Development of soil health benchmarks for managed and semi-natural landscapes.

Efforts to improve soil health require that target values of key soil properties are established. No agreed targets exist but providing population data as benchmarks is a useful step to standardise soil health comparison between landscapes. We exploited nationally representative topsoil (0-15 cm) measurements to derive soil health benchmarks for managed and semi-natural environments across Great Britain. In total, 4587 soil organic matter (SOM), 3860 pH, 2908 bulk density (BD), and 465 earthworm abundance (EA) datapoints were used. As soil properties are sensitive to site-specific characteristics, data were stratified by habitat, soil type, and mean annual precipitation, with benchmarks defined as the middle 80 % of values in each distribution - yielding 135 benchmarks. BD and pH decreased with land management intensity (agriculture > semi-natural grasslands > woodlands > heathlands > wetlands), and vice versa for SOM and EA. Normalising benchmark ranges by medians revealed soil health indicator benchmark widths increased in the order: pH < BD < SOM < EA, while width increased with decreasing land management intensity. Arable and horticulture and improved grassland exhibited narrow benchmarks for SOM, pH and BD, yet the widest EA benchmark, suggesting additional drivers impact EA patterns. Upland wetlands had the widest BD benchmarks, important when determining carbon stocks. East Anglia currently possesses the largest proportions of atypical soils, including below typical SOM (19.2 %), above typical BD (17.4 %) and pH (39.1 %), and the smallest proportions of above typical SOM (2.4 %), and below typical BD (5.8 %) and pH (2.3 %). This is found even after land use, soil type and rainfall have been considered, underscoring how urgently soil health should be addressed here. Our benchmarking framework allows landowners to compare where their measured soil health indicators fall within expected ranges and is applicable to other biomes, national and multinational contexts.

Global meta-analysis of soil hydraulic properties on the same soils with differing land use.

Global land use change has resulted in more pasture and cropland, largely at the expense of woodlands, over the last 300 years. How this change affects soil hydraulic function with regard to feedbacks to the hydrological cycle is unclear for earth system modelling (ESM). Pedotransfer functions (PTFs) used to predict soil hydraulic conductivity (K) take no account of land use. Here, we synthesize >800 measurements from around the globe from sites that measured near-saturated soil hydraulic conductivity, or infiltration, at the soil surface, on the same soil type at each location, but with differing land use, woodland (W), grassland (G) and cropland (C). We found that texture based PTFs predict K reasonably well for cropland giving unbiased results, but increasingly underestimate K in grassland and woodland. In native woodland and grassland differences in K can usually be accounted for by differences in bulk density. However, heavy grazing K responses can be much lower indicating compaction likely reduces connectivity. We show that the K response ratios (RR) between land uses vary with cropland (C/W = 0.45 [W/C = 2.2]) and grassland (G/W = 0.63 [W/G = 1.6]) having about half the K of woodland.

Long-term cattle grazing shifts the ecological state of forest soils.

Cattle grazing profoundly affects abiotic and biotic characteristics of ecosystems. While most research has been performed on grasslands, the effect of large managed ungulates on forest ecosystems has largely been neglected. Compared to a baseline seminatural state, we investigated how long-term cattle grazing of birch forest patches affected the abiotic state and the ecological community (microbes and invertebrates) of the soil subsystem. Grazing strongly modified the soil abiotic environment by increasing phosphorus content, pH, and bulk density, while reducing the C:N ratio. The reduced C:N ratio was strongly associated with a lower microbial biomass, mainly caused by a reduction of fungal biomass. This was linked to a decrease in fungivorous nematode abundance and the nematode channel index, indicating a relative uplift in the importance of the bacterial energy-channel in the nematode assemblages. Cattle grazing highly modified invertebrate community composition producing distinct assemblages from the seminatural situation. Richness and abundance of microarthropods was consistently reduced by grazing (excepting collembolan richness) and grazing-associated changes in soil pH, Olsen P, and reduced soil pore volume (bulk density) limiting niche space and refuge from physical disturbance. Anecic earthworm species predominated in grazed patches, but were absent from ungrazed forest, and may benefit from manure inputs, while their deep vertical burrowing behavior protects them from physical disturbance. Perturbation of birch forest habitat by long-term ungulate grazing profoundly modified soil biodiversity, either directly through increased physical disturbance and manure input or indirectly by modifying soil abiotic conditions. Comparative analyses revealed the ecosystem engineering potential of large ungulate grazers in forest systems through major shifts in the composition and structure of microbial and invertebrate assemblages, including the potential for reduced energy flow through the fungal decomposition pathway. The precise consequences for species trophic interactions and biodiversity-ecosystem function relationships remain to be established, however.

Massively multiplex single-molecule oligonucleosome footprinting.

