Annual Partitioning Patterns of Labyrinthulomycetes Protists Reveal Their Multifaceted Role in Marine Microbial Food Webs

Oxygen levels differentially attenuate the structure and diversity of microbial communities in the oceanic oxygen minimal zones

Global change mediated shifts in ocean temperature and circulation patterns, compounded by human activities, are leading to the expansion of marine oxygen minimum zones (OMZs) with concomitant alterations in nutrient and climate-active trace gas cycling. While many studies have reported distinct bacterial communities within OMZs, much of this research compares across depths rather with oxygen status and does not include eukayrotic microbes. Here, we investigated the Bay of Bengal (BoB) OMZ, where low oxygen conditions are persistent, but trace levels of oxygen remain (< 20 μM from 200 to 500 m). As other environmental variables are similar between OMZ and non-OMZ (NOZ) stations, we compared the abundance, diversity, and community composition of several microbial groups (bacterioplankton, Labyrinthulomycetes, and fungi) across oxygen levels. While prokaryote abundance decreased with depth, no significant differences existed across oxygen groups. In contrast, Labyrinthulomycetes abundance was significantly higher in non-OMZ stations but did not change significantly with depth, while fungal abundance was patchy without clear depth or oxygen-related trends. Bacterial and fungal diversity was lower in OMZ stations at 500 m, while Labyrinthulomycetes diversity only showed a depth-related profile, decreasing below the euphotic zone. Surprisingly, previously reported OMZ-associated bacterial taxa were not significantly more abundant at OMZ stations. Furthermore, compared to the bacterioplankton, fewer Labyrinthulomycetes and fungi taxa showed responses to oxygen status. Thus, this research identifies stronger oxygen-level linkages within the bacterioplankton than in the examined microeukaryotes.

Labyrinthulomycetes thrives in organic matter-rich waters with ecological partitioning in the Pearl River Estuary

Labyrinthulomycetes play an important role in marine biogeochemical cycles, but their diversity, distribution patterns, and key regulatory factors remain unclear. This study measured the abundance and diversity of Labyrinthulomycetes in the Pearl River Estuary (PRE) to understand its distribution pattern and relationship with environmental and biological factors. The abundance of Labyrinthulomycetes ranged from 24 to 500 cells·mL-1, with an average of 144.37 ± 94.65 cells·mL-1, and its community composition showed obvious ecological partitioning in the PRE. The results of statistical analysis indicated that CDOM, salinity, and chlorophyll a contributed significantly (P < 0.01) to the community composition, explaining 46.59%, 11.34%, and 4.38% of the variance, respectively. The Labyrinthulomycetes distribution pattern combined with the niches of dominant species was revealed; low-salinity species mainly use terrigenous organic matter occupied dominant positions in the upper estuary and showed the highest abundance; moderate-salinity species that can use phytoplankton-derived resources thrived in the middle estuary; and seawater species dominated the lower estuary with the highest diversity but the lowest abundance. In addition, the results of phylogenetic tree analysis indicated that the existence of a novel lineage, and further study on the diversity and ecological functions of Labyrinthulomycetes is needed.IMPORTANCELabyrinthulomycetes play important roles in organic matter remineralization, carbon sinks, and food webs. However, the true diversity of Labyrinthulomycetes is still unclear due to limitations in isolation and culture methods. In addition, previous studies on their relationship with environmental factors are inconsistent and even contradictory, and it is speculated that their community composition may have spatial heterogeneity along the environmental gradient. In this study, the distribution pattern and key regulators of Labyrinthulomycetes in the PRE were revealed. Combining the niche of dominant species, it is suggested that salinity determines the spatial differences in Labyrinthulomycetes diversity, and the resources of substrate (terrestrial input or phytoplankton-derived) determine the dominant species, and its abundance is mainly determined by organic matter concentrations. Our study provided new information on the Labyrinthulomycetes diversity and verified the spatial heterogeneity of Labyrinthulomycetes community composition, providing reliable explanations for the inconsistencies in previous studies.

Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin

Stramenopiles represent a significant proportion of aquatic and terrestrial biota. Most biologists can name a few, but these are limited to the phototrophic (e.g. diatoms and kelp) or parasitic species (e.g. oomycetes, Blastocystis), with free-living heterotrophs largely overlooked. Though our attention is slowly turning towards heterotrophs, we have only a limited understanding of their biology due to a lack of cultured models. Recent metagenomic and single-cell investigations have revealed the species richness and ecological importance of stramenopiles-especially heterotrophs. However, our lack of knowledge of the cell biology and behaviour of these organisms leads to our inability to match species to their particular ecological functions. Because photosynthetic stramenopiles are studied independently of their heterotrophic relatives, they are often treated separately in the literature. Here, we present stramenopiles as a unified group with shared synapomorphies and evolutionary history. We introduce the main lineages, describe their important biological and ecological traits, and provide a concise update on the origin of the ochrophyte plastid. We highlight the crucial role of heterotrophs and mixotrophs in our understanding of stramenopiles with the goal of inspiring future investigations in taxonomy and life history. To understand each of the many diversifications within stramenopiles-towards autotrophy, osmotrophy, or parasitism-we must understand the ancestral heterotrophic flagellate from which they each evolved. We hope the following will serve as a primer for new stramenopile researchers or as an integrative refresher to those already in the field.

Comparative Genomic Analyses of Cellulolytic Machinery Reveal Two Nutritional Strategies of Marine Labyrinthulomycetes Protists

Labyrinthulomycetes are a group of ubiquitous and diverse unicellular Stramenopiles and have long been known for their vital role in ocean carbon cycling. However, their ecological function from the perspective of organic matter degradation remains poorly understood. This study reports high-quality genomes of two newly isolated Labyrinthulomycetes strains, namely, Botryochytrium sp. strain S-28 and Oblongichytrium sp. strain S-429, and provides molecular analysis of their ecological functions using comparative genomics and a biochemical assay. Our results suggest that Labyrinthulomycetes may occupy multiple ecological niches in marine ecosystems because of the significant differences in gene function among different genera. Certain strains could degrade wheat bran independently by secreting cellulase. The key glycoside hydrolase families (GH1, GH5, and GH9) related to cellulase and the functional domains of carbohydrate-active enzymes (CAZymes) were more enriched in their genomes. This group can actively participate in marine biochemical cycles as decomposers. In contrast, other strains that could not produce cellulase may thrive as "leftover scavengers" and act as a source of nutrients to the higher-trophic-level plankton. In addition, our findings emphasize the dual roles of endoglucanase, acting as both exo- and endoglucanases, in the process of cellulose degradation. Using genomic, biochemical, and phylogenetic analyses, our study provides a broader insight into the nutritional patterns and ecological functions of Labyrinthulomycetes. IMPORTANCE Unicellular heterotrophic eukaryotes are an important component of marine ecosystems. However, their ecological functions and modes of nutrition remain largely unknown. Our current understanding of marine microbial ecology is incomplete without integrating these heterotrophic microeukaryotes into the food web models. This study focuses on the unicellular fungus-like protists Labyrinthulomycetes and provides two high-quality genomes of cellulase-producing Labyrinthulomycetes. Our study uncovers the basis of their cellulase production by deciphering the results of genomic, biochemical, and phylogenetic analyses. This study instigates a further investigation of the molecular mechanism of organic matter utilization by Labyrinthulomycetes in the world's oceans.

Combining multi-marker metabarcoding and digital holography to describe eukaryotic plankton across the Newfoundland Shelf

The planktonic diversity throughout the oceans is vital to ecosystem functioning and linked to environmental change. Plankton monitoring tools have advanced considerably with high-throughput in-situ digital cameras and genomic sequencing, opening new challenges for high-frequency observations of community composition, structure, and species discovery. Here, we combine multi-marker metabarcoding based on nuclear 18S (V4) and plastidial 16S (V4–V5) rRNA gene amplicons with a digital in-line holographic microscope to provide a synoptic diversity survey of eukaryotic plankton along the Newfoundland Shelf (Canada) during the winter transition phase of the North Atlantic bloom phenomenon. Metabarcoding revealed a rich eukaryotic diversity unidentifiable in the imaging samples, confirming the presence of ecologically important saprophytic protists which were unclassifiable in matching images, and detecting important groups unobserved or taxonomically unresolved during similar sequencing campaigns in the Northwest Atlantic Ocean. In turn, imaging analysis provided quantitative observations of widely prevalent plankton from every trophic level. Despite contrasting plankton compositions portrayed by each sampling method, both capture broad spatial differences between the northern and southern sectors of the Newfoundland Shelf and suggest complementary estimations of important features in eukaryotic assemblages. Future tasks will involve standardizing digital imaging and metabarcoding for wider use and consistent, comparable ocean observations.

