Carlos Garbisu - Academia.edu (original) (raw)
Papers by Carlos Garbisu
Fuzzy logic is a suitable mathematical tool to treat data affected by uncertainty and inaccuracy ... more Fuzzy logic is a suitable mathematical tool to treat data affected by uncertainty and inaccuracy and to combine different subjective judgments in a joint assessment. For this reason, it is especially useful for the design of indexes addressed to assess with rigor the environmental quality from different points of view. This work proposes a new index for the evaluation of the dynamic quality of agricultural soil from a biological point of view (SQIBIO). It was designed according to a previously developed methodology based on fuzzy logic (Peche and Rodríguez, 2012). It allows the assessment of the biological changes induced in the soil by its use and/or management as well as by pollution.
Química Nova
ANTIOXIDATIVE RESPONSE, PHYTOCHELATIN PRODUCTION AND PHOTOPROTECTIVE PIGMENTS COMPOSITION OF Brac... more ANTIOXIDATIVE RESPONSE, PHYTOCHELATIN PRODUCTION AND PHOTOPROTECTIVE PIGMENTS COMPOSITION OF Brachiaria decumbens Stapf PLANTS EXPOSED TO Cd AND Zn. In order to evaluate the response of Brachiaria decumbens Stapf to Cd and Zn, plants were hydroponically exposed to 50 and 100 mu mol L-1 of Cd and 500 and 2000 mmol L-1 of Zn. Metal content of shoots and roots was determined, as well as alterations in photosynthetic and photoprotective pigments, antioxidant metabolites and phytochelatin synthesis. Plants concentrated elevated levels of Cd and Zn, especially in roots. Zinc exposure negatively affected chlorophyll and beta-carotene content, whereas the highest dose of Cd reduced VAZ cycle pigments and tocopherol levels in plant shoots. Cadmium was the maximum inducer of the phytochelatin synthesis pathway.
The intense mining activity in La Unión-Cartagena (Murcia, SE Spain) has given rise to highly con... more The intense mining activity in La Unión-Cartagena (Murcia, SE Spain) has given rise to highly contaminated soils with very unfavourable conditions, most of them without a vegetal cover to protect from erosion. A two-year field phytostabilisation experiment was carried out in a mine spoil soil contaminated with trace elements (pH 6.2; Zn 9686; Pb 10188; Cu 193; Cd 19; As 664 mg kg- 1). Three amendments were applied: olive mill-waste compost (60 t ha-1), pig slurry (60 m3 ha-1) and hydrated lime (2.3 t ha-1); and a native halophytic shrub (Atriplex halimus L.) was planted, leaving subplots without plants. In order to evaluate the efficiency of the phytostabilisation process for soil remediation, plant growth, soil pH, trace elements availability and microbial parameters with potential as indicators of soil health were analised at the end of the experiment. The amendments did not substantially modify metal availability in the soil and both organic amendments stimulated the growth of A....
Spanish Journal of Agricultural Research, 2012
Phytophthora root and crown rot is a plant disease responsible for important economic losses in p... more Phytophthora root and crown rot is a plant disease responsible for important economic losses in protected pepper crops. A greenhouse experiment was carried out in a temperate climate region (northern Spain) to assess the effects of repeated biodisinfection after three consecutive crop seasons with different organic amendments (a non-composted mixture of sheep manure and chicken litter, a semicomposted mixture of horse manure and chicken litter, Brassica carinata dehydrated pellets plus Sinapis alba fresh green manure) on disease incidence, crop yield and soil quality. Biodisinfection treatments were found to improve soil water properties through reduction in soil bulk density and increased water infiltration. Biodisinfested soils showed higher values of physicochemical and microbial properties than control (untreated) and plastic-mulched soils. In plots treated with the non-composted or semicomposted mixture, the observed higher levels of microbial activity were strongly related with an increase in soil microbial biomass. Brassica-Sinapis treatment had a weaker effect on soil properties than animal manure-based treatments. However, highest counts of total bacteria, actinomycetes and Pseudomonas spp. were found in Brassica-Sinapis-treated soils. It was concluded that repeated biodisinfection for the control of Phytophthora root and crown rot in protected pepper crops located in temperate climate regions can improve soil quality and suppressiveness, as well as allow for a reduction in the dose of organic amendment needed for biodisinfection. Among the studied organic amendments, the semicomposted amendment was the best option in terms of reduction in disease incidence.
