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 relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.
To improve physical characteristics of plastics such as flexibility and durability, producers enrich materials with phthalates such as di-2-(ethylhexyl) phthalate (DEHP). DEHP is a high production volume chemical associated with metabolic and immune disruption in animals and humans. To reveal mechanisms implicated in phthalate-related disruption in the gastrointestinal system, male and female zebrafish were fed DEHP (3 ppm) daily for two months. At the transcriptome level, DEHP significantly upregulated gene networks in the intestine associated with helper T cells (Th1, Th2 and Th17) specific pathways. The activation of gene networks associated with adaptive immunity were linked to the suppression of networks for tight junction, gap junctional intercellular communication, and transmembrane transporters, all of which are precursors for impaired gut integrity and performance. On a class level, DEHP exposure increased Bacteroidia and Gammaproteobacteria and decreased Verrucomicrobiae in both the male and female gastrointestinal system. Further, in males there was a relative increase in Fusobacteriia, Betaproteobacteria and a relative decrease in Saccharibacteria. Predictive algorithms revealed the functional shift in the microbiome community, and the metabolites they produce, act to modulate intestinal adaptive immunity. This finding suggests that the gut microbiota may contribute to the adverse effects of DEHP on the host by altering metabolites sensed by both intestinal and immune Th cells. Our results suggest that the microbiome-gut-immune axis can be modified by DEHP and emphasizes the value of multi-omics approaches to study microbiome-host interactions following chemical perturbations.
The Summary in Brief of my recently finalized project deals with the effect of plastic softeners on microbiome-gut axis, a key player in health, published in EU CORDIS.
Microbiomes are not only keystones of soil fertility, water quality and performance of engineered ecosystems but also major drivers of plant and animal health. Due to a recent decrease of sequencing cost, there are an increasing number of a broad spectrum of toxicologists that study the effect of stressors on microbiome. In our session, researchers presented new experimental results on the response of microbial community to a great diversity of chemicals (e.g. nanomaterials, pesticides, phthalates, triclosan, copper) and toxins (e.g. cyanobacteria). The session gathered scientists from aquatic, terrestrial and wildlife ecotoxicology that presented results on fish, soil, sediment, biofilm, invertebrates or bird microbiomes. However many studies still focus on the common model organisms (i.g. zebrafish, medaka fish or gammarus), there is increasing tendency to cover non-model species or communities such as stickleback fish, benthic, river and periphytic communities. The session clearly showed that the various environmental chemicals have a potency to significantly modify microbial communities and thus their functions for ecosystem or host health. To connect the chemical dependent microbial shift with the physiological outcomes of the host/ecosystem, the scientists presented latest bioinformatics approaches that help to predict metagenome functional content from 16s rRNA gene (i.g. PICRUSt, Tax4fun). In addition, a study on the effect of phthalate of zebrafish gut microbiome successfully adopted and presented new bioinformatics approach that can predict the effect of tested chemical on levels of microbial bioactive metabolites. However, 16s RNA amplification/sequencing and metagenomics are currently the standard technologies for microbiome studies, a very innovative proof of concept study suggested that mass spectrometry (MS) can be used to determine taxonomic and functional characterization of the microbiota. Advances in MS instrumentation and bioinformatics provide the ability to detect thousands of taxon-specific proteins and peptides, which can be used for deep characterization of organisms present in a sample. The functionality of microbial communities can be then directly assessed by inferring the functions of the corresponding proteins. New bioinformatic approaches were presented in the session and these methods open new possibilities in microbiome research. Specifically, the prediction of the changes in microbial metabolic capacity can help link microbial shifts in community structure with an adverse effect on the host health or ecosystem functioning. As discussed, such approach would be crucial for an Adverse Outcome Pathway (AOP) concept, where a shift in microbial community composition would be one of the key events. The session also stresses the need to adopt better data-sharing practices and that would allow the scientific community to conclusively assess the effect of various natural and anthropogenic stressors on microbiota in all types of environments. A newly introduced project, The Microbiome Stress Project (microbiomestressproject.weebly.com), was developed to identify how consistent are microbiome responses to the same stressor within the same environment, if there are there common microbiome responses to different stressors within the