The Ecology of Heterotrophic Microflagellates

Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning

Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.

Seasonality of top-down control of bacterioplankton at two central Red Sea sites with different trophic status

The role of bottom-up (nutrient availability) and top-down (grazers and viruses mortality) controls on tropical bacterioplankton have been rarely investigated simultaneously from a seasonal perspective. We have assessed them through monthly samplings over 2 years in inshore and offshore waters of the central Red Sea differing in trophic status. Flow cytometric analysis allowed us to distinguish five groups of heterotrophic bacteria based on physiological properties (nucleic acid content, membrane integrity and active respiration), three groups of cyanobacteria (two populations of Synechococcus and Prochlorococcus), heterotrophic nanoflagellates (HNFs) and three groups of viruses based on nucleic acid content. The dynamics of bacterioplankton and their top-down controls varied with season and location, being more pronounced in inshore waters. HNFs abundances showed a strong preference for larger prey inshore (r = -0.62 to -0.59, p = 0.001-0.002). Positive relationships between viruses and heterotrophic bacterioplankton abundances were more marked inshore (r = 0.67, p < 0.001) than offshore (r = 0.44, p = 0.03). The negative correlation between HNFs and viruses abundances (r = -0.47, p = 0.02) in shallow waters indicates a persistent seasonal switch between protistan grazing and viral lysis that maintains the low bacterioplankton stocks in the central Red Sea area.

Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory

BACKGROUND

Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations.

RESULTS

The most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes. Video Abstract CONCLUSIONS: Our results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.

Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study

To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.

Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory

Diplonemids are one of the most abundant groups of heterotrophic planktonic microeukaryotes in the world ocean and, thus, are likely to play an essential role in marine ecosystems. So far, only few species have been introduced into a culture, allowing basic studies of diplonemid genetics, morphology, ultrastructure, metabolism, as well as endosymbionts. However, it remains unclear whether these heterotrophic flagellates are parasitic or free-living and what are their predominant dietary patterns and preferred food items. Here we show that cultured diplonemids, maintained in an organic-rich medium as osmotrophs, can gradually switch to bacterivory as a sole food resource, supporting positive growth of their population, even when fed with a low biovolume of bacteria. We further observed remarkable differences in species-specific feeding patterns, size-selective grazing preferences, and distinct feeding strategies. Diplonemids can discriminate between low-quality food items and inedible particles, such as latex beads, even after their ingestion, by discharging them in the form of large waste vacuoles. We also detected digestion-related endogenous autofluorescence emitted by lysosomes and the activity of a melanin-like material. We present the first evidence that these omnipresent protists possess an opportunistic lifestyle that provides a considerable advantage in the generally food resource-limited marine environments.

Free-living Heterotrophic Flagellates (Protista) from Two Hypersaline Lakes in Turkey

This study was carried out in two hypersaline lakes (Acı and Meke Lakes) in Turkey to understand the diversity and geographic distribution of free-living heterotrophic flagellates. Heterotrophic flagellates of hypersaline environments have not previously been studied in Turkey. We found seventeen morphospecies of heterotrophic flagellates with one unidentified protist. The observed species belong to Craspedida, Heterolobosea, Apusomonadida, Neobodonida, Bicosoecida and Protista incertae sedis. Of the 17 species, ten species were new records for Turkey. All of the morphospecies described here except one unidentified protist were previously reported elsewhere and appear to be cosmopolitan.

The 2020 motile active matter roadmap

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of 'active matter' in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines. The 2020 motile active matter roadmap of Journal of Physics: Condensed Matter addresses the current state of the art of the field and provides guidance for both students as well as established scientists in their efforts to advance this fascinating area.

Bioaccumulation of metals in calanoid copepods by oral intake

We demonstrated that oral intake of water by two calanoid copepods, Pseudodiaptomus annandalei and Eurytemora affinis takes place and has implications for their ecotoxicology. In the first experiment, copepods were exposed to a dyed medium, which allowed us to visually examine the possibility of water uptake by the copepod. We observed that both copepod species were taking in water orally and evacuated dye at different speeds. This exposure left concentrated dye in the guts of the copepods indicating adsorption into the gut epithelium. This was further demonstrated by exposing both copepod species independently to dissolved metals (Cd,17 µg/L; Cu,13.8 µg/L; Ni, 29.3 µg/L) and to dietary metals (Cd,18.8 µg/g; Cu, 35.3 µg/g; Ni, 32.5 µg/g). The results showed that although the concentration of dissolved metals they were exposed to were lower than those of the dietary metals, nevertheless, uptake of metals by both copepod species from the dissolved phase alone was substantially higher than from dietary exposure. This provides clear evidence to support our hypothesis that higher metal body burden observed in copepods exposed to dissolved metals than in those exposed to dietary metals is an implication of oral intake of water. P. annandalei showed higher excretion rate of metals when exposed to dissolved metals than E. affinis. However, the excretion rate of metals from both copepod species exposed to dietary metal was similar. We conclude here that both copepod species take in water orally. Our study further showed that metal uptake depends on the exposure routes and the uptake and excretion rates are dependent on the type of metals, amounts and the species.

Effects of experimental addition of nitrogen and phosphorus on microbial and metazoan communities in a peatbog

Interactions between microbial communities and the classical grazing food chain are essential for understanding the functioning of peatbog ecosystems. However, little is known of how short-term intensification of eutrophication processes may influence microbial and metazoan communities in transitional peatbog. We addressed the hypothesis that an increase in the concentration of nutrients will affect the species richness and abundance of microorganisms and small metazoans and cause changes in the food web structure in a peatbog. The experiments were performed in a transitional peatbog. Four experimental variants were conducted (control and nutrient-enriched: +P, +N and P+N). Increased habitat fertility was found to modify the taxonomic composition and functioning of microbial communities. We observed a strong reduction in the species richness of testate amoebae-top predators, and a substantial increase in the abundance of bacteria, flagellates and ciliates. A better understanding of which parameters regulate microbial populations in peatbogs is critical for more accurate prediction of how peatbogs will respond to global climate change or anthropogenic disturbances.

