Standards in Genomic Sciences (2011) 4:54-62 DOI:10.4056/sigs.1523807 The Genomic Standards Consortium Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1T) Sam Pitluck1, Johannes Sikorski2, Ahmet Zeytun1,3, Alla Lapidus1, Matt Nolan1, Susan Lucas1, Nancy Hammon1, Shweta Deshpande1, Jan-Fang Cheng1, Roxane Tapia1,3, Cliff Han1,3, Lynne Goodwin1,3, Konstantinos Liolios1, Ioanna Pagani1, Natalia Ivanova1, Konstantinos Mavromatis1, Amrita Pati1, Amy Chen4, Krishna Palaniappan4, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, John C. Detter1, Evelyne Brambilla2, Oliver D. Ngatchou Djao6, Manfred Rohde6, Stefan Spring2, Markus Göker2, Tanja Woyke1, James Bristow1, Jonathan A. Eisen1,7, Victor Markowitz4, Philip Hugenholtz1,8, Nikos C. Kyrpides1, Hans-Peter Klenk2*, and Miriam Land1,5 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Hans-Peter Klenk Keywords: moderately thermophilic, strictly anaerobic, motile, Gram-negative, chemoorga- noheterotroph, hot spring, Deferribacteraceae, GEBA Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus Calditerrivibrio. The species is of interest because of its important role in the nitrate cycle as nitrate reducer and for its isolated phylogenetic position in the Tree of Life. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the third complete genome sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic En- cyclopedia of Bacteria and Archaea project. Introduction Strain Yu37-1T (= DSM 19672 = NBRC 101217) is the type strain of Calditerrivibrio nitroreducens which in turn is the type and sole species of the genus Calditerrivibrio [1]. The genus Calditerrivi- brio is one out of six genera in the family Deferri- bacteraceae [2-6]. The genus name is derived from Latin adjective “caldus”, hot, “terra”, the earth, and “vibrio”, a vibrio, referring to a vibroid shaped bac- terium in a hot terrestrial environment. The spe- cies epithet nitroreducens derives from the Greek name “nitron”, nitrite, nitrate, and “reducens”, drawing backwards, referring to its nitrate- reducing physiology [1]. Strain Yu37-1T was iso- lated from hot-spring water from Yumata, Nagano, Japan. No further cultivated strains belonging to the species C. nitroreducens have been described so far. Here we present a summary classification and a set of features for C. nitroreducens strain Yu37-1T, together with the description of the complete genomic sequencing and annotation. Classification and features A representative genomic 16S rRNA sequence of strain Yu37-1T was compared using BLAST under default settings (e.g., considering only only the

Pitluck et al. http://standardsingenomics.org 55 high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [7] and the relative frequen- cies of taxa and keywords (reduced to their stem [8]) were determined, weighted by BLAST scores. The most frequently occurring genera were Defer- ribacter (33.4%), Alteromonas (21.3%), Magneto- coccus (9.4%), Shuttleworthia (7.5%) and Geovibrio (7.3%) (61 hits in total). Regarding the single hit to sequences from members of the species, the aver- age identity within HSPs was 99.9%, whereas the average coverage by HSPs was 96.7%. Among all other species, the one yielding the highest score was Deferribacter desulfuricans, which corres- ponded to an identity of 88.1% and an HSP cover- age of 86.0%. The highest-scoring environmental sequence was DQ424925 ('Enrichment and Ther- mophilic Mediator-Less Microbial Fuel Cell ther- mophilic microbial fuel cell enriched artificial wastewater clone 1B62') [9], which showed an identity of 99.7% and an HSP coverage of 98.2%. The most frequently occurring keywords within the labels of environmental samples were 'microbiota' (4.1%), 'microbi' (4.1%), 'intestin' (4.0%), 'mous' (3.8%) and 'compet, exploit, inflamm, salmonella, typhimurium' (3.7%) (183 hits in total). The most frequently occurring keywords within the labels of environmental samples which yielded hits of a higher score than the highest scoring species were 'microbi' (8.6%), 'thermophil' (6.7%), 'enrich' (5.7%), 'cell, fuel' (5.3%) and 'spring' (3.6%) (21 hits in total), which seem to fit to the features known for C. nitroreducens. Figure 1 shows the phylogenetic neighborhood of C. nitroreducens Yu37-1T in a 16S rRNA based tree. The two copies of the 16S rRNA gene in the ge- nome differ by one nucleotide from each other any by up to one nucleotide from the previously pub- lished 16S rRNA sequence (AB364234). Cells of the strain Yu37-1T are vibrio-shaped, 0.4- 0.5 x 1.4-2.0 µm in size, occur singly or in pairs and stain Gram-negative [1] (Table 1 and Figure 2). No spore formation was detected for Yu37-1T [1]. No data is available on the generation time of strain Yu37-1T. Nitrate is the only electron accep- tor utilized, with ammonium as the end product [1]. Elemental sulfur, sulfate, sulfite, nitrite, iron (III) oxide, manganese (IV) oxide, selenate, sele- nite, arsenate, arsenite, fumarate and oxygen are not used as alternative electron acceptors [1]. Ace- tate, pyruvate, lactate, fumarate, succinate, malate, yeast extract, peptone and Casamino acids are uti- lized as electron donors with nitrate as the elec- tron acceptor fermentative growth has not been observed [1]. Strain Yu37-1T is strictly anaerobic and catalase negative [1]. Chemotaxonomy The predominant compounds in whole cell lipids of C. nitroreducens strain Yu37-1T are saturated branched-chain fatty acids: iso-C14:0 (26.3%), an- teiso-C15:0 (24.1%), iso-C13:0 (7.7%), C18:0 (7.2%), C16:0 (6.2%), iso-C16:0 (5.7%) and anteiso-C13:0 (5.3%) [1]. Menaquinone MK-8 was identified as the major quinone [1]. Figure 1. Phylogenetic tree highlighting the position of C. nitroreducens Yu37-1T relative to the other type strains within the family Deferribacteraceae. The tree was inferred from 1,470 aligned characters [10,11] of the 16S rRNA gene sequence under the maximum likelihood criterion [12] 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 sup- port values from 1,000 bootstrap replicates [13] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [14] are shown in blue, published genomes in bold [15].