Long lag times and high velocities in the motility of natural assemblages of marine bacteria

Morphogenesis of bacterial colonies in polymeric environments

Many bacteria live in polymeric fluids, such as mucus, environmental polysaccharides, and extracellular polymers in biofilms. However, lab studies typically focus on cells in polymer-free fluids. Here, we show that interactions with polymers shape a fundamental feature of bacterial life-how they proliferate in space in multicellular colonies. Using experiments, we find that when polymer is sufficiently concentrated, cells generically and reversibly form large serpentine "cables" as they proliferate. By combining experiments with biophysical theory and simulations, we demonstrate that this distinctive form of colony morphogenesis arises from an interplay between polymer-induced entropic attraction between neighboring cells and their hindered ability to diffusely separate from each other in a viscous polymer solution. Our work thus reveals a pivotal role of polymers in sculpting proliferating bacterial colonies, with implications for how they interact with hosts and with the natural environment, and uncovers quantitative principles governing colony morphogenesis in such complex environments.

A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments

In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.

Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility

Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [¹⁴ C]l-alanine, we confirmed that l-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate l-alanine oxidation at patch l-alanine concentrations, compared to <30 s for HTCC7211. By modelling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 min for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of l-alanine metabolism would produce 12% of their standing ATP stock upon encountering an l-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.

Particle-associated bacteria in seawater dominate the colony-forming microbiome on ZoBell marine agar

Planktonic particle-associated bacteria comprise particle-attached and motile free-living cells. These groups were obtained by settlement in Imhoff cones. Dilution plating on marine agar 2216 (ZoBell marine agar) and microscopic counts indicated a cultivability of 0.7% (0.4%-1.2%) of bacteria in coastal seawater collected at Helgoland Roads, North Sea. Particle-associated bacteria presented a minority population in seawater, but had a larger cultivability of 25% (0.9%-100%) for populations collected by settlement of particles and 5.7% (0.9%-24%) for populations collected by filtration. Partial 16S rRNA gene sequences indicated that 84% of the cultured taxa were either enriched in particle-associated microbiomes or only found in these microbiomes, including Sulfitobacter and other Rhodobacteraceae, Pseudoalteromonas, Psychromonas, Arcobacter and many Flavobacteriaceae. Illumina-based 16S rRNA V3V4 amplicon sequences of plate communities revealed that nearly all operational taxonomic units had a cultivated and described strain in close phylogenetic proximity. This suggested that decades of strain isolation from seawater on ZoBell marine agar had achieved a very good coverage of cultivable genera abundant in nature. The majority belonged to particle-associated bacteria, complementing observations that abundant free-living seawater bacteria often require cultivation conditions closer to their natural habitat like liquid cultivation in oligotrophic medium.

Investigating microscale patchiness of motile microbes under turbulence in a simulated convective mixed layer

Microbes play a primary role in aquatic ecosystems and biogeochemical cycles. Spatial patchiness is a critical factor underlying these activities, influencing biological productivity, nutrient cycling and dynamics across trophic levels. Incorporating spatial dynamics into microbial models is a long-standing challenge, particularly where small-scale turbulence is involved. Here, we combine a fully 3D direct numerical simulation of convective mixed layer turbulence, with an individual-based microbial model to test the key hypothesis that the coupling of gyrotactic motility and turbulence drives intense microscale patchiness. The fluid model simulates turbulent convection caused by heat loss through the fluid surface, for example during the night, during autumnal or winter cooling or during a cold-air outbreak. We find that under such conditions, turbulence-driven patchiness is depth-structured and requires high motility: Near the fluid surface, intense convective turbulence overpowers motility, homogenising motile and non-motile microbes approximately equally. At greater depth, in conditions analogous to a thermocline, highly motile microbes can be over twice as patch-concentrated as non-motile microbes, and can substantially amplify their swimming velocity by efficiently exploiting fast-moving packets of fluid. Our results substantiate the predictions of earlier studies, and demonstrate that turbulence-driven patchiness is not a ubiquitous consequence of motility but rather a delicate balance of motility and turbulent intensity.

Flagellar energy costs across the tree of life

Flagellar-driven motility grants unicellular organisms the ability to gather more food and avoid predators, but the energetic costs of construction and operation of flagella are considerable. Paths of flagellar evolution depend on the deviations between fitness gains and energy costs. Using structural data available for all three major flagellar types (bacterial, archaeal, and eukaryotic), flagellar construction costs were determined for Escherichia coli, Pyrococcus furiosus, and Chlamydomonas reinhardtii. Estimates of cell volumes, flagella numbers, and flagellum lengths from the literature yield flagellar costs for another ~200 species. The benefits of flagellar investment were analysed in terms of swimming speed, nutrient collection, and growth rate; showing, among other things, that the cost-effectiveness of bacterial and eukaryotic flagella follows a common trend. However, a comparison of whole-cell costs and flagellum costs across the Tree of Life reveals that only cells with larger cell volumes than the typical bacterium could evolve the more expensive eukaryotic flagellum. These findings provide insight into the unsolved evolutionary question of why the three domains of life each carry their own type of flagellum.

