scholarly journals Ferries and Environmental DNA: Underway Sampling From Commercial Vessels Provides New Opportunities for Systematic Genetic Surveys of Marine Biodiversity

2021 ◽  
Vol 8 ◽  
Author(s):  
Elena Valsecchi ◽  
Antonella Arcangeli ◽  
Roberto Lombardi ◽  
Elizabeth Boyse ◽  
Ian M. Carr ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Marine Biodiversity ◽  
Night Time ◽  
Operational Taxonomic Units ◽  
Reasonable Cost ◽  
Temperature Ranges ◽  
June July ◽  
Species Occurrences ◽  
Marine Environmental ◽  
Sample Heterogeneity

Marine environmental DNA (eDNA) is an important tool for biodiversity research and monitoring but challenges remain in scaling surveys over large spatial areas, and increasing the frequency of sampling in remote locations at reasonable cost. Here we demonstrate the feasibility of sampling from commercial vessels (Mediterranean ferries) while underway, as a strategy to facilitate replicable, systematic marine eDNA surveys in locations that would normally be challenging and expensive for researchers to access. Sixteen eDNA samples were collected from four fixed sampling stations, and in response to four cetacean sightings, across three cruises undertaken along the 300 km ferry route between Livorno (Tuscany) and Golfo Aranci (Sardinia) in the Ligurian/Tyrrhenian Seas, June-July 2018. Using 12SrDNA and 16SrDNA metabarcoding markers, we recovered diverse marine vertebrate Molecular Operational Taxonomic Units (MOTUs) from teleost fish, elasmobranchs, and cetaceans. We detected sample heterogeneity consistent with previously known variation in species occurrences, including putative species spawning peaks associated with specific sea surface temperature ranges, and increased night time abundance of bathypelagic species known to undertake diel migrations through the water column. We suggest commercial vessel based marine eDNA sampling using the global shipping network has potential to facilitate broad-scale biodiversity monitoring in the world’s oceans.

scholarly journals Scanning ferry routes: looking for eDNA traces of marine mammals and their preys

2021 ◽  
Vol 4 ◽  
Author(s):  
Elena Valsecchi
Keyword(s):  
Marine Mammals ◽  
High Throughput Sequencing ◽  
Simultaneous Detection ◽  
Environmental Dna ◽  
Trophic Levels ◽  
Systematic Sampling ◽  
Marine Biodiversity ◽  
Tyrrhenian Sea ◽  
Night Time ◽  
Species Specific

Marine environmental DNA (eDNA) surveys are becoming a promising approach to monitor biodiversity status and its variation over time. However, monitoring offshore areas could be extremely costly when using dedicated vessels, beside the impossibility to sample simultaneously geographically distant (even if adjacent) areas. The unexplored possibility of availing on operating ferries as an opportunistic platform for eDNA sampling offers several advantages besides opening limitless opportunities for systematic surveys on marine biodiversity.We present the results of both metabarcoding and barcoding approaches obtained from the analysis of water samples collected on board of a ferry boat along a pilot Mediterranean route crossing the Pelagos Sanctuary for Mediterranean Marine Mammals. The recently described MarVer primer sets (12SrDNA and 16SrDNA regions), specifically designed for the simultaneous detection of marine mammals and other marine vertebrates, were employed. The High Throughput Sequencing (HTS) outcome showed that the markers successfully detected most trophic levels of vertebrate marine communities, and classes, including bony fish, rays, cetaceans and birds. Ferry-based sampling allow to collect sample at any time of the day, and we indeed found diel differences in both quantitative and qualitative distribution of read counts. For instances, we observed an increased abundance of lantern fish amplicons in night-time collect samples (50%), reflecting nocturnal migration through the water column. In general, the number of read counts was significantly higher in nocturnal samples. Such diel differences within our sample indirectly provides evidence of the efficiency of the eDNA approach to detect contemporary signals in the sampled environment. Similarly, cetaceans were detected in correspondence of visual sightings (when these occurred, supplementary samples were collected). Rare species, such as the monk seal, are difficult to be detected in metabarcoding surveys, thus we opted to side the screening of the ferry-samples with a panel of species-specific qPCR assays, which were able to detect DNA traces of the endangered pinniped in the Tuscany archipelago (Tyrrhenian Sea) long before visual observations witnessed its presence in the same area. The study demonstrates the feasibility of using commercial shipping as a platform for eDNA marine sampling without dedicated survey cruises. Commercial shipping routes have potential to act as regular systematic sampling transects which can contribute to evaluating and monitoring marine biodiversity.

