Changes in the Microbiome of Mariculture Feed Organisms after Treatment with a Potentially Probiotic Strain of Phaeobacter inhibens.

The Phaeobacter genus has been explored as probiotics in mariculture as a sustainable strategy for the prevention of bacterial infections. Its antagonistic effect against common fish pathogens is predominantly due to the production of the antibacterial compound tropodithietic acid (TDA), and TDA-producing strains have repeatedly been isolated from mariculture environments. Despite many in vitro trials targeting pathogens, little is known about its impact on host-associated microbiomes in mariculture. Hence, the purpose of this study was to investigate how the addition of a TDA-producing Phaeobacter inhibens strain affects the microbiomes of live feed organisms and fish larvae. We used 16S rRNA gene sequencing to characterize the bacterial diversity associated with live feed microalgae (Tetraselmis suecica), live feed copepod nauplii (Acartia tonsa), and turbot (Scophthalmus maximus) eggs/larvae. The microbial communities were unique to the three organisms investigated, and the addition of the probiotic bacterium had various effects on the diversity and richness of the microbiomes. The structure of the live feed microbiomes was significantly changed, while no effect was seen on the community structure associated with turbot larvae. The changes were seen primarily in particular taxa. The Rhodobacterales order was indigenous to all three microbiomes and decreased in relative abundance when P. inhibens was introduced in the copepod and turbot microbiomes, while it was unaffected in the microalgal microbiome. Altogether, the study demonstrates that the addition of P. inhibens in higher concentrations, as part of a probiotic regime, does not appear to cause major imbalances in the microbiome, but the effects were specific to closely related taxa.IMPORTANCE This work is an essential part of the risk assessment of the application of roseobacters as probiotics in mariculture. It provides insights into the impact of TDA-producing Phaeobacter inhibens on the commensal bacteria related to mariculture live feed and fish larvae. Also, the study provides a sequencing-based characterization of the microbiomes related to mariculture-relevant microalga, copepods, and turbot larvae.

Mycosporine-Like Amino Acids (MAAs) in Zooplankton.

Organisms have different adaptations to avoid damage from ultraviolet radiation and one such adaptation is the accumulation of mycosporine-like amino acids (MAAs). These compounds are common in aquatic taxa but a comprehensive review is lacking on their distribution and function in zooplankton. This paper shows that zooplankton MAA concentrations range from non-detectable to ~13 µg mgDW-1. Copepods, rotifers, and krill display a large range of concentrations, whereas cladocerans generally do not contain MAAs. The proposed mechanisms to gain MAAs are via ingestion of MAA-rich food or via symbiotic bacteria providing zooplankton with MAAs. Exposure to UV-radiation increases the concentrations in zooplankton both via increasing MAA concentrations in the phytoplankton food and due to active accumulation. Concentrations are generally low during winter and higher in summer and females seem to deposit MAAs in their eggs. The concentrations of MAAs in zooplankton tend to increase with altitude but only up to a certain altitude suggesting some limitation for the uptake. Shallow and UV-transparent systems tend to have copepods with higher concentrations of MAAs but this has only been shown in a few species. A high MAA concentration has also been shown to lead to lower UV-induced mortality and an overall increased fitness. While there is a lot of information on MAAs in zooplankton we still lack understanding of the potential costs and constraints for accumulation. There is also scarce information in some taxa such as rotifers as well as from systems in tropical, sub(polar) areas as well as in marine systems in general.

Catching the complexity of salmon-louse interactions.

The study of host-parasite relationships is an integral part of the immunology of aquatic species, where the complexity of both organisms has to be overlayed with the lifecycle stages of the parasite and immunological status of the host. A deep understanding of how the parasite survives in its host and how they display molecular mechanisms to face the immune system can be applied for novel parasite control strategies. This review highlights current knowledge about salmon and sea louse, two key aquatic animals for aquaculture research worldwide. With the aim to catch the complexity of the salmon-louse interactions, molecular information gleaned through genomic studies are presented. The host recognition system and the chemosensory receptors found in sea lice reveal complex molecular components, that in turn, can be disrupted through specific molecules such as non-coding RNAs.

Attachment and antimicrobial susceptibility of bacterial associates of zooplanktonic copepod: Lesson for environmental safety.

