Modeling the ecological status response of rivers to multiple stressors using machine learning: A comparison of environmental DNA metabarcoding and morphological data

Fan, Jun; Wang, Shuping; Li, Hong; Yan, Zhenguang; Zhang, Yizhang; Zheng, Xin; Wang, Pengyuan

doi:10.1016/j.watres.2020.116004

Cited by 34 publications

(15 citation statements)

References 60 publications

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“…OTUs for the prediction. Despite these limitations, machine learning approaches have shown similar applicability for other biotic indicator taxa such as diatoms [ 24 ], macroinvertebrates [ 73 ], and taxonomy-free based approaches on prokaryotic and eukaryotic communities [ 39 ]. Overall, supervised machine learning can offer complementing or novel insights for the interpretation of big data in an ecological context, especially in the context of biotic indices when the like-for-like comparison is hindered by methodological differences.…”

Section: Discussionmentioning

confidence: 99%

Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

et al. 2021

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Anthropogenic activities are changing the state of ecosystems worldwide, affecting community composition and often resulting in loss of biodiversity. Rivers are among the most impacted ecosystems. Recording their current state with regular biomonitoring is important to assess the future trajectory of biodiversity. Traditional monitoring methods for ecological assessments are costly and time-intensive. Here, we compared monitoring of macroinvertebrates based on environmental DNA (eDNA) sampling with monitoring based on traditional kick-net sampling to assess biodiversity patterns at 92 river sites covering all major Swiss river catchments. From the kick-net community data, a biotic index (IBCH) based on 145 indicator taxa had been established. The index was matched by the taxonomically annotated eDNA data by using a machine learning approach. Our comparison of diversity patterns only uses the zero-radius Operational Taxonomic Units assigned to the indicator taxa. Overall, we found a strong congruence between both methods for the assessment of the total indicator community composition (gamma diversity). However, when assessing biodiversity at the site level (alpha diversity), the methods were less consistent and gave complementary data on composition. Specifically, environmental DNA retrieved significantly fewer indicator taxa per site than the kick-net approach. Importantly, however, the subsequent ecological classification of rivers based on the detected indicators resulted in similar biotic index scores for the kick-net and the eDNA data that was classified using a random forest approach. The majority of the predictions (72%) from the random forest classification resulted in the same river status categories as the kick-net approach. Thus, environmental DNA validly detected indicator communities and, combined with machine learning, provided reliable classifications of the ecological state of rivers. Overall, while environmental DNA gives complementary data on the macroinvertebrate community composition compared to the kick-net approach, the subsequently calculated indices for the ecological classification of river sites are nevertheless directly comparable and consistent.

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Section: Discussionmentioning

confidence: 99%

Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

et al. 2021

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“…Rivers provide fundamental ecosystem services for humans and their state is closely linked to socioeconomic development. − Unfortunately, these services are at stake through local to global river degradation, which accelerated within the last decades. − Establishing an effective assessment method that allows quick and reliable identification of the direction and the degree of ecosystem changes has become an urgent challenge for government managers and stakeholders. , Biological quality elements (BQEs) are an effective and legally implementable approach to explore human-induced environmental changes. A famous case is the European Union’s Water Framework Directive 2000/60/EC (WFD), which uses BQEs as key bioindicators to identify the ecological status of surface water. − Although the BQE-based system has promoted our understanding of the river’s ecological status, the current BQE system indeed does not cover all species present in ecosystems equally. ,− …”

Section: Introductionmentioning

confidence: 99%

Consideration of Multitrophic Biodiversity and Ecosystem Functions Improves Indices on River Ecological Status

Zhang

Altermatt

et al. 2021

Environ. Sci. Technol.

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Biological quality elements have been developed worldwide to assess whether a water body is in a good status or not. However, current studies mainly focus on a single taxonomic group or a small set of species, often limited by methods of morphological identification, and lack further aspects of biodiversity (e.g., across taxa and multiple attributes) and ecosystem functions. Here, we advance a framework for assessing the river’s ecological status based on complete biodiversity data measured by environmental DNA (eDNA) metabarcoding and measurements of ecosystem functions in addition to physicochemical elements across a large riverine system in China. We identified 40 indicators of biodiversity and ecosystem functions, covering five taxonomic groups from bacteria to invertebrates, and associated with multiple attributes of biodiversity and ecosystem functions. Our data show that human impact on ecosystems could be accurately predicted by these eDNA-based indicators and ecosystem functions, using cross-validation with a known stressor gradient. Moreover, indices based on these indicators of biodiversity and ecosystem functions not only distinguish the physicochemical characteristics of the sites but also improve the assessment accuracy of 20–30% for the river’s ecological status. Overall, by incorporating eDNA-based biodiversity with physicochemical and ecosystem functional elements, the multidimensional perspectives of ecosystem states provide additional information to protect and maintain a good ecological status of rivers.

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“…are placed. Furthermore, in the whole genus Colacium, ranges of its interspecific and intraspecific variability significantly overlap (Łukomska-Kowalczyk et al, 2016), On the other hand, an incomplete database and errors in the taxonomic assignment of some reference sequences are considered to be the main issues that can hamper metabarcoding studies (Pawlowski et al, 2018;Sawaya et al, 2019;Fan et al, 2020). Euglenids are one of the taxa with a limited number of reference sequences, thus their molecular identification is strongly affected by this problem.…”

Section: Dna Metabarcoding Performancementioning

confidence: 99%

Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids

Gumińska

Łukomska‐Kowalczyk

Chaber

et al. 2021

Environmental Microbiology

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Even though the interest in metabarcoding in environmental studies is growing, euglenids are still underrepresented in both sea and freshwater bodies researches. The reason for this situation could be the unsuitability of universal eukaryotic DNA barcodes and primers as well as the lack of a verified protocol, suitable to assess euglenid diversity. In this study, using specific primers for the V2 hypervariable region of 18S rDNA for metabarcoding resulted in obtaining a high fraction (85%) of euglenid reads and species-level identification of almost 90% of them. Fifty species were detected by the metabarcoding method, including almost all species observed using a light microscope. We investigated three biomass harvesting methods (filtering, centrifugation and scraping the side of a collection vessel) and determined that centrifugation and filtration outperformed scrapes, but the choice between them is not crucial for the reliability of the analysis. In addition, eight DNA extraction methods were evaluated. We compared five commercially available DNA isolation kits, two CTAB-based protocols and a chelating resin. For this purpose, the efficiency of extraction, quality of obtained DNA, preparation time and generated costs were taken into consideration. After examination of the aforementioned criteria, we chose the GeneMATRIX Soil DNA Purification Kit as the most suitable for DNA isolation.

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Modeling the ecological status response of rivers to multiple stressors using machine learning: A comparison of environmental DNA metabarcoding and morphological data

Cited by 34 publications

References 60 publications

Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

Environmental DNA gives comparable results to morphology-based indices of macroinvertebrates in a large-scale ecological assessment

Consideration of Multitrophic Biodiversity and Ecosystem Functions Improves Indices on River Ecological Status

Evaluation of V2 18S rDNA barcode marker and assessment of sample collection and DNA extraction methods for metabarcoding of autotrophic euglenids

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