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Karasov TL, Lundberg DS. The changing influence of host genetics on the leaf fungal microbiome throughout plant development. PLoS Biol 2022; 20:e3001748. [PMID: 35960709 PMCID: PMC9374218 DOI: 10.1371/journal.pbio.3001748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Talia L. Karasov
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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2
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Shirsekar G, Devos J, Latorre SM, Blaha A, Queiroz Dias M, González Hernando A, Lundberg DS, Burbano HA, Fenster CB, Weigel D. Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia. Mol Biol Evol 2021; 38:5328-5344. [PMID: 34499163 PMCID: PMC8662644 DOI: 10.1093/molbev/msab268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.
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Affiliation(s)
- Gautam Shirsekar
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jane Devos
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Andreas Blaha
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | - Derek S Lundberg
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hernán A Burbano
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Charles B Fenster
- Oak Lake Field Station, Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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3
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Lundberg DS, Pramoj Na Ayutthaya P, Strauß A, Shirsekar G, Lo WS, Lahaye T, Weigel D. Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition. eLife 2021; 10:e66186. [PMID: 34292157 PMCID: PMC8387020 DOI: 10.7554/elife.66186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 07/19/2021] [Indexed: 12/26/2022] Open
Abstract
The ratio of microbial population size relative to the amount of host tissue, or 'microbial load', is a fundamental metric of colonization and infection, but it cannot be directly deduced from microbial amplicon data such as 16S rRNA gene counts. Because existing methods to determine load, such as serial dilution plating, quantitative PCR, and whole metagenome sequencing add substantial cost and/or experimental burden, they are only rarely paired with amplicon sequencing. We introduce host-associated microbe PCR (hamPCR), a robust strategy to both quantify microbial load and describe interkingdom microbial community composition in a single amplicon library. We demonstrate its accuracy across multiple study systems, including nematodes and major crops, and further present a cost-saving technique to reduce host overrepresentation in the library prior to sequencing. Because hamPCR provides an accessible experimental solution to the well-known limitations and statistical challenges of compositional data, it has far-reaching potential in culture-independent microbiology.
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Affiliation(s)
- Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | | | - Annett Strauß
- Department of Evolutionary Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Wen-Sui Lo
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Thomas Lahaye
- ZMBP-General Genetics, University of TübingenTübingenGermany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
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4
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Cambiagno DA, Giudicatti AJ, Arce AL, Gagliardi D, Li L, Yuan W, Lundberg DS, Weigel D, Manavella PA. HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. Mol Plant 2021; 14:426-439. [PMID: 33385584 DOI: 10.1016/j.molp.2020.12.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 05/23/2023]
Abstract
Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis. We found that Arabidopsis mutants with impaired HST shuttling exhibit normal subcellular distribution of miRNAs. Interestingly, protein-protein interaction and microscopy assays showed that HST directly interacts with the microprocessor core component DCL1 through its N-terminal domain. Moreover, mass spectrometry analysis revealed that HST also interacts independently of its N-terminal domain with the mediator complex subunit MED37. Further experiments revealed that HST could act as a scaffold to facilitate the recruitment of DCL1 to genomic MIRNA loci by stabilizing the DCL1-MED37 complex, which in turn promotes the transcription and proper processing of primary miRNA transcripts (pri-miRNAs). Taken together, these results suggest that HST is likely associated with the formation of the miRNA biogenesis complex at MIRNA genes, promoting the transcription and processing of pri-miRNAs rather than the direct export of processed miRNAs from the nucleus.
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Affiliation(s)
- Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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5
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Regalado J, Lundberg DS, Deusch O, Kersten S, Karasov T, Poersch K, Shirsekar G, Weigel D. Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves. ISME J 2020; 14:2116-2130. [PMID: 32405027 PMCID: PMC7368051 DOI: 10.1038/s41396-020-0665-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/27/2020] [Accepted: 04/15/2020] [Indexed: 12/23/2022]
Abstract
Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, support the acquisition of nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of the 16S rRNA gene and/or the internal transcribed spacer (ITS) of rRNA genomic loci, which show the relative abundance of the microbes to each other. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S and eukaryotic ITS1 rRNA amplicon data from 176 of these samples. Shotgun data, which unlike the amplicon data capture the ratio of microbe to plant DNA, enable scaling of microbial read abundances to reflect the microbial load on the host. In a more cost-effective hybrid strategy, we show they also allow a similar scaling of amplicon data to overcome compositionality problems. Our wild plants were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. Microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. Critically, considering absolute microbial load led to fundamentally different conclusions about microbiome assembly and the interaction networks among major taxa.
