Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont

Abstract

Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (F_ST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.

Keywords: 16S RNA; bacterioplankton; environmental microbiology; fish; genotype; gill; metagenomics; microbial ecology; population genetics; transcription.

FIG 1

Relative abundance of the phyla detected in active gill bacterial communities samples based on 16S rRNA gene transcripts, according to the water type and the genetic cluster of the fish found at each sampling site. “GC” stands for “Genetic cluster”.

FIG 2

Principal coordinates analyses (PCoA) of gill bacterial communities samples, based on Bray-Curtis distances. Ellipses represent groups with default confidence intervals of 0.05. In (a) samples are colored according to their genetic cluster of origin. “GC” stands for “Genetic cluster”. In (b) samples are colored according to their water type of origin. The genetic clusters GC1 and GC3 are not shown in (b) as they were not found in both water types.

FIG 3

Bacterial biomarkers (at the ASV level) specific to one of the four genetic clusters (a) and (b) or one of the two water types (c) and (d). In (a) and (c) the relative abundance of these biomarkers in each genetic cluster (a) or water type (c) is shown on heatmaps where each column is a gill bacterial community sample and each row represents one of the biomarker ASV (colors at the right end of each row represent biomarker phylogeny at the Class level). Darker shades of orange indicate higher relative abundance of the ASV in the sample. In (b) and (d) the relative abundance of the biomarkers in each genetic cluster (b) or water type (d) is shown on stacked barplots. In these plots, biomarker ASVs are colored according to their phylogeny (Class level).

FIG 4

(a) Relative abundance of the main phyla detected in bacterioplankton samples. In (b) and (c): Constrained analysis of principal coordinates (CAP) on bacterioplanktonic communities (b) and on gill bacterial community samples (c). Each data point in the CAP plots represents a sample, and their color and shape correspond to the water type at the sampling site. The results of permutation tests for CAP under reduced model (5 environmental variables) are shown in red in the upper left corner of each plot. “df res” stands for residual degrees of freedom and “***” for “P value < 0.001”. “Al” stands for dissolved aluminum (μg L⁻¹), “DOC” for the concentration of dissolved organic carbon (mg L⁻¹), “Silicate” for the concentration of silicates (mg L⁻¹), “Chl_a” for the concentration of chlorophyll a (μg L⁻¹), “Cond.” for the conductivity (μS).

FIG 5

Linear mixed-effects modeling analysis of the explicative variables potentially associated to gill bacterial community 16S rRNA gene transcripts. The 4 following explicative variables (transformed in distance matrices) are included in the global model (a) used for predicting dissimilarity values: bacterioplankton 16S rRNA gene transcripts (BC distance), genotypic distances between hosts (F_ST), geographic distances between sites (Euclidean distance), and the ensemble of the 34 environmental parameters measured in this study (Euclidean distance). Each row of the gray diagram in (b) corresponds to one of the models tested, and colored circles represent the elements that were included in the models. The upper three rows of the diagram represent significant models, with Akaike scores superior to the null (random) model (fourth row), while the lower four rows correspond to models with low explicative power. Linear correlation plots (c), (d), (e), and (f) for each of the 4 explicative variables considered in the model represent the linear correlation between the normalized distance/dissimilarity of each variable with the gill microbiome Bray-Curtis (BC) dissimilarity, when assessed separately outside of the LMER model. The linear correlations with BC gill bacterial community dissimilarity are displayed with the following variables: (c) BC bacterioplankton dissimilarity, (d) F_ST genotypic distances, (e) Euclidean distances of geographical distances, (f) Euclidean distances of environmental parameters.

FIG 6

(a) Map of the 12 sampling sites including information on the water type and the genetic cluster of fish found at each site. “GC” stands for “Genetic cluster”. (b) Observed values of the environmental parameters commonly used to differentiate black from white water. “Al” refers to dissolved aluminum, “DOC” refers to dissolved organic carbon.