Niche Partitioning of Labyrinthulomycete Protists Across Sharp Coastal Gradients and Their Putative Relationships With Bacteria and Fungi

While planktonic microbes play key roles in the coastal oceans, our understanding of heterotrophic microeukaryotes’ ecology, particularly their spatiotemporal patterns, drivers, and functions, remains incomplete. In this study, we focus on a ubiquitous marine fungus-like protistan group, the Labyrinthulomycetes, whose biomass can exceed that of bacterioplankton in coastal oceans but whose ecology is largely unknown. Using quantitative PCR and amplicon sequencing of their 18S rRNA genes, we examine their community variation in repeated five-station transects across the nearshore-to-offshore surface waters of North Carolina, United States. Their total 18S rRNA gene abundance and phylotype richness decrease significantly from the resource-rich nearshore to the oligotrophic offshore waters, but their Pielou’s community evenness appears to increase offshore. Similar to the bacteria and fungi, the Labyrinthulomycete communities are significantly structured by distance from shore, water temperature, and other environmental factors, suggesting potential niche partitioning. Nevertheless, only several Labyrinthulomycete phylotypes, which belong to aplanochytrids, thraustochytrids, or unclassified Labyrinthulomycetes, are prevalent and correlated with cohesive bacterial communities, while more phylotypes are patchy and often co-occur with fungi. Overall, these results complement previous time-series observations that resolve the Labyrinthulomycetes as persistent and short-blooming ecotypes with distinct seasonal preferences, further revealing their partitioning spatial patterns and multifaceted roles in coastal marine microbial food webs.

Riverine Inputs Impact the Diversity and Population Structure of Heterotrophic Fungus-like Protists and Bacterioplankton in the Coastal Waters of the South China Sea

Labyrinthulomycetes protists (LP) play an important role in ocean carbon cycling with an ubiquitous presence in marine ecosystems. As one of the most important environmental factors, salinity is known to regulate their diverse metabolic activities. However, impacts of salinity gradient on their distribution and ecological functions in natural habitats remain largely unknown. In this study, the dynamics of LP abundance and community structure were examined in the surface water of plume, offshore, and pelagic habitats in the South China Sea (SCS). The highest (5.59 × 105 copies L−1) and lowest (5.28 × 104 copies L−1) abundance of LP were found to occur in the waters of plume and pelagic habitats, respectively. Multiple dimensional scaling (MDS) analysis revealed a strong relationship between salinity and LP community variation (p < 0.05, rho = 0.67). Unexpectedly, relative low LP diversity was detected in the brackish water samples of the plume. Moreover, our results indicated the genus Aplanochytrium dominated LP communities in offshore and pelagic, while Aurantiochytrium and Ulkenia were common in the plume. Physiological and metabolic features of these genera suggested that LP ecological functions were also largely varied along this salinity gradient. Clearly, the salinity gradient likely regulates the diversity and functional partitioning of marine protistan micro-eukaryotes in the world’s oceans.

Patchy Blooms and Multifarious Ecotypes of Labyrinthulomycetes Protists and Their Implication in Vertical Carbon Export in the Pelagic Eastern Indian Ocean

