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Palleronia Soli Sp Nova, Isolated from a Soil Sample on Reclaimed Tidal

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International Journal of Systematic and Evolutionary Microbiology (2015), 65, 2516–2521 DOI 10.1099/ijs.0.000297 Palleronia soli sp. nov., isolated from a soil sample on reclaimed tidal land, and emended description of the genus Palleronia Yena Kim,1 Jong-Hwa Kim,1 Keun Chul Lee,2 Jung-Sook Lee2 and Wonyong Kim1 Correspondence 1Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea Wonyong Kim 2Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, [email protected] Daejeon, Republic of Korea A Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, short rod-shaped and moderately halophilic bacterial strain, CAU 1105T, was isolated from soil on reclaimed tidal land in Modo, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. Strain CAU 1105T grows optimally at a temperature of 37 8C at pH 7 in the presence of 3 % (w/v) sea salt. Based on 16S rRNA gene sequence similarity analyses, the novel isolate was assigned to the genus Palleronia within the class Alphaproteobacteria and showed the highest 16S rRNA gene sequence similarity with Palleronia marisminoris B33T (95.4 %). Strain CAU 1105T contained ubiquinone-10 as the only respiratory quinone and T C18 : 1v7c as the major cellular fatty acid. The DNA G+C content of strain CAU 1105 was 64.3 mol%. On the basis of phenotypic differentiation, phylogenetic and chemotaxonomic data, strain CAU 1105T represents a novel species of the genus Palleronia, for which the name Palleronia soli sp. nov. is proposed. The type strain is CAU 1105T (5KCTC 42298T5NBRC 110740T). An emended description of the genus Palleronia is also provided. Since Gram-negative bacteria belonging to the Roseobacter from a hypersaline soil bordering a saline saltern on the Med- clade within the family Rhodobacteraceae (class Alphaproteo- iterranean seaboard near Murcia, South-eastern Spain (Mar- bacteria) were first described by Shiba (1991), 17 different tı´nez-Checa et al., 2005). During the past 10 years, no new genera have been described. The Roseobacter clade is species of this genus with validly published names have marine or hypersaline, with characterized isolates demon- been described (Parte, 2014). The Yellow Sea coast of the strating either a salt tolerance or requirement (Buchan Republic of Korea comprises huge tidal flats, which are et al., 2005; Zan et al., 2014). Members of the Roseobacter rich in valuable biological resources. A novel Gram-stain- clade are known to be numerically abundant and ecologically negative, aerobic, moderately halophilic bacterium, desig- important in marine environments, and they have been iso- nated CAU 1105T, was isolated from a soil sample on lated from many marine environments such as seawater, reclaimed tidal land, collected in Modo (378 329 12.280 N sediment, tidal flats, marine algae, hypersaline microbial 1268 249 51.470 E), Republic of Korea. The objective of mats and coastal biofilms (Choi et al., 2007; Lee et al., 2007; this study was to evaluate the taxonomic position of this Kim et al., 2008; Yoon et al., 2009; Vandecandelaere et al., bacterial strain using a polyphasic approach. 2009; Wang et al., 2009; Zheng et al., 2010). The genus Paller- A marine environmental sample was serially diluted and onia was created by Martı´nez-Checa et al. (2005) as a member plated on marine agar 2216 (MA; Difco) at 30 8C for of the Roseobacter clade. The genus Palleronia consists of 7 days under aerobic conditions as described by Gordon Gram-negative, rod-shaped, moderately halophilic bacteria. & Mihm (1962). Colonies were randomly selected and Ubiquinone Q-10 is the dominating respiratory quinone. T strain CAU 1105 was purified from a single colony on At the time of writing, this genus consists of only one recog- MA. The strain was grown aerobically on MA at 37 8C nized species, Palleronia marisminoris, which was isolated for 3 days. The strain was preserved at 280 8C in marine broth 2216 (MB; Difco) containing 25 % glycerol. Strain The GenBank/EMBL/DDBJ accession number for the 16S rRNA CAU 1105T has been deposited in the Korean Collection T gene sequence of strain CAU 1105 is KP064190. for Type Cultures (KCTC; Taejon, Korea) and the Biologi- A supplementary figure is available with the online Supplementary cal Resource Center, NITE (NBRC; Chiba, Japan) as KCTC T T Material. 42298 and NBRC 110740 , respectively. 