Exploring the plant environmental DNA diversity in soil from two sites on Deception Island (Antarctica, South Shetland Islands) using metabarcoding

2021 ◽  
pp. 1-10
Author(s):  
Micheline Carvalho-Silva ◽  
Luiz Henrique Rosa ◽  
Otávio H.B. Pinto ◽  
Thamar Holanda Da Silva ◽  
Diego Knop Henriques ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Crater Lake ◽  
Environmental Dna ◽  
Food Sources ◽  
South Shetland Islands ◽  
Deception Island ◽  
Shetland Islands ◽  
Operational Taxonomic Units ◽  
First Time ◽  
Impacted Site

Abstract The few Antarctic studies to date to have applied metabarcoding in Antarctica have primarily focused on microorganisms. In this study, for the first time, we apply high-throughput sequencing of environmental DNA to investigate the diversity of Embryophyta (Viridiplantae) DNA present in soil samples from two contrasting locations on Deception Island. The first was a relatively undisturbed site within an Antarctic Specially Protected Area at Crater Lake, and the second was a heavily human-impacted site in Whalers Bay. In samples obtained at Crater Lake, 84% of DNA reads represented fungi, 14% represented Chlorophyta and 2% represented Streptophyta, while at Whalers Bay, 79% of reads represented fungi, 20% represented Chlorophyta and < 1% represented Streptophyta, with ~1% of reads being unassigned. Among the Embryophyta we found 16 plant operational taxonomic units from three Divisions, including one Marchantiophyta, eight Bryophyta and seven Magnoliophyta. Sequences of six taxa were detected at both sampling sites, eight only at Whalers Bay and two only at Crater Lake. All of the Magnoliophyta sequences (flowering plants) represent species that are exotic to Antarctica, with most being plausibly linked to human food sources originating from local national research operator and tourism facilities.

scholarly journals Environmental DNA variability in lake sediment cores

2021 ◽  
Vol 4 ◽  
Author(s):  
John Pearman ◽  
Georgia Thomson-Laing ◽  
Jamie Howarth ◽  
Marcus Vandergoes ◽  
Lucy Thompson ◽  
...  
Keyword(s):  
16S Rrna ◽  
General Trend ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Biological Communities ◽  
The Core ◽  
Community Dissimilarity ◽  
Sample Heterogeneity ◽  
Read Abundance ◽  
Natural Archives

Lake sediments are natural archives that accumulate information about biological communities and their surrounding catchments. Paleolimnology has traditionally focussed on identifying fossilized organisms to reconstruct past environments. In the last decade, the application of molecular methodologies has increased in paleolimnological studies, but further studies investigating factors such as sample heterogeneity and DNA degradation are required. Here we investigated bacterial community heterogeneity (16S rRNA metabarcoding) within depth slices. Sediment cores were collected from three lakes with differing sediment compositions. Samples were collected from a variety of depths (1-cm width) which represent a period of time of approximately 1,200 years. Triplicate samples were collected from each slice and bacterial 16S rRNA metabarcoding was undertaken on each sample. Rarefaction curves showed that except for the deepest (oldest) slices, the combination of three replicate samples were insufficient to characterise the entire bacterial diversity. However, shared Amplicon Sequence Variants (ASVs) accounted for the majority of the reads in each slice (max. shared proportional read abundance 96%, 86%, 65% in the three lakes). Within slice similarity was higher than between slice similarity. No general trend was observed in variability among replicates with depth amongst the lakes. In one core. there was a higher community dissimilarity in older sediment, which may be due to laminae not being horizontal. These results highlight the fact that microbial communities can be differentiated with depth however it is critical to interpret these results in the context of the stratigraphic data of the core.

