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Teresa A Coutinho - One of the best experts on this subject based on the ideXlab platform.
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The Distribution of Onion Virulence Gene Clusters Among Pantoea spp.
Frontiers in plant science, 2021Co-Authors: Shaun P. Stice, Teresa A Coutinho, Gi Yoon Shin, Stefanie De Armas, Santosh Koirala, Guillermo A. Galván, María Inés Siri, Paul M. Severns, Bhabesh Dutta, Brian H. KvitkoAbstract:Pantoea ananatis 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 alt, associated with center rot. The HiVir gene cluster is required to induce necrosis on onion tissues via synthesis of a predicted small molecule toxin. The alt gene cluster aids in tolerance to thiosulfinates generated during onion tissue damage. Whole genome sequencing of other Pantoea species suggest that these gene clusters are present outside of P. ananatis. To assess the distribution of these gene clusters, two PCR primer sets were designed to detect the presence of HiVir and alt. Two hundred fifty-two strains of Pantoea spp. were phenotyped using the red onion scale necrosis (RSN) assay and were assayed using PCR for the presence of these virulence genes. A diverse panel of strains from three distinct culture collections comprised of 24 Pantoea species, 41 isolation sources, and 23 countries, collected from 1946-2019, were tested. There is a significant association between the alt PCR assay and Pantoea strains recovered from symptomatic onion (P
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Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites
Standards in Genomic Sciences, 2016Co-Authors: Marike Palmer, Teresa A Coutinho, Pieter De Maayer, Michael Poulsen, Emma T. Steenkamp, Elritha Van Zyl, Stephanus N. VenterAbstract:The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.
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the large universal Pantoea plasmid lpp 1 plays a major role in biological and ecological diversification
BMC Genomics, 2012Co-Authors: Pieter De Maayer, S N Venter, Theo H. M. Smits, Jochen Blom, Brion Duffy, Waiyin Chan, Teresa A CoutinhoAbstract:Pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant and animal hosts. This suggests that members of this genus have undergone extensive genotypic diversification. One means by which this occurs among bacteria is through the acquisition and maintenance of plasmids. Here, we have analyzed and compared the sequences of a large plasmid common to all sequenced Pantoea spp. The L arge P antoea P lasmids (LPP-1) of twenty strains encompassing seven different Pantoea species, including pathogens and endo-/epiphytes of a wide range of plant hosts as well as insect-associated strains, were compared. The LPP-1 plasmid sequences range in size from ~281 to 794 kb and carry between 238 and 750 protein coding sequences (CDS). A core set of 46 proteins, encompassing 2.2% of the total pan-plasmid (2,095 CDS), conserved among all LPP-1 plasmid sequences, includes those required for thiamine and pigment biosynthesis. Phylogenetic analysis reveals that these plasmids have arisen from an ancestral plasmid, which has undergone extensive diversification. Analysis of the proteins encoded on LPP-1 also showed that these plasmids contribute to a wide range of Pantoea phenotypes, including the transport and catabolism of various substrates, inorganic ion assimilation, resistance to antibiotics and heavy metals, colonization and persistence in the host and environment, pathogenesis and antibiosis. LPP-1 is universal to all Pantoea spp. whose genomes have been sequenced to date and is derived from an ancestral plasmid. LPP-1 encodes a large array of proteins that have played a major role in the adaptation of the different Pantoea spp. to their various ecological niches and their specialization as pathogens, biocontrol agents or benign saprophytes found in many diverse environments.
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Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus.
International journal of systematic and evolutionary microbiology, 2011Co-Authors: Carrie L Brady, Ilse Cleenwerck, Teresa A Coutinho, Stephanus N. Venter, Lorinda Van Der Westhuizen, Paul De VosAbstract:Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa, Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA-DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273(T)=BD 943(T) (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa)=BCC 581(T) (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275(T)=BD 944(T)=BCC 571(T)) and Pantoea wallisii sp. nov. (type strain LMG 26277(T)=BD 946(T)=BCC 682(T)) are proposed.
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Pantoea allii sp. nov., isolated from onion plants and seed
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Paul De Vos, Teresa Goszczynska, Ronald D. Gitaitis, Teresa A CoutinhoAbstract:Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed .97% 16S rRNA gene sequence similarity with strain BD 390 T , the isolates exhibited 11–55% whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390 T (5LMG 24248 T ).
