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The constant increase in aquaculture production has led to extensive use of antibiotics as a means to prevent and treat diseases, with adverse implications on the environment, animal health and commensal microbes. Gut microbes are important for the host proper functioning, thus evaluating such impacts is highly crucial. Examining the antibiotic impact on gut segments with different physiological roles may provide insight into their effects on these microhabitats. Hence, we evaluated the effect of feed-administrated antibiotics on the composition and metabolic potential of the gut microbiome in the European seabass, an economically important aquaculture species. We used quantitative PCR to measure bacterial copy numbers, and amplicon sequencing of the 16S rRNA gene to describe the composition along the gut, after 7-days administration of two broad-range antibiotic mixtures at two concentrations. While positive correlation was found between antibiotic concentration and bacterial abundance, we showed a differential effect of antibiotics on the composition along the gut, highlighting distinct impacts on these microbial niches. Moreover, we found an increase in abundance of predicted pathways related to antibiotic-resistance. Overall, we show that a high portion of the European seabass gut microbiome persisted, despite the examined antibiotic intake, indicating high stability to perturbations.

The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment. Animals and plants host diverse microbial communities that are vital for their survival. In fact, the host organisms and their associated ‘microbiome’ are so closely linked that they are often described as a single entity: the holobiont unit. This suggests that when the host adapts to cope with stressful conditions, similar changes should also occur in its microbiome. Fish are unable to maintain a stable body temperature and can be greatly affected by temperature fluctuations. Some fish are better able to tolerate cold conditions than others, but it was not known if their gut microbes are similarly affected by changes in temperature. To investigate, Kokou et al. selectively bred tropical blue tilapia to create families of fish that could either tolerate the cold well, or that were highly sensitive to the cold. The gut microbiomes of cold-resistant fish were different from the cold-sensitive ones, even though the fish lived in the same tank. Moreover, the gut microbiomes of the cold-tolerant fish showed higher resilience to temperature changes than the microbes in the guts of the cold-sensitive fish. It remains to be determined whether the response of the microbiome directly affects how its host fish responds to temperature changes. However, the results presented by Kokou et al. show that there are links between how the host and its microbes adapt to environmental stress. As well as helping us to understand how holobionts evolved, this knowledge could also potentially be applied broadly in clinical sciences or agriculture, for example to select for efficient crops.

MYC transcription factors have critical roles in facilitating a variety of cellular functions that have been highly conserved among species during evolution. However, despite circumstantial evidence for an involvement of MYC in animal osmoregulation, mechanistic links between MYC function and osmoregulation are missing. Mozambique tilapia ( Oreochromis mossambicus ) represents an excellent model system to study these links because it is highly euryhaline and highly tolerant to osmotic (salinity) stress at both the whole organism and cellular levels of biological organization. Here, we utilize an O. mossambicus brain cell line and an optimized vector-based CRISPR/Cas9 system to functionally disrupt MYC in the tilapia genome and to establish causal links between MYC and cell functions, including cellular osmoregulation. A cell isolation and dilution strategy yielded polyclonal myca (a gene encoding MYC) knockout (ko) cell pools with low genetic variability and high gene editing efficiencies (as high as 98.2%). Subsequent isolation and dilution of cells from these pools produced a myca ko cell line harboring a 1-bp deletion that caused a frameshift mutation. This frameshift functionally inactivated the transcriptional regulatory and DNA-binding domains predicted by bioinformatics and structural analyses. Both the polyclonal and monoclonal myca ko cell lines were viable, propagated well in standard medium, and differed from wild-type cells in morphology. As such, they represent a new tool for causally linking myca to cellular osmoregulation and other cell functions.

Nile tilapia (Oreochromis niloticus) is the world's most widely cultured fish species. Therefore, its nutritional physiology is of great interest from an aquaculture perspective. Studies conducted on several fish species, including tilapia, demonstrated the beneficial effects of dietary salt supplementation on growth; however, the mechanism behind these beneficial effects is still not fully understood. The fish intestine is a complex system, with functions, such as nutrient absorption, ion equilibrium and acid-base balance that are tightly linked and dependent on each other's activities and products. Ions are the driving force in the absorption of feed components through pumps, transporters and protein channels. In this study, we examined the impact of 5% increase in dietary NaCl on protein, lipid, ash and dry matter digestibility, as well as on the expression of intestinal peptide transporters (PepTs) and ion pumps (Na+/K+-ATPase, V-H+-ATPase, N+/H+-Exchanger) in Nile tilapia. In addition, effects on the gut microbiome were evaluated. Our results show that dietary salt supplementation significantly increased digestibility of all measured nutritional components, peptide transporters expression and ion pumps activity. Moreover, changes in the gut microbial diversity were observed, and were associated with lipid digestibility and Na+/K+-ATPase expression.

