The use of molecular techniques to characterize the microbial communities in contaminated soil and water
TL;DR: This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water and methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies.
About: This article is published in Environment International.The article was published on 2008-02-01. It has received 204 citations till now. The article focuses on the topics: Microbial population biology & Bioremediation.
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TL;DR: This review selectively examines and provides a critical view on the knowledge gaps and limitations in field application strategies, approaches such as composting, electrobioremediation and microbe-assisted phytoremediating, and the use of probes and assays for monitoring and testing the efficacy of bioremediations of polluted sites.
795 citations
Cites background or methods from "The use of molecular techniques to ..."
..., 1995) and molecular ecological techniques for community profiling (Malik et al., 2008), soil metagenomics using isotope distribution analysis (Villas-Boas and Bruheim, 2007), and functional genomics and proteomics (Zhao and Poh, 2008) can help in identifying the partners and the patterns of responses to external stimuli within the network and the ‘system complexities’ of contaminated sites....
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...The application of molecular site assessment (Fleming et al., 1998; Sayler et al., 1995) and molecular ecological techniques for community profiling (Malik et al., 2008), soil metagenomics using isotope distribution analysis (Villas-Boas and Bruheim, 2007), and functional genomics and proteomics…...
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TL;DR: The changes of different microbiological indices and the mechanism of microbial response to heavy metal stress in soils are comprehensively summarized and future directions of the microbial ecotoxicological diagnosis of soil contamination by heavy metals are proposed and discussed.
222 citations
06 Jul 2011
TL;DR: Microbial methods for monitoring bioremediation of hydrocarbons include chemical, biochemical and microbiological molecular indices that measure rates of microbial activities to show that in the end the target goal of pollutant reduction to a safe and permissible level has been achieved.
Abstract: Bioremediation of hydrocarbon pollutants is advantageous owing to the cost-effectiveness of the technology and the ubiquity of hydrocarbon-degrading microorganisms in the soil. Soil microbial diversity is affected by hydrocarbon perturbation, thus selective enrichment of hydrocarbon utilizers occurs. Hydrocarbons interact with the soil matrix and soil microorganisms determining the fate of the contaminants relative to their chemical nature and microbial degradative capabilities, respectively. Provided the polluted soil has requisite values for environmental factors that influence microbial activities and there are no inhibitors of microbial metabolism, there is a good chance that there will be a viable and active population of hydrocarbon-utilizing microorganisms in the soil. Microbial methods for monitoring bioremediation of hydrocarbons include chemical, biochemical and microbiological molecular indices that measure rates of microbial activities to show that in the end the target goal of pollutant reduction to a safe and permissible level has been achieved. Enumeration and characterization of hydrocarbon degraders, use of micro titer plate-based most probable number technique, community level physiological profiling, phospholipid fatty acid analysis, 16S rRNA- and other nucleic acid-based molecular fingerprinting techniques, metagenomics, microarray analysis, respirometry and gas chromatography are some of the methods employed in bio-monitoring of hydrocarbon remediation as presented in this review.
162 citations
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...diversity pattern. In addition, biases may be introduced during PCR-amplification and cloning steps ( Malik et al. 2008 )....
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...Because of this immense genotypic and phenotypic diversity, microbial communities in the soil remain some of the most difficult to characterize (Atlas and Bartha 1998; Maila 2005; Smalla et al. 2007; Malik et al. 2008 )....
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...Because of this immense genotypic and phenotypic diversity, microbial communities in the soil remain some of the most difficult to characterize (Atlas and Bartha 1998; Maila 2005; Smalla et al. 2007; Malik et al. 2008)....
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...In addition, biases may be introduced during PCR-amplification and cloning steps (Malik et al. 2008)....
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...There are also emerging techniques of molecular microbial ecology that do not rely on cultivation because of the viable, but nonculturable, phenomenon, which has been found to be very useful for monitoring the progress of bioremediation (Siciliano et al. 2003; Kloos et al. 2006; Brons and van Elsas 2008; Malik et al. 2008; Zengler 2008)....
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TL;DR: It is proposed that in‐soil environmental risk assessments are made at in‐ and off‐field scale considering field boundary levels, and a new testing strategy which takes into account the relevant exposure routes for in‐ soil organisms and the potential direct and indirect effects is proposed.
