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Microorganisms Dec 2022, the causative agent of fire blight, leads to important economic losses of apple and pear crops worldwide. This study aimed to investigate the potential of the resident...
, the causative agent of fire blight, leads to important economic losses of apple and pear crops worldwide. This study aimed to investigate the potential of the resident microbiota of the apple blossom in combatting plant disease-causing organisms, with a focus on controlling fire blight. We obtained 538 isolates from sites around Canton Zurich, which we tested for activity against and We also evaluated the isolates' activity against oomycete and fungal pathogens. Nine isolates showed activity against , and eight of these against . Furthermore, 117 showed antifungal, and 161 anti-oomycete, activity. We assigned genera and in some cases species to 238 of the isolates by sequencing their 16S RNA-encoding gene. Five strains showed activity against all pathogens and were tested in a detached apple model for anti- activity. Of these five strains, two were able to antagonize , namely #124 and #378. We sequenced the #378 genome and analyzed it for secondary metabolite clusters using antiSMASH, revealing the presence of a putative bacteriocin cluster. We also showed that #124 exhibits strong activity against three different fungi and two oomycetes in vitro, suggesting a broader capacity for biocontrol. Our results showcase the protective potential of the natural apple blossom microbiota. We isolated two candidate biocontrol strains from apple blossoms, suggesting that they might persist at the most common entry point for the causative agent of fire blight. Furthermore, they are probably already part of the human diet, suggesting they might be safe for consumption, and thus are promising candidates for biocontrol applications.
PubMed: 36557734
DOI: 10.3390/microorganisms10122480 -
International Journal of Molecular... Jul 2021A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp)...
A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a gene encoding a preQ DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of phages. Thus, the data presented in this study provide new information on -infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
Topics: DNA, Viral; Genome, Viral; Guanosine; Open Reading Frames; Pantoea; Siphoviridae; Viral Proteins
PubMed: 34298953
DOI: 10.3390/ijms22147333 -
Microorganisms May 2022a gram-negative bacterium belonging to the family, is a well-known phytopathogen isolated from many ecological niches and plant hosts. However, this bacterium also... (Review)
Review
a gram-negative bacterium belonging to the family, is a well-known phytopathogen isolated from many ecological niches and plant hosts. However, this bacterium also provides us with various beneficial characteristics, such as the growth promotion of their host plants and increased crop yield. Some isolated non-pathogenic strains are promising for the microbial production of useful substances. AJ13355 was isolated as an acidophilic bacterium and was used as an excellent host to produce L-glutamic acid under acidic conditions. The genome sequence of AJ13355 was determined, and specific genome-engineering technologies were developed. As a result, was successfully used to construct a bacterial strain that produces cysteine, a sulfur-containing amino acid that has been difficult to produce through fermentation because of complex regulation. Furthermore, by heterologous expression including plant-derived genes, construction of a strain that produces isoprenoids such as isoprene and linalool as secondary metabolites was achieved. is shown to be a useful host for the production of secondary metabolites, as well as amino acids, and is expected to be used as a platform for microbial production of bioactive substances, aromatic substances, and other high-value-added substances of plant origin in the future.
PubMed: 35744651
DOI: 10.3390/microorganisms10061133 -
The Science of the Total Environment Jul 2022Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when...
