DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species

The loss of aquatic biodiversity is increasing at a rapid rate globally. There is a worldwide effort to protect, preserve and restore aquatic ecosystems. For efficient biodiversity monitoring and reliable management tools, comprehensive biodiversity data are required. The abundance and species diversity of benthic macroinvertebrates are commonly used as indicators of the aquatic ecosystem condition. Currently, macroinvertebrate species biodiversity assessment is based on morpho-taxonomy, which could be enhanced by recent advances in DNA-based tools for species identification. In particular, DNA metabarcoding has the potential to identify simultaneously many different taxa in a pool of species and to improve aquatic biomonitoring significantly, especially for indicator species. This review is focused on the current state of DNA-based aquatic biomonitoring using benthic macroinvertebrates in the Mediterranean region.

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The Orthoptera fauna of the Stelvio National Park

Bollettino della Società Entomologica Italiana ◽

10.4081/bollettinosei.2018.3 ◽

2018 ◽

pp. 3-20

Author(s):

Daniele Baroni ◽

Marco Bonifacino ◽

Luca Cristiano ◽

Roberta Rossi ◽

Luca Pedrotti ◽

...

Keyword(s):

Habitat Loss ◽

Species Distribution ◽

Protected Area ◽

National Park ◽

Conservation Value ◽

Geographic Differentiation ◽

Biodiversity Monitoring ◽

Check List ◽

Alpine Environment ◽

High Conservation

Within the Project “Animal Biodiversity Monitoring in the Alpine Environment” the Orthoptera fauna has been studied in a three-year period (2013-2015). The first check-list of the protected area, with ecological and biogeographical notes, is presented. We found 40 species (16 Ensifera, 24 Caelifera), corresponding to 11% of the Italian Orthoptera fauna. A geographic differentiation in species distribution among the three areas (Alto Adige - BZ, Trentino - TN and Lombardy - BS and SO) has been detected. The genus Barbitistes is represented by B. serricauda in Alto Adige and B. alpinus in Trentino and Lombardy. Kisella irena is restricted to Peio and Rabbi Valleys only, in connection with this species distribution in Trentino. Within the Park, Euthystira brachyptera is distributed only in Lombardy, despite its habitat is apparently extensively available also in Trentino and Alto Adige. We found Omocestus haemorrhoidalis and Chorthippus vagans only in Val Venosta (BZ). Only two species, previously reported for the study area, has not been detected during our surveys: Celes variabilis and Ruspolia nitidula. The first site of presence of Tettigonia caudata, rare in Italy, within the Park boundaries has been discovered near Martello (BZ). Two endangered taxa of high conservation value, Epacromius tergestinus ponticus and Crysochraon dispar, reported in the last Century just outside the Park boundaries, are probably extinct today due to habitat loss.

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Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA metabarcoding

Molecular Ecology Resources ◽

10.1111/1755-0998.13148 ◽

2020 ◽

Vol 20 (3) ◽

pp. 732-745 ◽

Cited By ~ 5

Author(s):

Mieke Heyde ◽

Michael Bunce ◽

Grant Wardell‐Johnson ◽

Kristen Fernandes ◽

Nicole E. White ◽

...

Keyword(s):

Environmental Dna ◽

Biodiversity Monitoring ◽

Multiple Substrates ◽

Dna Metabarcoding ◽

Terrestrial Biodiversity

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Biodiversity monitoring in seaweed farms by DNA metabarcoding using settlement plates and water samples

10.18174/496237 ◽

2019 ◽

Author(s):

M.S. Bernard ◽

◽

L. Tonk ◽

G.A. de Groot ◽

S. Glorius ◽

...

Keyword(s):

Water Samples ◽

Biodiversity Monitoring ◽

Dna Metabarcoding

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Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

PeerJ ◽

10.7717/peerj.3006 ◽

2017 ◽

Vol 5 ◽

pp. e3006 ◽

Cited By ~ 60

Author(s):

Matthieu Leray ◽

Nancy Knowlton

Keyword(s):