Biodegradation, 1998
We have studied the reduction of hexavalent chromium (chromate) to the less toxic trivalent form ... more We have studied the reduction of hexavalent chromium (chromate) to the less toxic trivalent form by using cell suspensions and cell-free extracts from the common soil bacterium, Bacillus subtilis. B. subtilis was able to grow and reduce chromate at concentrations ranging from 0.1 to 1 mM K2CrO4. Chromate reduction was not affected by a 20-fold excess of nitrate-compound that serves as alternate electron acceptor and antagonizes chromate reduction by anaerobic bacteria. Metabolic poisons including sodium azide and sodium cyanide inhibited chromate reduction. Reduction was effected by a constitutive system associated with the soluble protein fraction and not with the membrane fraction. The reducing activity was heat labile and showed a Km of 188 microns CrO4(2)-. The reductase can mediate the transfer of electrons from NAD(P)H to chromate. The results suggest that chromate is reduced via a detoxification system rather than dissimilatory electron transport.
Microbiología (Madrid, Spain), 1997
Ten bacterial strains were isolated from the activated sludge waste treatment system (BIOX) at th... more Ten bacterial strains were isolated from the activated sludge waste treatment system (BIOX) at the Exxon refinery in Benicia, California. Half of these isolates could be grown in minimal medium. When tested for selenite detoxification capability, these five isolates (members of the genera Bacillus, Pseudomonas, Enterobacter and Aeromonas), were capable of detoxifying selenite with kinetics similar to those of a well characterized Bacillus subtilis strain (168 Trp+) studied previously. The selenite detoxification phenotype of the Exxon isolates was stable to repeated transfer on culture media which did not contain selenium. Microorganisms isolated from the Exxon BIOX reactor were capable of detoxifying selenite. Treatability studies using the whole BIOX microbial community were also carried out to evaluate substrates for their ability to support growth and selenite bioremediation. Under the appropriate conditions, indigenous microbial communities are capable of remediating selenite i...
BioFactors (Oxford, England), 1995
We have demonstrated that the common soil bacterium, Bacillus subtilis, reduces selenite to an in... more We have demonstrated that the common soil bacterium, Bacillus subtilis, reduces selenite to an insoluble and much less toxic product--the red form of elemental selenium. Reduction was effected by an inducible system that appears to deposit elemental selenium between the cell wall and the plasma membrane. Glucose and sucrose supported selenite reduction. Although malate and citrate supported growth, no significant reduction of selenite occurred, indicating the importance of the redox state of the culture substrate. Selenite reduction in the millimolar concentration range (i.e., cultures supplemented with 1 mM selenite) was not affected by a ten-fold excess of nitrate or sulfate--compounds that serve as alternate electron acceptors and antagonize selenite reduction by anaerobic bacteria. Similarly, nitrite and sulfite did not significantly affect the rate or extent of selenite reduction. B.subtilis was able to grow and produce selenium (Se degree) at selenite concentrations ranging fr...
FEMS Microbiology Ecology, 2014
Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity... more Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination.
International Journal of Phytoremediation, 2014
Phytostabilization is a promising option for the remediation of metal contaminated soils which re... more Phytostabilization is a promising option for the remediation of metal contaminated soils which requires the implementation of long-term monitoring programs. We here propose to incorporate the paradigm of "adaptive monitoring", which enables monitoring programs to evolve iteratively as new information emerges and research questions change, to metal phytostabilization. Posing good questions that cover the chemical, toxicological and ecological concerns associated to metal contaminated soils is critical for an efficient long-term phytostabilization monitoring program. Regarding the ecological concerns, soil microbial parameters are most valuable indicators of the effectiveness of metal phytostabilization processes in terms of recovery of soil health. We suggest to group soil microbial parameters in higher-level categories such as "ecological attributes" (vigor, organization, stability) or "ecosystem services" in order to facilitate interpretation and, most importantly, to provide long-term phytostabilization monitoring programs with the required stability through time against changes in techniques, methods, interests, etc. that will inevitably occur during the monitoring program. Finally, a Phytostabilization Monitoring Card, based on both ecological attributes and ecosystem services, for soil microbial properties is provided.
Soil Biology, 2009
... of Remediation Efficiency Lur Epelde, José Ma Becerril, Itziar Alkorta, and Carlos Garbisu ..... more ... of Remediation Efficiency Lur Epelde, José Ma Becerril, Itziar Alkorta, and Carlos Garbisu ... 2002). The technical aspects of phytoremediation, together with the advantages and limitations of this technology, have been extensively reviewed elsewhere (Chaney et al. ...