The present study emphasizes on the antimicrobial susceptibility of different bacterial strains isolated from the external body surface of a commonly found zooplanktonic copepod (Heliodiaptomus viduus, Gurney, 1916) inhabiting both in fresh and brackish water bodies of Midnapore (West and East) Districts, West Bengal, India. Out of 62 bacterial isolated strains, 38 isolates were identified as Gram-positive while the remaining 24 isolates were found to be Gram-negative. Antimicrobial properties of all those bacterial strains were determined by Vitek 2 compact system using minimum inhibitory concentration (MIC) values. All isolated bacterial strains had exhibited differential susceptibilities against some selected antibiotics. Field Emission Scanning Electron Microscope (FE-SEM) analysis revealed the considerable association of bacteria on the cuticular body parts of the studied zooplankton. The outcomes of the present research are expected to enable health professionals in identifying two major problems -1) bacterial association with zooplankton which is so far mostly considered as a novel source of food for fish in aquatic ecosystems. 2) Selection of antibiotics as treatment measure because of the pathogenic effects of zooplankton associated bacteria on human being. This unattended arena of research is also supposed to evoke a new dimension not only because of bacteria-zooplankton interactions but also on undertaking of judicious strategies to find out proper ways and means to make the surface water suitable for the utilization by the common peoples (minimising bacterial contamination) in the context of human health and environmental safety.

Effects of the vertically transmitted microsporidian Facilispora margolisi and the parasiticide emamectin benzoate on salmon lice (Lepeophtheirus salmonis).

BACKGROUND: Microsporidia are highly specialized, parasitic fungi that infect a wide range of eukaryotic hosts from all major taxa. Infections cause a variety of damaging effects on host physiology from increased stress to death. The microsporidian Facilispora margolisi infects the Pacific salmon louse (Lepeophtheirus salmonis oncorhynchi), an economically and ecologically important ectoparasitic copepod that can impact wild and cultured salmonids. RESULTS: Vertical transmission of F. margolisi was demonstrated by using PCR and in situ hybridization to identify and localize microsporidia in female L. salmonis and their offspring. Spores and developmental structures of F. margolisi were identified in 77% of F1 generation copepods derived from infected females while offspring from uninfected females all tested negative for the microsporidia. The transcriptomic response of the salmon louse to F. margolisi was profiled at both the copepodid larval stage and the pre-adult stage using microarray technology. Infected copepodids differentially expressed 577 transcripts related to stress, ATP generation and structural components of muscle and cuticle. The infection also impacted the response of the copepodid to the parasiticide emamectin benzoate (EMB) at a low dose of 1.0 ppb for 24 h. A set of 48 transcripts putatively involved in feeding and host immunomodulation were up to 8-fold underexpressed in the F. margolisi infected copepodids treated with EMB compared with controls or either stressor alone. Additionally, these infected lice treated with EMB also overexpressed 101 transcripts involved in stress resistance and signalling compared to the other groups. In contrast, infected pre-adult lice did not display a stress response, suggesting a decrease in microsporidian virulence associated with lice maturity. Furthermore, copepodid infectivity and moulting was not affected by the microsporidian infection. CONCLUSIONS: This study demonstrated that F. margolisi is transmitted vertically between salmon louse generations and that biological impacts of infection differ depending on the stage of the copepod host. The infection caused significant perturbations of larval transcriptomes and therefore must be considered in future studies in which impacts to host development and environmental factors are assessed. Fitness impacts are probably minor, although the interaction between pesticide exposure and microsporidian infection merits further study.

Seasonal variation in the copepod gut microbiome in the subtropical North Atlantic Ocean.

Characterisation of marine copepod gut microbiome composition and its variability provides information on function of marine food webs, biogeochemical cycles and copepod health. Copepod gut microbiomes were investigated quarterly over two years at the Bermuda Atlantic Time-series Station in the North Atlantic Subtropical Gyre, while assessing seasonal shifts in stable and transient communities. Microbial communities were analysed using amplicon sequencing targeting the bacterial 16S rRNA V3-V4 region and the cyanobacterial ntcA gene. Persistent bacterial groups belonging to Firmicutes, Bacteroidetes and Actinobacteria were present in the copepod guts throughout the year, and showed synchronous changes, suggesting a link to variability in copepod nutritional content. The gut communities were separate from those in the seawater, suggesting the copepod gut hosts long-term, specialized communities. Major temporal variations in the gut communities during the early winter and spring, specifically a high relative abundance of Synechococcus (up to 65%), were attributed to bacterioplankton shifts in the water column, and copepod grazing on these picoplanktonic cyanobacteria. The presence of obligate and facultative anaerobes, including Clostridiales year round, suggests that anaerobic bacterial processes are common in these dynamic microhabitats in the oligotrophic open ocean.

