- Extended genome report
- Open Access
Complete genome sequence analysis of Archaeoglobus fulgidus strain 7324 (DSM 8774), a hyperthermophilic archaeal sulfate reducer from a North Sea oil field
© The Author(s). 2017
- Received: 24 July 2017
- Accepted: 5 December 2017
- Published: 16 December 2017
Archaeoglobus fulgidus is the type species of genus Archaeoglobus Stetter 1998, a hyperthermophilic sulfate reducing group within the Archaeoglobi class of the euryarchaeota phylum. Members of this genus grow heterotrophically or chemolithoautotrophically with sulfate or thiosulfate as electron acceptors. Except for A. fulgidus strain 7324 and the candidate species “Archaeoglobus lithotrophicus”, which both originate from deep oil-fields, the other members of this genus have been recovered from marine hydrothermal systems. Here we describe the features of the A. fulgidus strain 7324 genome as compared to the A. fulgidus VC16 type strain. The 2.3 Mbp genome sequence of strain 7324 shares about 93.5% sequence identity with that of strain VC16T but is about 138 Kbp longer, which is mostly due to two large ‘insertions’ carrying one extra cdc6 (cell-cycle control protein 6) gene, extra CRISPR elements and mobile genetic elements, a high-GC ncRNA gene (hgcC) and a large number of hypothetical gene functions. A comparison with four other Archaeoglobus spp. genomes identified 1001 core Archaeoglobus genes and more than 2900 pan-genome orthologous genes.
- Sulfate reduction
Archaeoglobus fulgidus strain 7324 was recovered from hot oil-field water originating from a deep oil-well in the North Sea . It shares many features with the A. fulgidus type strain VC16, e.g. dissimilatory sulfate reduction, utilization of lactate and pyruvate as carbon sources, irregular coccoid to disc-shaped cells, and blue-green fluorescence under the UV microscope due to the presence of Coenzyme F420. Strain VC16T was isolated from a shallow marine hydrothermal system at Volcano island, Italy . The complete genome sequence of strain VC16T was reported in 1997 as the third archaeal genome to be fully sequenced  and A. fulgidus has since served as a prototype for studies of archaeal and hyperthermophilic sulfate reduction . Here we report a summary of the features of A. fulgidus strain 7324, together with the description of the complete genomic sequencing and annotation and comparison with the genome of the A. fulgidus type strain and other Archaeoglobus spp.
Classification and features
Classification and general features of Archaeoglobus fulgidus strain 7324 (DSM 8774)
Species Archaeoglobus fulgidus
Irregular coccoid to disc shaped
60 to 85 °C
Lactate, pyruvate, valerate
Lactate, pyruvate, valerate + H2
Terminal electron receptor
Sulfate and thiosulfate
3–500 mM NaCl (optimum at 300 mM)
Sample collection time
1993 or earlier
Genome project history
454 Titanium paired-end, Solexa paired end
454-GS-FLX, Solexa, Illumina
Newbler, Velvet v. 1.0.18; Consed v.20.0
Gene calling method
GenBank Date of Release
Source Material Identifier
Environmental, evolution of anaerobic respiration
Growth conditions and genomic DNA preparation
A. fulgidus strain 7324 was from our own collection at the University of Bergen. It was cultivated in anaerobic medium containing lactate and sulfate as described previously . The incubation temperature was 80 °C. Genomic DNA was isolated using a modification of the cetyl trimethylammonium bromide method as described .
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 . The initial assembly of 454 raw data suggested a contamination of the sequenced sample. Using blast search, all contigs (>500 nt in length) could be assigned either to A. fulgidus or Thermococcus litoralis , an archaeon that shares the same habitat . To overcome this issue, two additional blast searches including all contigs longer than 500 nt were performed against the previously sequenced genome of A. fulgidus VC-16T (NCBI/GenBank:AE000782) and all available genomic sequences of Thermococcus species in Genebank (Dec. 2010). Only sequences in length sharing more than 90% sequence identity with A. fulgidus VC-16T and having no hits in the Thermococcus blast database were kept. A total of 84 Newbler contigs could be assigned to A. fulgidus . Illumina raw reads were assembled to 223 contigs. Both draft assemblies were merged in a hybrid approach using the phred/phrap/consed pipeline . After manual curation, a total of 27 ordered gaps were closed by bridging PCRs at LGC Genomics (Berlin). The final consensus sequence represents a single circular chromosomal element (103× coverage).