Our understanding of the beads-on-a-string arrangement of nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge the divide between these approaches, we present the single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput single-molecule sequencing method that combines adenine methyltransferase footprinting and single-molecule real-time DNA sequencing to natively and nondestructively measure nucleosome positions on individual chromatin fibres. SAMOSA data allows unbiased classification of single-molecular 'states' of nucleosome occupancy on individual chromatin fibres. We leverage this to estimate nucleosome regularity and spacing on single chromatin fibres genome-wide, at predicted transcription factor binding motifs, and across human epigenomic domains. Our analyses suggest that chromatin is comprised of both regular and irregular single-molecular oligonucleosome patterns that differ subtly in their relative abundance across epigenomic domains. This irregularity is particularly striking in constitutive heterochromatin, which has typically been viewed as a conformationally static entity. Our proof-of-concept study provides a powerful new methodology for studying nucleosome organization at a previously intractable resolution and offers up new avenues for modeling and visualizing higher order chromatin structure.

A systematic evaluation of the design and context dependencies of massively parallel reporter assays.

Massively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. To date, there are limited studies that systematically compare differences in MPRA design. Here, we screen a library of 2,440 candidate liver enhancers and controls for regulatory activity in HepG2 cells using nine different MPRA designs. We identify subtle but significant differences that correlate with epigenetic and sequence-level features, as well as differences in dynamic range and reproducibility. We also validate that enhancer activity is largely independent of orientation, at least for our library and designs. Finally, we assemble and test the same enhancers as 192-mers, 354-mers and 678-mers and observe sizable differences. This work provides a framework for the experimental design of high-throughput reporter assays, suggesting that the extended sequence context of tested elements and to a lesser degree the precise assay, influence MPRA results.

Decadal shifts in soil pH and organic matter differ between land uses in contrasting regions in China.

Soil organic matter (SOM) and pH are critical soil properties strongly linked to carbon storage, nutrient cycling and crop productivity. Land use is known to have a dominant impact on these key soil properties, but we often lack the ability to examine temporal trajectories across extensive spatial scales. Large-scale monitoring programmes provide the data to evaluate these longer-term changes, and under different climatic conditions. This study used data from Chinese soil surveys to examine changes in soil pH and SOM across different land uses (dry farmland, paddy fields, grassland, woodland, unused land), with surface soil (0-20 cm) collected in the periods 1985-90 (Survey 1; 890 samples) and 2006-10 (Survey 2; 5005 samples) from two contrasting areas. In the southern part of China the mean pH of paddy soils fell sharply over the two decades between surveys - from pH 5.81 to 5.19 (p < 0.001), while dry farmlands in the northern sampling area fell slightly (from pH 8.15 to 7.82; p < 0.001). The mean SOM content of dry farmland soil rose in both areas and the mean SOM of paddy fields in the southern area also rose (all p < 0.001). Woodland soil pH in the south showed an increase from 4.71 to 5.29 (p < 0.001) but no significant difference was measured in the woodlands of the northern area, although the trend increased. The SOM content of woodland top soils rose in the northern (p = 0.003) and southern (p < 0.001) study areas. The implications and potential causes of these changes over the two decade timespan between surveys are discussed and suggestions made as to how large scale soil sampling campaigns can be designed to monitor for changes and potential controlling factors.

Zones of influence for soil organic matter dynamics: A conceptual framework for data and models.

Soil organic matter (SOM) is an indicator of sustainable land management as stated in the global indicator framework of the United Nations Sustainable Development Goals (SDG Indicator 15.3.1). Improved forecasting of future changes in SOM is needed to support the development of more sustainable land management under a changing climate. Current models fail to reproduce historical trends in SOM both within and during transition between ecosystems. More realistic spatio-temporal SOM dynamics require inclusion of the recent paradigm shift from SOM recalcitrance as an 'intrinsic property' to SOM persistence as an 'ecosystem interaction'. We present a soil profile, or pedon-explicit, ecosystem-scale framework for data and models of SOM distribution and dynamics which can better represent land use transitions. Ecosystem-scale drivers are integrated with pedon-scale processes in two zones of influence. In the upper vegetation zone, SOM is affected primarily by plant inputs (above- and belowground), climate, microbial activity and physical aggregation and is prone to destabilization. In the lower mineral matrix zone, SOM inputs from the vegetation zone are controlled primarily by mineral phase and chemical interactions, resulting in more favourable conditions for SOM persistence. Vegetation zone boundary conditions vary spatially at landscape scales (vegetation cover) and temporally at decadal scales (climate). Mineral matrix zone boundary conditions vary spatially at landscape scales (geology, topography) but change only slowly. The thicknesses of the two zones and their transport connectivity are dynamic and affected by plant cover, land use practices, climate and feedbacks from current SOM stock in each layer. Using this framework, we identify several areas where greater knowledge is needed to advance the emerging paradigm of SOM dynamics-improved representation of plant-derived carbon inputs, contributions of soil biota to SOM storage and effect of dynamic soil structure on SOM storage-and how this can be combined with robust and efficient soil monitoring.

