Recent Submissions

• Journal Article

Exfoliated near infrared fluorescent silicate nanosheets for (bio)photonics ﻿

Nature Communications 2020; 11(1) p.1-11: Art. 1495
Imaging of complex (biological) samples in the near-infrared (NIR) is beneficial due toreduced light scattering, absorption, phototoxicity, and autofluorescence. However, there arefew NIRfluorescent materials known and suitable for biomedical applications. Here weexfoliate the layered pigment $CaCuSi_4O_{10}$ (Egyptian Blue, EB) via ball milling and facile tipsonication into NIRfluorescent nanosheets (EB-NS). The size of EB-NS can be tailored todiameters <20 nm and heights down to 1 nm. EB-NSfluoresce at 910 nm and thefluorescenceintensity correlates with the number of $Cu^{2+}$ ions. Furthermore, EB-NS display no bleachingand high brightness compared with other NIRfluorophores. The versatility of EB-NS isdemonstrated by in-vivo single-particle tracking and microrheology measurements inDro-sophila melanogasterembryos. EB-NS can be uptaken by plants and remotely detected in alow-cost stand-off detection setup. In summary, EB-NS have the potential for a wide range ofbioimaging applications.
• Journal Article

In silico quality assessment of SNPs—A case study on the Axiom® Wheat genotyping arrays ﻿

Current Plant Biology 2020; 21 p.1-6: Art. 100140
Genotyping arrays proved to be an exemplary tool for the simultaneous analysis of a multitude of single nucleotide polymorphisms (SNPs), a special case of genomic variants. By the example of SNPs represented on the Axiom® Wheat HD genotyping array as well as on the Axiom® Wheat Breeder's genotyping array, we applied a three way classification system to assess the quality of SNPs in bread wheat (Triticum aestivum L.) and subsequently the quality of these genotyping arrays. Class 1 SNPs could be aligned uniquely to the reference genome and did not show any genomic variants in their flanking sequence. Class 2 SNPs could also be aligned uniquely to the reference genome but showed genomic variants in their flanking sequence. The remaining SNPs were assigned to class 3. To determine the number of genomic variants in a SNP's flanking sequence, we used all currently available SNPs in the Ensembl Plants database. From the 819,571 SNPs on the Axiom® Wheat HD genotyping array, we assigned 24,343 to class 1 and from the 35,143 SNPs on the Axiom® Wheat Breeder's genotyping array we classified 2295 SNPs as class 1. We show that class 1 SNPs of the Axiom® Wheat HD genotyping array result in an equidistant coverage of the reference genome. We make the classification table as well as R-scripts available to give breeders and researchers the possibility to reproduce our analysis in an easy way. Moreover, we discuss the possibilities and limitations of such an in silico analysis of genotyping arrays as well as future research possibilities for this approach.
• Journal Article

Effect of sexed semen on different production and functional traits in German Holsteins ﻿

Veterinary and Animal Science 2020; 9 p.1-7: Art. 100101
The aim of this study was to analyze possible effects of semen type (conventional vs. female sexed) and calf sex on fertility and production traits. For this purpose, field data of German Holstein heifers in Lower Saxony were evaluated. Sexed semen was mainly used for first insemination. 87.0% female calves were born from sexed semen, while 52.7% female calves were born from conventional semen. Heifers inseminated with sexed semen were on average 43 to 48 days younger at their first calving than heifers inseminated with conventional semen. Calf sex had an influence on the average calving ease and the dystocia rates. Male calves showed higher calving ease scores and caused a higher risk for dystocia than female calves. The semen type had no influence on these characteristics. Within the same calf sex, sexed semen had only minor effects on most traits, except for stillbirth rates: the stillbirth rate for male calves from female sexed semen was 30.6%, which was 2.86 times the stillbirth rate of male calves from conventional semen, possibly due to trisomies. Sexed semen played only a minor role for production traits in first lactations. The extrapolated 305-day milk yield was 200 kg lower for first calf heifers, which were inseminated with sexed semen compared to heifers inseminated with conventional semen. Fat and protein yield were 6 kg to 8 kg lower after use of sexed semen. Animals with female offspring from sexed semen showed higher survival rates than the other groups.
• Journal Article

