Microscale nutrient patches in planktonic habitats shown by chemotactic bacteria

Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients

Diffusion-based microfluidic devices can generate steady, arbitrarily shaped chemical gradients without requiring fluid flow and are ideal for studying chemotaxis of free-swimming cells such as bacteria. However, if microfluidic gradient generators are to be used to systematically study bacterial chemotaxis, it is critical to evaluate their performance with actual quantitative chemotaxis tests. We characterize and compare three diffusion-based gradient generators by confocal microscopy and numerical simulations, select an optimal design and apply it to chemotaxis experiments with Escherichia coli in both linear and nonlinear gradients. Comparison of the observed cell distribution along the gradients with predictions from an established mathematical model shows very good agreement, providing the first quantification of chemotaxis of free-swimming cells in steady nonlinear microfluidic gradients and opening the door to bacterial chemotaxis studies in gradients of arbitrary shape.

Fold-change detection and scalar symmetry of sensory input fields

Recent studies suggest that certain cellular sensory systems display fold-change detection (FCD): a response whose entire shape, including amplitude and duration, depends only on fold changes in input and not on absolute levels. Thus, a step change in input from, for example, level 1 to 2 gives precisely the same dynamical output as a step from level 2 to 4, because the steps have the same fold change. We ask what the benefit of FCD is and show that FCD is necessary and sufficient for sensory search to be independent of multiplying the input field by a scalar. Thus, the FCD search pattern depends only on the spatial profile of the input and not on its amplitude. Such scalar symmetry occurs in a wide range of sensory inputs, such as source strength multiplying diffusing/convecting chemical fields sensed in chemotaxis, ambient light multiplying the contrast field in vision, and protein concentrations multiplying the output in cellular signaling systems. Furthermore, we show that FCD entails two features found across sensory systems, exact adaptation and Weber's law, but that these two features are not sufficient for FCD. Finally, we present a wide class of mechanisms that have FCD, including certain nonlinear feedback and feed-forward loops. We find that bacterial chemotaxis displays feedback within the present class and hence, is expected to show FCD. This can explain experiments in which chemotaxis searches are insensitive to attractant source levels. This study, thus, suggests a connection between properties of biological sensory systems and scalar symmetry stemming from physical properties of their input fields.

Aggregation of chemotactic organisms in a differential flow

We study the effect of advection on the aggregation and pattern formation in chemotactic systems described by Keller-Segel-type models. The evolution of small perturbations is studied analytically in the linear regime complemented by numerical simulations. We show that a uniform differential flow can significantly alter the spatial structure and dynamics of the chemotactic system. The flow leads to the formation of anisotropic aggregates that move following the direction of the flow, even when the chemotactic organisms are not directly advected by the flow. Sufficiently strong advection can stop the aggregation and coarsening process that is then restricted to the direction perpendicular to the flow.

Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment

Lake mixing disrupts chemical and physical gradients that structure bacterial communities. A transplant experiment was designed to investigate the influence of post-mixing environmental conditions and biotic interactions on bacterial community composition. The experimental design was 3x2 factorial, where water was incubated from three different sources (epilimnion, hypolimnion, and mixed epilimnion and hypolimnion) at two different locations in the water column (epilimnion or hypolimnion). Three replicate mesocosms of each treatment were removed every day for 5 days for bacterial community profiling, assessed by automated ribosomal intergenic spacer analysis. There were significant treatment effects observed, and temperature was the strongest measured driver of community change (r=-0.66). Epilimnion-incubated communities changed more than hypolimnion-incubated. Across all treatments, we classified generalist, layer-preferential and layer-specialist populations based on occurrence patterns. Most classified populations were generalists that occurred in both strata, suggesting that communities were robust to mixing. In a network analysis of the mixed-inocula treatments, there was correlative evidence of inter-population biotic interactions, where many of these interactions involved generalists. These results reveal differential responses of bacterial populations to lake mixing and highlight the role of generalist taxa in structuring an emergent community-level response.

Resource patch formation and exploitation throughout the marine microbial food web

Exploitation of microscale (microm-mm) resource patches by planktonic microorganisms may influence oceanic trophodynamics and nutrient cycling. However, examinations of microbial behavior within patchy microhabitats have been precluded by methodological limitations. We developed a microfluidic device to generate microscale resource patches at environmentally realistic spatiotemporal scales, and we examined the exploitation of these patches by marine microorganisms. We studied the foraging response of three sequential levels of the microbial food web: a phytoplankton (Dunaliella tertiolecta), a heterotrophic bacterium (Pseudoalteromonas haloplanktis), and a phagotrophic protist (Neobodo designis). Population-level chemotactic responses and single-cell swimming behaviors were quantified. Dunaliella tertiolecta accumulated within a patch of NH4(+), simulating a zooplankton excretion, within 1 min of its formation. Pseudoalteromonas haloplanktis cells also exhibited a chemotactic response to patches of D. tertiolecta exudates within 30 s, whereas N. designis shifted swimming behavior in response to bacterial prey patches. Although they relied on different swimming strategies, all three organisms exhibited behaviors that permitted efficient and rapid exploitation of resource patches. These observations imply that microscale nutrient patchiness may subsequently trigger the sequential formation of patches of phytoplankton, heterotrophic bacteria, and protozoan predators in the ocean. Enhanced uptake and predation rates driven by patch exploitation could accelerate carbon flux through the microbial loop.

