16S rRNA Region Research Articles

Integrated skin microbiome and metabolome analyses reveal altered bacterial community composition and metabolites in psoriasis

Objective: Current theories highlight the role of the microbiome in the pathogenesis of psoriasis. Additionally, abnormal metabolism can alter disease processes in terms of occurrence, progression, and prognosis. Therefore, an integrative microbiome and metabolome analysis of the skin may aid in understanding the disease pathogenesis and identify therapeutic targets for psoriasis. Methods: We recruited 22 patients with psoriasis and 22 age- and sex-matched healthy controls. Skin swabs were collected from the participants’ scalps. All samples underwent amplicon sequencing of the ITS1 and V3V4 16S rRNA regions and metabolome analysis. Results: The psoriatic lesions were characterized by higher bacterial diversity, significantly higher abundances of Corynebacterium and Staphylococcus, and a lower abundance of Cutibacterium compared with healthy controls. However, no significant alterations in the fungal diversity or fungal taxonomies were detected. Metabolome analysis revealed that prostaglandin-related metabolites, nucleotides, and cysteine- and methionine-related metabolites were significantly enriched in patients with psoriasis, and these metabolites were positively correlated with the disease-associated bacteria Staphylococcus and Corynebacterium. Conclusions: We demonstrated significant alterations in the skin microbiome and metabolome in patients with psoriasis compared with healthy controls.

Soil Microbial Community Composition and Diversity Are Insusceptible to Nitrogen Addition in a Semi-Arid Grassland in Northwestern China

Human-caused nitrogen (N) deposition is a global environmental issue that can change community composition, functions, and ecosystem services. N deposition affects plants, soil, and microorganisms regionally and is linked to ecosystem, soil, and climate factors. We examined the effects of six N addition levels (0, 2.34 g, 4.67, 9.34,18.68, and 37.35 g N m−2 yr−1) on aboveground vegetation, surface soil properties, and microbial community. Alterations in microbial communities in response to N addition were monitored using 16S rRNA (16S ribosomal ribonucleic acid, where S donates a sedimentation coefficient) and ITS (internal transcribed spacer) regions for bacterial and fungal communities, respectively. N addition positively affected aboveground vegetation traits, such as biomass and community weighted mean of leaf nitrogen. N addition also limited phosphorus (P) availability and altered the microbial community assembly process from random processes to deterministic processes. The microbial community diversity and composition, however, were not sensitive to N addition. Partial least squares structural equation models showed that the composition of bacterial communities was mainly driven by the composition of plant communities and total nitrogen, while the composition of fungal communities was driven by soil pH and community weighted mean of leaf nitrogen. Taken together, the results of this research improved our understanding of the response of grassland ecosystems to N deposition and provided a theoretical basis for grassland utilization and management under N deposition.

Molecular characterization of multidrug resistant (MDR) clinical isolates of Pseudomonas aeruginosa from Nsukka, South Eastern Nigeria.

P. aeruginosa is an important nosocomial pathogen with increasing resistance to antibiotics. Objective: This study was performed to evaluate the genetic relatedness of MDR clinical isolates of P. aeruginosa. A total of 1000 samples were analysed in the study. Antibiotic resistance profiles of the isolates were determined using Kirby Bauer disk diffusion method. Polymerase chain reaction (PCR) and sequencing were simultaneously used to detect the consensus region of 16S rRNA. Genetic relatedness of the isolates was determined using restriction patterns from ALU 1 digest and random amplified polymorphic DNA. Out of the 192 P. aeruginosa isolates recovered, 136 (78.83%) were multidrug resistant. Sequence analysis of the confirmed isolates (80.68%) revealed that all the isolates shared homology with each other and also showed sequence similarity to known strains of P. aeruginosa (ATCC 27853; KT 315654; KU 321274 and KT894767). The PCR-Restriction fragment length polymorphism (PCR-RFLP) analysis revealed that there was a lot of genetic relatedness among the isolates. The RFLP finger printing technique detected seven distinct RFLP types among the isolates. Thus, study shows that there is high prevalence of MDRPA and high degree of genetic relatedness among the MDRPA isolates circulating in Nsukka area.

