Protistan grazing impacts microbial communities and carbon cycling at deep-sea hydrothermal vents

Insights into a novel exopolysaccharide from Mariana Trench-derived Aspergillus versicolor SCAU214: Structure and immune activity

A novel exopolysaccharide AVP-214-1was isolated and purified from the metabolites of a Mariana Trench-derived fungus Aspergillus versicolor SCAU214. AVP-214-1 exhibited a heteropolysaccharide architecture composed of mannose, galactose, and glucose residues. The linear backbone adopted α-(1 → 4)-linked d-galactopyranose and d-glucopyranose units with the following sequence: →[4,6)-α-D-Glcp-(1 → 4)-α-D-Glcp-(1]4 → [4)-α-D-Glcp-(1 → 6)-α-D-Glcp-(1 → 3)-α-D-Glcp-(1]3 → [4,6)-α-D-Glcp-(1 → 4)-α-D-Glcp-(1]2 → [4)-α-D-Glcp-(1]19 → [4)-α-D-Glcp-(1 → 4)-α-D-Galp-(1]2→. Structural complexity arose from two distinct branching motifs: single α-d-glucopyranosyl and an α-D-mannopyranosyl, both attached via C-6 positions of the backbone residues 1,4,6-α-D-Glcp. The molecular weight of AVP-214-1 was determined to be 8277 Da. In functional assays, AVP-214-1 was found to significantly enhance the proliferation of RAW 264.7 macrophage cells and promote the secretion of cytokines, such as IL-6, TNF-α and IL-1β. Metabolomic analysis revealed that AVP-214-1 primarily influences pyrimidine metabolism and amino acid-related metabolic pathways, these metabolic pathways were likely related to immune regulation. These results suggest that AVP-214-1 from a Mariana Trench-derived fungus was a novel immune-stimulating polysaccharide, opening up new avenues for the development of bioactive polysaccharides from deep-sea organisms for potential biotechnological applications.

Nanopore Sequencing of Amoebophrya Species Reveals Novel Collection of Bacteria Putatively Associated With Karlodinium veneficum

The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate K. veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole-genome sequencing of an Amoebophrya sp. ex K. veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, 13 were identifiable at the generic level by BLAST (8 of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for <2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of metagenome-assembled genomes are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.

Shallow Hydrothermal Fluids Shape Microbial Dynamics at the Tagoro Submarine Volcano (Canary Islands, Spain)

Shallow underwater hydrothermal systems are often overlooked despite their potential contribution to marine diversity and biogeochemistry. Over a decade after its eruption, the Tagoro submarine volcano continues to emit heat, reduced compounds, and nutrients into shallow waters, serving as a model system for studying the effects of diffuse hydrothermal fluids on surface microbial communities. The impact on both phytoplankton and bacterial communities was examined through experimental manipulations mimicking dilution levels up to ~100 m from the primary crater of Tagoro. Chlorophyll a concentration doubled in the presence of hydrothermal products, with peak levels detected about a day earlier than in controls. Picoeukaryotes and Synechococcus cell abundances moderately increased, yet small eukaryotic phytoplankton (≤ 5 μm) predominated in the hydrothermally enriched bottles. Dinoflagellates, diatoms, small green algae and radiolarians particularly benefited from the hydrothermal inputs, along with phototrophic and chemoautotrophic bacteria. Our results indicate that hydrothermal products in shallow waters enhance primary production driven by phototrophic microbes, potentially triggering a secondary response associated with increased organic matter availability. Additionally, protistan grazing and parasitism emerged as key factors modulating local planktonic communities. Our findings highlight the role of shallow submarine hydrothermal systems in enhancing local primary production and element cycling.

