scholarly journals Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12458
Author(s):  
Laurence J. Clarke ◽  
Leonie Suter ◽  
Bruce E. Deagle ◽  
Andrea M. Polanowski ◽  
Aleks Terauds ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Sediment Cores ◽  
Spatial Dynamics ◽  
Environmental Dna ◽  
Extreme Environment ◽  
Sample Type ◽  
Biodiversity Survey ◽  
Water And Sediment ◽  
Vestfold Hills ◽  
Benthic Ecosystems

Antarctic benthic ecosystems support high biodiversity but their characterization is limited to a few well-studied areas, due to the extreme environment and remoteness making access and sampling difficult. Our aim was to compare water and sediment as sources of environmental DNA (eDNA) to better characterise Antarctic benthic communities and further develop practical approaches for DNA-based biodiversity assessment in remote environments. We used a cytochrome c oxidase subunit I (COI) metabarcoding approach to characterise metazoan communities in 26 nearshore sites across 12 locations in the Vestfold Hills (East Antarctica) based on DNA extracted from either sediment cores or filtered seawater. We detected a total of 99 metazoan species from 12 phyla across 26 sites, with similar numbers of species detected in sediment and water eDNA samples. However, significantly different communities were detected in the two sample types at sites where both were collected (i.e., where paired samples were available). For example, nematodes and echinoderms were more likely to be detected exclusively in sediment and water eDNA samples, respectively. eDNA from water and sediment core samples are complementary sample types, with epifauna more likely to be detected in water column samples and infauna in sediment. More reference DNA sequences are needed for infauna/meiofauna to increase the proportion of sequences and number of taxa that can be identified. Developing a better understanding of the temporal and spatial dynamics of eDNA at low temperatures would also aid interpretation of eDNA signals from polar environments. Our results provide a preliminary scan of benthic metazoan communities in the Vestfold Hills, with additional markers required to provide a comprehensive biodiversity survey. However, our study demonstrates the choice of sample type for eDNA studies of benthic ecosystems (sediment, water or both) needs to be carefully considered in light of the research or monitoring question of interest.

scholarly journals Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mizuki Ogata ◽  
Reiji Masuda ◽  
Hiroya Harino ◽  
Masayuki K. Sakata ◽  
Makoto Hatakeyama ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Oil Spills ◽  
Sediment Cores ◽  
Environmental Dna ◽  
Target Species ◽  
Tank Experiment ◽  
Polycyclic Aromatic ◽  
Flow Through ◽  
High Concentrations ◽  
One Year

AbstractEnvironmental DNA (eDNA) can be a powerful tool for detecting the distribution and abundance of target species. This study aimed to test the longevity of eDNA in marine sediment through a tank experiment and to use this information to reconstruct past faunal occurrence. In the tank experiment, juvenile jack mackerel (Trachurus japonicus) were kept in flow-through tanks with marine sediment for two weeks. Water and sediment samples from the tanks were collected after the removal of fish. In the field trial, sediment cores were collected in Moune Bay, northeast Japan, where unusual blooms of jellyfish (Aurelia sp.) occurred after a tsunami. The samples were analyzed by layers to detect the eDNA of jellyfish. The tank experiment revealed that after fish were removed, eDNA was not present in the water the next day, or subsequently, whereas eDNA was detectable in the sediment for 12 months. In the sediment core samples, jellyfish eDNA was detected at high concentrations above the layer with the highest content of polycyclic aromatic hydrocarbons, reflecting tsunami-induced oil spills. Thus, marine sediment eDNA preserves a record of target species for at least one year and can be used to reconstruct past faunal occurrence.

Using sediment cores to establish targets for the remediation of aquatic environments

2015 ◽  
Vol 73 (3) ◽  
pp. 628-635 ◽  
Author(s):  
Anna Lintern ◽  
Marion Anderson ◽  
Paul Leahy ◽  
Ana Deletic ◽  
David McCarthy
Keyword(s):  
Sediment Cores ◽  
Sediment Quality ◽  
Aquatic Systems ◽  
Quality Data ◽  
Aquatic Environments ◽  
Site Specific ◽  
European Settlement ◽  
Quality Guidelines ◽  
Water And Sediment ◽  
Water And Sediment Quality

When assigning site-specific restoration targets for deteriorating aquatic systems, it is necessary to have an understanding of the undisturbed or background state of the system. However, the site-specific characteristics of aquatic systems prior to disturbance are mostly unknown, due to the lack of historical water and sediment quality data. This study aims to introduce a method for filling this gap in our understanding, using dated sediment cores from the beds of aquatic environments. We used Bolin Billabong, a floodplain lake of the Yarra River (South-East Australia), as a case study to demonstrate the application of this method. We identified the concentrations of aluminium, cadmium, chromium, copper, iron, lead, manganese, nickel, tin and zinc at 8 cm intervals through the sediment core. This showed that aluminium, chromium, copper, iron, lead, nickel, tin and zinc concentrations in Bolin Billabong sediments significantly increased after European settlement in the river catchment in the mid-19th century. The differences between current Australian sediment quality guidelines trigger values and the background metal concentrations in Bolin Billabong sediments underscore the value of using locally relevant background toxicant concentrations when setting water and sediment quality targets.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
O. Nurul Fizatul Nabilah ◽  
A. R. Ramizah ◽  
A. B. Adibah ◽  
S. Syazwan ◽  
A.G. Intan Faraha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Coi Gene ◽  
Alien Invasive Species ◽  
Survey Method ◽  
Specific Primers ◽  
Invasive Fishes ◽  
Specific Amplification ◽  
Species Specific ◽  
High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

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.

