The potential of soil protein-based methods to indicate metal contamination

Singleton, Ian; Merrington, Graham; Colvan, S.; Delahunty, J. S.

doi:10.1016/s0929-1393(03)00004-0

Cited by 61 publications

(59 citation statements)

References 17 publications

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“…However, even in the lane of the phenol phase there was no defined band visible. A likely reason is the lack of dominant organisms and enzymes in the highly complex and heterogeneous control soil (Singleton et al, 2003). Another possibility is that our procedure also extracted large amounts of extracellular protein from soil particles (Nannipieri, 2006) which is presumably also heterogeneous and prevented the detection of bands.…”

Section: Resultsmentioning

confidence: 99%

“…In this approach, minerals were dissolved by hydrofluoric acid and the extracted proteins identified by MS coupled to liquid chromatography. Methods based on freeze-thawing or bead beating of soil for extracting intra-or extracellular proteins were also proposed (Singleton et al, 2003). The greatest difficulty lies in the separation of proteins from humic acids.…”

Section: Introductionmentioning

confidence: 99%

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Functional metaproteome analysis of protein extracts from contaminated soil and groundwater

et al. 2007

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Using proteins from soil or groundwater as functional biomarkers requires efficient extraction. We developed an extraction method in which the separation of proteins from the inorganic and organic constituents of the soil matrix was achieved by a combination of 0.1 m NaOH treatment and phenol extraction. Incubation with NaOH released humic acids and proteins from soil minerals, and simultaneously, disrupted microorganisms. The subsequent phenol extraction separated the proteins from the humic organic matter. Protein extracts were applied to sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and 2D-electrophoresis (2-DE). Spots and bands were excised and individual proteins identified by liquid chromatography online linked to mass spectrometry (MS) via electrospray ionization source (LC-ESI-MS). To assess the suitability of the method for the functional analysis of environmental metaproteomes, it was applied to soil that had been enriched in chlorophenoxy acid-degrading bacteria by incubation with 2,4-dichlorophenoxy acetic acid (2,4-D) for 22 days. The method was also used to analyze groundwater from the aquifer of a chlorobenzene-contaminated site. The identification of enzymes such as chlorocatechol dioxygenases was consistent with bacterial metabolic pathways expected to be expressed in these samples. The protocol enabled thus the analysis of the metaproteome of soil and groundwater samples. It thereby provides a means to study the diversity of environmental microbial communities while addressing functional aspects more directly than metagenome or even metatranscriptome analysis.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Functional metaproteome analysis of protein extracts from contaminated soil and groundwater

et al. 2007

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“…The increase of soil pH by liming is thus usually favourable for the microbial growth and it was found that microbial biomass increased already after two years after liming in comparison to unlimed control (Bezdicek et al 2003). Moreover, liming significantly increased total soil protein and these results were related to similar but less pronounced changes in microbial biomass in Cd contaminated and limed control soils (Singleton et al 2003). In addition, the growth of microbial biomass and the growth of bacteria as the response to increased pH in limed soils were commonly found (i.e.…”

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confidence: 93%

Effects of liming on the microbial biomass and its activities in soils long-term contaminated by toxic elements

Mühlbachová¹,

Tlustoš²

2006

PLANT SOIL ENVIRON

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The effects of liming by CaO and CaCO 3 on soil microbial characteristics were studied during laboratory incubation of long-term contaminated arable and grassland soils from the vicinity of lead smelter near Příbram (Czech Republic). The CaO treatment showed significant negative effects on soil microbial biomass C and its respiratory activity in both studied soils, despite the fact that microbial biomass C in the grassland soil increased sharply during the first day of incubation. The metabolic quotient (qCO 2 ) in soils amended by CaO showed greater values than the control from the second day of incubation, indicating a possible stress of soil microbial pool. The vulnerability of organic matter to CaO could be indicated by the availability of K 2 SO 4 -extractable carbon that increased sharply, particularly at the beginning of the experiment. The amendment of soils by CaCO 3 moderately increased the soil microbial biomass. The respiratory activity and qCO 2 increased sharply during the first day of incubation, however it is not possible to ascribe them only to microbial activities, but also to CaCO 3 decomposition in hydrogen carbonates, water and CO 2 . The pH values increased more sharply under CaO treatment in comparison to CaCO 3 treatment. The improvement of soil pH by CaCO 3 could be therefore more convenient for soil microbial communities.

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“…Subsequently, Craig and Collins (2002) initiated a research program to detect proteins markers of human settlements in archaeological surveys, for archaeological site interpretation. The 'lag phase' of environmental proteomics ended in mid-2000s with a series of studies beginning with the soil metaproteomic study of soil microbial communities in Cd contaminated soils published by Singleton et al (2003). Since then, the potential of research on proteins in the environment as an unprecedented approach for monitoring past and current biochemical processes in the environment became clear, also supported by the development of the mass spectrometry (MS) based proteomics (Aebersold and Mann, 2003).…”

Section: Advances In Environmental Proteomicsmentioning

confidence: 99%