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Identification of therapeutic targets from genome-wide association studies (GWAS) requires insights into downstream functional consequences. We harmonized 8,613 RNA-sequencing samples from 14 brain datasets to create the MetaBrain resource and performed cis - and trans -expression quantitative trait locus (eQTL) meta-analyses in multiple brain region- and ancestry-specific datasets ( n  ≤ 2,759). Many of the 16,169 cortex cis -eQTLs were tissue-dependent when compared with blood cis -eQTLs. We inferred brain cell types for 3,549 cis -eQTLs by interaction analysis. We prioritized 186 cis -eQTLs for 31 brain-related traits using Mendelian randomization and co-localization including 40 cis -eQTLs with an inferred cell type, such as a neuron-specific cis -eQTL ( CYP24A1 ) for multiple sclerosis. We further describe 737 trans -eQTLs for 526 unique variants and 108 unique genes. We used brain-specific gene-co-regulation networks to link GWAS loci and prioritize additional genes for five central nervous system diseases. This study represents a valuable resource for post-GWAS research on central nervous system diseases. Brain expression quantitative trait locus (eQTL) and network analyses encompassing 8,613 RNA-sequencing samples from 14 eQTL datasets reveal downstream effects and putative drivers for brain-related diseases.

Distributed temperature sensing (DTS) systems can be used to estimate the temperature along optic fibers of several kilometers at a sub-meter interval. DTS systems function by shooting laser pulses through a fiber and measuring its backscatter intensity at two distinct wavelengths in the Raman spectrum. The scattering-loss coefficients for these wavelengths are temperature-dependent, so that the temperature along the fiber can be estimated using calibration to fiber sections with a known temperature. A new calibration approach is developed that allows for an estimate of the uncertainty of the estimated temperature, which varies along the fiber and with time. The uncertainty is a result of the noise from the detectors and the uncertainty in the calibrated parameters that relate the backscatter intensity to temperature. Estimation of the confidence interval of the temperature requires an estimate of the distribution of the noise from the detectors and an estimate of the multi-variate distribution of the parameters. Both distributions are propagated with Monte Carlo sampling to approximate the probability density function of the estimated temperature, which is different at each point along the fiber and varies over time. Various summarizing statistics are computed from the approximate probability density function, such as the confidence intervals and the standard uncertainty (the estimated standard deviation) of the estimated temperature. An example is presented to demonstrate the approach and to assess the reasonableness of the estimated confidence intervals. The approach is implemented in the open-source Python package “dtscalibration”.

PurposeThe impact of vermicompost on tree-soil systems is not yet fully understood. This study aimed to comparatively investigate the effects of chemical fertilizer, compost and vermicompost on soil enzymatic activities, seedling mycorrhizal colonization, growth and nutrition of one exotic tree species (radiata pine, Pinus radiata D. Don) and two native tree species (mānuka, Leptospermum scoparium and tōtara, Podocarpus totara).MethodsA 12-month-long pot trial was set up in the glasshouse with a factorial design of three tree species (radiata pine, tōtara and manuka) by six treatments, including T1-control, T2-chemical fertilizer, T3-HS compost, T4-HS vermicompost, T5-LS vermicompost and T6-CM vermicompost. We assessed the main effects and interactions of treatment and species on soil chemical and biological properties, plant growth and nutritional responses.ResultsCompared to the untreated control (T1), application of vermicomposts (T4-T6) and compost (T3) significantly improved soil chemical properties and enzymatic activities, and increased total seedling dry weight by 160–260%, shoot concentrations of nitrogen (N) by 54–97% and phosphorus (P) by 61–91%. Vermicomposts were comparable to diammonium phosphate (DAP) applied at 133 kg N ha−1 (T2) in stimulating the growth of native species (mānuka and tōtara) without negative impact on mycorrhizal colonization, with T5 being better than DAP (T2) in promoting mānuka growth. However, application of vermicompost alone was less effective than DAP in stimulating the exotic radiata pine growth. Overall, soil activities of dehydrogenase, urease, acid phosphatase and invertase were significantly and positively correlated to total C and N and exchangeable Ca and Mg.ConclusionThe increased growth of three tree species after application of vermicomposts was mainly related to improved N and P nutrition associated with enhanced root growth and soil enzymatic activities. Our findings imply that the vermicomposting products from septic tank waste could be a promising alternative to inorganic fertilizers in land application or greenhouse potting media of native tree species.

Forests provide essential ecosystem services such as wood production and soil carbon storage, which can be influenced by forest management. Fertilisation and understory removal are common practices set up in managed forests to reduce tree mortality and relieve trees from their main limitations, but their effects on belowground functioning and soil carbon storage are still unclear. In this study, we investigated the effects of phosphorus fertilisation, understory removal and their interaction on the carbon stored in the ecosystem and soil enzyme activities in two contrasting moorlands in south-western France (dry and wet moorlands) planted with maritime pines (Pinus pinaster Ait.). In the wet moorland, we found that fertilisation and understory removal had a positive effect on tree biomass, but they did not affect soil carbon stocks nor carbon-related enzyme activities. In the dry moorland, understory removal had a significant positive effect on tree biomass and a strong negative effect on topsoil organic carbon stocks and carbon-related enzyme activities. Overall, understory removal did not affect total carbon stocks at the ecosystem scale due to compensatory effects between carbon pools, i.e. the increase in carbon stored in the aboveground biomass was cancelled by a decrease in carbon stored in the soil. These results highlight the importance of adapting forest practices depending on the environmental context and carbon sequestration objectives.

