An agarose-in-plug bridge method to study chemotaxis in the Archaeon Halobacterium salinarum

A Review of the Advantages, Disadvantages and Limitations of Chemotaxis Assays for Campylobacter spp

Reproducible qualitative and quantitative assessment of bacterial chemotactic motility, particularly in response to chemorepellent effectors, is experimentally challenging. Here we compare several established chemotaxis assays currently used to investigate Campylobacter jejuni chemotaxis, with the aim of improving the correlation between different studies and establishing the best practices. We compare the methodologies of capillary, agar, and chamber-based assays, and discuss critical technical points, in terms of reproducibility, accuracy, and the advantages and limitations of each.

Innovations to culturing the uncultured microbial majority

Despite the surge of microbial genome data, experimental testing is important to confirm inferences about the cell biology, ecological roles and evolution of microorganisms. As the majority of archaeal and bacterial diversity remains uncultured and poorly characterized, culturing is a priority. The growing interest in and need for efficient cultivation strategies has led to many rapid methodological and technological advances. In this Review, we discuss common barriers that can hamper the isolation and culturing of novel microorganisms and review emerging, innovative methods for targeted or high-throughput cultivation. We also highlight recent examples of successful cultivation of novel archaea and bacteria, and suggest key microorganisms for future cultivation attempts.

Combining two optimized and affordable methods to assign chemoreceptors to a specific signal

Chemotaxis allows bacteria to detect specific compounds and move accordingly. This pathway involves signal detection by chemoreceptors (MCPs). Attributing a chemoreceptor to a ligand is difficult because there is a lot of redundancy in the MCPs that recognize a single ligand. We propose a methodology to define which chemoreceptors bind a given ligand. First, an MCP is overproduced to increase sensitivity to the ligand(s) it recognizes, thus promoting accumulation of cells around an agarose plug containing a low attractant concentration. Second, the ligand-binding domain (LBD) of the chemoreceptor is fused to maltose-binding protein (MBP), which facilitates purification and provides a control for a thermal shift assay (TSA). An increase in the melting temperature of the LBD in the presence of the ligand indicates that the chemoreceptor directly binds it. We showed that overexpression of two Shewanella oneidensis chemoreceptors (SO_0987 and SO_1056) promoted swimming toward an agarose plug containing a low concentration of chromate. The LBD of each of the two chemoreceptors was fused to MBP. A TSA revealed that only the LBD from SO_1056 had its melting temperature increased by chromate. In conclusion, we describe an efficient approach to define chemoreceptor-ligand pairs before undertaking more-sophisticated biochemical and structural studies.

Quantification of Bacterial Chemotaxis Responses at the Mouths of Hydrogel Capillaries

Many chemotaxis assays allow for the assessment of bacterial chemotaxis by determining the number of cells migrating toward a chemoattractant or away from a chemorepellent. Some of these assays use a capillary filled with a chemoeffector/agarose mixture to allow cells to accumulate at the mouth of the capillary. Subsequently, assumptions about the relative strengths of chemotaxis strength are based on visual comparisons. Here, we describe a modification of this assay that uses a hydrogel matrix to enable quantitative time-course measurements by analyzing image pixel intensities. This approach allows a high-throughput method when coupled with the aid of a motorized microscope stage.

Heterologous Expression of Pseudomonas putida Methyl-Accepting Chemotaxis Proteins Yields Escherichia coli Cells Chemotactic to Aromatic Compounds

Escherichia coli, commonly used in chemotaxis studies, is attracted mostly by amino acids, sugars, and peptides. We envisioned modifying the chemotaxis specificity of E. coli by expressing heterologous chemoreceptors from Pseudomonas putida enabling attraction either to toluene or benzoate. The mcpT gene encoding the type 40-helical bundle (40H) methyl-accepting chemoreceptor for toluene from Pseudomonas putida MT53 and the pcaY gene for the type 40H receptor for benzoate and related molecules from P. putida F1 were expressed from the trg promoter on a plasmid in motile wild-type E. coli MG1655. E. coli cells expressing McpT accumulated in chemoattraction assays to sources with 60 to 200 μM toluene, although less strongly than the response to 100 μM serine, but statistically significantly stronger than that to sources without any added attractant. An McpT-mCherry fusion protein was detectably expressed in E. coli and yielded weak but distinguishable membranes and polar foci in 1% of cells. E. coli cells expressing PcaY showed weak attraction to 0.1 to 1 mM benzoate, but 50 to 70% of cells localized the PcaY-mCherry fusion to their membrane. We conclude that implementing heterologous receptors in the E. coli chemotaxis network is possible and, upon improvement of the compatibility of the type 40H chemoreceptors, may bear interest for biosensing.IMPORTANCE Bacterial chemotaxis might be harnessed for the development of rapid biosensors, in which chemical availability is deduced from cell accumulation to chemoattractants over time. Chemotaxis of Escherichia coli has been well studied, but the bacterium is not attracted to chemicals of environmental concern, such as aromatic solvents. We show here that heterologous chemoreceptors for aromatic compounds from Pseudomonas putida at least partly functionally complement the E. coli chemotaxis network, yielding cells attracted to toluene or benzoate. Complementation was still inferior to native chemoattractants, like serine, but our study demonstrates the potential for obtaining selective sensing for aromatic compounds in E. coli.

A Static Microfluidic Device for Investigating the Chemotaxis Response to Stable, Non-linear Gradients

Microfluidic technology allows fast and precise measurement of chemotaxis responses to both attractant and repellent signals. One of the major drawbacks of current microfluidic chemotaxis assays is the presence of bacterial cells within the concentration gradient flow field, which has the potential for flow effects masking the chemotaxis response. This chapter describes a new microfluidic device for producing stable concentration gradients and measuring the response of cells to the gradient without exposing them to any flow. Unlike other methods described in the literature, this method is capable of producing gradients of any shape, almost instantaneously, allowing the measurement of time-dependent response of cells to a variety of signals.

