High-temporal Resolution Sediment Fingerprinting in the River Wensum Demonstration Test Catchment, UK: A Bayesian Approach

A high-temporal resolution fluvial sediment source apportionment model, set within an empirical Bayesian framework, is presented for the River Wensum Demonstration Test Catchment (DTC), UK. Direct X-ray fluorescence (XRF) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) analysis of sediment covered filter papers were used in conjunction with ISCO automatic water samplers to monitor suspended particulate matter (SPM) geochemistry at high-temporal resolution throughout the progression of five heavy precipitation events during 2012-2013. Exploiting the spatial and temporal variation in four potential sediment source areas and SPM geochemistry respectively, we are able to apportion sediment contributions from eroding stream channel banks, arable topsoils, damaged road verges and agricultural field drains at 60-120 minute resolution. For all monitored precipitation episodes, pre- and post-event conditions are dominated by elevated SPM calcium concentrations that indicate major sediment inputs from carbonate-rich subsurface sources. Conversely, precipitation events coincide with an increase in concentrations of clay-associated elements and a consequent increase in predicted contributions from surface sources. Employing a Gibbs sampling Markov Chain Monte-Carlo mixing model procedure has enabled full characterisation of both spatial geochemical variability and instrument precision to quantify uncertainty around posterior distributions. All model source apportionment estimates correspond favourably with understanding of the regional geology, analysis of hysteresis behaviour, and visual observations of catchment processes. The results presented here demonstrate how to directly analyse SPM trapped on filter papers by spectroscopy to yield the high-temporal resolution source apportionment estimates required by catchment managers to help mitigate the deleterious effects of land-to-river sediment transfer

Intermittent Small Baseline Subset (ISBAS) monitoring of land covers unfavourable for conventional C-band InSAR: proof-of-concept for peatland environments in North Wales, UK

This paper provides a proof-of-concept for the use of the new Intermittent Small Baseline Subset (ISBAS) approach to study ground elevation changes in areas of peat and organic soils in north Wales, which are generally, unfavourable for conventional C-band interferometric applications. A stack of 53 ERS-1/2 C-band SAR scenes acquired between 1993 and 2000 in descending mode was processed with both the standard low-pass SBAS method and ISBAS. The latter revealed exceptional improvements in the coverage of ground motion solutions with respect to the standard approach. The number of identified coherent and intermittently coherent pixels increased by a factor of 26 with respect to the SBAS solution, and extended the coverage of results across unfavourable land covers, particularly for coniferous woodland, bog, acid grassland and heather. The greatest increase was achieved over coniferous woodland, which showed ISBAS/SBAS pixel density ratios above 300. Despite the intermittent nature of the ISBAS solutions, ISBAS provided velocity standard errors generally below 1-1.5 mm/yr, thus preserving good quality of the estimated ground motion rates

Combining Two Filter Paper-Based Analytical Methods to Monitor Temporal Variations in Fluvial Suspended Solid Properties

Many of the commonly used analytical techniques for assessing the properties of fluvial suspended solids are neither cost-effective nor time-efficient, making them prohibitive to long-term high-resolution monitoring.We propose a novel methodology utilising two types of spectroscopy which, when combined with automatic water samplers, can generate accurate, high-temporal resolution sediment property data, inexpensively and non-destructively, directly from sediment covered filter papers. A dual X-ray fluorescence spectroscopy (XRFS) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) approach is developed to estimate concentrations for a range of elements (Al, Ca, Ce, Fe, K, Mg, Mn, Na, P, Si, Ti) and compounds (organic carbon, Aldithionate, Aloxalate, Fedithionate, and Feoxalate) within sediments trapped on quartz fibre filters at masses as low as 3 mg. Calibration models with small prediction errors are produced for a total of 16 elements and compounds for which the geochemical signal is demonstrated to be time stable enabling samples to be stored for several weeks prior to analysis. Spectral pre-processing methods are shown to enhance the reproducibility of results for some compounds, whilst corrections for sediment mass retention are derived, and the importance of filter paper selection and homogeneous sample preparation in minimising spectral interference are emphasized. The results presented here demonstrate the potential for a combined XRFS and DRIFTS analysis of sediment covered filter papers to be utilized under a range of in-stream hydrological conditions where there is an environmental requirement for high-resolution monitoring of suspended solid properties

Spatial scaling of CO2 efflux in a temperate grazed grassland

Understanding CO2 efflux from soil at different scales is important when up-scaling CO2 measurements from plot to larger scales, but there have been few studies investigating spatial CO2 efflux in temperate environments. We conducted a nested analysis of variation to explore how the CO2 efflux variation occurs between different spatial scales. Ninety-six manual dynamic chamber flux measurements of CO2 were undertaken during three, four hour surveys within seven grouped sites, each containing an optimised nested design with lag distances of 0.3m, 1m, 3m and 9m across six hectares of grazed hillslope grassland. This design also included continuous logging soil moisture sensors (plus conductivity and temperature) at 10cm soil depth. A previous study showed at this site that the variation of soil moisture is divided relatively equally between the four spatial scales 9m. The proportion of large-scale (>9m) variation increased after rainfall. In contrast in the three surveys analysed to date, the vast majority of the variation in CO2 flux occurred over the two smallest scales. No significant correlation between CO2 and soil moisture was observed over any of the spatial scales. All of these three surveys were conducted on relatively dry soils. We also investigated whether there were significant temporal variations in CO2 efflux over a period of three weeks using an automated soil flux system. These data showed there was no significant temporal variability between 10:00 to 16:00 hrs during late summer. There has recently been substantial rainfall at the field site and we are now conducting additional surveys to examine how the total CO2 fluxes and their spatial variation is effected by these wetter conditions

