IRON-REGULATED TRANSPORTER1 (IRT1) is the root high-affinity ferrous iron uptake system and indispensable for the completion of the life cycle ofArabidopsis thalianawithout vigorous iron (Fe) supplementation. Here we provide evidence supporting a second role of IRT1 in root-to-shoot mobilization of Fe. We show that theirt1-2 (pam42) mutant over-accumulates Fe in roots, most prominently in the cortex of the differentiation zone, when compared to the wild type. Shoots ofirt1-2 are severely Fe-deficient according to Fe content and marker transcripts, as expected. We generatedirt1-2 lines producing IRT1 mutant variants carrying single amino-acid substitutions of key residues in transmembrane helices IV and V, Ser206and His232, which are required for transport activity in yeast. In the transgenic Arabidopsis lines, short-term root Fe uptake rates and secondary substrate Mn accumulation resemble those ofirt1-2, suggesting that these plants remain incapable of IRT1-mediated root Fe uptake. Yet, IRT1S206Apartially complements rosette dwarfing and leaf chlorosis, as well as root-to-shoot Fe partitioning and gene expression defects ofirt1-2, all of which are fully complemented by wild-type IRT1. Taken together, these results suggest a function for IRT1 in root-to-shoot Fe partitioning that does not require Fe transport activity of IRT1. Among the genes of which transcript levels are partially dependent on IRT1, we identifyMYB DOMAIN PROTEIN10,MYB DOMAIN PROTEIN72andNICOTIANAMINE SYNTHASE4as candidates for effecting IRT1-dependent Fe mobilization in roots. Understanding the biological functions of IRT1 will help to improve iron nutrition and the nutritional quality of agricultural crops.Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1 \uffc2\uffb5m-sized metabolite producer, receiver and competitor cells in different spatial structures. We show that receivers cannot interact with producers \uffe2\uff88\uffbc15 \uffc2\uffb5m away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and created variants of the receiver cells\uffe2\uff80\uff99 import system, to show that within producer-receiver aggregates even low affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces the interaction distance to the low micrometer-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.Rhizobial infection of legume roots during development of nitrogen fixing root nodules occurs either intracellularly though plant derived infection threads traversing the epidermal and cortical cell layers to deliver the bacteria or intercellularly via bacterial entry between epidermal plant cells. Although, around 25% of all legume genera are postulated to be intercellularly infected, the pathways and mechanisms supporting this process has remained virtually unexplored due to lack of genetically amenable legumes that have this infection mode. In this study, we report that the model legume Lotus japonicus is infected intercellularly by Rhizobium sp. IRBG74 and demonstrate that the resources available in Lotus enable insight into the genetic requirements and the fine-tuning of the pathway governing intercellular infection. Inoculation of Lotus mutants shows that Ern1 and RinRK1 are dispensable for intercellular infection in contrast to intracellular infection. Other symbiotic genes, including Nfr5, SymRK, CCaMK, Epr3, Cyclops, Nin, Nsp1, Nsp2, Cbs and Vpy1 are equally important for both entry modes. Comparative RNAseq analysis of roots inoculated with IRBG74 revealed a distinctive transcriptome response compared to intracellular colonization. In particular, a number of cytokinin-related genes were differentially regulated. Corroborating this observation cyp735A and ipt4 cytokinin biosynthesis mutants were significantly affected in their nodulation with IRBG74 while lhk1 cytokinin receptor mutants did not form any nodules. These results indicate that a differential requirement for cytokinin signalling conditions intercellular rhizobial entry and highlight the distinct modalities of the inter- and intra-cellular infection mechanisms.Plants synthesize and release specialized metabolites into their environment that can serve as chemical cues for other organisms. Metabolites that are released from the roots are important factors in determining which microorganisms will colonize the root and become part of the plant rhizosphere. Root exudates can be converted by soil microorganisms, which can result in the formation of toxic compounds. How individual