Paolo Nannipieri - Academia.edu (original) (raw)
Papers by Paolo Nannipieri
Biology and Fertility of Soils, 2014
Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurr... more Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurrence, and role of its different microbial populations are largely unknown. Here, two sterilized soils (from England and Italy) were inoculated with a subsample of their initial microbial communities and/or those from the other soil to study their microbial community evolution. This approach compared two driving factors (original community and soil physicochemical characteristics) for microbial community definition. After 2 months of incubation and based on metagenomic datasets, the two inoculated communities (from an English grassland and an Italian forest) possessed similar functional and taxonomical structures when inoculated in the same sterile soil. For example, the newly colonized Italian soil was dominated by Actinobacteria related organisms (>66 % of the detected community) with a functional distribution independent of the inoculated soil origin. In addition, some of the organisms that dominated the different inoculated communities after 2 months were similar for a given sterile soil whether they came from the English grassland or the Italian forest, and they had not been detected in the original microbial community from either soil. Thus, similar microorganisms with low representation from the two distinct communities emerged in each sterilized soil, thus increasing the microbial diversity recovered from the microbial community of the donor soil. So far, these observations support the idea that different temperate soil microbial communities have different evenness due to environmental physico-chemical variations, yet have similar community composition (richness), and thus develop similarly when colonizing the same habitat.
Biology and Fertility of Soils, 2004
This review mainly discusses three related topics: the application of ecological theories to soil... more This review mainly discusses three related topics: the application of ecological theories to soil, the measurement of microbial diversity by molecular techniques and the impact of transgenic plants and microorganisms on genetic diversity of soil. These topics were debated at the Meeting on Soil Emergency held in Erice (Trapani, Italy) in 2001 for the celebration of the 50th anniversary of
Effects of indoleacetic acid (IAA) and ethylene (E) precursors on microbial biomass, respiration,... more Effects of indoleacetic acid (IAA) and ethylene (E) precursors on microbial biomass, respiration, and various hydrolase activities of the rhizosphere and bulk soil, were studied using a model system simulating this environment. The effects of IAA and E precursors were compared to those of glucose-C, N and S (GNS) applied at the same rate to soils. None of the treatments significantly affected respiration rates and ATP contents of soils. The IAA precursor significantly increased phosphatase, -glycosidase, urease and protease activities of the rhizosphere layer of both soils; the E precursor significantly increased phosphodiesterase, urease and protease activities of both soils. The GNS treatment did not significantly increase any hydrolase activity. The IAA precursor also stimulated the phosphatase activity of the bulk layer of the sandy soil after 7 d of incubation, possibly due to its diffusion from the rhizosphere to the bulk soil, whereas no stimulation in the bulk soil layer was observed in either E or GNS treatments. The increased hydrolase activities in the rhizosphere upon addition of both IAA and E precursors may be due to the role of these precursors as microbial metabolic activators, and may be involved in stimulation of plant growth through other processes involving IAA and E producing root associated microorganisms.
Aims of this work were to understand the effects of metal oxide (CeO 2 , Fe 3 O 4 , SnO 2 ) engin... more Aims of this work were to understand the effects of metal oxide (CeO 2 , Fe 3 O 4 , SnO 2 ) engineered nanoparticles (NPs) on microbial biomass and to evaluate their availability and distribution among soil particles. Two organ-mineral horizons (A1 and A2) of Epileptic Cambisol were polluted with NPs at rates of 0, 10 and 100 mg kg À1 of dry soil of Ce, Fe and Sn and incubated for 7 and 60 days at 60% WHC and at 25 C. Both microbial biomass C and N were not statistically affected by NPs pollution whereas the microbial C/N ratio increased with Fe 3 O 4 and SnO 2 -NPs probably due to the predominance of microbial communities such as ectomycorrhizae. The metabolic quotient (qCO 2 ) significantly (P < 0.001) increased in polluted soils indicating microbial stress or changes in the bacterial/fungal biomass ratio. The CHCl 3labile amounts of free Ce and Fe were found in soil polluted with CeO 2 and Fe 3 O 4 , indicating these elements were taken up by soil microorganisms. The chemical methods used for NPs bioavailability were not adequately sensitive to evaluate availability of elements in nanoparticles, and the best evaluation was from the wateresoil partition coefficient (log Kd) showing a low solubility of NPs. Nanoparticles were found in soil small aggregates (2e53 and <2 mm) by infrared spectrometry (FTIR) and electron microscopy (ESEM-EDS). The study of interactions between NPs and both organic or inorganic compounds can give insights about the potential risks of NPs in soil. Furthermore the study on diversity of microbial communities will clarify the NPs toxicity on soil microbial communities.
