Description of Dryocola gen. nov. and two novel species, Dryocola boscaweniae sp. nov. and Dryocola clanedunensis sp. nov. isolated from the rhizosphere of native British oaks
While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these...
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| Published in | Systematic and applied microbiology Vol. 46; no. 2; p. 126399 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
| Published |
Germany
Elsevier GmbH
01.04.2023
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0723-2020 1618-0984 1618-0984 |
| DOI | 10.1016/j.syapm.2023.126399 |
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| Abstract | While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4T = CCUG 76177T = LMG 32610T) and Dryocola clanedunesis sp. nov. (type strain H11S18T = CCUG 76181T = LMG 32611T). |
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| AbstractList | While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4
= CCUG 76177
= LMG 32610
) and Dryocola clanedunesis sp. nov. (type strain H11S18
= CCUG 76181
= LMG 32611
). While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4T = CCUG 76177T = LMG 32610T) and Dryocola clanedunesis sp. nov. (type strain H11S18T = CCUG 76181T = LMG 32611T). While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4ᵀ = CCUG 76177ᵀ = LMG 32610ᵀ) and Dryocola clanedunesis sp. nov. (type strain H11S18ᵀ = CCUG 76181ᵀ = LMG 32611ᵀ). While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4T = CCUG 76177T = LMG 32610T) and Dryocola clanedunesis sp. nov. (type strain H11S18T = CCUG 76181T = LMG 32611T).While investigating the role of the rhizosphere in the development of Acute Oak Decline, bacterial strains belonging to the family Enterobacteriaceae were isolated from rhizosphere soil following enrichment for the Enterobacterales. Partial sequencing of several housekeeping genes showed that these strains could not be assigned to an existing genus. Overall, 16 strains were investigated using a polyphasic approach to determine their taxonomic status. This involved phenotypic testing and fatty acid analysis paired with phylogenetic analyses of 16S rRNA and housekeeping gene sequences, as well as phylogenomic analysis of whole genome sequences. Phylogenomic and phylogenetic analyses consistently demonstrated that the 16 isolates could be separated into two distinct clusters in a monophyletic clade situated between the genera Cedecea and Buttiauxella. The two clusters could be genotypically and phenotypically differentiated from each other and from their closest neighbours. As such we propose the description of Dryocola boscaweniae gen. nov. sp. nov. (type strain H6W4T = CCUG 76177T = LMG 32610T) and Dryocola clanedunesis sp. nov. (type strain H11S18T = CCUG 76181T = LMG 32611T). |
| ArticleNumber | 126399 |
| Author | Arnold, Dawn Maddock, Daniel Brady, Carrie Denman, Sandra |
| Author_xml | – sequence: 1 givenname: Daniel surname: Maddock fullname: Maddock, Daniel organization: Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom – sequence: 2 givenname: Carrie orcidid: 0000-0001-8035-9491 surname: Brady fullname: Brady, Carrie email: carrie.brady@uwe.ac.uk organization: Centre for Research in Bioscience, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom – sequence: 3 givenname: Sandra surname: Denman fullname: Denman, Sandra organization: Centre for Ecosystems, Society and Biosecurity, Forest Research, Farnham, United Kingdom – sequence: 4 givenname: Dawn surname: Arnold fullname: Arnold, Dawn organization: Harper Adams University, Newport, Shropshire, United Kingdom |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36689899$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1046/j.1365-2672.1997.00141.x 10.4103/amhs.amhs_24_18 10.1007/s00284-020-02253-3 10.46490/BF563 10.1093/jxb/erw108 10.1007/s11356-018-2322-6 10.1101/2021.12.13.472471 10.1038/s41396-020-00801-0 10.1038/s41467-019-10210-3 10.1128/JCM.01916-08 10.1007/s00299-019-02447-5 10.1099/ijsem.0.001755 10.1099/mgen.0.000240 10.1038/s41467-018-07641-9 10.1099/ijsem.0.001485 10.1016/S0723-2020(97)80028-8 10.1111/1462-2920.13389 10.1038/s41592-021-01101-x 10.1128/JB.187.18.6258-6264.2005 10.1099/00207713-49-2-405 10.1016/j.ijid.2020.09.036 10.1086/282802 10.1099/00207713-31-3-317 10.1093/nar/gkw569 10.1099/ijs.0.64483-0 10.4161/viru.25730 10.1093/nar/gks1195 10.1093/molbev/msv150 10.1111/efp.12535 10.1093/molbev/msab120 10.3390/f11111153 10.1128/CMR.00174-20 10.1002/9781118960608.gbm01142 10.1099/00207713-46-1-50 10.1002/9781118960608.gbm01139 10.1093/bioinformatics/btu170 10.1089/cmb.2012.0021 10.1080/10635150390235520 10.1094/PDIS-09-20-1886-PDN 10.1093/bioinformatics/btac087 10.1186/1471-2105-14-60 10.1128/jcm.16.4.775-778.1982 10.3390/microorganisms8020309 10.1093/bioinformatics/btu153 10.1146/annurev.micro.62.081307.162918 10.1007/s00239-008-9115-3 10.1093/bioinformatics/bts091 10.5197/j.2044-0588.2020.041.018 10.1093/molbev/msx149 10.1093/bioinformatics/btab090 10.1093/nar/19.24.6823 10.1093/nar/gkab1107 10.1007/s00284-021-02714-3 |
