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 at quantifying ecological processes influencing community assembly in cod larvae and at elucidating 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 bacteria was highly dissimilar from the fish bacteria. Still, differences in the environmental bacteria strongly influenced the fish bacteria. 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 for 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.

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

“…The Phusion buffer HF, 0.015 units/µL of Phusion Hot Start II DNA polymerase, 1 µL of DNA template and dH20 to a total volume of 25 µL. The amplicon library was prepared as described previously (30). In brief, we used the SequalPrep Normalisation plate (96) kit (Invitrogen) to normalise and purify PCR products and the Illumina Nextera XT Index kits (FC-131-2001 andFC-131-2004) for amplicon indexing.…”

Key Drivers of Ecological Assembly in the Hindgut of Atlantic Cod (Gadus morhua) when Fed with a Macroalgal Supplemented diet – How Robust Is the Gut to Taxonomic Perturbation?

“…However, host pressures in the juvenile or adult cod gut are not widely described, a study design similar to the zebrafish study but with Atlantic cod could help elucidate these factors. Research on the Atlantic cod larval phase has suggested that selective pressures in the gut, associated with host intestinal development combined with stochastic pressures, shaped the gut microbiota 47,48 . Ecological theory has been loosely applied to manipulate the microbiome of Atlantic cod larvae by changing the tank water to improve survival rates using selection 49 .…”

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

“…The amplicon library preparation and processing of the Illumina sequencing data was performed as described by Vestrum et al [28]. In short, for the first stage of amplification, the reactions were run for 38 cycles for water samples and 40 cycles for cod larval samples (98 • C 15 s, 55 • C 20 s, 72 • C 20 s), with 0.3 µM of each primer, 0.25 mM of each dNTP, 2 mM of MgCl 2 , 12 µM of BSA, glycerol (10%), Phusion Hot Start II High-Fidelity DNA Polymerase and reaction buffer from Thermo Scientific in a total volume of 20 µL.…”