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  • 1
    In: Diversity and Distributions, Wiley, Vol. 27, No. 10 ( 2021-10), p. 1942-1957
    Abstract: Environmental DNA (eDNA) metabarcoding has demonstrated its applicability as a highly sensitive biomonitoring tool across small spatial and temporal scales in marine ecosystems. However, it has rarely been tested across large spatial scales or biogeographical barriers. Here, we scale up marine eDNA metabarcoding, test its ability to detect a major marine biogeographic break and evaluate its use as a regional biomonitoring tool in Australia. Location North‐western Australia (NWA). Methods We applied metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes to 284 surface seawater eDNA samples collected from 71 mid‐shelf, inshore, coastal and nearshore estuarine sites over 700 km of the NWA coastline. Results Metabarcoding detected a wide range of bony fish (404 taxa), elasmobranchs (44) and aquatic reptiles (5). We detected bioregional and depth differentiation within inshore bony fish communities. These findings support the presence of a marine biogeographic break, which is purported to occur in the vicinity of Cape Leveque, demarcating the border between the Kimberley and Canning bioregions. Inshore bony fish and elasmobranch communities, as well as coastal bony fish assemblages, were additionally found to differ between the South and North Kimberley regions suggesting previously unrecognized subregional differentiation amongst these taxa. The overall compositional data have been used to update distribution information for a number of endangered, elusive and data‐deficient taxa, including sawfish (family: Pristidae), northern river shark ( Glyphis garricki ) and wedgefish (genus: Rhynchobatus ). Main conclusions eDNA metabarcoding demonstrated a high level of sensitivity that was able to discern fine‐scale patterns across the large‐scale, remote and oceanographically complex region of North‐western Australia. Importantly, this study highlights the potential of integrating broad‐scale eDNA metabarcoding alongside other baseline surveys and long‐term monitoring approaches, which are crucial for the sustainable management and conservation of marine biodiversity in this unique marine region.
    Type of Medium: Online Resource
    ISSN: 1366-9516 , 1472-4642
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020139-4
    detail.hit.zdb_id: 1443181-6
    SSG: 12
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  • 2
    In: Molecular Ecology, Wiley, Vol. 29, No. 6 ( 2020-03), p. 1069-1086
    Abstract: Environmental DNA (eDNA) metabarcoding, a technique for retrieving multispecies DNA from environmental samples, can detect a diverse array of marine species from filtered seawater samples. There is a growing potential to integrate eDNA alongside existing monitoring methods in order to establish or improve the assessment of species diversity. Remote island reefs are increasingly vulnerable to climate‐related threats and as such there is a pressing need for cost‐effective whole‐ecosystem surveying to baseline biodiversity, study assemblage changes and ultimately develop sustainable management plans. We investigated the utility of eDNA metabarcoding as a high‐resolution, multitrophic biomonitoring tool at the Cocos (Keeling) Islands, Australia (CKI)—a remote tropical coral reef atoll situated within the eastern Indian Ocean. Metabarcoding assays targeting the mitochondrial 16S rRNA and CO1 genes, as well as the 18S rRNA nuclear gene, were applied to 252 surface seawater samples collected from 42 sites within a 140 km 2 area. Our assays successfully detected a wide range of bony fish and elasmobranchs (244 taxa), crustaceans (88), molluscs (37) and echinoderms (7). Assemblage composition varied significantly between sites, reflecting habitat partitioning across the island ecosystem and demonstrating the localisation of eDNA signals, despite extensive tidal and oceanic movements. In addition, we document putative new occurrence records for 46 taxa and compare the efficiency of our eDNA approach to visual survey techniques at CKI. Our study demonstrates the utility of a multimarker metabarcoding approach in capturing multitrophic biodiversity across an entire coral reef atoll and sets an important baseline for ongoing monitoring and management.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 3
    In: Environmental DNA, Wiley, Vol. 2, No. 4 ( 2020-10), p. 614-626
