Skeletonema marinoi ecotypes show specific habitat-related responses to fluctuating light supporting high potential for growth under photobioreactor light regime.

Diatoms are a diverse group of phytoplankton usually dominating areas characterized by rapidly shifting light conditions. Because of their high growth rates and interesting biochemical profile, their biomass is considered for various commercial applications. This study aimed at identifying strains with superior growth in a photobioreactor (PBR) by screening the natural intraspecific diversity of ecotypes isolated from different habitats. We investigated the effect of PBR light fluctuating on a millisecond scale (FL, simulating the light in a PBR) on 19 ecotypes of the diatom Skeletonema marinoi isolated from the North Sea-Baltic Sea area. We compare growth, pigment ratios, phylogeny, photo-physiological variables and photoacclimation strategies between all strains and perform qPCR and absorption spectra analysis on a subset of strains. Our results show that the ecotypes responded differently to FL, and have contrasting photo-physiological and photoprotective strategies. The strains from Kattegat performed better in FL, and shared common photoacclimation and photoprotection strategies that are the results of adaptation to the specific light climate of the Kattegat area. The strains that performed better with FL conditions had a high light (HL)-acclimated phenotype coupled with unique nonphotochemical quenching features. Based on their characteristics, three strains were identified as good candidates for growth in PBRs.

Effect of Food Amounts on Larval Performance, Bacteriome and Molecular Immunologic Development during First-Feeding Culture of European Eel.

Production of European eel offspring has become a reality, but liquid diets during larval culture hold new challenges. This study focused on increasing food amounts without compromising well-being or healthy larvae-bacteria interactions. First-feeding larvae were fed two food amounts (Low = 0.5 mL food/L water vs. High = 1.5 mL food/L water) until 30 days post-hatch (dph). Results indicated that ~75% of larvae ingested the diet in both treatments, but upregulation of a stress/repair-related gene (hsp90) on 25 and 30 dph indicated nutritional inadequacy. Larvae fed a High amount of food were 3.68% bigger, while larvae in the Low-food group showed 45.2% lower gut fullness and upregulated expression of the gene encoding the "hunger hormone" ghrelin (ghrl), indicating signs of starvation. The High-food group larvae exhibited a healthier bacteriome with a higher abundance of potentially beneficial orders (Lactobacillales and Bacillales), whereas the Low-food group showed more potentially harmful orders (Vibrionales, Rhodobacterales, and Alteromonadales). While survival was initially lower in the High-food group, both treatments had comparable survival by the end of the experiment. In conclusion, feeding European eel larvae with High food amounts seemed beneficial, supported by increased gut fullness, reduced ghrl expression (no starvation), enhanced growth, and the presence of a healthier bacteriome.

The impact of phage treatment on bacterial community structure is minor compared to antibiotics.

Phage treatment is suggested as an alternative to antibiotics; however, there is limited knowledge of how phage treatment impacts resident bacterial community structure. When phages induce bacterial lysis, resources become available to the resident community. Therefore, the density of the target bacterium is essential to consider when investigating the effect of phage treatment. This has never been studied. Thus, we invaded microcosms containing a lake-derived community with Flavobacterium columnare strain Fc7 at no, low or high densities, and treated them with either the bacteriophage FCL-2, the antibiotic Penicillin or kept them untreated (3 × 3 factorial design). The communities were sampled over the course of one week, and bacterial community composition and density were examined by 16S rDNA amplicon sequencing and flow cytometry. We show that phage treatment had minor impacts on the resident community when the host F. columnare Fc7 of the phage was present, as it caused no significant differences in bacterial density α- and ß-diversity, successional patterns, and community assembly. However, a significant change was observed in community composition when the phage host was absent, mainly driven by a substantial increase in Aquirufa. In contrast, antibiotics induced significant changes in all community characteristics investigated. The most crucial finding was a bloom of γ-proteobacteria and a shift from selection to ecological drift dominating community assembly. This study investigated whether the amount of a bacterial host impacted the effect of phage treatment on community structure. We conclude that phage treatment did not significantly affect the diversity or composition of the bacterial communities when the phage host was present, but introduced changes when the host was absent. In contrast, antibiotic treatment was highly disturbing to community structure. Moreover, higher amounts of the bacterial host of the phage increased the contribution of stochastic community assembly and resulted in a feast-famine like response in bacterial density in all treatment groups. This finding emphasises that the invader density used in bacterial invasion studies impacts the experimental reproducibility. Overall, this study supports that phage treatment is substantially less disturbing to bacterial communities than antibiotic treatments.

