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Microbial Genomics Apr 2024(Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in this genus...
(Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in this genus have been found to play important roles as insect endosymbionts supplementing the diet of their hosts. Here, I describe Erwinia impunctatus (Erwimp) associated with the Highland midge (Diptera: Ceratopogonidae), an abundant biting pest in the Scottish Highlands. The genome of this new species was assembled using hybrid long and short read techniques, and a comparative analysis was undertaken with other members of the genus to understand its potential ecological niche and impact. Genome composition analysis revealed that Erwimp is similar to other endophytic and ectophytic species in the genus and is unlikely to be restricted to its insect host. Evidence for an additional plant host includes the presence of a carotenoid synthesis operon implicated as a virulence factor in plant-associated members in the sister genus . Unique features of Erwimp include several copies of intimin-like proteins which, along with signs of genome pseudogenization and a loss of certain metabolic pathways, suggests an element of host restriction seen elsewhere in the genus. Furthermore, a screening of individuals over two field seasons revealed the absence of the bacteria in during the second year indicating this microbe-insect interaction is likely to be transient. These data suggest that may have an important role to play beyond a biting nuisance, as an insect vector transmitting Erwimp alongside any conferred impacts to surrounding biota.
Topics: Humans; Animals; Ceratopogonidae; Erwinia; Genomics; Insect Vectors; Ecosystem
PubMed: 38630610
DOI: 10.1099/mgen.0.001242 -
Chemistry & Biodiversity Jun 2024One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy,...
One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n : 10) and after pre-enrichment (n : 10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.
Topics: Bacteria; Metagenomics; Olea; Turkey; RNA, Ribosomal, 16S; Microbiota; High-Throughput Nucleotide Sequencing
PubMed: 38613509
DOI: 10.1002/cbdv.202302120 -
FEMS Microbiology Ecology May 2024Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the...
Coffee leaf rust, caused by the fungus Hemileia vastatrix, has become a major concern for coffee-producing countries. Additionally, there has been an increase in the resistance of certain races of the fungus to fungicides and breeding cultivars, making producers use alternative control methods. In this work, we transplanted the leaf surface microbiota of rust-resistant coffee species (Coffea racemosa and Coffea stenophylla) to Coffea arabica and tested whether the new microbiota would be able to minimize the damage caused by H. vastatrix. It was seen that the transplant was successful in controlling rust, especially from C. stenophylla, but the protection depended on the concentration of the microbiota. Certain fungi, such as Acrocalymma, Bipolaris, Didymella, Nigrospora, Setophaeosphaeria, Simplicillium, Stagonospora and Torula, and bacteria, such as Chryseobacterium, Sphingobium and especially Enterobacter, had their populations increased and this may be related to the antagonism seen against H. vastatrix. Interestingly, the relative population of bacteria from genera Pantoea, Methylobacterium and Sphingomonas decreased after transplantation, suggesting a positive interaction between them and H. vastatrix development. Our findings may help to better understand the role of the microbiota in coffee leaf rust, as well as help to optimize the development of biocontrol agents.
Topics: Coffea; Plant Diseases; Plant Leaves; Basidiomycota; Microbiota; Disease Resistance; Bacteria; Fungi
PubMed: 38599638
DOI: 10.1093/femsec/fiae049 -
FEMS Microbiology Ecology Apr 2024As an important habitat for microorganisms, the phyllosphere has a great impact on plant growth and health, and changes in phyllosphere microorganisms are closely...
As an important habitat for microorganisms, the phyllosphere has a great impact on plant growth and health, and changes in phyllosphere microorganisms are closely related to the occurrence of leaf diseases. However, there remains a limited understanding regarding alterations to the microbial community in the phyllosphere resulting from pathogen infections. Here, we analyzed and compared the differences in phyllosphere microorganisms of powdery mildew cucumber from three disease severity levels (0% < L1 < 30%, 30% ≤ L2 < 50%, L3 ≥ 50%, the number represents the lesion coverage rate of powdery mildew on leaves). There were significant differences in α diversity and community structure of phyllosphere communities under different disease levels. Disease severity altered the community structure of phyllosphere microorganisms, Rosenbergiella, Rickettsia, and Cladosporium accounted for the largest proportion in the L1 disease grade, while Bacillus, Pantoea, Kocuria, and Podosphaera had the highest relative abundance in the L3 disease grade. The co-occurrence network analysis of the phyllosphere microbial community indicated that the phyllosphere bacterial community was most affected by the severity of disease. Our results suggested that with the development of cucumber powdery mildew, the symbiotic relationship between species was broken, and the entire bacterial community tended to compete.
