Phagotrophic Protists Research Articles

Migrating ripples create streambed heterogeneity altering microbial diversity and metabolic activity

AbstractSandy sediments of lowland streams are typically transported at low flow in the form of migrating ripples. In these bedforms, microbial communities spanning all trophic guilds (heterotrophic bacteria, fungi, photoautotrophic and phagotrophic protists) are exposed to highly frequent moving–resting cycles of sediment grains. Up to date, it is unknown to what extent ripple migration impacts community metabolism and composition as well as the vertical zonation of sediment‐associated multitrophic microbial communities compared to stationary sediments. We hypothesize that, as a result of mechanical abrasion and limited light supply, migrating ripple sediments have lower microbial abundance, diversity, metabolism and resource acquisition and no vertical zonation compared to stationary sediments. We collected samples from five lowland streams in north‐eastern Germany between May and June 2020. The coarser and better sorted sediments of migrating ripples had a higher oxygen concentration and less organic matter than stationary sediments. Photosynthetic pigments, potential extracellular enzyme activities, bacterial cell counts, and fungal gene copies were lower in migrating ripples than in stationary sediments. In contrast, cell‐specific bacterial production was higher in migrating ripples. Metabarcoding revealed that bedform migration was important in shaping the community structure of bacteria, fungi, and phagotrophic protists. Dry mass‐related net community production, respiration, and bacterial production were higher in superficial compared to underlying layers irrespective of sediment transport. By modulating the abundance, diversity, and structure of different trophic guilds of microbial communities and their resource acquisition, migrating bedforms create streambed heterogeneity, shaping regional biodiversity and the flow of matter through the benthic food web.

Size exclusion experiment in a grassland field unravels top–down control of the soil fauna on microbial community assembly

AbstractHighly diverse and abundant organisms coexist in soils. However, the contribution of biotic interactions between soil organisms to microbial community assembly remains to be explored. Here, we assess the extent to which soil fauna can shape microbial community assembly using an exclusion experiment in a grassland field to sort soil biota based on body size. After 1 year, the exclusion of larger fauna favoured phagotrophic protists, with increases up to 32% in their proportion compared to the no‐mesh treatment. In contrast, members of the bacterial community and to a lesser extent of the fungal community were negatively impacted. Shifts in bacterial but not in fungal communities were best explained by the response of the protistan community to exclusion. Our findings provide empirical evidence of top–down control on the soil microbial communities and underline the importance of integrating higher trophic levels for a better understanding of the soil microbiome assembly.

Promotion of the symbiotic interaction between phagotrophic protists and beneficial bacteria, mediated via a balancing of soil nutrients, reduces the incidence of watermelon Fusarium wilt

Elucidating the microbial mechanisms that trigger Fusarium wilt represents a key step in addressing the barriers to sustainable cropping. However, from the perspective of the complete microbiome, the integrated role of soil nutrients and the microbial community in fields with different rate of wilt disease remains unclear. In this study, we examined the potential interrelationships among rhizosphere soil nutrients, bacteria, fungi, and protists in soils collected from fields in which watermelon had been cultivated for 8 years, and which were characterized by high (HW: 81.25%) or low (LW: 6.25%) incidence of watermelon Fusarium wilt. Soil from HW fields was found to contain a higher density of F. oxysporum (1.30-fold higher than that in the LW soil), along with higher contents of available phosphorus (1.31-fold higher), and available potassium (2.39-fold higher). In addition, the inter-kingdom correlation between protists and bacteria in the HW soil was 2.08-fold higher than that in LW soil. Furthermore, structural equation modeling revealed that an excess of soil available potassium enhances predation by potentially detrimental phagotrophic protists on potentially beneficial bacteria. Collectively, our findings indicate that a balanced nutrient input and the interaction between protists and beneficial bacteria play important roles in controlling the incidence of watermelon Fusarium wilt. These findings have implications for controlling the incidence of watermelon Fusarium wilt based on modifying the nutrient balance of soil and increasing the flora of certain beneficial protists (Cercomonas and Colpoda) that interact symbiotically with species of Bacillus.

Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome.

Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.

Intercropping with Trifolium repens contributes disease suppression of banana Fusarium wilt by reshaping soil protistan communities

Fusarium wilt disease of bananas, caused by the soil-borne pathogen Fusarium oxysporum, threatens banana production. Intercropping, cultivation of more than one crop simultaneously on the same field, has emerged as efficient and sustainable land management for suppressing Fusarium wilt disease. Although previous studies have proven the changes in soil microbial communities including bacteria and fungi under intercropping contributed to disease suppression, little is known about the role of protistan communities in driving this effect. In a field experiment, we assessed microbiome shifts with a focus on protists under intercropping of banana with the legume Trifolium repens. Our results showed that the reduced Fusarium wilt disease incidence and the decreased Fusarium pathogen density under intercropping could be attributed to the changes in protistan community compositions. Specially, we observed a significant negative correlation between the relative abundance of phagotrophic protists and Fusarium oxysporum. We further conducted a pot experiment to examine the impacts of the legume crop on phagotrophic protists across different spatial distances, which showing that intercropping enriched the relative abundance of phagotrophic protists, especially Cercomonas, with members of this group showing the capacity to directly inhibit the growth of Fusarium pathogen in vitro. We highlight that predatory protists are important agents underlying disease suppression in intercropping system, which can offer new venues to promote plant health in sustainable agriculture.

Urban greenspaces shape soil protist communities in a location-specific manner

The impacts of urbanization on aboveground biodiversity are well studied, and its impact on soil microorganisms are also receiving increased attention. However, the impact of urbanization on the soil protists are hardly investigated. Here, we studied how urbanization and distinct urban greenspaces affect protist communities. We used amplicon sequencing of the18 S rRNA gene of samples from five types of urban greenspaces (parks, greenbelts, industrial areas, residential areas and hospital lawns), neighboring natural forests and agricultural ecosystems in Ningbo, China. We found that urban greenspaces harbored higher protist α-diversity than forests, while protist β-diversity increased from agricultural systems to urban greenspaces to forests. Among the studied driving factors, soil bacterial α- and β-diversity best predicted phagotrophic protist α- and β-diversity in urban greenspaces, while differences in α- and β-diversity of phototrophic protists were best explained by soil carbon-to-nitrogen ratio and fungal β-diversity, respectively. Abiotic factors i.e., total phosphorus and carbon-to-nitrogen ratio, best predicted the α- and β-diversity of protist parasites in urban greenspaces, respectively. The results revealed that the composition and drivers of protist communities vary between functional groups and urban ecosystems. Overall, our findings contribute to a better understanding of drivers of soil protist communities and indicate that soil protist communities and associated soil functions could be managed in predictable ways in urban greenspaces.

Phagotrophic protists preserve antibiotic-resistant opportunistic human pathogens in the vegetable phyllosphere

Food safety of leafy greens is an emerging public health issue as they can harbor opportunistic human pathogens (OHPs) and expose OHPs to consumers. Protists are an integral part of phyllosphere microbial ecosystems. However, our understanding of protist-pathogen associations in the phyllosphere and their consequences on public health remains poor. Here, we examined phyllosphere protists, human pathogen marker genes (HPMGs), and protist endosymbionts from four species of leafy greens from major supermarkets in Xiamen, China. Our results showed that Staphylococcus aureus and Klebsiella pneumoniae were the dominant human pathogens in the vegetable phyllosphere. The distribution of HPMGs and protistan communities differed between vegetable species, of which Chinese chive possessed the most diverse protists and highest abundance of HPMGs. HPMGs abundance positively correlated with the diversity and relative abundance of phagotrophic protists. Whole genome sequencing further uncovered that most isolated phyllosphere protists harbored multiple OHPs which carried antibiotic resistance genes, virulence factors, and metal resistance genes and had the potential to HGT. Colpoda were identified as key phagotrophic protists which positively linked to OHPs and carried diverse resistance and virulence potential endosymbiont OHPs including Pseudomonas nitroreducens, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. We highlight that phyllosphere protists contribute to the transmission of resistant OHPs through internalization and thus pose risks to the food safety of leafy greens and human health. Our study provides insights into the protist-OHP interactions in the phyllosphere, which will help in food safety surveillance and human health.

