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12 results for “environmental biomonitoring”
A molecular method for biomonitoring of an exotic plant-pest: leafmining for environmental DNA
<p><span>1. Understanding how invasive species respond to novel environments is limited by a lack of sensitivity and throughput in conventional biomonitoring methods.<i> </i>Arthropods in particular are often difficult to monitor due to their small size, rapid lifecycles, and/or visual similarities with co-occurring species<i>. </i>This is true for the agromyzid leafminer fly, <i>Liriomyza sativae</i>, a global pest of vegetable and nursery industries that has recently established in Australia. </span></p> <p><span>2. A robust method based on environmental DNA (eDNA) was developed exploiting traces of DNA left inside 'empty' leaf mines, which are straightforward to collect and persist longer in the environment than the fly. This extends the window of possible diagnosis to at least 28 days after a leaf mine becomes empty. The test allowed for visually indistinguishable leafmining damage caused by <i>L. sativae</i> to be genetically differentiated from that of other flies. </span></p> <p><span> 3. Field application resulted in the identification of new local plant hosts for <i>L. sativae</i>, including widely distributed weeds and common garden crops, which has important implications for the pest's ability to spread. Moreover, the test confirmed the presence of a previously unknown population of <i>L. sativae</i> on an island in the Torres Strait. </span></p> <p>4. The developed eDNA method is likely to become an important tool for <i>L. sativae</i> and other leafmining species of biosecurity significance, which, historically, have been difficult to detect, diagnose and monitor. More generally, eDNA is emerging as a highly sensitive and labour-efficient surveillance tool for difficult to survey species to improve outcomes for agricultural industries, global health, and the environment.</p>
Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates
Recent studies have advocated biomonitoring using DNA techniques. In this study, two high-throughput sequencing (HTS)-based methods were evaluated: amplicon metabarcoding of the cytochrome C oxidase subunit I (COI) mitochondrial gene and gene enrichment using MYbaits (targeting nine different genes including COI). The gene-enrichment method does not require PCR amplification and thus avoids biases associated with universal primers. Macroinvertebrate samples were collected from 12 New Zealand rivers. Macroinvertebrates were morphologically identified and enumerated, and their biomass determined. DNA was extracted from all macroinvertebrate samples and HTS undertaken using the illumina miseq platform. Macroinvertebrate communities were characterized from sequence data using either six genes (three of the original nine were not used) or just the COI gene in isolation. The gene-enrichment method (all genes) detected the highest number of taxa and obtained the strongest Spearman rank correlations between the number of sequence reads, abundance and biomass in 67% of the samples. Median detection rates across rare (<1% of the total abundance or biomass), moderately abundant (1–5%) and highly abundant (>5%) taxa were highest using the gene-enrichment method (all genes). Our data indicated primer biases occurred during amplicon metabarcoding with greater than 80% of sequence reads originating from one taxon in several samples. The accuracy and sensitivity of both HTS methods would be improved with more comprehensive reference sequence databases. The data from this study illustrate the challenges of using PCR amplification-based methods for biomonitoring and highlight the potential benefits of using approaches, such as gene enrichment, which circumvent the need for an initial PCR step.
Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats
<p>Conservation and management of marine biodiversity depends on biomonitoring of marine habitats,<br> but current approaches are resource-intensive and require different approaches for different organisms. Environmental<br> DNA (eDNA) extracted from water samples is an efficient and versatile approach to detecting aquatic<br> animals. In the ocean, eDNA composition reflects local fauna at fine spatial scales, but little is known about the<br> effectiveness of eDNA-based monitoring of marine communities at larger scales. We investigated the potential of<br> eDNA to characterize and distinguish marine communities at large spatial scales by comparing vertebrate species<br> composition among marine habitats in Qatar, the Arabian Gulf (also known as the Persian Gulf), based on eDNA<br> metabarcoding of seawater samples. We conducted species accumulation analyses to estimate how much of the<br> vertebrate diversity we detected. We obtained eDNA sequences from a diverse assemblage of marine vertebrates,<br> spanning 191 taxa in 73 families. These included rare and endangered species and covered 36% of the bony fish<br> genera previously recorded in the gulf. Sites of similar habitat type were also similar in eDNA composition. The<br> species accumulation analyses showed that the number of sample replicates was insufficient for some sampling<br> sites but suggested that a few hundred eDNA samples could potentially capture >90% of the marine vertebrate<br> diversity in the study area. Our results confirm that seawater samples contain habitat-characteristic molecular<br> signatures and that eDNA monitoring can efficiently cover vertebrate diversity at scales relevant to national and<br> regional conservation and management.</p>
Data from: Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates
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Using vertebrate environmental DNA from seawater in biomonitoring of marine habitats
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Data from: Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events
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A molecular method for biomonitoring of an exotic plant-pest: leafmining for environmental DNA
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Supplementary material 1 from: Zangaro F, Saccomanno B, Tzafesta E, Bozzeda F, Specchia V, Pinna M (2021) Current limitations and future prospects of detection and biomonitoring of NIS in the Mediterranean Sea through environmental DNA. NeoBiota 70: 151-165. https://doi.org/10.3897/neobiota.70.71862
Table S1
Assessing environmental DNA metabarcoding and camera trap surveys as complementary tools for biomonitoring of remote desert water bodies
<p>Biodiversity assessments are indispensable tools for planning and monitoring conservation strategies. Camera traps (CT) are widely used to monitor wildlife and have proven their usefulness. Environmental DNA (eDNA)-based approaches are increasingly implemented for biomonitoring, combining sensitivity, high taxonomic coverage and resolution, non-invasiveness and easiness of sampling, but remain challenging for terrestrial fauna. However, in remote desert areas where scattered water bodies attract terrestrial species, which release their DNA into the water, this method presents a unique opportunity for their detection. In order to identify the most efficient method for a given study system, comparative studies are needed. Here, we compare CT and DNA metabarcoding of water samples collected from two desert ecosystems, the Trans-Altai Gobi in Mongolia and the Kalahari in Botswana. We recorded with CT the visiting patterns of wildlife and studied the correlation with the biodiversity captured with the eDNA approach. The aim of the present study was threefold: a) to investigate how well waterborne eDNA captures signals of terrestrial fauna in remote desert environments, which have been so far neglected in terms of biomonitoring efforts; b) to compare two distinct approaches for biomonitoring in such environments and c) to draw recommendations for future eDNA-based biomonitoring. We found significant correlations between the two methodologies and describe a detectability score based on variables extracted from CT data and the visiting patterns of wildlife. This supports the use of eDNA-based biomonitoring in these ecosystems and encourages further research to integrate the methodology in the planning and monitoring of conservation strategies.</p>
Assessing environmental DNA metabarcoding and camera trap surveys as complementary tools for biomonitoring of remote desert water bodies
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Optimising environmental DNA biomonitoring for Kakadu National Park's freshwater fish communities
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Biomonitoring of Environmental Pollution: An Exploratory Investigation Using Mosses and X-Ray Fluorescence(XRF) Spectroscopy
<p>Raw data and voucher information used for a study</p>
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