Soils contaminated with heavy metals also contain a number of organic ligands, particularly in th... more Soils contaminated with heavy metals also contain a number of organic ligands, particularly in the rhizosphere and thus, a fraction of the bioavailable metals in soils likely exists in a complexed form. The presence of soluble, metal-complexing organic ligands can influence the fate and transport of metals as well as mineralisation of organic compounds. Oxalate and citrate complexed with Cd, Cu, Mg, Pb and Zn were used as model metal -organic complexes possibly occurring in heavy metal contaminated soils. Soil respiration was used to determine the biodegradation of these compounds in a clay alkaline soil kept under different management regimes. Overall, the results indicated that metal complexes with citrate generally were more degradable than oxalate -metal complexes. For each organic acid, biodegradability of the metal -organic complexes varied for different metals, following the ranking order: Mg>Zn>CuiPb>Cd. Addition of Cd complexes decreased the soil respiration.
We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and ... more We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and activity, microbial and plant species richness, of an As-contaminated mine spoil, amended with compost (C) alone and in combination with beringite (B) or zerovalent iron grit (Z), to increase organic matter content and reduce trace elements mobility, and to allow Holcus lanatus and Pinus pinaster growth. Untreated spoil showed the lowest microbial biomass and activity and hydrolase activities, and H. lanatus as sole plant species, whereas the presented aided phytostabilisation option, especially CBZ treatment, significantly increased microbial biomass and activity and allowed colonisation by several plant species, comparable to those of an uncontaminated sandy soil. Microbial species richness was only increased in spoils amended with C alone. No clear correlation occurred between trace element mobility and microbial parameters and plant species richness. Our results indicate that the choice of indicators of soil remediation practices is a bottleneck.
![Research paper thumbnail of Erratum to “The chemical and functional characterization of soil N and its biotic components” [Soil Biology & Biochemistry, Vol. 41, Issue 12 (2009), 2357–2369]](https://attachments.academia-assets.com/46306293/thumbnails/1.jpg)
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Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltra... more Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltrated separating the extracted material into three fractions: A I with nominal molecular weight (nmw) > 100 kD, A II with nmw between 10 kD and 100 kD and R with nmw < 10 kD. Protease activity was determined in the fractions by using three different substrates: N-benzoyl-L-argininamide (BAA), specific for trypsin; N-benzyloxy-carbonyl-L-phenylalanyl L-leucine (ZPL), specific for carboxypeptidases; and casein, essentially a non-specific substrate. The derivative fractions were also analysed for their amino acid N and humic (HA) and fulvic (FA) acid contents. The organic matter of extracts and derivative fractions obtained from the pasture soil was analysed by isoelectric focusing (IEF) and that of fractions analysed by pyrolysis gas chromatography (Py-GC). Activities of the extract were monitored for their thermal stability and those of the extract and derivative fractions for their optimal pH. Due to the mechanical disintegrating action of sodium pyrophosphate over the humic substances during the fractionation process the amount of total organic C and FA in the fractions was ranked as R > A II > A I . The lowest amino acid N/organic C was found in the R fraction, whereas A II fraction was rich in humic acids, carbohydrates and amino acid N and A I fraction showed the lowest carbohydrate content. At least 70% of the total BAA-and ZPL-hydrolysing activity was associated to particles with nmw higher than 10 kD and at least 30% of these activities were present in particles with nmw higher 100 kD. Caseinhydrolysing activity was quite evenly distributed among the three fractions (A I , A II and R). The extracted protease-organic complexes were resistant to thermal denaturation and some of them showed optimal activity at pH values higher than 10 as a result of the polyanionic characteristics of the humic material surrounding enzyme molecules and of the presence of alkaline protease. Comparison of data obtained in Py-GC analyses and in protease activity suggests that BAA-hydrolysing activity was associated to a highly condensed humic matter and ZPL-hydrolysing activity to less resistant humic substances, while at least some of the extracted casein-hydrolysing activity was present as glyco-proteins not associated to humus. BAA-hydrolysing activity was probably inhibited by fresh organic matter of carbohydrate origin whereas lignin derived organic matter probably inhibited ZPL-and casein-hydrolysing activity.
