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The oxygen isotope composition of atmospheric carbon dioxide (CO2) is intimately linked to large-scale variations in the cycling of CO2 and water across the Earth's surface. Understanding the role the biosphere plays in modifying the oxygen isotope composition of atmospheric CO2 is particularly important as this isotopic tracer has the potential to constrain estimates of important processes such as gross primary production at large scales. However, constraining the atmospheric mass budget for the oxygen isotope composition of CO2 also requires that we understand better the contribution of soil communities and how they influence the rate of oxygen isotope exchange between soil water and CO2 (kiso) across a wide range of soil types and climatic zones. As the carbonic anhydrases (CAs) group of enzymes enhances the rate of CO2 hydration within the water-filled pore spaces of soils, it is important to develop understanding of how environmental drivers can impact kiso through changes in their activity. Here we estimate kiso and measure associated soil properties in laboratory incubation experiments using 44 soils sampled from sites across western Eurasia and north-eastern Australia. Observed values for kiso always exceeded theoretically derived uncatalysed rates, indicating a significant influence of CAs on the variability of kiso across the soils studied. We identify soil pH as the principal source of variation, with greater kiso under alkaline conditions suggesting that shifts in microbial community composition or intra–extra-cellular dissolved inorganic carbon gradients induce the expression of more or higher activity forms of CAs. We also show for the first time in soils that the presence of nitrate under naturally acidic conditions reduces kiso, potentially reflecting a direct or indirect inhibition of CAs. This effect appears to be supported by a supplementary ammonium nitrate fertilisation experiment conducted on a subset of the soils. Greater microbial biomass also increased kiso under a given set of chemical conditions, highlighting a putative link between CA expression and the abundance of soil microbes. These data provide the most extensive analysis of spatial variations in soil kiso to date and indicate the key soil trait datasets required to predict variations in kiso at large spatial scales, a necessary next step to constrain the important role of soil communities in the atmospheric mass budget of the oxygen isotope composition of CO2.

The oxygen isotope composition (δ18O) of atmospheric carbon dioxide (CO2) can be used to estimate gross primary production at the ecosystem-scale and above. Understanding how and why the rate of oxygen isotope exchange between soil water and CO2 (kiso) varies can help to reduce uncertainty in the retrieval of such estimates. The expression and activity of carbonic anhydrases in soils are important drivers of variations in kiso. Here we estimate kiso and measure associated soil properties in laboratory incubation experiments using 44 soils sampled from sites across western Eurasia and northeastern Australia. Observed kiso exceeded theoretical uncatalysed rates indicating the significant influence of carbonic anhydrases on the variability observed among the soils studied. We identify soil pH as the principal source of variation, with greater kiso under alkaline conditions suggesting that shifts in microbial community composition or intra-extra cellular dissolved inorganic carbon gradients induce the expression of more or higher activity forms of carbonic anhydrases. We also show for the first time in soils that the presence of nitrate under acidic conditions reduces kiso, potentially reflecting the direct or indirect inhibition of carbonic anhydrases. This effect was confirmed by a supplementary ammonium nitrate fertilisation experiment conducted on a subset of the soils. Future changes in atmospheric nitrogen deposition or land-use may thus influence carbonic anhydrase activity. Greater microbial biomass also increased kiso under a given set of chemical conditions likely highlighting the ubiquity of carbonic anhydrase expression by soil microbial communities. These data provide the most extensive analysis of spatial variations in soil kiso to date and indicate key controls required to predict variations in kiso at the scales needed to improve efforts to constrain gross primary productivity using the δ18O of atmospheric CO2.

Recent interest in the seasonal and spatial variability of atmospheric COS has intensified as its use as an atmospheric tracer of biosphere productivity in the carbon cycle has recently been demonstrated. The key link between the COS and CO2 cycles in the biosphere is a family of enzymes called the carbonic anhydrases (CA) that catalyse both the hydration of CO2 and the hydrolysis of COS in both plants and soil microbes. Recently studies have demonstrated that the variability in soil COS and CO2 fluxes are modified significantly by fertilisation with inorganic N, indicating a strong coupling between soil carbon (C), nitrogen (N) and sulphur (S) cycling (Kaisermann et al., 2018). However, it is currently not clear whether the observed changes in COS and CO2 gas exchange were principally driven by important shifts in the microbial community size, structure or function or some combination of the three.To elucidate the underlying mechanism(s) we used a functional metagenomic and metatranscriptomic approach coupled with climate controlled gas exchange measurements on soils. A set of 6 soils collected from boreal and temperate sites were sieved and re-packed in microcosms and incubated in the lab for 2 weeks at 23oC and 30% water holding capacity in the dark. For each site half the microcosms were fertilised with 5 mg N in the form of NH4NO3 at the start of the incubation period. At the end of the incubation period soil COS, CO2 fluxes were measured, and soil samples transported at -80oC to the Genosol platform for DNA and RNA extraction. For each soil microcosm we quantified the abundance of bacterial, fungal and algal genes in each community using 16S, 18S and 23S amplicon sequencing. After assembling and cross-mapping the metagenomes and metatranscriptomes we used a HMM model (Meredith et al. 2018) to estimate and comparatively assess the abundance of CA genes between the different sites and treatments.Our results indicate that the N treatment caused a relative increase in the abundance of fungi in N treated soils compared to those in the control. Generally, we also found that the total number of CAs in soils shifted when treated with N compared to the controls and that the β-D CA sub-family were the most prevalent CAs in all of the soils. In our presentation we will demonstrate how both the community structure and the abundance of CAs were modified upon N fertilisation and provide vital clues on the most likely mechanism(s) controlling COS and CO2 fluxes in soil communities and the significance of these results for interpreting atmospheric signals.Kaisermann, Aurore, Sam P. Jones, Steven Wohl, Jérôme Ogée, and Lisa Wingate. 2018 Nitrogen Fertilization Reduces the Capacity of Soils to take up Atmospheric Carbonyl Sulphide. Soil Systems 2 (4), 62 doi.org/10.3390/soilsystems2040062Meredith, Laura K, Jérôme Ogée, Kristin Boye, Esther Singer, Lisa Wingate, Christian von Sperber, Aditi Sengupta, et al. 2018. “Soil Exchange Rates of COS and CO18O Differ with the Diversity of Microbial Communities and Their Carbonic Anhydrase Enzymes.” ISME Journal, 2018. https://doi.org/10.1038/s41396-018-0270-2.

