Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Background: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment

The genome of the plant-colonizing bacterium Pseudomonas fluorescens SBW25 harbors a subset of genes that are expressed specifically on plant surfaces. The function of these genes is central to the ecological success of SBW25, but their study poses significant challenges because no phenotype is discernable in vitro. Here, we describe a genetic strategy with general utility that combines suppressor analysis with IVET (SPyVET) and provides a means of identifying regulators of niche-specific genes. Central to this strategy are strains carrying operon fusions between plant environment-induced loci (EIL) and promoterless 'dapB. These strains are prototrophic in the plant environment but auxotrophic on laboratory minimal medium. Regulatory elements were identified by transposon mutagenesis and selection for prototrophs on minimal medium. Approximately 106 mutants were screened for each of 27 strains carrying 'dapB fusions to plant EIL and the insertion point for the transposon determined in approximately 2,000 putative regulator mutants. Regulators were functionally characterized and used to provide insight into EIL phenotypes. For one strain carrying a fusion to the cellulose-encoding wss operon, five different regulators were identified including a diguanylate cyclase, the flagella activator, FleQ, and alginate activator, AmrZ (AlgZ). Further rounds of suppressor analysis, possible by virtue of the SPyVET strategy, revealed an additional two regulators including the activator AlgR, and allowed the regulatory connections to be determined.

Development and application of in vivo expression technology (IVET) for analysing microbial gene expression in complex environments

Establishing the mechanisms by which microbes interact with their environment, including eukaryotic hosts, is a major challenge that is essential for the economic utilisation of microbes and their products. Techniques for determining global gene expression profiles of microbes, such as microarray analyses, are often hampered by methodological restraints, particularly the recovery of bacterial transcripts (RNA) from complex mixtures and rapid degradation of RNA. A pioneering technology that avoids this problem is In Vivo Expression Technology (IVET). IVET is a 'promoter-trapping' methodology that can be used to capture nearly all bacterial promoters (genes) upregulated during a microbe-environment interaction. IVET is especially useful because there is virtually no limit to the type of environment used (examples to date include soil, oomycete, a host plant or animal) to select for active microbial promoters. Furthermore, IVET provides a powerful method to identify genes that are often overlooked during genomic annotation, and has proven to be a flexible technology that can provide even more information than identification of gene expression profiles. A derivative of IVET, termed resolvase-IVET (RIVET), can be used to provide spatio-temporal information about environment-specific gene expression. More recently, niche-specific genes captured during an IVET screen have been exploited to identify the regulatory mechanisms controlling their expression. Overall, IVET and its various spin-offs have proven to be a valuable and robust set of tools for analysing microbial gene expression in complex environments and providing new targets for biotechnological development.

Structure determination, magnetic and optical properties of a new chromium(II) thioantimonate, [Cr((NH2CH2CH2)(3)N)]Sb4S7

The chromium(II) antimony(III) sulphicle, [Cr((NH2CH2CH2)(3)N)]Sb4S7, was synthesised under solvothermal conditions from the reaction of Sb2S3. Cr and S dissolved in tris(2-aminoethyl)amine (tren) at 438 K. The products were characterised by single-crystal X-ray diffraction. elemental analysis, SQUID magnetometry and diffuse reflectance spectroscopy. The compound crystallises in the monoclinic space group P2(1)/n with a = 7.9756(7), b = 10.5191(9), c = 25.880(2) angstrom and beta = 90.864(5)degrees. Alternating SbS33- trigonal pyramids and Sb36 semi-cubes generate Sb4S72- chains which are directly bonded to Cr(tren pendant units. The effective magnetic moment of 4.94(6)mu(B) shows a negligible orbital contribution, in agreement with expectations for Cr(II):d(4) in a (5)A ground state. The measured band gap of 2.14(3) eV is consistent with a correlation between optical band gap and framework density that is established from analysis of a wide range of antimony sulphides. (C) 2007 Elsevier Ltd. All rights reserved.

Testing temperature-induced proteomic changes in the plant-associated bacterium Pseudomonas fluorescens SBW25.

