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The New Phytologist Mar 2020At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structure - a plant gall - accommodates various... (Review)
Review
At the colonization site of a foreign entity, plant cells alter their trajectory of growth and development. The resulting structure - a plant gall - accommodates various needs of the foreigner, which are phylogenetically diverse: viruses, bacteria, protozoa, oomycetes, true fungi, parasitic plants, and many types of animals, including rotifers, nematodes, insects, and mites. The plant species that make galls also are diverse. We assume gall production costs the plant. All is well if the foreigner provides a gift that makes up for the cost. Nitrogen-fixing nodule-inducing bacteria provide nutritional services. Gall wasps pollinate fig trees. Unfortunately for plants, most galls are made for foes, some of which are deeply studied pathogens and pests: Agrobacterium tumefaciens, Rhodococcus fascians, Xanthomonas citri, Pseudomonas savastanoi, Pantoea agglomerans, 'Candidatus' phytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges. Galls are an understudied phenomenon in plant developmental biology. We propose gall inception for discovering unifying features of the galls that plants make for friends and foes, talk about molecules that plants and gall-inducers use to get what they want from each other, raise the question of whether plants colonized by arbuscular mycorrhizal fungi respond in a gall-like manner, and present a research agenda.
Topics: Animals; Emigrants and Immigrants; Host-Parasite Interactions; Humans; Plant Tumors; Pseudomonas; Rhodococcus; Xanthomonas
PubMed: 31774564
DOI: 10.1111/nph.16340 -
Journal of Applied Microbiology Jul 2021Isolation, characterization and identification of possible microbial contaminant(s) in the inflated foil bag containing hop pellets packed and stored in a modified...
AIMS
Isolation, characterization and identification of possible microbial contaminant(s) in the inflated foil bag containing hop pellets packed and stored in a modified atmosphere.
METHODS AND RESULTS
Package gas of the inflated foil bag containing hop pellets was analysed by gas chromatography. Compared with the reference modified atmosphere, containing about 16 vol.% of CO , the inflated bag atmosphere contained 53 vol.% CO , suggesting possible microbial contamination. Therefore, several standard and mineral media, with added hop pellets or hop infusion, were used for cultivation at different temperatures under an anaerobic atmosphere. Cultivation in mineral medium with hop pellets yielded a bacterial isolate that was identified by MALDI-TOF mass spectrometry and verified by partial 16S rRNA gene analysis as Pantoea agglomerans, a known plant epiphyte.
CONCLUSIONS
A novel strain of P. agglomerans (designed as DBM 3696) was found to be suspicious of causing inflation of the foil bag containing dried hop pellets packed in modified atmosphere.
SIGNIFICANCE AND IMPACT OF THE STUDY
This study suggests that P. agglomerans, probably hop epiphyte, could cause sporadic inflation of bags with hop pellets packed in modified atmosphere causing logistical problems during bags transport.
Topics: Atmosphere; Food Packaging; Food Storage; Humulus; Mass Spectrometry; Pantoea; RNA, Ribosomal, 16S
PubMed: 33320407
DOI: 10.1111/jam.14970 -
Plant Disease Oct 2022Species of represent a group of plant pathogenic bacteria that infect a variety of agro-economically important plant species. Among these, a complex of , , , and...
Species of represent a group of plant pathogenic bacteria that infect a variety of agro-economically important plant species. Among these, a complex of , , , and subsp. cause center rot in onion, resulting in significant economic losses. As species of are phenotypically closely related, identification of species relies on the sequencing and phylogenetic analysis of housekeeping genes. To aid in rapid identification of species, efforts have been made in developing species-specific primers to be used in PCR assays. In the current study, two , one , one , and three published primers as well as newly developed PagR primers were evaluated for their specificity against 79 strains, belonging to 15 different species. To ensure that selected primers were evaluated against accurately identified species, sequencing and phylogenetic analysis of housekeeping gene were conducted. Thereafter, PCR assays using selected species-specific primers were performed. The results showed that previously described -specific PANA_1008; -specific allii-leuS; -specific PANST_rpoB, 3614galE, and DC283galE primers; and one newly designed -specific PagR primer pair were highly specific for their target species. They accurately identified these strains into their species and, in some cases, their subspecies level. The findings of the current study will facilitate rapid and reliable identification of , , , and
Topics: Pantoea; Phylogeny; Polymerase Chain Reaction; Species Specificity
PubMed: 35171633
DOI: 10.1094/PDIS-08-21-1810-SC -
Virus Research May 2023In this study, the genome of the lytic broad-host-range phage Key infecting Erwinia amylovora, Erwinia horticola, and Pantoea agglomerans strains was characterized. Key...