Most creatures on Earth are single cell organisms. The tree of life comprises three domains, two of which – bacteria and archaea – are formed exclusively of creatures that spend their existence as independent cells. Yet even eukaryotes, the domain which include animals and plants, feature single cell species such as yeasts and algae.

Regardless of which group they belong to, all single-celled organisms must find food in their environment. For this, many are equipped with flagella, whip-like structures that protrude from the cell and allow it to swim. In fact, archaea, bacteria and eukaryotes have all independently evolved these structures.

However, flagella are also expensive for an organism to build, maintain and operate. They are only worth having if the advantages they bring to the cell compensate for their cost; many single-cell species do not carry flagella and obtain their food without having to swim.

To explore this trade-off, Schavemaker and Lynch calculated the cost of building and using flagella for about 200 species across the tree of life. The analysis show that the amount of energy spent on flagella varied between 0.1% and 40% of the entire cell budget. This investment is only worthwhile if the cell is above a certain size. Smaller than this, and the organism is better off obtaining its food passively.

The results also show that while eukaryotic flagella are much bigger and quite different than their bacterial counterpart, both appendages share the same patterns of cost effectiveness. However only eukaryotic cells, which are on average larger than bacteria, can afford to evolve such sizable and complex structures; making just one would cost more than the entire energy budget of a bacterial cell.

Many single-cell species which are critical for the health of the planet are equipped with flagella, such as the microorganisms which recycle matter in the oceans and release carbon dioxide. Understanding the costs and benefits of flagella could explain more about this aspect of the carbon cycle, and therefore global warming.

Leave or Stay: Simulating Motility and Fitness of Microorganisms in Dynamic Aquatic Ecosystems

Motility is a key adaptation factor in scarce marine environments inhabited by bacteria. The question of how a capacity for adaptive migrations influences the success of a microbial population in various conditions is a challenge addressed in this study. We employed the agent-based model of competition of motile and sedentary microbial populations in a confined aquatic environment supplied with a periodic batch nutrient source to assess the fitness of both. Such factors as nutrient concentration in a batch, batch period, mortality type and energetic costs of migration were considered to determine the conditions favouring different strategies: Nomad of a motile population and Settler of a sedentary one. The modelling results demonstrate that dynamic and nutrient-scarce environments favour motile populations, whereas nutrient-rich and stagnant environments promote sedentary microorganisms. Energetic costs of migration determine whether or not the Nomad strategy of the motile population is successful, though it also depends on such conditions as nutrient availability. Even without penalties for migration, under certain conditions, the sedentary Settler population dominates in the ecosystem. It is achieved by decreasing the local nutrient availability near the nutrient source, as motile populations relying on a local optimizing strategy tend to follow benign conditions and fail, enduring stress associated with crossing the valleys of suboptimal nutrient availability.

Seasonal Variation in Viral Infection Rates and Cell Sizes of Infected Prokaryotes in a Large and Deep Freshwater Lake (Lake Biwa, Japan)

As viruses regulate prokaryotic abundance and the carbon cycle by infecting and lysing their prokaryotic hosts, the volume of infected prokaryotes is an important parameter for understanding the impact of viruses on aquatic environments. However, literature regarding the seasonal and spatial variations in the cell volume of infected prokaryotes is limited, despite the volume of the prokaryotic community varying dynamically with season and water column depth. Here, we conducted a field survey for two annual cycles in a large and deep freshwater lake (Lake Biwa, Japan), where large prokaryotes inhabit the deeper layer during the stratified period. We used transmission electron microscopy to reveal the seasonal and spatial variation in the frequency of viral infection and cell volume of infected prokaryotes. We found that the viral infection rate in the surface layer increased when estimated contact rates increased during the middle of the stratified period, whereas the infection rate in the deeper layer increased despite low estimated contact rates during the end of the stratified period. In addition, in the deeper layer, the fraction of large prokaryotes in the total and infected prokaryotic communities increased progressively while the number of intracellular viral particles increased. We suggest different ways in which the viral abundance is maintained in the two water layers. In the surface layer, it is speculated that viral abundance is supported by the high viral infection rate because of the high activity of prokaryotes, whereas in the deeper layer, it might be supported by the larger number of intracellular viral particles released from large prokaryotes. Moreover, large prokaryotes could contribute as important sources of organic substrates via viral lysis in the deeper layer, where labile dissolved organic matter is depleted.

Particle Collection in Imhoff Sedimentation Cones Enriches Both Motile Chemotactic and Particle-Attached Bacteria