Cell Biology and Toxicology, 2015
The molecular response of Pseudomonas fluorescens cells exposed to a mixture of heavy metals rema... more The molecular response of Pseudomonas fluorescens cells exposed to a mixture of heavy metals remains largely unknown. Here, we studied the temporal changes in the early gene expression of P. fluorescens cells exposed to three doses of a polymetallic solution over two exposure times, through the application of a customized cDNA microarray. At the lowest metal dose (MD/4), we observed a repression of the Hsp70 chaperone system, MATE and MFS transporters, TonB membrane transporter and histidine kinases, together with an overexpression of metal transport (ChaC, CopC), chemotaxis and glutamine synthetase genes. At the intermediate metal dose (MD), several amino acid transporters, a response regulator (CheY), a TonBdependent receptor and the mutT DNA repair gene were repressed; by contrast, an overexpression of genes associated with the antioxidative stress system and the transport of chelates and sulfur was observed. Finally, at the highest metal dose (4MD), a repression of genes encoding metal ion transporters, drug resistance and alginate biosynthesis was found, together with an overexpression of genes encoding antioxidative proteins, membrane transporters, ribosomal proteins, chaperones and proteases. It was concluded that P. fluorescens cells showed, over exposure time, a highly complex molecular response when exposed to a polymetallic solution, involving mechanisms related with chemotaxis, signal transmission, membrane transport, cellular redox state, and the regulation of transcription and ribosomal activity.
Reviews on Environmental Health, 2002
Fuzzy logic is a suitable mathematical tool to treat data affected by uncertainty and inaccuracy ... more Fuzzy logic is a suitable mathematical tool to treat data affected by uncertainty and inaccuracy and to combine different subjective judgments in a joint assessment. For this reason, it is especially useful for the design of indexes addressed to assess with rigor the environmental quality from different points of view. This work proposes a new index for the evaluation of the dynamic quality of agricultural soil from a biological point of view (SQIBIO). It was designed according to a previously developed methodology based on fuzzy logic (Peche and Rodríguez, 2012). It allows the assessment of the biological changes induced in the soil by its use and/or management as well as by pollution.
Química Nova
ANTIOXIDATIVE RESPONSE, PHYTOCHELATIN PRODUCTION AND PHOTOPROTECTIVE PIGMENTS COMPOSITION OF Brac... more ANTIOXIDATIVE RESPONSE, PHYTOCHELATIN PRODUCTION AND PHOTOPROTECTIVE PIGMENTS COMPOSITION OF Brachiaria decumbens Stapf PLANTS EXPOSED TO Cd AND Zn. In order to evaluate the response of Brachiaria decumbens Stapf to Cd and Zn, plants were hydroponically exposed to 50 and 100 mu mol L-1 of Cd and 500 and 2000 mmol L-1 of Zn. Metal content of shoots and roots was determined, as well as alterations in photosynthetic and photoprotective pigments, antioxidant metabolites and phytochelatin synthesis. Plants concentrated elevated levels of Cd and Zn, especially in roots. Zinc exposure negatively affected chlorophyll and beta-carotene content, whereas the highest dose of Cd reduced VAZ cycle pigments and tocopherol levels in plant shoots. Cadmium was the maximum inducer of the phytochelatin synthesis pathway.
The intense mining activity in La Unión-Cartagena (Murcia, SE Spain) has given rise to highly con... more The intense mining activity in La Unión-Cartagena (Murcia, SE Spain) has given rise to highly contaminated soils with very unfavourable conditions, most of them without a vegetal cover to protect from erosion. A two-year field phytostabilisation experiment was carried out in a mine spoil soil contaminated with trace elements (pH 6.2; Zn 9686; Pb 10188; Cu 193; Cd 19; As 664 mg kg- 1). Three amendments were applied: olive mill-waste compost (60 t ha-1), pig slurry (60 m3 ha-1) and hydrated lime (2.3 t ha-1); and a native halophytic shrub (Atriplex halimus L.) was planted, leaving subplots without plants. In order to evaluate the efficiency of the phytostabilisation process for soil remediation, plant growth, soil pH, trace elements availability and microbial parameters with potential as indicators of soil health were analised at the end of the experiment. The amendments did not substantially modify metal availability in the soil and both organic amendments stimulated the growth of A....
