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The extracellular release of dissolved organic carbon (DOC) from marine macroalgae supports coastal ecosystem function by supplying photosynthetically fixed carbon to higher trophic levels via the microbial loop. Despite its widely acknowledged biogeochemical importance, DOC is not typically included in primary production estimates of coastal systems. Additionally, little is known about how changes in species composition and coverage will affect the supply of DOC to coastal systems. Within the context of the Baltic Sea, anthropogenic forces are driving a decline in habitat forming kelp species (Fucus vesiculosus) which is superseded by filamentous/turfing algal species, a pattern of change observed globally in numerous other aquatic systems. To evaluate how the drivers of this change may impact the flow of carbon within the Baltic Sea coastal system, the production of DOC by the filamentous algae (Ectocarpus siliculosus) was examined and its rate of release determined (0.095 mg C · g DW-1 · h-1 in light and 0.070 mg C · g DW-1 · h-1 in dark). In addition, bioassays were used to assess the short-term DOC use by bacteria as a proxy of the lability of the released products, with the majority (28.7% released in light and 18.6% released in dark) of the products remaining after 120 hours. This data was linked with long term macroalgae biomass and coverage surveys in order to assess changes in macroalgae community structure through time and to produce standing stock estimates of F. vesiculosus. DOC production as a metric of algal coverage was used to make a preliminary estimation of how changes in community structure may impact the flow of carbon within the system. Our results suggest that decreased levels of DOC released by filamentous algae relative to F. vesiculosus will act to reduce microbial activity. Our model estimates the presence of approximately 150,000 tonnes of F. vesiculosus (dry weight) within the Estonian coastal system translating to an annual release of 7,391 tonnes of DOC. Our study indicates that filamentous-dominated systems have likely altered carbon flow, impacting the broader ecology of the Baltic Sea. Consequently, the loss of kelp species and the expansion of filamentous algae may alter carbon dynamics, with important ecological consequences for other coastal systems globally. [ABSTRACT FROM AUTHOR]

Prokaryotes play a fundamental role in global ocean biogeochemical cycles. However, how the abundance and metabolic activity of ecologically distinct subgroups (i.e., high nucleic acid (HNA) and low nucleic acid (LNA) cells), and their regulating factors, change in response to changing marine environmental conditions remains poorly understood. Here, we delved into the time-evolving dynamic responses of the HNA and LNA prokaryotic subgroups to declining resource availability and selective grazing by protozoa by conducting a 73-day incubation experiment in a large-volume (117,000 L) macrocosm that facilitates community-level exploration. We found that the metabolic activity of the HNA subgroup was higher than that of the LNA subgroup when the macrocosm was resource replete but that the HNA subgroup declined more rapidly than the LNA subgroup as the resources became increasingly scarce, leading to a steadily increasing contribution of LNA cells to prokaryotic activity. Meanwhile, as resources in the macrocosm became limited, protozoan grazing preference shifted from the HNA to the LNA subgroup and the contributions of the LNA subgroup to the carbon flow within the macrocosm increased. The findings highlight the resilience of LNA cells in resource-limited environments, illuminate the critical role of selective grazing by protozoa in balancing distinct prokaryotic subgroups under changing resource conditions, and demonstrate the complex and adaptive interactions between protozoa and prokaryotes across diverse environmental contexts. [ABSTRACT FROM AUTHOR]

Ciliate interactions including mode of nutrition contribute significantly to freshwater and marine ecosystems. Ciliates associations with their bacterial communities, and symbionts have crucial contributions to biomass productivity, transfer of nutrients to higher trophic levels and thus to sustain the ecosystems. The mixotrophic and heterotrophic ciliates are crucial in nutrient cycling by increasing nitrogen, phosphorus, and sulphur. Bacterial predator ciliates regulate the bacterial population and function as bioindicators. Endosymbionts in ciliates illustrate the incorporation of photosynthesis, nitrogen fixation and recycling, and methanogenesis, into ciliate hosts by endosymbionts. Endosymbiosis represents an evolutionary strategy of protists to acquire novel biochemical functions. Herein, I briefly give an account for the impact of ciliate nutrition on aquatic systems. [ABSTRACT FROM AUTHOR]

The extracellular release of dissolved organic carbon (DOC) from marine macroalgae supports coastal ecosystem function by supplying photosynthetically fixed carbon to higher trophic levels via the microbial loop. Despite its widely acknowledged biogeochemical importance, DOC is not typically included in primary production estimates of coastal systems. Additionally, little is known about how changes in species composition and coverage will affect the supply of DOC to coastal systems. Within the context of the Baltic Sea, anthropogenic forces are driving a decline in habitat forming kelp species (Fucus vesiculosus) which is superseded by filamentous/turfing algal species, a pattern of change observed globally in numerous other aquatic systems. To evaluate how the drivers of this change may impact the flow of carbon within the Baltic Sea coastal system, the production of DOC by the filamentous algae (Ectocarpus siliculosus) was examined and its rate of release determined (0.095 mg C · g DW−1 · h−1 in light and 0.070 mg C · g DW−1 · h−1 in dark). In addition, bioassays were used to assess the short-term DOC use by bacteria as a proxy of the lability of the released products, with the majority (28.7% released in light and 18.6% released in dark) of the products remaining after 120 hours. This data was linked with long term macroalgae biomass and coverage surveys in order to assess changes in macroalgae community structure through time and to produce standing stock estimates of F. vesiculosus. DOC production as a metric of algal coverage was used to make a preliminary estimation of how changes in community structure may impact the flow of carbon within the system. Our results suggest that decreased levels of DOC released by filamentous algae relative to F. vesiculosus will act to reduce microbial activity. Our model estimates the presence of approximately 150,000 tonnes of F. vesiculosus (dry weight) within the Estonian coastal system translating to an annual release of 7,391 tonnes of DOC. Our study indicates that filamentous-dominated systems have likely altered carbon flow, impacting the broader ecology of the Baltic Sea. Consequently, the loss of kelp species and the expansion of filamentous algae may alter carbon dynamics, with important ecological consequences for other coastal systems globally.

Eastern Boundary Systems support major fisheries whose early life stages depend on upwelling production. Upwelling can be highly variable at the regional scale, with substantial repercussions for new productivity and microbial loop activity. Studies that integrate the classic trophic web based on new production with the microbial loop are rare due to the range in body forms and sizes of the taxa. Underwater imaging can overcome this limitation, and with machine learning, enables fine resolution studies spanning large spatial scales. We used the In-situ Ichthyoplankton Imaging System (ISIIS) to investigate the drivers of plankton community structure in the northern California Current, sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA, respectively. The non-invasive imaging of particles and plankton over 1644km in the winters and summers of 2018 and 2019 yielded 1.194 billion classified plankton images. Combining nutrient analysis, flow cytometry, and 16S rRNA gene sequencing of the microbial community with mesoplankton underwater imaging enabled us to study taxa from 0.2µm to 15cm, including prokaryotes, copepods, ichthyoplankton, and gelatinous forms. To assess community structure, >2000 single-taxon distribution profiles were analyzed using high resolution spatial correlations. Co-occurrences on the NH line were consistently significantly higher off-shelf while those at TR were highest on-shelf. Random Forests models identified the concentrations of microbial loop associated taxa such as protists, Oithona copepods, and appendicularians as important drivers of co-occurrences at NH line, while at TR, cumulative upwelling and chlorophyll a were of the highest importance. Our results indicate that the microbial loop is driving plankton community structure in intermittent upwelling systems such as the NH line and supports temporal stability, and further, that taxa such as protists, Oithona copepods, and appendicularians connect a diverse and functionally redundant microbial community to stable plankton community structure. Where upwelling is more continuous such as at TR, primary production may dominate patterns of community structure, obscuring the underlying role of the microbial loop. Future changes in upwelling strength are likely to disproportionately affect plankton community structure in continuous upwelling regions, while high microbial loop activity enhances community structure resilience. [ABSTRACT FROM AUTHOR]