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Affiliation(s)
- Julian Regalado
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Oliver Deusch
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Sonja Kersten
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, 70599, Stuttgart, Germany
| | - Talia Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Karin Poersch
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
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6
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Karasov TL, Almario J, Friedemann C, Ding W, Giolai M, Heavens D, Kersten S, Lundberg DS, Neumann M, Regalado J, Neher RA, Kemen E, Weigel D. Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host Microbe 2018; 24:168-179.e4. [PMID: 30001519 PMCID: PMC6054916 DOI: 10.1016/j.chom.2018.06.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/16/2018] [Accepted: 06/21/2018] [Indexed: 11/23/2022]
Abstract
Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild pathosystems, we carried out a multi-year, multi-site survey of Pseudomonas in its natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a ubiquitous pathogenic clade. Sequencing of 1,524 genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically identifiable pathogenic sublineages. There is differentiation at the level of both gene content and disease phenotype, although the differentiation may not provide fitness advantages to specific sublineages. The coexistence of sublineages indicates that in contrast to crop systems, no single strain has been able to overtake the studied A. thaliana populations in the recent past. Our results suggest that selective pressures acting on a plant pathogen in wild hosts are likely to be much more complex than those in agricultural systems.
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Affiliation(s)
- Talia L Karasov
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Juliana Almario
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, IMITP, University of Tübingen, 72076 Tübingen, Germany
| | - Claudia Friedemann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Ding
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Michael Giolai
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Darren Heavens
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich NR4 7UZ, UK
| | - Sonja Kersten
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Julian Regalado
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Richard A Neher
- University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Eric Kemen
- Max Planck Research Group Fungal Biodiversity, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany; Interfaculty Institute of Microbiology and Infection Medicine Tübingen, IMITP, University of Tübingen, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
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7
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Levy A, Salas Gonzalez I, Mittelviefhaus M, Clingenpeel S, Herrera Paredes S, Miao J, Wang K, Devescovi G, Stillman K, Monteiro F, Rangel Alvarez B, Lundberg DS, Lu TY, Lebeis S, Jin Z, McDonald M, Klein AP, Feltcher ME, Rio TG, Grant SR, Doty SL, Ley RE, Zhao B, Venturi V, Pelletier DA, Vorholt JA, Tringe SG, Woyke T, Dangl JL. Genomic features of bacterial adaptation to plants. Nat Genet 2017; 50:138-150. [PMID: 29255260 PMCID: PMC5957079 DOI: 10.1038/s41588-017-0012-9] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 11/10/2017] [Indexed: 01/10/2023]
Abstract
Plants intimately associate with diverse bacteria. Plant-associated (PA) bacteria have ostensibly evolved genes enabling adaptation to the plant environment. However, the identities of such genes are mostly unknown and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3837 bacterial genomes to identify thousands of PA gene clusters. Genomes of PA bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant associated genomes. We experimentally validated candidates from two sets of PA genes, one involved in plant colonization, the other serving in microbe-microbe competition between PA bacteria. We also identified 64 PA protein domains that potentially mimic plant domains; some are shared with PA fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides leads for efficient and sustainable agriculture through microbiome engineering.
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Affiliation(s)
- Asaf Levy
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Isai Salas Gonzalez
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | | | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Jiamin Miao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.,The Grassland College, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Kunru Wang
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Giulia Devescovi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | - Freddy Monteiro
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Derek S Lundberg
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tse-Yuan Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sarah Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Zhao Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Meredith McDonald
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Andrew P Klein
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Meghan E Feltcher
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,BD Technologies and Innovation, Research Triangle Park, NC, USA
| | | | - Sarah R Grant
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Sharon L Doty
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Ruth E Ley
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA, USA
| | - Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Susannah G Tringe
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA. .,School of Natural Sciences, University of California, Merced, Merced, CA, USA.
