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The increasing frequency and intensity of heatwaves driven by climate change significantly impact microbial communities in freshwater habitats, particularly eukaryotic microorganisms. Heterotrophic nanoflagellates are important bacterivorous grazers and play a crucial role in aquatic food webs, influencing the morphological and taxonomic structure of bacterial communities. This study investigates the responses of three flagellate taxa to heatwave conditions through single-strain and mixed culture experiments, highlighting the impact of both biotic and abiotic factors on functional redundancy between morphologically similar protist species under thermal stress. Our results indicate that temperature can significantly impact growth and community composition. However, density-dependent factors also had a significant impact. In sum, stabilizing effects due to functional redundancy may be pronounced as long as density-dependent factors play a minor role and can be overshadowed when flagellate abundances increase. [ABSTRACT FROM AUTHOR]

The soil microbial food web plays a vital role in soil health, nutrient cycling and agricultural productivity. Notably, there is a distinct paucity of information regarding the effects of heavy metal contamination on trophic-level interactions within the microbial food web of agricultural soils, which experience appreciably metal contamination worldwide. Herein, we investigated trophic interactions among predators (protists), their preys (bacteria and fungi) and competitors (nematodes) under four metal contamination levels using high-throughput sequencing and a laboratory verification experiment. Metal contamination decreased growth of protist-preferential prey (e.g., small-sized and gram-negative bacteria), increased the growth of protist-nonpreferential prey (e.g., pathogenic fungi and Actinobacteria), and had a limited effect on the soil protist-competitor (i.e., nematodes). This resulted in a considerable decrease in the diversity and abundance of protistan consumers and a re-arrangement of their interactions with other organisms. From a systemic view, the direct link was weaker between heavy metal contamination and the protist community than the indirect linkage, i.e., metal-induced changes in the prey community. We further validated these results with laboratory incubation trials that documented growth inhibition of protist (Colpoda) and protist-preferential prey (Spingomonas) versus growth stimulation of protist-nonpreferential prey (Arthrobacter) under metal contamination. These findings indicate that metal contamination collapses trophic-level interactions within the soil microbial food web via bottom-up regulation, providing important implications for managing trophic interactions to maintain agricultural ecosystem services under the challenge of worldwide metal contamination.

The increasing frequency and intensity of heatwaves driven by climate change significantly impact microbial communities in freshwater habitats, particularly eukaryotic microorganisms. Heterotrophic nanoflagellates are important bacterivorous grazers and play a crucial role in aquatic food webs, influencing the morphological and taxonomic structure of bacterial communities. This study investigates the responses of three flagellate taxa to heatwave conditions through single-strain and mixed culture experiments, highlighting the impact of both biotic and abiotic factors on functional redundancy between morphologically similar protist species under thermal stress. Our results indicate that temperature can significantly impact growth and community composition. However, density-dependent factors also had a significant impact. In sum, stabilizing effects due to functional redundancy may be pronounced as long as density-dependent factors play a minor role and can be overshadowed when flagellate abundances increase.

BackgroundCold environments dominate the Earth's biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000-7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles.ResultsThe lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts.ConclusionOver-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract.

Context: We studied the virus component in the microbial food-web in the tropical coastal Sunda Shelf waters. Aims: We investigated viral processes, including the lysogenic to lytic shift dynamics with seawater warming and nutrient enrichment. Methods: We sampled nearshore and offshore waters of Peninsular Malaysia to provide a natural trophic gradient for correlational analyses. We also conducted laboratory experiments to investigate the changes in virus production rates and lysogeny, when temperature (range: 25–37°C) and nutrient concentrations (range: 0.1–1.0× marine-broth concentration) were manipulated. Key results: Observations showed site-dependent differences in dissolved inorganic nutrient concentration, Chl- a (0.21–3.54 μg L−1) and bacterial abundance (4.09 × 105−9.41 × 105 cells mL−1), but not in viral abundance (measured as virus-like particles or VLP) (1.04 × 106−2.39 × 106 VLP mL−1) and virus production rates (0.59 × 105−4.55 × 105 VLP mL−1 h−1). From laboratory experiments, both warming and nutrient enrichment increased virus production (R 2 > 0.651), decreased lysogeny (R 2 > 0.743), and resulted in an increase of the viral lysis:bacterial production ratio, and a stronger viral control on bacterial production. Conclusions: Although both seawater warming and nutrient enrichment increased virus production and reduced lysogeny, nutrient enrichment was a more important factor. Implications: The increasing nutrient concentrations in these waters will increase virus production and virus top-down control of bacteria, and drive the ecosystem towards heterotrophy. Tropical coastal waters are experiencing warming and nutrient enrichment, and these environmental changes increased both bacterial and virus production. Nutrient enrichment increased virus production and resulted in a stronger virus top-down control on bacterial production. Therefore, eutrophication will drive the ecosystem towards heterotrophy. [ABSTRACT FROM AUTHOR]

To quantitatively evaluate the role of copepod nauplii as predators in the microbial food web, the ingestion rate (IR) of copepod nauplii and the food requirement (FR) of microzooplankton were estimated monthly for 3 consecutive years in temperate embayment waters. The IR of dominant copepod nauplii (Acartia spp. nauplii) was estimated from water temperature, individual carbon weight and food concentration and peaked (>0.50 μgC ind−1 d−1) with relatively high food concentration (>57.5 μgC L−1). This result suggests that food concentration should be considered to estimate copepod naupliar IR in marine environments, especially where biological conditions fluctuate largely. The comparison of copepod naupliar and microprotozoan FR showed the dominance of naked ciliate FR (77.0–90.2%) during the study period except in spring when comparable values were observed between the FR of naked ciliates (41.6%) and copepod nauplii (33.6%). During spring, transfer efficiency (10.5%) from primary production (PP) to microzooplankton production was lower than in other seasons (16.2–17.1%). This study indicates that copepod nauplii are seasonally important micro-sized predators in the microbial food web of temperate embayment waters and that carbon flow through copepod nauplii is a pathway which inefficiently transfers PP to higher trophic levels. [ABSTRACT FROM AUTHOR]

Climate change has been projected to cause increased temperature and amplified inflows of terrestrial organic matter to coastal areas in northern Europe. Consequently, changes at the base of the food web favoring heterotrophic bacteria over phytoplankton are expected, affecting the food web structure. We tested this hypothesis using an outdoor shallow mesocosm system in the northern Baltic Sea in early summer, where the effects of increased temperature (+ 3°C) and terrestrial matter inputs were studied following the system dynamics and conducting grazing experiments. Juvenile perch constituted the highest trophic level in the system, which exerted strong predation on the zooplankton community. Perch subsequently released the microbial food web from heavy grazing by mesozooplankton. Addition of terrestrial matter had a stronger effect on the microbial food web than the temperature increase, because terrestrial organic matter and accompanying nutrients promoted both heterotrophic bacterial production and phytoplankton primary production. Moreover, due to the shallow water column in the experiment, terrestrial matter addition did not reduce the light below the photosynthesis saturation level, and in these conditions, the net-autotrophy was strengthened by terrestrial matter enrichment. In combination with elevated temperature, the terrestrial matter addition effects were intensified, further shifting the size distribution of the microbial food web base from picoplankton to microphytoplankton. These changes up the food web led to increase in the biomass and proportion of large-sized ciliates (>60 µm) and rotifers. Despite the shifts in the microbial food web size structure, grazing experiments suggested that the pathway from picoplankton to nano- and microzooplankton constituted the major energy flow in all treatments. The study implies that the microbial food web compartments in shallow coastal waters will adjust to climate induced increased inputs of terrestrial matter and elevated temperature, and that the major energy path will flow from picoplankton to large-sized ciliates during the summer period.