Marine ciliates play important roles not only in linking the microbial loop to the classic pelagic and benthic food chains but also in regenerating nutrients, yet how dietary nutrient imbalance impacts their nutrient regeneration has not been thoroughly addressed. The growth and physiological responses of Euplotes vannus to low dietary nitrogen (LN) and low dietary phosphorus (LP) conditions were studied, with the bacterium Pseudomonas putida as prey. Feeding on LN prey reduced the growth rate of E. vannus. Dietary nutrient limitation changed the types and quantities of nutrient recycling. Feeding on LP prey enhanced dissolved organic carbon excretion but reduced orthophosphate excretion, whereas feeding on LN prey generally resulted in decreases in the excretion rate in all N forms (ammonium, urea, and nitrate). In addition, the proportion of ammonium in regenerated N increased significantly under the LN condition. These findings indicate that a nutrient-imbalanced diet triggers E. vannus to retain limited macronutrients and promotes the recycling of excessive macronutrients, which may potentially form positive and negative feedback to ambient N and P limitations, respectively. [ABSTRACT FROM AUTHOR]

Ratios between viruses, heterotrophic prokaryotes and chlorophyll a are key indicators of microbial food structure and both virus–prokaryote and prokaryote–chlorophyll ratios have been proposed to decrease with system productivity. However, the mechanisms underlying these responses are still insufficiently resolved and their consistency across aquatic ecosystem types requires critical evaluation. We assessed microbial community ratios in highly productive African soda-lakes and used our data from naturally hypereutrophic systems which are largely underrepresented in literature, to complement earlier across-system meta-analyses. In contrast to marine and freshwater systems, prokaryote–chlorophyll ratios in African soda-lakes did not decrease along productivity gradients. High-resolution time series from two soda-lakes indicated that this lack of response could be driven by a weakened top–down control of heterotrophic prokaryotes. Our analysis of virus–prokaryote relationships, revealed a reduction of virus–prokaryote ratios by high suspended particle concentrations in soda-lakes. This effect, likely driven by the adsorption of free-living viruses, was also found in three out of four additionally analysed marine datasets. However, the decrease of virus–prokaryote ratios previously reported in highly productive marine systems, was neither detectable in soda-lakes nor freshwaters. Hence, our study demonstrates that system-specific analyses can reveal the diversity of mechanisms that structure microbial food-webs and shape their response to productivity increases. [ABSTRACT FROM AUTHOR]

A seagrass meadow is one of the most important ecosystems around the world, both economically and ecologically. An important feature of this ecosystem is the presence of large coastal seagrass beds, which dominate the primary production and contribute to the secondary productivity of the ecosystem. The microbial loop (consuming bacterial biomass by grazers and using seagrass-derived detritus by bacteria) may be an important mechanism for transferring seagrass-derived organic matter to aquatic food chains. The goal of this study is to gain a better understanding of how bacterial growth and mortality (grazing and viral lysis rates) differ in unvegetated meadow habitats and seagrass habitats. According to this study, DOC levels were higher in seagrass habitats (1685 g L−1) than in unvegetated water surroundings. The instantaneous growth rate of bacteria in seagrass habitats was 2.05 d−1, higher than that of unvegetated water. In a seagrass environment during the summer, we have found that viral lysis and grazing both result in similar mortality rates of bacteria during the summer season. It has been found, however, that bacterial production is controlled by the availability of resources (bottom-up control) in adjacent unvegetated waters, and is thus cycled internally within the bacteria–virus–DOC loop within those waters. [ABSTRACT FROM AUTHOR]

Eastern Boundary Systems support major fisheries whose early life stages depend on upwelling production. Upwelling can be highly variable at the regional scale, with substantial repercussions for new productivity and microbial loop activity. Studies that integrate the classic trophic web based on new production with the microbial loop are rare due to the range in body forms and sizes of the taxa. Underwater imaging can overcome this limitation, and with machine learning, enables fine resolution studies spanning large spatial scales. We used the In-situ Ichthyoplankton Imaging System (ISIIS) to investigate the drivers of plankton community structure in the northern California Current, sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA, respectively. The non-invasive imaging of particles and plankton over 1644km in the winters and summers of 2018 and 2019 yielded 1.194 billion classified plankton images. Combining nutrient analysis, flow cytometry, and 16S rRNA gene sequencing of the microbial community with mesoplankton underwater imaging enabled us to study taxa from 0.2µm to 15cm, including prokaryotes, copepods, ichthyoplankton, and gelatinous forms. To assess community structure, >2000 single-taxon distribution profiles were analyzed using high resolution spatial correlations. Co-occurrences on the NH line were consistently significantly higher off-shelf while those at TR were highest on-shelf. Random Forests models identified the concentrations of microbial loop associated taxa such as protists, Oithona copepods, and appendicularians as important drivers of co-occurrences at NH line, while at TR, cumulative upwelling and chlorophyll a were of the highest importance. Our results indicate that the microbial loop is driving plankton community structure in intermittent upwelling systems such as the NH line and supports temporal stability, and further, that taxa such as protists, Oithona copepods, and appendicularians connect a diverse and functionally redundant microbial community to stable plankton community structure. Where upwelling is more continuous such as at TR, primary production may dominate patterns of community structure, obscuring the underlying role of the microbial loop. Future changes in upwelling strength are likely to disproportionately affect plankton community structure in continuous upwelling regions, while high microbial loop activity enhances community structure resilience.

Viruses impact host cells and have indirect effects on ecosystem processes. Plankton such as ciliates can reduce the abundance of virions in water, but whether virus consumption translates into demographic consequences for the grazers is unknown. Here, we show that small protists not only can consume viruses they also can grow and divide given only viruses to eat. Moreover, the ciliate Halteria sp. foraging on chloroviruses displays dynamics and interaction parameters that are similar to other microbial trophic interactions. These results suggest that the effect of viruses on ecosystems extends beyond (and in contrast to) the viral shunt by redirecting energy up food chains. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The impacts and toxicological mechanisms of microplastics (MPs) or heavy metals on aquatic ecosystems have been the subject of extensive research and initial understanding. However, the combined toxicity of co-pollutants on organisms and cumulative toxic effects along the food chain are still underexplored. In this study, the ciliate protozoan Paramecium caudatum and zebrafish Danio rerio were used to represent the microbial loop and the higher trophic level, respectively, to illustrate the progressive exposure of MPs and cadmium (Cd2+). The findings indicate that MPs (ca. 1 ×105 items/L) containing with Cd2+ (below 0.1 µg/L) could permeate the bodies of zebrafish through trophic levels after primary ingestion by ciliates. This could cause adverse effects on zebrafish, including alterations in bioindicators (total sugar, triglycerides, lactate, and glycogen) associated with metabolism, delayed hepatic development, disruption of intestinal microbiota, DNA damage, inflammatory responses, and abnormal cellular apoptosis. In addition, the potential risks associated with the transfer of composite pollutants through the microbial loop into traditional food chain were examined, offering novel insights on the evaluation of the ecological risks associated with MPs. As observed, understanding the bioaccumulation and toxic effects of combined pollutants in zebrafish holds crucial implications for food safety and human health. [Display omitted] • MPs could transport Cd2+ into zebrafish via ciliate of the microbial loop. • Transfer of MPs+Cd2+ induced nutrient alterations within zebrafish. • MPs+Cd2+ disrupt the intestinal microbiota and lead to immune response. • The induction of apoptosis by MPs+Cd2+ is the key factor of toxicity in zebrafish. [ABSTRACT FROM AUTHOR]

