The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils
Ano de defesa: | 2021 |
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Autor(a) principal: | |
Orientador(a): | |
Banca de defesa: | , , |
Tipo de documento: | Tese |
Tipo de acesso: | Acesso aberto |
Idioma: | eng |
Instituição de defesa: |
Universidade de São Paulo
|
Programa de Pós-Graduação: |
Agronomia (Microbiologia Agrícola)
|
Departamento: |
Não Informado pela instituição
|
País: |
BR
|
Link de acesso: | https://doi.org/10.11606/T.11.2021.tde-11102021-134636 |
Resumo: | Soil microbiome is essential for providing ecosystem services. The relationship between microbial diversity and ecosystem services is well elucidated for soil microbiome collective functions (i.e. organic matter decomposition and carbon assimilation). However, this relationship remains poorly understood for more specific functions (pesticides and o other xenobiotics degradation). Here, the dilution-to-extinction approach, radiorespirometry and high-throughput sequencing of 16S rRNA gene were used to assess the role of bacterial diversity depletion in the dissipation of antibiotic sulfadiazine (SDZ) and herbicide atrazine (ATZ), which are widely used in pig farming and agriculture, respectively. SDZ microcosm was assembled using paralel soils without (S1) and with (S2) a long-term of swine manure application. While the ATZ microcosm was assembled using Pasture Soil (GS, without long- term of ATZ application) and Cultivated Soil (CS, with long-term of ATZ application). Swine manure application promoted increases in pH and organic carbon and macronutrient contents, as well as impacted the soil bacterial community structure and diversity. The bacterial diversity depletion reduced SDZ mineralization (14C-CO2) and non-extractable residue (NER) formation, but NER recovered after 42 d of incubation. Surprisingly, the non-manured soil ( treatment NS- S1) had a faster SDZ dissipation rate (DT90 = 2.0 versus 21 d) and had a large number of bacterial families involved in the main SDZ dissipation pathways (14C-CO2 and mainly NER), such as Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_Subgroup_1, Micromonosporaceae and Sphingobacteriaceae. Similarly, land use and the long-term of atrazine application promoted changes in the soil physico-chemical attributes, bacterial community structure, diversity and composition, as well as in its capacity to dissipate atrazine. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes and Gemmatimonadetes were the dominant phyla in both soils (GS and CS). Atrazine minerazation was reduced by 12-fold when compared to the worst scenarios of bacterial diversity depletion. Long-term atrazine application resulted in greater bacterial community efficiency in herbicide dissipation. Bacterial diversity depletion reflected in the reduction of complexity, classification of species (specialists, generalists and very rare), in addition to increases in the abundance of functions related to obtaining energy and nitrogen transformations. Twelve bacterial genera (Ralstonia, Nitrospira, Hirschia, MND1, Candidatus_Koribacter, OM27_clade, Arenimonas, Occallatibacter, Bryobacter, UTBCD1, Ellin6067 and Crenobacter) correlated with atrazine mineralization, suggesting the selection of these genera as potential atrazine degraders. The NER formation was the SDZ primary dissipation route and had the greatest impact of the bacterial diversity depletion. While mineralization was the ATZ primary dissipation route in cultivated soil (CS). The bacterial diversity depletion resulted in simplified bacterial communities, greater imbalance in the niches occupation, as well as higher abundance of functions associated with obtaining energy. |