Three-dimensional soil organic matter distribution, accessibility and microbial respiration in macroaggregates using osmium staining and synchrotron X-ray computed tomography

The spatial distribution and accessibility of organic matter (OM) to soil microbes in aggregates – determined by the fine-scale, 3-D distribution of OM, pores and mineral phases – may be an important control on the magnitude of soil heterotrophic respiration (SHR). Attempts to model SHR on fine scales requires data on the transition probabilities between adjacent pore space and soil OM, a measure of microbial accessibility to the latter. We used a combination of osmium staining and synchrotron X-ray computed tomography (CT) to determine the 3-D (voxel) distribution of these three phases (scale 6.6 μm) throughout nine aggregates taken from a single soil core (range of organic carbon (OC) concentrations: 4.2–7.7 %). Prior to the synchrotron analyses we had measured the magnitude of SHR for each aggregate over 24 h under controlled conditions (moisture content and temperature). We test the hypothesis that larger magnitudes of SHR will be observed in aggregates with (i) shorter length scales of OM variation (more aerobic microsites) and (ii) larger transition probabilities between OM and pore voxels. After scaling to their OC concentrations, there was a 6-fold variation in the magnitude of SHR for the nine aggregates. The distribution of pore diameters and tortuosity index values for pore branches was similar for each of the nine aggregates. The Pearson correlation between aggregate surface area (normalized by aggregate volume) and normalized headspace C gas concentration was both positive and reasonably large (r D0.44), suggesting that the former may be a factor that influences SHR. The overall transition probabilities between OM and pore voxels were between 0.07 and 0.17, smaller than those used in previous simulation studies. We computed the length scales over which OM, pore and mineral phases vary within each aggregate using 3-D indicator variograms. The median range of models fitted to variograms of OM varied between 38 and 175 μm and was generally larger than the other two phases within each aggregate, but in general variogram models had ranges <250 μm. There was no evidence to support the hypotheses concerning scales of variation in OM and magnitude of SHR; the linear correlation was 0.01. There was weak evidence to suggest a statistical relationship between voxel-based OM–pore transition probabilities and the magnitudes of aggregate SHR (r D0.12).We discuss how our analyses could be extended and suggest improvements to the approach we used

Sensitivity of fluvial sediment source apportionment to mixing model assumptions: A Bayesian model comparison

Mixing models have become increasingly common tools for apportioning fluvial sediment load to various sediment sources across catchments using a wide variety of Bayesian and frequentist modeling approaches. In this study, we demonstrate how different model setups can impact upon resulting source apportionment estimates in a Bayesian framework via a one-factor-at-a-time (OFAT) sensitivity analysis. We formulate 13 versions of a mixing model, each with different error assumptions and model structural choices, and apply them to sediment geochemistry data from the River Blackwater, Norfolk, UK, to apportion suspended particulate matter (SPM) contributions from three sources (arable topsoils, road verges, and subsurface material) under base flow conditions between August 2012 and August 2013. Whilst all 13 models estimate subsurface sources to be the largest contributor of SPM (median ∼76%), comparison of apportionment estimates reveal varying degrees of sensitivity to changing priors, inclusion of covariance terms, incorporation of time-variant distributions, and methods of proportion characterization. We also demonstrate differences in apportionment results between a full and an empirical Bayesian setup, and between a Bayesian and a frequentist optimization approach. This OFAT sensitivity analysis reveals that mixing model structural choices and error assumptions can significantly impact upon sediment source apportionment results, with estimated median contributions in this study varying by up to 21% between model versions. Users of mixing models are therefore strongly advised to carefully consider and justify their choice of model structure prior to conducting sediment source apportionment investigations

Apportioning sources of organic matter in streambed sediments: An integrated molecular and compound-specific stable isotope approach