Top-down structuring of freshwater bacterial communities by mixotrophic flagellates

Mixotrophic and heterotrophic protists hold a key position in aquatic microbial food webs. Whereas they can account for the bulk of bacterivory in pelagic systems, the potential structuring effect of these consumers on bacterial communities is far from clear. We conducted short-term grazing experiments to test for the overall impact on bacterial community structure and possible prey preferences of phagotrophic protists. The protist taxa selected for this study include three mixotrophic flagellates, comprising two obligate- and one facultative mixotroph, and one phagoheterotrophic flagellate lacking phototrophic capacity. Bacterioplankton from seven different lakes were enriched and used to represent semi-natural prey communities. Our study demonstrated protist strain specific impacts on bacterial community composition linked to grazing. The three mixotrophs had variable impacts on bacterial communities where the two obligate mixotrophs exhibited lower grazing rates, while showing a tendency to promote higher bacterial diversity. The phagoheterotroph displayed the highest grazing rates and structured the bacterial communities via apparent selective grazing. Consistent selectivity trends were observed throughout the experiments, such as the apparent avoidance of all flagellates of Actinobacteria, and high grazing on dominant Burkholderiales taxa. However, there was no consistent “fingerprint” of mixotrophic grazing on prey communities, but the structuring impact rather seemed to depend on the trophic mode of the individual protist taxa, i.e. their dependence on phototrophy vs. phagotrophy. Our findings highlight the differential structuring impact of protist taxa on bacterial communities which may have important ecological implications, for example during periodic dominance of obligate mixotrophic bacterivores in changing lake ecosystems.

Phosphorus Fertilization Boosts Mineral-Associated Soil Organic Carbon Formation Associated with Phagotrophic Protists.

Long-term fertilization affects soil organic C accumulation. A growing body of research has revealed critical roles of bacteria in soil organic C accumulation, particularly through mineral-associated organic C (MAOC) formation. Protists are essential components of soil microbiome, but the relationships between MAOC formation and protists under long-term fertilization remain unclear. Here, we used cropland soil from a long-term fertilization field trial and conducted two microcosm experiments with 13C-glucose addition to investigate the effects of N and P fertilizations on MAOC formation and the relationships with protists. The results showed that long-term fertilization (especially P fertilization) significantly (P < 0.05) increased 13C-MAOC content. Compared with P-deficient treatment, P replenishment enriched the number of protists (mainly Amoebozoa and Cercozoa) and bacteria (mainly Acidobacteriota, Bacteroidota, and Gammaproteobacteria), and significantly (P < 0.001) promoted the abundances of bacterial functional genes controlling C, N, P, and S metabolisms. The community composition of phagotrophic protists prominently (P < 0.001) correlated with the bacterial community composition, bacterial functional gene abundance, and 13C-MAOC content. Co-occurrence networks of phagotrophic protists and bacteria were more connected in soil with the N inoculum added than in soil with the NP inoculum added. P replenishment strengthened bacterial 13C assimilation (i.e., 13C-phospholipid fatty acid content), which negatively (P < 0.05) correlated with the number and relative abundance of phagotrophic Cercozoa. Together, these results suggested that P fertilization boosts MAOC formation associated with phagotrophic protists. Our study paves the way for future research to harness the potential of protists to promote belowground C accrual in agroecosystems.

