Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella Shih-Yi Sheu, Li-Chu Chen, Che-Chia Yang, Aurélien Carlier, Wen-Ming Chen To cite this version: Shih-Yi Sheu, Li-Chu Chen, Che-Chia Yang, Aurélien Carlier, Wen-Ming Chen. Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella. International Journal of Systematic and Evo- lutionary Microbiology, Microbiology Society, 2020, 70 (12), pp.6381-6389. 10.1099/ijsem.0.004538. hal-03151291 HAL Id: hal-03151291 https://hal.inrae.fr/hal-03151291 Submitted on 24 Feb 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. TAXONOMIC DESCRIPTION Sheu et al., Int. J. Syst. Evol. Microbiol. 2020;70:6381–6389 DOI 10.1099/ijsem.0.004538 Orrella amnicola sp. nov., isolated from a freshwater river, reclassification of Algicoccus marinus as Orrella marina comb. nov., and emended description of the genus Orrella Shih- Yi Sheu1, Li- Chu Chen1, Che- Chia Yang1, Aurelien Carlier2,3 and Wen- Ming Chen4,* Abstract A novel Gram- negative, aerobic, non- motile, ovoid to rod- shaped bacterium, designated NBD-18T, was isolated from a freshwa- ter river in Taiwan. Optimal growth occurred at 30 °C, at pH 6 and in the absence of NaCl. The predominant fatty acids of strain T NBD-18 were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 0 cyclo and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyldimeth- ylethanolamine. The major polyamine was putrescine. The major isoprenoid quinone was Q-8. The genomic DNA G+C content of strain NBD-18T was 50.9 %. Strain NBD-18T was most closely related to Orrella dioscoreae LMG 29303T and Algicoccus marinus HZ20T at a 16S rRNA gene sequence similarity of 97.7 %. 16S rRNA gene sequence similarity between O. dioscoreae LMG 29303T and A. marinus HZ20T was 97.7 %. Phylogenetic analyses based on 16S rRNA gene sequences and an up- to- date bacterial core gene set indicated that strain NBD-18T, O. dioscoreae LMG 29303T and A. marinus HZ20T are affiliated with the same genus. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values among these three strains supported that they belong to the same genus and that strain NBD-18T represents a novel species. Thus, A. marinus HZ20T should be reclassified as Orrella marina comb. nov. based on the rules for priority of publication and validation. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain NBD-18T represents a novel species in the genus Orrella, for which the name Orrella amnicola sp. nov. is proposed. The type strain is NBD-18T (=BCRC 81197T=LMG 31338T). The genus Orrella, belonging to the family Alcaligenaceae belonging to the family Alcaligenaceae within the order Bur- within the order Burkholderiales of the class Betaproteobacte- kholderiales of the class Betaproteobacteria, was proposed by ria, was proposed by Carlier et al. [1]. To date, this genus com- Ying et al. [2]. The genus Algicoccus presently comprises only prises only one recognized species: Orrella dioscoreae, isolated one species with a validly published name: Algicoccus mari- from leaf acumens of Dioscorea sansibarensis [1]. Members nus, a marine bacterium isolated from the surface of brown of the genus Orrella are characterized as Gram- negative, seaweed Laminaria japonica. Cells of the genus Algicoccus facultatively anaerobic, non- motile, coccobacillus- shaped are Gram- negative, strictly aerobic, chemo-organotrophic, and oxidase- positive. Chemotaxonomically, members of the non- motile, ovoid to rod-shaped, mesophilic, neutrophilic, genus Orrella are characterized by C16 : 0, C18 : 1ω7c and summed chemotrophic, and catalase- and oxidase- positive. Chemo- feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty taxonomically, cells of the genus Algicoccus possess Q-8 as acids, by Q-8 as the major respiratory quinone and by hav- the sole respiratory quinone, C17 : 0 cyclo, C16 : 0 and summed ing a DNA G+C content of ˜67.4 % [1]. The genus Algicoccus, feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the predominant fatty Author affiliations: 1Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, ROC; 2Laboratory of Microbiology, Faculty of Sciences, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; 3LIPM, Université de Toulouse, INRAE, CNRS, Castanet- Tolosan, France; 4Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung University of Science and Technology, Kaohsiung City 811, Taiwan, TOC. *Correspondence: Wen- Ming Chen, p62365@ ms28. hinet. net Keywords: Orrella amnicola sp. nov.; Alcaligenaceae; Burkholderiales; Betaproteobacteria. Abbreviations: AAI, average amino acid identity; ANI, average nucleotide identity; APL, unidentified aminophospholipid; CAD, cadaverine; dDDH, digital DNA–DNA hybridization; DPG, diphosphatidylglycerol; HPUT, homoputrescine; L, unidentified lipid; ML, maximum- likelihood; MP, maximum- parsimony; NJ, neighbour- joining; PDE, phosphatidyldimethylethanolamine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PUT, putrescine; Q-8, ubiquinone-8; UBCG, up- to- date bacterial core gene set. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the whole genome of Orrella amnicola NBD-18T are MK272950 and NZ_JAAGRN000000000, respectively. Six supplementary figures and four supplementary tables are available with the online version of this article. 004538 © 2020 The Authors 6381 Sheu et al., Int. J. Syst. Evol. Microbiol. 2020;70:6381–6389 Table 1. Differential characteristics between strains NBD-18T, acids, phosphatidylethanolamine, phosphatidylglycerol, T T O. dioscoreae LMG 29303 and A. marinus HZ20 diphosphatidylglycerol, an unidentified aminophospholipid Strains: 1, NBD-18T; 2, O. dioscoreae LMG 29303T; 3, A. marinus HZ20T. and unidentified phospholipid as the major polar lipids, and Data were obtained in this study except the G+C content of O. dioscoreae a DNA G+C content of around 55.5 % [2]. LMG 29303T [1], and data for A. marinus HZ20T from Ying et al. [2]. +, Positive reaction; w, weakly positive reaction; −, negative reaction. The 16S rRNA gene sequence similarity between O. dioscoreae The three strains are positive for oxidase, leucine arylamidase and LMG 29303T and A. marinus HZ20T is 97.7 %. Unfortunately, acid phosphatase activities, and nitrate reduction. The three strains there is no conclusive evidence available to elucidate the are negative for: Gram staining; motility; indol production; glucose taxonomic relationship between these taxa due to the lack fermentation; hydrolysis of aesculin and CM- cellulose; and arginine of experimental comparisons. In the course of a study on dihydrolase, C14 lipase, trypsin, α-chymotrypsin, α-galactosidase, -galactosidase, -glucuronidase, -glucosidase, -glucosidase, N- cultivable bacteria from a freshwater river, a bacterial strain β β α β T acetyl-β-glucosaminidase, α-mannosidase and α-fucosidase activities. designated NBD-18 was isolated and selected for detailed analysis. Phylogenetic analysis of the 16S rRNA gene sequence Characteristic 1 2 3 of strain NBD-18T revealed that the closest relatives of this Isolation source Freshwater Plant Brown isolate were members of the genera Orrella and Algicoccus. T river seaweed Strain NBD-18 occupied an intermediate position between these two genera. Sequence similarity calculations indicated Colony pigmentation White White Yellow that strain NBD-18T was closely related to O. dioscoreae T T Temperature range for growth 25–37 (30) 15–40 (30) 4–50 (37) LMG 29303 and A. marinus HZ20 at 97.7 % similarity. In (°C) (optimum) this study, the taxonomic relationship between these taxa was NaCl range for growth (%) 0–0.5 (0) 0–0.5 (0) 0–10 clarified by means of experimental comparisons. Based on (optimum) (1–1.5) the results of phylogenetic, phenotypic and chemotaxonomic analyses, we conclude that strain NBD-18T should be placed pH range for growth (optimum) 5.5–8 (6) 8–9 (8.5) 5–9.5 in the genus Orrella as the type strain of a novel species and (7–7.5) that the nearest neighbour, A. marinus HZ20T, should be Oxygen requirement Strictly Facultatively Strictly reclassified as a member of the genus Orrella. aerobic anaerobic aerobic Hydrolysis of: ISOLATION AND ECOLOGY Tweens 20, 40, 60 − + + During investigations on the biodiversity of bacteria present Tween 80 − − + in freshwater, a water sample (25 °C, pH 7.2, 0 %, w/v, NaCl) Casein + − + was collected from the Dahanxi River (GPS location: 25° 02′ 27″ N 121° 29′ 05″ E) in New Taipei City, Taiwan, on 10 Starch − − + October 2018 (Fig. S1, available in the online version of this Urea − − + article). The water sample was spread on R2A agar (BD Difco)