Modelling Climate Change Impact on Irrigation Water Requirement and Yield of Winter Wheat (Triticum aestivum L.), Barley (Hordeum vulgare L.), and Fodder Maize (Zea mays L.) in the Semi-Arid Qazvin Plateau, Iran ﻿

Agriculture 2020; 10(3) p.1-14: Art. 60
It is very important to determine the irrigation water requirement (IR) of crops for optimal irrigation scheduling under the changing climate. This study aimed to investigate the impact of climate change on the future IR and yield of three strategic crops (winter wheat, barley, fodder maize) in the semi-arid Qazvin Plateau, Iran, for the periods 2016–2040, 2041–2065, and 2066–2090. The Canadian Earth System Model (CanESM2), applying IPCC scenarios rcp2.6, rcp4.5, and rcp8.5, was used to project the monthly maximum and minimum temperatures and monthly precipitation of the region. The results indicated that the maximum and minimum temperatures will increase by 1.7 °C and 1.2 °C, respectively, under scenario rcp8.5 in the period 2066–2090. The precipitation will decrease (1%–13%) under all scenarios in all months of the future periods, except in August, September, and October. The IR of winter wheat and barley will increase by 38%–79% under scenarios rcp2.6 and rcp8.5 in the future periods. The increase in the IR of fodder maize will be very slight (0.7%–4.1%). The yield of winter wheat and barley will decrease by ~50%–100% under scenarios rcp2.6 and rcp8.5 in the future periods. The reduction in the yield of maize will be ~4%. Serious attention has to be paid to the water resources management of the region. The use of drought-tolerant cultivars in the region can be a good strategy to deal with the predicted future climatic conditions.
• Journal Article

Biomass, Morphology, and Dynamics of the Fine Root System Across a 3,000-M Elevation Gradient on Mt. Kilimanjaro ﻿

Frontiers in Plant Science 2020; 11 p.1-16: Art. 13
Fine roots (≤2 mm) consume a large proportion of photosynthates and thus play a key role in the global carbon cycle, but our knowledge about fine root biomass, production, and turnover across environmental gradients is insufficient, especially in tropical ecosystems. Root system studies along elevation transects can produce valuable insights into root trait-environment relationships and may help to explore the evidence for a root economics spectrum (RES) that should represent a trait syndrome with a trade-off between resource acquisitive and conservative root traits. We studied fine root biomass, necromass, production, and mean fine root lifespan (the inverse of fine root turnover) of woody plants in six natural tropical ecosystems (savanna, four tropical mountain forest types, tropical alpine heathland) on the southern slope of Mt. Kilimanjaro (Tanzania) between 900 and 4,500 m a.s.l. Fine root biomass and necromass showed a unimodal pattern along the slope with a peak in the moist upper montane forest (~2,800 m), while fine root production varied little between savanna and upper montane forest to decrease toward the alpine zone. Root:shoot ratio (fine root biomass and production related to aboveground biomass) in the tropical montane forest increased exponentially with elevation, while it decreased with precipitation and soil nitrogen availability (decreasing soil C:N ratio). Mean fine root lifespan was lowest in the ecosystems with pronounced resource limitation (savanna at low elevation, alpine heathland at high elevation) and higher in the moist and cool forest belt (~1,800–3,700 m). The variation in root traits across the elevation gradient fits better with the concept of a multi-dimensional RES, as root tissue density and specific root length showed variable relations to each other, which does not agree with a simple trade-off between acquisitive and conservative root traits. In conclusion, despite large variation in fine root biomass, production, and morphology among the different plant species and ecosystems, a general belowground shift in carbohydrate partitioning is evident from 900 to 4,500 m a.s.l., suggesting that plant growth is increasingly limited by nutrient (probably N) shortage toward higher elevations.
• Journal Article