Natural resource landscapes of a marine bacterium reveal distinct fitness-determining genes across the genome.

Heterotrophic bacteria exploit diverse microhabitats in the ocean, from particles to transient gradients. Yet the degree to which genes and pathways can contribute to an organism's fitness on such complex and variable natural resource landscapes remains poorly understood. Here, we determine the gene-by-gene fitness of a generalist saprophytic marine bacterium (Vibrio sp. F13 9CS106) on complex resources derived from its natural habitats - copepods (Apocyclops royi) and brown algae (Fucus vesiculosus) - and as reference substrates, glucose and the polysaccharide alginate, derived from brown algal cell walls. We find that resource complexity strongly buffers fitness costs of mutations, and that anabolic rather than catabolic pathways are more stringently required, likely due to functional redundancy in the latter. Moreover, while carbohydrate-rich algae requires several synthesis pathways, protein-rich Apocyclops does not, suggesting this ancestral habitat for Vibrios is a replete medium with metabolically redundant substrates. We also identify a candidate fitness trade-off for algal colonization: deletion of mshA increases mutant fitness. Our results demonstrate that gene fitness depends on habitat composition, and suggest that this generalist uses distinct resources in different natural habitats. The results further indicate that substrate replete conditions may lead to relatively relaxed selection on catabolic genes.

Vibrio tapetis from wrasse used for ectoparasite bio-control in salmon farming: phylogenetic analysis and serotyping.

So-called 'cleaner fish', including various wrasse (Labridae) species, have become increasingly popular in Norwegian salmon farming in recent years for biocontrol of the salmon louse Lepeophtheirus salmonis. Cleaner fish mortalities in salmon farms are, however, often high. Various bacterial agents are frequently associated with episodes of increased cleaner fish mortality, and Vibrio tapetis is regularly cultured from diseased wrasse. In the present study, we investigated the genetic relationships among 54 V. tapetis isolates (34 from wrasse species) by multilocus sequence analysis (MLSA; rpoD, ftsZ, pyrH, rpoA and atpA). In the resulting phylogenetic tree, all wrasse isolates belonged to sub-clusters within V. tapetis subsp. tapetis. Slide agglutination testing further confirmed the complete dominance amongst these isolates of 4 O-antigen serotypes, designated here as V. tapetis subsp. tapetis serotypes O1, O3, O4 and O5, respectively. A pilot challenge trial using serotypes O3, O4 and O5 did not indicate high pathogenicity towards ballan wrasse Labrus bergylta, thus questioning the role of V. tapetis as a primary pathogen of this fish species.

Survival, growth performance and immune capacity of the juvenile lined seahorse Hippocampus erectus fed with rifampicin-treated copepods.

Gastrointestinal disease is one of the most serious diseases in cultured seahorse juveniles. Treatment with antimicrobials of live food (i.e. copepods and Artemia) that is used to feed the juveniles may be a promising measure to alleviate the occurrence of gastrointestinal disease. However, relevant investigations are rare. In the present study, we first investigated the antimicrobial efficacies on bacteria within copepods that were treated with 4 antimicrobials, including 3 antibiotics (i.e. enrofloxacin hydrochloride, oxytetracycline and rifampicin [RFP]) that are approved for use in aquaculture and 1 disinfectant (i.e. povidone iodine). We then assessed the effects of copepods treated with the antimicrobial that had the best antimicrobial efficacy on survival, growth performance and immune capacity of juvenile lined seahorses Hippocampus erectus. The results showed that RFP had the best antimicrobial efficacy on both Pseudoalteromonas spp. and Vibrio spp., 2 dominant bacteria with potential pathogenicity within the copepods; the proper concentration of RFP was 6 mg l-1. Moreover, H. erectus juveniles fed with RFP-treated copepods demonstrated an improved survivorship and immune capacity and had a lower abundance of pathogenic bacteria within their gastrointestinal tracts compared to juveniles fed with untreated copepods. These results suggest that treating live food with RFP is a potential measure for reducing the incidence of gastrointestinal disease in seahorse juveniles.

