Nutritional Endosymbionts Research Articles

PacBio Hi-Fi genome assembly of Sipha maydis, a model for the study of multipartite mutualism in insects

Dependence on multiple nutritional endosymbionts has evolved repeatedly in insects feeding on unbalanced diets. However, reference genomes for species hosting multi-symbiotic nutritional systems are lacking, even though they are essential for deciphering the processes governing cooperative life between insects and anatomically integrated symbionts. The cereal aphid Sipha maydis is a promising model for addressing these issues, as it has evolved a nutritional dependence on two bacterial endosymbionts that complement each other. In this study, we used PacBio High fidelity (HiFi) long-read sequencing to generate a highly contiguous genome assembly of S. maydis with a length of 410 Mb, 3,570 contigs with a contig N50 length of 187 kb, and BUSCO completeness of 95.5%. We identified 117 Mb of repetitive sequences, accounting for 29% of the genome assembly, and predicted 24,453 protein-coding genes, of which 2,541 were predicted enzymes included in an integrated metabolic network with the two aphid-associated endosymbionts. These resources provide valuable genetic and metabolic information for understanding the evolution and functioning of multi-symbiotic systems in insects.

Retention of an Endosymbiont for the Production of a Single Molecule.

Sap-feeding insects often maintain two or more nutritional endosymbionts that act in concert to produce compounds essential for insect survival. Many mealybugs have endosymbionts in a nested configuration: one or two bacterial species reside within the cytoplasm of another bacterium, and together, these bacteria have genomes that encode interdependent sets of genes needed to produce key nutritional molecules. Here, we show that the mealybug Pseudococcus viburni has three endosymbionts, one of which contributes only two unique genes that produce the host nutrition-related molecule chorismate. All three bacterial endosymbionts have tiny genomes, suggesting that they have been coevolving inside their insect host for millions of years.

Unveiling metabolic integration in psyllids and their nutritional endosymbionts through comparative transcriptomics analysis

Psyllids, a group of insects that feed on plant sap, have a symbiotic relationship with an endosymbiont called Carsonella. Carsonella synthesizes essential amino acids and vitamins for its psyllid host, but lacks certain genes required for this process, suggesting a compensatory role of psyllid host genes. To investigate this, gene expression was compared between two psyllid species, Bactericera cockerelli and Diaphorina citri, in specialized cells where Carsonella resides (bacteriomes). Collaborative psyllid genes, including horizontally transferred genes, showed patterns of conserved gene expression; however, species-specific patterns were also observed, suggesting differences in the nutritional metabolism between psyllid species. Also, the recycling of nitrogen in bacteriomes may primarily rely on glutamate dehydrogenase (GDH). Additionally, lineage-specific gene clusters were differentially expressed in B.cockerelli and D.citri bacteriomes and are highlighted here. These findings shed light on potential host adaptations for the regulation of this symbiosis due to host, microbiome, and environmental differences.

Genomic Comparisons Reveal Selection Pressure and Functional Variation Between Nutritional Endosymbionts of Cave-Adapted and Epigean Hawaiian Planthoppers.

Planthoppers in the family Cixiidae (Hemiptera: Auchenorrhyncha: Fulgoromorpha) harbor a diverse set of obligate bacterial endosymbionts that provision essential amino acids and vitamins that are missing from their plant-sap diet. "Candidatus Sulcia muelleri" and "Ca. Vidania fulgoroidea" have been associated with cixiid planthoppers since their origin within the Auchenorrhyncha, whereas "Ca. Purcelliella pentastirinorum" is a more recent endosymbiotic acquisition. Hawaiian cixiid planthoppers occupy diverse habitats including lava tube caves and shrubby surface landscapes, which offer different nutritional resources and environmental constraints. Genomic studies have focused on understanding the nutritional provisioning roles of cixiid endosymbionts more broadly, yet it is still unclear how selection pressures on endosymbiont genes might differ between cixiid host species inhabiting such diverse landscapes, or how variation in selection might impact symbiont evolution. In this study, we sequenced the genomes of Sulcia, Vidania, and Purcelliella isolated from both surface and cave-adapted planthopper hosts from the genus Oliarus. We found that nutritional biosynthesis genes were conserved in Sulcia and Vidania genomes in inter- and intra-host species comparisons. In contrast, Purcelliella genomes retain different essential nutritional biosynthesis genes between surface- and cave-adapted planthopper species. Finally, we see the variation in selection pressures on symbiont genes both within and between host species, suggesting that strong coevolution between host and endosymbiont is associated with different patterns of molecular evolution on a fine scale that may be associated with the host diet.

