Genomics Analyses of Rose Crown Gall-Associated Bacteria Revealed Two New Agrobacterium species: Agrobacterium burrii sp. nov. and Agrobacterium shirazense sp. nov.

2021 ◽  
Author(s):  
Hamzeh Mafakheri ◽  
S. Mohsen Taghavi ◽  
Kamran Khezerpour ◽  
Nemanja Kuzmanović ◽  
Ebrahim Osdaghi
Keyword(s):  
Crown Gall ◽  
Type Strain ◽  
Species Complex ◽  
Whole Genome Sequence ◽  
Bacterial Strains ◽  
Associated Bacteria ◽  
Molecular Phylogenetic ◽  
Genome Phylogeny ◽  
Agricultural Plants ◽  
Molecular Phylogenetic Data

Agrobacterium tumefaciens species complex contains a set of diverse bacterial strains most of which are well known for their pathogenicity on agricultural plants causing crown gall diseases. Members of A. tumefaciens species complex are classified into several taxonomically distinct lineages called “genomospecies” (13 genomospecies until early 2021). Recently, two genomospecies, i.e., G19 (strains RnrT, Rew and Rnw) and G20 (strains OT33T and R13) infecting Rose sp. plants in Iran were described based on biochemical and molecular-phylogenetic data. Whole genome sequence-based core-genome phylogeny followed by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) calculations performed in this study suggested that genomospecies G19 and G20 could be described as two novel and standalone species. In the phylogenetic tree, these two new genomospecies were clustered separately from other genomospecies/species of A. tumefaciens species complex. Moreover, both ANI and dDDH indices between the G19/G20 strains and other Rhizobiaceae members are clearly below the accepted thresholds for prokaryotic species description. Hence, Agrobacterium burrii sp. nov. is proposed to encompass the G19 strains, with RnrT = CFBP 8705T = DSM 112541T as type strain. Agrobacterium shirazense sp. nov. is also proposed to include G20 strains, with OT33T = CFBP 8901T = DSM 112540T as type strain.

scholarly journals Teredinibacter haidensis sp. nov., Teredinibacter purpureus sp. nov. and Teredinibacter franksiae sp. nov., marine, cellulolytic endosymbiotic bacteria isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter

2021 ◽  
Author(s):  
Marvin A. Altamia ◽  
J. Reuben Shipway ◽  
David Stein ◽  
Meghan A. Betcher ◽  
Jennifer M. Fung ◽  
...  
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Sequence Data ◽  
Amino Acid Identity ◽  
Whole Genome Sequence ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Content Type ◽  
Link Type

Here, we describe three endosymbiotic bacterial strains isolated from the gills of the shipworm, Bankia setacea (Teredinidae: Bivalvia). These strains, designated as Bs08T, Bs12T and Bsc2T, are Gram-stain-negative, microaerobic, gammaproteobacteria that grow on cellulose and a variety of substrates derived from lignocellulose. Phenotypic characterization, phylogeny based on 16S rRNA gene and whole genome sequence data, amino acid identity and percentage of conserved proteins analyses, show that these strains are novel and may be assigned to the genus Teredinibacter . The three strains may be differentiated and distinguished from other previously described Teredinibacter species based on a combination of four characteristics: colony colour (Bs12T, purple; others beige to brown), marine salt requirement (Bs12T, Bsc2T and Teredinibacter turnerae strains), the capacity for nitrogen fixation (Bs08T and T. turnerae strains) and the ability to respire nitrate (Bs08T). Based on these findings, we propose the names Teredinibacter haidensis sp. nov. (type strain Bs08T=ATCC TSD-121T=KCTC 62964T), Teredinibacter purpureus sp. nov. (type strain Bs12T=ATCC TSD-122T=KCTC 62965T) and Teredinibacter franksiae sp. nov. (type strain Bsc2T=ATCC TSD-123T=KCTC 62966T).

