131 research outputs found
The future of biotic indices in the ecogenomic era: Integrating (e)DNA metabarcoding in biological assessment of aquatic ecosystems
The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/
or abundance of selected taxonomic groups to define ecological status. These conventional indices have some
limitations, often related to difficulties inmorphological identification of bioindicator taxa. Recent development
of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences
instead of morphology to identify organisms and to characterize a given ecosystem. In this paper,we review
the structure of conventional biotic indices, andwe present the results of pilotmetabarcoding studies using
environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches
to assess parameters such as richness, abundance, taxonomic composition and species ecological
values, to be used for calculation of biotic indices.We present some future developments to fully exploit the potential
of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some
recommendations for the future integration of DNA metabarcoding to routine biomonitoring program
A comparison of biotic groups as dry-phase indicators of ecological quality in intermittent rivers and ephemeral streams
Intermittent rivers and ephemeral streams (IRES) are dynamic ecosystems that shift between aquatic and terrestrial states. IRES are widespread, abundant and increasing in extent, but developing biomonitoring programmes to determine their ecological quality is challenging. To date, quality assessments have focused on the aquatic organisms present during wet phases, whereas dry-phase communities remain poorly characterized. We examined multiple biotic groups present in dry IRES channels, to compare assemblages at sites impacted and unimpacted by human activity and to evaluate the potential of each group as an ecological quality indicator. We explored existing, unpublished data for three biotic groups: an aquatic microflora (diatoms), an aquatic fauna (the invertebrate ‘seedbank’), and a mixed flora (aquatic and terrestrial plants); notably, we did not source data for terrestrial assemblages with high potential to act as indicators. Diatom and plant assemblage composition differed between impacted and unimpacted sites, and the latter assemblages were more diverse and included more indicator taxa. Invertebrate seedbank taxa richness was higher at unimpacted sites but compositional differences were not detected, probably due to the coarse taxonomic resolution to which abundant taxa were identified. Performance of standard indices of ecological quality was variable, but differences were identified between impacted and unimpacted conditions for all biotic groups. Our results can inform the enhancement of biomonitoring programmes designed to characterize IRES ecological quality in relation to legislative targets. We highlight the need to integrate wet- and dry-phase survey data in holistic quality assessments. Although we suggest diatoms, aquatic plants and the aquatic invertebrate seedbank as having the potential to inform assessment of dry-phase ecological quality, we highlight the need for research to further characterize these aquatic groups and, crucially, to explore terrestrial assemblages with high potential to act as dry-phase quality indicators
Simonsenia aveniformis sp nov (Bacillariophyceae), molecular phylogeny and systematics of the genus, and a new type of canal raphe system
The genus Simonsenia is reviewed and S. aveniformis described as new for science by light and electron microscopy. The new species originated from estuarine environments in southern Iberia (Atlantic coast) and was isolated into culture. In LM, Simonsenia resembles Nitzschia, with bridges (fibulae) beneath the raphe, which is marginal. It is only electron microscope (EM) examination that reveals the true structure of the raphe system, which consists of a raphe canal raised on a keel (wing), supported by rib like braces (fenestral bars) and tube-like portulae; between the portulae the keel is perforated by open windows (fenestrae). Based on the presence of portulae and a fenestrated keel, Simonsenia has been proposed to be intermediate between Bacillariaceae and Surirellaceae. However, an rbcL phylogeny revealed that Simonsenia belongs firmly in the Bacillariaceae, with which it shares a similar chloroplast arrangement, rather than in the Surirellaceae. Lack of homology between the surirelloid and simonsenioid keels is reflected in subtle differences in the morphology and ontogeny of the portulae and fenestrae. The diversity of Simonsenia has probably been underestimated, particularly in the marine environment.Polish National Science Centre in Cracow within the Maestro program [N 2012/04/A/ST10/00544]; Sciences and Technologies Foundation-FCT (Portugal) [SFRH/BD/62405/2009]info:eu-repo/semantics/publishedVersio
DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work
Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding) requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD) and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants) are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%) in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.This paper is a deliverable of the European Cooperation in Science and Technology (COST) Action DNAqua-Net (CA15219) Working Group 1, led by Torbjørn Ekrem and Fedor Čiampor. Thanks to the University of
