Innovative approaches to understand complex microbial communities for

GIULIETTI, AM; FLOCCO, CG; MERINI, LJ; CUADRADO, V

2002-11-01/2005-10-30

Biotecnología ambiental

Rec.Nat.Renov.-Conservacion y preservacion

The primary objective of ACCESS has been to generate and establish the knowledge base for the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy. primary objective of ACCESS has been to generate and establish the knowledge base for the eco-engineering of soil ecosystems polluted with herbicides, atrazine, 2,4-D, and their derivatives. This was proposed to be achieved by 1) the detailed physical, chemical and microbiological characterization of herbicide contaminated agricultural soils; 2) the design and optimization of molecular methods to study changes in gene expression of the responses to stress in microbial isolates and communities, the changes in diversity and catabolic performance of complex microbial communities; 3) extension of the knowledge base of microbial capabilities for degrading the target compounds and the influences on degradation through community interactions; 4) evaluation, with newly developed tools and methods, of the factors that positively affect biodegradation by microbial communities in microcosms of increasing complexity, including plant-microbe interactions and 5) design of knowledgebased farming practices to more actively reduce pollution caused by organochlorine herbicides. To reach the objectives, experimental areas in Chile and Argentina were chosen based upon the applied agricultural practice. Monitoring tools were optimized with a special emphasis on molecular biology diagnostics. DNA extraction procedures were adapted to the soil types under study and a new RNA extraction method for agricultural soils rich in humic acids was developed. Nucleic acid profiling and sequencing methods were optimized and applied for rapid assessments of microbial community structure and function and a prototype phylogenybased DNA array system was developed for identifying individual members of complex communities. Catabolic gene profiling methods were developedand applied, to assess their diversity under changing environmental conditions. Dedicated DNA arrays were developed and successfully applied, to assess the effects of stress caused by substrate addition on the general physiological status of soil bacteria. An in silico system was established to simulate the degradation of any given compound through the global biodegradation network. Advanced molecular diagnostic tools in combination with accurate analytic determinations were applied, to evaluate the effects of environmental stress factors, specifically herbicides, on microbial community composition and degradation performance in different experimental systems ranging from pure cultures and consortia, soil microcosms, including plant microcosms and field studies. New isolates capable of degrading the target herbicides were obtained, specifically simazine degrading isolates were identified to be promising candidates for bioaugmentation. Soil microcosms of different complexities were shown to be useful tools for analyzing the degradation of herbicides, the effectiveness of bioaugmentation procedures, the catabolic potential of microbial communities and the changes in bacterial communities after herbicide exposure. Overall, the project developed a variety of new molecular tools which focused on assessing community and catabolic gene structure and gene expression, as well as linking biodegradation to host physiology. A multifaceted approach at the different scales of complexity succeeded in generating a knowledge base which can be applicable for the eco-engineering of sites polluted with atrazine, 2,4-D, and their derivatives. Information on new molecular tools has been published or is in the process of being published. The Meta-Router web page is available to the general public. All partners are available for consultancy.