The protist community of the oligotrophic waters of the Gulf of Mexico is distinctly shaped by depth-specific physicochemical conditions during the warm season

Marine protists are key components of biogeochemical cycles and microbial food webs, which respond quickly to environmental factors. In the Gulf of Mexico (GoM), the Loop Current intensifies in summer and supplies the gulf with warm and oligotrophic waters. However, the cyclonic eddies within the GoM create favorable conditions for biological productivity by bringing nutrient-rich water to the subsurface layer. In this study, we investigated the response of the protist community to the regional physicochemical conditions, its spatial and temporal variability, the influence of mesoscale structures, and its ecological roles in the mixed layer (ML) and deep chlorophyll maximum (DCM). This is the first study to conduct a V9-18S rRNA gene survey for this community in the Mexican Exclusive Economic Zone of the GoM. The regional distribution, temporal changes, and mesoscale structures significantly affected the structure of the protist community in the ML. In contrast, only mesoscale structures significantly affected the protist community in the DCM. Different protist assemblages were also present between the ML and DCM, with the Alveolata representing ∼60% of the community in both layers, followed by haptophytes and MAST (Marine Stramenopiles) in the ML; pelagophytes and radiolarians were the more prevalent taxa in the DCM. Finally, co-occurrence analyses revealed that competition, parasitism, and predation were the potential interactions shaping these communities at both depths.

Novel oil-associated bacteria in Arctic seawater exposed to different nutrient biostimulation regimes

The Arctic Ocean is an oligotrophic ecosystem facing escalating threats of oil spills as ship traffic increases owing to climate change-induced sea ice retreat. Biostimulation is an oil spill mitigation strategy that involves introducing bioavailable nutrients to enhance crude oil biodegradation by endemic oil-degrading microbes. For bioremediation to offer a viable response for future oil spill mitigation in extreme Arctic conditions, a better understanding of the effects of nutrient addition on Arctic marine microorganisms is needed. Controlled experiments tracking microbial populations revealed a significant decline in community diversity along with changes in microbial community composition. Notably, differential abundance analysis highlighted the significant enrichment of the unexpected genera Lacinutrix, Halarcobacter and Candidatus Pseudothioglobus. These groups are not normally associated with hydrocarbon biodegradation, despite closer inspection of genomes from closely related isolates confirming the potential for hydrocarbon metabolism. Co-occurrence analysis further revealed significant associations between these genera and well-known hydrocarbon-degrading bacteria, suggesting potential synergistic interactions during oil biodegradation. While these findings broaden our understanding of how biostimulation promotes enrichment of endemic hydrocarbon-degrading genera, further research is needed to fully assess the suitability of nutrient addition as a stand-alone oil spill mitigation strategy in this sensitive and remote polar marine ecosystem.

Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage 'omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.

Protists play important roles in the assembly and stability of denitrifying bacterial communities in copper-tailings drainage

Unraveling the drivers controlling the assembly and stability of functional communities is a central issue in ecology. Despite extensive research and data, relatively little attention has been paid on the importance of biotic factors and, in particular, on the trophic interaction for explaining the assembly of microbial community. Here, we examined the diversity, assembly, and stability of nirS-, nirK-, and nosZ-type denitrifying bacterial communities in copper-tailings drainages of the Shibahe tailings reservoir in Zhongtiao Mountain, China's. We found that components of nirS-, nirK-, and nosZ-type denitrifying bacterial community diversity, such as taxon relative abundance, richness, and copy number, were strongly correlated with protist community composition and diversity. Assembly of the nirK-type denitrifying bacterial community was governed by dispersal limitation, whereas those of nirS- and nosZ-type communities were controlled by homogeneous selection. The relative importance of protist diversity in the assembly of nirK- and nosZ-type denitrifying bacterial communities was greater than that in nirS-type assembly. In addition, protists reduced the stability of the co-occurrence network of the nosZ-type denitrifying bacterial community. Compared with eukaryotic algae, protozoa had a greater impact on the stability of denitrifying bacterial community co-occurrence networks. Generally, protists affected the assembly and community stability of denitrifying bacteria in copper-tailings drainages. Our findings thus emphasize the importance of protists on affecting the assembly and community stability of denitrifying bacteria in copper-tailings drainages and may be useful for predicting changes in the ecological functions of microorganisms.

Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity

Active hydrothermal vents are oases for productivity in the deep ocean, but the flow of dissolved substrates that fuel such abundant life ultimately ceases, leaving behind inactive mineral deposits. The rates of microbial activity on these deposits are largely unconstrained. Here we show primary production occurs on inactive hydrothermal deposits and quantify its contribution to new organic carbon production in the deep ocean. Measured incorporation of 14C-bicarbonate shows that microbial communities on inactive deposits fix inorganic carbon at rates comparable to those on actively venting deposits. Single-cell uptake experiments and nanoscale secondary ion mass spectrometry showed chemoautotrophs comprise a large fraction (>30%) of the active microbial cells. Metagenomic and lipidomic surveys of inactive deposits further revealed that the microbial communities are dominated by Alphaproteobacteria and Gammaproteobacteria using the Calvin-Benson-Bassham pathway for carbon fixation. These findings establish inactive vent deposits as important sites for microbial activity and organic carbon production on the seafloor.