Maize root and shoot litter quality controls short-term $CO_2$ and $N_2O$ emissions and bacterial community structure of arable soil ﻿

Biogeosciences 2020; 17(4) p.1181-1198
Chemical composition of root and shoot litter controls decomposition and, subsequently, C availability for biological nitrogen transformation processes in soils. While aboveground plant residues have been proven to increase $N_2O$ emissions, studies on root litter effects are scarce. This study aimed (1) to evaluate how fresh maize root litter affects $N_2O$ emissions compared to fresh maize shoot litter, (2) to assess whether $N_2O$ emissions are related to the interaction of C and N mineralization from soil and litter, and (3) to analyze changes in soil microbial community structures related to litter input and $N_2O$ emissions. To obtain root and shoot litter, maize plants (Zea mays L.) were cultivated with two N fertilizer levels in a greenhouse and harvested. A two-factorial 22 d laboratory incubation experiment was set up with soil from both N levels (N1, N2) and three litter addition treatments (control, root, root + shoot). We measured $CO_2$ and $N_2O$ fluxes, analyzed soil mineral N and water-extractable organic C (WEOC) concentrations, and determined quality parameters of maize litter. Bacterial community structures were analyzed using 16S rRNA gene sequencing. Maize litter quality controlled $NO^−_3$ and WEOC availability and decomposition-related $CO_2$ emissions. Emissions induced by maize root litter remained low, while high bioavailability of maize shoot litter strongly increased $CO_2$ and $N_2O$ emissions when both root and shoot litter were added. We identified a strong positive correlation between cumulative $CO_2$ and $N_2O$ emissions, supporting our hypothesis that litter quality affects denitrification by creating plant-litter-associated anaerobic microsites. The interdependency of C and N availability was validated by analyses of regression. Moreover, there was a strong positive interaction between soil $NO^−_3$ and WEOC concentration resulting in much higher $N_2O$ emissions, when both $NO^−_3$ and WEOC were available. A significant correlation was observed between total $CO_2$ and $N_2O$ emissions, the soil bacterial community composition, and the litter level, showing a clear separation of root + shoot samples of all remaining samples. Bacterial diversity decreased with higher N level and higher input of easily available C. Altogether, changes in bacterial community structure reflected degradability of maize litter with easily degradable C from maize shoot litter favoring fast-growing C-cycling and N-reducing bacteria of the phyla Actinobacteria, Chloroflexi, Firmicutes, and Proteobacteria. In conclusion, litter quality is a major driver of $N_2O$ and $CO_2$ emissions from crop residues, especially when soil mineral N is limited.
• Journal Article

Notes on the leaf insects of the genus Phyllium of Sumatra and Java, Indonesia, including the description of two new species with purple coxae (Phasmatodea, Phylliidae) ﻿

ZooKeys 2020; 913 p.89-126
Within the last two years, the leaf insects of the genus Phyllium of both the islands of Java and Sumatra have been reviewed extensively based on morphological observations. However, cryptic species which cannot be differentiated morphologically may be present among the various populations. Since it has frequently been demonstrated that analyses based on molecular data can bring clarity in such cases, we conducted a phylogenetic analysis based on three genes (nuclear gene 28S and mitochondrial genes COI and 16S) from the Phyllium species of these islands. The results show distinct molecular divergence for several populations and suggest the presence of two new cryptic species, morphologically inseparable from Phyllium hausleithneri Brock, 1999. From Sumatra, the population originally thought to be a range expansion for Phyllium hausleithneri, is now here described as Phyllium nisus sp. nov., with the only consistent morphological difference being the color of the eggs between the two populations (dark brown in P. hausleithneri and tan in P. nisus sp. nov.). Further, an additional population with purple coxae from Java was morphologically examined and found to have no consistent features to separate it morphologically from the other purple coxae species. This cryptic species from Java was however shown to be molecularly distinct from the other purple coxae populations from Sumatra and Peninsular Malaysia and is here described as Phyllium gardabagusi sp. nov. In addition, Phyllium giganteum is here officially reported from Java for the first time based on both historic and modern records of male specimens.
• Journal Article

