Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.

Detalhes bibliográficos
Autor(a) principal: LAMMEL, D. R.
Data de Publicação: 2018
Outros Autores: BARTH, G., OVASKAINEN, O., CRUZ, L. M., ZANATTA, J. A., RYO, M., SOUZA, E. M. de, PEDROSA, F. O.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1099575
Resumo: Background: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to ?spillover effects? on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. Results: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical?chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Conclusions: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and ?spillover effects? of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.
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spelling Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.Sub-tropical soil16S rRNAIllumina sequencingEcologia microbianaSolo sub tropicalPhBactériaQuímica do SoloMicrobial ecologySoil chemistryArchaeaBackground: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to ?spillover effects? on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. Results: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical?chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Conclusions: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and ?spillover effects? of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.Daniel R. Lammel, UFPR; Gabriel Barth, ABC Research Foundation; Otso Ovaskainen, University of Helsinki; Leonardo M. Cruz, UFPR; JOSILEIA ACORDI ZANATTA, CNPF; Masahiro Ryo, 3Freie Universität Berlin and Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB); Emanuel M. de Souza, UFPR; Fábio O. Pedrosa, UFPR.LAMMEL, D. R.BARTH, G.OVASKAINEN, O.CRUZ, L. M.ZANATTA, J. A.RYO, M.SOUZA, E. M. dePEDROSA, F. O.2018-11-22T00:48:49Z2018-11-22T00:48:49Z2018-11-1920182019-02-22T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleMicrobiome, v. 6, article 106, June 2018. 13 p.http://www.alice.cnptia.embrapa.br/alice/handle/doc/109957510.1186/s40168-018-0482-8enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2018-11-22T00:48:56Zoai:www.alice.cnptia.embrapa.br:doc/1099575Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542018-11-22T00:48:56falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542018-11-22T00:48:56Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
title Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
spellingShingle Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
LAMMEL, D. R.
Sub-tropical soil
16S rRNA
Illumina sequencing
Ecologia microbiana
Solo sub tropical
Ph
Bactéria
Química do Solo
Microbial ecology
Soil chemistry
Archaea
title_short Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
title_full Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
title_fullStr Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
title_full_unstemmed Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
title_sort Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures.
author LAMMEL, D. R.
author_facet LAMMEL, D. R.
BARTH, G.
OVASKAINEN, O.
CRUZ, L. M.
ZANATTA, J. A.
RYO, M.
SOUZA, E. M. de
PEDROSA, F. O.
author_role author
author2 BARTH, G.
OVASKAINEN, O.
CRUZ, L. M.
ZANATTA, J. A.
RYO, M.
SOUZA, E. M. de
PEDROSA, F. O.
author2_role author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Daniel R. Lammel, UFPR; Gabriel Barth, ABC Research Foundation; Otso Ovaskainen, University of Helsinki; Leonardo M. Cruz, UFPR; JOSILEIA ACORDI ZANATTA, CNPF; Masahiro Ryo, 3Freie Universität Berlin and Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB); Emanuel M. de Souza, UFPR; Fábio O. Pedrosa, UFPR.
dc.contributor.author.fl_str_mv LAMMEL, D. R.
BARTH, G.
OVASKAINEN, O.
CRUZ, L. M.
ZANATTA, J. A.
RYO, M.
SOUZA, E. M. de
PEDROSA, F. O.
dc.subject.por.fl_str_mv Sub-tropical soil
16S rRNA
Illumina sequencing
Ecologia microbiana
Solo sub tropical
Ph
Bactéria
Química do Solo
Microbial ecology
Soil chemistry
Archaea
topic Sub-tropical soil
16S rRNA
Illumina sequencing
Ecologia microbiana
Solo sub tropical
Ph
Bactéria
Química do Solo
Microbial ecology
Soil chemistry
Archaea
description Background: pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to ?spillover effects? on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarely investigated. Usually, pH also co-varies with some confounding factors, such as land use, soil management (e.g., tillage and chemical inputs), plant cover, and/or edapho-climatic conditions. So, a more comprehensive analysis of the direct and indirect effects of pH brings a better understanding of the mechanisms driving prokaryotic (archaeal and bacterial) community structures. Results: We evaluated an agricultural soil pH gradient (from 4 to 6, the typical range for tropical farms), in a liming gradient with confounding factors minimized, investigating relationships between prokaryotic communities (16S rRNA) and physical?chemical parameters (indirect effects). Correlations, hierarchical modeling of species communities (HMSC), and random forest (RF) modeling indicated that both direct and indirect effects of the pH gradient affected the prokaryotic communities. Some OTUs were more affected by the pH changes (e.g., some Actinobacteria), while others were more affected by the indirect pH effects (e.g., some Proteobacteria). HMSC detected a phylogenetic signal related to the effects. Both HMSC and RF indicated that the main indirect effect was the pH changes on the availability of some elements (e.g., Al, Fe, and Cu), and secondarily, effects on plant growth and nutrient cycling also affected the OTUs. Additionally, we found that some of the OTUs that responded to pH also correlated with CO2, CH4, and N2O greenhouse gas fluxes. Conclusions: Our results indicate that there are two distinct pH-related mechanisms driving prokaryotic community structures, the direct effect and ?spillover effects? of pH (indirect effects). Moreover, the indirect effects are highly relevant for some OTUs and consequently for the community structure; therefore, it is a mechanism that should be further investigated in microbial ecology.
publishDate 2018
dc.date.none.fl_str_mv 2018-11-22T00:48:49Z
2018-11-22T00:48:49Z
2018-11-19
2018
2019-02-22T11:11:11Z
dc.type.driver.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv Microbiome, v. 6, article 106, June 2018. 13 p.
http://www.alice.cnptia.embrapa.br/alice/handle/doc/1099575
10.1186/s40168-018-0482-8
identifier_str_mv Microbiome, v. 6, article 106, June 2018. 13 p.
10.1186/s40168-018-0482-8
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/1099575
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.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron:EMBRAPA
instname_str Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
instacron_str EMBRAPA
institution EMBRAPA
reponame_str Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
collection Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
repository.name.fl_str_mv Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
repository.mail.fl_str_mv cg-riaa@embrapa.br
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