Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence

Colin, Y.; Nicolitch, O.; Van Nostrand, J. D.; Zhou, J. Z.; Turpault, M. -P.; Uroz, S.

doi:10.1038/s41598-017-07639-1

Title: Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence

Journal Article · 29 August 2017 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-07639-1 · OSTI ID:1567096

Colin, Y. ^[1];

^[1];

^[2]; Zhou, J. Z. ^[3]; Turpault, M. -P. ^[1]; Uroz, S. ^[1]

Univ. de Lorraine, Champenoux (France)
Univ. of Oklahoma, Norman, OK (United States)
Univ. of Oklahoma, Norman, OK (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; Tsinghua Univ., Beijing (China)

It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1567096

Journal Information:: Scientific Reports, Vol. 7, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 41 works

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References (136)

The ecological engineering impact of a single tree species on the soil microbial community: Tree impacts on the soil microbial community Mitchell, Ruth J.; Campbell, Colin D.; Chapman, Stephen J. Journal of Ecology, Vol. 98, Issue 1 https://doi.org/10.1111/j.1365-2745.2009.01601.x	journal	January 2010
Effects of soil water content, fertilization, light, weed competition and seedbed type on natural regeneration of beech (Fagus sylvatica) Madsen, Palle Forest Ecology and Management, Vol. 72, Issue 2-3 https://doi.org/10.1016/0378-1127(95)97453-Y	journal	April 1995
Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase Uroz, S.; Tech, J. J.; Sawaya, N. A. Soil Biology and Biochemistry, Vol. 69 https://doi.org/10.1016/j.soilbio.2013.11.002	journal	February 2014
The Structure, Distribution, and Biomass of the World's Forests Pan, Yude; Birdsey, Richard A.; Phillips, Oliver L. Annual Review of Ecology, Evolution, and Systematics, Vol. 44, Issue 1 https://doi.org/10.1146/annurev-ecolsys-110512-135914	journal	November 2013
Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities Paula, Fabiana S.; Rodrigues, Jorge L. M.; Zhou, Jizhong Molecular Ecology, Vol. 23, Issue 12 https://doi.org/10.1111/mec.12786	journal	June 2014
Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soil Priha, Outi; Grayston, Susan J.; Pennanen, Taina FEMS Microbiology Ecology, Vol. 30, Issue 2 https://doi.org/10.1111/j.1574-6941.1999.tb00647.x	journal	October 1999
Functional Diversity of Culturable Bacterial Communities in the Rhizosphere in Relation to Fine-root and Soil Parameters in Alder Stands on Forest, Abandoned Agricultural, and Oil-shale Mining Areas Lõhmus, K.; Truu, M.; Truu, J. Plant and Soil, Vol. 283, Issue 1-2 https://doi.org/10.1007/s11104-005-2509-8	journal	May 2006
Influence of Forest Trees on the Distribution of Mineral Weathering-Associated Bacterial Communities of the Scleroderma citrinum Mycorrhizosphere Calvaruso, C.; Turpault, M. -P.; Leclerc, E. Applied and Environmental Microbiology, Vol. 76, Issue 14 https://doi.org/10.1128/aem.03040-09	journal	May 2010
Root exudates as mediators of mineral acquisition in low-nutrient environments Dakora, Felix D.; Phillips, Donald A. Plant and Soil, Vol. 245, Issue 1, p. 35-47 https://doi.org/10.1023/A:1020809400075	journal	January 2002
Antibiotic-producing ability by representatives of a newly discovered lineage of actinomycetes Busti, E. Microbiology, Vol. 152, Issue 3 https://doi.org/10.1099/mic.0.28335-0	journal	March 2006
Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants Poomthongdee, Nalin; Duangmal, Kannika; Pathom-aree, Wasu The Journal of Antibiotics, Vol. 68, Issue 2 https://doi.org/10.1038/ja.2014.117	journal	August 2014
Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests Kaiser, Kristin; Wemheuer, Bernd; Korolkow, Vera Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep33696	journal	September 2016
Beyond the Venn diagram: the hunt for a core microbiome: The hunt for a core microbiome Shade, Ashley; Handelsman, Jo Environmental Microbiology, Vol. 14, Issue 1 https://doi.org/10.1111/j.1462-2920.2011.02585.x	journal	October 2011
The CRISPR-Cas immune system: Biology, mechanisms and applications Rath, Devashish; Amlinger, Lina; Rath, Archana Biochimie, Vol. 117 https://doi.org/10.1016/j.biochi.2015.03.025	journal	October 2015