Minho and University of Pécs for hosting workshops and working group meetings. We also thank staff at National Environment Agencies and others that provided national checklists of taxa used in biomonitoring,
and otherwise assisted with checklist proof-reading: Jarmila Makovinská and Emília Mišíková Elexová (Slovakia); Steinar Sandøy and Dag Rosland (Norway); Mišel Jelič (Croatia); Marlen Vasquez
(Cyprus); Adam Petrusek (Czech Republic); Kristel Panksep (Estonia);
Panagiotis Kaspiditis (Greece); Matteo Montagna (Italy); Marija
Katarzyte (Lithuania); Ana Rotter (Slovenia); Rosa Trabajo (Spain);
Florian Altermatt (Switzerland); Kristian Meissner (Finland), Rigers
Bakiu (Albania), Valentina Stamenkovic and Jelena Hinic (Macedonia);
Patricia Mergen (Belgium); Gael Denys & the French Biodiversity
Agency (France); Mary Kelly-Quinn (Ireland); Piotr Panek and Andrzej
Zawal (Poland); Cesare Mario Puzzi (Italy); Carole Fitzpatrick (United
Kingdom); Simon Vitecek (Austria); Ana Filipa Filipe (Portugal); Peter
Anton Stæhr & Anne Winding (Denmark); Michael Monaghan
(Germany); Alain Dohet, Lionel L'Hoste, Nora Welschbillig & Luc Ector
(Luxembourg), Lujza Keresztes, (Romania). The authors also want to
thank Dirk Steinke for providing the original European ERMS list for marine taxa and Florian Malard for comments on the manuscript. The preparation of the AMBI checklist was carried out in the scope of a
Short-term Scientific Mission (ECOST-STSM-CA15219-150217- 082111) granted to SD visiting AZTI, Spain. ZC was supported by grants EFOP-3.6.1.-16-2016-00004 and 20765-3/2018/FEKUTSTRAT. TE was
supported by the NorBOL-grant (226134/F50) from the Research Coun cil of Norway. BR, FL and MFG contributed through support from the GBOL project, which is generously funded by the German Federal Min istry of Education and Research (FKZ 01LI1101 and 01LI1501). MG contributed through support of the Polish National Science Centre, grants N N303 5794 39 and 2014/15/B/NZ8/00266. SF was funded by the project PORBIOTA - Portuguese E-Infrastructure for Information and Research
on Biodiversity (POCI-01-0145-FEDER-022127), supported by Operational Thematic Program for Competitiveness and Internationalization (POCI), under the PORTUGAL 2020 Partnership Agreement, through
the European Regional Development Fund (FEDER)
Molecular biogeography of planktonic and benthic diatoms in the Yangtze River
Background: Diatoms are of great significance to primary productivity in oceans, yet little is known about their biogeographic distribution in oligotrophic rivers.
Results: With the help of metabarcoding analysis of 279 samples from the Yangtze River, we provided the first integral biogeographic pattern of planktonic and benthic diatoms over a 6030 km continuum along the world's third largest river. Our study revealed spatial dissimilarity of diatoms under varying landforms, including plateau, mountain, foothill, basin, foothill-mountain, and plain regions, from the river source to the estuary. Environmental drivers of diatom communities were interpreted in terms of photosynthetically active radiation, temperature, channel slope and nutrients, and human interference. Typical benthic diatoms, such as Pinnularia, Paralia, and Aulacoseira, experienced considerable reduction in relative abundance downstream of the Three Gorges Dam and the Xiluodu Dam, two of the world's largest dams.
Conclusions: Our study revealed that benthic diatoms are of particular significance in characterizing motile guild in riverine environments, which provides insights into diatom biogeography and biogeochemical cycles in large river ecosystems
A 2-year survey of phytoplankton in the Marne Reservoir (France): A case study to validate the use of an in situ spectrofluorometer by comparison with algal taxonomy and chlorophyll a measurements
For almost two years (2006–2007), phytoplankton structure and distribution were monitored
using a combination of methods in the Marne Reservoir (France). We used the bbe
FluoroprobeTM spectrofluorometer, which provides vertical profiles for
different algal classes and chlorophyll analysis, based on the in vivo
autofluorescence characteristics of the phytoplankton. In parallel, we measured
chlorophyll a (chl a) concentrations using the classical
extraction method coupled with spectrophotometric analyses, and calculated the biovolume
of all the taxa identified using inverted light microscopy. A very close correlation
(ρ = 0.93, n = 243, p <
0.0001) was found between the total equivalent chl a concentrations given
by the bbe FluoroprobeTM and the total chl a concentrations
(g·L−1) provided by the spectrophotometric analysis. The closest correlation
was obtained for concentrations below 6.9 μg·L−1 whereas
little or no correlation was found for those above 21.6
μg·L−1. The relationship was highly significant when total
phytoplankton biovolume was compared with data from the probe (ρ = 0.6,
n = 243, p < 0.0001), the strongest correlation
being found for the group composed of diatoms, dinoflagellates and chrysophyceae
(ρ = 0.67, p < 0.0001), while the weakest
relationship was for the blue-green cyanobacteria (ρ = 0.33,
p < 0.0001), although it was still highly significant. Our
analysis, based on a large dataset, indicates that the FluoroprobeTM appears to
be a reliable tool suitable for use by fresh water managers to monitor phytoplankton on
any relevant time and space scales
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