Optimal concentrations of three anesthetics for use with juvenile cobia (Rachycentron canadum) were determined using time-to-recovery and hematological datasets. Buffered MS-222, clove oil and 2-phenoxyethanol (2-PE) were examined. Juvenile cobia were exposed to three concentrations of each anesthetic at 24 °C. Based on time to recovery, optimal doses for MS-222 was determined as 120-mg L−1, that for 2-PE, 0.4-mL L−1 and, for clove oil, 5-mL L−1. The hematological response of cobia to anesthesia included quantification of whole blood pH, pCO2, pO2, and Ca2+, K+, Na+, Cl−, hematocrit and glucose. Irrespective of anesthetic employed, cobia expressed metabolic acidosis, with changes in blood pH (p < 0.001) being matched by increases (p < 0.001) in pCO2. Anesthesia tended to increase blood Na+, hematocrit, pO2, Ca2+, and K+ although differential responses between anesthetics were recorded, suggesting different modes of action. A combination of recovery and hematological data indicated that when anesthesia is necessary, MS-222 represents the sedative of choice.

The physiological response of Mozambique and Nile tilapia transferred from fresh to brackish (15 ppt) water was compared during a one-week time course. Response in the pituitary was measured by the gene expression pattern of prolactin (PRL I), growth hormone (GH), and calcium-sensing receptor (CaSR), while the response in the gills was measured by the gene expression pattern of the prolactin receptor (PRL-R), Na + /K + /2Cl − cotransporter (NKCC) and Na + /Cl − cotransporter (NCC), and by activity and expression of Na + /K + -ATPase (NKA). The time-course curves of plasma osmolality levels indicate a rapid elevation 24 h after transfer, which later decreased and maintained at stable level. PRL I expression decreased in both species, but with stronger response in the Nile tilapia, while no differences were found in the slightly elevated levels of GH mRNA. The branchial response demonstrated a faster up-regulation of NKA and NKCC in the Mozambique tilapia, but similar levels after a week, while Nile tilapia had stronger and constant down-regulation of NCC. The time-course response of the measured osmoregulatory parameters indicate that 24 h after transfer is a critical time point for brackish-water adaptation. The differences in responses to saltwater challenge between Mozambique and Nile tilapia shown in this study may be associated with the differences in saltwater tolerance between these two tilapiine species.

Recent studies have revealed that the major genes of the mammalian sex determination pathway are also involved in sex determination of fish. Several studies have reported QTL in various species and strains of tilapia, regions contributing to sex determination have been identified on linkage groups 1, 3, and 23. Genes contributing to sex-specific mortality have been detected on linkage groups 2, 6, and 23. To test whether the same genes might control sex determination in mammals and fishes, we mapped 11 genes that are considered putative master key regulators of sex determination: Amh, Cyp19, Dax1, Dmrt2, Dmrta2, Fhl3l, Foxl2, Ixl, Lhx9, Sf1, and Sox8. We identified polymorphisms in noncoding regions of these genes and genotyped these sites for 90 individuals of an F2 mapping family. Mapping of Dax1 joined LG16 and LG21 into a single linkage group. The Amh and Dmrta2 genes were mapped to two distinct regions of LG23. The Amh gene was mapped 5 cM from UNH879 within a QTL region for sex determination and 2 cM from UNH216 within a QTL region for sex-specific mortality. Dmrta2 was mapped 4 cM from UNH848 within another QTL region for sex determination. Cyp19 was mapped to LG1 far from a previously reported QTL region for sex determination on this chromosome. Seven other candidate genes mapped to LG4, -11, -12, -14, and -17.

The term core microbiome describes microbes that are consistently present in a particular habitat. If the conditions in that habitat are highly variable, core microbes may also be considered to be ecological generalists. However, little is known about whether metabolic competition and microbial interactions influence the ability of some microbes to persist in the core microbiome while others cannot. We investigated microbial communities at three sites in the guts of European seabass under four dietary conditions. We identified generalist core microbial populations in each gut site that are shared across fish, present under multiple diets and persistent over time. We found that core microbes tend to show synergistic growth in co-culture, and low levels of predicted and validated metabolic competition. Within core microbial species, we found high levels of intraspecific variability and strain-specific habitat specialization. Thus, both intraspecific variability and interspecific facilitation may contribute to the ecological stability of the animal core microbiome. Core microbial populations across distinct gut habitats and diets were identified in a European seabass model indicating that microbial generalists persist and coexist by maintaining low competition, beneficial interactions and strain variability.

Abstract Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.

In accordance with their tropical origin, the optimal water temperature for most tilapia species is between 25 and 28  ° C. The lethal temperature varies as a function of environmental effects, individual fish histories and genetic effects; however, the genetic basis of cold tolerance in tilapia has not been investigated in detail. Blue tilapia ( Oreochromis aureus ) is considered as one of the most cold-tolerant tilapia species, and, in this study, we have used a fish from a three-generation selective breeding program for enhanced cold tolerance. Four crosses within and between resistant and sensitive fish were used in this study. Forty families were challenged for cold tolerance, and a strong maternal effect was observed in two consecutive experiments. Expression patterns of the mitochondrial ATP6 gene were strongly correlated with cold tolerance; however, an analysis that applied an individual animal model restricted maximum likelihood on a three-generation pedigree, implies that an epigenetic effect rather than mitochondrial inheritance is the main source of the observed maternal effect. This study demonstrates that maternal effects can play a significant role in the inheritance of cold tolerance and that maternally-transferred genetic components should be targeted when adaptation to low temperature is studied in tilapia.