European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation

Abstract

Marine ecosystems, ranging from coastal seas and wetlands to the open ocean, accommodate a wealth of biological diversity from small microorganisms to large mammals. This biodiversity and its associated ecosystem function occurs across complex spatial and temporal scales and is not yet fully understood. Given the wide range of external pressures on the marine environment, this knowledge is crucial for enabling effective conservation measures and defining the limits of sustainable use. The development and application of omics-based approaches to biodiversity research has helped overcome hurdles, such as allowing the previously hidden community of microbial life to be identified, thereby enabling a holistic view of an entire ecosystem’s biodiversity and functioning. The potential of omics-based approaches for marine ecosystems observation is enormous and their added value to ecosystem monitoring, management, and conservation is widely acknowledged. Despite these encouraging prospects, most omics-based studies are short-termed and typically cover only small spatial scales which therefore fail to include the full spatio-temporal complexity and dynamics of the system. To date, few attempts have been made to establish standardised, coordinated, broad scaled, and long-term omics observation networks. Here we outline the creation of an omics-based marine observation network at the European scale, the European Marine Omics Biodiversity Observation Network (EMO BON). We illustrate how linking multiple existing individual observation efforts increases the observational power in large-scale assessments of status and change in biodiversity in the oceans. Such large-scale observation efforts have the added value of cross-border cooperation, are characterised by shared costs through economies of scale, and produce structured, comparable data. The key components required to compile reference environmental datasets and how these should be linked are major challenges that we address.

Marine Microbiomes: Towards Standard Methods and Best Practices

“…The Marine Biodiversity Observation Network (MBON) is one of the first biodiversity monitoring programs to perform method comparisons to establish standardized workflows for sampling and analysis of eDNA, including for prokaryotic targets (e.g., Djurhuus et al, 2017;McElroy et al, 2020). Several current efforts feature protocols of the Tara Oceans expedition (Pesant et al, 2015), such as AtlantECO Mission Microbiomes (Pesant et al, 2022) and EMO BON (Santi et al, 2021; Table 1). Others, such as the Bio-GO-SHIP program (Clayton et al, 2022), have expanded to incorporate a subset of these protocols (Pesant et al, 2022).…”

“…Despite the challenges, simple steps can be applied in field settings to minimize potential contamination. A variety of detailed marine microbiome sampling protocols are available to guide researchers (e.g., Santi et al, 2021;Pesant et al, 2022), with a few key highlights provided here. In general, aseptic practices form the foundation of clean molecular technique.…”

“…Commercially available buffers like RNAlater and DNA/RNA Shield (Catalog no. R1100-250; Zymo Research, Irvine, CA) can protect all nucleic acids and are often recommended for broadly applicable sampling practices; for example, the European Marine Omics Biodiversity Observation Network (EMO BON) Handbook (Santi et al, 2021).…”

metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data

“…To demonstrate metaGOflow and its key features, the analysis of a sediment and a water column sample from EMO BON was performed. As mentioned in the EMO BON handbook [ 72 ] and the EMO BON paper [ 14 ], DNA extraction, cleaning, library preparation, and sequencing are performed at a centralized facility to minimize biases and maximize consistency in sequence quality. DNA extraction is performed using commercially available kits, to minimize deviations among samples.…”

“…The analysis of data resulting from these studies has greatly increased our understanding of the importance, the role, and the mechanisms governing microbial communities in some of the most common, sensitive, or threatened marine environments [ 11–13 ]. European Marine Omics Biodiversity Observation Network (EMO BON) [ 14 ], a European Marine Biological Resource Centre (EMBRC-ERIC) [ 15 ] initiative, is designed to continue and expand this effort by regular bimonthly microbial genomic biodiversity samplings at designated marine coastal stations around the European coastline. In the first 2 years of the EMO BON (2021–2022), it is expected that more than 540 shotgun metagenomic data sets from water column and sediment samples will be generated from 17 European sites.…”