Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates

Henry, Sonia; Texier, Stéphanie; Hallet, Stéphanie; Bru, David; Dambreville, Christophe; Chèneby, Dominique; Bizouard, Florian; Germon, Jean-Claude; Philippot, Laurent

doi:10.1111/j.1462-2920.2008.01599.x

Cited by 262 publications

(213 citation statements)

References 67 publications

(85 reference statements)

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“…The lower concentration of nitrate might be because of the increased microbial activity observed in the rhizosphere, especially in contaminated soils, where bacteria were significantly more active and nitrate at its lowest concentration, being below the detection limit for two of the three replicates analyzed. Nitrate reduction was shown to be stimulated by root exudates (Henry et al, 2008), and, in this study, several nitrate reductase genes were more expressed in the rhizosphere of willow, offering another potential explanation for the lower nitrate concentration observed in the rhizosphere. Taken together, these data suggest that the stimulation of the rhizosphere hydrocarbon-degrading microorganisms by willows is not because of an increased nitrate input from the roots.…”

Section: Metatranscriptomics Of the Rhizospheresupporting

confidence: 49%

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

et al. 2013

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The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation.

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Section: Metatranscriptomics Of the Rhizospheresupporting

confidence: 49%

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

et al. 2013

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“…The addition of wheat residues had very limited effect on the denitrifier abundance monitored during 1 month. Accordingly, Miller et al (2008) showed that the number of the denitrifiers was not modified by the short-term addition of wheat, rape or alfafa residues and several studies suggest that carbon is not a strong driver of the denitrifier abundance in soil (Henry et al, 2008;Bru et al, 2011). Overall, serial dilution of the soil did not lead to a reduction in denitrifier abundances in the amended or non-amended microcosms after the pre-incubation period.…”

Section: Discussionmentioning

confidence: 87%

Loss in microbial diversity affects nitrogen cycling in soil

et al. 2013

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Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequencing. As expected, the diversity metrics indicated a decrease in diversity in the 1/10 3 and 1/10 5 dilution treatments compared with the undiluted one. However, the extent of dilution and the corresponding reduction in diversity were not commensurate, as a dilution of five orders of magnitude resulted in a 75% decrease in estimated richness. This reduction in denitrifier diversity resulted in a significantly lower potential denitrification activity in soil of up to 4-5 folds. Addition of wheat residues significantly increased differences in potential denitrification between diversity levels, indicating that the resource level can influence the shape of the microbial diversityfunctioning relationship. This study shows that microbial diversity loss can alter terrestrial ecosystem processes, which suggests that the importance of functional redundancy in soil microbial communities has been overstated.

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“…Similar nosZ clones have also been obtained from other paddy fields (for example, GenBank Accession No. ACI48848) and maize rhizospheric soils (Mounier et al, 2004;Dambreville et al, 2006;Henry et al, 2008). Considering the general agreement between the 16S rRNA gene and nosZ phylogenies (Jones et al, 2008;Palmer et al, 2009), these results suggested that Herbaspirillum and other Burkholderiales bacteria may be important players in N 2 O reduction, not only in rice paddy soils but also in other environments.…”

Section: Discussionmentioning

confidence: 99%

Identification and isolation of active N2O reducers in rice paddy soil

et al. 2011

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Dissolved N 2 O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N 2 O is emitted to the atmosphere above these fields. This indicates the occurrence of N 2 O reduction in rice paddy fields; however, identity of the N 2 O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N 2 O reducers in rice paddy soil. In a soil microcosm, N 2 O and succinate were added as the electron acceptor and donor, respectively, for N 2 O reduction. For the stable isotope probing (SIP) experiment, 13 C-labeled succinate was used to identify succinate-assimilating microbes under N 2 O-reducing conditions. DNA was extracted 24 h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N 2 O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N 2 O-reducing conditions in the presence of cell-division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N 2 O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N 2 O-reducing conditions, in contrast to the control sample (soil incubated with only 13 C-succinate). Results of the single-cell isolation technique also indicated that the majority of the N 2 O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N 2 O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N 2 O reduction in rice paddy soils.

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Disentangling the rhizosphere effect on nitrate reducers and denitrifiers: insight into the role of root exudates

Cited by 262 publications

References 67 publications

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

Microbial expression profiles in the rhizosphere of willows depend on soil contamination

Loss in microbial diversity affects nitrogen cycling in soil

Identification and isolation of active N2O reducers in rice paddy soil

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