Effects of Wolbachia elimination and B-vitamin supplementation on bed bug development and reproduction

Obligate blood feeders, such as Cimex lectularius (common bed bug), have symbiotic associations with nutritional endosymbionts that produce B-vitamins. To quantify the symbiont’s contribution to host fitness in these obligate mutualisms, the symbiont must be eliminated and its absence rigorously confirmed. We developed and validated procedures for complete elimination of Wolbachia (Wb) in bed bugs and quantified development and reproduction in bed bugs with and without Wb and with and without B-vitamins supplementation. Aposymbiotic bed bugs had slower nymphal development, reduced adult survivorship, smaller adult size, fewer eggs per female, and lower hatch rate than bed bugs that harbored Wb. In aposymbiotic bed bugs that were fed B-vitamins-supplemented blood, nymph development time, adult survivorship and hatch rate recovered to control levels, but adult size and egg number only partially recovered. These results underscore the nutritional dependence of bed bugs on their Wb symbiont and suggest that Wb may provide additional nutritional benefits beyond the B-vitamin mix that we investigated.

Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont

The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host’s cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.

Ecological Contacts and Host Specificity Promote Replacement of Nutritional Endosymbionts in Ticks.

Symbiosis with vitamin-provisioning microbes is essential for the nutrition of animals with somespecialized feeding habits. While coevolution favors the interdependence between symbiotic partners, their associations are not necessarily stable: Recently acquired symbionts can replace ancestral symbionts. In this study, we demonstrate successful replacement by Francisella-like endosymbionts (-LE), a group of B-vitamin-provisioning endosymbionts, across tick communities driven by horizontal transfers. Using a broad collection of Francisella-LE-infected tick species, we determined the diversity of Francisella-LE haplotypes through a multi-locus strain typing approach and further characterized their phylogenetic relationships and their association with biological traits of their tick hosts. The patterns observed showed that Francisella-LE commonly transfer through similar ecological networks and geographic distributions shared among different tick species and, in certain cases, through preferential shuffling across congeneric tick species. Altogether, these findings reveal the importance of geographic, ecological, and phylogenetic proximity in shaping the replacement pattern in which new nutritional symbioses are initiated.

The Evolution of Interdependence in a Four-Way Mealybug Symbiosis.

Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provision these same nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in its cytoplasm. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared with their closest nonendosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to an endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved codependencies with each other, Tremblaya, and their insect host.

Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis

Glyphosate is widely used as a herbicide, but recent studies begin to reveal its detrimental side effects on animals by targeting the shikimate pathway of associated gut microorganisms. However, its impact on nutritional endosymbionts in insects remains poorly understood. Here, we sequenced the tiny, shikimate pathway encoding symbiont genome of the sawtoothed grain beetle Oryzaephilus surinamensis. Decreased titers of the aromatic amino acid tyrosine in symbiont-depleted beetles underscore the symbionts’ ability to synthesize prephenate as the precursor for host tyrosine synthesis and its importance for cuticle sclerotization and melanization. Glyphosate exposure inhibited symbiont establishment during host development and abolished the mutualistic benefit on cuticle synthesis in adults, which could be partially rescued by dietary tyrosine supplementation. Furthermore, phylogenetic analyses indicate that the shikimate pathways of many nutritional endosymbionts likewise contain a glyphosate sensitive 5-enolpyruvylshikimate-3-phosphate synthase. These findings highlight the importance of symbiont-mediated tyrosine supplementation for cuticle biosynthesis in insects, but also paint an alarming scenario regarding the use of glyphosate in light of recent declines in insect populations.

Characterization and comparison of the bacterial microbiota of Lysiphlebia japonica parasitioid wasps and their aphid host Aphis gosypii.

