Establishment of New Genetic Traits in a Microbial Biofilm Community

Conjugational transfer of the TOL plasmid (pWWO) was analyzed in a flow chamber biofilm community engaged in benzyl alcohol degradation. The community consisted of three species, Pseudomonas putida RI, Acinetobacter sp. strain C6, and an unidentified isolate, D8. Only P. putida RI could act as a recipient for the TOL plasmid. Cells carrying a chromosomally integrated lacI^q gene and a lacp-gfp-tagged version of the TOL plasmid were introduced as donor strains in the biofilm community after its formation. The occurrence of plasmid-carrying cells was analyzed by viable-count-based enumeration of donors and transconjugants. Upon transfer of the plasmids to the recipient cells, expression of green fluorescence was activated as a result of zygotic induction of the gfp gene. This allowed a direct in situ identification of cells receiving the gfp-tagged version of the TOL plasmid. Our data suggest that the frequency of horizontal plasmid transfer was low, and growth (vertical transfer) of the recipient strain was the major cause of plasmid establishment in the biofilm community. Employment of scanning confocal laser microscopy on fixed biofilms, combined with simultaneous identification of P. putida cells and transconjugants by 16S rRNA hybridization and expression of green fluorescence, showed that transconjugants were always associated with noninfected P. putida RI recipient microcolonies. Pure colonies of transconjugants were never observed, indicating that proliferation of transconjugant cells preferentially took place on preexisting P. putida RI microcolonies in the biofilm.     

In Situ Gene Expression in Mixed-Culture Biofilms: Evidence of Metabolic Interactions between Community Members

Microbial communities growing in laboratory-based flow chambers were investigated in order to study compartmentalization of specific gene expression. Among the community members studied, the focus was in particular on Pseudomonas putida and a strain of an Acinetobacter sp., and the genes studied are involved in the biodegradation of toluene and related aromatic compounds. The upper-pathway promoter (Pu) and the meta-pathway promoter (Pm) from the TOL plasmid were fused independently to the gene coding for the green fluorescent protein (GFP), and expression from these promoters was studied in P. putida, which was a dominant community member. Biofilms were cultured in flow chambers, which in combination with scanning confocal laser microscopy allowed direct monitoring of promoter activity with single-cell spatial resolution. Expression from the Pu promoter was homogeneously induced by benzyl alcohol in both community and pure-culture biofilms, while the Pm promoter was induced in the mixed community but not in a pure-culture biofilm. By sequentially adding community members, induction of Pm was shown to be a consequence of direct metabolic interactions between an Acinetobacter species and P. putida. Furthermore, in fixed biofilm samples organism identity was determined and gene expression was visualized at the same time by combining GFP expression with in situ hybridization with fluorescence-labeled 16S rRNA targeting probes. This combination of techniques is a powerful approach for investigating structure-function relationships in microbial communities.     

Dual Labeling of Pseudomonas putida with Fluorescent Proteins for In Situ Monitoring of Conjugal Transfer of the TOL Plasmid

We describe here a dual-labeling technique involving the green fluorescent protein (GFP) and the red fluorescent protein (DsRed) for in situ monitoring of horizontal gene transfer via conjugation. A GFPmut3b-tagged derivative of narrow-host-range TOL plasmid (pWWO) was delivered to Pseudomonas putida KT2442, which was chromosomally labeled with dsRed by transposon insertion via biparental mating. Green and red fluorescent proteins were coexpressed in donor P. putida cells. Cells expressing both fluorescent proteins were smaller in size than cells expressing GFP alone. Donors and transconjugants in mixed culture or sludge samples were discriminated on the basis of their fluorescence by using confocal laser scanning microscopy. Conjugal plasmid transfer frequencies on agar surfaces and in sludge microcosms were determined microscopically without cultivation. This method worked well for in situ monitoring of horizontal gene transfer in addition to tracking the fate of microorganisms released into complex environments. To the best of our knowledge, this is the first study that discusses the coexpression of GFP and DsRed for conjugal gene transfer studies.     

