Dataset Information

Aquatic suspended particulate matter as source of eDNA for fish metabarcoding.

ABSTRACT: The use of environmental DNA (eDNA) for monitoring aquatic macrofauna allows the non-invasive species determination and measurement of their DNA abundance and typically involves the analysis of eDNA captured from water samples. In this proof-of-concept study, we focused on the novel use of eDNA extracted from archived suspended particulate matter (SPM) for identifying fish species using metabarcoding, which benefits from the prospect of retrospective monitoring and also analysis of fish communities through time. We used archived SPM samples of the German Environmental Specimen Bank (ESB), which were collected using sedimentation traps from different riverine points in Germany. Environmental DNA was extracted from nine SPM samples differing in location, organic content, and porosity (among other factors) using four different methods for the isolation of high-quality DNA. Application of the PowerSoil DNA Isolation Kit with an overnight incubation in lysis buffer, resulted in DNA extraction with the highest purity and eDNA metabarcoding of these eDNA fragments was used to detect a total of 29 fish taxa among the analyzed samples. Here we demonstrated for the first time that SPM is a promising source of eDNA for metabarcoding analysis, which could provide valuable retrospective information (when using archived SPM) for fish monitoring, complementing the currently used approaches.

SUBMITTER: Diaz C

PROVIDER: S-EPMC7463230 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Aquatic suspended particulate matter as source of eDNA for fish metabarcoding.

Díaz Cecilia C Wege Franziska-Frederike FF Tang Cuong Q CQ Crampton-Platt Alexandra A Rüdel Heinz H Eilebrecht Elke E Koschorreck Jan J

Scientific reports 20200901 1

The use of environmental DNA (eDNA) for monitoring aquatic macrofauna allows the non-invasive species determination and measurement of their DNA abundance and typically involves the analysis of eDNA captured from water samples. In this proof-of-concept study, we focused on the novel use of eDNA extracted from archived suspended particulate matter (SPM) for identifying fish species using metabarcoding, which benefits from the prospect of retrospective monitoring and also analysis of fish communit ...[more]

PMID: 32873823

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Project description:Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.

Project description:BackgroundEvidence from various epidemiological studies has shown an association between particulate matter 2.5 (PM2.5) and diabetes mellitus. A prospective study from the United States reported that exposure to PM2.5 alters endothelial function, and leads to insulin resistance and reduction in peripheral glucose uptake. There is a paucity of data on the relation between air pollution and diabetes in low- and middle-income countries.ObjectivesTo estimate the prevalence of type 2 diabetes among people living in areas with higher exposures of suspended PM2.5 compared to people living in areas with lower exposures in Chennai, Tamil Nadu, India.MethodsA cross-sectional study was carried out in two areas of Chennai city. The PM2.5 affecting vulnerable areas were stratified from a list of air quality monitoring stations in Tamil Nadu Pollution Control Board and Central Pollution Control Board. The highest and lowest areas of exposure were selected from the list. Households were randomly selected for the study. A total of 201 (67 male, 134 female) individuals from a high exposure area (HEA) and 209 (76 male 133 female) individuals from a low exposure area (LEA) were recruited for the study. Adults over 18 years of age were screened for random capillary blood glucose (RCBG) by glucometer (OneTouch Ultra).ResultsThe prevalence of diabetes (34.8% vs 19.6% p =0.001) was 77.5% higher among people living in areas of high particulate matter exposure compared to people living in less exposed areas. Multivariable logistic regression analysis showed that age, gender, residential area, and family history of diabetes were significantly associated with the prevalence of diabetes (p<0.05).ConclusionsThe present study indicates a link between high levels of exposure to PM2.5 and diabetes mellitus. Further prospective studies on populations exposed to elevated pollution are needed to establish whether this association has a causative link.Participant consentObtained.Ethics approvalThe study was approved by the Ethics Committee of the Prof. M Viswanathan Diabetes Research Centre, Chennai, India.Competing interestsThe authors declare no competing financial interests.

Dataset Information

Aquatic suspended particulate matter as source of eDNA for fish metabarcoding.

Publications

Aquatic suspended particulate matter as source of eDNA for fish metabarcoding.

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