Projecting the impacts of the bioeconomy on Nordic land use and freshwater quality and quantity-An overview

This paper synthesizes a five-year project (BIOWATER) that assessed the effects of a developing bioeconomy on Nordic freshwaters. We used a catchment perspective and combined several approaches: comparative analyses of long-term data sets from well-monitored catchments (agricultural, with forestry, and near pristine) across Fennoscandia, catchment biogeochemical modelling and ecosystem services assessment for integration. Various mitigation measures were also studied. Benchmark Shared Socio-economic Pathways were downscaled and articulated in dialogue with national stakeholder representatives leading to five Nordic Bioeconomy Pathways (NBPs) describing plausible but different trajectories of societal development towards 2050.These were then used for catchment modelling and ecosystem service assessment. Key findings from the work synthesized here are: (a) The monitoring results from 69 catchments demonstrate that agricultural lands exported an order of magnitude more nutrients than natural catchments (medians 44 vs 4 kg P km-2 y-1 and 1450 vs 139 kg N km-2 y-1) whilst forests were intermediate (7 kg P km-2 y-1 and 200 kg N km-2 y-1). (b) Our contrasting scenarios led to substantial differences in land use patterns, which affected river flow as well as nutrient loads in two of the four modelled catchments (Danish Odense angstrom and Norwegian Skuterud), but not in two others (Swedish catchment C6 and Finnish Simojoki). (c) Strongly contrasting scenarios (NBP1 maximizing resource circularity versus NBP5 maximizing short-term profit) were found to lead to similar monetary estimates of total societal benefits, though for different underlying reasons - a pattern similar across the six studied Nordic catchments. (d) The ecological status of small to medium sized rivers in agricultural landscapes benefitted greatly from an increase in riparian forest cover from 10 % to 60 %. Riparian buffer strips, constructed wetlands, rewetting of ditched peatlands, and similar nature-based solutions optimize natural biogeochemical processes and thus can help in mitigating negative impacts of intensified biomass removal on water quality

Catchment effects of a future Nordic bioeconomy : From land use to water resources

In the future, the world is expected to rely increasingly on renewable biomass resources for food, fodder, fibre and fuel. The sustainability of this transition to bioeconomy for our water systems depends to a large extent on how we manage our land resources. Changes in land use together with climate change will affect water quantity and quality, which again will have implications for the ecosystem services provided by water resources. These are the main topics of this Ambio special issue on “Environmental effects of a green bio-economy”. This paper offers a summary of the eleven papers included in this issue and, at the same time, outlines an approach to quantify and mitigate the impacts of bioeconomy on water resources and their ecosystem services, with indications of useful tools and knowledge needs

Seasonality and depth zonation of intertidal Halophila ovalis and Zostera japonica in Ha Long Bay (northern Vietnam)

Abstract Seasonality and depth zonation of two common intertidal northern Vietnamese seagrass species, Halophila ovalis and Zostera japonica, were investigated in a 50 m long intertidal transect from 1999 till 2001. Z. japonica occurred in the middle intertidal (1.2 m above mean chart datum to mean sea level at

Assessing the societal benefits of river restoration using the ecosystem services approach

This paper is a contribution from the EU seventh framework funded research project REFORM (Grant Agreement 282656).The success of river restoration was estimated using the ecosystem services approach. In eight pairs of restored–unrestored reaches and floodplains across Europe, we quantified provisioning (agricultural products, wood, reed for thatching, infiltrated drinking water), regulating (flooding and drainage, nutrient retention, carbon sequestration) and cultural (recreational hunting and fishing, kayaking, biodiversity conservation, appreciation of scenic landscapes) services for separate habitats within each reach, and summed these to annual economic value normalized per reach area. We used locally available data and literature, did surveys among inhabitants and visitors, and used a range of economic methods (market value, shadow price, replacement cost, avoided damage, willingness-to-pay survey, choice experiment) to provide final monetary service estimates. Total ecosystem service value was significantly increased in the restored reaches (difference 1400 ± 600 € ha−1 year−1; 2500 − 1100, p = 0.03, paired t test). Removal of one extreme case did not affect this outcome. We analysed the relation between services delivered and with floodplain and catchment characteristics after reducing these 23 variables to four principal components explaining 80% of the variance. Cultural and regulating services correlated positively with human population density, cattle density and agricultural N surplus in the catchment, but not with the fraction of arable land or forest, floodplain slope, mean river discharge or GDP. Our interpretation is that landscape appreciation and flood risk alleviation are a function of human population density, but not wealth, in areas where dairy farming is the prime form of agriculture.PostprintPeer reviewe

Occupational exposure to gases/fumes and mineral dust affect DNA methylation levels of genes regulating expression

Many workers are daily exposed to occupational agents like gases/fumes, mineral dust or biological dust, which could induce adverse health effects. Epigenetic mechanisms, such as DNA methylation, have been suggested to play a role. We therefore aimed to identify differentially methylated regions (DMRs) upon occupational exposures in never-smokers and investigated if these DMRs associated with gene expression levels. To determine the effects of occupational exposures independent of smoking, 903 never-smokers of the LifeLines cohort study were included. We performed three genome-wide methylation analyses (Illumina 450 K), one per occupational exposure being gases/fumes, mineral dust and biological dust, using robust linear regression adjusted for appropriate confounders. DMRs were identified using comb-p in Python. Results were validated in the Rotterdam Study (233 never-smokers) and methylation-expression associations were assessed using Biobank-based Integrative Omics Study data (n = 2802). Of the total 21 significant DMRs, 14 DMRs were associated with gases/fumes and 7 with mineral dust. Three of these DMRs were associated with both exposures (RPLP1 and LINC02169 (2x)) and 11 DMRs were located within transcript start sites of gene expression regulating genes. We replicated two DMRs with gases/fumes (VTRNA2-1 and GNAS) and one with mineral dust (CCDC144NL). In addition, nine gases/fumes DMRs and six mineral dust DMRs significantly associated with gene expression levels. Our data suggest that occupational exposures may induce differential methylation of gene expression regulating genes and thereby may induce adverse health effects. Given the millions of workers that are exposed daily to occupational exposures, further studies on this epigenetic mechanism and health outcomes are warranted