Endosymbiotic bacteria have been reported to mediate interactions between parasitoids and their insect hosts. How parasitic wasps influence changes in host microbial communities and the relationship between them are of great importance to the study of host-parasitoid co-evolutionary and ecological interactions. However, these interactions remain largely unreported for interactions between Aphis gossypii and Lysiphlebia japonica. In this study, we characterize the bacterial microbiota of L. japonica wasps at different developmental stages and monitor changes over time in the bacterial microbiota of their parasitized and nonparasitized aphid hosts, using metagenomic analysis of 16S rDNA sequencing data. Proteobacteria, Firmicutes, and Actinobacteria were the three most abundant bacterial phyla identified in L. japonica. We found that parasitism was associated with an increased abundance of Buchnera nutritional endosymbionts, but decreased abundance of Acinetobacter, Arsenophonus, Candidatus_Hamiltonella, and Pseudomonas facultative symbionts in aphid hosts. Functional analysis of enriched pathways of parasitized aphids showed significant differences in the 'transport and metabolism of carbohydrates' and 'amino acid, lipid, and coenzyme biosynthesis' pathways. Notably, the composition of symbiotic bacteria in wasp larvae was highly similar to that of their aphid hosts, especially the high abundance of Buchnera. The results provide a conceptual framework for L. japonica interactions with A. gossypii in which the exchange of symbiotic microbes provides a means by which microbiota can potentially serve as evolutionary drivers of complex, multilevel interactions underlying the ecology and co-evolution of these hosts and parasites. © 2021 Society of Chemical Industry.

Cicada Endosymbionts Have tRNAs That Are Correctly Processed Despite Having Genomes That Do Not Encode All of the tRNA Processing Machinery.

Gene loss and genome reduction are defining characteristics of endosymbiotic bacteria. The most highly reduced endosymbiont genomes have lost numerous essential genes related to core cellular processes such as replication, transcription, and translation. Computational gene predictions performed for the genomes of the two bacterial symbionts of the cicada Diceroprocta semicincta, "Candidatus Hodgkinia cicadicola" (Alphaproteobacteria) and "Ca Sulcia muelleri" (Bacteroidetes), have found only 26 and 16 tRNA genes and 15 and 10 aminoacyl tRNA synthetase genes, respectively. Furthermore, the original "Ca Hodgkinia cicadicola" genome annotation was missing several essential genes involved in tRNA processing, such as those encoding RNase P and CCA tRNA nucleotidyltransferase as well as several RNA editing enzymes required for tRNA maturation. How these cicada endosymbionts perform basic translation-related processes remains unknown. Here, by sequencing eukaryotic mRNAs and total small RNAs, we show that the limited tRNA set predicted by computational annotation of "Ca Sulcia muelleri" and "Ca Hodgkinia cicadicola" is likely correct. Furthermore, we show that despite the absence of genes encoding tRNA processing activities in the symbiont genomes, symbiont tRNAs have correctly processed 5' and 3' ends and seem to undergo nucleotide modification. Surprisingly, we found that most "Ca Hodgkinia cicadicola" and "Ca Sulcia muelleri" tRNAs exist as tRNA halves. We hypothesize that "Ca Sulcia muelleri" and "Ca Hodgkinia cicadicola" tRNAs function in bacterial translation but require host-encoded enzymes to do so.IMPORTANCE The smallest bacterial genomes, in the range of about 0.1 to 0.5 million base pairs, are commonly found in the nutritional endosymbionts of insects. These tiny genomes are missing genes that encode proteins and RNAs required for the translation of mRNAs, one of the most highly conserved and important cellular processes. In this study, we found that the bacterial endosymbionts of cicadas have genomes which encode incomplete tRNA sets and lack genes required for tRNA processing. Nevertheless, we found that endosymbiont tRNAs are correctly processed at their 5' and 3' ends and, surprisingly, that mostly exist as tRNA halves. We hypothesize that the cicada host must supply its symbionts with these missing tRNA processing activities.

Genome Evolution of Bartonellaceae Symbionts of Ants at the Opposite Ends of the Trophic Scale.

Many insects rely on bacterial symbionts to supply essential amino acids and vitamins that are deficient in their diets, but metabolic comparisons of closely related gut bacteria in insects with different dietary preferences have not been performed. Here, we demonstrate that herbivorous ants of the genus Dolichoderus from the Peruvian Amazon host bacteria of the family Bartonellaceae, known for establishing chronic or pathogenic infections in mammals. We detected these bacteria in all studied Dolichoderus species, and found that they reside in the midgut wall, that is, the same location as many previously described nutritional endosymbionts of insects. The genomic analysis of four divergent strains infecting different Dolichoderus species revealed genes encoding pathways for nitrogen recycling and biosynthesis of several vitamins and all essential amino acids. In contrast, several biosynthetic pathways have been lost, whereas genes for the import and conversion of histidine and arginine to glutamine have been retained in the genome of a closely related gut bacterium of the carnivorous ant Harpegnathos saltator. The broad biosynthetic repertoire in Bartonellaceae of herbivorous ants resembled that of gut bacteria of honeybees that likewise feed on carbohydrate-rich diets. Taken together, the broad distribution of Bartonellaceae across Dolichoderus ants, their small genome sizes, the specific location within hosts, and the broad biosynthetic capability suggest that these bacteria are nutritional symbionts in herbivorous ants. The results highlight the important role of the host nutritional biology for the genomic evolution of the gut microbiota—and conversely, the importance of the microbiota for the nutrition of hosts.