members of the plant rhizosphere respond to individual compounds and how the differential response of individual microorganisms contributes to the response of a microbial community remains an open question. Here, we investigated the impact of derivatives of benzoxazinoids, a class of plant root exudates released by important crops such as wheat and maize, on a collection of 180 root-associated bacteria. Phenoxazine, derived in soil from benzoxazinoids, inhibited the growth of root-associated bacteriain vitroin an isolate-specific manner, with sensitive and resistant isolates present in most of the studied clades. Using synthetic communities, we show that community stability is a consequence of the resilience of its individual members, with communities assembled from tolerant isolates being overall more tolerant to benzoxazinoids. However, the performance of an isolate in a community context was not correlated with its individual performance but appeared to be shaped by interactions between isolates. These interactions were independent of the overall community composition and were strain-specific, with interactions between different representatives of the same bacterial genera accounting for differential community composition.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "15. Life on land"]}, "links": [{"href": "https://doi.org/10.1101/2021.01.12.425818"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2021.01.12.425818", "name": "item", "description": "10.1101/2021.01.12.425818", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2021.01.12.425818"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-01-12T00:00:00Z"}}, {"id": "10.1101/2021.02.09.430461", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:40Z", "type": "Journal Article", "created": "2021-02-10", "title": "Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome", "description": "AbstractConventional methods of agricultural pest control and crop fertilisation are contributing to a crisis of biodiversity loss, biogeochemical cycle dysregulation, and ecosystem collapse. Thus, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome may contribute to this goal as microbes can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. We applied 16S rRNA gene & fungal 18S rRNA gene (ITS2 region) amplicon sequencing to profile the diversity of the bacterial, archaeal & fungal communities associated with the roots of UK elite spring bread wheat varietyTriticum aestivum var.Paragon in different soils and developmental stages. This revealed that community composition shifted significantly for all three groups across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these wereStreptomycetaceaeandBurkholderiaceae.Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. To understand which microbes are using wheat root exudates in the rhizosphere, root exudates were labelled in a13CO2DNA stable isotope probing experiment. This shows that bacterial taxa within theBurkholderiaceaefamily among other core enriched taxa, such asPseudomonadaceae,were able to use root exudates butStreptomycetaceaewere not. Overall, this work provides a better understanding of the wheat microbiome, including the endosphere community. Understanding crop microbiome formation will contribute to ecologically responsible methods for yield improvement and biocontrol in the future.To address the challenge of predicting tomato yields in the field, we used whole-plant functional phenotyping to evaluate water relations under well-irrigated and drought conditions. The genotypes tested are known to exhibit variability in their yields in wet and dry fields. The examined lines included two lines with recessive mutations that affect carotenoid biosynthesis, zetaz2083and tangerinet3406, both isogenic to the processing tomato variety M82. The two mutant lines were reciprocally grafted onto M82, and multiple physiological characteristics were measured continuously, before, during and after drought treatment in the greenhouse. A comparative analysis of greenhouse and field yields showed that the whole-canopy stomatal conductance (gsc) in the morning and cumulative transpiration (CT) were strongly correlated with field measurements of total yield (TY:r2= 0.9 and 0.77, respectively) and plant vegetative weight (PW:r2= 0.6 and 0.94, respectively). Furthermore, the minimum CT during drought and the rate of recovery when irrigation was resumed were both found to predict resilience.
", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Dehydration", "Genotype", "Genetic Variation", "15. Life on land", "Genes", " Plant", "Adaptation", " Physiological", "6. Clean water", "Droughts", "03 medical and health sciences", "Phenotype", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Mutation", "Plant Physiological Phenomena", "Forecasting"]}, "links": [{"href": "https://doi.org/10.1101/2021.03.18.435447"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2021.03.18.435447", "name": "item", "description": "10.1101/2021.03.18.435447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2021.03.18.435447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-19T00:00:00Z"}}, {"id": "10.1101/2021.03.20.436100", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-03T16:19:40Z", "type": "Journal Article", "created": "2021-03-21", "title": "Marchantia polymorphamodel reveals conserved infection mechanisms in the vascular wilt fungal pathogenFusarium oxysporum", "description": "AbstractThe non-vascular plantMarchantia polymorphahas emerged as a valuable model for studying evolutionarily conserved microbial infection strategies and plant immune responses. However, only a handful of fungal pathogens ofMarchantiahave been described so far. Here we establish a new pathosystem using the root-infecting vascular wilt fungusFusarium oxysporum. On angiosperms, this fungus exhibits exquisite adaptation to the plant vascular niche and host-specific pathogenicity, both of which are conferred by lineage-specific effectors secreted during growth in the xylem. We show thatF. oxysporumisolates with different lifestyles - pathogenic or endophytic - are able to infect this non-vascular liverwort causing tissue maceration and plant cell killing. Similar to bacterial pathogens,F. oxysporuminduces a PAMP-triggered immune response inM. polymorpha. Analysis of isogenic fungal mutants established that infection ofMarchantiarequires conserved fungal pathogenicity mechanisms such as mitogen activated protein kinases, transcriptional regulators and cell wall remodeling enzymes. Remarkably, lineage-specific virulence effectors are dispensable for infection, most likely due to the absence of xylem tissue in this non-vascular plant. TheF. oxysporum-M. polymorphasystem provides new insights into the mechanism and evolution of pathogenic and endophytic fungus-plant interactions.
Significance statementRoot-infecting vascular fungi cause wilt diseases and provoke devastating losses in hundreds of crops. It is currently unknown how these pathogens evolved and whether they infect non-vascular plants, which diverged from vascular plants over 450 million years ago. Here we show that two strains of the fungusFusarium oxysporumwith opposed lifestyles, causing either wilting and death or beneficial protection on tomato, produce similar disease symptoms on the non-vascular plantMarchantia polymorpha.We define a set of core fungal pathogenicity factors required on both vascular and non-vascular plants and show that host-specific effectors contributing to disease on tomato are dispensable onMarchantia. These findings suggest that systemic wilt disease evolved in fungal pathogens after the emergence of vascular land plants.Recently, it has been shown that several bacterial strains can be very efficient in cancer treatment since they possess many important properties such as self-targeting, ease of detection, sensing and toxicity against tumors. However, there are only a few relevant \uffe2\uff80\uff9ccandidates\uffe2\uff80\uff9d for such an approach, as targeting and detection one of the biggest challenges as well as there are many limitations in the use of genetic approaches. Here, it is proposed the solution that enables surface modification of alive bacterial cells without interfering with their genetic material and potentially reduces their toxic side effect. By the electrostatic interaction fluorescently labeled polyelectrolytes (PEs) and magnetite nanoparticles (NPs) were deposited on the bacterial cell surface to control the cell growth, distribution and detection of bacteria. According to the results obtained in vivo, by the magnet entrapment of the modified bacteria the local concentration of the cells was increased more than 5 times, keeping the high concentrations even when the magnet is removed. Since the PEs create a strong barrier, in vitro it was shown that the division time of the cells can be regulated for better immune presentation.Although electrostatic modification of bacterial surfaces using polyelectrolytes (PEs) is a convenient and versatile tool for biotechnological processes, the ambiguities in toxicity of PEs between various bacteria and the insufficient understanding of the mechanism of action of cationic PEs and their nano-thick shells formed around the bacteria create a bottleneck of the approach. Here, we show how the viability of two bacterial strains, Escherichia coli and Pseudomonas stutzeri, both from the Gram-negative group differs, when the cells are exposed to cationic PEs under different conditions. Although the cell wall architecture of the strains should be structurally similar, we found that the viability of E. coli was not affected by the electrostatic deposition of polyethyleneimine (PEI) or poly(allylamine) hydrochloride (PAH), whereas for P. stutzeri the deposition resulted in high death rates. The cells of E. coli proved to be suitable templates for Layer-by-Layer (LbL) modification, while in P. stutzeri a modified protocol with mild conditions had to be used to ensure the viability of the cells. Super resolution stimulated emission depletion (STED) microscopy allowed us to clearly visualize that after PE deposition onto the surface of the cells, the PEs could penetrate inside the cells of P. stutzeri, while forming a capsule around E. coli as expected. Therefore, this knowledge will help us select the most appropriate combinations of strains and PEs, for biotechnological processes or biomedical application, preventing unwanted toxicity.Soil-transmitted helminth infections represent a large burden across the globe with over a quarter of the world\uffe2\uff80\uff99s population at risk. The outcome of available treatments is species-specific with a large proportion of unexplained treatment failure. Administration of albendazole is the standard of care, but because of low cure rates (CR) observed in treatingTrichuris trichiurainfections, a significantly more efficacious alternative therapy combining albendazole and ivermectin is being investigated.
