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Rhizosphere Microbiomes Of Potato Cultivated In The High Andes Show Stable And Dynamic Core Microbiomes With Different Responses To Plant Development

S. Pfeiffer, B. Mitter, A. Oswald, B. Schloter-Hai, M. Schloter, S. Declerck, A. Sessitsch
Published 2017 · Biology, Medicine

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&NA; The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3245 to 4070 m.a.s.l., differing in soil characteristics, climate and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions. A detailed statistical analysis on the operational taxonomic unit (OTU) level, representing bacterial species, revealed a complex community structure of the rhizosphere. We identified an opportunistic microbiome which comprises OTUs that occur randomly or under specific environmental conditions. In contrast, core microbiome members were found at all sites. The ‘stable’ component of the core microbiome consisted of few ubiquitous OTUs that were continuously abundant in all samples and vegetation stages, whereas the ‘dynamic’ component comprised OTUs that were enriched at specific vegetation stages.
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Über neuere Erfahrungen und Probleme auf dem Gebiete der Bodenbakteriologie unter besonderer Berücksichtigung der Gründüngung und Brache
L. Hiltner (1904)
10.1111/J.1469-8137.1920.TB07331.X
PLANT FAMILIES: A PLEA FOR AN INTERNATIONAL SEQUENCE.
A. Gundersen (1920)
10.1128/jb.173.2.697-703.1991
16S ribosomal DNA amplification for phylogenetic study
W. Weisburg (1991)
10.1016/0006-3207(92)91201-3
Conservation evaluation and phylogenetic diversity
D. Faith (1992)
Einheitliche Codierung der phänologischen Entwicklungsstadien mono - und dikotyler Pflanzen - Erweiterte BBCH - Skala
H Hack (1992)
Einheitliche Codierung der phänologischen Entwicklungsstadien mono- und dikotyler Pflanzen - Erweiterte BBCH-Skala.Nachrichtenbl Deut Pflanzenschutzd 1992;44:265–70
H Hack (1992)
10.1128/AEM.59.3.695-700.1993
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
G. Muyzer (1993)
10.1111/J.1442-9993.1993.TB00438.X
Non‐parametric multivariate analyses of changes in community structure
K. R. Clarke (1993)
10.1093/nar/26.13.3309
Efficient removal of PCR inhibitors using agarose-embedded DNA preparations
D. Moreira (1998)
PAST: PALEONTOLOGICAL STATISTICAL SOFTWARE PACKAGE FOR EDUCATION AND DATA ANALYSIS
Ø. Hammer (2001)
10.1186/1471-2105-4-2
An automated method for finding molecular complexes in large protein interaction networks
Gary D Bader (2002)
10.1101/GR.1239303
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
P. Shannon (2003)
An automatedmethod for findingmolec - ular complexes in large protein interaction networks
GD Bader (2003)
An automatedmethod for findingmolecular complexes in large protein interaction networks. BMC Bioinformatics 2003;4:2
GD Bader (2003)
10.1146/ANNUREV.PHYTO.42.012604.135455
Microbial diversity in soil: selection microbial populations by plant and soil type and implications for disease suppressiveness.
P. Garbeva (2004)
10.1023/A:1004326910584
Potential of Rhizobium and Bradyrhizobium species as plant growth promoting rhizobacteria on non-legumes: Effect on radishes (Raphanus sativus L.)
H. Antoun (2004)
10.1093/NAR/GKH340
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
R. Edgar (2004)
10.1128/AEM.71.12.8228-8235.2005
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
C. Lozupone (2005)
10.1111/J.1574-6941.2005.00027.X
Rhizosphere bacteria affected by transgenic potatoes with antibacterial activities compared with the effects of soil, wild-type potatoes, vegetation stage and pathogen exposure.
Frank Rasche (2006)
10.1139/W06-059
Chilling and cultivar type affect the diversity of bacterial endophytes colonizing sweet pepper (Capsicum anuum L.).