Background: Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus-like species becomes the most abundant member in the upper sunlit waters during summer while persisting annually even in the absence of sunlight and at depth in the anoxic zone. Here, we analysed ~ 300 Gb of Ace Lake metagenome data including 59 Synechococcus-like metagenome-assembled genomes (MAGs) to determine depth-related variation in cyanobacterial population structure. Metagenome data were also analysed to investigate viruses associated with this cyanobacterium and the host's capacity to defend against or evade viruses. Results: A single Synechococcus-like species was found to exist in Ace Lake, Candidatus Regnicoccus frigidus sp. nov., consisting of one phylotype more abundant in the oxic zone and a second phylotype prevalent in the oxic-anoxic interface and surrounding depths. An important aspect of genomic variation pertained to nitrogen utilisation, with the capacity to perform cyanide assimilation and asparagine synthesis reflecting the depth distribution of available sources of nitrogen. Both specialist (host specific) and generalist (broad host range) viruses were identified with a predicted ability to infect Ca. Regnicoccus frigidus. Host-virus interactions were characterised by a depth-dependent distribution of virus type (e.g. highest abundance of specialist viruses in the oxic zone) and host phylotype capacity to defend against (e.g. restriction-modification, retron and BREX systems) and evade viruses (cell surface proteins and cell wall biosynthesis and modification enzymes). Conclusion: In Ace Lake, specific environmental factors such as the seasonal availability of sunlight affects microbial abundances and the associated processes that the microbial community performs. Here, we find that the population structure for Ca. Regnicoccus frigidus has evolved differently to the other dominant phototroph in the lake, Candidatus Chlorobium antarcticum. The geography (i.e. Antarctica), limnology (e.g. stratification) and abiotic (e.g. sunlight) and biotic (e.g. microbial interactions) factors determine the types of niches that develop in the lake. While the lake community has become increasingly well studied, metagenome-based studies are revealing that niche adaptation can take many paths; these paths need to be determined in order to make reasonable predictions about the consequences of future ecosystem perturbations. 2GZ5fuYNnhGp9HukxerBaX Video Abstract [ABSTRACT FROM AUTHOR]

[Display omitted] • Transport and transformation processes of detritus in rivers were decoupled. • The decreased velocity promoted detritus availability. • Detritus availability promoted the diversity of multi-trophic microbiota. • The increased detritus availability promoted the trophic transfer efficiency. Detritus is the vital support for the microbial food web, which would further affect river ecological conditions. Determining the effects of detritus availability on microbial food webs in rivers is critical for protecting river ecological functions. However, the detritus availability was difficult to estimate directly, since the detritus transformation processes (i.e. detritus availability) and flow-induced transport processes are interdependent in rivers. Therefore, this study quantified the detritus transformation processes in a natural river and further identified the impacts of detritus availability on microbial food web patterns. Results revealed that the flow velocity was the main physical driver determining the detritus availability. The decreased velocity would promote detritus availability. Moreover, the increased detritus availability significantly promoted the diversity of bacteria, protozoan and metazoan (p < 0.05). The responses of low trophic levels to detritus availability were significantly greater than those of higher trophic levels, emphasizing the bottom-up cascading effect of detritus availability on microbial food web composition (p < 0.05). From microbial food web perspectives, the detritus availability was amplified with flow velocity decreased, promoting trophic transfer efficiency between different trophic levels. Results and findings revealed the ecological effect of detritus transformation processes on multi-trophic levels in rivers and provided advantageous information for river management. [ABSTRACT FROM AUTHOR]

Microbial food web (MFW) dominates the energy flow in oligotrophic tropical open ocean pelagic ecosystems. Understanding biogeographic patterns and driving mechanisms of key components of the MFW is one of the central topics in current marine ecology. Investigations were conducted along an 1,100-km horizontal gradient and in the full-water column vertical gradient of the oligotrophic tropical western Pacific Ocean. High-throughput sequencing and association networking methods were used to analyze the community structure and interspecies interactions of MFW. The structure of MFW significantly differed with depths, but not across horizontal gradients. Bacteria and microeukaryotes were interconnected and had more predominantly positive and negative linkages in the aphotic layers. Key components of MFW exhibited similar biogeographic patterns and driving mechanisms. Geographic distance exerted minimal effects on the distribution patterns of the microbial food web, while environmental factors played more important roles, especially for temperature and inorganic nutrients. Stochastic processes were more important in the microbial food webs of the 5–200 m layer than the >500 m layer, and drift explained the majority of stochastic processes. Moreover, only a weak but not significant driving force for North Equatorial Current on the east–west connectivity of the microbial food web was found in the upper layers. This knowledge is a critical fundamental data for future planning of marine protected areas targeting the protection of tuna fishing in the western Pacific Ocean.

Background: Biological conversion of the surplus of renewable electricity and carbon dioxide (CO2) from biogas plants to biomethane (CH4) could support energy storage and strengthen the power grid. Biological methanation (BM) is linked closely to the activity of biogas-producing Bacteria and methanogenic Archaea. During reactor operations, the microbiome is often subject to various changes, e.g., substrate limitation or pH-shifts, whereby the microorganisms are challenged to adapt to the new conditions. In this study, various process parameters including pH value, CH4 production rate, conversion yields and final gas composition were monitored for a hydrogenotrophic-adapted microbial community cultivated in a laboratory-scale BM reactor. To investigate the robustness of the BM process regarding power oscillations, the biogas microbiome was exposed to five hydrogen (H2)-feeding regimes lasting several days. Results: Applying various "on–off" H2-feeding regimes, the CH4 production rate recovered quickly, demonstrating a significant resilience of the microbial community. Analyses of the taxonomic composition of the microbiome revealed a high abundance of the bacterial phyla Firmicutes, Bacteroidota and Thermotogota followed by hydrogenotrophic Archaea of the phylum Methanobacteriota. Homo-acetogenic and heterotrophic fermenting Bacteria formed a complex food web with methanogens. The abundance of the methanogenic Archaea roughly doubled during discontinuous H2-feeding, which was related mainly to an increase in acetoclastic Methanothrix species. Results also suggested that Bacteria feeding on methanogens could reduce overall CH4 production. On the other hand, using inactive biomass as a substrate could support the growth of methanogenic Archaea. During the BM process, the additional production of H2 by fermenting Bacteria seemed to support the maintenance of hydrogenotrophic methanogens at non-H2-feeding phases. Besides the elusive role of Methanothrix during the H2-feeding phases, acetate consumption and pH maintenance at the non-feeding phase can be assigned to this species. Conclusions: Taken together, the high adaptive potential of microbial communities contributes to the robustness of BM processes during discontinuous H2-feeding and supports the commercial use of BM processes for energy storage. Discontinuous feeding strategies could be used to enrich methanogenic Archaea during the establishment of a microbial community for BM. Both findings could contribute to design and improve BM processes from lab to pilot scale. [ABSTRACT FROM AUTHOR]

