified using a set of PCR primers (Ma et al. 2007) followed by sequencing (MZ643221-MZ643232). No sequence variation was observed at any MLSA locus between isolates BY21211 and BY21212. To determine the species of the Erwinia isolate BY21211 and BY21212, multi-locus sequence analysis (MLSA) was performed with six housekeeping genes, and phylogenetic tree was reconstructed using RAxML v8.2.12 (github.com/stamatak/standard-RAxML). The result of phylogenetic analysis showed that the celery stalk rot isolate BY21211 and BY21212 was clustered with E. persicina type strain NBRC102418T (Hao et al. 1990). When celery plants (cv. Queen of France) have eight to nine true leaves, plants were inoculated with the isolate BY21211 by injecting 20 µl of bacterial suspensions (107 CFU·mL-1) into the celery stalks, and negative controls were injected with 20 µl of 0.9% saline. The seedlings were grown at 25°C and 50% relative humidity. Three days after inoculation, only the bacterial-inoculated seedlings showed disease symptoms resembled to those observed in greenhouses. Bacterial colonies were obtained from the infected stalks and were identified using the same PCR primers of housekeeping genes as described above. Therefore, E. persicina isolate BY21211 fulfill Koch's postulates for stalk rot of celery. Isolates BY21211 and BY21212 produce water-soluble pink pigment on sucrose-peptone agar. These isolates were gram negative and rod shaped, negative for oxidase, urease, indole production, gelatin liquefaction and acid production from xylose and glycerol. They were positive for catalase, citrate utilization, acid production from sorbitol, raffinose, glucose, arabinose, cellobiose, rhamnose, maltose, saccharose, inositol, lactose and esculin (hydrolysis). E. persicina has been reported to cause pink seed, crown and stem rot, soft rot or leaf spot on many plant hosts including pea (Pisum sativum), soybean (Glycine max), common bean (Phaseolus vulgaris), lucerne (Medicago sativa), barley (Hordeum vulgare), onion (Allium cepa), garlic bulbs (Allium sativum), tomato (Lycopersicon esculentum) and cucumber (Cucumis sativus) (Hao et al. 1990; González et al. 2005, 2007; Zhang and Nan 2014; Gálvez et al. 2015; Cho et al. 2019; Kawaguchi et al. 2021). To our knowledge, this is the first report of E. persicina causing stalk rot in celery. Stalk rot of celery has increased in prevalence over recent years in the Baoding region, it can cause significant yield loss and no cultivar has been found to be resistant to this disease so far. The stalk rot poses significant threat to local celery production, and further research on epidemiology and disease management options is needed.

The mosquito microbiome includes habitat-specific but rare symbionts

Microbial communities are known to influence mosquito lifestyles by modifying essential metabolic and behavioral processes that affect reproduction, development, immunity, digestion, egg survival, and the ability to transmit pathogens. Many studies have used 16S rRNA gene amplicons to characterize mosquito microbiota and investigate factors that influence host-microbiota dynamics. However, a relatively low taxonomic resolution due to clustering methods based on arbitrary threshold and the overall dominance of Wolbachia or Asaia symbionts obscured the investigation of rare members of mosquito microbiota in previous studies. Here, we used high resolution Shannon entropy-based oligotyping approach to analyze the microbiota of Culex pipiens, Culex quinquefasciatus and Aedes individuals from continental Southern France and overseas Guadeloupe as well as from laboratories with or without antibiotics treatment. Our experimental design that resulted in a series of mosquito samples with a gradient of Wolbachia density and relative abundance along with high-resolution analyses of amplicon sequences enabled the recovery of a robust signal from typically less accessible bacterial taxa. Our data confirm species-specific mosquito-bacteria associations with geography as a primary factor that influences bacterial community structure. But interestingly, they also reveal co-occurring symbiotic bacterial variants within single individuals for both Elizabethkingia and Erwinia genera, distinct and specific Asaia and Chryseobacterium in continental and overseas territories, and a putative rare Wolbachia variant. Overall, our study reveals the presence of previously overlooked microdiversity and multiple closely related symbiotic strains within mosquito individuals with a remarkable habitat-specificity.

Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection.

Our previous study identified a new β-galactosidase in Erwinia sp. E602. To further understand the lactose metabolism in this strain, de novo genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of Erwinia sp. E602 includes a 4.8 Mb chromosome and a 326 kb large plasmid. A total of 4,739 genes, including 4,543 protein-coding genes, 25 rRNAs, 82 tRNAs and 7 other ncRNAs genes were annotated. The plasmid was the largest one characterized in genus Erwinia by far, and it contained a number of genes and pathways responsible for lactose metabolism and regulation. Moreover, a new plasmid-borne lac operon that lacked a typical β-galactoside transacetylase (lacA) gene was identified in the strain. Phylogenetic analysis showed that the genes lacY and lacZ in the operon were under positive selection, indicating the adaptation of lactose metabolism to the environment in Erwinia sp. E602. Our current study demonstrated that the hybrid de novo genome assembly using Illumina and PacBio sequencing technologies, as well as the metabolic pathway analysis, provided a useful strategy for better understanding of the evolution of undiscovered microbial species or strains.

Analysis of Total Acidity toward Bacterial and Endophytic Fungi Profile dur-ing Black Garlic Processing from Garlic (Allium sativum L.) and Shallot (Allium ascalonicum L.)

