Two-Dimensional Patterns in Bacterial Veils Arise from Self-generated,Three-Dimensional Fluid Flows

The behavior of collections of oceanic bacteria is controlled by metabolic (chemotaxis) and physical (fluid motion) processes. Some sulfur-oxidizing bacteria, such as Thiovulum majus, unite these two processes via a material interface produced by the bacteria and upon which the bacteria are transiently attached. This interface, termed a bacterial veil, is formed by exo-polymeric substances (EPS) produced by the bacteria. By adhering to the veil while continuing to rotate their flagella, the bacteria are able to exert force on the fluid surroundings. This behavior induces a fluid flow that, in turn, causes the bacteria to aggregate leading to the formation of a physical pattern in the veil. These striking patterns are very similar in flavor to the classic convection instability observed when a shallow fluid is heated from below. However, the physics are very different since the flow around the veil is mediated by the bacteria and affects the bacterial densities.     

Conspicuous veils formed by vibrioid bacteria on sulfidic marine sediment

We describe the morphology and behavior of a hitherto unknown bacterial species that forms conspicuous veils (typical dimensions, 30 by 30 mm) on sulfidic marine sediment. The new bacteria were enriched on complex sulfidic medium within a benthic gradient chamber in oxygen-sulfide countergradients, but the bacteria have so far not been isolated in pure culture, and a detailed characterization of their metabolism is still lacking. The bacteria are colorless, gram-negative, and vibrioid-shaped (1.3- to 2.5- by 4- to 10- micro m) cells that multiply by binary division and contain several spherical inclusions of poly-beta-hydroxybutyric acid. The cells have bipolar polytrichous flagella and exhibit a unique swimming pattern, rotating and translating along their short axis. Free-swimming cells showed aerotaxis and aggregated at ca. 2 micro M oxygen within opposing oxygen-sulfide gradients, where they were able to attach via a mucous stalk, forming a cohesive whitish veil at the oxic-anoxic interface. Bacteria attached to the veil kept rotating and adapted their stalk lengths dynamically to changing oxygen concentrations. The joint action of rotating bacteria on the veil induced a homogeneous water flow from the oxic water region toward the veil, whereby the oxygen uptake rate could be enhanced up to six times, as shown by model calculations. The veils showed a pronounced succession pattern. New veils were generated de novo within 24 h and had a homogeneous whitish translucent appearance. Bacterial competitors or eukaryotic predators were apparently kept away by the low oxygen concentration prevailing at the veil surface. Frequently, within 2 days the veil developed a honeycomb pattern of regularly spaced holes. After 4 days, most veils were colonized by grazing ciliates, leading to the fast disappearance of the new bacteria. Several-week-old veils finally developed into microbial mats consisting of green, purple, and colorless sulfur bacteria.     

Collective swimming and the dynamics of bacterial turbulence

To swim, a bacterium pushes against the fluid within which it is immersed, generating fluid flow that dies off on a length scale comparable to the size of the bacterium. However, in dense colonies of bacteria, the bacteria are close enough that flow generated by swimming is substantial. For these cases, complex flows can arise due to the interaction and feedback between the bacteria and the fluid. Recent experiments on dense populations of swimming Bacillus subtilis have revealed a volume fraction-dependent transition from random swimming to transient jet and vortex patterns in the bacteria/fluid mixture. The fluid motions that are observed are reminiscent of flows that are observed around translating objects at moderate to high Reynolds numbers. In this work, I present a two-phase model for the bacterial/fluid mixture. The model explains turbulent flows in terms of the dipole stress that the bacteria exert on the fluid, entropic elasticity due to the rod shape of each bacterium, and the torque on the bacteria due to fluid gradients. Solving the equations in two dimensions using realistic parameters, the model reproduces empirically observed velocity fields. Dimensional analysis provides scaling relations for the dependence of the characteristic scales on the model parameters.     

Upcoming flow promotes the bundle formation of bacterial flagella

Flagellated bacteria swim by rotating a bundle of helical flagella and commonly explore the surrounding environment in a “run-and-tumble” motility mode. Here, we show that the upcoming flow could impact the bacterial run-and-tumble behavior by affecting the formation and dispersal of the flagellar bundle. Using a dual optical tweezers setup to trap individual bacteria, we characterized the effects of the imposed fluid flow and cell body rotation on the run-and-tumble behavior. We found that the two factors affect the behavior differently, with the imposed fluid flow increasing the running time and decreasing the tumbling time and the cell body rotation decreasing the tumbling time only. Using numerical simulations, we computed the flagellar bundling time as a function of flow velocity, which agrees well with our experimental observations. The mechanical effects we characterized here provide novel, to our knowledge, ingredients for further studies of bacterial chemotaxis in complex environments such as dynamic fluid environments.     

