Genomic characterization of symbiotic mycoplasmas from the stomach of deep‐sea isopod bathynomus sp

Abstract

Deep-sea isopod scavengers such as Bathynomus sp. are able to live in nutrient-poor environments, which is likely attributable to the presence of symbiotic microbes in their stomach. In this study we recovered two draft genomes of mycoplasmas, Bg1 and Bg2, from the metagenomes of the stomach contents and stomach sac of a Bathynomus sp. sample from the South China Sea (depth of 898 m). Phylogenetic trees revealed a considerable genetic distance to other mycoplasma species for Bg1 and Bg2. Compared with terrestrial symbiotic mycoplasmas, the Bg1 and Bg2 genomes were enriched with genes encoding phosphoenolpyruvate-dependent phosphotransferase systems (PTSs) and sodium-driven symporters responsible for the uptake of sugars, amino acids and other carbohydrates. The genome of mycoplasma Bg1 contained sialic acid lyase and transporter genes, potentially enabling the bacteria to attach to the stomach sac and obtain organic carbons from various cell walls. Both of the mycoplasma genomes contained multiple copies of genes related to proteolysis and oligosaccharide degradation, which may help the host survive in low-nutrient conditions. The discovery of the different types of mycoplasma bacteria in the stomach of this deep-sea isopod affords insights into symbiotic model of deep-sea animals and genomic plasticity of mycoplasma bacteria.

Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish

“…The full-length 16S rRNA genes of the microbes from snailfish guts were amplified with a pair of universal primers (27F: 5 -AGAGTTTGATC[C/A]TGGCTCAG-3 ; 1492R: 5 -TACGG[C/T]TACCTTGTTACGAC-3 ) (Wang et al, 2016). PCR amplification was performed in a 50 µl reaction containing 5 ng of bacterial DNA as template, 10 µl of 5 × PCR buffer, 4 µl of 10 mM dNTPs, 0.5 µl of Prime STAR HS DNA Polymerase (TaKaRa, Japan), 32.5 µl of ddH 2 O, and 2 µl of 10 µM each primer.…”

“…This phenomenon is particularly evident for organisms in deep sea. In the stomach microbiota of Bathynomus sp., a deep-sea isopod living at a depth of 898 m in the South China Sea, symbiotic mycoplasmas occupy 42.8-100% of the microbial communities and might provide sugars and amino acids to the hosts (Wang et al, 2016). A sea cucumber from a depth of > 6,000 m in the Mariana Trench harbored obligate symbiotic spiroplasmas, with 63.5% occupation in the hindgut bacterial community.…”

Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

“…In deep-sea isopod gut, we also identified two types of Tenericutes bacteria, Mycoplasma sp. Bg1 and Bg2 (6). M. sp.…”

“…A total of 857 Tenericutes genomes were downloaded from the NCBI database. Three genomes of deep-sea symbiotic Tenericutes were collected from the previous studies (6, 7). Completeness and contamination of the genomes were evaluated by CheckM (v1.0.5) (42).…”

“…Environmental Tenericutes might be pathogens and/or mutualistic symbionts in the gut of their host species. For example, mycoplasmas and hepatoplasmas affiliated with Mycoplasmatales play a role in degrading recalcitrant carbon sources in the stomach and pancreas of isopods (5, 6). Spiroplasma symbionts discovered in sea cucumber guts possibly protect the host intestine from invading viruses (7).…”