Penguin occupation in the Vestfold Hills

2008 ◽  
Vol 21 (2) ◽  
pp. 131-134 ◽  
Author(s):  
Tao Huang ◽  
Liguang Sun ◽  
Yuhong Wang ◽  
Renbin Zhu
Keyword(s):  
Sediment Core ◽  
Environmental Changes ◽  
Sediment Cores ◽  
East Antarctica ◽  
Before Present ◽  
The Holocene ◽  
History Of ◽  
Vestfold Hills ◽  
Free Area ◽  
Ornithogenic Sediment

AbstractDuring CHINARE-22 (December 2005–March 2006), we investigated six penguin colonies in the Vestfold Hills, East Antarctica, and collected several penguin ornithogenic sediment cores, samples of fresh guano and modern penguin bone and feather. We selected seven penguin bones and feathers and six sediments from the longest sediment core and performed AMS14C dating. The results indicate that penguins occupied the Vestfold Hills as early as 8500 calibrated years before present (cal. yrbp), following local deglaciation and the formation of the ice free area. This is the first report on the Holocene history of penguins in the Vestfold Hills. As in other areas of Antarctica, penguins occupied this area as soon as local ice retreated and the ice free area formed, and they are very sensitive to climatic and environmental changes. This work provides the foundation for understanding the history of penguins occupation in Vestfold Hills, East Antarctica.

scholarly journals Blooms of Toxic Cyanobacterium Nodularia spumigena in Norwegian Fjords During Holocene Warm Periods

Toxins ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 257
Author(s):  
Robert Konkel ◽  
Anna Toruńska-Sitarz ◽  
Marta Cegłowska ◽  
Žilvinas Ežerinskis ◽  
Justina Šapolaitė ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Phytoplankton Community ◽  
Sediment Cores ◽  
Specific Chemical ◽  
Nodularia Spumigena ◽  
History Of ◽  
Recent Sediments ◽  
Species Specific ◽  
Ecosystem Changes ◽  
Deep Sediments

In paleoecological studies, molecular markers are being used increasingly often to reconstruct community structures, environmental conditions and ecosystem changes. In this work, nodularin, anabaenopeptins and selected DNA sequences were applied as Nodularia spumigena markers to reconstruct the history of the cyanobacterium in the Norwegian fjords. For the purpose of this study, three sediment cores collected in Oslofjorden, Trondheimsfjorden and Balsfjorden were analyzed. The lack of nodularin in most recent sediments is consistent with the fact that only one report on the sporadic occurrence and low amounts of the cyanobacterium in Norwegian Fjords in 1976 has been published. However, analyses of species-specific chemical markers in deep sediments showed that thousands of years ago, N. spumigena constituted an important component of the phytoplankton community. The content of the markers in the cores indicated that the biomass of the cyanobacterium increased during the warmer Holocene periods. The analyses of genetic markers were less conclusive; they showed the occurrence of microcystin/nodularin producing cyanobacteria of Nostocales order, but they did not allow for the identification of the organisms at a species level.

scholarly journals MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

BMC Genomics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 461 ◽  
Author(s):  
Manuel Stark ◽  
Simon A Berger ◽  
Alexandros Stamatakis ◽  
Christian von Mering
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Environmental Dna

scholarly journals Metabolic network-guided binning of metagenomic sequence fragments

2015 ◽  
Vol 32 (6) ◽  
pp. 867-874 ◽  
Author(s):  
Matthew B. Biggs ◽  
Jason A. Papin
Keyword(s):  
Metabolic Network ◽  
Dna Sequences ◽  
Metabolic Networks ◽  
Human Microbiome ◽  
Environmental Dna ◽  
Human Microbiome Project ◽  
Supplementary Information ◽  
Metagenomic Sequence ◽  
Connectivity Score ◽  
Genome Scale

Abstract Motivation: Most microbes on Earth have never been grown in a laboratory, and can only be studied through DNA sequences. Environmental DNA sequence samples are complex mixtures of fragments from many different species, often unknown. There is a pressing need for methods that can reliably reconstruct genomes from complex metagenomic samples in order to address questions in ecology, bioremediation, and human health. Results: We present the SOrting by NEtwork Completion (SONEC) approach for assigning reactions to incomplete metabolic networks based on a metabolite connectivity score. We successfully demonstrate proof of concept in a set of 100 genome-scale metabolic network reconstructions, and delineate the variables that impact reaction assignment accuracy. We further demonstrate the integration of SONEC with existing approaches (such as cross-sample scaffold abundance profile clustering) on a set of 94 metagenomic samples from the Human Microbiome Project. We show that not only does SONEC aid in reconstructing species-level genomes, but it also improves functional predictions made with the resulting metabolic networks. Availability and implementation: The datasets and code presented in this work are available at: https://bitbucket.org/mattbiggs/sorting_by_network_completion/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.

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