The Experts below are selected from a list of 270 Experts worldwide ranked by ideXlab platform
Carlos García - One of the best experts on this subject based on the ideXlab platform.
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can the labile carbon contribute to carbon immobilization in Semiarid Soils priming effects and microbial community dynamics
Soil Biology & Biochemistry, 2013Co-Authors: Felipe Bastida, Teresa Hernández, I F Torres, Petra Bombach, Hans H Richnow, Carlos GarcíaAbstract:Abstract Tracer experiments with isotopic-enriched carbon compounds can provide information regarding the carbon cycling in Semiarid Soils. We studied priming effects and microbial utilization of glucose as an example of bioavailable labile molecule in the carbon cycle of a Semiarid soil. The soil, which has low content of total organic carbon (5.0 g kg −1 ), was amended with U 13 C-glucose (99 atom %) at concentration of 75 μg C g −1 soil (LD) or 300 μg C g −1 soil (HD). Glucose-derived carbon remained in soil after two months of incubation. The percentage of residual carbon stabilized was greater in LD with 40% of the initial 13 C added compared to 30% of the initial 13 C added in the HD. Comparison of 13 C content in water- and sodium-pyrophosphate extracts pointed to a significant humification of up to 2.4% of the initial 13 C-glucose. Glucose was subjected to an intense mineralization in the first 17-days of 22.8% and 40.94% for the LD and HD, respectively. The stable isotope probing (SIP) of phospholipid fatty acids (PLFAs) by gas-chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) showed that bacteria dominated glucose metabolism in comparison to fungi. Gram-negative populations were initially more involved in glucose assimilation than Gram-positive bacteria. In the fatty acids fraction, up to 95% of the 13 C was predominantly found in fatty acids typical for Gram-negative bacteria. However, after 4 and 17 days the 13 C-enrichment in Gram-positive biomarkers increased. The mineralization of soil organic matter triggered by glucose additions was more intense in HD (3.6% of soil TOC) than LD (1.0% of soil TOC) and reached the highest level after 4 days in HD. Priming was controlled by Gram-negative populations but fungi and, particularly actinobacteria played an important role in latter steps. Our data indicated that the intense metabolism of SOM due to priming phenomena compromises the potential carbon sequestration in this Semiarid soil amended with glucose.
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Semiarid Soils submitted to severe drought stress influence on humic acid characteristics in organic amended Soils
Journal of Soils and Sediments, 2012Co-Authors: Sara Hueso, Teresa Hernández, Gennaro Brunetti, N Senesi, Karam Farrag, Carlos GarcíaAbstract:Purpose The objective of this work was to assess the effect of severe drought conditions on the characteristics of Semiarid soil humic acids (HAs) as well as the effect of organic amendment on such changes.
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influence of stability and origin of organic amendments on humification in Semiarid Soils
Soil Science Society of America Journal, 2011Co-Authors: Keiji Jindo, Teresa Hernández, Carlos García, Miguel Angel SanchezmonederoAbstract:Th e application of soil organic amendments is a widely accepted strategy to maintain soil fertility by maintaining and increasing the levels of soil organic matter. Th e objective of this study was to evaluate the eff ect of land application of organic wastes of diff erent sources and stabilization degrees on the soil organic matter humifi cation, measured by changes in the chemical and structural characteristics of humic and fulvic acids by cross-polarization magic angle spinning 13 C nuclear magnetic resonance (CPMAS 13 C-NMR) and Fourier-transform infrared (FT-IR) spectroscopy. A microcosm experiment lasting 360 d was performed with 500 g of a Semiarid soil amended with diff erent materials: sewage sludge from a wastewater treatment plant, composted sewage sludge, the organic fraction of municipal solid wastes, and composted municipal solid wastes. Th e addition of the organic amendments increased the amount of humic acids in the soil in all cases, whereas the amount of fulvic acids remained very similar to that of the control soil. Th e humic acids of the amended Soils were characterized by an enrichment of N and aromatic C compounds, along with carboxylic groups, which increased their aromatic and hydrophobic characteristics. Aft er the 360-d incubation, some of the labile compounds added with the organic amendments had been incorporated into the soil humic pool and protected from degradation, contributing to the buildup of soil organic matter. Land application of organic wastes represents a key waste management option in Semiarid regions where these materials can be used as an exogenous source of organic matter for soil rehabilitation.
