- Open Access
Complete genome sequence of Haliscomenobacter hydrossis type strain (OT)
Standards in Genomic Sciences volume 4, pages352–360(2011)
Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Haliscomenobacter, which belongs to order “Sphingobacteriales”. The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically uncharted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family “Saprospiraceae”. The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Strain OT (= DSM 1100 = ATCC 27775) is the type strain of Haliscomenobacter hydrossis which is the type and only species within the genus Haliscomenobacter [1,2]. The generic name derives from the Greek word haliskomai, to be imprisoned, and the Neo-Latin bacter, a rod, meaning the imprisoned rod. The species epithet is derived from the Greek word hudôr, water, and Oss, a town in the Netherlands, hydrossis, from water of Oss. The imprisoned rod from the water of Oss. Five morphologically and physiologically congruent strains belonging to the species, including the type strain OT, were isolated from activated sludge samples in the early 1970s . H. hydrossis was sporadically observed in aeration tanks of sewage treatment plants in Germany  and in paper industry wastewater treatment plants in France . As a recent biotechnological application, biomass bulking caused by H. hydrossis was controlled by lytic bacteriophages . An improved high quality draft sequence of Saprospira grandis strain Sa g1 (=HR1, DSM 2844, GOLD ID Gi033955) is the only other genomic information currently available from the family “Saprospiraceae”. Here we present a summary classification and a set of features for H. hydrossis OT, together with the description of the complete genomic sequencing and annotation.
Classification and features
The single genomic 16S rRNA sequence of H. hydrossis OT was compared using NCBI BLAST  under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database  and the relative frequencies of taxa and keywords (reduced to their stem ) were determined, weighted by BLAST scores. The most frequently occurring genera were Haliscomenobacter (83.9%) and Lewinella (16.1%) (3 hits in total). Regarding the two hits to sequences from members of the species, the average identity within HSPs was 99.2%, whereas the average coverage by HSPs was 98.1%. Among all other species, the one yielding the highest score was Lewinella antarctica (EF554367), which corresponded to an identity of 89.1% and an HSP coverage of 66.6%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was AJ786323 (‘Lake Wolfgangsee freshwater enrichment clone MS-Wolf2-H’), which showed an identity of 98.8% and an HSP coverage of 97.9%. The most frequently occurring keywords within the labels of environmental samples which yielded hits were ‘lake’ (10.6%), ‘tin’ (5.3%), ‘microbi’ (3.4%), ‘freshwat’ (3.2%) and ‘mat’ (3.2%) (247 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 ‘lake’ (11.1%), ‘tin’ (5.6%), ‘microbi’ (3.5%), ‘freshwat’ (3.4%) and ‘mat’ (3.3%) (225 hits in total). These keywords reflect the ecological properties reported for strain OT in the original description .
Figure 1 shows the phylogenetic neighborhood of H. hydrossis in a 16S rRNA based tree. The sequences of the two 16S rRNA gene copies in the genome differ from each other by two nucleotides and do not differ from the previously published 16S rRNA sequence AJ784892, which contains two ambiguous base calls.
The cells of H. hydrossis are rod-shaped, 0.35–0.45 µm wide and 3–5 µl long, mostly occurring in chains and nearly always enclosed by a narrow hyaline sheath (Figure 2) . The sheath is sometimes disrupted by branching cells . Flagella were never visible in EM images nor was motility ever observed . Growing bacteria excrete so far unidentified polysaccharides . Strain OT grows strictly aerobically and produces intracellular carotenoid pigments . Optimal growth temperature was 26°C, with a span of 8–30°C . Optimal pH for growth was 7.5 . Organic acids, peptides, proteins, mono- and polysaccharides were reported as carbon and energy sources . Starch and gelatine were decomposed by all strains of the species , sorbitol, glycerol, lactate, acetate, succinate and β-hydroxybutyrate were not utilized . The authors of the original description of the strain suggested that OT accumulates polysaccharides either intra- or extracellularily .
Nothing is known about the structure of the cell wall of H. hydrossis. The six major fatty acids of strain OT were iso-C15:0 3-OH (22.8%), iso-C15:0 (21.0%), C16:1 (17.3%), iso-C15:0 2-OH (15.5%), and C18:0 (6.9%) and C16:0 (5.7%) . The type strain contained significantly more hydroxylated fatty acids than several analyzed reference strains from the genus . Observed quinones were mainly of the MK-7 type (70-90%), with 10–30% MK-6 .