A seagrass meadow is one of the most important ecosystems around the world, both economically and ecologically. An important feature of this ecosystem is the presence of large coastal seagrass beds, which dominate the primary production and contribute to the secondary productivity of the ecosystem. The microbial loop (consuming bacterial biomass by grazers and using seagrass-derived detritus by bacteria) may be an important mechanism for transferring seagrass-derived organic matter to aquatic food chains. The goal of this study is to gain a better understanding of how bacterial growth and mortality (grazing and viral lysis rates) differ in unvegetated meadow habitats and seagrass habitats. According to this study, DOC levels were higher in seagrass habitats (1685 g L−1) than in unvegetated water surroundings. The instantaneous growth rate of bacteria in seagrass habitats was 2.05 d−1, higher than that of unvegetated water. In a seagrass environment during the summer, we have found that viral lysis and grazing both result in similar mortality rates of bacteria during the summer season. It has been found, however, that bacterial production is controlled by the availability of resources (bottom-up control) in adjacent unvegetated waters, and is thus cycled internally within the bacteria–virus–DOC loop within those waters.

The increase in the frequency of peatland fires is due to both global climate change and deliberate human activity. The primary aim of the study was to investigate the structure of microbial communities and nematodes before and after a peat bog fire, as well as to analyse the relationships between food web components. Hydrological and physicochemical parameters were analysed during the period before the fire (2018 and 2019) and after the fire (2020 and 2021—2, 4, 8, and 12 months after the fire). The fire clearly modified the physicochemical properties of the peat bog, increasing the temperature, pH, conductivity, and concentrations of biogenic compounds and organic matter. It also caused a pronounced deterioration in oxygen conditions. The fire clearly modified the qualitative and quantitative structure and functioning of microbial food webs. This was reflected in a decrease in the species number and abundance of testate amoebae, with various groups of microbes showing pronounced fluctuations during the study period. The functioning of food webs in peatlands after fires is still very little understood, although an understanding of the functioning of these habitats, which increasingly undergo this type of catastrophe due to global climate change, is crucial. [ABSTRACT FROM AUTHOR]

Extensive oceanographic data sets were combined with microbiological parameters to elucidate the tight coupling between glacial meltwater and heterotrophic bacterial production (BP) on the Getz Ice Shelf (GtzIS) in the Amundsen Sea. BP in the eastern GtzIS (EG; 85.8 pM Leu. h−1), where basal glacier meltwater upwells, was significantly higher than BP measured in the western GtzIS (WG; 50.6 pM Leu. h−1) and the Amundsen Sea Polynya (ASP; 27.8 pM Leu. h−1). BP in the EG accounted for 49% of primary production, which was greater than that of the WG (10%) and ASP (9.2%). Enhanced BP in the eastern GtzIS was not coupled with phytoplankton biomass, but correlated significantly with the freshwater fraction containing meltwater‐derived dissolved organic carbon (MW‐DOC). These results suggest that warming‐induced glacier melting weakens carbon sequestration efficiency in Antarctic coastal waters by stimulating heterotrophic metabolism that converts MW‐DOC to CO2. Plain Language Summary: The Getz Ice Shelf (GtzIS) in the Amundsen Sea, the third‐largest ice shelf (34,018 km2) on the West Antarctic Ice Sheet, is regarded as a hot spot for producing large amount of glacier meltwater (144.9 ± 14 Gt yr−1). In general, the amount of dissolved organic carbon (DOC) from terrestrial sources is negligible in Antarctic waters, making DOC supplied by phytoplankton a major carbon source for heterotrophic bacteria growth. Although Antarctica's glacial ice shelves are presumably a large reservoir of organic carbon (ca. 5.5 Pg C), little is known about the effect of glacial melting on the supply of DOC available to heterotrophic bacteria. On the eastern GtzIS, where glacial meltwater upwells to the surface water column, heterotrophic bacteria production has no significant positive relationship with phytoplankton biomass, but is positively correlated with freshwater fraction. This suggests that DOC in glacial meltwater, rather than phytoplankton, provides DOC to support enhanced bacteria production. Our results imply that global warming–related increases in glacial meltwater may stimulate heterotrophic bacterial metabolism that respires DOC to CO2, thereby reducing carbon sequestration efficiency in Antarctic coastal waters. Key Points: Unlike the sea‐ice melting system, enhanced bacterial production (BP) in the eastern Getz Ice Shelf (GtzIS) was uncoupled with phytoplankton biomassDissolved organic carbon in glacier meltwater likely stimulates BP on the eastern GtzISWarming‐induced glacial melting may weaken carbon sequestration in the Antarctic Ocean by stimulating heterotrophic bacterial metabolism [ABSTRACT FROM AUTHOR]

Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events. [ABSTRACT FROM AUTHOR]

The Wadden Sea is the world’s largest intertidal ecosystem and provides vital food resources for a large number of migratory bird and fish species during seasonal stopovers. Previous work using bulk stable isotope analysis of carbon found that microphytobenthos (MPB) was the dominant resource fueling the food web with particulate organic matter making up the remainder. However, this work was unable to account for the trophic structure of the food web or the considerable increase in δ15N values of bulk tissue throughout the benthic food web occurring in the Eastern regions of the Dutch Wadden Sea. Here, we combine compound-specific and bulk analytical stable isotope techniques to further resolve the trophic structure and resource use throughout the benthic food web in the Wadden Sea. Analysis of δ15N for trophic and source amino acids allowed for better identification of trophic relationships due to the integration of underlying variation in the nitrogen resources supporting the food web. Baseline-integrated trophic position estimates using glutamic acid (Glu) and phenylalanine (Phe) allow for disentanglement of baseline variations in underlying δ15N sources supporting the ecosystem and trophic shifts resulting from changes in ecological relationships. Through this application, we further confirmed the dominant ecosystem support by MPB-derived resources, although to a lesser extent than previously estimated. In addition to phytoplankton-derived particulate, organic matter and MPB supported from nutrients from the overlying water column there appears to be an additional resource supporting the benthic community. From the stable isotope mixing models, a subset of species appears to focus on MPB supported off recycled (porewater) N and/or detrital organic matter mainly driven by increased phenylalanine δ15N values. This additional resource within MPB may play a role in subsidizing the exceptional benthic productivity observed within the Wadden Sea ecosystem and reflect division in MPB support along green (herbivory) and brown (recycled/detrital) food web pathways.