A trophic framework for animal origins

Metazoans emerged in a microbial world and play a unique role in the biosphere as the only complex multicellular eukaryotes capable of phagocytosis. While the bodyplan and feeding mode of the last common metazoan ancestor remain unresolved, the earliest multicellular stem-metazoans likely subsisted on picoplankton (planktonic microbes 0.2-2 μm in diameter) and dissolved organic matter (DOM), similarly to modern sponges. Once multicellular stem-metazoans emerged, they conceivably modulated both the local availability of picoplankton, which they preferentially removed from the water column for feeding, and detrital particles 2-100 μm in diameter, which they expelled and deposited into the benthos as waste products. By influencing the availability of these heterotrophic food sources, the earliest multicellular stem-metazoans would have acted as ecosystem engineers, helping create the ecological conditions under which other metazoans, namely detritivores and non-sponge suspension feeders incapable of subsisting on picoplankton and DOM, could emerge and diversify. This early style of metazoan feeding, specifically the phagocytosis of small eukaryotic prey, could have also encouraged the evolution of larger, even multicellular, eukaryotic forms less prone to metazoan consumption. Therefore, the first multicellular stem-metazoans, through their feeding, arguably helped bridge the strictly microbial food webs of the Proterozoic Eon (2.5-0.541 billion years ago) to the more macroscopic, metazoan-sustaining food webs of the Phanerozoic Eon (0.541-0 billion years ago).

Colonization in the photic zone and subsequent changes during sinking determine bacterial community composition in marine snow

Due to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washed in situ to prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather than de novo colonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

Prey-Specific Growth Responses of Freshwater Flagellate Communities Induced by Morphologically Distinct Bacteria from the Genus Limnohabitans

Because their large growth potential is counterbalanced with grazing by heterotrophic nanoflagellates (HNF), bacteria of the genus Limnohabitans, which are common in many freshwater habitats, represent a valuable model for examining bacterial carbon flow to the grazer food chain. We conducted experiments with natural HNF communities taken from two distinct habitats, the meso-eutrophic Římov Reservoir and the oligo-mesotrophic Lake Cep (South Bohemia). HNF communities from each habitat at distinct seasonal phases, a late April algal bloom and a late May clear water phase, were each fed 3 Limnohabitans strains of differing cell sizes. Water samples were prefiltered (5 μm) to release natural HNF communities from zooplankton control and then amended with the Limnohabitans strains L. planktonicus II-D5 (medium sized, rod shaped), Limnohabitans sp. strain T6-5 (thin, long, curved rod), and Limnohabitans sp. strain 2KL-3 (large solenoid). Using temporal sampling and prey treatment, we determined HNF growth parameters such as doubling time, growth efficiency, and length of lag phase prior starting to exponential growth. All three Limnohabitans strains supported HNF growth but in significant prey-, site-, and season-dependent fashions. For instance, addition of the moderately large T6-5 strain yielded very rapid HNF growth with a short lag phase. In contrast, the curved morphology and larger cell size of strain 2KL-3 made this prey somewhat protected against grazing by smaller HNF, resulting in slower HNF growth and longer lag phases. These trends were particularly pronounced during the late May clear-water phase, which was dominated by smaller HNF cells. This may indicate a longer "adaptation time" for the flagellate communities toward the large prey size offered.

Enrichment of specific protozoan populations during in situ bioremediation of uranium-contaminated groundwater

The importance of bacteria in the anaerobic bioremediation of groundwater polluted with organic and/or metal contaminants is well recognized and in some instances so well understood that modeling of the in situ metabolic activity of the relevant subsurface microorganisms in response to changes in subsurface geochemistry is feasible. However, a potentially significant factor influencing bacterial growth and activity in the subsurface that has not been adequately addressed is protozoan predation of the microorganisms responsible for bioremediation. In field experiments at a uranium-contaminated aquifer located in Rifle, CO, USA, acetate amendments initially promoted the growth of metal-reducing Geobacter species, followed by the growth of sulfate reducers, as observed previously. Analysis of 18S rRNA gene sequences revealed a broad diversity of sequences closely related to known bacteriovorous protozoa in the groundwater before the addition of acetate. The bloom of Geobacter species was accompanied by a specific enrichment of sequences most closely related to the ameboid flagellate, Breviata anathema, which at their peak accounted for over 80% of the sequences recovered. The abundance of Geobacter species declined following the rapid emergence of B. anathema. The subsequent growth of sulfate-reducing Peptococcaceae was accompanied by another specific enrichment of protozoa, but with sequences most similar to diplomonadid flagellates from the family Hexamitidae, which accounted for up to 100% of the sequences recovered during this phase of the bioremediation. These results suggest a prey-predator response with specific protozoa responding to increased availability of preferred prey bacteria. Thus, quantifying the influence of protozoan predation on the growth, activity and composition of the subsurface bacterial community is essential for predictive modeling of in situ uranium bioremediation strategies.

