Real time computer-controlled tracking of motile microorganisms

Biological early warning system based on the responses of aquatic organisms to disturbances: a review

Aquatic ecosystems are subject to a number of anthropogenic disturbances, including environmental toxicants. The efficient monitoring of water resources is fundamental for effective management of water quality and aquatic ecosystems. Spot sampling and continuous water quality monitoring based on physicochemical factors are conducted to assess water quality. However, not all contaminants or synergistic and antagonistic toxic effects can be determined by solely analyzing the physicochemical factors. Thus, various biotests have been developed using long-term and automatic observation studies based on the ability of the aquatic organisms to continuously sense a wide range of pollutants. In addition, a biological early warning system (BEWS) has been developed based on the response behaviors of organisms to continuously detect a wide range of pollutants for effective water quality monitoring and management. However, large amounts of data exhibiting non-linearity and individual behavioral variation are continuously accumulated over long-term and continuous behavioral monitoring studies. Thus, appropriate mathematical and computational data analyses are necessary to manage and interpret such large datasets. Here, we review the development and application of BEWS by using various groups of organisms and the computational methods used to process the behavioral monitoring data.

Novel methods for analysing bacterial tracks reveal persistence in Rhodobacter sphaeroides

Tracking bacteria using video microscopy is a powerful experimental approach to probe their motile behaviour. The trajectories obtained contain much information relating to the complex patterns of bacterial motility. However, methods for the quantitative analysis of such data are limited. Most swimming bacteria move in approximately straight lines, interspersed with random reorientation phases. It is therefore necessary to segment observed tracks into swimming and reorientation phases to extract useful statistics. We present novel robust analysis tools to discern these two phases in tracks. Our methods comprise a simple and effective protocol for removing spurious tracks from tracking datasets, followed by analysis based on a two-state hidden Markov model, taking advantage of the availability of mutant strains that exhibit swimming-only or reorientating-only motion to generate an empirical prior distribution. Using simulated tracks with varying levels of added noise, we validate our methods and compare them with an existing heuristic method. To our knowledge this is the first example of a systematic assessment of analysis methods in this field. The new methods are substantially more robust to noise and introduce less systematic bias than the heuristic method. We apply our methods to tracks obtained from the bacterial species Rhodobacter sphaeroides and Escherichia coli. Our results demonstrate that R. sphaeroides exhibits persistence over the course of a tumbling event, which is a novel result with important implications in the study of this and similar species.

Many species of planktonic bacteria are able to propel themselves through a liquid medium by the use of one or more helical flagella. Commonly, the observed motile behaviour consists of a series of approximately straight-line movements, interspersed with random, approximately stationary, reorientation events. This phenomenon is of current interest as it is known to be linked to important bacterial processes such as pathogenicity and biofilm formation. An accepted experimental approach for studying bacterial motility in approximately indigenous conditions is the tracking of cells using a microscope. However, there are currently no validated methods for the analysis of such tracking data. In particular, the identification of reorientation phases, which is complicated by various sources of noise in the data, remains an open challenge. In this paper we present novel methods for analysing large bacterial tracking datasets. We assess the performance of our new methods using computational simulations, and show that they are more reliable than a previously published method. We proceed to analyse previously unpublished tracks from the bacterial species Rhodobacter sphaeroides, an emerging model organism in the field of bacterial motility, and Escherichia coli, a well-studied model bacterium. The analysis demonstrates the novel result that R. sphaeroides exhibits directional persistence over the course of a reorientation event.

Application of a novel open-source program for measuring the effects of toxicants on the swimming behavior of large groups of unmarked fish

The aim of this study was to demonstrate a novel method for measuring the effects of toxicants on the behavior of groups of unmarked fish. Ctrax is an open source Python-based machine vision program that was originally designed to track fruit flies (Drosophila). The effects of the fish anaesthetic quinaldine sulfate on the behavior of groups of 10 unmarked Arabian killifish (Aphanias dispar) in a small arena were measured. Ctrax was able to identify and track the X-Y coordinates of the individual fish over 1 min recording periods. The data was analyzed using specifically written Matlab (The Mathworks™) toolboxes and the effects of quinaldine sulfate on absolute swimming velocity, forward swimming velocity, rate of change in orientation and distance to wall were calculated. Additionally the effects of quinaldine sulfate on path tortuosity were also measured. Ctrax has significant benefits over other available technologies for tracking the 2-dimensional coordinates of fish. In particular the software is open source and thus freely available, it is accurate, requires only simple easily available equipment and able to track potentially large groups of fish (possibly >50) while maintaining their individual identities.

