Soil – Microbiome – Contaminant Interactions: Pre and Post Remediation of Chromated Copper Arsenate Contaminated Soil

Stacie Tardif

Soil – Microbiome – Contaminant Interactions: Pre and Post Remediation of Chromated Copper Arsenate Contaminated Soil

Stacie Tardif

Abstract

Soil contamination with trace elements is a major global threat to soil quality and ecosystem functioning. Its impact on soil microorganisms and the critical processes they undergo remains a challenge to predict under natural field conditions. Soil remediation aims to not only reduce contaminant toxicity in soil, but also to improve overall soil quality. Yet, few studies investigate microbial recovery following soil remediation, particularly when employing harsher remediation technologies such as soil washing with chemical ligands. To better predict the response and recovery of microbial communities in these complex soil systems, a comprehensive understanding of the interplay between soil-microbe-contaminant is needed. This can be achieved by using an integrative multi-disciplinary approach that combines soil chemistry, microbial ecology and multivariate statistics. To this end, this PhD thesis aims to infer specific effects of multi-element contaminatio n on soil bacterial communities in the field and to assess the recovery of the soil microbiome after remediation. Additionally, we evaluated the ability of the soil microbiome to function as an ecological indicator of soil quality before and after remediation. Chromated copper arsenate (CCA) contaminated sites, a by-product of the wood impregnation industry, were used as a multi-element contamination model system of global relevance. First, in Manuscript I, we characterized the chemical composition of soil at a heterogeneous CCA contaminated field site and established a contamination gradient with highly variable soil edaphic factors. The distribution of Cr, Cu and As amongst different soil solid phases was assessed using an advanced sequential extraction method called CISED – Chemometric Identification of Substrates and Element Distributions. This study demonstrated that, even after long-term ageing, Cu and As were associated with readily available phases in soil, constituting the highest potential ecological risk. Furthermore, pH was identified as the most important factor affecting the distribution of all three elements in soil, with other element-specific effects in evidence. This study further demonstrated that bioavailable Cu, as determined with a bacterial bioreporter, could not be modelled using sequential extractions. As such, we suggested that receptor-specific tests of bioavailability are required to complement chemical tests in risk assessments. In Manuscript II, we characterized soil bacterial community abundance (16S rRNA gene copy number), structure, both at the taxonomic (16S rRNA amplicon sequencing) and functional group level (high-throughput quantitative PCR quantification of 90 functional genes), and function (bacterial growth activity) along this CCA contamination gradient. Further, a trait-based approach with pollution-induced community tolerance (PICT) was applied to infer causal effects of Cr, Cu and As on these community attributes in the presence of strong confoing factors such as pH and soilorganic matter. This study revealed strong Cu, and possibly As, filtering of soil bacterial communities, whereas Cr displayed negligible effects. We showed that CCA contamination caused a shift in community composition and identified a marked increase in potential bioindicator taxa such as Chloroflexi and Bacilli, which may have sophisticated survival strategies. Despite signs of adaptation in the communities, toxic legacy effects persisted as shown by decreased bacterial and functional diversity, as well as reduced bacterial growth activity. In Manuscript III, we assessed the ability of coarse- and fine-grain biochar, and zero-valent ironamendments to improve soil quality of CCA contaminated soil from the gradient. A soil quality TRIAD approach was employed to evaluate the efficiency of these amendments, which integrates tests from soil chemistry (total, water-extractable and bioavailable fractions of elements), ecotoxicology (bioluminescence inhibition assay) and ecology (bacterial growth activity). This study demonstrated that the combination of fine-grain biochar and zero-valent iron showed promise as an effective and low-cost in-situ stabilization strategy for CCA contaminated soil. This approach also led to the highest ecological recovery and significant reduction in water-extractable concentration of Cr, Cu and As by 45, 45 and 43%, respectively. In Manuscript IV, we determined the recovery of the microbiome after soil washing with a tailor-made group of organic ligands (melanoidins) as compared with ethylenediaminetetraacetic acid(EDTA), and assessed the effect of biochar as a follow-up treatment. Using non-contaminated and CCA contaminated soil from the CCA gradient, we monitored bacterial community composition and diversity (16S rRNA gene amplicon sequencing), abundance (16S rRNA copy number), growth activity, and tolerance to As and Cu (PICT) after 30 and 100 days. This study demonstrated that soil washing imposed stringent conditions on soil microbes, and as such, only a modest recovery on growth, abundance and diversity soil occurred. The relative abundance of certain bioindicator taxa (Chloroflexi and Bacilli) that were specifically associated with CCA contamination in Manuscript II were reduced, but even after significant reduction of Cu toxicity, bacterial community structure remained similar to the community composition in the original CCA contaminated soil. Furthermore, biochar was central to the modest recovery detected in bacterial communities, and hence, demonstrates the importance of post soil washing treatments. Collectively, results presented in this thesis brings new insights on the interactions between soilmicrobiome- contamination, pre and post remediation of aged CCA contaminated soils.