Coding genes were predicted by GeneMark  as part of the genome annotation pipeline in the Integrated Microbial Genomes Expert Review system . The tRNAs were identified by tRNAScan-SE-1.23 , while ribosomal RNA genes within the genome were predicted using the tool RNAmmer . Other non-coding RNA genes were predicted using Infernal . CRISPR elements were identified by the program CRT . Manual functional annotation was performed within the IMG platform  and the Artemis Genome Browser .
% of Total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, Cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational 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
InsII also contains a gene encoding an extra homologue of the Orc1/Cdc6 family of replication initiation control proteins in addition to the two other cdc6 homologous in the 7324 and VC16T genomes. The closest homologue identified by a blast search is from A. veneficus (62% amino acid sequence identity). The majority of the other genes are hypothetical or have a general function prediction only. InsI carries two CRISPR repeat regions and 14 genes encoding CRISPR-associated proteins including a Cas6 homologue (Fig. 5a). The rest of this insert mostly contains hypothetical genes.
Archaeoglobus fulgidus strain 7324 has been reported to degrade starch  and several enzymes involved in starch degradation have been purified from cells grown on starch. These enzymes include cyclodextrin gluconotransferase, cyclodextrinase, maltodextrin phosphorylase, and phosphoglucomutase, ADP-dependent glucokinase, ADP-dependent phosphofructokinase and pyruvate kinase [34–37]. The enzymes were biochemically characterized and the N-termini (with exception of cyclodextrinase) have been determined. They showed highest sequence identity to proteins from Thermococcales , e.g. from Thermococcus litoralis . However, in the genome of A. fulgidus presented here, genes encoding sugar degrading enzymes have not been identified. Rather, various analyses indicated that A. fulgidus strain 7324, deposited as DSM 8774, was contaminated with a Thermococcus strain. The genome of this Thermococcus strain has also been sequenced and all genes encoding the sugar degrading enzymes, originally attributed to A. fulgidus strain 7324, were found in the Thermococcus strain genome. Also, glutamate dehydrogenase from a DSM 8774 culture grown in the presence of small amounts of yeast extract (0.3 gL−) was previously purified and characterized [38, 39], but appears also to be encoded by the Thermococcus strain genome. The purity of the original A. fulgidus 7324 isolate was not assessed by 16S rRNA gene sequencing prior to deposition at DSMZ  and whether the Thermococcus contamination was present in the original culture or has been introduced at a different stage is not known. The genome analysis of this Thermococcus strain, which appears to represent a novel Thermococcus species, will be published separately.
The complete genome of A. fulgidus strain 7324, recovered from hot water produced from an oil well in the North Sea was sequenced and annotated. In addition to the A. fulgidus type strain, VC16, isolated from a shallow hot vent in the Mediterranean, this is the second A. fulgidus genome to be characterized. The two strains share 93.5% genome sequence similarity, and differ mostly by two large insertions of 64 and 109 Kbp in strain 7324 that seem to have originated from an AT-rich archaeon. The insertions carry two additional CRISPR elements, an extra cdc6 gene, a variety of mobile genetic elements and a large number of hypothetical and unassigned genes. Based on comparison with four other Archaeoglobus spp. genomes, the Archaeoglobus core genome was estimated to 1001 genes. No particular traits indicating adaptation to the petroleum reservoir subsurface environment could be identified.
NKB, PS and HPK conceived and designed this project, and were involved in interpretation of the data. NKB, HPK and AF performed the sequencing, assembly and the bioinformatics analysis. LP performed the electron microscopy. NKB prepared the first draft of the manuscript. All authors were involved in critical revision of the manuscript and approved the final version.
The authors declare that they have no competing interests.
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