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  • Soil Biology and Biochemistry

  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: orcid Pedro Martins da Silva;
    Pedro Martins da Silva
    ORCID
    Harvested from ORCID Public Data File

    Pedro Martins da Silva in OpenAIRE
    orcid Jean-Christophe Clément;
    Jean-Christophe Clément
    ORCID
    Harvested from ORCID Public Data File

    Jean-Christophe Clément in OpenAIRE
    José Paulo Sousa; Laura B. Martínez-García; +9 Authors

    The functional trait framework provides a powerful corpus of integrated concepts and theories to assess how environmental factors influence ecosystem functioning through community assembly. While common in plant ecology, this approach is under-used in microbial ecology. After an introduction of this framework in the context of microbial ecology and enzymology, we propose an approach 1) to elucidate new links between soil microbial community composition and microbial traits; and 2) to disentangle mechanisms underlying “total” potential enzyme activity in soil (sum of 7 hydrolase potential activities). We address these objectives using a terrestrial grassland ecosystem model experiment with intact soil monoliths from three European countries (Switzerland, France and Portugal) and two management types (Conventional-intensive and Ecological-intensive), subjected to 4 rain regimes (Dry, Wet, Intermittent and Normal) under controlled conditions in a common climate chamber. We found tight associations between proxies of microbial ecoenzymatic community-weighted mean traits (enzymatic stoichiometry and biomass-specific activity) and community composition, bringing new information on resource acquisition strategy associated with fungi, Gram positive and Gram negative bacteria. We demonstrate that microbial biomass explained most of the total enzyme activity before altered rain regimes, whereas adjustments in biomass-specific activity (enzyme activity per unit of microbial biomass) explained most variation under altered rain regime scenarios. Furthermore, structural equation models revealed that the variation of community composition was the main driver of the variation in biomass-specific enzyme activity prior to rain perturbation, whereas physiological acclimation or evolutionary adaptation became an important driver only under altered rain regimes. This study presents a promising trait-based approach to investigate soil microbial community response to environmental changes and potential consequences for ecosystem functioning. We argue that the functional trait framework should be further implemented in microbial ecology to guide experimental and analytical design.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Université François-...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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    Soil Biology and Biochemistry
    Article . 2020 . Peer-reviewed
    License: Elsevier TDM
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Soil Biology and Biochemistry
      Article . 2020 . Peer-reviewed
      License: Elsevier TDM
      Data sources: Crossref
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Ari Fina Bintarti; orcid bw Elena Kost;
    Elena Kost
    ORCID
    Derived by OpenAIRE algorithms or harvested from 3rd party repositories

    Elena Kost in OpenAIRE
    Dominika Kundel; orcid Rafaela Feola Conz;
    Rafaela Feola Conz
    ORCID
    Harvested from ORCID Public Data File

    Rafaela Feola Conz in OpenAIRE
    +5 Authors

    The severity of drought is predicted to increase across Europe due to climate change. Droughts can substantially impact terrestrial nitrogen (N) cycling and the corresponding microbial communities. Here, we investigated how ammonia-oxidizing bacteria (AOB), archaea (AOA), and complete ammonia oxidizers (comammox) as well as inorganic N pools and N2O fluxes respond to simulated drought under different cropping systems. A rain-out shelter experiment was conducted as part of a long-term field experiment comparing cropping systems that differed mainly in fertilization strategy (organic, mineral, or mixed mineral and organic) and plant protection management (biodynamic versus conventional pesticide use). We found that the effect of drought varied depending on the specific ammonia-oxidizing (AO) groups and the type of cropping system. Drought had the greatest impact on the structure of the AOA community compared to the other AO groups. The abundance of ammonia oxidizers was also affected by drought, with comammox clade B exhibiting the highest sensitivity. Additionally, drought had, overall, a stronger impact on the AO community structure in the biodynamic cropping system than in the mixed and mineral-fertilized conventional systems. The responses of ammonia-oxidizing communities to drought were comparable between bulk soil and rhizosphere. We observed a significant increase in NH4+ and NO3− pools during the drought period, which then decreased after rewetting, indicating a strong resilience. We further found that drought altered the complex relationships between AO communities and mineral N pools, as well as N2O fluxes. These results highlight the importance of agricultural management practices in influencing the response of nitrogen cycling guilds and their processes to drought. Soil Biology and Biochemistry, 201 ISSN:0038-0717 ISSN:1879-3428