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| Keywords | Oak Soil Rhizosphere AOD Enterobacteriaceae |
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| References | Okonechnikov, Golosova, Fursov, Varlamov, Vaskin, Efremov, German Grehov, Kandrov, Rasputin, Syabro, Tleukenov (b0205) 2012; 28 Ruffner, Schneider, Meyer, Queloz, Rigling (b0235) 2020; 41 Sinclair (b0250) 1967; 17–31 Wagner, Avram, Gold-Binshtok, Zerah, Teper, Pupko (b0295) 2022; 38 Seemann (b0245) 2014; 30 Moradi-Amirabad, Rahimian, Babaeizad, Denman (b0180) 2019; 49 Buchfink, Reuter, Drost (b0030) 2021; 18 Yoon, Ha, Kwon, Lim, Kim, Seo, Chun (b0315) 2017; 67 Sinclair, Hudler (b0255) 1988; 14 Fernandes, Duarte, Naves, Sousa, Cruz (b0080) 2022; 143 Meier-Kolthoff, Göker (b0175) 2019; 10 York, Carminati, Mooney, Ritz, Bennett (b0320) 2016; 67 Denman, Brown, Vanguelova, Crampton (b0055) 2022 Pinho, Barroso, Froufe, Brown, Vanguelova, Egas, Denman (b0225) 2020; 11 Bankevich, Nurk, Antipov, Gurevich, Dvorkin, Kulikov, Lesin, Nikolenko, Pham, Prjibelski, Pyshkin, Sirotkin, Vyahhi, Tesler, Alekseyev, Pevzner (b0010) 2012; 19 Tatusova, Dicuccio, Badretdin, Chetvernin, Nawrocki, Zaslavsky, Lomsadze, Pruitt, Borodovsky, Ostell (b0270) 2016; 44 de Araújo, Rodrigues, Nadal, Ribeiro, Antônio, Rodrigues, de Souza, Pasqual, Dória (b0045) 2021; 248 Versalovic, Koeuth, Lupski (b0285) 1991; 19 Manion (b0160) 1981 Ferragut, Izard, Gavini (b0085) 1981; 2 Müller, Brenner, Fanning, Grimont, Kampfer (b0185) 1996; 46 Adeolu, Alnajar, Naushad, Gupta (b0005) 2016; 66 Thompson, Sharkady (b0275) 2020; 100 Janda, Abbott (b0115) 2021; 34 Meier-Kolthoff, Auch, Klenk, Göker (b0170) 2013; 14 Delétoile, Decré, Courant, Passet, Audo, Grimont, Arlet, Brisse (b0050) 2009; 47 Tkaczyk, Celma, Ruņģis, Bokuma (b0280) 2021; 27 Patra, N., Prakash, M.R., Patil, S., Rao, M.B., 2018. First case report of surgical site infection due to Buttiauxella agrestis in a Neurocare Center in India, 117–8, Doi: 10.4103/amhs.amhs. Naum, Brown, Mason-Gamer (b0190) 2008; 66 Zgheib, Hasni, Mbaye, Anani, Haddad, Armstrong, Chartier, Caputo, Raoult, Fenollar, Fournier (b0325) 2022; 79 Guindon, Gascuel (b0105) 2003; 52 Patz, S., Gautam, A., Becker, M., Ruppel, S., Rodríguez-Palenzuela, P., Huson, D., 2021. PLaBAse: a comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria. BioRxiv (3), 2021.12.13.472471. Coenye, Falsen, Vancanneyt, Hoste, Govan, Kersters, Vandamme (b0035) 1999; 49 Lugtenberg, Kamilova (b0155) 2009; 63 Jain, Rodriguez-R, Phillippy, Konstantinidis, Aluru (b0110) 2018; 9 Bolger, Lohse, Usadel (b0025) 2014; 30 González, Ciordia (b0090) 2019 Singh, Wurtele (b0260) 2021; 37 Boath, Dakhal, Van, Moore, Dekiwadia, Macreadie (b0020) 2020; 8 Farris, J.S., 1972. Estimating Phlogenetic Trees from Distance Matrices 106(951), 645–70. Benson, Cavanaugh, Clark, Karsch-Mizrachi, Lipman, Ostell, Sayers (b0015) 2013; 41 Grimont, Grimont, Farmer, Asbury (b0100) 1981; 31 Scarlett, Denman, Clark, Forster, Vanguelova, Brown, Whitby (b0240) 2021; 15 Martínez-García, López-Solanilla, Ramos, Rodríguez-Palenzuela (b0165) 2016; 18 Tamura, Stecher, Kumar (b0265) 2021; 38 Goris, Konstantinidis, Klappenbach, Coenye, Vandamme, Tiedje (b0095) 2007; 57 Liu, Zheng, Zhou, Chen, Yang (b0150) 2022; 50 Liu, Z., Zhou, S., Zhang, W., Wu, S., 2021. First Report of Cedecea neteri Causing Yellow Rot Disease in Pleurotus pulmonarius in China. Plant Dis. (April), 1189. Niu, Yu, Wang, Ren, Jin, Zhou, Li, Cheng, Yue, Gao, Liang (b0200) 2013; 4 Crampton, B., Brady, C., Denman, S., 2022. Bacterial Tree Disease Fact Sheets. Yan, Liu, Wang, Mukhtar, Liu, Lin, Jiang, Xie (b0310) 2019; 103 Philippot, Raaijmakers, Lemanceau, Van Der Putten (b0220) 2013; 789–99 Lefort, Longueville, Gascuel (b0140) 2017; 34 Farmer (b0065) 2015; 1–14 Farmer, Sheth, Hudzinski, Rose, Asbury (b0070) 1982; 16 Konstantinidis, Tiedje (b0130) 2005; 187 Lefort, Desper, Gascuel (b0135) 2015; 32 Rodriguez-R, Konstantinidis (b0230) 2016; 4 Doonan, Denman, Pachebat, McDonald (b0060) 2019; 5 Kämpfer (b0120) 2015; 1–16 Niemann, Pühler, Tichy, Simon, Selbitschka (b0195) 1997; 82 Wu, Luo, Li, An, Yang, Liang, Li (b0300) 2018; 25 Vives-Peris, de Ollas, Gómez-Cadenas, Pérez-Clemente (b0290) 2020; 39 Kämpfer, Meyer, Müller (b0125) 1997; 20 Xu, Yan, Liu, Zhao, Song, Gu, Song, Xie, Rong (b0305) 2021; 78 Fernandes (10.1016/j.syapm.2023.126399_b0080) 2022; 143 Konstantinidis (10.1016/j.syapm.2023.126399_b0130) 2005; 187 Jain (10.1016/j.syapm.2023.126399_b0110) 2018; 9 Xu (10.1016/j.syapm.2023.126399_b0305) 2021; 78 Tamura (10.1016/j.syapm.2023.126399_b0265) 2021; 38 Liu (10.1016/j.syapm.2023.126399_b0150) 2022; 50 Goris (10.1016/j.syapm.2023.126399_b0095) 2007; 57 Yoon (10.1016/j.syapm.2023.126399_b0315) 2017; 67 Lugtenberg (10.1016/j.syapm.2023.126399_b0155) 2009; 63 Rodriguez-R (10.1016/j.syapm.2023.126399_b0230) 