Marine heterotrophic microorganisms remineralize about half of the annual primary production, with the microbiomes on and around algae and particles having a major contribution. These microbiomes specifically include free-living chemotactic and particle-attached bacteria, which are often difficult to analyze individually, as the standard method of size-selective filtration only gives access to particle-attached bacteria. In this study, we demonstrated that particle collection in Imhoff sedimentation cones enriches microbiomes that included free-living chemotactic bacteria and were distinct from particle microbiomes obtained by filtration or centrifugation. Coastal seawater was collected during North Sea phytoplankton spring blooms, and the microbiomes were investigated using 16S rRNA amplicon sequencing and fluorescence microscopy. Enrichment factors of individual operational taxonomic units (OTUs) were calculated for comparison of fractionated communities after separation with unfractionated seawater communities. Filtration resulted in a loss of cells and yielded particle fractions including bacterial aggregates, filaments, and large cells. Centrifugation had the lowest separation capacity. Particles with a sinking rate of >2.4 m day^-1 were collected in sedimentation cones as a bottom fraction and enriched in free-living chemotactic bacteria, i.e., Sulfitobacter, Pseudoalteromonas, and Vibrio. Subfractions of these bottom fractions, obtained by centrifugation, showed enrichment of either free-living or particle-attached bacteria. We identified five distinct enrichment patterns across all separation techniques: mechano-sensitive and mechano-stable free-living bacteria and three groups of particle-attached bacteria. Simultaneous enrichment of particle-attached and chemotactic free-living bacteria in Imhoff sedimentation cones is a novel experimental access to these groups providing more insights into the diversity, structure, and function of particle-associated microbiomes, including members of the phycosphere.

Bacterial foraging facilitates aggregation of Chlamydomonas microsphaera in an organic carbon source-limited aquatic environment

Microalgal aggregation is a key to many ecosystem functions in aquatic environments. Yet mechanistic understanding of microalgae aggregation, especially the interactions with ubiquitous bacteria populations, remains elusive. We reported an experimental study illustrating how the emerging bacterial populations interacted with a model microalga (Chlamydomonas microsphaera) cells and the consequent aggregation patterns. Results showed that the emergence of bacterial populations significantly stimulated C. microsphaera aggregation. Both bacterial and C. microsphaera motilities were remarkably excited upon coculturing, with the mean cell velocity being up to 2.67 and 1.80 times of those of separate bacterial and C. microsphaera cultures, respectively. The stimulated bacterial and C. microsphaera cell velocity upon coculturing would likely provide a mechanism for enhanced probability of cell-cell collisions that led to amplified aggregation of C. microsphaera population. Correlation analysis revealed that bacterial resource foraging (for polysaccharides) was likely a candidate mechanism for stimulated cell motility in an organic carbon source-limited environment, whereby C. microsphaera-derived polysaccharides serve as the sole organic carbon source for heterotrophic bacteria which in turns facilitates bacteria-C. microsphaera aggregation. Additional analysis showed that bacterial populations capable of successive decomposing algal-derived organic matters dominated the cocultures, with the top five abundant genera of Brevundimonas (24.78%), Shinella (17.94%), Sphingopyxis (11.62%), Dongia (5.82%) and Hyphomicrobium (5.45%). These findings provide new insights into full understanding of microalgae-bacteria interactions and consequent microbial aggregation characteristics in aquatic ecosystems.

Distinct niche partitioning of marine and freshwater microbes during colonisation

Bacteria are ubiquitous on the Earth, and many use chemotaxis to colonise favourable microenvironments. The colonisation process is continuous, where animals, plants, protists, viruses and chemical and physical factors frequently remove bacteria from wide volume ranges. Colonisation processes are poorly understood in natural communities. Here, we investigated niche partitioning during colonisation in aquatic microbial communities using bands of bacterial chemotaxis in petri dishes from mixed-species communities. The community partitioned into loiterers, primary and secondary colonisers, each having distinct abundances and taxonomy. Within marine samples, Shewanella dominated the primary colonisers, whilst Enterobacteriaceae dominated this group within the freshwater samples. Whether the success of these specific groups translates to what occurs within natural communities is uncertain, but here we show these taxa have the capacity to colonise new, unexplored environments. A strong negative association existed between the primary colonisers and viral abundance, suggesting that successful colonisers simultaneously move toward areas of heightened resources, which correlated with lower virus-like particles. Here, we show that microbial communities constantly sort themselves into distinct taxonomic groups as they move into new environments. This sorting during colonisation may be fundamental to microbial ecology, industry, technology, and disease development by setting the initial conditions that determine the winners as a community develops.

Connecting single-cell properties to collective behavior in multiple wild isolates of the Enterobacter cloacae complex

Some strains of motile bacteria self-organize to form spatial patterns of high and low cell density over length scales that can be observed by eye. One such collective behavior is the formation in semisolid agar media of a high cell density swarm band. We isolated 7 wild strains of the Enterobacter cloacae complex capable of forming this band and found its propagation speed can vary 2.5 fold across strains. To connect such variability in collective motility to strain properties, each strain’s single-cell motility and exponential growth rates were measured. The band speed did not significantly correlate with any individual strain property; however, a multilinear analysis revealed that the band speed was set by a combination of the run speed and tumbling frequency. Comparison of variability in closely-related wild isolates has the potential to reveal how changes in single-cell properties influence the collective behavior of populations.

Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile

The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.

This study assessed the dispersal of five bacterial communities from contrasting compartments along a fractured clay till depth profile comprising plow layer soil, preferential flow paths (biopores and the tectonic fractures below), and matrix sediments, down to 350 cm below the surface. A recently developed expansion of the porous surface model (PSM) was used to capture bacterial communities dispersing under controlled hydration conditions on a soil-like surface. All five communities contained bacteria capable of active dispersal under relatively low hydration conditions (−3.1 kPa). Further testing of the plow layer community revealed active dispersal even at matric potentials of −6.3 to −8.4 kPa, previously thought to be too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, the dispersing communities were found to be less diverse than their corresponding total communities. The dominant dispersers in most compartments belonged to the genus Pseudomonas and, in the plow layer soil, to Rahnella as well. An exception to this was the dispersing community in the matrix at 350 cm below the surface, which was dominated by Pantoea. Hydrologically connected compartments shared proportionally more dispersing than nondispersing amplicon sequence variants (ASVs), suggesting that active dispersal is important for colonizing these compartments. These results highlight the importance of including soil profile heterogeneity when assessing the role of active dispersal and contribute to discerning the importance of active dispersal in the soil environment.