Spanish Journal of Agricultural Research, 2012
Phytophthora root and crown rot is a plant disease responsible for important economic losses in p... more Phytophthora root and crown rot is a plant disease responsible for important economic losses in protected pepper crops. A greenhouse experiment was carried out in a temperate climate region (northern Spain) to assess the effects of repeated biodisinfection after three consecutive crop seasons with different organic amendments (a non-composted mixture of sheep manure and chicken litter, a semicomposted mixture of horse manure and chicken litter, Brassica carinata dehydrated pellets plus Sinapis alba fresh green manure) on disease incidence, crop yield and soil quality. Biodisinfection treatments were found to improve soil water properties through reduction in soil bulk density and increased water infiltration. Biodisinfested soils showed higher values of physicochemical and microbial properties than control (untreated) and plastic-mulched soils. In plots treated with the non-composted or semicomposted mixture, the observed higher levels of microbial activity were strongly related with an increase in soil microbial biomass. Brassica-Sinapis treatment had a weaker effect on soil properties than animal manure-based treatments. However, highest counts of total bacteria, actinomycetes and Pseudomonas spp. were found in Brassica-Sinapis-treated soils. It was concluded that repeated biodisinfection for the control of Phytophthora root and crown rot in protected pepper crops located in temperate climate regions can improve soil quality and suppressiveness, as well as allow for a reduction in the dose of organic amendment needed for biodisinfection. Among the studied organic amendments, the semicomposted amendment was the best option in terms of reduction in disease incidence.
Biodegradation, 1998
We have studied the reduction of hexavalent chromium (chromate) to the less toxic trivalent form ... more We have studied the reduction of hexavalent chromium (chromate) to the less toxic trivalent form by using cell suspensions and cell-free extracts from the common soil bacterium, Bacillus subtilis. B. subtilis was able to grow and reduce chromate at concentrations ranging from 0.1 to 1 mM K2CrO4. Chromate reduction was not affected by a 20-fold excess of nitrate-compound that serves as alternate electron acceptor and antagonizes chromate reduction by anaerobic bacteria. Metabolic poisons including sodium azide and sodium cyanide inhibited chromate reduction. Reduction was effected by a constitutive system associated with the soluble protein fraction and not with the membrane fraction. The reducing activity was heat labile and showed a Km of 188 microns CrO4(2)-. The reductase can mediate the transfer of electrons from NAD(P)H to chromate. The results suggest that chromate is reduced via a detoxification system rather than dissimilatory electron transport.
Microbiología (Madrid, Spain), 1997
Ten bacterial strains were isolated from the activated sludge waste treatment system (BIOX) at th... more Ten bacterial strains were isolated from the activated sludge waste treatment system (BIOX) at the Exxon refinery in Benicia, California. Half of these isolates could be grown in minimal medium. When tested for selenite detoxification capability, these five isolates (members of the genera Bacillus, Pseudomonas, Enterobacter and Aeromonas), were capable of detoxifying selenite with kinetics similar to those of a well characterized Bacillus subtilis strain (168 Trp+) studied previously. The selenite detoxification phenotype of the Exxon isolates was stable to repeated transfer on culture media which did not contain selenium. Microorganisms isolated from the Exxon BIOX reactor were capable of detoxifying selenite. Treatability studies using the whole BIOX microbial community were also carried out to evaluate substrates for their ability to support growth and selenite bioremediation. Under the appropriate conditions, indigenous microbial communities are capable of remediating selenite i...
BioFactors (Oxford, England), 1995
We have demonstrated that the common soil bacterium, Bacillus subtilis, reduces selenite to an in... more We have demonstrated that the common soil bacterium, Bacillus subtilis, reduces selenite to an insoluble and much less toxic product--the red form of elemental selenium. Reduction was effected by an inducible system that appears to deposit elemental selenium between the cell wall and the plasma membrane. Glucose and sucrose supported selenite reduction. Although malate and citrate supported growth, no significant reduction of selenite occurred, indicating the importance of the redox state of the culture substrate. Selenite reduction in the millimolar concentration range (i.e., cultures supplemented with 1 mM selenite) was not affected by a ten-fold excess of nitrate or sulfate--compounds that serve as alternate electron acceptors and antagonize selenite reduction by anaerobic bacteria. Similarly, nitrite and sulfite did not significantly affect the rate or extent of selenite reduction. B.subtilis was able to grow and produce selenium (Se degree) at selenite concentrations ranging fr...
