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Fulvimarina Manganoxydans Sp. Nov., Isolated from a Deep-Sea Hydrothermal Plume in the South-West Indian Ocean

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Fulvimarina Manganoxydans Sp. Nov., Isolated from a Deep-Sea Hydrothermal Plume in the South-West Indian Ocean International Journal of Systematic and Evolutionary Microbiology (2014), 64, 2920–2925 DOI 10.1099/ijs.0.060558-0 Fulvimarina manganoxydans sp. nov., isolated from a deep-sea hydrothermal plume in the south-west Indian Ocean Fei Ren,13 Limin Zhang,13 Lei Song,2 Shiyao Xu,1 Lijun Xi,1 Li Huang,1 Ying Huang1 and Xin Dai1 Correspondence 1State Key Laboratory of Microbial Resources, Institute of Microbiology, Xin Dai Chinese Academy of Sciences, Beijing 100101, PR China [email protected] or [email protected]. 2China General Microbiological Culture Collection Center, Institute of Microbiology, cn Chinese Academy of Sciences, Beijing 100101, PR China An aerobic, Mn(II)-oxidizing, Gram-negative bacterium, strain 8047T, was isolated from a deep- sea hydrothermal vent plume in the south-west Indian Ocean. The strain was rod-shaped and motile with a terminal flagellum, and formed yellowish colonies. It produced catalase and oxidase, hydrolysed gelatin and reduced nitrate. 16S rRNA gene sequence analysis showed that strain 8047T belonged to the order Rhizobiales of the class Alphaproteobacteria, and was phylogenetically most closely related to the genus Fulvimarina, sharing 94.4 % sequence identity with the type strain of the type species. The taxonomic affiliation of strain 8047T was supported by phylogenetic analysis of four additional housekeeping genes, gyrB, recA, rpoC and rpoB. The predominant respiratory lipoquinone of strain 8047T was Q-10, the major fatty acid was C18 : 1v7c and the DNA G+C content was 61.7 mol%. On the basis of the phenotypic and genotypic characteristics determined in this study, strain 8047T represents a novel species within the genus Fulvimarina, for which the name Fulvimarina manganoxydans sp. nov. is proposed. The type strain is strain 8047T (5CGMCC1.10972T5JCM 18890T). As the biggest group in the a2-proteobacteria, the order genus Fulvimarina was proposed by Cho & Giovannoni Rhizobiales comprises more than ten families, and the (2003) and its description was emended by Rathsack et al. majority of the members of this order were isolated from (2011). At the time of writing, it comprises only one species, terrestrial ecosystems (Cho & Giovannoni, 2003; Weon Fulvimarina pelagi, which was isolated from water of the et al., 2007). Members of only a few genera were retrieved Sargasso Sea by using high-throughput culturing methods from marine environments, which are distributed primarily (Cho & Giovannoni, 2003). in the families Rhodobiaceae (Hiraishi et al., 1995; Brettar During a survey of the microbial diversity of a deep-sea et al., 2007) and ‘Aurantimonadaceae’ (Cho & Giovannoni, hydrothermal plume in the south-west Indian Ocean, where 2003; Denner et al., 2003). The latter includes four genera, total Fe and dissolved Mn were found in high concentra- Aurantimonas (Denner et al., 2003), Fulvimarina (Cho & tions (Wang et al., 2012), an aerobic, Gram-negative, yellow Giovannoni, 2003), Martelella (Rivas et al., 2005) and bacterium, strain 8047T, was isolated. Based on 16S rRNA Aureimonas (Rathsack et al., 2011). Except for the genus gene sequence analysis, the strain was related phylogeneti- Aureimonas, which was created by division from the genus cally to F. pelagi HTCC2506T and formed a branch within Aurantimonas (Rathsack et al., 2011), the members of the the order Rhizobiales. Here, we describe the characterization family ‘Aurantimonadaceae’ were all derived from marine of strain 8047T using a polyphasic taxonomic approach. environments. Furthermore, several strains of this family are capable of Mn(II) oxidation (Anderson et al., 2009). The Seawater was collected at 37u 479 S49u 399 E from ~2800 m below sea level and concentrated in situ 1000-fold with an 3These authors contributed equally to this work. integrated biological sampling device (Beijing Pioneer High The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA, Technology Development Co.) during cruise DY-115-21 gyrB, recA, rpoC and rpoB gene sequences of strain 8047T are of the DaYang YiHao in January 2010. The geochemical HQ622550, HG764651, HG764652, HG764653 and HG764654, characteristics of the hydrothermal plume at the sampling respectively. site were described by Wang et al. (2012). Strain 8047T was Four supplementary figures and a supplementary table are available with isolated from the concentrated sample following growth on the online version of this paper. seawater GYM agar (0.4 % yeast extract, 1 % malt extract, Downloaded from www.microbiologyresearch.org by 2920 060558 G 2014 IUMS Printed in Great Britain IP: 54.70.40.11 On: Fri, 07 Dec 2018 15:01:17 Fulvimarina manganoxydans sp. nov. 0.4 % glucose, 1.5 % agar and 60 % seawater) at 28 uC for implemented in the software package MEGA version 5.0 2–3 days. Individual colonies were picked and transferred (Tamura et al., 2011). Evolutionary distances were calcu- to YTSS agar [0.5 % yeast extract, 1 % tryptone, 1.5 % agar lated by using Kimura’s two-parameter model. The resultant and 2 % sea salt (Sigma)] for further purification. Culture tree topologies were evaluated by bootstrap analysis purity was checked by microscopic examination and KOH- with 1000 resamplings. As revealed by the phylogenetic lysis test (Smibert & Krieg, 1994). Colonies of strain 8047T tree, strain 8047T formed a stable clade with F. pelagi were smooth, circular, yellow, flat and non-translucent HTCC2506T, and the clade was associated closely with the after cultivation at 28 uC for 48 h. genera Aurantimonas and Martelella, two members of the family ‘Aurantimonadaceae’ within the order Rhizobiales Genomic DNA was extracted from strain 8047T using an (Fig. 1). Therefore, F. pelagi HTCC 2506T, Aurantimonas AxyPrep bacterial genomic DNA extraction kit (Axygen) coralicida DSM 14790T and Martelella mediterranea DSM and used as the template for amplification of the 16S rRNA 17316T were used as reference strains for investigation of gene by PCR with primers 27F and 1492R, as described some properties under the same laboratory conditions. previously (Cho & Giovannoni, 2003). The amplification product was purified and sequenced at Invitrogen Inc. To learn more about the relationship between strain 8047T A sequence search in GenBank with the 16S rRNA and other strains of the family ’Aurantimonadaceae’, we gene sequence of strain 8047T (1449 bp) as a query was generated a draft genome sequence of strain 8047T with a performed using the BLAST algorithm. Sequence comparison 454 Genome Sequencer FLX instrument (Roche Applied of the retrieved 16S rRNA gene sequences indicated that Science). The complete sequences of four housekeeping strain 8047T was most closely related to species of the order genes, gyrB (2439 bp), recA (1074 bp), rpoC (4197 bp) Rhizobiales of the class Alphaproteobacteria. On the basis of and rpoB (4140 bp), were obtained from contigs 00036 pairwise 16S rRNA gene sequence comparisons using the (66 660 bp), 00085 (130 247 bp) and 00088 (134 521 bp, EzTaxon-e server (Kim et al., 2012), the highest similarity containing both rpoC and rpoB) in the genome sequence (94.4 %) was found to F. pelagi HTCC2506T. A phyloge- of strain 8047T. Phylogenetic trees based on the sequences netic tree was reconstructed using the neighbour-joining, of the housekeeping genes were reconstructed using maximum-parsimony and maximum-likelihood methods the same methods as described for the reconstruction of SI85-9A1 (U53824) 100 Aurantimonas manganoxydans 0.02 Aurantimonas coralicida WP1T (AJ786361) 85 100 Aureimonas altamirensis S21BT (DQ372921) 86 Aureimonas frigidaquae CW5T (EF373540) 90 Aureimonas ureilytica 5715S-12T (DQ883810) 96 Fulvimarina manganoxydans 8047T (HQ622550) Fulvimarina pelagi HTCC2506T (AY178860) Martelella mediterranea MACL11T (AY649762) T 75 68 Agrobacterium tumefaciens IAM 13129 (D12784) T 64 Rhizobium leguminosarum IAM 12609 (D14513) IAM 13154T (D12786) 81 Mycoplana dimorpha 100 Brucella melitensis ATCC 23456T (L26166) 94 Ochrobactrum anthropi IAM 14119T (D12794) Aquamicrobium defluvium DSM 11603T (Y15403) Mesorhizobium loti LMG 6125T (X67229) Ahrensia kielensis IAM 12618T (D88524) Afifella marina DSM 2698T (D30790) Escherichia coli ATCC 11775T (X80725) Fig. 1. Phylogenetic dendrogram of strain 8047T and related species based on 16S rRNA gene sequences. The tree was reconstructed using the neighbour-joining method, and Rhodobacter capsulatus ATCC 11166T (GenBank accession no. D16428) was used as an outgroup (not shown). Numbers at nodes represent percentage levels of bootstrap support based on a neighbour-joining analysis of 1000 resampled datasets; only values .50 % are shown. GenBank accession numbers are given in parentheses. Filled circles indicate branches also recovered using the maximum-likelihood and maximum-parsimony methods. Bar, 2 % sequence divergence. Downloaded from www.microbiologyresearch.org by http://ijs.sgmjournals.org 2921 IP: 54.70.40.11 On: Fri, 07 Dec 2018 15:01:17 F. Ren and others the 16S rRNA gene tree (Fig. S1, available in the online pH 4.0–9.0, with optimal growth at pH 6.0–7.0, as deter- Supplementary Material). The topological structures of the mined in YTSS medium adjusted to pH 2–12 with KH2PO4/ housekeeping gene trees were consistent with that of the HCl, KH2PO4/K2HPO4 and K2HPO4/NaOH buffer systems 16S rRNA gene tree, and strain 8047T again clustered with (Zhang et al., 2013). The strain grew in sea-salt-free YTSS F. pelagi HTCC2506T. As shown in Table S1, the sequence medium supplemented with 0–10 % (w/v) NaCl, and identities of the housekeeping genes between strain 8047T optimal
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