Grazing by protozoa as selection factor for activated sludge bacteria

Formation of multicellular colonies by choanoflagellates increases susceptibility to capture by amoeboid predators

Many heterotrophic microbial eukaryotes are size-selective feeders. Some microorganisms increase their size by forming multicellular colonies. We used choanoflagellates, Salpingoeca helianthica, which can be unicellular or form multicellular colonies, to study the effects of multicellularity on vulnerability to predation by the raptorial protozoan predator, Amoeba proteus, which captures prey with pseudopodia. Videomicrography used to measure the behavior of interacting S. helianthica and A. proteus revealed that large choanoflagellate colonies were more susceptible to capture than were small colonies or single cells. Swimming colonies produced larger flow fields than did swimming unicellular choanoflagellates, and the distance of S. helianthica from A. proteus when pseudopod formation started was greater for colonies than for single cells. Prey size did not affect the number of pseudopodia formed and the time between their formation, pulsatile kinematics and speed of extension by pseudopodia, or percent of prey lost by the predator. S. helianthica did not change swimming speed or execute escape maneuvers in response to being pursued by pseudopodia, so size-selective feeding by A. proteus was due to predator behavior rather than prey escape. Our results do not support the theory that the selective advantage of becoming multicellular by choanoflagellate-like ancestors of animals was reduced susceptibility to protozoan predation.

Enterobacter sp. Strain SM1_HS2B Manifests Transient Elongation and Swimming Motility in Liquid Medium

Many species of bacteria change their morphology and behavior under external stresses. In this study, we report transient elongation and swimming motility of a novel Enterobacter sp. strain, SM1_HS2B, in liquid broth under a standard growth condition. When growing in the Luria-Bertani medium, HS2B cells delay their cell division and elongate. Although transient over a few hours, the average cell length reaches over 10 times that of the stationary-state cells. The increase is also cumulative following repeated growth cycles stimulated by taking cells out of the exponential phase and adding them into fresh medium every 2 hours. The majority of the cells attain swimming motility during the exponential growth phase, and then they lose swimming motility over the course of several hours. Both daughter cells due to division of a long swimming cell retain the ability to swim. We confirm that the long HS2B cells swim with rigid-body rotation along their body axis. These findings based on microscopic observation following repeated cycles of growth establish HS2B as a prototype strain with sensitive dependence of size and motility on its physical and biochemical environment. IMPORTANCE Bacteria undergo morphological changes in order to cope with external stresses. Among the best-known examples are cell elongation and hyperflagellation in the context of swarming motility. The subject of this report, SM1_HS2B, is a hyperswarming strain of a newly identified species of enterobacteria, noted as Enterobacter sp. SM1. The key finding that SM1_HS2B transiently elongates to extreme length in fresh liquid medium offers new insights on regulation in bacterial growth and division. SM1_HS2B also manifests transient but vigorous swimming motility during the exponential phase of growth in liquid medium. These properties establish HS2B as a prototype strain with sensitive dependence of size and motility on its physical and biochemical environment. Such a dependence may be relevant to swarming behavior with a significant environmental or physiological outcome.

The wastewater protist Rhogostoma minus (Thecofilosea, Rhizaria) is abundant, widespread, and hosts Legionellales

Wastewater is treated by concerted actions of the microbial communities within bioreactors. Although protists (unicellular eukaryotes) are good bioindicators and important players influencing denitrification, nitrification, and flocculation, they are the least known organisms in WWTPs. The few recent environmental surveys of the protistan diversity in WWTPs show that the most abundant protistan sequences in WWTPs belong to Thecofilosea (Rhizaria). We re-investigated previously published environmental sequencing data and gathered strains from seven WWTPs to determine which species dominate WWTPs worldwide. We found that all highly abundant thecofilosean sequences represent a single species - Rhogostoma minus. Considering that Thecofilosea are frequent hosts for Legionellales, i.e. bacteria linked to waterborne diseases, we confirm that Rhogostoma minus functions as a host for Legionellales in WWTPs. Whether the highly abundant Rhogostoma minus also serves as a host for known human pathogenic Legionellales requires further attention.

Biocontrol Traits Correlate With Resistance to Predation by Protists in Soil Pseudomonads

Root-colonizing bacteria can support plant growth and help fend off pathogens. It is clear that such bacteria benefit from plant-derived carbon, but it remains ambiguous why they invest in plant-beneficial traits. We suggest that selection via protist predation contributes to recruitment of plant-beneficial traits in rhizosphere bacteria. To this end, we examined the extent to which bacterial traits associated with pathogen inhibition coincide with resistance to protist predation. We investigated the resistance to predation of a collection of Pseudomonas spp. against a range of representative soil protists covering three eukaryotic supergroups. We then examined whether patterns of resistance to predation could be explained by functional traits related to plant growth promotion, disease suppression and root colonization success. We observed a strong correlation between resistance to predation and phytopathogen inhibition. In addition, our analysis highlighted an important contribution of lytic enzymes and motility traits to resist predation by protists. We conclude that the widespread occurrence of plant-protective traits in the rhizosphere microbiome may be driven by the evolutionary pressure for resistance against predation by protists. Protists may therefore act as microbiome regulators promoting native bacteria involved in plant protection against diseases.

Shaving and breaking bacterial chains with a viscous flow

Some food and ferment manufacturing steps such as spray-drying result in the application of viscous stresses to bacteria. This study explores how a viscous flow impacts both bacterial adhesion functionality and bacterial cell organization using a combined experimental and modeling approach. As a model organism we study Lactobacillus rhamnosus GG (LGG) "wild type" (WT), known to feature strong adhesive affinities towards beta-lactoglobulin thanks to pili produced by the bacteria on cell surfaces, along with three cell-surface mutant strains. Applying repeated flows with high shear-rates reduces bacterial adhesive abilities up to 20% for LGG WT. Bacterial chains are also broken by this process, into 2-cell chains at low industrial shear rates, and into single cells at very high shear rates. To rationalize the experimental observations we study numerically and analytically the Stokes equations describing viscous fluid flow around a chain of elastically connected spheroidal cell bodies. In this model setting we examine qualitatively the relationship between surface traction (force per unit area), a proxy for pili removal rate, and bacterial chain length (number of cells). Longer chains result in higher maximal surface tractions, particularly at the chain extremities, while inner cells enjoy a small protection from surface tractions due to hydrodynamic interactions with their neighbors. Chain rupture therefore may act as a mechanism to preserve surface adhesive functionality in bacteria.

Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats

Many bacteria drastically change their cell size and morphology in response to changing environmental conditions. Here, we demonstrate that the freshwater bacterium Caulobacter crescentus and related species transform into filamentous cells in response to conditions that commonly occur in their natural habitat as a result of algal blooms during the warm summer months. These filamentous cells may be better able to scavenge nutrients when they grow in biofilms and to escape from protist predation during planktonic growth. Our findings suggest that seasonal changes and variations in the microbial composition of the natural habitat can have profound impact on the cell biology of individual organisms. Furthermore, our work highlights that bacteria exist in morphological and physiological states in nature that can strongly differ from those commonly studied in the laboratory.

All living cells are characterized by certain cell shapes and sizes. Many bacteria can change these properties depending on the growth conditions. The underlying mechanisms and the ecological relevance of changing cell shape and size remain unclear in most cases. One bacterium that undergoes extensive shape-shifting in response to changing growth conditions is the freshwater bacterium Caulobacter crescentus. When incubated for an extended time in stationary phase, a subpopulation of C. crescentus forms viable filamentous cells with a helical shape. Here, we demonstrated that this stationary-phase-induced filamentation results from downregulation of most critical cell cycle regulators and a consequent block of DNA replication and cell division while cell growth and metabolism continue. Our data indicate that this response is triggered by a combination of three stresses caused by prolonged growth in complex medium, namely, the depletion of phosphate, alkaline pH, and an excess of ammonium. We found that these conditions are experienced in the summer months during algal blooms near the surface in freshwater lakes, a natural habitat of C. crescentus, suggesting that filamentous growth is a common response of C. crescentus to its environment. Finally, we demonstrate that when grown in a biofilm, the filamentous cells can reach beyond the surface of the biofilm and potentially access nutrients or release progeny. Altogether, our work highlights the ability of bacteria to alter their morphology and suggests how this behavior might enable adaptation to changing environments.

Towards an eDNA metabarcode-based performance indicator for full-scale municipal wastewater treatment plants

Knowledge-driven management for wastewater treatment plant (WWTP) performance becomes increasingly important considering the globally growing production of wastewater and the rising demand of clean water supply. Even though the potential of microbial organisms (bacteria and protists) as bioindicators for WWTP performance is well known, it is far from being fully exploited for routine monitoring programs. Therefore, we here used massive sequencing of environmental (e)DNA metabarcodes from bacterial (V3-V4 region of the SSU rRNA gene) and eukaryote (V9 region of the SSU rRNA gene) communities in 21 activated sludge samples obtained from full-scale municipal WWTPs in Germany. Microbial community patterns were compared to standard WWTP operating parameters and two traditionally used WWTP performance indicators (Sludge Biotic Index and Sludge Index). Both indices showed low concordance and hardly correlated with chemical WWTP performance parameters nor did they correlate with microbial community structures. In contrast, microbial community profiles significantly correlated with WWTP performance parameters and operating conditions of the plants under study. Therefore, eDNA metabarcode profiles of whole microbial communities indicate the performance of WWTP and can provide useful information for management strategies. We here suggest a strategy for the development of an eDNA metabarcode based bioindicator system, which can be implemented in future standard monitoring programs for WWTP performance and effluent quality.

Phagocytosis: what's on the menu? 1

Phagocytosis is an evolutionarily conserved process. In Protozoa, phagocytosis fulfills a feeding mechanism, while in Metazoa, phagocytosis diversified to play multiple organismal roles, including immune defence, tissue homeostasis, and remodeling. Accordingly, phagocytes display a high level of plasticity in their capacity to recognize, engulf, and process targets that differ in composition and morphology. Here, we review how phagocytosis adapts to its multiple roles and discuss in particular the effect of target morphology in phagocytic uptake and phagosome maturation.

Interaction Between a Bacterivorous Ciliate Aspidisca cicada and a Rotifer Lecane inermis: Doozers and Fraggles in Aquatic Flocs

Activated sludge is a semi-natural habitat composed of macroaggregates made by flocculating bacteria and inhabited by numerous protozoans and metazoans, creating a complicated interactome. The activated sludge resembles the biological formation of naturally occurring floc habitats, such as "marine snow." So far, these two types of habitat have been analyzed separately, despite their similarities. We examined the effect of a bacterivorous ciliate, Aspidisca cicada, on the quality of the macroaggregate ecosystem by estimating (i) the floc characteristics, (ii) the proliferation of other bacterivores (rotifers), and (iii) the chemical processes. We found that A. cicada (i) positively affected floc quality by creating flocs of larger size; (ii) promoted the population growth of the rotifer Lecane inermis, an important biological agent in activated sludge systems; and (iii) increased the efficiency of ammonia removal while at the same time improving the oxygen conditions. The effect of A. cicada was detectable long after its disappearance from the system. We therefore claim that A. cicada is a very specialized scavenger of flocs with a key role in floc ecosystem functioning. These results may be relevant to the ecology of any natural and engineered aggregates.

