Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov.
© The Author(s) 2013
Published: 16 October 2013
Halopiger djelfamassiliensis strain IIH2T sp. nov. is the type strain of Halopiger djelfamassiliensis sp. nov., a new species within the genus Halopiger. This strain, whose genome is described here, was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria). H. Djelfamassiliensis is a Gram-negative, polymorphic-shaped and strictly aerobic archaeon. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,771,216 bp long genome-contains 3,761 protein-coding and 51 RNA genes, including 4 rRNA genes.
Halopiger djelfamassiliensis sp. nov. strain IIH2T (= KC430939 = DSM on-going deposit) is the type strain of H. djelfamassiliensis sp. nov. It is a Gram-negative, aerobic, non-motile and polymorphic archaeon that was isolated from evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region (Algeria) as part of a project studying archaeal diversity in hypersaline Lakes of Algeria.
Classically, the classification of prokaryotes is based on a combination of phenotypic and genotypic characteristics  also known as polyphasic taxonomy. To date, only 192 archaeal genomes have been sequenced . As the cost of genomic sequencing is constantly decreasing, the number of archaeal sequenced genomes is expected to grow in the next few years. We propose to describe new archaeal species by adding genomic information [3,4] to phenotypic criteria, including the proteic profile [5,6], as it was previously used for the description of new bacterial species [7–19].
The genus Halopiger created in 2007 by Gutiérrez , contains only three species, Halopiger xanaduensis SH-6T isolated from the Shangmatala salt lake, Inner Mongolia, china , Halopiger aswanensis 56T isolated from the surface of hypersaline salt soils close to Aswan, Egypt  and Halopiger salifodinae KCY07-B2T recently isolated from a salt mine in Kuche county, Xinjiang province, China . So far, this genus is composed of aerobic, Gram-negative, polymorphic and pigmented strains [20–22].
Here, we present a summary classification and a set of features for H. Djelfamassiliensis sp. nov. strain IIH2T (= KC430939 = DSM ongoing deposit) together with the description of the complete genome sequencing and annotation. These characteristics support the circumscription of the H. Djelfamassiliensis species.
Classification and features
Classification and general features of Halopiger djelfamassiliensis according to the MIGS recommendations .
Evidence code a
Species Halopiger djelfamassiliensis
Type strain IIH2T
Between 37°C and 55°C
Halophile, 25% (optimum)
Sugar or amino acids
Salt Lake sediment
Sediment of Zahrez Gharbi Lake
Phenotypic tests of strain were performed according to the proposed minimal standards for the description of new taxa in the order Halobacteriales . Different growth temperatures (30, 37, 40, 50, 55, 60°C), pH (5, 6, 7, 7.5, 8, 8.5, 9, 10, 11, 12) and NaCl concentration (0, 10, 12, 15, 20, 22.5, 25, 30%) were tested. The requirement of Mg2+ for growth was determined in media containing 0, 1, 2.5, and 5g MgSO4. Growth occurred between 37°C and 55°C (optimum at 40°C), between 15% and 30% NaCl (optimum at 25% NaCl) and between pH 7–11 (optimum at pH 8). Mg2+ was not required for growth.
All the following biochemical and nutritional tests were realized in duplicate. Strain IIH2T was found to be oxidase- and catalase-positive. Negative results were obtained for tryptophanase, β-galactosidase, arginine decarboxylase, H2S and indole production. Tween 80, gelatin, casein and lipids from egg yolk were hydrolysed at 40°C and 55°C, whereas urea, starch, and phosphatase were not. Methyl red and Voges-Proskauer tests were negative.
Differential phenotypic characteristics between strain IIH2T and related species
Cell diameter (µm)
NaCl range (%, w/v)
NaCl optimum (%, w/v)
Temperature range (°C)
Temperature optimum (°C)
Lipids from egg yolk
Halopiger djelfamassiliensis strain IIH2T was susceptible to bacitracin (10 µg), novobiocin (30 µg) and tetracycline (30 µg) but resistant to ampicillin (10 µg), cephalothin (30 µg), chloramphenicol (30 µg), streptomycin (10 µg), erythromycin (15 µg), gentamicin (10 µg), kanamycin (30 µg), nalidixic acid (30 µg), penicillin G (10 µg) and vancomycin (30 µg).