... project no. BL 91/35-1 and the State of Schleswig-Holstein. Birgit Vogt and Astrid Menzel are... more ... project no. BL 91/35-1 and the State of Schleswig-Holstein. Birgit Vogt and Astrid Menzel are acknowledged for their excellent assistance and Prof. Dr. Dr. hc H.-P. Blume for his helpful comments on the results. References Alef ...
We investigated Cd, Zn, and Cd+Zn toxicity to soil microbial biomass and activity, and indigenous... more We investigated Cd, Zn, and Cd+Zn toxicity to soil microbial biomass and activity, and indigenous Rhizobium leguminosarum biovar trifolii, in two near neutral pH clay loam soils, under long-term arable and grassland management, in a 6-month laboratory incubation, with a view to determining the causative metal. Both soils were amended with Cd-or Zn-enriched sewage sludge, to produce soils with total Cd concentrations at four times (12 mg Cd g −1 soil), and total Zn concentrations (300 mg Zn kg −1 soil) at the EU upper permitted limit. The additive effects of Cd plus Zn at these soil concentrations were also investigated. There were no significant differences in microbial biomass C (B C ), biomass ninhydrin N (B N ), ATP, or microbial respiration between the different treatments. Microbial metabolic quotient (defined as qCO 2 =units of CO 2 -C evolved unit −1 biomass C unit −1 time) also did not differ significantly between treatments. However, the microbial maintenance energy (in this study defined as qCO 2 -to-μ ratio value, where μ is the growth rate) indicated that more energy was required for microbial synthesis in metal-rich sludgetreated soils (especially Zn) than in control sludge-treated soils. Indigenous R.leguminosarum bv. trifolii numbers were not significantly different between untreated and sludgetreated grassland soils after 24 weeks regardless of metal or metal concentrations. However, rhizobial numbers in the arable soils treated with metal-contaminated sludges decreased significantly (P<0.05) compared to the untreated control and uncontaminated sludge-treated soils after 24 weeks. The order of decreasing toxicity to rhizobia in the arable soils was Zn>Cd>Cd+Zn.
Journal of genomics, 2015
Here we report a benchmark of the effect of bootstrap cut-off values of the RDP Classifier tool i... more Here we report a benchmark of the effect of bootstrap cut-off values of the RDP Classifier tool in terms of data retention along the different taxonomic ranks by using Illumina reads. Results provide guidelines for planning sequencing depths and selection of bootstrap cut-off in taxonomic assignments.
Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltra... more Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltrated separating the extracted material into three fractions: A I with nominal molecular weight (nmw) > 100 kD, A II with nmw between 10 kD and 100 kD and R with nmw < 10 kD. Protease activity was determined in the fractions by using three different substrates: N-benzoyl-L-argininamide (BAA), specific for trypsin; N-benzyloxy-carbonyl-L-phenylalanyl L-leucine (ZPL), specific for carboxypeptidases; and casein, essentially a non-specific substrate. The derivative fractions were also analysed for their amino acid N and humic (HA) and fulvic (FA) acid contents. The organic matter of extracts and derivative fractions obtained from the pasture soil was analysed by isoelectric focusing (IEF) and that of fractions analysed by pyrolysis gas chromatography (Py-GC). Activities of the extract were monitored for their thermal stability and those of the extract and derivative fractions for their optimal pH. Due to the mechanical disintegrating action of sodium pyrophosphate over the humic substances during the fractionation process the amount of total organic C and FA in the fractions was ranked as R > A II > A I . The lowest amino acid N/organic C was found in the R fraction, whereas A II fraction was rich in humic acids, carbohydrates and amino acid N and A I fraction showed the lowest carbohydrate content. At least 70% of the total BAA-and ZPL-hydrolysing activity was associated to particles with nmw higher than 10 kD and at least 30% of these activities were present in particles with nmw higher 100 kD. Caseinhydrolysing activity was quite evenly distributed among the three fractions (A I , A II and R). The extracted protease-organic complexes were resistant to thermal denaturation and some of them showed optimal activity at pH values higher than 10 as a result of the polyanionic characteristics of the humic material surrounding enzyme molecules and of the presence of alkaline protease. Comparison of data obtained in Py-GC analyses and in protease activity suggests that BAA-hydrolysing activity was associated to a highly condensed humic matter and ZPL-hydrolysing activity to less resistant humic substances, while at least some of the extracted casein-hydrolysing activity was present as glyco-proteins not associated to humus. BAA-hydrolysing activity was probably inhibited by fresh organic matter of carbohydrate origin whereas lignin derived organic matter probably inhibited ZPL-and casein-hydrolysing activity.