2016; 4 Ferragut (10.1016/j.syapm.2023.126399_b0085) 1981; 2 Niemann (10.1016/j.syapm.2023.126399_b0195) 1997; 82 Vives-Peris (10.1016/j.syapm.2023.126399_b0290) 2020; 39 Buchfink (10.1016/j.syapm.2023.126399_b0030) 2021; 18 Wu (10.1016/j.syapm.2023.126399_b0300) 2018; 25 Guindon (10.1016/j.syapm.2023.126399_b0105) 2003; 52 Grimont (10.1016/j.syapm.2023.126399_b0100) 1981; 31 Tkaczyk (10.1016/j.syapm.2023.126399_b0280) 2021; 27 Lefort (10.1016/j.syapm.2023.126399_b0140) 2017; 34 Naum (10.1016/j.syapm.2023.126399_b0190) 2008; 66 10.1016/j.syapm.2023.126399_b0075 10.1016/j.syapm.2023.126399_b0215 Ruffner (10.1016/j.syapm.2023.126399_b0235) 2020; 41 González (10.1016/j.syapm.2023.126399_b0090) 2019 Tatusova (10.1016/j.syapm.2023.126399_b0270) 2016; 44 Seemann (10.1016/j.syapm.2023.126399_b0245) 2014; 30 Versalovic (10.1016/j.syapm.2023.126399_b0285) 1991; 19 Niu (10.1016/j.syapm.2023.126399_b0200) 2013; 4 Lefort (10.1016/j.syapm.2023.126399_b0135) 2015; 32 Kämpfer (10.1016/j.syapm.2023.126399_b0120) 2015; 1–16 Meier-Kolthoff (10.1016/j.syapm.2023.126399_b0175) 2019; 10 Delétoile (10.1016/j.syapm.2023.126399_b0050) 2009; 47 Farmer (10.1016/j.syapm.2023.126399_b0065) 2015; 1–14 Farmer (10.1016/j.syapm.2023.126399_b0070) 1982; 16 10.1016/j.syapm.2023.126399_b0145 York (10.1016/j.syapm.2023.126399_b0320) 2016; 67 Scarlett (10.1016/j.syapm.2023.126399_b0240) 2021; 15 Martínez-García (10.1016/j.syapm.2023.126399_b0165) 2016; 18 Müller (10.1016/j.syapm.2023.126399_b0185) 1996; 46 Benson (10.1016/j.syapm.2023.126399_b0015) 2013; 41 Adeolu (10.1016/j.syapm.2023.126399_b0005) 2016; 66 Thompson (10.1016/j.syapm.2023.126399_b0275) 2020; 100 de Araújo (10.1016/j.syapm.2023.126399_b0045) 2021; 248 Okonechnikov (10.1016/j.syapm.2023.126399_b0205) 2012; 28 Singh (10.1016/j.syapm.2023.126399_b0260) 2021; 37 Bolger (10.1016/j.syapm.2023.126399_b0025) 2014; 30 Moradi-Amirabad (10.1016/j.syapm.2023.126399_b0180) 2019; 49 Sinclair (10.1016/j.syapm.2023.126399_b0250) 1967; 17–31 Zgheib (10.1016/j.syapm.2023.126399_b0325) 2022; 79 Wagner (10.1016/j.syapm.2023.126399_b0295) 2022; 38 Sinclair (10.1016/j.syapm.2023.126399_b0255) 1988; 14 Bankevich (10.1016/j.syapm.2023.126399_b0010) 2012; 19 Boath (10.1016/j.syapm.2023.126399_b0020) 2020; 8 Janda (10.1016/j.syapm.2023.126399_b0115) 2021; 34 Kämpfer (10.1016/j.syapm.2023.126399_b0125) 1997; 20 Meier-Kolthoff (10.1016/j.syapm.2023.126399_b0170) 2013; 14 10.1016/j.syapm.2023.126399_b0210 Pinho (10.1016/j.syapm.2023.126399_b0225) 2020; 11 Coenye (10.1016/j.syapm.2023.126399_b0035) 1999; 49 Manion (10.1016/j.syapm.2023.126399_b0160) 1981 10.1016/j.syapm.2023.126399_b0040 Yan (10.1016/j.syapm.2023.126399_b0310) 2019; 103 Doonan (10.1016/j.syapm.2023.126399_b0060) 2019; 5 Philippot (10.1016/j.syapm.2023.126399_b0220) 2013; 789–99 Denman (10.1016/j.syapm.2023.126399_b0055) 2022 |
| References_xml | – year: 2019 ident: b0090 article-title: Brenneria goodwinii and Gibbsiella quercinecans isolated from weeping cankers on Quercus robur L. in Spain publication-title: Eur. J. Plant Pathol. – volume: 18 start-page: 366 year: 2021 end-page: 368 ident: b0030 article-title: Sensitive protein alignments at tree-of-life scale using DIAMOND publication-title: Nat. Methods – volume: 49 start-page: 1 year: 2019 end-page: 14 ident: b0180 article-title: Brenneria spp. and Rahnella victoriana associated with acute oak decline symptoms on oak and hornbeam in Iran publication-title: For. Pathol. – volume: 8 year: 2020 ident: b0020 article-title: Polyphasic characterisation of Cedecea colo sp. Nov., a new enteric bacterium isolated from the koala hindgut publication-title: Microorganisms – volume: 31 start-page: 317 year: 1981 end-page: 326 ident: b0100 article-title: Cedecea davisae gen. nov., sp. nov. and Cedecea lapagei sp. nov., New Entero bacteriaceae from Clinical Specimens publication-title: Int. J. Syst. Bacteriol. – volume: 17–31 year: 1967 ident: b0250 article-title: Decline of Hardwoods: Possible Causes publication-title: Int. Shade Tree Conf. – volume: 52 start-page: 696 year: 2003 end-page: 704 ident: b0105 article-title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood publication-title: Syst. Biol. – volume: 1–14 year: 2015 ident: b0065 article-title: Cedecea publication-title: Bergey’s Man. Syst. Archaea Bact. – volume: 4 start-page: 473 year: 2013 end-page: 482 ident: b0200 article-title: Common and pathogen-specific virulence factors are different in function and structure publication-title: Virulence – volume: 79 start-page: 1 year: 2022 end-page: 9 ident: b0325 article-title: Buttiauxella massiliensis sp. nov., Isolated from a Human Bone Infection publication-title: Curr. Microbiol. – volume: 39 start-page: 3 year: 2020 end-page: 17 ident: b0290 article-title: Root exudates: from plant to rhizosphere and beyond publication-title: Plant Cell Rep. – volume: 38 start-page: 2341 year: 2022 end-page: 2343 ident: b0295 