For the first time in the Mekong delta (Vietnam), the abundance and biomass of the main components of the planktonic microbial food web, and namely: bacteria, picophytoplankton, and heterotrophic and phototrophic flagellates were determined; the features of their spatial distribution and the species diversity of heterotrophic flagellates were studied. In this productive polluted tropical river ecosystem, heterotrophic bacteria were large in size and their biomass reached high values characteristic of hypertrophic waters. They made the main contribution (73.8%, on average) to the formation of the total biomass of the planktonic microbial community. The contribution of picophytoplankton and heterotrophic and phototrophic flagellates was 20.5, 3.9, and 1.9%, respectively. Twenty-nine species and forms of heterotrophic flagellates belonging to eight large taxa and a group of uncertain taxonomic position were identified. [ABSTRACT FROM AUTHOR]

Through the fixation of large quantities of dissolved inorganic carbon (DIC), macroalgae facilitate the energetic foundation of highly productive coastal ecosystems. While the processes controlling photosynthesis and carbon fixation by macroalgae are well known, the fate of organic matter fixed by macroalgae is less well understood. This study quantified release rates of DOC by three ecologically significant Baltic macroalgae species: the perennial habitat forming Fucus vesiculosus and Furcellaria lumbricalis, and the seasonal fast-growing Ulva intestinalis, under both light and dark conditions. The released products were assessed using bacterial incubations whereby radiolabeled leucine was used to evaluate the uptake and lability of these products by marine heterotrophic bacteria. DOC was found to be released by both F. vesiculosus and U. intestinalis at rates of 0.27 mg C·h−1 under light and 0.13 mg C·h−1 per unit of dry mass under dark treatments, respectively, whereas F. lumbricalis DOC release was observed to be negligible under both light and dark. Our findings further validate previous hypotheses that factors such as photosynthetic activity are a primary driver behind DOC release and that DOC release is not an entirely passive process. Additionally, we reaffirm the need to relate a given species life characteristics and habitat in order to understand why DOC products are released. The consumption of macroalgae-derived DOC by heterotrophic bacteria reveals that released DOC is variable in its lability. After a period of 12 h and under maximum photosynthetic conditions, the release of DOC by F. vesiculosus and U. intestinalis achieved a peak rate of 219 µg C·L−1·day−1 and 214 µg C·L−1·day−1 for each gram of dry weight material, respectively, directly into the microbial loop via heterotrophic bacterial consumption. In contrast, F. lumbricalis’ low rate of DOC release and the subsequent low bacterial consumption indicate that habitats dominated by this species have a reduced importance in the transfer energy via the microbial loop. These findings have implications for how we view carbon transfer within coastal food webs and highlight how changes in species composition and coverage may dramatically affect coastal ecosystem productivity through the microbial loop.

ABSTRACT Lake Cadagno, a permanently stratified high-alpine lake with a persistent microbial bloom in its chemocline, has long been considered a model for the low-oxygen, high-sulfide Proterozoic ocean. Although the lake has been studied for over 25 years, the absence of concerted study of the bacteria, phytoplankton, and viruses, together with primary and secondary production, has hindered a comprehensive understanding of its microbial food web. Here, the identities, abundances, and productivity of microbes were evaluated in the context of Lake Cadagno biogeochemistry. Photosynthetic pigments together with 16S rRNA gene phylogenies suggest the prominence of eukaryotic phytoplankton chloroplasts, primarily chlorophytes. Chloroplasts closely related to those of high-alpine-adapted Ankyra judayi persisted with oxygen in the mixolimnion, where photosynthetic efficiency was high, while chloroplasts of Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. The anoxygenic phototrophic sulfur bacterium Chromatium dominated the chemocline along with Lentimicrobium, a genus of known fermenters. Secondary production peaked in the chemocline, which suggested that anoxygenic primary producers depended on heterotrophic nutrient remineralization. The virus-to-microbe ratio peaked with phytoplankton abundances in the mixolimnion and were at a minimum where Chromatium abundance was highest, trends that suggest that viruses may play a role in the modulation of primary production. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical spatial dynamics, we provide a comprehensive synthesis of the Lake Cadagno microbial loop. This study offers a new ecological perspective on how biological and geochemical connections may have occurred in the chemocline of the Proterozoic ocean, where eukaryotic microbial life is thought to have evolved. IMPORTANCE As a window into the past, this study offers insights into the potential role that microbial guilds may have played in the production and recycling of organic matter in ancient Proterozoic ocean chemoclines. The new observations described here suggest that chloroplasts of eukaryotic algae were persistent in the low-oxygen upper chemocline along with the purple and green sulfur bacteria known to dominate the lower half of the chemocline. This study provides the first insights into Lake Cadagno’s viral ecology. High viral abundances suggested that viruses may be essential components of the chemocline, where their activity may result in the release and recycling of organic matter. The integration of diverse geochemical and biological data types provides a framework that lays the foundation to quantitatively resolve the processes performed by the discrete populations that comprise the microbial loop in this early anoxic ocean analogue.

We investigated changes in heterotrophic bacterial metabolic activities and associated carbon cycles in response to a change in dominant phytoplankton communities during two contrasting environmental conditions in austral summer in the Amundsen Sea polynya (ASP), Antarctica: the closed polynya condition in 2014 (ANA04) and the open polynya condition in 2016 (ANA06). In ANA04, Phaeocystis antarctica predominated phytoplankton biomass, comprising 78% of total phytoplankton carbon biomass, whereas diatoms and Dictyocha speculum accounted for 45% and 48% of total phytoplankton carbon biomass, respectively, in ANA06. Bacterial production (BP) showed a significant positive correlation with only chlorophyll-a (Chl-a, rho = 0.66, p < 0.001) in P. antarctica-dominated ANA04, whereas there were significant positive relationships of BP with various organic carbon pools, such as chromophoric dissolved organic matter (CDOM, rho = 0.84, p < 0.001), Chl-a (rho = 0.59, p < 0.001), and dissolved organic carbon (DOC, rho = 0.51, p = 0.001), in ANA06 when diatoms and D. speculum co-dominated. These results indicate that BP depended more on DOC directly released from P. antarctica in ANA04, but was supported by DOC derived from various food web processes in the diatom-dominated system in ANA06. The BP to primary production (BP : PP) ratio was three-fold higher in P. antarctica-dominated ANA04 (BP: PP = 0.09), than in diatom- and D. speculum-co-dominated ANA06 (BP : PP = 0.03). These results suggested that the microbial loop is more significant in Phaeocystis-dominated conditions than in diatom-dominated conditions. In addition, the decreases in BP : PP ratio and bacterial respiration with increasing diatom proportion in the surface mixed layer indicated that the change from P. antarctica to diatom predominance enhanced biological carbon pump function by increasing particulate organic carbon export efficiency. Consequently, our results suggest that bacterial metabolic response to shifts in phytoplankton communities could ultimately affect larger-scale ecological and biogeochemical processes in the water column of the ASP.