Random Sampling ◽

Marine Invertebrates ◽

Illumina Miseq ◽

Pcr Primers ◽

Biodiversity Monitoring ◽

Analysis Pipeline ◽

Operational Taxonomic Units ◽

Abundance Patterns ◽

Dna Metabarcoding ◽

Data Reproducibility

DNA metabarcoding, the PCR-based profiling of natural communities, is becoming the method of choice for biodiversity monitoring because it circumvents some of the limitations inherent to traditional ecological surveys. However, potential sources of bias that can affect the reproducibility of this method remain to be quantified. The interpretation of differences in patterns of sequence abundance and the ecological relevance of rare sequences remain particularly uncertain. Here we used one artificial mock community to explore the significance of abundance patterns and disentangle the effects of two potential biases on data reproducibility: indexed PCR primers and random sampling during Illumina MiSeq sequencing. We amplified a short fragment of the mitochondrial Cytochrome c Oxidase Subunit I (COI) for a single mock sample containing equimolar amounts of total genomic DNA from 34 marine invertebrates belonging to six phyla. We used seven indexed broad-range primers and sequenced the resulting library on two consecutive Illumina MiSeq runs. The total number of Operational Taxonomic Units (OTUs) was ∼4 times higher than expected based on the composition of the mock sample. Moreover, the total number of reads for the 34 components of the mock sample differed by up to three orders of magnitude. However, 79 out of 86 of the unexpected OTUs were represented by <10 sequences that did not appear consistently across replicates. Our data suggest that random sampling of rare OTUs (e.g., small associated fauna such as parasites) accounted for most of variation in OTU presence–absence, whereas biases associated with indexed PCRs accounted for a larger amount of variation in relative abundance patterns. These results suggest that random sampling during sequencing leads to the low reproducibility of rare OTUs. We suggest that the strategy for handling rare OTUs should depend on the objectives of the study. Systematic removal of rare OTUs may avoid inflating diversity based on commonβdescriptors but will exclude positive records of taxa that are functionally important. Our results further reinforce the need for technical replicates (parallel PCR and sequencing from the same sample) in metabarcoding experimental designs. Data reproducibility should be determined empirically as it will depend upon the sequencing depth, the type of sample, the sequence analysis pipeline, and the number of replicates. Moreover, estimating relative biomasses or abundances based on read counts remains elusive at the OTU level.

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Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey

Scientific Reports ◽

10.1038/s41598-021-98926-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Masaaki Sato ◽

Nariaki Inoue ◽

Ryogen Nambu ◽

Naoki Furuichi ◽

Tomohito Imaizumi ◽

...

Keyword(s):

Fish Species ◽

Internal Standard ◽

Environmental Dna ◽

Artificial Reefs ◽

Sampling Station ◽

Biodiversity Monitoring ◽

Dna Metabarcoding ◽

Positive Correlations ◽

Multiple Species ◽

Echo Sounder

AbstractSince the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.

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Detection of Macrobenthos Species With Metabarcoding Is Consistent in Bulk DNA but Dependent on Body Size and Sclerotization in eDNA From the Ethanol Preservative

Frontiers in Marine Science ◽

10.3389/fmars.2021.637858 ◽

2021 ◽

Vol 8 ◽

Author(s):

Sofie Derycke ◽

Sara Maes ◽

Laure Van den Bulcke ◽

Joran Vanhollebeke ◽

Jan Wittoeck ◽

...

Keyword(s):

Body Size ◽

Reference Database ◽

Biodiversity Monitoring ◽

Marine Monitoring ◽

Diversity Patterns ◽

The North ◽

Dna Metabarcoding ◽

The North Sea ◽

Primer Sets ◽

Marine Macrobenthos

DNA metabarcoding is a promising method to increase cost and time efficiency of marine monitoring. While substantial evidence exists that bulk DNA samples adequately reflect diversity patterns of marine macrobenthos, the potential of eDNA in the ethanol preservative of benthic samples for biodiversity monitoring remains largely unexplored. We investigated species detection in bulk DNA and eDNA from the ethanol preservative in samples from four distinct macrobenthic communities in the North Sea. Bulk DNA and eDNA were extracted with different extraction kits and five COI primer sets were tested. Despite the availability of a nearly complete reference database, at most 22% of the amplicon sequence variants (ASVs) were assigned taxonomy at the phylum level. However, the unassigned ASVs represented only a small fraction of the total reads (13%). The Leray primer set outperformed the four other primer sets in the number of non-chimeric reads and species detected, and in the recovery of beta diversity patterns. Community composition differed significantly between bulk DNA and eDNA samples, but both sample types were able to differentiate the four communities. The probability of detecting a species in the eDNA from the ethanol preservative was significantly lower than for bulk DNA for macrobenthos species having small to medium body size and for species having chitine or CaCO3 in their cuticula. Detection in the bulk DNA samples was not affected by the investigated morphological traits, indicating that monitoring of macrobenthos species will be most robust when using bulk DNA as template for metabarcoding.