... Maria Rosanna Favretto 1, Maurizio Guido Paoletti 1, Fabio Caporali 2, Paolo Nannipieri 3, An... more ... Maria Rosanna Favretto 1, Maurizio Guido Paoletti 1, Fabio Caporali 2, Paolo Nannipieri 3, Antonio Onnis 4, and Paolo Emilio Tomei 4 ... use of natural resources, no-tillage in association with living mulch has attracted increasing attention (Finch and Sharp 1981; Hargrove 1982). ...
The long-term physical persistence and biological activity of transplastomic plant DNA (transgene... more The long-term physical persistence and biological activity of transplastomic plant DNA (transgenes contained in the chloroplast genome) either purified and added to soil or naturally released by decaying tobacco leaves in soil was determined. Soil microcosms were amended with transplastomic tobacco leaves or purified plant DNA and incubated for up to 4 years. Total DNA was extracted from soil and the number of transgenes (aadA, which confers resistance to both spectinomycin and streptomycin) was quantified by quantitative PCR. The biological activity of these transgenes was assessed by transformation in the bacterial strain Acinetobacter sp. BD413(pBAB2) in vitro. While the proportion of transgenes recovered increased with the increasing amount of transplastomic DNA added, plant DNA was rapidly degraded over time. The number of transgenes recovered decreased about 10,000 fold within 2 weeks. Data reveal, however, that a small fraction of the plant DNA escaped degradation. Transgene sequences were still detected after 4 years and transformation assays showed that extracted DNA remained biologically active and could still transform competent cells of Acinetobacter sp. BD413(pBAB2). The approach presented here quantified the number of transgenes (based on quantitative PCR of 50% of the gene) released and persisting in the environment over time and provided new insights into the fate of transgenic plant DNA in soil. 326e334 www.elsevier.com/locate/resmic A. Pontiroli et al. / Research in Microbiology 161 (2010) 326e334
Applied Soil Ecology, 2007
Books by Paolo Nannipieri
Biology and Fertility of Soils, 2014
Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurr... more Soil is considered as one of the most biodiverse environments on Earth; yet, the taxonomy, occurrence, and role of its different microbial populations are largely unknown. Here, two sterilized soils (from England and Italy) were inoculated with a subsample of their initial microbial communities and/or those from the other soil to study their microbial community evolution. This approach compared two driving factors (original community and soil physicochemical characteristics) for microbial community definition. After 2 months of incubation and based on metagenomic datasets, the two inoculated communities (from an English grassland and an Italian forest) possessed similar functional and taxonomical structures when inoculated in the same sterile soil. For example, the newly colonized Italian soil was dominated by Actinobacteria related organisms (>66 % of the detected community) with a functional distribution independent of the inoculated soil origin. In addition, some of the organisms that dominated the different inoculated communities after 2 months were similar for a given sterile soil whether they came from the English grassland or the Italian forest, and they had not been detected in the original microbial community from either soil. Thus, similar microorganisms with low representation from the two distinct communities emerged in each sterilized soil, thus increasing the microbial diversity recovered from the microbial community of the donor soil. So far, these observations support the idea that different temperate soil microbial communities have different evenness due to environmental physico-chemical variations, yet have similar community composition (richness), and thus develop similarly when colonizing the same habitat.