Ilse Cleenwerck - One of the best experts on this subject based on the ideXlab platform.
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Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus.
International journal of systematic and evolutionary microbiology, 2011Co-Authors: Carrie L Brady, Ilse Cleenwerck, Teresa A Coutinho, Stephanus N. Venter, Lorinda Van Der Westhuizen, Paul De VosAbstract:Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa, Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA-DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273(T)=BD 943(T) (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa)=BCC 581(T) (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275(T)=BD 944(T)=BCC 571(T)) and Pantoea wallisii sp. nov. (type strain LMG 26277(T)=BD 946(T)=BCC 682(T)) are proposed.
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Pantoea allii sp. nov., isolated from onion plants and seed
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Paul De Vos, Teresa Goszczynska, Ronald D. Gitaitis, Teresa A CoutinhoAbstract:Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed .97% 16S rRNA gene sequence similarity with strain BD 390 T , the isolates exhibited 11–55% whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390 T (5LMG 24248 T ).
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Pantoea gaviniae sp nov and Pantoea calida sp nov isolated from infant formula and an infant formula production environment
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Alexandra Popp, Ilse Cleenwerck, Paul De Vos, Carol Iversen, Roger StephanAbstract:Five Gram-negative, facultatively anaerobic, non-spore-forming, coccoid rod-shaped bacterial isolates were obtained from infant formula and an infant formula production environment and were investigated by use of a polyphasic taxonomic study. Biochemical tests and partial rpoB gene sequence analysis of the five isolates revealed that they formed two distinct groups in the family Enterobacteriaceae, closely related to several species of the genera Pantoea and Erwinia, which indicated a phylogenetic position within the genus Pantoea or the genus Erwinia. Multilocus sequence analysis of concatenated partial atpD, gyrB, infB and rpoB gene sequences of two of the isolates suggested that they represented two novel species of the genus Pantoea, phylogenetically related most closely to Pantoea septica. The five isolates had general characteristics consistent with those of the genus Pantoea, and DNA–DNA hybridizations between two representatives and the type strains of their phylogenetically closest relatives based on comparative 16S rRNA gene sequence analysis showed that the isolates represented two novel genospecies. These two genospecies could be differentiated from each other based on fermentation of galacturonate, sorbitol and potassium 5-ketogluconate. They could be differentiated from phylogenetically related Pantoea species based on their ability to ferment lactose and to utilize β-gentiobiose and raffinose, their inability to ferment or utilize d-arabitol, and their inability to produce indole. On the basis of the results obtained, the five isolates are considered to represent two novel species of the genus Pantoea, for which the names Pantoea gaviniae sp. nov. (type strain A18/07T =LMG 25382T =DSM 22758T) and Pantoea calida sp. nov. (type strain 1400/07T =LMG 25383T =DSM 22759T) are proposed.