article-title: Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors publication-title: Bioinformatics – volume: 41 start-page: 36 year: 2013 end-page: 42 ident: b0015 article-title: GenBank publication-title: Nucl. Acids Res. – volume: 82 start-page: 477 year: 1997 end-page: 484 ident: b0195 article-title: Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population publication-title: J. Appl. Microbiol. – volume: 67 start-page: 3629 year: 2016 end-page: 3643 ident: b0320 article-title: The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots publication-title: J. Exp. Bot. – volume: 143 year: 2022 ident: b0080 article-title: First report of Brenneria goodwinii causing acute oak decline on Quercus suber in Portugal publication-title: J. Plant Pathol. – reference: Patra, N., Prakash, M.R., Patil, S., Rao, M.B., 2018. First case report of surgical site infection due to Buttiauxella agrestis in a Neurocare Center in India, 117–8, Doi: 10.4103/amhs.amhs. – volume: 2 start-page: 33 year: 1981 end-page: 44 ident: b0085 article-title: Buttiauxella, a new genus of the family Enterobacteraceae. Zentralblatt Fur Bakteriol publication-title: Angew. Und Okol. Microbiol. Abt. 1 Orig.C Hyg. – volume: 50 start-page: D912 year: 2022 end-page: D917 ident: b0150 article-title: VFDB 2022: A general classification scheme for bacterial virulence factors publication-title: Nucleic Acids Res. – year: 1981 ident: b0160 article-title: Tree disease concepts – volume: 187 start-page: 6258 year: 2005 end-page: 6264 ident: b0130 article-title: Towards a genome-based taxonomy for prokaryotes publication-title: J. Bacteriol. – volume: 10 year: 2019 ident: b0175 article-title: TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy publication-title: Nat. Commun. – reference: Farris, J.S., 1972. Estimating Phlogenetic Trees from Distance Matrices 106(951), 645–70. – volume: 28 start-page: 1166 year: 2012 end-page: 1167 ident: b0205 article-title: Unipro UGENE: a unified bioinformatics toolkit publication-title: Bioinformatics – volume: 103 start-page: 6 year: 2019 end-page: 11 ident: b0310 article-title: First report of Cedecea neteri causing yellow sticky disease in Flammulina velutipes in China publication-title: Plant Dis. – volume: 18 start-page: 4847 year: 2016 end-page: 4861 ident: b0165 article-title: Prediction of bacterial associations with plants using a supervised machine-learning approach publication-title: Environ. Microbiol. – reference: Crampton, B., Brady, C., Denman, S., 2022. Bacterial Tree Disease Fact Sheets. – volume: 27 year: 2021 ident: b0280 article-title: First report of Brenneria goodwinii and Gibbsiella quercinecans bacteria, detected on weaken oak trees in Poland publication-title: Balt. For. – volume: 32 start-page: 2798 year: 2015 end-page: 2800 ident: b0135 article-title: FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program publication-title: Mol. Biol. Evol. – volume: 34 start-page: 2422 year: 2017 end-page: 2424 ident: b0140 article-title: SMS: Smart Model Selection in PhyML publication-title: Mol. Biol. Evol. – volume: 11 start-page: 1 year: 2020 end-page: 19 ident: b0225 article-title: Linking tree health, rhizosphere physicochemical properties, and microbiome in acute oak decline publication-title: Forests – volume: 46 start-page: 50 year: 1996 end-page: 63 ident: b0185 article-title: Emended description of Buttiauxella agrestis with recognition of six new species of Buttiauxella and two new species of Kluyvera: Buttiauxella ferragutiae sp. nov., Buttiauxella gaviniae sp. nov., Buttiauxella brennerae sp. nov., Buttiauxella izardii sp publication-title: Int. J. Syst. Bacteriol. – volume: 248 year: 2021 ident: b0045 article-title: Acclimatization of Musa spp. seedlings using endophytic Bacillus spp. and Buttiauxella agrestis strains publication-title: Microbiol. Res. – volume: 14 year: 2013 ident: b0170 article-title: Genome sequence-based species delimitation with confidence intervals and improved distance functions publication-title: BMC Bioinformatics – volume: 57 start-page: 81 year: 2007 end-page: 91 ident: b0095 article-title: DNA-DNA hybridization values and their relationship to whole-genome sequence similarities publication-title: Int. J. Syst. Evol. Microbiol. – reference: Liu, Z., Zhou, S., Zhang, W., Wu, S., 2021. First Report of Cedecea neteri Causing Yellow Rot Disease in Pleurotus pulmonarius in China. Plant Dis. (April), 1189. – volume: 16 start-page: 775 year: 1982 end-page: 778 ident: b0070 article-title: Bacteremia due to Cedecea neteri sp. nov publication-title: J. Clin. Microbiol. – volume: 78 start-page: 179 year: 2021 end-page: 189 ident: b0305 article-title: A Re-evaluation of the Taxonomy and Classification of the Type III Secretion System in a Pathogenic Bacterium Causing Soft Rot Disease of Pleurotus eryngii publication-title: Curr. Microbiol. – volume: 30 start-page: 2114 year: 2014 end-page: 2120 ident: b0025 article-title: Trimmomatic: a flexible trimmer for Illumina sequence data publication-title: Bioinformatics – volume: 66 start-page: 630 year: 2008 end-page: 642 ident: b0190 article-title: Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the enterobacteriaceae? publication-title: J. Mol. Evol. – volume: 789–99 year: 2013 ident: b0220 article-title: Going back to the roots: the microbial ecology of the rhizosphere publication-title: Nat. Rev. Microbiol. – volume: 37 start-page: 3019 year: 2021 end-page: 3020 ident: b0260 article-title: orfipy: a fast and flexible tool for extracting ORFs publication-title: Bioinformatics – volume: 1–16 year: 2015 ident: b0120 article-title: Buttiauxella publication-title: Bergey’s Man. Syst. Archaea Bact. – volume: 66 start-page: 5575 year: 2016 end-page: 5599 ident: b0005 article-title: Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: Proposal for enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov. publication-title: Morgane. Int. J. Syst. Evol. Microbiol. – volume: 63 start-page: 541 year: 2009 end-page: 556 ident: b0155 article-title: Plant-Growth-Promoting Rhizobacteria publication-title: Annu. Rev. Microbiol. – volume: 5 year: 2019 ident: b0060 article-title: Genomic analysis of bacteria in the Acute Oak Decline pathobiome publication-title: Microb. Genomics – volume: 100 start-page: 461 year: 2020 end-page: 469 ident: b0275 article-title: Expanding spectrum of opportunistic Cedecea infections: Current clinical status and multidrug resistance publication-title: Int. J. Infect. Dis. – volume: 20 start-page: 566 year: 1997 end-page: 571 ident: b0125 article-title: Characterization of Buttiauxella and Kluyvera species by analysis of whole cell fatty acid patterns publication-title: Syst. Appl. Microbiol. – volume: 41 start-page: 18 year: 2020 ident: b0235 article-title: First report of acute oak decline disease of native and non-native oaks in Switzerland publication-title: New Dis. Rep. – volume: 38 start-page: 3022 year: 2021 end-page: 3027 ident: b0265 article-title: MEGA11: molecular evolutionary genetics analysis Version 11 publication-title: Mol. Biol. Evol. – reference: Patz, S., Gautam, A., Becker, M., Ruppel, S., Rodríguez-Palenzuela, P., Huson, D., 2021. PLaBAse: a comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria. BioRxiv (3), 2021.12.13.472471. – volume: 30 start-page: 2068 year: 2014 end-page: 2069 ident: b0245 article-title: Prokka: Rapid prokaryotic genome annotation publication-title: Bioinformatics – volume: 25 start-page: 21844 year: 2018 end-page: 21854 ident: b0300 article-title: Endophytic bacterium Buttiauxella sp. SaSR13 improves plant growth and cadmium accumulation of hyperaccumulator Sedum alfredii publication-title: Environ. Sci. Pollut. Res. – volume: 14 start-page: 29 year: 1988 end-page: 35 ident: b0255 article-title: Tree delince: four concepts of causality publication-title: J. Arboric. – volume: 44 start-page: 6614 year: 2016 end-page: 6624 ident: b0270 article-title: NCBI prokaryotic genome annotation pipeline publication-title: Nucleic Acids Res. – volume: 4 start-page: e1900v1 year: 2016 ident: b0230 article-title: The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes publication-title: PeerJ Prepr. – volume: 9 start-page: 1 year: 2018 end-page: 8 ident: b0110 article-title: High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries publication-title: Nat. Commun. – volume: 19 start-page: 455 year: 2012 end-page: 477 ident: b0010 article-title: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing publication-title: J. Comput. Biol. – start-page: 239 year: 2022 end-page: 263 ident: b0055 article-title: Temperate oak declines: biotic and abiotic predisposition drivers publication-title: For. Microbiol., Academic Press – volume: 47 start-page: 300 year: 2009 end-page: 310 ident: b0050 article-title: Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing publication-title: J. Clin. Microbiol. – volume: 67 start-page: 1613 year: 2017 end-page: 1617 ident: b0315 article-title: Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies publication-title: Int. J. Syst. Evol. Microbiol. – volume: 49 start-page: 405 year: 1999 end-page: 413 ident: b0035 article-title: Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov publication-title: Int. J. Syst. Bacteriol. – volume: 34 start-page: 1 year: 2021 end-page: 45 ident: b0115 article-title: The changing face of the family Enterobacteriaceae (order:“Enterobacterales”): new members, taxonomic issues, geographic expansion, and new diseases and disease syndromes publication-title: Clin. Microbiol. Rev. – volume: 15 start-page: 623 year: 2021 end-page: 635 ident: b0240 article-title: Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline publication-title: ISME J. – volume: 19 start-page: 6823 year: 1991 end-page: 6831 ident: b0285 article-title: Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes publication-title: Nucleic