    Abstract: Environmental DNA (eDNA) metabarcoding methods have demonstrated their potential as noninvasive techniques for the monitoring and conservation of marine fishes, including rare and endangered taxa. However, the majority of these investigations have focused on large‐bodied taxa such as sharks and sturgeons. In contrast, eDNA studies on small‐bodied cryptic taxa are much less common. As a case in point, seahorses (members of the Syngnathidae family) have never been detected by eDNA, despite the fact that globally there are 14 species classified as “Threatened” by the IUCN. Here, we critically evaluate the ability of two existing broad‐spectrum fish metabarcoding assays (MiFish and 16S Fish) and explore the efficacy of two newly designed fish metabarcoding assays (16S_FishSyn_Short and 16S_FishSyn_Long) to detect Syngnathidae amidst a wide spectrum of fish species. Furthermore, a custom Western Australian 16S rRNA fish database was created to increase the likelihood of correct taxonomic assignments. With the newly designed assays, we detected four Syngnathidae species in a targeted eDNA survey of the Perth metropolitan area (Western Australia). These detections include the seahorse species Hippocampus subelongatus and Hippocampus breviceps , which represents the first time seahorse species have been detected using eDNA. The existing MiFish and 16S Fish assays did not detect any Syngnathidae. This evaluation of all four fish metabarcoding assays reinforces the view that every PCR assay has “blind spots”. In the context of complex environmental samples, no assay is universal and false negatives will occur due to a combination of PCR efficacy, primer binding, assay sensitivity, degeneracies in the primers, template competition, and amplicon length. Taken together, these data indicate that eDNA methodologies, with ongoing optimizations, will become an integral part of monitoring small‐bodied cryptic taxa such as seahorses, gobies, and blennies and can assist in mapping species’ distributions and prioritizing conservation areas.
    Type of Medium: Online Resource
    ISSN: 2637-4943 , 2637-4943
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 3001165-6
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  • 4
    In: Molecular Ecology Resources, Wiley, Vol. 19, No. 2 ( 2019-03), p. 366-376
    Abstract: Effective biomonitoring is critical for driving management outcomes that ensure long‐term sustainability of the marine environment. In recent years, environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data are needed on how to best implement eDNA field sampling approaches to maximize their utility for each specific application. The effect of the substrate chosen for eDNA sampling on the diversity of marine taxa detected by DNA metabarcoding has not yet been systematically analysed, despite aquatic systems being those most commonly targeted for eDNA studies. We investigated the effect of four commonly used eDNA substrates to explore taxonomic diversity: (a) surface water, (b) marine sediment, (c) settlement plates and (d) planktonic tows. With a focus on coastal ports, 332 eDNA samples from Australia (Indian and Southern oceans) and Kazakhstan (Caspian Sea) were collected and analysed by multi‐assay DNA metabarcoding. Across study locations, between 30% and 52% of eukaryotic families detected were unique to a particular substrate and 〈 6% of families were found in all four substrates. Taxonomic composition varied significantly depending on the substrate sampled implying that the suitability (and bias) of an eDNA substrate will depend on the focal taxa. These findings demonstrate that single substrate eDNA metabarcoding likely underestimates the total eukaryotic diversity. Future eDNA experimental design should consider incorporating multiple substrates or select substrate(s) best suited to the specific detection of target taxa.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 5
    In: British Journal of Urology, Wiley, Vol. 79, No. 3 ( 1997-03), p. 439-444
    Abstract: Objective  To assess the detection of prostate cancer using the Ciba Corning ACS 180 prostate‐specific antigen (PSA) assay and transrectal ultrasonography (TRUS) in a district general hospital. Patients and methods  In a preliminary study, the serum PSA level in 130 patients was measured using both the Ciba Corning and the Hybritech Tandem‐R PSA assay and the results assessed using linear regression analysis. A further study comprised 204 consecutive patients who underwent TRUS and biopsy. The histology of the prostatic biopsies was analysed according to the pre‐biopsy PSA level (Ciba Corning assay), digital rectal examination (DRE) and TRUS findings. Results  The PSA levels measured using the Ciba Corning assay were about 50% higher than those using the Hybritech Tandem‐R assay. Of 204 men who