The authors wish to make the following two corrections to this paper [...]

Large, persistent seed banks contribute to the invasiveness of non-native plants, and maternal plant size is an important contributory factor. We explored the relationships between plant vegetative size (V) and soil seed bank size (S) for the invasive shrub Ulex europaeus in its native range and in non-native populations, and identified which other factors may contribute to seed bank variation between native and invaded regions. We compared the native region (France) with two regions where Ulex is invasive, one with seed predators introduced for biological control (New Zealand) and another where seed predators are absent (La Réunion). We quantified seed bank size, plant dimensions, seed predation and soil fertility for six stands in each of the three regions. Seed banks were 9-14 times larger in the two invaded regions compared to native France. We found a positive relationship between current seed bank size and actual plant size, and that any deviation from this relationship was probably due to large differences in seed predation and/or soil fertility. We further identified three possible factors explaining larger seed banks in non-native environments: larger maternal plant size, lower activity of seed predators and higher soil fertility. In highlighting a positive relationship between maternal plant size and seed bank size, and identifying additional factors that regulate soil seed bank dynamics in non-native ranges, our data offer a number of opportunities for invasive weed control. For non-native Ulex populations specifically, management focusing on 'S' (i.e. the reduction of the seed bank by stimulating germination, or the introduction of seed predators as biological control agents) and/or on 'V' (i.e. by cutting mature stands to reduce maternal plant biomass) offers the most probable combination of effective control options.

Key message Pine fine root biomass, live fraction and specific root length studied after collection with ingrowth cores do not correspond with those collected with ingrowth meshes. Root studies are a challenging task, yet they are primordial to improve our understanding of biogeochemical cycles in many ecosystems. Methods reducing operator time and minimizing disturbance while permitting adequate assessment of root dimensions in space and time would naturally be of great relevance. Recently, ingrowth meshes have been proposed as a valuable alternative to existing methods, deployable in remote areas and potentially yielding smaller disturbances along with a reduction in time spent per sample. In this study, we used flexible mesh material in Pinus pinaster production forests. The mesh material (pore size 6 by 6 mm) was either applied as cores (15 cm deep, 8 cm diameter) or as linear meshes (15 cm deep, 50 cm long), and left in soils for 9, 24, or 36 months. Roots were retrieved from both devices and separated over plant species (pine and understory species), diameter class and vitality (live or dead). We expected 1) improved assessment of larger diameter roots in the linear meshes due to a larger mesh surface and 2) less disturbance of the soil for the linear meshes. Results indicate that most patterns were similar between both devices and species, but the meshes resulted in lower ingrowth for all diameter classes, and the cores better reflected the standing biomass. The larger surface of the linear meshes resulted in larger disturbance and did not permit to reduce time per sample. Future research may target ingrowth meshes of reduced size and perhaps of more rigid material.

Aims We investigated whether tree species growing in mixtures and under different water supply would segregate their fine roots vertically, produce more fine roots overall, or only in specific soil layers. Methods We examined the biomass, morphology, and distribution of fine roots down to 90 cm (forest floor, 0–5, 5–15, 15–30, 30–60, 60–90 cm) in pure and mixed stands of 10-year-old birch and pine trees, planted on a sandy podzol with discontinuous hardpan and seasonal high water table, following a randomized block design with four blocks receiving irrigation and four blocks left unirrigated during summer. Results Our results did not show any vertical root segregation between birch and pine in mixed plots. None of the species overyielded belowground throughout, but pine developed more roots in the top soil layer under irrigation. Both species had shallower fine root distributions in wet conditions, especially birch that was more plastic than pine in response to irrigation. Conclusions Both species followed similar ecological strategies, occupying and competing for the same layers of the soil profile, under both control and irrigated conditions. However, the greater allocation of pine roots at the top soil horizons under irrigated conditions suggests locally favourable niches can lead to depth-specific asymmetric competition. This sheds new light on vertical niche partitioning of young tree mixtures under varying environmental conditions.

Climate change is particularly strong in northern Eurasia and substantial ecological changes are expected in this extensive region. The reshaping and migration northwards of bioclimatic zones may offer opportunities for agricultural development in western and central Siberia. However, the bioclimatic vegetation models currently employed for projections still do not consider soil fertility, in spite of this being highly critical for plant growth. In the present study, we surveyed the phosphorus (P) status in the south-west of Siberia where soils have developed on loess parent material. We selected six sites differing in pedoclimatic conditions and the soil was sampled at different depths down to 1 m in aspen (Populus tremula L.) forest as well as in grassland areas. The P status was assessed by conventional methods and by isotope dilution kinetics. We found that P concentrations and stocks, as well as their distribution through the soil profile, were fairly homogeneous on the regional scale studied, although there were some differences between sites (particularly in organic P). The young age of the soils, together with slow kinetics of soil formation processes have probably not yet resulted in a sufficiently wide range of soil physico-chemical conditions to observe a more diverging P status. The comparison of our data set with similar vegetation contexts on the global scale revealed that the soils of south-western Siberia, and more generally of northern Eurasia, often have (very) high levels of total, organic and inorganic P. The amount of plant-available P in topsoils, estimated by the isotopically exchangeable phosphate ions, was not particularly high but was intermediate on the global scale. However, large stocks of plant-available P are stored in subsurface layers which currently have low fine-root exploration intensities. These results suggest that the P resource is unlikely to constrain vegetation growth and agricultural development under the present conditions or in the near future.