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Soil Biology and Bio...arrow_drop_down
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    Soil Biology and Biochemistry
    Article . 2025 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Research Collection
    Article . 2025
    License: CC BY
    Research Collection
    Article . 2025
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Soil Biology and Bio...arrow_drop_down
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      Soil Biology and Biochemistry
      Article . 2025 . Peer-reviewed
      License: CC BY
      Data sources: Crossref
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Research Collection
      Article . 2025
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      Research Collection
      Article . 2025
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    Authors: Stephan Hättenschwiler; orcid Nathalie Fromin;
    Nathalie Fromin
    ORCID
    Harvested from ORCID Public Data File

    Nathalie Fromin in OpenAIRE
    orcid Virginie Baldy;
    Virginie Baldy
    ORCID
    Harvested from ORCID Public Data File

    Virginie Baldy in OpenAIRE
    Anaïs Rancon; +5 Authors

    The consequences of predicted climate change on ecosystem processes is difficult to evaluate, because biodiversity is also susceptible to change resulting in complex interactions on ecosystem functioning. With an experimental approach, we aimed to understand how plant community diversity (through different plant litter mixtures) and climate change (through decreased precipitation) may impact microbial abundance and diversity and affect C and N cycling in a Mediterranean shrubland. Along a natural plant diversity gradient, we manipulated the amount of precipitation and followed leaf litter decomposition during one year. We found that multi-species litter mixtures had higher microbial abundance, lower bacterial diversity and higher fungal diversity than predicted from single-species litter. In addition, C and N release increased with increasing litter species richness. Microbial abundance and diversity were positively, but weakly, correlated to the litter mixture effects on C and N release. Drier conditions increased microbial diversity but had no effect on microbial abundance. The net release of N from decomposing litter was lower with reduced precipitation irrespective of litter species richness and composition, while that of C was higher or lower depending on litter species composition. The relationships between microbial communities and litter mixture effects on C and N release were altered under drier conditions. Our data provide clear evidence that microbial decomposers and the processes they drive, respond to changing plant community diversity and composition in a Mediterranean shrubland. We highlighted the importance of Quercus coccifera that appears to be a key species in shaping microbial communities and driving synergistic effects on C and N release more than the three other shrub species. Our study also suggests that shifts in the plant community composition may have stronger impacts on litter decomposition and nutrient cycling than relatively subtle changes in precipitation as simulated in our study.

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    Soil Biology and Biochemistry
    Article . 2017 . Peer-reviewed
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      Soil Biology and Biochemistry
      Article . 2017 . Peer-reviewed
      License: Elsevier TDM
      Data sources: Crossref
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    Authors: orcid Villenave, C.;
    Villenave, C.
    ORCID
    Harvested from ORCID Public Data File

    Villenave, C. in OpenAIRE
    Ekschmitt, K.; Nazaret, S.; Bongers, A.M.T.;

    The carrying capacity for microflora and nematofauna was manipulated (using a bactericide, a fungicide, manure or a growing millet plant) in a poor tropical soil, in order to identify relationships between the soil microbes and nematodes and to assess the influences of these organisms on nitrogen flux. The experiment was conducted for 4 months in containers under greenhouse conditions, with analyses of soil, nematofauna and microbial characteristics at regular intervals. Manure input and initial bactericide application led to a significant increase in bacterial-feeding and fungal-feeding nematodes of coloniser-persister classes 1 and 2, respectively, whereas high manure input stimulated omnivorous nematodes (i.e. Microdorylaimus rapsus) which became the dominant trophic group. Changes in abundance of the different bacterial-feeding nematode taxa between treatments seemed to be more related to changes in the structure of the microbial communities than to the total amount of micro-organisms, as suggested by the RISA fingerprint analysis of the bacterial communities. Canonical analysis of nematode feeding guilds, combined with soil microbial and mineral nitrogen parameters as well as multiple regression showed that the bacterial-feeding nematodes influenced the inorganic N content in the soil whereas microbial biomass was determined by total nematode abundance and not by any specific trophic group. (C) 2004 Elsevier Ltd. All rights reserved.

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    Soil Biology and Biochemistry
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      Soil Biology and Biochemistry
      Article . 2004 . Peer-reviewed
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    Authors: Kaurin, Anela; orcid Mihelič, Rok;
    Mihelič, Rok
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    Mihelič, Rok in OpenAIRE
    Kastelec, Damijana; orcid Grčman, Helena;
    Grčman, Helena
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    Grčman, Helena in OpenAIRE
    +3 Authors

    Climate change causes droughts, which in turn cause significant physiological stress for soil microorganisms. In this study, we investigated how the abundance of total bacterial, crenarchaeal and fungal communities and the abundance of N-cycling microbial guilds responded to a severe agricultural drought event in a long-term experiment of minimum tillage (MT) and conventional ploughing (CT) at two soil depths. This study was financially supported by the European Commission within the EcoFINDERS project (FP7-264465), CORE Organic Plus funding bodies within the FertilCrop project, and by the Slovenian Research Agency within the programme P4-0085.