Black garlic or shallot are products of processed garlic and shallots obtained through a heating process conducted over a certain period. Black garlic/shallots have a mild aroma with a sweet and sour taste. The heating process causes chemical compound transition in the garlic, including acidity. In addition to the chemical process, the garlic’s color and component changes are due to the role of microorganisms during black garlic processing. However, the presence and function of such microorganisms have not been identified. Therefore, this research explores the black garlic’s microorganisms, their role in black garlic processing, and their relation to the total acidity changes. Total acidity test was completed using the potentiometric titration method, while the onion’s microorganisms were explored through isolation and characterization. Data show that black garlic’s total acidity of both garlic and shallot increases during the heating period day by day. Endophytic microbes that were successfully isolated during black garlic processing were observed on days 0 and 6. According to the rough data, the bacteria that emerged on day 0 are presumed to come from genus Erwinia, Pseudomonas, Xanthomonas, Agrobacterium, Ralstonia, Xylophilus, Pantoea, Acidovorax, Burkholderia, Coryneform, and Streptomyces, while the bacteria observed on day 6 are assumed to be generated from genus Coryneform and Streptomyces.

The Bacteriophage pEp_SNUABM_08 Is a Novel Singleton Siphovirus with High Host Specificity for Erwinia pyrifoliae.

Species belonging to the genus Erwinia are predominantly plant pathogens. A number of bacteriophages capable of infecting Erwinia have been used for the control of plant diseases such as fire blight. Public repositories provide the complete genome information for such phages, which includes genomes ranging from 30 kb to 350 kb in size. However, limited information is available regarding bacteriophages belonging to the family Siphoviridae. A novel lytic siphophage, pEp_SNUABM_08, which specifically infects Erwinia pyrifoliae, was isolated from the soil of an affected apple orchard in South Korea. A comprehensive genome analysis was performed using the Erwinia-infecting siphophage. The whole genome of pEp_SNUABM_08 comprised 62,784 bp (GC content, 57.24%) with 79 open reading frames. The genomic characteristics confirmed that pEp_SNUABM_08 is a singleton lytic bacteriophage belonging to the family Siphoviridae, and no closely related phages have been reported thus far. Our study not only characterized a unique phage, but also provides insight into the genetic diversity of Erwinia bacteriophages.

Gut Bacterial Diversity in Different Life Cycle Stages of Adelphocoris suturalis (Hemiptera: Miridae).

Bacteria and insects have a mutually beneficial symbiotic relationship. Bacteria participate in several physiological processes such as reproduction, metabolism, and detoxification of the host. Adelphocoris suturalis is considered a pest by the agricultural industry and is now a major pest in cotton, posing a serious threat to agricultural production. As with many insects, various microbes live inside A. suturalis. However, the microbial composition and diversity of its life cycle have not been well-studied. To identify the species and community structure of symbiotic bacteria in A. suturalis, we used the HiSeq platform to perform high-throughput sequencing of the V3–V4 region in the 16S rRNA of symbiotic bacteria found in A. suturalis throughout its life stages. Our results demonstrated that younger nymphs (1st and 2nd instar nymphs) have higher species richness. Proteobacteria (87.06%) and Firmicutes (9.43%) were the dominant phyla of A. suturalis. At the genus level, Erwinia (28.98%), Staphylococcus (5.69%), and Acinetobacter (4.54%) were the dominant bacteria. We found that the relative abundance of Erwinia was very stable during the whole developmental stage. On the contrary, the relative abundance of Staphylococcus, Acinetobacter, Pseudomonas, and Corynebacterium showed significant dynamic changes at different developmental stages. Functional prediction of symbiotic bacteria mainly focuses on metabolic pathways. Our findings document symbiotic bacteria across the life cycle of A. suturalis, as well as differences in both the composition and richness in nymph and adult symbiotic bacteria. Our analysis of the bacteria in A. suturalis provides important information for the development of novel biological control strategies.

Identification and Characterization of a New Quorum-Quenching N-acyl Homoserine Lactonase in the Plant Pathogen Erwinia amylovora.

Quorum quenching (QQ) is the ability to interfere with bacterial cell to cell communication, known as quorum sensing (QS). QQ enzymes that degrade or modify acyl homoserine lactones (AHLs) have been attracting increasing interest as promising agents for inhibiting QS-mediated bacterial pathogenicity. Plant pathogens from the genus Erwinia cause diseases in several economically important crops. Fire blight is a devastating plant disease caused by Erwinia amylovora, affecting a wide range of host species within the Rosaceae and posing a major global threat for commercial apple and pear production. While QS has been described in Erwinia species, no AHL-degrading enzymes were identified and characterized. Here, phylogenetic analysis and structural modeling were applied to identify an AHL lactonase in E. amylovora (dubbed EaAiiA). Following recombinant expression and purification, the enzyme was biochemically characterized. EaAiiA lactonase activity was dependent on metal ions and effectively degraded AHLs with high catalytic efficiency. Its highest specific activity (kcat/KM value) was observed against one of the AHLs (3-oxo-C6-homoserine lactone) secreted from E. amylovora. Exogenous addition of the purified enzyme to cultures of E. amylovora reduced the formation of levan, a QS-regulated virulence factor, by 40% and the transcription level of the levansucrase-encoding gene by 55%. Furthermore, preincubation of E. amylovora cultures with EaAiiA inhibited the progress of fire blight symptoms in immature Pyrus communis fruits. These results demonstrate the ability of the identified enzyme from E. amylovora to act as a quorum-quenching lactonase.