F. Rasche (2006)
vegan : Community Ecology Package. R package version 1.8-5
J. Oksanen (2007)
10.1038/ismej.2007.53
Pyrosequencing enumerates and contrasts soil microbial diversity
L. F. Roesch (2007)
10.1128/MICROBE.3.151.1
Streptomyces in Nature and Medicine: the Antibiotic Makers
P. A. Hoskisson (2008)
10.1104/pp.108.127613
Root-Secreted Malic Acid Recruits Beneficial Soil Bacteria1[C][W][OA]
T. Rudrappa (2008)
10.1007/s11104-008-9568-6
The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms
J. Raaijmakers (2008)
10.1002/pro.250
KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
Vincent B. Chen (2009)
10.1128/AEM.00120-09
Assessment of Bias Associated with Incomplete Extraction of Microbial DNA from Soil
Larry M. Feinstein (2009)
10.1111/j.1574-6941.2009.00654.x
Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere.
G. Berg (2009)
10.1128/AEM.00335-09
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale
C. Lauber (2009)
10.1099/ijs.0.006163-0
Sphingobium vermicomposti sp. nov., isolated from vermicompost.
Ivone Vaz-Moreira (2009)
10.1093/molbev/msp077
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
M. Price (2009)
10.1371/journal.pone.0023321
Comparative Analysis of Bacterial Communities in a Potato Field as Determined by Pyrosequencing
Özgül Inceoğlu (2011)
10.1111/j.1574-6941.2011.01073.x
Effects of genetically modified starch metabolism in potato plants on photosynthate fluxes into the rhizosphere and on microbial degraders of root exudates.
Silvia Gschwendtner (2011)
10.1111/j.1574-6941.2010.01025.x
PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa.
N. Weinert (2011)
10.7490/F1000RESEARCH.1089522.1
Metagenomic biomarker discovery and explanation
N. Segata (2011)
10.1128/AEM.00133-11
Protection of Arabidopsis thaliana against Leaf-Pathogenic Pseudomonas syringae by Sphingomonas Strains in a Controlled Model System†
G. Innerebner (2011)
10.1093/jxb/ers301
Multiple impacts of the plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2 on nutrient and ABA relations of Pisum sativum
F. Jiang (2012)
10.1007/s11104-012-1495-x
Possible contribution of Bradyrhizobium on nitrogen fixation in sweet potatoes
Junko Terakado-Tonooka (2012)
10.1038/ismej.2012.84
Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests
M. Hartmann (2012)
10.1128/AEM.07308-11
Microbial Scout Hypothesis and Microbial Discovery
S. Buerger (2012)
10.1038/nature11237
Defining the core Arabidopsis thaliana root microbiome
Derek S. Lundberg (2012)
10.1128/AEM.02811-12
Normal Operating Range of Bacterial Communities in Soil Used for Potato Cropping
Özgül Inceoğlu (2012)
10.1099/ijs.0.035097-0
Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts.
J. Ardley (2012)
10.1111/j.1574-6941.2012.01420.x
Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing
M. Kuffner (2012)
10.1371/journal.pcbi.1002606
Microbial Co-occurrence Relationships in the Human Microbiome
K. Faust (2012)
Gavrish E et al.Microbial scout hypothesis andmicrobial discovery.Appl EnvironMicrob 2012;78:3229–33
S Buerger (2012)
10.1371/journal.pone.0061217
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
P. McMurdie (2013)
10.1016/j.syapm.2013.03.007
Centrosema is a promiscuous legume nodulated by several new putative species and symbiovars of Bradyrhizobium in various American countries.