Microbial eukaryotic predation pressure and biomass at deep-sea hydrothermal vents

Deep-sea hydrothermal vent geochemistry shapes the foundation of the microbial food web by fueling chemolithoautotrophic microbial activity. Microbial eukaryotes (or protists) play a critical role in hydrothermal vent food webs as consumers and hosts of symbiotic bacteria, and as a nutritional source to higher trophic levels. We measured microbial eukaryotic cell abundance and predation pressure in low-temperature diffuse hydrothermal fluids at the Von Damm and Piccard vent fields along the Mid-Cayman Rise in the Western Caribbean Sea. We present findings from experiments performed under in situ pressure that show cell abundances and grazing rates higher than those done at 1 atmosphere (shipboard ambient pressure); this trend was attributed to the impact of depressurization on cell integrity. A relationship between the protistan grazing rate, prey cell abundance, and temperature of end-member hydrothermal vent fluid was observed at both vent fields, regardless of experimental approach. Our results show substantial protistan biomass at hydrothermally fueled microbial food webs, and when coupled with improved grazing estimates, suggest an important contribution of grazers to the local carbon export and supply of nutrient resources to the deep ocean.

Role of Syndiniales parasites in depth-specific networks and carbon flux in the oligotrophic ocean

Microbial associations that result in phytoplankton mortality are important for carbon transport in the ocean. This includes parasitism, which in microbial food webs is dominated by the marine alveolate group, Syndiniales. Parasites are expected to contribute to carbon recycling via host lysis; however, knowledge on host dynamics and correlation to carbon export remain unclear and limit the inclusion of parasitism in biogeochemical models. We analyzed a 4-year 18S rRNA gene metabarcoding dataset (2016-19), performing network analysis for 12 discrete depths (1-1000 m) to determine Syndiniales-host associations in the seasonally oligotrophic Sargasso Sea. Analogous water column and sediment trap data were included to define environmental drivers of Syndiniales and their correlation with particulate carbon flux (150 m). Syndiniales accounted for 48-74% of network edges, most often associated with Dinophyceae and Arthropoda (mainly copepods) at the surface and Rhizaria (Polycystinea, Acantharea, and RAD-B) in the aphotic zone. Syndiniales were the only eukaryote group to be significantly (and negatively) correlated with particulate carbon flux, indicating their contribution to flux attenuation via remineralization. Examination of Syndiniales amplicons revealed a range of depth patterns, including specific ecological niches and vertical connection among a subset (19%) of the community, the latter implying sinking of parasites (infected hosts or spores) on particles. Our findings elevate the critical role of Syndiniales in marine microbial systems and reveal their potential use as biomarkers for carbon export.

Globally-distributed microbial eukaryotes exhibit endemism at deep-sea hydrothermal vents

Single-celled microbial eukaryotes inhabit deep-sea hydrothermal vent environments and play critical ecological roles in the vent-associated microbial food web. 18S rRNA amplicon sequencing of diffuse venting fluids from four geographically- and geochemically-distinct hydrothermal vent fields was applied to investigate community diversity patterns among protistan assemblages. The four vent fields include Axial Seamount at the Juan de Fuca Ridge, Sea Cliff and Apollo at the Gorda Ridge, all in the NE Pacific Ocean, and Piccard and Von Damm at the Mid-Cayman Rise in the Caribbean Sea. We describe species diversity patterns with respect to hydrothermal vent field and sample type, identify putative vent endemic microbial eukaryotes, and test how vent fluid geochemistry may influence microbial community diversity. At a semi-global scale, microbial eukaryotic communities at deep-sea vents were composed of similar proportions of dinoflagellates, ciliates, Rhizaria, and stramenopiles. Individual vent fields supported distinct and highly diverse assemblages of protists that included potentially endemic or novel vent-associated strains. These findings represent a census of deep-sea hydrothermal vent protistan communities. Protistan diversity, which is shaped by the hydrothermal vent environment at a local scale, ultimately influences the vent-associated microbial food web and the broader deep-sea carbon cycle.

