Metagenomic insights into feasibility of agricultural wastes on optimizing water quality and natural bait by regulating microbial loop

Effective screening feed substitutes for improving water quality in aquaculture systems has become a trending research topic now. In this study, three typical organic agricultural wastes, including sugar cane bagasse (SC), coconut shell powder (CS), and corn cob powder (CC), were selected to evaluate their potential roles on the optimization of water quality and natural bait compared to aquafeeds. Fish feed resulted in the highest growth rate of fish but the worst water quality. Organic detritus addition markedly improved the water quality, especially soluble reactive phosphorus (SRP, decrease of 56-61%) and ammonium (decrease of 16% in SC, 47% in CC). Specially, SC induced core microbes to mediate nutrients transformation and recycling (N₂-fixation, ammonification, nitrification, dissimilatory nitrate reduction to ammonia and organic nutrients decomposition), which facilitated the primary productivity based on their positive relationships. This further reduced the available nutrients (especially SRP) in the water and built a mutually beneficial microbial loop. In addition, SC addition increased the abundance of genes involved in amino acids biosynthesis pathways, photosynthesis, and carbon fixation. These results led to energy transfer to higher trophic levels. The addition of CC had a better effect than SC in terms of lower nitrogen levels and a higher fish growth rate (19% in CC, 5% in SC). However, low temperatures and carbon accumulation jointly drive the anaerobic decomposition, resulting in unhealthy microbial loops and low fish growth rates. In contrast to the direct consumption of fish feed, organic detritus can induce more natural bait to provide food for fish by regulating the microbial loop, as showed by the microbial community composition in the water and fish gut. To comprehensively assess water quality, natural bait, and fish growth and quality, certain organic detritus should be considered as an auxiliary material to partially replace feed for healthy and sustainable aquaculture systems.

Light dependence in the phototrophy-phagotrophy balance of constitutive and non-constitutive mixotrophic protists

Mixotrophic protists display contrasting nutritional strategies and are key groups connecting planktonic food webs. They comprise constitutive mixotrophs (CMs) that have an innate photosynthetic ability and non-constitutive mixotrophs (NCMs) that acquire it from their prey. We modelled phototrophy and phagotrophy of two mixotrophic protists as a function of irradiance and prey abundance. We hypothesised that differences in their physiology (constitutive versus non-constitutive mixotrophy) can result in different responses to light gradients. We fitted the models with primary production and bacterivory data from laboratory and field experiments with the nanoflagellate Chrysochromulina parva (CM) and the ciliate Ophrydium naumanni (NCM) from north Andean Patagonian lakes. We found a non-monotonic response of phototrophy and phagotrophy to irradiance in both mixotrophs, which was successfully represented by our models. Maximum values for phototrophy and phagotrophy were found at intermediate irradiance coinciding with the light at the deep chlorophyll maxima in these lakes. At lower and higher irradiances, we found a decoupling between phototrophy and phagotrophy in the NCM while these functions were more coupled in the CM. Our modelling approach revealed the difference between both mixotrophic functional types on the balance between their nutritional strategies under different light scenarios. Thus, our proposed models can be applied to account how changing environmental conditions affect both primary and secondary production within the planktonic microbial food web.

Nanoparticle pre- or co-exposure affects bacterial ingestion by the protozoan Tetrahymena thermophila

Although nanoparticles' (NPs) toxicity has been intensively studied, their effects on bacterial ingestion by protozoans (as an important component of the microbial loop) is unknown. This study investigated the effects of NPs of different chemical composition [hematite (HemNPs), anatase (AnaNPs), and silica (SiNPs) NPs] and size [SiNPs with particle size of 20 (Si-20), 100 (Si-100), and 500 (Si-500) nm] on the ingestion of Escherichia coli by the protozoan Tetrahymena thermophila. Potential differences between pre- vs. co-exposure were also assessed. Pre-exposure to HemNPs had no effects on bacterial ingestion but the other NPs caused a significant inhibition, due to their inhibition of ATP synthesis and the down-regulation of phagocytosis-related genes (ACT1 and CTHB). Contrastively, co-exposure to HemNPs and Si-20 didn't affect bacterial ingestion while co-exposure to AnaNPs (Si-100 and Si-500) induced (inhibited) ingestion. The stimulatory effect of AnaNPs was due to their induction of an increase in the intracellular Ca concentration of T. thermophila whereas the inhibitory effects of Si-100 and Si-500 were attributable to ATP synthesis reduction, enhanced bacterial cell aggregation, and competition between the bacterial cells and the NPs. These findings provide insights into the mechanisms underlying the environmental risks of NPs.

