Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance

Thion, Cécile; Poirel, Jessica; Cornulier, Thomas; Vries, Franciska T. de; Bardgett, Richard D.; Prosser, James I.

doi:10.1093/femsec/fiw091

Cited by 80 publications

(69 citation statements)

References 81 publications

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“…Moreover, the increased mineralization of organic P by legume is also possible, because phosphatase activity is higher in the rhizosphere of legume than in the rhizosphere of grass regardless of organic P addition (Li et al, 2004). Plant nutritional strategy is an important factor involved in shaping the SMC structure (Thion et al, 2016; Guyonnet et al, 2017), however, the plant biomass and nutritional traits of different species were not monitored in this study. The nutritional strategy of these species and its influence on the SMC deserves further investigation in the future.…”

Section: Discussionmentioning

confidence: 99%

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Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

Yang¹,

Zhu

et al. 2017

Front. Microbiol.

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Plants are the essential factors shaping soil microbial community (SMC) structure. When most studies focus on the difference in the SMC structure associated different plant species, the variation in the SMC structure associated with phylogenetically close species is less investigated. Legume (Fabaceae) and grass (Poaceae) are functionally important plant groups; however, their influences on the SMC structure are seldom compared, and the variation in the SMC structure among legume or grass species is largely unknown. In this study, we grew three legume species vs. three grass species in mesocosms, and monitored the soil chemical property, quantified the abundance of bacteria and fungi. The SMC structure was also characterized using PCR-DGGE and Miseq sequencing. Results showed that legume and grass differentially affected soil pH, dissolved organic C, total N content, and available P content, and that legume enriched fungi more greatly than grass. Both DGGE profiling and Miseq-sequencing indicated that the bacterial diversity associated with legume was higher than that associated with grass. When legume increased the abundance of Verrucomicrobia, grass decreased it, and furthermore, linear discriminant analysis identified some group-specific microbial taxa as potential biomarkers of legume or grass. These data suggest that legume and grass differentially select for the SMC. More importantly, clustering analysis based on both DGGE profiling and Miseq-sequencing demonstrated that the variation in the SMC structure associated with three legume species was greater than that associated with three grass species.

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Section: Discussionmentioning

confidence: 99%

“…Legume is less effective mainly due to the release of proton during the biological N-fixation by symbionts (Haynes, 1983). The differential uptake of different nutrient forms can also modify the soil pH (Thion et al, 2016). In addition to the lower soil pH, the DOC content was also lower in the legume soils than in the grass soils.…”

Section: Discussionmentioning

confidence: 99%

Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

Yang¹,

Zhu

et al. 2017

Front. Microbiol.

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“…Second, we measured potentially leached ammonium (

{NH}_{4}^{+}

–N) and nitrate (

{NO}_{3}^{-}

–N) which represent good proxies for soil mineral N‐retention. While nitrification and denitrification processes directly influence N‐leaching, there are also growing evidences that specific root functional traits directly affect these microbial soil processes (Cantarel et al., ; Legay et al., ; Moreau et al., ), their relative abundances (Thion et al., ) or through the release of labile C sources (Kuzyakov, ). Plant roots, therefore, directly drive the amount of N in soil but also indirectly affect soil N‐retention through their regulating activities on microbial processes (Hayatsu et al., ).…”

Section: Introductionmentioning

confidence: 99%

The added value of including key microbial traits to determine nitrogen‐related ecosystem services in managed grasslands