Differential freshwater flagellate community response to bacterial food quality with a focus on Limnohabitans bacteria

Different bacterial strains can have different value as food for heterotrophic nanoflagellates (HNF), thus modulating HNF growth and community composition. We examined the influence of prey food quality using four Limnohabitans strains, one Polynucleobacter strain and one freshwater actinobacterial strain on growth (growth rate, length of lag phase and growth efficiency) and community composition of a natural HNF community from a freshwater reservoir. Pyrosequencing of eukaryotic small subunit rRNA amplicons was used to assess time-course changes in HNF community composition. All four Limnohabitans strains and the Polynucleobacter strain yielded significant HNF community growth while the actinobacterial strain did not although it was detected in HNF food vacuoles. Notably, even within the Limnohabitans strains we found significant prey-related differences in HNF growth parameters, which could not be related only to size of the bacterial prey. Sequence data characterizing the HNF communities showed also that different bacterial prey items induced highly significant differences in community composition of flagellates. Generally, Stramenopiles dominated the communities and phylotypes closely related to Pedospumella (Chrysophyceae) were most abundant bacterivorous flagellates rapidly reacting to addition of the bacterial prey of high food quality.

Phylogenetic composition and distribution of picoeukaryotes in the hypoxic northwestern coast of the Gulf of Mexico

Coastal marine hypoxic, or low-oxygen, episodes are an increasing worldwide phenomenon, but its effect on the microbial community is virtually unknown by far. In this study, the community structure and phylogeny of picoeukaryotes in the Gulf of Mexico, which are exposed to severe hypoxia in these areas was explored through a clone library approach. Both oxic surface waters and suboxic bottom waters were collected in August 2010 from three representative stations on the inner Louisiana shelf near the Atchafalaya and Mississippi River plumes. The bottom waters of the two more western stations were much more hypoxic in comparison to those of the station closest to the Mississippi River plume, which were only moderately hypoxic. A phylogenetic analysis of a total 175 sequences, generated from six 18S rDNA clone libraries, demonstrated a clear dominance of parasitic dinoflagellates from Marine alveolate clades I and II in all hypoxic waters as well as in the surface layer at the more western station closest to the Atchafalaya River plume. Species diversity was significantly higher at the most hypoxic sites, and many novel species were present among the dinoflagellate and stramenopile clades. We concluded that hypoxia in the Gulf of Mexico causes a significant shift in picoeukaryote communities, and that hypoxia may cause a shift in microbial food webs from grazing to parasitism.

Microbial community response during the iron fertilization experiment LOHAFEX

Iron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean, Bacteria and Archaea were monitored within and outside an induced bloom, dominated by Phaeocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescence in situ hybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such as Roseobacter and Gammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers.

Prey detection in a cruising copepod

Small cruising zooplankton depend on remote prey detection and active prey capture for efficient feeding. Direct, passive interception of prey is inherently very inefficient at low Reynolds numbers because the viscous boundary layer surrounding the approaching predator will push away potential prey. Yet, direct interception has been proposed to explain how rapidly cruising, blind copepods feed on non-motile phytoplankton prey. Here, we demonstrate a novel mechanism for prey detection in a cruising copepod, and describe how motile and non-motile prey are discovered by hydromechanical and tactile or, likely, chemical cues, respectively.

How zooplankton feed: mechanisms, traits and trade-offs

Zooplankton is a morphologically and taxonomically diverse group and includes organisms that vary in size by many orders of magnitude, but they are all faced with the common problem of collecting food from a very dilute suspension. In order to maintain a viable population in the face of mortality, zooplankton in the ocean have to clear daily a volume of ambient water for prey particles that is equivalent to about 10(6) times their own body volume. While most size-specific vital rates and mortality rates decline with size, the clearance requirement is largely size-independent because food availability also declines with size. There is a limited number of solutions to the problem of concentrating dilute prey from a sticky medium: passive and active ambush feeding; feeding-current feeding, where the prey is either intercepted directly, retained on a filter, or individually perceived and extracted from the feeding current; cruise feeding; and colonization of large particles and marine snow aggregates. The basic mechanics of these food-collection mechanisms are described, and it is shown that their efficiencies are inherently different and that each of these mechanisms becomes less efficient with increasing size. Mechanisms that compensate for this decline in efficiency are described, including inflation of feeding structures and development of vision. Each feeding mode has implications beyond feeding in terms of risk of encountering predators and chance of meeting mates, and they partly target different types of prey. The main dichotomy is between (inefficient) ambush feeding on motile prey and the more efficient active feeding modes; a secondary dichotomy is between (efficient) hovering and (less efficient) cruising feeding modes. The efficiencies of the various feeding modes are traded off against feeding-mode-dependent metabolic expenses, predation risks, and mating chances. The optimality of feeding strategies, evaluated as the ratio of gain over risk, varies with the environment, and may explain both size-dependent and spatio-temporal differences in distributions of various feeding types as well as other aspects of the biology of zooplankton (mating behaviour, predator defence strategies).

Food quality of heterotrophic bacteria for Daphnia magna: evidence for a limitation by sterols

The quality of heterotrophic bacteria as food for metazoan grazers has been investigated poorly. We conducted growth experiments with juvenile Daphnia magna feeding on different strains of heterotrophic bacteria that represent typical pelagic bacteria of five phylogenetically distinct groups. The bacterial food suspensions were supplemented with cholesterol and/or the polyunsaturated fatty acid eicosapentaenoic acid (EPA), two essential nutrients that are either absent or scarcely represented in bacteria. Our data imply that the selected heterotrophic bacteria are of poor food quality for D. magna, which was indicated either by very low somatic growth rates or by high mortality. However, with four out of six bacterial strains tested, the somatic growth rates increased significantly upon supplementation with cholesterol, which shows that the lack of sterols in bacteria is a major food quality constraint. We did not find clear evidence for a limitation by EPA on bacterial diets within our growth experiments. High mortality was observed when D. magna was fed with Hydrogenophaga sp. or Pseudomonas sp., which indicates that these two bacterial strains are toxic to D. magna. Our findings highlight the limitations of bacteria as a carbon source for Daphnia and point to a so far underestimated diversity of interactions between grazers and its bacterial food.

