Thioautotrophic bacterial endosymbionts are degraded by enzymatic digestion during starvation: Case study of two lucinidsCodakia orbicularisandC. orbiculata

Host Species and Environment Shape the Gut Microbiota of Cohabiting Marine Bivalves

Pacific oysters (Crassostrea gigas) and Mediterranean mussels (Mytilus galloprovincialis) are commercially important marine bivalves that frequently coexist and have overlapping feeding ecologies. Like other invertebrates, their gut microbiota is thought to play an important role in supporting their health and nutrition. Yet, little is known regarding the role of the host and environment in driving these communities. Here, bacterial assemblages were surveyed from seawater and gut aspirates of farmed C. gigas and co-occurring wild M. galloprovincialis in summer and winter using Illumina 16S rRNA gene sequencing. Unlike seawater, which was dominated by Pseudomonadata, bivalve samples largely consisted of Mycoplasmatota (Mollicutes) and accounted for >50% of the total OTU abundance. Despite large numbers of common (core) bacterial taxa, bivalve-specific species (OTUs) were also evident and predominantly associated with Mycoplasmataceae (notably Mycoplasma). An increase in diversity (though with varied taxonomic evenness) was observed in winter for both bivalves and was associated with changes in the abundance of core and bivalve-specific taxa, including several representing host-associated and environmental (free-living or particle-diet associated) organisms. Our findings highlight the contribution of the environment and the host in defining the composition of the gut microbiota in cohabiting, intergeneric bivalve populations.

Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Nutrient stoichiometry (N:P) controls nitrogen fixation and distribution of diazotrophs in a tropical eutrophic estuary

Nitrogen fixation and its ecological regulation are poorly understood in the tropical estuaries, which are highly influenced by anthropogenic disturbances. In this study, we investigated the role of nutrient stoichiometry in the diversity, abundance and activity of N₂-fixing bacterial community and their seasonal variations in the water column of a tropical eutrophic estuary (Cochin estuary). The N₂ fixation rates in the estuary ranged from 0.1 to 2.0 nmol N₂ l^-1 h^-1, with higher activity during post-monsoon and lower during monsoon. The rates are appeared to be primarily controlled by dissolved inorganic nitrogen and phosphorous (N:P) ratio. Clone library analysis of nitrogenase (nifH) gene revealed that the major N₂ fixing phylotypes belong to Cluster I and Cluster III diazotrophs. The overall findings of this study suggest that monsoon induced seasonal changes in nutrient stoichiometry control the distribution and activity of diazotrophs in a tropical estuary.

Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis

All animals are associated with microorganisms; hence, host-microbe interactions are of fundamental importance for life on earth. However, we know little about the molecular basis of these interactions. Therefore, we studied the deep-sea Riftia pachyptila symbiosis, a model association in which the tubeworm host is associated with only one phylotype of endosymbiotic bacteria and completely depends on this sulfur-oxidizing symbiont for nutrition. Using a metaproteomics approach, we identified both metabolic interaction processes, such as substrate transfer between the two partners, and interactions that serve to maintain the symbiotic balance, e.g., host efforts to control the symbiont population or symbiont strategies to modulate these host efforts. We suggest that these interactions are essential principles of mutualistic animal-microbe associations.

The deep-sea tubeworm Riftia pachyptila lacks a digestive system but completely relies on bacterial endosymbionts for nutrition. Although the symbiont has been studied in detail on the molecular level, such analyses were unavailable for the animal host, because sequence information was lacking. To identify host-symbiont interaction mechanisms, we therefore sequenced the Riftia transcriptome, which served as a basis for comparative metaproteomic analyses of symbiont-containing versus symbiont-free tissues, both under energy-rich and energy-limited conditions. Our results suggest that metabolic interactions include nutrient allocation from symbiont to host by symbiont digestion and substrate transfer to the symbiont by abundant host proteins. We furthermore propose that Riftia maintains its symbiont by protecting the bacteria from oxidative damage while also exerting symbiont population control. Eukaryote-like symbiont proteins might facilitate intracellular symbiont persistence. Energy limitation apparently leads to reduced symbiont biomass and increased symbiont digestion. Our study provides unprecedented insights into host-microbe interactions that shape this highly efficient symbiosis.

Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve

BACKGROUND

The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam's physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts.

RESULTS

The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont's clear reliance on chemosynthesis, the clam's visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment.

CONCLUSIONS

The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.

NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host

The giant colonial ciliate Zoothamnium niveum harbors a monolayer of the gammaproteobacteria Cand. Thiobios zoothamnicoli on its outer surface. Cultivation experiments revealed maximal growth and survival under steady flow of high oxygen and low sulfide concentrations. We aimed at directly demonstrating the sulfur-oxidizing, chemoautotrophic nature of the symbionts and at investigating putative carbon transfer from the symbiont to the ciliate host. We performed pulse-chase incubations with 14C- and 13C-labeled bicarbonate under varying environmental conditions. A combination of tissue autoradiography and nanoscale secondary ion mass spectrometry coupled with transmission electron microscopy was used to follow the fate of the radioactive and stable isotopes of carbon, respectively. We show that symbiont cells fix substantial amounts of inorganic carbon in the presence of sulfide, but also (to a lesser degree) in the absence of sulfide by utilizing internally stored sulfur. Isotope labeling patterns point to translocation of organic carbon to the host through both release of these compounds and digestion of symbiont cells. The latter mechanism is also supported by ultracytochemical detection of acid phosphatase in lysosomes and in food vacuoles of ciliate cells. Fluorescence in situ hybridization of freshly collected ciliates revealed that the vast majority of ingested microbial cells were ectosymbionts.

Nitrogen fixation in a chemoautotrophic lucinid symbiosis

The shallow water bivalve Codakia orbicularis lives in symbiotic association with a sulfur-oxidizing bacterium in its gills. The endosymbiont fixes CO₂ and thus generates organic carbon compounds, which support the host's growth. To investigate the uncultured symbiont's metabolism and symbiont-host interactions in detail we conducted a proteogenomic analysis of purified bacteria. Unexpectedly, our results reveal a hitherto completely unrecognized feature of the C. orbicularis symbiont's physiology: the symbiont's genome encodes all proteins necessary for biological nitrogen fixation (diazotrophy). Expression of the respective genes under standard ambient conditions was confirmed by proteomics. Nitrogenase activity in the symbiont was also verified by enzyme activity assays. Phylogenetic analysis of the bacterial nitrogenase reductase NifH revealed the symbiont's close relationship to free-living nitrogen-fixing Proteobacteria from the seagrass sediment. The C. orbicularis symbiont, here tentatively named 'Candidatus Thiodiazotropha endolucinida', may thus not only sustain the bivalve's carbon demands. C. orbicularis may also benefit from a steady supply of fixed nitrogen from its symbiont-a scenario that is unprecedented in comparable chemoautotrophic symbioses.

Multiple I-Type Lysozymes in the Hydrothermal Vent Mussel Bathymodiolus azoricus and Their Role in Symbiotic Plasticity

The aim of this study was first to identify lysozymes paralogs in the deep sea mussel Bathymodiolus azoricus then to measure their relative expression or activity in different tissue or conditions. B. azoricus is a bivalve that lives close to hydrothermal chimney in the Mid-Atlantic Ridge (MAR). They harbour in specialized gill cells two types of endosymbiont (gram-bacteria): sulphide oxidizing bacteria (SOX) and methanotrophic bacteria (MOX). This association is thought to be ruled by specific mechanism or actors of regulation to deal with the presence of symbiont but these mechanisms are still poorly understood. Here, we focused on the implication of lysozyme, a bactericidal enzyme, in this endosymbiosis. The relative expression of Ba-lysozymes paralogs and the global anti-microbial activity, were measured in natural population (Lucky Strike--1700 m, Mid-Atlantic Ridge), and in in situ experimental conditions. B. azoricus individuals were moved away from the hydrothermal fluid to induce a loss of symbiont. Then after 6 days some mussels were brought back to the mussel bed to induce a re-acquisition of symbiotic bacteria. Results show the presence of 6 paralogs in B. azoricus. In absence of symbionts, 3 paralogs are up-regulated while others are not differentially expressed. Moreover the global activity of lysozyme is increasing with the loss of symbiont. All together these results suggest that lysozyme may play a crucial role in symbiont regulation.