Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus)

Abstract

Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.

Fig. 1

Average bacterial profiles of all animals sampled over 52 weeks. Bacterial genera representing more than 2% of entire 16S community. Genera coloured according to key. Time increases towards to extremities of the x axis from the pre-deployment control (0 PDC) at the centre. Green = land-based culture (LBC). Blue = sea-based container culture (SBCC)

Fig. 2

Three-dimensional non-metric multidimensional scaling (NMDS) of all gut samples. Unweighted non-metric multidimensional scaling (NMDS) using the Bray-Curtis measure of dissimilarity over three axes. Stress = 0.130. a Coloured according to sample group. b Coloured according to culture environment

Fig. 3

Alpha diversity measures of all sample groups. a Shannon’s measure of species diversity across all sample groups. b Chao1 estimate of species richness across all sample groups. Green = land-based culture (LBC). Blue = sea-based container culture (SBCC). Environmental comparison “LBC” (including day 0) and “SBCC” represent combined data of all corresponding groups. Boxes labelled with groups that are significantly different. **p < =0.01, ***p < =0.001

Fig. 4

Standard effect size of mean-nearest-taxon index (ses.MNTD) indicating phylogenetic clustering of sequence variants. Standard deviation of mean nearest taxon index (MNTD) from random model. Ses.MNTD values >2 indicate phylogenetic overdispersion of taxa, 2 < & > −2 indicate stochastic distribution across phylogeny, < −2 indicate phylogenetic clustering. Green = land-based culture (LBC). Blue = sea-based container culture (SBCC). Environmental comparison “LBC” (including day 0) and “SBCC” represent combined data of all corresponding groups. Boxes labelled with groups that are significantly different. ***p < =0.001

Fig. 5

Changes to gut microbiota in the presence of Homarus gammarus nudivirus (HgNV). a Shannon’s measure of species diversity across healthy and infected individuals sampled at 104 weeks. b Chao1 estimate of species richness. c Bacterial genera representing more than 2% of entire 16S community. Yellow = HgNV-negative samples (n = 3). Pink = HgNV-positive samples (n = 6). Genera coloured according to key