• A simulator has been created that links metagenomic data on transporter proteins to the growth and succession of a set of bacterial taxa. • The model is based on a classical microbial food web, but with the addition of virtual transporter proteins to control the nutrient uptake of the bacteria. • The simulator generates a realistic annual pattern for the development of a microbial food web and a diverse bacterial community can be maintained in the simulator over several annual cycles. A platform using virtual transporter proteins to simulate nutrient uptake and bacterial multispecies dynamics has been created. The purpose of this simulator is to explore the extent to which different bacterial taxa can coexist based on a mechanistic understanding of their fitness. In the simulator, taxa with different combinations of fitness traits such as the abundance of specific transporter proteins, cell size, motility, metabolic strategies, and predation are allowed to freely compete for available resources. The bacterial taxa represented in the simulator feature bacterial stereotypes at the taxonomic level of order. Metagenomic data on the taxonomic distribution of molecular transporters, from a Baltic Sea time series, provide a framework for the uptake of nutrients by the bacteria. Physical space is not explicitly simulated, so the arena in the experiment is inherently homogeneous as this appears to be a good approximation to an aquatic microbial food web. However, the simulation scenario is based on physical constraints such as the diffusion encounter of nutrients and viruses as well as swimming predators. Examples of mechanisms that are parameterized include growth rate, virus infection, and predation. The overall structure is a classical pelagic microbial food web, where protozoa graze on bacteria and algae and are in turn grazed by microzooplankton. The annual growth pattern of primary producers, and thus the input of organic material over the course of a season, is driven by the flux of light at a given latitude. The results show that the model generates a realistic annual pattern for the development of an aquatic microbial food web and that a diverse bacterial community can be maintained in the simulator over several annual cycles. Notably, the simulator generated similar bacterial population dynamics compared to in situ data. [ABSTRACT FROM AUTHOR]

Ciliates of the genus Urotricha are widely distributed and occur in almost any freshwater body. Thus far, almost all species have been described from morphology only. Here, we applied an integrative approach on the morphology, molecular phylogeny and biogeography of two species isolated from high mountain lakes in the Central Alps, Austria. As these remote lakes are known to have water temperatures <15 °C, our hypothesis was that these urotrichs might prefer 'cold' environments. We studied the morphological details from living and silver-stained individuals, and their molecular sequences (ribosomal operon, ITS), and screened available datasets for their biogeography. The two Urotricha species resembled morphological features of several congeners. An accurate species assignment was difficult due to several overlapping characteristics. However, we tentatively attributed the investigated species to Urotricha nais and Urotricha globosa. The biogeographic analyses revealed their occurrence in Europe, Africa and Asia, and no correlations to (cold) temperatures were found. Our findings suggest that these two urotrichs, originating from two cold and remote habitats, are probably cryptic species well adapted to their harsh environment. [ABSTRACT FROM AUTHOR]

Theory and some evidence suggest that biodiversity promotes stability. However, evidence of how trophic interactions and environmental changes modulate this relationship in multitrophic communities is lacking. Given the current scenario of biodiversity loss and climate changes, where top predators are disproportionately more affected, filling these knowledge gaps is crucial. We simulated climate warming and top predator loss in natural microcosms to investigate their direct and indirect effects on temporal stability of microbial communities and the role of underlying stabilising mechanisms. Community stability was insensitive to warming, but indirectly decreased due to top predator loss via increased mesopredator abundance and consequent reduction of species asynchrony and species stability. The magnitude of destabilising effects differed among trophic levels, being disproportionally higher at lower trophic levels (e.g. producers). Our study unravels major patterns and causal mechanisms by which trophic downgrading destabilises large food webs, regardless of climate warming scenarios. [ABSTRACT FROM AUTHOR]

Abstract Background Cold environments dominate the Earth’s biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000–7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles. Results The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts. Conclusion Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract

Background: In Antarctica, summer sunlight enables phototrophic microorganisms to drive primary production, thereby "feeding" ecosystems to enable their persistence through the long, dark winter months. In Ace Lake, a stratified marine-derived system in the Vestfold Hills of East Antarctica, a Chlorobium species of green sulphur bacteria (GSB) is the dominant phototroph, although its seasonal abundance changes more than 100-fold. Here, we analysed 413 Gb of Antarctic metagenome data including 59 Chlorobium metagenome-assembled genomes (MAGs) from Ace Lake and nearby stratified marine basins to determine how genome variation and population structure across a 7-year period impacted ecosystem function. Results: A single species, Candidatus Chlorobium antarcticum (most similar to Chlorobium phaeovibrioides DSM265) prevails in all three aquatic systems and harbours very little genomic variation (≥ 99% average nucleotide identity). A notable feature of variation that did exist related to the genomic capacity to biosynthesize cobalamin. The abundance of phylotypes with this capacity changed seasonally ~ 2-fold, consistent with the population balancing the value of a bolstered photosynthetic capacity in summer against an energetic cost in winter. The very high GSB concentration (> 108 cells ml−1 in Ace Lake) and seasonal cycle of cell lysis likely make Ca. Chlorobium antarcticum a major provider of cobalamin to the food web. Analysis of Ca. Chlorobium antarcticum viruses revealed the species to be infected by generalist (rather than specialist) viruses with a broad host range (e.g., infecting Gammaproteobacteria) that were present in diverse Antarctic lakes. The marked seasonal decrease in Ca. Chlorobium antarcticum abundance may restrict specialist viruses from establishing effective lifecycles, whereas generalist viruses may augment their proliferation using other hosts. Conclusion: The factors shaping Antarctic microbial communities are gradually being defined. In addition to the cold, the annual variation in sunlight hours dictates which phototrophic species can grow and the extent to which they contribute to ecosystem processes. The Chlorobium population studied was inferred to provide cobalamin, in addition to carbon, nitrogen, hydrogen, and sulphur cycling, as critical ecosystem services. The specific Antarctic environmental factors and major ecosystem benefits afforded by this GSB likely explain why such a coherent population structure has developed in this Chlorobium species. FJebgLEuwcBu4fPtsFrHHT Video abstract [ABSTRACT FROM AUTHOR]