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    Soil Biology and Biochemistry
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      Soil Biology and Biochemistry
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    Authors: Kam-Rigne Laossi; Juan Andrés Cardoso; Patrick Lavelle; Patrick Lavelle; +5 Authors

    The aim of this work was to compare the effects of biochar and earthworms on rice growth and to investigate the possible interactions between both. In addition to classic macroscopic variables we also monitored some leaf-level cellular processes involved in protein turnover. Both biochar and earthworms significantly increased shoot biomass production. However, biochar had a higher effect on the number of leaves (þ87%) and earthworms on leaf area (þ89%). Biochar also significantly increased the leaf turnover. At the cellular level, biochar but not earthworms enhanced protein catabolism by an increase in leaf proteolytic activities. This could be related to the increased expression of three of the six genes tested related to protein catabolism, one serine protease gene OsSP2 (þ24%), one aspartic acid protease gene, Oryzasin (þ162%) and one cysteine protease gene OsCatB (þ257%). Furthermore, biochar also enhanced the expression level of two genes linked to protein anabolism, coding for the small and large subunits of rubisco (þ33% and þ30%, for rbcS and rbcL, respectively), the most abundant protein in leaves. In conclusion, our data gives evidence that biochar increased rice biomass production through increased leaf protein turnover (both catabolism and anabolism) whereas earthworms also increased rice biomass production but not through changes in the rate of protein turnover. We hypothesize that earthworms increase nitrogen uptake at a low cost for the plant through a simultaneous increase in mineralization rate and root biomass, probably through the release in the soil of plant growth factors. This could allow plants to accumulate more biomass without an increase in nitrogen metabolism at the leaf level, and without having to support the consecutive energy cost that must bear plants in the biochar treatment. 2012 Elsevier Ltd. All rights reserved.

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    Soil Biology and Biochemistry
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      Soil Biology and Biochemistry
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    Authors: Congreves, KA; orcid Wagner-Riddle, C;
    Wagner-Riddle, C
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    Wagner-Riddle, C in OpenAIRE
    Si, BC; Clough, Timothy;

    Abstract Soil freeze-thaw (FT) and dry-wet (DW) cycles are brief transitory biophysical changes, but these events have important implications in determining the timing and magnitude of N2O emissions and may represent a significant proportion of annual N2O emissions from agricultural systems. It is often assumed that FT and DW cycles influence the processes of N2O production and emission in a similar manner, however, research has yet to systematically identify the similarities and differences in the mechanisms which lead to potentially higher N2O fluxes during FT compared to DW cycles. Herein, we present the first review to do so; in addition, we identify strategic research areas required for improving the understanding of FT and DW processes leading to N2O emissions. There are key differences between the mechanisms that contribute to N2O fluxes during FT and DW cycles, centered on the duration and spatial extent of anaerobiosis, temperature sensitivity of microbial activity, relative gas diffusivity, and soil water dynamics. These differences might increase the risk of N2O emissions during FT cycles relative to soil DW cycles. Current research gaps include (i) the identification of organic substrates made available due to FT and DW cycles, and their contribution to ensuing N2O fluxes, (ii) an understanding of how cryosuction dynamics potentially influence N2O production and emission, (iii) understanding and predicting the air-entry potential of soil as it relates to N2O fluxes, (iv) identifying the relative significance of dissolved N2O in soil water and its solubility changes during FT and DW phases, and (v) determining microbial community and functional changes across soil spatial and temporal scales. Advances in these areas are recommended for improving process descriptions in biogeochemical models in order to more accurately predict N2O emissions from soils prone to FT and DW cycles.