Dbp5/DDX19 between Translational Readthrough and Nonsense Mediated Decay ﻿

International Journal of Molecular Sciences 2020; 21(3) p.1-13: Art. 1085
The DEAD-box protein Dbp5 (human DDX19) remodels RNA-protein complexes. Dbp5 functions in ribonucleoprotein export and translation termination. Termination occurs, when the ribosome has reached a stop codon through the Dbp5 mediated delivery of the eukaryotic termination factor eRF1. eRF1 contacts eRF3 upon dissociation of Dbp5, resulting in polypeptide chain release and subsequent ribosomal subunit splitting. Mutations in DBP5 lead to stop codon readthrough, because the eRF1 and eRF3 interaction is not controlled and occurs prematurely. This identifies Dbp5/DDX19 as a possible potent drug target for nonsense suppression therapy. Neurodegenerative diseases and cancer are caused in many cases by the loss of a gene product, because its mRNA contained a premature termination codon (PTC) and is thus eliminated through the nonsense mediated decay (NMD) pathway, which is described in the second half of this review. We discuss translation termination andNMDin the light of Dbp5/DDX19 and subsequently speculate on reducing Dbp5/DDX19 activity to allow readthrough of the PTC and production of a full-length protein to detract the RNA from NMD as a possible treatment for diseases.
• Journal Article

A Collection of 13 Archaeal and 46 Bacterial Genomes Reconstructed from Marine Metagenomes Derived from the North Sea ﻿

Data 2020; 5(1) p.1-5: Art. 15
Marine bacteria are key drivers of ocean biogeochemistry. Despite the increasing number of studies, the complex interaction of marine bacterioplankton communities with their environment is still not fully understood. Additionally, our knowledge about prominent marine lineages is mostly based on genomic information retrieved from single isolates, which do not necessarily represent these groups. Consequently, deciphering the ecological contributions of single bacterioplankton community members is one major challenge in marine microbiology. In the present study, we reconstructed 13 archaeal and 46 bacterial metagenome-assembled genomes (MAGs) from four metagenomic data sets derived from the North Sea. Archaeal MAGs were a liated to Marine Group II within the Euryarchaeota. Bacterial MAGs mainly belonged to marine groups within the Bacteroidetes as well as alpha- and gammaproteobacteria. In addition, two bacterial MAGs were classified as members of the Actinobacteria and Verrucomicrobiota, respectively. The reconstructed genomes contribute to our understanding of important marine lineages and may serve as a basis for further research on functional traits of these groups.
• Journal Article

Stochastic and Arbitrarily Generated Input Patterns to the Mushroom Bodies Can Serve as Conditioned Stimuli in Drosophila ﻿

Frontiers in Physiology 2020; 11 p.1-15: Art. 53
Single neurons in the brains of insects often have individual genetic identities and can be unambiguously identified between animals. The overall neuronal connectivity is also genetically determined and hard-wired to a large degree. Experience-dependent structural and functional plasticity is believed to be superimposed onto this more-or-less fixed connectome. However, in Drosophila melanogaster, it has been shown that the connectivity between the olfactory projection neurons (OPNs) and Kenyon cells, the intrinsic neurons of the mushroom body, is highly stochastic and idiosyncratic between individuals. Ensembles of distinctly and sparsely activated Kenyon cells represent information about the identity of the olfactory input, and behavioral relevance can be assigned to this representation in the course of associative olfactory learning. Previously, we showed that in the absence of any direct sensory input, artificially and stochastically activated groups of Kenyon cells could be trained to encode aversive cues when their activation coincided with aversive stimuli. Here, we have tested the hypothesis that the mushroom body can learn any stochastic neuronal input pattern as behaviorally relevant, independent of its exact origin. We show that fruit flies can learn thermogenetically generated, stochastic activity patterns of OPNs as conditioned stimuli, irrespective of glomerular identity, the innate valence that the projection neurons carry, or inter-hemispheric symmetry.
• Journal Article