M. Ramı́rez-Bahena (2013)
10.1073/pnas.1302837110
Diversity and heritability of the maize rhizosphere microbiome under field conditions
Jason Peiffer (2013)
10.1016/J.APSOIL.2012.09.004
Shifts in soil bacterial communities associated with the potato rhizosphere in response to aromatic sulfonate amendments
Özgül Inceoğlu (2013)
10.1038/nmeth.2604
UPARSE: highly accurate OTU sequences from microbial amplicon reads
R. Edgar (2013)
10.1038/nrmicro3109
Going back to the roots: the microbial ecology of the rhizosphere
L. Philippot (2013)
10.3389/fpls.2013.00356
Plant growth-promoting rhizobacteria and root system functioning
J. Vacheron (2013)
10.1016/j.mimet.2013.04.003
Development of a simple root model to study the effects of single exudates on the development of bacterial community structure.
M. Ziegler (2013)
10.1111/nph.12124
Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior.
D. Badri (2013)
10.1007/s00572-013-0549-0
Potato-associated arbuscular mycorrhizal fungal communities in the Peruvian Andes
Carolina Senés-Guerrero (2013)
10.1371/journal.pone.0055731
Root Exudation of Phytochemicals in Arabidopsis Follows Specific Patterns That Are Developmentally Programmed and Correlate with Soil Microbial Functions
J. M. Chaparro (2013)
A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, 2013, http://www.R-project.org
R R Core Team (2013)
10.1186/1471-2105-15-293
jvenn: an interactive Venn diagram viewer
Philippe Bardou (2014)
10.1007/s12230-014-9405-9
Site and Clone Effects on the Potato Root-Associated Core Microbiome and its Relationship to Tuber Yield and Nutrients
B. Barnett (2014)
10.1371/journal.pone.0100709
Changes in the Bacterial Community of Soybean Rhizospheres during Growth in the Field
Akifumi Sugiyama (2014)
10.3389/fmicb.2014.00002
Root exudation and root development of lettuce (Lactuca sativa L. cv. Tizian) as affected by different soils
G. Neumann (2014)
10.1111/1462-2920.12350
Improved group-specific primers based on the full SILVA 16S rRNA gene reference database.
S. Pfeiffer (2014)
10.3389/fmicb.2014.00144
Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce
Susanne Schreiter (2014)
10.1038/ismej.2013.196
Rhizosphere microbiome assemblage is affected by plant development
Jacqueline M. Chaparro (2014)
10.1128/mBio.00746-15
Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons
Shengjing Shi (2015)
10.1038/nature16192
Functional overlap of the Arabidopsis leaf and root microbiota
Y. Bai (2015)
10.1038/srep15839
Littoral lichens as a novel source of potentially bioactive Actinobacteria
Delphine Parrot (2015)
10.1128/genomeA.00432-15
Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments
Erika Corretto (2015)
10.1111/1462-2920.12452
Evolution of bacterial communities in the wheat crop rhizosphere.
S. Donn (2015)
10.3389/fmicb.2015.00856
Mangrove rare actinobacteria: taxonomy, natural compound, and discovery of bioactivity
A. Azman (2015)
Draft genome sequences of 10 Microbacterium spp., with emphasis on heavy metal-contaminated environments. Genome Announc 2015;3:e00432–15
E Corretto (2015)
Potato - associated arbuscular
C Senés-Guerrero



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10.1007/S11104-021-04945-6
Wheat-root associated prokaryotic community: interplay between plant selection and location
Yuyin Zheng (2021)
10.3390/microorganisms9081785
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Gavriel Friesem (2021)
10.3390/D13030125
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Cristina P. Fernández-Baca (2021)
10.1007/s00122-021-03791-5
Nitrogen fixation in maize: breeding opportunities.
Seema Sheoran (2021)
10.1016/J.SCITOTENV.2021.146021
Stochastic processes drive bacterial and fungal community assembly in sustainable intensive agricultural soils of Shanghai, China.