Determinants of Bacterial Morphology: From Fundamentals to Possibilities for Antimicrobial Targeting

Bacterial morphology is extremely diverse. Specific shapes are the consequence of adaptive pressures optimizing bacterial fitness. Shape affects critical biological functions, including nutrient acquisition, motility, dispersion, stress resistance and interactions with other organisms. Although the characteristic shape of a bacterial species remains unchanged for vast numbers of generations, periodical variations occur throughout the cell (division) and life cycles, and these variations can be influenced by environmental conditions. Bacterial morphology is ultimately dictated by the net-like peptidoglycan (PG) sacculus. The species-specific shape of the PG sacculus at any time in the cell cycle is the product of multiple determinants. Some morphological determinants act as a cytoskeleton to guide biosynthetic complexes spatiotemporally, whereas others modify the PG sacculus after biosynthesis. Accumulating evidence supports critical roles of morphogenetic processes in bacteria-host interactions, including pathogenesis. Here, we review the molecular determinants underlying morphology, discuss the evidence linking bacterial morphology to niche adaptation and pathogenesis, and examine the potential of morphological determinants as antimicrobial targets.

Interplay between microbial trait dynamics and population dynamics revealed by the combination of laboratory experiment and computational approaches

Filament formation is a common bacterial defense mechanism and possibly has a broad impact on microbial community dynamics. In order to examine the impact of filament formation on population dynamics, we developed an experimental system with a filamentous bacterium Flectobacillus sp. MWH38 and a ciliate predator Tetrahymena pyriformis. In this system, the effective defense of Flectobacillus resulted in the extinction of Tetrahymena by allowing almost no population growth. The result of a kairomone experiment suggested the existence of chemical signals for filament formation. To examine the mechanism further, we developed a quantitative mechanistic model and optimized the model for the experimental result using the simulated annealing method. We also performed a global parameter sensitivity analysis using an approximated Bayesian computation based on the sequential Monte Carlo method to reveal parameters to which the model behavior is sensitive to. Our model reproduced the population dynamics, as well as the cell size dynamics of Flectobacillus. The model behavior is sensitive to the nutrient uptake of Flectobacillus and the propensity of filament formation. It robustly predicts the extinction of Tetrahymena at the condition used in the experiment and predicts the transition from equilibrium to population cycle at higher nutrient conditions. Contrary to the previous study that disproved the presence of chemical signals for filament formation, our result suggested the importance of chemical signals at low predator density, suggesting the variety in bacterial resistance mechanisms that act at different stages of predator-prey interactions.

Green algae and the origins of multicellularity in the plant kingdom

The green lineage of chlorophyte algae and streptophytes form a large and diverse clade with multiple independent transitions to produce multicellular and/or macroscopically complex organization. In this review, I focus on two of the best-studied multicellular groups of green algae: charophytes and volvocines. Charophyte algae are the closest relatives of land plants and encompass the transition from unicellularity to simple multicellularity. Many of the innovations present in land plants have their roots in the cell and developmental biology of charophyte algae. Volvocine algae evolved an independent route to multicellularity that is captured by a graded series of increasing cell-type specialization and developmental complexity. The study of volvocine algae has provided unprecedented insights into the innovations required to achieve multicellularity.

Differential growth of and nanoscale TiO₂ accumulation in Tetrahymena thermophila by direct feeding versus trophic transfer from Pseudomonas aeruginosa

Nanoscale titanium dioxide (TiO2) is increasingly used in consumer goods and is entering waste streams, thereby exposing and potentially affecting environmental microbes. Protozoans could either take up TiO2 directly from water and sediments or acquire TiO2 during bactivory (ingestion of bacteria) of TiO2-encrusted bacteria. Here, the route of exposure of the ciliated protozoan Tetrahymena thermophila to TiO2 was varied and the growth of, and uptake and accumulation of TiO2 by, T. thermophila were measured. While TiO2 did not affect T. thermophila swimming or cellular morphology, direct TiO2 exposure in rich growth medium resulted in a lower population yield. When TiO2 exposure was by bactivory of Pseudomonas aeruginosa, the T. thermophila population yield and growth rate were lower than those that occurred during the bactivory of non-TiO2-encrusted bacteria. Regardless of the feeding mode, T. thermophila cells internalized TiO2 into their food vacuoles. Biomagnification of TiO2 was not observed; this was attributed to the observation that TiO2 appeared to be unable to cross the food vacuole membrane and enter the cytoplasm. Nevertheless, our findings imply that TiO2 could be transferred into higher trophic levels within food webs and that the food web could be affected by the decreased growth rate and yield of organisms near the base of the web.

Emergent multicellular life cycles in filamentous bacteria owing to density-dependent population dynamics

Filamentous bacteria are the oldest and simplest known multicellular life forms. By using computer simulations and experiments that address cell division in a filamentous context, we investigate some of the ecological factors that can lead to the emergence of a multicellular life cycle in filamentous life forms. The model predicts that if cell division and death rates are dependent on the density of cells in a population, a predictable cycle between short and long filament lengths is produced. During exponential growth, there will be a predominance of multicellular filaments, while at carrying capacity, the population converges to a predominance of short filaments and single cells. Model predictions are experimentally tested and confirmed in cultures of heterotrophic and phototrophic bacterial species. Furthermore, by developing a formulation of generation time in bacterial populations, it is shown that changes in generation time can alter length distributions. The theory predicts that given the same population growth curve and fitness, species with longer generation times have longer filaments during comparable population growth phases. Characterization of the environmental dependence of morphological properties such as length, and the number of cells per filament, helps in understanding the pre-existing conditions for the evolution of developmental cycles in simple multicellular organisms. Moreover, the theoretical prediction that strains with the same fitness can exhibit different lengths at comparable growth phases has important implications. It demonstrates that differences in fitness attributed to morphology are not the sole explanation for the evolution of life cycles dominated by multicellularity.

A guide to the natural history of freshwater lake bacteria

Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.

Biomagnification of cadmium selenide quantum dots in a simple experimental microbial food chain

Previous studies have shown that engineered nanomaterials can be transferred from prey to predator, but the ecological impacts of this are mostly unknown. In particular, it is not known if these materials can be biomagnified-a process in which higher concentrations of materials accumulate in organisms higher up in the food chain. Here, we show that bare CdSe quantum dots that have accumulated in Pseudomonas aeruginosa bacteria can be transferred to and biomagnified in the Tetrahymena thermophila protozoa that prey on the bacteria. Cadmium concentrations in the protozoa predator were approximately five times higher than their bacterial prey. Quantum-dot-treated bacteria were differentially toxic to the protozoa, in that they inhibited their own digestion in the protozoan food vacuoles. Because the protozoa did not lyse, largely intact quantum dots remain available to higher trophic levels. The observed biomagnification from bacterial prey is significant because bacteria are at the base of environmental food webs. Our findings illustrate the potential for biomagnification as an ecological impact of nanomaterials.

