The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors

Buée, Marc; Boer, Wietse de; Martin, Francis; Overbeek, L.S. van; Jurkevitch, Édouard

doi:10.1007/s11104-009-9991-3

Cited by 399 publications

(255 citation statements)

References 196 publications

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“…This consistency suggests that generally maize selects independent of its variety, age or soil in which it was cultivated for a similar core bacterial community, which is also quite similar to dominant members from other plant species (Buee et al, 2009;da Rocha et al, 2009). In contrast to the low-throughput sequencing methods that are typically limited to the most dominant 100 phylotypes (rRNA genes; Dunbar et al, 2001;Janssen, 2006;Schü tte et al, 2008;Aiken, 2011), the pyrosequencing applied here detected 510 different genera and 61 000 superior OTUs, thus, opening the view on the less abundant, 'rare' community members by a factor of more than two orders of magnitude.…”

Section: Discussionmentioning

confidence: 83%

“…The easily available carbon sources exert a great selective power on the enrichment of soil bacteria and may attract both beneficial and detrimental bacteria. Differences in rhizodeposition by the plants are reflected by differently composed bacterial communities in the rhizosphere (Brimecombe et al, 2001) as they become evident between different plant species (Dohrmann and Tebbe, 2005) or cultivars grown in the same soil (Buee et al, 2009) and even across different root sections of the same plant (Watt et al, 2006). GM Bt-maize events produce Cry proteins, typically also in their root tissue.…”

Section: Introductionmentioning

confidence: 99%

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Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties

et al. 2012

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Ribosomal 16S rRNA gene pyrosequencing was used to explore whether the genetically modified (GM) Bt-maize hybrid MON 89034 × MON 88017, expressing three insecticidal recombinant Cry proteins of Bacillus thuringiensis, would alter the rhizosphere bacterial community. Fine roots of field cultivated Bt-maize and three conventional maize varieties were analyzed together with coarse roots of the Bt-maize. A total of 547 000 sequences were obtained. Library coverage was 100% at the phylum and 99.8% at the genus rank. Although cluster analyses based on relative abundances indicated no differences at higher taxonomic ranks, genera abundances pointed to variety specific differences. Genera-based clustering depended solely on the 49 most dominant genera while the remaining 461 rare genera followed a different selection. A total of 91 genera responded significantly to the different root environments. As a benefit of pyrosequencing, 79 responsive genera were identified that might have been overlooked with conventional cloning sequencing approaches owing to their rareness. There was no indication of bacterial alterations in the rhizosphere of the Bt-maize beyond differences found between conventional varieties. B. thuringiensis-like phylotypes were present at low abundance (0.1% of Bacteria) suggesting possible occurrence of natural Cry proteins in the rhizospheres. Although some genera indicated potential phytopathogenic bacteria in the rhizosphere, their abundances were not significantly different between conventional varieties and Bt-maize. With an unprecedented sensitivity this study indicates that the rhizosphere bacterial community of a GM maize did not respond abnormally to the presence of three insecticidal proteins in the root tissue.

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Section: Discussionmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties

et al. 2012

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“…The rhizosphere may be more limited to millimeters around roots and more severe influence by roots would be expected. 24 The mass-flow of As from bulk soil during water assimilation into rice roots, together with the fast efflux of As(III) from roots, 42 also contributed to the replenishment of dissolved As to the rice rhizosphere. Thus, the actual effects of As oxidation and sequestration in the rice rhizosphere are likely more profound than the observed (16.8% and 13.5% lower than in bulk soil solution for YD and NK, respectively), shown by the fact that As accumulation on the root surface alone was higher than that accumulated in the whole plant.…”

Section: ■ Discussionmentioning

confidence: 99%

Arsenic Uptake by Rice Is Influenced by Microbe-Mediated Arsenic Redox Changes in the Rhizosphere

Jia

Huang

Chen

et al. 2014

Environ. Sci. Technol.