Defining the core Arabidopsis thaliana root microbiome Lundberg, Derek S.; Lebeis, Sarah L.; Paredes, Sur Herrera Nature, Vol. 488, Issue 7409 https://doi.org/10.1038/nature11237	journal	August 2012
DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes Plagens, André; Richter, Hagen; Charpentier, Emmanuelle FEMS Microbiology Reviews, Vol. 39, Issue 3 https://doi.org/10.1093/femsre/fuv019	journal	April 2015
Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition de Ridder-Duine, Annelies S.; Kowalchuk, George A.; Klein Gunnewiek, Paulien J. A. Soil Biology and Biochemistry, Vol. 37, Issue 2 https://doi.org/10.1016/j.soilbio.2004.08.005	journal	February 2005
Seasons differently impact the structure of mineral weathering bacterial communities in beech and spruce stands Collignon, C.; Uroz, S.; Turpault, M-P. Soil Biology and Biochemistry, Vol. 43, Issue 10 https://doi.org/10.1016/j.soilbio.2011.05.008	journal	October 2011
The Human Microbiome Project Turnbaugh, Peter J.; Ley, Ruth E.; Hamady, Micah Nature, Vol. 449, Issue 7164 https://doi.org/10.1038/nature06244	journal	October 2007
Plant-Growth-Promoting Rhizobacteria Lugtenberg, Ben; Kamilova, Faina Annual Review of Microbiology, Vol. 63, Issue 1 https://doi.org/10.1146/annurev.micro.62.081307.162918	journal	October 2009
Multiple dimensions of resource limitation in tropical forests Townsend, A. R.; Asner, G. P. Proceedings of the National Academy of Sciences, Vol. 110, Issue 13 https://doi.org/10.1073/pnas.1301606110	journal	March 2013
Soil acidity affects fine root turnover of European beech Richter, A. K.; Hajdas, I.; Frossard, E. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, Vol. 147, Issue 1 https://doi.org/10.1080/11263504.2012.742471	journal	November 2012
On the niche breadth of Fagus sylvatica : soil nutrient status in 50 Central European beech stands on a broad range of bedrock types Leuschner, Christoph; Meier, Ina C.; Hertel, Dietrich Annals of Forest Science, Vol. 63, Issue 4 https://doi.org/10.1051/forest:2006016	journal	May 2006
Rhizosphere Microbial Community Structure in Relation to Root Location and Plant Iron Nutritional Status Yang, C. -H.; Crowley, D. E. Applied and Environmental Microbiology, Vol. 66, Issue 1 https://doi.org/10.1128/AEM.66.1.345-351.2000	journal	January 2000
Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees Graff, Andrea; Conrad, Ralf FEMS Microbiology Ecology, Vol. 53, Issue 3 https://doi.org/10.1016/j.femsec.2005.01.009	journal	August 2005
Biological costs and benefits to plant–microbe interactions in the rhizosphere Morgan, J. A. W.; Bending, G. D.; White, P. J. Journal of Experimental Botany, Vol. 56, Issue 417 https://doi.org/10.1093/jxb/eri205	journal	May 2005
Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce Schreiter, Susanne; Ding, Guo-Chun; Heuer, Holger Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00144	journal	April 2014
454 Pyrosequencing Analysis of Fungal Assemblages from Geographically Distant, Disparate Soils Reveals Spatial Patterning and a Core Mycobiome Orgiazzi, Alberto; Bianciotto, Valeria; Bonfante, Paola Diversity, Vol. 5, Issue 1 https://doi.org/10.3390/d5010073	journal	February 2013
Selective progressive response of soil microbial community to wild oat roots DeAngelis, Kristen M.; Brodie, Eoin L.; DeSantis, Todd Z. The ISME Journal, Vol. 3, Issue 2 https://doi.org/10.1038/ismej.2008.103	journal	November 2008
Viruses in soils: morphological diversity and abundance in the rhizosphere Swanson, M. M.; Fraser, G.; Daniell, T. J. Annals of Applied Biology, Vol. 155, Issue 1 https://doi.org/10.1111/j.1744-7348.2009.00319.x	journal	August 2009
Root distribution of Fagus sylvatica in a chronosequence in western France Bakker, M. R.; Turpault, M. -P.; Huet, S. Journal of Forest Research, Vol. 13, Issue 3 https://doi.org/10.1007/s10310-008-0068-6	journal	June 2008
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley Bulgarelli, Davide; Garrido-Oter, Ruben; Münch, Philipp C. Cell Host & Microbe, Vol. 17, Issue 3 https://doi.org/10.1016/j.chom.2015.01.011	journal	March 2015