Rapid chemotactic response enables marine bacteria to exploit ephemeral microscale nutrient patches

Because ocean water is typically resource-poor, bacteria may gain significant growth advantages if they can exploit the ephemeral nutrient patches originating from numerous, small sources. Although this interaction has been proposed to enhance biogeochemical transformation rates in the ocean, it remains questionable whether bacteria are able to efficiently use patches before physical mechanisms dissipate them. Here we show that the rapid chemotactic response of the marine bacterium Pseudoalteromonas haloplanktis substantially enhances its ability to exploit nutrient patches before they dissipate. We investigated two types of patches important in the ocean: nutrient pulses and nutrient plumes, generated for example from lysed algae and sinking organic particles, respectively. We used microfluidic devices to create patches with environmentally realistic dimensions and dynamics. The accumulation of P. haloplanktis in response to a nutrient pulse led to formation of bacterial hot spots within tens of seconds, resulting in a 10-fold higher nutrient exposure for the fastest 20% of the population compared with nonmotile cells. Moreover, the chemotactic response of P. haloplanktis was >10 times faster than the classic chemotaxis model Escherichia coli, leading to twice the nutrient exposure. We demonstrate that such rapid response allows P. haloplanktis to colonize nutrient plumes for realistic particle sinking speeds, with up to a 4-fold nutrient exposure compared with nonmotile cells. These results suggest that chemotactic swimming strategies of marine bacteria in patchy nutrient seascapes exert strong influence on carbon turnover rates by triggering the formation of microscale hot spots of bacterial productivity.

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

Multiple forces structure natural microbial communities, but the relative roles and interactions of these drivers are poorly understood. Gradients of physical and chemical parameters can be especially influential. In traditional ecological theory, variability in environmental conditions across space and time represents habitat heterogeneity, which may shape communities. Here we used aquatic microbial communities as a model to investigate the relationship between habitat heterogeneity and community composition and dynamics. We defined spatial habitat heterogeneity as vertical temperature and dissolved oxygen (DO) gradients in the water column, and temporal habitat heterogeneity as variation throughout the open-water season in these environmental parameters. Seasonal lake mixing events contribute to temporal habitat heterogeneity by destroying and re-creating these gradients. Because of this, we selected three lakes along a range of annual mixing frequency (polymictic, dimictic, meromictic) for our study. We found that bacterial community composition (BCC) was distinct between the epilimnion and hypolimnion within stratified lakes, and also more variable within the epilimnia through time. We found stark differences in patterns of epilimnion and hypolimnion dynamics over time and across lakes, suggesting that specific drivers have distinct relative importance for each community.

The flow generated by an active olfactory system of the red swamp crayfish

Crayfish are nocturnal animals that mainly rely on their chemoreceptors to locate food. On a crayfish scale, chemical stimuli received from a distant source are dispersed by an ambient flow rather than molecular diffusion. When the flow is weak or absent, food searching can be facilitated by currents generated by the animal itself. Crayfish employ their anterior fan organs to produce a variety of flow patterns. Here we study the flow generated by Procambarus clarkii in response to odour stimulation. We found that while searching for food the crayfish generates one or two outward jets. These jets induce an inflow that draws odour to the crayfish's anterior chemoreceptors. We quantified velocity fields in the inflow region using Particle Image Velocimetry. The results show that the inflow velocity decreases proportionally to the inverse distance from the animal so that it takes about 100 s for an odour plume to reach the animal's chemoreceptors from a distance of 10 cm. We compare the inflow generated by live crayfish with that produced by a mechanical model. The model consists of two nozzles and an inlet and provides two jets and a sink so that the overall mass flux is zero. Use of the model enabled us to analyze the inflow at various jet parameters. We show that variation of directions and relative intensities of the jets allows the direction of odour attraction to be changed. These results provide a rationale for biomimetic robot design. We discuss sensitivity and efficiency of such a robot.

Neuroecology, chemical defense, and the keystone species concept

Neuroecology unifies principles from diverse disciplines, scaling from biophysical properties of nerve and muscle cells to community-wide impacts of trophic interactions. Here, these principles are used as a common fabric, woven from threads of chemosensory physiology, behavior, and population and community ecology. The "keystone species" concept, for example, is seminal in ecological theory. It defines a species whose impacts on communities are far greater than would be predicted from its relative abundance and biomass. Similarly, neurotoxins could function in keystone roles. They are rare within natural habitats but exert strong effects on species interactions at multiple trophic levels. Effects of two guanidine alkaloids, tetrodotoxin (TTX) and saxitoxin (STX), coalesce neurobiological and ecological perspectives. These molecules compose some of the most potent natural poisons ever described, and they are introduced into communities by one, or only a few, host species. Functioning as voltage-gated sodium channel blockers for nerve and muscle cells, TTX and STX serve in chemical defense. When borrowed by resistant consumer species, however, they are used either in chemical defense against higher order predators or for chemical communication as chemosensory excitants. Cascading effects of the compounds profoundly impact community-wide attributes, including species compositions and rates of material exchange. Thus, a diverse array of physiological traits, expressed differentially across many species, renders TTX and STX fully functional as keystone molecules, with vast ecological consequences at multiple trophic levels.

