Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up

Environmental DNA (eDNA) based methods (Fig. 1) are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Freshwater fish are actively involved in aquatic ecosystems functioning and diversity, contributing to the health, well-being and economy in every geographic realm. Unfortunately, many freshwater fish are experiencing critical population decline with risk of local or global extinction because of intense anthropogenic pressure. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. To evaluate the performance of the metabarcoding approach specifically designed to measure freshwater fish biodiversity in Alpine lakes and rivers, an intercalibration test was performed. This exercise forecasted the use of mock samples containing either tissue-extracted DNA of different target species or water collected from aquaculture tanks to mimic real environmental water sampling and processing. Moreover, three water samples collected in Lake Bourget (France) were used to compare the efficiency of taxonomic assignments in natural and mock community samples. Our results highlighted a good efficiency of the molecular laboratory protocols for HTS and a good amplification success of the selected primers, providing essential information concerning the taxonomic resolution of the 12S mitochondrial marker. As further confirmation, different concentration of species DNA in the mock samples were well represented by the relative read abundance. This preliminary test confirmed the applicability of eDNA metabarcoding analyses for the biomonitoring of freshwater fish inhabiting Alpine and perialpine lakes and rivers.

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New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment

Scientific Reports ◽

10.1038/s41598-020-74902-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

David T. Milan ◽

Izabela S. Mendes ◽

Júnio S. Damasceno ◽

Daniel F. Teixeira ◽

Naiara G. Sales ◽

...

Keyword(s):

Fish Species ◽

Species Delimitation ◽

Fish Fauna ◽

Environmental Dna ◽

Threshold Value ◽

Full Length ◽

Taxonomic Resolution ◽

Reference Database ◽

Biodiversity Assessment ◽

Neotropical Fish

Abstract The megadiverse Neotropical fish fauna lacks a comprehensive and reliable DNA reference database, which hampers precise species identification and DNA based biodiversity assessment in the region. Here, we developed a mitochondrial 12S ribosomal DNA reference database for 67 fish species, representing 54 genera, 25 families, and six major Neotropical orders. We aimed to develop mini-barcode markers (i.e. amplicons with less than 200 bp) suitable for DNA metabarcoding by evaluating the taxonomic resolution of full-length and mini-barcodes and to determine a threshold value for fish species delimitation using 12S. Evaluation of the target amplicons demonstrated that both full-length library (565 bp) and mini-barcodes (193 bp) contain enough taxonomic resolution to differentiate all 67 fish species. For species delimitation, interspecific genetic distance threshold values of 0.4% and 0.55% were defined using full-length and mini-barcodes, respectively. A custom reference database and specific mini-barcode markers are important assets for ecoregion scale DNA based biodiversity assessments (such as environmental DNA) that can help with the complex task of conserving the megadiverse Neotropical ichthyofauna.

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Spatial Representativeness of Environmental DNA Metabarcoding Signal for Fish Biodiversity Assessment in a Natural Freshwater System

PLoS ONE ◽

10.1371/journal.pone.0157366 ◽

2016 ◽

Vol 11 (6) ◽

pp. e0157366 ◽

Cited By ~ 77

Author(s):

Raphaël Civade ◽

Tony Dejean ◽

Alice Valentini ◽

Nicolas Roset ◽

Jean-Claude Raymond ◽

...

Keyword(s):

Environmental Dna ◽

Biodiversity Assessment ◽

Fish Biodiversity ◽

Dna Metabarcoding ◽

Freshwater System

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Development and validation of an environmental DNA protocol to detect an invasive Caribbean freshwater fish, the guppy ( Poecilia reticulata )

Environmental DNA ◽

10.1002/edn3.248 ◽

2021 ◽

Author(s):

Sierra N. Smith ◽

Ingo Schlupp ◽

Edward D. Higgins ◽

Jessa L. Watters ◽

Kerri‐Ann Bennett ◽

...

Keyword(s):

Freshwater Fish ◽

Poecilia Reticulata ◽

Environmental Dna ◽

Development And Validation

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Extracellular DNA in environmental samples: Occurrence, extraction, quantification, and impact on microbial biodiversity assessment

Applied and Environmental Microbiology ◽

10.1128/aem.01845-21 ◽

2021 ◽

Author(s):

Sakcham Bairoliya ◽

Jonas Koh Zhi Xiang ◽

Bin Cao

Keyword(s):

Dna Sequencing ◽

Microbial Communities ◽

Dna Extraction ◽

Environmental Samples ◽

Environmental Dna ◽

Extracellular Dna ◽

Biodiversity Assessment ◽

Microbial Biodiversity ◽

Technical Details ◽

The Impact

Environmental DNA, i.e., DNA directly extracted from environmental samples, has been applied to understand microbial communities in the environments and to monitor contemporary biodiversity in the conservation context. Environmental DNA often contains both intracellular DNA (iDNA) and extracellular DNA (eDNA). eDNA can persist in the environment and complicate environmental DNA sequencing-based analyses of microbial communities and biodiversity. Although several studies acknowledged the impact of eDNA on DNA-based profiling of environmental communities, eDNA is still being neglected or ignored in most studies dealing with environmental samples. In this article, we summarize key findings on eDNA in environmental samples and discuss the methods used to extract and quantify eDNA as well as the importance of eDNA on the interpretation of experimental results. We then suggest several factors to consider when designing experiments and analyzing data to negate or determine the contribution of eDNA to environmental DNA-based community analyses. This field of research will be driven forward by: (i) carefully designing environmental DNA extraction pipelines by taking into consideration technical details in methods for eDNA extraction/removal and membrane-based filtration and concentration; (ii) quantifying eDNA in extracted environmental DNA using multiple methods including qPCR and fluorescent DNA binding dyes; (iii) carefully interpretating effect of eDNA on DNA-based community analyses at different taxonomic levels; and (iv) when possible, removing eDNA from environmental samples for DNA-based community analyses.