Viability of meta-populations of wetland birds in a fragmented landscape: Testing the key-patch approach

The key patch approach assumes that metapopulations in fragmented landscapes are likely to be viable with at least one "key" sub-population that is sufficiently large to ensure re-colonization of surrounding minor habitat patches. It is based on a minimum viable number of breeding pairs and within-breeding season dispersal distance, linked to size of the animal and longevity. It was tested using census data of 15 wetland bird species (bearded tit, bluethroat, great reed warbler, sedge warbler, Savi's warbler, grasshopper warbler, spotted crake, water rail, common snipe, common teal, garganey, little bittern, night heron, great bittern and marsh harrier) in 14 wetland complexes of variable size (3-55 k

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare variants have not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped variants for association. Here we present the results of imputation using a large, new population-specific panel: the Genome of The Netherlands (GoNL). We benchmarked the performance of the 1000G and GoNL reference sets by comparing imputation genotypes with ‘true' genotypes typed on ImmunoChip in three European populations (Dutch, British, and Italian). GoNL showed significant improvement in the imputation quality for rare variants (MAF 0.05–0.5%) compared with 1000G. In Dutch samples, the mean observed Pearson correlation, r2, increased from 0.61 to 0.71. We also saw improved imputation accuracy for other European populations (in the British samples, r2 improved from 0.58 to 0.65, and in the Italians from 0.43 to 0.47). A combined reference set comprising 1000G and GoNL improved the imputation of rare variants even further. The Italian samples benefitted the most from this combined reference (the mean r2 increased from 0.47 to 0.50). We conclude that the creation of a large population-specific reference is advantageous for imputing rare variants and that a combined reference panel across multiple populations yields the best imputation results

Next-generation sequencing-based genome diagnostics across clinical genetics centers: Implementation choices and their effects

Implementation of next-generation DNA sequencing (NGS) technology into routine diagnostic genome care requires strategic choices. Instead of theoretical discussions on the consequences of such choices, we compared NGS-based diagnostic practices in eight clinical genetic centers in the Netherlands, based on genetic testing of nine pre-selected patients with cardiomyopathy. We highlight critical implementation choices, including the specific contributions of laboratory and medical specialists, bioinformaticians and researchers to diagnostic genome care, and how these affect interpretation and reporting of variants. Reported pathogenic mutations were consistent for all but one patient. Of the two centers that were inconsistent in their diagnosis, one reported to have found 'no causal variant', thereby underdiagnosing this patient. The other provided an alternative diagnosis, identifying another variant as causal than the other centers. Ethical and legal analysis showed that informed consent procedures in all centers were generally adequate for diagnostic NGS applications that target a limited set of genes, but not for exome- and genome-based diagnosis. We propose changes to further improve and align these procedures, taking into account the blurring boundary between diagnostics and research, and specific counseling options for exome- and genome-based diagnostics. We conclude that alternative diagnoses may infer a certain level of 'greediness' to come to a positive diagnosis in interpreting sequencing results. Moreover, there is an increasing interdependence of clinic, diagnostics and research departments for comprehensive diagnostic genome care. Therefore, we invite clinical geneticists, physicians, researchers, bioinformatics experts and patients to reconsider their role and position in future diagnostic genome care

Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation

This is the final version of the article. Available from Springer Nature via the DOI in this record.Raw data were submitted to the European Genome-phenome Archive (EGA) under accession EGAS00001001077.X-chromosome inactivation (XCI), i.e., the inactivation of one of the female X chromosomes, restores equal expression of X-chromosomal genes between females and males. However, ~10% of genes show variable degrees of escape from XCI between females, although little is known about the causes of variable XCI. Using a discovery data-set of 1867 females and 1398 males and a replication sample of 3351 females, we show that genetic variation at three autosomal loci is associated with female-specific changes in X-chromosome methylation. Through cis-eQTL expression analysis, we map these loci to the genes SMCHD1/METTL4, TRIM6/HBG2, and ZSCAN9. Low-expression alleles of the loci are predominantly associated with mild hypomethylation of CpG islands near genes known to variably escape XCI, implicating the autosomal genes in variable XCI. Together, these results suggest a genetic basis for variable escape from XCI and highlight the potential of a population genomics approach to identify genes involved in XCI.This research was financially supported by several institutions: BBMRI-NL, a Research Infrastructure financed by the Dutch government (NWO, numbers 184.021.007 and 184.033.111); the UK Medical Research Council; Wellcome (www.wellcome.ac.uk; [grant number 102215/2/13/2 to ALSPAC]); the University of Bristol to ALSPAC; the UK Economic and Social Research Council (www.esrc.ac.uk; [ES/N000498/1] to CR); the UK Medical Research Council (www.mrc.ac.uk; grant numbers [MC_UU_12013/1, MC_UU_12013/2 to JLM, CR]); the Helmholtz Zentrum München – German Research Center for Environmental Health, which is funded by the German Federal Ministry of Education and Research (BMBF) and by the State of Bavaria; the Munich Center of Health Sciences (MC-Health), Ludwig-Maximilians-Universität, as part of LMUinnovativ; the Wellcome Trust, Medical Research Council, European Union (EU), and the National Institute for Health Research (NIHR)- funded BioResource, Clinical Research Facility, and Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust in partnership with King’s College London