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Microbiota play a pivotal role in holobionts, influencing nutrient intake, growth, and overall health. In this context, microbial dysbiosis of Penaeus stylirostris larvae seem to be associated with huge larval mortalities in hatcheries in New Caledonia. To understand larval dysbiosis establishment, our purpose was to identify bacterial biomarkers, as bioindicators, related to a given larval stage and health condition. To this end, larvae were sampled daily to access their active microbiota through sequencing of the V4 region of the 16S rRNA molecule, while their stage and their health were also observed. We identified three biomarkers strongly related to healthy zoea, and some may act as probiotics or play key roles in larval ontogeny and nutrition. We also found six biomarkers linked to unhealthy zoea and eight related to healthy mysis. Biomarkers were mostly related to diseased shrimps (Lewinella) or healthy shrimps (Cognitishimia, Thalassolituus) or were known to prey on cells (P30B-42), suggesting that the larvae might be battling against detrimental conditions. No biomarker related to unhealthy mysis was identified. Finally, our data showed that bacterial bioindicators could be used as an effective biosurveillance proxy in hatcheries, to monitor larval development, and as an early warning tool to predict rearing outcomes.

During their entire lifecycle, mariculture animals are farmed in water that contains various microorganisms with which they are in close associations. Microbial exchanges between the animals and their surrounding water can occur. However, little is known about the interactions between shrimp larvae and water, and more especially, about larval bacterial selection and microbiota modulation across ontogeny. To address this gap, using HiSeq sequencing targeting the V4 region of the 16S rRNA molecule, we investigated the active prokaryotic diversity and structure of healthy Penaeus stylirostris larvae and seawater. Comparisons between different larval stages revealed evidence of stage-specific microbiotas and biomarkers, a core microbiota common to all stages, and shared taxa between successive stages, suggesting vertical transmission of bacterial taxa. Comparisons between stage-specific microbiotas and core microbiotas with water storages highlighted that many taxa associated with the larvae were originally present in the natural seawater, underlining horizontal transmission of bacteria from water to larvae. As some of these lineages became active at specific larval stages, we suggest that larvae were able to modulate their microbiota. This study provides insight into larvae-microbiota interactions at the larval stage scale.

Background In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species ( Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata ) on active sediment microbial communities and their implications on organic matter degradation. Results Drying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture. Conclusion The efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.

Microbial communities associated with animals are known to be key elements in the development of their hosts. In marine environments, these communities are largely under the influence of the surrounding water. In aquaculture, understanding the interactions existing between the microbiotas of farmed species and their rearing environment could help establish precise bacterial management. In light of these facts, we studied the active microbial communities associated with the eggs and the nauplii of the Pacific blue shrimp ( ) and their rearing water. All samples were collected in September 2018, November 2018 and February 2019. After RNA extractions, two distinct Illumina HiSeq sequencings were performed. Due to different sequencing depths and in order to compare samples, data were normalized using the Count Per Million method. We found a core microbiota made of taxa related to , , , , , and associated with all the samples indicating that these bacterial communities could be transferred from the water to the animals. We also highlighted specific bacterial taxa in the eggs and the nauplii affiliated to , , , , , , , , , and genera suggesting a possible prokaryotic vertical transmission from the breeders to their offspring. This study is the first to focus on the active microbiota associated with early developmental stages of a farmed shrimp species and could serve as a basis to comprehend the microbial interactions involved throughout the whole rearing process.

Estuaries are a key component of the land‐sea continuum, and their microbial diversity depends on the connection with terrestrial ecosystems. This work aimed to demonstrate that the terrestrial matter carried by rivers influences the structuration of microeukaryote communities of superficial (0–3 cm) sediments collected at the interface between the land and marine coastal areas. To demonstrate this hypothesis, we have chosen the main island of New Caledonia as a study site, a French overseas territory located in the South West Pacific. Using amplicon sequencing of the 18S‐V4 rDNA extracted from sediments, we analyzed microeukaryote community composition in relation to numerous environmental parameters. Samples were collected in five bays influenced by riverine inputs and corresponding to distinct geological features of the watersheds, as revealed by high variations in metal concentrations released from specific minerals in the sediment. Particularly, the influence of ultramafic soils was highlighted by higher nickel concentration (correlated to Co, Cr, Mn, and Fe). Diatoms were the dominant taxonomic group, especially the classes of Bacillariophyceae and Mediophyceae. Then Apicomplexa, Ciliophora, Dinoflagellata, and Cercozoa followed. The metallic composition of the sediment explained 18.46% of the community spatial variability. The selection of ASVs based on their contribution to beta diversity and their correlation with metallic concentrations enabled us to identify spatial patterns. This information could lead to identifying microeukaryote bioindicators of terrestrial influences, particularly of ultramafic origin. We hypothesized that the association between microeukaryotes and metallic compositions is linked to selection processes, given the resistance of some microeukaryotes to some high metallic concentrations. In vitro experiments are needed to confirm this hypothesis. Our results emphasized the role of terrestrial inputs in shaping estuarine diversity and the need to consider the entire land–sea continuum for studying these ecosystems. Changes in the matter origin are reflected in estuarine benthic microeukaryote diversity. Specific taxa are associated with different metal inputs, which are linked to the geological characteristics of watersheds. The study of New Caledonian ecosystems can lead to the development of marine bioindicators of metallic inputs from land.