Antimicrobial resistance (AMR) is becoming an increasing global concern and the anaerobic digestion (AD) process represents a potential transmission route when digestates are used as fertilizing agents. AMR contaminants, e.g. antibiotic-resistant bacteria (ARB) and plasmid-mediated antibiotic resistance genes (ARGs) have been found in different substrates and AD systems, but not yet been investigated in plant-based substrates. AMR transfer from soils to vegetable microbiomes has been observed, and thus crop material potentially represents a so far neglected AMR load in agricultural AD processes, contributing to AMR spread. In order to test this hypothesis, this study examined the AMR situation throughout the process of three biogas plants using plant-based substrates only, or a mixture of plant-based and manure substrates. The evaluation included a combination of culture-independent and -dependent methods, i.e., identification of ARGs, plasmids, and pathogenic bacteria by DNA arrays, and phylogenetic classification of bacterial isolates and their phenotypic resistance pattern. To our knowledge, this is the first study on AMR in plant-based substrates and the corresponding biogas plant. The results showed that the bacterial community isolated from the investigated substrates and the AD processing facilities were mainly Gram-positive Bacillus spp. Apart from Pantoea agglomerans, no other Gram-negative species were found, either by bacteria culturing or by DNA typing array. In contrast, the presence of ARGs and plasmids clearly indicated the existence of Gram-negative pathogenic bacteria, in both substrate and AD process. Compared with substrates, digestates had lower levels of ARGs, plasmids, and culturable ARB. Thus, digestate could pose a lower risk of spreading AMR than substrates per se. In conclusion, plant-based substrates are associated with AMR, including culturable Gram-positive ARB and Gram-negative pathogenic bacteria-associated ARGs and plasmids. Thus, the AMR load from plant-based substrates should be taken into consideration in agricultural biogas processing.
Topics: Angiotensin Receptor Antagonists; Angiotensin-Converting Enzyme Inhibitors; Anti-Bacterial Agents; Bacteria; Biofuels; Drug Resistance, Bacterial; Genes, Bacterial; Gram-Negative Bacteria; Phylogeny
PubMed: 35306061
DOI: 10.1016/j.scitotenv.2022.154556 -
Journal of Applied Microbiology Nov 2022The rhizosphere is the region around the plant roots where maximum microbial activities occur. In the rhizosphere, microorganisms' beneficial and harmful activities... (Review)
Review
The rhizosphere is the region around the plant roots where maximum microbial activities occur. In the rhizosphere, microorganisms' beneficial and harmful activities affect plant growth and development. The mutualistic rhizospheric bacteria which improve plant growth and health are known as plant growth-promoting rhizobacteria (PGPR). They are very important due to their ability to help the plant in diverse ways. PGPR such as Pseudomonas, Bacillus, Azospirillum, Azotobacter, Arthrobacter, Achromobacter, Micrococcus, Enterobacter, Rhizobium, Agrobacterium, Pantoea and Serratia are now very well known. Rhizomicrobiome plays critical roles in nutrient acquisition and assimilation, improved soil texture, secreting and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics and various signal compounds, all leading to the enhancement of plant growth and development. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. In this review, we highlight the rhizobacteria diversity and cutting-edge findings focusing on the role of a PGPR in plant growth and development. We also discussed the role of PGPR in resisting the adverse effects arising from various abiotic (drought, salinity, heat, heavy metals) stresses.
Topics: Plant Development; Rhizosphere; Stress, Physiological; Plant Roots; Soil Microbiology; Soil; Metals, Heavy; Pantoea; Anti-Bacterial Agents; Hormones
PubMed: 36017561
DOI: 10.1111/jam.15796 -
Plant Disease Feb 2022Peanut ( L.) is cultivated in tropical and subtropical regions of the world as an important source of oil and protein. Until now, bacterial wilt, caused by , was the...
Peanut ( L.) is cultivated in tropical and subtropical regions of the world as an important source of oil and protein. Until now, bacterial wilt, caused by , was the only known bacterial disease of peanut. In 2020, widespread incidence of poor stand establishment was observed in multiple production fields planted to the Spanish-type peanut varieties in the Texas Panhandle. The observed symptoms included seed rot, pre- and postemergence damping-off, poor seedling vigor, poorly developed root systems with little or no nodule formation, and death. Subsequent diagnosis of symptomatic seedlings recovered two bacterial species identified by BLAST using 676- and 661-bp 16S rRNA fragments as a sp. and a sp., respectively. To investigate a possible causative role of these bacteria in the observed peanut disease, the pathogenicity of the two isolates was evaluated under greenhouse conditions relying on Koch's postulates. Cell suspensions of the two bacteria, separately and in combination, were used to inoculate seeds of a Valencia-type peanut variety with no history of the disease and found to be pathogenic on the resultant seedling plants. Symptoms that developed on the inoculated plants were similar to the symptoms initially observed in the field, including seed rot, pre- and postemergence damping-off, poor seedling vigor, and root establishment. The two bacteria were also successfully recovered from inoculated and symptomatic plants, thus satisfying Koch's postulates. Given the early onset of symptom development on affected seeds and seedlings, a seedborne origin of the disease, described here as early-decline bacterial disease of peanut, was investigated in the same batches of peanut seeds that were planted, as well as seeds later harvested in some of the affected fields. Identical bacterial species, on the basis of 16S rRNA identity, were recovered from all of the seeds evaluated indicating that the bacteria are both seedborne and seed-transmissible. Multilocus sequence analysis involving six genes (, , , , , and ) showed that these new strains are most closely related to and , but also phylogenetically distinct. The two bacteria were designated sp. strain B265 and sp. strain B270. Losses from the disease in affected fields in 2020 averaged 50% (US$1.12 million) from a total of nine production fields. Findings from this study provide evidence for two new bacterial pathogens of peanuts capable of infecting Spanish and Valencia peanut varieties.