Coexistence of mixotrophs, autotrophs, and heterotrophs in planktonic microbial communities

We examine what circumstances allow the coexistence of microorganisms following different nutritional strategies, using a mathematical model. This model incorporates four nutritional types commonly found in planktonic ecosystems: (1) heterotrophic bacteria that consume dissolved organic matter and are prey to some of the other organisms; (2) heterotrophic zooflagellates that depend entirely on bacterial prey; (3) phototrophic algae that depend only on light and inorganic nutrients, and (4) mixotrophs that photosynthesize, take up inorganic nutrients, and consume bacterial prey. Mixotrophs are characterized by a parameter representing proportional mixing of phototrophic and heterotrophic nutritional strategies. Varying this parameter, a range of mixotrophic strategies was examined in hypothetical habitats differing in supplies of light, dissolved organic carbon, and dissolved inorganic phosphorous. Mixotrophs expressing a wide range of mixotrophic strategies persisted in model habitats with low phosphorus supply, but only those with a strategy that is mostly autotrophic persisted with high nutrient supply, and then only when light supply was also high. Organisms representing all four nutritional strategies were predicted to coexist in habitats with high phosphorus and light supplies. Coexistence involves predation by zooflagellates and mixotrophs balancing the high competitive ability of bacteria for phosphorus, the partitioning of partially overlapping resources between all populations, and possibly nonequlibrium dynamics. In most habitats, the strategy predicted to maximize the abundance of mixotrophs is to be mostly photosynthetic and supplement nutritional needs by consuming bacteria.

Mechanisms and feasibility of prey capture in ambush-feeding zooplankton

Many marine zooplankters, particularly among copepods, are "ambush feeders" that passively wait for their prey and capture them by fast surprise attacks. This strategy must be very demanding in terms of muscle power and sensing capabilities, but the detailed mechanisms of the attacks are unknown. Using high-speed video we describe how copepods perform spectacular attacks by precision maneuvering during a rapid jump. We show that the flow created by the attacking copepod is so small that the prey is not pushed away, and that the attacks are feasible because of their high velocity (approximately 100 mm x s(-1)) and short duration (few ms), which leaves the prey no time for escape. Simulations and analytical estimates show that the viscous boundary layer that develops around the attacking copepod is thin at the time of prey capture and that the flow around the prey is small and remains potential flow. Although ambush feeding is highly successful as a feeding strategy in the plankton, we argue that power requirements for acceleration and the hydrodynamic constraints restrict the strategy to larger (> 0.25 mm), muscular forms with well-developed prey perception capabilities. The smallest of the examined species is close to this size limit and, in contrast to the larger species, uses its largest possible jump velocity for such attacks. The special requirements to ambush feeders with such attacks may explain why this strategy has evolved to perfection only a few times among planktonic suspension feeders (few copepod families and chaetognaths).

Distribution of the uncultured protist MAST-4 in the Indian Ocean, Drake Passage and Mediterranean Sea assessed by real-time quantitative PCR

Molecular surveys of marine picoeukaryotes have revealed a large number of sequences unrelated to cultured organisms, such as those forming the marine stramenopile (MAST)-4 clade. Recent FISH (fluorescent in situ hybridization) data have shown that MAST-4 cells are uncultured heterotrophic flagellates of 2-3 microm in size that have a global distribution in non-polar marine waters. However, FISH is time-consuming and hard to apply to the many samples generated during oceanographic cruises, so we developed a real-time quantitative polymerase chain reaction (Q-PCR) protocol to determine rapidly the abundance of this group using environmental DNA. We designed a primer set targeting the 18S rRNA genes (rDNA) of MAST-4 and optimized and calibrated the Q-PCR protocol using a plasmid with the target sequence as insert. The Q-PCR was then applied to quantify MAST-4 rDNA molecules along three marine transects, longitudinal in the Indian Ocean, latitudinal in the Drake Passage and coastal-offshore in the Mediterranean Sea, and to a temporal study in a Mediterranean Sea coastal station. MAST-4 was detected in all samples processed (averaged abundances between 500 and 1000 rDNA molecules ml(-1)) except in mesopelagic and Antarctic samples, where it was virtually absent. In general, it was more abundant in the coast than offshore and in the deep chlorophyll maximum than at surface. A comparison of Q-PCR and FISH signals in well-controlled microbial incubations indicated that MAST-4 cells have around 30 copies of the rDNA operon. This Q-PCR assay quickly yielded quantitative data of uncultured MAST-4 cells and confirmed their wide distribution and putative ecological importance.

Microeukaryote diversity in a marine methanol-fed fluidized denitrification system

The marine methanol-fed fluidized denitrification system operated by the Montreal Biodome includes carriers on which a denitrifying biofilm has developed. Previous observations showed a high abundance of microeukaryotes living in and around the biofilm. These eukaryotes may influence the system's denitrification efficiency. The composition of the microeukaryote population was determined. Microscopic observations showed at least 20 different morphologies that included large numbers of ciliates. Molecular analyses of an 18S ribosomal RNA (rDNA) gene library revealed 31 different phylotypes. Alveolobiontes were the most abundant phylotypes and made up 75% of the 159 screened clones. Other eukaryotic groups, including Stramenopiles, Fungi, Amoebozoa, and nematodes, were also present. From 18S rDNA specific sequences, one of the Amoebozoa-affiliated phylotypes was visualized by fluorescence in situ hybridization. It had a rod-like irregular shape and measured less than 5 mum in length. We determined the impact of protozoans on the denitrifying activity. In a laboratory-scale batch culture assays, the denitrifying biofilm was treated with cycloheximide and nystatin that eliminated the protozoans. No difference in the denitrification rate was found. However, planktonic bacteria were more abundant in the treated culture medium.