Moving pictures of the human microbiome Caporaso, J. Gregory; Lauber, Christian L.; Costello, Elizabeth K. Genome Biology, Vol. 12, Issue 5 https://doi.org/10.1186/gb-2011-12-5-r50	journal	January 2011
Defining the core Arabidopsis thaliana root microbiome E., Ley, Ruth; Julien, Tremblay,; L., Dangl, Jeffery The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/w03e-5q36	text	January 2012
Going back to the roots: the microbial ecology of the rhizosphere Philippot, Laurent; Raaijmakers, Jos M.; Lemanceau, Philippe Nature Reviews Microbiology, Vol. 11, Issue 11 https://doi.org/10.1038/nrmicro3109	journal	September 2013
Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees Nicolitch, O.; Colin, Y.; Turpault, M. -P. Soil Biology and Biochemistry, Vol. 103 https://doi.org/10.1016/j.soilbio.2016.09.018	journal	December 2016
Soil pH controls the environmental availability of phosphorus: Experimental and mechanistic modelling approaches Devau, Nicolas; Cadre, Edith Le; Hinsinger, Philippe Applied Geochemistry, Vol. 24, Issue 11 https://doi.org/10.1016/j.apgeochem.2009.09.020	journal	November 2009
Soil bacterial and fungal communities across a pH gradient in an arable soil Rousk, Johannes; Bååth, Erland; Brookes, Philip C. The ISME Journal, Vol. 4, Issue 10 https://doi.org/10.1038/ismej.2010.58	journal	May 2010
Effect of the Mycorrhizosphere on the Genotypic and Metabolic Diversity of the Bacterial Communities Involved in Mineral Weathering in a Forest Soil Uroz, S.; Calvaruso, C.; Turpault, M. P. Applied and Environmental Microbiology, Vol. 73, Issue 9 https://doi.org/10.1128/aem.00121-07	journal	March 2007
Soil and plant effects on microbial community structure Buyer, Jeffrey S.; Roberts, Daniel P.; Russek-Cohen, Estelle Canadian Journal of Microbiology, Vol. 48, Issue 11 https://doi.org/10.1139/w02-095	journal	November 2002
Fine Root Biomass, Production, Turnover Rates, and Nutrient Contents in Boreal Forest Ecosystems in Relation to Species, Climate, Fertility, and Stand Age: Literature Review and Meta-Analyses Yuan, Z. Y.; Chen, Han Y. H. Critical Reviews in Plant Sciences, Vol. 29, Issue 4 https://doi.org/10.1080/07352689.2010.483579	journal	July 2010
Carbon flow in the rhizosphere: carbon trading at the soil–root interface Jones, D. L.; Nguyen, C.; Finlay, R. D. Plant and Soil, Vol. 321, Issue 1-2 https://doi.org/10.1007/s11104-009-9925-0	journal	February 2009
The influence of soil properties on the structure of bacterial and fungal communities across land-use types Lauber, Christian L.; Strickland, Michael S.; Bradford, Mark A. Soil Biology and Biochemistry, Vol. 40, Issue 9 https://doi.org/10.1016/j.soilbio.2008.05.021	journal	September 2008
Effect of the soil type on the microbiome in the rhizosphere of field-grown lettuce Schreiter, Susanne; Ding, Guo-Chun; Heuer, Holger Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00144	journal	April 2014
Soil and plant effects on microbial community structure Buyer, Jeffrey S.; Roberts, Daniel P.; Russek-Cohen, Estelle Canadian Journal of Microbiology, Vol. 48, Issue 11 https://doi.org/10.1139/w02-095	journal	November 2002
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota Bulgarelli, Davide; Rott, Matthias; Schlaeppi, Klaus Nature, Vol. 488, Issue 7409 https://doi.org/10.1038/nature11336	journal	August 2012
Saliva microbiomes distinguish caries-active from healthy human populations Yang, Fang; Zeng, Xiaowei; Ning, Kang The ISME Journal, Vol. 6, Issue 1 https://doi.org/10.1038/ismej.2011.71	journal	June 2011
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities Schloss, P. D.; Westcott, S. L.; Ryabin, T. Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541 https://doi.org/10.1128/AEM.01541-09	journal	October 2009
Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization Rousk, J.; Brookes, P. C.; Baath, E. Applied and Environmental Microbiology, Vol. 75, Issue 6 https://doi.org/10.1128/AEM.02775-08	journal	January 2009
Manipulating the soil microbiome to increase soil health and plant fertility Chaparro, Jacqueline M.; Sheflin, Amy M.; Manter, Daniel K. Biology and Fertility of Soils, Vol. 48, Issue 5 https://doi.org/10.1007/s00374-012-0691-4	journal	May 2012
