Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome
Autor(a) principal: | |
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Data de Publicação: | 2021 |
Outros Autores: | , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.micres.2021.126866 http://hdl.handle.net/11449/222430 |
Resumo: | Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations. |
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Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiomeMetabarcodingMicrobial networkOrganic farmingSugarcane microbiomeSustainabilitySugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Laboratory of Bioinformatics Department of Agricultural and Environmental Biotechnology São Paulo State University (UNESP) School of Agricultural and Veterinary SciencesGraduate Program in Agricultural and Livestock Microbiology São Paulo State University (UNESP) School of Agricultural and Veterinary SciencesCenter for Molecular Biology and Genetic Engineering University of Campinas (UNICAMP)Genomics for Climate Change Research Center (GCCRC) University of Campinas (UNICAMP)Department of Genetics Evolution and Bioagents Institute of Biology University of Campinas (UNICAMP)Department of Botany and Ecology Federal University of Mato Grosso (UFMT), Av. Fernando Corrêa 2367Laboratory of Bioinformatics Department of Agricultural and Environmental Biotechnology São Paulo State University (UNESP) School of Agricultural and Veterinary SciencesGraduate Program in Agricultural and Livestock Microbiology São Paulo State University (UNESP) School of Agricultural and Veterinary SciencesFAPESP: 2017/09008-5Universidade Estadual Paulista (UNESP)Universidade Estadual de Campinas (UNICAMP)Federal University of Mato Grosso (UFMT)de Carvalho, Lucas Amoroso Lopes [UNESP]Teheran-Sierra, Luis Guillermo [UNESP]Funnicelli, Michelli Inácio Gonçalves [UNESP]da Silva, Rafael Correia [UNESP]Campanari, Maria Fernanda Zaneli [UNESP]de Souza, Rafael Soares CorreaArruda, PauloSoares, Marcos AntônioPinheiro, Daniel Guariz [UNESP]2022-04-28T19:44:41Z2022-04-28T19:44:41Z2021-11-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.micres.2021.126866Microbiological Research, v. 252.0944-5013http://hdl.handle.net/11449/22243010.1016/j.micres.2021.1268662-s2.0-85115038158Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengMicrobiological Researchinfo:eu-repo/semantics/openAccess2022-04-28T19:44:41Zoai:repositorio.unesp.br:11449/222430Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T21:19:51.264164Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome |
title |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome |
spellingShingle |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome de Carvalho, Lucas Amoroso Lopes [UNESP] Metabarcoding Microbial network Organic farming Sugarcane microbiome Sustainability |
title_short |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome |
title_full |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome |
title_fullStr |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome |
title_full_unstemmed |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome |
title_sort |
Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome |
author |
de Carvalho, Lucas Amoroso Lopes [UNESP] |
author_facet |
de Carvalho, Lucas Amoroso Lopes [UNESP] Teheran-Sierra, Luis Guillermo [UNESP] Funnicelli, Michelli Inácio Gonçalves [UNESP] da Silva, Rafael Correia [UNESP] Campanari, Maria Fernanda Zaneli [UNESP] de Souza, Rafael Soares Correa Arruda, Paulo Soares, Marcos Antônio Pinheiro, Daniel Guariz [UNESP] |
author_role |
author |
author2 |
Teheran-Sierra, Luis Guillermo [UNESP] Funnicelli, Michelli Inácio Gonçalves [UNESP] da Silva, Rafael Correia [UNESP] Campanari, Maria Fernanda Zaneli [UNESP] de Souza, Rafael Soares Correa Arruda, Paulo Soares, Marcos Antônio Pinheiro, Daniel Guariz [UNESP] |
author2_role |
author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) Universidade Estadual de Campinas (UNICAMP) Federal University of Mato Grosso (UFMT) |
dc.contributor.author.fl_str_mv |
de Carvalho, Lucas Amoroso Lopes [UNESP] Teheran-Sierra, Luis Guillermo [UNESP] Funnicelli, Michelli Inácio Gonçalves [UNESP] da Silva, Rafael Correia [UNESP] Campanari, Maria Fernanda Zaneli [UNESP] de Souza, Rafael Soares Correa Arruda, Paulo Soares, Marcos Antônio Pinheiro, Daniel Guariz [UNESP] |
dc.subject.por.fl_str_mv |
Metabarcoding Microbial network Organic farming Sugarcane microbiome Sustainability |
topic |
Metabarcoding Microbial network Organic farming Sugarcane microbiome Sustainability |
description |
Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations. |
publishDate |
2021 |
dc.date.none.fl_str_mv |
2021-11-01 2022-04-28T19:44:41Z 2022-04-28T19:44:41Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.micres.2021.126866 Microbiological Research, v. 252. 0944-5013 http://hdl.handle.net/11449/222430 10.1016/j.micres.2021.126866 2-s2.0-85115038158 |
url |
http://dx.doi.org/10.1016/j.micres.2021.126866 http://hdl.handle.net/11449/222430 |
identifier_str_mv |
Microbiological Research, v. 252. 0944-5013 10.1016/j.micres.2021.126866 2-s2.0-85115038158 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Microbiological Research |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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1808129310296375296 |