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resistance and resilience of the soil microbial biomass to severe drought in Semiarid Soils the importance of organic amendments
Applied Soil Ecology, 2011Co-Authors: Sara Hueso, Teresa Hernández, Carlos GarcíaAbstract:Abstract Changes in mean global air temperature and precipitation patterns, leading to longer drought periods and more extremely dry years, are predicted. The objective of this work was to assess whether a long period of severe drought can affect the growth and activity of the microbiota of a Semiarid soil, as well as the effect of organic amendments on soil resistance and resilience to this severe drought. A soil incubation experiment was carried out over 60 days, under controlled conditions (25 °C and 60/80% day/night relative humidity), with two treatments: unamended (US) and amended (AS) with manure compost (100 t ha−1). Two levels of irrigation were imposed: (1) well-watered (MUS and MAS), the soil being maintained at 60% of its water-holding capacity (WHC), and (2) dry, without irrigation (DUS and DAS). Then, a single level of irrigation was established for 37 days, dry Soils being irrigated under the same conditions than well-watered Soils, to assess soil resilience to this period of drought. Under well-watered conditions, the soil water-soluble nitrogen contents were 73 and 88% higher, the microbial biomass carbon 63 and 48% higher, alkaline phosphomonoesterase activity 46 and 32% higher, β-glucosidase activity 16 and 25% higher and urease activity 30 and 19% higher for the US and AS treatments, respectively, compared with the dry conditions at the end of the experimental period. Furthermore, the organic amendment helped the soil to retain moisture and encouraged the growth and activity of soil microbial populations. However, a 2-month drought seems insufficient to destroy the native microbial biomass in the arid soil used in this study, indicating that it is well adapted to adverse climate conditions. Thus, microbiological and biochemical parameters experienced a rapid recovery after soil rewetting, DUS and DAS showing values similar to MUS and MAS, after rewetting, highlighting the resilience of this type of soil against drought stress.
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soil organic carbon buffers heavy metal contamination on Semiarid Soils effects of different metal threshold levels on soil microbial activity
European Journal of Soil Biology, 2009Co-Authors: J L Moreno, Felipe Bastida, Teresa Hernández, Margarita Ros, Carlos GarcíaAbstract:Abstract Traditionally, three threshold levels have been accepted for heavy metal concentrations in agricultural Soils, depending on soil pH. The aim of this work was to ascertain how the three threshold values proposed for Cd (3, 6.5, and 12.5 mg kg−1) and Zn (300, 650, and 1300 mg kg−1) really affect soil microbial activity. Two Soils, a scrubland soil and a forest soil, differing widely in their organic C content, were used in this study. Despite the different soil characteristics, the fractions of Cd and Zn extracted with a solution of diethylenetriaminepentaacetic acid (DTPA) showed little difference between Soils. Parameters, such as microbial biomass C (Cmic), soil basal respiration (BR), adenosine triphosphate (ATP) content, dehydrogenase activity (DHA), urease activity (UA), alkaline phosphatase activity (APA), and β-glucosidase (β-GA), were less affected by heavy metals in the forest soil than in the scrubland soil. In general, the simultaneous addition of both metals had a synergistic effect on microbial activity, and this treatment produced a significant decrease of microbial activity of both Soils with respect to control. The highest level (L3) of Cd, Zn and Cd + Zn treatments produced significant decrease of microbial and biochemical parameters in both Soils.
Felipe Bastida - One of the best experts on this subject based on the ideXlab platform.
