Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell

Abstract

Termites harbor a symbiotic gut microbial community that is responsible for their ability to thrive on recalcitrant plant matter. The community comprises diverse microorganisms, most of which are as yet uncultivable; the detailed symbiotic mechanism remains unclear. Here, we present the first complete genome sequence of a termite gut symbiont-an uncultured bacterium named Rs-D17 belonging to the candidate phylum Termite Group 1 (TG1). TG1 is a dominant group in termite guts, found as intracellular symbionts of various cellulolytic protists, without any physiological information. To acquire the complete genome sequence, we collected Rs-D17 cells from only a single host protist cell to minimize their genomic variation and performed isothermal whole-genome amplification. This strategy enabled us to reconstruct a circular chromosome (1,125,857 bp) encoding 761 putative protein-coding genes. The genome additionally contains 121 pseudogenes assigned to categories, such as cell wall biosynthesis, regulators, transporters, and defense mechanisms. Despite its apparent reductive evolution, the ability to synthesize 15 amino acids and various cofactors is retained, some of these genes having been duplicated. Considering that diverse termite-gut protists harbor TG1 bacteria, we suggest that this bacterial group plays a key role in the gut symbiotic system by stably supplying essential nitrogenous compounds deficient in lignocelluloses to their host protists and the termites. Our results provide a breakthrough to clarify the functions of and the interactions among the individual members of this multilayered symbiotic complex.gut bacteria ͉ insect ͉ phi29 ͉ symbiosis T he termite gut harbors 10 6 -10 8 microorganisms comprising Ͼ300 species of protists, bacteria, and archaea (1-5). These are mostly unique to termites and are essential, as a highly structured symbiotic community, for the host to survive on recalcitrant plant matter (1, 6-9). Although this symbiosis has long been attracting researchers for both basic and applied interests, the complexity and formidable unculturability of the gut microbiota have hampered clarification of the symbiotic mechanism. Among the as-yet-uncultivable gut symbionts, bacteria belonging to the candidate phylum Termite Group 1 (TG1) are common and often predominate in the gut microbial communities (8, 10, 11). Recently, these TG1 bacteria have been identified as intracellular symbionts of diverse cellulolytic gut protists (10, 12, 13). Because of its predominance, commonness, and specific localization confined to the gut protist cells, we assumed that the TG1 bacteria play a key role in the termite gut symbiotic system. However, TG1 is one of the Ϸ40 candidate phyla without isolated representatives (Fig. 1a) (5, 14), and no physiological information have been obtained thus far.In the present study, we aimed to acquire a complete genome sequence of the TG1 bacteria to clarify their functions, which will provide a breakthrough to disentangle the complicated symbiotic web. We targeted phylotype...

Acetogenesis from H2plus CO2and nitrogen fixation by an endosymbiotic spirochete of a termite-gut cellulolytic protist

“…The endosymbionts of termite-gut cellulolytic protists in the genus Pseudotrichonympha and Trichonympha have smaller genomes (1.1 Mb in each case) rich in pseudogenes, and thus their ongoing genome erosion is suggested (20,21). In contrast, the estimated genome size of the endosymbiont of Eucomonympha does not look severely reduced.…”

“…It is possible that, after the two lineages separated, they acquired the endosymbionts independently or that the endosymbiont of one lineage was replaced by another. In either case, the endosymbionts of both lineages seem to share many functions, such as nitrogen fixation, utilization of urea and ammonia, glycogen metabolism, and H 2 consumption, although H 2 is not used for reductive acetogenesis in the endosymbiont of Pseudotrichonympha, in addition to upgrading nitrogenous nutrients and the utilization of sugars, which are also common to the genome-sequenced endosymbiont of Trichonympha that belongs to the phylum Elusimicrobia (21). These common features suggest that different bacterial species have convergently established the similar intracellular niches of the cellulolytic protists and that these functions are important for the establishment of the endosymbiotic relationships.…”

“…The genome sequences of the two endosymbiont bacteria of two different gut protists have been reported, and their roles are inferred (20,21). These endosymbionts have the genetic potential to use sugars produced during cellulose degradation in the protist cells and to upgrade nitrogenous nutrients for the host protists.…”

Bacteroidales ectosymbionts of gut flagellates shape the nitrogen-fixing community in dry-wood termites

“…The lack of any nitrogenase genes from 'Endomicrobium trichonymphae' (Hongoh et al, 2008a)-the closest relative of the second symbiont of D. arta -and the apparent absence of 'Endomicrobia' from S. tabogae strongly suggest that both the Arma-1 (anfH) and the Bact-1a (nifH) paralogs stem from 'A. devescovinae' and the closely related symbiont of S. tabogae.…”

Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut

“…Furthermore, spirochetes and Bacteroidales bacteria are attached to its cell surface (Hongoh et al, 2007b). The complete genome sequence analysis of phylotype Rs-D17 suggested that the endosymbionts contribute to the host protists and termites by the synthesis of amino acids and cofactors, which are deficient in the ingested wood materials (Hongoh et al, 2008a). Likewise, termite gut protists generally harbor diverse intracellular and/or extracellular symbiotic prokaryotes comprising members of the orders Spirochaetales, Bacteroidales, 'Endomicrobiales', Desulfovibrionales, Actinomycetales and Methanobacteriales (Hongoh and Ohkuma, 2011;Desai and Brune, 2012;Strassert et al, 2012).…”