Endophytic Bacillus aerophilus from the Leaves of Azadirachta indica as a Potential Biocontrol against Staphylococcus aureus

Aims: The study entailed isolation and identification of Bacillus aerophilus in the leaves of young Azadirachta indica plants, establishing the antimicrobial activity of the endophyte against Staphylococcus aureus, and screening for phytochemicals. The study investigated the potential of the endophytic Bacillus aerophilus in pathogen inhibition and phytochemical screening for bioactive compounds produced by the endophyte that can be used in drug development. The research contributes to the wider scientific goal of curbing rising cases of antibiotic resistance.
 Place and Duration of Study: Sample: collected from Kanyonyoo in Kitui County, between August 2022 and June 2023.
 Methodology: The bacteria were aseptically isolated and sub-cultured on nutrient agar. For identification, the bacteria underwent biochemical tests and molecular characterization. The 16S rRNA region was amplified and sequenced using universal primers 27F and 1492R. Bacterial isolate K1L003 was identified as Bacillus aerophilus. For antimicrobial testing, the agar disk diffusion method was used against pathogenic Staphylococcus aureus on Mueller Hinton Agar plates (MHA). The controls were doxycycline and vancomycin.
 Results: The endophytic isolate only inhibited Staphylococcus aureus (P < .001), with an inhibition mean similar to doxycycline (26 mm), against the pathogen. The endophytic isolate produced terpenoids, saponins, alkaloids, and flavonoids.
 Conclusion: Endophytic Bacillus aerophilus has better antimicrobial inhibition potential than vancomycin, against Staphylococcus aureus and produces diverse bioactive secondary metabolites. The endophyte has the potential to produce compounds that are useful in treating drug-resistant Staphylococcal infections.

Decoding Microbial Networks: An Insight into 16S rRNA and Whole Genome Sequencing Approaches in Metagenomic Studies

The exploration of microbial communities is pivotal in understanding environmental, human, and animal ecosystem dynamics. Advances in high-throughput sequencing technologies have significantly enriched our insights into microbiomes, with 16S rRNA and Whole Genome Sequencing (WGS) being central methodologies. This review delineates a comparative analysis of these sequencing techniques, particularly focusing on different hypervariable regions of 16S rRNA (V3-V4 and V2-3-4-6-7-8-9) and WGS. The 16S rRNA sequencing, despite being cost-effective and less computationally demanding, often limits identification to the genus level. In contrast, WGS, while being resource-intensive, provides a broader spectrum of microbial identification including bacteria, viruses, fungi, and parasites, alongside a deeper insight into microbial functional attributes. The challenges associated with sequencing depth in WGS are discussed, alongside emerging mitigating strategies like host DNA depletion. The choice between these methodologies hinges on the project objectives and available resources. This comparative assessment aims to guide researchers in selecting the apt sequencing approach for their metagenomic studies, thereby facilitating a more extensive understanding of microbial ecosystems.

Extreme weather events as an important factor for the evolution of plastisphere but not for the degradation process