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Environmental flow envelopes: quantifying ecosystem-threatening flow alterations

10.5194/egusphere-egu21-14627 ◽

2021 ◽

Author(s):

Vili Virkki ◽

Elina Alanärä ◽

Miina Porkka ◽

Lauri Ahopelto ◽

Tom Gleeson ◽

...

Keyword(s):

Lower Bound ◽

Upper Bound ◽

Human Impacts ◽

Well Being ◽

Environmental Flow ◽

Freshwater Ecosystems ◽

Low Flow ◽

Anthropogenic Pressure ◽

Basin Scale ◽

Climate Forcings

The benefits of harnessing rivers into human use should not come with a disproportionate expense on the Earth system. Especially, freshwater ecosystems suffer greatly from direct and indirect human impacts, such as excessive water withdrawals and climate change, which are expected to only increase in the near future. Here, we aim for quantifying the extent and degree of considerable flow alterations that threaten the well-being of freshwater ecosystems, across the world.At the global scale, the ecological status of river systems is often assessed using global hydrological models (GHMs) and hydrological environmental flow (EF) methods. These suffer from substantial uncertainties: 1) the GHMs parameterised with variable climate forcings may give highly dispersed discharge estimates and 2) individual hydrological EF methods capture ecosystem water needs poorly. We tackle these sources of uncertainty by introducing a novel methodology: environmental flow envelopes (EFEs). The EFE is an envelope of safe discharge variability between a lower and an upper bound, defined at the sub-basin scale in monthly time resolution. It is based on pre-industrial (1801-1860) discharge and a large ensemble of EF methods, GHMs, and climate forcings, using ISI-MIP2b data. Using the EFE, we can simultaneously assess the frequency and severity of ecosystem-threatening flow alterations.Comparing post-industrial (1976-2005) discharge to the EFEs, discharge in 32.7% of the total 3860 sub-basins, covering 28.4% of the global landmass, violates the EFE during more than 10% of all months across four GHMs. These violations are considered as severe threats to freshwater ecosystems. The most impacted regions include areas with high anthropogenic pressure, such as the Middle East, India, Eastern Asia, and Middle America. The violations clearly concentrate on the EFE lower bound during low or intermediate flow seasons. Discharge in 61.4% of sub-basins violates the EFE during more than 10% of low flow season months, average violation being 47.5% below the safe limit denoted by EFE lower bound. Indications of significantly increased flows by violations of the EFE upper bound are fewer and further apart, as well as lower bound violations during high flow season.Although fractional discharge allocations alone cannot fully capture the ecosystem water needs, this study is a step towards less uncertainty in global EF assessments. The introduced method provides a novel, globally robust way of estimating ecosystem water needs at the sub-basin scale. The results of this study underline the importance of the low flow season, during which EFE violations are the most prevalent. While only preliminary evidence of significantly increased flows emerges in relatively few areas, the EFE upper bound would benefit from further research. The EFE methodology can be used for exploring macro-regional areas where anthropogenic flow alteration threatens freshwater ecosystems the most. However, case-specific studies incorporating factors beyond quantitative flow only are required for practical implications.

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Freshwater Fish Biodiversity in Iraq: Importance, Threats, Status, and Conservation Challenges

10.1007/978-3-030-57570-0_19 ◽

2021 ◽

pp. 479-497

Author(s):

Laith A. Jawad

Keyword(s):

Freshwater Fish ◽

Fish Biodiversity

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Complete Field Guide to Dragonflies of Australia

10.1071/9780643094109 ◽

2006 ◽

Cited By ~ 21

Author(s):

Gunther Theischinger ◽

John Hawking

Keyword(s):

Environmental Protection ◽

Freshwater Fish ◽

Well Being ◽

Detailed Knowledge ◽

Field Guide ◽

Distribution Maps ◽

Identification Keys ◽

Complete Field ◽

First Time ◽

Important Basis

Dragonflies and damselflies are conspicuous insects – many are large and brightly coloured. Here for the first time is a comprehensive guide to the Australian dragonfly fauna. The book includes identification keys not only for adults but also for their larvae, commonly known as ‘mud eyes’ and often used as bait for freshwater fish. With stunning full-colour images and distribution maps, the book covers all 30 families, 110 genera and 324 species found in Australia. Dragonflies are valuable indicators of environmental well-being. A detailed knowledge of the dragonfly fauna and its changes is therefore an important basis for decisions about environmental protection and management. Their extraordinary diversity will interest entomologists and amateur naturalists alike.

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