Marine Microbiomes: Towards Standard Methods and Best Practices DOI Open Access

Frontiers research topics, Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 1, 2023

A decade of technological advances and research on the human microbiome has re-defined our understanding biological systems, now offers diagnostic tools new approaches to health. Likewise, marine ecosystems are driven by their microbiome, ensemble microscopic organisms that inhabit water column, sediments aquatic organisms, regulate most fluxes energy matter. While is composed principally bacteria, a much broader with sizes spanning from viruses few tens nanometres metazoans several centimetres. Advances in high throughput imaging sequencing emerging science, providing important insights into ecosystem structure functions, contributing develop indicators health potential hazards living resources humans. number exploration monitoring programs such as Tara Oceans global expedition Marine Biological Observing Network (MBON), rising popularity environmental DNA (eDNA) already led wealth data. However, wide range methodologies used this early phase poses challenge integrative studies, prompting community responses Genomic Standards Consortium. This Research Topic will foster cross-community exchange standards best practices. It an opportunity for different communities working microbiomes discuss advantages limitations sampling analysis methods. The collection papers constitute knowledge base aimed at (1) addressing integration existing observations heterogenous methods data types, (2) towards cross-communities practices future experiments. publish comprehensive methodological review sufficiently large body field or experimental work. Supporting (meta)data, context, materials, sample treatments, extraction yields, must be provided should preferably uploaded online registry BioSamples. Protocols analytical repository Protocols.io. We welcome contributions environments: · focus but also interested estuarine freshwater systems coastal, open ocean deep-sea regions benthic, pelagic aerosol environments strongly encourage involved in: networks local observatories long-term regional & basin-scale surveys, expeditions biodiscovery linked economic sectors pharmaceutics bioengineering assessments aquaculture, fisheries, seabed mining, wind-farms, oil gas

Language: Английский

Next-generation data filtering in the genomics era DOI
William Hemstrom, Jared A. Grummer, Gordon Luikart

et al.

Nature Reviews Genetics, Journal Year: 2024, Volume and Issue: unknown

Published: June 14, 2024

Language: Английский

Citations

16
Decoding dissolved information: environmental DNA sequencing at global scale to monitor a changing ocean DOI Creative Commons
Luke Thompson, Peter Thielen

Current Opinion in Biotechnology, Journal Year: 2023, Volume and Issue: 81, P. 102936 - 102936

Published: April 14, 2023

Language: Английский

Citations

16
Comparing eDNA metabarcoding and conventional pelagic netting to inform biodiversity monitoring in deep ocean environments DOI Creative Commons
David Côté, M B McClenaghan, Jessica E. Desforges

et al.

ICES Journal of Marine Science, Journal Year: 2023, Volume and Issue: 80(10), P. 2545 - 2562

Published: Nov. 9, 2023

Abstract The performance of environmental DNA (eDNA) metabarcoding has rarely been evaluated against conventional sampling methods in deep ocean mesopelagic environments. We assessed the biodiversity patterns generated with eDNA and two co-located methods, oblique midwater trawls vertical multinets, to compare regional sample-level diversity. then concordance ecological across water column habitats how markers level effort influenced inferred community. found characterized diversity well, detecting more taxa while identifying similar as samples. Within locations, detected than one replicate. While were within sample stations, fewer compared multinets. Our simulations show greater would improve methods. also observed that using taxonomic data from multiple most those Patterns Exact Sequence Variants stable suggesting they are powerful for change. is a valuable tool monitoring biological hotspots but some methodological adjustments recommended

Language: Английский

Citations

13
Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems DOI

Suxiang Lu,

Honghui Zeng, Fan Xiong

et al.

Science China Life Sciences, Journal Year: 2024, Volume and Issue: 67(7), P. 1368 - 1384

Published: March 18, 2024

Language: Английский

Citations

4
Applying environmental DNA approaches to inform marine biodiversity conservation: The case of the Ocean Twilight Zone DOI Creative Commons

Nina Yang,

Di Jin, Annette F. Govindarajan

et al.

Marine Policy, Journal Year: 2024, Volume and Issue: 165, P. 106151 - 106151

Published: May 6, 2024

Effective governance of the global ocean under accelerating environmental and social changes depends on sufficient scientific knowledge that unravels complexity dynamic marine ecosystems. In case vast remote twilight zone (OTZ), management is particularly challenged by lack data. Traditional biodiversity monitoring methods are unable to scale efficiently or effectively address these gaps new technologies needed inform policy. Environmental DNA (eDNA) has quickly gained traction in recent years as an enabling technology for conservation will play a transformative role OTZ high seas general. Through comprehensive review science policy literature analysis existing data, we discuss importance OTZ, gaps, summarize developments eDNA research. We identify key components framework implications relevant Biodiversity Beyond National Jurisdiction (BBNJ) Agreement. show integrated science-policy approach based transdisciplinary research essential achieving sustainability 30×30 target conserving biodiversity.