We present a novel application for quantitatively apportioning sources of organic matter in streambed sediments via a coupled molecular and compound-specific isotope analysis (CSIA) of long-chain leaf wax n-alkane biomarkers using a Bayesian mixing model. Leaf wax extracts of 13 plant species were collected from across two environments (aquatic and terrestrial) and four plant functional types (trees, herbaceous perennials, and C3 and C4 graminoids) from the agricultural River Wensum catchment, UK. Seven isotopic (δ13C27, δ13C29, δ13C31, δ13C27–31, δ2H27, δ2H29, and δ2H27–29) and two n-alkane ratio (average chain length (ACL), carbon preference index (CPI)) fingerprints were derived, which successfully differentiated 93% of individual plant specimens by plant functional type. The δ2H values were the strongest discriminators of plants originating from different functional groups, with trees (δ2H27–29 = − 208‰ to − 164‰) and C3 graminoids (δ2H27–29 = − 259‰ to − 221‰) providing the largest contrasts. The δ13C values provided strong discrimination between C3 (δ13C27–31 = − 37.5‰ to − 33.8‰) and C4 (δ13C27–31 = − 23.5‰ to − 23.1‰) plants, but neither δ13C nor δ2H values could uniquely differentiate aquatic and terrestrial species, emphasizing a stronger plant physiological/biochemical rather than environmental control over isotopic differences. ACL and CPI complemented isotopic discrimination, with significantly longer chain lengths recorded for trees and terrestrial plants compared with herbaceous perennials and aquatic species, respectively. Application of a comprehensive Bayesian mixing model for 18 streambed sediments collected between September 2013 and March 2014 revealed considerable temporal variability in the apportionment of organic matter sources. Median organic matter contributions ranged from 22% to 52% for trees, 29% to 50% for herbaceous perennials, 17% to 34% for C3 graminoids and 3% to 7% for C4 graminoids. The results presented here clearly demonstrate the effectiveness of an integrated molecular and stable isotope analysis for quantitatively apportioning, with uncertainty, plant-specific organic matter contributions to streambed sediments via a Bayesian mixing model approach

National-scale geodata describe widespread accelerated soil erosion

Accelerated soil erosion can result in substantial declines in soil fertility and has devastating environmental impacts. Consequently, understanding if rates of soil erosion are acceptable is of local and global importance. Herein we use empirical soil erosion observations collated into an open access geodatabase to identify the extent to which existing data and methodological approaches can be used to develop an empirically-derived understanding of soil erosion in the UK (by way of an example). The findings indicate that whilst mean erosion rates in the UK are low, relative to the rest of Europe for example, 16% of observations on arable land were greater than the supposedly tolerable rate of 1 t ha−1 yr−1 and maximum erosion rates were as high as 91.7 t ha−1 yr−1. However, the analysis highlights a skew in existing studies towards locations with a known erosion likelihood and methods that are biased towards single erosion pathways, rather than an all-inclusive study of erosion rates and processes. Accordingly, we suggest that future soil erosion research and policy must address these issues if an accurate assessment of soil erosion rates at the national-scale are to be established. The interactive geodatabase published alongside this paper offers a platform for the simultaneous development of soil erosion research, formulation of effective policy and better protection of soil resource

An Amish founder variant consolidates disruption of CEP55 as a cause of hydranencephaly and renal dysplasia

This is the author accepted manuscript. The final version is available from Springer Nature via the DOI in this record.The centrosomal protein 55 kDa (CEP55 (OMIM 610000)) plays a fundamental role in cell cycle regulation and cytokinesis. However, the precise role of CEP55 in human embryonic growth and development is yet to be fully defined. Here we identified a novel homozygous founder frameshift variant in CEP55, present at low frequency in the Amish community, in two siblings presenting with a lethal foetal disorder. The features of the condition are reminiscent of a Meckel-like syndrome comprising of Potter sequence, hydranencephaly, and cystic dysplastic kidneys. These findings, considered alongside two recent studies of single families reporting loss of function candidate variants in CEP55, confirm disruption of CEP55 function as a cause of this clinical spectrum and enable us to delineate the cardinal clinical features of this disorder, providing important new insights into early human development.Medical Research CouncilNewlife Foundation for disabled childre

Lung epithelial stem cells and their niches : Fgf10 takes center stage

Throughout life adult animals crucially depend on stem cell populations to maintain and repair their tissues to ensure life-long organ function. Stem cells are characterized by their capacity to extensively self-renew and give rise to one or more differentiated cell types. These powerful stem cell properties are key to meet the changing demand for tissue replacement during normal lung homeostasis and regeneration after lung injury. Great strides have been made over the last few years to identify and characterize lung epithelial stem cells as well as their lineage relationships. Unfortunately, knowledge on what regulates the behavior and fate specification of lung epithelial stem cells is still limited, but involves communication with their microenvironment or niche, a local tissue environment that hosts and influences the behaviors or characteristics of stem cells and that comprises other cell types and extracellular matrix. As such, an intimate and dynamic epithelial-mesenchymal cross-talk, which is also essential during lung development, is required for normal homeostasis and to mount an appropriate regenerative response after lung injury. Fibroblast growth factor 10 (Fgf10) signaling in particular seems to be a well-conserved signaling pathway governing epithelial-mesenchymal interactions during lung development as well as between different adult lung epithelial stem cells and their niches. On the other hand, disruption of these reciprocal interactions leads to a dysfunctional epithelial stem cell-niche unit, which may culminate in chronic lung diseases such as chronic obstructive pulmonary disease (COPD), chronic asthma and idiopathic pulmonary fibrosis (IPF)