Viral lysing can alleviate microbial nutrient limitations and accumulate recalcitrant dissolved organic matter components in soil

Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.

Effects of livestock grazing on the relationships between soil microbial community and soil carbon in grassland ecosystems

Livestock grazing of grassland ecosystems may induce shifts in microbe community traits and soil carbon (C) cycling; however, impacts of grassland management (grazing) on soil C- microbe community trait (microbial biomass, diversity, community structure, and enzyme activity) relationships are unclear. To address this, we conducted a global meta-analysis of 95 articles of livestock grazing studies that vary in grazing intensities (light, moderate, and high) and durations (<5 years, 5-10 years, and > 10 years). We found that gazing decreased soil organic carbon content (SOC; 10.1 %), and activities of the enzymes of saccharase (SA; 31.1 %), urease (UA; 7.0 %), and acid phosphatase (11.9 %) in topsoil. Meanwhile, the SOC, soil microbial biomass and enzyme activities consistently decreased as grazing intensity and duration prolonged. Furthermore, we observed strong linear relationships of microbe community traits with SOC (p < 0.05), but weak relationships with soil N or P (p > 0.05) in grasslands, which also depends on the grazing intensity and duration. In conclusion, our results indicate that traits of soil carbon content, soil microbe community, and in particular their relationships in global grasslands are overall significantly affected by livestock grazing, but the effects strongly depend on the grazing intensity and duration.

Protist Predation Influences the Temperature Response of Bacterial Communities

Temperature strongly influences microbial community structure and function, in turn contributing to global carbon cycling that can fuel further warming. Recent studies suggest that biotic interactions among microbes may play an important role in determining the temperature responses of these communities. However, how predation regulates these microbiomes under future climates is still poorly understood. Here, we assess whether predation by a key global bacterial consumer-protists-influences the temperature response of the community structure and function of a freshwater microbiome. To do so, we exposed microbial communities to two cosmopolitan protist species-Tetrahymena thermophila and Colpidium sp.-at two different temperatures, in a month-long microcosm experiment. While microbial biomass and respiration increased with temperature due to community shifts, these responses changed over time and in the presence of protists. Protists influenced microbial biomass and respiration rate through direct and indirect effects on bacterial community structure, and predator presence actually reduced microbial respiration at elevated temperature. Indicator species analyses showed that these predator effects were mostly determined by phylum-specific bacterial responses to protist density and cell size. Our study supports previous findings that temperature is an important driver of microbial communities but also demonstrates that the presence of a large predator can mediate these responses to warming.

Heterogeneous viral contribution to dissolved organic matter processing in a long-term macrocosm experiment

Viruses saturate environments throughout the world and play key roles in microbial food webs, yet how viral activities affect dissolved organic matter (DOM) processing in natural environments remains elusive. We established a large-scale long-term macrocosm experiment to explore viral dynamics and their potential impacts on microbial mortality and DOM quantity and quality in starved and stratified ecosystems. High viral infection dynamics and the virus-induced cell lysis (6.23-64.68% d^-1) was found in the starved seawater macrocosm, which contributed to a significant transformation of microbial biomass into DOM (0.72-5.32 μg L^-1 d^-1). In the stratified macrocosm, a substantial amount of viral lysate DOM (2.43-17.87 μg L^-1 d^-1) was released into the upper riverine water, and viral lysis and DOM release (0.35-5.75 μg L^-1 d^-1) were reduced in the mixed water layer between riverine water and seawater. Viral lysis was stimulated at the bottom of stratified macrocosm, potentially fueled by the sinking of particulate organic carbon. Significant positive and negative associations between lytic viral production and different fluorescent DOM components were found in the starved and stratified macrocosm, indicating the potentially complex viral impacts on the production and utilization of DOM. Results also revealed the significant viral contribution to pools of both relatively higher molecular weight labile DOM and lower molecular weight recalcitrant DOM. Our study suggests that viruses have heterogeneous impact on the cycling and fate of DOM in aquatic environments.