This paper presents a global model‐based country‐scale quantification of urban N and P mass flows from humans, animals, and industries and their waste N and P discharges to surface water and urban ...waste recycling in agriculture. Agricultural recycling was practiced commonly in early twentieth century Europe, Asia, and North America. During the twentieth century, global urban discharge to surface water increased ~3.5‐fold to 7.7 Tg yr‐1 for N and ~4.5‐fold to 1.0 Tg yr‐1 for P; the major part of this increase occurred between 1950 and 2000. Between 1900 and ~1940, industrial N and P flows dominated global surface water N and P loadings from urban areas; since ~1940, human wastes are the major source of urban nutrient discharge to both surface water and agricultural recycling. During the period 1900–2000, total global recycling of urban nutrients in agriculture increased from 0.4 to 0.6 Tg N yr‐1 and from 0.07 to 0.08 Tg P yr‐1. A large number of factors (the major ones related to food consumption, urban population, sewer connection, and industrial emissions) contribute to the uncertainty of −18% to +42% for N and −21% to +45% for P around the calculated surface water loading estimate for 2000.
Key Points
A global model was made to inventory urban 20th century nutrient flows
Global surface water discharge increased ~3.5‐fold for N and ~4.5‐fold for P
At present human excreta and detergents are the major urban nutrient sources
We present the experimental protocol and data analysis toolbox for multi-contact 4C (MC-4C), a new proximity ligation method tailored to study the higher-order chromatin contact patterns of selected ...genomic sites. Conventional chromatin conformation capture (3C) methods fragment proximity ligation products for efficient analysis of pairwise DNA contacts. By contrast, MC-4C is designed to preserve and collect large concatemers of proximity ligated fragments for long-molecule sequencing on an Oxford Nanopore or Pacific Biosciences platform. Each concatemer of proximity ligation products represents a snapshot topology of a different individual allele, revealing its multi-way chromatin interactions. By inverse PCR with primers specific for a fragment of interest (the viewpoint) and DNA size selection, sequencing is selectively targeted to thousands of different complex interactions containing this viewpoint. A tailored statistical analysis toolbox is able to generate background models and three-way interaction profiles from the same dataset. These profiles can be used to distinguish whether contacts between more than two regulatory sequences are mutually exclusive or, conversely, simultaneously occurring at chromatin hubs. The entire procedure can be completed in 2 w, and requires standard molecular biology and data analysis skills and equipment, plus access to a third-generation sequencing platform.
As Chinese aquaculture production accounts for over half of the global aquaculture production and has increased by 50% since 2006, there is growing concern about eutrophication caused by aquaculture ...in China. This paper presents a model-based estimate of nutrient flows in China’s aquaculture system during 2006–2017 using provincial scale data, to spatially distribute nutrient loads with a 0.5° resolution. The results indicate that with the increase in fish and shellfish production from 30 to 47 million tonnes (Mt) during 2006–2017, the nitrogen (N) release increased from 1.0 to 1.6 Mt/year and that of phosphorus (P) from 0.1 to 0.2 Mt/year. Nutrient release from freshwater aquaculture was concentrated in Guangdong, Jiangsu, and Hubei, and that from mariculture in Shandong, Fujian, and Guangdong. Aquaculture is an important strongly concentrated nutrient source in both freshwater and marine environments. Its nutrient release is >20% of total nutrient inputs to freshwater environments in some provinces, and nutrients from mariculture are comparable to river nutrient export to Chinese coastal seas. Aquaculture production and nutrient excretions are now comparable to those of livestock production systems in China and need to be accounted for when analyzing causes of eutrophication and harmful algal blooms and possible mitigation strategies.
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•In 2050 anthropogenic sources will contribute up to 80% to river nutrient loading.•Curbing the global nutrient cycles requires paradigm shifts in food and waste systems.•N:P ratios ...in global rivers will further increase due to selective system retention of P.•Waste systems need to change from a disposal orientation towards conservation.
This global spatially explicit (0.5 by 0.5 degree) analysis presents the nitrogen (N) and phosphorus (P) inputs, processing and biogeochemical retention and delivery to surface waters and river export to coastal seas according to the five shared socioeconomic pathways (SSP). Four systems are considered: (i) human system; (ii) agriculture; (iii) aquaculture; (iv) nature. Exploring the changes during 1980–2015 and 2015–2050 according to the SSPs shows that the natural nutrient sources have been declining in the past decades and will continue to decline in all SSPs in future decades due to massive land transformations, while agriculture, human sewage and aquaculture are becoming increasingly dominant (globally up to 80% of nutrient delivery). More efforts than those employed in any of the SSPs are needed to slow down the global nutrient cycles. One of the drivers of the proliferation of harmful algal blooms is the tendency towards increasing N:P ratios in global freshwaters and export to the global coastal seas; this is the result of increasing N:P in inputs in food production, more efficient biogeochemical retention of P than of N in river basins, and groundwater N legacies, which seems to be most pronounced in a united world that strives after sustainability. The diverging strategies to achieve UN Sustainable Development Goals 14 (life below water), 2 (zero hunger) and 6 (clean water and sanitation) therefore require a balanced management system for both N and P in all systems, that accounts for future nutrient legacies.