Assessment of plausible bioindicators for plant performance in advanced wastewater treatment systems

Three full-scale advanced biological systems for nitrogen removal showing different efficiencies were assessed during one year, to investigate the protist communities supported in these wastewater treatment plants (WWTP). The main goal of this research was to explore the differences of these communities from those observed in conventional activated sludge systems. The final objective was to provide background support for the proposal of bioindicators in this type of biological systems, where scarce information was available until now, since only conventional systems had been previously studied from this point of view. Results obtained indicate that, in fact, protist population density and diversity in advanced systems for N-elimination are quite different from other wastewater systems studied before. A statistical approach through multivariate analysis was developed to search for association between protist species and physical-chemical system performance, and specifically N-removal efficiencies. The original hypothesis proposing that previous indicators from conventional systems are not adequate in advanced N-removal mechanisms was proved to be correct. Efficient processes on N-removal, despite what it had been usually found in conventional systems, show important flagellate and amoeba populations and these populations tend to reduce their abundances as nitrogen removal performance decreases (moderate to low). Ciliates are however less abundant in these N-removal efficient systems. Certain groups and genera of protist such as flagellates and small amoebae are thus proposed as indicative of high performance N-removal, while in this case the appearance of certain ciliates were indicative of low performance on N- or high organic matter removal (as COD) efficiencies.

Impact of protozoan grazing on nitrification and the ammonia- and nitrite-oxidizing bacterial communities in activated sludge

In activated sludge, protozoa feed on free-swimming bacteria and suspended particles, inducing flocculation and increasing the turnover rate of nutrients. In this study, the effect of protozoan grazing on nitrification rates under various conditions in municipal activated sludge batch reactors was examined, as was the spatial distribution of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) within the activated sludge. The reactors were monitored for ammonia, nitrite, nitrate, and total nitrogen concentrations, and bacterial numbers in the presence and absence of cycloheximide (a protozoan inhibitor), allylthiourea (an inhibitor of ammonia oxidation), and EDTA (a deflocculating agent). The accumulations of nitrate, nitrite, and ammonia were lower in batches without than with protozoa grazing. Inhibition of ammonia oxidation also decreased the amount of nitrite and nitrate accumulation. Inhibiting protozoan grazing along with ammonia oxidation further decreased the amounts of nitrite and nitrate accumulated. Induction of deflocculation led to high nitrate accumulation, indicating high levels of nitrification; this effect was lessened in the absence of protozoan grazing. Using fluorescent in situ hybridization and confocal laser scanning microscopy, AOB and NOB were found clustered within the floc, and inhibiting the protozoa, inhibiting ammonia oxidation, or inducing flocculation did not appear to lower the number of AOB and NOB present or affect their position within the floc. These results suggest that the AOB and NOB are present but less active in the absence of protozoa.

The selective value of bacterial shape

Why do bacteria have shape? Is morphology valuable or just a trivial secondary characteristic? Why should bacteria have one shape instead of another? Three broad considerations suggest that bacterial shapes are not accidental but are biologically important: cells adopt uniform morphologies from among a wide variety of possibilities, some cells modify their shape as conditions demand, and morphology can be tracked through evolutionary lineages. All of these imply that shape is a selectable feature that aids survival. The aim of this review is to spell out the physical, environmental, and biological forces that favor different bacterial morphologies and which, therefore, contribute to natural selection. Specifically, cell shape is driven by eight general considerations: nutrient access, cell division and segregation, attachment to surfaces, passive dispersal, active motility, polar differentiation, the need to escape predators, and the advantages of cellular differentiation. Bacteria respond to these forces by performing a type of calculus, integrating over a number of environmental and behavioral factors to produce a size and shape that are optimal for the circumstances in which they live. Just as we are beginning to answer how bacteria create their shapes, it seems reasonable and essential that we expand our efforts to understand why they do so.

Mesocosm-scale evaluation of faunal and microbial communities of aerated and unaerated leachfield soil

Aeration improves the capacity of leachfields to decontaminate and reduce the nutrient load of wastewater. To gain a better understanding of the effects of aeration, we examined the faunal and microbial communities of septic system leachfield soil (0-4 and 4-13 cm) using replicated (n = 3) mesocosms that were actively aerated (AIR) or unaerated (LEACH). Protozoa were 40 to 140 times more abundant in AIR than in LEACH soil. No nematodes were found in LEACH soil, whereas AIR soil contained 5 to 14 x 10(3) nematodes (all bacteriovores) kg(-1). Active microbial biomass was four to five times higher in AIR than LEACH soil. Proteobacteria and actinomycetes/sulfate-reducing bacteria constituted a higher proportion of the community in AIR soil, whereas anaerobic Gram-negative bacteria/firmicutes were more prominent in LEACH soil. Ratios of prokaryotic to eukaryotic phospholipid fatty acids (PLFAs) were higher in LEACH soil, as were membrane stress index values, whereas the starvation index was higher in AIR soil. Community-level physiological profiles showed that 29 and 30 different substrates were used for growth by LEACH and AIR soil microorganisms, respectively. The AIR soil had more microorganisms capable of growing on 10 substrates, whereas growth on two substrates was higher in LEACH soil. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S rRNA gene fragments revealed greater diversity of dominant phylotypes in AIR than LEACH soil, with communities separated by treatment. Aerated leachfield soil had a larger and more diverse faunal and microbial community than unaerated soil, possibly due to differences in the type and availability of electron acceptors.

