Variable phylosymbiosis and cophylogeny patterns in wild fish gut microbiota of a large subtropical river

Abstract

The persistence and specificity of fish host-microbial interaction during evolution is an important part of exploring the host-microbial symbiosis mechanism. However, it remains unclear how the environmental and host factors shape fish host-microbe symbiotic relationships in subtropical rivers with complex natural environments. Freshwater fish are important consumers in rivers and lakes and are considered keystone species in maintaining the stability of food webs there. In this study, patterns and mechanisms shaping gut microbiota community in 42 fish species from the Pearl River, in the subtropical zone of China, were investigated. The results showed that fish host specificity is a key driver of gut microbiota evolution and diversification. Different taxonomic levels of the host showed different degrees of contribution to gut microbiota variation. Geographical location and habitat type were the next most important factors in shaping gut microbiota across the 42 fishes, followed by diet and gut trait. Our results emphasized the contribution of stochastic processes (drift and homogenizing dispersal) in the gut microbial community assembly of freshwater fishes in the middle and lower reaches of the Pearl River. Phylosymbiosis is evident at both global and local levels, which are jointly shaped by complex factors including ecological or host physiological filtration and evolutionary processes. The core microbiota showed co-evolutionary relationships of varying degrees with different taxonomic groups. We speculate that host genetic isolation or habitat variation facilitates the heterogeneous selection (deterministic process), which occurs and results in different host-core bacterium specificity.

Importance: Freshwater fish are regarded as the dominant consumers in rivers and lakes. Due to their diverse feeding modes, fish significantly enhance the trophic link and nutrient recycling/retention in aquatic habitats. For this, they are often considered keystone species in maintaining the stability of food webs in rivers and lakes. A significant part of fish nutrition is essentially mediated by their gut microbiota, which can enhance fish tolerance to fluctuations in external resources and improve the efficiency of nutrients extracted from various food sources. As gut bacterial symbionts have a profound impact on the nutrition and development of their hosts, as well as their overall fitness, it is critical to answer the question of how hosts maintain these benefits by procuring or inheriting these vital symbionts, which is still largely unanswered, especially for freshwater fish. Our study provides new insights into the co-evolutionary relationship between wild fish and their symbiotic microbiome, the hidden diversity of gut microbiome, and the ecological adaptation potential of wild freshwater fish.

Keywords: Pearl River; assembly; co-evolution; fish; gut microbiota; phylosymbiosis.

Fig 1

Broad microbiome in the fish gut in the middle and lower research of the Pearl River. (A) Map showing the geographical locations of fish samples analyzed in this study. (B) Relative abundance of bacterial taxa in the gut microbiome in fish host species. Microbial community compositions are displayed based on the phylum level. Host phylogeny was inferred from COI gene evolution history using iq-tree. For convenience, the lengths of branches do not represent evolutionary distance. Host metadata are labeled using different colors and shapes.

Fig 2

Abundance and prevalence of bacterial genera in all fish hosts. The prevalent rate of genus of all samples ≥ 90% was highlighted in different colors, and another genus ≤90% was shown in gray color.

Fig 3

Ecological processes about the gut microbial community assembly. Quantification of deterministic and stochastic processes governing the microbial community assembly and the percentages are relative contributions of each process turnover for different orders (A), families (B), diet (C), stomach types (D), habitat (E), and sex (F). (G) The relationship between βNTI and the microbiome similarity (Bray-Curtis distance). Linear regression models (shown as red lines) and associated correlation coefficients are provided on each panel

Fig 4

Phylosymbiosis patterns of fish gut microbiome in the middle and lower research of the Pearl River. (A) Linear regression analysis with the slope of the regression line for host COI gene similarity versus microbial dissimilarity. (B) β-Dispersion analysis indicating microbial community composition heterogeneity at different host taxonomic levels. (C) Sharing and specificity ASVs of fish gut microbiota from different orders. (D) Neighbor-joining phylogenetic tree of common ASVs. (E) Procrustean approach to co-phylogeny (PACo) analysis between fish hosts and microbiome. (F) Local indicator of phylogenetic association (LIPA) values for correlations between abundances of ASVs (different genera) and specific hosts using heatmap. The host species tree on the left was found to have significant associations with at least one ASV of microbiome (P-value < 0.05). Branch colors are determined by host order in the phylogenetic tree.