Contrasting patterns in diversity and community assembly of bacterioplankton and three size fractions of protists in the South China Sea

Abstract

The microbial food web plays a critical role in marine ecosystems, composed of various cell sizes of microbial organisms. Here, high-throughput sequencing of the 16S and 18S rRNA genes was conducted to detect the community structure and distribution patterns of bacterioplankton (0.2 µm-2 µm) and three size fractions of protist communities, i.e., pico-protist (0.2 µm-2 µm), nano-protist (2 µm-20 µm), and micro-protist (20 µm-200 µm), in the euphotic zone of the South China Sea. The trophic mode compositions of protist communities varied significantly across three size fractions, characterized by a substantial prevalence of parasitic pico-protists (40% amplicon sequence variants) and a greater predominance of mixotrophic taxa within nano- and micro-protist communities. Furthermore, we detected stronger vertical stratification of bacterial and pico-protist communities, corresponding to the wider niche breadth of smaller cells and reliance on passive dispersal. Additionally, both bacterial and protist community assemblies were dominated by stochastic processes. The relative contribution of homogeneous selection in nano-protist community assembly was greater compared to other size fractions, probably related to high relative abundance of mixotrophs. In summary, our results suggest that both cell size and trophic mode affect marine microbial community assembly, and that neither the "size-plasticity" hypothesis nor the "size-dispersal" hypothesis fully matched microbial communities. Our analyses are important for a better understanding of the assemblage processes of marine epipelagic microbial communities and how they will respond to global change.IMPORTANCECell size is a key feature that influences microbial biology at both the cellular and community levels. Poorly understood is the extent to which diverse ecological factors influence the assembly of microbial communities of various sizes. Two important hypotheses addressing the mechanisms of biome assembly are "size-plasticity" and "size-dispersal." Here, we investigated epipelagic microbial communities to reveal differences in the ecological functions of various microbial sizes, to explore the association of ecological processes with niche and cell size, and to expand the current understanding of marine microbial community assemblages and their possible responses to future global change.

Keywords: South China Sea; community assembly; diversity; marine microbes.

Fig 1

Overview of sampling area and environmental factors. (A) Location of 18 sampling stations (blue circles) in the South China Sea. Map is from Ocean Data View (Schlitzer, Reiner, Ocean Data View, https://odv.awi.de, 2025). (B) Water column profiles. (C) Environmental factors at different water layers. Asterisk indicates significant differences at the level of P < 0.05 (*, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001). The abbreviations of environmental variables are NO₃-N, nitrate; NO₂-N, nitrite; NH₄-N, ammonium; PO₄-P, phosphate; SiO₄-Si, silicate; HNF, heterotrophic nano-sized flagellates; PNF, pigmented nano-sized flagellates; PPE, photosynthetic picoeukaryotes; Syn, Synechococcus; Pro, Prochlorococcus; HB, heterotrophic bacteria.

Fig 2

Community compositions of bacterioplankton and pico-, nano-, and micro-protists (A) at the phylum level (top 10 phyla and others) and (B) at the class level (relative abundance >5% in at least one of samples) across 54 samples for each size fraction.

Fig 3

Community compositions of pico-, nano-, and micro-protists, grouped by trophic modes across 54 samples for each size fraction.

Fig 4

(A) NMDS ordination of microbial communities in three water layers. (B) Violin plots of Bray-Curtis dissimilarity of microbial communities in each water layer. Black points and error bars represent the mean values and standard deviations, respectively. Letters indicate significant differences (P < 0.05) among water layers calculated by LSD tests.

Fig 5

The variations of bacterioplankton and pico-, nano-, and micro-protist communities are explained by spatial, environmental abiotic, and biotic variables, respectively. (A) RDAs show the microbial communities’ compositions in relation to non-significant (P > 0.1, gray fonts) and significant (P < 0.1, black fonts; P < 0.05, bold fonts) variables. (B) VPAs show the contributions of spatial factors (S), environmental abiotic factors (E), and biotic factors (B) on the compositions of the microbial communities, values <0 are not shown. The abbreviations of environmental and spatial variables are Tem, temperature; NO₂-N, nitrite; NH₄-N, ammonium; PO₄-P, phosphate; Syn, Synechococcus; HB, heterotrophic bacteria; PPE, photosynthetic picoeukaryotes; HNFs, heterotrophic nano-sized flagellates; PNFs, pigmented nano-sized flagellates; MEM1, 2, 3, 4, 6, 10, and 11, a set of spatial factors which were generated by distance-based Moran’s eigenvector maps. Note: Only variables with variance inflation factors less than 10 and significant in the forward model choice based on R² and P-values were retained in the analysis.

Fig 6

Boxplots of community-level niche breadth of bacterial and three size fractions of protist communities (A) across all depths and (B) in each water layer. LSD tests are calculated among groups. The numbers below the box indicate the mean values. Letters indicate significant differences (P < 0.05).

Fig 7

Relative contribution of different processes for microbial assembly at the (A) horizontal scale and (B) vertical scale based on phylogenetic bin-based null model analysis (iCAMP). Drift (and others) includes drift, diversification, weak selection, and/or weak dispersal.