Direct and indirect effects of protist predation on population size structure of a bacterial strain with high phenotypic plasticity

We studied the impact of grazing and substrate supply on the size structure of a freshwater bacterial strain (Flectobacillus sp.) which showed pronounced morphological plasticity. The cell length varied from 2 to >40 microm and encompassed rods, curved cells, and long filaments. Without grazers and with a sufficient substrate supply, bacteria grew mainly in the form of medium-sized rods (4 to 7 microm), with a smaller proportion (<10%) of filamentous forms. Grazing experiments with the bacterivorous flagellate Ochromonas sp. showed that freely suspended cells of <7 microm were highly vulnerable to grazers, whereas filamentous cells were resistant to grazing and became enriched during predation. A comparison of long-term growth in carbon-limited chemostats with and without grazers revealed that strikingly different bacterial populations developed: treatments with flagellates were composed of >80% filamentous cells. These attained a biomass comparable to that of populations in chemostats without grazers, which were composed of medium-sized rods and c-shaped cells. Carbon starvation resulted in a fast decrease in cell length and a shift towards small rods, which were highly vulnerable to grazing. Dialysis bag experiments in combination with continuous cultivation revealed that filament formation was significantly enhanced even without direct contact of bacteria with bacterivores and was thus probably stimulated by grazer excretory products.

Integrating decay, storage, kinetic selection, and filamentous backbone factors in a bacterial competition model

Filamentous bulking in activated sludge systems occurs when filamentous organisms outgrow floc-forming bacteria and interfere with sludge settling. The competition between filaments and floc formers has been described previously using the kinetic selection and filamentous backbone theories. We hypothesized that differences in decay rates and storage abilities also affect this competition. We tested this hypothesis by integrating these four factors into a substrate-utilization model to predict and explain coexistence in a completely mixed reactor. In addition, filamentous and nonfilamentous sludges were developed in laboratory-scale reactors and analyzed to determine decay rates. The modeling results showed coexistence of the two organism types, and sensitivity analysis showed that the kinetic parameters, storage rate constants, and backbone coefficient had the greatest effect on the simulation results. Monte Carlo simulation showed the effect of storage, and the ranges of dilution rates wherein one group outcompeted the other were delineated.

Low-temperature growth of Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is a mesophilic bacterium with a maximum growth temperature of approximately 35 degrees C but the ability to grow over a wide range of temperatures, including temperatures near zero. At room temperature ( approximately 22 degrees C) MR-1 grows with a doubling time of about 40 min, but when moved from 22 degrees C to 3 degrees C, MR-1 cells display a very long lag phase of more than 100 h followed by very slow growth, with a doubling time of approximately 67 h. In comparison to cells grown at 22 degrees C, the cold-grown cells formed long, motile filaments, showed many spheroplast-like structures, produced an array of proteins not seen at higher temperature, and synthesized a different pattern of cellular lipids. Frequent pilus-like structures were observed during the transition from 3 to 22 degrees C.

Influence of aquatic microbiota on the survival in water of the human and eel pathogen Vibrio vulnificus serovar E

The eel and human pathogen Vibrio vulnificus serovar E (biotype 2) is seldom isolated from natural waters, although it can survive in sterilized artificial seawater microcosms for years. The main objective of the present study was to investigate whether aquatic microbiota can limit its survival and recovery from water samples. A set of preliminary experiments of survival in microcosms containing natural seawater and water from eel farms showed that the persistence of this pathogen was mainly controlled by grazing, and secondarily by bacterial competition. The bacterial competition was further analysed in artificial seawater microcosms co-inoculated with selected virulent serovar E (VSE) strains and potential competitors. Competitors included V. vulnificus biotype 1 isolates and strains of selected species that can grow on the selective media designed for V. vulnificus isolation from water samples. Evidences of bacterial competition that was detrimental for VSE recovery were recorded. Thus, some species produced a deleterious effect on VSE strains under starvation, and others were able to use the resources more efficiently under nutrient input. These results suggest that an overgrowth of more efficient competitor bacteria in conventional media used for isolation of V. vulnificus could mask the recovery of VSE strains and explain the scarcity of reports on the isolation of this human and eel pathogen from natural waters.

Successful predation of filamentous bacteria by a nanoflagellate challenges current models of flagellate bacterivory

Current models suggest that (i) filamentous bacteria are protected against predation by nanoflagellates, (ii) prey size is positively correlated with prey-predator contact probability, and (iii) contact probability is mainly responsible for size-selective predation by interception-feeding flagellates. We used five strains of filamentous bacteria and one bacterivorous nanoflagellate, Ochromonas sp. strain DS, to test these assumptions. The five strains, including one spirochete and four Betaproteobacteria strains, were isolated by the filtration-acclimatization method. All five strains possess flexible cells, but they differ in average cell length, which ranged from 4.5 to 13.7 micro m. High-resolution video microscopy was used to measure contact, capture, and ingestion rates, as well as selectivity of the flagellate feeding. Growth and feeding experiments with satiating and nonsatiating food conditions, as well as experiments including alternative well-edible prey, were performed. In contrast to predictions by current models, the flagellate successfully consumed all the tested filamentous strains. The ingestion rate was negatively correlated with bacterial length. On the other hand, the lengths of the filamentous bacteria were not positively correlated to the contact rate and capture rate but were negatively correlated to ingestion efficiency. In experiments including alternative nonfilamentous prey, the flagellates showed negative selection for filamentous bacteria, which was independent of food concentration and is interpreted as a passive selection. Our observations indicate that (i) size alone is not sufficient to define a refuge for filamentous bacteria from nanoflagellate predation and (ii) for the investigated filamentous bacteria, prey-predator contact probability could be more influenced by factors other than the prey size.