Bioaugmentation of microbial communities in laboratory and pilot scale sequencing batch biofilm reactors using the TOL plasmid

The aim of this study was to investigate the effectiveness of bioaugmentation and transfer of plasmid pWWO (TOL plasmid) to mixed microbial populations in pilot and laboratory scale sequencing batch biofilm reactors (SBBRs) treating synthetic wastewater containing benzyl alcohol (BA) as a model xenobiotic. The plasmid donor was a Pseudomonas putida strain chromosomally tagged with the gene for the red fluorescent protein carrying a green fluorescent protein labeled TOL plasmid, which confers degradation capacity for several compounds including toluene and BA. In the pilot scale SBBR donor cells were disappeared 84 h after inoculation while transconjugants were not detected at all. In contrast, both donor and transconjugant cells were detected in the laboratory scale reactor where the ratio of transconjugants to donors fluctuated between 1.9 × 10^?1 and 8.9 × 10^?1 during an experimental period of 32 days. BA degradation rate was enhanced after donor inoculation from 0.98 mg BA/min prior to inoculation to 1.9 mg BA/min on the seventeenth day of operation. Survival of a bioaugmented strain, conjugative plasmid transfer and enhanced BA degradation was demonstrated in the laboratory scale SBBR but not in the pilot scale SBBR.     

EVOLUTION OF BROAD AND SPECIFIC COMPETITIVE ABILITY IN NOVEL VERSUS FAMILIAR ENVIRONMENTS IN DROSOPHILA SPECIES

We used nine pairs of competing Drosophila melanogaster and Drosophila simulans populations to test three hypotheses. (1) Weaker competitors undergo greater evolutionary increases in competitive ability, compared with stronger ones. (2) Increased competitive ability against a specific competitor population causes a correlated increase in competitive ability against other competitor populations. (3) In a novel environment, adaptation to the abiotic environment contributes more to competitive ability than adaptation to the competitor population. After 11 generations of competition, initially weaker competitor populations showed relatively greater increases in competitive ability. Broad and specific competitive abilities, the latter being specific to a particular competitor population, were positively correlated in both familiar and novel environments. Adaptation to the abiotic environment seemed to be a more important component of competitive ability in the novel environments. We conclude that in geographically structured species, biotic and abiotic factors affecting the evolution of competitive ability may interact to help create a mosaic of outcomes that can affect the evolutionary dynamics of the interaction over the range of the competing species.     

In situ monitoring of biofilm formations ofEscherichia coli andPseudomonas putida by use of lux and GFP reporters

A plasmid vector containing two reporter genes,mer-lux andlac-GFP, was transformed to bothEscherichia coli andPseudomonas putida. Their cellular activities and biofilm characteristics were investigated in flow-cell units by measuring bioluminescent lights and fluorescent levels of GFP. Bioluminescence was effective to monitor temporal cell activities, whereas fluorescent level of GFP was useful to indicate the overall cell activities during biofilm development. The light production rates ofE. coli andP. putida cultures were dependent upon concentrations of HgCl₂. Mercury molecules entrapped inP. putida biofilms were hardly washed out in comparison with those inE. coli biofilms, indicating thatP. putida biofilms may have higher affinity to mercury molecules thanE. coli biofilms. It was observed thatP. putida expressed GFP cDNA in biofilms but not in liquid cultures. This may indicate that the genetic mechanisms ofP. putida were favorably altered in biofilm conditions to make a foreign gene expression possible.     

Protein as Chemical Cue: Non-Nutritional Growth Enhancement by Exogenous Protein in Pseudomonas putida KT2440

Research pertaining to microbe-microbe and microbe-plant interactions has been largely limited to small molecules like quorum sensing chemicals. However, a few recent reports have indicated the role of complex molecules like proteins and polysaccharides in microbial communication. Here we demonstrate that exogenous proteins present in culture media can considerably accelerate the growth of Pseudomonas putida KT2440, even when such proteins are not internalized by the cells. The growth enhancement is observed when the exogenous protein is not used as a source of carbon or nitrogen. The data show non-specific nature of the protein inducing growth; growth enhancement was observed irrespective of the protein type. It is shown that growth enhancement is mediated via increased siderophore secretion in response to the exogenous protein, leading to better iron uptake. We highlight the ecological significance of the observation and hypothesize that exogenous proteins serve as chemical cues in the case of P.putida and are perceived as indicator of the presence of competitors in the environment. It is argued that enhanced siderophore secretion in response to exogenous protein helps P.putida establish numerical superiority over competitors by way of enhanced iron assimilation and quicker utilization of aromatic substrates.     