The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts D. Ainsworth, Tracy; Krause, Lutz; Bridge, Thomas The ISME Journal, Vol. 9, Issue 10 https://doi.org/10.1038/ismej.2015.39	journal	April 2015
A global analysis of root distributions for terrestrial biomes Jackson, R. B.; Canadell, J.; Ehleringer, J. R. Oecologia, Vol. 108, Issue 3 https://doi.org/10.1007/BF00333714	journal	November 1996
Plant host habitat and root exudates shape soil bacterial community structure Haichar, Feth el Zahar; Marol, Christine; Berge, Odile The ISME Journal, Vol. 2, Issue 12 https://doi.org/10.1038/ismej.2008.80	journal	August 2008
Bacterial diversity promotes community stability and functional resilience after perturbation Girvan, M. S.; Campbell, C. D.; Killham, K. Environmental Microbiology, Vol. 7, Issue 3 https://doi.org/10.1111/j.1462-2920.2005.00695.x	journal	March 2005
Distribution of above-ground and below-ground carbohydrate reserves in adult trees of two contrasting broad-leaved species (Quercus petraea and Fagus sylvatica) Barbaroux, C.; Breda, N.; Dufrene, E. New Phytologist, Vol. 157, Issue 3 https://doi.org/10.1046/j.1469-8137.2003.00681.x	journal	March 2003
Modeling wave-like dynamics of oligotrophic and copiotrophic bacteria along wheat roots in response to nutrient input from a growing root tip Zelenev, V. V.; van Bruggen, A. H. C.; Semenov, A. M. Ecological Modelling, Vol. 188, Issue 2-4 https://doi.org/10.1016/j.ecolmodel.2005.01.046	journal	November 2005
Development of a Common Oligonucleotide Reference Standard for Microarray Data Normalization and Comparison across Different Microbial Communities Liang, Y.; He, Z.; Wu, L. Applied and Environmental Microbiology, Vol. 76, Issue 4 https://doi.org/10.1128/AEM.02749-09	journal	December 2009
The CRISPR-Cas immune system: Biology, mechanisms and applications Rath, Devashish; Amlinger, Lina; Rath, Archana Biochimie, Vol. 117 https://doi.org/10.1016/j.biochi.2015.03.025	journal	October 2015
Bioactive Microbial Metabolites: A Personal View Bérdy, János The Journal of Antibiotics, Vol. 58, Issue 1 https://doi.org/10.1038/ja.2005.1	journal	January 2005
Species distributions in response to individual soil nutrients and seasonal drought across a community of tropical trees Condit, R.; Engelbrecht, B. M. J.; Pino, D. Proceedings of the National Academy of Sciences, Vol. 110, Issue 13 https://doi.org/10.1073/pnas.1218042110	journal	February 2013
Root exudation and root development of lettuce (Lactuca sativa L. cv. Tizian) as affected by different soils Neumann, G.; Bott, S.; Ohler, M. A. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00002	journal	January 2014
Rhizospheric P and K in forest soil manipulated with ammonium sulfate and water Clegg, Stephen; Gobran, George R. Canadian Journal of Soil Science, Vol. 77, Issue 4 https://doi.org/10.4141/s95-070	journal	November 1997
Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification Wu, L.; Liu, X.; Schadt, C. W. Applied and Environmental Microbiology, Vol. 72, Issue 7 https://doi.org/10.1128/AEM.02738-05	journal	July 2006
On the niche breadth of Fagus sylvatica : soil nutrient status in 50 Central European beech stands on a broad range of bedrock types Leuschner, Christoph; Meier, Ina C.; Hertel, Dietrich Annals of Forest Science, Vol. 63, Issue 4 https://doi.org/10.1051/forest:2006016	journal	May 2006
Vertical distribution and radial growth of coarse roots in pure and mixed stands of Fagus sylvatica and Picea abies Schmid, Iris; Kazda, Marian Canadian Journal of Forest Research, Vol. 31, Issue 3 https://doi.org/10.1139/x00-195	journal	March 2001
Land use change alters functional gene diversity, composition and abundance in Amazon forest soil microbial communities Paula, Fabiana S.; Rodrigues, Jorge L. M.; Zhou, Jizhong Molecular Ecology, Vol. 23, Issue 12 https://doi.org/10.1111/mec.12786	journal	June 2014
Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession Wang, Miao; Yang, Pu; Falcão Salles, Joana Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.01188	journal	January 2016
