Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

• Published in: Frontiers in Microbiology
• Main Authors: Sehnal, Ludek, Brammer-Robbins, Elizabeth, Wormington, Alexis, Blaha, Ludek, Bisesi, Joe, Larkin, Iske, Martyniuk, Christopher, Simonin, Marie, Adamovsky, Ondrej
• Other Authors: Masaryk University Brno (MUNI), University of Florida Gainesville (UF), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), National Science Foundation (NSF) : 2019285699; National Science Foundation Grant (CBET Award) : 1605119; RECETOX research infrastructure (Ministry of Education, Youth and Sport of the Czech Republic) : LM2018121; CETOCOEN EXCELLENCE Teaming 2 project - Horizon2020 : 857560; Ministry of Education, Youth & Sports - Czech Republic : CZ.02.1.01/0.0/0.0/17_043/0009632.
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2021
• Subjects: microbiome; fish; aquatic mammals; stressors; biomonitoring; ecosystem health; [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology; [SDE.MCG]Environmental Sciences/Global Changes; [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology; Ocean acidification
• Online Access: https://hal.inrae.fr/hal-03238365; https://doi.org/10.3389/fmicb.2021.567408

International audience Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic ...