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

ABSTRACT 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.

Transcriptome profiling reveals exposure to predicted end-of-century ocean acidification as a stealth stressor for Atlantic cod larvae

Ocean acidification (OA), a direct consequence of increasing atmospheric CO2 concentration dissolving in ocean waters, is impacting many fish species. Little is known about the molecular mechanisms underlying the observed physiological impacts in fish. We used RNAseq to characterize the transcriptome of 3 different larval stages of Atlantic cod (Gadus morhua) exposed to simulated OA at levels (1179 µatm CO2) representing end-of-century predictions compared to controls (503 µatm CO2), which were shown to induce tissue damage and elevated mortality in G. morhua. Only few genes were differentially expressed in 6 and 13 days-post-hatching (dph) (3 and 16 genes, respectively), during a period when maximal mortality as a response to elevated pCO2 occurred. At 36 dph, 1413 genes were differentially expressed, most likely caused by developmental asynchrony between the treatment groups, with individuals under OA growing faster. A target gene analysis revealed only few genes of the universal and well-defined cellular stress response to be differentially expressed. We thus suggest that predicted ocean acidification levels constitute a “stealth stress” for early Atlantic cod larvae, with a rapid breakdown of cellular homeostasis leading to organismal death that was missed even with an 8-fold replication implemented in this study.

Annual and spatial variability in endo- and ectoparasite infections of North Sea cod (Gadus morhua Linnaeus, 1758) larvae, post-larvae and juveniles

A parasitological investigation was performed on a total of 5380 Atlantic cod larvae, post-larvae and small juveniles sampled from the North Sea during a period of five years. The copepod Caligus elongatus (Von Nordmann, 1832) and the nematode Hysterothylacium aduncum (Rudolphi, 1802) were found at a relatively high prevalence of infection (4.6% and 5.2%, respectively). The infection by both parasites showed annual and spatial variability. C. elongatus showed a higher prevalence in 1992 compared to the following years, whereas the prevalence of H. aduncum increased from 1992 to 2001.We observed a relation between parasite distribution and parameters such as latitude and water depth. Adult digeneans (Lecithaster gibbosus and Derogenes varicus) and larval cestodes were also found with lower infection rates. Since changes of infection levels coincided with increasing North Sea water temperature in the studied period, it is hypothesized that temperature may affect parasite population levels. However, it is likely that other environmental factors may contribute to the observed variations. Absence of infection intensities higher than one nematode per fish in small larvae and post-larvae suggests that host survival may be affected by a high infection pressure. The relatively high levels of infection in the younger stages of cod, and the annual/spatial variability of these infections should be considered in the understanding of the early life dynamics of the species.