Toluene biodegradation by <Emphasis Type="Italic">Pseudomonas putida</Emphasis> F1: targeting culture stability in long-term operation

The stability of Pseudomonas putida F1, a strain harbouring the genes responsible for toluene degradation in the chromosome was evaluated in a bioscrubber under high toluene loadings and nitrogen limiting conditions at two dilution rates (0.11 and 0.27 h⁻¹). Each experiment was run for 30 days, period long enough for microbial instability to occur considering previously reported studies carried out with bacterial strains encoding the catabolic genes in the TOL plasmid. At all tested conditions, P. putida F1 exhibited stable performance as shown by the constant values of the specific toluene degradation yield, CO₂ produced versus toluene degraded yield, and biomass concentration within each steady state. Benzyl alcohol, a curing agent causing TOL plasmid deletion in Pseudomonas strains, was present in the cultivation medium as a result of the monooxygenation of toluene by the diooxygenase system of P. putida F1. However, no mutant population growing at the expense of the extracellular excreted carbon or lysis products was established in the chemostat as confirmed by the constant dissolved total organic carbon (TOC) concentration and fraction of toluene degrading cells (approx. 100%). In addition, batch experiments conducted with both lysis substrate and toluene simultaneously confirmed that P. putida F1 preferentially consumed toluene rather than extracellular excreted carbon.     

Role of the ptsN Gene Product in Catabolite Repression of the Pseudomonas putida TOL Toluene Degradation Pathway in Chemostat Cultures▿

The Pseudomonas putida KT2440 TOL upper pathway is repressed under nonlimiting conditions in cells growing in chemostat with succinate as a carbon source. We show that the ptsN gene product IIA^Ntr participates in this repression. Crc, involved in yeast extract-dependent repression in batch cultures, did not influence expression when cells were growing in a chemostat with succinate at maximum rate.     

Effects of Iron Limitation on the Degradation of Toluene by Pseudomonas Strains Carrying the TOL (pWWO) Plasmid

Most aerobic biodegradation pathways for hydrocarbons involve iron-containing oxygenases. In iron-limited environments, such as the rhizosphere, this may influence the rate of degradation of hydrocarbon pollutants. We investigated the effects of iron limitation on the degradation of toluene by Pseudomonas putida mt2 and the transconjugant rhizosphere bacterium P. putida WCS358(pWWO), both of which contain the pWWO (TOL) plasmid that harbors the genes for toluene degradation. The results of continuous-culture experiments showed that the activity of the upper-pathway toluene monooxygenase decreased but that the activity of benzyl alcohol dehydrogenase was not affected under iron-limited conditions. In contrast, the activities of three meta-pathway (lower-pathway) enzymes were all found to be reduced when iron concentrations were decreased. Additional experiments in which citrate was used as a growth substrate and the pathways were induced with the gratuitous inducer o-xylene showed that expression of the TOL genes increased the iron requirement in both strains. Growth yields were reduced and substrate affinities decreased under iron-limited conditions, suggesting that iron availability can be an important parameter in the oxidative breakdown of hydrocarbons.     

Effects of leaf litter on inter-specific competitive ability of the invasive plant <Emphasis Type="Italic">Wedelia trilobata</Emphasis>

Allelochemicals released by invasive plants contribute to the successful invasion of new habitats. However, the relationship between allelopathic effects and competitive ability of invasive plants has not been characterized. We quantified the neighbor effects of Wedelia trilobata (family: Asteraceae) and the allelopathic effects of its leaf litter on two Asteraceae competitor species (invasive Eupatorium catarium and non-invasive Lactuca sativa) and on its own ramet growth. The seed germination rate and seedling biomass of the two competitor species decreased following treatment with W. trilobata leaf extracts. When co-cultured with W. trilobata, the total biomass of the two competitor species significantly decreased regardless of whether leaf extracts were present. Under low plant density co-culture conditions, W. trilobata leaf extracts enhanced the inhibitory effects on E. catarium. In contrast, W. trilobata leaf extracts promoted the growth of W. trilobata adventitious roots, resulting in increased competitive ability. Therefore, W. trilobata growth was promoted by its own allelochemicals in leaf extracts, whereas the growth of the invasive and non-invasive competitors was inhibited by the same chemicals. These responses facilitated the invasion by W. trilobata. Our study demonstrates that leaf litter of invasive plants may inhibit the growth of neighboring species to enhance the competitive ability of the invasive plants during the early stages of invasion.     

