Exploring the capacity of aquatic biofilms to act as environmental DNA samplers: Test on macroinvertebrate communities in rivers

Assessing the relevance of DNA metabarcoding compared to morphological identification for lake phytoplankton monitoring

Phytoplankton is a key biological group used to assess the ecological status of lakes. The classical monitoring approach relies on microscopic identification and counting of phytoplankton species, which is time-consuming and requires high taxonomic expertise. High-throughput sequencing, combined with metabarcoding, has recently demonstrated its potential as an alternative approach for plankton surveys. Several studies have confirmed the relevance of the diatom metabarcoding approach to calculate biotic indices based on species ecology. However, phytoplankton communities have not yet benefited from such validation. Here, by comparing the results obtained with the two methods (molecular and microscopic counting), we evaluated the relevance of metabarcoding approach for phytoplankton monitoring by considering different metrics: alpha diversity, taxonomic composition, community structure and a phytoplankton biotic index used to assess the trophic level of lakes. For this purpose, 55 samples were collected in four large alpine lakes (Aiguebelette, Annecy, Bourget, Geneva) during the year 2021. For each sample, a metabarcoding analysis based on two genetic markers (16S and 23S rRNA) was performed, in addition to the microscopic count. Regarding the trophic level of lakes, significant differences were found between index values obtained with the two approaches. The main hypothesis to explain these differences comes from the incompleteness, particularly at the species level, of the barcode reference library for the two genetic markers. It is therefore necessary to complete reference libraries for using such species-based biotic indices with metabarcoding data. Besides this, species richness and diversity were higher in the molecular inventories than in the microscopic ones. Moreover, despite differences in taxonomic composition of the floristic lists obtained by the two approaches, their community structures were similar. These results support the possibility of using metabarcoding for phytoplankton monitoring but in a different way. We suggest exploring alternative approaches to index development, such as a taxonomy-free approach.

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

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.

Multi-group biodiversity distributions and drivers of metacommunity organization along a glacial-fluvial-limnic pathway on the Tibetan plateau

Extensive global glacial retreats are threatening cryosphere ecosystem functioning and the associated biota in glacier-fed water systems. Understanding multi-group biodiversity distributions and compositional variation across diverse but hydrologically linked habitats under varying glacial influences will help explain the mechanisms underlying glacial community organization and ecosystem processes. However, such data are generally lacking due to the difficulty of obtaining biodiversity information across wide taxonomic ranges. Here, we used a multi-marker environmental DNA metabarcoding approach to simultaneously investigate the spatial patterns of community compositions and assembly mechanisms of four taxonomic groups (cyanobacteria, diatoms, invertebrates, and vertebrates) along the flowpaths of a tributary of Lake Nam Co on the Tibetan Plateau-from its glacier headwaters, through its downstream river and wetlands, to its estuary. We detected 869 operational taxonomic units: 119 cyanobacterial, 395 diatom, 269 invertebrate, and 86 vertebrate. Taxonomic richnesses consistently increased from upstream to downstream, and although all groups showed community similarity distance decay patterns, the trend for vertebrates was the weakest. Cyanobacteria, diatom, and invertebrate community compositions were significantly correlated with several environmental factors, while the vertebrate community was only correlated with waterway width. Variation partitioning analysis indicated that varying extents of environmental conditions and spatial factors affected community organizations for different groups. Furthermore, stochastic processes contributed prominently to the microorganisms' community assembly (Sloan's neutral model R² = 0.77 for cyanobacteria and 0.73 for diatoms) but were less important for macroorganisms (R² = 0.21 for invertebrates and 0.15 for vertebrates). That trend was further substantiated by modified stochasticity ratio analyses. This study provides the first holistic picture of the diverse biotic communities residing in a series of hydrologically connected glacier-influenced habitats. Our results both uncovered the distinct mechanisms that underlie the metacommunity organizations of different glacial organisms and helped comprehensively predict the ecological impacts of the world's melting glaciers.

