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Thermaerobacter Marianensis Type Strain (7P75a)

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Thermaerobacter Marianensis Type Strain (7P75a) Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Thermaerobacter marianensis type strain (7p75a). Permalink https://escholarship.org/uc/item/2km2g1rj Journal Standards in genomic sciences, 3(3) ISSN 1944-3277 Authors Han, Cliff Gu, Wei Zhang, Xiaojing et al. Publication Date 2010-12-15 DOI 10.4056/sigs.1373474 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 3:337-345 DOI:10.4056/sigs.1373474 Complete genome sequence of Thermaerobacter T marianensis type strain (7p75a ) Cliff Han1,2, Wei Gu1,2, Xiaojing Zhang1,2, Alla Lapidus1, Matt Nolan1, Alex Copeland1, Susan Lucas1, Tijana Glavina Del Rio1, Hope Tice1, Jan-Fang Cheng1, Roxane Tapia1,2, Lynne Goodwin1,2, Sam Pitluck1, Ioanna Pagani1, Natalia Ivanova1, Konstantinos Mavromatis1, Natalia Mikhailova1, Amrita Pati1, Amy Chen3, Krishna Palaniappan3, Miriam Land1,4, Loren Hauser1,4, Yun-Juan Chang1,4, Cynthia D. Jeffries1,4, Susanne Schneider5, Manfred Rohde6, Markus Göker5, Rüdiger Pukall5, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz3, Philip Hugenholtz1, Nikos C. Kyrpides1, Hans-Peter Klenk5*, and John C. Detter1,2 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 3 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Hans-Peter Klenk Keywords: strictly aerobic, none-motile, Gram-variable, thermophilic, chemoheterotrophic, deep-sea, family Incertae Sedis XVII, Clostridiales, GEBA Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus Thermaero- bacter, which belongs to the Clostridiales family Incertae Sedis XVII. The species is of special interest because T. marianensis is an aerobic, thermophilic marine bacterium, originally iso- lated from the deepest part in the western Pacific Ocean (Mariana Trench) at the depth of 10, 897 m. Interestingly, the taxonomic status of the genus has not been clarified until now. The genus Thermaerobacter may represent a very deep group within the Firmicutes or potentially a novel phylum. The 2,844,696 bp long genome with its 2,375 protein-coding and 60 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain 7p75aT (= DSM 12885 = ATCC 700841 = which the strain was isolated from [2]. T. maria- JCM 10246) is the type strain of T. marianensis nensis strain 7p75aT was isolated from a mud which is the type species of the genus Thermaero- sample of the Challenger Deep in the Mariana bacter [1,2]. Currently, there are five species Trench at the depth of 10,897 m [2]. No further placed in the genus Thermaerobacter [1,3]. The isolates have been obtained for T. marianensis. generic name derives from the Greek words Other members of the genus Thermaerobacter ‘thermos’ meaning ‘hot’, ‘aeros’(air) and the Neo- were isolated from mud of the bottom of the Chal- Latin word ‘bacter’ meaning ‘a rod’, which alto- lenger Deep [2], shallow marine hydrothermal gether means able to grow at high temperatures in vent, Japan [4], water sediment slurries of the run- the presence of air [2]. The species epithet is de- off channel of New Lorne Bore, Australia [5], a rived from the Neo-Latin word ‘marianensis’ per- coastal hydrothermal beach, Japan [6] and from taining to the Mariana Trench, the location from food sludge compost, Japan [7]. Here we present a The Genomic Standards Consortium Han et al. summary classification and a set of features for T. The cells of T. marianensis are generally rod-shaped marianensis 7p75aT, together with the description (0.3-0.6 × 2-7 µm), straight to slightly curved with of the complete genomic sequencing and annota- rounded ends (Figure 2). The cells can be arranged tion. in pairs [2]. T. marianensis is a Gram-positive, spore-forming bacterium (Table 1). At stationary Classification and features phase cells, may stain Gram-negative. Motility and The 16S rRNA gene sequences of T. marianensis flagella have not been observed [2], but genes for 7p75aT share 98.3 to 98.6% sequence identity with biosynthesis and assembly of flagella have been the other type strains of the genus Thermaerobac- identified in the here reported genome sequence. ter [2,8] and T. nagasakiensis being the closest rela- The organism is a strictly aerobic chemohetero- tive. Outside the genus members of the recently troph. T. marianensis is a typical marine bacterium proposed genus “Calditerricola” (88.6%) [9] and and requires sea salts (0.5-5%, optimum 2%) in the genus Moorella (88.1%) [10] share the highest media for good growth [2]. The temperature range degree of sequence similarity. The genomic survey for growth is between 50°C and 80°C, with an op- sequence database (gss) contains as best hits sev- timum at 75°C [2]. The pH range for growth is 5.4- eral 16S rRNA gene sequence from The Sorcerer II 9.5, with an optimum at pH 7.0-7.5 [2]. T. maria- Global Ocean Sampling Expedition: Northwest At- nensis is able to grow on yeast extract, peptone and lantic through Eastern Tropical Pacific [11] at a si- casein. It utilizes carbohydrates like starch, xylan, milarity level of only 84%. No phylotypes from en- chitin, maltose, maltotriose, cellobiose, lactose, tre- vironmental samples database (env_nt) could be halose, sucrose, glucose, galactose, xylose, manni- linked to the species T. marianensis or even the ge- tol, inositol. The strain is also able to grow on ami- nus Thermaerobacter, indicating a rather rare oc- no acids like casamino acids, valine, isoleucine, currence of members of this genus in the habitats cysteine, proline, serine, threonine, asparagine, glu- screened thus far (as of November 2010). tamine, aspartate, glutamate, lysine, arginine and histidine. T. marianensis is able to grow well on var- A representative genomic 16S rRNA sequence of T. ious carboxylic acids like propionate, 2- marianensis 7p75aT was compared using NCBI aminobutyric acid, malate, pyruvate, tartarate, suc- BLAST under default values (e.g., considering only cinate, lactate, acetate and glycerol [2]. the best 250 hits) with the most recent release of the Greengenes database [12] and the relative fre- quencies of taxa and keywords, weighted by BLAST Chemotaxonomy The cellular polyamines of the strain 7p75aT were scores, were determined. The five most frequent genera were Thermaerobacter (39.7%), Moorella identified as N4-bis(aminopropyl)spermidine, (35.3%), Geobacillus (6.4%), Thermoactinomyces agmatine, spermidine, and spermine [30,31]. The (3.6%) and Bacillus (3.4%). Regarding hits to se- major cellular fatty acids were composed of 15- quences from other members of the genus, the av- methyl-hexadecanic acid (52.3%), myristoleic acid erage identity within HSPs (high-scoring segment (27.6%) and 14-methyl hexadecanoic acid (9.3%) pairs) was 98.1%, whereas the average coverage by [2]. No data are available for polar lipids and pep- HSPs was 96.3%. The species yielding the highest tidoglycan type of the cell wall. score was Thermaerobacter subterraneus. The five most frequent keywords within the labels of envi- Genome sequencing and annotation ronmental samples which yielded hits were Genome project history 'compost(ing)' (6.1%), 'municipal' (2.9%), 'scale' This organism was selected for sequencing on the (2.7%) and 'process/stages' (2.6%). Environmental basis of its phylogenetic position [32], and is part samples which yielded hits of a higher score than of the Genomic Encyclopedia of Bacteria and Arc- the highest scoring species were not found. haea project [33]. The genome project is depo- Figure 1 shows the phylogenetic neighborhood of sited in the Genome OnLine Database [17,34] and T. marianensis 7p75aT in a 16S rRNA based tree. the complete genome sequence is deposited in The sequences of the two 16S rRNA gene copies GenBank. Sequencing, finishing and annotation differ from each other by two nucleotides, and dif- were performed by the DOE Joint Genome Insti- fer by up to two nucleotides from the previously tute (JGI). A summary of the project information is published 16S rRNA sequence (AB011495), which shown in Table 2. contains one ambiguous base call. http://standardsingenomics.org 338 Thermaerobacter marianensis type strain (7p75aT) Figure 1. Phylogenetic tree highlighting the position of T. marianensis 7p75aT relative to the other type strains within the family. The tree was inferred from 1,489 aligned characters [13,14] of the 16S rRNA gene sequence under the maximum likelihood criterion [15] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates [16] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are shown in blue, published genomes in bold. Growth conditions and DNA isolation T. marianensis 7p75aT, DSM 12885, was grown in the standard protocol as recommended by the half strength DSMZ medium 514 (Bacto Marine manufacturer, with modification st/LALM for cell Broth)
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