Vent Shrimp Rimicaris Exoculata Research Articles

A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata

BackgroundIn deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential.ResultsWe reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this.ConclusionOverall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont.FJvM6igKFE6x_yqS3roQ38Video

Anatomy and Symbiosis of the Digestive System of the Vent Shrimp Rimicaris Exoculata and Rimicaris Chacei Revealed Through Imaging Approaches

The shrimp Rimicaris exoculata and Rimicaris chacei are visually dominant fauna co-occurring at deep-sea hydrothermal sites of the Mid-Atlantic Ridge (MAR). Their co-existence was related to contrasted life-history traits, including differences in their diet and reliance on chemoautotrophic symbionts at the adult stage. Both species of shrimp are colonized by diversified chemosynthetic symbiotic microbial communities in their cephalothoracic cavity. Symbiotic association with bacteria was also evidenced in their digestive system, and the major lineages were identified through sequencing (with Mycoplasmatales in the foregut and Deferribacteres in the midgut) but their precise distribution within each host species was not assessed. For the first time, we used Fluorescence in situ Hybridization (FISH) to visualize these lineages and describe their association with digestive structures of their host. The aim of the study was to identify possible differences between host species that could be related to their different life-history traits. For this purpose, we developed new specific FISH probes targeting Deferribacteres and Mycoplasmatales lineages identified in the digestive system of these shrimp. Our FISH results showed a partitioning of the bacterial lineages according to the digestive organ corroborating sequencing data, and highlighted their association with specific anatomical structures. Despite morphological differences between the foreguts of R. exoculata and R. chacei that could be related to the adult diet, our FISH results showed overall similar distribution of digestive symbionts for the two host species. However, a more comprehensive study is needed with specimens at different life or molt stages to reveal potential host specific patterns. Such comparisons are now possible thanks to our newly designed FISH probes. The tools used in our study are valuable for tracking symbiont lineages in the environment, allowing a better understanding of their relationship with their host along its life cycle, including their acquisition mechanisms.

Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata

Characterization of DNA polymerase δ from deep-sea hydrothermal vent shrimp Rimicaris exoculata

Is It First the Egg or the Shrimp? - Diversity and Variation in Microbial Communities Colonizing Broods of the Vent Shrimp Rimicaris exoculata During Embryonic Development.

Rimicaris exoculata is one of the most well-known and emblematic species of endemic vent fauna. Like many other species from these ecosystems, Rimicaris shrimps host important communities of chemosynthetic bacteria living in symbiosis with their host inside the cephalothorax and gut. For many of these symbiotic partners, the mode of transmission remains to be elucidated and the starting point of the symbiotic relationship is not yet defined, but could begin with the egg. In this study, we explored the proliferation of microbial communities on R. exoculata broods through embryonic development using a combination of NGS sequencing and microscopy approaches. Variations in abundance and diversity of egg microbial communities were analyzed in broods at different developmental stages and collected from mothers at two distinct vent fields on the Mid-Atlantic Ridge (TAG and Snake Pit). We also assessed the specificity of the egg microbiome by comparing communities developing on egg surfaces with those developing on the cuticle of pleopods, which are thought to be exposed to similar environmental conditions because the brood is held under the female’s abdomen. In terms of abundance, bacterial colonization clearly increases with both egg developmental stage and the position of the egg within the brood: those closest to the exterior having a higher bacterial coverage. Bacterial biomass increase also accompanies an increase of mineral precipitations and thus clearly relates to the degree of exposure to vent fluids. In terms of diversity, most bacterial lineages were found in all samples and were also those found in the cephalothorax of adults. However, significant variation occurs in the relative abundance of these lineages, most of this variation being explained by body surface (egg vs. pleopod), vent field, and developmental stage. The occurrence of symbiont-related lineages of Epsilonbacteraeota, Gammaproteobacteria, Zetaproteobacteria, and Mollicutes provide a basis for discussion on both the acquisition of symbionts and the potential roles of these bacterial communities during egg development.