The newly described dinoflagellate, Shimiella gracilenta, is known to survive for approximately 1 month on the plastids of ingested prey cells during starvation, indicating kleptoplastidy. To understand the population dynamics of this dinoflagellate in marine planktonic food webs, its growth and mortality rate due to predation should be assessed. Thus, we investigated the feeding occurrence of eight common heterotrophic protists on S. gracilenta. We also determined the growth and ingestion rates of Oxyrrhis marina and the naked ciliate, Rimostrombidium sp. on S. gracilenta as a function of the prey concentration. The common heterotrophic dinoflagellates (HTDs) Gyrodinium dominans, O. marina, and Pfiesteria piscicida and a naked ciliate Rimostrombidium sp. were able to feed on S. gracilenta; whereas the HTDs Aduncodinium glandula, Gyrodinium jinhaense, Oblea rotunda, and Polykrikos kofoidii were not. Shimiella gracilenta supported positive growth of O. marina and Rimostrombidium sp. but did not support that of G. dominans and P. piscicida. With increasing prey concentrations, the growth and ingestion rates of O. marina and Rimostrombidium sp. on S. gracilenta increased and became saturated. The maximum growth rates of O. marina and Rimostrombidium sp. on S. gracilenta were 0.645 and 0.903 day−1, respectively. Furthermore, the maximum ingestion rates of O. marina and Rimostrombidium sp. on S. gracilenta were 0.11 ng C predator day−1 (1.6 cells predator−1 day−1) and 35 ng C predator day−1 (500 cells predator−1 day−1), respectively. The maximum ingestion rate of O. marina on S. gracilenta was lower than that on any other algal prey reported to date, although its maximum growth rate was moderate. In conclusion, S. gracilenta had only a few common heterotrophic protist predators but could support moderate growth rates of the predators. Thus, S. gracilenta may not be a common prey species for diverse heterotrophic protists but may be a suitable prey for a few heterotrophic protists.

The food web is a cycle of matter and energy within river ecosystems. River environmental changes resulting from human activities are increasingly threatening the composition and diversity of global aquatic organisms and the multi-trophic networks. How multiple environmental factors influence food web patterns among multi-trophic microbial communities in rivers remains largely unknown. Using water quality evaluation and meta-omics techniques, we investigated the composition, structure and interaction characteristics, and drivers of food webs of microorganisms (archaea, bacteria, fungi, protists, metazoa, viridiplantae and viruses) at multiple trophic levels in different water quality environments (Classes II, III, and IV). First, water quality deterioration led to significant changes in the composition of the microbial community at multiple trophic levels, which were represented by the enrichment of Euryarchaeota in the archaeal community, the increase of r-strategists in the bacterial community, and the increase of the proportion of predators in the protist community. Second, deteriorating water quality resulted in a significant reduction in the dissimilarity of community structure (homogenization of community structure in Class III and IV waters). Of the symbiotic, parasitic, and predatory networks, the community networks in Class II water all showed the most stable symbiotic, parasitic, and predatory correlations (higher levels of modularity in the networks). In Class III and IV waters, nutrient inputs have led to increased reciprocal symbiosis and decreased competition between communities, which may have the risk of a positive feedback loop driving a system collapse. Finally, inputs of phosphorus and organic matter could be the main drivers of changes in the planktonic microbial food web in the Fen River. Overall, the results indicated the potential ecological risks of exogenous nutrient inputs, which were important for aquatic ecosystem conservation. [Display omitted] • Water quality deterioration drove shift in bacterial community to r-strategists. • Water quality degradation increased the proportion of heterotrophic protists. • Trophic transfer efficiency of bacteria, fungi, and metazoa was greatly affected. • Positive feedback loops and associated ecological destabilization risk increased. • TP and CODcr are the main factors driving the microbial food web in the Fen River. [ABSTRACT FROM AUTHOR]

Anthropogenic carbon emissions are causing changes in seawater carbonate chemistry including a decline in the pH of the oceans. While its aftermath for calcifying microbes has been widely studied, the effect of ocean acidification (OA) on marine viruses and their microbial hosts is controversial, and even more in combination with another anthropogenic stressor, i.e., human-induced nutrient loads. In this study, two mesocosm acidification experiments with Mediterranean waters from different seasons revealed distinct effects of OA on viruses and viral-mediated prokaryotic mortality depending on the trophic state and the successional stage of the plankton community. In the winter bloom situation, low fluorescence viruses, the most abundant virus-like particle (VLP) subpopulation comprising mostly bacteriophages, were negatively affected by lowered pH with nutrient addition, while the bacterial host abundance was stimulated. High fluorescence viruses, containing cyanophages, were stimulated by OA regardless of the nutrient conditions, while cyanobacteria of the genus Synechococcus were negatively affected by OA. Moreover, the abundance of very high fluorescence viruses infecting small haptophytes tended to be lower under acidification while their putative hosts' abundance was enhanced, suggesting a direct and negative effect of OA on viral–host interactions. In the oligotrophic summer situation, we found a stimulating effect of OA on total viral abundance and the viral populations, suggesting a cascading effect of the elevated pCO2 stimulating autotrophic and heterotrophic production. In winter, viral lysis accounted for 30 ± 16% of the loss of bacterial standing stock per day (VMMBSS) under increased pCO2 compared to 53 ± 35% in the control treatments, without effects of nutrient additions while in summer, OA had no significant effects on VMMBSS (35 ± 20% and 38 ± 5% per day in the OA and control treatments, respectively). We found that phage production and resulting organic carbon release rates significantly reduced under OA in the nutrient replete winter situation, but it was also observed that high nutrient loads lowered the negative effect of OA on viral lysis, suggesting an antagonistic interplay between these two major global ocean stressors in the Anthropocene. In summer, however, viral-mediated carbon release rates were lower and not affected by lowered pH. Eutrophication consistently stimulated viral production regardless of the season or initial conditions. Given the relevant role of viruses for marine carbon cycling and the biological carbon pump, these two anthropogenic stressors may modulate carbon fluxes through their effect on viruses at the base of the pelagic food web in a future global change scenario.