In this study, the genome of the lytic broad-host-range phage Key infecting Erwinia amylovora, Erwinia horticola, and Pantoea agglomerans strains was characterized. Key phage has a 115,651 bp long double-stranded DNA genome with the G + C ratio of 39.03%, encoding 182 proteins and 27 tRNA genes. The majority (69%) of predicted coding sequences (CDSs) encode proteins with unknown functions. The protein products of 57 annotated genes were found to have probable functions in nucleotide metabolism, DNA replication, recombination, repair, and packaging, virion morphogenesis, phage-host interaction and lysis. Furthermore, the product of gene 141 shared amino acid sequence similarity and conserved domain architecture with the exopolysaccharide (EPS) degrading proteins of Erwinia and Pantoea infecting phages as well as bacterial EPS biosynthesis proteins. Due to the genome synteny and similarity to the proteins of T5-related phages, phage Key, together with its closest relative, Pantoea phage AAS21, was suggested to represent a novel genus within the Demerecviridae family, for which we tentatively propose the name "Keyvirus".
Topics: Bacteriophages; Erwinia amylovora; Host Specificity; Virion; Genome, Viral
PubMed: 36907559
DOI: 10.1016/j.virusres.2023.199088 -
Plant Disease Nov 2023Nearly 5,400 hectares of long-day onions () are cultivated in the Central Zone of Chile (UTM 33°3´S to 37°24´S). During summer 2021-22 and 2022-23 (December to...
Nearly 5,400 hectares of long-day onions () are cultivated in the Central Zone of Chile (UTM 33°3´S to 37°24´S). During summer 2021-22 and 2022-23 (December to February), followed by high temperatures (around 35°C) and high humidity conditions, symptoms showing yellowing, soft rot, blight on old leaves, necrotic tips, and soft bulbs were observed. The affected plants were observed in "spots" into the fields, and the incidence reached 5-10%. The severity was high, and 70-80% of the affected plants died. Symptomatic plants from different fields from the Coquimbo, Metropolitan, O´Higgins and Maule regions were sampled. Isolations were made using casamino-acid peptone glucose (CPG) agar medium (Schaad, 2001). Yellow-pigmented, circular to irregular shaped colonies were observed. Molecular identification was carried out by partial 16S rRNA gene sequencing, resulting in the identification of 18 isolates of spp. from twelve different fields. Selected strains were biochemically analyzed using the GEN III BIOLOG microtest system (Hayward, CA) and were identified as spp. BLAST analyses of the 16S rRNA sequences (602 nt) of selected strains (GenBank Accession No. OR527817 to OR527819) against the NCBI Database resulted in the identification of species with 100% coverage and 100% identity. To determine the species of each strain, housekeeping gene (Delétoile et al. 2009) was amplified and sequenced (GenBank Accessions No. OR544061 to OR544063). BLAST analysis (802 nt) of selected strains resulted in 100% coverage and 100% identity, identifying three different species: , , and . species were isolated from both leaves and bulbs and no more than one species was observed per field. Pathogenicity assays in onion plants and bulbs were performed based on the methodology described by Asselin et al. (2018). Five onion plants cv. Cimarron of thirteen-week-old were inoculated by wounding an external leave with a sterile toothpick previously immersed in a bacterial suspension at ~ 108 CFU/mL and maintained at 26-28°C for 30 days in high humidity conditions. Control plants were inoculated with sterile water. Plants inoculated with spp. showed chlorosis, soft rot, and necrosis mainly in older leaves, as observed in the field, while negative control plants remained healthy. Pantoea spp. were re-isolated from the inoculated onion plants. Toothpicks dipped in the inoculum were stuck 4 cm into the shoulders of onion bulbs and incubated at 26°C for 20 days. Water was inoculated as a negative control. At the end of the incubation period, the bulbs were opened longitudinally across their inoculation sites and shrunken, brownish, watery scales were observed. species have been previously described as causing leaf blight of onions in Georgia and Michigan in the USA and South Africa, Brazil, and Uruguay (Hattingh and Walters 1981; Gitaitis and Gay 1997; Edens et al. 2006; Tho et al. 2015; De Armas et al. 2022; Rosende et al. 2022). was recently reported in Chile (Sepúlveda et al. 2023), but this is the first report of and affecting onions in central Chile. This detection is an alert call for the onion's growers and exporters in Chile for upcoming seasons, where conditions predisposing to disease may continue to occur. It is crucial to continue analyzing the factors that caused the appearance of this new disease in onions.
PubMed: 37990524
DOI: 10.1094/PDIS-09-23-1884-PDN -
Frontiers in Microbiology 2019Members of the genus are Gram-negative bacteria isolated from various environments. Taxonomic affiliation based on multilocus sequence analysis (MLSA) is used routinely...