Intoxicated copepods: ingesting toxic phytoplankton leads to risky behaviour.

Understanding interactions between harmful algal bloom (HAB) species and their grazers is essential for determining mechanisms of bloom proliferation and termination. We exposed the common calanoid copepod, Temora longicornis to the HAB species Alexandrium fundyense and examined effects on copepod survival, ingestion, egg production and swimming behaviour. A. fundyense was readily ingested by T. longicornis and significantly altered copepod swimming behaviour without affecting copepod survival or fitness. A. fundyense caused T. longicornis to increase their swimming speed, and the straightness of their path long after the copepods had been removed from the A. fundyense treatment. Models suggest that these changes could lead to a 25-56% increase in encounter frequency between copepods and their predators. This work highlights the need to determine how ingesting HAB species alters grazer behaviour as this can have significant impacts on the fate of HAB toxins in marine systems.

Are natural reservoirs important for cholera surveillance? The case of an outbreak in a Brazilian estuary.

UNLABELLED: Paranaguá Bay is one of the largest estuarine systems on the Southern Brazilian coast. The only recorded cholera outbreak in this region since the early 20th century occurred in 1999 and resulted in 467 cases and at least three reported deaths in a population of approx. 150 000 people. This short communication reports historical, unpublished data related to that outbreak. Water, zooplankton and bivalve samples were collected and evaluated using direct fluorescence assay to determine whether Vibrio cholerae serogroups O1 and O139 were present in the estuarine system at that time. Most of the water (83%) and zooplankton samples (75%) were positive for V. cholerae O1, while V. cholerae O139 was not detected. Shellfish (Mytella sp.) were also positive for V. cholerae O1. These results indicate that the estuary, including biological vectors such as copepods and bivalves, comprise an important reservoir of V. cholerae O1 and a probable waterborne pathway for the disease, in addition to contamination with untreated sewage. SIGNIFICANCE AND IMPACT OF THE STUDY: Despite most of the cholera cases that occurred in Brazil during the 7th pandemic were located in the northern areas of the country, a significant outbreak in Paranaguá, an estuary in the south coast, resulted in at least three deaths in 1999. We report here the detection of Vibrio cholerae O1 in water, zooplankton and bivalve samples during the outbreak, using direct fluorescence assay as an alternative method for the traditional plate culture employed at the time by the Brazilian Sanitary Agency. Results demonstrate that aquatic natural reservoirs comprise a potential route of transmission of cholera, in addition to untreated sewage and routine monitoring is recommended.

Impacts of temperature and crowding on sex ratio, fecundity and Wolbachia infection intensity in the copepod, Mesocyclops thermocyclopoides.

Wolbachia are a group of intracellular bacteria that cause reproductive alterations in arthropods. Here, we describe the effects of two environmental factors (crowding and temperature) on phenotypic expression of feminization, the host's fecundity and Wolbachia infection intensity among life cycle stages in the naturally Wolbachia-infected copepod, Mesocyclops thermocyclopoides. The copepod was first found to be co-infected with Wolbachia A- and B-supergroups Wolbachia strains based on wsp primers. The relative Wolbachia infection intensity within individuals was determined using quantitative real-time PCR and was significantly higher in the B-supergroup than in the A-supergroup. Experimental results of temperature effect on bacterial density in each developmental stage revealed a significant decrease in Wolbachia infection intensity following exposure to high temperature (37°C) in both sexes and implied that Wolbachia might survive in room temperature (25°C) better than in high temperature. Experimental results of crowding effects on Wolbachia infection intensity suggested a negative correlation between copepod nauplii and Wolbachia infection intensity. No effect of rearing temperature on the sex ratio was reported although the fecundity was significantly decreased by high temperature. The results showed that Wolbachia infection intensity to be correlated with crowding conditions and was decreased following exposure of elevated temperature.

Investigations on the role of the salmon louse, Lepeophtheirus salmonis (Caligidae), as a vector in the transmission of Aeromonas salmonicida subsp. salmonicida.