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emended description of the genus Pantoea description of four species from human clinical samples Pantoea septica sp nov Pantoea eucrina sp nov Pantoea brenneri sp nov and Pantoea conspicua sp nov and transfer of pectobacterium cypripedii hori 1911 br
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Carrie L Brady, S N Venter, Katrien Engelbeen, Ilse Cleenwerck, Teresa A CoutinhoAbstract:Bacterial strains belonging to DNA hybridization groups (HG) II, IV and V, in the Erwinia herbicola-Enterobacter agglomerans complex, of Brenner et al. [Int J Syst Bacteriol 34 (1984), 45-55] were suggested previously to belong to the genus Pantoea, but have never been formally described and classified. Additionally, it has been shown in several studies that Pectobacterium cypripedii is more closely related to species of Pantoea than to those of Pectobacterium. In this study, the phylogenetic positions of Brenner's DNA HG II, IV and V and Pectobacterium cypripedii were re-examined by both 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) based on the gyrB, rpoB, atpD and infB genes. The analyses revealed that DNA HG II, IV and V and Pectobacterium cypripedii form five separate branches within the genus Pantoea (strains from HG V were split into two branches). DNA-DNA hybridization data further confirmed that DNA HG II, IV and V constitute four separate species. Pectobacterium cypripedii was shown to be a close phylogenetic relative of Pantoea dispersa and DNA HG IV by both 16S rRNA gene sequence and MLSA analyses. Biochemical analyses performed on strains from DNA HG II, IV and V and Pectobacterium cypripedii confirmed their taxonomic position within the genus Pantoea and revealed phenotypic characteristics that allow the differentiation of these species from each other and from their closest phylogenetic neighbours. It is proposed to emend the description of the genus Pantoea and to describe Pantoea septica sp. nov. for DNA HG II (type strain LMG 5345(T) =BD 874(T) =CDC 3123-70(T)), Pantoea eucrina sp. nov. for DNA HG IV (type strain LMG 2781(T) =BD 872(T) =CDC 1741-71(T) = LMG 5346(T)), Pantoea brenneri sp. nov. for strains of DNA HG V excluding LMG 24534 (type strain LMG 53431 =BD 873(T) =CDC 3482-71(T)) and Pantoea conspicua sp. nov. for the remaining strain of DNA HG V (type strain LMG 245341 =BD 805(T) =CDC 3527-71(T)) and to transfer Pectobacterium cypripedii to the genus as Pantoea cypripedii comb. nov. (type strain LMG 2657(T) =ATCC 29267(T) =DSM 3873(T) =LMG 2655(T)).
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Transfer of Pantoea citrea, Pantoea punctata and Pantoea terrea to the genus Tatumella emend. as Tatumella citrea comb. nov., Tatumella punctata comb. nov. and Tatumella terrea comb. nov. and description of Tatumella morbirosei sp. nov.
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Paul De Vos, Katrien Vandemeulebroecke, Teresa A CoutinhoAbstract:Pantoea citrea, Pantoea punctata and Pantoea terrea were described for strains isolated from fruit and soil originating in Japan. These three 'Japanese' species have been shown to be phylogenetically distant from other species of the genus Pantoea. It has been observed previously that, using multilocus sequence analysis (MLSA), the 'Japanese' species consistently formed a distinct clade with an extended branch length, casting doubt on the inclusion of these species within the genus Pantoea. Furthermore, the 'Japanese' species are closely related to Tatumella ptyseos, strains of which originate from human clinical specimens. DNA-DNA hybridization and phenotypic tests confirmed the observed phylogenetic distance of P. citrea, P. punctata and P. terrea from the genus Pantoea and the affiliation of these species with Tatumella. In addition, strains causing pink disease of pineapple, identified previously as P. citrea , were shown to represent a separate species by using 16S rRNA gene sequence analysis, and MLSA and DNA-DNA hybridization data. The name Tatumella morbirosei sp. nov. with the type strain LMG 23360(T) (=BD 878(T)=NCPPB 4036(T)=CMC6(T)) is proposed to accommodate these strains. The new combinations Tatumella citrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2003(T)=ATCC 31623(T)=BD 875( T)=CCUG 30156(T)=CIP 105599(T)=DSM 13699(T)=JCM 8882(T)=LMG 22049(T)), Tatumella punctata (Kageyama et al. 1992) comb. nov. (type strain, SHS 2006(T)=ATCC 31626(T)=BD 876( T)=CCUG 30159(T)=CIP 105598(T)=DSM 13700(T)=JCM 8885(T)=LMG 22050(T)) and Tatumella terrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2008(T)=ATCC 31628(T)=BD 877(T)=CCUG 30161(T)=CIP 105600(T)=DSM 13701(T)=JCM 8887(T)=LMG 22051(T)) are proposed for P. citrea, P. punctata and P. terrea , respectively.
Stephanus N. Venter - One of the best experts on this subject based on the ideXlab platform.
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Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites
Standards in Genomic Sciences, 2016Co-Authors: Marike Palmer, Teresa A Coutinho, Pieter De Maayer, Michael Poulsen, Emma T. Steenkamp, Elritha Van Zyl, Stephanus N. VenterAbstract:The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.
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Pantoea rodasii sp. nov., Pantoea rwandensis sp. nov. and Pantoea wallisii sp. nov., isolated from Eucalyptus.
