Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO ₂ Fixation

Abstract

Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO2 by the symbionts drives these nutritional associations. In this study, we investigated “Candidatus Kentron,” the clade of symbionts hosted by Kentrophoros, a diverse genus of ciliates which are found in marine coastal sediments around the world. Despite being the main food source for their hosts, Kentron bacteria lack the key canonical genes for any of the known pathways for autotrophic carbon fixation and have a carbon stable isotope fingerprint that is unlike other thiotrophic symbionts from similar habitats. Our genomic and transcriptomic analyses instead found metabolic features consistent with growth on organic carbon, especially organic and amino acids, for which they have abundant uptake transporters. All known thiotrophic symbionts have converged on using reduced sulfur to gain energy lithotrophically, but they are diverse in their carbon sources. Some clades are obligate autotrophs, while many are mixotrophs that can supplement autotrophic carbon fixation with heterotrophic capabilities similar to those in Kentron. Here we show that Kentron bacteria are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotrophic symbionts studied to date, which possess either the Calvin-Benson-Bassham or the reverse tricarboxylic acid cycle for autotrophy. IMPORTANCE Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO2, serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, “Candidatus Kentron,” associated with marine ciliates. They lack genes for known autotrophic pathways and have a carbon stable isotope fingerprint heavier than other symbionts from similar habitats. Instead, they have the potential to oxidize sulfur to fuel the uptake of organic compounds for heterotrophic growth, a metabolic mode called chemolithoheterotrophy that is not found in other symbioses. Although several symbionts have heterotrophic features to supplement primary production, in Kentron they appear to supplant it entirely.

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

“…All these compounds may be relevant heterotrophic substrates in large Endoriftia, which could channel amino acids and peptides into protein biosynthesis, while sugars could be stored as glycogen. Heterotrophy in thiotrophic symbionts was previously shown for a ciliate symbiont ( Seah et al, 2019 ) and for ectosymbionts of shrimp ( Ponsard et al, 2013 ). Although the Riftia symbiont’s potential for mixotrophy, that is, for both autotrophy and heterotrophy, had been predicted from the symbiont’s genome, it was previously assumed that heterotrophy might be particularly relevant in free-living Endoriftia, but not during symbiosis ( Robidart et al, 2008 ).…”

Host-associated microbiomes drive structure and function of marine ecosystems

“…Previously unrecognized metabolic innovations of marine microbial symbioses that are ecologically important are discovered regularly [24]. For example, Candidatus Kentron (a clade of Gammaproteobacteria found in association with ciliates) nourish their ciliate hosts in the genus Kentrophoros and recycle acetate and propionate, which are low-value cellular waste products from their hosts, into biomass [25]. Another interesting example is found in the anaerobic marine ciliate Strombidium purpureum [26].…”

Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces

“…Reduced sulfur compounds stimulate carbon fixation in thioautotrophic symbionts (7, 11, 18, 19, 68-70, 126, 127). Our bulk isotope-ratio mass spectrometry (EA-IRMS) analysis indicates that, even though expression of the sulfur oxidation pathway was stimulated (Figures 1 and 2), fixation of 13 symbionts (71,73,131). No other known carboxylases are found in the symbiont genome.…”

“…Notably, sulfide oxidation without matching CO2 fixation has been described before for the symbiont of Riftia pachyptila (132,133) and an example of extreme decoupling of sulfur oxidation and carbon fixation was recently reported for Kentrophoros ectosymbionts. Strikingly, these lack genes for autotrophic carbon fixation altogether and thus represent the first heterotrophic sulfuroxidizing symbionts (71).…”