Chemotaxis to Atypical Chemoattractants by Soil Bacteria

Although the mechanism of bacterial chemotaxis has been extensively studied in enteric bacteria, the hunt for novel and atypical chemoeffectors (in enterics and distantly-related species alike) has necessitated the modification of classic chemotaxis assays to deal with recalcitrant and potentially toxic chemicals. Here, we describe detailed protocols for the quantitative and qualitative assessment of chemotaxis responses that are categorized into short-term direct population response assays and long-term metabolism-based assays that can be used to identify novel chemoeffector molecules and the specific chemoreceptors involved. We emphasize the importance of behavior-based assays to verify the biochemical and physiological relevance of newly identified chemoeffector-receptor pairs.

Two Spatial Chemotaxis Assays: The Nutrient-Depleted Chemotaxis Assay and the Agarose-Plug-Bridge Assay

This chapter describes two spatial chemotaxis assays, the nutrient-depleted chemotaxis assay and agarose-plug-bridge assay, which enable the evaluation of putative chemoeffectors. These two assays have worked well with Campylobacter jejuni and Helicobacter pylori, and techniques for using these assays with these microbes are described.

The Norepinephrine Metabolite 3,4-Dihydroxymandelic Acid Is Produced by the Commensal Microbiota and Promotes Chemotaxis and Virulence Gene Expression in Enterohemorrhagic Escherichia coli

Enterohemorrhagic Escherichia coli (EHEC) is a commonly occurring foodborne pathogen responsible for numerous multistate outbreaks in the United States. It is known to infect the host gastrointestinal tract, specifically, in locations associated with lymphoid tissue. These niches serve as sources of enteric neurotransmitters, such as epinephrine and norepinephrine, that are known to increase virulence in several pathogens, including enterohemorrhagic E. coli The mechanisms that allow pathogens to target these niches are poorly understood. We previously reported that 3,4-dihydroxymandelic acid (DHMA), a metabolite of norepinephrine produced by E. coli, is a chemoattractant for the nonpathogenic E. coli RP437 strain. Here we report that DHMA is also a chemoattractant for EHEC. In addition, DHMA induces the expression of EHEC virulence genes and increases attachment to intestinal epithelial cells in vitro in a QseC-dependent manner. We also show that DHMA is present in murine gut fecal contents and that its production requires the presence of the commensal microbiota. On the basis of its ability to both attract and induce virulence gene expression in EHEC, we propose that DHMA acts as a molecular beacon to target pathogens to their preferred sites of infection in vivo.

Chemotaxis detection towards chlorophenols using video processing analysis

To our knowledge, this communication is the first report of chemotaxis towards chlorophenols by any bacteria. We used a recently published method based on the agarose in-plug assay combined with video processing analysis and we also present a new index of bacterial mean speed for these assays.

A cyclic di-GMP-binding adaptor protein interacts with a chemotaxis methyltransferase to control flagellar motor switching

The bacterial messenger cyclic diguanylate monophosphate (c-di-GMP) binds to various effectors, the most common of which are single-domain PilZ proteins. These c-di-GMP effectors control various cellular functions and multicellular behaviors at the transcriptional or posttranslational level. We found that MapZ (methyltransferase-associated PilZ; formerly known as PA4608), a single-domain PilZ protein from the opportunistic pathogen Pseudomonas aeruginosa, directly interacted with the methyltransferase CheR1 and that this interaction was enhanced by c-di-GMP. In vitro assays indicated that, in the presence of c-di-GMP, MapZ inhibited CheR1 from methylating the chemoreceptor PctA, which would be expected to increase its affinity for chemoattractants and promote chemotaxis. MapZ localized to the poles of P. aeruginosa cells, where the flagellar motor and other chemotactic proteins, including PctA and CheR1, are also located. P. aeruginosa cells exhibit a random walk behavior by frequently switching the direction of flagellar rotation in a uniform solution. We showed that binding of c-di-GMP to MapZ decreased the frequency of flagellar motor switching and that MapZ was essential for generating the heterogeneous motility typical of P. aeruginosa cell populations and for efficient surface attachment during biofilm formation. Collectively, the studies revealed that c-di-GMP affects flagellar motor output by regulating the methylation of chemoreceptors through a single-domain PilZ adaptor protein.

Video processing analysis for the determination and evaluation of the chemotactic response in bacterial populations

The aim of the present work was to design a methodology based on video processing to obtain indicators of bacterial population motility that allow the quantitative and qualitative analysis and comparison of the chemotactic phenomenon with different attractants in the agarose-in plug bridge method. Video image sequences were processed applying Shannon's entropy to the intensity time series of each pixel, which conducted to a final pseudo colored image resembling a map of the dynamic bacterial clusters. Processed images could discriminate perfectly between positive and negative attractant responses at different periods of time from the beginning of the assay. An index of spatial and temporal motility was proposed to quantify the bacterial response. With this index, this video processing method allowed obtaining quantitative information of the dynamic changes in space and time from a traditional qualitative assay. We conclude that this computational technique, applied to the traditional agarose-in plug assay, has demonstrated good sensitivity for identifying chemotactic regions with a broad range of motility.

The Helicobacter pylori CZB Cytoplasmic Chemoreceptor TlpD Forms an Autonomous Polar Chemotaxis Signaling Complex That Mediates a Tactic Response to Oxidative Stress

Cytoplasmic chemoreceptors are widespread among prokaryotes but are far less understood than transmembrane chemoreceptors, despite being implicated in many processes. One such cytoplasmic chemoreceptor is Helicobacter pylori TlpD, which is required for stomach colonization and drives a chemotaxis response to cellular energy levels. Neither the signals sensed by TlpD nor its molecular mechanisms of action are known. We report here that TlpD functions independently of the other chemoreceptors. When TlpD is the sole chemoreceptor, it is able to localize to the pole and recruits CheW, CheA, and at least two CheV proteins to this location. It loses the normal membrane association that appears to be driven by interactions with other chemoreceptors and with CheW, CheV1, and CheA. These results suggest that TlpD can form an autonomous signaling unit. We further determined that TlpD mediates a repellent chemotaxis response to conditions that promote oxidative stress, including being in the presence of iron, hydrogen peroxide, paraquat, and metronidazole. Last, we found that all tested H. pylori strains express TlpD, whereas other chemoreceptors were present to various degrees. Our data suggest a model in which TlpD coordinates a signaling complex that responds to oxidative stress and may allow H. pylori to avoid areas of the stomach with high concentrations of reactive oxygen species.

