Implications of taxonomic and numerical resolution on DNA metabarcoding-based inference of benthic macroinvertebrate responses to river restoration

Serrana, Joeselle M.; Li, Bin; Takemon, Yasuhiro; Watanabe, Kozo

doi:10.1016/j.ecolind.2021.108508

Cited by 7 publications

(4 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, quantitative data require detailed work and are susceptible to being influenced by the dominant species. In contrast, qualitative data only consider the presence or absence of species, and cannot be interfered by the dominant species, while being able to work better for rare and diagnostic species (Serrana et al, 2022). The combination of environmental factors identified by quantitative and qualitative data corresponding to taxonomic levels in the four seasons had high similarity, while the amount of explanatory environmental factors by qualitative data was lower than that explained by quantitative data in all cases.…”

Section: Analysis Of the Correlation Between Macrofaunal Assemblages ...mentioning

confidence: 88%

Applicability of taxonomic sufficiency of macrofaunal assemblages in benthic ecological quality assessments: Insights from a semi-enclosed bay

Liu

Xu²,

Liu³

2023

Front. Mar. Sci.

View full text Add to dashboard Cite

To explore the applicability of taxonomic sufficiency in benthic ecological quality assessments, we analyzed the similarity of data matrices under different taxonomic levels and transformations based on macrofaunal data sampled from a semi-enclosed bay. The data matrix similarity revealed a highly significant correlation among the similarity matrices at the species level and those at the higher taxonomic levels (genus, family and order), while the correlation coefficients among the matrices decreased with increasing taxonomic levels. Second-stage CLUSTER plots showed that the quantitative genus level was the closest to the quantitative species level. The loss of family level data varied among seasons. The results of the response to environmental factors at the genus and family levels were similar to those at the species level. In the assessment of the benthic ecological quality of semi-enclosed bays, the level of macrofauna identification can be at the genus or family level to improve the cost performance, depending on logistical conditions.

show abstract

Section: Analysis Of the Correlation Between Macrofaunal Assemblages ...mentioning

confidence: 88%

Applicability of taxonomic sufficiency of macrofaunal assemblages in benthic ecological quality assessments: Insights from a semi-enclosed bay

Liu

Xu²,

Liu³

2023

Front. Mar. Sci.

View full text Add to dashboard Cite

show abstract

“…Stochastic variation among counts may even reduce a user's power to discriminate ecological condition among sites (Bush et al, 2019). Despite this understanding, and a growing body of evidence to show occurrence data are sufficient and potentially more effective at detecting changes in habitat condition (Beentjes et al, 2018; Buchner et al, 2019; Serrana et al, 2022), the application of metabarcoding to support more effective biomonitoring has been hindered by practitioners and legislation demanding authorities collect abundance information (e.g., European Water Framework Directive; Leese et al, 2018). Current biomonitoring practitioners should instead ask themselves if they really need abundance data to answer simple questions based on variations in community composition.…”

Section: Discussionmentioning

confidence: 99%

Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages

Буш

Compson

Rideout

et al. 2023

Molecular Ecology Resources

View full text Add to dashboard Cite

The delivery of consistent and accurate fine‐resolution data on biodiversity using metabarcoding promises to improve environmental assessment and research. Whilst this approach is a substantial improvement upon traditional techniques, critics note that metabarcoding data are suitable for establishing taxon occurrence, but not abundance. We propose a novel hierarchical approach to recovering abundance information from metabarcoding, and demonstrate this technique using benthic macroinvertebrates. To sample a range of abundance structures without introducing additional changes in composition, we combined seasonal surveys with fish‐exclusion experiments at Catamaran Brook in northern New Brunswick, Canada. Five monthly surveys collected 31 benthic samples for DNA metabarcoding divided between caged and control treatments. A further six samples per survey were processed using traditional morphological identification for comparison. By estimating the probability of detecting a single individual, multispecies abundance models infer changes in abundance based on changes in detection frequency. Using replicate detections of 184 genera (and 318 species) from metabarcoding samples, our analysis identified changes in abundance arising from both seasonal dynamics and the exclusion of fish predators. Counts obtained from morphological samples were highly variable, a feature that limited the opportunity for more robust comparison, and emphasizing the difficulty standard methods also face to detect changes in abundance. Our approach is the first to demonstrate how quantitative estimates of abundance can be made using metabarcoding, both among species within sites as well as within species among sites. Many samples are required to capture true abundance patterns, particularly in streams where counts are highly variable, but few studies can afford to process entire samples. Our approach allows study of responses across whole communities, and at fine taxonomic resolution. We discuss how ecological studies can use additional sampling to capture changes in abundance at fine resolution, and how this can complement broad‐scale biomonitoring using DNA metabarcoding.

