-
BMC Genomics Nov 2022Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand...
Pantoea agglomerans DAPP-PG 734 was isolated as endophyte from knots (tumors) caused by Pseudomonas savastanoi pv. savastanoi DAPP-PG 722 in olive trees. To understand the plant pathogen-endophyte interaction on a genomic level, the whole genome of P. agglomerans DAPP-PG 734 was sequenced and annotated. The complete genome had a total size of 5'396'424 bp, containing one circular chromosome and four large circular plasmids. The aim of this study was to identify genomic features that could play a potential role in the interaction between P. agglomerans DAPP-PG 734 and P. savastanoi pv. savastanoi DAPP-PG 722. For this purpose, a comparative genomic analysis between the genome of P. agglomerans DAPP-PG 734 and those of related Pantoea spp. was carried out. In P. agglomerans DAPP-PG 734, gene clusters for the synthesis of the Hrp-1 type III secretion system (T3SS), type VI secretion systems (T6SS) and autoinducer, which could play an important role in a plant-pathogenic community enhancing knot formation in olive trees, were identified. Additional gene clusters for the biosynthesis of two different antibiotics, namely dapdiamide E and antibiotic B025670, which were found in regions between integrative conjugative elements (ICE), were observed. The in-depth analysis of the whole genome suggested a characterization of the P. agglomerans DAPP-PG 734 isolate as endophytic bacterium with biocontrol activity rather than as a plant pathogen.
Topics: Pantoea; Plant Diseases; Olea; Endophytes; Genomics
PubMed: 36344949
DOI: 10.1186/s12864-022-08966-y -
Applied and Environmental Microbiology Mar 2022Pantoea ananatis is an emerging plant pathogen that causes disease in economically important crops such as rice, corn, onion, melon, and pineapple, and it also infects...
Negatively Regulated Aerobactin and Desferrioxamine E by Fur in Pantoea ananatis Are Required for Full Siderophore Production and Antibacterial Activity, but Not for Virulence.
Pantoea ananatis is an emerging plant pathogen that causes disease in economically important crops such as rice, corn, onion, melon, and pineapple, and it also infects humans and insects. In this study, we identified biosynthetic gene clusters of aerobactin and desferrioxamine E (DFO-E) siderophores by using the complete genome of PA13 isolated from rice sheath rot. PA13 exhibited the strongest antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (). Mutants of aerobactin or DFO-E maintained antibacterial activity against E. amylovora and Y. enterocolitica, as well as in a siderophore activity assay. However, double aerobactin and DFO-E gene deletion mutants completely lost siderophore and antibacterial activity. These results reveal that both siderophore biosynthetic gene clusters are essential for siderophore production and antibacterial activity in PA13. A ferric uptake regulator protein (Fur) mutant exhibited a significant increase in siderophore production, and a Fur-overexpressing strain completely lost antibacterial activity. Expression of the , and genes was significantly increased in the Δ mutant background, and expression of these genes returned to wild-type levels after compensation. These results indicate that Fur negatively regulates aerobactin and DFO-E siderophores. However, siderophore production was not required for virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment. This study is the first to report the regulation and functional characteristics of siderophore biosynthetic genes in . Pantoea ananatis is a bacterium that causes diseases in several economically important crops, as well as in insects and humans. This bacterium has been studied extensively as a potentially dangerous pathogen due to its saprophytic ability. Recently, the types, biosynthetic gene clusters, and origin of the siderophores in the genus were determined by using genome comparative analyses. However, few genetic studies have investigated the characteristics and functions of siderophores in . The results of this study revealed that the production of aerobactin and desferrioxamine E in the rice pathogen PA13 is negatively regulated by Fur and that these siderophores are essential for antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (). However, siderophore production was not required for virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment.
Topics: Anti-Bacterial Agents; Humans; Hydroxamic Acids; Lactams; Pantoea; Siderophores; Virulence
PubMed: 35108090
DOI: 10.1128/aem.02405-21 -
Microorganisms Jul 2022Two bacteria belonging to the and genera were isolated from olive knots. Both bacterial strains were omnipresent in this study's olive orchard with high susceptibility...
Two bacteria belonging to the and genera were isolated from olive knots. Both bacterial strains were omnipresent in this study's olive orchard with high susceptibility of the autochthonous olive genotypes indicating coevolution of bacteria with host plants. Genomes of two endemic bacteria show conserved core genomes and genome plasticity. The ST1 genome has conserved virulence-related genes including genes for quorum sensing, pilus, and flagella biosynthesis, two copies of indole acetic acid biosynthesis (IAA) operons, type I-VI secretions systems, and genes for alginate and levan biosynthesis. Development of knots depends only on the presence of the ST1 strain which then allows paga strain co-infection and cohabitation in developed knots. The two bacteria are sensitive to a large number of antimicrobials, antibiotics, HO, and Cu (II) salts that can be efficiently used in propagation of bacterial free olive cultivars.