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA. .,Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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8
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Abstract
Many microbes associate with higher eukaryotes and impact their vitality. To engineer microbiomes for host benefit, we must understand the rules of community assembly and maintenance that, in large part, demand an understanding of the direct interactions among community members. Toward this end, we have developed a Poisson-multivariate normal hierarchical model to learn direct interactions from the count-based output of standard metagenomics sequencing experiments. Our model controls for confounding predictors at the Poisson layer and captures direct taxon-taxon interactions at the multivariate normal layer using an ℓ1 penalized precision matrix. We show in a synthetic experiment that our method handily outperforms state-of-the-art methods such as SparCC and the graphical lasso (glasso). In a real in planta perturbation experiment of a nine-member bacterial community, we show our model, but not SparCC or glasso, correctly resolves a direct interaction structure among three community members that associates with Arabidopsis thaliana roots. We conclude that our method provides a structured, accurate, and distributionally reasonable way of modeling correlated count-based random variables and capturing direct interactions among them.
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Affiliation(s)
- Surojit Biswas
- 1 Department of Statistics, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Meredith Mcdonald
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Derek S Lundberg
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Jeffery L Dangl
- 2 Department of Biology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,3 Howard Hughes Medical Institute, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina.,4 Department of Immunology, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
| | - Vladimir Jojic
- 5 Department of Computer Science, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina
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Abstract
A major goal for biologists is to understand the connection between genes and phenotypic traits, and genetic mapping in experimental populations remains a powerful approach for discovering the causal genes underlying phenotypes. For genetic mapping, the process of genotyping was previously a major rate-limiting step. Modern sequencing technology has greatly improved the resolution and speed of genetic mapping by reducing the time, labor, and cost per genotyping marker. In addition, the ability to perform genotyping-by-sequencing (GBS) has facilitated large-scale population genetic analyses by providing a simpler way to survey segregating genetic variation in natural populations. Here we present two protocols for GBS, using the Illumina platform, that can be applied to a wide range of genotyping projects in different species. The first protocol is for genotyping a subset of marker positions genome-wide using restriction digestion, and the second is for preparing inexpensive paired-end whole-genome libraries. We discuss the suitability of each approach for different genotyping applications and provide notes for adapting these protocols for use with a liquid-handling robot.
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Affiliation(s)
- Beth A Rowan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076, Tübingen, Germany
| | - Danelle K Seymour
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076, Tübingen, Germany
| | - Eunyoung Chae
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076, Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37-39, 72076, Tübingen, Germany.
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10
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Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T. Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nat Commun 2016; 7:12151. [PMID: 27402057 PMCID: PMC4945892 DOI: 10.1038/ncomms12151] [Citation(s) in RCA: 416] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 06/06/2016] [Indexed: 01/01/2023] Open
Abstract
Bacteria living on and in leaves and roots influence many aspects of plant health, so the extent of a plant's genetic control over its microbiota is of great interest to crop breeders and evolutionary biologists. Laboratory-based studies, because they poorly simulate true environmental heterogeneity, may misestimate or totally miss the influence of certain host genes on the microbiome. Here we report a large-scale field experiment to disentangle the effects of genotype, environment, age and year of harvest on bacterial communities associated with leaves and roots of Boechera stricta (Brassicaceae), a perennial wild mustard. Host genetic control of the microbiome is evident in leaves but not roots, and varies substantially among sites. Microbiome composition also shifts as plants age. Furthermore, a large proportion of leaf bacterial groups are shared with roots, suggesting inoculation from soil. Our results demonstrate how genotype-by-environment interactions contribute to the complexity of microbiome assembly in natural environments.
