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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.

Two methods were evaluated to extract ergosterol for quantitation of fungal biomass in Marshan, Zurich, and Batavia soils. Yields of ergosterol from hyphae and from fungal-colonized soil were greater when fungal tissue was extracted with an alkaline solvent mixture than when base was added to neutral extracts following removal of solids. A lyophilization treatment prior to extraction increased yields from Marshan but not from Zurich and Batavia soils. Losses of ergosterol during lyophilization were prevented by a rapid freezing treatment before lyophilization of soil samples. Recoveries from soil fortified with pure ergosterol did not accutately model recoveries from fungal tissue in these substrates. Thus, determinations of extraction efficiencies should be based upon recoveries from fungal tissue added to soils. Ergosterol was quantitatively recovered from Marshan and Zurich soils fortified with fungal tissue; however, only ca 66% was recovered from Batavia soil, a subsoil with a high clay content. The limit of detection of Phanerochaete chrysosporium from the three soils ranged from 8 to 15 μg biomass g soil−1.

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

Abstract We studied the effects of O 3 and CO 2 alone and in combination on soil microbial communities by assessing the changes in total PLFA biomass, profiles and specific subgroups. Meadow mesocosms were exposed to slightly elevated O 3 (40–50 ppb) and CO 2 (+100 ppm) in open-top chambers for three subsequent growing seasons (2002–2004). Decreased total, bacterial, actinobacterial, fungal PLFA biomass values as well as fungal:bacterial PLFA biomass ratio were measured after three growing seasons of fumigations with elevated O 3 . There were significant differences in the relative proportions of individual PLFAs between the control and elevated O 3 treatments. Moreover, enhanced O 3 alone and in combination with CO 2 modified the structure of the microbial community. The effects of elevated CO 2 given alone on PLFA profiles were negligible. Our results show that elevated O 3 alone and in combination with CO 2 even at moderate levels may cause changes in the biomass and composition of the microbial community in meadow soils, which may lead to functional changes in soil ecosystem processes.

Abstract Although most land-plants form associations with arbuscular mycorrhizal fungi (AMF) as a means of optimising nutrient capture, legacy effects of altered soil moisture regimes on plant responses to arbuscular mycorrhizas (AM) have not been studied. As rainfall patters change with climate change, soil moisture legacy effects, and their impact on plants, soil and microbes may become increasingly important. Results of an experiment are presented in which soil was subjected to a range of different soil moisture regimes prior to planting a mycorrhiza-defective tomato mutant and its mycorrhizal wild-type progenitor. There were clear legacy effects of the soil moisture regime prior to planting on soil physicochemical properties, plant growth and nutrition, the formation of AM and mycorrhizal responsiveness. For example, in the Dry treatment the plants were well colonized by AM, there was a clear benefit to the plants in terms of mycorrhizal growth responses and mycorrhizal P responses. In contrast, in the Intermediate treatment AM colonisation was lower, there was little benefit in terms of mycorrhizal responses. Finally, in the Wet and Wet/Dry treatments AM colonization levels were similar (albeit lower) to those in the Dry treatment, but mycorrhizal growth responses were lower and more variable. Together, these results clearly indicate that soil nutrients, plant growth and nutrition and mycorrhizal responsiveness are affected by soil moisture legacy effect. Consequently, as we move into a period where more variable and intense rainfall amounts and patterns have been projected, we need to consider soil moisture legacy effects.

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.

Abstract Plant roots are the primary source of soil organic carbon (C) and critically support the growth and activities of microbes in the rhizosphere. Climate change factors may, however, modify root-microbial interactions and impact C dynamics in the rhizosphere. Yet, the direction and magnitude of interactive climate change effects, as well as the underlying mechanisms, remain unclear. Here we show evidence from a field experiment demonstrating that warming and precipitation changes strengthen root controls over litter decomposition in a semi-arid grassland. While warming and precipitation reduction suppressed microbial decomposition of root litter regardless of the root presence, precipitation increase stimulated litter decomposition only in the absence of roots, suggesting that plant competition for water constraints the activities of saprophytic microbes. Root presence increased microbial biomass but reduced microbial activities such as respiration, C cycling enzymes and litter decomposition, indicating that roots exert differential effects on microbes through altering C or water availability. In addition, nitrogen (N) input significantly reduced microbial biomass and microbial activities (respiration). Together, these results showed that alterations in soil moisture induced by climate change drivers critically modulate root controls over microbial decomposition in soil. Our findings suggest that warming-enhanced plant water utilization, combined with N-induced suppression of microbes, may provide a unique mechanism through which moderate increases in precipitation, warming and N input interactively suppress microbial decomposition, thereby facilitating short-term soil C sequestration in the arid and semi-arid grasslands.