The ecological engineering impact of a single tree species on the soil microbial community: Tree impacts on the soil microbial community Mitchell, Ruth J.; Campbell, Colin D.; Chapman, Stephen J. Journal of Ecology, Vol. 98, Issue 1 https://doi.org/10.1111/j.1365-2745.2009.01601.x	journal	January 2010
A Core Human Microbiome as Viewed through 16S rRNA Sequence Clusters Huse, Susan M.; Ye, Yuzhen; Zhou, Yanjiao PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0034242	journal	June 2012
Plant-Growth-Promoting Rhizobacteria Lugtenberg, Ben; Kamilova, Faina Annual Review of Microbiology, Vol. 63, Issue 1 https://doi.org/10.1146/annurev.micro.62.081307.162918	journal	October 2009
Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase Uroz, S.; Tech, J. J.; Sawaya, N. A. Soil Biology and Biochemistry, Vol. 69 https://doi.org/10.1016/j.soilbio.2013.11.002	journal	February 2014
DNA and RNA interference mechanisms by CRISPR-Cas surveillance complexes Plagens, André; Richter, Hagen; Charpentier, Emmanuelle FEMS Microbiology Reviews, Vol. 39, Issue 3 https://doi.org/10.1093/femsre/fuv019	journal	April 2015
Microbial activities related to C and N cycling and microbial community structure in the rhizospheres of Pinus sylvestris, Picea abies and Betula pendula seedlings in an organic and mineral soil Priha, Outi; Grayston, Susan J.; Pennanen, Taina FEMS Microbiology Ecology, Vol. 30, Issue 2 https://doi.org/10.1111/j.1574-6941.1999.tb00647.x	journal	October 1999
Viruses in soils: morphological diversity and abundance in the rhizosphere Swanson, M. M.; Fraser, G.; Daniell, T. J. Annals of Applied Biology, Vol. 155, Issue 1 https://doi.org/10.1111/j.1744-7348.2009.00319.x	journal	August 2009
Biological costs and benefits to plant–microbe interactions in the rhizosphere Morgan, J. A. W.; Bending, G. D.; White, P. J. Journal of Experimental Botany, Vol. 56, Issue 417 https://doi.org/10.1093/jxb/eri205	journal	May 2005
454 Pyrosequencing Analysis of Fungal Assemblages from Geographically Distant, Disparate Soils Reveals Spatial Patterning and a Core Mycobiome Orgiazzi, Alberto; Bianciotto, Valeria; Bonfante, Paola Diversity, Vol. 5, Issue 1 https://doi.org/10.3390/d5010073	journal	February 2013
Functional Diversity of Culturable Bacterial Communities in the Rhizosphere in Relation to Fine-root and Soil Parameters in Alder Stands on Forest, Abandoned Agricultural, and Oil-shale Mining Areas Lõhmus, K.; Truu, M.; Truu, J. Plant and Soil, Vol. 283, Issue 1-2 https://doi.org/10.1007/s11104-005-2509-8	journal	May 2006
Selective progressive response of soil microbial community to wild oat roots DeAngelis, Kristen M.; Brodie, Eoin L.; DeSantis, Todd Z. The ISME Journal, Vol. 3, Issue 2 https://doi.org/10.1038/ismej.2008.103	journal	November 2008
Impact of forest tree species on feldspar weathering rates Augusto, Laurent; Turpault, Marie-Pierre; Ranger, Jacques Geoderma, Vol. 96, Issue 3 https://doi.org/10.1016/s0016-7061(00)00021-5	journal	June 2000
Toward an Ecological Classification of soil Bacteria Fierer, Noah; Bradford, Mark A.; Jackson, Robert B. Ecology, Vol. 88, Issue 6 https://doi.org/10.1890/05-1839	journal	June 2007
Vertical distribution and radial growth of coarse roots in pure and mixed stands of Fagus sylvatica and Picea abies Schmid, Iris; Kazda, Marian Canadian Journal of Forest Research, Vol. 31, Issue 3 https://doi.org/10.1139/x00-195	journal	March 2001
Soil acidity affects fine root turnover of European beech Richter, A. K.; Hajdas, I.; Frossard, E. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, Vol. 147, Issue 1 https://doi.org/10.1080/11263504.2012.742471	journal	November 2012
Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale Lauber, C. L.; Hamady, M.; Knight, R. Applied and Environmental Microbiology, Vol. 75, Issue 15 https://doi.org/10.1128/AEM.00335-09	journal	June 2009
Influence of chronic ozone stress on carbon translocation pattern into rhizosphere microbial communities of beech trees (Fagus sylvatica L.) during a growing season Esperschütz, Jürgen; Pritsch, Karin; Gattinger, Andreas Plant and Soil, Vol. 323, Issue 1-2 https://doi.org/10.1007/s11104-009-0090-2	journal	July 2009