Impact of protozoan grazing on bacterial community structure in soil microcosms

The influence of grazing by a mixed assemblage of soil protozoa (seven flagellates and one amoeba) on bacterial community structure was studied in soil microcosms amended with a particulate resource (sterile wheat roots) or a soluble resource (a solution of various organic compounds). Sterilized soil was reinoculated with mixed soil bacteria (obtained by filtering and dilution) or with bacteria and protozoa. Denaturing gradient gel electrophoresis (DGGE) of PCR amplifications of 16S rRNA gene fragments, as well as community level physiological profiling (Biolog plates), suggested that the mixed protozoan community had significant effects on the bacterial community structure. Excising and sequencing of bands from the DGGE gels indicated that high-G+C gram-positive bacteria closely related to Arthrobacter spp. were favored by grazing, whereas the excised bands that decreased in intensity were related to gram-negative bacteria. The percentages of intensity found in bands related to high G+C gram positives increased from 4.5 and 12.6% in the ungrazed microcosms amended with roots and nutrient solution, respectively, to 19.3 and 32.9% in the grazed microcosms. Protozoa reduced the average bacterial cell size in microcosms amended with nutrient solution but not in the treatment amended with roots. Hence, size-selective feeding may explain some but not all of the changes in bacterial community structure. Five different protozoan isolates (Acanthamoeba sp., two species of Cercomonas, Thaumatomonas sp., and Spumella sp.) had different effects on the bacterial communities. This suggests that the composition of protozoan communities is important for the effect of protozoan grazing on bacterial communities.

Ciliate communities of rotating biological contactor biofilms: a multivariate approach

Physical-chemical monitoring and characterization of ciliate communities from a full-scale rotating biological system (RBC) have been carried out for a year. RBC system operated efficiently in removing the organic matter, as the decrease of the BOD5 loading along the successive RBC units revealed. 55 species of ciliated protozoa were identified in the RBC biofilms. Differences in abundance, occurrence and type of species were found along the different units of the RBC system; the last RBC held a more stable and diverse ciliate community. The complexity of interspecific relationships among the ciliates has been outlined using multivariate methods (Cluster and Correspondence analysis). Correlation between ciliate species and physical-chemical conditions were obtained by regression analysis. Results show that 12 species of ciliates were related to an optimal efficiency in organic matter removal, Litonotus crystallinus being the most sensitive species. The presence and abundance of Litonotus crystallinus and Acineria uncinata was associated with a decrease in the organic factor. Metopus es was the only species related to a decrease in process efficiency due to its association with an increase in organic factor. The results provide statistical evidence of the use of certain ciliate species as reliable bioindicators in full-scale RBC wastewater treatment plants.

The interaction of protozoa with their potential prey bacteria in the rhizosphere

Extensive colonization of the rhizosphere by beneficial bacteria is desirable but it is not yet clear whether the feeding patterns of protozoa exert any ecological impact on the competence of bacteria in the rhizosphere. To determine whether the successful colonization of the rhizosphere by bacteria can be explained by inherent abilities of the bacteria to resist predation, six bacteria categorized as poor, mediocre or good rhizosphere colonists were tested. The populations of protozoa in the rhizosphere consistently increased to a maximum density in two days but then declined to a stable level. Grazing by protozoa increased the doubling time of all of the test bacteria but did not significantly affect the final densities of bacteria in the rhizosphere. The differences in the colonization ability of the six bacteria tested were not attributable to inherent differences in their susceptibility to predation by protozoa.

Grazing of protozoa and its effect on populations of aquatic bacteria

Predation by bacterivorous protists in aquatic habitats can influence the morphological structure, taxonomic composition and physiological status of bacterial communities. The protistan grazing can result in bacterial responses at the community and the species level. At the community level, grazing-induced morphological shifts have been observed, which were directed towards either larger or smaller bacterial sizes or in both directions. Morphological changes have been accompanied by changes in taxonomic community structure and bacterial activity. Responses at the species level vary from species to species. Some taxa have shown a pronounced morphological plasticity and demonstrated complete or partial shifts in size distribution to larger growth forms (filaments, microcolonies). However, other taxa with weak plasticity have shown no ability to reduce grazing mortality through changes in size. The impact of protistan grazing on bacterial communities is based on the complex interplay of several parameters. These include grazing selectivity (by size and other features), differences in sensitivity of bacterial species to grazing, differences in responses of single bacterial populations to grazing (size and physiology), as well as the direct and indirect influence of grazing on bacterial growth conditions (substrate supply) and bacterial competition (elimination of competitors).

Particle handling during interception feeding by four species of heterotrophic nanoflagellates

High resolution video-microscopy was used to observe grazing patterns of the heterotrophic nanoflagellates Cafeteria roenbergensis, Bodo saltans, Spumella sp., and Ochromonas sp. Spumella and Ochromonas enclose food particles with pseudopodia while Cafeteria and Bodo engulf particles by invagination of the cell surface. The following parameters of the feeding process were quantified: frequency of flagellar beating, speed of particles in different positions of the feeding current, food size selection, feeding rate, and the time budget for the handling of particles. The mean handling times differed between 94 s for Cafeteria and 4 s for Ochromonas for ingested particles. Handling times for ingested particles were significantly longer than for non-captured particles. Long handling times were calculated to be disadvantageous only for flagellates which propel a high water volume per hour (esp. Ochromonas) or live in a bacteria-rich environment. Our model calculations may provide a reasonable theoretical explanation for a concentration-dependent behavioural variability of the feeding strategy of different heterotrophic nanoflagellates (HNF) species.