Soils are an important carbonyl sulphide (COS) sink. However, they can also act as sources of COS to the atmosphere. Here we demonstrate that variability in the soil COS sink and source strength is strongly linked to the available soil inorganic nitrogen (N) content across a diverse range of biomes in Europe. We revealed in controlled laboratory experiments that a one-off addition of ammonium nitrate systematically decreased the COS uptake rate whilst simultaneously increasing the COS production rate of soils from boreal and temperate sites in Europe. Furthermore, we found strong links between variations in the two gross COS fluxes, microbial biomass, and nitrate and ammonium contents, providing new insights into the mechanisms involved. Our findings provide evidence for how the soil&ndash, atmosphere exchange of COS is likely to vary spatially and temporally, a necessary step for constraining the role of soils and land use in the COS mass budget.

Soils both emit and consume the trace gas carbonyl sulfide (COS) leading to a soil–air COS exchange rate that is the net result of two opposing fluxes. Partitioning these two gross fluxes and understanding their drivers are necessary to estimate the contribution of soils to the current and future atmospheric COS budget.Previous efforts to disentangle the gross COS fluxes from soils have used flux measurements on air-dried soils as a proxy for the COS emission rates of moist soils. However, this method implicitly assumes that COS uptake becomes negligible and that COS emission remains steady while soils are drying. We tested this assumption by simultaneously estimating the soil COS sources and sinks and their temperature sensitivity (Q10); these estimates were based on soil–air COS flux measurements on fresh soils at different COS concentrations and two soil temperatures. Measurements were performed on 27 European soils from different biomes and land use types in order to obtain a large range of physical–chemical properties and identify the drivers of COS consumption and production rates.We found that COS production rates from moist and air-dried soils were not significantly different for a given soil and that the COS production rates had Q10 values (3.96 ± 3.94) that were larger and more variable than the Q10 for COS consumption (1.17 ± 0.27). COS production generally contributed less to the net flux at lower temperatures but this contribution of COS production increased rapidly at higher temperatures, lower soil moisture contents and lower COS concentrations. Consequently, measurements at higher COS concentrations (viz. 1000 ppt) always increased the robustness of COS consumption estimates. Across the range of biomes and land use types COS production rates co-varied with total soil nitrogen concentrations (r = 0.52, P r = 0.53, P r = −0.74 and 0.64, P P

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO 2 emission by up to 40%, and (ii) shaped the source of CO 2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil. IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil.

• Interactions between aboveground and belowground biota have the potential to modify ecosystem responses to climate change, yet little is known about how drought influences plant–soil feedbacks with respect to microbial mediation of plant community dynamics. • We tested the hypothesis that drought modifies plant–soil feedback with consequences for plant competition. We measured net pairwise plant–soil feedbacks for two grassland plant species grown in monoculture and competition in soils that had or had not been subjected to a previous drought; these were then exposed to a subsequent drought. To investigate the mechanisms involved, we assessed treatment responses of soil microbial communities and nutrient availability. • We found that previous drought had a legacy effect on bacterial and fungal community composition that decreased plant growth in conspecific soils and had knock-on effects for plant competitive interactions. Moreover, plant and microbial responses to subsequent drought were dependent on a legacy effect of the previous drought on plant–soil interactions. • We show that drought has lasting effects on belowground communities with consequences for plant–soil feedbacks and plant–plant interactions. This suggests that drought, which is predicted to increase in frequency with climate change, may change soil functioning and plant community composition via the modification of plant–soil feedbacks.