Phage therapy minimally affects the water microbiota in an Atlantic salmon (Salmo salar) rearing system while still preventing infection.

Excessive usage of antibiotics threatens the bacterial diversity in the microbiota of animals. An alternative to antibiotics that has been suggested to not disturb the microbiota is (bacterio)phage therapy. In this study, we challenged germ-free and microbially colonized yolk sac fry of Atlantic salmon with Flavobacterium columnare and observed that the mere presence of a microbiota protected the fish against lethal infection. We then investigated the effect of phage- or oxytetracycline treatment on fish survival and rearing water bacterial community characteristics using 16S rRNA gene amplicon sequencing. Phage treatment led to an increased survival of F. columnare-challenged fish and reduced the relative amounts of the pathogen in the water microbiota. In the absence of F. columnare, phage treatment did not affect the composition or the α-diversity of the rearing water microbiota. In the presence of the phage's host, phage treatment induced minor changes to the bacterial community composition, without affecting the α-diversity. Surprisingly, oxytetracycline treatment had no observable effect on the water microbiota and did not reduce the relative abundance of F. columnare in the water. In conclusion, we showed that phage treatment prevents mortality while not negatively affecting the rearing water microbiota, thus suggesting that phage treatment may be a suitable alternative to antibiotics. We also demonstrated a protective effect of the microbiota in Atlantic salmon yolk sac fry.

The stability and composition of the gut and skin microbiota of Atlantic salmon throughout the yolk sac stage.

The bacterial colonization of newly hatched fish is important for the larval development and health. Still, little is known about the ontogeny of the early microbiota of fish. Here, we conducted two independent experiments with yolk sac fry of Atlantic salmon that were (1) either reared conventionally, with the eggs as the only source for bacteria (egg-derived microbiota; EDM) or (2) hatched germ-free and re-colonized using lake water (lake-derived microbiota; LDM). First, we characterized the gut and skin microbiota at 6, 9, and 13 weeks post hatching based on extracted RNA. In the second experiment, we exposed fry to high doses of either a fish pathogen or a commensal bacterial isolate and sampled the microbiota based on extracted DNA. The fish microbiota differed strongly between EDM and LDM treatments. The phyla Proteobacteria, Bacteroidetes, and Actinobacteria dominated the fry microbiota, which was found temporarily dynamic. Interestingly, the microbiota of EDM fry was more stable, both between replicate rearing flasks, and over time. Although similar, the skin and gut microbiota started to differentiate during the yolk sac stage, several weeks before the yolk was consumed. Addition of high doses of bacterial isolates to fish flasks had only minor effects on the microbiota.

Exploring bacterial community composition and immune gene expression of European eel larvae (Anguilla anguilla) in relation to first-feeding diets.

European eel (Anguilla anguilla) is a commercially important species for fisheries and aquaculture in Europe and the attempt to close the lifecycle in captivity is still at pioneering stage. The first feeding stage of this species is characterized by a critical period between 20 to 24 days post hatch (dph), which is associated with mortalities, indicating the point of no return. We hypothesized that this critical period might also be associated with larvae-bacterial interactions and the larval immune status. To test this, bacterial community composition and expression of immune and stress-related genes of hatchery-produced larvae were explored from the end of endogenous feeding (9 dph) until 28 dph, in response to three experimental first-feeding diets (Diet 1, Diet 2 and Diet 3). Changes in the water bacterial community composition were also followed. Results revealed that the larval stress/repair mechanism was activated during this critical period, marked by an upregulated expression of the hsp90 gene, independent of the diet fed. At the same time, a shift towards a potentially detrimental larval bacterial community was observed in all dietary groups. Here, a significant reduction in evenness of the larval bacterial community was observed, and several amplicon sequence variants belonging to potentially harmful bacterial genera were more abundant. This indicates that detrimental larvae-bacteria interactions were likely involved in the mortality observed. Beyond the critical period, the highest survival was registered for larvae fed Diet 3. Interestingly, genes encoding for pathogen recognition receptor TLR18 and complement component C1QC were upregulated in this group, potentially indicating a higher immunocompetency that facilitated a more successful handling of the harmful bacteria that dominated the bacterial community of larvae on 22 dph, ultimately leading to better survival, compared to the other two groups.

Aquaculture rearing systems induce no legacy effects in Atlantic cod larvae or their rearing water bacterial communities.

