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. 2016 Apr 21;4(2):e00308-16. doi: 10.1128/genomeA.00308-16

Draft Genome Sequence of Methanoculleus sediminis S3FaT, a Hydrogenotrophic Methanogen Isolated from a Submarine Mud Volcano in Taiwan

Sheng-Chung Chen a, Mei-Fei Chen a, Chieh-Yin Weng a, Mei-Chin Lai a,b,✉, Sue-Yao Wu a
PMCID: PMC4841145  PMID: 27103730

Abstract

Here, we announce the genome sequence of Methanoculleus sediminis S3FaT (DSM 29354T), a strict anaerobic methanoarchaeon, which was isolated from sediments near the submarine mud volcano MV4 located offshore in southwestern Taiwan. The 2.49-Mb genome consists of 2,459 predicted genes, 3 rRNAs, 48 tRNAs, and 1 ncRNA. The sequence of this novel strain may provide more information for species delineation and the roles that this strain plays in the unique marine mud volcano habitat.

GENOME ANNOUNCEMENT

Methanoculleus sediminis S3FaT, a mesophilic and hydrogenotrophic methanogen, was isolated from sediments near the submarine mud volcano MV4 located offshore in southwestern Taiwan and described as a novel species within the genus Methanoculleus (1). The genus Methanoculleus currently comprises 11 characterized and valid species: M. marisnigri JR1T (2), M. submarinus Nankai-1T (3), M. chikugoensis MG62T (4), M. thermophiles CR-1T (5), M. palmolei INSLUZT (6), M. bourgensis MS2T (7), M. receptaculi ZC-2T (8), M. hydrogenitrophicus HCT (9), M. horonobensis T10T (10), M. taiwanensis CYW4T (11), and M. sediminis S3FaT (1). The sources of these Methanoculleus spp. are truly diverse, including marine sediments, wastewater plants, wetlands, oil fields, and paddy fields. Here, we provide the draft genome sequence of M. sediminis S3FaT as a basis for future comparative studies and understanding the ecological roles of this genus.

Whole-genome shotgun sequencing was performed using the Illumina MiSeq platform with 2 × 300-bp reads. The reads were quality-filtered, trimmed, and assembled into contigs using the de novo assembler CLC Genomic Workbench version 7.5. The draft genome comprises 15 contigs with total length of ~2.49-Mb and a G+C content of 62.3%. Gene annotations were performed by using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP); 2,459 predicted genes, 3 rRNAs, 48 tRNAs, and 1 ncRNA were obtained.

The genome contains the genes of formate dehydrogenase, which is essential for formate utilization for methane production and growth of Methanoculleus sediminis S3FaT. Three clusters of regularly interspaced short palindromic repeat (CRISPR)-associated cas genes were identified. Furthermore, this genome contains three coding genes for trehalose synthases, which convert ADP-glucose to trehalose. This genome also comprises complete gene sets of heat shock proteins, including DnaK, DnaJ, GrpE, GroEL, GroES, prefoldin subunits, and small heat shock proteins. The genetic and physiological characteristics of strain S3FaT will be unveiled by comparative genomic analyses with Methanoculleus spp. and methanogens within other taxa.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JXOJ00000000. The version described in this paper is the first version, JXOJ01000000.

ACKNOWLEDGMENTS

This work is supported in part by the Ministry of Education, Taiwan, ROC, under the ATU plan (to M.-C.L.); by the Central Geological Survey, MOEA (100-5226904000-02-03); the National Science Council (NSC102-3113-P-005-002); and the Ministry of Science and Technology (MOST103-3113-M-005-001, MOST104-3113-M-005-001, and MOST105-3113-M-001), Taiwan, ROC.

Footnotes

Citation Chen S-C, Chen M-F, Weng C-Y, Lai M-C, Wu S-Y. 2016. Draft genome sequence of Methanoculleus sediminis S3FaT, a hydrogenotrophic methanogen isolated from a submarine mud volcano in Taiwan. Genome Announc 4(2):e00308-16. doi:10.1128/genomeA.00308-16.

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