Pommier

Cantarel

Grigulis

et al. 2017

Journal of Applied Ecology

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Abstract1. Despite playing central roles in nutrient cycles and plant growth, soil microbes are generally neglected in the study of ecosystem services (ES), due to difficulties to assess their diversity and functioning. However, to overcome these hurdles, new conceptual approaches and modern tools now provide a means to assess the role of micro-organisms in the evaluation of ES.2. In managed grasslands, soil microbes are central in providing nitrogen (N)-related ES such as maintenance of soil fertility and retention of mineral forms of N. Here, we applied state-of-the-art techniques in microbial ecology and plant functional ecology to uncover the intrinsic link between N-related bacterial functional groups, important plant functional traits, environmental factors and three proxies of maintenance of soil fertility and potential for N-leaching across managed grasslands in three regions of Europe.3. By constructing well-defined structural equation modelling, we showed that including key microbial traits improve on average more than >50% of the total variances of ES proxies, that is, ammonium (NH + 4 ) or nitrate (NO − 3 ) leaching, and soil organic matter content. Geographic differences arose when considering the direct relationships of these ES proxies with specific microbial traits: nitrate leaching was positively correlated to the maximum rate of nitrification, except in the Austrian site and potentially leached NH | Rationale of key microbial traits involved in two soil ESWe propose here a conceptual framework that integrate solid knowledge on the relationships between above-ground and F I G U R E 1 A priori model for three proxies of the maintenance of soil fertility and water quality (light grey boxes) and their relationships with microbial (white boxes) and plant (dark grey boxes) functional traits and soil characteristics (black boxes). Arrows indicate either positive or negative relationships, depending on the considered variables Zumft & Korner, 1997). Nitrification is a less common autotrophic process that is driven mostly by soil ammonium concentrations and soil water content (Patra et al., 2007;Prosser, 1989). These two important processes of the soil N-cycle are obviously driven by the relative abundances of functional groups performing key enzymatic steps, that is, nitrite and nitrate reducers for denitrification and ammonium and nitrite oxidizers for nitrification. Ultimately, the variations of potential leaching of ammonium and nitrate, as well as SOM content variance, are related to the different biotic and abiotic drivers described above.Here, to estimate the relative contribution of microbes to nitrogen-related ES in mountain managed grasslands, we applied this conceptual framework to eight different sampling fields across Europe. This broad perspective documents such dynamics in different grass-based agroecosystem under common climatic conditions of the Northern Hemisphere. We tested the hypothesis that integrating the measures of microbial traits would significantly improve the amount of var...

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“…Under aerobic conditions, the nitrogen loss was mainly attributable to ammonia oxidizers (Florio et al, 2016), and in this study the stimulating effects of plant roots on ammonia oxidizers still did not aid the accumulation of nitrogen. In the revegetation area, plant litter and root exudate contributed a large amount of organic nitrogen (Baxendale et al, 2014;Thion et al, 2016), and the inorganic nitrogen mineralized by this organic nitrogen was provided to plants and microbes (Thion et al, 2016). In the area revegetated by C. zizanioides, the phytocommunity obtained the inorganic nitrogen in the process of nitrogen transformation and grew well, but the TN in the tailings experienced no improvement compared to the bare wastelands assayed in our previous study (Li et al, 2016a).…”

Section: Discussionmentioning

confidence: 77%

“…In this study, the gene transcript abundance of nirK, norB, and nosZ were below the detection limit, maybe nitrite reduction was not the primary energy source for these denitrifiners in mine tailings. The general knowledge that plant roots can stimulate rhizosphere heterotrophs and activate root-derived N in a soil environment (Thion et al, 2016); formed the basis of our hypothesis that the rhizosphere stimulates the abundances and activities of Ncycling functional microorganisms. Although The primers in the study used to amplify the functional genes for qPCR do not target all genes, the two assayed plants I. cylindrica and C. zizanioides stimulated the abundances and activities of some nifH gene and archaeal amoA gene, respectively.…”

Section: Discussionmentioning

confidence: 95%

Plant-Mediated Changes in Soil N-Cycling Genes during Revegetation of Copper Mine Tailings

Jia

Sun

et al. 2017

Front. Environ. Sci.

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Nitrogen limitation represents a major bottleneck during the revegetation of mine tailings. However, controls over key nitrogen-cycling genes in rhizospheric soils under differential vegetation management remain poorly understood. The abundance and transcriptional activity of nitrogen-cycling genes and the enzymatic activity of nitrogen transformation are mediated differentially during revegetation of mine tailings by Imperata cylindrica and Chrysopogon zizanioides plants. Results showed that the highest total organic carbon (TOC), total nitrogen (TN), and NH + 4 -N contents were found in the rhizosphere of I. cylindrica. The nifH gene abundances differed between I. cylindrica and C. zizanioides, and were higher in I. cylindrica which demonstrated by 3.39-fold higher mRNA transcript abundance of the nifH gene and a 2.15-fold higher nitrogen fixation rate in the rhizosphere. In addition, C. zizanioides exhibited a 4.94-fold higher transcript abundance of the archaeal amoA gene and the highest nitrification rate (1.706 ± 0.293 µg N-NO − 2 g −1 h −1 ) in the rhizosphere. In conclusion, I. cylindrica and C. zizanioides stimulated the abundances and activities of nifH gene and archaeal amoA gene, respectively. In addition, I. cylindrica appears to be capable of enhancing nitrogen fixation and exhibited accelerated nitrogen accumulation, which may be particularly useful for the rehabilitation of mine tailings.

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Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance

Cited by 80 publications

References 81 publications

Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

Variation in Soil Microbial Community Structure Associated with Different Legume Species Is Greater than that Associated with Different Grass Species

The added value of including key microbial traits to determine nitrogen‐related ecosystem services in managed grasslands

Plant-Mediated Changes in Soil N-Cycling Genes during Revegetation of Copper Mine Tailings

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