1,721,216 research outputs found
Some new grand questions in soil biology and biochemistry
No full texthttp://dx.doi.org/10.13039/501100004434 Università degli Studi di Firenzehttp://dx.doi.org/10.13039/501100018647 RUDN Universit
Soil Proteomics
No full textProteomics is a post-genomic approach with the potential to interrogate natural complex systems such as soils. However, the great potentials of soil proteomics are currently limited by either the complexity of the soil matrix which is reactive, structured, teeming with microbial communities which are at the same time extremely diverse, in heterogeneous physiological state and normally poorly characterized. Taken together, these soil features pose problems of protein sampling, extraction and purification. This chapter, though not exhaustive, aims to illustrate the main approaches and achievements in soil proteomics and indicate some future directions for further developments soil proteomics
High montmorillonite content may affect soil microbial proteomic analysis
No full textWe studied the effects of high montmorillonite content in soil on the proteomic analysis of Cupriavidus
metallidurans CH34 inoculated into model soils, containing a montmorilonite gradient. Bacterial
proteomic analysis was conducted by two-dimensional gel electrophoresis (2-DE) coupled to mass spectrometry.
The results showed that increasing the montmorillonite content in artificial soil the bacterial
viability did not affect but the amount of extracted proteins and the number of protein spots in 2-DE
decreased. Higher soil montmorillonite content also affected the protein identification, likely due to
montomrillonite-induced conformational changes in proteins or degradation. Therefore the development
of soil proteomics needs to increase the studies of interaction between protein and soil components as
clays or humic substances. This experiment showed how the use of a model study can be an help to
achieve more information about the complexity of soil and the fate of proteins in soil
Activities of Proteolytic Enzymes
No full textProteases, also known as proteinases or proteolytic enzymes, are a large group of hydrolases that catalyze the cleavage of peptide bonds in proteins to produce peptides and/or amino acids. Classification of proteolytic enzymes is based on three major criteria: type of reaction catalyzed, functional group of the active site, and type of molecular structure and evolutionary relationship among the various enzymes. According to the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology, the proteolytic enzymes can be grouped into proteases and peptidases on the basis of their nature of attack. This chapter describes methods to estimate soil protease activity, utilizing two substrates: casein, essentially a nonspecific substrate, and N‐benzoyl‐L‐argininamide (BAA), a typical substrate for trypsin‐like enzyme. The assay is based on colorimetric estimation of products released by the protein and amide‐hydrolyzing enzymes when soil is incubated with buffered solutions of casein and BAA, respectively
Bacterial culturability and the viable but non-culturable (VBNC) state studied by a proteomic approach using an artificial soil
No full textGram-negative bacteria in soil rapidly adapt to various stresses, including nutrient limitation and desiccation, by adopting the viable but non-culturable (VBNC) state as a survival strategy. Due to the physico-chemical and microbiological complexity of soils, little is understood on the effects of nutrient availability and moisture level on the transition from the VBNC state to culturability in soil. We evaluated the effects of gluconate or water on the transition of the soil borne bacterium C. metallidurans strain CH34 from the VBNC state to culturability by experiments of inoculation into artificial soils and bacterial metaproteomic analysis. Incubation without water or nutrients reduced the bacterial culturability to zero in 12 d, and addition of both water or gluconate restored the bacterial culturability to high levels within 24 h. The proteomic analysis showed that under water and nutrient limitation, proteins related to the cell shape and protein synthesis were rapidly down-regulated and stress-related proteins were quickly up-regulated during the transition from culturability to VBNC state. Reversion from the VBNC state to a culturable state with water or gluconate led to highly different bacterial proteomic profiles of C. metallidurans. Gluconate availability restored main protein biosynthesis and energy metabolic pathways, whereas water addition led to up-regulation of only six proteins, one of which degrade sigma factors involved in expression of genes controlling bacterial resistance under nutrient limitation. Proteins regulated during the transition between culturable and VBNC states could also be involved in the phenotypic VBNC for other soil bacteria, and can highlight some of the microbial genetic mechanisms allowing the entering and exiting from the VBNC state. Implications of the VBNC in microbial diversity and soil functionality are discussed
