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- 2019
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Journal article (peer-reviewed)
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| 2. |
- Graf, Daniel, et al.
(author)
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Assembly of root-associated N₂O-reducing communities of annual crops is governed by selection for nosZ Glade I over Glade II
- 2022
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In: FEMS Microbiology Ecology. - : Oxford University Press (OUP). - 0168-6496 .- 1574-6941. ; 98
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Journal article (peer-reviewed)abstract
- The rhizosphere is a hotspot for denitrification. The nitrous oxide (N₂O) reductase among denitrifiers and nondenitrifying N₂O reducers is the only known N₂O sink in the biosphere. We hypothesized that the composition of root-associated N₂O-reducing communities when establishing on annual crops depend on soil type and plant species, but that assembly processes are independent of these factors and differ between nosZ clades I and II. Using a pot experiment with barley and sunflower and two soils, we analyzed the abundance, composition, and diversity of soil and root-associated N₂O reducing communities by qPCR and amplicon sequencing of nosZ. Clade I was more abundant on roots compared to soil, while clade II showed the opposite. In barley, this pattern coincided with N₂O availability, determined as potential N₂O production rates, but for sunflower no N₂O production was detected in the root compartment. Root and soil nosZ communities differed in composition and phylogeny-based community analyses indicated that assembly of root-associated N₂O reducers was driven by the interaction between plant and soil type, with inferred competition being more influential than habitat selection. Selection between clades I and II in the root/soil interface is suggested, which may have functional consequences since most clade I microorganisms can produce N₂O.
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| 3. |
- Graf, Daniel, et al.
(author)
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Lucerne (Medicago sativa) alters N2O-reducing communities associated with cocksfoot (Dactylis glomerata) roots and promotes N2O production in intercropping in a greenhouse experiment
- 2019
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In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 137
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Journal article (peer-reviewed)abstract
- Lower emissions of the greenhouse gas nitrous oxide (N2O) are generally observed from intercropped compared to sole cropped systems. This could be due to better N-use efficiency, but differences in microbial communities establishing in the rhizosphere may also play a role as the only known biological sink for N2O is its reduction to nitrogen gas (N-2) by bacteria and archaea that possess the nosZ gene encoding the N2O reductase. Nitrous oxide reducing communities can be divided into two clades, I and II, and their relative abundance and diversity may have important consequences for N2O emissions. Here, we examine how intercropping with a legume (Medicago sativa, "lucerne") and a grass (Dactylis glomerata, "cocksfoot") species, compared to sole cropping of each species, affects the N2O emission potential, and the structure and abundance of root-associated N2O-reducing microbial communities. In a rhizobox experiment, we show that intercropping resulted in higher total shoot biomass compared to sole cropping. Further, N2O production rates were significantly higher in intercropped cocksfoot roots compared to sole cropping of either species. This coincided with lower abundances of nosZ Glade II communities in intercropped compared to sole cropped cocksfoot roots, suggesting that these organisms likely act as a N2O sink. Phylogenetic placement of sequencing reads placed root-associated nosZ Glade II reads close to Ignavibacteria and Opitutaceae, which harbour non-denitrifying N2O reducers with the genetic capacity to also perform dissimilatory nitrate reduction to ammonium (DNRA). We observed a shift in the composition of the cocksfoot root-associated nosZI communities towards incomplete denitrifiers terminating with N2O in intercropped roots. Overall, we hypothesize that such alterations of plant-microbe and/or microbe-microbe interactions contributed to the higher potential N2O emission rate observed in intercropped cocksfoot roots. Understanding the nature of these interactions would represent an important step forward for the design of management practices that minimize N2O emissions.
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| 4. |
- Graf, Daniel, et al.
(author)
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Soil type overrides plant effect on genetic and enzymatic N2O production potential in arable soils
- 2016
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In: Soil Biology and Biochemistry. - : Elsevier BV. - 0038-0717 .- 1879-3428. ; 100, s. 125-128
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Journal article (peer-reviewed)abstract
- Nitrous oxide (N2O) is a potent greenhouse gas mainly produced by incomplete denitrification in agricultural soils. The rhizosphere is a hot spot for denitrification and this study aimed to discern the relative importance of soil type and crop on the genetic N2O production and reduction potential in soil and root associated communities in relation to denitrification activity. Based on a pot experiment with two agricultural soils planted with barley or sunflower, we showed that the effect of soil type overrode that of crop on both genetic and enzymatic potential. We also demonstrate niche differentiation between the nitrous oxide reductase genes nosZI and nosZII, with clade I dominating in the root-associated community and clade II in the soil. (C) 2016 Elsevier Ltd. All rights reserved.