Originalsprog	Engelsk

Forlag	Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen
Status	Udgivet - 2019

Adgang til dokumentet

PhD-STardifForlagets udgivne version, 15,7 MB

https://rex.kb.dk/permalink/f/h35n6k/KGL01012062025

Andre filer og links

Sign in to request a library copy

Citationsformater

@phdthesis{c6bbe84da40240538b615a3928f3b669,

title = "Soil – Microbiome – Contaminant Interactions: Pre and Post Remediation of Chromated Copper Arsenate Contaminated Soil",

abstract = "Soil contamination with trace elements is a major global threat to soil quality and ecosystem functioning. Its impact on soil microorganisms and the critical processes they undergo remains a challenge to predict under natural field conditions. Soil remediation aims to not only reduce contaminant toxicity in soil, but also to improve overall soil quality. Yet, few studies investigate microbial recovery following soil remediation, particularly when employing harsher remediation technologies such as soil washing with chemical ligands. To better predict the response and recovery of microbial communities in these complex soil systems, a comprehensive understanding of the interplay between soil-microbe-contaminant is needed. This can be achieved by using an integrative multi-disciplinary approach that combines soil chemistry, microbial ecology and multivariate statistics. To this end, this PhD thesis aims to infer specific effects of multi-element contaminatio n on soil bacterial communities in the field and to assess the recovery of the soil microbiome after remediation. Additionally, we evaluated the ability of the soil microbiome to function as an ecological indicator of soil quality before and after remediation. Chromated copper arsenate (CCA) contaminated sites, a by-product of the wood impregnation industry, were used as a multi-element contamination model system of global relevance. First, in Manuscript I, we characterized the chemical composition of soil at a heterogeneous CCA contaminated field site and established a contamination gradient with highly variable soil edaphic factors. The distribution of Cr, Cu and As amongst different soil solid phases was assessed using an advanced sequential extraction method called CISED – Chemometric Identification of Substrates and Element Distributions. This study demonstrated that, even after long-term ageing, Cu and As were associated with readily available phases in soil, constituting the highest potential ecological risk. Furthermore, pH was identified as the most important factor affecting the distribution of all three elements in soil, with other element-specific effects in evidence. This study further demonstrated that bioavailable Cu, as determined with a bacterial bioreporter, could not be modelled using sequential extractions. As such, we suggested that receptor-specific tests of bioavailability are required to complement chemical tests in risk assessments. In Manuscript II, we characterized soil bacterial community abundance (16S rRNA gene copy number), structure, both at the taxonomic (16S rRNA amplicon sequencing) and functional group level (high-throughput quantitative PCR quantification of 90 functional genes), and function (bacterial growth activity) along this CCA contamination gradient. Further, a trait-based approach with pollution-induced community tolerance (PICT) was applied to infer causal effects of Cr, Cu and As on these community attributes in the presence of strong confoing factors such as pH and soilorganic matter. This study revealed strong Cu, and possibly As, filtering of soil bacterial communities, whereas Cr displayed negligible effects. We showed that CCA contamination caused a shift in community composition and identified a marked increase in potential bioindicator taxa such as Chloroflexi and Bacilli, which may have sophisticated survival strategies. Despite signs of adaptation in the communities, toxic legacy effects persisted as shown by decreased bacterial and functional diversity, as well as reduced bacterial growth activity. In Manuscript III, we assessed the ability of coarse- and fine-grain biochar, and zero-valent ironamendments to improve soil quality of CCA contaminated soil from the gradient. A soil quality TRIAD approach was employed to evaluate the efficiency of these amendments, which integrates tests from soil chemistry (total, water-extractable and bioavailable fractions of elements), ecotoxicology (bioluminescence inhibition assay) and ecology (bacterial growth activity). This study demonstrated that the combination of fine-grain biochar and zero-valent iron showed promise as an effective and low-cost in-situ stabilization strategy for CCA contaminated soil. This approach also led to the highest ecological recovery and significant reduction in water-extractable concentration of Cr, Cu and As by 45, 45 and 43%, respectively. In Manuscript IV, we determined the recovery of the microbiome after soil washing with a tailor-made group of organic ligands (melanoidins) as compared with ethylenediaminetetraacetic acid(EDTA), and assessed the effect of biochar as a follow-up treatment. Using non-contaminated and CCA contaminated soil from the CCA gradient, we monitored bacterial community composition and diversity (16S rRNA gene amplicon sequencing), abundance (16S rRNA copy number), growth activity, and tolerance to As and Cu (PICT) after 30 and 100 days. This study demonstrated that soil washing imposed stringent conditions on soil microbes, and as such, only a modest recovery on growth, abundance and diversity soil occurred. The relative abundance of certain bioindicator taxa (Chloroflexi and Bacilli) that were specifically associated with CCA contamination in Manuscript II were reduced, but even after significant reduction of Cu toxicity, bacterial community structure remained similar to the community composition in the original CCA contaminated soil. Furthermore, biochar was central to the modest recovery detected in bacterial communities, and hence, demonstrates the importance of post soil washing treatments. Collectively, results presented in this thesis brings new insights on the interactions between soilmicrobiome- contamination, pre and post remediation of aged CCA contaminated soils.",