Spider webs as eDNA samplers: biodiversity assessment across the tree of life

The concept of environmental DNA (eDNA) utilizes nucleic acids of organisms directly from the environment. Recent breakthrough studies have successfully detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, ranging from ancient to modern, and from terrestrial to aquatic. With their diversity and ubiquity in nature, spider webs might act as powerful biofilters and could thus represent a promising new source of eDNA, but their utility under natural field conditions is severely understudied. Here, we bridge this knowledge gap to establish spider webs as a source of eDNA with far reaching implications. First, we conducted a field study to track specific arthropod targets from different spider webs. We then employed high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of spider web eDNA for biodiversity monitoring of animals, fungi, and bacteria. Our results show that genetic remains on spider webs allow the detection of even the smallest target organisms. We also demonstrate that eDNA from spider webs is useful in research of community compositions across the different domains of life, with potentially highly detailed temporal and spatial information.

DNA metabarcoding reveals human impacts on macroinvertebrate communities in polluted headwater streams: Evidence from the Liao River in northeast China

Headwater streams are a hotspot of freshwater biodiversity, carrying indispensable resource pools of aquatic species. However, up to now, there remain many challenges to accurately and efficiently characterize the responses of this vulnerable ecosystem to human-induced changes. Here, we collected macroinvertebrate data from 12 different headwater streams in the Liao River of northeast China by DNA metabarcoding approach, to reveal biodiversity changes and ecological thresholds affected by human beings. Our data showed that the community composition and structure of headwater streams had unique and significant differences under human impacts, and 5-day biological oxygen demand (BOD₅) and ammonia nitrogen (NH₃-N) were the key variables explaining the variation in community structure. Although α diversity had a unimodal relationship with nutrients and organic loads, β diversity and its turnover component (species replacement) increased significantly. In addition, 22 and 33 indicative taxa were identified to have significant negative responses to BOD₅ and NH₃-N, respectively, and the change points derived from Threshold Indicator Taxa Analysis (TITAN) for the negative response of their frequency and abundance were BOD₅ >3.42 mg/L and NH₃-N >0.14 mg/L. Overall, this study reveals the biodiversity changes in headwater streams from the aspects of α and β diversity, and also determines the thresholds of BOD₅ and NH₃-N pollutants for one reach at one date from 12 headwater streams, suggesting the potential of DNA metabarcoding approach for threshold analyses in headwater streams.

Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as water filtration and DNA precipitation are time consuming, require difficult-to-handle equipment and partially integrate eDNA signals. To overcome these limitations, we created the first proof of concept of a passive, 3D-printed and easy-to-use eDNA sampler. We designed the samplers from hydroxyapatite (HAp samplers), a natural mineral with a high DNA adsorption capacity. The porous structure and shape of the samplers were designed to optimise DNA adsorption and facilitate their handling in the laboratory and in the field. Here we show that HAp samplers can efficiently collect genomic DNA in controlled set-ups, but can also collect animal eDNA under controlled and natural conditions with yields similar to conventional methods. However, we also observed large variations in the amount of DNA collected even under controlled conditions. A better understanding of the DNA-hydroxyapatite interactions on the surface of the samplers is now necessary to optimise the eDNA adsorption and to allow the development of a reliable, easy-to-use and reusable eDNA sampling tool.

Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment

DNA metabarcoding is increasingly used for the assessment of aquatic communities, and numerous studies have investigated the consistency of this technique with traditional morpho‐taxonomic approaches. These individual studies have used DNA metabarcoding to assess diversity and community structure of aquatic organisms both in marine and freshwater systems globally over the last decade. However, a systematic analysis of the comparability and effectiveness of DNA‐based community assessment across all of these studies has hitherto been lacking. Here, we performed the first meta‐analysis of available studies comparing traditional methods and DNA metabarcoding to measure and assess biological diversity of key aquatic groups, including plankton, microphytobentos, macroinvertebrates, and fish. Across 215 data sets, we found that DNA metabarcoding provides richness estimates that are globally consistent to those obtained using traditional methods, both at local and regional scale. DNA metabarcoding also generates species inventories that are highly congruent with traditional methods for fish. Contrastingly, species inventories of plankton, microphytobenthos and macroinvertebrates obtained by DNA metabarcoding showed pronounced differences to traditional methods, missing some taxa but at the same time detecting otherwise overseen diversity. The method is generally sufficiently advanced to study the composition of fish communities and replace more invasive traditional methods. For smaller organisms, like macroinvertebrates, plankton and microphytobenthos, DNA metabarcoding may continue to give complementary rather than identical estimates compared to traditional approaches. Systematic and comparable data collection will increase the understanding of different aspects of this complementarity, and increase the effectiveness of the method and adequate interpretation of the results.

