skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot

Abstract

The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres, and to unravel new strategies for improved crop productivity in stressful environments.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [2];  [3];  [3];  [4]; ORCiD logo [2]; ORCiD logo [5];  [1]; ORCiD logo [6];  [6];  [6];  [6]; ORCiD logo [6];  [6];  [6]; ORCiD logo [6];  [6];  [6];  [6] more »;  [6]; ORCiD logo [6];  [6];  [6]; ORCiD logo [6];  [1]; ORCiD logo [2] « less
  1. Univ. Estadual de Campinas (UNICAMP), Campinas, SP (Brazil)
  2. Univ. Estadual de Campinas (UNICAMP), Campinas, SP (Brazil); Univ. of Western Australia, Perth, WA (Australia)
  3. Univ. Estadual de Campinas (UNICAMP), Campinas, SP (Brazil); Embrapa Informática Agropecuária, Campinas, SP (Brazil)
  4. Univ. Federal do Para (UFPA), Belem, PA (Brazil)
  5. Univ. of Western Australia, Perth, WA (Australia)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1559812
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Data
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2052-4463
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Camargo, Antonio Pedro, de Souza, Rafael Soares Correa, de Britto Costa, Patrícia, Gerhardt, Isabel Rodrigues, Dante, Ricardo Augusto, Teodoro, Grazielle Sales, Abrahão, Anna, Lambers, Hans, Carazzolle, Marcelo Falsarella, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Copeland, Alex, Chen, I. -Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Pennacchio, Christa, Eloe-Fadrosh, Emiley A., Arruda, Paulo, and Oliveira, Rafael Silva. Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. United States: N. p., 2019. Web. https://doi.org/10.1038/s41597-019-0141-3.
Camargo, Antonio Pedro, de Souza, Rafael Soares Correa, de Britto Costa, Patrícia, Gerhardt, Isabel Rodrigues, Dante, Ricardo Augusto, Teodoro, Grazielle Sales, Abrahão, Anna, Lambers, Hans, Carazzolle, Marcelo Falsarella, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Copeland, Alex, Chen, I. -Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Pennacchio, Christa, Eloe-Fadrosh, Emiley A., Arruda, Paulo, & Oliveira, Rafael Silva. Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. United States. https://doi.org/10.1038/s41597-019-0141-3
Camargo, Antonio Pedro, de Souza, Rafael Soares Correa, de Britto Costa, Patrícia, Gerhardt, Isabel Rodrigues, Dante, Ricardo Augusto, Teodoro, Grazielle Sales, Abrahão, Anna, Lambers, Hans, Carazzolle, Marcelo Falsarella, Huntemann, Marcel, Clum, Alicia, Foster, Brian, Foster, Bryce, Roux, Simon, Palaniappan, Krishnaveni, Varghese, Neha, Mukherjee, Supratim, Reddy, T. B. K., Daum, Chris, Copeland, Alex, Chen, I. -Min A., Ivanova, Natalia N., Kyrpides, Nikos C., Pennacchio, Christa, Eloe-Fadrosh, Emiley A., Arruda, Paulo, and Oliveira, Rafael Silva. Wed . "Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot". United States. https://doi.org/10.1038/s41597-019-0141-3. https://www.osti.gov/servlets/purl/1559812.
@article{osti_1559812,
title = {Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot},
author = {Camargo, Antonio Pedro and de Souza, Rafael Soares Correa and de Britto Costa, Patrícia and Gerhardt, Isabel Rodrigues and Dante, Ricardo Augusto and Teodoro, Grazielle Sales and Abrahão, Anna and Lambers, Hans and Carazzolle, Marcelo Falsarella and Huntemann, Marcel and Clum, Alicia and Foster, Brian and Foster, Bryce and Roux, Simon and Palaniappan, Krishnaveni and Varghese, Neha and Mukherjee, Supratim and Reddy, T. B. K. and Daum, Chris and Copeland, Alex and Chen, I. -Min A. and Ivanova, Natalia N. and Kyrpides, Nikos C. and Pennacchio, Christa and Eloe-Fadrosh, Emiley A. and Arruda, Paulo and Oliveira, Rafael Silva},
abstractNote = {The rocky, seasonally-dry and nutrient-impoverished soils of the Brazilian campos rupestres impose severe growth-limiting conditions on plants. Species of a dominant plant family, Velloziaceae, are highly specialized to low-nutrient conditions and seasonal water availability of this environment, where phosphorus (P) is the key limiting nutrient. Despite plant-microbe associations playing critical roles in stressful ecosystems, the contribution of these interactions in the campos rupestres remains poorly studied. Here we present the first microbiome data of Velloziaceae spp. thriving in contrasting substrates of campos rupestres. We assessed the microbiomes of Vellozia epidendroides, which occupies shallow patches of soil, and Barbacenia macrantha, growing on exposed rocks. The prokaryotic and fungal profiles were assessed by rRNA barcode sequencing of epiphytic and endophytic compartments of roots, stems, leaves and surrounding soil/rocks. We also generated root and substrate (rock/soil)-associated metagenomes of each plant species. We foresee that these data will contribute to decipher how the microbiome contributes to plant functioning in the campos rupestres, and to unravel new strategies for improved crop productivity in stressful environments.},
doi = {10.1038/s41597-019-0141-3},
journal = {Scientific Data},
number = 1,
volume = 6,
place = {United States},
year = {2019},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Save / Share:

Works referenced in this record:

MultiQC: summarize analysis results for multiple tools and samples in a single report
journal, June 2016


PILER-CR: Fast and accurate identification of CRISPR repeats
journal, January 2007


Cutadapt removes adapter sequences from high-throughput sequencing reads
journal, May 2011


The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015

  • Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
  • Standards in Genomic Sciences, Vol. 10, Issue 1
  • DOI: 10.1186/s40793-015-0077-y

TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
journal, January 2007

  • Selengut, J. D.; Haft, D. H.; Davidsen, T.
  • Nucleic Acids Research, Vol. 35, Issue Database
  • DOI: 10.1093/nar/gkl1043

Improving Microbial Genome Annotations in an Integrated Database Context
journal, February 2013


Rfam: annotating non-coding RNAs in complete genomes
journal, December 2004

  • Griffiths-Jones, S.
  • Nucleic Acids Research, Vol. 33, Issue Database issue
  • DOI: 10.1093/nar/gki081

Data, information, knowledge and principle: back to metabolism in KEGG
journal, November 2013

  • Kanehisa, Minoru; Goto, Susumu; Sato, Yoko
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1076

Single-molecule PCR analysis of an unstable microsatellite for detecting mutations in sperm of mice exposed to chemical mutagens
journal, May 2015

  • Beal, Marc A.; Rowan-Carroll, Andrea; Campbell, Caleigh
  • Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, Vol. 775
  • DOI: 10.1016/j.mrfmmm.2015.03.010

A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences
journal, June 2006

  • Morgulis, Aleksandr; Gertz, E. Michael; Schäffer, Alejandro A.
  • Journal of Computational Biology, Vol. 13, Issue 5
  • DOI: 10.1089/cmb.2006.13.1028

Practical innovations for high-throughput amplicon sequencing
journal, September 2013

  • Lundberg, Derek S.; Yourstone, Scott; Mieczkowski, Piotr
  • Nature Methods, Vol. 10, Issue 10
  • DOI: 10.1038/nmeth.2634

SignalP 4.0: discriminating signal peptides from transmembrane regions
journal, September 2011

  • Petersen, Thomas Nordahl; Brunak, Søren; von Heijne, Gunnar
  • Nature Methods, Vol. 8, Issue 10
  • DOI: 10.1038/nmeth.1701

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007

  • Wang, Q.; Garrity, G. M.; Tiedje, J. M.
  • Applied and Environmental Microbiology, Vol. 73, Issue 16
  • DOI: 10.1128/AEM.00062-07

Snakemake--a scalable bioinformatics workflow engine
journal, August 2012


fqtools: an efficient software suite for modern FASTQ file manipulation
journal, February 2016


Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
journal, June 2010

  • Caporaso, J. G.; Lauber, C. L.; Walters, W. A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue Supplement_1
  • DOI: 10.1073/pnas.1000080107

Bioconda: sustainable and comprehensive software distribution for the life sciences
journal, July 2018


tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Extraction of phosphorus, potassium, calcium, and magnesium from soils by an ion‐exchange resin procedure
journal, May 1986

  • van Raij, B.; Quaggio, J. A.; da Silva, N. M.
  • Communications in Soil Science and Plant Analysis, Vol. 17, Issue 5
  • DOI: 10.1080/00103628609367733

UNITE general FASTA release
dataset, January 2017


Search and clustering orders of magnitude faster than BLAST
journal, August 2010


phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
journal, April 2013


InterProScan 5: genome-scale protein function classification
journal, January 2014


Towards a unified paradigm for sequence-based identification of fungi
journal, September 2013

  • Kõljalg, Urmas; Nilsson, R. Henrik; Abarenkov, Kessy
  • Molecular Ecology, Vol. 22, Issue 21
  • DOI: 10.1111/mec.12481

Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014

  • Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1223

The Pfam Protein Families Database
journal, January 2000


Ecology and evolution of plant diversity in the endangered campo rupestre: a neglected conservation priority
journal, August 2015

  • Silveira, Fernando A. O.; Negreiros, Daniel; Barbosa, Newton P. U.
  • Plant and Soil, Vol. 403, Issue 1-2
  • DOI: 10.1007/s11104-015-2637-8

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012

  • Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1219

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
journal, June 2007

  • Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah
  • BMC Bioinformatics, Vol. 8, Issue 1
  • DOI: 10.1186/1471-2105-8-209

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012

  • Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
  • Journal of Computational Biology, Vol. 19, Issue 5
  • DOI: 10.1089/cmb.2012.0021

Buffer Methods for Determining Lime Requirement of Soils With Appreciable Amounts of Extractable Aluminum1
journal, January 1961


Accelerated Profile HMM Searches
journal, October 2011


Bioconductor workflow for microbiome data analysis: from raw reads to community analyses
journal, January 2016


A Mathematical Theory of Communication
journal, October 1948


Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome
journal, June 2016

  • de Souza, Rafael Soares Correa; Okura, Vagner Katsumi; Armanhi, Jaderson Silveira Leite
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep28774

Basic local alignment search tool
journal, October 1990

  • Altschul, Stephen F.; Gish, Warren; Miller, Webb
  • Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
  • DOI: 10.1016/S0022-2836(05)80360-2

DADA2: High-resolution sample inference from Illumina amplicon data
journal, May 2016

  • Callahan, Benjamin J.; McMurdie, Paul J.; Rosen, Michael J.
  • Nature Methods, Vol. 13, Issue 7
  • DOI: 10.1038/nmeth.3869

Determination of nitrogen in soil by the Kjeldahl method
journal, August 1960


Development of a DTPA Soil Test for Zinc, Iron, Manganese, and Copper1
journal, January 1978


IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
journal, October 2018

  • Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 47, Issue D1
  • DOI: 10.1093/nar/gky901

Infernal 1.0: inference of RNA alignments
journal, March 2009


Mineral nutrition of campos rupestres plant species on contrasting nutrient-impoverished soil types
journal, November 2014

  • Oliveira, Rafael S.; Galvão, Hugo C.; de Campos, Mariana C. R.
  • New Phytologist, Vol. 205, Issue 3
  • DOI: 10.1111/nph.13175

Specialized roots of Velloziaceae weather quartzite rock while mobilizing phosphorus using carboxylates
journal, April 2019

  • Teodoro, Grazielle Sales; Lambers, Hans; Nascimento, Diego L.
  • Functional Ecology, Vol. 33, Issue 5
  • DOI: 10.1111/1365-2435.13324

A Mathematical Theory of Communication
journal, July 1948


Infernal 1.0: inference of RNA alignments
journal, June 2009


The Pfam Protein Families Database
journal, January 2002


Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
journal, January 2016