Abstract: Following a request from EFSA, the Panel on Plant Protection Products and their Residues developed an opinion on the science behind the risk assessment of plant protection products for in-soil organisms. The current risk assessment scheme is reviewed, taking into account new regulatory frameworks and scientific developments. Proposals are made for specific protection goals for in-soil organisms being key drivers for relevant ecosystem services in agricultural landscapes such as nutrient cycling, soil structure, pest control and biodiversity. Considering the time-scales and biological processes related to the dispersal of the majority of in-soil organisms compared to terrestrial non-target arthropods living above soil, the Panel proposes that in-soil environmental risk assessments are made at in- and off-field scale considering field boundary levels. A new testing strategy which takes into account the relevant exposure routes for in-soil organisms and the potential direct and indirect effects is proposed. In order to address species recovery and long-term impacts of PPPs, the use of population models is also proposed.
142 citations
TL;DR: The SlipChip will be useful for applications involving PCR arrays and lays the foundation for new strategies for diagnostics, point-of-care devices, and immobilization-based arrays.
Abstract: The SlipChip platform was tested to perform high-throughput nanoliter multiplex PCR. The advantages of using the SlipChip platform for multiplex PCR include the ability to preload arrays of dry primers, instrument-free sample manipulation, small sample volume, and high-throughput capacity. The SlipChip was designed to preload one primer pair per reaction compartment and to screen up to 384 different primer pairs with less than 30 nanoliters of sample per reaction compartment. Both a 40-well and a 384-well design of the SlipChip were tested for multiplex PCR. In the geometries used here, the sample fluid was spontaneously compartmentalized into discrete volumes even before slipping of the two plates of the SlipChip, but slipping introduced additional capabilities that made devices more robust and versatile. The wells of this SlipChip were designed to overcome potential problems associated with thermal expansion. By using circular wells filled with oil and overlapping them with square wells filled with the ...
130 citations
References
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TL;DR: Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
Abstract: We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.
11,380 citations
TL;DR: A high-capacity system was developed to monitor the expression of many genes in parallel by means of simultaneous, two-color fluorescence hybridization, which enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA.
Abstract: A high-capacity system was developed to monitor the expression of many genes in parallel. Microarrays prepared by high-speed robotic printing of complementary DNAs on glass were used for quantitative expression measurements of the corresponding genes. Because of the small format and high density of the arrays, hybridization volumes of 2 microliters could be used that enabled detection of rare transcripts in probe mixtures derived from 2 micrograms of total cellular messenger RNA. Differential expression measurements of 45 Arabidopsis genes were made by means of simultaneous, two-color fluorescence hybridization.
10,287 citations
TL;DR: Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.
9,017 citations
TL;DR: The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
Abstract: Recent successes illustrate the role of mass spectrometry-based proteomics as an indispensable tool for molecular and cellular biology and for the emerging field of systems biology. These include the study of protein-protein interactions via affinity-based isolations on a small and proteome-wide scale, the mapping of numerous organelles, the concurrent description of the malaria parasite genome and proteome, and the generation of quantitative protein profiles from diverse species. The ability of mass spectrometry to identify and, increasingly, to precisely quantify thousands of proteins from complex samples can be expected to impact broadly on biology and medicine.
6,597 citations
TL;DR: Unlike other quantitative PCR methods, real-time PCR does not require post-PCR sample handling, preventing potential PCR product carry-over contamination and resulting in much faster and higher throughput assays.
Abstract: We have developed a novel "real time" quantitative PCR method. The method measures PCR product accumulation through a dual-labeled fluorogenic probe (i.e., TaqMan Probe). This method provides very accurate and reproducible quantitation of gene copies. Unlike other quantitative PCR methods, real-time PCR does not require post-PCR sample handling, preventing potential PCR product carry-over contamination and resulting in much faster and higher throughput assays. The real-time PCR method has a very large dynamic range of starting target molecule determination (at least five orders of magnitude). Real-time quantitative PCR is extremely accurate and less labor-intensive than current quantitative PCR methods.
6,367 citations
Additional excerpts
...This approach enables the detection and quantification of PCR amplicons during the early exponential phase of the reaction (Higuchi et al., 1993; Heid et al., 1996)....
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