Marine plastics, with their negative effects on marine life and the human health, have been recently recognized as a new niche for the colonization and development of marine biofilms. Members of the colonizing communities could possess the potential for plastic biodegradation. Thus, there is an urgent need to characterize these complex and geographically variable communities and elucidate the functionalities. In this work, we characterize the fungal and bacterial colonizers of 5 types of plastic films (High Density Polyethylene, Low Density Polyethylene, Polypropylene, Polystyrene and Polyethylene Terepthalate) over the course of a 242-day incubation in the south-eastern Mediterranean and relate them to the chemical changes observed on the surface of the samples via ATR-FTIR. The 16s rRNA and ITS2 ribosomal regions of the plastisphere communities were sequenced on four time points (35, 152, 202 and 242 days). The selection of the time points was dictated by the occurrence of a severe storm which removed biological fouling from the surface of the samples and initiated a second colonization period. The bacterial communities, dominated by Proteobacteria and Bacteroidetes, were the most variable and diverse. Fungal communities, characterized mainly by the presence of Ascomycota, were not significantly affected by the storm. Neither bacterial nor fungal community structure were related to the polymer type acting as substrate, while the surface of the plastic samples underwent weathering of oscillating degrees with time. This work examines the long-term development of Mediterranean epiplastic biofilms and is the first to examine how primary colonization influences the microbial community re-attachment and succession as a response to extreme weather events. Finally, it is one of the few studies to examine fungal communities, despite them containing putative plastic degraders.

First Report of Soft Rot Caused by Pectobacterium brasiliense on Cucumber in Korea

Wilted and water-soaked lesion symptoms were observed on cucumbers in greenhouses located in Daejeon, Chungcheongnam-do, Korea, in June 2021. A bacterial strain, designated KNUB-04-21, was isolated from the cucumbers, which was subsequently identified as <i>Pectobacterium brasiliense</i> through a phylogenetic analysis based on sequences of the 16S rRNA region, <i>dnaX, leuS</i>, and <i>recA</i> genes. The biochemical characteristics of KNUB-04-21 were also similar to those of <i>P. brasiliense</i> through investigation using the API ID 32 GN system. The pathogenicity of KNUB-04-21 was confirmed by inoculating it into healthy cucumber plants. The reisolated strains were also found to be same to the original strain. To our knowledge, this is the first report of <i>P. brasiliense</i> being identified as the causative agent of cucumber soft rot in Korea.

A simplified bacterial community found within the epidermis than at the epidermal surface of atopic dermatitis patients and healthy controls

There has been considerable research into the understanding of the healthy skin microbiome. Similarly, there is also a considerable body of research into whether specific microbes contribute to skin disorders, with atopic dermatitis (AD) routinely linked to increased Staphylococcus aureus (S. aureus) colonisation. In this study, the epidermal surface of participants was sampled using swabs, while serial tape-stripping (35 tapes) was performed to sample through the stratum corneum. Samples were taken from AD patients and healthy controls, and the bacterial communities were profiled by metabarcoding the universal V3-V4 16S rRNA region. Results show that the majority of bacterial richness is located within the outermost layers of the stratum corneum, however there were many taxa that were found almost exclusively at the very outermost layer of the epidermis. We therefore hypothesise that tape-stripping can be performed to investigate the ‘core microbiome’ of participants by removing environmental contaminants. Interestingly, significant community variation between AD patients and healthy controls was only observable at the epidermal surface, yet a number of individual taxa were found to consistently differ with AD status across the entire epidermis (i.e. both the epidermal surface and within the epidermis). Sampling strategy could therefore be tailored dependent on the hypothesis, with sampling for forensic applications best performed using surface swabs and outer tapes, while profiling sub-surface communities may better reflect host genome and immunological status.

Relative contribution of season, site, scion and rootstock genotype, and susceptibility to European canker to the variability in bacterial and fungal communities in apple leaf scar tissues