The microbial rearing quality influences the survival of marine larvae. Microbially matured water treatment systems (MMS) provide a more favourable rearing water microbiome than flow-through systems (FTS). It has previously been hypothesised, but not investigated, that initial rearing in MMS leaves a protective legacy effect in Atlantic cod larvae (Gadus morhua). We tested this hypothesis through a crossover 2 × 2 factorial experiment varying the rearing water treatment system (MMS vs FTS) and the microbial carrying capacity (+ /- added organic matter). At 9 days post-hatching, we switched the rearing water treatment system. By comparing switched and unswitched rearing tanks, we evaluated if legacy effects had been established in the larvae or their surrounding rearing water bacterial community. We analysed the bacterial communities with flow cytometry and 16S rRNA gene sequencing. We found no evidence that the initial rearing condition left a legacy effect in the communities by evaluating the bacterial community diversity and structure. Instead, the present rearing condition was the most important driver for differences in the rearing water microbiota. Furthermore, we found that MMS with high microbial carrying capacity appeared to seed a stable bacterial community to the rearing tanks. This finding highlights the importance of keeping a similar carrying capacity between the inlet and rearing water. Moreover, we reject the hypothesis that the initial rearing condition leaves a protective legacy effect in larvae, as the larval survival and robustness were linked to the present rearing condition. In conclusion, our results highlight the importance of maintaining a beneficial microbial rearing environment from hatching and throughout the larval rearing period.

Stochastic variation in gut bacterial community affects reproductive rates in the water flea Daphnia magna.

It is well-documented that perturbation of the gut bacterial community can influence the reproductive rates of the host. Less is known about how natural ecological processes can change the bacterial composition in the gut and how such changes influence the reproductive rate of the host. Here, we provide novel experimental insights into such processes using the clonally reproducing water flea, Daphnia magna. A total of 20 replicate cultures were reared for 5 weeks (Phase 1) to allow for divergence of bacterial communities through stochastic processes (i.e. drift, founder effects, and/or colonization). Duplicate cultures created from each of these were reared for 21 days (Phase 2) while recording reproductive rates. There was a significant repeatability in reproductive rates between these duplicates, suggesting that divergence of the bacterial communities during Phase 1 translated into reproductive rate effects during Phase 2. This was further supported by significant differences in the relative abundance of gut bacteria (investigated by amplicon sequencing of a part of the 16S rRNA gene) between cultures with high and low reproductive rate in Phase 2. These results are consistent with the hypothesis that stochastic processes can cause natural variation in the bacterial composition in the gut, which in turn affect host reproductive rates.

A novel gnotobiotic experimental system for Atlantic salmon (Salmo salar L.) reveals a microbial influence on mucosal barrier function and adipose tissue accumulation during the yolk sac stage.

Gnotobiotic models have had a crucial role in studying the effect that commensal microbiota has on the health of their animal hosts. Despite their physiological and ecological diversity, teleost fishes are still underrepresented in gnotobiotic research. Moreover, a better understanding of host-microbe interactions in farmed fish has the potential to contribute to sustainable global food supply. We have developed a novel gnotobiotic experimental system that includes the derivation of fertilized eggs of farmed and wild Atlantic salmon, and gnotobiotic husbandry of fry during the yolk sac stage. We used a microscopy-based approach to estimate the barrier function of the skin mucus layer and used this measurement to select the derivation procedure that minimized adverse effects on the skin mucosa. We also used this method to demonstrate that the mucus barrier was reduced in germ-free fry when compared to fry colonized with two different bacterial communities. This alteration in the mucus barrier was preceded by an increase in the number of cells containing neutral mucosubstances in the anterior segment of the body, but without changes in the number of cells containing acidic substances in any of the other segments studied along the body axis. In addition, we showed how the microbial status of the fry temporarily affected body size and the utilization of internal yolk stores during the yolk sac stage. Finally, we showed that the presence of bacterial communities associated with the fry, as well as their composition, affected the size of adipose tissue. Fry colonized with water from a lake had a larger visceral adipose tissue depot than both conventionally raised and germ-free fry. Together, our results show that this novel gnotobiotic experimental system is a useful tool for the study of host-microbe interactions in this species of aquacultural importance.

Nanocosm: a well plate photobioreactor for environmental and biotechnological studies.

