Compositional Dynamics of Gastrointestinal Tract Microbiomes Associated with Dietary Transition and Feeding Cessation in Lake Sturgeon Larvae

Abstract

Compromised nutritional conditions associated with dietary transitions and feeding cessation in the wild and during fish aquaculture operations are common and can impact growth and survival. These effects are especially prevalent during early ontogenetic stages. We quantified phenotypic and GI tract microbial community responses with an emphasis on protease-producing bacteria of lake sturgeon (Acipenser fulvescens) larvae, a species of aquacultural and conservational importance. To quantify responses associated with experimental food transition and feeding cessation, we performed a 36-day feeding experiment using two treatments: control and diet transition. However, larvae in the diet transition treatment failed to undergo transition and ceased feeding. Larvae in the diet transition treatment exhibited lower growth (total length and body weight) and survival than control larvae. Treatment had a greater effect than ontogenetic changes on taxonomic composition and diversity of the GI tract microbial community. Proteobacteria dominated the GI tract microbial community of the diet transition larvae whereas Firmicutes dominated the GI tracts of control larvae. Most of the 98 identified protease-producing isolates in both treatments were from genera Pseudomonas and Aeromonas: taxonomic groups that include known fish pathogens. Overall, failing to transition diets affected responses in growth and GI tract microbiome composition and diversity, with the later dysbiosis being an indicator of morbidity and mortality in larval lake sturgeon. Thus, microbiological interrogations can characterize responses to dietary regimes. The results can inform fish culturalists and microbiologists of the importance of dietary practices consistent with the establishment and maintenance of healthy GI tract microbiota and optimal growth during early ontogeny.

Keywords: aquaculture; diet transition; dysbiosis; feeding cessation; gut microbiome; high-throughput sequencing; lake sturgeon; microbiome; protease.

Figure 1

Mean cumulative survival (%; solid line) of lake sturgeon larvae from transition (TR) and control (CR) treatments with 95% CI (dashed line). Survival analyses were based on log-rank tests indicating that survival of fish in the TR treatment (0.527) was significantly lower compared to fish from the CR treatment (0.987) (chi-square value, χ² = 85.1, p-value < 0.01, df = 1).

Figure 2

Larval lake sturgeon morphometric data. (a) Mean total length (mm) by treatment, at each sampling point; (b) average body weight (g) of larvae from each feeding treatment. Significant differences in treatment mean test based on a Welch-t test (ns indicates non-significant; * p-value < 0.05; *** p-value < 0.001).

Figure 3

Measures of microbial community diversity including (a) inverse Simpson diversity index and (b) number of observed OTUs (taxa richness) for larval lake sturgeon from the control (CR) and transition (TR) feeding treatments at different sampling times.

Figure 4

(a) Relative abundance (%) of six most abundant bacterial phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria) found in the larval lake sturgeon GI tract for each treatment at different sampling times. The remaining taxa were assigned as others. (b) Relative abundance (%) of six most abundant bacterial phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia) found in aquatic samples. The remaining taxa were assigned as others.

Figure 5

Visualization of measures of microbial community beta diversity (Bray–Curtis distance) based on multivariate principal coordinates analyses (PCoA) plots showing variation in larval lake sturgeon GI tracts and water microbial community compositional differences among collections made at different times and between control (CR) and transition (TR) food treatments. Samples were taken from replicates of different treatments at three developmental stages (before transition at 14d pf, during transition week at 21 dpf, after transition at 36 dpf). (a) Plot based on Bray–Curtis distance axis 1 and 2, (b) plot based on Bray–Curtis distance axis 1 and 3, (c) plot based on Bray–Curtis distance axis 2 and 3.

Figure 6

Relative abundance of the 20 most prevalent annotated functional groups identified using KEGG orthologs pathway categorized at molecular-level 2 associated with lake sturgeon larval GI tract microbiome associated with two food treatments (control (CR) and transition (TR)) at each sampling point (a) 14 dpf; (b) 21 dpf; and (c) 36 dpf.

Figure 7

Distribution of protease-producing strains isolated from the gut of lake sturgeon fed different diet treatments. Larvae in control (CR) group were fed with live Artemia nauplii whereas treated (TR) group were fed with Artemia nauplii during the first 14 days post feedings (dpf) before transitioned to commercially grown bloodworm at 21 dpf. Isolates in bold text are microbial communities found larvae in the treated (TR) group and the remaining were from CR group. The maximum-likelihood phylogenetic tree was constructed using 16S rRNA sequence in MEGAX with general time reversible model and bootstrap support of 500 times. Protease-producers in both treatments were identified as Pseudomonas and Aeromonas with an isolate of Citrobacter sp. was identified in the control group. Pseudomonads and Aeromonads marked with an asterisk are species uniquely found in the TR group, and several are known to be associated with stress-related diseases in various fish species.