Seasons differently impact the structure of mineral weathering bacterial communities in beech and spruce stands Collignon, C.; Uroz, S.; Turpault, M-P. Soil Biology and Biochemistry, Vol. 43, Issue 10 https://doi.org/10.1016/j.soilbio.2011.05.008	journal	October 2011
Influence of mature Douglas fir roots on the solid soil phase of the rhizosphere and its solution chemistry Turpault, M. -P.; Utérano, C.; Boudot, J. -P. Plant and Soil, Vol. 275, Issue 1-2 https://doi.org/10.1007/s11104-005-2584-x	journal	August 2005
Soil properties and tree species drive ß-diversity of soil bacterial communities Landesman, William J.; Nelson, David M.; Fitzpatrick, Matthew C. Soil Biology and Biochemistry, Vol. 76 https://doi.org/10.1016/j.soilbio.2014.05.025	journal	September 2014
Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes: Research review Hinsinger, Philippe; Gobran, George R.; Gregory, Peter J. New Phytologist, Vol. 168, Issue 2 https://doi.org/10.1111/j.1469-8137.2005.01512.x	journal	August 2005
Defining the core Arabidopsis thaliana root microbiome Lundberg, Derek S.; Lebeis, Sarah L.; Paredes, Sur Herrera Nature, Vol. 488, Issue 7409 https://doi.org/10.1038/nature11237	journal	August 2012
Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil Uroz, Stéphane; Buée, Marc; Murat, Claude Environmental Microbiology Reports, Vol. 2, Issue 2 https://doi.org/10.1111/j.1758-2229.2009.00117.x	journal	April 2010
Effects of elevational range shift on the morphology and physiology of a carabid beetle invading the sub-Antarctic Kerguelen Islands Ouisse, T.; Day, E.; Laville, L. Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-57868-0	journal	January 2020
The Mineral Nutrition of Wild Plants Chapin, F. S. Annual Review of Ecology and Systematics, Vol. 11, Issue 1 https://doi.org/10.1146/annurev.es.11.110180.001313	journal	November 1980
Plant host habitat and root exudates shape soil bacterial community structure Haichar, Feth el Zahar; Marol, Christine; Berge, Odile The ISME Journal, Vol. 2, Issue 12 https://doi.org/10.1038/ismej.2008.80	journal	August 2008
Fine Root Biomass, Production, Turnover Rates, and Nutrient Contents in Boreal Forest Ecosystems in Relation to Species, Climate, Fertility, and Stand Age: Literature Review and Meta-Analyses Yuan, Z. Y.; Chen, Han Y. H. Critical Reviews in Plant Sciences, Vol. 29, Issue 4 https://doi.org/10.1080/07352689.2010.483579	journal	July 2010
The Diversity of Archaea and Bacteria in Association with the Roots of Zea mays L. Chelius, M. K.; Triplett, E. W. Microbial Ecology, Vol. 41, Issue 3 https://doi.org/10.1007/s002480000087	journal	February 2001
Plants impact structure and function of bacterial communities in Arctic soils Kumar, Manoj; Männistö, Minna K.; van Elsas, Jan Dirk Plant and Soil, Vol. 399, Issue 1-2 https://doi.org/10.1007/s11104-015-2702-3	journal	October 2015
Influence of Different Cultivars on Populations of Ammonia-Oxidizing Bacteria in the Root Environment of Rice Briones, A. M.; Okabe, S.; Umemiya, Y. Applied and Environmental Microbiology, Vol. 68, Issue 6 https://doi.org/10.1128/AEM.68.6.3067-3075.2002	journal	June 2002
Plant-driven selection of microbes Hartmann, Anton; Schmid, Michael; Tuinen, Diederik van Plant and Soil, Vol. 321, Issue 1-2 https://doi.org/10.1007/s11104-008-9814-y	journal	November 2008
A core gut microbiome in obese and lean twins Turnbaugh, Peter J.; Hamady, Micah; Yatsunenko, Tanya Nature, Vol. 457, Issue 7228 https://doi.org/10.1038/nature07540	journal	November 2008
Distribution of above-ground and below-ground carbohydrate reserves in adult trees of two contrasting broad-leaved species (Quercus petraea and Fagus sylvatica) Barbaroux, C.; Breda, N.; Dufrene, E. New Phytologist, Vol. 157, Issue 3 https://doi.org/10.1046/j.1469-8137.2003.00681.x	journal	March 2003
Vertical distribution and radial growth of coarse roots in pure and mixed stands of Fagus sylvatica and Picea abies Schmid, Iris; Kazda, Marian Canadian Journal of Forest Research, Vol. 31, Issue 3 https://doi.org/10.1139/cjfr-31-3-539	journal	January 2001
Does natural regeneration determine the limit of European beech distribution under climatic stress? E. Silva, D.; Rezende Mazzella, P.; Legay, M. Forest Ecology and Management, Vol. 266 https://doi.org/10.1016/j.foreco.2011.11.031	journal	February 2012