Reactive nitrogen (N) inputs in agriculture strongly outpace the outputs at the global scale due to inefficiencies in cropland N use. While improvement in agricultural practices and environmental ...legislation in developed regions such as Western Europe have led to a remarkable increase in the N use efficiency since 1985, this lower requirement for reactive N inputs via synthetic fertilizers has yet to occur in many developing and transition regions. Here, we explore future N input requirements and N use efficiency in agriculture for the five shared socioeconomic pathways. Results show that under the most optimistic sustainability scenario, the global synthetic fertilizer use in croplands stabilizes and even shrinks (85 Tg N yr−1 in 2050) regardless of the increase in crop production required to feed the larger estimated population. This scenario is highly dependent on projected increases in N use efficiency, particularly in South and East Asia. In our most pessimistic scenario, synthetic fertilization application rates are expected to increase almost threefold by 2050 (260 Tg N yr−1). Excepting the sustainability scenario, all other projected scenarios reveal that the areal N surpluses will exceed acceptable limits in most of the developing regions.
On the basis of the FAO projection ‘World Agriculture: Towards 2015/2030’ we direct our discussion to food production, the consequences for land use, efficiency of nitrogen (N) and losses of reactive ...N to the environment during 1995–2030. According the FAO, global food production can keep pace with the increase in food demand in the coming three decades. However, according the projection used here, there will be a major global increase (8%) in arable land, most of it in developing countries and with a major impact on the extent of tropical forests. Further forest clearing may occur to compensate for declining soil productivity due to land degradation. Despite improvements in the N use efficiency, total reactive N loss will grow strongly in the world's increasingly intensive agricultural systems. In the 1995–2030 period emissions of reactive N from intensive agricultural systems will continue to rise, particularly in developing countries. Therefore, the increase of N use efficiency and further improvement of agronomic management must remain high on the priority list of policy makers.
This paper presents a multiple linear regression model developed for describing global river export of sediments (suspended solids, TSS) to coastal seas, and approaches for estimating organic carbon, ...nitrogen, and phosphorous transported as particulate matter (POC, PN, and PP) associated with sediments. The model, with river‐basin spatial scale and a 1‐year temporal scale, is based on five factors with a significant influence on TSS yields (the extent of marginal grassland and wetland rice, Fournier precipitation, Fournier slope, and lithology), and accounts for sediment trapping in reservoirs. The model generates predictions within a factor of 4 for 80% of the 124 rivers in the data set. It is a robust model which was cross‐validated by using training and validation sets of data, and validated against independent data. In addition, Monte Carlo simulations were used to deal with uncertainties in the model coefficients for the five model factors. The global river export of TSS calculated thus is 19 Pg yr−1 with a 95% confidence interval of 11–27 Pg yr−1 when accounting for sediment trapping in regulated rivers. Associated POC, PN, and PP export is 197 Tg yr−1 (as C), 30 Tg yr−1 (N), and 9 Tg yr−1 (P), respectively. The global sediment trapping included in these estimates is 13%. Most particulate nutrients are transported by rivers to the Pacific (∼37% of global particulate nutrient export), Atlantic (28–29%), and Indian (∼20%) oceans, and the major source regions are Asia (∼50% of global particulate nutrient export), South America (∼20%), and Africa (12%).
Soil nitrogen (N) budgets are used in a global, distributed flow-path model with 0.5° × 0.5° resolution, representing denitrification and N2O emissions from soils, groundwater and riparian zones for ...the period 1900–2000 and scenarios for the period 2000–2050 based on the Millennium Ecosystem Assessment. Total agricultural and natural N inputs from N fertilizers, animal manure, biological N2 fixation and atmospheric N deposition increased from 155 to 345 Tg N yr−1 (Tg = teragram; 1 Tg = 1012 g) between 1900 and 2000. Depending on the scenario, inputs are estimated to further increase to 408–510 Tg N yr−1 by 2050. In the period 1900–2000, the soil N budget surplus (inputs minus withdrawal by plants) increased from 118 to 202 Tg yr−1, and this may remain stable or further increase to 275 Tg yr−1 by 2050, depending on the scenario. N2 production from denitrification increased from 52 to 96 Tg yr−1 between 1900 and 2000, and N2O–N emissions from 10 to 12 Tg N yr−1. The scenarios foresee a further increase to 142 Tg N2–N and 16 Tg N2O–N yr−1 by 2050. Our results indicate that riparian buffer zones are an important source of N2O contributing an estimated 0.9 Tg N2O–N yr−1 in 2000. Soils are key sites for denitrification and are much more important than groundwater and riparian zones in controlling the N flow to rivers and the oceans.
In livestock, many studies have reported the results of imputation to 50k single nucleotide polymorphism (SNP) genotypes for animals that are genotyped with low-density SNP panels. The objective of ...this paper is to review different measures of correctness of imputation, and to evaluate their utility depending on the purpose of the imputed genotypes. Across studies, imputation accuracy, computed as the correlation between true and imputed genotypes, and imputation error rates, that counts the number of incorrectly imputed alleles, are commonly used measures of imputation correctness. Based on the nature of both measures and results reported in the literature, imputation accuracy appears to be a more useful measure of the correctness of imputation than imputation error rates, because imputation accuracy does not depend on minor allele frequency (MAF), whereas imputation error rate depends on MAF. Therefore imputation accuracy can be better compared across loci with different MAF. Imputation accuracy depends on the ability of identifying the correct haplotype of a SNP, but many other factors have been identified as well, including the number of genotyped immediate ancestors, the number of animals with genotypes at the high-density panel, the SNP density on the low- and high-density panel, the MAF of the imputed SNP and whether imputed SNP are located at the end of a chromosome or not. Some of these factors directly contribute to the linkage disequilibrium between imputed SNP and SNP on the low-density panel. When imputation accuracy is assessed as a predictor for the accuracy of subsequent genomic prediction, we recommend that: (1) individual-specific imputation accuracies should be used that are computed after centring and scaling both true and imputed genotypes; and (2) imputation of gene dosage is preferred over imputation of the most likely genotype, as this increases accuracy and reduces bias of the imputed genotypes and the subsequent genomic predictions.
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