Extensive Thioautotrophic Gill Endosymbiont Diversity within a Single Ctena orbiculata (Bivalvia: Lucinidae) Population and Implications for Defining Host-Symbiont Specificity and Species Recognition

Abstract

Seagrass-dwelling members of the bivalve family Lucinidae harbor environmentally acquired gill endosymbionts. According to previous studies, lucinid symbionts potentially represent multiple strains from a single thioautotrophic gammaproteobacterium species. This study utilized genomic- and transcriptomic-level data to resolve symbiont taxonomic, genetic, and functional diversity from Ctena orbiculata endosymbiont populations inhabiting carbonate-rich sediment at Sugarloaf Key, FL (USA). The sediment had mixed seagrass and calcareous green alga coverage and also was colonized by at least five other lucinid species. Four coexisting, thioautotrophic endosymbiont operational taxonomic units (OTUs), likely representing four strains from two different bacterial species, were identified from C. orbiculata. Three of these OTUs also occurred at high relative abundances in the other sympatric lucinid species. Interspecies genetic differences averaged about 5% lower at both pairwise average nucleotide identity and amino acid identity than interstrain differences. Despite these genetic differences, C. orbiculata endosymbionts shared a high number of metabolic functions, including highly expressed thioautotrophy-related genes and a moderately to weakly expressed conserved one-carbon (C1) oxidation gene cluster previously undescribed in lucinid symbionts. Few symbiont- and host-related genes, including those encoding symbiotic sulfurtransferase, host respiratory functions, and host sulfide oxidation functions, were differentially expressed between seagrass- and alga-covered sediment locations. In contrast to previous studies, the identification of multiple endosymbiont taxa within and across C. orbiculata individuals, which were also shared with other sympatric lucinid species, suggests that neither host nor endosymbiont displays strict taxonomic specificity. This necessitates further investigations into the nature and extent of specificity of lucinid hosts and their symbionts. IMPORTANCE Symbiont diversity and host/symbiont functions have been comprehensively profiled for only a few lucinid species. In this work, unprecedented thioautotrophic gill endosymbiont taxonomic diversity was characterized within a Ctena orbiculata population associated with both seagrass- and alga-covered sediments. Endosymbiont metabolisms included known chemosynthetic functions and an additional conserved, previously uncharacterized C1 oxidation pathway. Lucinid-symbiont associations were not species specific because this C. orbiculata population hosted multiple endosymbiont strains and species, and other sympatric lucinid species shared overlapping symbiont 16S rRNA gene diversity profiles with C. orbiculata. Our results suggest that lucinid-symbiont association patterns within some host species could be more taxonomically diverse than previously thought. As such, this study highlights the importance of holistic analyses, at the population, community, and even ecosystem levels, in understanding host-microbe association patterns.

Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups

“…Thiodiazotropha formed two major clades, one comprising the four above-mentioned species and another containing Ca. T. endolucinida and the Thiodiazotropha-like species associated with Ctena orbiculata from Florida, previously reported by Lim et al (20) (Fig. 2).…”

Cutting out the middle clam: lucinid endosymbiotic bacteria are also associated with seagrass roots worldwide

“…Thiodiazotropha endolucinida indicated in Fig. S1), revealed not only genes relating to chemoautotrophy, but also diazotrophy, heterotrophy and oxidation of C1 compounds [5,[15][16][17]. Hence these bacteria may not only provide a means for lowering sediment sulphide levels, but may also provide an additional source of NH4 + via nitrogen fixation; the preferred source of N for seagrass uptake [18].…”

“…S1). Some lucinid species also exhibit diversity in their endosymbionts, possibly as a reflection of the diversity of free-living symbionts present in the environment [5,6]. To date, functional analysis of three gill edosymbionts (including Ca.…”

“…Lucinids acquire their endosymbionts in free-living stage from the environment, believed to be a result of chance encounters with potential symbionts during the juvenile phase [5,6]. It follows that seagrass roots, which provide a chemical environment that bears a striking resemblance to lucinid gills (i.e.…”

The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA

“…Intriguingly, Candidatus Thiodiazotropha is a recently described genus of endosymbionts discovered in the gills of lucinid bivalves (Petersen et al, 2016). Lucinid bivalves are not generally found in salt marshes, but they have been associated with reduced plant sulfide stress in seagrass meadows and mangroves (Lim et al, 2019a; Lim et al, 2019b; Gagnon et al, 2020). In these ecosystems, a tripartite symbiotic relationship occurs, whereby bivalves provide O 2 to endosymbiont sulfide-oxidizers that detoxify the plant’s environment from sulfide, a known phytotoxin (Gagnon et al, 2020).…”