Phytoplankton are key primary producers at the bottom of the aquatic food chain. They are a highly diverse group of organisms essential for the functioning of our ecosystems and because of their characteristics, their biomass is considered for various commercial applications. A full appreciation of their abundance, diversity and potential is only feasible by using systems that enable simultaneous testing of strains and/or variables in a fast and easy way. A major bottleneck is the lack of a cost-effective method with the capacity for complex experimental set-ups that enable fast and reproducible screening and analysis. In this study, we present nanocosm, a versatile LED-based micro-scale photobioreactor (PBR) that allows simultaneous testing of multiple variables such as temperature and light within the same plate. Every well can be independently controlled for intensity, temporal variation and light type (RGB, white, UV). We show that our systems guarantee homogeneous conditions because of controlled temperature and evaporation and adjustments for light crosstalk. By ensuring controlled environmental conditions the nanocosm is suitable for running factorial experimental designs where each well can be used as an independent micro-PBR. To validate culture performances, we assess well-to-well reproducibility and our results show minimal well-to-well variability for all the conditions tested. Possible modes of operation and application are discussed together with future development of the system.

Temporal dynamics of carbon sequestration in coastal North Atlantic fjord system as seen through dissolved organic matter characterisation.

Fjord systems in higher latitudes are unique coastal water ecosystems that facilitate the study of dissolved organic matter (DOM) dynamics from surface to deeper waters. The current work was undertaken in the Trondheim fjord characterized by North Atlantic waters, and compared DOM fractions from three depths - surface (3 m), intermediate (225 m) and deep (440 m) in four seasons, from late spring to winter in 2017. The high-resolution mass spectrometry data showed that DOM composition varies significantly in different seasons rather than in different depths in the fjord systems. The bacterial community composition was comparable except at spring surface and summer intermediate depths. Bacterial production was minimal below the euphotic layer, even with sufficient availability of inorganic nutrients. The bacterial production rate in the surface waters was about 7 times and over 50 times higher than that of the aphotic zone in the winter and the summer seasons, respectively. The surface heterotrophic microbial communities might have rapidly consumed the available labile DOM, with the production of more refractory DOM limiting bacterial production in aphotic layers. The greater number of CRAM-like formulas determined in the surface waters compared to other depths supports our hypothesis. The refractory DOM sequestered in the water column may either be exported into sediments attached to particulate matter and marine gels, or may escape into the atmosphere as carbon dioxide/monoxide during the photochemical oxidation pathways, suggesting that it is involved in climate change scenarios.

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater.

In this study, nitrification before and after abrupt cross-transfer in salinity was investigated in two moving bed biofilm reactors inoculated with nitrifying cultures that had adaptation to freshwater (FR) and seawater salinities (SR). FR and SR MBRRs were exposed to short and long term cross-transfer in salinity, and the functional capacity of nitrifying microbial communities was quantified by the estimation of ammonia and nitrite oxidation rates. Salinity induced successions were evaluated before and after salinity change by deep sequencing of 16S rRNA gene amplicons and statistical analysis. The bacterial community structure was characterized and Venn diagrams were included. The results indicated that after salinity cross-transfer, the FR was not significantly recovered at seawater salinity whereas SR showed high resistance to stress caused by low-salt. Succession and physiological plasticity were the main mechanisms of the long-term adaption of the nitrifying communities exposed to abrupt salinity changes. Independently of salinity, some nitrifiers presented high physiological plasticity towards salinity and were very successful at both zero and full seawater salinity. SR culture is robust and suitable inoculum for ammonium removal from recirculating aquaculture systems and industrial wastewaters with variable and fast salinity changes. Our findings contradict the current perspective of the significance of salinity on the structure of nitrifying communities.

Commensal and Opportunistic Bacteria Present in the Microbiota in Atlantic Cod (Gadus morhua) Larvae Differentially Alter the Hosts' Innate Immune Responses.

The roles of host-associated bacteria have gained attention lately, and we now recognise that the microbiota is essential in processes such as digestion, development of the immune system and gut function. In this study, Atlantic cod larvae were reared under germ-free, gnotobiotic and conventional conditions. Water and fish microbiota were characterised by 16S rRNA gene analyses. The cod larvae's transcriptional responses to the different microbial conditions were analysed by a custom Agilent 44 k oligo microarray. Gut development was assessed by transmission electron microscopy (TEM). Water and fish microbiota differed significantly in the conventional treatment and were dominated by different fast-growing bacteria. Our study indicates that components of the innate immune system of cod larvae are downregulated by the presence of non-pathogenic bacteria, and thus may be turned on by default in the early larval stages. We see indications of decreased nutrient uptake in the absence of bacteria. The bacteria also influence the gut morphology, reflected in shorter microvilli with higher density in the conventional larvae than in the germ-free larvae. The fact that the microbiota alters innate immune responses and gut morphology demonstrates its important role in marine larval development.