scholarly journals Revisiting the taxonomy of Allorhizobium vitis (i.e. Agrobacterium vitis) using genomics - emended description of All. vitis sensu stricto and description of Allorhizobium ampelinum sp. nov

2020 ◽  
Author(s):  
Nemanja Kuzmanović ◽  
Enrico Biondi ◽  
Jörg Overmann ◽  
Joanna Puławska ◽  
Susanne Verbarg ◽  
...  
Keyword(s):  
Type Strain ◽  
Species Complex ◽  
Gene Clusters ◽  
Sensu Stricto ◽  
Whole Genome Sequence ◽  
Polyamine Metabolism ◽  
Phylogenomic Analysis ◽  
Agrobacterium Vitis ◽  
Ecological Diversification ◽  
Allorhizobium Vitis

AbstractAllorhizobium vitis (formerly named Agrobacterium vitis or Agrobacterium biovar 3) is the primary causative agent of crown gall disease of grapevine worldwide. Whole-genome sequence comparisons and phylogenomic analysis of various All. vitis strains clearly indicated that All. vitis is not a single species, but represents a species complex composed of at least four genomic species. Thus, we amended the description of All. vitis which now refers to a restricted group of strains within the All. vitis complex (i.e. All. vitis sensu stricto) and proposed a description of a novel species All. ampelinum sp. nov. The type strain of All. vitis sensu stricto remains the existing type strain of All. vitis, K309T (= NCPPB 3554T =HAMBI 1817T = ATCC 49767T = CIP 105853T = ICMP 10752T = IFO 15140T = JCM 21033T = LMG 8750T = NBRC 15140T). The type strain of All. ampelinum sp. nov. is S4T (= DSM 112012T = ATCCBAA-846T). This genome-based classification was supported by differentiation of strains based on a MALDI-TOF MS analysis. We also identified gene clusters specific for All. vitis species complex, All. vitis sensu stricto and All. ampelinum, and attempted to predict their function and their role in ecological diversification of these clades, some of which were experimentally validated. Functions of All. vitis species complex-specific genes convergently indicate a role in adaptation to different stresses, including exposure to aromatic compounds. Similarly, All vitis sensu stricto-specific genes also confer the ability to degrade 4-hydroxyphenylacetate and a putative compound related to gentisic acid, while All. ampelinum-specific genes have putative functions related to polyamine metabolism and nickel assimilation. This suggests that these species have differentiated ecologies, each relying on specialized nutrient consumption or toxic compound degradation to adapt to their respective niche. Moreover, our genome-based analysis indicated that Allorhizobium and the “R. aggregatum complex” represent separate genera of the family Rhizobiaceae.

scholarly journals Occurrence of Crown Gall Disease on Japanese Spindle (Euonymus japonicas var. Green Rocket) Caused by Agrobacterium rosae in Iran

Plant Disease ◽  
2021 ◽  
Author(s):  
Hamzeh Mafakheri ◽  
Seied Mohsen Taghavi ◽  
Sadegh Zarei ◽  
Nemanja Kuzmanovic ◽  
Ebrahim Osdaghi
Keyword(s):  
Crown Gall ◽  
De Novo ◽  
Negative Control ◽  
Whole Genome Sequence ◽  
Reca Gene ◽  
Post Inoculation ◽  
Whole Genome ◽  
Bacterial Strains ◽  
Illumina Hiseq ◽  
Crown Gall Disease

