The Environmental Sample Processor (ESP) filtered seawater sequentially through 5.0 um and 0.2 um pore size polyvinylidene fluoride filters. Seawater was evacuated from filters and followed twice with a 2 minute incubation with 1 ml of RNAlater\u2122. RNAlater was evacuated, and filters were stored in the ESP until they were transferred to -80 C upon instrument recovery.\u00a0
\nGrab samples for sequencing while the ESP was not deployed were taken using Niskin bottles that collected seawater at the same depth and location of the ESP. Water was transferred to a low-density polyethylene cubitainer and maintained at ambient temperature until return to lab within 30 min. Seawater was filtered as above with vacuum filtration and preserved immediately in liquid nitrogen and transferred to -80 C.
\nSingle-cell sequencing: Seawater was transferred directly from the Niskin bottle to a 50 ml Falcon tube and placed on ice until brought back to lab. Each sampling day, 3 x 1 ml of seawater was preserved in cryovials using 100 ul of glyTe (5 ml glycerol, 3 ml Milli-Q H2O, 1 ml 100 x TE pH 8.0, 0.2 um filter sterilized after mixing the above, and stored in -20 C freezer). Preserved samples were then placed in a -80 C freezer. Samples were processed and sequenced at JGI
These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval.
ESP and grab sample filters were processed for DNA and RNA using the Zymobiomics DNA/RNA Mini Kit. Turbo DNase and RiboZero were performed on RNA samples. Illumina HiSeq-2500 1TB 2 x 151 bp sequencing was performed at the Joint Genome Institute (JGI).\u00a0
\nBBtools was used to trim and screen reads, followed by read correction using bfc (version r181). Reads with no mate pair were removed. Metagenomes were assembled using SPAdes assembler 3.11.1. The entire filtered read set was mapped to the final assembly and coverage information generated using bbmap (version 37.78). Metatranscriptomes were assembled using MEGAHIT v1.1.2 and reads were mapped to the assembly using BBMap. The JGI Integrated Microbial Genomes System (IMG) was used for annotation of the metagenomes and metatranscriptomes.
\nBCO-DMO Processing notes:
\n- added conventional header with dataset name, PI name, version date
\n- modified parameter names to conform with BCO-DMO naming conventions
\n- reformatted date from Mon-DD (Oct-04) to YYYYMMDD (20141004)