Quality assurance of diatom counts in Europe: towards harmonized datasets

Kahlert, Maria; Ács, Éva; Almeida, Salomé F.P.; Blanco, Saúl; Dreßler, Mirko; Éctor, Luc; Karjalainen, Satu Maaria; Liess, Antonia; Mertens, Adrienne; Wal, Jako van der; Vilbaste, Sirje; Werner, Petra

doi:10.1007/s10750-016-2651-8

Cited by 34 publications

(26 citation statements)

References 24 publications

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“…However, the taxonomic identification process often lacks a validation process or an assignment score. The classifications of diatoms to species level can vary between taxonomists, depending on skill level and availability of taxonomic keys and their updates [70][71][72]. It has been noted that quantifying diatom classification error based on the analyst's performance is difficult, as many factors can influence the results [73].…”

Section: Discussionmentioning

confidence: 99%

“…It has been noted that quantifying diatom classification error based on the analyst's performance is difficult, as many factors can influence the results [73]. Inconsistencies between classified diatom datasets can misinform diatom taxon-specific water quality assessments [70] and there has been limited research to date concerning the 'certainty' and 'precision' of ecological classifications based on diatoms as bioindicators [74]. For DNA metabarcoding approaches, despite incomplete reference libraries being a limiting factor [75], it is possible to ascertain a quantifiable level of identification certainty not currently possible, or at least not widely reported, with conventional identification.…”

Section: Discussionmentioning

confidence: 99%

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Freshwater diatom biomonitoring through benthic kick-net metabarcoding

et al. 2020

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Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms as well as macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes that currently only use the kick-net technique to sample macroinvertebrates.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

et al. 2020

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“…Secondly, there is a need to update and reevaluate the indicator and sensitivity values, since changes in diatom taxonomy happen very fast leading to new names and/or species descriptions. This in turn leads then to different results in quality indices calculations (Kahlert et al, 2016). Also, both values are inferred from aquatic surveys and many of them are probably not reflecting the behavior of soil diatoms in terrestrial habitats (Antonelli et al, 2017).…”

Section: Ips and Future Modificationsmentioning

confidence: 99%

Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on communities

Foets

Wetzel

Teuling

et al. 2020

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Diatoms are generally regarded as inhabitants of water bodies. However, numerous taxa are able to survive and reproduce in a variety of non-aquatic ecosystems. Although terrestrial diatoms are discussed extensively in the literature, most of those studies covered floristic aspects and few information exists on their ecology. This lack of knowledge thwarts their potential use as environmental markers in various applications. As a way forward, we investigated the seasonal patterns and the role of different disturbances on the community composition. We collected soil diatom samples in 16 sites across the Attert River basin (Luxembourg) every 4 weeks for a period of 14 months. Our results indicate that forests create a stable microhabitat for diatoms and that temporal variation of the diatom communities is mainly controlled by farming practices rather than seasonal changes in environmental variables. We also found out that communities need one to 2 months to reestablish a new, stable community after a significant change in the environment. We were able to confirm the applicability of the Pollution-Sensitivity Index (IPS) to identify anthropic disturbances.

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“…Many of taxa recognized in early studies have been overlooked in recent surveys and coerced into incorrect names. Inter-lab comparisons have made a significant improvement in coordination of analysts working in different countries (Kahlert et al 2009, Kelly 2013, Kahlert et al 2016, particularly for the coordination efforts to be made prior to analysis. This voucher flora is a part of a broader effort to improve taxonomic consistency in federal, state and local programs by communicating taxonomic practice and providing accessible identification resources (Spaulding et al 2010).…”

Section: Introductionmentioning

confidence: 99%

A diatom voucher flora from selected southeast rivers (USA)

et al. 2017

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This flora is intended to serve as an image voucher for samples analyzed for the U.S. Geological Survey Southeast Stream Quality Assessment (SESQA). The SESQA study included measurement of watershed and water quality parameters to determine the factors that have the greatest potential to alter biotic condition. Algal samples were collected at 108 sites in 2014, from streams representing gradients in chemical and physical alteration across the southeast region. More than 375 taxa were identified during analysis for species composition and abundance. This manuscript documents the flora with light micrographs of specimens representative of their morphologic range. We define "voucher flora" as images of specimens and the names applied to those specimens for a given project. Taxonomic vouchers from federal programs have generally not been made public, yet they are a salient element of a well-documented species dataset, particularly for long-term studies. This study is part of a broader effort to improve and encourage taxonomic consistency in federal, state and local programs by accessible identification resources and inter-lab comparisons.

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Quality assurance of diatom counts in Europe: towards harmonized datasets

Cited by 34 publications

References 24 publications

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

Temporal and spatial variability of terrestrial diatoms at the catchment scale: controls on communities

A diatom voucher flora from selected southeast rivers (USA)

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