16S rRNA metabarcoding data and analysis code from throughfall and soil samples in a Neotropical forest (Ubatuba, São Paulo, Brazil)

Version 2.0

Pereira, Tháles Augusto Coralli; Becker, Carlos Guilherme; Buttimer, Shannon Marie; Hidalgo Martinez, Kelly Johanna; Lemos, Leandro Nascimento; Oliveira, Valeria Maia de; Andreote, Fernando Dini; Dini-Andreote, Francisco; Romero, Gustavo Quevedo, 2026, "16S rRNA metabarcoding data and analysis code from throughfall and soil samples in a Neotropical forest (Ubatuba, São Paulo, Brazil)", https://doi.org/10.25824/redu/H2WXZN, Repositório de Dados de Pesquisa da Unicamp, V2

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Description	This repository contains processed data and analysis code associated with a 16S rRNA gene metabarcoding study of bacterial communities in throughfall water (rainwater passing through the forest canopy) and soil samples collected in a Neotropical forest in Ubatuba, São Paulo, Brazil. The dataset was generated to investigate how epiphytic tank bromeliads influence soil bacterial community structure and microbial functioning via canopy–soil coupling mediated by throughfall. Throughfall and soil samples were collected in field conditions and processed using eDNA metabarcoding targeting the 16S rRNA gene (V4 region), following the Illumina Amplicon Protocol from the Earth Microbiome Project. Sequence data were processed using QIIME 2, with denoising and amplicon sequence variant (ASV) inference performed using DADA2, and taxonomic assignment conducted with a Naive Bayes classifier trained on the SILVA 138 database. The repository includes ASV tables, taxonomic classifications, and associated metadata. In addition to sequencing data, this repository provides R scripts used for downstream analyses, including diversity metrics (alpha and beta diversity), ordination analyses (PCoA), redundancy analysis (RDA), and structural equation modeling (piecewise SEM). Soil chemical variables (e.g., pH, organic matter, and nutrients) and microbial functional indicators—such as microbial biomass carbon, soil respiration, and β-glucosidase activity—were integrated into the analytical framework as well. The data cannot be made publicly available due to intellectual property protection restrictions. For additional information, please contact the corresponding authors.
Subject	Earth and Environmental Sciences
Keyword	Soil biology, Soil microbial communities, Throughfall bacteria, Soil bacteria, Epiphytes, Neotropical forests, Tropical ecology
Related Publication	Epiphytic Tank Bromeliads in Tropical Forests: Unveiling their Role for Seedling and Soil Bacterial Communities Through Stable Isotopes and Metagenomics (Bromélias-Tanque Epífitas em Florestas Tropicais: Desvendando seu Papel para Comunidades de Plântulas e de Bactérias no Solo via Isótopos Estáveis e Metagenômica)
Notes	Data associated with the doctoral thesis: Epiphytic Tank Bromeliads in Tropical Forests: Unveiling their Role for Seedling and Soil Bacterial Communities Through Stable Isotopes and Metagenomics (Bromélias-Tanque Epífitas em Florestas Tropicais: Desvendando seu Papel para Comunidades de Plântulas e de Bactérias no Solo via Isótopos Estáveis e Metagenômica). Instituto de Biologia, Universidade Estadual de Campinas, 2025. Por motivos de propriedade intelectual, a tese será publicada um ano após sua defesa.
License/Data Use Agreement	CC BY-NC 4.0


