Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome

Detalhes bibliográficos
Autor(a) principal: de Carvalho, Lucas Amoroso Lopes [UNESP]
Data de Publicação: 2021
Outros Autores: 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]
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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spelling 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)
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