Insights into environmental bioremediation by microorganisms through functional genomics and proteomics

Zhao, Bing; Poh, Chit Laa

doi:10.1002/pmic.200701005

Cited by 75 publications

(29 citation statements)

References 67 publications

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“…Biological treatment (bioremediation) involves the conversion of toxic chemicals into benign or less toxic chemicals by biological means and typically by employing a single microorganism or a consortium of microorganisms (Pandey et al 2009;Bustard et al 2002Bustard et al , 2000Gupta et al 2006;Zhao and Poh 2008). The effectiveness of these microorganisms in degrading toxic chemicals depends on their natural, selected or engineered tolerance to the chemicals present during the remediation process.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of diesel fuel degradation in contaminated soil using organic wastes

Dadrasnia

Agamuthu

2013

Int. J. Environ. Sci. Technol.

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Bioremediation is an effective measure in dealing with such contamination, particularly those from petroleum hydrocarbon sources. The effect of soil amendments on diesel fuel degradation in soil was studied. Diesel fuel was introduced into the soil at the concentration of 5 % (w/w) and mixed with three different organic wastes tea leaf, soy cake, and potato skin, for a period of 3 months. Within 84 days, 35 % oil loss was recorded in the unamended polluted soil while 88, 81 and 75 % oil loss were recorded in the soil amended with soy cake, potato skin and tea leaf, respectively. Diesel fuel utilizing bacteria counts were significantly high in all organic wastes amended treatments, ranging from 111 9 106 to 152 9 106 colony forming unit/gram of soil, as compared to the unamended control soil which gave 31 9 106 CFU/g. The diesel fuel utilizing bacteria isolated from the oil-contaminated soil belongs to Bacillus licheniformis, Ochrobactrum tritici and Staphylococcus sp. Oil-polluted soil amended with soy cake recorded the highest oil biodegradation with a net loss of 53 %, as compared to the other treatments. Dehydrogenase enzyme activity, which was assessed by 2,3,5-triphenyltetrazolium chloride technique, correlated significantly with the total petroleum hydrocarbons degradation and accumulation of CO 2 . First-order kinetic model revealed that soy cake was the best of the three organic wastes used, with biodegradation rate constant of 0.148 day -1 and half life of 4.68 days. The results showed there is potential for soy cake, potato skin and tea leaf to enhance biodegradation of diesel in oil-contaminated soil.

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Section: Introductionmentioning

confidence: 99%

Dynamics of diesel fuel degradation in contaminated soil using organic wastes

Dadrasnia

Agamuthu

2013

Int. J. Environ. Sci. Technol.

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“…In order to obtain more accurate proteome measurements, quantitative proteomic methods, such as stable isotope labelling-based isotope-coded affinity tags (ICAT), isobaric tag for relative and absolute quantification (iTRAQ) (Yan et al, 2008) or label-free comparative quantitative proteomics, need to be employed (Haqqani et al, 2008). Proteomics has been extensively used to explore microbial metabolism, differentiation and relationship with environments (for recent reviews see Cash, 2000;Fraser & Rappuoli, 2005;Norbeck et al, 2006;Graham et al, 2007;Zhao & Poh, 2008;Lacerda & Reardon, 2009). …”

Section: Proteomicsmentioning

confidence: 99%

Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies

Zhang

Li²,

Nie³

2010

Microbiology

416

241

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Recent advances in various ‘omics’ technologies enable quantitative monitoring of the abundance of various biological molecules in a high-throughput manner, and thus allow determination of their variation between different biological states on a genomic scale. Several popular ‘omics’ platforms that have been used in microbial systems biology include transcriptomics, which measures mRNA transcript levels; proteomics, which quantifies protein abundance; metabolomics, which determines abundance of small cellular metabolites; interactomics, which resolves the whole set of molecular interactions in cells; and fluxomics, which establishes dynamic changes of molecules within a cell over time. However, no single ‘omics’ analysis can fully unravel the complexities of fundamental microbial biology. Therefore, integration of multiple layers of information, the multi-‘omics’ approach, is required to acquire a precise picture of living micro-organisms. In spite of this being a challenging task, some attempts have been made recently to integrate heterogeneous ‘omics’ datasets in various microbial systems and the results have demonstrated that the multi-‘omics’ approach is a powerful tool for understanding the functional principles and dynamics of total cellular systems. This article reviews some basic concepts of various experimental ‘omics’ approaches, recent application of the integrated ‘omics’ for exploring metabolic and regulatory mechanisms in microbes, and advances in computational and statistical methodologies associated with integrated ‘omics’ analyses. Online databases and bioinformatic infrastructure available for integrated ‘omics’ analyses are also briefly discussed.

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“…Applications of proteomics in environmental toxicology today range from microorganisms (bacteria, fungi) and plants, to invertebrates (clams, mussels, worms, insects) and vertebrates (freshwater and marine fish; Dowling & Sheehan, 2006;Zhao & Poh, 2008). However, the majority of the reports in this field still use traditional techniques (Santos, Benndorf, & Sá-Correia, 2004), thereby neglecting the progress made in mass spectrometry-based proteomics in recent years.…”

Section: Introductionmentioning

confidence: 98%

Analysis of environmental stress response on the proteome level

Nesatyy

Suter

2008

Mass Spectrometry Reviews

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Thousands of man-made chemicals are annually released into the environment by agriculture, transport, industries, and other human activities. In general, chemical analysis of environmental samples used to assess the pollution status of a specific ecosystem is complicated by the complexity of the mixture, and in some cases by the very low toxicity thresholds of chemicals present. In that sense, a proteomics approach, capable of detecting subtle changes in the level and structure of individual proteins within the whole proteome in response to the altered surroundings, has obvious applications in the field of ecotoxicology. In addition to identifying new protein biomarkers, it can also help to provide an insight into underlying mechanisms of toxicity. Despite being a comparatively new field with a number of caveats, proteomics applications have spread from microorganisms and plants to invertebrates and vertebrates, gradually becoming an established technology used in environmental research. This review article highlights recent advances in the field of environmental proteomics, mainly focusing on experimental approaches with a potential to understand toxic modes of action and to identify novel ecotoxicological biomarkers.

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Insights into environmental bioremediation by microorganisms through functional genomics and proteomics

Cited by 75 publications

References 67 publications

Dynamics of diesel fuel degradation in contaminated soil using organic wastes

Dynamics of diesel fuel degradation in contaminated soil using organic wastes

Integrating multiple ‘omics’ analysis for microbial biology: application and methodologies

Analysis of environmental stress response on the proteome level

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