author = "Stacie Tardif",

year = "2019",

language = "English",

publisher = "Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen",

}

TY - BOOK

T1 - Soil – Microbiome – Contaminant Interactions

T2 - Pre and Post Remediation of Chromated Copper Arsenate Contaminated Soil

AU - Tardif, Stacie

PY - 2019

Y1 - 2019

N2 - Soil contamination with trace elements is a major global threat to soil quality and ecosystem functioning. Its impact on soil microorganisms and the critical processes they undergo remains a challenge to predict under natural field conditions. Soil remediation aims to not only reduce contaminant toxicity in soil, but also to improve overall soil quality. Yet, few studies investigate microbial recovery following soil remediation, particularly when employing harsher remediation technologies such as soil washing with chemical ligands. To better predict the response and recovery of microbial communities in these complex soil systems, a comprehensive understanding of the interplay between soil-microbe-contaminant is needed. This can be achieved by using an integrative multi-disciplinary approach that combines soil chemistry, microbial ecology and multivariate statistics. To this end, this PhD thesis aims to infer specific effects of multi-element contaminatio n on soil bacterial communities in the field and to assess the recovery of the soil microbiome after remediation. Additionally, we evaluated the ability of the soil microbiome to function as an ecological indicator of soil quality before and after remediation. Chromated copper arsenate (CCA) contaminated sites, a by-product of the wood impregnation industry, were used as a multi-element contamination model system of global relevance. First, in Manuscript I, we characterized the chemical composition of soil at a heterogeneous CCA contaminated field site and established a contamination gradient with highly variable soil edaphic factors. The distribution of Cr, Cu and As amongst different soil solid phases was assessed using an advanced sequential extraction method called CISED – Chemometric Identification of Substrates and Element Distributions. This study demonstrated that, even after long-term ageing, Cu and As were associated with readily available phases in soil, constituting the highest potential ecological risk. Furthermore, pH was identified as the most important factor affecting the distribution of all three elements in soil, with other element-specific effects in evidence. This study further demonstrated that bioavailable Cu, as determined with a bacterial bioreporter, could not be modelled using sequential extractions. As such, we suggested that receptor-specific tests of bioavailability are required to complement chemical tests in risk assessments. In Manuscript II, we characterized soil bacterial community abundance (16S rRNA gene copy number), structure, both at the taxonomic (16S rRNA amplicon sequencing) and functional group level (high-throughput quantitative PCR quantification of 90 functional genes), and function (bacterial growth activity) along this CCA contamination gradient. Further, a trait-based approach with pollution-induced community tolerance (PICT) was applied to infer causal effects of Cr, Cu and As on these community attributes in the presence of strong confoing factors such as pH and soilorganic matter. This study revealed strong Cu, and possibly As, filtering of soil bacterial communities, whereas Cr displayed negligible effects. We showed that CCA contamination caused a shift in community composition and identified a marked increase in potential bioindicator taxa such as Chloroflexi and Bacilli, which may have sophisticated survival strategies. Despite signs of adaptation in the communities, toxic legacy effects persisted as shown by decreased bacterial and functional diversity, as well as reduced bacterial growth activity. In Manuscript III, we assessed the ability of coarse- and fine-grain biochar, and zero-valent ironamendments to improve soil quality of CCA contaminated soil from the gradient. A soil quality TRIAD approach was employed to evaluate the efficiency of these amendments, which integrates tests from soil chemistry (total, water-extractable and bioavailable fractions of elements), ecotoxicology (bioluminescence inhibition assay) and ecology (bacterial growth activity). This study demonstrated that the combination of fine-grain biochar and zero-valent iron showed promise as an effective and low-cost in-situ stabilization strategy for CCA contaminated soil. This approach also led to the highest ecological recovery and significant reduction in water-extractable concentration of Cr, Cu and As by 45, 45 and 43%, respectively. In Manuscript IV, we determined the recovery of the microbiome after soil washing with a tailor-made group of organic ligands (melanoidins) as compared with ethylenediaminetetraacetic acid(EDTA), and assessed the effect of biochar as a follow-up treatment. Using non-contaminated and CCA contaminated soil from the CCA gradient, we monitored bacterial community composition and diversity (16S rRNA gene amplicon sequencing), abundance (16S rRNA copy number), growth activity, and tolerance to As and Cu (PICT) after 30 and 100 days. This study demonstrated that soil washing imposed stringent conditions on soil microbes, and as such, only a modest recovery on growth, abundance and diversity soil occurred. The relative abundance of certain bioindicator taxa (Chloroflexi and Bacilli) that were specifically associated with CCA contamination in Manuscript II were reduced, but even after significant reduction of Cu toxicity, bacterial community structure remained similar to the community composition in the original CCA contaminated soil. Furthermore, biochar was central to the modest recovery detected in bacterial communities, and hence, demonstrates the importance of post soil washing treatments. Collectively, results presented in this thesis brings new insights on the interactions between soilmicrobiome- contamination, pre and post remediation of aged CCA contaminated soils.