International journal of systematic and evolutionary microbiology, 2011Co-Authors: Carrie L Brady, Ilse Cleenwerck, Teresa A Coutinho, Stephanus N. Venter, Lorinda Van Der Westhuizen, Paul De VosAbstract:Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa, Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA-DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273(T)=BD 943(T) (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa)=BCC 581(T) (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275(T)=BD 944(T)=BCC 571(T)) and Pantoea wallisii sp. nov. (type strain LMG 26277(T)=BD 946(T)=BCC 682(T)) are proposed.
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Pantoea allii sp. nov., isolated from onion plants and seed
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Paul De Vos, Teresa Goszczynska, Ronald D. Gitaitis, Teresa A CoutinhoAbstract:Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed .97% 16S rRNA gene sequence similarity with strain BD 390 T , the isolates exhibited 11–55% whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390 T (5LMG 24248 T ).
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Transfer of Pantoea citrea, Pantoea punctata and Pantoea terrea to the genus Tatumella emend. as Tatumella citrea comb. nov., Tatumella punctata comb. nov. and Tatumella terrea comb. nov. and description of Tatumella morbirosei sp. nov.
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Paul De Vos, Katrien Vandemeulebroecke, Teresa A CoutinhoAbstract:Pantoea citrea, Pantoea punctata and Pantoea terrea were described for strains isolated from fruit and soil originating in Japan. These three 'Japanese' species have been shown to be phylogenetically distant from other species of the genus Pantoea. It has been observed previously that, using multilocus sequence analysis (MLSA), the 'Japanese' species consistently formed a distinct clade with an extended branch length, casting doubt on the inclusion of these species within the genus Pantoea. Furthermore, the 'Japanese' species are closely related to Tatumella ptyseos, strains of which originate from human clinical specimens. DNA-DNA hybridization and phenotypic tests confirmed the observed phylogenetic distance of P. citrea, P. punctata and P. terrea from the genus Pantoea and the affiliation of these species with Tatumella. In addition, strains causing pink disease of pineapple, identified previously as P. citrea , were shown to represent a separate species by using 16S rRNA gene sequence analysis, and MLSA and DNA-DNA hybridization data. The name Tatumella morbirosei sp. nov. with the type strain LMG 23360(T) (=BD 878(T)=NCPPB 4036(T)=CMC6(T)) is proposed to accommodate these strains. The new combinations Tatumella citrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2003(T)=ATCC 31623(T)=BD 875( T)=CCUG 30156(T)=CIP 105599(T)=DSM 13699(T)=JCM 8882(T)=LMG 22049(T)), Tatumella punctata (Kageyama et al. 1992) comb. nov. (type strain, SHS 2006(T)=ATCC 31626(T)=BD 876( T)=CCUG 30159(T)=CIP 105598(T)=DSM 13700(T)=JCM 8885(T)=LMG 22050(T)) and Tatumella terrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2008(T)=ATCC 31628(T)=BD 877(T)=CCUG 30161(T)=CIP 105600(T)=DSM 13701(T)=JCM 8887(T)=LMG 22051(T)) are proposed for P. citrea, P. punctata and P. terrea , respectively.
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Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009Co-Authors: Carrie Brady, Katrien Engelbeen, Ilse Cleenwerck, Stephanus N. Venter, Marc Vancanneyt, Jean Swings, Teresa A CoutinhoAbstract:Bacteria isolated from eucalyptus leaves and shoots showing symptoms of blight and die-back collected in Uganda, Uruguay and Argentina and from maize displaying brown stalk rot symptoms in South Africa were tentatively placed in the genus Pantoea on the basis of phenotypic and biochemical tests. These isolates, together with two strains (LMG 2558 and LMG 2560) previously assigned to Pantoea agglomerans based on protein electrophoregrams but later excluded from this species, were further investigated using molecular techniques. 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) revealed that the strains were phylogenetically closely related to Pantoea agglomerans, Pantoea stewartii and Pantoea ananatis. MLSA and amplified fragment length polymorphism analysis placed the strains into four separate clusters, not containing any of the type strains of species of the genus Pantoea. DNA–DNA hybridization confirmed the classification of the isolates into four novel species, for which the names Pantoea vagans sp. nov. (type strain R-21566T =LMG 24199T =BCC 105T =BD 765T), Pantoea eucalypti sp. nov. (type strain R-25678T =LMG 24197T =BCC 076T =BD 769T), Pantoea deleyi sp. nov. (type strain R-31523T =LMG 24200T =BCC 109T =BD 767T) and Pantoea anthophila sp. nov. (type strain LMG 2558T =BD 871T =NCPPB 1682T) are proposed.