Microbial structuring of marine ecosystems

Despite the impressive advances that have been made in assessing the diversity of marine microorganisms, the mechanisms that underlie the participation of microorganisms in marine food webs and biogeochemical cycles are poorly understood. Here, we stress the need to examine the biochemical interactions of microorganisms with ocean systems at the nanometre to millimetre scale--a scale that is relevant to microbial activities. The local impact of microorganisms on biogeochemical cycles must then be scaled up to make useful predictions of how marine ecosystems in the whole ocean might respond to global change. This approach to microbial oceanography is not only helpful, but is in fact indispensable.

Evolution of microorganism locomotion induced by starvation

The search strategies of many organisms play a fundamental role in their competition to survive in a given environment. In this context, the propulsion systems of microorganisms have evolved during life history, to optimize the suitable use of energy they take from nutrients. Starting from a model for the motion of Brownian objects with internal energy depot, we show that the propulsion system of microorganisms has an optimal regimen while searching for new sources of food. Bacteria with a too low or too high energy expenditure in propulsion, moving in a nutrient-depleted environment, do not reach remote distances. In this sense, the mean square displacement has a maximum for a finite value of the propulsion rate. Species using the most efficient locomotion system have a considerable advantage for survival in hostile environments, a common situation in the ocean. Moreover, we found the existence of a lower size limit for useful locomotion. This suggests that, for organisms whose linear dimensions are below a certain threshold, it is advantageous not to use any propulsion mechanism at all, a result that is in agreement with what is observed in nature.

Power law rank-abundance models for marine phage communities

Metagenomic analyses suggest that the rank-abundance curve for marine phage communities follows a power law distribution. A new type of power law dependence based on a simple model in which a modified version of Lotka-Volterra predator-prey dynamics is sampled uniformly in time is presented. Biologically, the model embodies a kill the winner hypothesis and a neutral evolution hypothesis. The model can match observed power law distributions and uses very few parameters that are readily identifiable and characterize phage ecosystems. The model makes new untested predictions: (1) it is unlikely that the most abundant phage genotype will be the same at different time points and (2) the long-term decay of isolated phage populations follows a power law.

Prokaryotic lifestyles in deep sea habitats

Gradients of physicochemical factors influence the growth and survival of life in deep-sea environments. Insights into the characteristics of deep marine prokaryotes has greatly benefited from recent progress in whole genome and metagenome sequence analyses. Here we review the current state-of-the-art of deep-sea microbial genomics. Ongoing and future genome-enabled studies will allow for a better understanding of deep-sea evolution, physiology, biochemistry, community structure and nutrient cycling.

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

Microbes in the ocean dominate biogeochemical processes and are far more diverse than anticipated. Thus, in order to understand the ocean system, we need to delineate microbial populations with predictable ecological functions. Recent observations suggest that ocean communities comprise diverse groups of bacteria organized into genotypic (and phenotypic) clusters of closely related organisms. Although such patterns are similar to metazoan communities, the underlying mechanisms for microbial communities may differ substantially. Indeed, the potential among ocean microbes for vast population sizes, extensive migration and both homologous and illegitimate genetic recombinations, which are uncoupled from reproduction, challenges classical population models primarily developed for sexually reproducing animals. We examine possible mechanisms leading to the formation of genotypic clusters and consider alternative population genetic models for differentiation at individual loci as well as gene content at the level of whole genomes. We further suggest that ocean bacteria follow at least two different adaptive strategies, which constrain rates and bounds of evolutionary processes: the 'opportunitroph', exploiting spatially and temporally variable resources; and the passive oligotroph, efficiently using low nutrient concentrations. These ecological lifestyle differences may represent a fundamental divide with major consequences for growth and predation rates, genome evolution and population diversity, as emergent properties driving the division of labour within microbial communities.

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.

High-resolution fluorometer for mapping microscale phytoplankton distributions

A new high-resolution, in situ profiling fluorometer maps fluorescence distributions with a spatial resolution of 0.5 to 1.5 mm to a depth of 70 m in the open ocean. We report centimeter-scale patterns for phytoplankton distributions associated with gradients exhibiting 10- to 30-fold changes in fluorescence in contrasting marine ecosystems.

Volatile Foraging Kairomones in the Littoral Zone: Attraction of an Herbivorous Freshwater Gastropod to Algal Odors

Volatile organic compounds (VOCs) produced by algae and cyanobacteria are primarily responsible for odors in fresh waters. Among other functions, VOCs may serve as important infochemicals in biofilms of benthic primary producers. VOCs liberated by benthic, mat-forming cyanobacteria can be used as habitat-finding cues by insects, nematodes, and possibly other organisms. We developed a new gastropod behavioral assay that allows detection of food preference without offering food, thus allowing the distinction between taste, which requires direct contact with the food source, and the detection of odorous infochemicals, which work over distance. We demonstrated that VOCs released from disintegrated cells of a benthic, mat-forming, green alga (Ulothrix fimbriata) are food-finding cues ("foraging kairomones") that attract the herbivorous freshwater snail Radix ovata. A mixture of three C5 lipoxygenase compounds and 2(E),4(E)-heptadienal that mimic the major VOCs released by U. fimbriata attracted the snails, whereas neither the mixture of C5 compounds nor 2(E),4(E)-heptadienal were effective when given alone. This study suggests that VOCs can play a steering role as infochemicals in freshwater benthic habitats, as has been established for many organismic interactions in terrestrial ecosystems.