IMPORTANCE

Helicobacter pylori senses its environment with proteins called chemoreceptors. Chemoreceptors integrate this sensory information to affect flagellum-based motility in a process called chemotaxis. Chemotaxis is employed during infection and presumably aids H. pylori in encountering and colonizing preferred niches. A cytoplasmic chemoreceptor named TlpD is particularly important in this process, and we report here that this chemoreceptor is able to operate independently of other chemoreceptors to organize a chemotaxis signaling complex and mediate a repellent response to oxidative stress conditions. H. pylori encounters and must cope with oxidative stress during infection due to oxygen and reactive oxygen species produced by host cells. TlpD's repellent response may allow the bacteria to escape niches experiencing inflammation and elevated reactive oxygen species (ROS) production.

Pseudomonas chemotaxis

Pseudomonads sense changes in the concentration of chemicals in their environment and exhibit a behavioral response mediated by flagella or pili coupled with a chemosensory system. The two known chemotaxis pathways, a flagella-mediated pathway and a putative pili-mediated system, are described in this review. Pseudomonas shows chemotaxis response toward a wide range of chemicals, and this review includes a summary of them organized by chemical structure. The assays used to measure positive and negative chemotaxis swimming and twitching Pseudomonas as well as improvements to those assays and new assays are also described. This review demonstrates that there is ample research and intellectual space for future investigators to elucidate the role of chemotaxis in important processes such as pathogenesis, bioremediation, and the bioprotection of plants and animals.

Motile Geobacter dechlorinators migrate into a model source zone of trichloroethene dense non-aqueous phase liquid: experimental evaluation and modeling

Microbial migration towards a trichloroethene (TCE) dense non-aqueous phase liquid (DNAPL) could facilitate the bioaugmentation of TCE DNAPL source zones. This study characterized the motility of the Geobacter dechlorinators in a TCE to cis-dichloroethene dechlorinating KB-1(™) subculture. No chemotaxis towards or away from TCE was found using an agarose in-plug bridge method. A second experiment placed an inoculated aqueous layer on top of a sterile sand layer and showed that Geobacter migrated several centimeters in the sand layer in just 7days. A random motility coefficient for Geobacter in water of 0.24±0.02cm(2)·day(-1) was fitted. A third experiment used a diffusion-cell setup with a 5.5cm central sand layer separating a DNAPL from an aqueous top layer as a model source zone to examine the effect of random motility on TCE DNAPL dissolution. With top layer inoculation, Geobacter quickly colonized the sand layer, thereby enhancing the initial TCE DNAPL dissolution flux. After 19days, the DNAPL dissolution enhancement was only 24% lower than with an homogenous inoculation of the sand layer. A diffusion-motility model was developed to describe dechlorination and migration in the diffusion-cells. This model suggested that the fast colonization of the sand layer by Geobacter was due to the combination of random motility and growth on TCE.

Improving the design of the agarose spot assay for eukaryotic cell chemotaxis

Migration of cells along gradients of effector molecules, i.e., chemotaxis, is necessary in immune response and is involved in development and cancer metastasis. The experimental assessment of chemotaxis thus is of high interest. The agarose spot assay is a simple tissue culture system used to analyze chemotaxis. Although direction sensing requires gradients to be sufficiently steep, how the chemical gradients developed in this assay change over time, and thus, under what conditions chemotaxis is plausible, has not yet been determined. Here, we use numerical solution of the diffusion equation to determine the chemoattractant gradient produced in the assay. Our analysis shows that, for the usual spot size, the lifetime of the assay is optimized if the chemoattractant concentration in the spot is initially 30 times the dissociation constant of the chemoattractant-receptor bond. This result holds regardless of the properties of the chemoattractant. With this initial concentration, the chemoattractant gradient falls to the minimum threshold for directional sensing at the same time that the concentration drops to the optimal level for detecting gradient direction. If a higher initial chemoattractant concentration is used, the useful lifetime of the assay is likely to be shortened because receptor saturation may decrease the cells' sensitivity to the gradient; lower initial concentrations would result in too little chemoattractant for the cells to detect. Moreover, chemoattractants with higher diffusion coefficients would sustain gradients for less time. Based on previous measurements of the diffusion coefficients of the chemoattractants EGF and CXCL12, we estimate that the assay will produce gradients that cells can sense for a duration of 10 h for EGF and 5 h for CXCL12. These gradient durations are comparable to what can be achieved with the Boyden chamber assay. The analysis presented in this work facilitates determination of suitable parameters for the assay, and can be used to assess whether observed cell motility is likely due to chemotaxis or chemokinesis.

New paradigm for tumor theranostic methodology using bacteria-based microrobot

We propose a bacteria-based microrobot (bacteriobot) based on a new fusion paradigm for theranostic activities against solid tumors. We develop a bacteriobot using the strong attachment of bacteria to Cy5.5-coated polystyrene microbeads due to the high-affinity interaction between biotin and streptavidin. The chemotactic responses of the bacteria and the bacteriobots to the concentration gradients of lysates or spheroids of solid tumors can be detected as the migration of the bacteria and/or the bacteriobots out of the central region toward the side regions in a chemotactic microfluidic chamber. The bacteriobots showed higher migration velocity toward tumor cell lysates or spheroids than toward normal cells. In addition, when only the bacteriobots were injected to the CT-26 tumor mouse model, Cy5.5 signal was detected from the tumor site of the mouse model. In-vitro and in-vivo tests verified that the bacteriobots had chemotactic motility and tumor targeting ability. The new microrobot paradigm in which bacteria act as microactuators and microsensors to deliver microstructures to tumors can be considered a new theranostic methodology for targeting and treating solid tumors.