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info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesis The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils O papel da diversidade bacteriana na biodegradação de antibiótico e herbicida em solos agrícolas 2021-07-08Jussara Borges RegitanoGiselle Gomes Monteiro FracettoErika Valente de MedeirosTsai Siu MuiAdijailton José de SouzaUniversidade de São PauloAgronomia (Microbiologia Agrícola)USPBR Bacterial community Comunidade bacteriana Diluição para extinção Dilution-to-extinction Dissipação de pesticidas Pesticide dissipation S-triazinas S-triazines Sulfonamidas Sulfonamides Soil microbiome is essential for providing ecosystem services. The relationship between microbial diversity and ecosystem services is well elucidated for soil microbiome collective functions (i.e. organic matter decomposition and carbon assimilation). However, this relationship remains poorly understood for more specific functions (pesticides and o other xenobiotics degradation). Here, the dilution-to-extinction approach, radiorespirometry and high-throughput sequencing of 16S rRNA gene were used to assess the role of bacterial diversity depletion in the dissipation of antibiotic sulfadiazine (SDZ) and herbicide atrazine (ATZ), which are widely used in pig farming and agriculture, respectively. SDZ microcosm was assembled using paralel soils without (S1) and with (S2) a long-term of swine manure application. While the ATZ microcosm was assembled using Pasture Soil (GS, without long- term of ATZ application) and Cultivated Soil (CS, with long-term of ATZ application). Swine manure application promoted increases in pH and organic carbon and macronutrient contents, as well as impacted the soil bacterial community structure and diversity. The bacterial diversity depletion reduced SDZ mineralization (14C-CO2) and non-extractable residue (NER) formation, but NER recovered after 42 d of incubation. Surprisingly, the non-manured soil ( treatment NS- S1) had a faster SDZ dissipation rate (DT90 = 2.0 versus 21 d) and had a large number of bacterial families involved in the main SDZ dissipation pathways (14C-CO2 and mainly NER), such as Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_Subgroup_1, Micromonosporaceae and Sphingobacteriaceae. Similarly, land use and the long-term of atrazine application promoted changes in the soil physico-chemical attributes, bacterial community structure, diversity and composition, as well as in its capacity to dissipate atrazine. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes and Gemmatimonadetes were the dominant phyla in both soils (GS and CS). Atrazine minerazation was reduced by 12-fold when compared to the worst scenarios of bacterial diversity depletion. Long-term atrazine application resulted in greater bacterial community efficiency in herbicide dissipation. Bacterial diversity depletion reflected in the reduction of complexity, classification of species (specialists, generalists and very rare), in addition to increases in the abundance of functions related to obtaining energy and nitrogen transformations. Twelve bacterial genera (Ralstonia, Nitrospira, Hirschia, MND1, Candidatus_Koribacter, OM27_clade, Arenimonas, Occallatibacter, Bryobacter, UTBCD1, Ellin6067 and Crenobacter) correlated with atrazine mineralization, suggesting the selection of these genera as potential atrazine degraders. The NER formation was the SDZ primary dissipation route and had the greatest impact of the bacterial diversity depletion. While mineralization was the ATZ primary dissipation route in cultivated soil (CS). The bacterial diversity depletion resulted in simplified bacterial communities, greater imbalance in the niches occupation, as well as higher abundance of functions associated with obtaining energy. O microbioma do solo é essencial para o fornecimento de serviços ecossistêmicos. A relação entre diversidade microbiana e serviços ecossistêmicos é bem elucidada para funções coletivas do microbioma do solo (decomposição de matéria orgânica e assimilação de carbono). Contudo, esta relação ainda permanece pouco elucidada para funções mais específicas (degradação de pesticidas e outros xenobióticos). Aqui, foram utilizadas a abordagem da diluição para extinção, a radiorespirometria e o sequenciamento alto rendimento do gene 16S rRNA para avaliar o papel da depleção da diversidade bacteriana na dissipação do antibiótico sulfadiazina (SDZ) e herbicida atrazina (ATZ), que são amplamente usados na suinocultura e agricultura, respectivamente. O microcosmo da SDZ foi montado utilizando solos sem (S1) e com histórico de aplicação de esterco suíno (S2). Enquanto o microcosmo da ATZ foi montado usando Solo de Pastagem (GS, sem histórico de aplicação de ATZ) e Solo Cultivado (CS, com histórico de aplicação de ATZ). A aplicação de esterco promoveu aumentos no pH e nos teores de carbono orgânico e macronutrientes, bem como impactou a estrutura e diversidade da comunidade bacteriana do solo. A depleção da diversidade bacteriana reduziu a mineralização da SDZ (14C-CO2) e a formação de resíduo não extraível (NER), mas o NER se recuperou após 42 d de incubação. Surpreendentemente, o solo natural não adubado (NS-S1) apresentou taxa de dissipação da SDZ mais rápida (DT90 = 2.0 versus 21 d) e teve um grande número de famílias bacterianas envolvidas nas principais vias de dissipação da SDZ (14C-CO2 e principalmente NER), tais como Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_Subgroup_1, Micromonosporaceae e Sphingobacteriaceae. De forma similar, o uso da terra e longo período de aplicação da atrazina promoveu mudanças nos atributos físicos e químicos do solo, na estrutura, diversidade e composição da comunidade bacteriana, bem como em sua capacidade para dissipar a atrazina. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes e Gemmatimonadetes foram os filos dominantes ambos os solos (GS e CS). A mineralização da atrazina foi reduzida em 12 vezes quando comparada aos piores cenários de perda da diversidade bacteriana. O longo histórico de aplicação de atrazina resultou em maior eficiência da comunidade bacteriana na dissipação do herbicida. A perda da diversidade bacteriana refletiu na redução da complexidade, classificação das espécies (especialistas, generalistas e muito raras), além de aumentos na abundância de funções relacionadas à obtenção de transformações de energia e nitrogênio. Doze gêneros bacterianos (Ralstonia, Nitrospira, Hirschia, MND1, Candidatus_Koribacter, OM27_clade, Arenimonas, Occallatibacter, Bryobacter, UTBCD1, Ellin6067 e Crenobacter) se correlacionaram com a mineralização da atrazina, sugerindo a seleção desses gêneros como potenciais degradadores de atrazina. A formação de NER foi a rota primária de dissipação da SDZ e com maior impacto da depleção da diversidade bacteriana. Enquanto a mineralização foi a rota primária de dissipação da ATZ no solo cultivado (CS). A perda da diversidade bacteriana resultou em comunidades bacterianas simplificadas, maior desbalanço na ocupação de nichos, bem como maior abundância de funções associadas obtenção de energia. https://doi.org/10.11606/T.11.2021.tde-11102021-134636info:eu-repo/semantics/openAccessengreponame:Biblioteca Digital de Teses e Dissertações da USPinstname:Universidade de São Paulo (USP)instacron:USP2023-12-21T18:43:49Zoai:teses.usp.br:tde-11102021-134636Biblioteca Digital de Teses e Dissertaçõeshttp://www.teses.usp.br/PUBhttp://www.teses.usp.br/cgi-bin/mtd2br.plvirginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.bropendoar:27212021-10-14T13:07:02Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP)false |
dc.title.en.fl_str_mv |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils |
dc.title.alternative.pt.fl_str_mv |
O papel da diversidade bacteriana na biodegradação de antibiótico e herbicida em solos agrícolas |
title |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils |
spellingShingle |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils Adijailton José de Souza |
title_short |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils |
title_full |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils |
title_fullStr |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils |
title_full_unstemmed |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils |
title_sort |
The role of bacterial diversity on the antibiotic and herbicide biodegradation in agricultural soils |
author |
Adijailton José de Souza |
author_facet |
Adijailton José de Souza |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Jussara Borges Regitano |
dc.contributor.referee1.fl_str_mv |
Giselle Gomes Monteiro Fracetto |
dc.contributor.referee2.fl_str_mv |
Erika Valente de Medeiros |
dc.contributor.referee3.fl_str_mv |
Tsai Siu Mui |
dc.contributor.author.fl_str_mv |
Adijailton José de Souza |
contributor_str_mv |
Jussara Borges Regitano Giselle Gomes Monteiro Fracetto Erika Valente de Medeiros Tsai Siu Mui |
description |