Labyrinthulomycetes protists are an important heterotrophic component of microeukaryotes in the world’s oceans, but their distribution patterns and ecological roles are poorly understood in pelagic waters. This study employed flow cytometry and high-throughput sequencing to characterize the abundance, diversity, and community structure of Labyrinthulomycetes in the pelagic Eastern Indian Ocean. The total Labyrinthulomycetes abundance varied much more among stations than did the abundance of prokaryotic plankton, reaching over 1,000 cells mL⁻¹ at a few “bloom” stations. The total Labyrinthulomycetes abundance did not decline with depth throughout the whole water column (5 to 2,000 m) like the abundance of prokaryotic plankton did, and the Labyrinthulomycetes average projected biomass over all samples was higher than that of the prokaryotic plankton. However, Labyrinthulomycetes diversity showed obvious vertical variations, with richness, Shannon diversity, and evenness greatest in the upper epipelagic, lower epipelagic, and deep waters, respectively. Many abundant phylotypes were detected across multiple water layers, which aligned with the constant vertical Labyrinthulomycetes biomass, suggesting potential sinking and contribution to the biological pump. Hierarchical clustering revealed distinct ecotypes partitioning by vertical distribution patterns, suggesting their differential roles in the carbon cycle and storage processes. Particularly, most phylotypes showed patchy distributions (occurring in only few samples) as previously found in the coastal waters, but they were less associated with the Labyrinthulomycetes blooms than the prevalent phylotypes. Overall, this study revealed distinct patterns of Labyrinthulomycetes ecotypes and shed light on their importance in the pelagic ocean carbon cycling and sequestration relative to that of the prokaryotic plankton.

IMPORTANCE While prokaryotic heterotrophic plankton are well accepted as major players in oceanic carbon cycling, the ecological distributions and functions of their microeukaryotic counterparts in the pelagic ocean remain largely unknown. This study focused on an important group of heterotrophic (mainly osmotrophic) protistan microbes, the Labyrinthulomycetes, whose biomass can surpass that of the prokaryotic plankton in many marine ecosystems, including the bathypelagic ocean. We found patchy horizontal but persistent vertical abundance profiles of the Labyrinthulomycetes protists in the pelagic waters of the Eastern Indian Ocean, which were distinct from the spatial patterns of the prokaryotic plankton. Moreover, multiple Labyrinthulomycetes ecotypes with distinct vertical patterns were detected and, based on the physiologic, metabolic, and genomic understanding of their cultivated relatives, were inferred to play multifaceted key roles in the carbon cycle and sequestration, particularly as contributors to the vertical carbon export from the surface to the dark ocean, i.e., the biological pump.

Culturable Diversity of Thraustochytrids from Coastal Waters of Qingdao and Their Fatty Acids

Thraustochytrids have gained significant attention in recent years because of their considerable ecological and biotechnological importance. Yet, the influence of seasons and habitats on their culturable diversity and lipid profile remains poorly described. In this study, a total of 58 thraustochytrid strains were isolated from the coastal waters of Qingdao, China. These strains were phylogenetically close to five thraustochytrid genera, namely Botryochytrium, Oblongichytrium, Schizochytrium, Thraustochytrium, and Sicyoidochytrium. Most of the isolated strains were classified into the genera Thraustochytrium and Oblongichytrium. Further diversity analysis revealed that samples collected from nutrient-rich habitats and during summer/fall yielded significantly higher culturable diversity of thraustochytrids than those from low-nutrient habitats and winter/spring. Moreover, sampling habitats and seasons significantly impacted the fatty acid profiles of the strains. Particularly, the Oblongichytrium sp. OC931 strain produced a significant amount (153.99 mg/L) of eicosapentaenoic acid (EPA), accounting for 9.12% of the total fatty acids, which was significantly higher than that of the previously reported Aurantiochytrium strains. Overall, the results of this study fill the gap in our current understanding of the culturable diversity of thraustochytrids in the coastal waters and the impact of the sampling habitats and seasons on their capacity for lipid accumulation.

Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.

Patchy Distributions and Distinct Niche Partitioning of Mycoplankton Populations across a Nearshore to Open Ocean Gradient