A Model for Bacterial Colonization of Sinking Aggregates

Sinking aggregates provide important nutrient-rich environments for marine bacteria. Quantifying the rate at which motile bacteria colonize such aggregations is important in understanding the microbial loop in the pelagic food web. In this paper, a simple analytical model is presented to predict the rate at which bacteria undergoing a random walk encounter a sinking aggregate. The model incorporates the flow field generated by the sinking aggregate, the swimming behavior of the bacteria, and the interaction of the flow with the swimming behavior. An expression for the encounter rate is computed in the limit of large Péclet number when the random walk can be approximated by a diffusion process. Comparison with an individual-based numerical simulation is also given.

Bacterial motility: links to the environment and a driving force for microbial physics

Bacterial motility was recognized 300 years ago. Throughout this history, research into motility has led to advances in microbiology and physics. Thirty years ago, this union helped to make run and tumble chemotaxis the paradigm for bacterial movement. This review highlights how this paradigm has expanded and changed, and emphasizes the following points. The absolute magnitude of swimming speed is ecologically important because it helps determine vulnerability to Brownian motion, sensitivity to gradients, the type of receptors used and the cost of moving, with some bacteria moving at 1 mm s(-1). High costs for high speeds are offset by the benefit of resource translocation across submillimetre redox and other environmental gradients. Much of environmental chemotaxis appears adapted to respond to gradients of micrometres, rather than migrations of centimetres. In such gradients, control of ion pumps is particularly important. Motility, at least in the ocean, is highly intermittent and the speed is variable within a run. Subtleties in flagellar physics provide a variety of reorientation mechanisms. Finally, while careful physical analysis has contributed to our current understanding of bacterial movement, tactic bacteria are increasingly widely used as experimental and theoretical model systems in physics.

The effect of oxygen on chemotaxis to naphthalene byPseudomonas putida G7

Chemotactic bacteria can be attracted to electron donors they consume. In systems where donor is heterogeneously distributed, chemotaxis can lead to enhanced removal of donor relative to that achieved in the absence of chemotaxis. However, simultaneous consumption of an electron acceptor may result in the formation of an acceptor gradient to which the bacteria also respond, thus diminishing the positive effect of chemotaxis. Depletion of an electron acceptor can also reduce the rate of electron donor consumption in addition to its effect on chemotaxis. In this study, we examined the effect of oxygen on chemotaxis to naphthalene and on naphthalene consumption by Pseudomonas putida G7. The organism was able to move up an oxygen gradient when there was a naphthalene gradient in the opposite direction. In the absence of an oxygen gradient, low levels of oxygen attenuated chemotaxis to naphthalene but did not affect random motility. The rate of naphthalene consumption decreased at dissolved oxygen concentrations similar to those at which chemotaxis was attenuated. These results suggest that low dissolved oxygen concentrations can reduce naphthalene removal by P. putida G7 in systems where naphthalene is heterogeneously distributed by simultaneously attenuating chemotactic motion toward naphthalene and decreasing the rate of naphthalene degradation.

Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton

While several studies have suggested that bacterium-phytoplankton interactions have the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at the species composition level. The objective of the current study was to determine whether there are specific associations between diverse phytoplankton and the bacteria that co-occur with them. We determined the phylogenetic diversity of bacterial assemblages associated with 10 Alexandrium strains and representatives of the major taxonomic groups of phytoplankton in the Gulf of Maine. For this analysis we chose xenic phytoplankton cultures that (i) represented a broad taxonomic range, (ii) represented a broad geographic range for Alexandrium spp. isolates, (iii) grew under similar cultivation conditions, (iv) had a minimal length of time since the original isolation, and (v) had been isolated from a vegetative phytoplankton cell. 16S rRNA gene fragments of most Bacteria were amplified from DNA extracted from cultures and were analyzed by denaturing gradient gel electrophoresis and sequencing. A greater number of bacterial species were shared by different Alexandrium cultures, regardless of the geographic origin, than by Alexandrium species and nontoxic phytoplankton from the Gulf of Maine. In particular, members of the Roseobacter clade showed a higher degree of association with Alexandrium than with other bacterial groups, and many sequences matched sequences reported to be associated with other toxic dinoflagellates. These results provide evidence for specificity in bacterium-phytoplankton associations.