2516 000297 G 2015 IUMS Printed in Great Britain Palleronia soli sp. nov. Genomic DNA was extracted from strain CAU 1105T using API 20E and API 20NE systems (bioMe´rieux). Additionally, the method described by Marmur (1961). PCR amplifica- enzyme activities were determined using the API ZYM kit tion of 16S rRNA genes from the isolate was performed fol- (bioMe´rieux) according to the manufacturer’s instructions. lowing the procedures described in Lane (1991). API 20E and API ZYM strips were read after 24 h and API Sequencing of the amplified 16S rRNA gene was performed 20NE strips after 48 h. Antibiotic susceptibility was deter- using a BigDye Terminator Cycle Sequencing kit (Applied mined on MA at 37 8C by the disc diffusion method using Biosystems) and an automatic DNA sequencer (model Sensi-Disc susceptibility test discs (BBL). The following anti- 3730; Applied Biosystems). The 16S rRNA gene sequence biotics were examined (mg per disc unless otherwise stated): of strain CAU 1105T was determined and compared with amoxicillin (20), ampicillin (10), carbenicillin (100), cefoxi- available reference sequences in the GenBank database tin (30), cephalothin (30), chloramphenicol (30), erythro- (Benson et al., 2013) accessed December 2014. Sequence mycin (15), kanamycin (30), penicillin (10 U), polymyxin similarity levels between strain CAU 1105T and other B (300 U), rifampicin (5), streptomycin (10), tobramycin related strains were calculated using the EzTaxon-e server (10), nalidixic acid (30) and trimethoprim/sulfamethoxazole (Kim et al., 2012; http://www.ezbiocloud.net/eztaxon) (1.25/23.75). An inhibition zone .10 mm diameter indi- and multiple alignments with reference sequences were car- cated susceptibility and the absence of an inhibition zone rep- ried out using CLUSTAL X 2.1 (Larkin et al., 2007). The type resented resistance. strains of closely related taxa, including Palleronia marismi- Isoprenoid quinones were extracted according to Koma- noris B33T, Hwanghaeicola aestuarii Y26T, Maribius pelagius gata & Suzuki (1987) and analysed by HPLC. The isopre- B5-6T, Maribius salinus CL-SP27T and Maritimibacter alka- noid quinones were eluted by an isocratic solvent system liphilus HTCC2654T, were used as reference strains for the [methanol/isopropyl ether (3 : 1, v/v)] using a flow rate of phylogenetic analysis. Evolutionary distance matrices were 2 1 ml min 1. The cell mass of strain CAU 1105T for fatty generated through the neighbour-joining method (Jukes & acid analysis was harvested from tryptic soy agar (TSA; Cantor, 1969). Phylogenetic trees were reconstructed by Difco) in late-exponential growth phase after cultivation using the neighbour-joining (Saitou & Nei, 1987), maxi- for 3 days at 37 8C. Fatty acids were methylated, saponi- mum-likelihood (Felsenstein, 1981), maximum-parsimony fied, and extracted according to the standard MIDI proto- (Fitch, 1971) and least-squares (Fitch & Margoliash, 1967) col (Sherlock Microbial Identification System version 6.1). algorithms in the PHYLIP package (Felsenstein, 1989). The Fatty acid methyl esters were obtained by the method of tree topology reconstructed by the neighbour-joining Minnikin et al. (1980), and separated using an automated algorithm was evaluated using a bootstrap analysis based gas chromatography system (model 6890N and 7683 auto- on 1000 replicates (Felsenstein, 1985) using the SEQBOOT sampler; Agilent). The peaks were confirmed by using the and CONSENSE programs from the PHYLIP package. The Microbial Identification System software package G+C content of the DNA was performed using HPLC (MOORE library version 5.0; MIDI database TSBA6). according to Tamaoka & Komagata (1984) and analysed by reversed-phase HPLC. The 16S rRNA gene sequence of strain CAU 1105T (1447 bp) was determined and compared with the available reference The temperature range for growth of strain CAU 1105T was sequences in the GenBank database (accessed December determined by growing the isolate at different temperatures 2014). Phylogenetic analysis based on 16S rRNA gene (4, 10, 20, 30, 37, 40 and 45 8C) on MA. The pH range for sequences showed that strain CAU 1105T formed a distinct growth was examined at 37 8C in MB adjusted to pH 4.5– lineage within the genus Palleronia and the most closely 11.5 at 0.5 pH unit intervals. The pH values of ,6, 6–9 and related strain was P. marisminoris B33T (GenBank accession .9 were obtained by using sodium acetate/acetic acid, no. AY926462, similarity 95.4 %) (Fig. 1). Other closely Tris/HCl and sodium carbonate buffers, respectively. Salt related phylogenetic neighbours based on 16S rRNA gene requirement was determined in MY medium (Moraine & sequences were H. aestuarii Y26T (FJ230842, similarity Rogovin, 1966), and the salt concentrations examined 94.4 %), Maribius pelagius B5-6T (DQ514326, similar- ranged from 0–15 % (w/v) and consisted of a mixture of ity94.3 %),Maribiussalinus CL-SP27T (AY906863, similarity sea salts as described by Rodrı´guez-Valera et al. (1981). The 94.2 %) and Maritimibacter alkaliphilus HTCC2654T Gram reaction was performed using a Gram staining kit (bio- (DQ915443, similarity 92.9 %). The DNA G+C content of Me´rieux). Catalase and oxidase tests were carried out accord- strain CAU 1105T was 64.3 mol %. ing to Cappuccino & Sherman (2002). Hydrolysis of gelatin, casein, starch, aesculin and citrate were examined as Strain CAU 1105T grew at temperatures between 20 and described by La´nyı´ (1987) and Smibert & Krieg (1994). Cell 40 8C (optimum 37 8C) and sea salt concentrations from morphology was observed using light microscopy (DM 1–11 % sea salt (optimum 3 %).
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  • Appendix 1. Validly Published Names, Conserved and Rejected Names, And