The current article introduces and describes Haslea berepwari sp. nov. , a new species of diatom discovered in the vicinity of Boulouparis, New Caledonia. Under light microscopy, H. berepwari sp. nov. strongly resembles Haslea pseudostrearia , but preliminary molecular barcoding conducted using partial 18S and rbcL genes suggested that it was a distinct species. This was confirmed first by scanning electron microscopy which showed the differences in stria densities between both species. A short-reads genome-skimming protocol applied on H. berepwari sp. nov. led us to obtain its complete mitochondrial and plastid genomes. The mitogenome is 36,572 bp in length and as already observed among other species of Haslea spp., the nad6 and nad2 genes are fused within a single open-reading frame. The plastome is 131,897 bp length, and unlike the mitogenome, it is not colinear with those of H. pseudostrearia . The results derived from the sequencing of the plastome allowed to perform a 123-gene multigene maximum likelihood phylogeny that associates H. berepwari sp. nov. to H. pseudostrearia with maximum support at the nodes but also strictly distinguishes them, suggesting a greater genetic distance between these species than what has been previously observed between other marennine-producing species.

The Tetraconata (Pancrustacea) concept proposes that insects are more closely related to aquatic crustaceans than to terrestrial centipedes or millipedes. The question therefore arises whether insects have kept crustacean-specific genetic traits that could be targeted by specific toxins. Here we show that a toxin (nigritoxin), originally identified in a bacterial pathogen of shrimp, is lethal for organisms within the Tetraconata and non-toxic to other animals. X-ray crystallography reveals that nigritoxin possesses a new protein fold of the α/β type. The nigritoxin N-terminal domain is essential for cellular translocation and likely encodes specificity for Tetraconata. Once internalized by eukaryotic cells, nigritoxin induces apoptotic cell death through structural features that are localized in the C-terminal domain of the protein. We propose that nigritoxin will be an effective means to identify a Tetraconata evolutionarily conserved pathway and speculate that nigritoxin holds promise as an insecticidal protein. The Tetraconata concept suggests that insects and crustaceans may share evolutionarily conserved pathways. Here, the authors describe the animal tropism and structure-function relationship of nigritoxin, showing that this protein is lethal for insects and crustaceans but harmless to other animals.

Background In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FP). Results We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location. Conclusions Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions.

Vibrio nigripulchritudo is an emerging pathogen of farmed shrimp in New Caledonia and other regions in the Indo-Pacific. The molecular determinants of V. nigripulchritudo pathogenicity are unknown; however, molecular epidemiological studies have suggested that pathogenicity is linked to particular lineages. Here, we performed high-throughput sequencing-based comparative genome analysis of 16 V. nigripulchritudo strains to explore the genomic diversity and evolutionary history of pathogen-containing lineages and to identify pathogen-specific genetic elements. Our phylogenetic analysis revealed three pathogen-containing V. nigripulchritudo clades, including two clades previously identified from New Caledonia and one novel clade comprising putatively pathogenic isolates from septicemic shrimp in Madagascar. The similar genetic distance between the three clades indicates that they have diverged from an ancestral population roughly at the same time and recombination analysis indicates that these genomes have, in the past, shared a common gene pool and exchanged genes. As each contemporary lineage is comprised of nearly identical strains, comparative genomics allowed differentiation of genetic elements specific to shrimp pathogenesis of varying severity. Notably, only a large plasmid present in all highly pathogenic (HP) strains encodes a toxin. Although less/non-pathogenic strains contain related plasmids, these are differentiated by a putative toxin locus. Expression of this gene by a non-pathogenic V. nigripulchritudo strain resulted in production of toxic culture supernatant, normally an exclusive feature of HP strains. Thus, this protein, here termed ‘nigritoxin’, is implicated to an extent that remains to be precisely determined in the toxicity of V. nigripulchritudo.

The Pacific blue shrimp, Penaeus stylirostris , reared in New Caledonia, is economically important for the territory. However, since 2005, this sector has been facing huge larval mortalities occurring at all larval stages in hatcheries and for which no causes have yet been found. Microbial dysbiosis of the larvae are suspected as factors leading to larval death. To test this hypothesis, we monitored daily the larval health based on their survival rate and developmental stage and explored the active microbiota of the larvae by sequencing the V4 region of the 16S rRNA sequence. Richness proxies exhibited lower values in the unhealthy (high mortality rate) larval microbiota compared to the healthy one, highlighting a loss of microbial diversity in the unhealthy larvae. Venn diagram comparisons displayed specific taxa associated with a given larval stage and health with several taxa being vertically transmitted among multiple larval stages of a same health status as shown in the core microbiota. Besides, at the zoea stage, when the mortalities started, three ASVs related to Tenacibaculum , Microscilla and Bernardetia were specific of the unhealthy zoea suggesting that the zoea stage is crucial for dysbiosis induction. It is therefore probably at this stage that dysbiosis of the microbiota could evolve into larval pathobiome and lead to larval death. Thus, identifying specific lineages related to dysbiosis, being specific or correlated to unhealthy larvae or to the pathobiome, and demonstrating their pathogenicity, could ultimately support larval rearing by enabling targeted responses to mitigate their impact.