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    Soil Biology and Biochemistry
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      Soil Biology and Biochemistry
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    Authors: Pailler, A.; orcid Vennetier, M.;
    Vennetier, M.
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    orcid Torre, F.;
    Torre, F.
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    Torre, F. in OpenAIRE
    Ripert, C.; +1 Authors

    Little is known about how spatial and environmental patterns structure soil microbial activities. We investigated, on 47 soil samples collected in Mediterranean forests, the net and interaction effects of climatic-geographic and edaphic variables as well as vegetation cover and composition on soil microbial community-level physiological profiles (CLPPs) assessed by MicrorespTM. The effects of these variables were also analysed on CLPP response to an experimental drought treatment. CLPPs were shown to be mainly driven by climate-plant-soil and plant-soil interactions; even after drought treatment, there was a decrease in microbial activity but no change in CLPPs. Our findings highlight the robustness of these relationships, which need to be assessed within different ecosystems considering various spatial scales to reliably predict climate change effects on terrestrial ecosystems

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    Soil Biology and Biochemistry
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      Soil Biology and Biochemistry
      Article . 2014 . Peer-reviewed
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    Authors: Alexandre Buttler; Alexandre Buttler; Alexandre Buttler; orcid Thomas Spiegelberger;
    Thomas Spiegelberger
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    Thomas Spiegelberger in OpenAIRE
    +11 Authors

    Microbial communities drive soil organic matter (SOM) decomposition through the production of a variety of extracellular enzymes. Climate change impact on soil microbial communities and soil enzymatic activities can therefore strongly affect SOM turnover, and thereby determine the fate of ecosystems and their role as carbon sinks or sources. To simulate projected impacts of climate change on Swiss Jura subalpine grassland soils, an altitudinal soil transplantation experiment was set up in October 2009. On the fourth year of this experiment, we measured microbial biomass (MB), microbial community structure (MCS), and soil extracellular enzymatic activities (EEA) of nine hydrolytic and oxidative extracellular enzymes in the transplanted soils on a seasonal basis. We found a strong sampling date effect and a smaller but significant effect of the climate manipulation (soil transplantation) on EEA. Overall EEA was higher in winter and spring but enzymes linked to N and P cycles showed higher potential activities in autumn, suggesting that other factors than soil microclimate controlled their pool size, such as substrate availability. The climate warming manipulation decreased EEA in most cases, with oxidative enzymes more concerned than hydrolytic enzymes. In contrast to EEA, soil MB was more affected by the climate manipulation than by the seasons. Transplanting soils to lower altitudes caused a significant decrease in soil MB, but did not affect soil MCS. Conversely, a clear shift in soil MCS was observed between winter and summer. Mass-specific soil EEA (EEA normalized by MB) showed a systematic seasonal trend, with a higher ratio in winter than in summer, suggesting that the seasonal shift in MCS is accompanied by a change in their activities. Surprisingly, we observed a significant decrease in soil organic carbon (SOC) concentration after four years of soil transplantation, as compared to the control site, which could not be linked to any microbial data. We conclude that medium term (four years) warming and decreased precipitation strongly affected MB and EEA but not MCS in subalpine grassland soils, and that those shifts cannot be readily linked to the dynamics of soil carbon concentration under climate change. (C) 2014 Elsevier Ltd. All rights reserved.

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    Soil Biology and Biochemistry
    Article . 2015 . Peer-reviewed
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    Authors: orcid Barthès, Bernard, G.;
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    Brunet, Didier; Rabary, Bodovololona; Ba, Oumar; +1 Authors

    Abstract Studying soil nematofauna provides useful information on soil status and functioning but requires high taxonomic expertise. Near infrared reflectance (NIR) spectroscopy (NIRS) has been reported to allow fast and inexpensive determination of numerous soil attributes. Thus the present study aimed at assessing the potential of NIRS for determining the abundance and diversity of soil nematodes in a set of 103 clayey topsoil samples collected in 2005 and 2006 from agricultural soils in the highlands of Madagascar. The morphological characterization of soil nematofauna involved extraction through elutriation then counting under binoculars and identification at family or genus level using microscopy, on ca. 150-g fresh soil samples. Taxa were assigned to five trophic groups, namely bacterial feeders, fungal feeders, obligate plant feeders, facultative plant feeders, and omnivores and predators (together). In addition, four ecological indexes were calculated: the Enrichment index, Structure index, Maturity index, and Plant parasitic index. Oven-dried (40 °C) Examining wavelengths that contributed most to NIRS predictions, and chemical groups they have been assigned to, suggested that NIRS predictions regarding nematofauna depended on constituents of both nematodes and preys’ food. Predictions were thus based on both nematofauna and soil organic properties reflected by nematofauna.

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    Soil Biology and Biochemistry
    Article . 2011 . Peer-reviewed
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      Soil Biology and Biochemistry
      Article . 2011 . Peer-reviewed
      License: Elsevier TDM
      Data sources: Crossref
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