Morphological and compositional changes in a planktonic bacterial community in response to enhanced protozoan grazing

We analyzed changes in bacterioplankton morphology and composition during enhanced protozoan grazing by image analysis and fluorescent in situ hybridization with group-specific rRNA-targeted oligonucleotide probes. Enclosure experiments were conducted in a small, fishless freshwater pond which was dominated by the cladoceran Daphnia magna. The removal of metazooplankton enhanced protozoan grazing pressure and triggered a microbial succession from fast-growing small bacteria to larger grazing-resistant morphotypes. These were mainly different types of filamentous bacteria which correlated in biomass with the population development of heterotrophic nanoflagellates (HNF). Small bacterial rods and cocci, which showed increased proportion after removal of Daphnia and doubling times of 6 to 11 h, belonged nearly exclusively to the beta subdivision of the class Proteobacteria and the Cytophaga-Flavobacterium cluster. The majority of this newly produced bacterial biomass was rapidly consumed by HNF. In contrast, the proportion of bacteria belonging to the gamma and alpha subdivisions of the Proteobacteria increased throughout the experiment. The alpha subdivision consisted mainly of rods that were 3 to 6 microm in length, which probably exceeded the size range of bacteria edible by protozoa. Initially, these organisms accounted for less than 1% of total bacteria, but after 72 h they became the predominant group of the bacterial assemblage. Other types of grazing-resistant, filamentous bacteria were also found within the beta subdivision of Proteobacteria and the Cytophaga-Flavobacterium cluster. We conclude that the predation regimen is a major structuring force for the bacterial community composition in this system. Protozoan grazing resulted in shifts of the morphological as well as the taxonomic composition of the bacterial assemblage. Grazing-resistant filamentous bacteria can develop within different phylogenetic groups of bacteria, and formerly underepresented taxa might become a dominant group when protozoan predation is the major selective pressure.

Bacterial filament formation, a defense mechanism against flagellate grazing, is growth rate controlled in bacteria of different phyla

A facultatively filamentous bacterium was isolated from eutrophic lake water and was identified as Flectobacillus sp. strain MWH38 (a member of the Cytophaga-Flavobacterium-Bacteroides phylum) by comparative 16S rRNA gene sequence analysis. Filament formation by Flectobacillus sp. strain MWH38 and filament formation by Flectobacillus major, the closest known relative of strain MWH38, were studied in chemostat cultures under grazing pressure by the bacterivorous flagellate Ochromonas sp. strain DS and without predation at several growth rates. The results clearly demonstrated that filament formation by the two flectobacilli is growth rate controlled and thus independent of the presence of a predator. However, flagellate grazing positively influenced bacterial growth rates by decreasing bacterial biomass and thus indirectly stimulated filament formation. The results of investigations of cell elongation and filament formation by Comamonas acidovorans PX54 (a member of the beta subclass of the class Proteobacteria) supported the recent proposal that in this species the mechanism of filament formation is growth rate controlled. The finding that the grazing defense mechanism consisting of filament formation is growth rate controlled in the flectobacilli investigated and C. acidovorans PX54 (i.e., in bacteria belonging to divergent evolutionary phyla) may indicate that this mechanism is a phylogenetically widely distributed defense strategy against grazing.

Serratia liquefaciens swarm cells exhibit enhanced resistance to predation by Tetrahymena sp

Tetrahymena sp. was found to graze extensively on Serratia liquefaciens MG1 swim cells (1.5-3 microns long rods) resulting in the rapid elimination of the bacterial strain. However, when S. liquefaciens cells are exposed to certain surfaces they differentiate into elongated, highly motile swarm cells and these cells were found to be grazing-resistant provided their length exceeded 15 microns.

Grazing Pressure by a Bacterivorous Flagellate Reverses the Relative Abundance of Comamonas acidovorans PX54 and Vibrio Strain CB5 in Chemostat Cocultures

The response of the bacterial strains Comamonas acidovorans PX54 (beta subclass of the class Proteobacteria) and Vibrio strain CB5 (gamma subclass of the class Proteobacteria) to grazing by the bacterivorous flagellate Ochromonas sp. was examined in one-stage chemostat experiments under conditions of low growth rates with a complex carbon source. The two bacterial strains were cultured together; they were cultured without flagellates in the first phase of the experiments and in the presence of the flagellates in the second phase. Monoclonal and polyclonal antibodies were used to determine the numbers and sizes of C. acidovorans PX54 and Vibrio strain CB5 cells. The flagellates caused strong changes in total bacterial cell numbers, in the relative abundances of the individual bacterial strains, and in bacterial cell size distribution. Vibrio strain CB5 dominated the total bacterial cell numbers during the flagellate-free phase of the experiments with a relative abundance of 93%, but this declined to 33% after inoculation with the flagellate. In contrast to Vibrio strain CB5, C. acidovorans PX54 responded to grazing with a strong expansion of cell length distribution toward large, filamentous cells. These changes in cell morphology resulted in a high percentage of inedible cells in the C. acidovorans PX54 population but not in the Vibrio strain CB5 population, which caused the observed change in the relative abundances of the strains. Batch culture experiments without the flagellate demonstrated that the elongation of C. acidovorans PX54 cells was dependent on their growth rate. This indicates that the occurrence of filamentous C. acidovorans PX54 cells is not a direct response to chemical stimuli released by the flagellates but rather a response to increased growth rates due to flagellate grazing.

Grazing of Tetrahymena sp. on adhered bacteria in percolated columns monitored by in situ hybridization with fluorescent oligonucleotide probes

Predation of attached Pseudomonas putida mt2 by the small ciliate Tetrahymena sp. was investigated with a percolated column system. Grazing rates were examined under static and dynamic conditions and were compared to grazing rates in batch systems containing suspended prey. The prey densities were 2 x 10(8) bacteria per ml of pore space and 2 x 10(8) bacteria per ml of suspension, respectively. Postingestion in situ hybridization of bacteria with fluorescent oligonucleotide probes was used to quantify ingestion. During 30 min, a grazing rate of 1,382 +/- 1,029 bacteria individual-1 h-1 was obtained with suspended prey; this was twice the grazing rate observed with attached bacteria under static conditions. Continuous percolation at a flow rate of 73 cm h-1 further decreased the grazing rate to about 25% of the grazing rate observed with suspended prey. A considerable proportion of the protozoans fed on neither suspended bacteria nor attached bacteria. The transport of ciliates through the columns was monitored at the same time that predation was monitored. Less than 20% of the protozoans passed through the columns without being retained. Most of these organisms ingested no bacteria, whereas the retained protozoans grazed more efficiently. Retardation of ciliate transport was greater in columns containing attached bacteria than in bacterium-free columns. We propose that the correlation between grazing activity and retardation of transport is a consequence of the interaction between active predators and attached bacteria.

