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Raineya Orbicola Gen. Nov., Sp. Nov. a Slightly Thermophilic Bacterium of the Phylum Bacteroidetes and the Description of Raineyaceae Fam

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Raineya Orbicola Gen. Nov., Sp. Nov. a Slightly Thermophilic Bacterium of the Phylum Bacteroidetes and the Description of Raineyaceae Fam TAXONOMIC DESCRIPTION Albuquerque et al., Int J Syst Evol Microbiol 2018;68:982–989 DOI 10.1099/ijsem.0.002556 Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov. Luciana Albuquerque,1 Ana Rita M. Polónia,1 Cristina Barroso,1,2 Hugo J. C. Froufe,2 Olga Lage,3,4 Alexandre Lobo-da-Cunha,4,5 Conceiçao~ Egas1,2 and Milton S. da Costa1,* Abstract An isolate, designated SPSPC-11T, with an optimum growth temperature of about 50 C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85 %. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso- C15:0, iso-C15 : 0 2-OH and iso-C17 : 0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C content of strain SPSPC-11T was 37.6 mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11T. Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11T (=CECT 9012T=LMG 29233T) for which we propose the name Raineya orbicola gen. nov., sp. nov. We also describe the family Raineyaceae to accommodate this new genus and species. The vast majority of the species of the phylum Bacteroidetes optimum growth temperatures of over 65 C and maximum have optimum growth temperatures that range from about growth temperatures below 80 C, were included in the phy- 25 C and 45 C, while slightly thermophilic or thermophilic lum Bacteroidetes but are now classified in the novel phy- species are very rare. Some organisms, such as Pseudozobel- lum named ‘Rhodothermaeota’ [10]. lia thermophila [1] and Lutaonella thermophila [2], have We recently isolated one strain of a slightly thermophilic slightly elevated optimum growth temperatures of around organism with an optimum growth temperature of around 40–45 C, while other species, such as Anaerophaga thermohalophila, are slightly thermophilic [3], with an opti- 50 C and a maximum growth temperature of 60 C. Phylo- mum growth temperature of around 50 C. Two other spe- genetic analysis of the 16S rRNA gene sequence showed cies classified in the phylum Bacteroidetes are thermophilic, that this organism represents a distinct lineage within the namely Thermonema lapsum [4] and Thermonema rossia- phylum Bacteroidetes. Based on phylogenetic, physiological num [5] with optimum growth temperatures of about 60 C and biochemical parameters, we are of the opinion that and a maximum growth temperature of around 65 C. Until strain SPSPC-11T represents a novel genus and species, for recently, the two species of the genus Rhodothermus, Rhodo- which we propose the name Raineya orbicola gen. nov., sp. thermus marinus and Rhodothermus profundi [6–9], with nov. We also propose that this organism represents a new Author affiliations: 1Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; 2Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; 3Departamento de Biologia, Faculdade de Ciencias,^ Universidade do Porto, Rua do Campo Alegre s/n 4169-007 Porto, Portugal; 4CIMAR/CIIMAR – Centro Interdisciplinar de Investigaçao~ Marinha e Ambiental – Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; 5Laboratório de Biologia Celular, Instituto de Ciencias^ Biomedicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal. *Correspondence: Milton S. da Costa, [email protected] Keywords: new taxa; Bacteroidetes; Raineyaceae fam. nov.; Raineya gen. nov.; Raineya orbicola sp. nov. Abbreviations: CAPSO, 3-(Cyclohexylamino)-2-hydroxy-1-propanesulfonic acid; CECT, Colección Española de Cultivos Tipo; COG, clusters of ortholo- gous groups; CRISPR, clustered regularly interspaced short palindromic repeats; G+C, guanine plus cytosine; HEPES, 4-(2-hydroxyethyl)-1-piperazi- nethanesulfonic acid; LMG, Laboratorium voor Microbiologie Universiteit Gent; MIGS, minimum information genome sequence; SEM, scanning electron microscopy; TAPS, N-[Tris(hydroxymethyl)methyl]-3-aminopropanesulfonic acid; TEM, transmission electron microscopy. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strain SPSPC-11T are KY990922, MF125287 and MF125288, respectively. The draft genome accession number of strain SPSPC-11T is NKXO00000000. One supplementary figure and three supplementary tables are available with the online version of this article. 002556 ã 2018 IUMS This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. 