IMPORTANCE The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.

Novel Method Reveals a Narrow Phylogenetic Distribution of Bacterial Dispersers in Environmental Communities Exposed to Low-Hydration Conditions

In this study, we developed a method that provides profiles of community-level surface dispersal from environmental samples under controlled hydration conditions and enables us to isolate and uncover the diversity of the fastest bacterial dispersers. The method expands on the porous surface model (PSM), previously used to monitor the dispersal of individual bacterial strains in liquid films at the surface of a porous ceramic disc. The novel procedure targets complex communities and captures the dispersed bacteria on a solid medium for growth and detection. The method was first validated by distinguishing motile Pseudomonas putida and Flavobacterium johnsoniae strains from their nonmotile mutants. Applying the method to soil and lake water bacterial communities showed that community-scale dispersal declined as conditions became drier. However, for both communities, dispersal was detected even under low-hydration conditions (matric potential, -3.1 kPa) previously proven too dry for P. putida strain KT2440 motility. We were then able to specifically recover and characterize the fastest dispersers from the inoculated communities. For both soil and lake samples, 16S rRNA gene amplicon sequencing revealed that the fastest dispersers were substantially less diverse than the total communities. The dispersing fraction of the soil microbial community was dominated by Pseudomonas species cells, which increased in abundance under low-hydration conditions, while the dispersing fraction of the lake community was dominated by Aeromonas species cells and, under wet conditions (-0.5 kPa), also by Exiguobacterium species cells. The results gained in this study bring us a step closer to assessing the dispersal ability within complex communities under environmentally relevant conditions.IMPORTANCE Dispersal is a key process of bacterial community assembly, and yet, very few attempts have been made to assess bacterial dispersal at the community level, as the focus has previously been on pure-culture studies. A crucial factor for dispersal in habitats where hydration conditions vary, such as soils, is the thickness of the liquid films surrounding solid surfaces, but little is known about how the ability to disperse in such films varies within bacterial communities. Therefore, we developed a method to profile community dispersal and identify fast dispersers on a rough surface resembling soil surfaces. Our results suggest that within the motile fraction of a bacterial community, only a minority of the bacterial types are able to disperse in the thinnest liquid films. During dry periods, these efficient dispersers can gain a significant fitness advantage through their ability to colonize new habitats ahead of the rest of the community.

Microbial Morphology and Motility as Biosignatures for Outer Planet Missions

Meaningful motion is an unambiguous biosignature, but because life in the Solar System is most likely to be microbial, the question is whether such motion may be detected effectively on the micrometer scale. Recent results on microbial motility in various Earth environments have provided insight into the physics and biology that determine whether and how microorganisms as small as bacteria and archaea swim, under which conditions, and at which speeds. These discoveries have not yet been reviewed in an astrobiological context. This paper discusses these findings in the context of Earth analog environments and environments expected to be encountered in the outer Solar System, particularly the jovian and saturnian moons. We also review the imaging technologies capable of recording motility of submicrometer-sized organisms and discuss how an instrument would interface with several types of sample-collection strategies. Key Words: In situ measurement-Biosignatures-Microbiology-Europa-Ice. Astrobiology 16, 755-774.

Stygofauna enhance prokaryotic transport in groundwater ecosystems

More than 97% of the world’s freshwater reserves are found in aquifers, making groundwater one of the most important resources on the planet. Prokaryotic communities in groundwater underpin the turnover of energy and matter while also maintaining groundwater purity. Thus, knowledge of microbial transport in the subsurface is crucial for maintaining groundwater health. Here, we describe for the first time the importance of stygofauna as vectors for prokaryotes. The “hitch-hiking” prokaryotes associated with stygofauna may be up to 5 orders of magnitude higher in abundance and transported up to 34× faster than bulk groundwater flow. We also demonstrate that prokaryotic diversity associated with stygofauna may be higher than that of the surrounding groundwater. Stygofauna are a newly recognized prokaryotic niche in groundwater ecosystems that have the potential to transport remediating, water purifying and pathogenic prokaryotes. Therefore, stygofauna may influence ecosystem dynamics and health at a microbial level, and at a larger scale could be a new source of prokaryotic diversity in groundwater ecosystems.