International audience; Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO2. Climate change is predicted to increase the frequency of drought events, with uncertain consequences for soil microbial communities. In this study we tested the hypothesis that agricultural management used to enhance soil carbon stocks would increase the stability of microbial community structure and activity in response to water-stress. Soil was sampled from a long-term field trial with three soil carbon management systems and was used in a laboratory study of the effect of a dry wet cycle on organic C mineralisation and microbial community structure. After a drying-rewetting event, soil microcosms were maintained wet and microbial community structure and abundance as well as microbial respiration were measured for four weeks. The results showed that the NO-TILL management system, with the highest soil organic matter content and respiration rate, had a distinct bacterial community structure relative to the conventional and the TILL without fertiliser systems. In all management systems, the rewetting event clearly modified microbial community structure and activity. Both returned to their pre-drought state after 28 days. However, the magnitude of variation of C mineralisation was lower (i.e. the resistance to stress was higher) in the NO-TILL system. The genetic structure of the NO-TILL bacterial communities was most modified by water-stress and exhibited a slower recovery rate. This suggests that land use management can increase microbial functional resistance to drought stress via the establishment of bacterial communities with particular metabolic capacities. Nevertheless, the resilience rates of C mineralisation were similar among management regimes, suggesting that similar mechanisms occur, maybe due to a common soil microbial community legacy. (C) 2013 Elsevier Ltd. All rights reserved.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms., Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

International audience; Many studies have focused on the impact of intense drought and rain events on soil functioning and diversity, but little attention has been paid to the response of microbial communities to non-extreme soil moisture variations. However, small fluctuations of soil water content represent a common situation that ought to be examined before understanding and deciphering the impact of extreme events. Here, we tested the impact of a decrease in average soil water content and small water content fluctuations in non-extreme conditions on microbial community composition and C mineralisation rate of a temperate meadow soil. Two soil microcosm sets were incubated at high and low constant moisture and a third set was subjected to 4 short dry–wet cycles between these two soil moistures. No robust change in bacterial community composition, molecular microbial biomass, and fungal:bacterial ratio were associated with soil water content change. On the contrary, the fungal community composition rapidly alternated between states corresponding to the high and low levels of soil moisture content. In addition, gross C mineralisation was correlated with soil moisture, with a noteworthy absence of a Birch effect (C over-mineralisation) during the wetting. This study suggests that some fungal populations could coexist by occupying different moisture niches, and high fungal community plasticity would classify them as more sensitive indicators of soil moisture than bacteria. Moreover, under non-stressed conditions, the community composition did not affect metabolic performance so a future decrease in average soil moisture content should not result in a supplemental loss in soil carbon stocks by a Birch effect.

Heat waves, defined as events associating high temperatures with severe drought, are expected to become increasingly recurrent. Research has focused heavily on the impacts of drought and temperature increase on soil functioning and microbial diversity, but little attention has been paid to soil microbial community responses to combined heat-drought stresses. Heat waves, which combine heat and drought stresses, may induce different microbial responses to those observed in studies focusing on heat or drought alone. Microbial recovery strategies to withstand heat-drought conditions, along with patterns of microbial functional redundancy and complex interactions with the soil physical-chemical-biological interface may have marked effects on soil ecosystem functioning, particularly in agroecosystems through the rhizosphere. To better under stand how heat waves affect soil ecosystem functioning, we advocate the development of mechanistic approaches integrating individual to community level and biophysicochemical studies on the indirect effects of combined heat-drought stresses in microbial communities, observed through soil environment parameters in experimental and field studies. The challenge will be to define trait-based functional indicators of the microbial community response to heat waves, particularly the potential interrelatedness between the traits responsible for tolerance to drought and heat

13 pages; International audience; The turnover of organic matter in soil depends on the activity of microbial decomposers. However, little is known about how modifications of the diversity of soil microbial communities induced by fresh organic matter (FOM) inputs can regulate carbon cycling. Here, we investigated the decomposition of two 13C labeled crop residues (wheat and alfalfa) and the dynamics of the genetic structure and taxonomic composition of the soil bacterial communities decomposing 13C labeled FOM and native unlabeled soil organic matter (SOM), respectively. It was achieved by combining the stable isotope probing method with molecular tools (DNA genotyping and pyrosequencing of 16S rDNA). Although a priming effect (PE) was always induced by residue addition, its intensity increased with the degradability of the plant residue. The input of both wheat and alfalfa residues induced a rapid dynamics of FOM-degrading communities, corresponding to the stimulation of bacterial phyla which have been previously described as copiotrophic organisms. However, the dynamics and the identity of the bacterial groups stimulated depended on the residue added, with Firmicutes dominating in the wheat treatment and Proteobacteria dominating in the alfalfa treatment after 3 days of incubation. In both treatments, SOMdegrading communities were dominated by Acidobacteria, Verrucomicrobia, and Gemmatimonadetes phyla which have been previously described as oligotrophic organisms. An early stimulation of SOM-degrading populations mainly belonging to Firmicutes and Bacteroidetes groups was observed in the alfalfa treatment whereas no change occurred in the wheat treatment. Our findings support the hypothesis that the succession of bacterial taxonomic groups occurring in SOM- and FOMdegrading communities during the degradation process may be an important driver of the PE, and consequently of carbon dynamics in soil.