Carrie Brady - One of the best experts on this subject based on the ideXlab platform.
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Pantoea allii sp. nov., isolated from onion plants and seed
International Journal of Systematic and Evolutionary Microbiology, 2011Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Paul De Vos, Teresa Goszczynska, Ronald D. Gitaitis, Teresa A CoutinhoAbstract:Eight yellow-pigmented, Gram-negative, rod-shaped, oxidase-negative, motile, facultatively anaerobic bacteria were isolated from onion seed in South Africa and from an onion plant exhibiting centre rot symptoms in the USA. The isolates were assigned to the genus Pantoea on the basis of phenotypic and biochemical tests. 16S rRNA gene sequence analysis and multilocus sequence analysis (MLSA), based on gyrB, rpoB, infB and atpD sequences, confirmed the allocation of the isolates to the genus Pantoea. MLSA further indicated that the isolates represented a novel species, which was phylogenetically most closely related to Pantoea ananatis and Pantoea stewartii. Amplified fragment length polymorphism analysis also placed the isolates into a cluster separate from P. ananatis and P. stewartii. Compared with type strains of species of the genus Pantoea that showed .97% 16S rRNA gene sequence similarity with strain BD 390 T , the isolates exhibited 11–55% whole-genome DNA–DNA relatedness, which confirmed the classification of the isolates in a novel species. The most useful phenotypic characteristics for the differentiation of the isolates from their closest phylogenetic neighbours are production of acid from amygdalin and utilization of adonitol and sorbitol. A novel species, Pantoea allii sp. nov., is proposed, with type strain BD 390 T (5LMG 24248 T ).
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Transfer of Pantoea citrea, Pantoea punctata and Pantoea terrea to the genus Tatumella emend. as Tatumella citrea comb. nov., Tatumella punctata comb. nov. and Tatumella terrea comb. nov. and description of Tatumella morbirosei sp. nov.
International Journal of Systematic and Evolutionary Microbiology, 2010Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Paul De Vos, Katrien Vandemeulebroecke, Teresa A CoutinhoAbstract:Pantoea citrea, Pantoea punctata and Pantoea terrea were described for strains isolated from fruit and soil originating in Japan. These three 'Japanese' species have been shown to be phylogenetically distant from other species of the genus Pantoea. It has been observed previously that, using multilocus sequence analysis (MLSA), the 'Japanese' species consistently formed a distinct clade with an extended branch length, casting doubt on the inclusion of these species within the genus Pantoea. Furthermore, the 'Japanese' species are closely related to Tatumella ptyseos, strains of which originate from human clinical specimens. DNA-DNA hybridization and phenotypic tests confirmed the observed phylogenetic distance of P. citrea, P. punctata and P. terrea from the genus Pantoea and the affiliation of these species with Tatumella. In addition, strains causing pink disease of pineapple, identified previously as P. citrea , were shown to represent a separate species by using 16S rRNA gene sequence analysis, and MLSA and DNA-DNA hybridization data. The name Tatumella morbirosei sp. nov. with the type strain LMG 23360(T) (=BD 878(T)=NCPPB 4036(T)=CMC6(T)) is proposed to accommodate these strains. The new combinations Tatumella citrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2003(T)=ATCC 31623(T)=BD 875( T)=CCUG 30156(T)=CIP 105599(T)=DSM 13699(T)=JCM 8882(T)=LMG 22049(T)), Tatumella punctata (Kageyama et al. 1992) comb. nov. (type strain, SHS 2006(T)=ATCC 31626(T)=BD 876( T)=CCUG 30159(T)=CIP 105598(T)=DSM 13700(T)=JCM 8885(T)=LMG 22050(T)) and Tatumella terrea (Kageyama et al. 1992) comb. nov. (type strain, SHS 2008(T)=ATCC 31628(T)=BD 877(T)=CCUG 30161(T)=CIP 105600(T)=DSM 13701(T)=JCM 8887(T)=LMG 22051(T)) are proposed for P. citrea, P. punctata and P. terrea , respectively.
