Short-read metabarcoding analysis is the gold standard to access to partial 16S and ITS genes with high read quality. With the advent of long-read sequencing, the amplification of full-length target genes is possible but with low read accuracy. Moreover, the amplification of 16S rDNA genes in seaweed or plant samples results in a large proportion of plastid reads, which are directly or indirectly derived from cyanobacteria. Primers designed not to amplify plastid sequences are available for short-read sequencing, while Oxford Nanopore Technology offers adaptive sampling, a unique way to remove reads in real-time. In this study, we compare three options to address the plastid read issue: deleting plastid reads with adaptative sampling, using optimized primers with Illumina MiSeq technology, and sequencing large numbers of reads with Illumina NovaSeq technology with universal primers. We showed that adaptive sampling using default settings of the MinKNOW software was ineffective for plastid depletion. We also demonstrated with a mock community that the SAMBA workflow provided the most accurate taxonomic assignment at the bacterial genus level compared to the IDTAXA and KRAKEN2 pipelines, but many false positives were generated at species level. Although NovaSeq sequencing with universal primer stood out for studying the algal bacterial community due to its deep coverage, the inclusion of eukaryotes and bacteria in the same sequencing run, and the low error rate, the combination of Illumina and ONT sequencing helped us explore the fungal diversity and allowed for the retrieval taxonomic information for genera poorly represented in the sequence databases.

Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea, exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota, Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. Taxonomic richness of replicated co-cultures resulting from natural communities with axenic E. huxleyi rapidly shifted and then stabilized over time, presumably by ecological selection favoring more beneficial populations. Recruited microbiomes from the environment were consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom depth were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of both deterministic processes and stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.

The Ocean Barcode Atlas (OBA) is a user friendly web service designed for biologists who wish to explore the biodiversity and biogeography of marine organisms locked in otherwise difficult to mine planetary scale DNA metabarcode datasets. Using just a web browser, a comprehensive picture of the diversity of a taxon or a barcode sequence is visualized graphically on world maps and interactive charts. Interactive results panels allow dynamic threshold adjustments and the display of diversity results in their environmental context measured at the time of sampling (temperature, oxygen, latitude, etc.). Ecological analyses such as alpha and beta-diversity plots are produced via publication quality vector graphics representations. Currently, the Ocean Barcode Altas is deployed online with the i) Tara Oceans eukaryotic 18S-V9 rDNA metabarcodes, ii) Tara Oceans 16S/18S rRNA miTags, and iii) 16S-V4V5 metabarcodes collected during the Malaspina-2010 expedition. Additional prokaryotic or eukaryotic plankton barcode datasets will be added upon availability, given they provide the required complement of barcodes (including raw reads to compute barcode abundance) associated with their contextual environmental variables. Ocean Barcode Atlas is a freely-available web service at: http://oba.mio.osupytheas.fr/ocean-atlas/.