Welcoming more participation in open data science for the oceans DOI Creative Commons
Alexa Fredston, Julia Stewart Lowndes

Published: May 31, 2023

Open science is a global movement happening across all research fields. It builds on years of efforts by individual researchers and broad array institutions, agencies, grassroots organizations. Enabled technology the open web, goal to share knowledge broaden participation in science, from team formation early ideation making intermediate final outputs openly accessible (“open access”). Because its emphasis transparency collaboration, dovetails with increase diversity, equity, inclusion, belonging society. The Year Science (2023), as declared US Biden-Harris Administration many other government great opportunity boost for oceans. For day-to-day, critical piece modern workflows analyze, collaborate, communicate increasing amounts data. Therefore, we focus this data – tooling people enabling reproducible, transparent, inclusive practices data-intensive intersection marine sciences. We discuss state various technical dimensions such open-source programming academic publishing argue that advancements have outpaced our field’s culture change adopt incorporate them. believe inclusivity skill building are interlinked must be prioritized within community find collaborative solutions mitigating adapting climate threats food sources, biodiversity, habitats, As scientists whose careers been profoundly influenced continue benefit provide examples social transformation needed field become truly “open”.

Language: Английский

Towards a Standardized Operating Procedure for eDNA‐Based Biomonitoring in Coastal Marine Salmon Aquaculture DOI Creative Commons
Mahshid Oladi, Thomas A. Wilding, Adam J. Wyness

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(5)

Published: Sept. 1, 2024

ABSTRACT The marine aquaculture industry and regulators are in the process of implementing environmental DNA (eDNA) metabarcoding microbial communities for compliance monitoring. This requires standardization sampling, laboratory, data analysis protocols. Towards this goal, we study completed two further milestones using samples collected from Scottish salmon farms: (i) We tested effect different PCR protocols (i.e., polymerases, master mixes, annealing temperatures), which frequently being used eDNA biomonitoring installations, amplification taxonomic marker gene (V3‐V4 hypervariable region bacterial 16S rRNA gene). (ii) quantified sampling background noise obtained statistically compared results with bias observed macrofaunal same source sediments. detected differences community structures resulting performance protocols, profoundly influencing interpretation results. Furthermore, found that sampling‐induced errors were similar to according monitoring protocol (~25% variability both cases). Finally, showed within‐grab variances order magnitude (less than 10× difference all cases) as one replicate grabs locale (impact category). Based on our findings, suggest a consistent efforts improve comparability results, especially when service providers conducting biomonitoring. propose scheme be considered includes taking three at each locale, sample grab. minimizes makes upcoming eDNA‐based comparable previous data.

Language: Английский

Citations

0
rCRUX: A Rapid and Versatile Tool for Generating Metabarcoding Reference libraries in R DOI Open Access
Emily Curd,

Luna Gal,

Ramón Gallego

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 3, 2023

Key to making accurate taxonomic assignments are curated, comprehensive reference barcode databases. However, the generation and curation of such databases has remained challenging given large continuously growing volumes DNA sequence data novel targets. Monitoring research applications require a greater diversity specialized gene regions targeted taxa meet classification goals then currently curated by professional staff. Thus, there is need for an easy implement tool that can generate metabarcoding libraries any bespoke locus. We address this reimagining CRUX from Anacapa Toolkit present rCRUX package in R. The typical workflow involves searching plausible seed amplicons (

Language: Английский

Citations

1
Enhancing biodiversity monitoring efficiency through CRISPR-driven depletion and enrichment of aquatic environmental DNA DOI Creative Commons
Anya Kardailsky, Benjamín Durán‐Vinet, Georgia Nester

et al.

Published: May 14, 2024

Characterising biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex aquatic environments. However, eDNA is limited by biases towards certain species and low taxonomic resolution of current metabarcoding-based approaches. Shotgun metagenomics enables the collection whole ecosystem data sequencing all molecules present sample, allowing them to be characterised identified. Ongoing enhancements genome reference databases are improving shotgun metagenomics, reducing database related limitations individual identification metagenomic studies. metagenomics-based insights constrained preferential sequencing, favouring more abundant organisms water column like bacteria viruses over less target vertebrates. To improve probability detecting organisms, methods such as enrichment or removal non-target prior can employed. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR-associated proteins (Cas) have recently emerged novel technology that achieve both depletion. CRISPR-Cas-based potential efficiency simplify analysis filtration steps, however, they not been widely implemented due lack interest support past, well number studies demonstrating applied robust cost-effective manner. Here, we review approaches CRISPR-Cas study underrepresented taxa. We advocate further optimization depletion holds great promise rapidly evolving field through refining monitoring approaches, overcoming PCR bias, enabling efficient high-throughput applications.

Language: Английский

Citations

0
Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA DOI
Anya Kardailsky, Benjamín Durán‐Vinet, Georgia Nester

et al.

The CRISPR Journal, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 30, 2024

Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA is limited by biases toward certain species the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics enables collection whole ecosystem data sequencing all molecules present, allowing characterization identification. Clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated proteins (Cas)-based methods have potential to improve efficiency metagenomic low-abundant target organisms simplify analysis enrichment or nontarget depletion before sequencing. Implementation CRISPR-Cas has been due lack interest support past. This perspective synthesizes approaches study underrepresented taxa advocate further application optimization CRISPR-Cas, holding promise biomonitoring.

Language: Английский

Citations

0
Welcoming more participation in open data science for the oceans DOI Creative Commons
Alexa Fredston, Julia Stewart Lowndes

Published: May 31, 2023

Open science is a global movement happening across all research fields. It builds on years of efforts by individual researchers and broad array institutions, agencies, grassroots organizations. Enabled technology the open web, goal to share knowledge broaden participation in science, from team formation early ideation making intermediate final outputs openly accessible (“open access”). Because its emphasis transparency collaboration, dovetails with increase diversity, equity, inclusion, belonging society. The Year Science (2023), as declared US Biden-Harris Administration many other government great opportunity boost for oceans. For day-to-day, critical piece modern workflows analyze, collaborate, communicate increasing amounts data. Therefore, we focus this data – tooling people enabling reproducible, transparent, inclusive practices data-intensive intersection marine sciences. We discuss state various technical dimensions such open-source programming academic publishing argue that advancements have outpaced our field’s culture change adopt incorporate them. believe inclusivity skill building are interlinked must be prioritized within community find collaborative solutions mitigating adapting climate threats food sources, biodiversity, habitats, As scientists whose careers been profoundly influenced continue benefit provide examples social transformation needed field become truly “open”.

Language: Английский

Citations

0