A bacteria-parasite challenge model was used to study the role of sea lice, Lepeophtheirus salmonis (Copepoda), as a vector of Aeromonas salmonicida subsp. salmonicida. Three hypotheses were tested: (i) L. salmonis can acquire A. salmonicida subsp. salmonicida via water bath exposure; (ii) L. salmonis can acquire the bacteria via parasitizing infected Atlantic salmon, Salmo salar; and (iii) L. salmonis can transmit the bacteria to naïve Atlantic salmon via parasitism. Adult L. salmonis exposed to varying A. salmonicida subsp. salmonicida suspensions (10(1) -10(7)  cells mL(-1) ) for 1.0, 3.0 or 6.0 h acquired the bacteria externally (12.5-100%) and internally (10.0-100%), with higher prevalences associated with the highest concentrations and exposures. After exposure to 10(7)  cells mL(-1) , viable A. salmonicida subsp. salmonicida could be isolated from the external carapace of L. salmonis for 120 h. Lepeophtheirus salmonis also acquired the bacteria externally and internally from parasitizing infected fish. Bacterial transmission was observed only when L. salmonis had acquired the pathogen internally via feeding on 'donor fish' and then by parasitizing smaller (<50 g) 'naive' fish. Under specific experimental conditions, L. salmonis can transfer A. salmonicida subsp. salmonicida via parasitism; however, its role as a mechanical or biological vector was not defined.

Nitrogen-fixing bacteria associated with copepods in coastal waters of the North Atlantic Ocean.

The community composition of N2 -fixing microorganisms (diazotrophs) was investigated in copepods (primarily Acartia spp.) in parallel to that of seawater in coastal waters off Denmark (Øresund) and New England, USA. The unicellular cyanobacterial diazotroph UCYN-A was detected from seawater and full-gut copepods, suggesting that the new N contributed by UCYN-A is directly transferred to higher trophic levels in these waters. Deltaproteobacterial and Cluster 3 nifH sequences were detected in > 1 µm seawater particles and full-gut copepods, suggesting that they associate with copepods primarily via feeding. The dominant communities in starved copepods were Vibrio spp. and related Gammaproteobacteria, suggesting they represent the most permanent diazotroph associations in the copepods. N2 fixation rates were up to 3.02 pmol N copepod(-1) day(-1). Although at a typical copepod density in estuarine waters, these volumetric rates are low; considering the small size of a copepod, these mesozooplanktonic crustaceans may serve as hotspots of N2 fixation, at 12.9-71.9 µmol N dm(-3) copepod biomass day(-1). Taken together, diazotroph associations range from more permanent attachments to copepod feeding on some groups. Similar diazotroph groups detected on the eastern and western Atlantic Ocean suggest that these associations are a general phenomenon and play a role in the coastal N cycles.

Limnoithona sinensis as refuge for bacteria: protection from UV radiation and chlorine disinfection in drinking water treatment.

In this study, we tested the potential of Limnoithona sinensis to provide its attached bacteria refuge against disinfection. The experimental results indicated that in water devoid of zooplankton, both UV radiation and chlorine disinfection significantly decreased the viability of free-living bacteria. In the presence of L. sinensis, however, the attached bacteria could survive and rapidly recover from disinfection. This demonstrated that L. sinensis provided protection from external damage to various aquatic bacteria that were attached to its body. The surviving bacteria remained on L. sinensis after disinfection exposure, which enabled a rapid increase in the bacterial population followed by their subsequent release into the surrounding water. Compared with UV radiation, chlorine disinfection was more effective in terms of inactivating attached bacteria. Both UV radiation and chlorine disinfection had little effect in terms of preventing the spread of undesirable bacteria, due to the incomplete inactivation of the bacteria associated with L. sinensis.

Distribution, diversity and density of wolbachial infections in cladocerans and copepods from Thailand.

Species of the genus Wolbachia comprise a group of Rickettsia-like, maternally-inherited bacteria that cause several reproductive alterations in arthropod hosts. The best known are cytoplasmic incompatibility and feminization. Here, the first systematic surveys of wolbachial infections in cladocerans and copepods from six geographic regions of Thailand, including Northern, Northeastern, Western, Central, Eastern and Southern are reported. Using gene amplification assays with wsp and groE primers, wolbachiae were detected in 239 (4 spp.) of 1885 (57 spp.) copepods and cladocerans from all regions of Thailand surveyed. Screening results obtained with wsp primers or groE primers were similar in all cases. The presence of wolbachiae was only detected in copepods, not in cladocerans. Sex ratio analyses of the progeny of two species of copepods, Mesocyclops aspericornis and Mesocyclops thermocyclopoides, naturally or artificially infected with wolbachiae showed infection causes feminization (female-bias). The relative density if infection in naturally infected populations of three copepod species, M. thermocyclopoides, Heliodiaptomus elegans and Neodiaptomus blachei, were determined using real-time quantitative PCR assay based on the wsp gene. The density of wolbachiae in M. thermocyclopoides was significantly higher than in the other two species. These results suggest that wolbachial infections are distributed throughout Thailand, and that possibly the natural occurrence of these in copepods may be due to their predation on mosquito larvae. This apparent novel biology may have importance as a genetic drive system for control of vector borne diseases in the future.