Groundwater ecosystems are typically poor in organic carbon and productivity sustaining a low standing stock of microbial biomass. In consequence, microbial food webs in oligotrophic groundwater are hypothesized to be bottom-up controlled. To date, quantitative information on groundwater microbial communities, food web interactions, and carbon flow is relatively lacking in comparison to that of surface waters. Studying a shallow, porous alpine aquifer we collected data on the numbers of prokaryotes, virus-like particles and heterotrophic nanoflagellates (HNFs), the concentration of dissolved (DOC) and assimilable organic carbon (AOC), bacterial carbon production (BCP), and physical-chemical conditions for a 1 year hydrological cycle. The potential effects of protozoan grazing and viral lysis onto the prokaryotic biomass was tested. Flow of organic carbon through the microbial food web was estimated based on data from the literature. The abundance of prokaryotes in groundwater was low with 6.1 ± 6.9 × 104 cells mL–1, seasonally influenced by the hydrological dynamics, with higher densities coinciding with a lower groundwater table. Overall, the variability in cell numbers was moderate, and so it was for HNFs (179 ± 103 HNFs mL–1) and virus-like particles (9.6 ± 5.7 × 105 VLPs mL–1). The virus to prokaryotes and prokaryote to HNF ratios ranged between 2–230 and 33–2,084, respectively. We found no evidence for a viral control of prokaryotic biomass, and the biomass of HNFs being bottom-up controlled. First estimations point at carbon use efficiencies of 0.2–4.2% with prokaryotic production, and carbon consumed and recycled by HNFs and phages to be of minor importance. This first groundwater microbial food web analysis strongly hints at a bottom-up control on productivity and standing stock in oligotrophic groundwater ecosystems. However, direct measurement of protozoan grazing and phage mediated lysis rates of prokaryotic cells are urgently needed to deepen our mechanistic understanding. The effect of microbial diversity on the population dynamics still needs to be addressed.

Studies over the last two decades have shown that submicron particulates (SMPs) can be transferred from the seawater into sea spray aerosol (SSA), potentially impacting SSA cloud seeding ability. This work reports the first concurrent bulk and sea surface microlayer (SSML) SMP (0.4–1.0 μm) measurements, made during two mesocosm phytoplankton blooms in a region devoid of active wave breaking and bubble formation, providing insight into how biological and physicochemical processes influence seawater SMP distributions. Modal analyses of the SMP size distributions revealed contributions from multiple, biologically related particulate populations that were controlled by the microbial loop. With negligible bubble scavenging occurring, SSML enrichment of SMPs remained low throughout both experiments, suggesting scavenging is vital for SMP enrichment in the SSML. Our findings are discussed in the context of SMP transfer into SSA and its potential importance for SSA cloud seeding ability. Plain Language Summary: Research has shown that particulates can be transferred from the ocean into sea spray aerosol (SSA) when bubbles burst at the ocean surface. This transfer is important because incorporation of seawater particulates into SSA can impact its ability to seed water and ice clouds. During the Sea Spray Chemistry and Particulate Evolution (SeaSCAPE) study, submicron particulates (SMPs, 0.4–1.0 μm) were measured daily in the sea surface microlayer (SSML), the topmost 1–1,000 μm of the ocean surface, and the underlying bulk seawater over the course of two phytoplankton growth experiments. The objective of this study was to assess the influence of biological activity on SMP concentrations and distributions in the seawater. Our results indicate that biological growth led to increased SMP production, and the size distribution of SMPs produced was dependent on the phase of the bloom growth. Additionally, almost no SSML enrichment of SMPs occurred without active wave breaking and bubble formation, highlighting the significance of biological activity and bubble scavenging/bursting for particulate transfer into SSA. These findings are discussed in the context of potential SMP impacts on SSA cloud forming ability. Key Points: The concentration of 0.4–1.0 μm seawater particulates is higher during a phytoplankton bloomThe biologically induced increase in seawater submicron particulates is size dependent and influenced by the phase of the bloomParticulate enrichment in the sea surface microlayer is low in the absence of wave breaking and bubble scavenging [ABSTRACT FROM AUTHOR]

The annual global loss of organic carbon from terrestrial ecosystems into rivers is similar to the organic carbon stored in soils each year. Dissolved organic matter (DOM) flows through the food web to macroinvertebrates, but little is known about the effect of DOM increase on stream food webs and how much macroinvertebrates may contribute to the regulation of carbon fluxes in rivers. Using a before and after control impact (BACI) experimental design, we increased by 12% (+ 0.52 mg C L−1) the concentration of DOM in a stream for three weeks by adding sucrose, with a distinctive δ13C signature, to simulate a pulse of natural DOM supply from soils. We partitioned the diet of macroinvertebrates from carbon sources according to the green pathway (autotrophs) and detrital pathways (bacteria and terrestrial organic matter). Our flow food web approach based on C fluxes, with bacteria as a key node, showed the dominant contribution of the detrital pathways for macroinvertebrates in the reference stream. DOM addition induced changes in the diets of individual taxa, but did not have any strong effects on the relative overall contribution of the detrital pathways versus the green pathway. Autotrophic uptake of CO2 respired by bacteria was much larger than bacterial C flux to invertebrates (that is, the classic microbial loop) and allowed a significant fraction of natural allochthonous organic carbon to make its way to macroinvertebrates via autotrophs fixing CO2 respired by bacteria. Overall macroinvertebrates did not regulate directly to any great extent the flux of stream DOM towards downstream ecosystems. [ABSTRACT FROM AUTHOR]

The role of mixoplanktonic algae is increasingly recognised as an important link between primary production and microbial loop processes, particularly in dystrophic systems where staining can both limit light and nutrient availability and increase bacterial productivity. We hypothesised that these three factors would affect the relative abundance of mixotrophs (RAmixotrophs), with increased light and nutrient availability decreasing RAmixotrophs and increased bacterial availability increasing RAmixotrophs. We employed a fully factorial design within near-shore mesocosms in a highly stained lake, with light intensity, bacterial abundance, and phosphorus concentration as treatment variables. Over the initial 3 days of the experiment, when changes were greatest, we found no significant three-way interaction effect among light, phosphorus and nutrients on the RAmixotrophs. We did find significant two-way interactions between phosphorus and light, and phosphorus and bacteria. RAmixotrophs was decreased by the addition of phosphorus whether light was added or not, but light only significantly deceased RAmixotrophs when phosphorus was not added. Phosphorus concentration was also found to decrease RAmixotrophs whether bacterial food was supplemented or not, but bacteria increased RAmixotrophs only in mesocosms without phosphorus additions. Collectively, our results indicated that phosphorus concentrations may be the primary driver of mixoplanktonic phytoplankton dynamics in dystrophic systems. Mixoplanktonic algae may link important aspects of aquatic food webs, because they both provide energy to higher trophic levels as photosynthetic producers, and also consume bacteria involved in microbial recycling processes. We used in situ mesocosm experiments to assess the role of phosphorus, light and bacterial availability on the relative abundance and biomass of mixotrophic taxa in a highly stained lake. Our results indicated that phosphorus concentrations may be the primary driver of mixotrophic dynamics in such systems. [ABSTRACT FROM AUTHOR]