Poplar Rows in Temperate Agroforestry Croplands Promote Bacteria, Fungi, and Denitrification Genes in Soils ﻿

Frontiers in Microbiology 2020; 10 p.1-11: Art. 3108
Agroforestry, which is the integration of trees into monoculture cropland, can alter soil properties and nutrient cycling. Temperate agroforestry practices have been shown to affect soil microbial communities as indicated by changes in enzyme activities, substrate-induced respiration, and microbial biomass. Research exploring soil microbial communities in temperate agroforestry with the help of molecular tools which allow for the quantification of microbial taxa and selected genes is scarce. Here, we quantified 13 taxonomic groups of microorganisms and nine genes involved in N cycling (N2 fixation, nitrification, and denitrification) in soils of three paired temperate agroforestry and conventional monoculture croplands using real-time PCR. The agroforestry croplands were poplar-based alley-cropping systems in which samples were collected in the tree rows as well as within the crop rows at three distances from the tree rows. The abundance of Acidobacteria, Actinobacteria, Alpha- and Gammaproteobacteria, Firmicutes, and Verrucomicrobia increased in the vicinity of poplar trees, which may be accounted for by the presence of persistent poplar roots as well as by the input of tree litter. The strongest population increase was observed for Basidiomycota, which was likely related to high soil moisture, the accumulation of tree litter, and the absence of tillage in the tree rows. Soil microorganisms carrying denitrification genes were more abundant in the tree rows than in the crop rows and monoculture systems, suggesting a greater potential for nitrate removal through denitrification, which may reduce nitrate leaching. Since microbial communities are involved in critical soil processes, we expect that the combination of real-time PCR with soil process measurements will greatly enhance insights into the microbial control of important soil functions in agroforestry systems.
• Journal Article

Predictive context biases binocular rivalry in children and adults with no positive relation to two measures of social cognition ﻿

Scientific Reports 2020; 10 p.1-12: Art. 2059
Integration of prior experience and contextual information can help to resolve perceptually ambiguous situations and might support the ability to understand other peoples’ thoughts and intentions, called Theory of Mind. We studied whether the readiness to incorporate contextual information for resolving binocular rivalry is positively associated with Theory-of-Mind-related social cognitive abilities. In children (12 to 13 years) and adults (18 to 25 years), a predictive temporal context reliably modulated the onset of binocular rivalry to a similar degree. In contrast, adult participants scored better on measures of Theory of Mind compared to children. We observed considerable interindividual differences regarding the influence of a predictive context on binocular rivalry, which were associated with differences in sensory eye dominance. The absence of a positive association between predictive effects on perception and Theory of Mind performance suggests that predictive effects on binocular rivalry and higher-level Theory-of-Mind-related abilities stem from different neurocognitive mechanisms. We conclude that the influence of predictive contextual information on basic visual processes is fully developed at an earlier age, whereas social cognitive skills continue to evolve from adolescence to adulthood.
• Journal Article

Parenchyma Abundance in Wood of Evergreen Trees Varies Independently of Nutrients ﻿