Language: Английский

Citations

4
Environmental DNA and its role in identifying yeast biodiversity in mangrove ecosystem: A literature review DOI Creative Commons

Lila Kusuma Rahayu,

Tri Retnaningsih Soeprobowati, Budi Warsito

et al.

E3S Web of Conferences, Journal Year: 2025, Volume and Issue: 605, P. 03005 - 03005

Published: Jan. 1, 2025

Yeast biodiversity in mangrove ecosystems is crucial for their health and ecological functions. However, traditional methods often fail to detect yeast species that are difficult culture or slow growing, leaving a significant portion of this undetected. This study explores the use environmental DNA (eDNA) as an alternative method identifying ecosystems, addressing data gaps left by conventional methods. Data collected from various relevant literature sources, including scientific journals, books, research reports. The review reveals eDNA analysis can improve conservation management providing robust assessments. Future should focus on understanding persistence, implications, improving bioinformatics better interpretation. In-depth long-term studies recommended temporal spatial dynamics communities ecosystems. Further validation conditions needed ensure reliability. Research interactions with other ecosystem components impact human activities like pollution habitat change also important.

Language: Английский

Citations

0
What is environmental DNA? DOI Creative Commons
Haylea Power, Miwa Takahashi, Simon Jarman

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1743 - 1758

Published: Nov. 1, 2023

Abstract DNA collected from the environment (eDNA) can provide valuable understanding of ecological patterns and processes. eDNA is highly physically heterogeneous, but this has not been well‐characterized, so most sampling strategies do target any particular physical fraction. Consequently, we have limited evidence to understand interpret behavior eDNA, improve efficiency sampling, nor components spectrum for taxonomic molecular attributes. We perform first detailed characterization a marine sample using serial filtering an 80 <0.22 μm particle size gradient, tree life metabarcoding approach taxon‐specific universal assays, coupled with scanning electron microscopy fluorescent confocal microscopy. confirm that manifest in broad states, ranging extracellular fragments whole cells, tissue fragments, organisms. The largest these fractions were embedded microbial biofilms, rather than particulate. show choice filter types spectrum, affect detectable species richness, notably, also enrich samples specific groups. Our results imply there considerable scope collection aquatic environments, its informativeness.

Language: Английский

Citations

7
Advancing ecological assessment of the Arabian Gulf through eDNA metabarcoding: opportunities, prospects, and challenges DOI Creative Commons
Thadickal V. Joydas, Seerangan Manokaran, Jayanath Gopi

et al.

Frontiers in Marine Science, Journal Year: 2024, Volume and Issue: 11

Published: March 18, 2024

The Arabian Gulf (hereafter ‘the Gulf’) is renowned for its unique ecological characteristics and distinct marine life. It offers a diverse range of ecosystems that have adapted to the impacts posed by natural stress human activities. Regular biomonitoring diversity assessments are necessary document health ecosystem implement appropriate measures effective conservation management. Recently, environmental DNA (eDNA), total pool isolated from samples, has emerged as highly tool studies. This review explores opportunities, prospects, challenges associated with employing eDNA metabarcoding in assessment Gulf. provides an overview status discusses potential applications assessing biodiversity, monitoring invasive species, evaluating health. Additionally, investigation addresses inherent implementing this technique, considering complexities, methodological intricacies, data interpretation. Overall, emphasizes immense advancing calls further research collaboration harness benefits ecosystem.

Language: Английский

Citations

2
The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data DOI Creative Commons
Katy E. Klymus, Jacoby Baker, Cathryn L. Abbott

et al.

Metabarcoding and Metagenomics, Journal Year: 2024, Volume and Issue: 8

Published: Dec. 30, 2024

Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data metadata makes results difficult to reproduce synthesise. A working group scientists have collaborated produce set minimum reporting guidelines the constituent steps workflows, physical layout laboratories through archiving. We emphasise how suite should adhere findable, accessible, interoperable reproducible (FAIR) standards, thereby providing context evaluating understanding study results. An overview considerations each workflow step is presented then summarised in checklist that can accompany published or report. Ensuring workflows are transparent documented critical research allow more efficient uptake into management decision-making.

Language: Английский

Citations

2
Environmental DNA: Enhancing Species Detection and Study Comparability with Synthetic DNA Tracers DOI Open Access

George Stamatoyannopoulos,

Thalia Papayannopoulou

Published: Feb. 2, 2024

Environmental DNA (eDNA) sampling has emerged as a powerful approach for monitoring biodiversity in the context of diverse terrestrial and aquatic ecosystems, broad potential both environmental surveys species management. eDNA studies focusing on plant animal have capitalized analytical methodologies developed originally metagenomic microorganisms, technological improvements sample collection. However, while proliferated rapidly, efforts to standardize methods are still nascent. Critically, fundamental data concerning distribution persistence different ecological contexts lacking, complicating confidence detection comparability between studies. We propose that key deficits could be addressed by using well-designed synthetic standards or tracers, which widely used fields ranging from medical diagnostics hydrology. In-field application standardized mixture barcoded fragments varying lengths concentrations recovered concommitantly with should provide critical yet missing turnover, well an internal molecular standard enhance

Language: Английский

Citations

1