scholarly journals Metabarcoding on the deep seafloor: optimizing multigene approaches and sampling methods for large-scale biodiversity assessments.

2018 ◽  
Author(s):  
Miriam I Brandt ◽  
Daniela Zeppilli ◽  
Caroline Dussart ◽  
Erwan Aublet ◽  
Florence Pradillon ◽  
...  
Keyword(s):  
Deep Sea ◽  
Large Scale ◽  
Sampling Methods ◽  
Environmental Dna ◽  
Ecological Impacts ◽  
Extracellular Dna ◽  
Baseline Knowledge ◽  
Ecosystem Diversity ◽  
Central Atlantic ◽  
Large Scale Project

The deep sea, the largest and most poorly known biome on Earth, is under increasing threat from human-induced ecological impacts. Improved baseline knowledge and environmental impact assessment protocols are required to be able to alleviate potential changes in ecosystem diversity and functioning in the deep-sea. Metabarcoding of environmental DNA (eDNA) enables broader and faster biodiversity assessments, and is increasingly used to study eukaryote and prokaryote diversity. Whether metabarcoding provides reliable diversity inventories that meet the quality standards for accurate baseline data and biomonitoring is still uncertain in the deep-sea benthos, the latter being associated with specific taxonomic and sampling challenges. In particular, it is crucial to develop multigene metabarcoding protocols targeting living organisms and not extracellular, archived DNA. Before launching a large-scale project for the reassessment of deep-sea biodiversity, we addressed these technical challenges using bathyal and abyssal sediments sampled in the Mediterranean and central Atlantic. Our aim was to setup optimized protocols and evaluate the strengths and limitations of multigene metabarcoding in the deep sea by 1) comparing eDNA-based with traditional morphology-based diversity inventories and 2) assessing the accuracy and/or bias associated with distinct sample processing methods, including RNA and size-selected DNA extracts lacking short (extracellular) DNA fragments.

scholarly journals Metabarcoding on the deep seafloor: optimizing multigene approaches and sampling methods for large-scale biodiversity assessments.

2018 ◽  
Author(s):  
Miriam I Brandt ◽  
Daniela Zeppilli ◽  
Caroline Dussart ◽  
Erwan Aublet ◽  
Florence Pradillon ◽  
...  
Keyword(s):  
Deep Sea ◽  
Large Scale ◽  
Sampling Methods ◽  
Environmental Dna ◽  
Ecological Impacts ◽  
Extracellular Dna ◽  
Baseline Knowledge ◽  
Ecosystem Diversity ◽  
Central Atlantic ◽  
Large Scale Project

The deep sea, the largest and most poorly known biome on Earth, is under increasing threat from human-induced ecological impacts. Improved baseline knowledge and environmental impact assessment protocols are required to be able to alleviate potential changes in ecosystem diversity and functioning in the deep-sea. Metabarcoding of environmental DNA (eDNA) enables broader and faster biodiversity assessments, and is increasingly used to study eukaryote and prokaryote diversity. Whether metabarcoding provides reliable diversity inventories that meet the quality standards for accurate baseline data and biomonitoring is still uncertain in the deep-sea benthos, the latter being associated with specific taxonomic and sampling challenges. In particular, it is crucial to develop multigene metabarcoding protocols targeting living organisms and not extracellular, archived DNA. Before launching a large-scale project for the reassessment of deep-sea biodiversity, we addressed these technical challenges using bathyal and abyssal sediments sampled in the Mediterranean and central Atlantic. Our aim was to setup optimized protocols and evaluate the strengths and limitations of multigene metabarcoding in the deep sea by 1) comparing eDNA-based with traditional morphology-based diversity inventories and 2) assessing the accuracy and/or bias associated with distinct sample processing methods, including RNA and size-selected DNA extracts lacking short (extracellular) DNA fragments.

scholarly journals Ecological impacts of large-scale disposal of mining waste in the deep sea

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
David J. Hughes ◽  
Tracy M. Shimmield ◽  
Kenneth D. Black ◽  
John A. Howe
Keyword(s):  
Deep Sea ◽  
Large Scale ◽  
Mining Waste ◽  
Ecological Impacts

scholarly journals Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Miriam I. Brandt ◽  
Florence Pradillon ◽  
Blandine Trouche ◽  
Nicolas Henry ◽  
Cathy Liautard-Haag ◽  
...  
Keyword(s):  
Deep Sea ◽  
Sampling Methods ◽  
Alpha Diversity ◽  
Environmental Dna ◽  
Size Class ◽  
Sampling Strategies ◽  
Water Sampling ◽  
Dna Metabarcoding ◽  
Genetic Assessment

