• Energy Research
• 2016-2025close
• FR close
• Soil Biology and Biochemistry close

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.

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

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.

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.

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.

Fluctuations in soil moisture create drying-rewetting events affecting the activity of microorganisms. Microbial responses to drying-rewetting are mostly studied in soils that are air-dried before rewetting. Upon rewetting, two patterns of bacterial growth have been observed. In the Type 1 pattern, bacterial growth rates increase immediately in a linear fashion. In the Type 2 pattern, bacterial growth rates increase exponentially after a lag period. However, soils are often only partially dried. Partial drying (higher remaining moisture content before rewetting) may be considered a less harsh treatment compared with air-drying. We hypothesized that a soil with a Type 2 response upon rewetting air-dried soil would transform into a Type 1 response if dried partially before rewetting. Two soils were dried to a gradient of different moisture content. Respiration and bacterial growth rates were then measured before and during 48 h after rewetting to 50% of water holding capacity (WHC). Initial moisture content determined growth and respiration in a sigmoidal fashion, with lowest activity in air-dried soil and maximum above ca. 30% WHC. Partial drying resulted in shorter lag periods, shorter recovery times and lower maximum bacterial growth rates after rewetting. The respiration after rewetting was lower when soil was partially dried and higher when soils were air-dried. The threshold moisture content where transition from a Type 2 to a Type 1 response occurred was about 14% WHC, while >30% WHC resulted in no rewetting effect. We combine our result with other recent reports to propose a framework of response patterns after drying-rewetting, where the harshness of drying determines the response pattern of bacteria upon rewetting dried soils.

Abstract Nitrous oxide (N2O) is an important greenhouse gas and fundamental questions about the capacity of soil microbial communities to act not only as sources, but also as sinks for N2O remains unanswered. We evaluated the capacity of non-denitrifying N2O-reducers to mitigate the production of this greenhouse gas in soil. We showed experimentally that the addition of the non-denitrifying strain Dyadobacter fermentans, which possesses the previously unaccounted N2O reductase NosZII, to 11 different soils significantly reduced N2O production of up to 189% in more than 1/3 of the soils. The magnitude of this effect was significantly influenced by the soil pH and C/N ratio. Overall, our results provide unambiguous evidence that the overlooked non-denitrifying NosZII-type bacteria can contribute to N2O consumption in soil.