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Past, Present and Future in Soil Enzymology
No full textThe bibliography on soil enzymes is extensive as showed by books and many review chapters devoted to the subject. The assays of soil enzymes are generally simple, accurate, sensitive and relatively rapid and for this reasons they have been extensively used to determine the effects of contaminants, changes in management practices and effects of environmental factors and plant cover on soil metabolism. However, the present enzyme assays determine potential rather than real enzyme activities due to the optimal conditions of the assays and they do not discriminate the contribution of extracellular stabilised enzymes from that of intracellular enzyme activities. The determination of the latter is important to evaluate the answer of soil microorganisms to any effect on soil. Methods based on fumigation of soil with chloroform or with the physiological response of soil microorganisms to glucose addition to soil present drawbacks. Presently, enzyme activities are still used to evaluate the response of soil metabolism to any effect not only in arable soils but also in forest soils. However, not always the past bibliography and the limits of the present enzyme assays are considered. A few innovative studies have been carried out. Measurements of enzyme activities have been combined with those on microbial diversity evaluated by molecular techniques. Both synthesis and persistence of phosphomonoesterases have been quantified in studies based on the stimulation of microbial growth by adding easily degradable organic compounds to soil. Metcalfe et al. (Metcalfe AC, Krsek M, Gooday GW, Prosseer JI, Wellington EM (2002) Appl Environ Microbiol 68:5042–5050) covered all events from gene presence, through gene expression and up to the detection of target enzyme in soil. The addition of sludge to a pasture soil increased chitinase activity and the number of actinobacteria but selected actinobacterium-like chitinase sequences. Enzyme assays distinguishing the contribution of extracellular stabilised enzymes from that of intracellular enzyme activities are needed. Future research should increase the number of enzyme activities which can be determined in soil. For example, an accurate assay for determining nuclease activity in soil is not available. It is important to set up accurate methods for extracting intracellular and stabilised extracellular proteins, which are largely prevailing, so as to be able to carry out the proteomic approach in soil. The understanding of microbial synthesis of proteins (functional proteomic) as affected by different environmental conditions can increase our knowledge on the synthesis of enzymes in soil whereas the characterization of proteins protected against microbial degradation by their interactions with surface-reactive particles or their inclusion within humic component (structural proteomic) can give insights on the stabilization of organic N, including enzymes, in soil. The set up of suitable techniques is needed to visualise the location of stabilised enzymes in soil sections by both scanning electron microscopy and transmission electron microscopy. Acid phosphatase activity has been detected in small (7 × 20 nm) fragments of microbial membranes, roots, mycorrhizae, etc. of soil but not in naturally-electron dense soil components (minerals) and in soil components reacting with OsO4 (humus) and this does not permit to localize extracellular enzymes or proteins stabilized by clay minerals or humic materials (Ladd JN, Butler JHA (1966) Aust J Soil Res 4:41–54)
Interactions between proteins and humic substances affect protein identification by mass spectrometry
No full textSoil proteomics is facing problems such as low yields of protein extraction from soil and low protein identification rates as compared to theoretical estimates of soil proteome. This work aimed to evaluate the effect of soilborne humic substances (HS) on the identification of model proteins with different properties, such as myoglobin (Mb), α-glucosidase (αG), and β-glucosidase (βG), by using electrophoretic and ESI- and MALDI-mass spectrometry (MS) methodologies. Results showed that the contact between proteins and HS did not alter protein electrophoretic mobility but led to protein modifications that affected protein identification by MS. The decrease in protein identification parameters was more evident for Mb than for αG and βG, probably due to its lower molecular weight and less complex molecular structure. Analysis of MS data indicated that hydrophobic interactions could be responsible for the observed effects of contact between proteins and HS
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