Topics: Cucumis sativus; Plant Diseases; Microbiota; Ascomycota; Plant Leaves; Bacteria; RNA, Ribosomal, 16S
PubMed: 38599637
DOI: 10.1093/femsec/fiae050 -
Plant Disease Apr 2024Rice (Oryza sativa L.) is a crucial staple crop worldwide, and bacterial diseases are among the primary factors affecting rice yield. In late October 2022, bacterial...
Rice (Oryza sativa L.) is a crucial staple crop worldwide, and bacterial diseases are among the primary factors affecting rice yield. In late October 2022, bacterial leaf streak disease was observed on the leaves of the rice variety Meixiangzhan 2 across multiple fields (approximately 130 hm2) in Leizhou City, Guangdong Province, China. The incidence rate was up to 30% in each field. Infected rice leaves exhibited distinctive symptoms at the boundary between diseased and healthy tissue, featuring dark green to yellow-brown streaks, while most of the leaf margin exhibited symptoms of either leaf edge or sheath rot. Disease progression from the leaf tip inwards revealed gray-white or dehydrated lesions with a bluish-gray color. Some leaves exhibited wrinkling at the edges, and severe symptoms at the leaf tip resembled those of bacterial leaf blight in rice. Ten leaves were collected from 10 infected rice plants in three distinct fields, and leaf pieces at the border of diseased and healthy areas were surface disinfected with 75% anhydrous ethanol for 60 seconds, rinsed three times with sterile water, and then soaked in sterile water for 8 hours. The obtained bacterial suspension was diluted at a ratio of 1: 106, and 100 μL of the diluted samples were plated on Potato Dextrose Agar (PDA) plates. After incubation at 28°C for 48 hours, the yellow bacterial colonies that appeared, were purified on PDA plates. To confirm the bacterial species, the amplification of genes gyrB, leuS, rpoB, and 16S rDNA was performed on six randomly selected isolates from the three different fields using the primers 27F/1492R, gyrB-F/R, leuS-F/R and rpoB-F/R, as reported by Yu et al (2022), respectively. PCR products were sequenced. All six isolates had identical sequences for all genes sequenced.The gene sequences of 16S rDNA (960 bp), gyrB (953 bp), leuS (733 bp), and rpoB (877 bp) for LZ1, were deposited in the NCBI database under accession numbers PP048830 , PP068625 , PP068626, and PP068627, respectively. These sequences were subsequently compared using BLASTn tool against the NCBI nr/nt database. The 16S rDNA, gyrB, leuS, and rpoB of LZ1 showed similarities of 99.90%, 99.16%, 99.73%, and 99.89%, with the corresponding sequences of P. ananatis TZ39 (GenBank accession numbers MZ800600.1 for 16S rDNA, and CP081342.1 for gyrB, leuS and rpoB ). MLSA analysis using concatenated sequences of gyrB, leuS, and rpoB genes indicated that the isolated strain LZ1 belongs to P. ananatis. In the tillering stage of rice varieties Meixiangzhan 2 and Huahangyuzhan, P. ananatis LZ1 was inoculated at a concentration of 108 CFU/mL using the leaf-cutting method, with sterile water used as a control (Toh et al., 2019). After 14 days of bacterial inoculation, the inoculated leaves gradually became necrotic, changing from light green to brown showing identical symptoms as those in the field, while the control plants remained symptom-free. Subsequent 16S rDNA, gyrB, leuS and rpoB gene sequencing results further confirmed the identity of the pathogen as P. ananatis, thereby fulfilling Koch's postulates. Previous reports have already identified P. ananatis as the pathogen causing rice bacterial leaf streak (Kini et al., 2017; Arayaskul et al., 2019; Yu et al., 2022; Lu et al., 2022; Luna et al., 2023; Yuan et al., 2023). This is the first report of rice bacterial leaf streak caused by P. ananatis in Guangdong Province, China, laying the foundation for future research to establish strategies for the prevention and control of this disease.
PubMed: 38595062
DOI: 10.1094/PDIS-02-24-0421-PDN -
Frontiers in Microbiology 2024P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the order. In lysogens, it is maintained as a plasmid. We tested P1...