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Affiliation(s)
- Maggie R. Wagner
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708, USA
| | - Derek S Lundberg
- Department of Biology, Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Tijana G. del Rio
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Susannah G. Tringe
- Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jeffery L. Dangl
- Department of Biology, Curriculum in Genetics and Molecular Biology, Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Howard Hughes Medical Institute, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Thomas Mitchell-Olds
- Program in Genetics and Genomics, Department of Biology, Duke University, Durham, North Carolina 27708, USA
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11
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Lebeis SL, Paredes SH, Lundberg DS, Breakfield N, Gehring J, McDonald M, Malfatti S, Glavina del Rio T, Jones CD, Tringe SG, Dangl JL. PLANT MICROBIOME. Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa. Science 2015; 349:860-4. [PMID: 26184915 DOI: 10.1126/science.aaa8764] [Citation(s) in RCA: 576] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 06/26/2015] [Indexed: 12/29/2022]
Abstract
Immune systems distinguish "self" from "nonself" to maintain homeostasis and must differentially gate access to allow colonization by potentially beneficial, nonpathogenic microbes. Plant roots grow within extremely diverse soil microbial communities but assemble a taxonomically limited root-associated microbiome. We grew isogenic Arabidopsis thaliana mutants with altered immune systems in a wild soil and also in recolonization experiments with a synthetic bacterial community. We established that biosynthesis of, and signaling dependent on, the foliar defense phytohormone salicylic acid is required to assemble a normal root microbiome. Salicylic acid modulates colonization of the root by specific bacterial families. Thus, plant immune signaling drives selection from the available microbial communities to sculpt the root microbiome.
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Affiliation(s)
- Sarah L Lebeis
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA. Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
| | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Derek S Lundberg
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Natalie Breakfield
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Jase Gehring
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Meredith McDonald
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Stephanie Malfatti
- Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA
| | | | - Corbin D Jones
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599-3280, USA
| | - Susannah G Tringe
- Joint Genome Institute, U.S. Department of Energy, Walnut Creek, CA, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599-3280, USA. Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
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12
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Tennessen K, Andersen E, Clingenpeel S, Rinke C, Lundberg DS, Han J, Dangl JL, Ivanova N, Woyke T, Kyrpides N, Pati A. ProDeGe: a computational protocol for fully automated decontamination of genomes. ISME J 2015; 10:269-72. [PMID: 26057843 PMCID: PMC4681846 DOI: 10.1038/ismej.2015.100] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/29/2015] [Accepted: 05/08/2015] [Indexed: 11/09/2022]
Abstract
Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes--clean and contaminant--using a combination of homology and feature-based methodologies. On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). The procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.
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Affiliation(s)
- Kristin Tennessen
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Evan Andersen
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Scott Clingenpeel
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Christian Rinke
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Derek S Lundberg
- Department of Biology and Curriculum in Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - James Han
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jeff L Dangl
- Department of Biology and Howard Hughes Medical Institute, Curriculum in Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Natalia Ivanova
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos Kyrpides
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Amrita Pati
- Prokaryotic Super Program, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
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13
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Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. Corrigendum to Wagneret al.: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 2014. [DOI: 10.1111/ele.12400] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maggie R. Wagner
- Duke University Program in Genetics and Genomics; Department of Biology, Box 90338; Duke University; Durham NC 27708 USA
| | - Derek S. Lundberg
- Department of Biology; Howard Hughes Medical Institute
- Curriculum in Genetics and Molecular Biology; Carolina Center for Genome Sciences; University of North Carolina; Chapel Hill NC 27599 USA
| | | | | | - Jeffery L. Dangl
- Department of Biology; Howard Hughes Medical Institute
- Curriculum in Genetics and Molecular Biology; Department of Microbiology and Immunology; Carolina Center for Genome Sciences; University of North Carolina; Chapel Hill NC 27599 USA
| | - Thomas Mitchell-Olds
- Institute for Genome Sciences & Policy; Department of Biology, Box 90338; Duke University; Durham NC 27708 USA
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14
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Yourstone SM, Lundberg DS, Dangl JL, Jones CD. MT-Toolbox: improved amplicon sequencing using molecule tags. BMC Bioinformatics 2014; 15:284. [PMID: 25149069 PMCID: PMC4153912 DOI: 10.1186/1471-2105-15-284] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 08/12/2014] [Indexed: 01/18/2023] Open
Abstract
Background Short oligonucleotides can be used as markers to tag and track DNA sequences. For example, barcoding techniques (i.e. Multiplex Identifiers or Indexing) use short oligonucleotides to distinguish between reads from different DNA samples pooled for high-throughput sequencing. A similar technique called molecule tagging uses the same principles but is applied to individual DNA template molecules. Each template molecule is tagged with a unique oligonucleotide prior to polymerase chain reaction. The resulting amplicon sequences can be traced back to their original templates by their oligonucleotide tag. Consensus building from sequences sharing the same tag enables inference of original template molecules thereby reducing effects of sequencing error and polymerase chain reaction bias. Several independent groups have developed similar protocols for molecule tagging; however, user-friendly software for build consensus sequences from molecule tagged reads is not readily available or is highly specific for a particular protocol. Results MT-Toolbox recognizes oligonucleotide tags in amplicons and infers the correct template sequence. On a set of molecule tagged test reads, MT-Toolbox generates sequences having on average 0.00047 errors per base. MT-Toolbox includes a graphical user interface, command line interface, and options for speed and accuracy maximization. It can be run in serial on a standard personal computer or in parallel on a Load Sharing Facility based cluster system. An optional plugin provides features for common 16S metagenome profiling analysis such as chimera filtering, building operational taxonomic units, contaminant removal, and taxonomy assignments. Conclusions MT-Toolbox provides an accessible, user-friendly environment for analysis of molecule tagged reads thereby reducing technical errors and polymerase chain reaction bias. These improvements reduce noise and allow for greater precision in single amplicon sequencing experiments. Electronic supplementary material The online version of this article (doi:10.1186/1471-2105-15-284) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Scott M Yourstone
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill 27599, USA.