Crown gall disease caused by diverse Agrobacterium species is one of the main biotic constraints in the ornamental plants industry in Iran (Mafakheri et al. 2017). In August 2019, Japanese spindle (Euonymus japonicus var. Green Rocket) plants showing crown gall symptoms were observed in a commercial greenhouse in Tehran, Iran. Infected plants were characterized by a visible overgrowth on their stems and crown. Bacterial isolation from the gall tissues was performed on nutrient agar (NA) and 1A media as described by Moore et al. (2001). The six resulted bacterial strains (A.E1 to A.E6) were evaluated using PCR primer pair F8360/F8361 amplifying a 453 bp DNA fragment in recA gene and confirmed as Agrobacterium sp. (Shams et al. 2013). Pathogenicity of the strains was evaluated in two independent assays on Japanese spindle plantlets as well as 10-15 day old tomato (Solanum lycopersicum cv. Sunseed 6189) and sunflower (Helianthus annuus cv. Armavirski) plants in greenhouse conditions using the needle prick method as described previously (Mafakheri et al. 2019). The reference strain A. radiobacter ICMP 5856 and sterile distilled water were used as positive and negative controls, respectively. Crown gall symptoms appeared 20-25 days post inoculation on the Japanese spindle plantlets as well as tomato and sunflower plants inoculated with the strains isolated in this study, while the negative control plants remained asymptomatic. Koch’s postulates were accomplished by re-isolating on NA medium and PCR-based identification of the inoculated strains from the symptomatic plants. The representative strain A.E1 was subjected to multilocus sequence analysis (MLSA) using the sequences of four housekeeping genes (i.e. atpD, gyrB, recA, and rpoB) as described previously (Mafakheri et al. 2019). MLSA results revealed that the strain A.E1 is phylogenetically closely related to A. rosae. The sequences were deposited into GenBank under the accession numbers MT007962 to MT007965 for atpD, gyrB, recA, and rpoB, respectively. Further, the strain A.E1 was subjected to whole genome sequencing using Illumina HiSeq X platform. DNA extraction was performed using NucleoSpin Microbial DNA kit (Macherey-Nagel, Germany), DNA libraries were obtained with Nextera XT DNA Library Prep Kit (Illumina, USA), and de novo sequence assembly was performed using SPAdes genome assembler. The resulting whole genome sequence was deposited into the GenBank database under the accession number JAFJZW000000000. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were calculated among all the type strains of Agrobacterium species/genomospecies using standard criteria as detailed previously (Osdaghi et al. 2020; Chen et al. 2021). The strain A.E1 had 97% ANI and 72% dDDH values with A. rosae strain NCPPB 1650, suggesting that the bacterial strains isolated from Japanese spindle in Iran belong to A. rosae. This is the first report of A. rosae causing crown gall disease on Japanese spindle in Iran. The new crown gall disease could negatively affect the ornamental shrub production industry in central Iran unless strict sanitary measures are taken into the account in the nurseries in these areas. Further nationwide surveys and samplings are warranted to elucidate the economic impact of the pathogen on ornamental plant industry in the country.

Floral ontogeny of Aeschynomene falcata and A. sensitiva (Leguminosae: Papilionoideae) supports molecular phylogenetic data

2012 ◽  
Vol 299 (3) ◽  
pp. 499-513 ◽  
Author(s):  
Diana Salles Sampaio ◽  
Maria Cecília de Chiara Moço ◽  
Jorge Ernesto Araujo Mariath
Keyword(s):  
Floral Ontogeny ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
Molecular Phylogenetic Data

scholarly journals Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2931-2936 ◽  
Author(s):  
Xiao-Xia Zhang ◽  
Ju-Sheng Gao ◽  
Yan-Hua Cao ◽  
Rizwan Ali Sheirdil ◽  
Xiu-Cheng Wang ◽  
...  
Keyword(s):  
Type Strain ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Astragalus Sinicus ◽  
Dna Relatedness ◽  
Rice Roots ◽  
Long Term Experiment ◽  
Plant Growth Promoting

