Evaluation of a diatom eDNA-based technique for assessing water quality variations in tropical lakes and reservoirs

Kutty, Sujatha Narayanan; Loh, Rebecca Ker; Bannister, Wayne; Taylor, David

doi:10.1016/j.ecolind.2022.109108

Cited by 12 publications

(5 citation statements)

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“…However, challenges such as the necessity for region-specific indices due to regional variation and the requirement for taxonomic expertise to avoid misidentification and inaccurate assessments persist. The laborious process of collecting and analyzing diatom samples raises concerns about the practicality of the index and the potential for delays in diatom response, thus affecting the timeliness of ecosystem health assessments [32][33][34].…”

Section: The Evolution Of Microscopy-enabled Diatom-based Water Quali...mentioning

confidence: 99%

Advancing River Health Assessments: Integrating Microscopy and Molecular Techniques through Diatom Indices

Kim,

Cho,

Hwang

et al. 2024

Water

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This paper reviews the evolution and integration of diatom-based water quality assessments with environmental DNA (eDNA) techniques for advancing river ecosystem health evaluations. Traditional methods, relying on microscopy and diatom indices, have significantly contributed to our understanding of aquatic ecosystems but face challenges such as the need for taxonomic expertise and the labor-intensive nature of sample collection. Recent advancements in molecular biology, particularly eDNA analysis, offer opportunities to overcome these limitations, providing more accurate and comprehensive assessments. This study highlights the benefits of combining traditional microscopy with modern molecular techniques, enhancing the precision and efficiency of water quality evaluations. By addressing the challenges of standardizing methods and improving species identification through comprehensive reference libraries and advanced bioinformatics tools, this integrated approach aims to refine and advance the effectiveness of diatom-based strategies in monitoring and managing river health amidst environmental changes.

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Section: The Evolution Of Microscopy-enabled Diatom-based Water Quali...mentioning

confidence: 99%

Advancing River Health Assessments: Integrating Microscopy and Molecular Techniques through Diatom Indices

Kim,

Cho,

Hwang

et al. 2024

Water

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“…Others proposed taxonomy-free indexes (Apotheloz-Perret- Gentil et al, 2017). However, little congruence has been observed when these methods are compared with morphology-based methods at the species level in tropical environments (Kutty et al, 2022).…”

Section: Taxonomic Impedimentmentioning

confidence: 99%

Relevance of DNA barcodes for biomonitoring of freshwater animals

Elías‐Gutiérrez

Valdéz-Moreno²

2023

Front. Environ. Sci.

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The COI gene, colloquially named the DNA barcode, is a universal marker for species identification in the animal kingdom. Nevertheless, due to the taxonomic impediment, there are various proposals for molecular operational taxonomic units (MOTUs) because high-throughput sequencers can generate millions of sequences in one run. In the case of freshwater systems, it is possible to analyze whole communities through their DNA using only water or sediment as a sample. Using DNA barcodes with these technologies is known as metabarcoding. More than 90% of studies based on eDNA work with MOTUs without previous knowledge of the biodiversity in the habitat. Despite this problem, it has been proposed as the future for biomonitoring. All these studies are biased toward the Global North and focused on freshwater macrofaunae. Few studies include other regions of the world or other communities, such as zooplankton and phytoplankton. The future of biomonitoring should be based on a standardized gene, for example, COI, the most studied gene in animals, or another secondary consensual gene. Here, we analyzed some proposals with 28S or 12S. The studies on eDNA can focus on analyses of the whole community or a particular species. The latter can be an endangered or exotic species. Any eDNA study focused on a community study should have a well-documented DNA baseline linked to vouchered specimens. Otherwise, it will be tough to discriminate between false positives and negatives. Biomonitoring routines based on eDNA can detect a change in a community due to any perturbation of the aquatic ecosystem. Also, it can track changes along the history of an epicontinental environment through the analyses of sediments. However, their implementation will be complex in most megadiverse Neotropical countries due to the lack of these baselines. It has been demonstrated that a rapid functional construction of a DNA baseline is possible, although the curation of the species can take more time. However, there is a lack of governmental interest in this kind of research and subsequent biomonitoring.

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“…There is also a significant proportion of macroinvertebrate taxa which do not have assigned indicator values, leading to confusion and inconsistencies in analytical approaches, with some authorities excluding/omitting them from site calculations and some creating indicator values based on their professional judgment ( Stark & Maxted, 2007 ). Importantly, both methods have limited taxonomic scope, and do not include bioindicators with rapid generation times that respond quickly to environmental disturbance, such as fungi, phytoplankton and bacteria which can be responsive indicators ( Kutty et al, 2022 ). Despite the drawbacks, and through necessity, biological assessment of both fish and macroinvertebrate communities is standard and common practice, and both attributes are now mandatory monitoring requirements for regional and unitary councils under the NPSFM ( New Zealand Ministry for the Environment, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

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

Wilkinson,

Gault,

Welsh

et al. 2024

PeerJ

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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.

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Evaluation of a diatom eDNA-based technique for assessing water quality variations in tropical lakes and reservoirs

Cited by 12 publications

References 97 publications

Advancing River Health Assessments: Integrating Microscopy and Molecular Techniques through Diatom Indices

Advancing River Health Assessments: Integrating Microscopy and Molecular Techniques through Diatom Indices

Relevance of DNA barcodes for biomonitoring of freshwater animals

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

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