982 Albuquerque et al., Int J Syst Evol Microbiol 2018;68:982–989 family for which we propose the name Raineyaceae fam. medium composed of Thermus basal salts containing filter- À nov. sterilized single carbon sources (2.0 g l 1), ammonium sul- À1 T fate (0.5 g l ) and a vitamin and nucleotide solution at a Strain SPSPC-11 was isolated from a reddish biofilm at the À1 final concentration of 40 µg l [15] consisting of thiamine, hot spring at S~ao Pedro do Sul in Central Portugal (40 46¢ riboflavin, pyridoxine, biotin, folic acid, inositol, nicotinic N, 8 4¢ W). The sample was maintained without tempera- acid, pantothenic acid, p-aminobenzoic acid, cyanocobala- ture control for 1 day, and then 0.001 to 0.1 ml in 10 ml min, adenine, thymine, cytosine, guanine, cytidine, uracil water were filtered through membrane filters (Gelman type À and inosine (10 ml l 1). Growth of the strain on single GN-6; pore size 0.45 µm; diameter 47 mm). The filters were carbon sources was examined by measuring the turbidity placed on the surface of solidified Thermus medium [11], of cultures in 20 ml screw capped tubes containing 10 ml the plates were wrapped in plastic to prevent evaporation medium for up to 7 days. and incubated at 45 C for up to 5 days. Cultures were puri- fied by sub-culturing and the isolates stored at –70 C in The polar lipids were extracted from freeze-dried cells and Thermus medium with 15 % (w/v) glycerol. the individual polar lipids were separated by two-dimen- sional thin-layer chromatography. To visualize phospholi- Unless otherwise stated, all biochemical and tolerance tests pids, aminolipids, glycolipids and total lipids, the following were performed, as described previously [12, 13], in liquid reagents were used, respectively, molybdenum blue, ninhy- Thermus medium or on Thermus agar plates [11] at 45 C drin, a-naphthol-sulfuric acid and molybdophosphoric acid for up to 7 days, rather than at the optimum growth temper- [16]. Lipoquinones were extracted from freeze-dried cells ature of about 50 C, because the cultures remained viable and purified by thin-layer chromatography. The purified for longer periods of time. Cell morphology and motility lipoquinones were separated by high-performance liquid were examined by phase contrast microscopy during the chromatography (HPLC) as described previously [17]. Cul- exponential growth phase. For transmission electron tures for fatty acid analysis were grown in Thermus liquid microscopy (TEM), bacteria were fixed for 2 h with 2.5 % medium at 45 C for 5, 8 and 24 h. Fatty acid methyl esters glutaraldehyde in 0.1 M cacodylate buffer (pH 7.2), washed were obtained from fresh wet biomass, separated, identified in buffer, postfixed for 4 h with buffered 2 % OsO , washed 4 and quantified with the standard MIS Library Generation in buffer, followed by 1 h in 1 % uranyl acetate, dehydrated Software, version 6.0, aerobe TSBA method (Microbial ID in ethanol and embedded in Epon. Ultrathin sections were Inc., MIDI) as described previously [18]. stained with uranyl acetate and lead citrate. For scanning electron microscopy (SEM), bacteria were initially processed Total genomic DNA was extracted following the method of as for TEM, but after postfixation a drop of bacteria sus- Nielsen et al. [19], and used for the different analyses per- pended in buffer was laid on each coverslip coated with formed. The G+C content of DNA was determined by poly-lysine. After resting for 15 min with the buffer, the bac- HPLC as described by Mesbah et al. [20] and by genome teria on the coverslips were dehydrated in ethanol and criti- sequencing (see below). PCR-amplification of 16S rRNA cal-point dried. Samples were coated with Au before being genes was carried out as described by Rainey et al. [21]. The observed. 16S rRNA gene sequence was determined by Sanger sequencing (Macrogen). The presence of flexirubin-type pigments was determined by flooding bacterial cells with 20 % KOH [14]. The absorp- The genomic DNA was prepared with the Nextera XT DNA tion spectra of pigments extracted using acetone/methanol Library Preparation Kit and sequenced using paired-end 7 : 2 (v/v) were determined at 200–900 nm with a UV–visi- 2Â300 bp on the MiSeq system (Illumina). Sequenced reads ble spectrophotometer (ThermoScientific). The growth were quality filtered with Trimmomatic [22] and assembled temperature range of the strain was examined at 5 C incre- with SPAdes (version 3.7.1; [23]) and the resulting contigs ments between 30 and 65 C by measuring the turbidity annotated with prokaryotic genome prediction [24]. Genome (610 nm) of cultures incubated in 300 ml metal-capped estimated completeness and contamination were verified Erlenmeyer flasks, containing 100 ml medium in a rotary with CheckM (version 1.0.7) [25].
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