A Worldwide Competition to Compare the Speed and Chemotactic Accuracy of Neutrophil-Like Cells

Chemotaxis is the ability to migrate towards the source of chemical gradients. It underlies the ability of neutrophils and other immune cells to hone in on their targets and defend against invading pathogens. Given the importance of neutrophil migration to health and disease, it is crucial to understand the basic mechanisms controlling chemotaxis so that strategies can be developed to modulate cell migration in clinical settings. Because of the complexity of human genetics, Dictyostelium and HL60 cells have long served as models system for studying chemotaxis. Since many of our current insights into chemotaxis have been gained from these two model systems, we decided to compare them side by side in a set of winner-take-all races, the Dicty World Races. These worldwide competitions challenge researchers to genetically engineer and pharmacologically enhance the model systems to compete in microfluidic racecourses. These races bring together technological innovations in genetic engineering and precision measurement of cell motility. Fourteen teams participated in the inaugural Dicty World Race 2014 and contributed cell lines, which they tuned for enhanced speed and chemotactic accuracy. The race enabled large-scale analyses of chemotaxis in complex environments and revealed an intriguing balance of speed and accuracy of the model cell lines. The successes of the first race validated the concept of using fun-spirited competition to gain insights into the complex mechanisms controlling chemotaxis, while the challenges of the first race will guide further technological development and planning of future events.

A Submersible, Off-Axis Holographic Microscope for Detection of Microbial Motility and Morphology in Aqueous and Icy Environments

Sea ice is an analog environment for several of astrobiology’s near-term targets: Mars, Europa, Enceladus, and perhaps other Jovian or Saturnian moons. Microorganisms, both eukaryotic and prokaryotic, remain active within brine channels inside the ice, making it unnecessary to penetrate through to liquid water below in order to detect life. We have developed a submersible digital holographic microscope (DHM) that is capable of resolving individual bacterial cells, and demonstrated its utility for immediately imaging samples taken directly from sea ice at several locations near Nuuk, Greenland. In all samples, the appearance and motility of eukaryotes were conclusive signs of life. The appearance of prokaryotic cells alone was not sufficient to confirm life, but when prokaryotic motility occurred, it was rapid and conclusive. Warming the samples to above-freezing temperatures or supplementing with serine increased the number of motile cells and the speed of motility; supplementing with serine also stimulated chemotaxis. These results show that DHM is a useful technique for detection of active organisms in extreme environments, and that motility may be used as a biosignature in the liquid brines that persist in ice. These findings have important implications for the design of missions to icy environments and suggest ways in which DHM imaging may be integrated with chemical life-detection suites in order to create more conclusive life detection packages.

Chemotaxis toward phytoplankton drives organic matter partitioning among marine bacteria

The microenvironment surrounding individual phytoplankton cells is often rich in dissolved organic matter (DOM), which can attract bacteria by chemotaxis. These "phycospheres" may be prominent sources of resource heterogeneity in the ocean, affecting the growth of bacterial populations and the fate of DOM. However, these effects remain poorly quantified due to a lack of quantitative ecological frameworks. Here, we used video microscopy to dissect with unprecedented resolution the chemotactic accumulation of marine bacteria around individual Chaetoceros affinis diatoms undergoing lysis. The observed spatiotemporal distribution of bacteria was used in a resource utilization model to map the conditions under which competition between different bacterial groups favors chemotaxis. The model predicts that chemotactic, copiotrophic populations outcompete nonmotile, oligotrophic populations during diatom blooms and bloom collapse conditions, resulting in an increase in the ratio of motile to nonmotile cells and in the succession of populations. Partitioning of DOM between the two populations is strongly dependent on the overall concentration of bacteria and the diffusivity of different DOM substances, and within each population, the growth benefit from phycospheres is experienced by only a small fraction of cells. By informing a DOM utilization model with highly resolved behavioral data, the hybrid approach used here represents a new path toward the elusive goal of predicting the consequences of microscale interactions in the ocean.

Microbial Surface Colonization and Biofilm Development in Marine Environments

Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

Seeking sunlight: rapid phototactic motility of filamentous mat-forming cyanobacteria optimize photosynthesis and enhance carbon burial in Lake Huron's submerged sinkholes

We studied the motility of filamentous mat-forming cyanobacteria consisting primarily of Oscillatoria-like cells growing under low-light, low-oxygen, and high-sulfur conditions in Lake Huron's submerged sinkholes using in situ observations, in vitro measurements and time-lapse microscopy. Gliding movement of the cyanobacterial trichomes (100-10,000 μm long filaments, composed of cells ∼10 μm wide and ∼3 μm tall) revealed individual as well as group-coordinated motility. When placed in a petri dish and dispersed in ground water from the sinkhole, filaments re-aggregated into defined colonies within minutes, then dispersed again. Speed of individual filaments increased with temperature from ∼50 μm min(-1) or ∼15 body lengths min(-1) at 10°C to ∼215 μm min(-1) or ∼70 body lengths min(-1) at 35°C - rates that are rapid relative to non-flagellated/ciliated microbes. Filaments exhibited precise and coordinated positive phototaxis toward pinpoints of light and congregated under the light of foil cutouts. Such light-responsive clusters showed an increase in photosynthetic yield - suggesting phototactic motility aids in light acquisition as well as photosynthesis. Once light source was removed, filaments slowly spread out evenly and re-aggregated, demonstrating coordinated movement through inter-filament communication regardless of light. Pebbles and pieces of broken shells placed upon intact mat were quickly covered by vertically motile filaments within hours and became fully buried in the anoxic sediments over 3-4 diurnal cycles - likely facilitating the preservation of falling debris. Coordinated horizontal and vertical filament motility optimize mat cohesion and dynamics, photosynthetic efficiency and sedimentary carbon burial in modern-day sinkhole habitats that resemble the shallow seas in Earth's early history. Analogous cyanobacterial motility may have played a key role in the oxygenation of the planet by optimizing photosynthesis while favoring carbon burial.