Chemotaxis to furan compounds by furan-degrading Pseudomonas strains

Two Pseudomonas strains known to utilize furan derivatives were shown to respond chemotactically to furfural, 5-hydroxymethylfurfural, furfuryl alcohol, and 2-furoic acid. In addition, a LysR-family regulatory protein known to regulate furan metabolic genes was found to be involved in regulating the chemotactic response.

Impact of fluorochrome stains used to study bacterial transport in shallow aquifers on motility and chemotaxis of Pseudomonas species

One of the most common methods of tracking movement of bacteria in groundwater environments involves a priori fluorescent staining. A major concern in using these stains to label bacteria in subsurface injection-and-recovery studies is the effect they may have on the bacterium's transport properties. Previous studies investigated the impact of fluorophores on bacterial surface properties (e.g. zeta potential). However, no previous study has looked at the impact of fluorescent staining on swimming speed and chemotaxis. It was found that DAPI lowered the mean population swimming speed of Pseudomonas putida F1 by 46% and Pseudomonas stutzeri by 55%. DAPI also inhibited the chemotaxis in both strains. The swimming speeds of P. putida F1 and P. stutzeri were diminished slightly by CFDA/SE, but not to a statistically significant extent. CFDA/SE had no effect on chemotaxis of either strain to acetate. SYBR(®) Gold had no effect on swimming speed or the chemotactic response to acetate for either strain. This research indicates that although DAPI may not affect sorption to grain surfaces, it adversely affects other potentially important transport properties such as swimming and chemotaxis. Consequently, bacterial transport studies conducted using DAPI are biased to nonchemotactic conditions and do not appear to be suitable for monitoring the effect of chemotaxis on bacterial transport in shallow aquifers.

Transverse chemotactic migration of bacteria from high to low permeability regions in a dual permeability microfluidic device

Low permeability regions such as clay lenses are difficult to remediate using conventional treatment methods. Bacterial chemotaxis (directed migration toward a contaminant source) may be helpful in enhancing bioremediation of such contaminated sites. This study experimentally simulates a two-dimensional dual-permeability groundwater contamination scenario using a microfluidic device (MFD) and evaluates transverse chemotactic migration of bacteria from high to low permeability regions under various flow velocities. Chemotaxis of Escherichia coli (E. coli) HCB33 to the chemoattractant dl-aspartic acid was quantified in terms of change in total bacterial counts in pore throats in low permeability regions containing attractant. An increase in total bacterial counts, ranging from 1.09 to 1.74 times, was observed in low permeability regions in experiments under chemotactic conditions. Experiments with no attractant showed no increase in total bacterial counts in low permeability regions. A large increase in bacterial counts in the pore throats just outside the low permeability region was also observed in chemotaxis experiments. The bacterial chemotactic response was observed to decrease linearly with increase in flow velocity, with no observed response at the highest flow velocity (Darcy velocity = 0.22 mm/s), where chemotaxis was offset by advective flow.

A MotN mutant of Ralstonia solanacearum is hypermotile and has reduced virulence

Ralstonia solanacearum is a soil-borne plant pathogen that causes bacterial wilt disease on many plant species. We previously showed that swimming motility contributes to virulence of this bacterium in the early stages of host invasion and colonization. In this study we identified a new negative regulator of motility, named motN, that is located in a cluster of motility-related genes. A motN mutant was hypermotile both on 0.3% agar motility plates and in rich and minimal medium broth. However, like its wild-type parent, it was largely nonmotile inside plants. The motN mutant cells appeared hyperflagellated, and sheared cell protein preparations from motN contained more flagellin than preparations from wild-type cells. The motN strain was significantly reduced in virulence in a naturalistic soil soak assay on tomato plants. However, the motN mutant had wild-type virulence when it was inoculated directly into the plant vascular system. This suggests that motN makes its contribution to virulence early in disease development. The motN mutant formed weaker biofilms than the wild type, but it attached normally to tomato roots and colonized tomato stems as well as its wild-type parent. Phenotypic analysis and gene expression studies indicated that MotN directly or indirectly represses transcription of the major motility regulator FlhDC. MotN was also connected with other known motility and virulence regulators, PehSR, VsrBC, and VsrAD, via uncertain mechanisms. Together, these results demonstrate the importance of precise regulation of flagellum-mediated motility in R. solanacearum.

An agarose spot chemotaxis assay for chemokine receptor antagonists

INTRODUCTION

Chemokines are important players in directing the migration of cancer cells as part of the metastatic process. The aim of this study is to develop an easy-to-perform, reliable, and inexpensive assay for rapid analysis of anti-chemotactic activity of chemokine antagonists under a number of experimental conditions.

METHODS

An agarose spot containing the chemokine chemoattractant is applied to a glass petri dish. Live cells in a media, both with and without a chemokine antagonist, are added to the dish and, following cell adhesion, the migration under the agarose spot is observed and analysed by microscopy.

RESULTS

In the absence of CXCL12 in the agarose, no migration under the agarose spot is detected. In the presence of CXCL12, significant migration under the agarose spot is observed which can be retarded if a neutralising monoclonal antibody or a small molecule antagonist is added to the media.

DISCUSSION

This experimental configuration is a reliable, inexpensive and easy-to-perform chemotaxis assay, which enables assessment of the activity of CXCR4 antagonists.

A histidine-kinase cheA gene of Pseudomonas pseudoalcaligens KF707 not only has a key role in chemotaxis but also affects biofilm formation and cell metabolism

A histidine-kinase cheA gene in Pseudomonas pseudoalcaligenes KF707 plays a central role in the regulation of metabolic responses as well as in chemotaxis. Non-chemotactic mutants harboring insertions into the cheA gene were screened for their ability to form biofilms in the Calgary biofilm device. Notably, ≥95% decrease in the number of cells attached to the polystyrene surface was observed in cheA mutants compared to the KF707 wild-type biofilm phenotype. The ability to form mature biofilms was restored to wild-type levels, providing functional copies of the KF707 cheA gene to the mutants. In addition, phenotype micro-arrays and proteomic analyses revealed that several basic metabolic activities and a few periplasmic binding proteins of cheA mutant cells differed compared to those of wild-type cells. These results are interpreted as evidence of a strong integration between chemotactic and metabolic pathways in the process of biofilm development by P. pseudoalcaligenes KF707.

