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

   https://doi.org/10.1016/j.dsr2.2025.105563  

   Selph, Karen E; Yingling, Natalia; Traboni, Claudia; Landry, Michael R (December 2025, Deep Sea Research Part II: Topical Studies in Oceanography)

   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 chlorophyllcontaining 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 region’s nutrient-poor status. 

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2. Differential clearance rates of microbial phylotypes by four appendicularian species

   https://doi.org/10.3354/meps14233  

   Dadon-Pilosof, A; Conley, K; Lombard, F; Sutherland, KR; Genin, A; Richter, M; Glöckner, FO; Yahel, G (February 2023, Marine Ecology Progress Series)

   Appendicularians are abundant planktonic filter feeders that play a significant role in the pelagic food web due to their high clearance rates. Their diet and feeding rates have typically been measured as bulk chlorophyll or cell removal, with some attention given to prey size but no differentiation between the microbial phylotypes. Using a combination of in situ and laboratory incubations with flow cytometry and next-generation sequencing, we found species-specific differences in clearance rates and diet compositions of 4 common species: Oikopleura albicans , O. fusiformis , O. longicauda , and O. dioica . While O. albicans most efficiently removed nano-eukaryotic algae, the other smaller species preferentially removed micron-sized pico-eukaryotic algae. Pico- and nano-eukaryotic cells constituted the major food source of the studied appendicularians despite their occurrence in oligotrophic water dominated by prokaryotic cells. Across species, pico- and nano-planktonic microalgae biomass comprised 45 to 75% of the appendicularian diets. Although non-photosynthetic bacteria were removed at lower rates than all other prey groups, their total contribution to the appendicularian diet was not trivial, representing 5 to 19% of the planktonic carbon in the appendicularian diet; pico-cyanobacteria contributed an additional 9 to 18%. Removal rates and efficiencies of pico-eukaryotes were higher than those of prokaryotes of similar size. Strikingly different clearance rates were observed for different prokaryotic phylotypes, indicating that factors other than size are involved in determining the capturability of the cells. Collectively, our findings provide additional evidence for differential retention of microbial prey among mucous-mesh grazers and its substantial effect on the upper-ocean microbial community. 

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3. Phytoplankton community composition and biomass in the oligotrophic Gulf of Mexico

   https://doi.org/10.1093/plankt/fbab006  

   E Selph, Karen; Swalethorp, Rasmus; R Stukel, Michael; B Kelly, Thomas; N Knapp, Angela; Fleming, Kelsey; Hernandez, Tabitha; R Landry, Michael (March 2021, Journal of Plankton Research)

   Campbell, Lisa (Ed.)

   Abstract Biomass and composition of the phytoplankton community were investigated in the deep-water Gulf of Mexico (GoM) at the edges of Loop Current anticyclonic eddies during May 2017 and May 2018. Using flow cytometry, high-performance liquid chromatography pigments and microscopy, we found euphotic zone integrated chlorophyll a of ~10 mg m−2 and autotrophic carbon ranging from 463 to 1268 mg m−2, dominated by picoplankton (<2 μm cells). Phytoplankton assemblages were similar to the mean composition at the Bermuda Atlantic Time-series Study site, but differed from the Hawaii Ocean Times-series site. GoM phytoplankton biomass was ~2-fold higher at the deep chlorophyll maximum (DCM) relative to the mixed layer (ML). Prochlorococcus and prymnesiophytes were the dominant taxa throughout the euphotic zone; however, other eukaryotic taxa had significant biomass in the DCM. Shallower DCMs were correlated with more prymnesiophytes and prasinophytes (Type 3) and reduced Prochlorococcus. These trends in ML and DCM taxonomic composition likely reflect relative nutrient supply—with ML populations relying on remineralized ammonium as a nitrogen source, and the taxonomically diverse DCM populations using more nitrate. These spatially separated phytoplankton communities represent different pathways for primary production, with a dominance of picoplankton in the ML and more nano- and microplankton at the DCM. 

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4. Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series

   https://doi.org/10.1038/s43705-022-00121-8  

   Yeh, Yi-Chun; Fuhrman, Jed A. (December 2022, ISME Communications)

   Abstract Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005–2018), using SSU rRNA gene sequencing from two size fractions (0.2–1 and 1–80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46–93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships. 

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5. Distribution Patterns of Ciliate Diversity in the South China Sea

   https://doi.org/10.3389/fmicb.2021.689688  

   Liu, Weiwei; McManus, George B.; Lin, Xiaofeng; Huang, Honghui; Zhang, Wenjing; Tan, Yehui (September 2021, Frontiers in Microbiology)

   Ciliates are abundant microplankton that are widely distributed in the ocean. In this paper, the distribution patterns of ciliate diversity in the South China Sea (SCS) were analyzed by compiling community data from previous publications. Based on morphological identification, a total of 592 ciliate species have been recorded in the SCS. The ciliate communities in intertidal, neritic and oceanic water areas were compared in terms of taxonomy, motility and feeding habit composition, respectively. Significant community variation was revealed among the three areas, but the difference between the intertidal area and the other two areas was more significant than that between neritic and oceanic areas. The distributions of ciliates within each of the three areas were also analyzed. In the intertidal water, the community was not significantly different among sites but did differ among habitat types. In neritic and oceanic areas, the spatial variation of communities among different sites was clearly observed. Comparison of communities by taxonomic and ecological traits (motility and feeding habit) indicated that these traits similarly revealed the geographical pattern of ciliates on a large scale in the SCS, but to distinguish the community variation on a local scale, taxonomic traits has higher resolution than ecological traits. In addition, we assessed the relative influences of environmental and spatial factors on assembly of ciliate communities in the SCS and found that environmental selection is the major process structuring the taxonomic composition in intertidal water, while spatial processes played significant roles in influencing the taxonomic composition in neritic and oceanic water. Among ecological traits, environmental selection had the most important impact on distributions. 

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