Biology and Fertility of Soils, 2004
This review mainly discusses three related topics: the application of ecological theories to soil... more This review mainly discusses three related topics: the application of ecological theories to soil, the measurement of microbial diversity by molecular techniques and the impact of transgenic plants and microorganisms on genetic diversity of soil. These topics were debated at the Meeting on Soil Emergency held in Erice (Trapani, Italy) in 2001 for the celebration of the 50th anniversary of
Effects of indoleacetic acid (IAA) and ethylene (E) precursors on microbial biomass, respiration,... more Effects of indoleacetic acid (IAA) and ethylene (E) precursors on microbial biomass, respiration, and various hydrolase activities of the rhizosphere and bulk soil, were studied using a model system simulating this environment. The effects of IAA and E precursors were compared to those of glucose-C, N and S (GNS) applied at the same rate to soils. None of the treatments significantly affected respiration rates and ATP contents of soils. The IAA precursor significantly increased phosphatase, -glycosidase, urease and protease activities of the rhizosphere layer of both soils; the E precursor significantly increased phosphodiesterase, urease and protease activities of both soils. The GNS treatment did not significantly increase any hydrolase activity. The IAA precursor also stimulated the phosphatase activity of the bulk layer of the sandy soil after 7 d of incubation, possibly due to its diffusion from the rhizosphere to the bulk soil, whereas no stimulation in the bulk soil layer was observed in either E or GNS treatments. The increased hydrolase activities in the rhizosphere upon addition of both IAA and E precursors may be due to the role of these precursors as microbial metabolic activators, and may be involved in stimulation of plant growth through other processes involving IAA and E producing root associated microorganisms.
Aims of this work were to understand the effects of metal oxide (CeO 2 , Fe 3 O 4 , SnO 2 ) engin... more Aims of this work were to understand the effects of metal oxide (CeO 2 , Fe 3 O 4 , SnO 2 ) engineered nanoparticles (NPs) on microbial biomass and to evaluate their availability and distribution among soil particles. Two organ-mineral horizons (A1 and A2) of Epileptic Cambisol were polluted with NPs at rates of 0, 10 and 100 mg kg À1 of dry soil of Ce, Fe and Sn and incubated for 7 and 60 days at 60% WHC and at 25 C. Both microbial biomass C and N were not statistically affected by NPs pollution whereas the microbial C/N ratio increased with Fe 3 O 4 and SnO 2 -NPs probably due to the predominance of microbial communities such as ectomycorrhizae. The metabolic quotient (qCO 2 ) significantly (P < 0.001) increased in polluted soils indicating microbial stress or changes in the bacterial/fungal biomass ratio. The CHCl 3labile amounts of free Ce and Fe were found in soil polluted with CeO 2 and Fe 3 O 4 , indicating these elements were taken up by soil microorganisms. The chemical methods used for NPs bioavailability were not adequately sensitive to evaluate availability of elements in nanoparticles, and the best evaluation was from the wateresoil partition coefficient (log Kd) showing a low solubility of NPs. Nanoparticles were found in soil small aggregates (2e53 and <2 mm) by infrared spectrometry (FTIR) and electron microscopy (ESEM-EDS). The study of interactions between NPs and both organic or inorganic compounds can give insights about the potential risks of NPs in soil. Furthermore the study on diversity of microbial communities will clarify the NPs toxicity on soil microbial communities.
Soils contaminated with heavy metals also contain a number of organic ligands, particularly in th... more Soils contaminated with heavy metals also contain a number of organic ligands, particularly in the rhizosphere and thus, a fraction of the bioavailable metals in soils likely exists in a complexed form. The presence of soluble, metal-complexing organic ligands can influence the fate and transport of metals as well as mineralisation of organic compounds. Oxalate and citrate complexed with Cd, Cu, Mg, Pb and Zn were used as model metal -organic complexes possibly occurring in heavy metal contaminated soils. Soil respiration was used to determine the biodegradation of these compounds in a clay alkaline soil kept under different management regimes. Overall, the results indicated that metal complexes with citrate generally were more degradable than oxalate -metal complexes. For each organic acid, biodegradability of the metal -organic complexes varied for different metals, following the ranking order: Mg>Zn>CuiPb>Cd. Addition of Cd complexes decreased the soil respiration.
We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and ... more We studied the effectiveness of remediation on microbial endpoints, namely microbial biomass and activity, microbial and plant species richness, of an As-contaminated mine spoil, amended with compost (C) alone and in combination with beringite (B) or zerovalent iron grit (Z), to increase organic matter content and reduce trace elements mobility, and to allow Holcus lanatus and Pinus pinaster growth. Untreated spoil showed the lowest microbial biomass and activity and hydrolase activities, and H. lanatus as sole plant species, whereas the presented aided phytostabilisation option, especially CBZ treatment, significantly increased microbial biomass and activity and allowed colonisation by several plant species, comparable to those of an uncontaminated sandy soil. Microbial species richness was only increased in spoils amended with C alone. No clear correlation occurred between trace element mobility and microbial parameters and plant species richness. Our results indicate that the choice of indicators of soil remediation practices is a bottleneck.
Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltra... more Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltrated separating the extracted material into three fractions: A I with nominal molecular weight (nmw) > 100 kD, A II with nmw between 10 kD and 100 kD and R with nmw < 10 kD. Protease activity was determined in the fractions by using three different substrates: N-benzoyl-L-argininamide (BAA), specific for trypsin; N-benzyloxy-carbonyl-L-phenylalanyl L-leucine (ZPL), specific for carboxypeptidases; and casein, essentially a non-specific substrate. The derivative fractions were also analysed for their amino acid N and humic (HA) and fulvic (FA) acid contents. The organic matter of extracts and derivative fractions obtained from the pasture soil was analysed by isoelectric focusing (IEF) and that of fractions analysed by pyrolysis gas chromatography (Py-GC). Activities of the extract were monitored for their thermal stability and those of the extract and derivative fractions for their optimal pH. Due to the mechanical disintegrating action of sodium pyrophosphate over the humic substances during the fractionation process the amount of total organic C and FA in the fractions was ranked as R > A II > A I . The lowest amino acid N/organic C was found in the R fraction, whereas A II fraction was rich in humic acids, carbohydrates and amino acid N and A I fraction showed the lowest carbohydrate content. At least 70% of the total BAA-and ZPL-hydrolysing activity was associated to particles with nmw higher than 10 kD and at least 30% of these activities were present in particles with nmw higher 100 kD. Caseinhydrolysing activity was quite evenly distributed among the three fractions (A I , A II and R). The extracted protease-organic complexes were resistant to thermal denaturation and some of them showed optimal activity at pH values higher than 10 as a result of the polyanionic characteristics of the humic material surrounding enzyme molecules and of the presence of alkaline protease. Comparison of data obtained in Py-GC analyses and in protease activity suggests that BAA-hydrolysing activity was associated to a highly condensed humic matter and ZPL-hydrolysing activity to less resistant humic substances, while at least some of the extracted casein-hydrolysing activity was present as glyco-proteins not associated to humus. BAA-hydrolysing activity was probably inhibited by fresh organic matter of carbohydrate origin whereas lignin derived organic matter probably inhibited ZPL-and casein-hydrolysing activity.
... project no. BL 91/35-1 and the State of Schleswig-Holstein. Birgit Vogt and Astrid Menzel are... more ... project no. BL 91/35-1 and the State of Schleswig-Holstein. Birgit Vogt and Astrid Menzel are acknowledged for their excellent assistance and Prof. Dr. Dr. hc H.-P. Blume for his helpful comments on the results. References Alef ...
We investigated Cd, Zn, and Cd+Zn toxicity to soil microbial biomass and activity, and indigenous... more We investigated Cd, Zn, and Cd+Zn toxicity to soil microbial biomass and activity, and indigenous Rhizobium leguminosarum biovar trifolii, in two near neutral pH clay loam soils, under long-term arable and grassland management, in a 6-month laboratory incubation, with a view to determining the causative metal. Both soils were amended with Cd-or Zn-enriched sewage sludge, to produce soils with total Cd concentrations at four times (12 mg Cd g −1 soil), and total Zn concentrations (300 mg Zn kg −1 soil) at the EU upper permitted limit. The additive effects of Cd plus Zn at these soil concentrations were also investigated. There were no significant differences in microbial biomass C (B C ), biomass ninhydrin N (B N ), ATP, or microbial respiration between the different treatments. Microbial metabolic quotient (defined as qCO 2 =units of CO 2 -C evolved unit −1 biomass C unit −1 time) also did not differ significantly between treatments. However, the microbial maintenance energy (in this study defined as qCO 2 -to-μ ratio value, where μ is the growth rate) indicated that more energy was required for microbial synthesis in metal-rich sludgetreated soils (especially Zn) than in control sludge-treated soils. Indigenous R.leguminosarum bv. trifolii numbers were not significantly different between untreated and sludgetreated grassland soils after 24 weeks regardless of metal or metal concentrations. However, rhizobial numbers in the arable soils treated with metal-contaminated sludges decreased significantly (P<0.05) compared to the untreated control and uncontaminated sludge-treated soils after 24 weeks. The order of decreasing toxicity to rhizobia in the arable soils was Zn>Cd>Cd+Zn.
Journal of genomics, 2015
Here we report a benchmark of the effect of bootstrap cut-off values of the RDP Classifier tool i... more Here we report a benchmark of the effect of bootstrap cut-off values of the RDP Classifier tool in terms of data retention along the different taxonomic ranks by using Illumina reads. Results provide guidelines for planning sequencing depths and selection of bootstrap cut-off in taxonomic assignments.
Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltra... more Pyrophosphate (140 mM, pH 7.1) extracts of two arable soils and one pasture soil were ultrafiltrated separating the extracted material into three fractions: A I with nominal molecular weight (nmw) > 100 kD, A II with nmw between 10 kD and 100 kD and R with nmw < 10 kD. Protease activity was determined in the fractions by using three different substrates: N-benzoyl-L-argininamide (BAA), specific for trypsin; N-benzyloxy-carbonyl-L-phenylalanyl L-leucine (ZPL), specific for carboxypeptidases; and casein, essentially a non-specific substrate. The derivative fractions were also analysed for their amino acid N and humic (HA) and fulvic (FA) acid contents. The organic matter of extracts and derivative fractions obtained from the pasture soil was analysed by isoelectric focusing (IEF) and that of fractions analysed by pyrolysis gas chromatography (Py-GC). Activities of the extract were monitored for their thermal stability and those of the extract and derivative fractions for their optimal pH. Due to the mechanical disintegrating action of sodium pyrophosphate over the humic substances during the fractionation process the amount of total organic C and FA in the fractions was ranked as R > A II > A I . The lowest amino acid N/organic C was found in the R fraction, whereas A II fraction was rich in humic acids, carbohydrates and amino acid N and A I fraction showed the lowest carbohydrate content. At least 70% of the total BAA-and ZPL-hydrolysing activity was associated to particles with nmw higher than 10 kD and at least 30% of these activities were present in particles with nmw higher 100 kD. Caseinhydrolysing activity was quite evenly distributed among the three fractions (A I , A II and R). The extracted protease-organic complexes were resistant to thermal denaturation and some of them showed optimal activity at pH values higher than 10 as a result of the polyanionic characteristics of the humic material surrounding enzyme molecules and of the presence of alkaline protease. Comparison of data obtained in Py-GC analyses and in protease activity suggests that BAA-hydrolysing activity was associated to a highly condensed humic matter and ZPL-hydrolysing activity to less resistant humic substances, while at least some of the extracted casein-hydrolysing activity was present as glyco-proteins not associated to humus. BAA-hydrolysing activity was probably inhibited by fresh organic matter of carbohydrate origin whereas lignin derived organic matter probably inhibited ZPL-and casein-hydrolysing activity.
... Maria Rosanna Favretto 1, Maurizio Guido Paoletti 1, Fabio Caporali 2, Paolo Nannipieri 3, An... more ... Maria Rosanna Favretto 1, Maurizio Guido Paoletti 1, Fabio Caporali 2, Paolo Nannipieri 3, Antonio Onnis 4, and Paolo Emilio Tomei 4 ... use of natural resources, no-tillage in association with living mulch has attracted increasing attention (Finch and Sharp 1981; Hargrove 1982). ...
The long-term physical persistence and biological activity of transplastomic plant DNA (transgene... more The long-term physical persistence and biological activity of transplastomic plant DNA (transgenes contained in the chloroplast genome) either purified and added to soil or naturally released by decaying tobacco leaves in soil was determined. Soil microcosms were amended with transplastomic tobacco leaves or purified plant DNA and incubated for up to 4 years. Total DNA was extracted from soil and the number of transgenes (aadA, which confers resistance to both spectinomycin and streptomycin) was quantified by quantitative PCR. The biological activity of these transgenes was assessed by transformation in the bacterial strain Acinetobacter sp. BD413(pBAB2) in vitro. While the proportion of transgenes recovered increased with the increasing amount of transplastomic DNA added, plant DNA was rapidly degraded over time. The number of transgenes recovered decreased about 10,000 fold within 2 weeks. Data reveal, however, that a small fraction of the plant DNA escaped degradation. Transgene sequences were still detected after 4 years and transformation assays showed that extracted DNA remained biologically active and could still transform competent cells of Acinetobacter sp. BD413(pBAB2). The approach presented here quantified the number of transgenes (based on quantitative PCR of 50% of the gene) released and persisting in the environment over time and provided new insights into the fate of transgenic plant DNA in soil. 326e334 www.elsevier.com/locate/resmic A. Pontiroli et al. / Research in Microbiology 161 (2010) 326e334
Applied Soil Ecology, 2007