CECILIA, a versatile research tool for cellular responses to gravity

We describe a centrifuge designed and constructed according to current demands for a versatile instrument in cellular gravitational research, in particular protists (ciliates, flagellates). The instrument (called CECILIA, centrifuge for ciliates) is suited for videomonitoring, videorecording, and quantitative evaluation of data from large numbers of swimming cells in a ground-based laboratory or in a drop tower/drop shaft under microgravity conditions. The horizontal rotating platform holds up to six 8mm-camcorders and six chambers holding the experimental cells. Under hypergravity conditions (up to 15 g) chambers can be rotated about 2 axes to adjust the swimming space at right angles or parallel to the resulting gravity vector. Evaluations of cellular responses to central acceleration-- in the presence of gravitational 1 g--are used for extrapolation of cellular behaviour under hypogravity conditions. CECILIA is operated and monitored by computer using a custom-made software. Times and slopes of rising and decreasing acceleration, values and and quality of steady acceleration are supervised online. CECILIA can serve as an on-ground research instrument for precursor investigations of the behaviour of ciliates and flagellates under microgravity conditions such as long-term experiments in the International Space Station.

A new approach for biological online testing of stack gas condensate from municipal waste incinerators

A biological testing system for the monitoring of stack gas condensates of municipal waste incinerators has been developed using Euglena gracilis as a test organism. The motility, velocity and cellular form of the organisms were the endpoints, calculated by an image analysis system. All endpoints showed statistically significant changes in a short time when organisms were exposed to samples collected during combustion situations with increased pollutant concentrations. The velocity of the organisms proved to be the most appropriate endpoint. A semi-continuous system with E. gracilis for monitoring stack gas condensate is proposed, which could result in an online system for testing stack gas condensates in the future.

Automated biomonitoring using real time movement analysis of Euglena gracilis

An automated biomonitoring system for early warning of pollutants in aquatic environments is described and characterized. The system uses sublethal changes in the movement behavior of the flagellate Euglena gracilis as biological endpoints. The movement is determined by real time image analysis. All parameters describing motility, velocity, orientation, and form of the cells are calculated during measurement, and changes of these parameters are interpreted as effect. By automatic dilution of the water sample, dose-effect relationships can be recorded automatically. A total measurement procedure, including control and sample measurement and filling and rinsing of the system, typically requires 8 min. Measurements with different organic and inorganic toxic compounds were performed and the calculated EC(50) values compared with literature data for the bioluminescence test with Vibrio fischeri. Also, measurements with waste water samples from different industrial plants were performed. The fast response time, the small size, the reliable image analysis system, the calculation of several endpoints, and the automatic measuring procedure are major advantages compared to other biological test systems.

Influence of extremely low frequency electromagnetic fields on the swimming behavior of ciliates

Different species of ciliates (Paramecium biaurelia, Loxodes striatus, Tetrahymena thermophila) have been taken as model systems to study the effects of extremely low-frequency electromagnetic fields (50 Hz, 0.5-2.0 mT) on the cellular level. A dose-dependent increase in the mean swimming velocity and a decrease in the linearity of cell tracks were observed in all wild-type cells. In contrast, field-exposure did not increase the number of directional turns of the Paramecium tetraurelia pawn mutant (d4-500r), which is characterized by defective Ca2+-channels. The described changes indicate a direct effect of low frequency electromagnetic fields on the transport mechanisms of the cell membrane for ions controlling the motile activity of cilia.

