Abstract
Fish-associated microbial communities play important roles in host growth, health and disease in the symbiont ecosystem; however, their diversity patterns and underlying mechanisms in different body habitats remain poorly understood. Siganus fuscescens is one of the most important consumers of macroalgae and an excellent natural marine source of nutritional lipids for humans, and widely distributes in shallow coastal areas. Here we systematically studied the microbial communities of 108 wild S. fuscescens in four body habitats (i.e., skin, gill, stomach, and hindgut) and surrounding water. We found that the β-diversity but not α-diversity of fish-associated microbial communities from each habitat significantly (p < 0.05) increased as body weight increased. Also, opportunistic pathogens and probiotics (e.g., Pseudomongs, Methylobacterium) appeared to be widely distributed in different body habitats, and many digestive bacteria (e.g., Clostridium) in the hindgut; the abundances of some core OTUs associated with digestive bacteria, “Anaerovorax” (OTU_6 and OTU_46724) and “Holdemania” (OTU_33295) in the hindgut increased as body weight increased. Additionally, the quantification of ecological processes indicated that heterogeneous selection was the major process (46–70%) governing the community assembly of fish microbiomes, whereas the undominated process (64%) was found to be more important for the water microbiome. The diversity pattern showed that β-diversity (75%) of the metacommunity overweight the α-diversity (25%), confirming that the niche separation of microbial communities in different habitats and host selection were important to shape the fish-associated microbial community structure. This study enhances our mechanistic understanding of fish-associated microbial communities in different habitats, and has important implications for analyzing host-associated metacommunities.
Highlights
Fish are continuously exposed to a microbe-rich water environment that circulates through and reaches epithelial barriers of their body
We found that niche and host selection could play important roles in shaping the S. fuscescens-associated microbial community structure, and they tended to assemble into distinct communities as body weight increased, and the relative abundance of some digestiverelated core operational taxonomy units (OTUs) increased as body weight increased
We found that the β-diversity of fish-associated microbial communities from all tested habitats increased as body weight increased, and the heterogeneous selection appeared to be the major force for the metacommunity assembly
Summary
Fish are continuously exposed to a microbe-rich water environment that circulates through and reaches epithelial barriers of their body. Gill and gastrointestinal tract are the main mucosal surfaces and immune barriers (Gomez et al, 2013), and these mucosal habitats are colonized by complex microbial communities, which interact with the host and regulate host immune systems and nutrient metabolism (Salinas and Magadan, 2017). The balance of these microbial communities is important to the fish development, immunity, health and resistance to external invasions (Fischbach and Segre, 2016; Li et al, 2017; Piazzon et al, 2017). Little is known about the other body habitats microbial communities, especially in the natural environment
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