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A new species of Derobrachus Audinet-Serville, 1832 (Coleoptera, Cerambycidae, Prioninae) from a cloud forest in Honduras

Zootaxa ◽

10.11646/zootaxa.4422.3.5 ◽

2018 ◽

Vol 4422 (3) ◽

pp. 395

Author(s):

ANTONIO SANTOS-SILVA ◽

NOËL MAL ◽

MARTIJN VAN ROIE ◽

MERLIJN JOCQUÉ

Keyword(s):

New Species ◽

National Park ◽

Cloud Forest ◽

Common Species ◽

Identification Key ◽

Biodiversity Monitoring ◽

Longhorned Beetles ◽

A New Species

A yearly biodiversity monitoring of longhorned beetles (Cerambycidae) in a Honduran cloud forest revealed a new species of prionine. Derobrachus cusucoensis sp. nov. is a locally relatively common species described from Cusuco National Park in Honduras, becoming the ninth species of this genus recorded for the country. Similar both in morphology and a montane habitat to D. dohrni, there is a possibility that this new species represents a disconnected population from the latter that evolved separately. An adapted insert for an existing identification key to all Derobrachus species is included.

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Environmental DNA metabarcoding for biodiversity monitoring of a highly diverse tropical fish community in a coral reef lagoon: Estimation of species richness and detection of habitat segregation

Environmental DNA ◽

10.1002/edn3.132 ◽

2020 ◽

Cited By ~ 3

Author(s):

Shin‐ichiro Oka ◽

Hideyuki Doi ◽

Kei Miyamoto ◽

Nozomi Hanahara ◽

Tetsuya Sado ◽

...

Keyword(s):

Species Richness ◽

Coral Reef ◽

Fish Community ◽

Environmental Dna ◽

Tropical Fish ◽

Habitat Segregation ◽

Biodiversity Monitoring ◽

Reef Lagoon ◽

Dna Metabarcoding ◽

Coral Reef Lagoon

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DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review

Frontiers in Marine Science ◽

10.3389/fmars.2021.730063 ◽

2021 ◽

Vol 8 ◽

Author(s):

Romy Gielings ◽

Maria Fais ◽

Diego Fontaneto ◽

Simon Creer ◽

Filipe Oliveira Costa ◽

...

Keyword(s):

Rrna Genes ◽

Biodiversity Monitoring ◽

Standard Tool ◽

Dna Metabarcoding ◽

High Species Richness ◽

Pre Treatment ◽

18S Rrna Genes ◽

Key Aspects ◽

Response To Environmental Change

Meiofaunal animals, roughly between 0.045 and 1 mm in size, are ubiquitous and ecologically important inhabitants of benthic marine ecosystems. Their high species richness and rapid response to environmental change make them promising targets for ecological and biomonitoring studies. However, diversity patterns of benthic marine meiofauna remain poorly known due to challenges in species identification using classical morphological methods. DNA metabarcoding is a powerful tool to overcome this limitation. Here, we review DNA metabarcoding approaches used in studies on marine meiobenthos with the aim of facilitating researchers to make informed decisions for the implementation of DNA metabarcoding in meiofaunal biodiversity monitoring. We found that the applied methods vary greatly between researchers and studies, and concluded that further explicit comparisons of protocols are needed to apply DNA metabarcoding as a standard tool for assessing benthic meiofaunal community composition. Key aspects that require additional consideration include: (1) comparability of sample pre-treatment methods; (2) integration of different primers and molecular markers for both the mitochondrial cytochrome c oxidase subunit I (COI) and the nuclear 18S rRNA genes to maximize taxon recovery; (3) precise and standardized description of sampling methods to allow for comparison and replication; and (4) evaluation and testing of bioinformatic pipelines to enhance comparability between studies. By enhancing comparability between the various approaches currently used for the different aspects of the analyses, DNA metabarcoding will improve the long-term integrative potential for surveying and biomonitoring marine benthic meiofauna.

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