A sRNA in a reduced mutualistic symbiont genome regulates its own gene expression.

Similar to other nutritional endosymbionts that are obligate for host survival, the mutualistic aphid endosymbiont, Buchnera, has a highly reduced genome with few regulatory elements. Until recently, it was thought that aphid hosts were primarily responsible for regulating their symbiotic relationship. However, we recently revealed that Buchnera displays differential protein regulation, but not mRNA expression. We also identified a number of conserved small RNAs (sRNAs) that are expressed among Buchnera taxa. In this study, we investigate whether differential protein regulation in Buchnera is the result of post-transcriptional gene regulation via sRNAs. We characterize the sRNA profile of two Buchnera life stages: (i) when Buchnera is transitioning from an extracellular proliferating state in aphid embryos and (ii) when Buchnera is in an intracellular nonproliferating state in aphid bacteriocytes (specialized symbiont cells). Overall, we identified 90 differentially expressed sRNAs, 97% of which were upregulated in aphid embryos. Of these sRNAs, the majority were predicted to be involved in the regulation of various metabolic processes, including arginine biosynthesis. Using a heterologous dual expression vector, we reveal for the first time that a Buchnera antisense sRNA can post-transcriptionally interact with its cognate Buchnera coding sequence, carB, a gene involved in arginine biosynthesis. These results corroborate our invivo RNAseq and proteomic data, where the candidate antisense sRNA carB and the protein CarB are significantly upregulated in aphid embryos. Overall, we demonstrate that Buchnera may regulate gene expression independently from its host by utilizing sRNAs.

Microbiota associated with tubes of Escarpia sp. from cold seeps in the southwestern Atlantic Ocean constitutes a community distinct from that of surrounding marine sediment and water

As the depth increases and the light fades in oceanic cold seeps, a variety of chemosynthetic-based benthic communities arise. Previous assessments reported polychaete annelids belonging to the family Siboglinidae as part of the fauna at cold seeps, with the 'Vestimentifera' clade containing specialists that depend on microbial chemosynthetic endosymbionts for nutrition. Little information exists concerning the microbiota of the external portion of the vestimentiferan trunk wall. We employed 16S rDNA-based metabarcoding to describe the external microbiota of the chitin tubes from the vestimentiferan Escarpia collected from a chemosynthetic community in a cold seep area at the southwestern Atlantic Ocean. The most abundant operational taxonomic unit (OTU) belonged to the family Pirellulaceae (phylum Planctomycetes), and the second most abundant OTU belonged to the order Methylococcales (phylum Proteobacteria), composing an average of 21.1 and 15.4% of the total reads on tubes, respectively. These frequencies contrasted with those from the surrounding environment (sediment and water), where they represent no more than 0.1% of the total reads each. Moreover, some taxa with lower abundances were detected only in Escarpia tube walls. These data constitute on the first report of an epibiont microbial community found in close association with external surface of a cold-seep metazoan, Escarpia sp., from a chemosynthetic community in the southwestern Atlantic Ocean.

The evolutionary development of plant-feeding insects and their nutritional endosymbionts.

Herbivorous insects have evolved diverse mechanisms enabling them to feed on plants with suboptimal nutrient availability. Low nutrient availability negatively impacts insect herbivore development and fitness. To overcome this obstacle numerous insect lineages have evolved intimate associations with nutritional endosymbionts. This is especially true for insects that specialize on nitrogen-poor substrates, as these insects are highly dependent on intracellular symbionts to provide nitrogen lacking in their insect host's diet. Emerging evidence in these systems suggest that the symbiont's and/or the insect's biosynthetic pathways are dynamically regulated throughout the insect's development to potentially cope with the insect's changing nutritional demands. In this review, we evaluate the evolutionary development of symbiotic insect cells (bacteriocytes) by comparing and contrasting genes and mechanisms involved in maintaining and regulating the nutritional symbiosis throughout insect development in a diversity of insect herbivore-endosymbiont associations. With new advances in genome sequencing and functional genomics, we evaluate to what extent nutritional symbioses are shaped by (i) the regulation of symbiont titer, (ii) the regulation of insect symbiosis genes, and (iii) the regulation of symbiont genes. We discuss how important these mechanisms are for the biosynthesis of essential amino acids and vitamins across insect life stages in divergent insect-symbiont systems. We conclude by suggesting future directions of research to further elucidate the evolutionary development of bacteriocytes and the impact of these nutritional symbioses on insect-plant interactions.