PubMed: 36013947
DOI: 10.3390/microorganisms10081529 -
Parasites & Vectors Feb 2022Emerging and re-emerging vector-borne diseases (VBDs) pose a recurring threat to tropical countries, mainly due to the abundance and distribution of the Aedes aegypti...
BACKGROUND
Emerging and re-emerging vector-borne diseases (VBDs) pose a recurring threat to tropical countries, mainly due to the abundance and distribution of the Aedes aegypti mosquito, which is a vector of the Zika, dengue, chikungunya, and yellow fever arboviruses.
METHODS
Female 3-5 day-old Ae. aegypti were distributed into two experimental groups: group I-survey of cultivable bacteria; sucrose group: fed only on sucrose, i.e., non-blood-fed (UF); blood-fed group: (i) fed with non-infected blood (BF); (ii) fed with blood infected with the Zika virus (BZIKV); (iii) pretreated with penicillin/streptomycin (pen/strep), and fed with non-infected blood (TBF); (iv) pretreated with pen/strep and fed blood infected with ZIKV, i.e., gravid with developed ovaries, (TGZIKV); group II-experimental co-infections: bacteria genera isolated from the group fed on sucrose, i.e., non-blood-fed (UF).
RESULTS
Using the cultivable method and the same mosquito colony and ZIKV strain described by in a previous work, our results reveled 11 isolates (Acinetobacter, Aeromonas, Cedecea, Cellulosimicrobium, Elizabethkingia, Enterobacter, Lysinibacillus, Pantoea, Pseudomonas, Serratia, and Staphylococcus). Enterobacter was present in all evaluated groups (i.e., UF, BF, BZIKV, TBF, and TGZIKV), whereas Elizabethkingia was present in the UF, BZIKV, and TBF groups. Pseudomonas was present in the BZIKV and TBF groups, whereas Staphylococcus was present in the TBF and TGZIKV groups. The only genera of bacteria that were found to be present in only one group were Aeromonas, Lysinibacillus, and Serratia (UF); Cedacea, Pantoea and Acinetobacter (BF); and Cellulosimicrobium (BZIKV). The mosquitoes co-infected with ZIKV plus the isolates group fed on sucrose (UF) showed interference in the outcome of infection.
CONCLUSIONS
We demonstrate that the distinct feeding aspects assessed herein influence the composition of bacterial diversity. In the co-infection, among ZIKV, Ae. aegypti and the bacterial isolates, the ZIKV/Lysinibacillus-Ae. aegypti had the lowest number of viral copies in the head-SG, which means that it negatively affects vector competence. However, when the saliva was analyzed after forced feeding, no virus was detected in the mosquito groups ZIKV/Lysinibacillus-Lu. longipalpis and Ae. aegypti; the combination of ZIKV/Serratia may interfere in salivation. This indicates that the combinations do not produce viable viruses and may have great potential as a method of biological control.
Topics: Aedes; Animals; Female; Microbiota; Mosquito Vectors; Zika Virus; Zika Virus Infection
PubMed: 35177110
DOI: 10.1186/s13071-022-05160-7 -
Microorganisms Aug 2021The bacterial genus has been widely evaluated as promising bacteria to increase phosphorus (P) availability in soil. The aim of this study was to characterize the...
The bacterial genus has been widely evaluated as promising bacteria to increase phosphorus (P) availability in soil. The aim of this study was to characterize the phosphate solubilizing (PS) activity of a strain and to evaluate the impact of its application in a semi-arid soil on phosphate availability and structure of the bacterial communities as a whole. An incubation experiment under close-to-natural soil environmental conditions was conducted for 15 days at 30 °C. High-throughput sequencing of the bacterial 16S rRNA gene was used to characterize and to compare the bacterial community structure of -inoculated soil with non-inoculated control. Furthermore, a qPCR-based method was developed for detection and quantification of the functional genes related to the expression of mineral phosphate solubilization (MPS) phenotype in . The results showed that in vitro solubilization of Ca(PO) by strain was very efficient (980 mg/L), and it was associated with a drop in pH due to the secretion of gluconic acid; these changes were concomitant with the detection of and genes. Moreover, inoculum application significantly increased the content of available P in semi-arid soil by 69%. Metagenomic analyses showed that treatment modified the overall edaphic bacterial community, significantly impacting its structure and composition. In particular, during inoculation the relative abundance of bacteria belonging to Firmicutes (mainly class) significantly increased, whereas the abundance of Actinobacteria together with Acidobacteria and Chloroflexi phyla decreased. Furthermore, genera known for their phosphate solubilizing activity, such as , , , and were exclusively detected in -treated soil. Pearson's correlation analysis revealed that changes in soil bacterial community composition were closely affected by soil characteristics, such as pH and available P. This study explores the effect of the inoculation of on the bacterial community structure of a semi-arid soil. The effectiveness in improving the phosphate availability and modification in soil bacterial community suggested that represent a promising environmental-friendly biofertilizer in arid and semi-arid ecosystems.
