Impacts of arable reforestation on soil carbon and nutrients are dependent upon interactions between soil depth and tree species

Recent interest in temperate farm woodland has focussed on strengthening delivery of ecological and economic benefits from land. However, impacts of temperate farm woodland on soil properties and carbon inventories are poorly studied. With field samples and measurements taken at 35-year-old agroforestry experiment we determine how functioning in three components of the soil column (forest floor, topsoil (0–30 cm) and subsoil (>30 cm)) respond to land-use change, tree species choice and small-scale random variability in soil properties. Tree species influenced soil nutrient dynamics in the forest floor and topsoil, with Hazel forest floor material 27 % less concentrated in phosphorus (P) but containing 50 % more soil organic carbon (SOC) stock than Cherry or Sycamore. Change in land use from arable to woodland controlled soil bulk density, organic matter content and C storage in topsoil, with 15 % (11.8 t ha−1) more SOC stock in 0–30 cm soil beneath woodland compared with arable. In subsoil, tree species and land cover influence over soil functioning was insignificant. Notably, no net difference between arable and woodland soil C storage was found when the 0–50 cm part of the profile was considered as a whole, although net C storage was highly variable by plot. 35 years following planting, soil structure and SOC storage were only different in the forest floor and topsoil compared to the adjacent arable system. Each soil component therefore has its own functioning ‘signature’ in response to afforestation. Future policy support for farm woodland must account for this complexity

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx

Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. Results: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. Conclusions: The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species

Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea

A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study

Multi-experiment assessment of soil nitrous oxide emissions in sugarcane

Soil nitrous oxide (N 2O) fluxes comprise a significant part of the greenhouse gas emissions of agricultural products but are spatially and tempo-rally variable, due to complex interactions between climate, soil and management variables. This study aimed to identify the main factors that affect N2Oemissions under sugarcane, using a multi-site data-base from field experiments. Greenhouse gas fluxes, soil, climate, and management data were obtained from 13 field trials spanning the 2011–2017 period. We conducted exploratory, descriptive and inferential data analyses in experiments with varying fertiliser and stillage (vinasse) type and rate, and crop residue rates. The most relevant period of high N2O fluxes was the first 46 days after fertiliser application. The results indicate a strong positive correlation of cumulative N2O with nitrogen (N) fertiliser rate, soil fungi community (18S rRNA gene), soil ammonium(NH 4+ ) and nitrate (NO3−); and a moderate negative correlation with amoA genes of ammonia-oxidising archaea (AOA) and soil organic matter content. The regression analysis revealed that easily routinely measured climate and management-related variables explained over 50% of the variation in cumulativeN2O emissions, and that additional soil chemical and physical parameters improved the regression fit within R2 = 0.65. Cross-wavelet analysis indicated significant correlations of N2O fluxes with rainfall and air temperature up to 64 days, associated with temporal lags of 2 to 4 days in some experiments, and presenting a good environmental control over fluxes in general. The nitrogen fertiliser mean emission factors ranged from 0.03 to 1.17% of N applied, with urea and ammonium nitrate plus vinasse producing high emissions, while ammonium sulphate, ammonium nitrate without vinasse, calcium nitrate, and mitigation alternatives (nitrification inhibitors and timing of vinasse application) producing low N2O-EFs. Measurements from multiple sites spanning several crop-ping seasons were useful for exploring the influence of environmental and management-related variables on soil N 2O emissions in sugarcane production, providing support for global warming mitigation strategies, nitrogen management policies, and increased agricultural input efficiency

Genetic Variation in the TP53 Pathway and Bladder Cancer Risk. A Comprehensive Analysis

