Acidic vacuole-containing organisms are a majority of the eukaryotic microbial community in oligotrophic Argo Basin waters (eastern Indian Ocean)

The Argo Basin of the eastern Indian Ocean in austral summer (February 2022) was characterized by warm (28.5-30.6°C), oligotrophic surface waters (nitrate and phosphate ≤0.1 μM), with relatively shallow mixed layers and deep chlorophyll biomass maxima. From euphotic zone depth-resolved samples analyzed by for DNA and acid vacuole staining (Hoechst and LysoTracker Green) by ship-board flow cytometry, we found that autotrophic populations were dominated by Prochlorococcus , followed by mixotrophs (58 and 28% of autotrophic community biomass, respectively), with only 14% obligate phototrophic phytoplankton (i.e., plastidic cells without acid vacuole fluorescence). Acid vacuole-containing microbes (mixotrophs and heterotrophs) were 34% of the microbial community, and 80% of the eukaryotic biomass. In shallow waters, the eukaryotic chlorophyll-containing community was comprised of pico-sized obligate phototrophs and mixotrophs (233-325 cells mL ^-1 ), nano-sized obligate phototrophs and mixotrophs (72 and 374 cells mL ^-1 , respectively), with all groups increasing several-fold in the deep chlorophyll maxima. Mixotrophs were a higher proportion of the chlorophyll-containing community in the shallow nutrient-poor mixed layer, consistent with a nutrient-acquisition argument for their prevalence. Heterotrophic eukaryotes averaged 524 ± 36 cells mL ^-1 in the euphotic zone, changing little with depth and showing a significant positive relationship with Prochlorococcus , but not any other group. In contrast, mixotrophs were positively correlated with heterotrophic bacteria, but not with Prochlorococcus . Overall, the high proportion of mixotrophs in the microbial community may channel more productivity to higher trophic levels than expected given the regions nutrient-poor status.