Frontiers in Plant Science 2020; 11 p.1-15: Art. 86
The abundance of living cells in wood—mainly as interconnected axial and ray parenchyma networks—varies widely between species. However, the functional significance of this variation and its role in plant ecological strategies is poorly understood, as is the extent to which different parenchyma fractions are favored in relation to soil nutrients and hydraulic functions. We analyzed wood tissue fractions of 16 Australian angiosperm species sampled from two nearby areas with similar climate but very different soil nutrient profiles and investigated structure-function links with soil and tissue nutrient concentrations and other plant traits. We expected the variation in parenchyma fractions to influence nutrient concentrations in wood xylem, and to find species with lower parenchyma fractions and accordingly lower nutrient requirements on lower-nutrient soils. Surprisingly, both axial and ray parenchyma fractions were mostly unrelated to tissue and soil nutrient concentrations, except for nitrogen concentration in stem sapwood. Species from low nutrient soils showed higher fractional P translocation from both leaves and sapwood, but little patterning with respect to tissue nitrogen. While species from high and low nutrient soils clearly clustered along the soil-fertility axis, their tissue composition varied independently from plant functional traits related to construction costs and hydraulic anatomy. Our findings imply that there is considerable variation among species in the nutrient concentrations within different parenchyma tissues. The anatomical composition of wood tissue seems unrelated to plant nutrient requirements. Even though xylem parenchyma is involved in metabolic functions such as nutrient translocation and storage, parenchyma abundance on its own does not directly explain variation in these functions, even in co-occurring species. While parenchyma is highly abundant in wood of angiosperm trees, we are still lacking a convincing ecological interpretation of its variability and role in whole-tree nutrient budgets.
• Journal Article

Association of α/β-Hydrolase D16B with Bovine Conception Rate and Sperm Plasma Membrane Lipid Composition ﻿

International Journal of Molecular Sciences 2020; 21(2) p.1-18: Art. 627
We have identified a Holstein sire named Tarantino who had been approved for artificial insemination that is based on normal semen characteristics (i.e., morphology, thermoresistance, motility, sperm concentration), but had no progeny after 412 first inseminations, resulting in a non-return rate (NRdev) of −29. Using whole genome association analysis and next generation sequencing, an associated nonsense variant in the α/β-hydrolase domain-containing 16B gene (ABHD16B) on bovine chromosome 13 was identified. The frequency of the mutant allele in the German Holstein population was determined to be 0.0018 in 222,645 investigated cattle specimens. The mutant allele was traced back to Whirlhill Kingpin (bornFeb. 13th, 1959) as potential founder. The expression of ABHD16B was detected by Western blotting and immunohistochemistry in testis and epididymis of control bulls. A lipidome comparison of the plasma membrane of fresh semen from carriers and controls showed significant differences in the concentration of phosphatidylcholine (PC), diacylglycerol (DAG), ceramide (Cer), sphingomyelin (SM), and phosphatidylcholine (-ether) (PC O-), indicating that ABHD16B plays a role in lipid biosynthesis. The altered lipid contents may explain the reduced fertilization ability of mutated sperms.
• Journal Article

Biological Control of Fusarium Crown and Root Rot of Wheat by Streptomyces Isolates – It’s Complicated ﻿

Phytobiomes Journal 2019; 3(1) p.52-60
The predominant causal agents of Fusarium crown and root rot(FCR) of wheat, along withFusarium pseudograminearum, areF. graminearumandF. culmorum. Members of the Gram-positivebacterial genusStreptomyceshave been shown to inhibit isolatesof the genusFusarium, andFusariumspp. isolates are also able toinhibitStreptomycesisolates in vitro. However, little is known aboutthese complex antagonistic interactions and the potential forinhibitoryStreptomycesto reduce FCR of wheat. The aim of thisstudy was to analyze whether inhibitoryStreptomycesisolatesaffect FCR of wheat and reduce root and stem base colonization byFusarium culmorum. We enriched sterilized potting soil with sporesuspensions of twoStreptomycesisolates, inoculated the soil withF. culmorum-colonized wheat straw, and planted pre-germinatedwheat seedlings. At 4 weeks,F. culmorum-inoculated plants hadsignificant FCR symptoms on roots and showed reduced freshweight of roots and above-ground plant biomass compared withthe non-inoculated controls. Enrichment of soil with an inhibitoryStreptomycesisolate reducedF. culmorumDNA in roots and stembases by 75% compared with inoculation withF. culmorumalone.Interestingly, co-inoculation ofF. culmorumwith a non-inhibitoryStreptomycesisolate led to the highest levelsF. culmorumDNA instem base tissue and greatestStreptomycesdensities (CFU per gof soil) in the rhizosphere. In vitro assays revealed thatF. culmorumshowed a strong inhibitory activity against thepathogen-inhibitoryStreptomycesisolate but not against the non-inhibitory isolate. In vitro tests with a larger set of 17StreptomycesandfiveFusariumspp. isolates revealed that there was littlevariation amongFusariumspp. isolates in capacities to inhibit thecollection ofStreptomycesisolates. In contrast, the sensitivity toinhibition by pathogenicFusariumspp. isolates varied widelyamongStreptomycesisolates. The results of this study suggestthe potential ofStreptomycesisolates for biocontrol of FCR ofwheat, while highlighting the specificity ofStreptomyces_Fusariuminteractions. Broader understanding of the variation insusceptibility withinFusariumspp. populations toStreptomycesinhibition and vice versa are needed to advance the potential forsuccessful biological control.
• Journal Article