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| 5. |
- Zhao, Enid Ming, et al.
(author)
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Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata
- 2017
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In: Applied Soil Ecology. - : Elsevier BV. - 0929-1393 .- 1873-0272. ; 119, s. 260-266
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Journal article (peer-reviewed)abstract
- The effect of intercropping on the genetic potential for N-cycle pathways promoting either retention or loss of N by the microbial communities associated to the roots or present in the bulk soil for two forage crops was studied in a greenhouse experiment. Medicago sativa ('lucerne') and Dactylis glomerata ('cocksfoot') were grown as sole crops or intercropped in soils with or without addition of biogas digestate to also evaluate fertilizer effects. Eight genes involved in inorganic N-cycling were quantified using real-time PCR to determine the genetic potential for different N-cycling pathways. Both plant species and intercropping affected the abundance of root-associated microbial-derived genes involved in N-cycling processes, while there was no effect of amendment with biogas digestate. The genetic potential for the various pathways differed between bulk soil and roots, as well as between the roots of the two plant species, suggesting that organisms involved in different N-cycling processes were favored in different compartments in the soil-root environment. Ammonia oxidizers involved in nitrification, a pathway resulting in N-leaching, dominated in soil whereas those related to N-2 fixation and gaseous N losses (denitrification) were more abundant on roots. We also observed niche differentiation between the two major groups of organisms with the capacity to reduce N2O in the root- and soil compartment. Legume-grass intercropping resulted in a decreasing trend for several root- associated functional communities. More specifically, the legume exerted an effect on the N-cycling communities on the roots of both the legume and grass species, which suggests altered plant-microbial or microbial-microbial interactions during intercropping.
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| 6. |
- Zhao, Enid Ming
(author)
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Nitrogen cycling communities associated to roots of arable crops in relation to management : plant, intercropping and soil effects
- 2016
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Doctoral thesis (other academic/artistic)abstract
- Management of terrestrial nitrogen (N) has been identified as a key challenge in the implementation of sustainable agricultural practices. Transformations of inorganic N are mainly performed by microbial functional guilds that regulate the retention or loss of N. Soil management may affect the diversity, composition, and functioning of N-cycling microbial communities. The aim was to define the influence of soil properties, crops and intercropping on root- and soil-associated N-cycling communities with a special focus on the genetic and enzymatic potential for denitrification and nitrous oxide (N₂O) reduction. A greenhouse experiment comparing intercropped cocksfoot and lucerne with sole cropping practices showed that plant species and intercropping significantly affected the abundances of root associated communities that drive the retention or loss of N, suggesting altered plant-microbial and/or microbial-microbial interactions. Addition of biogas digestate as fertilizer did not alter the intercropping effects. A higher N₂O production rate was found in root-associated microbial communities in cocksfoot during intercropping, which coincided with decreased genetic potential for N₂O reduction by organisms within nosZ clade II compared to sole cropped cocksfoot. Sequencing revealed that these N₂O reducers were related to Ignavibacteria, which have a truncated denitrification pathway that lacks the genetic capacity to produce N₂O. Soil type also had a strong influence on root-associated N-cycling communities. In a full-factorial experiment with two soil types and two different crops (barley and sunflower), soil type overrode crop effects regarding both genetic and enzymatic potential for denitrification. Thus, soil physical and chemical properties rather than plant species determine the denitrification and N₂O production rates of the root-associated communities. The genetic potential for the various N-cycling communities differed between bulk soil and roots, indicating that N-cycling functional organisms were favored in different compartments in the soil-root environment. The N₂O reducing organisms carrying nosZI were shown to have an affinity to plant roots, whereas those with nosZII prefer the bulk soil thus indicating a possible niche differentiation between the two clades.
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