An H-ferritin from the hydrothermal vent shrimp Rimicaris exoculata and its potential role in iron metabolism.

Rimicaris exoculata (Decapoda: Bresiliidae) is one of the dominant species among hydrothermal vent communities along the Mid-Atlantic Ridge. This shrimp can tolerate high concentrations of heavy metals such as iron, but the mechanisms used for detoxification and utilization of excess metals remain largely unknown. Ferritin is a major iron storage protein in most living organisms. The central heavy subunit of ferritin (H-ferritin) possesses ferroxidase activity and converts iron from Fe2+ to Fe3+, the non-toxic form used for storage. In the present study, the H-ferritin RexFrtH was identified in the hydrothermal vent shrimp R. exoculata, and found to be highly expressed in the gill, the main organ involved in bioaccumulation of metals, at both RNA and protein levels. Accumulation of RexFrtH decreased from efferent to afferent vessels, coinciding with the direction of water flow through the gills. Fe3+ was localized with RexFrtH, and in vitro iron-binding and ferroxidase assays using recombinant RexFrtH confirmed the high affinity for iron. Based on these results, we propose a model of iron metabolism in R. exoculata gills; ferrous iron from ambient hydrothermal water accumulates and is converted and stored in ferric form by RexFrtH as an iron reservoir when needed for metabolism, or excreted as an intermediate to prevent iron overload. The findings expand our understanding of the adaptation strategies used by shrimps inhabiting extreme hydrothermal vents to cope with extremely high heavy metal concentrations.

Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers.

Rimicaris exoculata is a caridean shrimp that dominates the fauna at several hydrothermal vent sites of the Mid-Atlantic Ridge. It has two distinct and stable microbial communities. One of these epibiontic bacterial communities is located in the shrimp gut and has a distribution and role that are poorly understood. The second colonizes its enlarged gill chamber and is involved in host nutrition. It is eliminated after each molt, and has colonization processes reminiscent of those of a biofilm. The presence and expression of genes usually involved in quorum sensing (QS) were then studied. At four sites, Rainbow, TAG, Snake Pit and Logatchev, two lux genes were identified in the R. exoculata epibiontic community at different shrimp molt stages and life stages. RT-PCR experiments highlighted lux gene expression activity at TAG, Snake Pit and Rainbow vent sites. Their potential QS activity and their possible roles in epibiont colonization processes are discussed. Moreover, phylogenetic analysis has shown the presence of three clades for luxS (Epsilonproteobacteria) and four clades for luxR (Gammaproteobacteria) genes, each clade being restricted to a single site. These genes are more divergent than the 16S rRNA one. They could therefore be used as biogeographical genetic markers.

Characterization of miRNAs from hydrothermal vent shrimp Rimicaris exoculata

Deep-sea hydrothermal vent shrimp Rimicaris exoculata is a dominant species aggregating in vent fields along the Mid-Atlantic Ocean Ridge. MicroRNAs play important roles in life cycles of eukaryotes. However, little is known about miRNAs of vent animals. In the present study, a small RNA cDNA library from the muscle of R. exoculata was constructed and the miRNA sequencing was performed. The results indicated that a total of 7,983,331 raw reads were obtained, representing 569,354 unique sequences. Based on sequence analysis, R. exoculata contained 159 conserved miRNAs and 34 novel miRNAs. The conserved miRNAs included 54 families belonging to three different taxonomic units (bilaterian, protostomes and arthropods). The results also showed that miR-2001, a lost miRNA in crustaceans, existed in R. exoculata. Among the conserved miRNAs, iso-miRs were detected. Therefore, this study presented the first insight into the miRNAs of deep-sea hydrothermal vent animals.