The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances ﻿

PLOS ONE 2020; 15(2) p.1-18: Art. e0228070
We study the number $N_k$ of length-k word matches between pairs of evolutionarily related DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two genome sequences—i.e. the number of substitutions per site that occurred since they evolved from their last common ancestor—can be estimated from the slope of a function $F$ that depends on $N_k$ and that is affine-linear within a certain range of $k$. Integers kmin and $k_{max}$ can be calculated depending on the length of the input sequences, such that the slope of $F$ in the relevant range can be estimated from the values $F(k_{min})$ and $F(k_{max})$. This approach can be generalized to so-called $Spaced-word$ $Matches$ $(SpaM)$, where mismatches are allowed at positions specified by a user-defined binary pattern. Based on these theoretical results, we implemented a prototype software program for alignment-free sequence comparison called $Slope-SpaM$. Test runs on real and simulated sequence data show that $Slope-SpaM$ can accurately estimate phylogenetic distances for distances up to around 0.5 substitutions per position. The statistical stability of our results is improved if spaced words are used instead of contiguous words. Unlike previous alignment-free methods that are based on the number of (spaced) word matches, $Slope-SpaM$ produces accurate results, even if sequences share only local homologies.
• Journal Article

Fresh groundwater discharge insignificant for the world’s oceans but important for coastal ecosystems ﻿

Nature Communications 2020; 11(1) p.1-12: Art. 1260
The flow of fresh groundwater may provide substantial inputs of nutrients and solutes to the oceans. However, the extent to which hydrogeological parameters control groundwater flow to the world’s oceans has not been quantified systematically. Here we present a spatially resolved global model of coastal groundwater discharge to show that the contribution of fresh groundwater accounts for ~0.6% (0.004%–1.3%) of the total freshwater input and ~2% (0.003%–7.7%) of the solute input for carbon, nitrogen, silica and strontium. However, the coastal discharge of fresh groundwater and nutrients displays a high spatial variability and for an estimated 26% (0.4%–39%) of the world’s estuaries, 17% (0.3%–31%) of the salt marshes and 14% (0.1–26%) of the coral reefs, the flux of terrestrial groundwater exceeds 25% of the river flux and poses a risk for pollution and eutrophication.
• Journal Article

Properties of a nonlinear bath: experiments, theory, and a stochastic Prandtl–Tomlinson model ﻿

