Monitoring of Biodegradative Pseudomonas putida Strains in Aquatic Environments Using Molecular Techniques

Wand, Helmut; Laht, Tiiu-Maie; Peters, Maire; Becker, P.M.; Stottmeister, U.; Heinaru, Ain

doi:10.1007/s002489900014

Cited by 14 publications

(20 citation statements)

References 24 publications

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“…However, no correlation was recorded for the pseudomonads (a major constituent of the ␥-Proteobacteria). This observation was unexpected, since pseudomonads are well characterized in their ability to degrade environmental phenol contamination, and the genetics of phenol degradation has been described by a variety of strains (1,5,7,8,18,23,34,39). However, the lack of correlation we observed in situ between phenolics and pseudomonad physiological status may not be unexpected, since culture isolation conditions for bioremediation organisms are highly selective (11,42) and the catabolic genes involved are often associated with the horizontal gene pool (17,20,46).…”

Section: Discussioncontrasting

confidence: 50%

Bacterial Community Structure and Physiological State within an Industrial Phenol Bioremediation System

Whiteley

Bailey

2000

Appl Environ Microbiol

175

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The structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. Rapid community fingerprinting by PCRbased denaturing gradient gel electrophoresis (DGGE) of 16S rDNA indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclusively within the Vitox biological reactor. Whole-cell targeting by fluorescent in situ hybridization with specific oligonucleotides (directed to the ␣, ␤ and ␥ subclasses of the class Proteobacteria [␣-, ␤-, and ␥-Proteobacteria, respectively], the Cytophaga-Flavobacterium group, and the Pseudomonas group) tended to mirror gross changes in bacterial community composition when compared with DGGE community fingerprinting. At the whole-cell level, the treatment compartments were numerically dominated by cells assigned to the Cytophaga-Flavobacterium group and to the ␥-Proteobacteria. The ␣ subclass Proteobacteria were of low relative abundance throughout the treatment system whilst the ␤ subclass of the Proteobacteria exhibited local dominance in several of the processing compartments. Quantitative image analyses of cellular fluorescence was used as an indicator of physiological state within the populations probed with rDNA. For cells hybridized with EUB338, the mean fluorescence per cell decreased with increasing phenolic concentration, indicating the strong influence of the primary pollutant upon cellular rRNA content. The ␥ subclass of the Proteobacteria had a ribosome content which correlated positively with total phenolics and thiocyanate. While members of the Cytophaga-Flavobacterium group were numerically dominant in the processing system, their abundance and ribosome content data for individual populations did not correlate with any of the measured chemical parameters. The potential importance of the ␥-Proteobacteria and the Cytophaga-Flavobacteria during this bioremediation process was highlighted.

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Section: Discussioncontrasting

confidence: 50%

Bacterial Community Structure and Physiological State within an Industrial Phenol Bioremediation System

Whiteley

Bailey

2000

Appl Environ Microbiol

175

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“…Bacillus and Aeromonas genera have previously been found to be dominant in the sediment of Lake Balaton by cultivation and chemotaxonomy studies (Langó, 1987;Tóth, 1996;Langó et al, 2002;Reskóné et al, 2006). Widespread metabolic potential contribute to the ubiquity of Bacillus, Aeromonas, and Pseudomas sp., in nature and little preference among the applied substrates make them well adapted to laboratory conditions (Rhodes & Kator, 1994;Nealson, 1997;Wand et al, 1997). Rheinheimera chrinomii was first cultivated from eggs of Chironomidae larvae (Halpern et al, 2007), which are dominating the macrobenthos in the sediment of Lake Balaton (Dévai, 1990;Specziár, 2008).…”