Engineering of Quasi-Natural Pseudomonas putida Strains for Toluene Metabolism through an ortho-Cleavage Degradation Pathway

To construct a bacterial catalyst for bioconversion of toluene and several alkyl and chloro- and nitro-substituted derivatives into the corresponding benzoates, the upper TOL operon of plasmid pWW0 of Pseudomonas putida was fully reassembled as a single gene cassette along with its cognate regulatory gene, xylR. The corresponding DNA segment was then targeted to the chromosome of a P. putida strain by using a genetic technique that allows deletion of all recombinant tags inherited from previous cloning steps and leaves the otherwise natural strain bearing exclusively the DNA segment encoding the phenotype of interest. The resulting strains grew on toluene as the only carbon source through a two-step process: conversion of toluene into benzoate, mediated by the upper TOL enzymes, and further metabolism of benzoate through the housekeeping ortho-ring cleavage pathway of the catechol intermediate.     

Mesopredators constrain a top predator: competitive release of ravens after culling crows

Although predator control programmes rarely consider complex competitive interactions among predators, it is becoming clear that removal of larger ‘superior’ competitors often releases the ‘inferior’ ones and can precipitate trophic cascades. In contrast, our study indicates that culling hooded crows Corvus cornix appears to release a larger competitor, the common raven Corvus corax. Ravens ranged more widely, and the predation of artificial nests was significantly faster (although total predation was similar), after the removal of crows. Our study provides evidence of a novel reversal of competitive release where a larger species was freed from constraints imposed on its distribution and behaviour by a smaller species, and emphasizes the importance of considering community and ecosystem effects of predator manipulations when undertaken for conservation or game management.     

Rats dying for mice: Modelling the competitor release effect

Abstract Introduced vertebrate predators are one of the most important threats to endemic species throughout a range of ecosystems, in particular on islands in biodiversity hot spots. Consequently, the reduction of predator numbers is considered a key conservation action in the management of many native vertebrates vulnerable to predators. It is now established that control attempts may affect non‐target species through trophic interactions, but little is known concerning their consequences on competitive relationships. We study a mathematical model mimicking the effects of controlling introduced species in the presence of their competitors. We used two competing rodents to illustrate our study: black rats, Rattus rattus, and mice, Mus musculus. Analyses of the model show that control of only one introduced species logically results in the dramatic increase of the overlooked competitor. We present empirical data that confirm our theoretical predictions. Less intuitively, this process, which we term ‘the competitor release effect’, may also occur when both introduced competitors are simultaneously controlled. In our setting, controlling both predators can promote their coexistence. This occurs as soon as the inferior competitor benefits from the differential effect of the simultaneous control of both competitors, that is, when the indirect positive effect of control (the removal of their competitors) exceeds its direct negative effect (their own removal). Both control levels and target specificity have a direct influence on the extent of this process: counter‐intuitively, the stronger and more specific the control, the greater the effect. The theoretical validation of the competitor release effect has important implications in conservation, especially for control management.     

<Emphasis Type="BoldItalic">In situ</Emphasis> real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe <Emphasis Type="BoldItalic">Deinococcus radiodurans</Emphasis>

A third generation promoter probe shuttle vector pKG was constructed, using the green fluorescent protein as a reporter, for in situ evaluation of Deinococcal promoter activity in Escherichia coli or Deinococcus radiodurans. The construct yielded zero background fluorescence in both the organisms, in the absence of promoter sequences. Fifteen Deinococcal promoters, either harbouring Radiation and Desiccation Response Motif (RDRM) or not, were cloned in vector pKG. Only the RDRM-promoter constructs displayed (i) gamma radiation inducible GFP expression in D. radiodurans, following gamma irradiation, (ii) DdrO-mediated repression of GFP expression in heterologous E. coli, or (iii) abolition in GFP induction following gamma irradiation, in pprI mutant of D. radiodurans. Utility of pKG vector for real-time in situ assessment of Deinococcal promoter function was, thus, successfully demonstrated.     