P1 is a model, temperate bacteriophage of the 94 kb genome. It can lysogenize representatives of the order. In lysogens, it is maintained as a plasmid. We tested P1 interactions with the biocontrol L15 strain to explore the utility of P1 in genome engineering. A P1 derivative carrying the Tn (cm) transposon could transfer a plasmid from to the L15 cells. The L15 cells infected with this derivative formed chloramphenicol-resistant colonies. They could grow in a liquid medium with chloramphenicol after adaptation and did not contain prophage P1 but the chromosomally inserted cm marker of P1 Tn (). The insertions were accompanied by various rearrangements upstream of the Tn gene promoter and the loss of IS (ISL) from the corresponding region. Sequence analysis of the L15 strain genome revealed a chromosome and three plasmids of 0.58, 0.18, and 0.07 Mb. The largest and the smallest plasmid appeared to encode partition and replication incompatibility determinants similar to those of prophage P1, respectively. In the L15 derivatives cured of the largest plasmid, P1 with Tn could not replace the smallest plasmid even if selected. However, it could replace the smallest and the largest plasmid of L15 if its Tn ISL sequence driving the Tn mobility was inactivated or if it was enriched with an immobile kanamycin resistance marker. Moreover, it could develop lytically in the L15 derivatives cured of both these plasmids. Clearly, under conditions of selection for P1, the mobility of the P1 selective marker determines whether or not the incoming P1 can outcompete the incompatible L15 resident plasmids. Our results demonstrate that can serve as a host for bacteriophage P1 and can be engineered with the help of this phage. They also provide an example of how antibiotics can modify the outcome of horizontal gene transfer in natural environments. Numerous plasmids of strains appear to contain determinants of replication or partition incompatibility with P1. Therefore, P1 with an immobile selective marker may be a tool of choice in curing these strains from the respective plasmids to facilitate their functional analysis.
PubMed: 38591037
DOI: 10.3389/fmicb.2024.1356206 -
Biomedical and Environmental Sciences :... Mar 2024The purpose of this study was to investigate the bacterial communities of biting midges and ticks collected from three sites in the Poyang Lake area, namely, Qunlu...
OBJECTIVE
The purpose of this study was to investigate the bacterial communities of biting midges and ticks collected from three sites in the Poyang Lake area, namely, Qunlu Practice Base, Peach Blossom Garden, and Huangtong Animal Husbandry, and whether vectors carry any bacterial pathogens that may cause diseases to humans, to provide scientific basis for prospective pathogen discovery and disease prevention and control.
METHODS
Using a metataxonomics approach in concert with full-length 16S rRNA gene sequencing and operational phylogenetic unit (OPU) analysis, we characterized the species-level microbial community structure of two important vector species, biting midges and ticks, including 33 arthropod samples comprising 3,885 individuals, collected around Poyang Lake.
RESULTS
A total of 662 OPUs were classified in biting midges, including 195 known species and 373 potentially new species, and 618 OPUs were classified in ticks, including 217 known species and 326 potentially new species. Surprisingly, OPUs with potentially pathogenicity were detected in both arthropod vectors, with 66 known species of biting midges reported to carry potential pathogens, including and , compared to 50 in ticks, such as and . We found that was the most dominant group in both midges and ticks. Furthermore, the outcomes demonstrated that the microbiota of midges and ticks tend to be governed by a few highly abundant bacteria. sp7 was predominant in biting midges, while sp1 was enriched in ticks. Meanwhile, spp., which may be essential for the survival of Neumann, were detected in all tick samples. The identification of dominant species and pathogens of biting midges and ticks in this study serves to broaden our knowledge associated to microbes of arthropod vectors.
CONCLUSION
Biting midges and ticks carry large numbers of known and potentially novel bacteria, and carry a wide range of potentially pathogenic bacteria, which may pose a risk of infection to humans and animals. The microbial communities of midges and ticks tend to be dominated by a few highly abundant bacteria.
Topics: Animals; Humans; Ticks; Ceratopogonidae; Phylogeny; RNA, Ribosomal, 16S; Prospective Studies; Microbiota; Coxiella
PubMed: 38582991
DOI: 10.3967/bes2024.030 -
The Science of the Total Environment Jun 2024Agriculture stands as a thriving enterprise in India, serving as both the bedrock of economy and vital source of nutrition. In response to the escalating demands for...
