Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). Item Type Article Authors Huntemann, Marcel; Lu, Megan; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D; Detter, John C; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Mavromatis, Konstantinos Citation Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)). 2011, 4 (3):303-11 Stand Genomic Sci DOI 10.4056/sigs.1814460 Journal Standards in genomic sciences Rights Archived with thanks to Standards in genomic sciences Download date 06/10/2021 02:13:06 Link to Item http://hdl.handle.net/10033/220772 This is an Open Access-journal’s PDF published in Huntemann, M., Lu, M., Nolan, M., Lapidus, A., Lucas, S., Hammon, N., Deshpande, S., Cheng, J.-F., Tapia, R., Han, C., Goodwin, L., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Ovchinikova, G., Pati, A., Chen, A., Palaniappan, K., Land, M., Hauser, L., Jeffries, C.D., Detter, J.C., Brambilla, E.-M., Rohde, M., Spring, S., Göker, M., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Kyrpides, N.C., Klenk, H.-P., Mavromatis, K. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH2T) (2011) Standards in Genomic Sciences, 4 (3), pp. 303-311 Standards in Genomic Sciences (2011) 4:303-311 DOI:10.4056/sigs.1814460 Complete genome sequence of the thermophilic T sulfur-reducer Hippea maritima type strain (MH2 ) Marcel Huntemann1, Megan Lu2,3, Matt Nolan2, Alla Lapidus2, Susan Lucas2, Nancy Hammon2, Shweta Deshpande2, Jan-Fang Cheng2, Roxanne Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Galina Ovchinikova2, Amrita Pati2, Amy Chen1, Krishna Palaniappan1, Miriam Land2,4, Loren Hauser2,4, Cynthia D. Jeffries2,4, John C. Detter2,3, Evelyne-Marie Brambilla5, Manfred Rohde6, Stefan Spring5, Markus Göker5, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz1, Philip Hugenholtz2,8, Nikos C. Kyrpides2, Hans-Peter Klenk5*, and Konstantinos Mavromatis2 1 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, 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 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Hans-Peter Klenk Keywords: anaerobic, motile, rod-shaped, Gram-negative, marine, moderately thermophilic, sulfur-reducer, Desulfurellaceae, GEBA Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome se- quencing because of its isolated phylogenetic location, as a distant next neighbor of the ge- T nus Desulfurella. Strain MH2 is the first type strain from the order Desulfurellales with a com- pletely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein- coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain MH2T (DSM 10411 = ATCC 700847) is the sulfur-reducing bacteria [1]. The genus is named type strain of the species Hippea maritima, which is after the German microbiologist Hans Hippe, in the type species of its genus Hippea [1]. The genus recognition of his significant contribution to the currently contains no other validly named species characterization of novel, obligately anaerobic pro- [2], but two other strains belonging to the species karyotes and the understanding of their physiology. were isolated from shallow-water hot vents in New The species epithet is derived from the Latin word Zealand and Papua New Guinea [1]. The type strain maritima (inhabiting marine environments) [2]. was isolated during a cruise of the Russian scientif- Here we present a summary classification and a set ic vessel A. Nesmeyanov through shallow-water hot of features for H. maritima strain MH2T, together vents of the south-western Pacific Ocean, environ- with the description of the complete genomic se- ments that are typical for anaerobic, thermophilic, quencing and annotation. The Genomic Standards Consortium Hippea maritima type strain (MH2T) Classification and features uses the INSDC (= EMBL/NCBI/DDBJ) annotation, A representative genomic 16S rRNA sequence of which is not an authoritative source for nomencla- ture or classification.) The highest-scoring envi- strain MH2T was compared using NCBI BLAST un- der default settings (e.g., considering only the ronmental sequence was AF232926 ('United high-scoring segment pairs (HSPs) from the best Kingdom: Montserrat geothermal springs clone 250 hits) with the most recent release of the MS10 proteobacterium'), which showed an identi- Greengenes database [3] and the relative frequen- ty of 88.9% and a HSP coverage of 73.0%. The cies, of taxa and keywords (reduced to their stem most frequently occurring keywords within the [4]) were determined, weighted by BLAST scores. labels of environmental samples which yielded The most frequently occurring genera were Desul- hits were 'microbi' (5.0%), 'spring' (2.9%), furella (38.7%), Desulfovibrio (15.2%), Deferribac- 'sediment' (2.4%), 'soil' (2.3%) and 'industri' ter (10.8%), Thermotoga (10.8%) and Hippea (2.2%) (206 hits in total). Environmental samples (8.6%) (44 hits in total). Regarding the single hit which yielded hits of a higher score than the high- to sequences from members of the species, the est scoring species were not found. average identity within HSPs was 99.9%, whereas The 16S rRNA based tree in Figure 1 shows the the average coverage by HSPs was 82.7%. Among phylogenetic neighborhood of H. maritima. The all other species, the one yielding the highest sequence of the two identical 16S rRNA genes dif- score was Desulfurella multipotens, which corres- fers by one nucleotide from the previously pub- ponded to an identity of 89.6% and an HSP cover- lished 16S rRNA sequence (Y18292). age of 82.6%. (Note that the Greengenes database Figure 1. Phylogenetic tree highlighting the position of H. maritima relative to the other type strains within the fam- ily Desulfurellaceae. The tree was inferred from 1,526 aligned characters [5,6] of the 16S rRNA gene sequence under the maximum likelihood criterion [7] and rooted in accordance to the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers next to bifurcations are support values from 700 bootstrap replicates [8] if larger than 60%. Lineages with type strain genome sequencing projects regis- tered in GOLD [9] are shown with an asterisk, those also listed as 'Complete and Published' with two asterisks. 304 Standards in Genomic Sciences Huntemann et al. The cells of H. maritima are short rods ranging Harbor, was the only H. maritima strain growing from 1-3 x 0.4–0.8 µm (Figure 2 and Table 1) that on ethanol in the presence of elemental sulfur [1]. occur singly or in pairs [1]. H. maritima is motile Fumarate supported only weak growth for all by one polar flagellum [1] (not visible in Figure 2). three known strains [1], whereas formate, propio- Colonies are whitish-gray with diameters up to 0.5 nate, butyrate, pyruvate, lactate, succinate, glu- mm [1]. H. maritima cultures require 2.5-3% NaCl cose, starch, peptone, methanol did not support and 0.02% (w/v) yeast extract for growth [1]. The growth [1]. CO2 and H2S were the only detected temperature range for growth is between 40°C end products [1]. and 65°C, with an optimum at 52–54°C [1]. Growth was observed over a pH range of 5.7 to 6.5 Chemotaxonomy with an optimum around 6.0 [1]. No chemotaxonomical data were reported in the All H. maritima strains can grow on molecular hy- initial description of the organism [1] nor else- drogen, acetate, and saturated fatty acids and re- where, subsequently. quire elemental sulfur as the only known electron acceptor [1]. Strain MH3, isolated from Matupi T Figure 2. Scanning electron micrograph of H. maritima MH2 http://standardsingenomics.org 305 Hippea maritima type strain (MH2T) T Table 1. Classification and general features of H. maritima MH2 according to the MIGS recommendations [10]. MIGS ID Property Term Evidence code Domain Bacteria TAS [11] Phylum Proteobacteria TAS [12] Class Deltaproteobacteria TAS [13,14] Order Desulfurellales TAS [13,14] Current classification Family Desulfurellaceae TAS [14,15] Genus Hippea TAS [1] Species Hippea maritima TAS [1] Type strain MH2