The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor

Abstract

Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.

Draft Genome Sequence of a Dictyoglomus sp. from an Enrichment Culture of a New Zealand Geothermal Spring

“…Due to the low number of representative genomes, their phylogenetic placement within the domain Bacteria is not certain as Dictyoglomus spp. are, although they appear to be affiliated most closely with a cluster containing Coprothermobacter , Synergistes , Acetothermia , and Thermotogales ( 1 , 12 , 13 ).…”

“… Dictyoglomus spp. form a distinct bacterial phylum, with only two described species with genome sequences, D. turgidum ( 1 ) and D. thermophilum ( 2 , 3 ). Dictyoglomus spp.…”

“…Further, Circos synteny plots ( 32 ) show that the Dictyoglomus sp. NZ13-RE01 genome does not share the highly syntenic genome arrangement found between D. turgidum and D. thermophilum ( 1 ). Considering the dissimilarity in genome nucleotide and amino acid sequences, and the low synteny in genome arrangement between NZ13-RE01 and either of the described Dictyoglomus spp., it is likely that NZ13-RE01 represents a new species within the genus Dictyoglomus .…”

“…The sporulation gene, spoVS , was also present and has been proposed to play a role in morphological changes in Dictyoglomus spp. ( 1 ).…”

Invited Review: Biodiversity of Plant Polysaccharide-Degrading Bacteria in Mangrove Ecosystem

“…In addition, xylan-degrading enzymes were also detected from cellulosome (Blouzard et al 2010;Kosugi et al 2002;Mohand-Oussaid et al 1999), indicating that the genus Clostridium is crucial for decomposition of cellulose and hemicellulose in anaerobic environments. Anaerobic bacteria Dictyoglomus thermophilum and D. turgidum belonging to the phylum Dicyoglomi known as xylan-degrading bacteria (Brumm et al 2016;Gibbs et al 1995) were also detected. Besides that, Opitutus terrae belonging to the phylum Verrucomicrobia was also found.…”