MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures

Chang, Jia Jin Marc; Ip, Yin Cheong Aden; Bauman, Andrew G.; Huang, Danwei

doi:10.3389/fmars.2020.00448

Cited by 38 publications

(39 citation statements)

References 73 publications

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“…Despite initial data analysis setbacks, we are confident that the final custom pipeline we developed is a suitable, reliable bioinformatics approach for handling the data with ease of reproducibility for any study system. Recently, several third-party freeware options have been developed to analyze long read data generated by nanopore sequencing devices (Chang et al, 2020a;de Koning et al, 2020;Rodríguez-pérez et al, 2020), offering promise for a standardized pipeline in the near future. For our homology search, we used a subset of all metazoan sequences in GenBank with species level identifications, called the MIDORI database (Machida et al, 2017).…”

Section: Discussionmentioning

confidence: 99%

Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

et al. 2021

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Recent advances in molecular sequencing technology and the increased availability of fieldable laboratory equipment have provided researchers with the opportunity to conduct real-time or near real-time gene-based biodiversity assessments of aquatic ecosystems. In this study, we developed a workflow and portable kit for fieldable environmental DNA sequencing (FeDS) and tested its efficacy by characterizing the breadth of jellyfish (Medusozoa) taxa in the coastal waters of the Upper and Lower Florida Keys. Environmental DNA was isolated from seawater collection events at eight sites and samples were subjected to medusozoan 16S rRNA gene and metazoan mitochondrial cytochrome oxidase 1 gene profiling via metabarcoding onsite. In total, FeDS yielded 175,326 processed sequence reads providing evidence for 53 medusozoan taxa. Our most salient findings revealed eDNA from: (1) two venomous box jellyfish (Cubozoa) species, including taxa whose stings cause the notorious Irukandji envenomation syndrome; (2) two species of potentially introduced stalked jellyfish (Staurozoa); and (3) a likely cryptic species of upside-down jellyfish (Scyphozoa). Taken together, the results of this study highlight the merits of FeDS in conducting biodiversity surveys of endemic and introduced species, and as a potential tool for assessing envenomation and/or conservation-related threats.

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Section: Discussionmentioning

confidence: 99%

Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

et al. 2021

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“…However, there are also other survey techniques that are not limited by turbid environments, where eDNA metabarcoding can potentially be used complementarily (Koziol et al, 2019;Ransome et al, 2017). We note that such surveys have also been done in Singapore (Guest et al, 2016 Toh et al, 2017), along with other techniques such as dredging, netting, and trapping fish (Larson et al, 2008(Larson et al, , 2016Toh et al, 2016) and settlement-recruitment studies (Chang et al, 2020).…”

Section: Introductionmentioning

confidence: 98%

Seeking life in sedimented waters: Environmental DNA from diverse habitat types reveals ecologically significant species in a tropical marine environment

Tay

Chang

et al. 2020

Environmental DNA

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Environmental DNA (eDNA) with metabarcoding or metagenomics will likely become a major biomonitoring tool in the 21st century, perhaps even more so in the face of increased coastal urbanization and its associated effects such as pollution, land reclamation, and seabed dredging. Together, these impacts and the consequent high turbidity pose severe challenges to traditional survey techniques that rely heavily on visual observations. We here demonstrate that eDNA can be used for biomonitoring in turbid waters, using Singapore as a case study. The cytochrome c oxidase subunit I (COI) locus was used to detect 525 metazoan molecular operational taxonomic units (MOTUs) based on eDNA obtained from 52 L of filtered seawater. Of these, 130 MOTUs (24.7%) were identifiable to species, including ecologically significant species that in some cases were invasive or rarely observed. Metazoan signals also enabled discrimination of discrete, but connected, environments from intertidal and subtidal zones. Taxa with known habitat preferences were found to have left trace eDNA at sites that matched putatively suitable habitats. Moreover, no coast-specific signals were detected in open water samples, which suggest that intermixing of water was limited. The study confirms that eDNA metabarcoding is a viable biomonitoring tool for coastal areas with highly sedimented waters.

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“…Although less used, the combination of primers mICOIintF/LoboR1 [132,133] has been tested successfully in mock communities [15,131] and shown to perform just as well as the pair mICOIintF/jgHCO2198 [134]. Moreover, compared to jgHCO2198, LoboR1 has the advantage of lacking inosine bases, which may be incompatible with high-fidelity Taq polymerases usually employed for amplifying the PCR amplicons to be high-throughput sequenced, and it is also a cost-effective solution [135,136]. On the other hand, the amplification of the whole COI region (i.e., barcode region) or of the 5 region have been less used and reported to recover fewer invertebrate taxa than primers amplifying the 3 end of the barcode region [15,43,131,132] (Table S3).…”

Section: Marker Loci and Primer Pairsmentioning

confidence: 99%

“…A cost-effective solution may be provided by Oxford Nanopore (Oxford, UK) or Pac-Bio (Menlo Park, CA, USA) platforms [135,148]. For instance, in a study employing ARMS in marine ecosystems biomonitoring, MinION (small handheld sequencer from Oxford Nanopore) barcodes, generated from macrofaunal samples (the fraction >2 mm) were highly accurate compared to Illumina reference barcodes [135]. In addition, data were available within 3.5-4 h, and at a lower price, but it still remains presently untested in metabarcoding and no established pipeline exists yet for metazoans [135].…”

Section: Sequencing Platformsmentioning

confidence: 99%

Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

Duarte

Leite

Feio

et al. 2021

Water

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Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.

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MinION-in-ARMS: Nanopore Sequencing to Expedite Barcoding of Specimen-Rich Macrofaunal Samples From Autonomous Reef Monitoring Structures

Cited by 38 publications

References 73 publications

Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

Fieldable Environmental DNA Sequencing to Assess Jellyfish Biodiversity in Nearshore Waters of the Florida Keys, United States

Seeking life in sedimented waters: Environmental DNA from diverse habitat types reveals ecologically significant species in a tropical marine environment

Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

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