Bacterial chemotaxis along vapor-phase gradients of naphthalene

The role of bacterial growth and translocation for the bioremediation of organic contaminants in the vadose zone is poorly understood. Whereas air-filled pores restrict the mobility of bacteria, diffusion of volatile organic compounds in air is more efficient than in water. Past research, however, has focused on chemotactic swimming of bacteria along gradients of water-dissolved chemicals. In this study we tested if and to what extent Pseudomonas putida PpG7 (NAH7) chemotactically reacts to vapor-phase gradients forming above their swimming medium by the volatilization from a spot source of solid naphthalene. The development of an aqueous naphthalene gradient by air-water partitioning was largely suppressed by means of activated carbon in the agar. Surprisingly, strain PpG7 was repelled by vapor-phase naphthalene although the steady state gaseous concentrations were 50-100 times lower than the aqueous concentrations that result in positive chemotaxis of the same strain. It is thus assumed that the efficient gas-phase diffusion resulting in a steady, and possibly toxic, naphthalene flux to the cells controlled the chemotactic reaction rather than the concentration to which the cells were exposed. To our knowledge this is the first demonstration of apparent chemotactic behavior of bacteria in response to vapor-phase effector gradients.

An agarose spot assay for chemotactic invasion

The directed motility of cells toward the source of a soluble chemical (chemotaxis) plays a role in events ranging from immune function to cancer progression. Numerous chemotaxis assays are commonly employed, yet none provides an optimal combination of the relevant parameters. The ideal chemotaxis assay for use in the analysis of cells crawling across a planar surface should be cost-effective, simple to perform, and suitable for high-throughput multiplexing, as well as permit alteration of experimental conditions during cell motility. Here we describe a novel chemotaxis assay based upon the invasion of cells into agarose spots into which chemoattractants are suspended. Our studies demonstrate that this system assays chemotaxis and not chemokinesis, and provide proof-of-principle for drug screening studies as well as analysis through high-resolution cellular imaging.

The chemical-in-plug bacterial chemotaxis assay is prone to false positive responses

Background

Chemical-in-plug assays are commonly used to study bacterial chemotaxis, sometimes in the absence of stringent controls.

Results

We report that non-chemotactic and non-motile mutants in two distinct bacterial species (Shewanella oneidensis and Helicobacter pylori) show apparent zones of accumulation or clearing around test plugs containing potential attractants or repellents, respectively.

Conclusions

Our results suggest that the chemical-in-plug assay should be used with caution, that non-motile or non-chemotactic mutants should be employed as controls, and that results should be confirmed with other types of assays.

Kinetics of trichloroethylene and toluene toxicity to Pseudomonas putida F1

The goal of the present study was to elucidate the distribution of viable bacteria in chemical gradients and to evaluate the toxic effect of high concentrations of contaminants on contaminant-degrading bacteria under prolonged exposure. Accumulations of viable Pseudomonas putida F1 (P. putida F1) cells were observed surrounding trichloroethylene (TCE)-containing plugs. Results from this work indicate that P. putida F1 immediately adjacent to a TCE source become nonviable, whereas cells accumulating farther away use chemotaxis to migrate toward regions with optimal chemical concentrations in the form of concentrated bacterial bands. A method was developed to test the toxicity of model contaminant stressors, TCE and toluene, to P. putida F1; data obtained from toxicity experiments were fit to linear and exponential bacterial viability-decay models. Toxicity of TCE to P. putida F1 was best described with an exponential viability-decay model, with a viability-decay constant k(TCE) = 0.025 h(-4.95) (r(2) = 0.965). Toluene toxicity showed a marginally better fit to the linear viability-decay model (r(2) = 0.976), with a viability-decay constant k(toluene) = 0.208 h(-1). Best-fit model parameters obtained for both TCE and toluene were used to predict bacterial viability in toxicity experiments with higher contaminant concentrations and matched well with experimental data. Results from the present study can be used to predict bacterial accumulation and viability near nonaqueous-phase liquid (NAPL) sources in groundwater and may be helpful in designing bioremediation strategies for sites contaminated with residual NAPLs.

Bacterial attraction and quorum sensing inhibition in Caenorhabditis elegans exudates

Caenorhabditis elegans, a bacterivorous nematode, lives in complex rotting fruit, soil, and compost environments, and chemical interactions are required for mating, monitoring population density, recognition of food, avoidance of pathogenic microbes, and other essential ecological functions. Despite being one of the best-studied model organisms in biology, relatively little is known about the signals that C. elegans uses to interact chemically with its environment or as defense. C. elegans exudates were analyzed by using several analytical methods and found to contain 36 common metabolites that include organic acids, amino acids, and sugars, all in relatively high abundance. Furthermore, the concentrations of amino acids in the exudates were dependent on developmental stage. The C. elegans exudates were tested for bacterial chemotaxis using Pseudomonas putida (KT2440), a plant growth promoting rhizobacterium, Pseudomonas aeruginosa (PAO1), a soil bacterium pathogenic to C. elegans, and Escherichia coli (OP50), a non-motile bacterium tested as a control. The C. elegans exudates attracted the two Pseudomonas species, but had no detectable antibacterial activity against P. aeruginosa. To our surprise, the exudates of young adult and adult life stages of C. elegans exudates inhibited quorum sensing in the reporter system based on the LuxR bacterial quorum sensing (QS) system, which regulates bacterial virulence and other factors in Vibrio fischeri. We were able to fractionate the QS inhibition and bacterial chemotaxis activities, thus demonstrating that these activities are chemically distinct. Our results demonstrate that C. elegans can attract its bacterial food and has the potential of partially regulating the virulence of bacterial pathogens by inhibiting specific QS systems.