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the extracellular metaproteome of Soils under Semiarid climate a methodological comparison of extraction buffers
Science of The Total Environment, 2018Co-Authors: Felipe Bastida, I F Torres, Nico Jehmlich, C GarciaAbstract:We compare the protein extraction efficiencies, as well as the phylogenetic and functional information provided, of two extraction protocols in Soils that differ mainly in their organic matter and clay contents, the main factors limiting protein extraction in Semiarid Soils. These protocols utilise extractants commonly used for the assay of extracellular enzyme activities. The first method was based on the utilisation of the modified universal buffer (MUB). The second was based on the extraction of humic substances with sodium pyrophosphate. When compared to the total amount of proteins in soil, the results indicate a very-low extraction efficiency for both protocols. Analysis in an Orbitrap Fusion mass spectrometer and further searching against an "ad hoc" metagenome evidenced that the phylogenetic and functional information retrieved from the extracellular soil metaproteome can be biased by the extraction buffer.
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the ecological and physiological responses of the microbial community from a Semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment
Journal of Proteomics, 2016Co-Authors: Felipe Bastida, Teresa Hernández, Hans H Richnow, Nico Jehmlich, K Lima, Brandon E L Morris, M Von Bergen, C GarciaAbstract:The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in Semiarid Soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted Semiarid Soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in Soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation.
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the role of lignin and cellulose in the carbon cycling of degraded Soils under Semiarid climate and their relation to microbial biomass
Soil Biology & Biochemistry, 2014Co-Authors: I F Torres, T Hernandez, Felipe Bastida, Petra Bombach, Hans H Richnow, C GarciaAbstract:Abstract A high level of biological degradation is usually observed in Soils under Semiarid climate where the low inputs of vegetal debris constraint the development of microbiota. Among vegetal inputs, cellulose and lignin are dominant substrates but their assimilation by the microbial community of Semiarid Soils is yet not understood. In the present study, 13C-labeled cellulose and 13C-labeled lignin (75 μg 13C g−1 soil) were added to two Semiarid Soils with different properties and degradation level. Abanilla soil is a bare, highly degraded soil without plant cover growing on it and a total organic C content of 5.0 g kg−1; Santomera soil is covered by plants (20% coverage) based on xerophytic shrubs and has a total organic C content of 12.0 g kg−1. The fate of added carbon was evaluated by analysis of the carbon isotope signature of bulk soil-derived carbon and extractable carbon fractions (water and sodium-pyrophosphate extracts). At long-term (120 days), we observed that the stability of cellulose- and lignin-derived carbon was dependent on their chemical nature. The contribution of lignin-derived carbon to the pool of humic substances was higher than that of cellulose. However, at short-term (30 days), the mineralization of the added substrates was more related to the degradation level of Soils (i.e. microbial biomass). Stable isotope probing (SIP) of phospholipid fatty acids (PLFA-SIP) analysis revealed that just a minor part of the microbial community assimilated the carbon derived from cellulose and lignin. Moreover, the relative contribution of each microbial group to the assimilation of lignin-derived carbon was different in each soil.
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metaproteomics of Soils from Semiarid environment functional and phylogenetic information obtained with different protein extraction methods
Journal of Proteomics, 2014Co-Authors: Felipe Bastida, Teresa Hernández, C GarciaAbstract:Abstract Microbial populations fulfil a critical role in the soil sustainability and their functionality can be ascertained by proteomics based on high-performance mass spectrometry (MS) measurements. However, soil proteomics is compromised by methodological issues, among which extraction is a limiting factor, and still has not been adequately applied in Semiarid Soils, which usually are nutrient limited. We aim to evaluate the functional and phylogenetic information retrieved from three Semiarid Soils with distinct edaphic properties and degradation levels. Three extraction methods with different physico-chemical bases were tested [1–3]. The HPLC-amino acid quantification of the extracted protein pellets revealed a tremendous inefficiency of the extraction methods, with a maximally 6.8% of the proteinaceous material being extracted in comparison with the protein content in the bulk soil. The composition of the proteomes extracted was analysed after SDS-PAGE and liquid chromatography coupled with electrospray-MS/MS. Chourey's method, based on boiling and DTT, yielded a high diversity of bacterial proteins and revealed differences in the community composition at the phylum level among the three Soils. The overall metabolic information obtained by both extraction methods was similar, but Chourey's method provided additionally valuable bio-geochemical insights which suggest an ecological adaptation of microbial communities from Semiarid Soils for carbon and nitrogen fixation. Biological significance Microbial communities inhabiting the soil perform critical reactions for the sustainability of the planet. At biochemical level, soil proteomics is starting to provide incipient insights into the microbial functionality of Soils. However, methodological comparisons are needed to assess which methods are more suitable. Precisely, such information under arid and Semiarid environments is missing. By using amino acid quantification of extracted proteomes and LC–MS/MS based proteomics, we provide a novel methodological evaluation of the functional, phylogenetic and bio-geochemical information obtained by three extraction methods in Semiarid Soils with distinct edaphic properties.