A UNIQUE LIFE CYCLE AND PERENNATION IN A COLORLESS CHRYSOPHYTE SPUMELLA SP.(1)

Life cycle and perennation of a colorless chrysophyte, Spumella sp., isolated from an ephemeral ditch were investigated. From a single resting cyst (statospore), only one nonmotile cell germinated. Shortly after germination, the cell generated flagella, started to swim, and formed a gelatinous sphere. The cell itself retained the ability to swim within the sphere. Cells fed on bacteria inhabiting the sphere and grew by longitudinal binary cell division very rapidly. The gelatinous sphere gradually enlarged as the number of cells increased. When it reached maximum size (∼500 μm in diameter), the gelatinous substance of the sphere weakened, and the sphere gradually broke into several pieces, forming cleavages between them. Cells swam away through the cleavages. Five to ∼40 swimming cells soon gathered and formed a swarm. In the swarm, some cells cannibalized other sibling cells and enlarged, resulting in giant cells that were two to three times larger in diameter than ordinary cells. The giant cells soon started statospore formation. Statospore formation was independent of any changes of environmental factors, such as increase or decrease in temperature or changes in nutrient or light levels, which are known to induce resting-cyst formation in other groups of algae and protists. Statospore formation started when cells divided 15 to 16 times after germination. This is congruent with the idea that statospore formation in planktonic chrysophytes directly depends on cell density. An extraordinarily high growth rate and cannibalism involved in the initiation of statospore formation are interpreted as adaptations to achieve the perennation in ephemeral aquatic environments.

Cyanophage Pf-WMP4, a T7-like phage infecting the freshwater cyanobacterium Phormidium foveolarum: complete genome sequence and DNA translocation

We report the complete 40,938-bp genome sequence of a cyanophage, Pf-WMP4, which infects the freshwater cyanobacterium Phormidium foveolarum Gom. Nine of the forty-five potential open reading frames in the Pf-WMP4 genome share similarities with the genes found in T7-like phages. Using in vitro transcription, we found that seven promoters at the leftmost end of the genome can be recognized by the host RNA polymerase. By blocking transcriptional and translational inhibitors, we found that Pf-WMP4 DNA translocation, with an average translocation rate of 19.8+/-2.7 bp s(-1) at 28 degrees C, requires both host transcription and protein synthesis of an unknown factor. Therefore the mechanism of cyanophage Pf-WMP4 DNA injection may be driven both by a T7-like internalization mechanism as well as an additional unknown mechanism requiring de novo protein synthesis. Our analysis of the Pf-WMP4 genome sheds new light on the translocation strategies and evolutionary traces of phages belonging to the T7 supergroup.

Distribution and abundance of uncultured heterotrophic flagellates in the world oceans

Heterotrophic flagellates play fundamental roles in marine ecosystems as picoplankton grazers. This recognized importance contrasts with our ignorance of the taxonomic composition of this functional group, which remains mostly unidentified by microscopical and culturing approaches. Recent molecular marine surveys based on 18S rDNA genes have retrieved many sequences unrelated to cultured organisms and marine stramenopiles were among the first reported uncultured eukaryotes. However, little is known about the organisms corresponding to these sequences. Here we determine the abundance of several marine stramenopile lineages in surface marine waters using molecular probes and fluorescent in situ hybridization. We show that these protists are free-living bacterivorous heterotrophic flagellates. They were widely distributed, occurring in the five world oceans, and accounted for a significant fraction (up to 35%) of heterotrophic flagellates in diverse geographic regions. A single group, MAST-4, represented 9% of cells within this functional assemblage, with the intriguing exception of polar waters where it was absent. MAST-4 cells likely contribute substantially to picoplankton grazing and nutrient re-mineralization in vast areas of the oceans and represent a key eukaryotic group in marine food webs.

Unveiling fungal zooflagellates as members of freshwater picoeukaryotes: evidence from a molecular diversity study in a deep meromictic lake

This study presents an original 18S rRNA PCR survey of the freshwater picoeukaryote community, and was designed to detect unidentified heterotrophic picoflagellates (size range 0.6-5 microm) which are prevalent throughout the year within the heterotrophic flagellate assemblage in Lake Pavin. Four clone libraries were constructed from samples collected in two contrasting zones in the lake. Computerized statistic tools have suggested that sequence retrieval was representative of the in situ picoplankton diversity. The two sampling zones exhibited similar diversity patterns but shared only about 5% of the operational taxonomic units (OTUs). Phylogenetic analysis clustered our sequences into three taxonomic groups: Alveolates (30% of OTUs), Fungi (23%) and Cercozoa (19%). Fungi thus substantially contributed to the detected diversity, as was additionally supported by direct microscopic observations of fungal zoospores and sporangia. A large fraction of the sequences belonged to parasites, including Alveolate sequences affiliated to the genus Perkinsus known as zooparasites, and chytrids that include host-specific parasitic fungi of various freshwater phytoplankton species, primarily diatoms. Phylogenetic analysis revealed five novel clades that probably include typical freshwater environmental sequences. Overall, from the unsuspected fungal diversity unveiled, we think that fungal zooflagellates have been misidentified as phagotrophic nanoflagellates in previous studies. This is in agreement with a recent experimental demonstration that zoospore-producing fungi and parasitic activity may play an important role in aquatic food webs.