Bacterial swimming strategies and turbulence

Most bacteria in the ocean can be motile. Chemotaxis allows bacteria to detect nutrient gradients, and hence motility is believed to serve as a method of approaching sources of food. This picture is well established in a stagnant environment. In the ocean a shear microenvironment is associated with turbulence. This shear flow prevents clustering of bacteria around local nutrient sources if they swim in the commonly assumed "run-and-tumble" strategy. Recent observations, however, indicate a "back-and-forth" swimming behavior for marine bacteria. In a theoretical study we compare the two bacterial swimming strategies in a realistic ocean environment. The "back-and-forth" strategy is found to enable the bacteria to stay close to a nutrient source even under high shear. Furthermore, rotational diffusion driven by thermal noise can significantly enhance the efficiency of this strategy. The superiority of the "back-and-forth" strategy suggests that bacterial motility has a control function rather than an approach function under turbulent conditions.     

Effects of deflected droplet electrostatic cell sorting on the viability and exoproteolytic activity of bacterial cultures and marine bacterioplankton

The cell-sorting capability of flow cytometers makes it possible to isolate specific populations of cells with pre-defined cytometric characteristics. A better knowledge of the biological effects of the sorting process is necessary for the future cell sorting applications. In this paper we report the effects of flow cytometric sorting on bacterial viability and exoproteolytic activity (EPA) of bacterial cultures and marine bacterioplankton. Sorting bacterial cultures and bacterioplankton samples reduce viability as assessed by plate counts and produce variations in the exoproteolytic activity. These effects indicate that deflected electrostatic sorting may significantly alter the biological properties of the sorted bacteria.     

Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy

The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.Subject terms: Microbial ecology, Bacteria     

Sheared bioconvection in a horizontal tube

The recent interest in using microorganisms for biofuels is motivation enough to study bioconvection and cell dispersion in tubes subject to imposed flow. To optimize light and nutrient uptake, many microorganisms swim in directions biased by environmental cues (e.g. phototaxis in algae and chemotaxis in bacteria). Such taxes inevitably lead to accumulations of cells, which, as many microorganisms have a density different to the fluid, can induce hydrodynamic instabilites. The large-scale fluid flow and spectacular patterns that arise are termed bioconvection. However, the extent to which bioconvection is affected or suppressed by an imposed fluid flow and how bioconvection influences the mean flow profile and cell transport are open questions. This experimental study is the first to address these issues by quantifying the patterns due to suspensions of the gravitactic and gyrotactic green biflagellate alga Chlamydomonas in horizontal tubes subject to an imposed flow. With no flow, the dependence of the dominant pattern wavelength at pattern onset on cell concentration is established for three different tube diameters. For small imposed flows, the vertical plumes of cells are observed merely to bow in the direction of flow. For sufficiently high flow rates, the plumes progressively fragment into piecewise linear diagonal plumes, unexpectedly inclined at constant angles and translating at fixed speeds. The pattern wavelength generally grows with flow rate, with transitions at critical rates that depend on concentration. Even at high imposed flow rates, bioconvection is not wholly suppressed and perturbs the flow field.     

RecA Expression in Response to Solar UVR in the Marine Bacterium Vibrio natriegens

Solar ultraviolet radiation may produce daily stress on marine and estuarine communities as cells are damaged and repair that damage. Reduction in the earth's stratospheric ozone layer has increased awareness of the potential effects that ultraviolet radiation may have in the environment, including how marine bacteria respond to changes in solar radiation. We examined the use of the bacterial RecA protein as an indicator of the potential of bacteria to repair DNA damage caused by solar UV irradiation using the marine bacterium Vibrio natriegens as a model. RecA is universally present in bacteria and is a regulator protein for the so-called Dark Repair Systems, which include excision repair, postreplication recombinational repair, and mutagenic or SOS repair. Solar UVB and UVA both reduced V. natriegens viability in seawater microcosms. After exposure to unfiltered solar radiation or radiation in which UVB was blocked, survival dropped below 1%, whereas visible light from which UVA and UVB had been filtered had no effect on survival. Using a RecA-specific antibody for detection, RecA protein was induced by solar radiation in a diel pattern in marine microcosms conducted in the Gulf of Mexico. Peak induction was observed at dusk each day. Although RecA expression was correlated with the formation of UVB-induced cyclobutyl pyrimidine dimers, longer wavelength UVA radiation also induced recA gene expression. Our results demonstrate that RecA-regulated, light-independent repair is an important component in the ability of marine bacteria to survive exposure to solar ultraviolet radiation and that RecA expression is a useful monitor of bacterial repair after exposure to solar UVR.     