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Persistent Identifier	doi:10.25824/redu/H2WXZN
Publication Date	2026-03-04
Title	16S rRNA metabarcoding data and analysis code from throughfall and soil samples in a Neotropical forest (Ubatuba, São Paulo, Brazil)
Alternative URL	https://doi.org/10.6084/m9.figshare.c.7678838
Author	Pereira, Tháles Augusto Coralli (Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia.) - ORCID: https://orcid.org/0000-0002-4999-8604 Becker, Carlos Guilherme - ORCID: https://orcid.org/0000-0002-5122-8238 Buttimer, Shannon Marie - ORCID: https://orcid.org/0000-0002-4128-5482 Hidalgo Martinez, Kelly Johanna (Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia.) - ORCID: https://orcid.org/0000-0003-4607-3750 Lemos, Leandro Nascimento (Universidade Estadual de Campinas (UNICAMP). Centro Nacional de Pesquisa em Energia e Materiais.) - ORCID: https://orcid.org/0000-0002-0898-568X Oliveira, Valeria Maia de (Universidade Estadual de Campinas (UNICAMP). Centro Nacional de Pesquisa em Energia e Materiais.) - ORCID: https://orcid.org/0000-0001-8817-4758 Andreote, Fernando Dini (Universidade de São Paulo (USP).) - ORCID: https://orcid.org/0000-0002-9883-9968 Dini-Andreote, Francisco - ORCID: https://orcid.org/0000-0002-6654-0769 Romero, Gustavo Quevedo (Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia.) - ORCID: https://orcid.org/0000-0003-3736-4759
Point of Contact	Use email button above to contact. Romero, Gustavo Quevedo (Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia.)
Description	This repository contains processed data and analysis code associated with a 16S rRNA gene metabarcoding study of bacterial communities in throughfall water (rainwater passing through the forest canopy) and soil samples collected in a Neotropical forest in Ubatuba, São Paulo, Brazil. The dataset was generated to investigate how epiphytic tank bromeliads influence soil bacterial community structure and microbial functioning via canopy–soil coupling mediated by throughfall. Throughfall and soil samples were collected in field conditions and processed using eDNA metabarcoding targeting the 16S rRNA gene (V4 region), following the Illumina Amplicon Protocol from the Earth Microbiome Project. Sequence data were processed using QIIME 2, with denoising and amplicon sequence variant (ASV) inference performed using DADA2, and taxonomic assignment conducted with a Naive Bayes classifier trained on the SILVA 138 database. The repository includes ASV tables, taxonomic classifications, and associated metadata. In addition to sequencing data, this repository provides R scripts used for downstream analyses, including diversity metrics (alpha and beta diversity), ordination analyses (PCoA), redundancy analysis (RDA), and structural equation modeling (piecewise SEM). Soil chemical variables (e.g., pH, organic matter, and nutrients) and microbial functional indicators—such as microbial biomass carbon, soil respiration, and β-glucosidase activity—were integrated into the analytical framework as well. The data cannot be made publicly available due to intellectual property protection restrictions. For additional information, please contact the corresponding authors.
Subject	Earth and Environmental Sciences
Keyword	Soil biology (DLC (LCSH)) Soil microbial communities Throughfall bacteria Soil bacteria Epiphytes Neotropical forests Tropical ecology
Related Publication	Epiphytic Tank Bromeliads in Tropical Forests: Unveiling their Role for Seedling and Soil Bacterial Communities Through Stable Isotopes and Metagenomics (Bromélias-Tanque Epífitas em Florestas Tropicais: Desvendando seu Papel para Comunidades de Plântulas e de Bactérias no Solo via Isótopos Estáveis e Metagenômica)
Notes	Data associated with the doctoral thesis: Epiphytic Tank Bromeliads in Tropical Forests: Unveiling their Role for Seedling and Soil Bacterial Communities Through Stable Isotopes and Metagenomics (Bromélias-Tanque Epífitas em Florestas Tropicais: Desvendando seu Papel para Comunidades de Plântulas e de Bactérias no Solo via Isótopos Estáveis e Metagenômica). Instituto de Biologia, Universidade Estadual de Campinas, 2025. Por motivos de propriedade intelectual, a tese será publicada um ano após sua defesa.
Funding Information	Conselho Nacional de Desenvolvimento Científico e Tecnológico: CNPq: 140793/2020-8 Fundação de Amparo à Pesquisa do Estado de São Paulo: FAPESP: 2020/06778-7 Fundação de Amparo à Pesquisa do Estado de São Paulo: FAPESP: 2019/08474-8 Fundação de Amparo à Pesquisa do Estado de São Paulo: FAPESP: 2022/10765-3 Fundação de Amparo à Pesquisa do Estado de São Paulo: FAPESP: 2023/01589-0
Depositor	Pereira, Tháles Augusto Coralli
Deposit Date	2025-07-23
Declarações obrigatórias sobre ética e privacidade	o projeto que gerou os dados foi aprovado pelo Comite de Ética em Pesquisa da Unicamp ou não envolve questões que requeiram tal aprovação; os dados que serão depositados estão de acordo com a LGPD (Lei Geral de Proteção de Dados)

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