Anthropogenic carbon emissions are causing changes in seawater carbonate chemistry including a decline in the pH of the oceans. While its aftermath for calcifying microbes has been widely studied, the effect of ocean acidification (OA) on marine viruses and their microbial hosts is controversial, and even more in combination with another anthropogenic stressor, i.e., human-induced nutrient loads. In this study, two mesocosm acidification experiments with Mediterranean waters from different seasons revealed distinct effects of OA on viruses and viral-mediated prokaryotic mortality depending on the trophic state and the successional stage of the plankton community. In the winter bloom situation, low fluorescence viruses, the most abundant virus-like particle (VLP) subpopulation comprising mostly bacteriophages, were negatively affected by lowered pH with nutrient addition, while the bacterial host abundance was stimulated. High fluorescence viruses, containing cyanophages, were stimulated by OA regardless of the nutrient conditions, while cyanobacteria of the genus Synechococcus were negatively affected by OA. Moreover, the abundance of very high fluorescence viruses infecting small haptophytes tended to be lower under acidification while their putative hosts' abundance was enhanced, suggesting a direct and negative effect of OA on viral–host interactions. In the oligotrophic summer situation, we found a stimulating effect of OA on total viral abundance and the viral populations, suggesting a cascading effect of the elevated p CO2 stimulating autotrophic and heterotrophic production. In winter, viral lysis accounted for 30 ± 16% of the loss of bacterial standing stock per day (VMMBSS) under increased p CO2 compared to 53 ± 35% in the control treatments, without effects of nutrient additions while in summer, OA had no significant effects on VMMBSS (35 ± 20% and 38 ± 5% per day in the OA and control treatments, respectively). We found that phage production and resulting organic carbon release rates significantly reduced under OA in the nutrient replete winter situation, but it was also observed that high nutrient loads lowered the negative effect of OA on viral lysis, suggesting an antagonistic interplay between these two major global ocean stressors in the Anthropocene. In summer, however, viral-mediated carbon release rates were lower and not affected by lowered pH. Eutrophication consistently stimulated viral production regardless of the season or initial conditions. Given the relevant role of viruses for marine carbon cycling and the biological carbon pump, these two anthropogenic stressors may modulate carbon fluxes through their effect on viruses at the base of the pelagic food web in a future global change scenario. [ABSTRACT FROM AUTHOR]

Ciliates of the genus Urotricha are widely distributed and occur in almost any freshwater body. Thus far, almost all species have been described from morphology only. Here, we applied an integrative approach on the morphology, molecular phylogeny and biogeography of two species isolated from high mountain lakes in the Central Alps, Austria. As these remote lakes are known to have water temperatures Urotricha species resembled morphological features of several congeners. An accurate species assignment was difficult due to several overlapping characteristics. However, we tentatively attributed the investigated species to Urotricha nais and Urotricha globosa. The biogeographic analyses revealed their occurrence in Europe, Africa and Asia, and no correlations to (cold) temperatures were found. Our findings suggest that these two urotrichs, originating from two cold and remote habitats, are probably cryptic species well adapted to their harsh environment.

Microbial food web (MFW) in the seawater encompasses the smallest organisms: viruses, autotrophic prokaryotes and heterotrophic prokaryotes (HP), nanoflagellates, eukaryotic phytoplankton and ciliates. For many years, scientists investigated the MFW structure differences in distinct water masses. However, the MFW structure seasonal variation in coastal areas remains poorly documented. In this study, we report on the seasonal and spatial variations of the MFW structure in the temperate Sanggou Bay in four successive seasons, from spring to winter. With a temperature increase from 1.90 to 24.20°C, HP biomass increased from 3.77 to 135.77 μg C dm–3, almost covering the whole variation range for the global ocean. The autotrophic (AUTO) components, including Synechococcus, phototrophic picoeukaryotes (PEUK) and pigmented nanoflagellates (PNF), exhibited biomass variation ranges as large as previously reported. The MFW structure seasonal variation was driven by MFW relative biomasses (biomass ratios of MFW components to HP). With the increase of HP biomass, PNF and PEUK relative biomasses increased more rapidly than those of other groups while that of ciliates slightly decreased. The HETE:AUTO (biomass ratio of heterotroph to autotroph organisms) decreased with temperature, it was 1 in other seasons. Cluster analyses distinguished Inside Bay and Outside Bay on the basis of hydrological characteristics. Consistently, the two subdivisions of Sanggou Bay exhibited different MFW structures as well as distinct tintinnid communities. The main MFW structure difference between Inside and Outside Bay was the biomass ratios of AUTO components to HP. Our results showed that the variations of autotrophic component biomass ratios relative to HP were the main factor responsible for the MFW structure seasonal variation. The spatial difference in MFW structure as well as in tintinnid taxonomic composition between Inside and Outside Bay was linked to the semienclosed nature of the Bay that does not favor efficient mixing with outside Yellow Sea waters.

Microbial food web organisms are at the base of the functioning of pelagic ecosystems and support the whole marine food web. They are very reactive to environmental changes and their interactions are modified in response to different productive periods such as phytoplankton bloom and non-bloom as well as contrasted climatic years. To study ecological associations, identify potential interactions between microorganisms and study the structure of the microbial food web in coastal waters, a weekly monitoring was carried out in the Thau Lagoon on the French Mediterranean coast. The monitoring lasted from winter to late spring during two contrasting climatic years, a typical Mediterranean (2015) and a year with an extreme warm winter (2016). Correlation networks comprising 110 groups/taxa/species were constructed to characterize potential possible interactions between the microorganisms during bloom and non-bloom periods. Complex correlation networks during the bloom and dominated by negative intraguild correlations and positive correlations of phytoplankton with bacteria. Such pattern can be interpreted as a dominance of competition and mutualism. In contrast, correlation networks during the non-bloom period were less complex and mostly dominated by tintinnids associations with bacteria mostly referring to potential feeding on bacteria, which suggests a shift of biomass transfer from phytoplankton-dominated food webs during bloom to more bacterioplankton-based food webs during non-bloom. Inter-annual climatic conditions significantly modified the structure of microbial food webs. The warmer year favored relationships among smaller group/taxa/species at the expense of large phytoplankton and ciliates, possibly due to an intensification of the trophic cascade with a potential shift in energy circulation through microbial food web. Our study compares a typical Mediterranean spring with another mimicking the prospected intensification of global warming; if such consideration holds true, the dominance of future coastal marine ecosystems will be shifted from the highly productive herbivorous food web to the less productive microbial food web.

Microbialmats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions. [ABSTRACT FROM AUTHOR]

Microbial food web organisms are at the base of the functioning of pelagic ecosystems and support the whole marine food web. They are very reactive to environmental changes and their interactions are modified in response to different productive periods such as phytoplankton bloom and non-bloom as well as contrasted climatic years. To study ecological associations, identify potential interactions between microorganisms and study the structure of the microbial food web in coastal waters, a weekly monitoring was carried out in the Thau Lagoon on the French Mediterranean coast. The monitoring lasted from winter to late spring during two contrasting climatic years, a typical Mediterranean (2015) and a year with an extreme warm winter (2016). Correlation networks comprising 110 groups/taxa/species were constructed to characterize potential possible interactions between the microorganisms during bloom and non-bloom periods. Complex correlation networks during the bloom and dominated by negative intraguild correlations and positive correlations of phytoplankton with bacteria. Such pattern can be interpreted as a dominance of competition and mutualism. In contrast, correlation networks during the non-bloom period were less complex and mostly dominated by tintinnids associations with bacteria mostly referring to potential feeding on bacteria, which suggests a shift of biomass transfer from phytoplankton-dominated food webs during bloom to more bacterioplankton-based food webs during non-bloom. Inter-annual climatic conditions significantly modified the structure of microbial food webs. The warmer year favored relationships among smaller group/taxa/species at the expense of large phytoplankton and ciliates, possibly due to an intensification of the trophic cascade with a potential shift in energy circulation through microbial food web. Our study compares a typical Mediterranean spring with another mimicking the prospected intensification of global warming; if such consideration holds true, the dominance of future coastal marine ecosystems will be shifted from the highly productive herbivorous food web to the less productive microbial food web. [ABSTRACT FROM AUTHOR]