Bacterial communities in Arctic fjelds of Finnish Lapland are stable but highly pH-dependent: Bacterial communities in Arctic fjelds of Finnish Lapland MÃ¤nnistÃ¶, Minna K.; Tiirola, Marja; HÃ¤ggblom, Max M. FEMS Microbiology Ecology, Vol. 59, Issue 2 https://doi.org/10.1111/j.1574-6941.2006.00232.x	journal	February 2007
A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees Shakya, Migun; Gottel, Neil; Castro, Hector PLoS ONE, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pone.0076382	journal	October 2013
Acidophilic actinomycetes from rhizosphere soil: diversity and properties beneficial to plants Poomthongdee, Nalin; Duangmal, Kannika; Pathom-aree, Wasu The Journal of Antibiotics, Vol. 68, Issue 2 https://doi.org/10.1038/ja.2014.117	journal	August 2014
Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences Jeanbille, M.; Buée, M.; Bach, C. Microbial Ecology, Vol. 71, Issue 2 https://doi.org/10.1007/s00248-015-0669-5	journal	September 2015
Vertical distribution of the soil microbiota along a successional gradient in a glacier forefield Rime, Thomas; Hartmann, Martin; Brunner, Ivano Molecular Ecology, Vol. 24, Issue 5 https://doi.org/10.1111/mec.13051	journal	January 2015
Soil bacterial and fungal communities across a pH gradient in an arable soil Rousk, Johannes; Bååth, Erland; Brookes, Philip C. The ISME Journal, Vol. 4, Issue 10 https://doi.org/10.1038/ismej.2010.58	journal	May 2010
Soil type determines the distribution of nutrient mobilizing bacterial communities in the rhizosphere of beech trees Nicolitch, O.; Colin, Y.; Turpault, M. -P. Soil Biology and Biochemistry, Vol. 103 https://doi.org/10.1016/j.soilbio.2016.09.018	journal	December 2016
A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees Shakya, Migun; Gottel, Neil; Castro, Hector PLoS ONE, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pone.0076382	journal	October 2013
The influence of soil properties on the structure of bacterial and fungal communities across land-use types Lauber, Christian L.; Strickland, Michael S.; Bradford, Mark A. Soil Biology and Biochemistry, Vol. 40, Issue 9 https://doi.org/10.1016/j.soilbio.2008.05.021	journal	September 2008
Carbon flow in the rhizosphere: carbon trading at the soil–root interface Jones, D. L.; Nguyen, C.; Finlay, R. D. Plant and Soil, Vol. 321, Issue 1-2 https://doi.org/10.1007/s11104-009-9925-0	journal	February 2009
Bioactive Microbial Metabolites: A Personal View Bérdy, János The Journal of Antibiotics, Vol. 58, Issue 1 https://doi.org/10.1038/ja.2005.1	journal	January 2005
Enrichment of specific bacterial and eukaryotic microbes in the rhizosphere of switchgrass ( P anicum virgatum L.) through root exudates : Root exudate-utilizing microbes in switchgrass rhizosphere Mao, Yuejian; Li, Xiangzhen; Smyth, Eoghan M. Environmental Microbiology Reports, Vol. 6, Issue 3 https://doi.org/10.1111/1758-2229.12152	journal	March 2014
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley Bulgarelli, Davide; Garrido-Oter, Ruben; Münch, Philipp C. Cell Host & Microbe, Vol. 17, Issue 3 https://doi.org/10.1016/j.chom.2015.01.011	journal	March 2015
Moving pictures of the human microbiome Caporaso, J. Gregory; Lauber, Christian L.; Costello, Elizabeth K. Genome Biology, Vol. 12, Issue 5 https://doi.org/10.1186/gb-2011-12-5-r50	journal	January 2011
Changes in water extractable metals, pH and organic carbon concentrations at the soil-root interface of forested soils Séguin, Véronique; Gagnon, Christian; Courchesne, François Plant and Soil, Vol. 260, Issue 1/2 https://doi.org/10.1023/B:PLSO.0000030170.49493.5f	journal	March 2004
Bacterial diversity promotes community stability and functional resilience after perturbation Girvan, M. S.; Campbell, C. D.; Killham, K. Environmental Microbiology, Vol. 7, Issue 3 https://doi.org/10.1111/j.1462-2920.2005.00695.x	journal	March 2005
The coral core microbiome identifies rare bacterial taxa as ubiquitous endosymbionts D. Ainsworth, Tracy; Krause, Lutz; Bridge, Thomas The ISME Journal, Vol. 9, Issue 10 https://doi.org/10.1038/ismej.2015.39	journal	April 2015
