An improved Tn7-lux reporter for broad host range, chromosomally-integrated promoter fusions in Gram-negative bacteria.

An improved vector for chromosomally-integrated promoter-lux fusions is described. The modified vector was tested in parallel with the unmodified vector using the well-characterized Escherichia coli araBAD promoter in the Pseudomonas aeruginosa attTn7 site. The modified mini-Tn7 showed reduced background luminescence, and increased luminescence upon induction, giving >16-fold higher induction ratio.

Role for ferredoxin:NAD(P)H oxidoreductase (FprA) in sulfate assimilation and siderophore biosynthesis in Pseudomonads.

Pyridine-2,6-bis(thiocarboxylate) (PDTC), produced by certain pseudomonads, is a sulfur-containing siderophore that binds iron, as well as a wide range of transition metals, and it affects the net hydrolysis of the environmental contaminant carbon tetrachloride. The pathway of PDTC biosynthesis has not been defined. Here, we performed a transposon screen of Pseudomonas putida DSM 3601 to identify genes necessary for PDTC production (Pdt phenotype). Transposon insertions within genes for sulfate assimilation (cysD, cysNC, and cysG [cobA2]) dominated the collection of Pdt mutations. In addition, two insertions were within the gene for the LysR-type transcriptional activator FinR (PP1637). Phenotypic characterization indicated that finR mutants were cysteine bradytrophs. The Pdt phenotype of finR mutants could be complemented by the known target of FinR regulation, fprA (encoding ferredoxin:NADP(+) oxidoreductase), or by Escherichia coli cysJI (encoding sulfite reductase). These data indicate that fprA is necessary for effective sulfate assimilation by P. putida and that the effect of finR mutation on PDTC production was due to deficient expression of fprA and sulfite reduction. fprA expression in both P. putida and P. aeruginosa was found to be regulated by FinR, but in a manner dependent upon reduced sulfur sources, implicating FinR in sulfur regulatory physiology. The genes and phenotypes identified in this study indicated a strong dependence upon intracellular reduced sulfur/cysteine for PDTC biosynthesis and that pseudomonads utilize sulfite reduction enzymology distinct from that of E. coli and possibly similar to that of chloroplasts and other proteobacteria.

The role of the siderophore pyridine-2,6-bis (thiocarboxylic acid) (PDTC) in zinc utilization by Pseudomonas putida DSM 3601.

Previous work had suggested that in addition to serving the function of a siderophore, pyridine-2,6-bis(thiocarboxylic acid) (PDTC) may also provide producing organisms with the ability to assimilate other divalent transition metals. This was tested further by examining regulation of siderophore production, expression of pdt genes, and growth in response to added zinc. In media containing 10-50 microM ZnCl2, the production of PDTC was found to be differentially repressed, as compared with the production of pyoverdine. The expression of PdtK, the outer membrane receptor involved in PDTC transport, was also reduced in response to added zinc whereas other iron-regulated outer membrane proteins were not. Expression of a chromosomal pdtI: xylE fusion was repressed to a similar extent in response to zinc or iron. Mutants that cannot produce PDTC did not show a growth enhancement with micromolar concentrations of zinc as seen in the wild type strain. The phenotype of the mutant strains was suppressed by the addition of PDTC. The outer membrane receptor and inner membrane permease components of PDTC utilization were necessary for relief of chelator (1,10-phenanthroline)-induced growth inhibition by Zn:PDTC. Iron uptake from 55Fe:PDTC was not affected by a 32-fold molar excess of Zn:PDTC. The data indicate that zinc present as Zn:PDTC can be utilized by strains possessing PDTC utilization functions but that transport is much less efficient than for Fe:PDTC.

Identification and characterization of Pseudomonas membrane transporters necessary for utilization of the siderophore pyridine-2,6-bis(thiocarboxylic acid) (PDTC).