Widespread N-acetyl-D-glucosamine uptake among pelagic marine bacteria and its ecological implications

Dissolved free and combined N-acetyl-D-glucosamine (NAG) is among the largest pools of amino sugars in the ocean. NAG is a main structural component in chitin and a substantial constituent of bacterial peptidoglycan and lipopolysaccharides. We studied the distribution and kinetics of NAG uptake by the phosphoenolpyruvate:NAG phosphotransferase systems (PTS) in marine bacterial isolates and natural bacterial assemblages in near-shore waters. Of 78 bacterial isolates examined, 60 took up 3H-NAG, while 18 showed no uptake. No systematic pattern in NAG uptake capability relative to phylogenetic affiliation was found, except that all isolates within Vibrionaceae took up NAG. Among 12 isolates, some showed large differences in the relationship between polymer hydrolysis (measured as chitobiase activity) and uptake of the NAG, the hydrolysis product. Pool turnover time and estimated maximum ambient concentration of dissolved NAG in samples off Scripps Pier (La Jolla, Calif.) were 5.9 +/- 3.0 days (n = 10) and 5.2 +/- 0.9 nM (n = 3), respectively. Carbohydrate competition experiments indicated that glucose, glucosamine, mannose, and fructose were taken up by the same system as NAG. Sensitivity to the antibiotic and NAG structural analog streptozotocin (STZ) was developed into a culture-independent approach, which demonstrated that approximately one-third of bacteria in natural marine assemblages that were synthesizing DNA took up NAG. Isolates possessing a NAG PTS system were found to be predominantly facultative anaerobes. These results suggest the hypothesis that a substantial fraction of bacteria in natural pelagic assemblages are facultative anaerobes. The adaptive value of fermentative metabolism in the pelagic environment is potentially significant, e.g., to bacteria colonizing microenvironments such as marine snow that may experience periodic O2-limitation.     

Factors Influencing Bacterial Production in a Shallow Estuarine System

The bacterioplankton of the marine and brackish water zones of the complex system Ria de Aveiro was characterized as profiles of bacterial abundance and biomass productivity. During the warm season, total bacteria ranged from 0.2 to 8.5 x 109 cells L-1 and active bacteria number from 0.1 to 3.1 x 109 cells L-1. Total and active bacterial numbers were, on average, three times higher in brackish than in marine water. Bacterial productivity on different dates and different tides in the marine zone varied from 0.05 to 4.5 mg C L-1 h-1. Here the average productivity (1.1 mg C L-1 h-1) was 3.5 times less than in brackish water (average 3.8 mg C L-1 h-1; range 0.7-14.2 mg C L-1 h-1). Specific productivity varied from 0.05 to 2.61 fg C cell-1 h-1, a range that was similar throughout the ecosystem. However, specific productivity per active cell was 19% higher in brackish water. Bacterial production variation was best explained by the number of active bacteria, which, in turn, was highly associated with total bacterial number, temperature, and particulate organic carbon. In the marine zone, bacterial production was also influenced by depth and salinity. In the brackish zone, the set of independent variables explained a smaller percentage of bacterial production variation than in marine zone, suggesting greater importance of other variables. In the marine zone, and mainly near low tide, productivity was significantly higher (average 3.3 times) at the surface (down to 0.5 m) than in the deeper layers of the water column. This stratification of bacterial productivity was linked to the increased specific productivity per active cell, as no modification in the proportion of active cells in the population could be detected. The vertical profile of bacterial production in the deeper zone of this estuarine ecosystem, in which no clear salinity or thermal stratification occurs throughout the tidal cycle, seemed to reflect a biochemical stratification generated by increased phytoplankton exudation and/or by photochemical transformation of semilabile or recalcitrant organic compounds. Shallower water masses tend to blur this surface effect. The relative importance of photochemical transformation in the pattern of estuarine bacterial production will therefore tend to vary with the bathymetry of the system.     