The effect of periodic disturbances and carrying capacity on the significance of selection and drift in complex bacterial communities.

Understanding how periodical disturbances affect the community assembly processes is vital for predicting temporal dynamics in microbial communities. However, the effect of dilutions as disturbances are poorly understood. We used a marine bacterial community to investigate the effect of disturbance (+/-) and carrying capacity (high/low) over 50 days in a dispersal-limited 2 × 2 factorial study in triplicates, with a crossover in the disturbance regime between microcosms halfway in the experiment. We modelled the rate of change in community composition between replicates and used this rate to quantify selection and ecological drift. The disturbed communities increased in Bray-Curtis similarity with 0.011 ± 0.0045 (Period 1) and 0.0092 ± 0.0080 day-1 (Period 2), indicating that selection dominated community assembly. The undisturbed communities decreased in similarity at a rate of -0.015 ± 0.0038 day-1 in Period 1 and were stable in Period 2 at 0.00050 ± 0.0040 day-1, suggesting drift structured community assembly. Interestingly, carrying capacity had minor effects on community dynamics. This study is the first to show that stochastic effects are suppressed by periodical disturbances resulting in exponential growth periods due to density-independent biomass loss and resource input. The increased contribution of selection as a response to disturbances implies that ecosystem prediction is achievable.

Bacterial community assembly in Atlantic cod larvae (Gadus morhua): contributions of ecological processes and metacommunity structure.

Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host-microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host-microbe interactions and improved fish health and survival.

A salty start: Brackish water start-up as a microbial management strategy for nitrifying bioreactors with variable salinity.

Nitrifying biofilms developed in brackish water are reported to be more robust to salinity changes than freshwater biofilms. This makes them a promising strategy for water treatment systems with variable salinity, such as recirculating aquaculture systems for Atlantic salmon. However, little is known about the time required for nitrification start-up in brackish water or the microbial community dynamics. To investigate the development of nitrifying biofilms at intermediate salinity, we compared the startup of moving bed biofilm reactors with virgin carriers in brackish- (12‰ salinity) and freshwater. After 60 days, the brackish water biofilm had half the nitrification capacity of the freshwater biofilm, with a less diverse microbial community, lower proportion of nitrifiers, and a significantly different nitrifying community composition. Nitrosomonas and Nitrosospira-like bacteria were the main ammonia oxidizers in the brackish water biofilms, whereas Nitrosomonas was dominant in freshwater biofilms. Nitrotoga was the dominant nitrite oxidizer in both treatments. Despite the lower nitrification capacity in the brackish water treatment, the low ammonia and nitrite concentration with rapidly increasing nitrate concentration indicated that complete nitrification was established in both reactors within 60 days. The results suggest that biofilms develop nitrification in brackish water in comparable time as in freshwater, and brackish start-up can be a strategy for bioreactors with varying salinity.

Biofilms remember: Osmotic stress priming as a microbial management strategy for improving salinity acclimation in nitrifying biofilms.

With increasing freshwater scarcity and greater use of seawater, fluctuating salinities are becoming common in water treatment systems. This can be challenging for salinity-sensitive processes like nitrification, especially in recirculating aquaculture systems (RAS), where maintaining nitrification efficiency is crucial for fish health. This study was undertaken to determine if prior exposure to seawater (priming) could improve nitrification in moving bed biofilm reactors (MBBR) under salinity increase from freshwater to seawater. The results showed that seawater-primed freshwater MBBRs had less than 10% reduction in nitrification activity and twice the ammonia oxidation capacity of the unprimed bioreactors after seawater transfer. The primed biofilms had different microbial community composition but the same nitrifying taxa, suggesting that priming promoted physiological adaptation of the nitrifiers. Priming may also have strengthened the extrapolymeric matrix protecting the nitrifiers. In MBBRs started up in brackish water (12‰ salinity), seawater priming had no significant impact on the nitrification activity and the microbial community composition. These bioreactors were inherently robust to salinity increase, likely because they were already primed to osmotic stress by virtue of their native salinity of 12‰. The results show that osmotic stress priming is an effective strategy for improving salinity acclimation in nitrifying biofilms and can be applied to water treatment systems where salinity variations are expected.