The compound pyridine-2,6-bis(thiocarboxylic acid) (PDTC) is known to be produced and excreted by three strains of Pseudomonas. Its reactivity includes the complete dechlorination of the environmental contaminant carbon tetrachloride. PDTC functions as a siderophore; however, roles as a ferric reductant and antimicrobial agent have also been proposed. PDTC function and regulation were further explored by characterizing the phenotypes of mutants in predicted membrane transporter genes. The functions of a predicted outer-membrane transporter (PdtK) and a predicted inner-membrane permease (PdtE) were examined in Pseudomonas putida DSM 3601. Uptake of iron from (55)Fe(III):PDTC, and bioutilization of PDTC in a chelated medium, were dependent upon PdtK and PdtE. Another strain of P. putida (KT2440), which lacks pdt orthologues, showed growth inhibition by PDTC that could be relieved by introducing a plasmid containing pdtKCPE. Transcriptional activation in response to exogenously added PDTC (25 muM) was unaltered by the pdtK or pdtE mutations; each mutant showed activation of a pdt transcriptional reporter, indistinguishable from an isogenic PDTC utilization-proficient strain. The data demonstrate that PdtK and PdtE constitute a bipartite outer-membrane/inner-membrane transport system for iron acquisition from Fe(III):PDTC. Disruptions in this portion of the P. putida DSM 3601 pdt gene cluster do not abolish PDTC-dependent transcriptional signalling.

Transcriptional regulation of the pdt gene cluster of Pseudomonas stutzeri KC involves an AraC/XylS family transcriptional activator (PdtC) and the cognate siderophore pyridine-2,6-bis(thiocarboxylic acid).

In order to gain an understanding of the molecular mechanisms dictating production of the siderophore and dechlorination agent pyridine-2,6-bis(thiocarboxylic acid) (PDTC), we have begun characterization of a gene found in the pdt gene cluster of Pseudomonas stutzeri KC predicted to have a regulatory role. That gene product is an AraC family transcriptional activator, PdtC. Quantitative reverse transcription-PCR and expression of transcriptional reporter fusions were used to assess a role for pdtC in the transcription of pdt genes. PdtC and an upstream, promoter-proximal DNA segment were required for wild-type levels of expression from the promoter of a predicted biosynthesis operon (P(pdtF)). At least two other transcriptional units within the pdt cluster were also dependent upon pdtC for expression at wild-type levels. The use of a heterologous, Pseudomonas putida host demonstrated that pdtC and an exogenously added siderophore were necessary and sufficient for expression from the pdtF promoter, i.e., none of the PDTC utilization genes within the pdt cluster were required for transcriptional signaling. Tests using the promoter of the pdtC gene in transcriptional reporter fusions indicated siderophore-dependent negative autoregulation similar to that seen with other AraC-type regulators of siderophore biosynthesis and utilization genes. The data increase the repertoire of siderophore systems known to be regulated by this type of transcriptional activator and have implications for PDTC signaling.

Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP).

Wetlands are major sources of carbon dioxide, methane, and other greenhouse gases released during microbial degradation. Despite the fact that decomposition is mainly driven by bacteria and fungi, little is known about the taxonomic diversity of bacterial communities in wetlands, particularly Sphagnum bogs. To explore bacterial community composition, 24 bogs in Vermont and Massachusetts were censused for bacterial diversity at the surface (oxic) and 1 m (anoxic) regions. Bacterial diversity was characterized by a terminal restriction fragment length (T-RFLP) fingerprinting technique and a cloning strategy that targeted the 16S rRNA gene. T-RFLP analysis revealed a high level of diversity, and a canonical correspondence analysis demonstrated marked similarity among bogs, but consistent differences between surface and subsurface assemblages. 16S rDNA sequences derived from one of the sites showed high numbers of clones belonging to the Deltaproteobacteria group. Several other phyla were represented, as well as two Candidate Division-level taxonomic groups. These data suggest that bog microbial communities are complex, possibly stratified, and similar among multiple sites.

Bioremediation of soils contaminated with explosives.