Soil aggregates affect the legacy effect of copper pollution on the microbial communities

Soil aggregates provide spatially heterogeneous microhabitats for microorganisms and their activities. In metal contaminated soil, the microbial community is shaped by both metal stress and aggregate sizes. However, it remains unclear whether and how aggregate sizes affect the legacy effect of metal pollution on microbial communities. Here, we investigated the legacy effect of long-term copper (Cu) pollution on the distribution patterns of the bacterial and protistan communities in soil aggregates. Our results showed that soil aggregates of different sizes possessed distinct bacterial and protistan communities under Cu-polluted and unpolluted conditions (aggregate effects), as reflected by distinct α-diversity and community compositions. The bacterial and protistan communities in micro- and macro-aggregates were more responsive to Cu pollution than those in mega-aggregates, primarily because micro- and macro-aggregates contained a greater number of Cu susceptible bacterial and protistan species. Ciliophora and Chlorophyta displayed great sensitivity to Cu, especially in small aggregate-size fractions, and could serve as a bio-indicator of Cu pollution. Furthermore, the magnitude of aggregate effects on microbial communities was weakened in Cu-polluted soils compared to unpolluted soils. With decreasing aggregate sizes, the co-occurrence networks between bacteria and protists became more complex, connected and compact. Robustness analysis showed that phagotrophic protists played essential roles in sustaining the network stability, especially in mega-aggregates. Our findings highlight the asymmetrical changes in microorganisms in aggregates under long-term Cu pollution, providing a novel insight into the legacy effects of metal pollution on soil microbiomes at the micro-level.

Phagotrophic Protists Modulate Copper Resistance of the Bacterial Community in Soil.

Protist predation is a crucial biotic driver modulating bacterial populations and functional traits. Previous studies using pure cultures have demonstrated that bacteria with copper (Cu) resistance exhibited fitness advantages over Cu-sensitive bacteria under the pressure of protist predation. However, the impact of diverse natural communities of protist grazers on bacterial Cu resistance in natural environments remains unknown. Here, we characterized the communities of phagotrophic protists in long-term Cu-contaminated soils and deciphered their potential ecological impacts on bacterial Cu resistance. Long-term field Cu pollution increased the relative abundances of most of the phagotrophic lineages in Cercozoa and Amoebozoa but reduced the relative abundance of Ciliophora. After accounting for soil properties and Cu pollution, phagotrophs were consistently identified as the most important predictor of the Cu-resistant (CuR) bacterial community. Phagotrophs positively contributed to the abundance of a Cu resistance gene (copA) through influencing the cumulative relative abundance of Cu-resistant and -sensitive ecological clusters. Microcosm experiments further confirmed the promotion effect of protist predation on bacterial Cu resistance. Our results indicate that the selection by protist predation can have a strong impact on the CuR bacterial community, which broadens our understanding of the ecological function of soil phagotrophic protists.

Changes in Phylogenetic and Functional Diversity of Ciliates along the Course of a Mediterranean Karstic River.

Ciliates are a group of phagotrophic protists found in a wide variety of ecosystems. This study builds on recent studies of ciliates in the Krka river and investigates changes in the phylogenetic and functional diversity of ciliates in biofilm to predict the phylogenetic and functional structure of ciliates in other karstic rivers. Biofilm samples were collected from four representative locations: upstream (Krka spring), midstream (Marasovine), and downstream (Roški slap, Skradinski buk) of the Krka river to test for differences in phylogenetic and functional diversity of ciliates in relation to location and positioning on tufa stones (light/dark-exposed side of tufa stone). Our results showed that Krka spring had higher phylogenetic species variability, lower phylogenetic diversity, and lower functional richness than Skradinski buk, suggesting phylogenetic overdispersal at Krka spring. This could be due to environmental filtering, competitive exclusion, or a combination of these factors. As the first study of its kind in the Mediterranean, our results shed light on the phylogenetic and functional diversity of ciliates in karst ecosystems and provide a basis for future ecological and conservation efforts.

