Does DNA barcoding improve performance of traditional stream bioassessment metrics?

Stein, Eric D.; White, Bryan P.; Mazor, Raphael D.; Jackson, John K.; Battle, Juliann M.; Miller, Peter E.; Pilgrim, Erik M.; Sweeney, Bernard W.

doi:10.1086/674782

Cited by 64 publications

(53 citation statements)

References 39 publications

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“…A promising alternative to morphological identification is DNA based determination of macroinvertebrates, which has been demonstrated in multiple case studies (Hajibabaei et al, 2011;Sweeney et al, 2011;Carew et al, 2013;Stein et al, 2013;Elbrecht and Leese, 2015). Prerequisite of such "DNA barcoding" techniques is an appropriate reference data base.…”

Section: Introductionmentioning

confidence: 99%

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Elbrecht

Leese

2017

Front. Environ. Sci.

198

221

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A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for such bioassessments as many taxa show specific responses to environmental conditions. However, generating accurate macroinvertebrate inventories based on primarily larval morphology is difficult and error-prone. Here, DNA metabarcoding provides new opportunities. Its potential to accurately identify invertebrates in bulk samples to the species level has been demonstrated in several case studies. However, DNA based identification is often limited by primer bias, potentially leading to taxa in the sample remaining undetected. Thus, the success of DNA metabarcoding as an emerging technique for bioassessment critically relies on carefully evaluated primers. We used the R package PrimerMiner to obtain and process cytochrome c oxidase I (COI) sequence data for the 15 globally most relevant freshwater invertebrate groups for stream assessment. Using these sequence alignments, we developed four primer combinations optimized for freshwater macroinvertebrates. All primers were evaluated by sequencing 10 mock community samples, each consisting of 52 freshwater invertebrate taxa. Additionally, popular metabarcoding primers from the literature and the developed primers were tested in silico against these 15 relevant invertebrate groups. The developed primers varied in amplification efficiency and the number of detected taxa, yet, all detected more taxa than standard "Folmer" barcoding primers. Two new primer combinations showed even more consistent amplification than a previously tested ribosomal marker (16S) and detected all 42 insect taxa present in the mock community samples. In silico evaluation revealed critical design flaws in some commonly used primers from the literature. We demonstrate a reliable strategy to develop optimized primers using the tool PrimerMiner. The developed primers detected almost all taxa present in the mock samples, and we argue that high base degeneracy is necessary to decrease primer bias as confirmed by experimental results and in silico primer evaluation. We further demonstrate that some primers currently Elbrecht and Leese Freshwater Primer Development and Evaluation used in metabarcoding studies may not be suitable for amplification of freshwater macroinvertebrates. Therefore, careful primer evaluation and more region/ecosystem specific primers are needed before DNA metabarcoding can be used for routine bioassessment of freshwater ecosystems.

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Section: Introductionmentioning

confidence: 99%

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Elbrecht

Leese

2017

Front. Environ. Sci.

198

221

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“…Thus, with appropriate analyses, it will be possible to differentiate communities in a subtler way (Stein et al . ) and to gain capacity in distinguishing the effects of various pressures.…”

Section: Biomonitoring As a Source Of Massive Datamentioning

confidence: 99%

Freshwater biomonitoring in the Information Age

Keck

Vasselon

Tapolczai

et al. 2017

Frontiers in Ecol & Environ

110

100

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Freshwaters worldwide face serious threats, making their protection increasingly important. Freshwater monitoring has historically produced valuable data and continues to develop. Rapid improvements to biomolecular techniques are revolutionizing the way scientists describe biological communities and are bringing about major changes in biomonitoring. Combined with high‐throughput sequencing, DNA metabarcoding is fast and cost‐effective, generating massive amounts of data. In a world with numerous ecological threats, “big data” constitute a tremendous opportunity to improve the efficiency of biological monitoring. These fundamental changes in biomonitoring will require freshwater ecologists and environmental managers to reconsider how they handle large amounts of data.

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“…Misidentification, low comparability, and limited taxonomic resolution for difficult groups, such as chironomids, can lead to inaccurate assessments and potentially to the mismanagement of stream ecosystems (Stein et al . ). Moreover, the use of human experts for morphological identification is time‐consuming and therefore expensive (Yu et al .…”

Section: Introductionmentioning

confidence: 97%

Assessing strengths and weaknesses of DNA metabarcoding‐based macroinvertebrate identification for routine stream monitoring

et al. 2017

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Summary DNA metabarcoding holds great promise for the assessment of macroinvertebrates in stream ecosystems. However, few large‐scale studies have compared the performance of DNA metabarcoding with that of routine morphological identification. We performed metabarcoding using four primer sets on macroinvertebrate samples from 18 stream sites across Finland. The samples were collected in 2013 and identified based on morphology as part of a Finnish stream monitoring program. Specimens were morphologically classified, following standardised protocols, to the lowest taxonomic level for which identification was feasible in the routine national monitoring. DNA metabarcoding identified more than twice the number of taxa than the morphology‐based protocol, and also yielded a higher taxonomic resolution. For each sample, we detected more taxa by metabarcoding than by the morphological method, and all four primer sets exhibited comparably good performance. Sequence read abundance and the number of specimens per taxon (a proxy for biomass) were significantly correlated in each sample, although the adjusted R2 values were low. With a few exceptions, the ecological status assessment metrics calculated from morphological and DNA metabarcoding datasets were similar. Given the recent reduction in sequencing costs, metabarcoding is currently approximately as expensive as morphology‐based identification. Using samples obtained in the field, we demonstrated that DNA metabarcoding can achieve comparable assessment results to current protocols relying on morphological identification. Thus, metabarcoding represents a feasible and reliable method to identify macroinvertebrates in stream bioassessment, and offers powerful advantage over morphological identification in providing identification for taxonomic groups that are unfeasible to identify in routine protocols. To unlock the full potential of DNA metabarcoding for ecosystem assessment, however, it will be necessary to address key problems with current laboratory protocols and reference databases.

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Does DNA barcoding improve performance of traditional stream bioassessment metrics?

Cited by 64 publications

References 39 publications

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment

Freshwater biomonitoring in the Information Age

Assessing strengths and weaknesses of DNA metabarcoding‐based macroinvertebrate identification for routine stream monitoring

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