AbstractDespite representing one of the largest biomes on earth, biodiversity of the deep seafloor is still poorly known. Environmental DNA metabarcoding offers prospects for fast inventories and surveys, yet requires standardized sampling approaches and careful choice of environmental substrate. Here, we aimed to optimize the genetic assessment of prokaryote (16S), protistan (18S V4), and metazoan (18S V1–V2, COI) communities, by evaluating sampling strategies for sediment and aboveground water, deployed simultaneously at one deep-sea site. For sediment, while size-class sorting through sieving had no significant effect on total detected alpha diversity and resolved similar taxonomic compositions at the phylum level for all markers studied, it effectively increased the detection of meiofauna phyla. For water, large volumes obtained from an in situ pump (~ 6000 L) detected significantly more metazoan diversity than 7.5 L collected in sampling boxes. However, the pump being limited by larger mesh sizes (> 20 µm), only captured a fraction of microbial diversity, while sampling boxes allowed access to the pico- and nanoplankton. More importantly, communities characterized by aboveground water samples significantly differed from those characterized by sediment, whatever volume used, and both sample types only shared between 3 and 8% of molecular units. Together, these results underline that sediment sieving may be recommended when targeting metazoans, and aboveground water does not represent an alternative to sediment sampling for inventories of benthic diversity.

scholarly journals Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

2021 ◽  
Vol 8 ◽  
Author(s):  
Franck Lejzerowicz ◽  
Andrew John Gooday ◽  
Inés Barrenechea Angeles ◽  
Tristan Cordier ◽  
Raphaël Morard ◽  
...  
Keyword(s):  
Deep Sea ◽  
Large Scale ◽  
Benthic Communities ◽  
Experimental Studies ◽  
Alpha Diversity ◽  
Environmental Dna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Data Resource ◽  
Dna And Rna

The abyssal seafloor is a mosaic of highly diverse habitats that represent the least known marine ecosystems on Earth. Some regions enriched in natural resources, such as polymetallic nodules in the Clarion-Clipperton Zone (CCZ), attract much interest because of their huge commercial potential. Since nodule mining will be destructive, baseline data are necessary to measure its impact on benthic communities. Hence, we conducted an environmental DNA and RNA metabarcoding survey of CCZ biodiversity targeting microbial and meiofaunal eukaryotes that are the least known component of the deep-sea benthos. We analyzed two 18S rRNA gene regions targeting eukaryotes with a focus on Foraminifera (37F) and metazoans (V1V2), sequenced from 310 surface-sediment samples from the CCZ and other abyssal regions. Our results confirm huge unknown deep-sea biodiversity. Over 60% of benthic foraminiferal and almost a third of eukaryotic operational taxonomic units (OTUs) could not be assigned to a known taxon. Benthic Foraminifera are more common in CCZ samples than metazoans and dominated by clades that are only known from environmental surveys. The most striking results are the uniqueness of CCZ areas, both datasets being characterized by a high number of OTUs exclusive to the CCZ, as well as greater beta diversity compared to other abyssal regions. The alpha diversity in the CCZ is high and correlated with water depth and terrain complexity. Topography was important at a local scale, with communities at CCZ stations located in depressions more diverse and heterogeneous than those located on slopes. This could result from eDNA accumulation, justifying the interim use of eRNA for more accurate biomonitoring surveys. Our descriptions not only support previous findings and consolidate our general understanding of deep-sea ecosystems, but also provide a data resource inviting further taxon-specific and large-scale modeling studies. We foresee that metabarcoding will be useful for deep-sea biomonitoring efforts to consider the diversity of small taxa, but it must be validated based on ground truthing data or experimental studies.

Forensic botany: time to embrace natural history collections, large scale environmental data and environmental DNA

2021 ◽  
Author(s):  
Mark A. Spencer
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Environmental Dna ◽  
Ecological Impacts ◽  
Environmental Data ◽  
Physical Assault ◽  
Trade Disputes ◽  
Sequencing Technologies ◽  
Natural History Collections ◽  
The Impact

Forensic botany is a diverse discipline that spans many aspects of plant sciences, particularly taxonomy, field botany, anatomy, and ecology. Internationally, there is a significant opportunity to expand the application of forensic botany in criminal investigations, especially war crimes, genocide, homicide, sexual violence, serious physical assault, illegal trade in endangered species and wildlife crime. In civil proceedings, forensic botany may, for example, be called upon in trade disputes such as accidental contamination of commodities. Despite the potential, there are barriers to the wider application of forensic botany in criminal cases; there is a widespread need to improve the efficiency of botanical trace evidence identification. This could partly be addressed by embracing innovations in image recognition and by accessing the huge quantity of specimens and images housed in natural history collections worldwide. Additionally, the recent advances in DNA sequencing technologies and the expansion of environmental DNA (eDNA) and forensic ecogenomics, offers opportunities to more rapidly provide species-level identifications. The impact of taphonomic processes upon vegetation, and vice versa, remains poorly understood; improved understanding of these interactions and their ecological impacts may be invaluable in improving clandestine burial search protocols.