Fate of heterotrophic microbes in pelagic habitats: focus on populations

Major biogeochemical processes in the water columns of lakes and oceans are related to the activities of heterotrophic microbes, e.g., the mineralization of organic carbon from photosynthesis and allochthonous influx or its transport to the higher trophic levels. During the last 15 years, cultivation-independent molecular techniques have substantially contributed to our understanding of the diversity of the microbial communities in different aquatic systems. In parallel, the complexity of aquatic habitats at a microscale has inspired research on the ecophysiological properties of uncultured microorganisms that thrive in a continuum of dissolved to particulate organic matter. One possibility to link these two aspects is to adopt a"Gleasonian" perspective, i.e., to study aquatic microbial assemblages in situ at the population level rather than looking at microbial community structure, diversity, or function as a whole. This review compiles current knowledge about the role and fate of different populations of heterotrophic picoplankton in marine and inland waters. Specifically, we focus on a growing suite of techniques that link the analysis of bacterial identity with growth, morphology, and various physiological activities at the level of single cells. An overview is given of the potential and limitations of methodological approaches, and factors that might control the population sizes of different microbes in pelagic habitats are discussed.

Predation on prokaryotes in the water column and its ecological implications

The oxic realms of freshwater and marine environments are zones of high prokaryotic mortality. Lysis by viruses and predation by ciliated and flagellated protists result in the consumption of microbial biomass at approximately the same rate as it is produced. Protist predation can favour or suppress particular bacterial species, and the successful microbial groups in the water column are those that survive this selective grazing pressure. In turn, aquatic bacteria have developed various antipredator strategies that range from simply 'outrunning' protists to the production of highly effective cytotoxins. This ancient predator-prey system can be regarded as an evolutionary precursor of many other interactions between prokaryotic and eukaryotic organisms.

Continuous-flow capillary assay for measuring bacterial chemotaxis

Bacterial chemotaxis may have a significant impact on the structure and function of bacterial communities. Quantification of chemotactic motion is necessary to identify chemoeffectors and to determine the bacterial transport parameters used in predictive models of chemotaxis. When the chemotactic bacteria consume the chemoeffector, the chemoeffector gradient to which the bacteria respond may be significantly perturbed by the consumption. Therefore, consumption of the chemoeffector can confound chemotaxis measurements if it is not accounted for. Current methods of quantifying chemotaxis use bacterial concentrations that are too high to preclude chemoeffector consumption or involve ill-defined conditions that make quantifying chemotaxis difficult. We developed a method of quantifying bacterial chemotaxis at low cell concentrations ( approximately 10(5) CFU/ml), so metabolism of the chemoeffector is minimized. The method facilitates quantification of bacterial-transport parameters by providing well-defined boundary conditions and can be used with volatile and semivolatile chemoeffectors.

High motility reduces grazing mortality of planktonic bacteria

We tested the impact of bacterial swimming speed on the survival of planktonic bacteria in the presence of protozoan grazers. Grazing experiments with three common bacterivorous nanoflagellates revealed low clearance rates for highly motile bacteria. High-resolution video microscopy demonstrated that the number of predator-prey contacts increased with bacterial swimming speed, but ingestion rates dropped at speeds of >25 microm s(-1) as a result of handling problems with highly motile cells. Comparative studies of a moderately motile strain (<25 microm s(-1)) and a highly motile strain (>45 microm s(-1)) further revealed changes in the bacterial swimming speed distribution due to speed-selective flagellate grazing. Better long-term survival of the highly motile strain was indicated by fourfold-higher bacterial numbers in the presence of grazing compared to the moderately motile strain. Putative constraints of maintaining high swimming speeds were tested at high growth rates and under starvation with the following results: (i) for two out of three strains increased growth rate resulted in larger and slower bacterial cells, and (ii) starved cells became smaller but maintained their swimming speeds. Combined data sets for bacterial swimming speed and cell size revealed highest grazing losses for moderately motile bacteria with a cell size between 0.2 and 0.4 microm(3). Grazing mortality was lowest for cells of >0.5 microm(3) and small, highly motile bacteria. Survival efficiencies of >95% for the ultramicrobacterial isolate CP-1 (< or =0.1 microm(3), >50 microm s(-1)) illustrated the combined protective action of small cell size and high motility. Our findings suggest that motility has an important adaptive function in the survival of planktonic bacteria during protozoan grazing.

Chemotaxis of Silicibacter sp. strain TM1040 toward dinoflagellate products

The alpha-proteobacteria phylogenetically related to the Roseobacter clade are predominantly responsible for the degradation of organosulfur compounds, including the algal osmolyte dimethylsulfoniopropionate (DMSP). Silicibacter sp. strain TM1040, isolated from a DMSP-producing Pfiesteria piscicida dinoflagellate culture, degrades DMSP, producing 3-methylmercaptopropionate. TM1040 possesses three lophotrichous flagella and is highly motile, leading to a hypothesis that TM1040 interacts with P. piscicida through a chemotactic response to compounds produced by its dinoflagellate host. A combination of a rapid chemotaxis screening assay and a quantitative capillary assay were used to measure chemotaxis of TM1040. These bacteria are highly attracted to dinoflagellate homogenates; however, the response decreases when homogenates are preheated to 80 degrees C. To help identify the essential attractant molecules within the homogenates, a series of pure compounds were tested for their ability to serve as attractants. The results show that TM1040 is strongly attracted to amino acids and DMSP metabolites, while being only mildly responsive to sugars and the tricarboxylic acid cycle intermediates. Adding pure DMSP, methionine, or valine to the chemotaxis buffer resulted in a decreased response to the homogenates, indicating that exogenous addition of these chemicals blocks chemotaxis and suggesting that DMSP and amino acids are essential attractant molecules in the dinoflagellate homogenates. The implication of Silicibacter sp. strain TM1040 chemotaxis in establishing and maintaining its interaction with P. piscicida is discussed.