Nitrifying biofilms deprived of organic carbon show higher functional resilience to increases in carbon supply.

In nitrifying biofilms, the organic carbon to ammonia nitrogen (C/N) supply ratio can influence resource competition between heterotrophic and nitrifying bacteria for oxygen and space. We investigated the impact of acute and chronic changes in carbon supply on inter-guild competition in two moving bed biofilm reactors (MBBR), operated with (R1) and without (R0) external organic carbon supply. The microbial and nitrifying community composition of the reactors differed significantly. Interestingly, acute increases in the dissolved organic carbon inhibited nitrification in R1 ten times more than in R0. A sustained increase in the carbon supply decreased nitrification efficiency and increased denitrification activity to a greater extent in R1, and also increased the proportion of potential denitrifiers in both bioreactors. The findings suggest that autotrophic biofilms subjected to increases in carbon supply show higher nitrification and lower denitrification activity than carbon-fed biofilms. This has significant implications for the design of nitrifying bioreactors. Specifically, efficient removal of organic matter before the nitrification unit can improve the robustness of the bioreactor to varying influent quality. Thus, maintaining a low C/N ratio is important in nitrifying biofilters when acute carbon stress is expected or when anoxic activity (e.g. denitrification or H2S production) is undesirable, such as in recirculating aquaculture systems (RAS).

Comparative transcriptomics reveals domestication-associated features of Atlantic salmon lipid metabolism.

Domestication of animals imposes strong targeted selection for desired traits but can also result in unintended selection due to new domestic environments. Atlantic salmon (Salmo salmar) was domesticated in the 1970s and has subsequently been selected for faster growth in systematic breeding programmes. More recently, salmon aquaculture has replaced fish oils (FOs) with vegetable oils (VOs) in feed, radically changing the levels of essential long-chain polyunsaturated fatty acids (LC-PUFAs). Our aim here was to study the impact of domestication on metabolism and explore the hypothesis that the shift to VO diets has unintentionally selected for a domestication-specific lipid metabolism. We conducted a 96-day feeding trial of domesticated and wild salmon fed diets based on FOs, VOs or phospholipids, and compared transcriptomes and fatty acids in tissues involved in lipid absorption (pyloric caeca) and lipid turnover and synthesis (liver). Domesticated salmon had faster growth and higher gene expression in glucose and lipid metabolism compared to wild fish, possibly linked to differences in regulation of circadian rhythm pathways. Only the domesticated salmon increased expression of LC-PUFA synthesis genes when given VOs. This transcriptome response difference was mirrored at the physiological level, with domesticated salmon having higher LC-PUFA levels but lower 18:3n-3 and 18:2n-6 levels. In line with this, the VO diet decreased growth rate in wild but not domesticated salmon. Our study revealed a clear impact of domestication on transcriptomic regulation linked to metabolism and suggests that unintentional selection in the domestic environment has resulted in evolution of stronger compensatory mechanisms to a diet low in LC-PUFAs.

Gut Microbiota of Migrating Wild Rabbit Fish (Siganus guttatus) Larvae Have Low Spatial and Temporal Variability.

We investigated the gut microbiota of rabbit fish larvae at three locations in Vietnam (ThuanAn-northern, QuangNam-intermediate, BinhDinh-southern sampling site) over a three-year period. In the wild, the first food for rabbit fish larvae remains unknown, while the juveniles and adults are herbivores, forming schools near the coasts, lagoons, and river mouths, and feeding mainly on filamentous algae. This is the first study on the gut microbiota of the wild fish larvae and with a large number of individuals analyzed spatially and temporally. The Clostridiales order was the most predominant in the gut, and location-by-location alpha diversity showed significant differences in Chao-1, Hill number 1, and evenness. Analysis of beta diversity indicated that the location, not year, had an effect on the composition of the microbiota. In 2014, the gut microbiota of fish from QuangNam was different from that in BinhDinh; in 2015, the gut microbiota was different for all locations; and, in 2016, the gut microbiota in ThuanAn was different from that in the other locations. There was a time-dependent trend in the north-south axis for the gut microbiota, which is considered to be tentative awaiting larger datasets. We found limited variation in the gut microbiota geographically and in time and strong indications for a core microbiome. Five and fifteen OTUs were found in 100 and 99% of the individuals, respectively. This suggests that at this life stage the gut microbiota is under strong selection due to a combination of fish-microbe and microbe-microbe interactions.