The gill chamber epibiosis of deep‐sea shrimp Rimicaris exoculata: an in‐depth metagenomic investigation and discovery of Zetaproteobacteria

The gill chamber of deep-sea hydrothermal vent shrimp Rimicaris exoculata hosts a dense community of epibiotic bacteria dominated by filamentous Epsilonproteobacteria and Gammaproteobacteria. Using metagenomics on shrimp from the Rainbow hydrothermal vent field, we showed that both epibiont groups have the potential to grow autotrophically and oxidize reduced sulfur compounds or hydrogen with oxygen or nitrate. For carbon fixation, the Epsilonproteobacteria use the reductive tricarboxylic acid cycle, whereas the Gammaproteobacteria use the Calvin-Benson-Bassham cycle. Only the epsilonproteobacterial epibionts had the genes necessary for producing ammonium. This ability likely minimizes direct competition between epibionts and also broadens the spectrum of environmental conditions that the shrimp may successfully inhabit. We identified genes likely to be involved in shrimp-epibiont interactions, as well as genes for nutritional and detoxification processes that might benefit the host. Shrimp epibionts at Rainbow are often coated with iron oxyhydroxides, whose origin is intensely debated. We identified 16S rRNA sequences and functional genes affiliated with iron-oxidizing Zetaproteobacteria, which indicates that biological iron oxidation might play a role in forming these deposits. Fluorescence in situ hybridizations confirmed the presence of active Zetaproteobacteria in the R. exoculata gill chamber, thus providing the first evidence for a Zetaproteobacteria-invertebrate association.

Comparison of heat-shock responses between the hydrothermal vent shrimp Rimicaris exoculata and the related coastal shrimp Palaemonetes varians

The deep-sea vent shrimp Rimicaris exoculata is believed to occur at the hot end of the hydrothermal biotope in order to provide essential elements to its epibiosis. Because it is found close to hot venting water, R. exoculata lives in a highly fluctuating environment where temperature (2–40 °C in the swarms) can exceed its critical maximal temperature (33–38.5 ± 2 °C). In order to understand how this vent shrimp copes with hyperthermia, we compared its molecular heat stress response following an acute but non-lethal heat-shock (1 h at 30 °C) with that of its monophyletic shallow-water relative, the shrimp Palaemonetes varians, known to frequently undergo prolonged exposure at temperatures up to 30 °C in its natural environment during summer. We isolated four isoforms of heat-shock proteins 70 (HSP70) in R. exoculata (2 constitutive and 2 inducible isoforms) and two isoforms in P. varians (1 constitutive and 1 inducible isoform) and quantitatively compared their magnitude of induction at mRNA level, using real-time PCR, in the case of experimentally heat-stressed shrimps, with respect to control (unstressed) animals. Here, we report the first quantification of the expression of multiple hsp70 genes following heat stress in a deep-sea vent species living at 2300 m depth. Our results show a strong increase of hsp70 inducible genes in the vent shrimp (∼ 400-fold) compared to the coastal shrimp (∼ 15-fold). We therefore propose that, the highly inducible molecular response observed in R. exoculata may contribute to the ability of this species to tolerate thermal extremes.

Morphological adaptations to chronic hypoxia in deep-sea decapod crustaceans from hydrothermal vents and cold seeps

Animals inhabiting hydrothermal vents and cold seeps face conditions that are challenging for survival. In particular, these two habitats are characterized by chronic hypoxia, sometimes reaching complete anoxia. The characteristics of the scaphognathite and gills were studied in four species of shrimp and three species of crabs from hydrothermal vents and cold seeps, in order to highlight potential adaptations that could enhance oxygen acquisition in comparison with shallow-water relatives. All the vent and seep species studied here exhibit significantly larger scaphognathites, likely allowing more water to flow over their gills per stroke of this appendage. This is probably more energetically efficient that prolonged hyperventilation. In contrast to annelids, vent and seep decapods usually do not possess enlarged gills, a phenomenon likely due to the physical limitations imposed by the size of the gill chamber. In the vent shrimp Rimicaris exoculata and the vent crab Bythograea thermydron, however, there is a significantly higher specific gill surface area linked to a higher number of lamellae per gram of gill. Again in contrast to annelids, the diffusion distance through the gills is not strikingly different between the vent shrimp Alvinocaris komaii and the shallow-water species Palaemon spp. This may indicate that the epithelium and cuticle of the decapod gills are already optimized for oxygen uptake and that reducing the thickness of these compartments is not physically possible without affecting the physical integrity of the gills.