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can the labile carbon contribute to carbon immobilization in Semiarid Soils priming effects and microbial community dynamics
Soil Biology & Biochemistry, 2013Co-Authors: Felipe Bastida, Teresa Hernández, I F Torres, Petra Bombach, Hans H Richnow, Carlos GarcíaAbstract:Abstract Tracer experiments with isotopic-enriched carbon compounds can provide information regarding the carbon cycling in Semiarid Soils. We studied priming effects and microbial utilization of glucose as an example of bioavailable labile molecule in the carbon cycle of a Semiarid soil. The soil, which has low content of total organic carbon (5.0 g kg −1 ), was amended with U 13 C-glucose (99 atom %) at concentration of 75 μg C g −1 soil (LD) or 300 μg C g −1 soil (HD). Glucose-derived carbon remained in soil after two months of incubation. The percentage of residual carbon stabilized was greater in LD with 40% of the initial 13 C added compared to 30% of the initial 13 C added in the HD. Comparison of 13 C content in water- and sodium-pyrophosphate extracts pointed to a significant humification of up to 2.4% of the initial 13 C-glucose. Glucose was subjected to an intense mineralization in the first 17-days of 22.8% and 40.94% for the LD and HD, respectively. The stable isotope probing (SIP) of phospholipid fatty acids (PLFAs) by gas-chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) showed that bacteria dominated glucose metabolism in comparison to fungi. Gram-negative populations were initially more involved in glucose assimilation than Gram-positive bacteria. In the fatty acids fraction, up to 95% of the 13 C was predominantly found in fatty acids typical for Gram-negative bacteria. However, after 4 and 17 days the 13 C-enrichment in Gram-positive biomarkers increased. The mineralization of soil organic matter triggered by glucose additions was more intense in HD (3.6% of soil TOC) than LD (1.0% of soil TOC) and reached the highest level after 4 days in HD. Priming was controlled by Gram-negative populations but fungi and, particularly actinobacteria played an important role in latter steps. Our data indicated that the intense metabolism of SOM due to priming phenomena compromises the potential carbon sequestration in this Semiarid soil amended with glucose.
Teresa Hernández - One of the best experts on this subject based on the ideXlab platform.
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the ecological and physiological responses of the microbial community from a Semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment
Journal of Proteomics, 2016Co-Authors: Felipe Bastida, Teresa Hernández, Hans H Richnow, Nico Jehmlich, K Lima, Brandon E L Morris, M Von Bergen, C GarciaAbstract:The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in Semiarid Soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted Semiarid Soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in Soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation.