Manipulating the soil microbiome to increase soil health and plant fertility Chaparro, Jacqueline M.; Sheflin, Amy M.; Manter, Daniel K. Biology and Fertility of Soils, Vol. 48, Issue 5 https://doi.org/10.1007/s00374-012-0691-4	journal	May 2012
Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems Uroz, Stéphane; Oger, Phil; Lepleux, Cendrella Research in Microbiology, Vol. 162, Issue 9 https://doi.org/10.1016/j.resmic.2011.01.013	journal	November 2011
Role of root derived organic acids in the mobilization of nutrients from the rhizosphere Jones, David L.; Darrah, Peter R. Plant and Soil, Vol. 166, Issue 2 https://doi.org/10.1007/BF00008338	journal	October 1994
Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere: Plant species, soil type and rhizosphere communities Berg, Gabriele; Smalla, Kornelia FEMS Microbiology Ecology, Vol. 68, Issue 1 https://doi.org/10.1111/j.1574-6941.2009.00654.x	journal	April 2009
Modeling wave-like dynamics of oligotrophic and copiotrophic bacteria along wheat roots in response to nutrient input from a growing root tip Zelenev, V. V.; van Bruggen, A. H. C.; Semenov, A. M. Ecological Modelling, Vol. 188, Issue 2-4 https://doi.org/10.1016/j.ecolmodel.2005.01.046	journal	November 2005
Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota Bulgarelli, Davide; Rott, Matthias; Schlaeppi, Klaus Nature, Vol. 488, Issue 7409 https://doi.org/10.1038/nature11336	journal	August 2012
The diversity and biogeography of soil bacterial communities Fierer, N.; Jackson, R. B. Proceedings of the National Academy of Sciences, Vol. 103, Issue 3 https://doi.org/10.1073/pnas.0507535103	journal	January 2006
Low-molecular organic acids in the rhizosphere soil solution of beech forest (Fagus sylvatica L.) cambisols determined by ion chromatography using supported liquid membrane enrichment technique Shen, Yin; Ström, Lena; Jönsson, Jan-Åke Soil Biology and Biochemistry, Vol. 28, Issue 9 https://doi.org/10.1016/0038-0717(96)00119-8	journal	September 1996
Impact of flooding on soil bacterial communities associated with poplar (Populus sp.) trees Graff, Andrea; Conrad, Ralf FEMS Microbiology Ecology, Vol. 53, Issue 3 https://doi.org/10.1016/j.femsec.2005.01.009	journal	August 2005
Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip Van Nostrand, Joy D.; Yin, Huaqin; Wu, Liyou Microbial Environmental Genomics (MEG) https://doi.org/10.1007/978-1-4939-3369-3_11	book	January 2016
Rhizosphere bacterial community composition in natural stands of Carex arenaria (sand sedge) is determined by bulk soil community composition de Ridder-Duine, Annelies S.; Kowalchuk, George A.; Klein Gunnewiek, Paulien J. A. Soil Biology and Biochemistry, Vol. 37, Issue 2 https://doi.org/10.1016/j.soilbio.2004.08.005	journal	February 2005
Saliva microbiomes distinguish caries-active from healthy human populations Yang, Fang; Zeng, Xiaowei; Ning, Kang The ISME Journal, Vol. 6, Issue 1 https://doi.org/10.1038/ismej.2011.71	journal	June 2011
The Structure, Distribution, and Biomass of the World's Forests Pan, Yude; Birdsey, Richard A.; Phillips, Oliver L. Annual Review of Ecology, Evolution, and Systematics, Vol. 44, Issue 1 https://doi.org/10.1146/annurev-ecolsys-110512-135914	journal	November 2013
Rhizosphere geometry and heterogeneity arising from root-mediated physical and chemical processes: Research review Hinsinger, Philippe; Gobran, George R.; Gregory, Peter J. New Phytologist, Vol. 168, Issue 2 https://doi.org/10.1111/j.1469-8137.2005.01512.x	journal	August 2005
Toward an Ecological Classification of soil Bacteria Fierer, Noah; Bradford, Mark A.; Jackson, Robert B. Ecology, Vol. 88, Issue 6 https://doi.org/10.1890/05-1839	journal	June 2007
Iron Dynamics in the Rhizosphere Robin, A.; Vansuyt, G.; Hinsinger, P. Advances in Agronomy https://doi.org/10.1016/S0065-2113(08)00404-5	book	January 2008
FactoMineR : An R Package for Multivariate Analysis Lê, Sébastien; Josse, Julie; Husson, François Journal of Statistical Software, Vol. 25, Issue 1 https://doi.org/10.18637/jss.v025.i01	journal	January 2008

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