scholarly journals Phylogenetic and Chemical Diversity of a Hybrid-Isoprenoid-Producing Streptomycete Lineage

2013 ◽  
Vol 79 (22) ◽  
pp. 6894-6902 ◽  
Author(s):  
Kelley A. Gallagher ◽  
Kristin Rauscher ◽  
Laura Pavan Ioca ◽  
Paul R. Jensen
Keyword(s):  
Secondary Metabolites ◽  
Secondary Metabolite ◽  
Sequence Data ◽  
Environmental Dna ◽  
Chemical Diversity ◽  
Phenotypic Trait ◽  
Content Type ◽  
Operational Taxonomic Units ◽  
Culture Independent ◽  
Structural Classes

ABSTRACTStreptomycesspecies dedicate a large portion of their genomes to secondary metabolite biosynthesis. A diverse and largely marine-derived lineage within this genus has been designated MAR4 and identified as a prolific source of hybrid isoprenoid (HI) secondary metabolites. These terpenoid-containing compounds are common in nature but rarely observed as bacterial secondary metabolites. To assess the phylogenetic diversity of the MAR4 lineage, complementary culture-based and culture-independent techniques were applied to marine sediment samples collected off the Channel Islands, CA. The results, including those from an analysis of publically available sequence data and strains isolated as part of prior studies, placed 40 new strains in the MAR4 clade, of which 32 originated from marine sources. When combined with sequences cloned from environmental DNA, 28 MAR4 operational taxonomic units (0.01% genetic distance) were identified. Of these, 82% consisted exclusively of either cloned sequences or cultured strains, supporting the complementarity of these two approaches. Chemical analyses of diverse MAR4 strains revealed the production of five different HI structure classes. All 21 MAR4 strains tested produced at least one HI class, with most strains producing from two to four classes. The two major clades within the MAR4 lineage displayed distinct patterns in the structural classes and the number and amount of HIs produced, suggesting a relationship between taxonomy and secondary metabolite production. The production of HI secondary metabolites appears to be a phenotypic trait of the MAR4 lineage, which represents an emerging model with which to study the ecology and evolution of HI biosynthesis.

scholarly journals Environmental DNA (eDNA) Metabarcoding in the Fish Market and Nearby Seafood Restaurants in Taiwan Reveals the Underestimation of Fish Species Diversity in Seafood

Biology ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1132
Author(s):  
Hung-Tai Lee ◽  
Cheng-Hsin Liao ◽  
Te-Hua Hsu
Keyword(s):  
Species Diversity ◽  
Species Identification ◽  
Fish Species ◽  
Large Scale ◽  
Environmental Dna ◽  
Universal Primers ◽  
Similar Species ◽  
Operational Taxonomic Units ◽  
Fish Market ◽  
Fish Species Identification

Seafood, especially in traditional food Taiwan, is rarely sourced from a fixed species and routinely from similar species depending on their availability. Hence, the species composition of seafood can be complicated. While a DNA-based approach has been routinely utilized for species identification, a large scale of seafood identification in fish markets and restaurants could be challenging (e.g., elevated cost and time-consuming only for a limited number of species identification). In the present study, we aimed to identify the majority of fish species potentially consumed in fish markets and nearby seafood restaurants using environmental DNA (eDNA) metabarcoding. Four eDNA samplings from a local fish market and nearby seafood restaurants were conducted using Sterivex cartridges. Nineteen universal primers previously validated for fish species identification were utilized to amplify the fragments of mitochondrial DNA (12S, COI, ND5) of species in eDNA samples and sequenced with NovaSeq 6000 sequencing. A total of 153 fish species have been identified based on 417 fish related operational taxonomic units (OTUs) generated from 50,534,995 reads. Principal Coordinate Analysis (PCoA) further showed the differences in fish species between the sampling times and sampling sites. Of these fish species, 22 chondrichthyan fish, 14 Anguilliformes species, and 15 Serranidae species were respectively associated with smoked sharks, braised moray eels, and grouper fish soups. To our best knowledge, this work represents the first study to demonstrate the feasibility of a large scale of seafood identification using eDNA metabarcoding approach. Our findings also imply the species diversity in traditional seafood might be seriously underestimated and crucial for the conservation and management of marine resources.