Influences of temperature, salinity and starvation on the motility and chemotactic response of Vibrio anguillarum

The role of growth factors for the motility and chemotaxis of the fish pathogenVibrio anguillarumwas determined. Cells ofV. anguillarumwere chemotactic to serine in the temperature range 5–25 °C and in 0·8–2·7 % NaCl. The chemotactic response was significantly higher at 25 °C than at 5 or 15 °C. Growth in medium with 1·5 % NaCl gave a higher response than growth with 3 % NaCl; when the salinity of the chemotaxis buffer was raised, the chemotactic response was reduced. The role of starvation was also studied;V. anguillarumshowed a high chemotactic response after starvation for 2 and 8 days. Motility and chemotaxis are important virulence factors for this bacterium. Not only was the ability to perform chemotactic motility maintained after starvation, but also it was shown that starvation does not interfere with the ability of the organism to cause infection in rainbow trout after a bath challenge. The swimming speed was reduced at lower temperatures. Within the range of salinity and starvation studied, the motile cells swam with the same velocity, indicating thatV. anguillarumunder all the examined conditions has a functional flagellum and rotates it with constant speed. Phenamil, a specific inhibitor of Na+-driven flagella, reduced the motility of both starved and non-starved cells ofV. anguillarumindicating that, in both cases, a Na+motive force drives the flagellum.

Ecological role of energy taxis in microorganisms

Motile microorganisms rapidly respond to changes in various physico-chemical gradients by directing their motility to more favorable surroundings. Energy generation is one of the most important parameters for the survival of microorganisms in their environment. Therefore it is not surprising that microorganisms are able to monitor changes in the cellular energy generating processes. The signal for this behavioral response, which is called energy taxis, originates within the electron transport system. By coupling energy metabolism and behavior, energy taxis is fine-tuned to the environment a cell finds itself in and allows efficient adaptation to changing conditions that affect cellular energy levels. Thus, energy taxis provides cells with a versatile sensory system that enables them to navigate to niches where energy generation is optimized. This behavior is likely to govern vertical species stratification and the active migration of motile cells in response to shifting gradients of electron donors and/or acceptors which are observed within microbial mats, sediments and soil pores. Energy taxis has been characterized in several species and might be widespread in the microbial world. Genome sequencing revealed that many microorganisms from aquatic and soil environments possess large numbers of chemoreceptors and are likely to be capable of energy taxis. In contrast, species that have a fewer number of chemoreceptors are often found in specific, confined environments, where relatively constant environmental conditions are expected. Future studies focusing on characterizing behavioral responses in species that are adapted to diverse environmental conditions should unravel the molecular mechanisms underlying sensory behavior in general and energy taxis in particular. Such knowledge is critical to a better understanding of the ecological role of energy taxis.

Bacterial colonization of particles: growth and interactions

Marine particles in the ocean are exposed to diverse bacterial communities, and colonization and growth of attached bacteria are important processes in the degradation and transformation of the particles. In an earlier study, we showed that the initial colonization of model particles by individual bacterial strains isolated from marine aggregates was a function of attachment and detachment. In the present study, we have investigated how this colonization process was further affected by growth and interspecific interactions among the bacteria. Long-term incubation experiments showed that growth dominated over attachment and detachment after a few hours in controlling the bacterial population density on agar particles. In the absence of grazing mortality, this growth led to an equilibrium population density consistent with the theoretical limit due to oxygen diffusion. Interspecific interaction experiments showed that the presence of some bacterial strains ("residents") on the agar particles either increased or decreased the colonization rate of other strains ("newcomers"). Comparison between an antibiotic-producing strain and its antibiotic-free mutant showed no inhibitory effect on the newcomers due to antibiotic production. On the contrary, hydrolytic activity of the antibiotic-producing strain appeared to benefit the newcomers and enhance their colonization rate. These results show that growth- and species-specific interactions have to be taken into account to adequately describe bacterial colonization of marine particles. Changes in colonization pattern due to such small-scale processes may have profound effects on the transformation and fluxes of particulate matter in the ocean.

Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization

We describe here an automated system for the counting of multiple samples of double-stained microbial cells on sections of membrane filters. The application integrates an epifluorescence microscope equipped with motorized z-axis drive, shutters, and filter wheels with a scanning stage, a digital camera, and image analysis software. The relative abundances of specific microbial taxa are quantified in samples of marine picoplankton, as detected by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition. Pairs of microscopic images are automatically acquired from numerous positions at two wavelengths, and microbial cells with both general DNA and FISH staining are counted after object edge detection and signal-to-background ratio thresholding. Microscopic fields that are inappropriate for cell counting are automatically excluded prior to measurements. Two nested walk paths guide the device across a series of triangular preparations until a user-defined number of total cells has been analyzed per sample. A backup autofocusing routine at incident light allows automated refocusing between individual samples and can reestablish the focal plane after fatal focusing errors at epifluorescence illumination. The system was calibrated to produce relative abundances of FISH-stained cells in North Sea samples that were comparable to results obtained by manual evaluation. Up to 28 preparations could be analyzed within 4 h without operator interference. The device was subsequently applied for the counting of different microbial populations in incubation series of North Sea waters. Automated digital microscopy greatly facilitates the processing of numerous FISH-stained samples and might thus open new perspectives for bacterioplankton population ecology.

