Thermosipho spp. immune system differences affect variation in genome size and geographical distributions

Abstract

Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs, and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents, and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: The widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.

Lysogeny in the oceans: Lessons from cultivated model systems and a reanalysis of its prevalence

“…2B). Regarding the Thermotogae, prophage‐like elements have been found within SAGs belonging to this phylum (Labonté et al ., 2019) as well as cultured members of the genera Marinitoga and Thermosipho (Lossouarn et al ., 2015; Touchon et al ., 2016; Haverkamp et al ., 2018; Mercier et al ., 2018). Some of these prophage harbouring strains were present in our analysis (i.e., Marinitoga piezophile KA3, Thermosipho melanesiensis 431, and Thermosipho sp.…”

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing

“…Analysis of 111 Thermotogota genomes identified 20 proviruses, including the three already characterized viruses from Marinitoga (MPV1, MCV1 and MCV2; Lossouarn et al ., 2015; Mercier et al ., 2018) and four likely remnants of proviruses (Supporting Tables S1A and S2). One of the 20 proviruses is present with 100% nucleotide sequence identity in all six available Thermosipho melanesiensis genomes (Haverkamp et al ., 2018), and therefore is counted as just one novel provirus. An additional provirus was reported in a Marinitoga lauensis genome after we completed the screening (L'Haridon et al ., 2019).…”

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing

“…Analysis of 111 Thermotogota genomes identified proviruses, including the three already characterized viruses from Marinitoga [15,16] and four likely partial proviruses ( Supplementary Table S1 and Supplementary Table S2). One of the proviruses is present with 100% nucleotide sequence identity in all six available Thermosipho melanesiensis genomes [41], and therefore is counted as just one novel provirus. An additional provirus (MLaV1) was reported in a Marinitoga lauensis genome after we completed the screening [42].…”

“…Analysis of 111 Thermotogota genomes identified 20 proviruses, including the three already characterized viruses from Marinitoga and four partial proviruses (Supplementary Table S1). All available Thermosipho melanesiensis genomes have identical provirus sequences [35] and only one representative of these genomes were included in our analyses below. Annotation of coding sequences (CDS) in the proviruses are reported in Supplementary Table S2.…”