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

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

doi:10.1038/s41597-019-0141-3

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:

^[1];

^[1]; de Britto Costa, Patrícia ^[2]; Gerhardt, Isabel Rodrigues ^[3]; Dante, Ricardo Augusto ^[3]; Teodoro, Grazielle Sales ^[4];

^[2];

^[5]; Carazzolle, Marcelo Falsarella ^[1];

^[6]; Clum, Alicia ^[6]; Foster, Brian ^[6]; Foster, Bryce ^[6];

^[6]; Palaniappan, Krishnaveni ^[6]; Varghese, Neha ^[6];

^[6]; Reddy, T. B. K. ^[6]; Daum, Chris ^[6]; Copeland, Alex ^[6] more »

Univ. Estadual de Campinas (UNICAMP), Campinas, SP (Brazil)
Univ. Estadual de Campinas (UNICAMP), Campinas, SP (Brazil); Univ. of Western Australia, Perth, WA (Australia)
Univ. Estadual de Campinas (UNICAMP), Campinas, SP (Brazil); Embrapa Informática Agropecuária, Campinas, SP (Brazil)
Univ. Federal do Para (UFPA), Belem, PA (Brazil)
Univ. of Western Australia, Perth, WA (Australia)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:: 2019-07-31

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.  doi:10.1038/s41597-019-0141-3.

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                    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

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                    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.

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@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}

}

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Works referenced in this record:

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

Ewels, Philip; Magnusson, Måns; Lundin, Sverker
Bioinformatics, Vol. 32, Issue 19
DOI: 10.1093/bioinformatics/btw354

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

Edgar, Robert C.
BMC Bioinformatics, Vol. 8, Issue 1
DOI: 10.1186/1471-2105-8-18

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

Martin, Marcel
EMBnet.journal, Vol. 17, Issue 1
DOI: 10.14806/ej.17.1.200

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

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
PLoS ONE, Vol. 8, Issue 2
DOI: 10.1371/journal.pone.0054859

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

Koster, J.; Rahmann, S.
Bioinformatics, Vol. 28, Issue 19
DOI: 10.1093/bioinformatics/bts480

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

Droop, Alastair P.
Bioinformatics, Vol. 32, Issue 12
DOI: 10.1093/bioinformatics/btw088

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

Grüning, Björn; Dale, Ryan; Sjödin, Andreas
Nature Methods, Vol. 15, Issue 7
DOI: 10.1038/s41592-018-0046-7

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

Lowe, Todd M.; Eddy, Sean R.
Nucleic Acids Research, Vol. 25, Issue 5
DOI: 10.1093/nar/25.5.0955

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

Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
BMC Bioinformatics, Vol. 11, Issue 1
DOI: 10.1186/1471-2105-11-119

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

Community, Unite
UNITE Community
DOI: 10.15156/BIO/587475

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

Edgar, Robert C.
Bioinformatics, Vol. 26, Issue 19, p. 2460-2461
DOI: 10.1093/bioinformatics/btq461

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

McMurdie, Paul J.; Holmes, Susan
PLoS ONE, Vol. 8, Issue 4
DOI: 10.1371/journal.pone.0061217

An Examination of the Degtjareff Method for Determining soil Organic Matter, and a Proposed Modification of the Chromic acid Titration Method
journal, January 1934

Walkley, A.; Black, I. Armstrong
Soil Science, Vol. 37, Issue 1
DOI: 10.1097/00010694-193401000-00003

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

Jones, P.; Binns, D.; Chang, H. -Y.
Bioinformatics, Vol. 30, Issue 9
DOI: 10.1093/bioinformatics/btu031

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

Bateman, A.
Nucleic Acids Research, Vol. 28, Issue 1
DOI: 10.1093/nar/28.1.263

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

Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis
journal, February 2009

Brundrett, Mark C.
Plant and Soil, Vol. 320, Issue 1-2
DOI: 10.1007/s11104-008-9877-9

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

Shoemaker, H. E.; McLean, E. O.; Pratt, P. F.
Soil Science Society of America Journal, Vol. 25, Issue 4
DOI: 10.2136/sssaj1961.03615995002500040014x