Functional testing of thousands of osteoarthritis-associated variants for regulatory activity.

To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. Here, we functionally test 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identify six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that the most significant SNP, rs4730222, exhibits differential nuclear protein binding in electrophoretic mobility shift assays and drives increased expression of an alternative isoform of HBP1 in a heterozygote chondrosarcoma cell line, in a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.

Model-based hypervolumes for complex ecological data.

Developing a holistic understanding of the ecosystem impacts of global change requires methods that can quantify the interactions among multiple response variables. One approach is to generate high dimensional spaces, or hypervolumes, to answer ecological questions in a multivariate context. A range of statistical methods has been applied to construct hypervolumes but have not yet been applied in the context of ecological data sets with spatial or temporal structure, for example, where the data are nested or demonstrate temporal autocorrelation. We outline an approach to account for data structure in quantifying hypervolumes based on the multivariate normal distribution by including random effects. Using simulated data, we show that failing to account for structure in data can lead to biased estimates of hypervolume properties in certain contexts. We then illustrate the utility of these "model-based hypervolumes" in providing new insights into a case study of afforestation effects on ecosystem properties where the data has a nested structure. We demonstrate that the model-based generalization allows hypervolumes to be applied to a wide range of ecological data sets and questions.

Vinasse application and cessation of burning in sugarcane management can have positive impact on soil carbon stocks.

Bioenergy crops, such as sugarcane, have the potential to mitigate greenhouse gas emissions through fossil fuel substitution. However, increased sugarcane propagation and recent management changes have raised concerns that these practices may deplete soil carbon (C) stocks, thereby limiting the net greenhouse gas benefit. In this study, we use both a measured and modelled approach to evaluate the impacts of two common sugarcane management practices on soil C sequestration potential in Brazil. We explore how transitions from conventional (mineral fertiliser/burning) to improved (vinasse application/unburned) practices influence soil C stocks in total and in physically fractionated soil down to one metre. Results suggest that vinasse application leads to an accumulation of soil C of 0.55 Mg ha-1yr-1 at 0-30 cm depth and applying unburned management led to gains of ∼0.7 Mg ha-1yr-1 at 30-60 cm depth. Soil C concentration in the Silt+Clay fraction of topsoil (0-20 cm) showed higher C content in unburned management but it did not differ under vinasse application. The CENTURY model was used to simulate the consequences of management changes beyond the temporal extent of the measurements. Simulations indicated that vinasse was not the key factor driving increases in soil C stocks but its application may be the most readily available practice to prevent the soil C losses under burned management. Furthermore, cessation of burning may increase topsoil C by 40% after ∼50 years. These are the first data comparing different sugarcane management transitions within a single area. Our findings indicate that both vinasse application and the cessation of burning can play an important role in reducing the time required for sugarcane ethanol production to reach a net C benefit (payback time).

Soil bacterial networks are less stable under drought than fungal networks.

Soil microbial communities play a crucial role in ecosystem functioning, but it is unknown how co-occurrence networks within these communities respond to disturbances such as climate extremes. This represents an important knowledge gap because changes in microbial networks could have implications for their functioning and vulnerability to future disturbances. Here, we show in grassland mesocosms that drought promotes destabilising properties in soil bacterial, but not fungal, co-occurrence networks, and that changes in bacterial communities link more strongly to soil functioning during recovery than do changes in fungal communities. Moreover, we reveal that drought has a prolonged effect on bacterial communities and their co-occurrence networks via changes in vegetation composition and resultant reductions in soil moisture. Our results provide new insight in the mechanisms through which drought alters soil microbial communities with potential long-term consequences, including future plant community composition and the ability of aboveground and belowground communities to withstand future disturbances.

Functional characterization of enhancer evolution in the primate lineage.

BACKGROUND: Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Previous efforts to understand the evolution of enhancers in primates have typically studied many enhancers at low resolution, or single enhancers at high resolution. Although comparative genomic studies reveal large-scale turnover of enhancers, a specific understanding of the molecular steps by which mammalian or primate enhancers evolve remains elusive. RESULTS: We identified candidate hominoid-specific liver enhancers from H3K27ac ChIP-seq data. After locating orthologs in 11 primates spanning around 40 million years, we synthesized all orthologs as well as computational reconstructions of 9 ancestral sequences for 348 active tiles of 233 putative enhancers. We concurrently tested all sequences for regulatory activity with STARR-seq in HepG2 cells. We observe groups of enhancer tiles with coherent trajectories, most of which can be potentially explained by a single gain or loss-of-activity event per tile. We quantify the correlation between the number of mutations along a branch and the magnitude of change in functional activity. Finally, we identify 84 mutations that correlate with functional changes; these are enriched for cytosine deamination events within CpGs. CONCLUSIONS: We characterized the evolutionary-functional trajectories of hundreds of liver enhancers throughout the primate phylogeny. We observe subsets of regulatory sequences that appear to have gained or lost activity. We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution.