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15
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Wagner MR, Lundberg DS, Coleman-Derr D, Tringe SG, Dangl JL, Mitchell-Olds T. Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative. Ecol Lett 2014; 17:717-26. [PMID: 24698177 DOI: 10.1111/ele.12276] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/09/2014] [Accepted: 02/28/2014] [Indexed: 02/03/2023]
Abstract
Plant phenology is known to depend on many different environmental variables, but soil microbial communities have rarely been acknowledged as possible drivers of flowering time. Here, we tested separately the effects of four naturally occurring soil microbiomes and their constituent soil chemistries on flowering phenology and reproductive fitness of Boechera stricta, a wild relative of Arabidopsis. Flowering time was sensitive to both microbes and the abiotic properties of different soils; varying soil microbiota also altered patterns of selection on flowering time. Thus, soil microbes potentially contribute to phenotypic plasticity of flowering time and to differential selection observed between habitats. We also describe a method to dissect the microbiome into single axes of variation that can help identify candidate organisms whose abundance in soil correlates with flowering time. This approach is broadly applicable to search for microbial community members that alter biological characteristics of interest.
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Affiliation(s)
- Maggie R Wagner
- Duke University Program in Genetics and Genomics, Department of Biology, Duke University, Durham, NC, 27708, USA
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16
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Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL. Practical innovations for high-throughput amplicon sequencing. Nat Methods 2013; 10:999-1002. [PMID: 23995388 DOI: 10.1038/nmeth.2634] [Citation(s) in RCA: 493] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/31/2013] [Indexed: 11/09/2022]
Abstract
We describe improvements for sequencing 16S ribosomal RNA (rRNA) amplicons, a cornerstone technique in metagenomics. Through unique tagging of template molecules before PCR, amplicon sequences can be mapped to their original templates to correct amplification bias and sequencing error with software we provide. PCR clamps block amplification of contaminating sequences from a eukaryotic host, thereby substantially enriching microbial sequences without introducing bias.
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Affiliation(s)
- Derek S Lundberg
- 1] Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA. [2] Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina, USA. [3]
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17
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Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL. Defining the core Arabidopsis thaliana root microbiome. Nature 2012; 488:86-90. [PMID: 22859206 PMCID: PMC4074413 DOI: 10.1038/nature11237] [Citation(s) in RCA: 1430] [Impact Index Per Article: 119.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 05/15/2012] [Indexed: 01/11/2023]
Abstract
Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities.