had TRUS and biopsy, 56 (28%) had detectable prostate cancer, but no patient with a PSA of 〈 6.0 ng/mL had. Five of 47 (11%), 21 of 83 (25%) and 30 of 65 (46%) patients with PSA levels in the range 6.1–15, 15.1–30 and 〉 30 ng/mL, respectively, had cancer detected. When the DRE was negative, 18 of 111 (16%) patients had a positive biopsy, compared with 38 of 93 (41%) patients when the DRE was positive ( P 〈 0.001). In men with a PSA level of 6.1–15.0 ng/mL, positive biopsies were found in 3% when the DRE was negative, compared with 27% when it was positive ( P 〈 0.025). A TRUS abnormality was detected in 54 of 204 (26%) patients, of whom 25 (46%) had positive biopsies. Of these 54, there were 43 with hypoechoic lesions, of whom 22 (51%) had positive biopsies. The cancer detection rate was higher when both TRUS and DRE were positive (62%), with the highest detection rate (86%) occurring when the PSA level was also 〉 30.0 ng/mL. When the DRE was positive, cancer was detected in 21 of 34 (62%) patients with a positive TRUS, but only in 17 of 59 (29%) patients with a negative TRUS ( P 〈 0.005). However, when the DRE was negative there was no significant difference in the cancer detection rates for TRUS‐positive and TRUS‐negative patients, where four of 20 and 14 of 91 (15%) patients were found to have cancer, respectively. Conclusions  The positive biopsy rates in this study were comparable with those from similar studies using other PSA assays. When the DRE was negative there was a low detection rate for cancer of 3% for men with PSA levels of 6.1–15.0 ng/mL. In patients with an elevated PSA level but a negative DRE, the positive biopsy rate for TRUS‐negative patients did not differ from TRUS‐positive patients, indicating the importance of random systematic biopsies.
    Type of Medium: Online Resource
    ISSN: 0007-1331
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 1997
    detail.hit.zdb_id: 2019983-1
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  • 6
    In: Diversity and Distributions, Wiley, Vol. 29, No. 7 ( 2023-07), p. 862-878
    Abstract: To use a long‐term collection of bulk plankton samples to test the capacity of DNA metabarcoding to characterize the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme. Location Samples were sourced seasonally for 3 years from nine Pan‐Australian marine sites (n = 90). Methods Here, we apply a multi‐assay metabarcoding approach to environmental DNA extracted from bulk plankton samples. Six assays (targeting 16SrRNA and COI genes) were used to target, amplify and sequence the zooplankton diversity found within each sample. The data generated from each assay were filtered and clustered into OTUs prior to analysis. Abiotic IMOS data collected contemporaneously enabled us to explore the physical and chemical drivers of community composition. Results From over 25 million sequences, we identified in excess of 500 distinct taxa and detected clear spatial differences. We found that site and sea surface temperature are the most consistent predictors of differences between zooplankton communities. We detected endangered and invasive species such as the bryozoan Membranipora membranacea and the mollusc Maoricolpus roseus , and seasonal occurrences of species such as humpback whales ( Megaptera novaeangliae ). We also estimated the number of samples required to detect any significant seasonal changes. For OTU richness, this was found to be assay dependent and for OTU assemblage, a minimum of nine samples per season would be required. Main Conclusion Our results demonstrate the ability of DNA to capture and map zooplankton community changes in response to seasonal and spatial stressors and provide vital evidence to environmental stakeholders. We confirm that a metabarcoding method offers a practical opportunity for an ecosystem‐wide approach to long‐term biomonitoring and understanding marine biomes where morphological analysis is not feasible.
    Type of Medium: Online Resource
    ISSN: 1366-9516 , 1472-4642
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2020139-4
    detail.hit.zdb_id: 1443181-6
    SSG: 12
    Location Call Number Limitation Availability
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  • 7
    In: Conservation Biology, Wiley, Vol. 33, No. 1 ( 2019-02), p. 196-205
    Abstract: Article impact statement : Use of video and environmental genomics in conservation will greatly improve capacity to effectively monitor fish biodiversity.
    Type of Medium: Online Resource
    ISSN: 0888-8892 , 1523-1739
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2020041-9
    SSG: 12
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