Genome sequencing and annotation
Genome project history
This organism was selected for sequencing on the basis of its phylogenetic position , and is part of the Genomic Encyclopedia of Bacteria and Archaea project . The genome project is deposited in the Genome On Line Database  and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Growth conditions and DNA isolation
H. hydrossis OT, DSM 1100, was grown in DSMZ medium 134 (Haliscomenobacter Medium)  at 26°C. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram-positive DNA purification kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer, with modification st/DL for cell lysis as described in Wu et al. . DNA is available through the DNA Bank Network .
Genome sequencing and assembly
The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website . Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 153 contigs in three scaffolds was converted into a phrap  assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library.
Illumina GAii sequencing data (1,273.3 Mb) was assembled with Velvet  and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 369.3 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package  was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution , Dupfinisher , or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 589 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI . The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 203.8 × coverage of the genome. The final assembly contained 1,005,536 pyrosequence and 35,370,321 Illumina reads.
Genes were identified using Prodigal  as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline . The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform .
The genome consists of an 8,371,686 bp long circular chromosome and three plasmids of 164,019 bp, 143,757 bp and 92,189 bp length, respectively, with a G+C content of 47.1% (Table 3 and Figure 3). Of the 6,918 genes predicted, 6,858 were protein-coding genes, and 60 RNAs; 106 pseudogenes were also identified. The majority of the protein-coding genes (58.6%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
van Veen WL, van der Kooij D, Geuze ECWA, van der Vlies AW. Investigations on the sheathed bacterium Haliscomenobacter hydrossis. Antonie van Leeuwenhoek 1973; 39:207–216. PubMed
Skerman VBD, McGowan V, Sneath PHA, eds. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. doi:10.1099/00207713-30-1-225
Emmrich M, Ziegler M, Rüden H. Filamentous bacteria in activated sludge (bulking sludge). I. Occurrence of filamentous bacteria in a sewage treatment plant working with the activated sludge process (plug flow system). Zentralbl. Bakteriol Microbiol Hyg B 1983; 177:436–450.
Fourest E, Craperi D, Deschamps-Roupert C, Pisicchio JL, Lenon G. Occurrence and control of filamentous bulking in aerated wastewater treatment plants of the French paper industry. Water Sci Technol 2004; 50:29–37. PubMed
Kotay SM, Datta T, Choi J, Goel R. Biocontrol of biomass bulking caused by Haliscomenobacter hydrossis using a newly isolated lytic bacteriophage. Water Res 2011; 45:694–704. PubMed doi:10.1016/j.watres.2010.08.038
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Bascic local alignment search tool. J Mol Biol 1990; 215:403–410. PubMed
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069–5072. PubMed doi:10.1128/AEM.03006-05
Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137.
Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452
Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642
Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669–674. doi:10.1111/J.1095-8312.2007.00864.x
Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184–200. doi:10.1007/978-3-642-02008-713
Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848
Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360
Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576
Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119–169.
Garrity GM, Holt JG. Taxonomic Outline of the Archaea and Bacteria. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 155–166.
Euzéby JP. List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed doi:10.1099/00207713-47-2-590
BAuA. 2010. Classification of bacteria and archaea in risk groups. TRBA 466.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556
Kämpfer P. Physiological and chemotaxonomic characteriation of filamentous bacteria belonging to the genus Hyalscomenobacter. Syst Appl Microbiol 1995; 18:363–367.
Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:10.1016/j.syapm.2010.03.003
Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656
List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51–55. doi:10.1089/bio.2010.0029
JGI website. http://www.jgi.doe.gov.
The Phred/Phrap/Consed software package. http://www.phrap.com
Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:10.1101/gr.074492.107
Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26–29, 2006: 141–146.
Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457
Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393
We would like to gratefully acknowledge the help of Anja Frühling (DSMZ) for growing H. hydrossis cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-1.
About this article
Cite this article
Daligault, H., Lapidus, A., Zeytun, A. et al. Complete genome sequence of Haliscomenobacter hydrossis type strain (OT). Stand in Genomic Sci 4, 352–360 (2011). https://doi.org/10.4056/sigs.1964579
- strictly aerobic