Genome Sequence of Halanaerobium saccharolyticum subsp. saccharolyticum Strain DSM 6643T, a Halophilic Hydrogen-Producing Bacterium.

Halanaerobium saccharolyticum is a halophilic anaerobic fermentative bacterium capable of producing hydrogen, a potential future energy carrier molecule. The high-quality draft genome of H. saccharolyticum subsp. saccharolyticum strain DSM 6643(T) consists of 24 contigs for 2,873,865 bp with a G+C content of 32.3%.

GENOME ANNOUNCEMENT

Halanaerobium saccharolyticum is a halophilic anaerobic fermentative bacterium belonging to the order Halanaerobiales and the family Halanaerobiaceae (1, 2). H. saccharolyticum is an interesting bacterium due to its efficient hydrogen (bioenergy molecule) production (3, 4), vitamin B12-dependent 1,3-propanediol (building block of polymers)-producing pathway that competes with hydrogen production (4, 5), and ability to utilize unpurified raw glycerol, a by-product of traditional biodiesel industry, as a substrate of fermentation (A. Kivistö, A. Ciranna, V. Santala, and M. Karp, submitted for publication). The genome of H. saccharolyticum was sequenced in order to provide insight into the halophilic fermentative metabolic pathways. Furthermore, three bacterial species of the family Halanaerobiaceae were sequenced recently (6–8). The genome sequence of H. saccharolyticum, together with those of the previously sequenced strains, provides valuable information on the adaptation strategies of this group of halophilic fermentative bacteria.

The genome of H. saccharolyticum subsp. saccharolyticum strain DSM 6643T was sequenced using Illumina paired-end sequencing and 454 technologies, assembled using MIRA (9), and manually edited with Gap5 (10) to fix sequencing and assembly errors and combine contigs. The RAST server (11; http://rast.nmpdr.org/) was used for annotation, and when needed, manual checking and revision of autoannotation were done according to BLAST analysis (12). The resulting “improved high-quality draft” (13) genome is 2,873,865 bp in size, comprising 24 contigs (>1 kb). The genome was predicted to contain 2,664 coding sequences, of which 72 are for RNAs. The maximum contig length in the assembly is 900,505 bp, and the N50 is 723,182 bp. The G+C content of the genome is 32.3%.

The glycerol fermentation pathways of H. saccharolyticum were reconstructed according to genome sequence analysis. The reconstruction revealed hydrogen, carbon dioxide, acetate, butyrate, butanol, ethanol, lactate, malate, and 1,3-propanediol (a vitamin B12-dependent route) as putative fermentation products. Four [FeFe]-hydrogenases, of which two are putative bifurcating hydrogenases requiring both reduced ferredoxin and NADH, were identified. The putative bifurcating hydrogenases are suggested to be involved in high-yield H2 production. Furthermore, the genes for a multidrug efflux pump (Acr type), β-lactamase, mercuric reductase, a copper-translocating ATPase, and a cobalt-zinc-cadmium resistance protein suggest that H. saccharolyticum is resistant to a wide variety of antibiotics and toxic compounds, including heavy metals.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. CAUI00000000. The version described in this paper is the first version, CAUI01000000.