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metaproteomics of Soils from Semiarid environment functional and phylogenetic information obtained with different protein extraction methods
Journal of Proteomics, 2014Co-Authors: Felipe Bastida, Teresa Hernández, C GarciaAbstract:Abstract Microbial populations fulfil a critical role in the soil sustainability and their functionality can be ascertained by proteomics based on high-performance mass spectrometry (MS) measurements. However, soil proteomics is compromised by methodological issues, among which extraction is a limiting factor, and still has not been adequately applied in Semiarid Soils, which usually are nutrient limited. We aim to evaluate the functional and phylogenetic information retrieved from three Semiarid Soils with distinct edaphic properties and degradation levels. Three extraction methods with different physico-chemical bases were tested [1–3]. The HPLC-amino acid quantification of the extracted protein pellets revealed a tremendous inefficiency of the extraction methods, with a maximally 6.8% of the proteinaceous material being extracted in comparison with the protein content in the bulk soil. The composition of the proteomes extracted was analysed after SDS-PAGE and liquid chromatography coupled with electrospray-MS/MS. Chourey's method, based on boiling and DTT, yielded a high diversity of bacterial proteins and revealed differences in the community composition at the phylum level among the three Soils. The overall metabolic information obtained by both extraction methods was similar, but Chourey's method provided additionally valuable bio-geochemical insights which suggest an ecological adaptation of microbial communities from Semiarid Soils for carbon and nitrogen fixation. Biological significance Microbial communities inhabiting the soil perform critical reactions for the sustainability of the planet. At biochemical level, soil proteomics is starting to provide incipient insights into the microbial functionality of Soils. However, methodological comparisons are needed to assess which methods are more suitable. Precisely, such information under arid and Semiarid environments is missing. By using amino acid quantification of extracted proteomes and LC–MS/MS based proteomics, we provide a novel methodological evaluation of the functional, phylogenetic and bio-geochemical information obtained by three extraction methods in Semiarid Soils with distinct edaphic properties.
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can the labile carbon contribute to carbon immobilization in Semiarid Soils priming effects and microbial community dynamics
Soil Biology & Biochemistry, 2013Co-Authors: Felipe Bastida, Teresa Hernández, I F Torres, Petra Bombach, Hans H Richnow, Carlos GarcíaAbstract:Abstract Tracer experiments with isotopic-enriched carbon compounds can provide information regarding the carbon cycling in Semiarid Soils. We studied priming effects and microbial utilization of glucose as an example of bioavailable labile molecule in the carbon cycle of a Semiarid soil. The soil, which has low content of total organic carbon (5.0 g kg −1 ), was amended with U 13 C-glucose (99 atom %) at concentration of 75 μg C g −1 soil (LD) or 300 μg C g −1 soil (HD). Glucose-derived carbon remained in soil after two months of incubation. The percentage of residual carbon stabilized was greater in LD with 40% of the initial 13 C added compared to 30% of the initial 13 C added in the HD. Comparison of 13 C content in water- and sodium-pyrophosphate extracts pointed to a significant humification of up to 2.4% of the initial 13 C-glucose. Glucose was subjected to an intense mineralization in the first 17-days of 22.8% and 40.94% for the LD and HD, respectively. The stable isotope probing (SIP) of phospholipid fatty acids (PLFAs) by gas-chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) showed that bacteria dominated glucose metabolism in comparison to fungi. Gram-negative populations were initially more involved in glucose assimilation than Gram-positive bacteria. In the fatty acids fraction, up to 95% of the 13 C was predominantly found in fatty acids typical for Gram-negative bacteria. However, after 4 and 17 days the 13 C-enrichment in Gram-positive biomarkers increased. The mineralization of soil organic matter triggered by glucose additions was more intense in HD (3.6% of soil TOC) than LD (1.0% of soil TOC) and reached the highest level after 4 days in HD. Priming was controlled by Gram-negative populations but fungi and, particularly actinobacteria played an important role in latter steps. Our data indicated that the intense metabolism of SOM due to priming phenomena compromises the potential carbon sequestration in this Semiarid soil amended with glucose.
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Semiarid Soils submitted to severe drought stress influence on humic acid characteristics in organic amended Soils
Journal of Soils and Sediments, 2012Co-Authors: Sara Hueso, Teresa Hernández, Gennaro Brunetti, N Senesi, Karam Farrag, Carlos GarcíaAbstract:Purpose The objective of this work was to assess the effect of severe drought conditions on the characteristics of Semiarid soil humic acids (HAs) as well as the effect of organic amendment on such changes.