Does microplastic ingestion dramatically decrease the biomass of protozoa grazers? A case study on the marine ciliate Uronema marinum

Microplastic debris has become a significant global environmental issue. Yet, the effects on ingestion of microplastics by protozoan grazers-an important link in the microbial loop-are scant. Feeding experiments were conducted with the free-living marine ciliate Uronema marinum grazing on cultured bacteria Pseudoaltermonas sp., exposing them to different concentrations or sizes of polystyrene beads for 96 h. The number of beads decreased during exposure experiments. Under the microplastic influence, the ciliate cells were observed to decrease in abundance, body size, and biomass. It was noted that the ciliate biomass in the highest microplastic density treatment was significantly lower than that in the control (98.1% lower) and that microplastics can be ingested by ciliate protozoa which performed an important role in the transportation of energy across the microbial loop. Moreover, carbon biomass of ciliates exposed to microplastics of different particle diameters decreased significantly compared to the control. However, this effect does not seem to vary depending on microplastic sizes. This study is a first step in providing experimental insight into the feeding relationship between microplastics and marine protozoan grazers. Further research based on components of the microbial loop is needed to explore the impacts of microplastics in marine food webs.

How do microplastics affect the marine microbial loop? Predation of microplastics by microzooplankton

Protozoans play an integral role in the microbial loop, an important process of material and energy transfer in marine ecosystems. The number of microplastics in the marine environment has greatly increased, but the potential impacts of small nanoplastics and microplastics on marine organisms remain unclear. Here, we conducted a series of feeding experiments with various concentrations of microplastic beads (ca. 1 μm) to characterize the response of the planktonic ciliated protozoan Strombidium sulcatum to microplastics and a set of additional exposure experiments with four different particle diameters of microplastics to explore whether the feeding response exhibited size selectivity. As the microplastic concentration increased, the number, body size, and biomass of ciliates decreased sharply during the exposure period. Predator biomass in all microplastic treatments was markedly reduced relative to the microplastic-free control. For example, at 72 h of exposure, the biomass in the highest microplastic concentration treatment was observed to decrease by 96.59% relative to the control. There was no obvious difference in the biomass of ciliates exposed to various diameters of microplastics; however, compared with the free bead control, the biomass still significantly decreased. These findings suggest that microplastics in the ocean negatively affect the growth of protozoan microzooplankton that might have accidentally ingested these tiny particles during the feeding process. Generally, this study provides basic and novel data for understanding the effect of microplastics on the microbial loop in marine ecosystems.

Particulate organic matter as causative factor to eutrophication of subtropical deep freshwater: Role of typhoon (tropical cyclone) in the nutrient cycling

Intense storms pose a serious threat to ecosystem functioning and services. However, the effects of typhoons (tropical cyclones) on the biogeochemical processes mediating risk of eutrophication in deep freshwater ecosystems remain unclear. Here, we conducted a three-year study to elucidate linkages between environmental change, stable isotopes and the stoichiometry of particulate organic matter (POM), and nutrient cycling (i.e., carbon, nitrogen and phosphorus) in a subtropical deep reservoir subjected to typhoon events. The typhoons significantly changed the nutrient levels in the deep waters as well as the thermocline position. Increased typhoon-driven organic matter input, algae sinking and heterotrophic decomposition interacted with each other to cause steep and prolonged increases of total nitrogen, ammonium nitrogen and total phosphorus in the bottom waters of the reservoir. Small-sized or pico-sized POM (i.e., 0.2-3 μm) showed a substantial increase in bottom waters, and it exhibited stronger response than large-sized POM (i.e., 3-20, 20-64, 64-200 μm) to the typhoons. Our results also indicated that typhoons boost the nutrient cycling in deep waters mainly through pico-sized POM.