Graviorientation in protists and plants

Gravitaxis, gravikinesis, and gravitropism are different graviresponses found in protists and plants. The phenomena have been intensively studied under variable stimulations ranging from microgravity to hypergravity. A huge amount of information is now available, e.g. about the time course of these events, their adaptation capacity, thresholds, and interaction between gravity and other environmental stimuli. There is growing evidence that a pure physical mechanism can be excluded for orientation of protists in the gravity field. Similarly, a physiological signal transduction chain has been postulated in plants. Current investigations focus on the question whether gravity is perceived by intracellular gravireceptors (e.g. the Muller organelle of the ciliate Loxodes, barium sulfate vacuoles in Chara rhizoids or starch statoliths in higher plants) or whether the whole cell acts as a sedimenting body exerting pressure on the lower membrane. Behavioral studies in density adjusted media, effects of inhibitors of mechano-sensitive ion channels or manipulations of the proposed gravireceptor structures revealed that both mechanisms have been developed in protists and plants. The threshold values for graviresponses indicate that even 10% of the normal gravitational field can be detected, which demands a focusing and amplifying system such as the cytoskeleton and second messengers.

Negative gravitactic behavior of Euglena gracilis can not be described by the mechanism of buoyancy-oriented upward swimming

Gravitactic behavior of microorganisms has been known for more than a hundred years. Euglena gracilis serves as a model system for gravity-triggered behavioral responses. Two basic mechanisms are discussed for gravitaxis: one is based on a physical mechanism where an asymmetric mass distribution pulls the cell passively in the correct orientation and, in contrast, the involvement of an active sensory system. A recently developed high-resolution motion-tracking system allows the analysis of single tracks during reorientation. The results are compared to a model developed by Fukui and Asai (1985) which describes gravitaxis of Paramecium caudatum on the basis of a physical mechanism. Taking into account the different size, different density, different mass distribution as well as the different velocity, results of the adapted model description of Paramecium were applied to measured data of Euglena. General shapes as well as the time scale of the predicted reorientational movement compared to measurements were different. The analysis clearly rules out the possibility that gravitaxis of Euglena gracilis is based on a pure physical phenomenon, and gives further support to the involvement of an active reorientational system. In addition, it could be shown that cell form changes during reorientation, even in an initial period where no angular change was observed.

Gravitaxis in unicellular microorganisms

Orientation of organisms with respect to the gravitational field of the Earth has been studied for more than 100 years in a number of unicellular microorganisms including flagellates and ciliates. Several hypotheses have been developed how the weak stimulus is perceived. Intracellular statoliths have been found to be involved in gravitaxis of Loxodes, while no specialized organelles have been detected in other ciliates, e.g. Paramecium. Also in the slime mold Physarum no specialized gravireceptors have been identified yet. In the flagellate Euglena gracilis the whole cell body, which is denser than the surrounding medium, seems to act as a statolith pressing onto the lower membrane where it activates mechanosensitive ion channels. Similar results were obtained for the ciliate Paramecium. In contrast to the flagellate Euglena, several ciliates have been found to show gravikinesis, which is defined as a dependence of the swimming velocity on the direction of movement in the gravity field.

Gravitaxis and graviperception in Euglena gracilis

Gravitactic orientation in the flagellate Euglena gracilis is mediated by an active physiological receptor rather than a passive alignment of the cells. During a recent space flight on the American shuttle Columbia the cells were subjected to different accelerations between 0 and 1.5 x g and tracked by computerized real-time image analysis. The dependence of orientation on acceleration followed a sigmoidal curve with a threshold at < or = 0.16 x g and a saturation at about 0.32 x g. No adaptation of the cells to the conditions of weightlessness was observed over the duration of the space mission (12 days). Under terrestrial conditions graviorientation was eliminated when the cells were suspended in a medium the density of which (Ficoll) equaled that of the cell body (1.04 g/ml) and was reversed at higher densities indicating that the whole cytoplasm exerts a pressure on the respective lower membrane. There it probably activates stretch-sensitive calcium specific ion channels since gravitaxis can be affected by gadolinium which is a specific inhibitor of calcium transport in these structures. The sensory transduction chain could involve modulation of the membrane potential since ion channel blockers, ionophores and ATPase inhibitors impair graviperception.