Spatial patterns and environmental constraints on ecosystem services at a catchment scale.

Improved understanding and prediction of the fundamental environmental controls on ecosystem service supply across the landscape will help to inform decisions made by policy makers and land-water managers. To evaluate this issue for a local catchment case study, we explored metrics and spatial patterns of service supply for water quality regulation, agriculture production, carbon storage, and biodiversity for the Macronutrient Conwy catchment. Methods included using ecosystem models such as LUCI and JULES, integration of national scale field survey datasets, earth observation products and plant trait databases, to produce finely resolved maps of species richness and primary production. Analyses were done with both 1×1km gridded and subcatchment data. A common single gradient characterised catchment scale ecosystem services supply with agricultural production and carbon storage at opposing ends of the gradient as reported for a national-scale assessment. Species diversity was positively related to production due to the below national average productivity levels in the Conwy combined with the unimodal relationship between biodiversity and productivity at the national scale. In contrast to the national scale assessment, a strong reduction in water quality as production increased was observed in these low productive systems. Various soil variables were tested for their predictive power of ecosystem service supply. Soil carbon, nitrogen, their ratio and soil pH all had double the power of rainfall and altitude, each explaining around 45% of variation but soil pH is proposed as a potential metric for ecosystem service supply potential as it is a simple and practical metric which can be carried out in the field with crowd-sourcing technologies now available. The study emphasises the importance of considering multiple ecosystem services together due to the complexity of covariation at local and national scales, and the benefits of exploiting a wide range of metrics for each service to enhance data robustness.

Land-use and land-management change: relationships with earthworm and fungi communities and soil structural properties.

BACKGROUND: Change in land use and management can impact massively on soil ecosystems. Ecosystem engineers and other functional biodiversity in soils can be influenced directly by such change and this in turn can affect key soil functions. Here, we employ meta-analysis to provide a quantitative assessment of the effects of changes in land use and land management across a range of successional/extensification transitions (conventional arable → no or reduced tillage → grassland → wooded land) on community metrics for two functionally important soil taxa, earthworms and fungi. An analysis of the relationships between community change and soil structural properties was also included. RESULTS: Meta-analysis highlighted a consistent trend of increased earthworm and fungal community abundances and complexity following transitions to lower intensity and later successional land uses. The greatest changes were seen for early stage transitions, such as introduction of reduced tillage regimes and conversion to grassland from arable land. Not all changes, however, result in positive effects on the assessed community metrics. For example, whether woodland conversion positively or negatively affects community size and complexity depends on woodland type and, potentially, the changes in soil properties, such as pH, that may occur during conversion. Alterations in soil communities tended to facilitate subsequent changes in soil structure and hydrology. For example, increasing earthworm abundances and functional group composition were shown to be positively correlated with water infiltration rate (dependent on tillage regime and habitat characteristics); while positive changes in fungal biomass measures were positively associated with soil microaggregate stability. CONCLUSIONS: These findings raise the potential to manage landscapes to increase ecosystem service provision from soil biota in relation to regulation of soil structure and water flow.

Increasing litter species richness reduces variability in a terrestrial decomposer system.

Debate on the relationship between diversity and stability has been driven by the recognition that species loss may influence ecosystem properties and processes. We conducted a litterbag experiment in the Scottish Highlands, United Kingdom, to examine the effects of altering plant litter diversity on decomposition, microbial biomass, and microfaunal abundance. The design of treatments was fully factorial and included five species from an upland plant community (silver birch, Betula pendula; Scots' pine, Pinus sylvestris; heather, Calluna vulgaris; bilberry, Vaccinium myrtillus; wavy-hair grass, Deschampsia flexuosa); species richness ranged from one to five species. We tested the effects of litter species richness and composition on variable means, whether increasing litter species richness reduced variability in the decomposer system, and whether any richness-variability relationships were maintained over time (196 vs. 564 days). While litter species composition effects controlled variable means, we revealed reductions in variability with increasing litter species richness, even after accounting for differences between litter types. These findings suggest that higher plant species richness per se may result in more stable ecosystem processes (e.g., decomposition) and decomposer communities. Negative richness-variation relationships generally relaxed over time, presumably because properties of litter mixtures became more homogeneous. However, given that plant litter inputs continue to enter the belowground system over time, we conclude that variation in ecosystem properties may be buffered by greater litter species richness.