Sara Hallin

Summary Global vegetation regimes vary in belowground carbon (C) and nitrogen (N) dynamics. However, disentangling large‐scale climatic controls from the effects of intrinsic plant–soil–microbial feedbacks on belowground processes is challenging. In local gradients with similar pedo‐climatic conditions, effects of plant–microbial feedbacks may be isolated from large‐scale drivers. Across a subarctic–alpine mosaic of historic grazing fields and surrounding heath and birch forest, we evaluated whether vegetation‐specific plant–microbial feedbacks involved contrasting N cycling characteristics and C and N stocks in the organic topsoil. We sequenced soil fungi, quantified functional genes within the inorganic N cycle, and measured 15N natural abundance. In grassland soils, large N stocks and low C : N ratios associated with fungal saprotrophs, archaeal ammonia oxidizers, and bacteria capable of respiratory ammonification, indicating maintained inorganic N cycling a century after abandoned reindeer grazing. Toward forest and heath, increasing abundance of mycorrhizal fungi co‐occurred with transition to organic N cycling. However, ectomycorrhizal fungal decomposers correlated with small soil N and C stocks in forest, while root‐associated ascomycetes associated with small N but large C stocks in heath, uncoupling C and N storage across vegetation types. We propose that contrasting, positive plant–microbial feedbacks stabilize vegetation trajectories, resulting in diverging soil C : N ratios at the landscape scale.

International audienceBiodiversity loss has become a global concern as increasing evidence highlights the importance of diverse species interactions as the main drivers of the ecosystem services on which society depends. This symposium focuses on the importance of above and belowground biodiversity for ecosystem functioning, multifunctionality and sustainability. Various talks will highlight the importance of biodiversity for agro-ecosystem functioning as this symposium is linked to the Biodiversa research project “Agricultural Diversification: Digging Deeper” investigating the importance of agricultural crop diversification

National audienceMicrobial communities are at the heart of all ecosystems and yet, a sound understanding of the ecological processes governing the assembly of these communities in the environment is missing. To address the role of biotic interactions in assembly and functioning of the soil microbiota, we used a top down manipulation approach based on the removal of various populations in a natural microbial community. Suspensions of the soil microbiota were subjected to various biocidal and filtration treatments before being inoculated into the same sterilized soil. We hypothesized that if biotic interactions are an important shaping force of the microbiota assembly, removal of microbial groups should largely affect the fitness of the remaining ones during soil recolonization. We show that nearly half of the dominant bacterial taxa were subjected to competitive interactions, underlining the importance of biotic interactions in the assembly of microbial community in soil. Moreover, evidence for competitive exclusion between members of Bacillales and Proteobacteriales suggests that potential general rules of microbial community assembly can be identified. Our findings also indicate that effects on biotic interactions results in more prominent changes in activities related to N- than to C-cycling. Such removal approach can provide a new avenue to study microbial interactions in complex ecosystem

Arable soils are a major source of nitrous oxide (N2O). The only known sink in Earth’s biosphere is the reduction of N2O to N2 via the N2O reductase encoded by the nosZ gene, identified as nosZ clade I and II. The nosZI gene is mainly found among denitrifying bacteria, whereas >50% of microorganisms with nosZII lack other denitrification genes. The abundance and phylogenetic diversity of nosZII was previously shown to correlate with a soils N2O sink capacity. To provide a proof of principle, we manipulated 11 indigenous soil microbial communities by increasing the abundance of a non-denitrifying N2O-reducing strain capable of growth with N2O as the only electron acceptor. Consequently, potential N2O emissions were lowered in 1/3 of the soils by 51% in average and the magnitude was significantly influenced by the soil pH and C/N ratio. These results provide direct evidence that non-denitrifying N2O-reducing bacteria can contribute to lowering the net N2O production in soil, which indicates that net N2O emissions are ultimately determined by the relative abundance of specific bacterial taxa with and without nosZ. The relative abundance of these bacterial taxa is known to be influenced by fertilization. Hence, we investigated predictable effects of N fertilizer on microbial communities across 14 Swedish longterm field trials, each with fertilized and non-fertilized treatments. The 16S rRNA and nosZ genes were sequenced, the abundance of denitrification genes quantified and the potential denitrification and N2O production rates determined. The genetic potential for denitrification correlated with the potential activity and high nosZ/nir gene ratios coincided with lower N2O:N2 emission ratios. The nosZII, but not nosZI, community was significantly affected by fertilization and the phylogenetic diversity of nosZII correlated negatively with the N2O:N2 emission ratio. The community data remains to be further analysed to identify factors influencing the overall bacterial and N2O reducing communities.

Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N 2 O. To curb soil N 2 O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed.