Hydrodynamic interactions between two swimming bacteria

This article evaluates the hydrodynamic interactions between two swimming bacteria precisely. We assume that each bacterium is force free and torque free, with a Stokes flow field around it. The geometry of each bacterium is modeled as a spherical or spheroidal body with a single helical flagellum. The movements of two interacting bacteria in an infinite fluid otherwise at rest are computed using a boundary element method, and the trajectories of the two interacting bacteria and the stresslet are investigated. The results show that as the two bacteria approach each other, they change their orientations considerably in the near field. The bacteria always avoided each other; no stable pairwise swimming motion was observed in this study. The effects of the hydrodynamic interactions between two bacteria on the rheology and diffusivity of a semidilute bacterial suspension are discussed.     

How the Motility Pattern of Bacteria Affects Their Dispersal and Chemotaxis

Most bacteria at certain stages of their life cycle are able to move actively; they can swim in a liquid or crawl on various surfaces. A typical path of the moving cell often resembles the trajectory of a random walk. However, bacteria are capable of modifying their apparently random motion in response to changing environmental conditions. As a result, bacteria can migrate towards the source of nutrients or away from harmful chemicals. Surprisingly, many bacterial species that were studied have several distinct motility patterns, which can be theoretically modeled by a unifying random walk approach. We use this approach to quantify the process of cell dispersal in a homogeneous environment and show how the bacterial drift velocity towards the source of attracting chemicals is affected by the motility pattern of the bacteria. Our results open up the possibility of accessing additional information about the intrinsic response of the cells using macroscopic observations of bacteria moving in inhomogeneous environments.     

Effects of Inorganic Particles on Metabolism by a Periphytic Marine Bacterium

Measurements were made of adsorption of a periphytic marine bacterium, glucose, and glutamic acid to inorganic particles in seawater and defined bacterial growth medium. Measurements of the metabolism of bacteria were made in the presence and absence of particles by microcalorimetry and radiorespirometry. It was found that hydroxyapatite adsorbs glutamic acid, but not glucose, from the experimental medium. It was also found that hydroxyapatite adsorbs essentially all of the bacteria from the medium when the bacterial concentration is approximately 6 × 10⁵ bacteria per ml. If the bacterial concentration is approximately 6 × 10⁷, then only a small fraction of cells become attached. It was therefore possible to select bacterial concentrations and organic nutrients so that bacterial attachment, organic nutrient adsorption, or both would occur in different experiments. In this experimental system the metabolism by attached and nonattached bacteria of adsorbing and nonadsorbing organic nutrients was measured. The results show that bacterial activity in this model system was not enhanced by the particles, regardless of whether the bacteria, the organic nutrient, or both were associated with the surface. In fact, the respiratory activity of the attached bacteria was diminished in comparison with that of free bacteria.     

Cytotoxicity and apoptosis induction of some selected marine bacteria metabolites

AIMS: To study the potential apoptosis effects of cytotoxic marine bacterial metabolites on human HeLa cell line. METHODS AND RESULTS: After HeLa cells were routinely cultured, tetrazolium-based colorimetric assay for cytotoxicity was performed to screen the marine bacteria extracts showing 12 strains active. To find the potential active strain with apoptosis mechanism, a battery of apoptosis assays, including AO/EB staining, TUNEL assay (terminal-deoxynucleotidyl transferase mediated nick end labelling), gel electrophoresis and flow cytometry, were used to determine whether apoptosis was involved in HeLa cell cytotoxicity of marine bacterial extracts. The results indicated that four strains could induce cell shrinkage, cell membrane blebbing, formation of apoptotic body and DNA fragmentation. CONCLUSIONS: Crude extracts of 12 of 153 strains of marine bacteria showed cytotoxic effects with ID50 ranged from 77.20 to 199.84 microg ml(-1), in which eight strains of bacteria were associated bacteria. The metabolites in the strains of QD1-2, NJ6-3-1, NJ1-1-1 and SS6-4 were able to induce HeLa cells apoptosis. Furthermore, the assessment by flow cytometry indicated that the hypodiploid apoptotic cells increased in a time-dependent manner, suggesting that induced apoptosis occurred from 24 h to 48 h after the extracts treatment. SIGNIFICANCE AND IMPACT OF THE STUDY: Our results suggested that the compounds from fermentation in these four marine bacterial strains could be candidates for developing apoptosis specific anti-tumour agents with lower toxicity. This study indicated that associated marine bacteria could be good source to find cytotoxic metabolites, and some cytotoxic marine bacterial metabolites could have apoptosis mechanisms.     