Complex interactions and different possible pathways among functional components of the aquatic microbial world in Farasan Archipelago, Southern Red Sea, Saudi Arabia

This work aims to outline the dynamics of trophic links between the three main microbial components (bacteria, nanoflagellates, and ciliates) of the Farasan Archipelago in order to establish a baseline for future research in this area. The Farasan Archipelago lies along the southwestern coast of the Saudi Arabia, southern Red Sea between 16°20′–17°10′N and 41°30′–42°30′E and had been declared as marine and terrestrial reserve by the year 1996. Three different sites were chosen for this study, with each site visited bimonthly for 18 months from September 2016 to February 2018. Bacteria, nanoflagellates and ciliates were enumerated in order to explore the complex interactions between the main microbial categories in sea waters of the Farasan Archipelago. High abundances were recorded during the present study for bacteria (8.7 × 10⁶ bacteria ml⁻¹), nanoflagellates (3.7 × 10⁴ TNAN ml⁻¹) and ciliates (40.4 ciliates ml⁻¹). The paper discusses the various potential pathways controlling the complex interactions between these microbial groups in this part of the southern Red Sea. It is concluded that a linear trophic chain consisting of bacteria; heterotrophic nanoflagellates; filter feeding ciliates is a major route by which the production of bacteria is transferred to the higher consuming levels, thereby confirming the high importance of t bottom-up control (food supply), alongside top-down control (predation) in regulating bacterial abundances in the Farasan Archipelago. During the present investigation, each nanoflagellate ingested between 11 and 87 bacteria in one hour, while each ciliate consumed between 20 and 185 nanoflagellates every hour. These calculated grazing rates of protistan eukaryotes confirmed the role of heterotrophic nanoflagellates as the main consumers of bacteria, and the role of ciliates as the major control for the heterotrophic nanoflagellate population dynamics, and thus the top predators within the microbial plankton assemblage in the Farasan Archipelago.

Seasonal dynamics of the epibiont food web on Unio tumidus (Philipsson, 1788) in a eutrophic reservoir

Bivalves represent one of the most important components of freshwater zoobenthos, and their shells provide a substrate for many organisms to create epibiotic communities of predominantly facultative nature. Thus far, information regarding colonization of Unio tumidus by microorganism assemblages has been almost absent. Moreover, data on the functioning of trophic networks created by epibionts are also unavailable. Therefore, the present study aimed to examine the assemblage of epibiotic microorganisms inhabiting live and dead bivalves with regard to the physicochemical properties of the habitat and determine whether stable isotope levels in primary producers and consumers colonizing bivalve shells exhibit significant seasonal variability. The substrate characteristic and physicochemical properties of water - primarily biogenic compounds and total organic carbon clearly modified the taxonomic composition of microorganisms and the function of the trophic network. This was reflected by the increased diversity of microorganisms (phycoflora, ciliates and rotifers) on live bivalves and the increase in their abundance on dead bivalves. The level of stable isotopes exhibited clear seasonal variability in individual components of the epibiotic trophic network, whereas food preferences of the potential consumers (protozoans and rotifers) depended significantly on the availability and abundance of food.

Inorganic mercury (Hg2+) accumulation in autotrophic and mixotrophic planktonic protists: Implications for Hg trophodynamics in ultraoligotrophic Andean Patagonian lakes

Microbial assemblages are typical of deep ultraoligotrophic Andean Patagonian lakes and comprise picoplankton and protists (phytoflagellates and mixotrophic ciliates), having a central role in the C cycle, primary production and in the incorporation of dissolved inorganic mercury (Hg²⁺) into lake food webs. In this study we evaluated the mechanisms of Hg²⁺ incorporation in hetero- and autotrophic bacteria, in the autotrophic dinoflagellate (Gymnodinium paradoxum) and in two mixotrophic ciliates (Stentor araucanus and Ophrydium naumanni) dominating the planktonic microbial assemblage. The radioisotope ¹⁹⁷Hg was used to trace the Hg²⁺ incorporation in microbiota. Hg uptake was analyzed as a function of cell abundance (BCF: bioconcentration factor), cell surface (SCF: surface concentration factor) and cell volume (VCF: volume concentration factor). Overall, the results obtained showed that these organisms incorporate substantial amounts of dissolved Hg²⁺ passively (adsorption) and actively (bacteria consumption or attachment), displaying different Hg internalization and therefore, varying potential for Hg transfer. Surface area and quality, and surface:volume ratio (S:V) control the passive uptake in all the organisms. Active incorporation depends on bacteria consumption in the mixotrophic ciliates, or on bacteria association to surface in the autotrophic dinoflagellate. Hg bioaccumulated by pelagic protists can be transferred to higher trophic levels through plankton and fish feeding, regenerated to the dissolved phase by excretion, and/or transferred to the sediments by particle sinking. In ultraoligotrophic Andean Patagonian lakes, picoplankton and planktonic protists are key components of lake food webs, linking the pelagic and benthic Hg pathways, and thereby playing a central role in Hg trophodynamics.

