Evolution of hydrothermal regime along a crustal shear zone, Tinos island, Greece

International audienceStructural, cathodoluminescence and SIMS δ18O analyses of quartz-calcite veins are combined to constrain the evolution in space and time of fluid infiltration in an exhuming detachment shear zone (Tinos Island, Cyclades, Greece). Careful description of vein arrays shows that the plumbing system evolved into an interconnected network just beneath the ductile-to-brittle transition. Micro-textures of quartz and calcite infilling veins display deformed relics and newly precipitated grains. High-resolution δ18O mapping in relics yield a steady quartz-calcite fractionation of 2 ‰ at ~400 °C, whereas fractionation increases in neo-grains from 2 to 5 ‰ in 190 m toward the fault, or a ~150 °C temperature fall. Cooling is associated with a shift of fluid stable isotope signature from 15 ‰ to 0 ‰ beneath the detachment. Results are interpreted as advective removal of heat by massive infiltration of surface-derived fluids over depths of 10-15 km. Fluid penetration was promoted by the coalescence of late ductile-early brittle veins, as the exhuming footwall crossed the ductile-brittle transition. Only small amounts of fluids penetrated the ductile crust beneath the transitional rheology

Loss in soil microbial diversity constrains microbiome selection and alters the abundance of N-cycling guilds in barley rhizosphere

Plant roots are shaping microbial communities that are distinct from the surrounding soil. These root-associated microbial communities can have both positive and negative effects on the host nutrient acquisition and thereby growth, yet how loss of soil microbial diversity will constrain the plant microbiome selection is relatively unknown. In this study, we manipulated the soil microbial community using a removal-by-dilution approach to examine how microbial diversity modulates microbiome selection in barley, including microbial guilds involved in nitrogen (N) cycling processes causing N loss, and its consequences for plant performance. We found that microbial diversity loss reduced the barley's ability to recruit specific microorganisms from the soil and only members of the Alphaproteobacteria and Bacteroidetes were enriched in both rhizosphere and root-associated compartments irrespective of dilution level. Loss in soil microbial diversity and the presence of plants affected the N-cycling communities, with the abundance of nitrous oxide reducers being 2-4 times higher in both barley compartments in the lower diversity soils. In these soils, the low abundance of bacterial ammonia oxidizers (close or below detection level in the barley compartments) was concomitant with an increase in leaf greenness (ca. 12%), an indicator of the plant N status. The reduction in soil microbial diversity was thus coupled to a change in functional traits of rhizosphere and root-associated communities, with consequences for plant performance. This work contributes to our understanding of plant-microbe interactions, which is needed to steer the crop microbiome towards increased N-use efficiency while minimizing negative environmental impact

Spatial patterns of bacteria show that members of higher taxa share ecological characteristics

Affiche, résuméWhether bacteria display spatial patterns of distribution and at which level of taxonomic organization such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR and geostatistical modelling. The distributions of the relative abundance of most taxa varied by a factor of 2.520136.5 and displayed strong spatial patterns at the field scale. These spatial patterns were taxon-specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high taxonomical levels shared specific ecological traits in the pasture. Ecologically meaningful assemblages of bacteria at the phylum or class level in the environment provides evidence that deep branching patterns of the 16S rRNA bacterial tree are actually mirrored in nature

Nitrogen Isotopic Composition and Density of the Archean Atmosphere

Understanding the atmosphere's composition during the Archean eon is a fundamental issue to unravel ancient environmental conditions. We show from the analysis of nitrogen and argon isotopes in fluid inclusions trapped in 3.0-3.5 Ga hydrothermal quartz that the PN2 of the Archean atmosphere was lower than 1.1 bar, possibly as low as 0.5 bar, and had a nitrogen isotopic composition comparable to the present-day one. These results imply that dinitrogen did not play a significant role in the thermal budget of the ancient Earth and that the Archean PCO2 was probably lower than 0.7 bar

Spatial patterns of bacteria show that members of higher taxa share ecological characteristics

Affiche, résuméWhether bacteria display spatial patterns of distribution and at which level of taxonomic organisation such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR. Geostatistical modelling was used to analyse the spatial patterns of the taxa distributions. To test whether the spatial distributions of the different taxa were related to soil heterogeneity, we performed exploratory analyses of relationships between abundance of the bacterial taxa and key soil properties. The distributions of the relative abundance of most taxa varied by a factor of 2.5 to 6.5 and displayed strong spatial patterns at the field scale with autocorrelation ranging between 2 to 37 m. These spatial patterns were taxon-specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high taxonomical levels shared specific ecological traits in the pasture. Overall, the present study showed spatial patterns of distribution of bacteria both at the meter scale and at high taxonomical levels of organisation. Such spatial patterns allow comprehensive observations and predictions of bacterial occurrence in nature, hence helping in the generation of hypotheses concerning the mechanisms generating and maintaining bacterial diversity. The taxa-specific spatial patterns observed here suggest that, in a given environment, ecological traits are shared at high taxonomic levels within the domain Bacteria. This is a piece of evidence that the 16S rRNA gene tree divisions are not only based on evolutionary theory, but also have an ecological reality

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

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 grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions: Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification

Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity

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 grasslands. Land-use intensity also affected the bacterial co-occurrence networks with increased complexity in the perennial grassland comparing to the other land-use systems. Similarly, co-occurrence networks within microbial groups showed a higher connectivity in the perennial grasslands. Protists, particularly Rhizaria, dominated in soil microbial associations, as they showed a higher number of connections than bacteria and fungi in all land uses. Conclusions Our findings provide evidence of legacy effects of prior land use on the composition of the soil microbiome. Whatever the land use, network analyses highlighted the importance of protists as a key element of the soil microbiome that should be considered in future work. Altogether, this work provides a holistic perspective of the differential responses of various microbial groups and of their associations to agricultural intensification