AbstractNeonectria ditissima infects apple trees through wounds, causing European canker. In the UK, the most important entry site for N. ditissima is leaf scar. Specific apple endophytes may contribute to cultivar resistance/tolerance to the pathogen. We assessed the relative effect of location, sampling time (season), and rootstock/scion genotype on bacterial and fungal endophyte communities in the apple leaf scar tissues of current‐season extension shoots and identified Operational Taxonomic Units (OTUs) with differential abundance between canker resistant and susceptible scions, and between rootstocks. Leaf scar tissues were sampled from two orchards at three times (10/2018, 06/2019 and 10/2019) for eight scion cultivars, each grafted onto two rootstocks, for profiling 16S and ITS rRNA regions. Endophyte composition was primarily affected by season (autumn vs. spring) and location (sites and blocks within site). There was a significant reduction in the community size in the spring, particularly for fungi, and species turnover between autumn and spring. This seasonal dynamics suggest that to protect leaf scars from N. ditissima infection in the autumn specific endophytes suppressing canker may have to be augmented annually around the leaf‐fall time. Scion and rootstock genotypes had limited effects on the endophyte community. A group of resistant cultivars differed from a group of susceptible ones in the relative abundance of many bacterial and fungal OTUs, most of which had low reads numbers. Nevertheless, several OTUs with high reads numbers differed in their relative abundance between resistant and susceptible scions, including OTUs from Sphingomonas, Methylobacterium, Vishniacozyma and Rhodotorula babjevae, and warrant further investigation for their potential role in host resistance/tolerance against N. ditissima.

Alterations of the bacterial ocular surface microbiome are found in both eyes of horses with unilateral ulcerative keratitis.

Next generation sequencing (NGS) studies in healthy equine eyes have shown a more diverse ocular surface microbiota compared to culture-based techniques. This study aimed to compare the bacterial ocular surface microbiota in both eyes of horses with unilateral ulcerative keratitis (UK) with controls free of ocular disease. Conjunctival swabs were obtained from both ulcerated eyes and unaffected eyes of 15 client-owned horses with unilateral UK following informed consent, as well as from one eye of 15 healthy horses. Genomic DNA was extracted from the swabs and sequenced on an Illumina platform using primers that target the V4 region of bacterial 16S rRNA. Data were analyzed using Quantitative Insights Into Molecular Ecology (QIIME2). The ocular surface of ulcerated eyes had significantly decreased species richness compared with unaffected fellow eyes (Chao1 q = 0.045, Observed ASVs p = 0.045) with no differences in evenness of species (Shannon q = 0.135). Bacterial community structure was significantly different between either eye of horses with UK and controls (unweighted UniFrac: control vs. unaffected, p = 0.03; control vs. ulcerated, p = 0.003; unaffected vs. ulcerated, p = 0.016). Relative abundance of the gram-positive taxonomic class, Bacilli, was significantly increased in ulcerated eyes compared with controls (q = 0.004). Relative abundance of the taxonomic family Staphylococcaceae was significantly increased in ulcerated and unaffected eyes compared with controls (q = 0.030). The results suggest the occurrence of dysbiosis in infected eyes and reveal alterations in beta diversity and taxa of unaffected fellow eyes. Further investigations are necessary to better understand the role of the microbiome in the pathophysiology of ocular surface disease.

Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods.

Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.

GENETIC DIVERSITY AND PHYLOGENY OF RHIZOBIA ISOLATED FROM NODULES USING RFLP-PCR TECHNIQUE IN NINEVEH PROVINCE, IRAQ

Rhizobia are important bacteria, playing a vital role in atmospheric nitrogen fixation. In addition, it increases soil fertility, enhancing crop production and preserving the soil from pollution resulting from inorganic fertilizers’ use. From 81 bacteria samples, nine isolates segregated from nine types of leguminous crops are economically valuable for cultivation within nine different locations in Nineveh Governorate, Iraq. The isolates underwent initial diagnosis by phenotypical and cultural characteristics and host specialization tests. Molecular characterization also ran on the selected bacterial isolates. Performing the 16S rRNA region amplification applied forward primer 27F and a reverse primer 1541R using the polymerase chain reaction (PCR) technique. The results of restriction fragment length polymorphism (RFLP-PCR) employing three endonuclease enzymes showed that EcoRI had similar sequences among the isolates under study but significantly different for MspI and HaeIII. Based on the analysis of results using the statistical program MVSP version 3.22, the degree of similarity divided the isolates into three groups. Results revealed that there were genetic differences between the isolates and the suppressing enzymes, providing more accurate results in recognizing the similarity among the bacterial isolates as a result of the difference in the location and environmental conditions from which the bacteria were isolated, in addition to the different agricultural processes used for those regions.

