Stressors Acting on Aquatic Ecosystems: High-Throughput Sequencing Approaches to Shed Light on Human-Nature Interactions

Molecular approaches such as DNA metabarcoding and metagenomics have revealed that aquatic ecosystems are characterized by rich biodiversity. Such high-throughput sequencing (HTS) techniques are particularly useful to identify microbial community composition and elucidate the associated metabolic potential when direct observation of morphology or physiology is difficult. Emblematic examples are the “uncultivated majority”, comprising the countless species of environmental bacteria and archaea harbored by natural and engineered water ecosystems that cannot be readily observed in-situ or grown in the laboratory. It is not only microscopic life that can be investigated with such an approach, but also macroorganisms that are difficult to observe and/or catch. Thus, application to natural freshwater environments and engineered water and wastewater treatment processes has revolutionized our capacity to observe the associated ecology.

It is increasingly documented that in aquatic environments, exogenous stressors, such as anthropogenic pressures, have a high impact on ecosystem equilibrium. Yet to date, there is no consensus on the most appropriate theoretical framework, methods and measures to study exogenous stressors and associated ecosystem impacts. Moreover, natural and engineered aquatic ecosystems are interconnected and subject to multiple natural and anthropogenic stressors that have not been characterized comprehensively.

For instance, the effects of acute and chronic stressors can be seen in variations in community structure and in the enrichment of mobile genetic elements and antibiotic resistance genes (ARGs). While natural antibiotics and their ARGs predate anthropogenic influence, emerging evidence indicates an association between anthropogenic stressors and increased (antibiotic) resistance: exogenous pressures serve to fix these genetic elements in the microbial communities of affected ecosystems, from watersheds to water treatment units and wastewater effluents. Another concern is plastic contamination, probably one of the major risks that we are facing today and a growing trend in ecological studies.

The historical approach based on the evaluation of a single stressor or target organism has not been effective in protecting the environment and its biodiversity, highlighting the urgency to address the issue from a broader perspective that considers human-nature interactions on the whole.

This Research Topic aims to highlight research that uses environmental DNA (eDNA) to reveal structural and evolutionary changes in communities due to stressors in natural and engineered aquatic ecosystems, with a particular focus on:

• detecting multidimensional changes to stressors, since eDNA can span the entire range of biodiversity, from prokaryotes to eukaryotes;
• revealing not only community shifts, but also functional shifts that show patterns of the distribution of genes of interest (i.e., resistance genes) related to relevant environmental variables;
• depicting the comprehensive health status of an ecosystem, considering biological and abiotic elements.

This Research Topic has the potential to introduce and showcase a comprehensive and multidimensional framework to study ecosystems under stress by integrating data that spans the entire spectrum of biodiversity and elucidating connections between natural and engineered systems. Finally, this approach based on multiple stressors and ecological interactions will permit the development of health indexes and prediction models, through meta-analyses coupled with machine learning analysis.

We welcome original research, reviews, perspective articles, and commentaries.