Topics: Arachis; Bacteria; Plant Diseases; RNA, Ribosomal, 16S; Seedlings; Texas
PubMed: 34597146
DOI: 10.1094/PDIS-07-21-1555-RE -
BMC Plant Biology Oct 2023In nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse...
BACKGROUND
In nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse pathogens. However, little is known about how the host plant initially responds to different beneficial bacteria. To reveal the impact of different bacteria on barley (Hordeum vulgare), bacterial colonization patterns, gene expression, and composition of seed endophytes were explored.
RESULTS
This study used the soil-borne Ensifer meliloti, as well as Pantoea sp. and Pseudomonas sp. isolated from barley seeds, individually. The results demonstrated that those bacteria persisted in the rhizosphere but with different colonization patterns. Although root-leaf translocation was not observed, all three bacteria induced systemic resistance (ISR) against foliar fungal pathogens. Transcriptome analysis revealed that ion- and stress-related genes were regulated in plants that first encountered bacteria. Iron homeostasis and heat stress responses were involved in the response to E. meliloti and Pantoea sp., even if the iron content was not altered. Heat shock protein-encoding genes responded to inoculation with Pantoea sp. and Pseudomonas sp. Furthermore, bacterial inoculation affected the composition of seed endophytes. Investigation of the following generation indicated that the enhanced resistance was not heritable.
CONCLUSIONS
Here, using barley as a model, we highlighted different responses to three different beneficial bacteria as well as the influence of soil-borne Ensifer meliloti on the seed microbiome. In total, these results can help to understand the interaction between ISR-triggering bacteria and a crop plant, which is essential for the application of biological agents in sustainable agriculture.
Topics: Hordeum; Pseudomonas; Endophytes; Bacteria; Iron; Soil; Plant Roots
PubMed: 37789272
DOI: 10.1186/s12870-023-04484-5 -
International Microbiology : the... Aug 2021Bdellovibrios are predatory bacteria that invade other live Gram-negative bacterial cells for growth and reproduction. They have recently been considered as potential...
Predatory and biocontrol potency of Bdellovibrio bacteriovorus toward phytopathogenic strains of Pantoea sp. and Xanthomonas campestris in the presence of exo-biopolymers: in vitro and in vivo assessments.
Bdellovibrios are predatory bacteria that invade other live Gram-negative bacterial cells for growth and reproduction. They have recently been considered as potential living antibiotics and biocontrol agents. In this study, the predatory activity and biocontrol potency of Bdellovibrio bacteriovorus strain SOIR-1 against Pantoea sp. strain BCCS and Xanthomonas campestris, two exo-biopolymer-producing phytopathogens, was evaluated. Plaque formation assays and lysis analysis in the broth co-cultures were used for the in vitro evaluation of bacteriolytic activity of strain SOIR-1. The in vivo biocontrol potential of strain SOIR-1 was evaluated by pathogenicity tests on the onion bulbs and potato tuber slices. The phytopathogens were also recovered from the infected plant tissues and confirmed using biochemical tests and PCR-based 16S rRNA gene sequence analysis. Typical bdellovibrios plaques were developed on the lawn cultures of Pantoea sp. BCCS and X. campestris. The killing rate of strain SOIR-1 toward Pantoea sp. BCCS and X. campestris was 84.3% and 76.3%, respectively. Exo-biopolymers attenuated the predation efficiency of strain SOIR-1 up to 10.2-18.2% (Pantoea sp. BCCS) and 12.2-17.3% (X. campestris). The strain SOIR-1 significantly reduced rotting symptoms in the onion bulbs caused by Pantoea sp. BCCS (69.0%) and potato tuber slices caused by X. campestris (73.1%). Although more field assessments are necessary, strain SOIR-1 has the preliminary potential as a biocontrol agent against phytopathogenic Pantoea sp. BCCS and X. campestris, especially in postharvest storage. Due to the particular physicochemical properties of evaluated exo-biopolymers, they can be used in the designing encapsulation systems for delivery of bdellovibrios.
Topics: Antibiosis; Bdellovibrio bacteriovorus; Biological Control Agents; Biopolymers; Coculture Techniques; DNA, Bacterial; Microbial Interactions; Pantoea; RNA, Ribosomal, 16S; Xanthomonas campestris
PubMed: 33956240
DOI: 10.1007/s10123-021-00177-x -
Frontiers in Microbiology 2022The experimental study was contrived to characterize two zinc-solubilizing bacteria (ZSB), namely BMRR126 and BMAR64, and their role in zinc (Zn) biofortification of...
The experimental study was contrived to characterize two zinc-solubilizing bacteria (ZSB), namely BMRR126 and BMAR64, and their role in zinc (Zn) biofortification of rice. These bacteria solubilized Zn profoundly, determined qualitatively by halo-zone formation on a solid medium and quantitatively in a liquid broth by AAS and SEM-EDX. The lowering of pH and contact angle assessment of the liquid broth unveiled the establishment of the acidic conditions in a medium suitable for Zn solubilization. The characterization of both isolates on the basis of 16S rRNA gene analysis was identified as and , respectively. These strains were also found to have some plant probiotic traits namely phosphate solubilization, production of siderophore, indole acetic acid (IAA), exopolysaccharide (EPS), and ammonia. The field experiments were performed at two diverse locations and under all treatments; the simultaneous use of BMRR126 and BMAR64 with zinc oxide (ZnO) resulted in the highest growth and productivity of the paddy crop. The utmost Zn achievement in the grain was estimated in a treatment (T9) (25.07 mg/kg) containing a consortium of BMRR126 and BMAR64 along with ZnO for the . The treatment containing single ZSB bioinoculant BMRR126 (T7) showed an elevated Zn amount in the rice grain (33.25 mg/kg) for the . The soil parameters (pH, EC, organic carbon, NPK, available Zn, and dehydrogenase activity) were also positively influenced under all bacterial treatments compared to the uninoculated control. Our study clearly accentuates the need for Zn solubilizing bacteria (ZSB) to provide the benefits of Zn-biofortification in different regions.
PubMed: 35602065
DOI: 10.3389/fmicb.2022.852192 -
Molecular Biotechnology Nov 2023In the past two decades, 25 different species of the genus Pantoea within the Enterobacteriaceae family, have been isolated from different environmental niches. These... (Review)
Review
In the past two decades, 25 different species of the genus Pantoea within the Enterobacteriaceae family, have been isolated from different environmental niches. These species have a wide range of biological roles. Versatility in functions and hosts indicate that this genus has undergone extensive genetic diversification, which can be attributed to the different extra-chromosomal genetic elements or plasmids found across this genus. We have analyzed the functions of these plasmids and categorized them into four major groups for a better understanding of their future applications. The first and second group includes plasmids that contribute to genetic diversification and pathogenicity, respectively. The third group comprises cryptic plasmids of Pantoea. The last group includes plasmids that play a role in the metabolic versatility of the genus Pantoea. We have analyzed the data available up to May 2023 from two databases (viz; NCBI and PLSDB). In our analysis we have found a vast gap in knowledge. Complete gene annotations are available for only a few of the plasmids. This review highlights these challenges as an avenue for future research.
PubMed: 38007817
DOI: 10.1007/s12033-023-00960-3