Coral Food, Feeding, Nutrition, and Secretion: A Review

Tropical scleractinian corals are dependent to varying degrees on their photosymbiotic partners. Under normal levels of temperature and irradiance, they can provide most, but not all, of the host's nutritional requirements. Heterotrophy is required to adequately supply critical nutrients, especially nitrogen and phosphorus. Scleractinian corals are known as mesozooplankton predators, and most employ tentacle capture. The ability to trap nano- and picoplankton has been demonstrated by several coral species and appears to fulfill a substantial proportion of their daily metabolic requirements. The mechanism of capture likely involves mucociliary activity or extracoelenteric digestion, but the relative contribution of these avenues have not been evaluated. Many corals employ mesenterial filaments to procure food in various forms, but the functional morphology and chemical activities of these structures have been poorly documented. Corals are capable of acquiring nutrition from particulate and dissolved organic matter, although the degree of reliance on these sources generally has not been established. Corals, including tropical, deep- and cold-water species, are known as a major source of carbon and other nutrients for benthic communities through the secretion of mucus, despite wide variation in chemical composition. Mucus is cycled through the planktonic microbial loop, the benthos, and the microbial community within the sediments. The consensus indicates that the dissolved organic fraction of mucus usually exceeds the insoluble portion, and both serve as sources for the growth of nano- and picoplankton. As many corals employ mucus to trap food, a portion is taken back during feeding. The net gain or loss has not been evaluated, although production is generally thought to exceed consumption. The same is true for the net uptake and loss of dissolved organic matter by mucus secretion. Octocorals are thought not to employ mucus capture or mesenterial filaments during feeding and generally rely on tentacular filtration of weakly swimming mesozooplankton, particulates, dissolved organic matter, and picoplankton. Nonsymbiotic species in the tropics favor phytoplankton and weakly swimming zooplankton. Azooxanthellate soft corals are opportunistic feeders and shift their diet according to the season from phyto- and nanoplankton in summer to primarily particulate organic matter (POM) in winter. Cold-water species favor POM, phytodetritus, microplankton, and larger zooplankton when available. Antipatharians apparently feed on mesozooplankton but also use mucus nets, possibly for capture of POM. Feeding modes in this group are poorly known.

Effects of temperature and UVR on organic matter fluxes and the metabolic activity of Acropora muricata

Coral bleaching events are predicted to occur more frequently in the coming decades with global warming. The susceptibility of corals to bleaching during thermal stress episodes depends on many factors, including the magnitude of thermal stress and irradiance. The interactions among these two factors, and in particular with ultra-violet radiation (UVR), the most harmful component of light, are more complex than assumed, and are not yet well understood. This paper explores the individual and combined effects of temperature and UVR on the metabolism of Acropora muricata, one of the most abundant coral species worldwide. Particulate and dissolved organic matter (POM/DOM) fluxes and organic matter (OM) degradation by the mucus-associated bacteria were also monitored in all conditions. The results show that UVR exposure exacerbated the temperature-induced bleaching, but did not affect OM fluxes, which were only altered by seawater warming. Temperature increase induced a shift from POM release and DOM uptake in healthy corals to POM uptake and DOM release in stressed ones. POM uptake was linked to a significant grazing of pico- and nanoplankton particles during the incubation, to fulfil the energetic requirements of A. muricata in the absence of autotrophy. Finally, OM degradation by mucus-associated bacterial activity was unaffected by UVR exposure, but significantly increased under high temperature. Altogether, our results demonstrate that seawater warming and UVR not only affect coral physiology, but also the way corals interact with the surrounding seawater, with potential consequences for coral reef biogeochemical cycles and food webs.