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influence of stability and origin of organic amendments on humification in Semiarid Soils
Soil Science Society of America Journal, 2011Co-Authors: Keiji Jindo, Teresa Hernández, Carlos García, Miguel Angel SanchezmonederoAbstract:Th e application of soil organic amendments is a widely accepted strategy to maintain soil fertility by maintaining and increasing the levels of soil organic matter. Th e objective of this study was to evaluate the eff ect of land application of organic wastes of diff erent sources and stabilization degrees on the soil organic matter humifi cation, measured by changes in the chemical and structural characteristics of humic and fulvic acids by cross-polarization magic angle spinning 13 C nuclear magnetic resonance (CPMAS 13 C-NMR) and Fourier-transform infrared (FT-IR) spectroscopy. A microcosm experiment lasting 360 d was performed with 500 g of a Semiarid soil amended with diff erent materials: sewage sludge from a wastewater treatment plant, composted sewage sludge, the organic fraction of municipal solid wastes, and composted municipal solid wastes. Th e addition of the organic amendments increased the amount of humic acids in the soil in all cases, whereas the amount of fulvic acids remained very similar to that of the control soil. Th e humic acids of the amended Soils were characterized by an enrichment of N and aromatic C compounds, along with carboxylic groups, which increased their aromatic and hydrophobic characteristics. Aft er the 360-d incubation, some of the labile compounds added with the organic amendments had been incorporated into the soil humic pool and protected from degradation, contributing to the buildup of soil organic matter. Land application of organic wastes represents a key waste management option in Semiarid regions where these materials can be used as an exogenous source of organic matter for soil rehabilitation.
C Garcia - One of the best experts on this subject based on the ideXlab platform.
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the extracellular metaproteome of Soils under Semiarid climate a methodological comparison of extraction buffers
Science of The Total Environment, 2018Co-Authors: Felipe Bastida, I F Torres, Nico Jehmlich, C GarciaAbstract:We compare the protein extraction efficiencies, as well as the phylogenetic and functional information provided, of two extraction protocols in Soils that differ mainly in their organic matter and clay contents, the main factors limiting protein extraction in Semiarid Soils. These protocols utilise extractants commonly used for the assay of extracellular enzyme activities. The first method was based on the utilisation of the modified universal buffer (MUB). The second was based on the extraction of humic substances with sodium pyrophosphate. When compared to the total amount of proteins in soil, the results indicate a very-low extraction efficiency for both protocols. Analysis in an Orbitrap Fusion mass spectrometer and further searching against an "ad hoc" metagenome evidenced that the phylogenetic and functional information retrieved from the extracellular soil metaproteome can be biased by the extraction buffer.
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the ecological and physiological responses of the microbial community from a Semiarid soil to hydrocarbon contamination and its bioremediation using compost amendment
Journal of Proteomics, 2016Co-Authors: Felipe Bastida, Teresa Hernández, Hans H Richnow, Nico Jehmlich, K Lima, Brandon E L Morris, M Von Bergen, C GarciaAbstract:The linkage between phylogenetic and functional processes may provide profound insights into the effects of hydrocarbon contamination and biodegradation processes in high-diversity environments. Here, the impacts of petroleum contamination and the bioremediation potential of compost amendment, as enhancer of the microbial activity in Semiarid Soils, were evaluated in a model experiment. The analysis of phospholipid fatty-acids (PLFAs) and metaproteomics allowed the study of biomass, phylogenetic and physiological responses of the microbial community in polluted Semiarid Soils. Petroleum pollution induced an increase of proteobacterial proteins during the contamination, while the relative abundance of Rhizobiales lowered in comparison to the non-contaminated soil. Despite only 0.55% of the metaproteome of the compost-treated soil was involved in biodegradation processes, the addition of compost promoted the removal of polycyclic aromatic hydrocarbons (PAHs) and alkanes up to 88% after 50 days. However, natural biodegradation of hydrocarbons was not significant in Soils without compost. Compost-assisted bioremediation was mainly driven by Sphingomonadales and uncultured bacteria that showed an increased abundance of catabolic enzymes such as catechol 2,3-dioxygenases, cis-dihydrodiol dehydrogenase and 2-hydroxymuconic semialdehyde. For the first time, metaproteomics revealed the functional and phylogenetic relationships of petroleum contamination in soil and the microbial key players involved in the compost-assisted bioremediation.