Protist Diversity Responses to Experimental N Deposition in Biological Crusts of a Semiarid Mediterranean Ecosystem

Biological soil crusts (BSC) are associations of different macro and microorganisms and aggregated soil particles located on the surface of soils in many different habitats. BSC harbour a diverse and complex community of ciliates and testate amoebae. These phagotrophic protists play an important role in C and N recycling in soil ecosystems but have not been frequently studied in BSC. In this context, the effects of three increasing N inputs on ciliates and testate amoebae in crusts from a semi-arid Mediterranean ecosystem were evaluated. A field experiment with artificial N-deposition was designed to mimic the effects caused by anthropogenic N depositions. The results have shown that the protist populations of these semi-arid Mediterranean environments have lower species richness than other soil environments. The increase in N produces a net loss of diversity in the populations studied and shifts in the community structure. It has also been shown that some ciliates and testate amoebae, due to their population responses to increased N concentrations, could potentially be used as bio-indicators of N contamination in these BSCs.

Algae and cyanobacteria in the aphotic habitats of Veternica Cave (Medvednica Mt., Croatia) and selected caves of the Dinaric karst (South-Eastern Europe)

Microphototrophs (algae and cyanobacteria) in karst environments have been intensively studied in aquatic epigean habitats. In recent decades knowledge about the communities inhabiting cave entrances and lampenflora has grown substantially, but the data about the communities in aphotic cave zone are scarce. This study aimed to investigate spatio-temporal presence of microphototrophs in the aphotic zone of Veternica Cave (Mt. Medvednica karst) and to present additional preliminary data from 22 caves of the Dinaric karst. The data were collected over ten years, in parallel with research on cave phagotrophic protists. In addition to the remains of microphototrophs, living algae and cyanobacteria were found in the cave aphotic zone. Diatoms (Bacillariophyta) were the most frequent group found, followed by green algae (Chlorophyta), golden-brown algae (Chrysophyta) and the filamentous cyanobacteria (Cyanobacteria). The presence of microphototrophs was detected throughout the year but showed spatio-temporal variations. Microphototrophs were absent in the parts of Veternica Cave with seeping and dripping water, while they were occasionally present in the hydrologically active parts of the cave. The presence of diatoms in the aphotic zone of Veternica Cave was related to hydrological conditions, and was not affected by the distance from the cave entrance. The presence of microphototrophs in caves of the Dinaric karst has been associated with caves subject to various types of flooding by endogenous and exogenous water. Despite the fact that microphototrophs are passively transported to the caves from the surface habitats, the presence of live individuals in the cave aphotic zone implies that they should not be neglected in discussions about cave food webs. Future research of microphototrophs should be focused on the species identification, their abundance, survival time, and detail description of conditions that determine their presence in caves.

Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies.

The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the "Opisthosporidia hypothesis"). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the "Aphelida $+$ Fungi hypothesis"). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida $+$ Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid-fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.].

Index to Titles and Authors/Editors of Books Reviewed

Index to Titles and Authors/Editors of Books Reviewed

Phagotrophic protists can change microbial nitrogen conversion patterns during swine manure composting

Phagotrophic protists can change microbial nitrogen conversion patterns during swine manure composting

Precipitation changes, warming, and N input differentially affect microbial predators in an alpine meadow: Evidence from soil phagotrophic protists

Soil phagotrophic protists are highly abundant and play a vital role in nutrient cycling through feeding on microbes. Global change factors, individually or in combination, often affect soil bacteria and fungi, but whether and how the resulting changes may cascade to affect phagotrophic protists remain largely unknown. Combining direct microscopic counting and high-throughput sequencing of 18s rRNA gene, we examined effects of precipitation changes, warming and nitrogen (N) input on soil phagotrophic protists in a 3-yr manipulation experiment with a Tibetan alpine meadow. Precipitation addition (+30%) enhanced but precipitation reduction (−30%) and warming decreased the alpha diversity of phagotrophic protists, primarily through altering soil moisture. However, N input (12 g N m−2 y−1) increased protist abundance, and in particular, offset the negative effect of precipitation reduction on the relative abundance of phagotrophic protists through increasing the microbial biomass, implying a bottom-up trophic control. Together, these findings indicate that interactions of multiple global change drivers may affect soil protist communities directly by modifying the soil physiochemical environment and indirectly through trophic cascading, which have implications for the potential changes in their ecosystem functions in alpine meadow under future global change scenarios.