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Pantoea vagans sp. nov., Pantoea eucalypti sp. nov., Pantoea deleyi sp. nov. and Pantoea anthophila sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009Co-Authors: Carrie Brady, Katrien Engelbeen, Ilse Cleenwerck, Stephanus N. Venter, Marc Vancanneyt, Jean Swings, Teresa A CoutinhoAbstract:Bacteria isolated from eucalyptus leaves and shoots showing symptoms of blight and die-back collected in Uganda, Uruguay and Argentina and from maize displaying brown stalk rot symptoms in South Africa were tentatively placed in the genus Pantoea on the basis of phenotypic and biochemical tests. These isolates, together with two strains (LMG 2558 and LMG 2560) previously assigned to Pantoea agglomerans based on protein electrophoregrams but later excluded from this species, were further investigated using molecular techniques. 16S rRNA gene sequencing and multilocus sequence analyses (MLSA) revealed that the strains were phylogenetically closely related to Pantoea agglomerans, Pantoea stewartii and Pantoea ananatis. MLSA and amplified fragment length polymorphism analysis placed the strains into four separate clusters, not containing any of the type strains of species of the genus Pantoea. DNA–DNA hybridization confirmed the classification of the isolates into four novel species, for which the names Pantoea vagans sp. nov. (type strain R-21566T =LMG 24199T =BCC 105T =BD 765T), Pantoea eucalypti sp. nov. (type strain R-25678T =LMG 24197T =BCC 076T =BD 769T), Pantoea deleyi sp. nov. (type strain R-31523T =LMG 24200T =BCC 109T =BD 767T) and Pantoea anthophila sp. nov. (type strain LMG 2558T =BD 871T =NCPPB 1682T) are proposed.
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phylogeny and identification of Pantoea species associated with plants humans and the natural environment based on multilocus sequence analysis mlsa
Systematic and Applied Microbiology, 2008Co-Authors: Carrie Brady, S N Venter, Ilse Cleenwerck, Marc Vancanneyt, Jean Swings, Teresa A CoutinhoAbstract:Species belonging to the genus of Pantoea are commonly isolated from plants, humans and the natural environment. The species of the genus are phenotypically closely related, making rapid identification of Pantoea strains to the species level difficult. Multilocus sequence analysis (MLSA) was evaluated as a means for rapid classification and identification of Pantoea strains. Four housekeeping genes, gyrB, rpoB, atpD and infB, were sequenced for strains assigned to the genus. Included in the study were (1) reference strains from the seven currently recognized species of Pantoea, (2) strains belonging to Brenner DNA groups II, IV and V, previously isolated from clinical samples and difficult to identify because of high phenotypic similarity to P. agglomerans or P. ananatis and (3) isolates from diseased Eucalyptus, maize and onion, assigned to the genus on the basis of phenotypic tests. Phylogenetic trees were constructed from the sequences of the four housekeeping genes. The "core"Pantoea species formed a cluster separate from the "Japanese" species which formed a tight cluster that included the genus Tatumella when the tree was based on concatenated sequences of the four genes. The MLSA data further suggested the existence of ten potential novel species, phylogenetically related to the currently recognized Pantoea species and the possible inclusion of Pectobacterium cypripedii in the genus Pantoea. When compared with DNA-DNA hybridization data, a good congruence was observed between both methods, with gyrB sequence data being the most consistent. In conclusion, MLSA of partial nucleotide sequences of the genes gyrB, rpoB, atpD and infB can be used for classification, identification and phylogenetic analyses of Pantoea strains.
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A FAFLP system for the improved identification of plant-pathogenic and plant-associated species of the genus Pantoea.