Dynamics and estimates of growth and loss rates of bacterioplankton in a temperate freshwater system

The growth rate and losses of bacterioplankton in the epilimnion of an oligo-mesotrophic reservoir were simultaneously estimated using three different methods for each process. Bacterial production was determined by means of the tritiated thymidine incorporation method, the dialysis bag method and the dilution method, while bacterial mortality was assessed with the dilution method, the disappearance of thymidine-labeled natural cells and ingestion of fluorescent bacterial tracers by heterotrophic flagellates. The different methods used to estimate bacterial growth rates yielded similar results. On the other hand, the mortality rates obtained with the dilution method were significantly lower than those obtained with the use of thymidine-labeled natural cells. The bacterial ingestion rate by flagellates accounted on average for 39% of total bacterial mortality estimated by the dilution method, but this value fell to 5% when the total mortality was measured by the thymidine-labeling method. Bacterial abundance and production varied in opposite phase to flagellate abundance and the various bacterial mortality rates. All this points to the critical importance of methodological aspects in the elaboration of quantitative models of matter and energy flows over the time through microbial trophic networks in aquatic systems, and highlights the role of bacterioplankton as a source of carbon for higher trophic levels in the studied system.

Prey selectivity of bacterivorous protists in different size fractions of reservoir water amended with nutrients

An experiment designed to examine food preferences of heterotrophic nanoflagellates (HNF) grazing on bacterioplankton was performed in the freshwater Rímov reservoir (Czech Republic). Water samples were size-fractionated to obtain < 5 microm filtrate containing bacteria and HNF. To manipulate resource availability, < 5 microm treatments were incubated in dialysis bags submerged in the barrels filled with the unfiltered reservoir water amended with either orthophosphate or glucose or combination of both. We employed rRNA-targeted probes to assess HNF prey preferences by analysing bacterial prey in HNF food vacuoles compared with available bacteria. Actinobacteria (the HGC69a probe) were avoided by HNF in all treatments. Cytophaga-Flavobacterium-Bacteroidetes bacteria (the CF319a probe) were positively selected mainly in treatments in which bacteria were heavily grazed, the < 5 microm treatments, but this trend was less pronounced towards the end of the study. The members of a small subcluster of Betaproteobacteria (the R-BT065 probe) were mostly positively selected. The nutrient amendments differentially affected bacterioplankton dynamics in almost all treatments, and together with the size fractionation, altered HNF overall bacterivory as well as prey selection. Analyses of bacterivores in unfiltered treatments allowed to detect the effect of different protists on shifts in HNF selectivity observed in < 5 microm compared with unfiltered treatments.

Halocafeteria seosinensis gen. et sp. nov. (Bicosoecida), a halophilic bacterivorous nanoflagellate isolated from a solar saltern

Recently, heterotrophic nanoflagellates (HNF) have been reported to actively ingest prokaryotes in high salinity waters. We report the isolation and culture of an HNF from a Korean saltern pond of 300 per thousand salinity. The organism is biflagellated with an acronematic anterior flagellum and never glides on surfaces. The mitochondria have tubular cristae. Neither transitional helix nor spiral fiber were observed in the transition zones of the flagella. The cell has a cytostome supported by an arc of eight microtubules, suggesting that our isolate is a bicosoecid. Our isolate had neither mastigonemes, lorica, body scales, nor cytopharynx and thus could not be placed in any of the presently described bicosoecid genera. Phylogenetic analysis of 18S rRNA gene sequences from stramenopiles confirmed the bicosoecid affinities of our isolate, but did not place it within any established genus or family. Its closest relatives include Caecitellus and Cafeteria. The optimal range of growth temperature was 30-35 degrees C. The isolated HNF grew optimally at 150 per thousand salinity and tolerated up to 363 per thousand salinity, but it failed to grow below 75 per thousand salinity, indicating that it could be a borderline extreme halophile. On the basis of its morphological features and position in 18S rRNA trees we propose a novel genus for our isolate; Halocafeteria, n. gen. The species name Halocafeteria seosinensis sp. nov. is proposed.

Assimilation efficiency of Vibrio bacterial protein biomass by the flagellate Pteridomonas: Assessment using flow cytometric sorting

A flow cytometric sorting technique for direct determination of bacterial biomass assimilation by phagotrophic flagellates was developed and tested in laboratory culture experiments. Living Vibrio bacteria were quantitatively pulse-chase labelled with [(35)S]methionine tracer and fed to Pteridomonas flagellates. Flow sorting revealed that the isotopically labelled material is in either bacterial prey or flagellate predators and the egested bacterial debris contained negligible amounts of tracer. These experimental results confirm an earlier hypothesis that flagellates release metabolised bacterial proteins primarily in a dissolved form. The assimilation efficiency of the Vibrio protein biomass by Pteridomonas was low, only about 20%, independently of the amount of consumed bacterial biomass, confirming our earlier indirect estimates. Additionally, against expectations that cells decrease their metabolic activity whilst preparing for and engaged in division, we found that the precursor uptake rates by flow sorted bacterial cells at the S+G(2) cell cycle stages were constantly 1.5 times higher than those of cells at the G(1) stage.

Grazing impact of different heterotrophic nanoflagellates on eukaryotic (Ostreococcus tauri ) and prokaryotic picoautotrophs (Prochlorococcus and Synechococcus)

Autotrophic picoplankton (<3 microm) composed of both prokaryotes and eukaryotes are the most abundant primary producers on Earth. In this study we examined the ingestion of the picoeukaryote Ostreococcus tauri by different marine heterotrophic nanoflagellates (HNF) with various morphologies, swimming and feeding behaviours. Cultures of specific bacterivorous nanoflagellates (Rhynchomonas nasuta, Jakoba libera, and a culture of Cafeteria sp./Monosiga sp.) and natural nanoflagellate populations were used as grazers. For comparison with Ostreococcus, we used similar-sized prokaryotes as prey, Prochlorococcus and Synechococcus. We observed large species-specific differences in terms of: use of picoautotrophs among nanoflagellates, time lag between prey addition and prey consumption (0-196 h), grazing rate (0-0.12 h(-1)), growth rate (0-0.3 h(-1)) and maximum abundance of HNF reached in experimental bottles (e.g. from 10(4) to 10(5) cells ml(-1), for a natural coastal population and a Cafeteria sp./Monosiga sp. culture feeding Ostreococcus respectively). Overall, this study shows that the nanoflagellate community composition is conclusive for picoautotrophic community structure and, vice versa, the picoautotrophic community structure favours or inhibits the growth of some nanoflagellate groups.