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Affiliation(s)
- Derek S Lundberg
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Sarah L Lebeis
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Scott Yourstone
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jase Gehring
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | | | - Julien Tremblay
- DOE Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Victor Kunin
- DOE Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | | | - Thilo Eickhorst
- Soil Science, Faculty of Biology and Chemistry, University of Bremen, Bremen 28359, Germany
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, New York 14853, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California 94598, USA.,Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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18
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Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, Gehring J, Malfatti S, Tremblay J, Engelbrektson A, Kunin V, Del Rio TG, Edgar RC, Eickhorst T, Ley RE, Hugenholtz P, Tringe SG, Dangl JL. Defining the core Arabidopsis thaliana root microbiome. Nature 2012; 41:325-50. [PMID: 22859206 DOI: 10.1146/annurev.phyto.41.052002.095514] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 05/15/2012] [Indexed: 05/20/2023]
Abstract
Land plants associate with a root microbiota distinct from the complex microbial community present in surrounding soil. The microbiota colonizing the rhizosphere (immediately surrounding the root) and the endophytic compartment (within the root) contribute to plant growth, productivity, carbon sequestration and phytoremediation. Colonization of the root occurs despite a sophisticated plant immune system, suggesting finely tuned discrimination of mutualists and commensals from pathogens. Genetic principles governing the derivation of host-specific endophyte communities from soil communities are poorly understood. Here we report the pyrosequencing of the bacterial 16S ribosomal RNA gene of more than 600 Arabidopsis thaliana plants to test the hypotheses that the root rhizosphere and endophytic compartment microbiota of plants grown under controlled conditions in natural soils are sufficiently dependent on the host to remain consistent across different soil types and developmental stages, and sufficiently dependent on host genotype to vary between inbred Arabidopsis accessions. We describe different bacterial communities in two geochemically distinct bulk soils and in rhizosphere and endophytic compartments prepared from roots grown in these soils. The communities in each compartment are strongly influenced by soil type. Endophytic compartments from both soils feature overlapping, low-complexity communities that are markedly enriched in Actinobacteria and specific families from other phyla, notably Proteobacteria. Some bacteria vary quantitatively between plants of different developmental stage and genotype. Our rigorous definition of an endophytic compartment microbiome should facilitate controlled dissection of plant-microbe interactions derived from complex soil communities.
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Affiliation(s)
- Derek S Lundberg
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Sarah L Lebeis
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Sur Herrera Paredes
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Scott Yourstone
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jase Gehring
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | | | - Julien Tremblay
- DOE Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | - Victor Kunin
- DOE Joint Genome Institute, Walnut Creek, California 94598, USA
| | | | | | - Thilo Eickhorst
- Soil Science, Faculty of Biology and Chemistry, University of Bremen, Bremen 28359, Germany
| | - Ruth E Ley
- Department of Microbiology, Cornell University, Ithaca, New York 14853, USA
| | - Philip Hugenholtz
- DOE Joint Genome Institute, Walnut Creek, California 94598, USA
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences & Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - Jeffery L Dangl
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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19
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Abstract
Chronic Pseudomonas aeruginosa lung infection is the major cause of morbidity and mortality in cystic fibrosis (CF) patients. One P. aeruginosa virulence factor unique to CF isolates is overproduction of alginate, phenotypically termed mucoidy. Mucoidy is the result of increased transcription from the algD gene and is activated by the transcriptional regulator AlgR. Mutations in algR result in a nonmucoid phenotype and loss of twitching motility. Additionally, AlgR controls transcription of algC, encoding a dual-function enzyme necessary for both lipopolysaccharide (LPS) and alginate production. Therefore, to determine the effect of algR on P. aeruginosa virulence, an algR mutant was examined for sensitivity to reactive oxygen intermediates, killing by phagocytes, systemic virulence, and the ability to maintain a murine lung infection. We found that P. aeruginosa PAO700 (algR::Gm(r)) was less lethal than PAO1, as tested in an acute septicemia infection mouse model, and was cleared more efficiently in a mouse pneumonia model. Additionally, the algR mutant (PAO700) was more sensitive to hypochlorite. However, PAO700 was more resistant to hydrogen peroxide and killed less readily in an acellular myeloperoxidase assay than PAO1. There was little difference in killing between PAO1 and PAO700 with macrophage-like J774 cells and human polymorhonuclear leukocytes. Two-dimensional gel analysis of P. aeruginosa algR mutant and wild-type protein extracts revealed 47 differentially regulated proteins, suggesting that AlgR plays both a positive role and a negative role in gene expression. Together, these results imply that AlgR is necessary for virulence and regulates genes in addition to the genes associated with alginate and LPS production and pilus function.
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Affiliation(s)
- Stephen E Lizewski
- Department of Microbiology and Immunology, Program in Molecular Pathogenesis and Immunity, Tulane University Health Sciences Center, New Orleans, Louisiana 70112-2699, USA
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