Blooms of marine phytoplankton fix complex pools of dissolved organic matter (DOM) that are thought to be partitioned among hundreds of heterotrophic microbes at the base of the food web. While the relationship between microbial consumers and phytoplankton DOM is a key component of marine carbon cycling, microbial loop metabolism is largely understood from model organisms and substrates. Here, we took an untargeted approach to measure and analyze partitioning of four distinct phytoplankton-derived DOM pools among heterotrophic populations in a natural microbial community using a combination of ecogenomics, stable isotope probing (SIP), and proteomics. Each 13C-labeled exudate or lysate from a diatom or a picocyanobacterium was preferentially assimilated by different heterotrophic taxa with specialized metabolic and physiological adaptations. Bacteroidetes populations, with their unique high-molecular-weight transporters, were superior competitors for DOM derived from diatom cell lysis, rapidly increasing growth rates and ribosomal protein expression to produce new relatively high C:N biomass. Proteobacteria responses varied, with relatively low levels of assimilation by Gammaproteobacteria populations, while copiotrophic Alphaproteobacteria such as the Roseobacter clade, with their diverse array of ABC- and TRAP-type transporters to scavenge monomers and nitrogen-rich metabolites, accounted for nearly all cyanobacteria exudate assimilation and produced new relatively low C:N biomass. Carbon assimilation rates calculated from SIP data show that exudate and lysate from two common marine phytoplankton are being used by taxonomically distinct sets of heterotrophic populations with unique metabolic adaptations, providing a deeper mechanistic understanding of consumer succession and carbon use during marine bloom events. [ABSTRACT FROM AUTHOR]

The increase in the frequency of peatland fires is due to both global climate change and deliberate human activity. The primary aim of the study was to investigate the structure of microbial communities and nematodes before and after a peat bog fire, as well as to analyse the relationships between food web components. Hydrological and physicochemical parameters were analysed during the period before the fire (2018 and 2019) and after the fire (2020 and 2021—2, 4, 8, and 12 months after the fire). The fire clearly modified the physicochemical properties of the peat bog, increasing the temperature, pH, conductivity, and concentrations of biogenic compounds and organic matter. It also caused a pronounced deterioration in oxygen conditions. The fire clearly modified the qualitative and quantitative structure and functioning of microbial food webs. This was reflected in a decrease in the species number and abundance of testate amoebae, with various groups of microbes showing pronounced fluctuations during the study period. The functioning of food webs in peatlands after fires is still very little understood, although an understanding of the functioning of these habitats, which increasingly undergo this type of catastrophe due to global climate change, is crucial.

Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.

Amino acids (AA) and carbohydrates (CHO) are important components of the marine organic carbon cycle. Produced mainly by phytoplankton as part of the particulate organic carbon (POC) fraction, these compounds can be released into the outer medium where they become part of the dissolved organic carbon (DOC) pool and are rapidly taken up by heterotrophs (e.g., bacteria). We investigated the quantity and quality of POC and DOC, AA and CHO composition in both pools in three different water masses in the Fram Strait (Arctic Ocean) in summer 2017. Polar Waters and Atlantic Waters showed similar concentrations of particulate and dissolved AA and CHO, despite Polar Waters showing the highest DOC concentrations. In Mixed Waters, where the two water masses mix with each other and with melting sea ice, the concentrations of particulate and dissolved AA and CHO were highest. AA and CHO composition differed substantially between the particulate and dissolved fractions. The particulate fraction (>0.7 μm) was enriched in essential AA and the CHO galactose, xylose/mannose, and muramic acid. In the dissolved fraction non-essential AA, several neutral CHO, and acidic and amino CHO were enriched. We further investigated different size fractions of the particulate matter using a separate size fractionation approach (0.2–0.7 μm, 0.7–10 μm and >10 μm). The chemical composition of the 0.2–0.7 μm size-fraction had a higher contribution of non-essential AA and acidic and amino sugars, setting them apart from the 0.7–10 μm and >10 μm fractions, which showed the same composition. We suggest that the relative differences observed between different size fractions and DOC with regards to AA and CHO composition can be used to evaluate the state of organic matter processing and evaluate the contribution of autotrophic phytoplankton or more heterotrophic biomass. In the future, changing conditions in the Central Arctic Ocean (Atlantification, warming, decreasing ice concentrations) may increase primary production and consequently degradation. The AA and CHO signatures left behind after production and/or degradation processes occurred, could be used as tracers after the fact to infer changes in microbial loop processes and food web interactions.

Despite worldwide efforts to restore degraded mangrove forests in the past decades, defining and tracking restoration success remains a major challenge. In this study, we used a multi-isotope approach to trace ecosystem responses to forest clearing and replanting in a tropical mangrove forest reserve at Matang, Malaysia. We measured δ2H or δD deuterium, δ13C and δ15N (HCN isotopes) in common macroinvertebrate consumers (barnacles, prawns, gastropods, and crabs) across a 70-year chronosequence of mangroves. Functional food web recovery was indicated by a decrease in δ13C and δ15N and increase in δD for gastropod and crab consumers in older forests. Timing of this shift in food web isotopic signals took place between 5 and 15 years post-clearing of mangroves. These changes in food web function paralleled changes in crab community composition, but also reflected changes in physicochemical conditions within the forest, such as increased tree cover and shading, which resulted in a shift of the food web base from microalgal-derived to mangrove-derived organic matter. Prawns and barnacles from tidal waters adjacent to the mangrove forests were estimated to derive 17 to 25% of their nutrition from mangroves, primarily from a microbial loop that was processing localised dissolved and particulate organic matter exported from mangrove marshes. The top-down mixing model approach using combined HCN isotope measurements clearly separated inputs from mangroves versus microalgae for the first time in estuarine food web studies, and tracked ecological mangrove ecosystem recovery. This combination of tracers is recommended for future studies of mangrove conservation and restoration. [ABSTRACT FROM AUTHOR]

The availability of phosphorus limits primary production in large regions of the oceans, and marine microbes use a variety of strategies to overcome this limitation. One strategy is the production of alkaline phosphatase (APase), which allows hydrolysis of larger dissolved organic phosphorus (DOP) compounds in the periplasm or at the cell surface for transport of orthophosphate into the cell. Cell lysis, driven by grazing and viral infection, releases phosphorus-containing cell components, along with active enzymes that could persist after lysis. The importance of this continued enzymatic activity for orthophosphate regeneration is unknown. We used three model bacteria – Escherichia coli K-12 MG1655, Synechococcus sp. WH7803, and Prochlorococcus sp. MED4 – to assess the impact of continued APase activity after cell lysis, via lysozyme treatment, on orthophosphate regeneration. Direct release of orthophosphate scaled with cell size and was reduced under phosphate-starved conditions where APase activity continued for days after lysis. All lysate incubations showed post-lysis orthophosphate generation suggesting phosphatases other than APase maintain activity. Rates of DOP hydrolysis and orthophosphate remineralization varied post-lysis among strains. Escherichia coli K-12 MG1655 rates of remineralization were 0.6 and 1.2 amol cell–1hr–1 under deplete and replete conditions; Synechococcus WH7803 lysates ranged from 0.04 up to 0.3 amol cell–1hr–1 during phosphorus deplete and replete conditions, respectively, while in Prochlorococcus MED4 lysates, rates were stable at 0.001 amol cell–1hr–1 in both conditions. The range of rates of hydrolysis and regeneration underscores the taxonomic and biochemical variability in the process of nutrient regeneration and further highlights the complexity of quantitatively resolving the major fluxes within the microbial loop.