Acids Res. – volume: 82 start-page: 477 issue: 4 year: 1997 ident: 10.1016/j.syapm.2023.126399_b0195 article-title: Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population publication-title: J. Appl. Microbiol. doi: 10.1046/j.1365-2672.1997.00141.x – ident: 10.1016/j.syapm.2023.126399_b0210 doi: 10.4103/amhs.amhs_24_18 – volume: 78 start-page: 179 issue: 1 year: 2021 ident: 10.1016/j.syapm.2023.126399_b0305 article-title: A Re-evaluation of the Taxonomy and Classification of the Type III Secretion System in a Pathogenic Bacterium Causing Soft Rot Disease of Pleurotus eryngii publication-title: Curr. Microbiol. doi: 10.1007/s00284-020-02253-3 – volume: 27 issue: 1 year: 2021 ident: 10.1016/j.syapm.2023.126399_b0280 article-title: First report of Brenneria goodwinii and Gibbsiella quercinecans bacteria, detected on weaken oak trees in Poland publication-title: Balt. For. doi: 10.46490/BF563 – volume: 67 start-page: 3629 issue: 12 year: 2016 ident: 10.1016/j.syapm.2023.126399_b0320 article-title: The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots publication-title: J. Exp. Bot. doi: 10.1093/jxb/erw108 – volume: 25 start-page: 21844 issue: 22 year: 2018 ident: 10.1016/j.syapm.2023.126399_b0300 article-title: Endophytic bacterium Buttiauxella sp. SaSR13 improves plant growth and cadmium accumulation of hyperaccumulator Sedum alfredii publication-title: Environ. Sci. Pollut. Res. doi: 10.1007/s11356-018-2322-6 – volume: 248 issue: March year: 2021 ident: 10.1016/j.syapm.2023.126399_b0045 article-title: Acclimatization of Musa spp. seedlings using endophytic Bacillus spp. and Buttiauxella agrestis strains publication-title: Microbiol. Res. – ident: 10.1016/j.syapm.2023.126399_b0215 doi: 10.1101/2021.12.13.472471 – volume: 15 start-page: 623 issue: 3 year: 2021 ident: 10.1016/j.syapm.2023.126399_b0240 article-title: Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline publication-title: ISME J. doi: 10.1038/s41396-020-00801-0 – volume: 10 issue: 1 year: 2019 ident: 10.1016/j.syapm.2023.126399_b0175 article-title: TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy publication-title: Nat. Commun. doi: 10.1038/s41467-019-10210-3 – volume: 47 start-page: 300 issue: 2 year: 2009 ident: 10.1016/j.syapm.2023.126399_b0050 article-title: Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing publication-title: J. Clin. Microbiol. doi: 10.1128/JCM.01916-08 – volume: 39 start-page: 3 issue: 1 year: 2020 ident: 10.1016/j.syapm.2023.126399_b0290 article-title: Root exudates: from plant to rhizosphere and beyond publication-title: Plant Cell Rep. doi: 10.1007/s00299-019-02447-5 – volume: 67 start-page: 1613 issue: 5 year: 2017 ident: 10.1016/j.syapm.2023.126399_b0315 article-title: Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies publication-title: Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001755 – volume: 5 issue: 1 year: 2019 ident: 10.1016/j.syapm.2023.126399_b0060 article-title: Genomic analysis of bacteria in the Acute Oak Decline pathobiome publication-title: Microb. Genomics doi: 10.1099/mgen.0.000240 – volume: 9 start-page: 1 issue: 1 year: 2018 ident: 10.1016/j.syapm.2023.126399_b0110 article-title: High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries publication-title: Nat. Commun. doi: 10.1038/s41467-018-07641-9 – volume: 66 start-page: 5575 issue: 12 year: 2016 ident: 10.1016/j.syapm.2023.126399_b0005 article-title: Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: Proposal for enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov. publication-title: Morgane. Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001485 – volume: 20 start-page: 566 issue: 4 year: 1997 ident: 10.1016/j.syapm.2023.126399_b0125 article-title: Characterization of Buttiauxella and Kluyvera species by analysis of whole cell fatty acid patterns publication-title: Syst. Appl. Microbiol. doi: 10.1016/S0723-2020(97)80028-8 – volume: 18 start-page: 4847 issue: 12 year: 2016 ident: 10.1016/j.syapm.2023.126399_b0165 article-title: Prediction of bacterial associations with plants using a supervised machine-learning approach publication-title: Environ. Microbiol. doi: 10.1111/1462-2920.13389 – volume: 18 start-page: 366 issue: 4 year: 2021 ident: 10.1016/j.syapm.2023.126399_b0030 article-title: Sensitive protein alignments at tree-of-life scale using DIAMOND publication-title: Nat. Methods doi: 10.1038/s41592-021-01101-x – volume: 187 start-page: 6258 issue: 18 year: 2005 ident: 10.1016/j.syapm.2023.126399_b0130 article-title: Towards a genome-based taxonomy for prokaryotes publication-title: J. Bacteriol. doi: 10.1128/JB.187.18.6258-6264.2005 – volume: 49 start-page: 405 issue: 2 year: 1999 ident: 10.1016/j.syapm.2023.126399_b0035 article-title: Classification of Alcaligenes faecalis-like isolates from the environment and human clinical samples as Ralstonia gilardii sp. nov publication-title: Int. J. Syst. Bacteriol. doi: 10.1099/00207713-49-2-405 – volume: 4 start-page: e1900v1 year: 2016 ident: 10.1016/j.syapm.2023.126399_b0230 article-title: The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes publication-title: PeerJ Prepr. – volume: 17–31 year: 1967 ident: 10.1016/j.syapm.2023.126399_b0250 article-title: Decline of Hardwoods: Possible Causes publication-title: Int. Shade Tree Conf. – volume: 100 start-page: 461 year: 2020 ident: 10.1016/j.syapm.2023.126399_b0275 article-title: Expanding spectrum of opportunistic Cedecea infections: Current clinical status and multidrug resistance publication-title: Int. J. Infect. Dis. doi: 10.1016/j.ijid.2020.09.036 – ident: 10.1016/j.syapm.2023.126399_b0040 – ident: 10.1016/j.syapm.2023.126399_b0075 doi: 10.1086/282802 – volume: 31 start-page: 317 issue: 3 year: 1981 ident: 10.1016/j.syapm.2023.126399_b0100 article-title: Cedecea davisae gen. nov., sp. nov. and Cedecea lapagei sp. nov., New Entero bacteriaceae from Clinical Specimens publication-title: Int. J. Syst. Bacteriol. doi: 10.1099/00207713-31-3-317 – volume: 44 start-page: 6614 issue: 14 year: 2016 ident: 10.1016/j.syapm.2023.126399_b0270 article-title: NCBI prokaryotic genome annotation pipeline publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkw569 – volume: 57 start-page: 81 issue: 1 year: 2007 ident: 10.1016/j.syapm.2023.126399_b0095 article-title: DNA-DNA hybridization values and their relationship to whole-genome sequence similarities publication-title: Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijs.0.64483-0 – volume: 4 start-page: 473 issue: 6 year: 2013 ident: 10.1016/j.syapm.2023.126399_b0200 article-title: Common and pathogen-specific virulence factors are different in function and structure publication-title: Virulence doi: 10.4161/viru.25730 – volume: 41 start-page: 36 issue: D1 year: 2013 ident: 10.1016/j.syapm.2023.126399_b0015 article-title: GenBank publication-title: Nucl. Acids Res. doi: 10.1093/nar/gks1195 – volume: 32 start-page: 2798 issue: 10 year: 2015 ident: 10.1016/j.syapm.2023.126399_b0135 article-title: FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msv150 – year: 1981 ident: 10.1016/j.syapm.2023.126399_b0160 – volume: 49 start-page: 1 issue: 4 year: 2019 ident: 10.1016/j.syapm.2023.126399_b0180 article-title: Brenneria spp. and Rahnella victoriana associated with acute oak decline symptoms on oak and hornbeam in Iran publication-title: For. Pathol. doi: 10.1111/efp.12535 – volume: 38 start-page: 3022 issue: 7 year: 2021 ident: 10.1016/j.syapm.2023.126399_b0265 article-title: MEGA11: molecular evolutionary genetics analysis Version 11 publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msab120 – volume: 11 start-page: 1 issue: 11 year: 2020 ident: 10.1016/j.syapm.2023.126399_b0225 article-title: Linking tree health, rhizosphere physicochemical properties, and microbiome in acute oak decline publication-title: Forests doi: 10.3390/f11111153 – volume: 34 start-page: 1 issue: 2 year: 2021 ident: 10.1016/j.syapm.2023.126399_b0115 article-title: The changing face of the family Enterobacteriaceae (order:“Enterobacterales”): new members, taxonomic issues, geographic expansion, and new diseases and disease syndromes publication-title: Clin. Microbiol. Rev. doi: 10.1128/CMR.00174-20 – volume: 2 start-page: 33 issue: 1 year: 1981 ident: 10.1016/j.syapm.2023.126399_b0085 article-title: Buttiauxella, a new genus of the family Enterobacteraceae. Zentralblatt Fur Bakteriol publication-title: Angew. Und Okol. Microbiol. Abt. 1 Orig.C Hyg. – volume: 1–14 year: 2015 ident: 10.1016/j.syapm.2023.126399_b0065 article-title: Cedecea publication-title: Bergey’s Man. Syst. Archaea Bact. doi: 10.1002/9781118960608.gbm01142 – volume: 14 start-page: 29 issue: 2 year: 1988 ident: 10.1016/j.syapm.2023.126399_b0255 article-title: Tree delince: four concepts of causality publication-title: J. Arboric. – start-page: 239 year: 2022 ident: 10.1016/j.syapm.2023.126399_b0055 article-title: Temperate oak declines: biotic and abiotic predisposition drivers publication-title: For. Microbiol., Academic Press – volume: 46 start-page: 50 issue: 1 year: 1996 ident: 10.1016/j.syapm.2023.126399_b0185 article-title: Emended description of Buttiauxella agrestis with recognition of six new species of Buttiauxella and two new species of Kluyvera: Buttiauxella ferragutiae sp. nov., Buttiauxella gaviniae sp. nov., Buttiauxella brennerae sp. nov., Buttiauxella izardii sp publication-title: Int. J. Syst. Bacteriol. doi: 10.1099/00207713-46-1-50 – volume: 1–16 year: 2015 ident: 10.1016/j.syapm.2023.126399_b0120 article-title: Buttiauxella publication-title: Bergey’s Man. Syst. Archaea Bact. doi: 10.1002/9781118960608.gbm01139 – volume: 30 start-page: 2114 issue: 15 year: 2014 ident: 10.1016/j.syapm.2023.126399_b0025 article-title: Trimmomatic: a flexible trimmer for Illumina sequence data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu170 – volume: 19 start-page: 455 issue: 5 year: 