The large-scale industrial production and processing of munitions such as 2,4,6-trinitrotoluene (TNT) over the past 100 years led to the disposal of wastes containing explosives and nitrated organic by-products into the environment. In the US, the Army alone has estimated that over 1.2 million tons of soil have been contaminated with explosives, and the impact of explosives contamination in other countries is of similar magnitude. In recent years, growing concern about the health and ecological threats posed by man-made chemicals have led to studies of the toxicology of explosives, which have identified toxic and mutagenic effects of the common military explosives and their transformation products (Bruns-Nagel et al., 1999a; Fuchs et al., 2001; Homma-Takeda et al., 2002; Honeycutt et al., 1996; Rosenblatt et al., 1991; Spanggord et al., 1982; Tan et al., 1992 and Won et al., 1976). Because the cleanup of areas contaminated by explosives is now mandated because of public health concerns, considerable effort has been invested in finding economical remediation technologies. Biological treatment processes are often considered, since these are usually the least expensive means of destroying organic pollution. This review examines the most important groups of chemicals that must be treated at sites contaminated by explosives processing, the chemical and biological transformations they undergo, and commercial processes developed to exploit these transformations for treatment of contaminated soil. We critically examine about 150 papers on the topic, including approximately 60 published within the past 5 years.

Physiological and molecular genetic evaluation of the dechlorination agent, pyridine-2,6-bis(monothiocarboxylic acid) (PDTC) as a secondary siderophore of Pseudomonas.

The bacterial metabolite and transition metal chelator pyridine-2,6-dithiocarboxylic acid (PDTC), promotes a novel and effective means of dechlorination of the toxic and carcinogenic pollutant, carbon tetrachloride. Pyridine-2,6-dithiocarboxylic acid has been presumed to act as a siderophore in the Pseudomonas strains known to produce it. To explore further the physiological function of PDTC production, we have examined its regulation, the phenotype of PDTC-negative (pdt) mutants, and envelope proteins associated with PDTC in P. putida strain DSM 3601. Aspects of the regulation of PDTC production and outer membrane protein composition were consistent with siderophore function. Pyridine-2,6-dithiocarboxylic acid production was coordinated with production of the well-characterized siderophore pyoverdine; exogenously added pyoverdine led to decreased PDTC production, and added PDTC led to decreased pyoverdine production. Positive regulation of a chromosomal pdtI-xylE transcriptional fusion, and of a 66 kDa outer membrane protein (IROMP), was seen in response to exogenous PDTC. Tests with transition metal chelators indicated that PDTC could provide a benefit under conditions of metal limitation; the loss of PDTC biosynthetic capacity caused by a pdtI transposon insertion resulted in increased sensitivity to 1,10-phenanthroline, a chelator that has high affinity for a range of divalent transition metals (e.g. Fe(2+), Cu(2+), Zn(2+)). Exogenously added PDTC could also suppress a phenotype of pyoverdine-negative (Pvd-) mutants, that of sensitivity to EDDHA, a chelator with higher affinity and specificity for Fe(3+). Measurement of 59Fe incorporation showed uptake from 59Fe:PDTC by DSM 3601 grown in low-iron medium, but not by cells grown in high iron medium, or by the pdtI mutant, which did not show expression of the 66 kDa envelope protein. These data verified a siderophore function for PDTC, and have implicated it in the uptake of transition metals in addition to iron.

Metal chelating properties of pyridine-2,6-bis(thiocarboxylic acid) produced by Pseudomonas spp. and the biological activities of the formed complexes.

We evaluated the ability of pyridine-2,6-bis(thiocarboxylic acid) (pdtc) to form complexes with 19 metals and 3 metalloids. Pdtc formed complexes with 14 of the metals. Two of these metal:pdtc complexes, Co:(pdtc)2 and Cu:pdtc, showed the ability to cycle between redox states, bringing to 4 the number of known redox-active pdtc complexes. A precipitant formed when pdtc was added to solutions of As, Cd, Hg, Mn, Pb, and Se. Additionally, 14 of 16 microbial strains tested were protected from Hg toxicity when pdtc was present. Pdtc also mediated protection from the toxic effects of Cd and Te, but for fewer strains. Pdtc by itself does not facilitate iron uptake, but increases the overall level of iron uptake of Pseudomonas stutzeri strain KC and P. putida DSM301. Both these pseudomonads could reduce amorphous Fe(III) oxyhydroxide in culture. In vitro reactions showed that copper and pdtc were required for this activity. This reaction may derive its reducing power from the hydrolysis of the thiocarboxyl groups of pdtc.