An Update of Knowledge of the Bacterial Assemblages Associated with the Mexican Caribbean Corals Acropora palmata, Orbicella faveolata, and Porites porites

In this study, the bacterial microbiota associated with apparently healthy corals of Acropora palmata, Orbicella faveolata, and Porites porites and the surrounding seawater and sediment were evaluated via the MiSeq Illumina sequencing of the V4 region of 16S rRNA at three reef sites in the Mexican Caribbean. Bacterial assemblages associated with apparently healthy corals and sediments showed no significant differences between sites. The colonies of A. palmata showed a dominance of families Amoebophilaceae, Spirochaetaceae, Myxococcaceae, and Cyclobacteriaceae. Meanwhile, the colonies of O. faveolata and P. porites revealed a high prevalence of the Rhodobacteraceae and Kiloniellaceae families. The families Rhodobacteraceae, Cryomorphaceae, Cyanobiaceae, and Flavobacteriaceae were predominant in seawater samples, while Pirellulaceae, Nitrosococcaceae, and Woeseiaceae were predominant in sediments. Variations in A. palmata bacterial assemblages were correlated with salinity, sea surface temperature, and depth. These variables, along with nitrate, phosphate, and ammonium concentrations, were also correlated with changes in the bacterial composition of P. porites, seawater, and sediments. However, none of the environmental variables were related to the bacterial taxa of O. faveolata. Aerobic chemoheterotrophy and fermentation, followed by nitrate reduction and ureolysis, were the metabolic functions with the highest occurrence in the bacterial assemblages associated with all substrates.

Standard- and large-sized eggs of Trichuris trichiura in the feces of schoolchildren in the Yangon Region, Myanmar: Morphological and molecular analyses.

Standard- and large-sized eggs of Trichuris trichiura were found in the feces of schoolchildren in Yangon, Myanmar during epidemiological surveys and mass deworming with albendazole in 2017-2019. The standard-sized eggs were identified as those of T. trichiura, but it was necessary to exclude the possibility of the large-sized eggs belonging to Trichuris vulpis, a dog whipworm. We conducted morphological and molecular studies to determine the species of the 2 types of Trichuris eggs. Individual eggs of both sizes were isolated from Kato-Katz fecal smears (n=20) and mechanically destroyed using a 23G injection needle. Nuclear DNA was extracted, and the 18S rRNA region was sequenced in 15 standard-sized eggs and 15 large-sized eggs. The average size of standard-sized eggs (T. trichiura) was 55.2×26.1 μm (range: 51.7-57.6×21.3-28.0 μm; n=97), whereas the size of large-sized eggs was 69.3×32.0 μm (range: 65.1-76.4×30.1-34.5 μm; n=20), slightly smaller than the known size of T. vulpis. Regarding standard-sized eggs, the 18S rRNA nucleotide sequences exhibited 100% homology with T. trichiura deposited in GenBank and 88.6-90.5% homology with T. vulpis. Regarding large-sized eggs, the nucleotide sequences showed 99.8-100% homology with T. trichiura in GenBank and 89.6-90.7% homology with T. vulpis. Both standard- and large-sized eggs of Trichuris spp. found in Myanmar schoolchildren during 2017-2019 were morphologically and molecularly confirmed to belong to T. trichiura. The conversion of eggs from smaller to large sizes might be due to anthelmintic treatments with albendazole.