Physiological diversity and niche adaptation in marine Synechococcus

During the twenty years or so since the discovery of tiny photosynthetic cells of the genus Synechococcus in marine oceanic systems, a tremendous expansion of interest has been seen in the literature pertaining to these organisms. The fact that they are ubiquitous and abundant in major oceanic regimes underlies their ecological importance as significant contributors to marine C fixation. Recent advances in the physiology and biochemistry of these organisms are presented here, focusing on strains of the MC-A and MC-B clusters; it is stressed that the data contained herein should be put into the context of the ecological niche occupied by particular genotypes in situ. This system is ripe for joining the often separate disciplines of molecular ecology and microbial physiology and provides a great opportunity to tease out the underlying processes that both mediate organism evolution and also the environmental factors that dictate this.

Chemical cues for surface colonization

Colonization of surfaces in marine benthic environments is often one of the most significant moments in the life history of benthic organisms, representing, for example, a change from a planktonic to a benthic existence, a shift from a mobile to a sessile life form, or the initiation of pathogenesis. Many of the surfaces that are colonized are, in fact, other marine organisms, and in a general sense there is widespread evidence that specific chemical cues derived from marine organisms affect colonization by both marine prokaryotes and eukaryotes. However, detailed information for any one system on the nature of such cues, their distribution in situ, and their effects on the demography of colonizers is rare. Here, we selectively review the literature on chemical cues for colonization in the sea, focussing on contrasts between positive (inducers) and negative (inhibitors, deterrents) cues and on prokaryote/eukaryote interactions. We also consider whether generalized life history or natural history characteristics of colonizers (i.e., the mobility of a propagule, the extent to which a species is a habitat generalist or specialist, etc.) affect their response to chemical cues, and we touch briefly on some recent highlights relevant to the critical interplay between hydrodynamics and chemistry. A number of important methodological concerns are now being addressed through the introduction of field assays and analyses for chemical cues, and through molecular techniques for the characterization of microbial biofilms. These developments are encouraging, as is the increasingly multidisciplinary and cross-taxonomic approach to research in this area.

Mechanisms and rates of bacterial colonization of sinking aggregates

Quantifying the rate at which bacteria colonize aggregates is a key to understanding microbial turnover of aggregates. We used encounter models based on random walk and advection-diffusion considerations to predict colonization rates from the bacteria's motility patterns (swimming speed, tumbling frequency, and turn angles) and the hydrodynamic environment (stationary versus sinking aggregates). We then experimentally tested the models with 10 strains of bacteria isolated from marine particles: two strains were nonmotile; the rest were swimming at 20 to 60 microm s(-1) with different tumbling frequency (0 to 2 s(-1)). The rates at which these bacteria colonized artificial aggregates (stationary and sinking) largely agreed with model predictions. We report several findings. (i) Motile bacteria rapidly colonize aggregates, whereas nonmotile bacteria do not. (ii) Flow enhances colonization rates. (iii) Tumbling strains colonize aggregates enriched with organic substrates faster than unenriched aggregates, while a nontumbling strain did not. (iv) Once on the aggregates, the bacteria may detach and typical residence time is about 3 h. Thus, there is a rapid exchange between attached and free bacteria. (v) With the motility patterns observed, freely swimming bacteria will encounter an aggregate in <1 day at typical upper-ocean aggregate concentrations. This is faster than even starving bacteria burn up their reserves, and bacteria may therefore rely solely on aggregates for food. (vi) The net result of colonization and detachment leads to a predicted equilibrium abundance of attached bacteria as a function of aggregate size, which is markedly different from field observations. This discrepancy suggests that inter- and intraspecific interactions among bacteria and between bacteria and their predators may be more important than colonization in governing the population dynamics of bacteria on natural aggregates.

Growth patterns of two marine isolates: adaptations to substrate patchiness?

During bottle incubations of heterotrophic marine picoplankton, some bacterial groups are conspicuously favored. In an earlier investigation bacteria of the genus Pseudoalteromonas rapidly multiplied in substrate-amended North Sea water, whereas the densities of Oceanospirillum changed little (H. Eilers, J. Pernthaler, and R. Amann, Appl. Environ. Microbiol. 66:4634-4640, 2000). We therefore studied the growth patterns of two isolates affiliating with Pseudoalteromonas and Oceanospirillum in batch culture. Upon substrate resupply, Oceanospirillum lagged threefold longer than Pseudoalteromonas but reached more than fivefold-higher final cell density and biomass. A second, mobile morphotype was present in the starved Oceanospirillum populations with distinctly greater cell size, DNA and protein content, and 16S rRNA concentration. Contrasting cellular ribosome concentrations during stationary phase suggested basic differences in the growth responses of the two strains to a patchy environment. Therefore, we exposed the strains to different modes of substrate addition. During cocultivation on a single batch of substrates, the final cell densities of Oceanospirillum were reduced three times as much as those Pseudoalteromonas, compared to growth yields in pure cultures. In contrast, the gradual addition of substrates to stationary-phase cocultures was clearly disadvantageous for the Pseudoalteromonas population. Different growth responses to substrate gradients could thus be another facet affecting the competition between marine bacteria and may help to explain community shifts observed during enrichments.