Methods80 patients from the village of Pak-Khan, in Laos, with confirmed STH infections (Trichuris trichiuraand hookworms), received either albendazole (400 mg) or albendazole (400 mg) and ivermectin (200 \uffc2\uffb5g/kg) together. A pre-treatment stool sample was collected as well as daily post-treatment stool samples for up to 28 days to measure treatment efficacy. Taxonomic profiling of pre-treatment stool samples was conducted using 16S rRNA gene sequencing, target-specific and total bacteria qPCR, as well as shotgun sequencing.
ResultsThree bacterial communities, or enterotypes (ET) 1-3, were identified. No association with pre-treatment enterotype and treatment outcome of bothTrichuris trichiuraand hookworm were found in the monotherapy arm with overall cure rates (CR) of 7.5% and 50%, respectively. Pre-treatment enterotype was strongly associated with efficacy of the combination therapy for both,T. trichiura(CRoverall= 33.3%; CRET1= 5.8%; CRET2= 16.6%; CRET3= 68.5%) and hookworm (CRoverall= 47.2%; CRET1= 31.2%; CRET2= 16.6%; CRET3= 78.5%) infections. Daily post-treatment egg per gram of stool counts recapitulated these observations and faster and increased egg reduction was observed in ET3 when compared to failure-associated ET1 and ET2. Species-level comparisons of these enterotypes highlighted a set of ten differentially enriched bacterial species.
ConclusionTaxonomically distinct gut microbiota communities were found in this setting in terms of both, relative and absolute abundances, of specific bacterial taxa. Pre-treatment enterotype was relevant for treatment outcome of the combination therapy, albendazole and ivermectin, forT. trichiuraas well as for hookworm infections. These observations indicate that pre-treatment microbial composition of stool samples should be monitored to ensure evidence-based administration of albendazole-ivermectin to treat these diseases.Fungal interactions with plant roots, either beneficial or detrimental, have a major impact on agriculture and ecosystems. The soil inhabiting ascomyceteFusarium oxysporum(Fo) constitutes a species complex of worldwide distribution causing vascular wilt in more than a hundred different crops. Individual isolates of the fungus exhibit host-specific pathogenicity, determined by proteinaceous effectors termed secreted in xylem (SIX). However, such isolates can also colonize roots of non-host plants asymptomatically as endophytes, or even protect them against pathogenic isolates. The molecular determinants of multi-host plant colonization are currently unknown. Here, we identified a set of fungal effectors termed ERCs (EarlyRootCompatibility effectors), which are secreted during early biotrophic growth of Fo on both host and non-host plants. In contrast to the strain-specific SIX effectors, which are encoded on accessory genomic regions, ERCs are encoded on core regions and are found across the entire Fo species complex as well as in other phytopathogens, suggesting a conserved role in fungus-plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence on the host plant and rapid activation of plant immune responses, while in a non-pathogenic isolate it led to impaired root colonization and loss of biocontrol ability. Strikingly, some ERCs also contribute to Fo infection on the non-vascular land plantMarchantia polymorpha. Our results reveal an evolutionarily conserved mechanism for multi-host colonization by root infecting fungi.
Soil cyanobacteria play essential ecological roles and are known to experience large changes in their diversity and abundance throughout early succession. However, much less is known about how and why soil cyanobacterial communities change as soil develops from centuries to millennia, and the effects of aboveground vegetation on these communities.