Fish eDNA metabarcoding from aquatic biofilm samples: Methodological aspects

Fish eDNA metabarcoding is usually performed from filtered water samples. The volume of filtered water depends on the study scope and can rapidly become time consuming according to the number of samples that have to be processed. To avoid time allocated to filtration, passive DNA samplers have been used to recover fish eDNA from marine environments faster. In freshwater ecosystems, aquatic biofilms were used to catch eDNA from macroinvertebrates. Here, we test the capacity of aquatic biofilms to entrap fish eDNA in a large lake and, therefore, the possibility to perform fish eDNA metabarcoding from this matrix compared to the traditional fish eDNA approach from filtered water samples. Methodological aspects of the use of aquatic biofilms for fish eDNA metabarcoding (e.g. PCR replicates, biological replicates, bioinformatics pipeline, reference database and taxonomic assignment) were validated against a mock community. When using biofilms from habitats sheltered from wind and waves, biofilm and water approach provided similar inventories. Richness and diversity were comparable between both approaches. Approaches differed only for rare taxa. Our results illustrate the capacity of aquatic biofilms to act as passive eDNA samplers of fish eDNA and, therefore, the possibility to use biofilms to monitor fish communities efficiently from biofilms. Furthermore, our results open up avenues of research to study a diversity of biological groups (among which bioindicators as diatoms, macroinvertebrates and fish) from eDNA isolated from a single environmental matrix reducing sampling efforts, analysis time and costs.

Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring

Traditional environmental biomonitoring approaches have limitations in terms of species detectability and their capacity to account for spatial and temporal variation. Furthermore, as invasive techniques they can be harmful to individual organisms, populations and habitats. The application of non-invasive sampling methods that extract, isolate and identify nucleic acid sequences (i.e. DNA, RNA) from environmental matrices have significant potential for complementing, or even ultimately replacing, current methods of biological environmental assessment. These environmental DNA (eDNA) and environmental RNA (eRNA) techniques increase spatial and temporal acuity of monitoring, and in the case of the latter, may provide functional information regarding the health of individuals, and thus ecosystems. However, these assessments require robust analysis of factors such as the detectability and specificity of the developed assays. The presented work highlights the current and future uses of nucleic acid-based biomonitoring regimes, with a focus on fish and aquatic invertebrates and their utility for water quality, biodiversity and species-specific monitoring. These techniques are compared to traditional approaches, with a particular emphasis on the potential insights that could be provided by eRNA analysis, including the benefits of microRNAs as assay targets.

Estimating aquatic plant diversity and distribution in rivers from Jingjinji region, China, using environmental DNA metabarcoding and a traditional survey method

Traditional survey methods (TSMs) are difficult to use to perform a census of aquatic plant diversity completely in river ecosystems, and improved aquatic plant community monitoring programs are becoming increasingly crucial with a continuous decline in diversity. Although environmental DNA (eDNA) metabarcoding has been applied successfully to assess aquatic biodiversity, limited work has been reported regarding aquatic plant diversity in rivers. In this study, the efficiency of eDNA to estimate the aquatic plant diversity and spatial distribution of rivers from the Jingjinji (JJJ) region was evaluated by comparing results obtained by the TSM. Based on a combination of the two methods, 157 aquatic plant species, including 24 hydrophytes, 61 amphibious plants, and 72 mesophytes, were identified. The spatial patterns in species richness and abundance by eDNA exhibited agreement with the TSM results with a gradual decline from the mountain area (MA) to the agricultural area (AA) and then to the urban area (UA). Compared to the TSM, eDNA identified a significantly greater number of species per site (p < 0.01) and obtained a significantly higher abundance in hydrophytes (p < 0.01), supplementing the unavailable abundance data from the TSM. Furthermore, the aquatic plant assemblages from the different areas were discriminated well using eDNA (p < 0.05), but they were better discriminated by the TSM (p < 0.01). Thus, our study provides more detailed data on aquatic plant diversity in rivers from the JJJ region, which is essential for biodiversity conservation. Our findings also highlight that eDNA can be reliable for evaluating aquatic plant diversity and has the potential to respond to landscape heterogeneity in river ecosystems.