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the role of lignin and cellulose in the carbon cycling of degraded Soils under Semiarid climate and their relation to microbial biomass
Soil Biology & Biochemistry, 2014Co-Authors: I F Torres, T Hernandez, Felipe Bastida, Petra Bombach, Hans H Richnow, C GarciaAbstract:Abstract A high level of biological degradation is usually observed in Soils under Semiarid climate where the low inputs of vegetal debris constraint the development of microbiota. Among vegetal inputs, cellulose and lignin are dominant substrates but their assimilation by the microbial community of Semiarid Soils is yet not understood. In the present study, 13C-labeled cellulose and 13C-labeled lignin (75 μg 13C g−1 soil) were added to two Semiarid Soils with different properties and degradation level. Abanilla soil is a bare, highly degraded soil without plant cover growing on it and a total organic C content of 5.0 g kg−1; Santomera soil is covered by plants (20% coverage) based on xerophytic shrubs and has a total organic C content of 12.0 g kg−1. The fate of added carbon was evaluated by analysis of the carbon isotope signature of bulk soil-derived carbon and extractable carbon fractions (water and sodium-pyrophosphate extracts). At long-term (120 days), we observed that the stability of cellulose- and lignin-derived carbon was dependent on their chemical nature. The contribution of lignin-derived carbon to the pool of humic substances was higher than that of cellulose. However, at short-term (30 days), the mineralization of the added substrates was more related to the degradation level of Soils (i.e. microbial biomass). Stable isotope probing (SIP) of phospholipid fatty acids (PLFA-SIP) analysis revealed that just a minor part of the microbial community assimilated the carbon derived from cellulose and lignin. Moreover, the relative contribution of each microbial group to the assimilation of lignin-derived carbon was different in each soil.
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metaproteomics of Soils from Semiarid environment functional and phylogenetic information obtained with different protein extraction methods
Journal of Proteomics, 2014Co-Authors: Felipe Bastida, Teresa Hernández, C GarciaAbstract:Abstract Microbial populations fulfil a critical role in the soil sustainability and their functionality can be ascertained by proteomics based on high-performance mass spectrometry (MS) measurements. However, soil proteomics is compromised by methodological issues, among which extraction is a limiting factor, and still has not been adequately applied in Semiarid Soils, which usually are nutrient limited. We aim to evaluate the functional and phylogenetic information retrieved from three Semiarid Soils with distinct edaphic properties and degradation levels. Three extraction methods with different physico-chemical bases were tested [1–3]. The HPLC-amino acid quantification of the extracted protein pellets revealed a tremendous inefficiency of the extraction methods, with a maximally 6.8% of the proteinaceous material being extracted in comparison with the protein content in the bulk soil. The composition of the proteomes extracted was analysed after SDS-PAGE and liquid chromatography coupled with electrospray-MS/MS. Chourey's method, based on boiling and DTT, yielded a high diversity of bacterial proteins and revealed differences in the community composition at the phylum level among the three Soils. The overall metabolic information obtained by both extraction methods was similar, but Chourey's method provided additionally valuable bio-geochemical insights which suggest an ecological adaptation of microbial communities from Semiarid Soils for carbon and nitrogen fixation. Biological significance Microbial communities inhabiting the soil perform critical reactions for the sustainability of the planet. At biochemical level, soil proteomics is starting to provide incipient insights into the microbial functionality of Soils. However, methodological comparisons are needed to assess which methods are more suitable. Precisely, such information under arid and Semiarid environments is missing. By using amino acid quantification of extracted proteomes and LC–MS/MS based proteomics, we provide a novel methodological evaluation of the functional, phylogenetic and bio-geochemical information obtained by three extraction methods in Semiarid Soils with distinct edaphic properties.