Considering the concept of the ecological civilization for conservation and sustainable use of marine biodiversity under the umbrella of the Biodiversity Beyond National Jurisdiction instrument

2021 ◽  
Vol 23 (3) ◽  
pp. 248-262
Author(s):  
Sabrina Hasan
Keyword(s):  
Environmental Governance ◽  
Sustainable Use ◽  
Marine Biodiversity ◽  
Ecological Civilization ◽  
National Jurisdiction ◽  
Marine Environmental

In exploring how the concept of ecological civilization can be applied to maintain adequate marine environmental governance for the conservation and sustainable use of marine biodiversity, the article first highlights the existing issues concerning conservation and sustainable use of marine biodiversity. It then suggests that ecological civilization can contribute as a norm to formulate the principles and approaches as well as to set goals and targets under the Biodiversity Beyond National Jurisdiction instrument.

scholarly journals Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

PLoS Genetics ◽  
2019 ◽  
Vol 15 (2) ◽  
pp. e1007943 ◽  
Author(s):  
Tina E. Berry ◽  
Benjamin J. Saunders ◽  
Megan L. Coghlan ◽  
Michael Stat ◽  
Simon Jarman ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Seasonal Patterns ◽  
Ecosystem Responses ◽  
Marine Environmental

scholarly journals Publisher Correction: Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Babett Günther ◽  
Thomas Knebelsberger ◽  
Hermann Neumann ◽  
Silke Laakmann ◽  
Pedro Martínez Arbizu
Keyword(s):  
Environmental Dna ◽  
Nuclear Genes ◽  
Marine Environmental

scholarly journals Ancient DNA complements microfossil record in deep-sea subsurface sediments

2013 ◽  
Vol 9 (4) ◽  
pp. 20130283 ◽  
Author(s):  
Franck Lejzerowicz ◽  
Philippe Esling ◽  
Wojciech Majewski ◽  
Witold Szczuciński ◽  
Johan Decelle ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Deep Sea ◽  
Environmental Dna ◽  
Small Subunit ◽  
Marine Biodiversity ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Core Sediment ◽  
Subsurface Sediments ◽  
Sediment Layers

Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.

scholarly journals Taxonomic identification of environmental DNA with informatic sequence classification trees.

2018 ◽  
Author(s):  
Shaun P Wilkinson ◽  
Simon K Davy ◽  
Michael Bunce ◽  
Michael Stat
Keyword(s):  
Classification Tree ◽  
Probabilistic Method ◽  
Query Sequence ◽  
Dna Barcode ◽  
Classification Trees ◽  
Environmental Dna ◽  
Training Data ◽  
Marine Biodiversity ◽  
Taxonomic Identification ◽  
Sequence Classification

High-throughput sequencing of environmental DNA (eDNA) offers a simple and cost-effective solution for marine biodiversity assessments. Yet several analytical challenges remain, including the incorporation of statistical inference in the assignment of taxonomic identities. We developed a probabilistic method for DNA barcode classification that can be used for both eDNA and traditional single-source sampling. The pipeline involves: (1) compiling a primer-specific database of barcode sequences to be used as training data (obtained from GenBank and other sequence repositories), (2) generating a classification tree using an iterative learning algorithm that divisively sorts the training data into hierarchical clusters based on profile hidden Markov models, (3) assignment of each query sequence to a cluster using a recursive series of model-comparison tests, and (4) taxonomic identification of the query sequences based on the lowest common taxonomic rank of the training sequences within the cluster. This method compares favorably to other DNA classification methods when tested on benchmark datasets, and offers the added features of classifying at higher taxonomic ranks and returning interpretable confidence values in the form of the Akaike weight statistic. This bioinformatics pipeline is available as an open source R package called ‘insect’ (informatic sequence classification trees).

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