Traits used by bacteria to enhance ecological performance in natural environments are not well understood. Recognizing that the saprophytic plant-colonizing bacterium Pseudomonas fluorescens SBW25 experiences temperatures in its natural environment significantly cooler than the 28°C routinely used in the laboratory, we identified proteins differentially expressed between 28°C and the more environmentally relevant temperature of 14°C. Of 2102 protein isoforms, 32 were temperature responsive and identified by mass spectrometry. Seven of these (OmpR, MucD, GuaD, OsmY and three of unknown function, Tee1, Tee2 and Tee3) were selected for genetic and ecological analyses. In each instance, changes in protein expression with temperature were mirrored by parallel transcriptional changes. The fitness contribution of the genes encoding each of the seven proteins was larger at 14°C than 28°C and included two cases of trade-offs (enhanced fitness at one temperature and reduced fitness at the other – mucD and tee2 deletions). The relationship between the fitness effects of genes in vitro and in vivo was variable, but two temperature-responsive genes – osmY and mucD – contribute substantially to the ability of P. fluorescens to colonize the plant environment.

Acquisition of automatic imitation is sensitive to sensorimotor contingency

The associative sequence learning model proposes that the development of the mirror system depends on the same mechanisms of associative learning that mediate Pavlovian and instrumental conditioning. To test this model, two experiments used the reduction of automatic imitation through incompatible sensorimotor training to assess whether mirror system plasticity is sensitive to contingency (i.e., the extent to which activation of one representation predicts activation of another). In Experiment 1, residual automatic imitation was measured following incompatible training in which the action stimulus was a perfect predictor of the response (contingent) or not at all predictive of the response (noncontingent). A contingency effect was observed: There was less automatic imitation indicative of more learning in the contingent group. Experiment 2 replicated this contingency effect and showed that, as predicted by associative learning theory, it can be abolished by signaling trials in which the response occurs in the absence of an action stimulus. These findings support the view that mirror system development depends on associative learning and indicate that this learning is not purely Hebbian. If this is correct, associative learning theory could be used to explain, predict, and intervene in mirror system development.

Using continuous ground-based radar and lidar measurements for evaluating the representation of clouds in four operational models

The ability of four operational weather forecast models [ECMWF, Action de Recherche Petite Echelle Grande Echelle model (ARPEGE), Regional Atmospheric Climate Model (RACMO), and Met Office] to generate a cloud at the right location and time (the cloud frequency of occurrence) is assessed in the present paper using a two-year time series of observations collected by profiling ground-based active remote sensors (cloud radar and lidar) located at three different sites in western Europe (Cabauw. Netherlands; Chilbolton, United Kingdom; and Palaiseau, France). Particular attention is given to potential biases that may arise from instrumentation differences (especially sensitivity) from one site to another and intermittent sampling. In a second step the statistical properties of the cloud variables involved in most advanced cloud schemes of numerical weather forecast models (ice water content and cloud fraction) are characterized and compared with their counterparts in the models. The two years of observations are first considered as a whole in order to evaluate the accuracy of the statistical representation of the cloud variables in each model. It is shown that all models tend to produce too many high-level clouds, with too-high cloud fraction and ice water content. The midlevel and low-level cloud occurrence is also generally overestimated, with too-low cloud fraction but a correct ice water content. The dataset is then divided into seasons to evaluate the potential of the models to generate different cloud situations in response to different large-scale forcings. Strong variations in cloud occurrence are found in the observations from one season to the same season the following year as well as in the seasonal cycle. Overall, the model biases observed using the whole dataset are still found at seasonal scale, but the models generally manage to well reproduce the observed seasonal variations in cloud occurrence. Overall, models do not generate the same cloud fraction distributions and these distributions do not agree with the observations. Another general conclusion is that the use of continuous ground-based radar and lidar observations is definitely a powerful tool for evaluating model cloud schemes and for a responsive assessment of the benefit achieved by changing or tuning a model cloud

A method for estimating the turbulent kinetic energy dissipation rate from a vertically pointing Doppler lidar, and independent evaluation from balloon-borne in situ measurements