    Appendix 1. Validly Published Names, Conserved and Rejected Names, And

    Appendix 1. Validly published names, conserved and rejected names, and taxonomic opinions cited in the International Journal of Systematic and Evolutionary Microbiology since publication of Volume 2 of the Second Edition of the Systematics* JEAN P. EUZÉBY New phyla Alteromonadales Bowman and McMeekin 2005, 2235VP – Valid publication: Validation List no. 106 – Effective publication: Names above the rank of class are not covered by the Rules of Bowman and McMeekin (2005) the Bacteriological Code (1990 Revision), and the names of phyla are not to be regarded as having been validly published. These Anaerolineales Yamada et al. 2006, 1338VP names are listed for completeness. Bdellovibrionales Garrity et al. 2006, 1VP – Valid publication: Lentisphaerae Cho et al. 2004 – Valid publication: Validation List Validation List no. 107 – Effective publication: Garrity et al. no. 98 – Effective publication: J.C. Cho et al. (2004) (2005xxxvi) Proteobacteria Garrity et al. 2005 – Valid publication: Validation Burkholderiales Garrity et al. 2006, 1VP – Valid publication: Vali- List no. 106 – Effective publication: Garrity et al. (2005i) dation List no. 107 – Effective publication: Garrity et al. (2005xxiii) New classes Caldilineales Yamada et al. 2006, 1339VP VP Alphaproteobacteria Garrity et al. 2006, 1 – Valid publication: Campylobacterales Garrity et al. 2006, 1VP – Valid publication: Validation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xv) (2005xxxixi) VP Anaerolineae Yamada et al. 2006, 1336 Cardiobacteriales Garrity et al. 2005, 2235VP – Valid publica- Betaproteobacteria Garrity et al. 2006, 1VP – Valid publication: tion: Validation List no. 106 – Effective publication: Garrity Validation List no. 107 – Effective publication: Garrity et al.
  • 1 Supplementary Information Genomic and Kinetic Analysis of Novel

    1 Supplementary Information Genomic and Kinetic Analysis of Novel

    Supplementary Information Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting Anna J. Mueller, Man-Young Jung, Cameron R. Strachan, Craig W. Herbold, Rasmus H. Kirkegaard, Michael Wagner, Holger Daims Supplementary Materials and Methods Isolation of accompanying heterotrophs Alphaproteobacterial heterotrophs were isolated from Nitrospinae containing co-cultures on Difco Marine Broth Agar 2216 (Difco, BD) at 28°C. Colonies were observed after ~3 days. After colony picking, the alphaproteobacterial strains were grown in liquid Difco Marine Broth (DB) media at 28°C for all subsequent experiments. To identify these organisms, their 16S rRNA genes were PCR-amplified, using the universal bacterial 16S rRNA gene-targeted primer pair 616V-1492R [1], and Sanger-sequenced (Microsynth). The obtained 16S rRNA gene sequences were subjected to BLASTN searches against the NCBI bacterial and archaeal 16S rRNA sequence database. The 16S rRNA gene sequences are available under the GenBank accession numbers MT338542 (Stappia sp.) and MT338538 (Maritimibacter sp.). Growth curves and nitrite oxidation Cells from 25 ml of nitrite-depleted cultures were harvested by centrifugation (4500×g, 20 min, 28°C using a swing-bucket rotor). The cells were subsequently washed with 2.5 ml and suspended in 500 µl of nitrite free medium. 100 µl of the washed and concentrated cells were inoculated into 25 ml of the strain-specific marine mineral medium (see main text Materials and Methods) with 1.1 mM and 0.55 mM nitrite for the EB and VA strain, respectively. The experiments were carried 1 out with biological quadruplicates. Samples for quantitative PCR (qPCR) and nitrite/nitrate quantification were regularly taken and stored at -20°C until further analysis.