We combined an extensive field survey including 16 global soil chronosequences across contrasting ecosystems (from deserts to tropical forests) with molecular analyses to investigate how the diversity and abundance of soil cyanobacteria under vegetation change during soil development from hundreds to thousands of years.
We show that, in most chronosequences, the abundance, species richness and community composition of soil cyanobacteria were relatively stable as soil develops (from centuries to millennia). Regardless of soil age, forest chronosequences were consistently dominated by non-photosynthetic cyanobacteria (Vampirovibrionia), while grasslands and shrublands were dominated by photosynthetic cyanobacteria. Chronosequences undergoing drastic vegetation shifts during soil development (e.g. transitions from grasslands to forests) experienced significant changes in the composition of soil cyanobacteria communities.
Our results advance our understanding of the ecology of cyanobacterial classes, specially the understudied non-photosynthetic ones and highlight the key role of vegetation as a major driver of their temporal dynamics as soil develops.
The terrestrial subsurface contains nearly all of Earth\uffe2\uff80\uff99s freshwater reserves1 and harbors upwards of 60% of our planet\uffe2\uff80\uff99s total prokaryotic biomass2,3. While genetic surveys suggest these organisms rely on in situ carbon fixation, rather than the translocation of photosynthetically derived organic carbon4\uffe2\uff80\uff936, corroborating measurements of carbon fixation in the subsurface are absent. Using a novel ultra-low level 14C-labeling technique, we show that in situ carbon fixation rates in a carbonate aquifer reached 10% of the median rates measured in oligotrophic marine surface waters, and were up to six-fold greater than those observed in lower euphotic zone waters where deep chlorophyll levels peak. Empirical carbon fixation rates were substantiated by both nitrification and anammox rate data. Metagenomic analyses revealed a remarkable abundance of putative chemolithoautotrophic members of an uncharacterized order of Nitrospiria \uffe2\uff80\uff93 the first representatives of this class expected to fix carbon via the Wood-Ljungdahl pathway. Based on these fixation rates, we extrapolate global primary production in carbonate groundwaters to be 0.11 Pg of carbon per year.Filling the global biodiversity financing gap will require significant investments from financial markets, which demand credible valuations of ecosystem services and natural capital. However, current valuation approaches discourage investment in conservation because their results cannot be verified using market-determined prices. Here, we bridge the gap between finance and conservation by valuing only wild animals\uffe2\uff80\uff99 carbon services for which market prices exist. By projecting the future path of carbon service production using a spatially-explicit demographic model, we place a credible value on the carbon-capture services produced by African forest elephants. If elephants were protected, their services would be worth $35.9 billion (24.3-41.2) and store 377 MtC (318-388) across tropical Africa. Our methodology can also place lower bounds on the social cost of nature degradation. Poaching would result in $10-14 billion of lost carbon services. Our methodology enables the integration of animal services into global financial markets with major implications for conservation, local socio-economies, and conservation.Bacterial attachment on root surfaces is an important step preceding the colonisation or internalisation and subsequent infection of plants by pathogens. Unfortunately, bacterial attachment is not well understood because the phenomenon is difficult to observe. Here we assessed whether this limitation could be overcome using optical trapping approaches. We have developed a system based on counter-propagating beams and studied its ability to guidePectobacterium atrosepticum(Pba) cells to different root cell types within the interstices of transparent soils. Bacterial cells were successfully trapped and guided to root hair cells, epidermis cells, border cells and tissues damaged by laser ablation. Finally, we used the system to quantify the bacterial cell detachment rate of Pba cells on root surfaces following reversible attachment. Optical trapping techniques could greatly enhance our ability to deterministically characterise mechanisms linked to attachment and formation of biofilms in the rhizosphere.Plants growing in proximity to other plants are exposed to a variety of metabolites that these neighbors release into the environment. Some species produce allelochemicals to inhibit growth of neighboring plants, which in turn have evolved ways to detoxify these compounds. In order to understand how the allelochemical-receiving target plants respond to chemically diverse compounds, we performed whole-genome transcriptome analysis ofArabidopsis thalianaexposed to either the benzoxazinoid derivative 2-amino-3H-phenoxazin-3-one (APO) or momilactone B. These two allelochemicals belong to two very different compound classes, benzoxazinoids and diterpenes, respectively, produced by different cereal crop species. Despite their distinct chemical nature, we observed similar molecular responses