2012 ident: 10.1016/j.syapm.2023.126399_b0010 article-title: SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing publication-title: J. Comput. Biol. doi: 10.1089/cmb.2012.0021 – volume: 52 start-page: 696 issue: 5 year: 2003 ident: 10.1016/j.syapm.2023.126399_b0105 article-title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood publication-title: Syst. Biol. doi: 10.1080/10635150390235520 – ident: 10.1016/j.syapm.2023.126399_b0145 doi: 10.1094/PDIS-09-20-1886-PDN – volume: 38 start-page: 2341 issue: 8 year: 2022 ident: 10.1016/j.syapm.2023.126399_b0295 article-title: Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors publication-title: Bioinformatics doi: 10.1093/bioinformatics/btac087 – volume: 14 year: 2013 ident: 10.1016/j.syapm.2023.126399_b0170 article-title: Genome sequence-based species delimitation with confidence intervals and improved distance functions publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-14-60 – volume: 16 start-page: 775 issue: 4 year: 1982 ident: 10.1016/j.syapm.2023.126399_b0070 article-title: Bacteremia due to Cedecea neteri sp. nov publication-title: J. Clin. Microbiol. doi: 10.1128/jcm.16.4.775-778.1982 – volume: 8 issue: 2 year: 2020 ident: 10.1016/j.syapm.2023.126399_b0020 article-title: Polyphasic characterisation of Cedecea colo sp. Nov., a new enteric bacterium isolated from the koala hindgut publication-title: Microorganisms doi: 10.3390/microorganisms8020309 – volume: 30 start-page: 2068 issue: 14 year: 2014 ident: 10.1016/j.syapm.2023.126399_b0245 article-title: Prokka: Rapid prokaryotic genome annotation publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu153 – volume: 63 start-page: 541 issue: 1 year: 2009 ident: 10.1016/j.syapm.2023.126399_b0155 article-title: Plant-Growth-Promoting Rhizobacteria publication-title: Annu. Rev. Microbiol. doi: 10.1146/annurev.micro.62.081307.162918 – volume: 66 start-page: 630 issue: 6 year: 2008 ident: 10.1016/j.syapm.2023.126399_b0190 article-title: Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the enterobacteriaceae? publication-title: J. Mol. Evol. doi: 10.1007/s00239-008-9115-3 – volume: 28 start-page: 1166 issue: 8 year: 2012 ident: 10.1016/j.syapm.2023.126399_b0205 article-title: Unipro UGENE: a unified bioinformatics toolkit publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts091 – volume: 143 year: 2022 ident: 10.1016/j.syapm.2023.126399_b0080 article-title: First report of Brenneria goodwinii causing acute oak decline on Quercus suber in Portugal publication-title: J. Plant Pathol. – volume: 789–99 year: 2013 ident: 10.1016/j.syapm.2023.126399_b0220 article-title: Going back to the roots: the microbial ecology of the rhizosphere publication-title: Nat. Rev. Microbiol. – volume: 41 start-page: 18 issue: 1 year: 2020 ident: 10.1016/j.syapm.2023.126399_b0235 article-title: First report of acute oak decline disease of native and non-native oaks in Switzerland publication-title: New Dis. Rep. doi: 10.5197/j.2044-0588.2020.041.018 – volume: 34 start-page: 2422 issue: 9 year: 2017 ident: 10.1016/j.syapm.2023.126399_b0140 article-title: SMS: Smart Model Selection in PhyML publication-title: Mol. Biol. Evol. doi: 10.1093/molbev/msx149 – volume: 37 start-page: 3019 issue: 18 year: 2021 ident: 10.1016/j.syapm.2023.126399_b0260 article-title: orfipy: a fast and flexible tool for extracting ORFs publication-title: Bioinformatics doi: 10.1093/bioinformatics/btab090 – volume: 19 start-page: 6823 issue: 24 year: 1991 ident: 10.1016/j.syapm.2023.126399_b0285 article-title: Distribution of repetitive DNA sequences in eubacteria and application to finerpriting of bacterial enomes publication-title: Nucleic Acids Res. doi: 10.1093/nar/19.24.6823 – volume: 103 start-page: 6 issue: 5 year: 2019 ident: 10.1016/j.syapm.2023.126399_b0310 article-title: First report of Cedecea neteri causing yellow sticky disease in Flammulina velutipes in China publication-title: Plant Dis. – year: 2019 ident: 10.1016/j.syapm.2023.126399_b0090 article-title: Brenneria goodwinii and Gibbsiella quercinecans isolated from weeping cankers on Quercus robur L. in Spain publication-title: Eur. J. Plant Pathol. – volume: 50 start-page: D912 issue: D1 year: 2022 ident: 10.1016/j.syapm.2023.126399_b0150 article-title: VFDB 2022: A general classification scheme for bacterial virulence factors publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkab1107 – volume: 79 start-page: 1 issue: 2 year: 2022 ident: 10.1016/j.syapm.2023.126399_b0325 article-title: Buttiauxella massiliensis sp. nov., Isolated from a Human Bone Infection publication-title: Curr. Microbiol. doi: 10.1007/s00284-021-02714-3 |
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| Title | Description of Dryocola gen. nov. and two novel species, Dryocola boscaweniae sp. nov. and Dryocola clanedunensis sp. nov. isolated from the rhizosphere of native British oaks |
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