Chemotaxis by natural populations of coral reef bacteria

Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately influence the health and stability of the coral holobiont.

Variability in microbial community composition and function between different niches within a coral reef

To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.

Enhancement of microbial motility due to speed-dependent nutrient absorption

Marine microorganisms often reach high swimming speeds, either to take advantage of evanescent nutrient patches or to beat Brownian forces. Since this implies that a sizable part of their energetic budget must be allocated to motion, it is reasonable to assume that some fast-swimming microorganisms may increase their nutrient intake by increasing their speed v. We formulate a model to investigate this hypothesis and its consequences, finding the steady-state solutions and analyzing their stability. Surprisingly, we find that even modest increases in nutrient absorption may lead to a significant increase of the microbial speed. In fact, evaluations obtained using realistic parameter values for bacteria indicate that the speed increase due to the enhanced nutrient absorption may be quite large.

Ecology and physics of bacterial chemotaxis in the ocean

Intuitively, it may seem that from the perspective of an individual bacterium the ocean is a vast, dilute, and largely homogeneous environment. Microbial oceanographers have typically considered the ocean from this point of view. In reality, marine bacteria inhabit a chemical seascape that is highly heterogeneous down to the microscale, owing to ubiquitous nutrient patches, plumes, and gradients. Exudation and excretion of dissolved matter by larger organisms, lysis events, particles, animal surfaces, and fluxes from the sediment-water interface all contribute to create strong and pervasive heterogeneity, where chemotaxis may provide a significant fitness advantage to bacteria. The dynamic nature of the ocean imposes strong selective pressures on bacterial foraging strategies, and many marine bacteria indeed display adaptations that characterize their chemotactic motility as "high performance" compared to that of enteric model organisms. Fast swimming speeds, strongly directional responses, and effective turning and steering strategies ensure that marine bacteria can successfully use chemotaxis to very rapidly respond to chemical gradients in the ocean. These fast responses are advantageous in a broad range of ecological processes, including attaching to particles, exploiting particle plumes, retaining position close to phytoplankton cells, colonizing host animals, and hovering at a preferred height above the sediment-water interface. At larger scales, these responses can impact ocean biogeochemistry by increasing the rates of chemical transformation, influencing the flux of sinking material, and potentially altering the balance of biomass incorporation versus respiration. This review highlights the physical and ecological processes underpinning bacterial motility and chemotaxis in the ocean, describes the current state of knowledge of chemotaxis in marine bacteria, and summarizes our understanding of how these microscale dynamics scale up to affect ecosystem-scale processes in the sea.

Swimming in light: a large-scale computational analysis of the metabolism of Dinoroseobacter shibae

The Roseobacter clade is a ubiquitous group of marine α-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae.

The oceans are home to a large variety of microorganisms, which interact in several ways with world-wide metabolic cycles. A representative of an important group of marine bacteria called the Roseobacter clade is Dinoroseobacter shibae. This organism is known to use a variant of photosynthesis to obtain energy from light. Another feature of D. shibae and many other Roseobacters is the ability to degrade an abundant compound in the ocean called dimethylsulfoniopropionate. Importantly, one degradation pathway of dimethylsulfoniopropionate releases a side product, which affects climate by seeding cloud formation. In this work, we constructed a genome-scale metabolic model of D. shibae and carried out a detailed computational analysis of its metabolism. Our model simulates the light-harvesting capabilities of D. shibae and also accounts for the energy needed to swim. Thanks to our exhaustive simulations we were able to elucidate the effect of light on the growth of D. shibae, to study the consequences of genetic perturbations, and to identify mutants which produce more cloud-seeding compounds. Foremost, our computational results help to understand an important part of the complex processes in the ocean in greater detail. Besides, they can be a valuable guide for future wet-lab experiments.

Vibrio coralliilyticus search patterns across an oxygen gradient

The coral pathogen, Vibrio coralliilyticus shows specific chemotactic search pattern preference for oxic and anoxic conditions, with the newly identified 3-step flick search pattern dominating the patterns used in oxic conditions. We analyzed motile V. coralliilyticus cells for behavioral changes with varying oxygen concentrations to mimic the natural coral environment exhibited during light and dark conditions. Results showed that 3-step flicks were 1.4× (P = 0.006) more likely to occur in oxic conditions than anoxic conditions with mean values of 18 flicks (95% CI = 0.4, n = 53) identified in oxic regions compared to 13 (95% CI = 0.5, n = 38) at anoxic areas. In contrast, run and reverse search patterns were more frequent in anoxic regions with a mean value of 15 (95% CI = 0.7, n = 46), compared to a mean value of 10 (95% CI = 0.8, n = 29) at oxic regions. Straight swimming search patterns remained similar across oxic and anoxic regions with a mean value of 13 (95% CI = 0.7, n = oxic: 13, anoxic: 14). V. coralliilyticus remained motile in oxic and anoxic conditions, however, the 3-step flick search pattern occurred in oxic conditions. This result provides an approach to further investigate the 3-step flick.