Sea surface temperature fronts in the Northeastern Arabian Sea (NEAS) facilitate nutrient enhancement in the surface layers, resulting in high primary production. Such high production areas contribute to the accumulation of fresh organic matter rich in carbohydrates, thereby supporting higher heterotrophic metabolism. Transparent exopolysaccharides (TEP) are one of the carbohydrate polymers released as exudates during primary production or decaying process and their breakdown is mediated by a set of ectoenzymes that includes glucosidases and chitinases. Observations were carried out in different aged NEAS fronts to elucidate the influence of frontal age on the abundance of TEP, bacterial nucleic acid content (high nucleic acid content, HNA and low nucleic acid content, LNA), and ectoenzymatic activities. The fronts were classified as younger and older, depending on their first appearance and sampling day. A clear transition from HNA to LNA bacteria, variations in TEP and related ectoenzymatic activities in the fronts was influenced by the frontal age. The younger fronts were dominated by HNA bacteria, α-glucosidase, and chitinase activity. In contrast, an acceleration in β-glucosidase activity, bacterial production, which was related to TEP concentration, was evident in the older fronts. Further, a significant increase in protist numbers in older fronts was related to effective grazing on HNA bacteria and TEP. The active turnover of TEP by bacteria and protists facilitates strong microbial loop in NEAS frontal regions. Elucidating contribution of such changes in the frontal areas will provide a basis for a better understanding of microbial carbon cycling. [ABSTRACT FROM AUTHOR]

Free-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytrid Batrachochytrium dendrobatidis (Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 μm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliate Tetrahymena pyriformis, which likely co-occurs with Bd, grew at near its maximum rate (r = 1.7 d–1). A functional response (ingestion vs. prey abundance) for T. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (Imax) of 1.63 × 103 zoospores d–1, with a half saturation constant (k) of 5.75 × 103 zoospores ml–1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could control Bd and potentially prevent chytridiomycosis (defined as 104 sporangia host–1). However, simulated inferior micrograzers (0.7 × Imax and 1.5 × k) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modeling disease dynamics for Bd and other zoosporic fungi.

Disturbances in the functioning of peatlands, due to growing human impact, climate change and the appearance of alien invasive species, are becoming increasingly common. Analysis of trophic relationships in the predator (invasive alien species)–prey system is extremely important for understanding the functioning of peat pools—small water bodies formed in peatlands by peat extraction. These issues are, as yet, very little understood. The aim of this study was to examine the impact of Ameiurus nebulosus, an alien and invasive fish species dominant in these pools, on the microbial communities and small metazoa (phycoflora, bacteria, heterotrophic flagellates, ciliates, and crustaceans) in peat pools. The laboratory experiment included two groups of treatments simulating natural conditions: treatments without fish and treatments with brown bullhead. The water temperature was manipulated as well. The presence of brown bullhead in combination with climate changes was shown to cause a change in the structure of microbial communities. This is reflected in a decrease in the abundance of planktonic crustaceans and an increase in ciliates. The overlapping effects of alien species and gradual climate warming may intensify the eutrophication of peatland ecosystems and the increase in the proportion of cyanobacteria, thereby affecting the carbon cycle in these ecosystems.

Marine fungi are an important component of pelagic planktonic communities. However, it is not yet clear how individual fungal taxa are integrated in marine processes of the microbial loop and food webs. Most likely, biotic interactions play a major role in shaping the fungal community structure. Thus, the aim of our work was to identify possible biotic interactions of mycoplankton with phytoplankton and zooplankton groups and among fungi, and to investigate whether there is coherence between interactions and the dynamics, abundance and temporal occurrence of individual fungal OTUs. Marine surface water was sampled weekly over the course of 1 year, in the vicinity of the island of Helgoland in the German Bight (North Sea). The mycoplankton community was analyzed using 18S rRNA gene tag-sequencing and the identified dynamics were correlated to environmental data including phytoplankton, zooplankton, and abiotic factors. Finally, co-occurrence patterns of fungal taxa were detected with network analyses based on weighted topological overlaps (wTO). Of all abundant and persistent OTUs, 77% showed no biotic relations suggesting a saprotrophic lifestyle. Of all other fungal OTUs, nearly the half (44%) had at least one significant negative relationship, especially with zooplankton and other fungi, or to a lesser extent with phytoplankton. These findings suggest that mycoplankton OTUs are embedded into marine food web chains via highly complex and manifold relationships such as parasitism, predation, grazing, or allelopathy. Furthermore, about one third of all rare OTUs were part of a dense fungal co-occurrence network probably stabilizing the fungal community against environmental changes and acting as functional guilds or being involved in fungal cross-feeding. Placed in an ecological context, strong antagonistic relationships of the mycoplankton community with other components of the plankton suggest that: (i) there is a top-down control by fungi on zooplankton and phytoplankton; (ii) fungi serve as a food source for zooplankton and thereby transfer nutrients and organic material; (iii) the dynamics of fungi harmful to other plankton groups are controlled by antagonistic fungal taxa.

When considering microbial biotic interactions, viruses as well as eukaryotic grazers are known to be important components of aquatic microbial food webs. It might be the same for bacterivorous bacteria but these groups have been comparatively less studied. This is typically the case of the Bdellovibrio and like organisms (BALOs), which are obligate bacterial predators of other bacteria. Recently, the abundance and distribution of three families of this functional group were investigated in perialpine lakes, revealing their presence and quantitative importance. Here, a more in-depth analysis is provided for Lake Geneva regarding the diversity of these bacterial predators at different seasons, sites and depths. We reveal a seasonal and spatial (vertical) pattern for BALOs. They were also found to be relatively diverse (especially Bdellovibrionaceae) and assigned to both known and unknown phylogenetic clusters. At last we found that most BALOs were positively correlated to other bacterial groups, mainly Gram-negative, in particular Myxococcales (among which many are predators of other microbes). This study is the first shedding light on this potentially important bacterial killing group in a large and deep lake.

Marine fungi are an important component of pelagic planktonic communities. However, it is not yet clear how individual fungal taxa are integrated in marine processes of the microbial loop and food webs. Most likely, biotic interactions play a major role in shaping the fungal community structure. Thus, the aim of our work was to identify possible biotic interactions of mycoplankton with phytoplankton and zooplankton groups and among fungi, and to investigate whether there is coherence between interactions and the dynamics, abundance and temporal occurrence of individual fungal OTUs. Marine surface water was sampled weekly over the course of 1 year, in the vicinity of the island of Helgoland in the German Bight (North Sea). The mycoplankton community was analyzed using 18S rRNA gene tag-sequencing and the identified dynamics were correlated to environmental data including phytoplankton, zooplankton, and abiotic factors. Finally, co-occurrence patterns of fungal taxa were detected with network analyses based on weighted topological overlaps (wTO). Of all abundant and persistent OTUs, 77% showed no biotic relations suggesting a saprotrophic lifestyle. Of all other fungal OTUs, nearly the half (44%) had at least one significant negative relationship, especially with zooplankton and other fungi, or to a lesser extent with phytoplankton. These findings suggest that mycoplankton OTUs are embedded into marine food web chains via highly complex and manifold relationships such as parasitism, predation, grazing, or allelopathy. Furthermore, about one third of all rare OTUs were part of a dense fungal co-occurrence network probably stabilizing the fungal community against environmental changes and acting as functional guilds or being involved in fungal cross-feeding. Placed in an ecological context, strong antagonistic relationships of the mycoplankton community with other components of the plankton suggest that: (i) there is a top-down control by fungi on zooplankton and phytoplankton; (ii) fungi serve as a food source for zooplankton and thereby transfer nutrients and organic material; (iii) the dynamics of fungi harmful to other plankton groups are controlled by antagonistic fungal taxa. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Cyanobacterial harmful algal blooms are known all around the world. Climate change (temperature increase) and human activity (eutrophication) are factors that promote the proliferation of cyanobacteria, leading to the development of blooms and the release of toxins. Abiotic and biotic factors are responsible for the development of blooms and how long they last. Although the abiotic factors controlling blooms are well known, knowledge of biotic factors and their interactions is still lacking. This paper reviews five levels of biotic interactions, namely cyanobacteria–zooplankton, cyanobacteria–ciliates, cyanobacteria–bacteria, cyanobacteria–viruses and cyanobacteria–fungi, showing a more complex food web network than was previously thought. New findings published recently, such as the relationships between cyanobacteria and viruses or cyanobacteria and fungi, indicate that cyanobacterial blooms are not the end of the cycle of events taking place in water habitats, but rather the middle of them. As such, a new approach needs to consider mutual connections, genetic response, horizontal gene transfer and non-linear flow of carbon. Food web network interactions among micro-organisms induce or inhibit blooms. This paper reviews interactions between cyanobacteria, zooplankton and other micro-organisms, because these biotic interactions are not well recognised. The paper describes new areas of research, the results of which provide us with a better understanding of the processes of proliferation, migration and invasion of cyanobacteria. [ABSTRACT FROM AUTHOR]

