Repository of community practices in Ocean Research, Applications and Data/Information Management
⇒ OBON: Ocean Biomolecular Observing Network
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Ocean life - from viruses to whales - is built from "biomolecules''. Biomolecules such as DNA infuse each drop of ocean water, grain of sediment, and breath of ocean air.
The Biomolecular Ocean Observing Network (OBON) will develop a global system that will allow science and society to understand ocean life like never before. The programme will transform how we sense, harvest, protect, and manage ocean life, which faces multiple stresses including pollution, habitat loss, and climate change. It will also help communities detect biological hazards like harmful algal blooms and pathogens and be a key component of next-generation ocean observing systems.
This Ocean Decade Programme hosts the following endorsed Decade Project: Mission Ocean Microbiomes (Tara Microbiomes)
Contact: mleinen@ucsd.edu
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Omics community protocols. EuroSea Deliverable D3.19.
(EuroSea Project, , 2023)The aim of the WP3 “Network Integration and Improvements” is to coordinate and enhance key aspects of integration of European observing technology (and related data flows) for its use in the context of international ocean ... -
Interoperable vocabulary for marine microbial flow cytometry.
(2022)The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms ... -
Marine microbiomes: Towards standard methods and best practices.
(Frontiers Media SA, Lausanne, Switzerland, 2023)The microbiome is key to understanding and sustaining the services that ocean ecosystems provide (Bolhuis et al., 2020). The marine microbiome—an ensemble of microscopic organisms that inhabit water columns, sediments, ... -
Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics.
(2023)Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host’s responses ... -
Collection Standand Operating Procedures: Omics size fractionation. Version 1.00.
(Naples Ecological Research Augmented Observatory (NEREA), Naples, Italy, 2021)The NEREA project aims to promote the development of new indicators for ocean health and new models of ocean microbiomes by coupling traditional physical, chemical, and biological measurements with omics approaches (i.e. ... -
Environmental DNA test validation guidelines.
(National eDNA Reference Centre, Canberra, Australia, 2022)These Environmental DNA test validation guidelines provide harmonised quality control and minimum standard considerations for developing or validating eDNA/eRNA assays for the purpose of single-species or multi-species ... -
Environmental DNA protocol development guide for biomonitoring.
(National eDNA Reference Centre, Canberra, Australia, 2022)The Environmental DNA protocol development guide for biomonitoring (EP guide for biomonitoring) provides harmonised quality control and minimum standard operating procedures. This document is complemented by the Environmental ... -
A practical guide to DNA-based methods for biodiversity assessment.
(Pensoft Advanced Books, Sofia, Bulgaria, 2021)This book represents a synthesis of knowledge and best practice in the field of DNA-based biomonitoring at the time of writing. It has been written with end-users of molecular tools in mind, as well as those who are new ... -
BBI: an R package for the computation of Benthic Biotic Indices from composition data.
(2018)The monitoring of impacts of anthropic activities in marine environments, such as aquaculture, oil-drilling platforms or deep-sea mining, relies on Benthic Biotic Indices (BBI). Several indices have been formalised to ... -
DNA Metabarcoding Methods for the Study of Marine Benthic Meiofauna: A Review.
(2021)Meiofaunal animals, roughly between 0.045 and 1 mm in size, are ubiquitous and ecologically important inhabitants of benthic marine ecosystems. Their high species richness and rapid response to environmental change make ... -
Framing Cutting-Edge Integrative Deep-Sea Biodiversity Monitoring via Environmental DNA and Optoacoustic Augmented Infrastructures.
(2022)Deep-sea ecosystems are reservoirs of biodiversity that are largely unexplored, but their exploration and biodiscovery are becoming a reality thanks to biotechnological advances (e.g., omics technologies) and their ... -
Toward a Global Public Repository of Community Protocols to Encourage Best Practices in Biomolecular Ocean Observing and Research
(2021)Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over ... -
Expanding "Tara" Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018).
(2019)Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition ... -
EMP Sample Submission Guide.
(NOAA Fisheries Southwest Fisheries Research Center, La Jolla,CA, 2018)This protocol was designed for collaborators with the Earth Microbiome Project to contribute samples in a standardized fashion. Raw, frozen samples are submitted in individually labeled tubes, 10 aliquots (identical ... -
Earth Microbiome Project (EMP) high throughput (HTP) DNA extraction protocol. Version 07112018.
(University of California, San Diego, San Diego, CA, 2018)This protocol accompanies the following publication: Marotz, Clarisse, et al. "DNA extraction for streamlined metagenomics of diverse environmental samples." BioTechniques 62.6 (2017):290-293 -
Quanti-iT™ Pico Green dsDNA Assay (Invitrogen P7589).
(Matthew Sullivan Lab, University of Arizona/Ohio State University, Tucson, AZ, 2019)This protocol accompanies the following publication: Ul-Hasan S, Bowers RM, Figueroa-Montiel A, Licea-Navarro AF, Beman JM, Woyke T, et al. (2019) Community ecology across bacteria, archaea and microbial eukaryotes in the ... -
Single cell rDNA amplification of Nassellaria (Radiolaria).
(Station Biologique de Roscoff, Roscoff, France, 2018) -
Confocal Microscopy imaging for Opaline Silica Single Cell Skeletons (Polycystines Radiolaria).
(Station Biologique de Roscoff, Roscoff, France, 2018) -
Transcriptome sequencing of 19 diverse species of choanoflagellates.
(Station Biologique de Roscoff, Roscoff, France, 2017)The origin of animals, which occurred over 600 million years ago, left no evidence in the fossil record. To trace the earliest events in animal prehistory, we compare extant animals to their closest living relatives, the ... -
Microscope video recording.
(Station Biologique de Roscoff, Roscoff, France, 2019)Protocol to record videos on SBR Microscope.
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