The impacts of grazing by meso- and microzooplankton on phytoplankton primary production (PP) was investigated in the surface layer of the western North Atlantic during spring. Shipboard experiments were performed on a latitudinal transect at three stations that differed in mixed layer depth, temperature, and mesozooplankton taxonomic composition. The mesozooplankton community was numerically dominated by Calanus finmarchicus at the northern and central station, with Calanus hyperboreus also present at the northern station. The southern station was >10 ffiC warmer than the other stations and had the most diverse mesozooplankton assemblage, dominated by small copepods including Paracalanus spp. Microzooplankton grazing was detected only at the northern station, where it removed 97% of PP. Estimated clearance rates by C. hyperboreus and C. finmarchicus suggested that at in-situ abundance these mesozooplankton were not likely to have a major impact on phytoplankton abundance, unless locally aggregated. Although mesozooplankton grazing impact on total phytoplankton was minimal, these grazers completely removed the numerically scarce > 10 mm particles, altering the particle-size spectrum. At the southern station, grazing by the whole mesozooplankton assemblage resulted in a removal of 14% of PP, and its effect on net phytoplankton growth rate was similar irrespective of ambient light. In contrast, reduction in light availability had an approximately 3-fold greater impact on net phytoplankton growth rate than mesozooplankton grazing pressure. The low mesozooplankton grazing impact across stations suggests limited mesozooplanktonmediated vertical export of phytoplankton production. The constraints provided here on trophic transfer, as well as quantitative estimates of the relative contribution of light and grazer controls of PP and of grazer-induced shifts in particle size spectra, illuminate food web dynamics and aid in parameterizing modeling-frameworks assessing global elemental fluxes and carbon export. [ABSTRACT FROM AUTHOR]

Thiamin (vitamin B1) is primarily produced by bacteria and phytoplankton in aquatic food webs and transferred by ingestion to higher trophic levels. However, much remains unknown regarding production, content and transfer of this water-soluble, essential micronutrient. Hence, the thiamin content of six phytoplankton species from different taxa was investigated, along with the effect of thiamin amendment on thiamin content. Furthermore, thiamin transfer to copepods was estimated in feeding experiments. Prey type, not phytoplankton thiamin content per se , was the most important factor for the transfer of thiamin, as it was lowest from filamentous Cyanophyceae and highest from more easily ingested prey like Dunaliella tertiolecta and Rhodomonas salina. Cyanophyceae had the highest thiamin content of the investigated species, eightfold higher than the lowest. Phytoplankton varied in thiamin content related to the supply of thiamin, where thiamin addition enabled higher thiamin content in some species, while copepod thiamin content was less variable. In all, thiamin transfer is not only dependent on the prey thiamin content, but also the edibility and/or digestibility is of importance. Thiamin is essential for all organisms, and this study constitutes an important building block to understanding the dynamics and transfer of thiamin in the aquatic food web. [ABSTRACT FROM AUTHOR]

Many marine microbial eukaryotes combine photosynthetic with phagotrophic nutrition, but incomplete understanding of such mixotrophic protists, their functional diversity, and underlying physiological mechanisms limits the assessment and modeling of their roles in present and future ocean ecosystems. We developed an experimental system to study responses of mixotrophic protists to availability of living prey and light, and used it to characterize contrasting physiological strategies in two stramenopiles in the genus Ochromonas. We show that oceanic isolate CCMP1393 is an obligate mixotroph, requiring both light and prey as complementary resources. Interdependence of photosynthesis and heterotrophy in CCMP1393 comprises a significant role of mitochondrial respiration in photosynthetic electron transport. In contrast, coastal isolate CCMP2951 is a facultative mixotroph that can substitute photosynthesis by phagotrophy and hence grow purely heterotrophically in darkness. In contrast to CCMP1393, CCMP2951 also exhibits a marked photoprotection response that integrates non‐photochemical quenching and mitochondrial respiration as electron sink for photosynthetically produced reducing equivalents. Facultative mixotrophs similar to CCMP2951 might be well adapted to variable environments, while obligate mixotrophs similar to CCMP1393 appear capable of resource efficient growth in oligotrophic ocean environments. Thus, the responses of these phylogenetically close protists to the availability of different resources reveals niche differentiation that influences impacts in food webs and leads to opposing carbon cycle roles. [ABSTRACT FROM AUTHOR]

In the Arctic, seasonal changes are substantial, and as a result, the marine bacterial community composition and functions differ greatly between the dark winter and light-intensive summer. While light availability is, overall, the external driver of the seasonal changes, several internal biological interactions structure the bacterial community during shorter timescales. These include specific phytoplankton–bacteria associations, viral infections and other top-down controls. Here, we uncover these microbial interactions and their effects on the bacterial community composition during a full annual cycle by manipulating the microbial food web using size fractionation. The most profound community changes were detected during the spring, with ‘mutualistic phytoplankton’—Gammaproteobacteria interactions dominating in the pre-bloom phase and ‘substrate-dependent phytoplankton’—Flavobacteria interactions during blooming conditions. Bacterivores had an overall limited effect on the bacterial community composition most of the year. However, in the late summer, grazing was the main factor shaping the community composition and transferring carbon to higher trophic levels. Identifying these small-scale interactions improves our understanding of the Arctic marine microbial food web and its dynamics.

Theory and empirical studies in metazoans predict that apex predators should shape the behavior and ecology of mesopredators and prey at lower trophic levels. Despite the ecological importance of microbial communities, few studies of predatory microbes examine such behavioral res-ponses and the multiplicity of trophic interactions. Here, we sought to assemble a three-level microbial food chain and to test for behavioral interactions between the predatory nematode Caenorhabditis elegans and the predatory social bacterium Myxococcus xanthus when cultured together with two basal prey bacteria that both predators can eat—Escherichia coli and Flavobacterium johnsoniae. We found that >90% of C. elegans worms failed to interact with M. xanthus even when it was the only potential prey species available, whereas most worms were attracted to pure patches of E. coli and F. johnsoniae. In addition, M. xanthus altered nematode predatory behavior on basal prey, repelling C. elegans from two-species patches that would be attractive without M. xanthus, an effect similar to that of C. elegans pathogens. The nematode also influenced the behavior of the bacterial predator: M. xanthus increased its predatory swarming rate in response to C. elegans in a manner dependent both on basal-prey identity and on worm density. Our results suggest that M. xanthus is an unattractive prey for some soil nematodes and is actively avoided when other prey are available. Most broadly, we found that nematode and bacterial predators mutually influence one another’s predatory behavior, with likely consequences for coevolution within complex microbial food webs.

