Genome of 'Ca. Desulfovibrio trichonymphae', an H2-oxidizing bacterium in a tripartite symbiotic system within a protist cell in the termite gut

Abstract

The cellulolytic protist Trichonympha agilis in the termite gut permanently hosts two symbiotic bacteria, 'Candidatus Endomicrobium trichonymphae' and 'Candidatus Desulfovibrio trichonymphae'. The former is an intracellular symbiont, and the latter is almost intracellular but still connected to the outside via a small pore. The complete genome of 'Ca. Endomicrobium trichonymphae' has previously been reported, and we here present the complete genome of 'Ca. Desulfovibrio trichonymphae'. The genome is small (1 410 056 bp), has many pseudogenes, and retains biosynthetic pathways for various amino acids and cofactors, which are partially complementary to those of 'Ca. Endomicrobium trichonymphae'. An amino acid permease gene has apparently been transferred between the ancestors of these two symbionts; a lateral gene transfer has affected their metabolic capacity. Notably, 'Ca. Desulfovibrio trichonymphae' retains the complex system to oxidize hydrogen by sulfate and/or fumarate, while genes for utilizing other substrates common in desulfovibrios are pseudogenized or missing. Thus, 'Ca. Desulfovibrio trichonymphae' is specialized to consume hydrogen that may otherwise inhibit fermentation processes in both T. agilis and 'Ca. Endomicrobium trichonymphae'. The small pore may be necessary to take up sulfate. This study depicts a genome-based model of a multipartite symbiotic system within a cellulolytic protist cell in the termite gut.

Figure 1

Fluorescence in situ hybridization (FISH) and transmission electron microscopy (TEM) of ‘Ca. Desulfovibrio trichonymphae' phylotype Rs-N31 cells associated with a Trichonympha agilis cell. (a) Phase-contrast image of T. agilis. (b) FISH analysis using oligonucleotide probes specific to ‘Ca. Desulfovibrio trichonymphae' (6-carboxyfluorescein-labelled, green) and to ‘Ca. Endomicrobium trichonymphae' (Texas red-labelled, red), respectively (Sato et al., 2009). (c) TEM image of ‘Ca. Desulfovibrio trichonymphae' cells in a T. agilis cell. Pores opening to the outside of the T. agilis cell were observed (arrows). H, hydrogenosome. (d) Magnified image of a ‘Ca. Desulfovibrio trichonymphae' cell in panel c. IM, inner membrane; OM, outer membrane; HPM, host plasma membrane. Bars: 20 μm (a, b); 500 nm (c); 100 nm (d).

Figure 2

Predicted metabolic pathways of ‘Ca. Desulfovibrio trichonymphae' phylotype Rs-N31. Genes responsible for the pathways marked with red X's are pseudogenized.

Figure 3

Predicted electron flows of ‘Ca. Desulfovibrio trichonymphae' phylotype Rs-N31. Hmc, high-molecular-weight cytochrome c; c₃, cytochrome c class III; MQ, menaquinone; Dsr, dissimilatory sulfite reductase; Qmo, quinone-modifying oxidoreductase; Apr, adenylylsulfate reductase; APS, adenylyl sulfate; Hdr, heterodisulfide reductase; Flx, NAD(P)H dehydrogenase; Nfn, ferredoxin-NADP(+) reductase; Coo-Hase, CO-induced membrane-bound hydrogenase; Ech-Hase, energy-conserving membrane-bound hydrogenase; Nrf, cytochrome c nitrite reductase; Frd, fumarate reductase; DcuA, anaerobic C₄-dicarboxylate antiporter.

Figure 4

Non-supervised orthologous groups (NOG) classification of genes in the genomes of ‘Ca. Desulfovibrio trichonymphae' phylotype Rs-N31 and reference organisms.

Figure 5

Proposed tripartite symbiotic relationship among ‘Ca. Desulfovibrio trichonymphae' phylotype Rs-N31, ‘Ca. Endomicrobium trichonymphae' phylotype Rs-D17, and Trichonympha agilis.