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies

Interactions between bacteria and protists are essential to the ecosystem ecology of fens. Until now, however, there has been almost no information on how restoration procedures in carbonate fens affect the functioning of microbial food webs. Changes in vegetation patterns resulting from restoration may take years to be observed, whereas microbial processes display effects even after short-term exposure to changes in environmental conditions caused by restoration. Therefore, microbial processes and patterns can be used as sensitive indicators of changes in environmental conditions. The present study attempts to verify the hypothesis that the species richness and abundance of microbial loop components would differ substantially before and after restoration. The effect of restoration processes on the functioning of the food web was investigated for a 10 years in a carbonate-rich fen, before and after restoration. The restoration procedure (particularly the improvement in hydrological conditions) distinctly modified the taxonomic composition and functioning of microbial food webs. This is reflected in the increased abundance and diversity of testate amoeba, i.e. top predators, within the microbial food web and in the pronounced increase in the abundance of bacteria. This study suggests potential use of microbial loop components as bio-indicators and bio-monitoring tools for hydrological status of fens and concentrations of nutrients. Better understanding of what regulates microbial populations and activity in fens and unravelling of these fundamental mechanisms are particularly critical in order to more accurately predict how fens will respond to global change or anthropogenic disturbances.

Mercury and selenium in seston, marine plankton and fish (Sardinella brasiliensis) as a tool for understanding a tropical food web

Mercury (Hg) and selenium (Se) concentrations were evaluated in a planktivorous fish and four size classes of organisms (FSCO), collected at an oligotrophic bay in the Southeastern Brazilian coast. No significant spatial differences between Hg and Se were found in the FSCO within the five sampling points in the bay. Hg and Se concentrations increased with successive increases in the size class of the analyzed plankton, i.e. approximately 3-and 2-fold, respectively, from microplankton to macroplankton. Hg and Se biomagnified throughout the planktonic food web. The smallest size class of organism, seston, composed of both biotic and abiotic portions, and fish showed the highest Hg concentrations. This indicates that Hg is not biomagnifying in the base of the bay food web. Selenium concentrations in fish were approximately 5.9 times higher than those in seston. Hg and Se concentrations in fish were approximately 3.5 and 14.6 times higher than those found in the plankton, respectively.

The influence of zooplankton enrichment on the microbial loop in a shallow, eutrophic lake

With increasing primary productivity, ciliates may become the most important members of the microbial loop and form a central linkage in the transformation of microbial production to upper trophic levels. How metazooplankters, especially copepods, regulate ciliate community structure in shallow eutrophic waters is not completely clear. We carried out mesocosm experiments with different cyclopoid copepod enrichments in a shallow eutrophic lake to examine the responses of ciliate community structure and abundance to changes in cyclopoid copepod biomass and to detect any cascading effects on bacterioplankton and edible phytoplankton. Our results indicate that an increase in copepod zooplankton biomass favours the development of small-sized bacterivorous ciliates. This effect is unleashed by the decline of predaceous ciliate abundance, which would otherwise graze effectively on the small-sized ciliates. The inverse relationship between crustacean zooplankton and large predaceous ciliates is an important feature adjusting not only the structure of the ciliate community but also the energy transfer between meta- and protozooplankton. Still we could not detect any cascading effects on bacterio- or phytoplankton that would be caused by the structural changes in the ciliate community.

The effects of predation by planktivorous juvenile fish on the microbial food web

The feeding impact of planktivorous fish on microbial organisms is still poorly understood. We followed the seasonal dynamics of the food web in two natural fishponds for two years: one was stocked with planktivorous whitefish while the other had no planktivorous fish. The aim of the study was the simultaneous assessment of the feeding behaviours of planktivorous fish and of bacterivorous meta-/protozooplankters. We hypothesized that in the presence of planktivorous fish there would be fewer metazooplankton, more protozoans and decreased numbers of bacteria. Our results showed that the amount of metazooplankton eaten by the fish was indeed negatively correlated with metazooplankton biomass. The feeding impact of planktivorous fish in shaping the microbial loop was remarkable. The main grazers of bacteria in the fishpond were ciliates, whereas in the pond without fish these were heterotrophic nanoflagellates. In the fishless pond the role of the top predator shifted to the predaceous metazooplankter Leptodora kindtii which controlled the abundance of herbivorous metazooplankters. We found a negative relationship between the number of bacteria and flagellates in the fishless pond, while the number of bacterivorous ciliates was suppressed by predaceous ciliates. Therefore the bacteria-grazing activity was higher in the absence of planktivorous fish.