Response of benthic protozoa and thraustochytrid protists to fish farm impact in seagrass (Posidonia oceanica) and soft-bottom sediments

We investigated the impact of fish farm biodeposition on benthic bacteria, thraustochytrid protists, and heterotrophic protozoa (nanoflagellates and ciliates) in an oligotrophic area of the Mediterranean Sea. The fish farm impact was investigated both on a seagrass (Posidonia oceanica) bed and on soft bottom sediments. In both systems, sediment samples were collected with a multicontrol sampling strategy (i.e., beneath the fish farm and at three control sites per system). The uneaten food pellets supplied to the fish determined the accumulation of sediment organic matter and the enhancement of protein content in impacted sediments (both seagrass bed and soft sediments). In both systems, the abundance and biomass of heterotrophic protists increased significantly beneath the fish farm, but the structure of the protist assemblages responded differently in vegetated and unvegetated sediments. Thraustochytrid abundance increased significantly in impacted seagrass. These results provide evidence that the structure of protist assemblages respond significantly to fish farm biodeposition and indicate that the monitoring of these benthic components provides complementary information for the assessment of the fish farm impact on the benthic systems.

Unexpected effects of prey dimensions and morphologies on the size selective feeding by two bacterivorous flagellates (Ochromonas sp. and Spumella sp.)

Current models on protistan size-selective feeding assume that contact probability is the factor that largely explains observed food preferences. Contact probability is generally expected to be positively correlated with prey size and therefore to explain observed food selection for larger prey items. We critically tested these basic assumptions on size-selective feeding using the interception-feeding chrysomonad nanoflagellates Ochromonas sp. and Spumella sp. Mechanisms of differential feeding were studied during distinct stages of the selection process (i.e. contact probability, capture efficiency, ingestion efficiency, and differential digestion) by means of high-resolution video microscopy. Food selection was investigated using a mixture of microspheres ranging from 0.3-2.2 microm in diam., as well as a mixed bacterial community. In contrast to current model assumptions, the contact probability was highest for microspheres of intermediate size (0.9-1.2 microm), but was not generally positively correlated with prey size over the whole prey size range. Capture and ingestion also proved to be involved in size selection: these patterns were also independent of the food concentration (p = 0.968 for Ochromonas, p = 0.971 for Spumella). Even though the capture rate was significantly higher for attached flagellates than for swimming flagellates (p < 0.001), size selectivity was not affected (p > 0.05). Our results indicate that: (i) size selection is not actively regulated by these flagellates, but is a passive process; (ii) contact probability is not generally positively correlated with prey size, but shows a maximum for intermediate-sized prey in the prey size spectrum of 0.3-2.2 microm; and (iii) selection steps other than contact probability are crucial for size selection and should be integrated in models on size selection.

Food selection by bacterivorous protists: insight from the analysis of the food vacuole content by means of fluorescence in situ hybridization

A modified fluorescence in situ hybridization (FISH) method was used to analyze bacterial prey composition in protistan food vacuoles in both laboratory and natural populations. Under laboratory conditions, we exposed two bacterial strains (affiliated with beta- and gamma-Proteobacteria -- Aeromonas hydrophila and Pseudomonas fluorescens, respectively) to grazing by three protists: the flagellates Bodo saltans and Goniomonas sp., and the ciliate Cyclidium glaucoma. Both flagellate species preferably ingested A. hydrophila over P. fluorescens, while C. glaucoma showed no clear preferences. Differences were found in the digestion of bacterial prey with B. saltans digesting significantly faster P. fluorescens compared to two other protists. The field study was conducted in a reservoir as part of a larger experiment. We monitored changes in the bacterial prey composition available compared to the bacteria ingested in flagellate food vacuoles. Bacteria detected by probe HGC69a (Actinobacteria) and R-BT065 were negatively selected by flagellates. Bacteria detected by probe CF319a were initially positively selected but along with a temporal shift in bacterial cell size, this trend changed to negative selection during the experiment. Overall, our analysis of protistan food vacuole content indicated marked effects of flagellate prey selectivity on bacterioplankton community composition.

Strain-specific differences in the grazing sensitivities of closely related ultramicrobacteria affiliated with the Polynucleobacter cluster

Ultramicrobacteria (cell volume < 0.1 microm(3)) are the numerically dominant organisms in the plankton of marine and freshwater habitats. Flagellates and other protists are assumed to be the most important predators of these ultramicrobacteria as well as of larger planktonic bacteria. However, due to controversial observations conducted previously, it is not clear as to whether fractions of the ultramicrobacteria are resistant to flagellate predation. Furthermore, it is not known if closely related bacteria vary significantly in their sensitivity to flagellate predation. We investigated the sensitivity of ultramicrobacteria affiliated with the cosmopolitan Polynucleobacter cluster to grazing by Spumella-like nanoflagellates. Laboratory grazing experiments with four closely related (> or =99.6% 16S rRNA gene sequence similarity) bacteria and three closely related (100% 18S rRNA gene sequence similarity) flagellates were performed. In comparison to larger bacteria, predation on the ultramicrobacterial Polynucleobacter strains was weak, and the growth of the predating flagellates was slow. Specific clearance rates ranged between 0.14 x 10(5) and 2.8 x 10(5) units of predator size h(-1). Feeding rates strongly depended on the flagellate and bacterial strain (P < 0.001). Grazing mortality rates of the three flagellate strains investigated varied for the same prey strain by up to almost fourfold. We conclude that (i) ultramicrobacteria affiliated with the Polynucleobacter cluster are not protected from grazing, (ii) strain-specific variations in grazing sensitivity even between closely related bacteria are high, and (iii) strain-specific differences in predator-prey interaction could be an important factor in the evolution and maintenance of microbial microdiversity.