Diversity in bacterial chemotactic responses and niche adaptation

The ability of microbes to rapidly sense and adapt to environmental changes plays a major role in structuring microbial communities, in affecting microbial activities, as well as in influencing various microbial interactions with the surroundings. The bacterial chemotaxis signal transduction system is the sensory perception system that allows motile cells to respond optimally to changes in environmental conditions by allowing cells to navigate in gradients of diverse physicochemical parameters that can affect their metabolism. The analysis of complete genome sequences from microorganisms that occupy diverse ecological niches reveal the presence of multiple chemotaxis pathways and a great diversity of chemoreceptors with novel sensory specificities. Owing to its role in mediating rapid responses of bacteria to changes in the surroundings, bacterial chemotaxis is a behavior of interest in applied microbiology as it offers a unique opportunity for understanding the environmental cues that contribute to the survival of bacteria. This chapter explores the diversity of bacterial chemotaxis and suggests how gaining further insights into such diversity may potentially impact future drug and pesticides development and could inform bioremediation strategies.

Microfluidic techniques for the analysis of bacterial chemotaxis

Anton van Leeuwenhoek first observed bacterial motility in the seventeenth century, and Wilhelm Pfeffer described bacterial chemotaxis in the late nineteenth century. A number of methods, briefly summarized here, have been developed over the years to quantify the motility and chemotaxis of bacteria, but none of them is totally satisfactory. In this chapter, we describe two new assays for chemotaxis that are based on microfabrication and microfluidic techniques. With easily culturable and manipulated bacteria like Escherichia coli, fluorescent labeling of the cells with green fluorescent protein (GFP) or red fluorescent protein (RFP) provides a convenient method for visualizing cells and differentiating two strains in the same experiment. The methods can be extended to environmental samples and mixed bacterial populations with suitable modifications of the optical recording system. The methods are equally useful for studying random motility, attractant chemotaxis, or repellent chemotaxis. The microfluidic system also provides a straightforward way to enrich for mutants that lose or gain responses to individual chemicals. The same approaches can presumably be used to isolate bacteria from environmental samples that respond, or do not respond, to particular chemicals or mixtures of chemicals.

Differential effects of epinephrine, norepinephrine, and indole on Escherichia coli O157:H7 chemotaxis, colonization, and gene expression

During infection in the gastrointestinal tract, enterohemorrhagic Escherichia coli (EHEC) O157:H7 is exposed to a wide range of signaling molecules, including the eukaryotic hormones epinephrine and norepinephrine, and bacterial signal molecules such as indole. Since these signaling molecules have been shown to be involved in the regulation of phenotypes such as motility and virulence that are crucial for EHEC infections, we hypothesized that these molecules also govern the initial recognition of the large intestine environment and attachment to the host cell surface. Here, we report that, compared to indole, epinephrine and norepinephrine exert divergent effects on EHEC chemotaxis, motility, biofilm formation, gene expression, and colonization of HeLa cells. Using a novel two-fluorophore chemotaxis assay, it was found that EHEC is attracted to epinephrine and norepinephrine while it is repelled by indole. In addition, epinephrine and norepinephrine also increased EHEC motility and biofilm formation while indole attenuated these phenotypes. DNA microarray analysis of surface-associated EHEC indicated that epinephrine/norepinephrine up-regulated the expression of genes involved in surface colonization and virulence while exposure to indole decreased their expression. The gene expression data also suggested that autoinducer 2 uptake was repressed upon exposure to epinephrine/norepinephrine but not indole. In vitro adherence experiments confirmed that epinephrine and norepinephrine increased attachment to epithelial cells while indole decreased adherence. Taken together, these results suggest that epinephrine and norepinephrine increase EHEC infection while indole attenuates the process.

Helicobacter pylori chemotaxis modulates inflammation and bacterium-gastric epithelium interactions in infected mice

The ulcer-causing pathogen Helicobacter pylori uses directed motility, or chemotaxis, to both colonize the stomach and promote disease development. Previous work showed that mutants lacking the TlpB chemoreceptor, one of the receptors predicted to drive chemotaxis, led to less inflammation in the gerbil stomach than did the wild type. Here we expanded these findings and examined the effects on inflammation of completely nonchemotactic mutants and mutants lacking each chemoreceptor. Of note, all mutants colonized mice to the same levels as did wild-type H. pylori. Infection by completely nonchemotactic mutants (cheW or cheY) resulted in significantly less inflammation after both 3 and 6 months of infection. Mutants lacking either the TlpA or TlpB H. pylori chemotaxis receptors also had alterations in inflammation severity, while mutants lacking either of the other two chemoreceptors (TlpC and HylB) behaved like the wild type. Fully nonchemotactic and chemoreceptor mutants adhered to cultured gastric epithelial cells and caused cellular release of the chemokine interleukin-8 in vitro similar to the release caused by the wild type. The situation appeared to be different in the stomach. Using silver-stained histological sections, we found that nonchemotactic cheY or cheW mutants were less likely than the wild type to be intimately associated with the cells of the gastric mucosa, although there was not a strict correlation between intimate association and inflammation. Because others have shown that in vivo adherence promotes inflammation, we propose a model in which H. pylori uses chemotaxis to guide it to a productive interaction with the stomach epithelium.

Characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis

Pseudomonas fluorescens strain KU-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-NBA) via the formation of 3-hydroxyanthranilate (3-HAA), a known antioxidant and reductant. The initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-HAA are catalyzed by a NADPH-dependent 2-NBA nitroreductase (NbaA) and 2-hydroxylaminobenzoate mutase (NbaB), respectively. The 216-amino-acid protein NbaA is 78% identical to a plasmid-encoded hypothetical conserved protein of Polaromonas strain JS666; structurally, it belongs to the homodimeric NADH:flavin mononucleotide (FMN) oxidoreductase-like fold family. Structural modeling of complexes with the flavin, coenzyme, and substrate suggested specific residues contributing to the NbaA catalytic activity, assuming a ping-pong reaction mechanism. Mutational analysis supports the roles of Asn40, Asp76, and Glu113, which are predicted to form the binding site for a divalent metal ion implicated in FMN binding, and a role in NADPH binding for the 10-residue insertion in the beta5-alpha2 loop. The 181-amino-acid sequence of NbaB is 35% identical to the 4-hydroxylaminobenzoate lyases (PnbBs) of various 4-nitrobenzoate-assimilating bacteria, e.g., Pseudomonas putida strain TW3. Coexpression of nbaB with nbaA in Escherichia coli produced a small amount of 3-HAA from 2-NBA, supporting the functionality of the nbaB gene. We also showed by gene knockout and chemotaxis assays that nbaY, a chemoreceptor NahY homolog located downstream of the nbaA gene, is responsible for strain KU-7 being attracted to 2-NBA. NbaY is the first chemoreceptor in nitroaromatic metabolism to be identified, and this study completes the gene elucidation of 2-NBA metabolism that is localized within a 24-kb chromosomal locus of strain KU-7.