Bacterial strains ZYY136T and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice–rice–Astragalus sinicus rotation. The 16S rRNA gene sequences of strains ZYY136T and ZYY9 showed the highest similarity, of 97.0  %, to Rhizobium tarimense PL-41T. Sequence analysis of the housekeeping genes recA, thrC and atpD clearly differentiated the isolates from currently described species of the genus Rhizobium. The DNA–DNA relatedness value between ZYY136T and ZYY9 was 82.3  %, and ZYY136T showed 34.0  % DNA–DNA relatedness with the most closely related type strain, R. tarimense PL-41T. The DNA G+C content of strain ZYY136T was 58.1 mol%. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C16 : 0 3-OH. Strains ZYY136T and ZYY9 could be differentiated from the previously defined species of the genus Rhizobium by several phenotypic characteristics. Therefore, we conclude that strains ZYY136T and ZYY9 represent a novel species of the genus Rhizobium, for which the name Rhizobium oryzicola sp. nov. is proposed (type strain ZYY136T = ACCC 05753T = KCTC 32088T).

The Effect of Curcumin against In Vitro Adhesion of Implant Device-Associated Bacteria on Nanosized Titanium Dioxide

2013 ◽  
Vol 23 ◽  
pp. 83-90
Author(s):  
Seung Han Oh ◽  
In Young Na ◽  
Kyoung Hee Choi
Keyword(s):  
Titanium Dioxide ◽  
Bacterial Adhesion ◽  
Curcuma Longa ◽  
Human Tooth ◽  
Bacterial Strains ◽  
Associated Bacteria ◽  
Tooth Surfaces ◽  
Titanium Surfaces ◽  
Main Component

Although titanium dioxide (TiO2) is an implantable biomaterial with its antibacterial activity, infection on TiO2 surfaces remains a problem for medical settings. According to our previous studies, curcumin, the main component of turmeric (Curcuma longa), partially hindered the attachment of Streptococcus mutans to human tooth surfaces. Therefore, it was examined whether several implant device-associated bacteria were able to adhere to nanosized TiO2 surfaces. In addition, the effect of curcumin on the bacterial adhesion was investigated. Bacterial strains were cultured on pure Ti and TiO2 surfaces with various nanotube sizes in the absence or presence of curcumin and observed by scanning electron microscopy. Consequently, most bacteria adhered to Ti and TiO2 surfaces. However, curcumin increased the adhesion of bacteria including S. mutans. The results suggest that bacterial adhesion to implant titanium surfaces can be augmented via curcumin ingestion.

scholarly journals Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

2021 ◽  
Author(s):  
Viola Kurm ◽  
Ilse Houwers ◽  
Claudia E. Coipan ◽  
Peter Bonants ◽  
Cees Waalwijk ◽  
...  
Keyword(s):  
Ralstonia Solanacearum ◽  
In Silico ◽  
Species Complex ◽  
Sequence Data ◽  
In Silico Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

Iljinskaea (Brassicaceae), a new genus based on Conringia planisiliqua

Phytotaxa ◽  
2021 ◽  
Vol 500 (2) ◽  
pp. 142-146
Author(s):  
IHSAN A. AL-SHEHBAZ ◽  
BARIŞ ÖZÜDOĞRU ◽  
DMITRY A. GERMAN
Keyword(s):  
New Genus ◽  
Critical Evaluation ◽  
New Combination ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
Molecular Phylogenetic Data

Iljinskaea is described as a new monospecific genus based on a critical evaluation of morphology and in light of the extensive molecular phylogenetic data. The new combination I. planisiliqua is proposed, and the distinguishing characters separating the new genus from Conringia are discussed. The new tribal assignment of Iljinskaea in the Isatideae is discussed and compared with the previous placement in the Conringieae.

Molecular phylogenetic relationships within the Phrynocephalus maculatus‐arabicus species complex (Sauria: Agamidae) in Iran

2021 ◽  
Vol 59 (7) ◽  
pp. 1583-1588
Author(s):  
Farnaz Ebrahimipour ◽  
Nasrullah Rastegar‐Pouyani ◽  
Eskandar Rastegar‐Pouyani ◽  
Seyyed Saeed Hosseinian Yousefkhani ◽  
Kamran Kamali
Keyword(s):  
Phylogenetic Relationships ◽  
Species Complex ◽  
Molecular Phylogenetic
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