Interactions between allelopathic properties and growth kynetics in four freshwater phytoplankton species studied by model simulations

We chose four species of freshwater phytoplankton: the chlorophyceans Ankistrodesmus falcatus, Chlamydomonas reinhardtii and Selenastrum capricornutum, and the cyanobacteria Oscillatoria sp. in order to study their competitive abilities for nitrate and their allelopathic properties. We parameterized models of nitrate uptake and growth with laboratory experiments. According to them, the species were ranked (from the best to the worst competitors): S. capricornutum, C. reinhardtii, A. falcatus and Oscillatoria sp. C. reinhardtii and Oscillatoria sp. were previously reported as allelopathic. In the present work, Oscillatoria sp. was allelopathic only against A. falcatus. However, none of our species was sensitive to C. reinhardtii. Additionally, we found an unknown allelopathic effect of A. falcatus against Oscillatoria sp. Our findings point out the high specificity of allelopathic interactions. With these data, we constructed a model of interspecific competition for nitrate, including allelopathic interactions. By performing model simulations, we studied how three factors influence the outcome of competition: relative abundance of competing species, resistance to allelopathy, and nitrate concentration. Our simulations showed that the initial ratio of species abundances will significantly determine the outcome of competition. If the worst competitor was the allelopathic species, the more it needs to outnumber the competing species, unless it is very sensitive to allelopathy (not defended). Nitrate has an important influence, showing a non-intuitive outcome of competition experiments at low nitrate concentrations, where the worst competitor (allelopathic species) wins competition in the majority of cases, whereas at intermediate concentrations, the better competitor dominates except for unfavorable ratios of abundances. With the increased amounts of nitrate, conditions again favor the worst competitor (the stronger allelopathic species). Despite the potential for two species coexistence showed by previous theoretical analysis of systems was similar to ours, our simulations did not detect this outcome. We hypothesized that this is due to the strong allelopathic effect of Oscillatoria sp.     

Competition-colonization trade-offs in a ciliate model community

There is considerable theoretical evidence that a trade-off between competitive and colonization ability enables species coexistence. However, empirical studies testing for the presence of a competition–colonization (CC) trade-off and its importance for species coexistence have found mixed results. In a microcosm experiment, we looked for a CC trade-off in a community of six benthic ciliate species. For each species, we measured the time needed to actively disperse to and colonize an empty microcosm. By measuring dispersal rates and growth rates of the species, we were able to differentiate between these two important components of colonization ability. Competitive ability was investigated by comparing species’ growth with or without a competitor in all pairwise species combinations. Species significantly differed in their colonization abilities, with good colonizers having either high growth rates or high dispersal rates or both. Although species showed a clear competitive hierarchy, competitive and colonization ability were uncorrelated. The weakest competitors were also the weakest colonizers, and the strongest competitor was an intermediate colonizer. However, some of the inferior competitors had higher colonization abilities than the strongest competitor, indicating that a CC trade-off may enable coexistence for a subset of the species. Absence of a community-wide CC trade-off may be based on the lack of strong relationships between the traits underlying competitive and colonization ability. We show that temporal effects and differential resource use are alternative mechanisms of coexistence for the species that were both slow colonizers and poor competitors.     

Efficiency of natural and engineered bacterial strains in the degradation of 4-chlorobenzoic acid in soil slurry

Two bacterial strains, the natural isolate Arthrobacter sp. FG1 and the engineered strain Pseudomonas putida PaW340/pDH5, were compared for their efficiency in the degradation of 4-chlorobenzoic acid in a slurry phase system. The recombinant strain was obtained by cloning the Arthrobacter sp. FG1 dehalogenase encoding genes in P. putida PaW340. In the slurry inoculated with pre-adapted cultures of Arthrobacter sp. FG1, the 4-chlorobenzoic acid degradation was found to be slower than that observed in the slurry inoculated with the recombinant strain P. putida PaW340/pDH5, regardless of the presence or absence of soil indigenous bacteria. Slurry inoculated with mixed cultures of Arthrobacter sp. FG1 and the 4-hyroxybenzoic acid degrader P. putida PaW340 did not show any improvement in 4-chlorobenzoic acid degradation.     

Species-Specific Oligonucleotides for Enumeration of Pseudomonas putida F1, Burkholderia sp. Strain JS150, and Bacillus subtilis ATCC 7003 in Biodegradation Experiments

Species-specific sequences were identified within the V4 variable region of 16S rRNA of two bacterial species capable of aromatic hydrocarbon metabolism, Pseudomonas putida F1 and Burkholderia sp. strain JS150, and a third, Bacillus subtilis ATCC 7003, that can function as a secondary degrader. Fluorescent in situ hybridization (FISH) with species-specific oligonucleotides was used for direct counting of these species throughout a phenol biodegradation experiment in batch culture. Traditional differential plate counting methods could not be used due to the similar metabolism and interactions of the primary degraders and difficulties in selecting secondary degraders in mixed culture. In contrast, the FISH method provided reliable quantitative results without interference from those factors.