Soil microbiome is essential for providing ecosystem services. The relationship between microbial diversity and ecosystem services is well elucidated for soil microbiome collective functions (i.e. organic matter decomposition and carbon assimilation). However, this relationship remains poorly understood for more specific functions (pesticides and o other xenobiotics degradation). Here, the dilution-to-extinction approach, radiorespirometry and high-throughput sequencing of 16S rRNA gene were used to assess the role of bacterial diversity depletion in the dissipation of antibiotic sulfadiazine (SDZ) and herbicide atrazine (ATZ), which are widely used in pig farming and agriculture, respectively. SDZ microcosm was assembled using paralel soils without (S1) and with (S2) a long-term of swine manure application. While the ATZ microcosm was assembled using Pasture Soil (GS, without long- term of ATZ application) and Cultivated Soil (CS, with long-term of ATZ application). Swine manure application promoted increases in pH and organic carbon and macronutrient contents, as well as impacted the soil bacterial community structure and diversity. The bacterial diversity depletion reduced SDZ mineralization (14C-CO2) and non-extractable residue (NER) formation, but NER recovered after 42 d of incubation. Surprisingly, the non-manured soil ( treatment NS- S1) had a faster SDZ dissipation rate (DT90 = 2.0 versus 21 d) and had a large number of bacterial families involved in the main SDZ dissipation pathways (14C-CO2 and mainly NER), such as Isosphaeraceae, Ktedonobacteraceae, Acidobacteriaceae_Subgroup_1, Micromonosporaceae and Sphingobacteriaceae. Similarly, land use and the long-term of atrazine application promoted changes in the soil physico-chemical attributes, bacterial community structure, diversity and composition, as well as in its capacity to dissipate atrazine. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes and Gemmatimonadetes were the dominant phyla in both soils (GS and CS). Atrazine minerazation was reduced by 12-fold when compared to the worst scenarios of bacterial diversity depletion. Long-term atrazine application resulted in greater bacterial community efficiency in herbicide dissipation. Bacterial diversity depletion reflected in the reduction of complexity, classification of species (specialists, generalists and very rare), in addition to increases in the abundance of functions related to obtaining energy and nitrogen transformations. Twelve bacterial genera (Ralstonia, Nitrospira, Hirschia, MND1, Candidatus_Koribacter, OM27_clade, Arenimonas, Occallatibacter, Bryobacter, UTBCD1, Ellin6067 and Crenobacter) correlated with atrazine mineralization, suggesting the selection of these genera as potential atrazine degraders. The NER formation was the SDZ primary dissipation route and had the greatest impact of the bacterial diversity depletion. While mineralization was the ATZ primary dissipation route in cultivated soil (CS). The bacterial diversity depletion resulted in simplified bacterial communities, greater imbalance in the niches occupation, as well as higher abundance of functions associated with obtaining energy. |
publishDate |
2021 |
dc.date.issued.fl_str_mv |
2021-07-08 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://doi.org/10.11606/T.11.2021.tde-11102021-134636 |
url |
https://doi.org/10.11606/T.11.2021.tde-11102021-134636 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Universidade de São Paulo |
dc.publisher.program.fl_str_mv |
Agronomia (Microbiologia Agrícola) |
dc.publisher.initials.fl_str_mv |
USP |
dc.publisher.country.fl_str_mv |
BR |
publisher.none.fl_str_mv |
Universidade de São Paulo |
dc.source.none.fl_str_mv |
reponame:Biblioteca Digital de Teses e Dissertações da USP instname:Universidade de São Paulo (USP) instacron:USP |
instname_str |
Universidade de São Paulo (USP) |
instacron_str |
USP |
institution |
USP |
reponame_str |
Biblioteca Digital de Teses e Dissertações da USP |
collection |
Biblioteca Digital de Teses e Dissertações da USP |
repository.name.fl_str_mv |
Biblioteca Digital de Teses e Dissertações da USP - Universidade de São Paulo (USP) |
repository.mail.fl_str_mv |
virginia@if.usp.br|| atendimento@aguia.usp.br||virginia@if.usp.br |
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1786376754986745856 |