Establishment of an animal-bacterial association: recruiting symbiotic vibrios from the environment

While most animal-bacterial symbioses are reestablished each successive generation, the mechanisms by which the host and its potential microbial partners ensure tissue colonization remain largely undescribed. We used the model association between the squid Euprymna scolopes and Vibrio fischeri to examine this process. This light organ symbiosis is initiated when V. fischeri cells present in the surrounding seawater enter pores on the surface of the nascent organ and colonize deep epithelia-lined crypts. We discovered that when newly hatched squid were experimentally exposed to natural seawater, the animals responded by secreting a viscous material from the pores of the organ. Animals maintained in filtered seawater produced no secretions unless Gram-negative bacteria, either living or dead, were reintroduced. The viscous material bound only lectins that are specific for either N-acetylneuraminic acid or N-acetylgalactosamine, suggesting that it was composed of a mucus-containing matrix. Complex ciliated fields on the surface of the organ produced water currents that focused the matrix into a mass that was tethered to, and suspended above, the light organ pores. When V. fischeri cells were introduced into the seawater surrounding the squid, the bacteria were drawn into its fluid-filled body cavity during ventilation and were captured in the matrix. After residing as an aggregate for several hours, the symbionts migrated into the pores and colonized the crypt epithelia. This mode of infection may be an example of a widespread strategy by which aquatic hosts increase the likelihood of successful colonization by rarely encountered symbionts.

A new system for three-dimensional tracking of motile microorganisms

A new three-dimensional (3D)-tracking system with optimized dark-field illumination is presented. It allows simultaneous 3D tracking of several free-swimming microorganisms with diameters of >10 microm. Resolution limits and illumination efficiencies for different size classes of microorganisms are treated analytically. First applications for 3D tracking of protists are demonstrated.

Physiological responses to starvation in the marine oligotrophic ultramicrobacterium Sphingomonas sp. strain RB2256

Sphingomonas sp. strain RB2256 is representative of the ultramicrobacteria that proliferate in oligotrophic marine waters. While this class of bacteria is well adapted for growth with low concentrations of nutrients, their ability to respond to complete nutrient deprivation has not previously been investigated. In this study, we examined two-dimensional protein profiles for logarithmic and stationary-phase cells and found that protein spot intensity was regulated by up to 70-fold. A total of 72 and 177 spots showed increased or decreased intensity, respectively, by at least twofold during starvation. The large number of protein spots (1,500) relative to the small genome size (ca. 1.5 Mb) indicates that gene expression may involve co- and posttranslational modifications of proteins. Rates of protein and RNA synthesis were examined throughout the growth phase and up to 7 days of starvation and revealed that synthesis was highly regulated. Rates of protein synthesis and cellular protein content were compared to ribosome content, demonstrating that ribosome synthesis was not directly linked to protein synthesis and that the function of ribosomes may not be limited to translation. By comparing the genetic capacity and physiological responses to starvation of RB2256 to those of the copiotrophic marine bacterium Vibrio angustum S14 (J. Ostling, L. Holmquist, and S. Kjelleberg, J. Bacteriol. 178:4901-4908, 1996), the characteristics of a distinct starvation response were defined for Sphingomonas strain RB2256. The capacity of this ultramicrobacterium to respond to starvation is discussed in terms of the ecological relevance of complete nutrient deprivation in an oligotrophic marine environment. These studies provide the first evidence that marine oligotrophic ultramicrobacteria may be expected to include a starvation response and the capacity for a high degree of gene regulation.

Mutations enhancing amino acid catabolism confer a growth advantage in stationary phase

Starved cultures of Escherichia coli undergo successive rounds of population takeovers by mutants of increasing fitness. These mutants express the growth advantage in stationary phase (GASP) phenotype. Previous work identified the rpoS819 allele as a GASP mutation allowing cells to take over stationary-phase cultures after growth in rich media (M. M. Zambrano, D. A. Siegele, M. A. Almirón, A. Tormo, and R. Kolter, Science 259:1757-1760, 1993). Here we have identified three new GASP loci from an aged rpoS819 strain: sgaA, sgaB, and sgaC. Each locus is capable of conferring GASP on the rpoS819 parent, and they can provide successively higher fitnesses for the bacteria in the starved cultures. All four GASP mutations isolated thus far allow for faster growth on both individual and mixtures of amino acids. Each mutation confers a growth advantage on a different subset of amino acids, and these mutations act in concert to increase the overall catabolic capacity of the cell. We present a model whereby this enhanced ability to catabolize amino acids is responsible for the fitness gain during carbon starvation, as it may allow GASP mutants to outcompete the parental cells when growing on the amino acids released by dying cells.