In many developing countries, aquaculture is key to ensuring food security for millions of people. It is thus important to measure the full implications of environmental changes on the sustainability of aquaculture. We conduct a double meta-analysis (460 articles) to explore how global warming and antimicrobial resistance (AMR) impact aquaculture. We calculate a Multi-Antibiotic Resistance index (MAR) of aquaculture-related bacteria (11,274 isolates) for 40 countries, of which mostly low- and middle-income countries present high AMR levels. Here we show that aquaculture MAR indices correlate with MAR indices from human clinical bacteria, temperature and countries’ climate vulnerability. We also find that infected aquatic animals present higher mortalities at warmer temperatures. Countries most vulnerable to climate change will probably face the highest AMR risks, impacting human health beyond the aquaculture sector, highlighting the need for urgent action. Sustainable solutions to minimise antibiotic use and increase system resilience are therefore needed.

This review is part of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) report on Europe and Central Asia (ECA) and provides a critical assessment of issues facing decision-makers, including freshwater biodiversity and ecosystem trends as well as drivers of change. Freshwater systems are well established as the most threatened ecosystem type in the ECA region, with the quantity and quality of habitats and abundance of many species rapidly declining. Only about half (53%) of the EU's rivers and lakes achieved good ecological status in 2015 (as defined by the Water Framework Directive in terms of the quality of the biological community), and many lakes, ponds, and streams are disappearing as a consequence of agricultural intensification and inefficient irrigation and urbanisation, combined with climate change. The situation regarding freshwater biodiversity remains highly critical in ECA as many species remain threatened with extinction, including >50% of known species for some groups (e.g., molluscs, amphibians). Drivers of ECA freshwater taxa include the destruction or modification of their habitat, including water abstraction, which affects ∼89% of all amphibian threatened species and ∼26% of threatened freshwater invertebrate species. Of particular concern is the lack of data for freshwater invertebrates. Current status is available for only a minority of species, and the impact of alien invasive species is often unknown, especially in Central Asia. Based on current freshwater biodiversity trends, it is highly unlikely that ECA will achieve either the respective Aichi biodiversity targets by 2020 (i.e., targets 2 to 4, 6 to 12, and 14) or Target 1 of the Biodiversity Strategy.

Despite increasingly sophisticated microbiological techniques, and long after the first discovery of microbes, basic knowledge is still lacking to fully appreciate the ecological importance of microbial parasites in fish. This is likely due to the nature of their habitats as many species of fish suffer from living beneath turbid water away from easy recording. However, fishes represent key ecosystem services for millions of people around the world and the absence of a functional ecological understanding of viruses, prokaryotes, and small eukaryotes in the maintenance of fish populations and of their diversity represents an inherent barrier to aquatic conservation and food security. Among recent emerging infectious diseases responsible for severe population declines in plant and animal taxa, fungal and fungal-like microbes have emerged as significant contributors. Here, we review the current knowledge gaps of fungal and fungal-like parasites and pathogens in fish and put them into an ecological perspective with direct implications for the monitoring of fungal fish pathogens in the wild, their phylogeography as well as their associated ecological impact on fish populations. With increasing fish movement around the world for farming, releases into the wild for sport fishing and human-driven habitat changes, it is expected, along with improved environmental monitoring of fungal and fungal-like infections, that the full extent of the impact of these pathogens on wild fish populations will soon emerge as a major threat to freshwater biodiversity.

With an ever-increasing human population, food security remains a central issue for the coming years. The magnitude of the environmental impacts of food production has motivated the assessment of the environmental and health benefits of shifting diets, from meat to fish and seafood. One of the main concerns for the sustainable development of aquaculture is the emergence and spread of infectious animal diseases in a warming climate. We conducted a meta-analysis to investigate the influence of global warming on mortality due to viral infections in farmed aquatic animals. We found a positive trend between increasing temperature and increasing viral virulence, with an increase in water temperature of 1 °C resulting in an increase in mortality of 1.47–8.33% in OsHV-1 infected oysters, 2.55–6.98% in carps infected with CyHV-3 and 2.18–5.37% in fishes infected with NVVs. We suggest that global warming is going to pose a risk of viral disease outbreaks in aquaculture and could compromise global food security.

Recent years have seen a global and rapid resurgence of fungal diseases with direct impact on biodiversity and local extinctions of amphibian, coral, or bat populations. Despite similar evidence of...