PubMed: 34442740
DOI: 10.3390/microorganisms9081661 -
Frontiers in Plant Science 2021is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and...
is a gram-negative bacterium and the primary causal agent of center rot of onions in Georgia. Previous genomic studies identified two virulence gene clusters, HiVir and , associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of pantaphos, (2-hydroxy[phosphono-methyl)maleate), a phosphonate phytotoxin. The gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other species suggests that these gene clusters are present outside of . To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and . Two hundred fifty-two strains of spp. were phenotyped using the red onion scale necrosis (RSN) assay and were genotyped using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 species, 41 isolation sources, and 23 countries, collected from 1946-2019, was tested. There is a significant association between the PCR assay and strains recovered from symptomatic onion ( < 0.001). There is also a significant association of a positive HiVir PCR and RSN assay among strains but not among spp., congeners. This may indicate a divergent HiVir cluster or different pathogenicity and virulence mechanisms. Last, we describe natural positive [RSN/HiVir/ ] strains, which cause extensive bulb necrosis in a neck-to-bulb infection assay compared to negative [RSN/HiVir/ ] strains. A combination of assays that include PCR of virulence genes [HiVir and ] and an RSN assay can potentially aid in identification of onion-bulb-rotting pathogenic strains.
PubMed: 33777079
DOI: 10.3389/fpls.2021.643787 -
Frontiers in Microbiology 2020Sugarcane is a major crop in tropical and subtropical regions of the world. In China, the application of large amounts of nitrogen (N) fertilizer to boost sugarcane...
Sugarcane is a major crop in tropical and subtropical regions of the world. In China, the application of large amounts of nitrogen (N) fertilizer to boost sugarcane yield is commonplace, but it causes substantial environmental damages, particularly soil, and water pollution. Certain rhizosphere microbes are known to be beneficial for sugarcane production, but much of the sugarcane rhizosphere microflora remains unknown. We have isolated several sugarcane rhizosphere bacteria, and 27 of them were examined for N-fixation, plant growth promotion, and antifungal activity. 16S rRNA gene sequencing was used to identify these strains. Among the isolates, several strains were found to have a relatively high activity of nitrogenase and ACC deaminase, the enzyme that reduces ethylene production in plants. These strains were found to possess and genes associated with N-fixation and ethylene production, respectively. Two of these strains, -AA7 and -BY4 showed maximum plant growth promotion (PGP) and nitrogenase activity, and thus they were selected for detailed analysis. The results show that they colonize different sugarcane tissues, use various growth substrates (carbon and nitrogen), and tolerate various stress conditions (pH and osmotic stress). The positive effect of AA7 and BY4 strains on and stress-related gene (, , , , and ) expression and the induction of defense-related processes in two sugarcane varieties, GT11 and GXB9, showed their potential for stress amelioration and PGP. Both bacterial strains increased several sugarcane physiological parameters. i.e., plant height, shoot weight, root weight, leaf area, chlorophyll content, and photosynthesis, in plants grown under greenhouse conditions. The ability of rhizobacteria on N-fixing in sugarcane was also confirmed by a N isotope-dilution study, and the estimate indicates a contribution of 21-35% of plant nitrogen by rhizobacterial biological N fixation (BNF). This is the first report of sugarcane growth promotion by N-fixing rhizobacteria and strains. Both strains could be used as biofertilizer for sugarcane to minimize nitrogen fertilizer use and better disease management.
PubMed: 33510724
DOI: 10.3389/fmicb.2020.600417 -
Scientific Reports Jul 2022The use of rhizobacteria provide great benefits in terms of nitrogen supply, suppression of plant diseases, or production of vitamins and phytohormones that stimulate...