Bioprotection of microbial communities from toxic phenol mixtures by a genetically designed pseudomonad

Pseudomonas sp. B13 SN45RE is a genetically engineered microorganism (GEM) that is able to simultaneously degrade mixtures of chloro- and methylaromatics ordinarily toxic for microbial communities via a designed novel ortho-cleavage pathway. The utility of the GEM was investigated in a laboratory scale sewage plant fed with mixtures of either 4-chlorophenol and 4-methyphenol or 3-chlorophenol and 4-methylphenol. In the model system the GEM significantly increased the rate and extent of degradation of the phenol mixtures. In the absence of the GEM, shock loads of the phenol mixtures (1 mM of each compound) reduced the numbers of culturable bacteria by three orders of magnitude, completely eliminated protozoa and metazoa, and caused a drastic decrease in oxygen consumption, whereas the presence of the GEM protected the indigenous microbial community and assured continued functioning of the sewage plant.

Permanent presence of grazing-resistant bacteria in a hypertrophic lake

The size structure of planktonic bacteria from a hypertrophic lake was investigated at 5- to 15-day intervals by means of a semiautomatic image analysis system during 1 year. Characteristic of this bacterial assemblage was the permanent presence of large filamentous bacteria and small cocci with cell sizes of <0.01 (mu)m(sup3). These filamentous bacteria, sometimes longer than 200 (mu)m and with cell volumes of up to 276 (mu)m(sup3), are larger than nanoflagellates (<20 (mu)m) and, even, metazoans living in the lake. Although they account for only 4 to 16% of bacterial abundance, their contribution to total bacterial biovolume was between 45 and 86%. An analysis of the food web structure indicates that this particular bacterial size structure may be the consequence of a strong bacterivory pressure by nanoflagellates and the absence of other larger bacterivores. The persistence of bacterial forms resistant to grazing has important consequences for the carbon flow within the microbial food web.

Notes on protozoa in agricultural soil with emphasis on heterotrophic flagellates and naked amoebae and their ecology

Heterotrophic flagellates and naked amoebae are usually very numerous in agricultural soils; with numbers in the magnitude of 10,000 to 100,000 (active+encysted) cells per gram of soil. In 'hotspots' influenced by living roots or by dead organic material, the number may occasionally be as high as several millions per gram of soil. An exact enumeration of these organisms is virtually impossible. As they most often adhere closely to the soil particles, direct counting will underestimate numbers since the organisms will be masked. The method usually applied for enumeration of these organisms, the 'most probable number (MPN) method', is based on the ability of the organisms to grow on particular culture media. This method will in many cases underestimate the total protozoan number (active+encysted). It is uncertain how many of the heterotrophic flagellates and naked amoebae are actively moving and how many are encysted at a particular time; the 'HCl-method' which has usually been used to discriminate between active and encysted has proven to be highly unreliable. Despite the methodological difficulties many investigations of these organisms indicate that they play an important role in agricultural soils as bacterial consumers, and to a minor extent as consumers of fungi. Because of their small size and their flexible body they are able to graze bacteria in small pores in the soil in which larger organisms are precluded from coming. Key factors restricting the number and activity of heterotrophic flagellates and naked amoebae in soils seem to be water potential and soil structure and texture. In micro-cosm experiments, small heterotrophic flagellates and naked amoebae regulate the size and composition of the bacterial community. Bacterial activity seems to be stimulated by these organisms in most cases as well as the mineralization of carbon and nitrogen and possibly other mineral nutrients. In the rhizosphere of living plants the activity of protozoa has proven to stimulate uptake of nitrogen in pot experiments, and it has been hypothesized that organic matter liberated by plants in the root zone will stimulate bacterial and protozoan activity, leading to mineralization of organic soil nitrogen which is subsequently taken up by the plants.

Family Spirosomaceae: gram-negative ring-forming aerobic bacteria

The bacteria having a unique ring-like morphology first isolated from nasal mucus by Weibel in 1887 were classified as a new genus Spirosoma by Migula in 1894. However, because these bacteria were not completely described for taxonomic purposes and their cultures were no longer available, the genus was deleted from the Bergey's Manual of Determinative Bacteriology, 6th edition, 1948. Orskov (1928) created a new genus "Microcyclus" (a name that has been found to be illegitimate and replaced with Ancylobacter by Raj 1983) to describe these nonmotile vibroid bacteria that occasionally formed ring-like structures. Several similar isolates found in many countries during the last 60 years were readily identified with this genus on the basis of the characteristic morphology alone. For the first time, these fascinating bacteria were extensively reviewed by Raj in 1977 and again in 1981. However, during the last decade, the systematics of these microcyclus bacteria has been reexamined and redefined. It has been shown that these Gram-negative ring-forming aerobic bacteria constitute a heterogeneous group of five genera: Ancylobacter, Cyclobacterium, Flectobacillus, Runella, and Spirosoma; the last four genera have been grouped into a family Spirosomaceace (reviving the old discarded name originally proposed by Migula 1894), thus separating them from the genus Ancylobacter which remains unaffiliated with any family yet (Bergey's Manual of Systematic Bacteriology, Vol. I, 9th ed., 1984). Also, this article reviews the recent studies reported on the ecology, morphogenesis, metabolism, and physiology of the picturesque bacteria.

Unusual bloom of star-like prosthecate bacteria and filaments as a consequence of grazing pressure

In seawater used for shrimp aquaculture in French Polynesia, the grazing of small bacteria (rods and coccoids) allowed the growth ofAncalomicrobium cells (to more than 2×10(6) cells ml(-1)) and large filaments > 10μm in length (5×10(6) cells ml(-1)). Their contribution to the increase in total bacterial number after grazing was 27.8 and 9.8%, respectively. These large bacteria are not grazed on by microflagellates, but are available for mesoplankton larvae.