Microbial food webs (MFW) play an indispensable role in marine pelagic ecosystem, yet their composition and response to abiotic variables were poorly documented in the oligotrophic tropical Western Pacific. During winter of 2015, we conducted a survey to examine key components of MFW, including Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic prokaryotes (HP), heterotrophic/pigmented nanoflagellates and ciliates, across water column from surface to 2000 m. Each MFW component exhibited unique vertical distribution pattern, with abundance ratio varying over six and three orders of magnitude across Pico/Microplankton (1.6 ± 1.0 × 10 6 ) and Nano/Microplankton (3.2 ± 2.8 × 10 3 ), respectively. Furthermore, HP was main component for MFW in the bathypelagic (>1000 m) zone. Multivariate biota-environment analysis demonstrated that environmental variables, particularly temperature, significantly impacted MFW composition, suggesting that bottom-up control (resource availability) dominated the water column. Our study provides benchmark information for future environmental dynamics forcing on MFW in the oligotrophic tropical seas., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

The microbial food web is an important part in aquatic ecosystem, but studies on the microbial food web in freshwater ecosystem, especially in freshwater eutrophic lakes, still need further investigation. In the present study, using eutrophic Lake Nanhu as model, the community changes of phytoplankton, zooplankton, and bacteria between the bloom and non-bloom period were analyzed, and microzooplankton grazing experiments were also conducted to measure the grazing pressure and selectivity of microzooplankton on phytoplankton community. Phytoplankton community in Lake Nanhu was mainly dominated by Cyanophyta (49.44%), especially Anabaena circinalis and Microcystis flos-aquae, during bloom period. Rotifers were the main components of zooplankton in Lake Nanhu (44.15%), Brachionus calyciflorus and Moina macrocopa were the most dominant zooplankton in the non-bloom and bloom period, respectively. Bacteroidetes showed significantly higher mean proportion in bloom period than that in non-bloom period (p < 0.001). The growth rates of phytoplankton ranged from −1.00 d−1 to 1.29 d−1, while grazing rates of microzooplankton ranged from −1.15 d−1 to 1.05 d−1. Results indicated that microzooplankton could respond quickly to the increase of phytoplankton during bloom period. Meanwhile, microzooplankton showed grazing preference on Cyanophyta and Cryptophyta during bloom period and non-bloom period, respectively. The microzooplankton grazing selectivity during bloom period might depend on phytoplankton community composition.

The simple view of the classical phytoplankton-zooplankton-fish food chain (CFC) has been replaced by a more complex framework, integrating microbial compartments (microbial food web, MFW). Few studies considered all components of the pelagic MFW in freshwaters and mostly are from temperate regions. We investigated carbon partitioning in the CFC and the MFW in an Amazonian floodplain system and analyzed the strength of interactions among components through structure equation modeling. We hypothesized that (i) MFW contributes highly to total plankton biomass throughout the year; and (ii) all plankton communities increase in biomass during low water, increasing the role of trophic interactions. We collected 30 subsurface samples (nutrients and plankton communities). MFW predominated over CFC in carbon biomass, and plankton components and their interactions changed according to the contrasting water level. Because phosphorus can be a potentially limiting resource for strict primary producers, higher biomass and a more complex MFW occurred during low water. We concluded that hydrology is a key factor shaping biotic interactions during low-water periods, and that MFW plays a key role in floodplain lakes, being potential mixotrophy an important strategy for phytoplankton. [ABSTRACT FROM AUTHOR]

An algorithm of a dynamic mass-balance model emulating the biotic energy flow in a planktonic community with the involvement of microbial organisms has been developed. The abiotic input parameters of the model are the latitude, mean depth of the water body, total phosphorus content, and water color. The model makes it possible to forecast the biomass and production of key plankton groups. It is shown that the food-base production for fish and their growth are determined by the degree of protozoan plankton involvement in the trophic web. [ABSTRACT FROM AUTHOR]

Pelagic copepods often couple the classical and microbial food webs by feeding on microzooplankton (e.g. ciliates) in oligotrophic aquatic systems, and this consumption can trigger trophic cascades within the microbial food web. Consumption of mixotrophic microzooplankton, which are both autotrophic and heterotrophic within the same individual, is of particular interest because of its influence on carbon transfer efficiency within aquatic food webs.In Lake Baikal, Siberia, it is unknown how carbon from a well‐developed microbial food web present during summer stratification moves into higher trophic levels within the classical food web.We conducted in situ experiments in August 2015 to test the hypotheses that: (a)  the lake's dominant endemic copepod (Epischura baikalensis), previously assumed to be an herbivore feeding on diatoms, connects the microbial and classical food webs by ingesting ciliates; and (b) this feeding initiates top‐down effects within the microbial food web.Our results supported these hypotheses. E. baikalensis individuals consumed on average 101–161 ciliates per day, obtaining 96%–98% of their ingested carbon from ciliates and the remainder from small diatoms. Clearly, E. baikalensis is omnivorous, and it is probably channelling more primary production from both the microbial food web and the classical food web of Lake Baikal to higher trophic levels than any other pelagic consumer.Most ciliates consumed were a mixotrophic oligotrich and such taxa are often abundant in summer in other oligotrophic lakes. Consumption of these mixotrophs is likely to boost substantially the transfer efficiency of biomass to higher trophic levels with potential implications for fish production, but this has seldom been investigated in oligotrophic lakes.Feeding of E. baikalensis initiated a three‐link predatory cascade which reduced the abundance of ciliates and elevated growth rates of heterotrophic nanoflagellates but did not affect abundance or growth rates of autotrophic picoplankton. This demonstration of a potential trophic cascade in Lake Baikal indicates that investigations at larger spatial–temporal scales are needed to identify the conditions promoting or precluding trophic cascades in this lake. [ABSTRACT FROM AUTHOR]

The distribution of bacterial and ciliate abundance, ciliate community composition and other parameters were studied during summer along a transect from the mouth of the Słupia River to offshore waters (southern Baltic Sea). Bacteria were examined under an epifluorescence microscope and ciliates were observed under an inverted microscope. Two water masses were identified along the transect. Less saline waters in the river mouth and in the surface layer in the port of Ustka were characterized by high bacterial abundance (5.51–6.16 × 106 ml−1) and low ciliate abundance (0.34–0.90 cells ml−1). More saline waters in the near-bottom zone in the port of Ustka and in the surface layer outside the port contained smaller numbers of bacteria (0.99–2.14 × 106 ml−1) and larger numbers of ciliates (2.65–5.40 cells ml−1). The differences were statistically significant. The separation of the two water masses indicated that the Słupia River exerted a minor impact on the marine waters. The ciliate community composition changed along the transect studied. The main statistically significant difference observed was the low contribution of oligotrichs and choreotrichs to ciliate biomass (3–4%) in less saline waters and their dominance (45–80% of ciliate biomass) in more saline waters. [ABSTRACT FROM AUTHOR]