The use of rhizobacteria provide great benefits in terms of nitrogen supply, suppression of plant diseases, or production of vitamins and phytohormones that stimulate the plant growth. At the same time, cyanobacteria can photosynthesize, fix nitrogen, synthesize substances that stimulate rhizogenesis, plant aerial growth, or even suppose an extra supply of carbon usable by heterotrophic bacteria, as well as act as biological control agents, give them an enormous value as plant growth promoters. The present study focused on the in vitro establishment of consortia using heterotrophic bacteria and cyanobacteria and the determination of their effectiveness in the development of tomato seedlings. Microbial collection was composed of 3 cyanobacteria (SAB-M612 and SAB-B866 belonging to Nostocaceae Family) and GS (unidentified cyanobacterium) and two phosphate and potassium solubilizing heterotrophic bacteria (Pseudomonas putida-BIO175 and Pantoea cypripedii-BIO175). The results revealed the influence of the culture medium, incubation time and the microbial components of each consortium in determining their success as biofertilizers. In this work, the most compatible consortia were obtained by combining the SAB-B866 and GS cyanobacteria with either of the two heterotrophic bacteria. Cyanobacteria GS promoted the growth of both rhizobacteria in vitro (increasing logarithmic units when they grew together). While Cyanobacteria SAB-B866 together with both rhizobacteria stimulated the growth of tomato seedlings in planta, leading to greater aerial development of the treated seedlings. Parameters such as fresh weight and stem diameter stood out in the plants treated with the consortia (SAB-B866 and both bacteria) compared to the untreated plants, where the values doubled. However, the increase was more discrete for the parameters stem length and number of leaves. These results suggest that the artificial formulation of microbial consortia can have positive synergistic effects on plant growth, which is of enormous agro-biotechnological interest.
Topics: Cyanobacteria; Solanum lycopersicum; Microbial Consortia; Nitrogen; Plant Roots; Seedlings
PubMed: 35909166
DOI: 10.1038/s41598-022-17547-8 -
Microorganisms Jan 2020Distinctive strains of are used as soil inoculants for their ability to promote plant growth. strain C1, previously isolated from the phyllosphere of lettuce, can...
Distinctive strains of are used as soil inoculants for their ability to promote plant growth. strain C1, previously isolated from the phyllosphere of lettuce, can produce indole-3-acetic acid (IAA), solubilize phosphate, and inhibit plant pathogens, such as . In this paper, the complete genome sequence of strain C1 is reported. In addition, experimental evidence is provided on how the strain tolerates arsenate As (V) up to 100 mM, and on how secreted metabolites like IAA and siderophores act as biostimulants in tomato cuttings. The strain has a circular chromosome and two prophages for a total genome of 4,846,925-bp, with a DNA G+C content of 55.2%. Genes related to plant growth promotion and biocontrol activity, such as those associated with IAA and spermidine synthesis, solubilization of inorganic phosphate, acquisition of ferrous iron, and production of volatile organic compounds, siderophores and GABA, were found in the genome of strain C1. Genome analysis also provided better understanding of the mechanisms underlying strain resistance to multiple toxic heavy metals and transmission of these genes by horizontal gene transfer. Findings suggested that strain C1 exhibits high biotechnological potential as plant growth-promoting bacterium in heavy metal polluted soils.
PubMed: 31979031
DOI: 10.3390/microorganisms8020153 -
MicrobiologyOpen Jan 2021Carotenoids are widely used in functional foods, cosmetics, and health supplements, and their importance and scope of use are continuously expanding. Here, we...
Carotenoids are widely used in functional foods, cosmetics, and health supplements, and their importance and scope of use are continuously expanding. Here, we characterized carotenoid biosynthetic genes of the plant-pathogenic bacterium Pantoea ananatis, which carries a carotenoid biosynthetic gene cluster (including crtE, X, Y, I, B, and Z) on a plasmid. Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that the crtEXYIB gene cluster is transcribed as a single transcript and crtZ is independently transcribed in the opposite direction. Using splicing by overlap extension with polymerase chain reaction (SOE by PCR) based on asymmetric amplification, we reassembled crtE-B, crtE-B-I, and crtE-B-I-Y. High-performance liquid chromatography confirmed that Escherichia coli expressing the reassembled crtE-B, crtE-B-I, and crtE-B-I-Y operons produced phytoene, lycopene, and β-carotene, respectively. We found that the carotenoids conferred tolerance to UV radiation and toxoflavin. Pantoea ananatis shares rice environments with the toxoflavin producer Burkholderia glumae and is considered to be the first reported example of producing and using carotenoids to withstand toxoflavin. We confirmed that carotenoid production by P. ananatis depends on RpoS, which is positively regulated by Hfq/ArcZ and negatively regulated by ClpP, similar to an important regulatory network of E. coli (Hfq →RpoS Ͱ ClpXP). We also demonstrated that Hfq-controlled quorum signaling de-represses EanR to activate RpoS, thereby initiating carotenoid production. Survival genes such as those responsible for the production of carotenoids of the plant-pathogenic P. ananatis must be expressed promptly to overcome stressful environments and compete with other microorganisms. This mechanism is likely maintained by a brake with excellent performance, such as EanR.
Topics: Bacterial Proteins; Carotenoids; Endopeptidase Clp; Escherichia coli; Escherichia coli Proteins; Host Factor 1 Protein; Multigene Family; Pantoea; Plasmids; Pyrimidinones; Quorum Sensing; Sigma Factor; Triazines; Ultraviolet Rays
PubMed: 33269542
DOI: 10.1002/mbo3.1143