Compounded Disturbance Chronology Modulates the Resilience of Soil Microbial Communities and N-Cycle Related Functions

There is a growing interest of overcoming the uncertainty related to the cumulative impacts of multiple disturbances of different nature in all ecosystems. With global change leading to acute environmental disturbances, recent studies demonstrated a significant increase in the possible number of interactions between disturbances that can generate complex, non-additive effects on ecosystems functioning. However, how the chronology of disturbances can affect ecosystems functioning is unknown even though there is increasing evidence that community assembly history dictates ecosystems functioning. Here, we experimentally examined the importance of the disturbances chronology in modulating the resilience of soil microbial communities and N-cycle related functions. We studied the impact of 3-way combinations of global change related disturbances on total bacterial diversity and composition, on the abundance of N-cycle related guilds and on N-cycle related activities in soil microcosms. The model pulse disturbances, i.e., short-term ceasing disturbances studied were heat, freeze-thaw and anaerobic cycles. We determined that repeated disturbances of the same nature can either lead to the resilience or to shifts in N-cycle related functions concomitant with diversity loss. When considering disturbances of different nature, we demonstrated that the chronology of compounded disturbances impacting an ecosystem determines the aggregated impact on ecosystem properties and functions. Thus, after 3 weeks the impact of the ‘anoxia/heat/freeze-thaw’ sequence was almost two times stronger than that of the ‘heat/anoxia/freeze-thaw’ sequence. Finally, we showed that about 29% of the observed variance in ecosystem aggregated impact caused by series of disturbances could be attributed to changes in the microbial community composition measured by weighted UniFrac distances. This indicates that surveying changes in bacterial community composition can help predict the strength of the impact of compounded disturbances on N-related functions and properties

Genome-wide detection of human variants that disrupt intronic branchpoints

The search for candidate variants underlying human disease in massive parallel sequencing data typically focuses on coding regions and essential splice sites, mostly ignoring noncoding variants. The RNA spliceosome recognizes intronic branchpoint (BP) motifs at the beginning of splicing and operates mostly within introns to define the exon-intron boundaries; however, BP variants have been paid little attention. We established a comprehensive genome-wide database and knowledgebase of BP and developed BPHunter for systematic and informative genome-wide detection of intronic variants that may disrupt BP and splicing, together with an effective strategy for prioritizing BP variant candidates. BPHunter not only constitutes an important resource for understanding BP, but should also drive discovery of BP variants in human genetic diseases and traits. Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 human genes have been reported to alter splicing and cause disease by disrupting BP. However, until now, no computational approach was available to efficiently detect such variants in massively parallel sequencing data. We established a comprehensive human genome-wide BP database by integrating existing BP data and generating new BP data from RNA sequencing of lariat debranching enzyme DBR1-mutated patients and from machine-learning predictions. We characterized multiple features of BP in major and minor introns and found that BP and BP-2 (two nucleotides upstream of BP) positions exhibit a lower rate of variation in human populations and higher evolutionary conservation than the intronic background, while being comparable to the exonic background. We developed BPHunter as a genome-wide computational approach to systematically and efficiently detect intronic variants that may disrupt BP recognition. BPHunter retrospectively identified 40 of the 48 known pathogenic BP variants, in which we summarized a strategy for prioritizing BP variant candidates. The remaining eight variants all create AG-dinucleotides between the BP and acceptor site, which is the likely reason for missplicing. We demonstrated the practical utility of BPHunter prospectively by using it to identify a novel germline heterozygous BP variant of STAT2 in a patient with critical COVID-19 pneumonia and a novel somatic intronic 59-nucleotide deletion of ITPKB in a lymphoma patient, both of which were validated experimentally. BPHunter is publicly available from an

Remotely Sensed Canopy Nitrogen Correlates With Nitrous Oxide Emissions in a Lowland Tropical Rainforest

Tropical forests exhibit significant heterogeneity in plant functional and chemical traits that may contribute to spatial patterns of key soil biogeochemical processes, such as carbon storage and greenhouse gas emissions. Although tropical forests are the largest ecosystem source of nitrous oxide (N2O), drivers of spatial patterns within forests are poorly resolved. Here, we show that local variation in canopy foliar N, mapped by remote‐sensing image spectroscopy, correlates with patterns of soil N2O emission from a lowland tropical rainforest. We identified ten 0.25 ha plots (assemblages of 40–70 individual trees) in which average remotely‐sensed canopy N fell above or below the regional mean. The plots were located on a single minimally‐dissected terrace (km2) where soil type, vegetation structure and climatic conditions were relatively constant. We measured N2O fluxes monthly for 1 yr and found that high canopy N species assemblages had on average three‐fold higher total mean N2O fluxes than nearby lower canopy N areas. These differences are consistent with strong differences in litter stoichiometry, nitrification rates and soil nitrate concentrations. Canopy N status was also associated with microbial community characteristics: lower canopy N plots had two‐fold greater soil fungal to bacterial ratios and a significantly lower abundance of ammonia‐oxidizing archaea, although genes associated with denitrification (nirS, nirK, nosZ) showed no relationship with N2O flux. Overall, landscape emissions from this ecosystem are at the lowest end of the spectrum reported for tropical forests, consist with multiple metrics indicating that these highly productive forests retain N tightly and have low plant‐available losses. These data point to connections between canopy and soil processes that have largely been overlooked as a driver of denitrification. Defining relationships between remotely‐sensed plant traits and soil processes offers the chance to map these processes at large scales, potentially increasing our ability to predict N2O emissions in heterogeneous landscapes