Genome sequencing information
Genome project history
Paired-end 5 kb library
454 GS FLX Titanium
Newbler version 2.5.3
Gene calling method
EMBL Date of Release
June 18, 2013
Study of the archaeal diversity in hypersaline lakes of Algeria
Growth conditions and DNA isolation
Halopiger djelfamassiliensis strain IIH2T sp. nov. (=CSUR P3035= DSM on-going deposit) was grown aerobically on SG medium at 40°C. Four petri dishes were spread and resuspended in 4×50µl of DTT buffer (60 mM). After incubation at 60°C for 20 min, proteinase K (0.2mg/mL) was added and the sample was incubated at 37°C for 2h. The lysate was extracted with an equal volume of buffered phenol followed by a classical phenol-chloroform extraction method . The quality of the DNA was checked on an agarose gel (0.8%) stained with SYBR safe. The yield and the concentration were measured using the Quant-it Picogreen kit (Invitrogen) on the Genios_Tecan fluorometer at 126 ng/µl.
Genome sequencing and assembly
A paired-end sequencing strategy was used (Roche). The library was pyrosequenced on a GS FLX Titanium sequencer (Roche). This project was loaded on a 1/4 region on PTP Picotiterplate (Roche). Three µg of DNA was mechanically fragmented on the Covaris device (KBioScience-LGC Genomics, Teddington, UK) using miniTUBE-Red 5Kb. The DNA fragmentation was visualized through the Agilent 2100 BioAnalyzer on a DNA labchip 7500 with an optimal size of 5.4 kb. After PCR amplification through 17 cycles followed by double size selection, the single stranded paired-end library was then loaded on a DNA labchip RNA pico 6000 on the BioAnalyzer. The pattern showed an optimal at 680 bp and the concentration was quantified on a Genios Tecan fluorometer at 456 pg/µL. The library concentration equivalence was calculated at 108 molecules/µL. The library was stored at −20°C until further use. The library was clonally amplified in 2 emPCR reactions at 0.25, 0.5 and 1 cpb with the GS Titanium SV emPCR Kit (Lib-L) v2 (Roche). The yield of the 3 types of paired-end emPCR reactions was 4.09%, 5.69% and 11.31% respectively, in the quality range of 5 to 20% expected from the Roche procedure. These emPCR were pooled. Approximately 480,000 beads were loaded on the GS Titanium PicoTiterPlates PTP Kit 70x75 and sequenced with the GS FLX Titanium Sequencing Kit XLR70 (Roche). The run was performed overnight and then analyzed on the cluster through the gsRunBrowser and Newbler Assembler (Roche). A total of 264,150 filter-passed wells were obtained and generated 89.81 Mb of DNA sequences with a length average of 381 bp. The filter-passed sequences were assembled using Newbler with 90% identity and 40 bp overlap. The final assembly identified 54 large contigs (>1,500 bp) arranged into 6 scaffolds and generated a genome size of 3.77 Mb which corresponds to a coverage of 23.8× genome equivalent.
Open Reading Frames (ORFs) were predicted using prodigal  with default parameters. ORFs spanning a sequencing gap region were excluded. Assessment of protein function was obtained by comparing the predicted protein sequences with sequences in the GenBank  and the Clusters of Orthologous Groups (COG) databases using BLASTP. RNAmmer  and tRNAscan-SE 1.21  were used for identifying the rRNAs and tRNAs, respectively. SignalP  and TMHMM  were used to predict signal peptides and transmembrane helices, respectively. ORFans of alignment length greater than 80 amino acids were identified if their BLASTP E-value was lower than 1e-03.. An E-value of 1e-05 was used if alignment lengths were smaller than 80 amino acids. DNA Plotter  was used for visualization of genomic features and Artemis  was used for data management. The mean level of nucleotide sequence similarity was estimated at the genome level between H. djelfamassiliensis and 5 other members of the Halobacteriaceae family (Table 6), by BLASTN comparison of orthologous ORFs in pairwise genomes. Orthologous proteins were detected using the Proteinortho software using the following parameters e-value 1e-05, 30% identity, 50% coverage and 50% of algebraic connectivity .