Oxygen and Redox Sensing by Two‐Component Systems That Regulate Behavioral Responses: Behavioral Assays and Structural Studies of Aer Using In Vivo Disulfide Cross‐Linking

A remarkable increase in the number of annotated aerotaxis (oxygen-seeking) and redox taxis sensors can be attributed to recent advances in bacterial genomics. However, in silico predictions should be supported by behavioral assays and genetic analyses that confirm an aerotaxis or redox taxis function. This chapter presents a collection of procedures that have been highly successful in characterizing aerotaxis and redox taxis in Escherichia coli. The methods are described in enough detail to enable investigators of other species to adapt the procedures for their use. A gas flow cell is used to quantitate the temporal responses of bacteria to a step increase or decrease in oxygen partial pressure or redox potential. Bacterial behavior in spatial gradients is analyzed using optically flat capillaries and soft agar plates (succinate agar or tryptone agar). We describe two approaches to estimate the preferred partial pressure of oxygen that attracts a bacterial species; this concentration is important for understanding microbial ecology. At the molecular level, we describe procedures used to determine the structure and topology of Aer, a membrane receptor for aerotaxis. Cysteine-scanning mutagenesis and in vivo disulfide cross-linking procedures utilize the oxidant Cu(II)-(1,10-phenanthroline)(3) and bifunctional sulfhydryl-reactive probes. Finally, we describe methods used to determine the boundaries of transmembrane segments of receptors such as Aer. These include 5-iodoacetamidofluorescein, 4-acetamido-4-disulfonic acid, disodium salt (AMS), and methoxy polyethylene glycol maleimide, a 5-kDa molecular mass probe that alters the mobility of Aer on SDS-PAGE.

Identification and characterization of the chemotactic transducer in Pseudomonas aeruginosa PAO1 for positive chemotaxis to trichloroethylene

Pseudomonas aeruginosa PAO1 is repelled by trichloroethylene (TCE), and the methyl-accepting chemotaxis proteins PctA, PctB, and PctC serve as the major chemoreceptors for negative chemotaxis to TCE. In this study, we found that the pctABC triple mutant of P. aeruginosa PAO1 was attracted by TCE. Chemotaxis assays of a set of mutants containing deletions in 26 potential mcp genes revealed that mcpA (PA0180) is the chemoreceptor for positive chemotaxis to TCE. McpA also detects tetrachloroethylene and dichloroethylene isomers as attractants.

Chemotaxis is required for virulence and competitive fitness of the bacterial wilt pathogen Ralstonia solanacearum

Ralstonia solanacearum, a soilborne plant pathogen of considerable economic importance, invades host plant roots from the soil. Qualitative and quantitative chemotaxis assays revealed that this bacterium is specifically attracted to diverse amino acids and organic acids, and especially to root exudates from the host plant tomato. Exudates from rice, a nonhost plant, were less attractive. Eight different strains from this heterogeneous species complex varied significantly in their attraction to a panel of carbohydrate stimuli, raising the possibility that chemotactic responses may be differentially selected traits that confer adaptation to various hosts or ecological conditions. Previous studies found that an aflagellate mutant lacking swimming motility is significantly reduced in virulence, but the role of directed motility mediated by the chemotaxis system was not known. Two site-directed R. solanacearum mutants lacking either CheA or CheW, which are core chemotaxis signal transduction proteins, were completely nonchemotactic but retained normal swimming motility. In biologically realistic soil soak virulence assays on tomato plants, both nonchemotactic mutants had significantly reduced virulence indistinguishable from that of a nonmotile mutant, demonstrating that directed motility, not simply random motion, is required for full virulence. In contrast, nontactic strains were as virulent as the wild-type strain was when bacteria were introduced directly into the plant stem through a cut petiole, indicating that taxis makes its contribution to virulence in the early stages of host invasion and colonization. When inoculated individually by soaking the soil, both nontactic mutants reached the same population sizes as the wild type did in the stems of tomato plants just beginning to wilt. However, when tomato plants were coinoculated with a 1:1 mixture of a nontactic mutant and its wild-type parent, the wild-type strain outcompeted both nontactic mutants by 100-fold. Together, these results indicate that chemotaxis is an important trait for virulence and pathogenic fitness in this plant pathogen.

Continuous-flow capillary assay for measuring bacterial chemotaxis

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

Chemotaxis of Pseudomonas stutzeri OX1 and Burkholderia cepacia G4 toward chlorinated ethenes

The chemotactic responses of Pseudomonas putida F1, Burkholderia cepacia G4, and Pseudomonas stutzeri OX1 were investigated toward toluene, trichloroethylene (TCE), tetrachloroethylene (PCE), cis-1,2-dichloroethylene (cis-DCE), trans-1,2-dichloroethylene (trans-DCE), 1,1-dichloroethylene (1,1-DCE), and vinyl chloride (VC). P. stutzeri OX1 and P. putida F1 were chemotactic toward toluene, PCE, TCE, all DCEs, and VC. B. cepacia G4 was chemotactic toward toluene, PCE, TCE, cis-DCE, 1,1-DCE, and VC. Chemotaxis of P. stutzeri OX1 grown on o-xylene vapors was much stronger than when grown on o-cresol vapors toward some chlorinated ethenes. Expression of toluene-o-xylene monooxygenase (ToMO) from touABCDEF appears to be required for positive chemotaxis attraction, and the attraction is stronger with the touR (ToMO regulatory) gene.