scholarly journals Experimental evaluation of genomic DNA degradation rates for the pathogen Pseudogymnoascus destructans (Pd) in bat guano

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8141
Author(s):  
Jenny Urbina ◽  
Tara Chestnut ◽  
Donelle Schwalm ◽  
Jenn Allen ◽  
Taal Levi
Keyword(s):  
North America ◽  
Environmental Conditions ◽  
Large Scale ◽  
Environmental Dna ◽  
Sampling Period ◽  
Dna Degradation ◽  
Washington State ◽  
Extracellular Dna ◽  
Pseudogymnoascus Destructans ◽  
Degradation Rates

Pseudogymnoascus destructans (Pd), the causative agent of white-nose syndrome in bats (WNS), has led to dramatic declines of bat populations in eastern North America. In the spring of 2016, WNS was first detected at several locations in Washington State, USA, which has prompted the need for large scale surveillance efforts to monitor the spread of Pd. Pd is typically detected in bats using invasive methods requiring capturing and swabbing individual bats. However, Pd can also be detected in guano, which may provide an efficient, affordable, and noninvasive means to monitor Pd in bats across North America. The widespread implementation of Pd surveillance in guano is hindered by substantial uncertainty about the probability of detecting Pd when present, and how this probability is influenced by the time since defecation, local environmental conditions, the amount of guano sampled, and the original concentration of DNA shed in the guano. In addition, the expected degradation rate of Pd DNA depends on whether the Pd DNA found in guano represents extracellular DNA fragments, intracellular DNA from dead Pd fungal cells, or from intracellular and viable Pd cells. While this is currently unknown, it has been posited that most environmental DNA, such as Pd found in guano long after defecation, is fragmented extracellular DNA. Using non-viable isolated DNA at precise quantities, we experimentally characterized the degradation rates of Pd DNA in guano samples. We spiked 450 guano samples with Pd gDNA in a 10-fold dilution series from 1 million to 1,000 fg and placed them in variable environmental conditions at five sites at Mount Rainier National Park in Washington State, which is a priority location for Pd surveillance. We evaluated DNA degradation over 70 days by quantifying the amount of DNA in samples collected every 14 days using real-time quantitative PCR (qPCR). Our sampling period was from July 10th to September 17th 2018 which overlaps with bat movement between summer roosts as well as movement from maternity colonies fall swarms. We detected Pd DNA in guano 56 and 70 days after inoculation with 1 million and 100,000 fg respectively, while the lowest quantity (1,000 fg) was detected until 42 days. Detection probability was variable among sites and lower where samples were left exposed without overhead cover. If Pd is shed as extracellular DNA in guano at quantities above 1,000 fg, then guano collection is likely to provide an effective tool for environmental screening of Pd that can be employed in an early detection and rapid response framework throughout Washington and other regions where this disease is rapidly emerging.

scholarly journals The Revitalization of the Historic Centre of the Town Slany

2014 ◽  
Vol 12 ◽  
pp. 3-11
Author(s):  
Zuzana Pešková
Keyword(s):  
Regional Policy ◽  
Large Scale ◽  
Test Theory ◽  
Team Members ◽  
Practical Design ◽  
Historic Centre ◽  
Reconstruction Project ◽  
One Year ◽  
The Town ◽  
Large Scale Project

In 2006, the town council of Slany decided to respond to the new trend of regional policy in the Central Bohemia region and focused on the revitalization of the historic core of the town. The large-scale project was assigned to a team of professionals (teachers and graduates of the Faculty of Civil Engineering of the Czech Technical University in Prague), led by Professor Sykora. Team members are to deal with issues of historical centre. The project presented a challenge to test theory, principles and procedures in practical design. The projected area featured Masaryk Square and 22 adjacent streets defined by the existing town walls. The reconstruction project of Vinarickeho Street was the first part of the overall project of revitalization of the historic core of the town chosen to implement. This reconstruction was one of the most technically, organizationally and financially complex works that have been undertaken in Slany recently. Construction started in November 2010 and lasted one year. Although this is a project of smaller scope, thanks to its complexity, sensitive approach and craftsmanship it brought the creators the price Construction of the Year 2012 in the Central Bohemia region and advanced to the second round in the competition Construction of the Year 2012 in Czech Republic.

Sign in / Sign up

Export Citation Format

Share Document