Shuangxi Li (2021)
10.1080/23766808.2021.1938900
The Ecuadorian Microbiome Project: a plea to strengthen microbial genomic research
Magdalena Díaz (2021)
10.3389/fagro.2021.714700
Effects of Microbial Consortia, Applied as Fertilizer Coating, on Soil and Rhizosphere Microbial Communities and Potato Yield
William Overbeek (2021)
10.1016/B978-0-12-819715-8.00004-5
Modern biotechnological tools: an opportunity to discover complex phytobiomes of horticulture crops
Shalini Rai (2021)
10.1038/s41598-021-82181-9
16S rRNA gene-based microbiome analysis identifies candidate bacterial strains that increase the storage time of potato tubers
Franziska Buchholz (2021)
10.3389/fpls.2021.634960
Life on the Rocks: First Insights Into the Microbiota of the Threatened Aquatic Rheophyte Hanseniella heterophylla
W. Purahong (2021)
10.1093/femsec/fiab107
Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices.
R. Ezazi (2021)
10.3390/applmicrobiol1020013
An Examination of Fungal and Bacterial Assemblages in Bulk and Rhizosphere Soils under Solanum tuberosum in Southeastern Wyoming, USA
Gordon Custer (2021)
10.1111/1462-2920.15469
Global analysis of the apple fruit microbiome: Are all apples the same?
A. Abdelfattah (2021)
10.1016/J.APSOIL.2021.104147
Soil bacterial diversity related to soil compaction and aggregates sizes in potato cropping systems
Yan Xu (2021)
10.1016/J.TIFS.2021.02.017
Technological aspects of kombucha, its applications and the symbiotic culture (SCOBY), and extraction of compounds of interest: A literature review
Marcelo Gomes Soares (2021)
10.1007/978-3-030-38453-1_14
Global Scenario of Plant–Microbiome for Sustainable Agriculture: Current Advancements and Future Challenges
Simranjeet Singh (2020)
10.1002/9781119505457.CH13
Biotechnology of Plant‐Associated Microbiomes
S. T. Dinh (2020)
10.1039/c9em00498j
Multi-element (C, H, Cl, Br) stable isotope fractionation as a tool to investigate transformation processes for halogenated hydrocarbons.
A. Ojeda (2020)
10.1007/978-3-030-38453-1
Plant Microbiomes for Sustainable Agriculture
Ajar Nath Yadav (2020)
10.1038/s41598-020-77417-z
The microbiota of farmed mink (Neovison vison) follows a successional development and is affected by early life antibiotic exposure
M. Bahl (2020)
10.1007/978-981-15-8249-3_18
Genetic and Management Options for Controlling Striga
P. J. Rich (2020)
10.7717/peerj.8541
Rhizosphere bacterial and fungal communities during the growth of Angelica sinensis seedlings cultivated in an Alpine uncultivated meadow soil
Zhigang An (2020)
10.1007/978-3-030-50395-6
Plant Microbiome Paradigm
A. Varma (2020)
10.1111/1462-2920.15240
The plant endosphere world - bacterial life within plants.
S. Compant (2020)
10.1007/s00227-020-03717-7
The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea
R. Xavier (2020)
10.1099/mic.0.000904
Microbiome diversity and composition varies across body areas in a freshwater turtle.
Donald T. McKnight (2020)
10.1101/2020.02.16.951384
What drives the assembly of plant-associated protist microbiomes?
Kenneth Dumack (2020)
10.3390/d12100392
Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity
Jennifer Estendorfer (2020)
10.1038/s41598-020-78891-1
An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health
Scott Sugden (2020)
10.3389/fmicb.2020.585690
Exploring the Microbiota of East African Indigenous Leafy Greens for Plant Growth, Health, and Resilience
J. Taffner (2020)
10.1080/24750263.2020.1844322
The microbiota of the Lasius fuliginosus – Pella laticollis myrmecophilous interaction
A. Kaczmarczyk-Ziemba (2020)
10.3390/microorganisms8020170
Revealing the Variation and Stability of Bacterial Communities in Tomato Rhizosphere Microbiota
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