Sampling campaigns was carried out at 15 stations along a transect from Antofagasta (Chile) to Wellington (New Zealand) during the R/V Sonne "UltraPac" cruise (SO245) in the Austral summer of 2015/2016. The research cruise covered a vast geographical area of 7 000 km along the SPG, conducting sampling that spanned the entire vertical profile from the surface to the depths of the bathypelagic waters. Our study comprised samples within the longitudinal scale of 5 5000 km in which we analyzed the diversity and composition of the protistan and fungal community using 18S and ITS region. Sequencing was performed at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna under the project ID JMF-2103-18.