A method of estimating dissipation rates from a vertically pointing Doppler lidar with high temporal and spatial resolution has been evaluated by comparison with independent measurements derived from a balloon-borne sonic anemometer. This method utilizes the variance of the mean Doppler velocity from a number of sequential samples and requires an estimate of the horizontal wind speed. The noise contribution to the variance can be estimated from the observed signal-to-noise ratio and removed where appropriate. The relative size of the noise variance to the observed variance provides a measure of the confidence in the retrieval. Comparison with in situ dissipation rates derived from the balloon-borne sonic anemometer reveal that this particular Doppler lidar is capable of retrieving dissipation rates over a range of at least three orders of magnitude. This method is most suitable for retrieval of dissipation rates within the convective well-mixed boundary layer where the scales of motion that the Doppler lidar probes remain well within the inertial subrange. Caution must be applied when estimating dissipation rates in more quiescent conditions. For the particular Doppler lidar described here, the selection of suitably short integration times will permit this method to be applicable in such situations but at the expense of accuracy in the Doppler velocity estimates. The two case studies presented here suggest that, with profiles every 4 s, reliable estimates of ϵ can be derived to within at least an order of magnitude throughout almost all of the lowest 2 km and, in the convective boundary layer, to within 50%. Increasing the integration time for individual profiles to 30 s can improve the accuracy substantially but potentially confines retrievals to within the convective boundary layer. Therefore, optimization of certain instrument parameters may be required for specific implementations.

Room reflections and constancy in speech-like sounds: within-band effects

The experiment asks whether constancy in hearing precedes or follows grouping. Listeners heard speech-like sounds comprising 8 auditory-filter shaped noise-bands that had temporal envelopes corresponding to those arising in these filters when a speech message is played. The „context‟ words in the message were “next you‟ll get _to click on”, into which a “sir” or “stir” test word was inserted. These test words were from an 11-step continuum that was formed by amplitude modulation. Listeners identified the test words appropriately and quite consistently, even though they had the „robotic‟ quality typical of this type of 8-band speech. The speech-like effects of these sounds appears to be a consequence of auditory grouping. Constancy was assessed by comparing the influence of room reflections on the test word across conditions where the context had either the same level of reflections, or where it had a much lower level. Constancy effects were obtained with these 8-band sounds, but only in „matched‟ conditions, where the room reflections were in the same bands in both the context and the test word. This was not the case in a comparison „mismatched‟ condition, and here, no constancy effects were found. It would appear that this type of constancy in hearing precedes the across-channel grouping whose effects are so apparent in these sounds. This result is discussed in terms of the ubiquity of grouping across different levels of representation.

Perceptual constancy, reverberation, and grouping: within-band effects

Perceptual constancy effects are observed when differing amounts of reverberation are applied to a context sentence and a test‐word embedded in it. Adding reverberation to members of a “sir”‐“stir” test‐word continuum causes temporal‐envelope distortion, which has the effect of eliciting more sir responses from listeners. If the same amount of reverberation is also applied to the context sentence, the number of sir responses decreases again, indicating an “extrinsic” compensation for the effects of reverberation. Such a mechanism would effect perceptual constancy of phonetic perception when temporal envelopes vary in reverberation. This experiment asks whether such effects precede or follow grouping. Eight auditory‐filter shaped noise‐bands were modulated with the temporal envelopes that arise when speech is played through these filters. The resulting “gestalt” percept is the appropriate speech rather than the sound of noise‐bands, presumably due to across‐channel “grouping.” These sounds were played to listeners in “matched” conditions, where reverberation was present in the same bands in both context and test‐word, and in “mismatched” conditions, where the bands in which reverberation was added differed between context and test‐word. Constancy effects were obtained in matched conditions, but not in mismatched conditions, indicating that this type of constancy in hearing precedes across‐channel grouping.

The role of spectral- and temporal-envelope room-acoustic cues in auditory selective attention

Listeners can attend to one of several simultaneous messages by tracking one speaker’s voice characteristics. Using differences in the location of sounds in a room, we ask how well cues arising from spatial position compete with these characteristics. Listeners decided which of two simultaneous target words belonged in an attended “context” phrase when it was played simultaneously with a different “distracter” context. Talker difference was in competition with position difference, so the response indicates which cue‐type the listener was tracking. Spatial position was found to override talker difference in dichotic conditions when the talkers are similar (male). The salience of cues associated with differences in sounds, bearings decreased with distance between listener and sources. These cues are more effective binaurally. However, there appear to be other cues that increase in salience with distance between sounds. This increase is more prominent in diotic conditions, indicating that these cues are largely monaural. Distances between spectra calculated using a gammatone filterbank (with ERB‐spaced CFs) of the room’s impulse responses at different locations were computed, and comparison with listeners’ responses suggested some slight monaural loudness cues, but also monaural “timbre” cues arising from the temporal‐ and spectral‐envelope differences in the speech from different locations.