show abstract

“…Additionally, we used a PCR annealing temperature of 55°C chosen after a temperature gradient PCR of each individual, which was also the optimal condition used from a previous bulk metabarcoding study on freshwater macroinvertebrate communities [ 13 ]. This temperature is relatively higher than the typical conditions, i.e., 50°C, previously used for the BF2 and BR2 fusion primers [e.g., 60 , 61 ].…”

Section: Discussionmentioning

confidence: 99%

“…The development and application of metabarcoding for biodiversity surveys have been considered a game-changer for ecological research, specifically for eukaryotic organisms [6]. Other than the taxonomic characterization of the community sample, metabarcoding data can be used to infer biodiversity indices and has been established as a robust method for environmental impact assessments of freshwater ecosystems [e.g., [9][10][11][12][13]. For these applications, biodiversity is generally quantified with taxonomic, functional, or phylogenetic diversity at the community level (i.e., interspecific diversity) [14].…”

Section: Introductionmentioning

confidence: 99%

Haplotype-level metabarcoding of freshwater macroinvertebrate species: A prospective tool for population genetic analysis

Serrana¹,

Watanabe²

2023

PLoS ONE

Self Cite

View full text Add to dashboard Cite

Metabarcoding is a molecular-based tool capable of large quantity high-throughput species identification from bulk samples that is a faster and more cost-effective alternative to conventional DNA-sequencing approaches. Still, further exploration and assessment of the laboratory and bioinformatics strategies are required to unlock the potential of metabarcoding-based inference of haplotype information. In this study, we assessed the inference of freshwater macroinvertebrate haplotypes from metabarcoding data in a mock sample. We also examined the influence of DNA template concentration and PCR cycle on detecting true and spurious haplotypes. We tested this strategy on a mock sample containing twenty individuals from four species with known haplotypes based on the 658-bp Folmer region of the mitochondrial cytochrome c oxidase gene. We recovered fourteen zero-radius operational taxonomic units (zOTUs) of 421-bp length, with twelve zOTUs having a 100% match with the Sanger haplotype sequences. High-quality reads relatively increased with increasing PCR cycles, and the relative abundance of each zOTU was consistent for each cycle. This suggests that increasing the PCR cycles from 24 to 64 did not affect the relative abundance of each zOTU. As metabarcoding becomes more established and laboratory protocols and bioinformatic pipelines are continuously being developed, our study demonstrated the method’s ability to infer intraspecific variability while highlighting the challenges that must be addressed before its eventual application for population genetic studies.

show abstract

Implications of taxonomic and numerical resolution on DNA metabarcoding-based inference of benthic macroinvertebrate responses to river restoration

Cited by 7 publications

References 70 publications

Applicability of taxonomic sufficiency of macrofaunal assemblages in benthic ecological quality assessments: Insights from a semi-enclosed bay

Applicability of taxonomic sufficiency of macrofaunal assemblages in benthic ecological quality assessments: Insights from a semi-enclosed bay

Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages

Haplotype-level metabarcoding of freshwater macroinvertebrate species: A prospective tool for population genetic analysis

Contact Info

Product

Resources

About