FEMS Microbiology Ecology, 2014
Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity... more Toxicity of metals released from mine tailings may cause severe damage to ecosystems. A diversity of microorganisms, however, have successfully adapted to such sites. In this study, our objective was to advance the understanding of the indigenous microbial communities of mining-impacted soils. To this end, a metatranscriptomic approach was used to study a heavily metal-contaminated site along a metal concentration gradient (up to 3220 000 and 97 000 mg kg(-1) of Cd, Pb and Zn, respectively) resulting from previous mining. Metal concentration, soil pH and amount of clay were the most important factors determining the structure of soil microbial communities. Interestingly, evenness of the microbial communities, but not its richness, increased with contamination level. Taxa with high metabolic plasticity like Ktedonobacteria and Chloroflexi were found with higher relative abundance in more contaminated samples. However, several taxa belonging to the phyla Actinobacteria and Acidobacteria followed opposite trends in relation to metal pollution. Besides, functional transcripts related to transposition or transfer of genetic material and membrane transport, potentially involved in metal resistance mechanisms, had a higher expression in more contaminated samples. Our results provide an insight into microbial communities in long-term metal-contaminated environments and how they contrast to nearby sites with lower contamination.
International Journal of Phytoremediation, 2014
Phytostabilization is a promising option for the remediation of metal contaminated soils which re... more Phytostabilization is a promising option for the remediation of metal contaminated soils which requires the implementation of long-term monitoring programs. We here propose to incorporate the paradigm of "adaptive monitoring", which enables monitoring programs to evolve iteratively as new information emerges and research questions change, to metal phytostabilization. Posing good questions that cover the chemical, toxicological and ecological concerns associated to metal contaminated soils is critical for an efficient long-term phytostabilization monitoring program. Regarding the ecological concerns, soil microbial parameters are most valuable indicators of the effectiveness of metal phytostabilization processes in terms of recovery of soil health. We suggest to group soil microbial parameters in higher-level categories such as "ecological attributes" (vigor, organization, stability) or "ecosystem services" in order to facilitate interpretation and, most importantly, to provide long-term phytostabilization monitoring programs with the required stability through time against changes in techniques, methods, interests, etc. that will inevitably occur during the monitoring program. Finally, a Phytostabilization Monitoring Card, based on both ecological attributes and ecosystem services, for soil microbial properties is provided.
Soil Biology, 2009
... of Remediation Efficiency Lur Epelde, José Ma Becerril, Itziar Alkorta, and Carlos Garbisu ..... more ... of Remediation Efficiency Lur Epelde, José Ma Becerril, Itziar Alkorta, and Carlos Garbisu ... 2002). The technical aspects of phytoremediation, together with the advantages and limitations of this technology, have been extensively reviewed elsewhere (Chaney et al. ...
Cell Biology and Toxicology, 2015
The molecular response of Pseudomonas fluorescens cells exposed to a mixture of heavy metals rema... more The molecular response of Pseudomonas fluorescens cells exposed to a mixture of heavy metals remains largely unknown. Here, we studied the temporal changes in the early gene expression of P. fluorescens cells exposed to three doses of a polymetallic solution over two exposure times, through the application of a customized cDNA microarray. At the lowest metal dose (MD/4), we observed a repression of the Hsp70 chaperone system, MATE and MFS transporters, TonB membrane transporter and histidine kinases, together with an overexpression of metal transport (ChaC, CopC), chemotaxis and glutamine synthetase genes. At the intermediate metal dose (MD), several amino acid transporters, a response regulator (CheY), a TonBdependent receptor and the mutT DNA repair gene were repressed; by contrast, an overexpression of genes associated with the antioxidative stress system and the transport of chelates and sulfur was observed. Finally, at the highest metal dose (4MD), a repression of genes encoding metal ion transporters, drug resistance and alginate biosynthesis was found, together with an overexpression of genes encoding antioxidative proteins, membrane transporters, ribosomal proteins, chaperones and proteases. It was concluded that P. fluorescens cells showed, over exposure time, a highly complex molecular response when exposed to a polymetallic solution, involving mechanisms related with chemotaxis, signal transmission, membrane transport, cellular redox state, and the regulation of transcription and ribosomal activity.
Reviews on Environmental Health, 2002