Marine microbes see a sea of gradients

Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. These large-scale consequences result from the combined effect of countless interactions occurring at the level of the individual cells. At these small scales, the ocean is surprisingly heterogeneous, and microbes experience an environment of pervasive and dynamic chemical and physical gradients. Many species actively exploit this heterogeneity, while others rely on gradient-independent adaptations. This is an exciting time to explore this frontier of oceanography, but understanding microbial behavior and competition in the context of the water column's microarchitecture calls for new ecological frameworks, such as a microbial optimal foraging theory, to determine the relevant trade-offs and global consequences of microbial life in a sea of gradients.

Bacterial tracking of motile algae

Abstract We investigated whether bacterial motility and chemotaxis in the ocean enables bacteria to approach and follow microscopic, moving, point sources of nutrients. The turbulent nature of the ocean combined with the imprecision of run and tumble chemotaxis has led to the assumption that marine bacteria cannot cluster around microscopic point sources. Recent work, however, shows that marine bacteria use a run and reverse strategy. We examine the ability of marine bacteria that use run and reverse chemotaxis to respond to and follow a moving point source. The addition of the 6 mum in diameter motile algae Pavlova lutheri to cultures of the marine bacteria Pseudoalteromonas haloplanktis and Shewanella putrefaciens revealed bacterial tracking individual free-swimming algae. The marine bacteria travelled at up to 445 mum s(-1) when tracking, up to 237 mum s(-1) when not tracking and up to 126 mum s(-1) in cultures without the algae. Tracking maintained bacteria within one run length of an alga. The bacteria appeared able to steer, consecutively turning up to 12 times toward the motile algae. They recovered from the occasional incorrect turn to continue moving around the swimming alga, indicating that marine bacteria can track moving point sources and form transient phyto-bacterial associations. Our analysis suggests tracking increases nutrient uptake by bringing cells into regions of high nutrient concentrations and by increased advection from high speeds. This result describes what is, apparently, one of the tightest spatial and temporal links between free-living primary and secondary producers in planktonic ecosystems.

Thalassospira sp. isolated from the oligotrophic eastern Mediterranean Sea exhibits chemotaxis toward inorganic phosphate during starvation

The eastern Mediterranean Sea represents an ultraoligotrophic environment where soluble phosphate limits the growth of bacterioplankton. Correspondingly, genes coding for high-affinity phosphate uptake systems and for organophosphonate utilization are highly prevalent in the plankton metagenome. Chemotaxis toward inorganic phosphate constitutes an alternative strategy to cope with phosphate limitation, but so far has only been demonstrated for two bacterial pathogens and an archaeon, and not in any free-living planktonic bacterium. In the present study, bacteria affiliated with the genus Thalassospira were found to constitute a regular, low-abundance member of the bacterioplankton that can be detected throughout the water column of the eastern Mediterranean Sea. A representative (strain EM) was isolated in pure culture and exhibited a strong positive chemotaxis toward inorganic phosphate that was induced exclusively in phosphate-starved cultures. Phosphate-depleted cells were 2-fold larger than in exponentially growing cultures, and 43% of the cells retained their motility even during prolonged starvation over 10 days. In addition, Thalassospira sp. strain EM was chemotactically attracted by complex substrates (yeast extract and peptone), amino acids, and 2-aminoethylphosphonate but not by sugar monomers. Similarly to the isolate from the eastern Mediterranean, chemotaxis toward phosphate was observed in starved cultures of the other two available isolates of the genus, T. lucentensis DSM 14000T and T. profundimaris WP0211T. Although Thalassospira sp. represents only up to 1.2% of the total bacterioplankton community in the water column of the eastern Mediterranean Sea, its chemotactic behavior potentially leads to an acceleration of nutrient cycling and may also explain the persistence of marine copiotrophs in this extremely nutrient-limited environment.

Clustering of marine bacteria in seawater enrichments

Seawater enrichments of marine bacteria clustered in 20- to 50-(mu)m-wide bands near air-water interfaces. The cells within the band travelled at up to 212 (mu)m s(sup-1) and at an average speed of 163 (mu)m s(sup-1). Mean cell speeds peaked mid-run at 187 (mu)m s(sup-1). At the end of the run, bacteria reversed direction rather than randomly reorienting. The duration of the stops during reversal was estimated at 18 ms, six to seven times shorter than that found in enteric bacteria. Cells hundreds of micrometers from the band travelled at half the speed of the bacteria in the band. The fastest isolate from the seawater enrichment was identified as Shewanella putrefaciens and had an average speed of 100 (mu)m s(sup-1) in culture. Air-water interfaces produced no clustering or speed changes in isolates derived from enrichments. Salinity and pH, however, both influenced speed. The speed and reversal times of the seawater enrichments indicate that the bacteria in them are better adapted for clustering around small point sources of nutrients than are either enteric or cultured marine bacteria.

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.