Evidence increasingly suggests planktonic fungi (or mycoplankton) play an important role in marine food webs and biogeochemical cycles. In order to better understand their ecological role and how oceanographic gradients from the coastal to open ocean shape the mycoplankton community, molecular approaches were used to study fungal dynamics along a repeatedly sampled, five-station transect beginning at the mouth of an estuary and continuing 87 km across the continental shelf to the oligotrophic waters at the boundary of the Sargasso Sea. Similar to patterns in chlorophyll a, fungal 18S rRNA gene abundance showed a sharp decrease from nearshore to offshore stations. While Shannon's diversity was not statistically different across the transect, nonmetric multidimensional scaling (NMDS) ordination revealed that fungal communities at the nearshore station were significantly different from those at other stations. Even though spatial gradients were consistently strong, the shelf mycoplankton were more similar to those of the offshore communities when temperature was high (>20°C) and while they shifted toward the nearshore communities when temperature was low (<19°C), suggesting a role for additional seasonal factors (such as temperature) in shaping mycoplankton distributions. However, overall phylotype distributions were patchy with few taxa observed at all stations and the majority observed at a single station with the nearshore station exhibiting the largest number of exclusive phylotypes. Overall, our findings revealed the patchy spatial distributions and distinct niche partitioning of mycoplankton populations across a nearshore to open ocean gradient, which improved our understanding of fungal ecology in coastal waters. IMPORTANCE Fungi are an important, but understudied, group of heterotrophic microbes in marine environments. Traditionally, fungi in the coastal ocean were largely assumed to be derived from terrestrial inputs. Yet here we find many fungal taxa are endemic to the open ocean environment but are rare or absent in nearshore waters, suggesting they are not washed into the ocean from the land. As observed for the bacterioplankton, coastal oceanographic gradients can function as habitat barriers to partition fungal communities. Compared to the bacterioplankton, however, the mycoplankton exhibit a much patchier distribution pattern, suggesting differential drivers and the potential for spatially/temporally limited habitats or strong density-dependent selection. Therefore, our results show that mycoplankton in the coastal ocean may play a significant but complementary role to that of the bacterioplankton.

Composition change and decreased diversity of microbial eukaryotes in the coastal upwelling waters of South China Sea

Upwelling plays an important role in marine ecosystems and potentially reshapes microbial communities by enhanced dispersal and distinct environmental drivers. Relative to that of bacterioplankton, however, the response of eukaryotic microbes to upwelling is largely unknown. Here, we investigated the influence of coastal upwelling in South China Sea on the microbial eukaryotic communities. Unlike several folds of increase in the cell abundance of bacterioplankton in upwelling than non-upwelling stations at corresponding water layers, no significant difference was detected for the total microbial eukaryotic 18S rRNA gene abundance. Moreover, the microbial eukaryotes in the upwelling stations exhibited increasing 18S rRNA gene abundance from the surface to the deep, contrasting the vertical cell abundance pattern of the bacterioplankton; but their vertical abundance patterns were similar in non-upwelling stations. Importantly, the coastal upwelling significantly reduced the community evenness of the microbial eukaryotes and slightly reduced their Shannon diversity. Their community composition also varied obviously especially between the surface waters of upwelling and non-upwelling stations. Among the dominant supergroups, Alveolata was found to be less abundant while Stramenopiles, particularly thraustochytrids and diatoms, to be more abundant in the surface water of upwelling than non-upwelling stations. Temperature was identified as the most important factor of the microbial eukaryotic community composition, suggesting potential effects of the cold upwelling water masses on specific taxa. Overall, our results reveal significant and distinct impacts of coastal upwelling on the abundance, diversity, and community structure of microbial eukaryotes, filling the knowledge gap about the microbial responses to this important marine phenomenon.

Vertical community patterns of Labyrinthulomycetes protists reveal their potential importance in the oceanic biological pump

The biological pump plays a vital role in exporting organic particles into the deep ocean for long-term carbon sequestration. However, much remains unknown about some of its key microbial players. In this study, Labyrinthulomycetes protists (LP) were used to understand the significance of heterotrophic microeukaryotes in the transport of particulate organic matter from the surface to the dark ocean. Unlike the sharp vertical decrease of prokaryotic biomass, the LP biomass only slightly decreased with depth and eventually exceeded prokaryotic biomass in the bathypelagic layer. Sequencing identified high diversity of the LP communities with a dominance of Aplanochytrium at all depths. Notably, ASVs that were observed in the surface layer comprised ~20% of ASVs and ~60% of sequences in each of the deeper (including bathypelagic) layers, suggesting potential vertical export of the LP populations to the deep ocean. Further analyses of the vertical patterns of the 50 most abundant ASVs revealed niche partitioning of LP phylotypes in the pelagic ocean, including those that could decompose organic detritus and/or facilitate the formation of fast-sinking particles. Overall, this study presents several lines of evidence that the LP can be an important component of the biological pump through their multiple ecotypes in the pelagic ocean.