Microbes are the key players in the global cycling of nitrogen (N) and carbon (C) processes, availability and fluxes, and losses through emission of nitrous oxide (N2O) and methane (CH4), two very potent greenhouse gases. Thus, characterization of microbial functional guilds involved in these processes is high on the political agenda. Yet, typical sequence based characterization often represents only a minor fraction of their diversity in nature due to their frequent low relative abundance, insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage and efficiency of PCR-based assays. Here, we developed and tested a targeted metagenomic approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic N and CH4cycling. We designed comprehensive probe libraries for each of the 15 selected marker genes, resulting in 264,000 unique probes in total. These p...

Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest dec...

International audienceNitrous oxide (N2O) is a major radiative forcing and stratospheric ozone depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to N2 by bacteria and archaea harboring the nitrous oxide reductase (N2OR), which is the only known N2O sink in the biosphere. Despite its crucial role in mitigating N2O emissions, knowledge of the N2OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N2OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N2O reducing communities. Examination of N2OR structural elements not considered in the phylogeny revealed that the two clades differ in their signal peptides, indicating differences in the translocation pathway of the N2OR across the membrane. Sequencing of environmental clones of the previously undetected nosZ lineage in various en...

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competit...

<p>Although nitrogen is not a traditional contaminant when considering the detrimental impacts of mine waste leachate on aquatic ecosystems, it is a common pollutant of concern in underground iron ore mining where waste rock leachate has a neutral pH and a low metal content. This is the case in northern Sweden, where environmental authorities, supported by the EU Water Framework Directive, have imposed strict regulations on nitrogen discharges to oligotrophic surface water systems. Requirements for lower nitrogen releases has driven the development and application of a bioreactor technology for nitrate removal at LKAB’s Kiruna iron ore mine.</p><p>A full-scale woodchip denitrifying bioreactor has been in operation since September 2018 in Kiruna for the removal of nitrate (NO<sub>3</sub><sup>-</sup>) from waste rock leachate. Drainage from the waste rock pile is intercepted in a subsurface groundwater collection reservoir at the toe of the waste rock pile and pumped at an average rate of 22 m<sup>3</sup>/d into the bioreactor. Leachate from the low-sulfur waste rock is characterized by neutral pH (average pH 7), moderate alkalinity (108 mg/L HCO<sub>3</sub><sup>-</sup>), and elevated concentrations of sulfate, NO<sub>3</sub><sup>-</sup> and chloride (average concentrations 670, 61 and 102 mg L<sup>-1</sup> respectively).</p><p>During 2019, and average nitrogen removal efficiency was 77%: during the 165 day sampling period, 189 kg NO<sub>3</sub>-N were removed in the bioreactor, which is primarily attributed to denitrification. A net production of 26 kg of…

Diversifying agriculture by rotating a greater number of crop species in sequence is a promising practice to reduce negative impacts of crop production on the environment and maintain yields. However, it is unclear to what extent cereal yields change with crop rotation diversity and external nitrogen fertilization level over time, and which functional groups of crops provide the most yield benefit. Here, using grain yield data of small grain cereals and maize from 32 long-term (10–63 years) experiments across Europe and North America, we show that crop rotational diversity, measured as crop species diversity and functional richness, enhanced grain yields. This yield benefit increased over time. Only the yields of winter-sown small grain cereals showed a decline at the highest level of species diversity. Diversification was beneficial to all cereals with a low external nitrogen input, particularly maize, enabling a lower dependence on nitrogen fertilisers and ultimately reducing gree...

Denitrifying woodchip bioreactors are potential low‐cost technologies for the removal of nitrate (NO3−) in water through denitrification. However, if environmental conditions do not support microbial communities performing complete denitrification, other N transformation processes will occur, resulting in the export of nitrite (NO2−), nitrous oxide (N2O), or ammonium (NH4+). To identify the factors controlling the relative accumulation of NO2−, N2O, and/or NH4+ in denitrifying woodchip bioreactors, porewater samples were collected over two operational years from a denitrifying woodchip bioreactor designed for removing NO3− from mine water. Woodchip samples were collected at the end of the operational period. Changes in the abundances of functional genes involved in denitrification, N2O reduction, and dissimilatory NO3− reduction to NH4+ were correlated with porewater chemistry and temperature. Temporal changes in the abundance of the denitrification gene nirS were significantly corr...

Background Soil microbial communities are major drivers of cycling of soil nutrients that sustain plant growth and productivity. Yet, a holistic understanding of the impact of land-use intensification on the soil microbiome is still poorly understood. Here, we used a field experiment to investigate the long-term consequences of changes in land-use intensity based on cropping frequency (continuous cropping, alternating cropping with a temporary grassland, perennial grassland) on bacterial, protist and fungal communities as well as on their co-occurrence networks. Results We showed that land use has a major impact on the structure and composition of bacterial, protist and fungal communities. Grassland and arable cropping differed markedly with many taxa differentiating between both land use types. The smallest differences in the microbiome were observed between temporary grassland and continuous cropping, which suggests lasting effects of the cropping system preceding the temporary gr...