The energetics and scaling of search strategies in bacteria

The influence of body size on the energetic cost of movement is well studied in animals but has been rarely investigated in bacteria. Here, I calculate the cost of four chemotactic strategies for different-sized bacteria by adding the costs of their locomotion and reorientation. Size differences of 0.1 microm result in 100,000-fold changes in the energetic cost of chemotaxis. The exact cost for any given size is a nonlinear function of flagella length, the minimum speed necessary to detect and respond to a signal, and the gradient of the signal. These parameters are interlinked in such a way that body size and strategy are tightly coupled to particular environmental gradients, offering avenues for explaining and exploring diversity and competition. The analysis here has implications beyond bacteria. Power-law regression through the minimum costs of transport for different kinds of chemotaxis has the same slope as that for swimming animals, suggesting a universal allometric equation for all swimming organisms.

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.

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.

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.

Plankton motility patterns and encounter rates

Many planktonic organisms have motility patterns with correlation run lengths (distances traversed before direction changes) of the same order as their reaction distances regarding prey, mates and predators (distances at which these organisms are remotely detected). At these scales, the relative measure of run length to reaction distance determines whether the underlying encounter is ballistic or diffusive. Since ballistic interactions are intrinsically more efficient than diffusive, we predict that organisms will display motility with long correlation run lengths compared to their reaction distances to their prey, but short compared to the reaction distances of their predators. We show motility data for planktonic organisms ranging from bacteria to copepods that support this prediction. We also present simple ballistic and diffusive motility models for estimating encounter rates, which lead to radically different predictions, and we present a simple criterion to determine which model is the more appropriate in a given case.

An application of statistics to comparative metagenomics

Background

Metagenomics, sequence analyses of genomic DNA isolated directly from the environments, can be used to identify organisms and model community dynamics of a particular ecosystem. Metagenomics also has the potential to identify significantly different metabolic potential in different environments.

Results

Here we use a statistical method to compare curated subsystems, to predict the physiology, metabolism, and ecology from metagenomes. This approach can be used to identify those subsystems that are significantly different between metagenome sequences. Subsystems that were overrepresented in the Sargasso Sea and Acid Mine Drainage metagenome when compared to non-redundant databases were identified.

Conclusion

The methodology described herein applies statistics to the comparisons of metabolic potential in metagenomes. This analysis reveals those subsystems that are more, or less, represented in the different environments that are compared. These differences in metabolic potential lead to several testable hypotheses about physiology and metabolism of microbes from these ecosystems.

Chemotaxis and behavioral physiology of not-yet-cultivated microbes

Chemotaxis assays provide a rapid and efficient means of (1) studying the chemotactic behavior of microorganisms in complex samples and (2) identifying potential growth substrates and generating inocula for subsequent isolation trials. The chemotaxis method thus complements the set of techniques currently available for the investigation of not-yet-cultured microbes. Although restricted to motile and chemotactically active microorganisms, a considerable fraction of species can be covered with this technique, particularly in bacterioplankton communities. Several formats of the chemotaxis assay have been developed. Capillaries are loaded with solutions of test compounds and are inserted in small microscopic chambers, in bottles containing culture suspensions, or incubated directly in situ. The latter two techniques are also suitable for experiments with anaerobic bacteria. In flat rectangular glass capillaries, the accumulating microorganisms can be observed directly by light microscopy in a dark field. Afterward, the chemotactically active bacteria can be identified by analyses of their 16S rRNA gene fragments. The method has been used to identify an essential carbon compound required for the growth of previously unculturable phototrophic consortia. This knowledge proved essential for the subsequent successful enrichment of these bacterial associations. Furthermore, it has been shown that different not-yet-cultured members of aerobic lake water bacterioplankton communities are chemotactically active and attracted by different carbon compounds.

Randomly curved runs interrupted by tumbling: a model for bacterial motion

Small bacteria are strongly buffeted by Brownian forces that make completely straight runs impossible. A model for bacterial motion is formulated in which the effects of fluctuational forces and torques on the run phase are taken into account by using coupled Langevin equations. An integrated description of the motion, including runs and tumbles, is then obtained by the use of convolution and Laplace transforms. The properties of the velocity-velocity correlation function, of the mean displacement, and of the two relevant diffusion coefficients are examined in terms of the bacterial sizes and of the magnitude of the propelling forces. For bacteria smaller than E. coli, the integrated diffusion coefficient crosses over from a jump-dominated to a rotational-diffusion-dominated form.

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.

Difference in bacterial motion between forward and backward swimming caused by the wall effect

A bacterial cell that has a single polar flagellum alternately repeats forward swimming, in which the flagellum pushes the cell body, and backward swimming, in which the flagellum pulls the cell body. We have reported that the backward swimming speeds of Vibrio alginolyticus are on average greater than the forward swimming speeds. In this study, we quantitatively measured the shape of the trajectory as well as the swimming speed. The trajectory shape in the forward mode was almost straight, whereas that in the backward mode was curved. The same parameters were measured at different distances from a surface. The difference in the motion characteristics between swimming modes was significant when a cell swam near a surface. In contrast, the difference was indistinguishable when a cell swam >60 microm away from any surfaces. In addition, a cell in backward mode tended to stay near the surface longer than a cell in forward mode. This wall effect on the bacterial motion was independent of chemical modification of the glass surface. The macroscopic behavior is numerically simulated on the basis of experimental results and the significance of the phenomenon reported here is discussed.