Littoral zones are the most productive areas of shallow lakes and make important contributions to energy transfer to higher trophic levels in aquatic ecosystems. Great habitat heterogeneity characterizes the littoral ecosystems, often encompassing macrophyte covered areas that provide microhabitats with diverse structural complexity, and several effects over the structure and function of biological communities. The effects of macrophytes on trophic interactions are more complex in subtropical lakes than in temperate lakes. The relationships between planktonic food web components and the effects of a highly dynamic environment in structuring plankton communities were studied in a large subtropical shallow lake. The study was conducted for twenty-five consecutive days in the summer of 2016 at two sites (Station 1 and Station 2) in the well-developed littoral zone of Lake Mangueira hosting different plant life forms. Strong spatial variation between sampling stations was evidenced in the density of most of the communities, with the highest means of bacterioplankton, phytoplankton, and ciliates density being recorded at the station surrounded mainly by submerged macrophytes (Station 1). These plants particularly modify microhabitat complexity by increasing the availability and functional diversity of niches. Furthermore, submerged macrophytes tend to accumulate more periphyton biomass, a quality food resource for many consumers. Important grazing relationships, nutrient demands, and trophic structure were assessed through carbon biomass of the communities. Phytoplankton accounted for a greater proportion of the entire plankton community than bacteria, while zooplankton had low carbon biomass of crustaceans and a high dominance of ciliates and rotifers, with a greater grazing impact on bacterioplankton than on phytoplankton. According to RDA and multiple-regression analysis, nutrients and humic substances were the main predictors of variability in the littoral food web components over a short-sampling interval. The carbon biomass of bacteria and metazooplankton were both positively related to humic substances and nutrients at Station 1, as well as the biomass ratio of metazooplankton to phytoplankton and metazooplankton to ciliates. This suggests that humic substances have been metabolized by bacteria and transferred to higher trophic levels through predation. On the other hand, humic substances negatively affected the carbon biomass of bacteria and cyanobacteria at Station 2, suggesting a mostly refractory DOC around the emergent plants. Results indicate that despite the greater importance of bacterial biomass in the energy transfer through zooplankton predation, the efficiency of carbon transfer in algal and bacteria-based food webs was both very low. The effects of macrophytes on the quantity and/or quality of nutrients and substrates for bacteria uptake and phytoplankton requirements, explained the spatial variability of plankton food web components, even over the short distance between stations, as well as the inefficient microbial loop found in the littoral zone inhabited by macrophytes. • High variability of the planktonic food web components occurred in a short distance. • The plankton communities quickly responded to fast changing in nutrients. • The carbon biomass ratios between metazooplankton and phytoplankton were very low. • Lower bacterial biomass indicated the low efficiency of the microbial patches. [ABSTRACT FROM AUTHOR]

A recent analysis of the Mediterranean Sea surface temperature showed significant annual warming. Since small picoplankton microorganisms play an important role in all major biogeochemical cycles, fluxes and processes occurring in marine systems (the changes at the base of the food web) as a response to human-induced temperature increase, could be amplified through the trophic chains and could also significantly affect different aspects of the structure and functioning of marine ecosystems. In this study, manipulative laboratory growth/grazing experiments were performed under in situ simulated conditions to study the structural and functional changes within the microbial food web after a 3 °C increase in temperature. The results show that a rise in temperature affects the changes in: (1) the growth and grazing rates of picoplankton, (2) their growth efficiency, (3) carrying capacities, (4) sensitivity of their production and grazing mortality to temperature, (5) satisfying protistan grazer carbon demands, (6) their preference in the selection of prey, (7) predator niche breadth and their overlap, (8) apparent uptake rates of nutrients, and (9) carbon biomass flow through the microbial food web. Furthermore, temperature affects the autotrophic and heterotrophic components of picoplankton in different ways.

ABSTRACT The role of protists and bacteriophages in bacterial predation in the microbial food web has been well studied. There is mounting evidence that Bdellovibrio and like organisms (BALOs) also contribute to bacterial mortality and, in some cases, more so than bacteriophages. A full understanding of the ecologic function of the microbial food web requires recognition of all major predators and the magnitude of each predator’s contribution. Here we investigated the contribution of Halobacteriovorax, one of the BALOs, and bacteriophages when incubated with their common prey, Vibrio vulnificus, in a seawater microcosm. We observed that Halobacteriovorax was the greatest responder to the prey, increasing 18-fold with a simultaneous 4.4-log-unit reduction of V. vulnificus at 40 h, whereas the bacteriophage population showed no significant increase. In subsequent experiments to formulate a medium that would support the predatory activities and replication of both predators, low-nutrient media favored the predation and replication of the Halobacteriovorax, whereas higher-nutrient media enhanced phage growth. The greatest prey reduction and replication of both Halobacteriovorax and phage were observed in media with moderate nutrient levels. Additional experiments show that the predatory activities of both predators were influenced by environmental conditions, specifically, temperature and salinity. The two predators combined exerted greater control on V. vulnificus, a synergism that may be exploited for practical applications to reduce bacterial populations. These findings suggest that along with bacteriophage and protists, Halobacteriovorax has the potential to have a prominent role in bacterial mortality and cycling of nutrients, two vital ecologic functions. IMPORTANCE Although much has been reported about the marine microbial food web and the role of micropredators, specifically viruses and protists, the contribution of Bdellovibrio-like predators has largely been ignored, posing a major gap in understanding food web processes. A complete scenario of the microbial food web cannot be developed until the roles of all major micropredators and the magnitude of their contributions to bacterial mortality, structuring of microbial communities, and cycling of nutrients are assessed. Here we show compelling evidence that Halobacteriovorax, a predatory bacterium, is a significant contributor to bacterial death and, in some cases, may rival viruses as agents of bacterial mortality. These results advance current understanding of the microbial loop and top-down control on the bacterial community.

Abstract: Aim: We aimed to assess the influence of bottom-up and top-down control mechanisms on the abundance and size structure of protist communities (heterotrophic flagellates and ciliates). We formulated the following hypothesis: bottom-up control mechanisms, related to the availability of resources in the environment, are responsible for structuring the abundance of these communities, whereas top-down control mechanisms, related to predation effects, determine the size pattern of these organisms. Methods Samples for planktonic organisms were taken in 20 shallow lakes belonging to the upper Paraná River floodplain. We evaluated linear regression models to select the best model which predicts the patterns observed according to Akaike Information Criterion. Results The best models selected to explain the abundance of heterotrophic flagellates included negative relations with picophytoplankton abundance and positive with rotifers abundance, while for their size structure, negative relationships were found with heterotrophic bacteria, ciliates and rotifers biovolumes. In relation to the ciliates, their abundances were positively related to the rotifers and picophytoplankton abundances and negatively with the heterotrophic bacteria abundance. On the other hand, for the size structure, the best models selected strong negative relations with the microcrustaceans biovolumes, in addition to relations with the different fractions of the phytoplankton. Conclusion For both flagellates and ciliates, their abundance is being mainly regulated by a bottom up control mechanism, whereas for the size structure the results showed that both food resources and predators were important, indicating that bottom-up and top-down mechanisms act simultaneously in determining the size of these microorganisms.