When considering microbial biotic interactions, viruses as well as eukaryotic grazers are known to be important components of aquatic microbial food webs. It might be the same for bacterivorous bacteria but these groups have been comparatively less studied. This is typically the case of the Bdellovibrio and like organisms (BALOs), which are obligate bacterial predators of other bacteria. Recently, the abundance and distribution of three families of this functional group were investigated in perialpine lakes, revealing their presence and quantitative importance. Here, a more in-depth analysis is provided for Lake Geneva regarding the diversity of these bacterial predators at different seasons, sites and depths. We reveal a seasonal and spatial (vertical) pattern for BALOs. They were also found to be relatively diverse (especially Bdellovibrionaceae) and assigned to both known and unknown phylogenetic clusters. At last we found that most BALOs were positively correlated to other bacterial groups, mainly Gram-negative, in particular Myxococcales (among which many are predators of other microbes). This study is the first shedding light on this potentially important bacterial killing group in a large and deep lake. [ABSTRACT FROM AUTHOR]

Species introduction can alter the structure and dynamics of biological communities and, therefore, understanding their feeding behavior and the effects that an exotic species can cause in the food web configuration is pivotal. We aimed to experimentally investigate the effects of the potential invasive species Kellicottia bostoniensis on different components of the microbial food web and to evaluate if the food preferences of this species change under different conditions of resource availability and interspecific interactions. We tested the hypothesis that the presence of K. bostoniensis would have direct and indirect effects on the different components of the planktonic food web. We designed three different assays (E) using prey size fractionation, being E1 composed of bacteria (HB) and picophytoplankton (PPP), E2 composed of HB, PPP and autotrophic and heterotrophic flagellates and, E3 with the whole planktonic community. Each one composed of a control in the absence of K. bostoniensis and a treatment with the presence of this species. Results showed that K. bostoniensis caused direct effects on its main food items, the heterotrophic and autotrophic flagellates, whereas no evidence of indirect effects was observed on the base components of the microbial web food, such as heterotrophic bacteria and picophytoplankton. In addition, a negative effect of the exotic rotifer on ciliates was observed. Finally, we emphasize that the impact of K. bostoniensis on aquatic ecosystem may be quite harmful, since this specie can act as a sink of matter and energy to higher trophic levels. [ABSTRACT FROM AUTHOR]

Quorum sensing (QS) describes a process by which bacteria can sense the local cell density of their own species, thus enabling them to coordinate gene expression and physiological processes on a community-wide scale. Small molecules called autoinducers or QS signals, which act as intraspecies signals, mediate quorum sensing. As our knowledge of QS has progressed, so too has our understanding of the structural diversity of QS signals, along with the diversity of bacteria conducting QS and the range of ecosystems in which QS takes place. It is now also clear that QS signals are more than just intraspecies signals. QS signals mediate interactions between species of prokaryotes, and between prokaryotes and eukaryotes. In recent years, our understanding of QS signals as mediators of algae–bacteria interactions has advanced such that we are beginning to develop a mechanistic understanding of their effects. This review will summarize the recent efforts to understand how different classes of QS signals contribute to the interactions between planktonic microalgae and bacteria in our oceans, primarily N-acyl-homoserine lactones, their degradation products of tetramic acids, and 2-alkyl-4-quinolones. In particular, this review will discuss the ways in which QS signals alter microalgae growth and metabolism, namely as direct effectors of photosynthesis, regulators of the cell cycle, and as modulators of other algicidal mechanisms. Furthermore, the contribution of QS signals to nutrient acquisition is discussed, and finally, how microalgae can modulate these small molecules to dampen their effects.

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.

Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using 13C and 15N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season.

Summary: Phytoplankton communities within the photic zones of the oceans and lakes are characterised by highly complex assemblages of unicellular microalgae and associated bacteria. The interconnected evolutionary history of algae and bacteria allowed the formation of a wide spectrum of associations defined by orchestrated nutrient exchange, mutual support with growth factors, quorum sensing mediation, and episodic killing of the partners to obtain more resources. In this review, we discuss how these cross‐kingdom interactions shape plankton communities that undergo annual, seasonal switching between alternative states with balanced multispecies consortia. We illustrate how these microscopic interactions can have consequences that scale up to influence global element cycling. [ABSTRACT FROM AUTHOR]

Many protist plankton are mixotrophs, combining phototrophy and phagotrophy. Their role in freshwater and marine ecology has emerged as a major developing feature of plankton research over recent decades. To better aid discussions, we suggest these organisms are termed "mixoplankton", as "planktonic protist organisms that express, or have potential to express, phototrophy and phagotrophy". The term "phytoplankton" then describes phototrophic organisms incapable of phagotrophy. "Protozooplankton" describes phagotrophic protists that do not engage in acquired phototrophy. The complexity of the changes to the conceptual base of the plankton trophic web caused by inclusion of mixoplanktonic activities are such that we suggest that the restructured description is termed the "mixoplankton paradigm". Implications and opportunities for revision of survey and fieldwork, of laboratory experiments and of simulation modelling are considered. The main challenges are not only with taxonomic and functional identifications, and with measuring rates of potentially competing processes within single cells, but with decades of inertia built around the traditional paradigm that assumes a separation of trophic processes between different organisms. In keeping with the synergistic nature of cooperative photo- and phagotrophy in mixoplankton, a comprehensive multidisciplinary approach will be required to tackle the task ahead. [ABSTRACT FROM AUTHOR]

A mass-balance model simulating a biotic energy flow in the plankton community with the participation of microbial organisms has been designed for a lake-type ecosystem. The input abiotic parameters of the model are latitude, mean depth, water color, and total phosphorus content in water. The model was constructed on the basis of the data published for the Rybinsk Reservoir and Mongolian lakes. An analysis of the model indicated that the addition of the microbial loop to the traditional linear trophic chain resulted in a twofold decrease in the biomass and production of metazoan plankton and planktivorous fish. The value of the final ecosystem production (fish production) is suggested to be closely associated with the degree of development of the microbial loop during the growing season. [ABSTRACT FROM AUTHOR]

Light plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using 13C and 15N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season. [ABSTRACT FROM AUTHOR]