180

119

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Arsenic (As) uptake by rice is largely determined by As speciation, which is strongly influenced by microbial activities. However, little is known about interactions between root and rhizosphere microbes, particularly on arsenic oxidation and reduction. In this study, two rice cultivars with different radial oxygen loss (ROL) ability were used to investigate the impact of microbially mediated As redox changes in the rhizosphere on As uptake. Results showed that the cultivar with higher ROL (Yangdao) had lower As uptake than that with lower ROL (Nongken). The enhancement of the rhizospheric effect on the abundance of the arsenite (As(III)) oxidase gene (aroA-like) was greater than on the arsenate (As(V)) reductase gene (arsC), and As(V) respiratory reductase gene (arrA), resulting in As oxidation and sequestration in the rhizosphere, particularly for cultivar Yangdao. The community of As(III)-oxidizing bacteria in the rhizosphere was dominated by α-Proteobacteria and β-Proteobacteria and was influenced by rhizospheric effects, rice straw application, growth stage, and cultivar. Application of rice straw into the soil increased As release and accumulation into rice plants. These results highlighted that uptake of As by rice is influenced by microbial processes, especially As oxidation in the rhizosphere, and these processes are influenced by root ROL and organic matter application. ■ INTRODUCTIONArsenic (As) contamination and its health impacts are widespread around the world. 1,2 Large areas of paddy soils are contaminated by As due to irrigation with As-tainted groundwater, mining, and other industrial activities. Rice is particularly efficient in accumulating As, compared with other cereal crops, as a result of its anaerobic growth conditions. 3 This poses potential harm to people through ingestion of rice, especially in Southeast Asia where rice is consumed as the staple food. 4−6 Rhizospheric chemical processes, such as iron oxidation−reduction and iron plaque formation on root surfaces, play an important role in affecting As uptake by rice plants, and they are largely influenced by oxygen release from rice roots. 7,8 The aerated rice rhizosphere and O 2 -releasing root surface are usually coated with iron (Fe) and manganese (Mn) oxides, while As is precipitated with these oxides mainly as arsenate (As(V)). 8,9 In addition to chemical processes, As speciation and mobility in soils, sediments, and natural water systems are mainly driven by microbial transformations. 10−12 Anaerobic bacteria containing the respiratory reductase (ArrA) can use As(V) as the terminal electron acceptor in respiration and conserve energy from this process. 13 Another pathway for microbial As(V) reduction lies in the widespread As detoxification by As(V) reductase (ArsC). 14,15 Arsenite (As(III)) is more weakly bound to most soil minerals than As(V); thus, As(V) reduction results in As release into soil solutions, especially under anaerobic conditions such as paddy soil. 16,17 On the other hand, some heterotrophic as well a...

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“…The ubiquitous presence of prokaryotes (archaea, bacteria) and eukaryotes in the mycorrhizosphere and on the surface of ectomycorrhizae is well documented (Garbaye 1994;Bomberg and Timonen 2007;Calvaruso et al 2007;Frey-Klett et al 2007, Buée et al 2009). There are increasing reports on interactions of saprotrophic fungi and bacteria with ECM in nutrient release from complex substrates (Koide and Kabir 2001;Leake et al 2002;Nurmiaho-Lassila et al 1997;Timonen et al 1998;Wu et al 2005;Wu et al 2003).…”

Section: Factors Influencing the Enzyme Activities Of Ecm Communitiesmentioning

confidence: 99%

Enzyme secretion by ECM fungi and exploitation of mineral nutrients from soil organic matter

Pritsch

Garbaye

2011

Annals of Forest Science

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Abstract· Introduction Important nutrients in forest soils such as nitrogen and phosphorus are mostly recycled from natural polymeric compounds contained in litter and organic debrisfor example nucleic acids, proteins, or chitin.· Objectives Activities of enzymes such as phosphatases, proteases, cellulases, chitinases and laccase were shown in saprotrophic but also in ectomycorrhizal fungi and there is increasing evidence that these enzymes contribute not only to the functioning of the symbiosis but also to the mobilisation of nutrients. In the present review, we describe how enzyme secretion and localisation on fungal hyphae may be connected to the potential role in soil nutrient cycling. · ResultsRecently developed methods for enzyme activity studies of ectomycorrhizae directly assayed in or collected from the field such as enzyme activity profiling and soil imprinting are described. Their value and limitations in different examples of ecological studies is highlighted and discussed also with respect to the role of other soil microorganisms associated with ectomycorrhizae. · ConclusionThe conclusion from our review is that enzyme activities of ECM and their associated microorganisms provide a potentially enormous plasticity of mycorrhizosphere functionality which is an open field for further research. Enzymes secrétés par les champignons ectomycorhiziens et exploitation des éléments minéraux contenus dans la matière organique du sol.

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The rhizosphere zoo: An overview of plant-associated communities of microorganisms, including phages, bacteria, archaea, and fungi, and of some of their structuring factors

Cited by 399 publications

References 196 publications

Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties

Importance of rare taxa for bacterial diversity in the rhizosphere of Bt- and conventional maize varieties

Arsenic Uptake by Rice Is Influenced by Microbe-Mediated Arsenic Redox Changes in the Rhizosphere

Enzyme secretion by ECM fungi and exploitation of mineral nutrients from soil organic matter

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