New Journal of Physics 2020; 22(2) p.1-19: Art. 023014
A colloidal particle is a prominent example of a stochastic system, and, if suspended in a simple viscous liquid, very closely resembles the case of an ideal random walker. A variety of new phenomena have been observed when such colloid is suspended in a viscoelastic fluid instead, for example pronounced nonlinear responses when the viscoelastic bath is driven out of equilibrium. Here, using a micron-sized particle in a micellar solution, we investigate in detail, how these nonlinear bath properties leave their fingerprints already in equilibrium measurements, for the cases where the particle is unconfined or trapped in a harmonic potential. We find that the coefficients in an effective linear (generalized) Langevin equation show intriguing inter-dependencies, which can be shown to arise only in nonlinear baths: for example, the friction memory can depend on the external potential that acts only on the colloidal particle (as recently noted in simulations of molecular tracers in water in (2017 Phys. Rev. X 7 041065)), it can depend on the mass of the colloid, or, in an overdamped setting, on its bare diffusivity. These inter-dependencies, caused by so-called fluctuation renormalizations, are seen in an exact small time expansion of the friction memory based on microscopic starting points. Using linear response theory, they can be interpreted in terms of microrheological modes of force-controlled or velocity-controlled driving. The mentioned nonlinear markers are observed in our experiments, which are astonishingly well reproduced by a stochastic Prandtl–Tomlinson model mimicking the nonlinear viscoelastic bath. The pronounced nonlinearities seen in our experiments together with the good understanding in a simple theoretical model make this system a promising candidate for exploration of colloidal motion in nonlinear stochastic environments.
• Journal Article

Diverse Swards and Mixed-Grazing of Cattle and Sheep for Improved Productivity ﻿

Frontiers in Sustainable Food Systems 2020; 3 p.1-14: Art. 125
Increasing sward phytodiversity has been suggested as having potential to increase primary production of grasslands, but whether any such gains are converted into secondary production, through improved performance of grazing livestock, remains uncertain. Animal production by cattle and sheep can also be enhanced by mixed-grazing. To our knowledge, this effect has never been studied in relation to differences in sward phytodiversity. Therefore, a rotational grazing experiment was conducted over 5 years (2007–2011) on permanent grassland in Germany using sheep and cattle in mono- (single-species) or mixed-grazing of swards differing in plant species richness. Herbicides against dicotyledonous plant species were used to create different sward types: species-poor, grass-dominated swards in contrast to untreated “diverse” control swards. We found no differences in herbage production between the sward types. However, compared to the grass-dominated sward, the diverse sward showed greater concentrations of crude protein and lower contents of acid detergent fiber in the herbage dry-matter. Lamb live weight gains were slightly greater on the diverse-swards (P < 0.05), but calf performance was unaffected by sward type. Mixed-grazing increased daily average live weight gains of suckler cows (g cow⁻¹ d⁻¹) (P < 0.05) as well as area-related daily live weight gains (kg ha⁻¹ d⁻¹) and total live weight gains (kg ha⁻¹) during the complete grazing season (P < 0.001). This indicates advantages of combining livestock species, attributed to complementary pasture use. We suggest that mixed-grazing of cattle and sheep on phytodiverse swards is an effective and sustainable means to enhance ecological and agronomic traits such as livestock production and plant species conservation. Lamb production especially showed benefits under mixed-grazing, with a 17% increase in live weight gain. Compared to the grass-dominated sward, diverse swards resulted in an average 12% increase of live weight gains (across grazing systems and livestock species).
• Journal Article

Substrate induced nanoscale resistance variation in epitaxial graphene ﻿

Nature Communications 2020; 11(1) p.1-9: Art. 555
Graphene, the first true two-dimensional material, still reveals the most remarkable transport properties among the growing class of two-dimensional materials. Although many studies have investigated fundamental scattering processes, the surprisingly large variation in the experimentally determined resistances is still an open issue. Here, we quantitatively investigate local transport properties of graphene prepared by polymer assisted sublimation growth using scanning tunneling potentiometry. These samples exhibit a spatially homogeneous current density, which allows to analyze variations in the local electrochemical potential with high precision. We utilize this possibility by examining the local sheet resistance finding a significant variation of up to 270% at low temperatures. We identify a correlation of the sheet resistance with the stacking sequence of the 6H silicon carbide substrate and with the distance between the graphene and the substrate. Our results experimentally quantify the impact of the graphene-substrate interaction on the local transport properties of graphene.