Soil properties have more significant effects on the community composition of protists than the rhizosphere effect of rice plants in alkaline paddy field soils

Protists are among the most diverse and major microbial groups in the soil ecosystem and play versatile functional roles for soil fertility and agricultural productivity. However, protist community composition is poorly understood in paddy field soil, especially in alkaline paddy fields. Here we aimed to characterise protist communities of alkaline paddy field soils with a particular focus on the effects of physicochemical properties of the soils and the rhizosphere effect of rice. We selected several alkaline paddy fields across three regions that differed in their soil physicochemical properties along the Kizilirmak River, Turkey, as a model ecosystem. The soils were incubated under submerged conditions with and without rice plants (Oryza sativa L.) to understand the rhizosphere effect on protist community composition. The protist communities were analysed with a high throughput sequencing method. The results showed that Amoebozoa (29.5%) were the most abundant taxonomic group of protists in the paddy fields, followed by Stramenopiles (23.7%), Rhizaria (19.5%), and Alveolata (12.6%). Among the functional groups, consumers (decomposers and predators) were the most dominant protist group (67.7%), followed by autotrophs (21.0%) and pathogens (microbial/animal parasites and plant pathogens) (9.2%). The soil properties have more significant effects driving the community composition of protists than the rhizosphere effect of rice in the paddy field soils. Among the soil properties, pH, exchangeable Na and Ca, EC, and lime were significantly correlated with the shift in the protist community composition. The rhizosphere effect of rice mainly affected phagotrophs and plant pathogens, especially Pythium sp. A significant negative correlation was observed in the relative abundances between phagotrophic protists and plant pathogens, which indicates that the plant pathogens could be top-down controlled by the phagotrophs.

Carbon and nitrogen isoscape of particulate organic matter in the East China Sea

The isoscape of particulate organic matters (POM) in the euphotic zone at the shelf of the East China Sea (ECS) is affected by hydrological interactions and biological activities. Based on the stable carbon and nitrogen isotope values (δ13C and δ15N) and C:N ratio of POM (0.7 to 50 μm) in the euphotic zone of the ECS from 2008 to 2018 with a total of 113 samples, we inferred their sources and then investigated what hydrographical and biological conditions determined these spatio-temporal variations through synoptic and intensive seasonal monitoring. The isotopic signatures (δ13C: −26.9 to −12.4‰, δ15N: −1.0 to 10.8‰) and C:N ratios (4.4–9.0) of euphotic POM varied within the range of values reported for marine phytoplankton, suggesting limited contribution of terrigenous POM to the shelf of the ECS. The δ13C values of POM increased with the increase of chlorophyll-a (chl-a) concentration at the depth of chl-a maximum and the δ15N values decreased near the Changjiang River plume and inner shelf with freshwater input and coastal upwelling in summer. This indicated that phytoplankton production was enhanced by high nutrient supply and warmer temperature. Besides, the δ15N values were higher under lower inorganic nitrogen nutrient concentrations, and were negatively correlated with POM C:N ratio (i.e., δ15N value was less negative with higher nitrogen content in POM). Such correlations may suggest the enhanced trophic interactions in microbial food chains in oligotrophic environments, where phagotrophic protists with high δ15N values could be included into the size fraction (0.7–50 μm) of POM. Based on our study, the spatial and temporal δ13C and δ15N isoscape of euphotic POM serves as an ecological indicator to infer primary production and plankton food web properties of the East China Sea.