DGGE_Weiker: Surface samples were collected while following a surface drifter (crosse window shade type). DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis. Sequencing use the Sanger method. Details can be found in Grattepanche, et al, 2014.

454 Long Island Sound: Surface and deep samples were taken from the Sound on several occasions. DNA was extracted and a ciliate clade-specific portion of the small subunit ribosomal gene was amplified using the polymerase chain reaction. Amplified fragments were sequenced using the Roche 454 platform. Details are reported in Santoferrara, et al, 2014.

454 and DGGE Hatteras: Vertically-resolved samples were collected along a section due south from Naragansett RI to the shelf break. DNA was extracted and amplified with PCR, and amplicons were separated with denaturant gradient gel electrophoresis or sequenced with Roche 454. Methodological details can be found in Grattepanche, et al, 2014 and Santoferrara, et al, 2014.

Single cells, Long Island Sound: Individual cells of tintinnid microzooplankton were picked with a micropipette, photo documented and placed in buffer for extraction and sequencing. Sequences of the internal transcribed spacer regions (ITS1-5.8S-ITS2), the small sub unit ribosomal gene (SSU), and the large subunit ribosomal gene (LSU) were obtained by Sanger sequencing.

References:

Grattepanche, J-D, L Santoferrara, J Andrade, AM Oliverio, GB McManus, and LA Katz. 2014. Distribution and diversity of oligotrich and choreotrich ciliates assessed by morphology and by DGGE in temperate coastal waters. Aquat. Microb. Ecol. 71:211-221. DOI:10.3354/ame01675.

Santoferrara, L, J-D Grattepanche, LA Katz, and GB McManus. 2014. Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods. Environ. Microbiol. DOI: 10.1111/1462-2920.12380.

Santoferrara, LF, GB McManus, and VA Alder. 2012. Utility of Genetic Markers and Morphology for Species Discrimination within the Order Tintinnida (Ciliophora, Spirotrichea). Protist , doi:10.1016/j.protis.2011.12.002