ofA. thalianato these allelochemicals. In particular, many of the same or closely related genes belonging to the three-phase detoxification pathway were upregulated in both treatments. Further, we observed an overlap between genes upregulated by allelochemicals and those involved in herbicide detoxification. Our findings highlight the overlap in the transcriptional response of a target plant to natural and synthetic phytotoxic compounds and illustrate how herbicide resistance could arise via pathways involved in plant-plant interaction.", "keywords": ["0301 basic medicine", "2. Zero hunger", "2-amino-3H-phenoxazin-3-one", "0303 health sciences", "Research", "Allelochemical", "Botany", "Arabidopsis", "Benzoxazinoid", "Plants", "Pheromones", "Benzoxazines", "03 medical and health sciences", "Momilactone B", "QK1-989", "Diterpenes", "Diterpene", "Detoxification"]}, "links": [{"href": "https://link.springer.com/content/pdf/10.1186/s12870-022-03780-w.pdf"}, {"href": "https://doi.org/10.1101/2022.02.21.480921"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2022.02.21.480921", "name": "item", "description": "10.1101/2022.02.21.480921", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2022.02.21.480921"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-02-22T00:00:00Z"}}, {"id": "10.1101/2022.02.24.481781", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-03T16:19:41Z", "type": "Report", "created": "2022-02-26", "title": "Database-independent analysis of probable post-translational modifications of soil proteins across ecosystems", "description": "AbstractThe identification rate of measured peptide spectra to proteins barely scratches 1% in best-case scenarios. Hundreds of thousands of valuable spectra are lost as no viable match in the database is found. Here, we apply the delta m/z plot that was previously implemented in MSnbase as tool for quality control to 63 soil samples from three ecosystems with different vegetation (39 forests, 11 grasslands, and 13 shrublands) with the aim to extract probable post-translational modifications (PTM) without the need of a reference database. The validity of the approach was verified with amino acids proposed for their respective 1 Da mass interval and compared to their relative abundance in proteins. We found that the average probable PTM and most known PTMs proposed for the mass intervals are similar across ecosystems. Otherwise, 11 mass intervals changed significantly in relative abundance in the three ecosystems but only for one an annotation could be proposed. Our approach not only highlights the opportunity of the database-independent analysis in soil metaproteomics but paves the way for targeted analysis of the yet unknown PTMs.Ecosystems worldwide receive large amounts of nutrients from both natural processes and human activities. While direct subsidy effects on primary productivity are relatively well known (the green food web), the indirect effects of subsidies on producers as mediated by the brown food web and predators have been neglected. With a dynamical green-brown food web model, parameterized using empirical estimates from the literature, we illustrate the effect of nutrient subsidies on net primary productivity (i.e., after removing loss to herbivory) in two generic ecosystems, terrestrial and aquatic. We find that nutrient subsidies increase net primary productivity because more nutrients are available, but this effect saturates with higher subsidies. Changing the quality of subsidies from inorganic to organic tends to increase net primary productivity in terrestrial ecosystems, but less often so in aquatic ecosystems. This occurs when organic nutrient inputs promote detritivores in the brown food web, and hence predators that in turn control herbivores, thus promoting primary productivity. This previously largely overlooked effect is further enhanced by ecosystem properties such as fast decomposition and low rates of nutrient additions, and demonstrates the importance of nutrient subsidy quality on ecosystem functioning.Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Many WGBS-based studies aim to identify biologically relevant loci that display differential methylation between genotypes, treatment groups, tissues, or developmental stages. Over the years, different tools have been developed to extract differentially methylated regions (DMRs) from whole-genome data. Often, such tools are built upon assumptions from mammalian data and do not consider the substantially more complex and variable nature of plant DNA methylation. Here, we present MethylScore, a pipeline to analyze WGBS data and to account for plant-specific DNA methylation properties. MethylScore processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. It uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation, substantially reducing the number of necessary statistical tests while increasing the signal-to-noise ratio and the statistical power. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1001 Genomes dataset to unveil known and unknown genotype-epigenotype associations. MethylScore is an accessible pipeline for plant WGBS data, with unprecedented features for DMR calling in small- and large-scale datasets; it is built as a Nextflow pipeline and its source code is available at https://github.com/Computomics/MethylScore.