Morpho-molecular Characterization of Carrot Soft Rot Incitant, Pectobacterium carotovorum subsp carotovoroum

Carrot is an important root vegetable which plays an important role in human health. Globally, Post harvest diseases are the major constraint in carrot production, especially soft rot which resulting in severe yield loss. Early diagnosis of these post-harvest diseases paves a way for reducing the economic losses. Carrot samples showing typical rotting symptoms were collected from markets of four different districts of Tamil Nadu and the pathogen involved were isolated. Severe carrot soft rot incidence (66.74%) was observed in samples collected from Ooty area of The Nilgiris district and the least disease incidence of (16.21%) was recorded in Perundurai of Erode district. Pathogenicity of soft rot pathogen were conducted and the virulent isolates were identified based on Percent Disease Index (PDI) showing >50% rotting falls under disease grade 9 using disease grade scale (0 to 9). The bacterial isolates (KPB-7 and OCB-5) causing soft rot were characterized using various biochemical assays where in they showed positive response for methyl red, H2S gas production, KOH and catalase tests besides showing negative response for gram’s reaction. Furthermore, molecular characterization of 16s rRNA region revealed the soft rot isolate (KPB-7) as Pectobacterium carotovorum subsp carotovorum (with an accession number OR251119).

First identification, molecular characterization, and pathogenicity assessment of Lactococcus garvieae isolated from cultured pompano in Taiwan.

Lactococcosis, caused by Lactococcus garvieae, is an acute hemorrhagic septicemia in fish recorded in marine and freshwater aquaculture during the summer months. In 2020-2021, several sea cage Pompano farms recorded sudden fish mortality events. Based on the results of phenotypic and biochemical tests, L. garvieae was predicted to be the cause. PCR with L. garvieae specific primers (pLG1 and pLG2) targeting the 16S rRNA region further confirmed the etiological agent as L. garvieae after amplifying an 1100 base pairs (bp) product. Furthermore, the 16S rRNA sequences of the two representative strains (AOD109-196-2B and AOD110-215-2B) shared 99.81% identity with L. garvieae (GenBank accession number: MT597707.1). The genetic profiles of the strains were classified using pulsed-field gel electrophoresis after digestion with SmaI and ApaI, which clustered our strains under the same pulsotype. Multiplex PCR targeting the capsule gene cluster and serotype-specific PCR collectively showed that the strains were non-capsulated; thus, they belonged to serotype I. An experimental infection was designed to fulfil Koch's postulates by infecting healthy Pompano with case-driven L. garvieae strains (AOD109-196-2B and AOD110-215-2B) with a cumulative mortality of 70%. Overall, L. garvieae infection in Pompano emphasizes the need for better monitoring and control procedures in aquaculture settings.

First molecular detection of Babesia vulpes and Babesia capreoli in wild boars from southern Italy.

Following the increase of wild boar (Sus scrofa) populations in Europe, a potential risk of emerging infections by vector-borne pathogens may occur. Despite this, the circulation of piroplasmid species in these ungulates is still a neglected topic, particularly in the Mediterranean basin. Therefore, this study aimed to investigate the presence of Babesia/Theileria spp. in wild boars from southern Italy to assess the epidemiological role of these ungulates in the circulation of piroplasmids. By using a citizen science approach among hunters and veterinarians, wild boar spleen samples were collected in the Campania region (southern Italy) between 2016 and 2022. A combined semi-nested PCR/sequencing analysis targeting the V4 hyper-variable region of 18S rRNA was run to detect Babesia/Theileria spp. DNA. Out of 243 boars, 15 (i.e., 6.2, 95% CI: 3.4-9.9) tested positive to Babesia/Theileria spp., Babesia vulpes (n = 13, 5.3, 95% CI: 3.1-8.9) the most prevalent, followed by Babesia capreoli (n = 2, 0.8, 95% CI: 0.2-2.9). Three different B. vulpes sequence types were identified (i.e., ST1, ST2, ST3), with the most representative as ST1 (60%), and a single B. capreoli sequence type. No statistically significant difference (p > 0.05) were found between the presence of the pathogens and boar age, sex, province and sample collection year. Data demonstrate for the first time the occurrence of B. vulpes and B. capreoli in wild boars, which may play a role in the biological cycle of piroplasmids. We emphasize the importance of monitoring these ungulates to prevent potential foci of infection. The engagement of hunters in epidemiological scientifically based surveys can constitute a technically sound control strategy of piroplasmids in a One Health perspective.

Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies.

Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared the amplicons generated by primers targeting different sites of the 16S rRNA gene found in the Human Oral Microbiome Database (HOMD). Six sets of primer targeting V1-V2, V1-V3, V3-V4, V4-V5, V5-V7 and V6-V8 regions of 16S rRNA were tested via in silico simulation. Primers targeting the V1-V2, V3-V4, and V4-V5 regions generated more than 90% of the original input sequences. Primers targeting the V1-V2 and V1-V3 regions exhibited a low number of mismatches and unclassified sequences at the taxonomic level, but there were notable discrepancies at the species level. Phylogenetic tree comparisons showed primers targeting the V1-V2 and V3-V4 regions showed performances similar to primers targeting the whole 16s RNA region in terms of separating total oral microbiomes and periodontopathogens. In an analysis of clinical oral samples, V1-V2 primers showed superior performance for identifying more taxa and had better resolution sensitivity for Streptococcus than V3-V4 primers. In conclusion, primers targeting the V1-V2 region of 16S rRNA showed the best performance for oral microbiome studies. In addition, the study demonstrates the need for careful PCR primer selections.

Characterization of Xanthomonas hortorum isolates causing leaf spot on Primula vulgaris

AbstractThe bacterial leaf spot of Primula vulgaris was reported from forest locations in Mazandaran province, Iran in 1995. The causative bacterium was initially identified as Xanthomonas campestris based on sequences of ITS and 16S rRNA regions. On the basis of sequences of gyrB and dnaK housekeeping genes, the isolates resembled strains of Xanthomonas hortorum. The present study was performed to clarify the taxonomic status of the incitant bacterium. Samples of P. vulgaris with leaf spot symptoms were collected from the Darabkola forest (Mazandaran province) and the bacterial strains were isolated on plates of glucose nutrient agar. Some isolates only induced hypersensitive reaction on geranium (Pelargonium × hortorum) leaves but a few isolates incited leaf spot symptoms when inoculated on P. vulgaris, P. heterochroma and P. × polyantha plants. The isolates were Gram stain, oxidase and urease negative but positive in tests for catalase and hydrolysis of gelatin, aesculin and Tween 80. Several unique nonpathogenic isolates were recovered with varying carbon source utilization profiles and different molecular features, including distinct ERIC‐PCR profiles. Representative gyrB, rpoD, dnaK and fyuA housekeeping genes were amplified by PCR and sequenced for comparison with Xanthomonas species in the GenBank database using maximum‐likelihood, maximum‐parsimony and Bayesian algorithms to construct phylogenetic trees. The pathogenic and nonpathogenic strains were closely related to X. hortorum pathovars. Therefore, it is likely that these isolates belong to a new pathovar of X. hortorum. Based on previous studies and our findings, we propose naming the strain causing primrose leaf spot as X. hortorum pv. primulicola.

The transcriptionally active bacterial communities of grapevine rhizosphere in dependence on rootstock and scion variety

The rhizosphere is where crucial processes for the productivity of viticultural systems occur. The composition of the bacterial communities associated with the rhizosphere of grapevines is known to depend on plant genotype. However, the genotype of grafted grapevines differs between scion and rootstock; the role of each genotype is unclear. To untangle the effect of scion and rootstock, the rRNA (V4–V5 region of 16S rRNA) extracted from the rhizosphere of the grape varieties Riesling and Mueller-Thurgau ungrafted vs grafted on different rootstocks was sequenced. The bioinformatic analysis with tools designed to be robust for compositional data showed that the investigated rootstocks or scions or combinations, respectively, recruited bacterial communities with distinguishable traits. Statistical differences were revealed between ungrafted Riesling vs Mueller-Thurgau, between grafted Riesling vs ungrafted Riesling, and between ungrafted Mueller-Thurgau vs grafted Mueller-Thurgau. Thus, confirming the role of scion and rootstock genotype as a driver of the structure and composition of bacterial communities in the rhizosphere of grapevines.