Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Simple Summary Freshwater ecosystems face various threats, especially in recent decades, that pose unprecedented challenges to human health, water supply, agriculture, forestry, ecology, and biodiversity. Although progress has been made in biomonitoring techniques tailored to specific countries and communities, significant constraints exist in assessing and quantifying biodiversity and its interaction with detrimental factors. The incorporation of modern techniques into biomonitoring is challenging, with multiple perspectives. This review aims to provide a comprehensive overview of contemporary advancements in freshwater biomonitoring, focusing on omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. Additionally, this work highlights the need for modernization by presenting case studies, examining studied organisms, and evaluating the benefits and drawbacks of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a departure from conventional practices, necessitating a significant shift. The contributions of omics techniques to biological quality elements (BQEs) and their interpretations of ecological problems are crucial for biomonitoring programs. These contributions identify interactions between different levels of biological organization and their responses to specific critical conditions. Abstract Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.