Laser impact assessment in a biofilm-forming bacterium Pseudoalteromonas carrageenovora using a flow cytometric system

Impact by pulsed laser irradiations from an Nd:YAG laser on the marine biofilm-forming bacterium Pseudoalteromonas carrageenovora has been studied using a flow cytometric system. The biofilm-forming bacteria in the planktonic state have been irradiated while flowing, and the mortality and bacterial attachment have been determined by exposing TiN coupons in the system. Coupons suspended in the non-irradiated bacterial flow were treated as the control. The fluence used in the study was 0.1 J/cm(2). Three flow rates (14, 28, and 42 cm/min) and two exposure durations (15 and 30 min) were tested. The results showed the increase in bacterial mortality with the decrease in flow rate. The maximum mortality of 27.5% was observed when the flow rate was 14 cm/min. The bacterial attachment increased with the increase in flow rate and exposure duration. The area of bacterial attachment on the experimental coupons exposed to the irradiated sample was significantly lesser than that for the nonirradiated sample. The results thus show in a flowing system, low power pulsed laser irradiations could reduce the bacterial attachment even though it did not cause significant mortality.     

Direct upstream motility in Escherichia coli

We provide an experimental demonstration of positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface. This hydrodynamic phenomenon is dominant below a critical shear rate and robust against Brownian motion and cell tumbling. We deduce that individual bacteria entering a flow system can rapidly migrate upstream (>20 μm/s) much faster than a gradually advancing biofilm. Given a bacterial population with a distribution of sizes and swim speeds, local shear rate near the surface determines the dominant hydrodynamic mode for motility, i.e., circular or random trajectories for low shear rates, positive rheotaxis for moderate flow, and sideways swimming at higher shear rates. Faster swimmers can move upstream more rapidly and at higher shear rates, as expected. Interestingly, we also find on average that both swim speed and upstream motility are independent of cell aspect ratio.     

Comparison of cell-specific activity between free-living and attached bacteria using isolates and natural assemblages

Marine snow aggregates are microbial hotspots that support high bacterial abundance and activities. We conducted laboratory experiments to compare cell-specific bacterial protein production (BPP) and protease activity between free-living and attached bacteria. Natural bacterial assemblages attached to model aggregates (agar spheres) had threefold higher BPP and two orders of magnitude higher protease activity than their free-living counterpart. These observations could be explained by preferential colonization of the agar spheres by bacteria with inherently higher metabolic activity and/or individual bacteria increasing their metabolism upon attachment to surfaces. In subsequent experiments, we used four strains of marine snow bacteria isolates to test the hypothesis that bacteria could up- and down-regulate their metabolism while on and off an aggregate. The protease activity of attached bacteria was 10-20 times higher than that of free-living bacteria, indicating that the individual strains could increase their protease activity within a short time (2 h) upon attachment to surfaces. Agar spheres with embedded diatom cells were colonized faster than plain agar spheres and the attached bacteria were clustered around the agar-embedded diatom cells, indicating a chemosensing response. Increased protease activity and BPP allow attached bacteria to quickly exploit aggregate resources upon attachment, which may accelerate remineralization of marine snow and reduce the downward carbon fluxes.     

Heat Transfer Analysis for Stationary Boundary Layer Slip Flow of a Power-Law Fluid in a Darcy Porous Medium with Plate Suction/Injection

In this paper, we investigate the slip effects on the boundary layer flow and heat transfer characteristics of a power-law fluid past a porous flat plate embedded in the Darcy type porous medium. The nonlinear coupled system of partial differential equations governing the flow and heat transfer of a power-law fluid is transformed into a system of nonlinear coupled ordinary differential equations by applying a suitable similarity transformation. The resulting system of ordinary differential equations is solved numerically using Matlab bvp4c solver. Numerical results are presented in the form of graphs and the effects of the power-law index, velocity and thermal slip parameters, permeability parameter, suction/injection parameter on the velocity and temperature profiles are examined.     

Cathodic protection and microbially induced corrosion

Cathodic protection, using sacrificial anodes or impressed current, has been recognized for a long time as an effective way to prevent marine corrosion. Cathodic polarization leads to the formation of a protective calcareous layer on the surfaces. It is well documented that the attachment of bacteria to metal surfaces and subsequent biofilm formation changes some physical and chemical parameters at the interface and influences the corrosion process. The objective of this study was to determine whether there is a relationship between cathodic polarization and development of biofilms on surfaces exposed to both synthetic and natural seawater. Experiments were conducted on clean surfaces, biofilmed surfaces, in natural or synthetic seawater using bacterial monocultures and cocultures. In marine sediments, cathodically produced hydrogen encouraged growth of hydrogenase-containing sulphate-reducing bacteria while in aerated seawater biofilms competed with the magnesium and calcium deposition. Both low pH induced by bacterial metabolism and exopolymers affect the deposition process and the stability of the calcareous layer.