TICI: a taxon-independent community index for eDNA-based ecological health assessment

Abstract

Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to provide a reliable, robust and low-cost assessment of ecological health that is accessible to environmental managers, decision makers, and the wider community.

The Tree of Life eDNA metabarcoding reveals a similar taxonomic richness but dissimilar evolutionary lineages between seaports and marine reserves

“…Such indicators would help to monitor and evaluate the efficiency of eco-certifications that are sometimes attributed to seaports (Hossain et al, 2021). Taxonindependent indices have recently been developed to overcome reference database incompleteness (Wilkinson et al, 2024). To go further, future works should explore beyond α-and β-biodiversity patterns to answer whether intraspecific variation is affected or not by coastal urbanization.…”

Developing an eDNA approach for wetland biomonitoring: Insights on technical and conventional approaches

“…This highlights the dependence of eDNA on reference databases (e.g., the National Centre for Biotechnology Information-NCBI GenBank; and the Barcode of Life Data System-BOLD) for matching unknown genetic sequences, that suffer from a significant amount of missing data (Hotaling et al, 2021). Indeed, more than a of the 3000 most encountered sequences across eight metabarcoding assays could not be appointed to a phylum in a recent study (Wilkinson et al, 2024), and >50% of sequences were unassigned to any taxonomic rank here in our study. This emphasizes the importance of current plans to de- Nevertheless, eDNA methods are continuing to improve, with the development of new assays, decreasing costs of sequencing, and regular additions to the reference database together enhancing their potential for species detection and identification.…”

“…Here, we explored the effects of filter size and spatial and temporal sampling schemes on biodiversity detection using eDNA in wetland environments. Outstanding questions include whether eDNA can detect macroorganisms in other challenging wetland environments (e.g., high-temperature geothermal wetlands and low pH bogs), and whether quantitative measures of ecosystem quality and health (e.g., the taxon-independent community index, "TICI"; Wilkinson et al, 2024) can be extended to wetlands and other environments.…”

“…The iSeq 100 output sequence fastq files were de-multiplexed in R (R Core Team, 2021) using the insect package (v.1.4.0; for further details). Following taxon assignment, any DNA identified as having human origin was removed for privacy reasons (Wilkinson et al, 2024).…”

“…PCR reactions were carried out in duplicate, with each reaction containing 5 μL SensiFAST 1 × LoRox SYBR Mix (Bioline), 0.25 μL forward primer (10 μM), 0.25 μL reverse primer (10 μM), 0.5 μL BSA (10 mg mL −1 , Sigma Aldrich), 2 μL deionized water and 2 μL template DNA. qPCR cycling conditions included initial denaturation of 3 min at 95°C, and then 40 cycles of 5 s at 95°C, 10 s at the appropriate annealing temperature (see Wilkinson et al, 2024),…”