Nucleotide content and gene count levels of the genome
% of totala
G+C content (bp)
Coding region (bp)
Genes with function prediction
Genes assigned to COGs
Genes with peptide signals
Genes with transmembrane helices
Number of genes associated with the 25 general COG functional categories
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, mitosis and meiosis
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Post-translational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
Comparison with other genomes of Archaea
Currently, only one genome from Halopiger species is available. Here, we compared the genome of H. djelfamassiliensis strain IIH2T with those of H. xanaduensis strain SH-6, Halalkalicoccus jeotgali strain B3, Natronomonas pharaonis strain DSM 2160, Haloterrigena turkmenica strain DSM 5511 and Natrialba magadii strain ATCC 43099. The draft genome of H. djelfamassiliensis (3.77 Mb) is larger than that of Halalkalicoccus jeotgali and Natronomonas pharaonis (3.69 and 2.75 Mb, respectively) but of a smaller size than H. xanaduensis, Natrialba magadii and Haloterrigena turkmenica (4.35, 4.44 and 5.44 Mb respectively). The G+C content (in %) of H. djelfaamassiliensis (64.30%) is higher than that of Haloterrigena turkmenica (64.26%), Natronomonas pharaonis (63.1%), Halalkalicoccus jeotgali (62.5%) and Natrialba magadii (61.1%) but smaller than H. xanaduensis (65.2%).
Orthologous gene comparison and average nucleotide identity of H. djelfamassiliensis with other compared genomes (upper right, numbers of orthologous genes; lower left, mean nucleotide identities of orthologous genes). Bold numbers indicate the numbers of genes for each genome.
Species (accession number)
Halopiger djelfamassiliensis (PRJEB1777)
Natronomonas pharaonis (NC_007426)
Haloterrigena turkmenica (NC_013743)
Natrialba magadii (NC_013922)
Halalkalicoccus jeotgali (NC_014297)
Halopiger xanaduensis (NC_015666)
On the basis of phenotypic, phylogenetic and genomic analyses, we formally propose the creation of Halopiger djelfamassiliensis sp. nov. that contains the strain IIH2T. This archaeal strain has been found in Algeria.
Description of Halopiger djelfamassiliensis sp. nov.
Halopiger djelfamassiliensis (dj. el. fa. ma. si. li. en’sis. L. gen. fem. n. djelfamassiliensis from the combination of Djelfa, the Algerian region where the strain was isolated, and massiliensis, of Massilia, the Latin name of Marseille, where the strain was sequenced). It has been isolated from an evaporitic sediment of the hypersaline Lake Zahrez Gharbi in the Djelfa region of Algeria.
Colonies were smooth, viscous and cream-pigmented with 3 to 4 mm in diameter on SG medium after incubation for 7 days at 40°C. Strain IIH2T is a Gram-negative, non-motile, strictly aerobic and extremely halophilic archeon. Growth occurs at NaCl concentrations of 15–30%, at pH values in the range 7–11, and within the temperature range 37–55 °C. Optimal NaCl concentration, pH and temperature for growth are 25%, 8.0 and 40 °C, respectively. Magnesium is not required for growth. Cells are polymorphic (0.9-2.2 µm) and lyse in distilled water. Tween 80, gelatin and lipids from egg yolk are hydrolysed, D-glucose, D-melibiose, L-rhamnose, D-xylose, D-galactose, D-mannose, D-ribose and D-sucrose are fermented. Cells are susceptible to bacitracin, novobiocin and tetracycline but resistant to ampicillin, cephalothin, chloramphenicol, erythromycin, gentamicin, kanamycin, nalidixic acid, penicillin G, streptomycin, and vancomycin. The G+C content of the genome is 64.30%. The 16S rRNA and genome sequences are deposited in GenBank and EMBL under accession numbers KC430939 and CBMA010000001-CBMA010000055 respectively. The type strain IIH2T (=CSUR P3035= DSM on-going deposit) was isolated from the sediment border of the hypersaline Lake Zahrez Gharbi, located in the Djelfa region of Algeria.
The authors thank the entire team of CD and more particularly Dr. Nikolay Popgeorgiev for his help with TEM and Sarah Temmam for her help with tree construction. The authors acknowledge the Xegen Company (www.xegen.fr) for automating the genomic annotation process.
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