Members of the genus are Gram-negative bacteria isolated from various environments. Taxonomic affiliation based on multilocus sequence analysis (MLSA) is used routinely for inferring accurate phylogeny and identification of bacterial species and genera. Partial sequences of five housekeeping genes (A, B, S, B, and G) were extracted from 206 draft or complete genomes of strains publicly available in databases and analyzed together with the representative sequences of the 25 validly published type strains to verify and assess their phylogenetic assignations. Of a total of 159 strains assigned to species level, 11.3% of the non-type strains were incorrectly assigned within suitable species. The highest proportion of misidentified strains was recorded in , 8 out of 15 (53.3%) inaccurate assignations at the species level. One probable reason for this incorrect classification could be the method previously used for strain identification. Forty-seven (22.8%) genome sequences were from strains identified at the genus level only ( sp.). A combination of MLSA, average nucleotide identities [ANI and MuMmer-based ANI (ANIm)], tetranucleotide usage pattern (TETRA), and genome-based DNA-DNA hybridization (gDDH) data was used to accurately assign 25 of the 47 strains to validly published species, while 17 strains could be assigned as putative novel species within the genus . Four genomes designed as sp. were identified as . Positive and significant correlation coefficients were computed between MLSA and all the indices derived from whole-genome sequences being proposed for species delimitation. gDDH exhibited the best correlation with MLSA while TETRA was the worst. Accurate species-level identification is key to a better understanding of bacterial diversity and evolution. The MLSA scheme used here could be instrumental to determine the correct taxonomic status of new whole-genome sequenced strains, especially non-type strains, before depositing into public databases.
PubMed: 31736906
DOI: 10.3389/fmicb.2019.02463 -
Microbiology Resource Announcements Nov 2023The Gram-negative bacterium has been isolated from various habitats including disease plants. Here, we present the genome of strain NBBC-01 obtained from rotten...
The Gram-negative bacterium has been isolated from various habitats including disease plants. Here, we present the genome of strain NBBC-01 obtained from rotten potatoes that were infected by . The genome information will prove advantageous in elucidating its ecological role.
PubMed: 37847025
DOI: 10.1128/MRA.00748-23 -
Microorganisms Sep 2020Bacteriophages are viruses capable of recognizing with high specificity, propagating inside of, and destroying their bacterial hosts. The phage lytic life cycle makes...
Bacteriophages are viruses capable of recognizing with high specificity, propagating inside of, and destroying their bacterial hosts. The phage lytic life cycle makes phages attractive as tools to selectively kill pathogenic bacteria with minimal impact on the surrounding microbiome. To effectively harness the potential of phages in therapy, it is critical to understand the phage-host dynamics and how these interactions can change in complex populations. Our model examined the interactions between the plant pathogen , the antagonistic epiphyte , and the bacteriophages that infect and kill both species. strains are used as a phage carrier; their role is to deliver and propagate the bacteriophages on the plant surface prior to the arrival of the pathogen. Using liquid cultures, the populations of the pathogen, carrier, and phages were tracked over time with quantitative real-time PCR. The jumbo phage ϕEa35-70 synergized with both the ϕEa21-4 and ϕEa46-1-A1 and was most effective in combination at reducing growth over 24 h. Phage ϕEa35-70, however, also reduced the growth of . Phage cocktails of ϕEa21-4, ϕEa46-1-A1, and ϕEa35-70 at multiplicities of infections (MOIs) of 10, 1, and 0.01, respectively, no longer inhibited growth of . When this cocktail was grown with for 8 h prior to pathogen introduction, pathogen growth was reduced by over four log units over 24 h. These findings present a novel approach to study complex phage-host dynamics that can be exploited to create more effective phage-based therapies.
PubMed: 32971807
DOI: 10.3390/microorganisms8091449 -
Molecular Plant-microbe Interactions :... Feb 2023The phytopathogen belongs to the Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Erwiniaceae in species classification. It causes disease symptoms in...
The phytopathogen belongs to the Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Erwiniaceae in species classification. It causes disease symptoms in many plants such as corn, banana, and walnut. This study aimed to report the complete genome of CHTF15, which represents the first whole-genome sequence of an isolate from diseased walnut leaves. The total length of the assembled genome was 4,820,607 bp, with an average GC content of 55.3%, including a circular chromosome and three circular plasmids, two of which were previously unreported sequences and one was announced previously. The CHTF15 genome helps understand the pathogenic mechanism of this important plant pathogen and provides an important theoretical basis for disease epidemic and field control. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
Topics: Pantoea; Juglans; Plasmids
PubMed: 36693088
DOI: 10.1094/MPMI-10-22-0216-A -
Frontiers in Microbiology 2023As the name of the genus ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils,...
As the name of the genus ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus . Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.
PubMed: 38029109
DOI: 10.3389/fmicb.2023.1254999