Aerotactic responses in bacteria to photoreleased oxygen

Bacterial aerotaxis is a rapid response towards or away from oxygen. Here we report on the use of computer-assisted motion analysis coupled to flash photolysis of caged oxygen to quantify aerotactic responses in bacteria. The caged compound (mu-peroxo)(mu-hydroxo)bis[bis(bipyridyl) cobalt(III)] perchlorate liberates molecular oxygen upon irradiation with near-UV light. A mixture of cells and the caged oxygen compound was placed in a capillary tube and challenged by discrete stimuli of molecular oxygen produced by photolysis. We then recorded the rate of change of direction (rcd) as an estimate of tumble frequency in response to liberated oxygen and measured the signal processing (excitation) times in Bacillus subtilis, Bacillus halodurans and Escherichia coli. This computer-assisted caged oxygen assay gives a unique physiological profile of different aerotaxis transducers in bacteria.

Bacterial chemotaxis to pollutants and plant-derived aromatic molecules

There is accumulating evidence that motile bacteria are chemotactically attracted to environmental pollutants that they can degrade. Chemotaxis, the ability of motile bacteria to detect and respond to specific chemicals in the environment, can increase an organism's chances of locating useful sources of carbon, nitrogen and energy, and could thus play an important role in the biodegradation process. Recent evidence demonstrating that chemotaxis and biodegradation genes are coordinately regulated suggests that these processes are intimately linked in nature.

Toluene-degrading bacteria are chemotactic towards the environmental pollutants benzene, toluene, and trichloroethylene

The bioremediation of polluted groundwater and toxic waste sites requires that bacteria come into close physical contact with pollutants. This can be accomplished by chemotaxis. Five motile strains of bacteria that use five different pathways to degrade toluene were tested for their ability to detect and swim towards this pollutant. Three of the five strains (Pseudomonas putida F1, Ralstonia pickettii PKO1, and Burkholderia cepacia G4) were attracted to toluene. In each case, the response was dependent on induction by growth with toluene. Pseudomonas mendocina KR1 and P. putida PaW15 did not show a convincing response. The chemotactic responses of P. putida F1 to a variety of toxic aromatic hydrocarbons and chlorinated aliphatic compounds were examined. Compounds that are growth substrates for P. putida F1, including benzene and ethylbenzene, were chemoattractants. P. putida F1 was also attracted to trichloroethylene (TCE), which is not a growth substrate but is dechlorinated and detoxified by P. putida F1. Mutant strains of P. putida F1 that do not oxidize toluene were attracted to toluene, indicating that toluene itself and not a metabolite was the compound detected. The two-component response regulator pair TodS and TodT, which control expression of the toluene degradation genes in P. putida F1, were required for the response. This demonstration that soil bacteria can sense and swim towards the toxic compounds toluene, benzene, TCE, and related chemicals suggests that the introduction of chemotactic bacteria into selected polluted sites may accelerate bioremediation processes.

BasT, a membrane-bound transducer protein for amino acid detection in Halobacterium salinarum

Halophilic archaea, such as eubacteria, use methyl-accepting chemotaxis proteins (MCPs) to sense their environment. We show here that BasT is a halobacterial transducer protein (Htp) responsible for chemotaxis towards five attractant amino acids. The C-terminus of the protein exhibits the highly conserved regions that are diagnostic for MCPs: the signalling domain for communication with the histidine kinase and the methylation sites that interact with the methylation/demethylation enzymes for adaptation. Hydropathy analysis predicts an enterobacterial-type transducer protein topology for BasT, with an extracellular putative ligand-binding domain flanked by two transmembrane helices and a cytoplasmic domain. BasT-inactivated mutant cells are missing a membrane protein radiolabelled with L-[methyl-3H]-methionine in wild-type cells, confirming that BasT is methylatable and membrane bound. Behavioural analysis of the basT mutant cells by capillary and chemical-in-plug assays demonstrates complete loss of chemotactic responses towards five (leucine, isoleucine, valine, methionine and cysteine) of the six attractant amino acids for Halobacterium salinarum, whereas they still respond to arginine. The volatile methyl group production assays also corroborate these findings and confirm that BasT signalling induces methyl group turnover. Our data identify BasT as the chemotaxis transducer protein for the branched chain amino acids leucine, isoleucine and valine as well as for methionine and cysteine. Thus, BasT and the arginine sensor Car cover the entire spectrum of chemotactic responses towards attractant amino acids in H. salinarum.

NahY, a catabolic plasmid-encoded receptor required for chemotaxis of Pseudomonas putida to the aromatic hydrocarbon naphthalene

Pseudomonas putida G7 exhibits chemotaxis to naphthalene, but the molecular basis for this was not known. A new gene, nahY, was found to be cotranscribed with meta cleavage pathway genes on the NAH7 catabolic plasmid for naphthalene degradation. The nahY gene encodes a 538-amino-acid protein with a membrane topology and a C-terminal region that resemble those of chemotaxis transducer proteins. A P. putida G7 nahY mutant grew on naphthalene but was not chemotactic to this aromatic hydrocarbon. The protein NahY thus appears to function as a chemoreceptor for naphthalene or a related compound. The presence of nahY on a catabolic plasmid implies that chemotaxis may facilitate biodegradation.

Sensory rhodopsin II transducer HtrII is also responsible for serine chemotaxis in the archaeon Halobacterium salinarum

Previously, we demonstrated that the methyl-accepting protein HtrII is the transducer for photoreceptor sensory rhodopsin II. Here, we provide experimental evidence that HtrII is also a chemotransducer. Using an agarose-in-plug bridge method, we show that an HtrII overexpression strain has a quicker response to serine than does an HtrII deletion strain. Furthermore, an in vivo flow assay demonstrates that the deletion strain is unable to modulate methylesterase activity after serine addition or photostimulation, while the overexpression strain shows distinct methanol peaks following both types of stimuli.