Dataset: A characterization of microbes at the San Pedro Ocean Time-series (SPOT) from 2005 to 2018, using SSU rRNA gene sequencing from two size fractions, with a universal primer set that amplifies from prokaryotes and eukaryotes

Monthly San Pedro Ocean Time-series (SPOT) cruises on R/V Yellowfin were conducted in the San Pedro Channel, off the coast of Los Angeles, California, USA (33 N, 118 W). Samples were collected monthly from five depths, including 5 meters (m), deep chlorophyll maximum (DCM), 150m, 500m, and 890 m, between the years 2005 and 2018. Ten to fifteen liters of seawater was sequentially filtered through an 80-micrometer (μm) mesh, a 1-μm A/E filter (Pall, Port Washington, NY), and a 0.2-μm Durapore filter (ED Millipore, Billerica, MA). Filters were stored at -80° Celsius (C) until DNA extraction. Durapore filters (collecting material 0.2 to 1 μm) were used for free-living prokaryotic community analysis, and A/E filters (collecting material between 1 to 80 μm) were used to analyze phytoplankton, microzooplankton, and particle-associated or larger prokaryotic communities. DNA was extracted from the Durapore filters using a hot SDS, phenol/chloroform/isoamyl alcohol, ethanol precipitation extraction protocol as described by Fuhrman et al. (1988). DNA on the A/E filters was extracted using a NaCl/CTAB bead-beating extraction protocol as described by Lie et al. (2013) with slight modification by adding an ethanol precipitation step after lysis to reduce the volume of crude extract, which helps minimize DNA loss during the subsequent purification.

The V4-V5 hyper-variable region of the 16S and 18S rRNA genes were amplified simultaneously using a universal primer set 515Y (GTGYCAGCMGCCGCGGTAA) and 926R (CCGYCAATTYMTTTRAGTTT). All DNA samples were amplified and purified using the same conditions described in Yeh et al. 2021). Purified PCR products were pooled in equal amount and then sequenced on Illumina HiSeq 2500 in PE250 mode or MiSeq PE300.