Ecological and Ontogenetic Components of Larval Lake Sturgeon Gut Microbiota Assembly, Successional Dynamics, and Ecological Evaluation of Neutral Community Processes

Abstract

Gastrointestinal (GI) or gut microbiotas play essential roles in host development and physiology. These roles are influenced partly by the microbial community composition. During early developmental stages, the ecological processes underlying the assembly and successional changes in host GI community composition are influenced by numerous factors, including dispersal from the surrounding environment, age-dependent changes in the gut environment, and changes in dietary regimes. However, the relative importance of these factors to the gut microbiota is not well understood. We examined the effects of environmental (diet and water sources) and host early ontogenetic development on the diversity of and the compositional changes in the gut microbiota of a primitive teleost fish, the lake sturgeon (Acipenser fulvescens), based on massively parallel sequencing of the 16S rRNA gene. Fish larvae were raised in environments that differed in water source (stream versus filtered groundwater) and diet (supplemented versus nonsupplemented Artemia fish). We quantified the gut microbial community structure at three stages (prefeeding and 1 and 2 weeks after exogenous feeding began). The diversity declined and the community composition differed significantly among stages; however, only modest differences associated with dietary or water source treatments were documented. Many taxa present in the gut were over- or underrepresented relative to neutral expectations in each sampling period. The findings indicate dynamic relationships between the gut microbiota composition and host gastrointestinal physiology, with comparatively smaller influences being associated with the rearing environments. Neutral models of community assembly could not be rejected, but selectivity associated with microbe-host GI tract interactions through early ontogenetic stages was evident. The results have implications for sturgeon conservation and aquaculture production specifically and applications of microbe-based management in teleost fish generally.IMPORTANCE We quantified the effects of environment (diet and water sources) and host early ontogenetic development on the diversity of and compositional changes in gut microbial communities based on massively parallel sequencing of the 16S rRNA genes from the GI tracts of larval lake sturgeon (Acipenser fulvescens). The gut microbial community diversity declined and the community composition differed significantly among ontogenetic stages; however, only modest differences associated with dietary or water source treatments were documented. Selectivity associated with microbe-host GI tract interactions through early ontogenetic stages was evident. The results have implications for lake sturgeon and early larval ecology and survival in their natural habitat and for conservation and aquaculture production specifically, as well as applications of microbe-based management in teleost fish generally.

Keywords: community ecology; diet; freshwater fish; gut microbiota; ontogeny.

FIG 1

Bacterial composition of different communities identified from lake sturgeon larval gut (A) and environmental samples (B). (A) Relative abundance of dominant bacterial phyla found in lake sturgeon larval gut microbiota across treatments and during different developmental stages. Only the dominant phyla are shown in the bar chart (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria). The remaining taxa were assigned to “other.” The four treatment groups are denoted S, Sp, GW, and GWp, as defined in the text. (B) Relative abundance of dominant bacterial phyla found in environmental microbiota. Only the dominant phyla are shown in the bar chart (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Verrucomicrobia). The remaining taxa were assigned to “other.”

FIG 2

Linear discriminant analysis (LDA) effect size (LEfSe) analyses identify OTUs in fish communities that respond significantly to feeding progression (from prefeeding and 1 week and 2 weeks after active feeding). Relative abundance was significant when P was <0.05 and the logarithmic LDA score was ≥2.0.

FIG 3

Estimates of alpha diversity for lake sturgeon gut microbial communities from all treatments across all developmental stages. The differences in the gut microbiota composition across the treatments at the different ages were evaluated using a two-way ANOVA. Each point indicates the mean value of the diversity index, colored by the different treatments. The four treatment groups are denoted S, Sp, GW, and GWp, as defined in the text. (A) Alpha diversity in the gut microbiota at each time point, as measured by the inverse Simpson diversity index. (B) OTU richness based on the number of taxa observed in the gut microbiota from all treatments and times.

FIG 4

Principal-coordinate analysis among microbial communities originating from the lake sturgeon larval gut across all four different treatments at three developmental stages (prefeeding and 1 week and 2 weeks after active feeding initiation) (A) and from environmental samples, including water, detritus, and Artemia fish (B). These environmental samples were collected at times corresponding to the times of fish sampling. Axes represent the first two principal coordinates maximizing the variance in the data (PCoA1 and PCoA2). Dissimilarity was calculated based on Bray-Curtis distances. The fish gut microbial communities from the four treatment groups are denoted S, Sp, GW, and GWp, as defined in the text. Water-GW and Water-S are water samples from groundwater and river water, respectively. Artemia-GW and Artemia-S are brine shrimp prepared using the respective water sources, and detritus was collected from a sock filter. Var, variation.

FIG 5

Interaction plots of marginal (least-squares [LS]) means for the first PCoA axes (axes that explained the largest variation in the data set) at different developmental stages. Additional information pertaining to the LS means is compiled in Table 6. (A) First PCoA axis at 1 week after active feeding; (B) first PCoA axis at 2 weeks after active feeding. The information in panel A indicates that significant interactions occurred between food and water treatments. Water and food treatments influenced the gut microbial community composition (represented by the first PCoA axis) during the sampling period at 1 week after active feeding. No significant difference in gut community composition between supplemented and nonsupplemented food treatments within the stream water environment was detected. However, a significant difference between the gut microbiota of fish raised in groundwater was observed on the basis of the food treatment (see the information in panel B). Significant effects of water treatment on gut composition (represented by the first PCoA axis) were observed in fish at 2 weeks after active feeding began. Diet effects were no longer observed. Food Suppl., food treatment in which live Artemia fish mixed with retentate was offered to the fish; Food No suppl., food treatment in which live Artemia fish only was offered to the fish.

FIG 6

Results of neutral model testing with water as the source of gut microbial communities at the prefeeding stage (a), at 1 week after active feeding initiation (b), and at 2 weeks after active feeding initiation (c). The solid black line represents the best-fit neutral model, generated using a beta probability distribution. The model was developed based only on taxa found in both gut and water sources. The dashed lines represents the 95% confidence intervals around the best-fitting neutral model. Species within the confidence intervals (gray points) are classified as neutrally dispersed taxa that were likely present in the gut as a result of neutral processes (such as dispersal or ecological drift). Species deviating from neutral model and identified by black and white points were classified as underrepresented and overrepresented taxa, respectively. These taxa were likely affected by deterministic processes or may have had a dispersal ability different from that of the other taxa in the water. The coefficient of determination (R²) represents the goodness of fit of the relative abundance under the neutral model. The value ranges from ≤0 (no fit) to 1 (perfect fit). The P value indicates that the neutral processes that were detected are significant and did not occur by random chance. In general, neutrality could not be rejected during all three developmental stages, but the fit of the data to the neutrality expectations was poor, as shown by the relatively low R² values.