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Seasonal dynamics alters taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands

, , , , , ,
1 Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa, São Gabriel, Brazil
2 Soil Department, “Luiz de Queiroz” College of Agriculture, Piracicaba, Brazil
3 Soil Department, Universidade Federal de Santa Maria, Santa Maria, Brazil
4 Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual da Agricultura, Pecuária e Irrigação, São Gabriel, Brazil
5 Department of Microbiology and Cell Science, University of Florida, Gainesville, United States
DOI
10.7287/peerj.preprints.26569v1
Published
Accepted
Subject Areas
Agricultural Science, Biodiversity, Bioinformatics, Ecology, Microbiology
Keywords
metatranscriptomics, 16S rRNA gene, abiotic factors, metataxonomics, seasons, soil microbial core, Ion Torrent PGM, NGS, subtropical ecosystems
Copyright
© 2018 Barboza et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Barboza A, Pylro VS, Jacques R, Gubiani P, Trindade J, Triplett E, Roesch L. 2018. Seasonal dynamics alters taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands. PeerJ Preprints 6:e26569v1

Abstract

Soil microbial communities’ assembly is strongly tied to changes in temperature and moisture. Although microbial functional redundancy seems to overcome taxonomical composition changes, the sensitivity and resilience of soil microbial communities from subtropical regions in response to seasonal variations are still poorly understood. Thus, the development of new strategies for biodiversity conservation and sustainable management require a complete understanding of the soil abiotic process involved in the selection of microbial taxa and functions. In this work, we used state of the art molecular methodologies (Next Generation Sequencing) to compare the taxonomic (metataxonomics) and functional (metatranscriptomics) profiles among soil samples from two subtropical natural grasslands located in the Pampa biome, Brazil, in response to short-term seasonal variations. We found consistent effects of season on both microbial community structure and functions, but with the former being more influenced than the latter. These variations were more related to the oscillation in the relative abundances of specific taxa along seasons, rather than extinction and recolonization of taxa along seasons. In conclusion, the most abundant microbial groups and functions were shared between seasons and locations reflecting the existence of a stable taxonomical and functional core microbiota.

Author Comment

This is a submission to PeerJ for review.

Supplemental Information

Table S1. Location, soil taxonomy and soil physicochemistry analysis for two grasslands located in Santa Maria and São Gabriel municipalities

(1) Extracted with Mehlich-1. (2) Extracted with KCl 1 mol L-1. (3) Walkey & Black method. (4) Extracted with hot water. (5) Pipet method.

DOI: 10.7287/peerj.preprints.26569v1/supp-1

Table S2. Sequencing coverage for 16S rRNA (taxa) and mRNA (function) libraries derived from two grasslands located in Santa Maria and São Gabriel municipalities

SM = Santa Maria municipality; SG = São Gabriel municipality.

DOI: 10.7287/peerj.preprints.26569v1/supp-2

raw data figure 1

raw data figure 1

DOI: 10.7287/peerj.preprints.26569v1/supp-3

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Anthony Barboza conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Victor S Pylro conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Rodrigo Jacques conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Paulo Gubiani conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Júlio Trindade conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Eric Triplett conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Luiz Roesch conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

Raw sequences obtained by metatranscriptome sequencing and associated metadata were submitted to MG-RAST server (http://metagenomics.anl.gov/) and are public available under the string mgp12046. All raw sequences obtained by amplicon sequencing were submitted to NCBI Sequence Read Archive (SRA) and are available under the experiment number SRX2779549 run number SRR5499445.

Data Deposition

The following information was supplied regarding data availability:

The raw data/code is included in the manuscript (in the section 2.5. Bioinformatics analysis and statistics).

Funding

The authors acknowledge Dra. Manoeli Lupatini for taking soil samples from the Santa Maria site. We also like to thank the Fundação Estadual a Pesquisa Agropecuária do Estado do Rio Grande do Sul (FEPAGRO) for providing the experimental area for sampling in São Gabriel. This study was funded by the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Pesquisa do Rio Grande do Sul (FAPERGS) and by the Brazilian Microbiome Project (http://www.brmicrobiome.org). VSP receives fellowship from FAPESP (Process number 2016/02219-8). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Seasonal dynamics alters taxonomical and functional microbial profiles in Pampa biome soils under natural grasslands
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