Surface mediated death of unconditioned Tetrahymena cells: effect of physical parameters, growth factors, hormones, and surfactants

A new form of cell death has been observed. The death occurs at liquid-air interfaces when Tetrahymena cells are grown in a chemically defined medium (CDM) at low inocula. The cells die by lysis at the liquid-air interface (medium surface), which they reach due to negative gravitaxis as well as positive aerotaxis. When the cells are grown in a closed compartment, with no liquid-air interface, the death is not observed, and the cells proliferate. Cloning of cells in CDM is thus possible. The addition of effectors such as NGF (10(-11) M), EGF (10(-10) M), PDGF (10(-10) M), and insulin (10(-7) M) to cells in CDM prevents the surface mediated death. Since detergents/surfactants like SDS (7 x 10(-5) M), NP-40 (2 x 10(-5) M), Tween 80 (10(-4))% w/v), Pluronic F-68 (10(-7) M), and the biosurfactant surfactin (10(-6) M) have the same effect, we suggest that the effectors act by stimulating the cells to exudate surfactant(s) of their own. Furthermore, lyzed cells and exudates from living cells (pre-conditioned medium) prevent the death. In conditions with liquid-air interfaces, certain physical parameters are of great importance for the survival of cells at low inocula. The parameters are the distance to the surface, the temperature, and the inoculum. By increasing the height of the medium, lowering the temperature, and increasing the inoculum of the culture, the survival can be greatly enhanced. There is no evidence for programmed cell death (PCD) or apoptosis.

Influence of accelerations on the spatial orientation of Loxodes and Paramecium

The gravitactic ciliates Paramecium and Loxodes were cultivated for 15 days in space during the IML-2 spacelab mission. At dedicated times their behavioral responses to different accelerations between 10(-3) x g and 1.5 x g were investigated by using a slow rotating centrifuge microscope (NIZEMI). The threshold for gravitaxis of Paramecium was found to be at > 0.16 x g and < or = 0.3 x g. No adaptation of Paramecium to the conditions of weightlessness was observed over the duration of 15 days. Loxodes showed no graviresponses to increasing accelerations, though it demonstrated gravitaxis after return to earth.

Orientation of Paramecium under the conditions of weightlessness

A cell culture of Paramecium with a precise negative gravitaxis was exposed to 4 x l0(-6) g during a parabolic flight of a sounding rocket for 6 min. Computer image analysis revealed that without gravity stimulus the individual swimming paths remained straight. In addition, three reactions could be distinguished. For about 30 s, paramecia maintained the swimming direction they had before onset of low gravity. During the next 20 s, an approximate reversal of the swimming direction occurred. This period was followed by the expected random swimming pattern. Similar behavior was observed under the condition of simulated weightlessness on a fast-rotating clinostat. Control experiments on the ground under hyper-gravity on a low-speed centrifuge microscope and on a vibration test facility proved that the observed effects were caused exclusively by the reduction of gravity.

Swimming behavior of Paramecium--first results with the low-speed centrifuge microscope (NIZEMI)

The low-speed centrifuge microscope NIZEMI (= Nieder-Geschwindigkeits-Zentrifugen-Mikroskop) is an excellent tool with which to investigate the effects of slightly increased gravity in the fields of biology and material sciences. We investigated the swimming behavior of Paramecium in the NIZEMI, by aid of a computer-controlled image analysis system. In the range of acceleration (1 g to 5 g), cells retained their swimming capability, did not sediment, and even increased the precision of their negative gravitaxis but reduced their mean swimming velocity.

Interactive image analysis system to determine the motility and velocity of cyanobacterial filaments

An interactive image analysis system has been developed to analyse and quantify the percentage of motile filaments and the individual linear velocities of organisms. The technique is based on the "difference" image between two digitized images taken from a time-lapse video recording 80 s apart which is overlaid on the first image. The bright lines in the difference image represent the paths along which the filaments have moved and are measured using a crosshair cursor controlled by the mouse. Even short exposure to solar ultraviolet radiation strongly impairs the motility of the gliding cyanobacterium Phormidium uncinatum, while its velocity is not likewise affected. These effects are not due to either type I (free radical formation) or type II (singlet oxygen production) photodynamic reactions, since specific quenchers and scavengers, indicative of these reactions, failed to be effective.

Image analysis techniques for automatic evaluation of two-dimensional electrophoresis

Techniques for automatic analysis of two-dimensional electrophoresis gels by computer-aided image analysis are described. Original gels or photographic films are scanned using a laser scanner and the files are transferred to a microcomputer. The program package first performs a compression and preevaluation of the files. Spot identification and quantification is performed by the chain code algorithm after appropriate zooming and cutting. Labeling facilitates spot identification and quantification in numerical and graphical (pseudocolor) representation on peripheral devices for camera ready output. Interpolation between measured basepoints is performed by cubic spline algorithms which are automatically switched on and off, depending on the need by the program. High speed analysis and graphic representation is achieved using fast Assembler language routines rather than high level languages. One-dimensional gels can be analyzed using the same software. Spot matching between parallel two-dimensional gels has not yet been implemented.