Introduction: Germline variants in TP63 have been consistently associated with several tumors, including bladder cancer, indicating the importance of TP53 pathway in cancer genetic susceptibility. However, variants in other related genes, including TP53 rs1042522 (Arg72Pro), still present controversial results. We carried out an in depth assessment of associations between common germline variants in the TP53 pathway and bladder cancer risk. Material and Methods: We investigated 184 tagSNPs from 18 genes in 1,058 cases and 1,138 controls from the Spanish Bladder Cancer/EPICURO Study. Cases were newly-diagnosed bladder cancer patients during 1998–2001. Hospital controls were age-gender, and area matched to cases. SNPs were genotyped in blood DNA using Illumina Golden Gate and TaqMan assays. Cases were subphenotyped according to stage/grade and tumor p53 expression. We applied classical tests to assess individual SNP associations and the Least Absolute Shrinkage and Selection Operator (LASSO)-penalized logistic regression analysis to assess multiple SNPs simultaneously. Results: Based on classical analyses, SNPs in BAK1 (1), IGF1R (5), P53AIP1 (1), PMAIP1 (2), SERINPB5 (3), TP63 (3), and TP73 (1) showed significant associations at p-value#0.05. However, no evidence of association, either with overall risk or with specific disease subtypes, was observed after correction for multiple testing (p-value$0.8). LASSO selected the SNP rs6567355 in SERPINB5 with 83% of reproducibility. This SNP provided an OR = 1.21, 95%CI 1.05–1.38, p-value = 0.006, and a corrected p-value = 0.5 when controlling for over-estimation. Discussion: We found no strong evidence that common variants in the TP53 pathway are associated with bladder cancer susceptibility. Our study suggests that it is unlikely that TP53 Arg72Pro is implicated in the UCB in white Europeans. SERPINB5 and TP63 variation deserve further exploration in extended studies.This work was supported by the Fondo de Investigacion Sanitaria, Spain (grant numbers 00/0745, PI051436, PI061614, G03/174); Red Tematica de Investigacion Cooperativa en Cancer (grant number RD06/0020-RTICC), Spain; Marato TV3 (grant number 050830); European Commission (grant numbers EU-FP7-HEALTH-F2-2008-201663-UROMOL; US National Institutes of Health (grant number USA-NIH-RO1-CA089715); and the Intramural Research Program of the Division of Cancer Epidemiology and Genetics, National Cancer Institute at the National Institutes of Health, USA; Consolider ONCOBIO (Ministerio de Economia y Competitividad, Madrid, Spain). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

piRNAs Are Associated with Diverse Transgenerational Effects on Gene and Transposon Expression in a Hybrid Dysgenic Syndrome of D. virilis

Sexual reproduction allows transposable elements (TEs) to proliferate, leading to rapid divergence between populations and species. A significant outcome of divergence in the TE landscape is evident in hybrid dysgenic syndromes, a strong form of genomic incompatibility that can arise when (TE) family abundance differs between two parents. When TEs inherited from the father are absent in the mother's genome, TEs can become activated in the progeny, causing germline damage and sterility. Studies in Drosophila indicate that dysgenesis can occur when TEs inherited paternally are not matched with a pool of corresponding TE silencing PIWI-interacting RNAs (piRNAs) provisioned by the female germline. Using the D. virilis syndrome of hybrid dysgenesis as a model, we characterize the effects that divergence in TE profile between parents has on offspring. Overall, we show that divergence in the TE landscape is associated with persisting differences in germline TE expression when comparing genetically identical females of reciprocal crosses and these differences are transmitted to the next generation. Moreover, chronic and persisting TE expression coincides with increased levels of genic piRNAs associated with reduced gene expression. Combined with these effects, we further demonstrate that gene expression is idiosyncratically influenced by differences in the genic piRNA profile of the parents that arise though polymorphic TE insertions. Overall, these results support a model in which early germline events in dysgenesis establish a chronic, stable state of both TE and gene expression in the germline that is maintained through adulthood and transmitted to the next generation. This work demonstrates that divergence in the TE profile is associated with diverse piRNA-mediated transgenerational effects on gene expression within populations

Factors affecting the net ecosystem productivity of agroecosystems on mineral soils: a meta-analysis

To optimize agricultural land management for soil carbon sequestration, it is necessary to identify whether agroecosystems are accumulating or gaining carbon. This can be done by determining an agroecosystem’s net ecosystem productivity (NEP). This study collated data from 40 papers, containing 242 annual measurements of NEP, to assess the impact of climate, soil type and management on the annual NEP of croplands and managed grasslands. Croplands lost significantly more carbon (110 g Cm−2) than managed grasslands (29.9 g Cm−2) and there was little statistical influence of climate, soil, or management practice on annual NEP. For agroecosystems to sequester carbon, there should be a shift in focus toward implementing management practices that increase carbon retention within agroecosystems

A restatement of the natural science evidence base concerning grassland management, grazing livestock and soil carbon storage

Approximately a third of all annual greenhouse gas emissions globally are directly or indirectly associated with the food system, and over a half of these are linked to livestock production. In temperate oceanic regions, such as the UK, most meat and dairy is produced in extensive systems based on pasture. There is much interest in the extent to which such grassland may be able to sequester and store more carbon to partially or completely mitigate other greenhouse gas emissions in the system. However, answering this question is difficult due to context-specificity and a complex and sometimes inconsistent evidence base. This paper describes a project that set out to summarize the natural science evidence base relevant to grassland management, grazing livestock and soil carbon storage potential in as policy-neutral terms as possible. It is based on expert appraisal of a systematically assembled evidence base, followed by a wide stakeholders engagement. A series of evidence statements (in the appendix of this paper) are listed and categorized according to the nature of the underlying information, and an annotated bibliography is provided in the electronic supplementary material