Agriculture stands as a thriving enterprise in India, serving as both the bedrock of economy and vital source of nutrition. In response to the escalating demands for high-quality food for swiftly expanding population, agricultural endeavors are extending their reach into the elevated terrains of the Himalayas, tapping into abundant resources for bolstering food production. Nonetheless, these Himalayan agro-ecosystems encounter persistent challenges, leading to crop losses. These challenges stem from a combination of factors including prevailing frigid temperatures, suboptimal farming practices, unpredictable climatic shifts, subdivided land ownership, and limited resources. While the utilization of chemical fertilizers has been embraced to enhance the quality of food output, genuine concerns have arisen due to the potential hazards they pose. Consequently, the present investigation was initiated with the objective of formulating environmentally friendly and cold-tolerant broad ranged bioinoculants tailored to enhance the production of Kidney bean while concurrently enriching its nutrient content across entire hilly regions. The outcomes of this study unveiled noteworthy advancements in kidney bean yield, registering a substantial increase ranging from 12.51 ± 2.39 % to 14.15 ± 0.83 % in regions of lower elevation (Jeolikote) and an even more remarkable surge ranging from 20.60 ± 3.03 % to 29.97 ± 5.02 % in higher elevated areas (Chakrata) compared to the control group. Furthermore, these cold-tolerant bioinoculants exhibited a dual advantage by fostering the enhancement of essential nutrients within the grains and fostering a positive influence on the diversity and abundance of microbial life in the rhizosphere. As a result, to effectively tackle the issues associated with chemical fertilizers and to achieve sustainable improvements in both the yield and nutrient composition of kidney bean across varying elevations, the adoption of cold-tolerant Enterobacter hormaechei CHM16, and Pantoea agglomerans HRM 23, including the consortium, presents a promising avenue. Additionally, this study has contributed significant insights-into the role of organic acids like oxalic acid in the solubilization of nutrients, thereby expanding the existing knowledge in this specialized field.
Topics: Rhizosphere; India; Cold Temperature; Biofortification; Phaseolus; Agriculture; Altitude; Soil Microbiology; Crops, Agricultural
PubMed: 38580128
DOI: 10.1016/j.scitotenv.2024.172204 -
Heliyon Apr 2024After harvesting, pathogens can infect fresh vegetables in different ways. Pathogenic bacteria associated with fresh vegetables can cause widespread epidemics associated...
After harvesting, pathogens can infect fresh vegetables in different ways. Pathogenic bacteria associated with fresh vegetables can cause widespread epidemics associated with foodborne illness. The aim of this study was to assess the microbiological quality of carrot slices after treatment with aqueous extracts of (AE) at different concentrations AE1 (10 mg/mL), AE2 (5 mg/mL), AE3 (2.5 mg/mL) and AE4 (1.25 mg/mL), and subsp. serovar Enteritidis, along with vacuum packaging and storage of carrots for 7 days at 4 °C. On days 1. and 7., total viable counts (TVC), and coliforms bacteria (CB), and count were all analysed. Microorganisms that were obtained from carrots were identified using MALDI-TOF MS Biotyper Mass Spectrometry. The total viable, coliform bacteria and counts were varied by the group of treatment. Higher counts were found in the control group on both days. The most isolated species of bacteria were and on the 1. day and on the 7. day. The current study adds useful information for a better understanding of how reacts to the effect of AE and its potential use as a sustainable washing method to eliminate bacteria from freshly cut carrots.
PubMed: 38576551
DOI: 10.1016/j.heliyon.2024.e29065 -
Frontiers in Microbiology 2024Lignocellulosic pretreatment is an important stage in biomass utilization, which usually requires high input. In this study, a low-cost method using combined ensiling...
Lignocellulosic pretreatment is an important stage in biomass utilization, which usually requires high input. In this study, a low-cost method using combined ensiling and NaOH was developed for lignocellulosic pretreatment. Sweet sorghum bagasse (SSB) was ensiled for 21 days and then treated with diluted NaOH (0%, 1%, and 2%) for fermentation. The results showed that the application of (L) reduced fermentation losses of the silages, mainly low water-soluble carbohydrate (WSC) and ammonia nitrogen loss. Meanwhile, the application of and ensiling enzyme (LE) promoted lignocellulosic degradation, as evidenced by low neutral detergent fiber (NDF), acid detergent fiber (ADF), lignin (ADL), and hemicellulosic (HC) contents. The dominant bacterial genera were , and after silage, which corresponded to the higher lactic acid and acetic contents and lower pH. The reducing sugar yields of SSB increased after combined pretreatment of silage and NaOH and were further enhanced by the 2% NaOH application, as evidenced by the high reducing sugar yield and microstructure damage, especially in the L-2% NaOH group and the LE-2% NaOH group, in which the reducing sugar yields were 87.99 and 94.45%, respectively, compared with those of the no additive control (CK)-0 NaOH group. Therefore, this study provides an effective method for SSB pretreatment to enhance biomass conservation.
PubMed: 38572245
DOI: 10.3389/fmicb.2024.1370686