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application of fresh and composted organic wastes modifies structure size and activity of soil microbial community under Semiarid climate
Applied Soil Ecology, 2008Co-Authors: Felipe Bastida, José L. Moreno, Ellen Kandeler, C Garcia, T HernandezAbstract:Abstract Although the application of organic amendments is considered a suitable tool for improving soil fertility, few studies have been conducted in Semiarid climates to evaluate the joint effect of such practice on the structure and function of the soil's microbial community. The aim of this work therefore was to make a comparative study of the effect of organic materials of differing degrees of stabilization (a sewage sludge and a compost made from the same) on the size, activity and structure of the microbial community in a Semiarid soil. In samples taken in spring, summer and autumn over a 2-year period we analysed parameters that indicate the size of the microbial community [microbial biomass C (MBC)], its general activity (ATP and respiration) and specific activity related to the N, P and C cycles in the soil (urease, phosphatase and β-glucosidase, respectively). Two years after the organic amendment, the structure of the microbial community was studied by analysing phospholipid fatty acids (PLFAs). At the end of the experiment, the MBC of the compost and sludge-treated Soils was 489 and 463 mg C mic kg −1 , respectively, while the MBC of the control Soils was 247 mg C mic kg −1 . Over the 2-year period, the higher β-glucosidase, urease and alkaline phosphatase activities of compost and sludge-treated Soils reflected higher substrate availability in these plots compared to the control plots. Indeed, plant abundance increased by about 25% with organic amendments. Whereas the bacterial to fungal ratio of signature PLFAs did not change, the ratio of monounsaturated/saturated and the ratio of Gram + /Gram − of the different treatments indicated that a different bacterial community developed 2 years after amendment with compost and sludge. Thus, factor analysis via PLFAs showed a change in microbial community structure in amended Soils versus control soil. It can be concluded that microbial biomass and activity of degraded Semiarid Soils can be improved by the addition of organic materials of differing degrees of stabilization (compost and sewage sludge). Compost-amended Soils showed the highest carbon contents, while in general no differences in activity or microbial biomass where found between compost or sludge treatments. Although phytotoxic substances in sewage sludge might negatively affect plant development, the similar density of plant cover developed in sludge and compost-treated Soils suggests that any phytotoxic substances had been degraded.
Sara Hueso - One of the best experts on this subject based on the ideXlab platform.
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Semiarid Soils submitted to severe drought stress influence on humic acid characteristics in organic amended Soils
Journal of Soils and Sediments, 2012Co-Authors: Sara Hueso, Teresa Hernández, Gennaro Brunetti, N Senesi, Karam Farrag, Carlos GarcíaAbstract:Purpose The objective of this work was to assess the effect of severe drought conditions on the characteristics of Semiarid soil humic acids (HAs) as well as the effect of organic amendment on such changes.
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resistance and resilience of the soil microbial biomass to severe drought in Semiarid Soils the importance of organic amendments
Applied Soil Ecology, 2011Co-Authors: Sara Hueso, Teresa Hernández, Carlos GarcíaAbstract:Abstract Changes in mean global air temperature and precipitation patterns, leading to longer drought periods and more extremely dry years, are predicted. The objective of this work was to assess whether a long period of severe drought can affect the growth and activity of the microbiota of a Semiarid soil, as well as the effect of organic amendments on soil resistance and resilience to this severe drought. A soil incubation experiment was carried out over 60 days, under controlled conditions (25 °C and 60/80% day/night relative humidity), with two treatments: unamended (US) and amended (AS) with manure compost (100 t ha−1). Two levels of irrigation were imposed: (1) well-watered (MUS and MAS), the soil being maintained at 60% of its water-holding capacity (WHC), and (2) dry, without irrigation (DUS and DAS). Then, a single level of irrigation was established for 37 days, dry Soils being irrigated under the same conditions than well-watered Soils, to assess soil resilience to this period of drought. Under well-watered conditions, the soil water-soluble nitrogen contents were 73 and 88% higher, the microbial biomass carbon 63 and 48% higher, alkaline phosphomonoesterase activity 46 and 32% higher, β-glucosidase activity 16 and 25% higher and urease activity 30 and 19% higher for the US and AS treatments, respectively, compared with the dry conditions at the end of the experimental period. Furthermore, the organic amendment helped the soil to retain moisture and encouraged the growth and activity of soil microbial populations. However, a 2-month drought seems insufficient to destroy the native microbial biomass in the arid soil used in this study, indicating that it is well adapted to adverse climate conditions. Thus, microbiological and biochemical parameters experienced a rapid recovery after soil rewetting, DUS and DAS showing values similar to MUS and MAS, after rewetting, highlighting the resilience of this type of soil against drought stress.