Effects of UV radiation on motility, photo-orientation and pigmentation in a freshwater Cryptomonas

The effects of UV radiation on photo-orientation, motility and pigmentation have been studied in a freshwater Cryptomonas species. The cells show a pronounced diaphototactic orientation which is affected by UV radiation at 50 mW m-2 within about 90 min. Both the average velocity of the swimming cells and the percentage of motile cells within the population decrease within about the same exposure time. UV radiation also bleaches the cellular pigments.

Effects of solar radiation on photoorientation, motility and pigmentation in a freshwater Peridinium

Solar radiation has a pronounced effect on photoorientation, motility and pigmentation in the freshwater dinoflagellate, Peridinium gatunense. Photoorientation (positive phototaxis) is impaired even after short exposure times and is totally inhibited after about 2.5 h. The percentage of motile cells decreases after short exposure times and after 4 h most cells are immotile. Likewise, the mean velocity decreases after an initial light-induced increase (photokinesis) under solar radiation. Solar UV-B (280-320 nm) radiation seems to be the major cause for the effects, since cutting off shorter wavelength by an ozone cuvette or WG filters prolongs the tolerated exposure times. Possible UV-B targets are the photoreceptor pigments since solar radiation causes a massive bleaching of the cells within a few hours.

Real time computer tracking of free-swimming and tethered rotating cells

A computerized image processing system has been developed that tracks individual free-swimming cells and rotating bacterial cell bodies tethered by their flagella in real time. Free-swimming bacteria of Rhodobacter sphaeroides, Rhodospirullum rubrum, and Salmonella typhimurium have been tracked swimming at speeds from 0 to over 120 microns s-1. A high level of discrimination is exerted against noncellular objects, allowing analysis of stopped as well as moving cells. This enabled detection of both speed and qualitative change in the swimming patterns of R. sphaeroides WS8 upon tactic stimulation. Comparison with darkfield microscopy indicated that the two techniques were in substantial agreement. The unidirectional rotation of cells of R. sphaeroides WS8 could be detected when the cells were either parallel to the microscope slide or end on. Frequencies of rotation of up to 10 Hz were monitored before image blurring became a problem. True rods would be easier to analyze at higher speeds of rotation. Although developed for photosynthetic bacteria, a wide range of bacteria, eucaryotic organisms, and subcellular organelles could be tracked with this system. Minor modifications to the software allow customization to different types of motility analysis.

Use of a computer to assay motility in bacteria

An assay was developed to study the movement of free-swimming Escherichia coli. Cells were videotaped through a microscope, and the videotape images were then digitized and analyzed with a computer. Angular and linear speeds were measured for wild-type E. coli and for a smooth and a tumbly mutant. The average angular and linear speeds of a population were directly and inversely proportional, respectively, to the time spent tumbling. Changes in angular and linear speeds were followed during the response of wild-type E. coli to attractant or repellent.

A rapid population method for action spectra applied to Halobacterium halobium

We have developed a simple and rapid technique for measuring the action spectra for phototaxis of populations of microorganisms and applied it to halobacteria. A microscope with a dark-field condenser was used to illuminate the cell suspension in a sealed chamber with light of wavelength greater than 750 nm; in this region of the spectrum, the halobacteria show no phototactic response. A 150-micron spot of light from a xenon arc lamp, whose wavelength and intensity can be varied, was projected through the objective lens into the center of the dark field. The objective lens imaged this measuring spot through a 780-nm cut-off filter on an aperture in front of a photomultiplier. The intensity of the scattered 750-nm light, and therefore the photomultiplier current, is proportional to the number of cells in the measuring spot. A third lamp provided background light of variable wavelength and intensity through the dark-field condenser. To minimize secondary effects due to large changes in cell density, we recorded the initial changes in the photomultiplier current over 1 min after the actinic light had been switched on. By plotting the rate of change against wavelength, we obtained action spectra after the proper corrections for changes in light intensity with wavelength were applied and saturation effects were avoided.