The ocean sampling day consortium

Abstract

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Methods for the Study of Marine Biodiversity

“…Global sampling of surface water marine microbes is also underway utilising genomic methods, including synchronised sampling of hundreds of stations on 'Ocean Sampling Day' (www.microb3.eu/osd) (e.g., Davies et al 2012a, b;Kopf et al 2015). These and related research into molecular indicators may fill gaps that complement more conventional metrics of biodiversity (Leray and Knowlton 2015).…”

“…These missions are uncovering marine planktonic communities from viruses to protists, up to metazoan larvae. The Malaspina project (http://scientific.expedicionmalaspina.es) complements these observations with samples of the deep seas at the global scale, and 'Ocean Sampling Day' with about 150 stations globally sampled on the same day (Kopf et al 2015). An increasing number of cruises include molecular high-throughput analyses of genes, transcripts, and metabolites of planktonic organisms, together with environmental variables such as physical and biochemical parameters (e.g., Atlantic Meridional Transect http://www.amt-uk.org).…”

Minimum Information about a Biosynthetic Gene cluster

“…This will generate opportunities for a range of analyses, such as the biogeographical mapping of secondary metabolite biosynthesis 22 , thereby identifying locations and ecosystems harboring rich biosynthetic diversity. But even if the contextual data associated with the genome sequences cannot always be made MIxS compliant (perhaps because the origin of a strain can no longer be traced), the MIBiG standard itself provides a comprehensive reference dataset for annotating large-scale MIxS-compliant metagenomic data from projects such as the Earth Microbiome Project 23 , Tara Oceans 24 and Ocean Sampling Day 25 . This will enable scientists to obtain a better understanding of the distribution of BGCs in the environment.…”

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

“…This culture-free application has spread widely into microbiology studies over the past decade [1], and is now applied to several domains such as clinical microbiology to obtain a microbiota signature associated with a clinical picture [2], industrial processes for quality control [3], or environmental communities studies [4,5]. The term metagenomics can refer to two distinct methods: shotgun metagenomics and targeted metagenomics.…”