The diversity of microsporidia in parasitic copepods (Caligidae: Siphonostomatoida) in the Northeast Pacific Ocean with description of Facilispora margolisi n. g., n. sp. and a new Family Facilisporidae n. fam.

Three distinct microsporidia were identified from parasitic copepods in the northeast Pacific Ocean. Sequencing and phylogenetic analysis of a partial small subunit ribosomal RNA gene (SSU rDNA) sequence identified a genetically distinct variety of Desmozoon lepeophtherii from Lepeophtheirus salmonis on cultured Atlantic salmon Salmo salar, and this was confirmed by transmission electron microscopy. Phylogenetic analysis resolved the SSU rDNA sequence of the second organism in a unique lineage that was most similar to microsporidia from marine and brackish water crustaceans. The second occurred in L. salmonis on Atlantic, sockeye Oncorhynchus nerka, chum O. keta and coho O. kisutch salmon, in Lepeophtheirus cuneifer on Atlantic salmon, and in Lepeophtheirus parviventris on Irish Lord Hemilepidotus hemilepidotus. Replication occurred by binary fission during merogony and sporogony, diplokarya were not present, and all stages were in contact with host cell cytoplasm. This parasite was identified as Facilispora margolisi n. g., n. sp. and accommodated within a new family, the Facilisporidae n. fam. The third, from Lepeophtheirus hospitalis on starry flounder Platichthys stellatus, was recognized only from its unique, but clearly microsporidian SSU rDNA sequence. Phylogenetic analysis placed this organism within the clade of microsporidia from crustaceans.

Bacterial communities in the gut of the freshwater copepod Eudiaptomus gracilis.

Eudiaptomus gracilis is the most abundant member of the zooplankton, plays a key role in the food web of Lake Balaton (Hungary). In the present study the composition of bacterial communities of this copepod was investigated based on cultivation and molecular cloning. The cultivated bacterial strains from the gut homogenate samples of Eudiaptomus gracilis belonged to four different clades: Firmicutes, Actinobacteria, Bacteriodetes and Proteobacteria. Clone library showed high species diversity, Firmicutes, Actinobacteria, Proteobacteria, representatives of Deinococcus-Thermus lineage and Cyanobacteria were detected. The isolated strains were very effective in degradation of different biopolymers. Many of the detected bacteria are known as opportunistic human or fish pathogens (Pseudomonas spp., Aeromonas spp., Chryseobacterium sp. and Staphylococcus sp.).

Proximity ligation strategy for the genomic reconstruction of microbial communities associated with the ectoparasite Caligus rogercresseyi.

The sea louse Caligus rogercresseyi has become one of the main constraints for the sustainable development of salmon aquaculture in Chile. Although this parasite's negative impacts are well recognized by the industry, some novel potential threats remain unnoticed. The recent sequencing of the C. rogercresseyi genome revealed a large bacterial community associated with the sea louse, however, it is unknown if these microorganisms should become a new focus of sanitary concern. Herein, chromosome proximity ligation (Hi-C) coupled with long-read sequencing were used for the genomic reconstruction of the C. rogercresseyi microbiota. Through deconvolution analysis, we were able to assemble and characterize 413 bacterial genome clusters, including six bacterial genomes with more than 80% of completeness. The most represented bacterial genome belonged to the fish pathogen Tenacibacullum ovolyticum (97.87% completeness), followed by Dokdonia sp. (96.71% completeness). This completeness allowed identifying 21 virulence factors (VF) within the T. ovolyticum genome and four antibiotic resistance genes (ARG). Notably, genomic pathway reconstruction analysis suggests putative metabolic complementation mechanisms between C. rogercresseyi and its associated microbiota. Taken together, our data highlight the relevance of Hi-C techniques to discover pathogenic bacteria, VF, and ARGs and also suggest novel host-microbiota mutualism in sea lice biology.