Systematic and applied microbiology, 2007Co-Authors: Carrie Brady, Ilse Cleenwerck, Stephanus N. Venter, Marc Vancanneyt, Jean Swings, Teresa A CoutinhoAbstract:The majority of Pantoea species are either plant-pathogenic or plant-associated and cause a wide variety of symptoms on a range of hosts. Identification of Pantoea species is difficult due to minor differences in phenotypic characteristics between them and related Enterobacteriaceae. Fluorescent amplified fragment length polymorphism (FAFLP) analysis was investigated for use as a rapid, molecular-based identification technique to the species level of the genus Pantoea. Following analysis of the band patterns generated by FAFLP, seven distinct clusters were observed, one for each validly published species of the genus. FAFLP has proven to be a rapid, reproducible identification technique for all species of the genus Pantoea.
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a carotenoid deficient mutant in Pantoea sp yr343 a bacteria isolated from the rhizosphere of populus deltoides is defective in root colonization
Frontiers in Microbiology, 2016Co-Authors: Amber N Bible, Sarah J Fletcher, Dale A Pelletier, Christopher W Schadt, Sara S Jawdy, David J Weston, Nancy L Engle, Timothy J Tschaplinski, Rachel N Masyuko, Sneha PolisettiAbstract:The complex interactions between plants and their microbiome can have a profound effect on the health and productivity of the plant host. A better understanding of the microbial mechanisms that promote plant health and stress tolerance will enable strategies for improving the productivity of economically-important plants. Pantoea sp. YR343 is a motile, rod-shaped bacterium isolated from the roots of Populus deltoides that possesses the ability to solubilize phosphate and produce the phytohormone indole-3-acetic acid. Pantoea sp. YR343 readily colonizes plant roots and does not appear to be pathogenic when applied to the leaves or roots of selected plant hosts. To better understand the molecular mechanisms involved in plant association and rhizosphere survival by Pantoea sp. YR343, we constructed a mutant in which the crtB gene encoding phytoene synthase was deleted. Phytoene synthase is responsible for converting geranylgeranyl pyrophosphate to phytoene, an important precursor to the production of carotenoids. As predicted, the ΔcrtB mutant is defective in carotenoid production, and shows increased sensitivity to oxidative stress. Moreover, we find that the ΔcrtB mutant is impaired in biofilm formation and production of indole-3-acetic acid. Finally we demonstrate that the ΔcrtB mutant shows reduced colonization of plant roots. Taken together, these data suggest that carotenoids are important for plant association and/or rhizosphere survival in Pantoea sp. YR343.
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raman chemical imaging of the rhizosphere bacterium Pantoea sp yr343 and its co culture with arabidopsis thaliana
Analyst, 2016Co-Authors: Sneha Polisetti, Amber N Bible, Jennifer L Morrellfalvey, Paul W BohnAbstract:Chemical imaging of plant-bacteria co-cultures makes it possible to characterize bacterial populations and behaviors and their interactions with proximal organisms, under conditions closest to the environment in the rhizosphere. Here Raman micro-spectroscopy and confocal Raman imaging are used as minimally invasive probes to study the rhizosphere bacterial isolate, Pantoea sp. YR343, and its co-culture with model plant Arabidopsis thaliana by combining enhanced Raman spectroscopies with electron microscopy and principal component analysis (PCA). The presence of carotenoid pigments in the wild type Pantoea sp. YR343 was characterized using resonance Raman scattering, which was also used to confirm successful disruption of the crtB gene in an engineered carotenoid mutant strain. Other components of the Pantoea sp. YR343 cells were imaged in the presence of resonantly enhanced pigments using a combination of surface enhanced Raman imaging and PCA. Pantoea sp. YR343 cells decorated with Ag colloid synthesized ex situ gave spectra dominated by carotenoid scattering, whereas colloids synthesized in situ produced spectral signatures characteristic of flavins in the cell membrane. Scanning electron microscopy (SEM) of whole cells and transmission electron microscopy (TEM) images of thinly sliced cross-sections were used to assess structural integrity of the coated cells and to establish the origin of spectral signatures based on the position of Ag nanoparticles in the cells. Raman imaging was also used to characterize senescent green Arabidopsis thaliana plant roots inoculated with Pantoea sp. YR343, and PCA was used to distinguish spectral contributions from plant and bacterial cells, thereby establishing the potential of Raman imaging to visualize the distribution of rhizobacteria on plant roots.