AB - Soil contamination with trace elements is a major global threat to soil quality and ecosystem functioning. Its impact on soil microorganisms and the critical processes they undergo remains a challenge to predict under natural field conditions. Soil remediation aims to not only reduce contaminant toxicity in soil, but also to improve overall soil quality. Yet, few studies investigate microbial recovery following soil remediation, particularly when employing harsher remediation technologies such as soil washing with chemical ligands. To better predict the response and recovery of microbial communities in these complex soil systems, a comprehensive understanding of the interplay between soil-microbe-contaminant is needed. This can be achieved by using an integrative multi-disciplinary approach that combines soil chemistry, microbial ecology and multivariate statistics. To this end, this PhD thesis aims to infer specific effects of multi-element contaminatio n on soil bacterial communities in the field and to assess the recovery of the soil microbiome after remediation. Additionally, we evaluated the ability of the soil microbiome to function as an ecological indicator of soil quality before and after remediation. Chromated copper arsenate (CCA) contaminated sites, a by-product of the wood impregnation industry, were used as a multi-element contamination model system of global relevance. First, in Manuscript I, we characterized the chemical composition of soil at a heterogeneous CCA contaminated field site and established a contamination gradient with highly variable soil edaphic factors. The distribution of Cr, Cu and As amongst different soil solid phases was assessed using an advanced sequential extraction method called CISED – Chemometric Identification of Substrates and Element Distributions. This study demonstrated that, even after long-term ageing, Cu and As were associated with readily available phases in soil, constituting the highest potential ecological risk. Furthermore, pH was identified as the most important factor affecting the distribution of all three elements in soil, with other element-specific effects in evidence. This study further demonstrated that bioavailable Cu, as determined with a bacterial bioreporter, could not be modelled using sequential extractions. As such, we suggested that receptor-specific tests of bioavailability are required to complement chemical tests in risk assessments. In Manuscript II, we characterized soil bacterial community abundance (16S rRNA gene copy number), structure, both at the taxonomic (16S rRNA amplicon sequencing) and functional group level (high-throughput quantitative PCR quantification of 90 functional genes), and function (bacterial growth activity) along this CCA contamination gradient. Further, a trait-based approach with pollution-induced community tolerance (PICT) was applied to infer causal effects of Cr, Cu and As on these community attributes in the presence of strong confoing factors such as pH and soilorganic matter. This study revealed strong Cu, and possibly As, filtering of soil bacterial communities, whereas Cr displayed negligible effects. We showed that CCA contamination caused a shift in community composition and identified a marked increase in potential bioindicator taxa such as Chloroflexi and Bacilli, which may have sophisticated survival strategies. Despite signs of adaptation in the communities, toxic legacy effects persisted as shown by decreased bacterial and functional diversity, as well as reduced bacterial growth activity. In Manuscript III, we assessed the ability of coarse- and fine-grain biochar, and zero-valent ironamendments to improve soil quality of CCA contaminated soil from the gradient. A soil quality TRIAD approach was employed to evaluate the efficiency of these amendments, which integrates tests from soil chemistry (total, water-extractable and bioavailable fractions of elements), ecotoxicology (bioluminescence inhibition assay) and ecology (bacterial growth activity). This study demonstrated that the combination of fine-grain biochar and zero-valent iron showed promise as an effective and low-cost in-situ stabilization strategy for CCA contaminated soil. This approach also led to the highest ecological recovery and significant reduction in water-extractable concentration of Cr, Cu and As by 45, 45 and 43%, respectively. In Manuscript IV, we determined the recovery of the microbiome after soil washing with a tailor-made group of organic ligands (melanoidins) as compared with ethylenediaminetetraacetic acid(EDTA), and assessed the effect of biochar as a follow-up treatment. Using non-contaminated and CCA contaminated soil from the CCA gradient, we monitored bacterial community composition and diversity (16S rRNA gene amplicon sequencing), abundance (16S rRNA copy number), growth activity, and tolerance to As and Cu (PICT) after 30 and 100 days. This study demonstrated that soil washing imposed stringent conditions on soil microbes, and as such, only a modest recovery on growth, abundance and diversity soil occurred. The relative abundance of certain bioindicator taxa (Chloroflexi and Bacilli) that were specifically associated with CCA contamination in Manuscript II were reduced, but even after significant reduction of Cu toxicity, bacterial community structure remained similar to the community composition in the original CCA contaminated soil. Furthermore, biochar was central to the modest recovery detected in bacterial communities, and hence, demonstrates the importance of post soil washing treatments. Collectively, results presented in this thesis brings new insights on the interactions between soilmicrobiome- contamination, pre and post remediation of aged CCA contaminated soils.

UR - https://rex.kb.dk/permalink/f/h35n6k/KGL01012062025

M3 - Ph.D. thesis

BT - Soil – Microbiome – Contaminant Interactions

PB - Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen

ER -