Retinal anatomy ofChorocaris chacei, a deep-sea hydrothermal vent shrimp from the mid-Atlantic ridge

Exploration of deep-sea hydrothermal vents over the past quarter century has revealed that they support unique and diverse biota. Despite the harsh nature of the environment, vents along the Mid-Atlantic Ridge are dominated by large masses of highly motile Bresiliid shrimp. Until 1989, when it was discovered that the vent shrimp Rimicaris exoculata possesses a hypertrophied dorsal eye, many believed that animals populating hydrothermal vents were blind. Chorocaris chacei (originally designated Rimicaris chacei) is a Bresiliid shrimp found at hydrothermal vent fields along the Mid-Atlantic Ridge. Like R. exoculata, C. chacei has a hypertrophied retina that appears to be specialized to detect the very small amount of light emitted from the orifices of black smoker hydrothermal vent chimneys. C. chacei lacks the sophisticated compound eyes common to other decapod crustaceans. Instead, it has a smooth cornea, with no dioptric apparatus, apposed by a tightly packed, massive array of photosensitive membrane. Photoreceptors in the C. chacei retina are segmented into a hypertrophied region that contains the photosensitive membrane and an atrophied cell body that is roughly ten times smaller in volume than the photosensitive segment. The microvillar photosensitive membrane is consistent in structure and ultrastructure with the rhabdoms of decapod and other invertebrate retinas. However, the volume density of photosensitive membrane (> or =60%) exceeds that typically observed in invertebrate retinas. The reflecting pigment cells commonly found in decapod retinas are represented in the form of a matrix of white diffusing cells that exhibit Tyndall scattering and form an axial sheath around the photoreceptors. All photoreceptor screening pigment granules and screening pigment cells are restricted to the region below the photoreceptor nuclei and are thereby removed from the path of incident light. No ultrastructural evidence of rhythmic cycling of photosensitive membrane was observed. The morphological adaptations observed in the C. chacei retina suggest that it is a high-sensitivity photodetector that is of functional significance to the animal.

Genetic comparison of two populations of the deep-sea vent shrimp Rimicaris exoculata (Decapoda: Bresiliidae) from the Mid-Atlantic Ridge

Allozyme data are presented for populations of the bresiliid shrimp Rimicaris exoculata from two hydrothermal vent fields, Trans-Atlantic Geotraverse (TAG) and Broken Spur, located along the Mid-Atlantic Ridge. These indicate that all morphotypes of R. exoculata examined, including those previously interpreted as representing separate species, are conspecific. Conversely, genetic identity between a single specimen of Chorocaris sp. and R. exoculata was high for intergeneric comparisons. Genetic variation in the populations of R. exoculata (Ho=0.034 to 0.056) was in the lower range of that estimated for other vent organisms, but similar to values obtained for other species of caridean shrimps in previous genetic studies. F-statistics were used to examine the population structure of R. exoculata. Estimates of variance of allele frequencies among populations (FST) between TAG and Broken Spur were very low (mean FST=0.001), indicating no significant genetic differentiation between these populations although they were separated by ≃ 370 km. The number of migrants per generation was estimated from FSTand by a private-alleles method, and indicates that migration between the two fields exceeds 100 individuals per generation. This may be because of efficient larval or adult migration or a combination of both. Estimates of the correlation between homologous alleles between individuals within local populations (FIS) of R. exoculata were high at two enzyme loci and indicate a heterozygote deficiency which caused a significant deviation from genotype frequencies expected under Hardy-Weinberg conditions. This deficiency was caused by the occurrence of rare homozygous genotypes in small individuals. In large individuals, rare alleles decreased in frequency or disappeared completely. This is discussed in relation to previous genetic investigations on other vent and nonvent organisms.