Genomic Evidence that Methanotrophic Endosymbionts Likely Provide Deep-Sea Bathymodiolus Mussels with a Sterol Intermediate in Cholesterol Biosynthesis.

Sterols are key cyclic triterpenoid lipid components of eukaryotic cellular membranes, which are synthesized through complex multi-enzyme pathways. Similar to most animals, Bathymodiolus mussels, which inhabit deep-sea chemosynthetic ecosystems and harbor methanotrophic and/or thiotrophic bacterial endosymbionts, possess cholesterol as their main sterol. Based on the stable carbon isotope analyses, it has been suggested that host Bathymodiolus mussels synthesize cholesterol using a sterol intermediate derived from the methanotrophic endosymbionts. To test this hypothesis, we sequenced the genome of the methanotrophic endosymbiont in Bathymodiolus platifrons. The genome sequence data demonstrated that the endosymbiont potentially generates up to 4,4-dimethyl-cholesta-8,14,24-trienol, a sterol intermediate in cholesterol biosynthesis, from methane. In addition, transcripts for a subset of the enzymes of the biosynthetic pathway to cholesterol downstream from a sterol intermediate derived from methanotroph endosymbionts were detected in our transcriptome data for B. platifrons. These findings suggest that this mussel can de novo synthesize cholesterol from methane in cooperation with the symbionts. By in situ hybridization analyses, we showed that genes associated with cholesterol biosynthesis from both host and endosymbionts were expressed exclusively in the gill epithelial bacteriocytes containing endosymbionts. Thus, cholesterol production is probably localized within these specialized cells of the gill. Considering that the host mussel cannot de novo synthesize cholesterol and depends largely on endosymbionts for nutrition, the capacity of endosymbionts to synthesize sterols may be important in establishing symbiont–host relationships in these chemosynthetic mussels.

Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida)

Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts.

Evolutionary radiation of shallow-water Lucinidae (Bivalvia with endosymbionts) as a result of the rise of seagrasses and mangroves

The Lucinidae (Bivalvia) originated in the Silurian Period with adaptations and life habits like those of modern members of this family. Nonetheless, the family remained at very low diversity until beginning a remarkable evolutionary radiation near the end of the Cretaceous Period, when seagrasses and mangroves arose. These marine angiosperms provided protective habitats in which the lucinids suddenly began to flourish, taking advantage of the dysaerobic sediments below roots and rhizomes to acquire sulfides for the endosymbiotic bacteria that they harbor in their gills and employ as food. Lucinids entered a symbiotic relationship with seagrasses, which benefit from the endosymbionts’ uptake of toxic sulfide, and it is in seagrass meadows that they have by far their highest diversity in shallow seas today. The terminal Cretaceous mass extinction had little impact on the taxonomic diversity of lucinids. Presumably they relied heavily on endosymbionts for nutrition at a time when marine pelagic productivity collapsed and many suspension-feeding taxa died out. The lucinids continued their radiation into the Cenozoic Era without interruption.

Highlight: Tiny Bacterial Genome Opens a Huge Mystery: AT Mutational Bias in Hodgkinia

Highlight: Tiny Bacterial Genome Opens a Huge Mystery: AT Mutational Bias in Hodgkinia

Complete genome sequence of Candidatus Ruthia magnifica

The hydrothermal vent clam Calyptogena magnifica (Bivalvia: Mollusca) is a member of the Vesicomyidae. Species within this family form symbioses with chemosynthetic Gammaproteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a rudimentary gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. The C. magnifica symbiont, Candidatus Ruthia magnifica, was the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced (Newton et al. 2007). Here we expand upon the original report and provide additional details complying with the emerging MIGS/MIMS standards. The complete genome exposed the genetic blueprint of the metabolic capabilities of the symbiont. Genes which were predicted to encode the proteins required for all the metabolic pathways typical of free-living chemoautotrophs were detected in the symbiont genome. These include major pathways including carbon fixation, sulfur oxidation, nitrogen assimilation, as well as amino acid and cofactor/vitamin biosynthesis. This genome sequence is invaluable in the study of these enigmatic associations and provides insights into the origin and evolution of autotrophic endosymbiosis.