Phylogenetic and ecological analysis of novel marine stramenopiles

Culture-independent molecular analyses of open-sea microorganisms have revealed the existence and apparent abundance of novel eukaryotic lineages, opening new avenues for phylogenetic, evolutionary, and ecological research. Novel marine stramenopiles, identified by 18S ribosomal DNA sequences within the basal part of the stramenopile radiation but unrelated to any previously known group, constituted one of the most important novel lineages in these open-sea samples. Here we carry out a comparative analysis of novel stramenopiles, including new sequences from coastal genetic libraries presented here and sequences from recent reports from the open ocean and marine anoxic sites. Novel stramenopiles were found in all major habitats, generally accounting for a significant proportion of clones in genetic libraries. Phylogenetic analyses indicated the existence of 12 independent clusters. Some of these were restricted to anoxic or deep-sea environments, but the majority were typical components of coastal and open-sea waters. We specifically identified four clusters that were well represented in most marine surface waters (together they accounted for 74% of the novel stramenopile clones) and are the obvious targets for future research. Many sequences were retrieved from geographically distant regions, indicating that some organisms were cosmopolitan. Our study expands our knowledge on the phylogenetic diversity and distribution of novel marine stramenopiles and confirms that they are fundamental members of the marine eukaryotic picoplankton.

Predation, competition, and nutrient recycling: a stoichiometric approach with multiple nutrients

A model for two competing prey species and one predator is formulated in which three essential nutrients can limit growth of all populations. Prey take up dissolved nutrients and predators ingest prey, assimilating a portion of ingested nutrients and recycling or respiring the balance. For all species, the nutrient contents of individuals vary and growth is coupled to increasing content of the limiting nutrient. This model was parameterized to describe a flagellate preying on two bacterial species, with carbon (C), nitrogen (N), and phosphorus (P) as nutrients. Parameters were chosen so that the two prey species would stably coexist without predators under some nutrient supply conditions. Using numerical simulations, the long-term outcomes of competition and predation were explored for a gradient of N:P supply ratios, varying C supply, and varying preference of the predator for the two prey. Coexistence and competitive exclusion both occurred under some conditions of nutrient supply and predator preference. As in simpler models of competition and predation these outcomes were largely governed by apparent competition mediated by the predator, and resource competition for nutrients whose effective supply was partly governed by nutrient recycling also mediated by the predator. For relatively small regions of parameter space, more complex outcomes with multiple attractors or three-species limit cycles occurred. The multiple constraints posed by multiple nutrients held the amplitudes of these cycles in check, limiting the influence of complex dynamics on competitive outcomes for the parameter ranges explored.

The impact of variable stoichiometry on predator-prey interactions: a multinutrient approach

A model for prey and predators is formulated in which three essential nutrients can limit growth of both populations. Prey take up dissolved nutrients, while predators ingest prey, assimilate a fraction of ingested nutrients that depends on their current nutrient status, and recycle the balance. Although individuals are modeled as identical within populations, amounts of nutrients within individuals vary over time in both populations, with reproductive rates increasing with these amounts. Equilibria and their stability depend on nutrient supply conditions. When nutrient supply increases, unusual results can occur, such as a decrease of prey density. This phenomenon occurs if, with increasing nutrient, predators sequester rather than recycle nutrients. Furthermore, despite use of a linear functional response for predators, high nutrient supply can destabilize equilibria. Responses to nutrient supply depend on the balance between assimilation and recycling of nutrients by predators, which differs depending on the identity of the limiting nutrient. Applied to microbial ecosystems, the model predicts that the efficiency of organic carbon mineralization is reduced when supply of mineral nutrients is low and when equilibria are unstable. The extent to which predators recycle or sequester limiting nutrients for their prey is of critical importance for the stability of predator-prey systems and their response to enrichment.

Dynamics of microbial communities on marine snow aggregates: colonization, growth, detachment, and grazing mortality of attached bacteria

We studied the dynamics of microbial communities attached to model aggregates (4-mm-diameter agar spheres) and the component processes of colonization, detachment, growth, and grazing mortality. Agar spheres incubated in raw seawater were rapidly colonized by bacteria, followed by flagellates and ciliates. Colonization can be described as a diffusion process, and encounter volume rates were estimated at about 0.01 and 0.1 cm(3) h(-1) for bacteria and flagellates, respectively. After initial colonization, the abundances of flagellates and ciliates remained approximately constant at 10(3) to 10(4) and approximately 10(2) cells sphere(-1), respectively, whereas bacterial populations increased at a declining rate to >10(7) cells sphere(-1). Attached microorganisms initially detached at high specific rates of approximately 10(-2) min(-1), but the bacteria gradually became irreversibly attached to the spheres. Bacterial growth (0 to 2 day(-1)) was density dependent and declined hyperbolically when cell density exceeded a threshold. Bacterivorous flagellates grazed on the sphere surface at an average saturated rate of 15 bacteria flagellate(-1) h(-1). At low bacterial densities, the flagellate surface clearance rate was approximately 5 x 10(-7) cm(2) min(-1), but it declined hyperbolically with increasing bacterial density. Using the experimentally estimated process rates and integrating the component processes in a simple model reproduces the main features of the observed microbial population dynamics. Differences between observed and predicted population dynamics suggest, however, that other factors, e.g., antagonistic interactions between bacteria, are of importance in shaping marine snow microbial communities.