Section: Discussionmentioning

confidence: 99%

Seasonal and spatial variability of sediment bacterial communities inhabiting the large shallow Lake Balaton

et al. 2010

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Seasonal studies of surface sediment bacterial communities, from two basins with differing trophic states within Lake Balaton (Hungary), were carried out using molecular (denaturing gradient gel electrophoresis, DGGE) and cultivation-based techniques. The presence of polyphosphate accumulates was tested using Neisser staining, and phosphatase activity was investigated on organic phosphorus (P) compound. Aerobic viable cell counts were significantly higher in the eutrophic than mesotrophic basin in each season. The lowest viable counts were observed in the autumn and the highest in spring and summer month in both basins. The DGGE fingerprints of the samples reflected that the composition of sediment bacterial communities in the two basins were distinct in spring and summer, and similar in autumn, but similarly diverse in all seasons. On the basis of partial 16S rDNA sequences, the 216 strains were affiliated with six major bacterial lineages: Firmicutes; Actinobacteria, Bacteroidetes, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Common species characterized from both basins constituted up to 66% of all identified phylotypes. Strains related to Bacillus sp. were dominant in all but one sample. Isolates affiliated with Aeromonas sp. prevailed in the sample taken from the mesotrophic basin in spring. The majority of the strains showed excess poly-P accumulation. Association of Neisser staining and phosphatase activity test results suggested that excess poly-P accumulation serves as P storage for sediment bacteria. Our study implied the importance of Firmicutes, Actinobacteria, Alphaproteobacteria, and Aeromonas species in benthic bacterial P retention.

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“…A set of C23DO primers has been described for quantifying organisms harboring this gene in toluene-contaminated soils, but they can detect only isolates mt-2, JI104, and IC (16). A different set of primers used to monitor phenol-degrading P. putida strains in an industrial wastewater process would be able to detect only isolates mt-2 and JI104 (39). C23DO primers identical to mt-2 genes alone have been used as a molecular marker for the identification of a fish pathogen in lakewater using PCR (30).…”

Section: Resultsmentioning

confidence: 99%

Development of Catechol 2,3-Dioxygenase-Specific Primers for Monitoring Bioremediation by Competitive Quantitative PCR

Mesarch

Nakatsu

Nies

2000

Appl Environ Microbiol

142

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Benzene, toluene, xylenes, phenol, naphthalene, and biphenyl are among a group of compounds that have at least one reported pathway for biodegradation involving catechol 2,3-dioxygenase enzymes. Thus, detection of the corresponding catechol 2,3-dioxygenase genes can serve as a basis for identifying and quantifying bacteria that have these catabolic abilities. Primers that can successfully amplify a 238-bp catechol 2,3-dioxygenase gene fragment from eight different bacteria are described. The identities of the amplicons were confirmed by hybridization with a 238-bp catechol 2,3-dioxygenase probe. The detection limit was 10 2 to 10 3 gene copies, which was lowered to 10 0 to 10 1 gene copies by hybridization. Using the dioxygenase-specific primers, an increase in catechol 2,3-dioxygenase genes was detected in petroleum-amended soils. The dioxygenase genes were enumerated by competitive quantitative PCR with a 163-bp competitor that was amplified using the same primers. Target and competitor sequences had identical amplification kinetics. Potential PCR inhibitors that could coextract with DNA, nonamplifying DNA, soil factors (humics), and soil pollutants (toluene) did not impact enumeration. Therefore, this technique can be used to accurately and reproducibly quantify catechol 2,3-dioxygenase genes in complex environments such as petroleum-contaminated soil. Direct, non-cultivationbased molecular techniques for detecting and enumerating microbial pollutant-biodegrading genes in environmental samples are powerful tools for monitoring bioremediation and developing field evidence in support of natural attenuation.

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Monitoring of Biodegradative Pseudomonas putida Strains in Aquatic Environments Using Molecular Techniques

Cited by 14 publications

References 24 publications

Bacterial Community Structure and Physiological State within an Industrial Phenol Bioremediation System

Bacterial Community Structure and Physiological State within an Industrial Phenol Bioremediation System

Seasonal and spatial variability of sediment bacterial communities inhabiting the large shallow Lake Balaton

Development of Catechol 2,3-Dioxygenase-Specific Primers for Monitoring Bioremediation by Competitive Quantitative PCR

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