", "keywords": ["0301 basic medicine", "03 medical and health sciences"]}, "links": [{"href": "https://doi.org/10.1101/2022.01.06.475031"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2022.01.06.475031", "name": "item", "description": "10.1101/2022.01.06.475031", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2022.01.06.475031"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2022-01-06T00:00:00Z"}}, {"id": "10.1101/2022.03.21.485206", "type": "Feature", "geometry": null, "properties": {"license": "unspecified", "updated": "2026-04-03T16:19:41Z", "type": "Report", "created": "2022-03-22", "title": "Cell-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil", "description": "AbstractWhen exposed to increased mechanical resistance from the soil, plant roots display non-linear growth responses that can not be solely explained by mechanical principles. Here, we aim to investigate how changes in tissue mechanical properties are biologically regulated in response to soil strength. A particle-based model was developed to solve root-soil mechanical interactions at the cellular scale, and a detailed numerical study explored factors that affect root responses to soil resistance. Results showed that growth through increasing soil strength is maintained through the softening of cell walls at the tip, a response likely linked to soil cavity expansion. The model also predicts the shortening and decreased anisotropy of the zone of cell elongation, which may improve the mechanical stability of the root against axial forces. The study demonstrates the potential of advanced modeling tools to help identify traits that confer plant resistance to abiotic stress.Acclimation of root growth is vital for plants to survive salt stress. Halophytes are great examples of plants that thrive under high salt concentrations but their salt tolerance mechanisms, especially those mediated by root responses, are still largely unknown. We compared root growth responses of the halophyteSchrenkiella parvulawith its glycophytic relative speciesArabidopsis thalianaunder salt stress, and performed root transcriptomic analysis to identify differences in gene regulatory networks underlying their physiological responses. Primary root growth ofS. parvulais less sensitive to salt compared with Arabidopsis. The root transcriptomic analysis ofS. parvularevealed the induction of sugar transporters and genes regulating cell expansion and suberization under salt stress.14C-labelled carbon partitioning analyses consistently showed thatS. parvulahad a higher incorporation rate of soluble sugars in roots under salt stress compared to Arabidopsis. Further physiological investigation revealed thatS. parvularoots do not show a halotropic response and maintain root cell expansion and enhanced suberization even under severe salt stress. In summary, our study demonstrates that roots ofS. parvuladeploy multiple physiological and developmental adjustments under salt stress to maintain growth, providing new avenues to improve salt tolerance of plants using root-specific strategies.Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology. Here, we performed metagenomic analyses on rocks from across Antarctica comprising >75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities potentially influencing bacterial adaptation and biogeochemistry. This catalog lays the foundation for expanding knowledge of the virosphere in extreme environments.We have developed a tuneable workflow for the study of soil microbes in an imitative 3D soil environment that is compatible with routine and advanced optical imaging, is chemically customisable, and is reliably refractive index matched based on the metabolic profile of the study organism. We demonstrate our transparent soil pipeline with two representative soil organisms,Bacillus subtilisandStreptomyces coelicolor, and visualise their colonisation behaviours using fluorescence microscopy and mesoscopy. This spatially structured, 3D approach to microbial culture has the potential to further study the behaviour of other difficult-to-culture bacteria in conditions matching their native environment and could be expanded to study microbial interactions, such as interaction, competition, and warfare.
3.Graphical AbstractA step-by-step method for creating a tailored 3D culture medium for study of soil microbes.
The complete workflow can be split into three parts: Growth and observation, metabolic profiling to provide a stable refractive index matching solution, and production of the 3D soil environment. The 3D culture scaffold was created by cryomilling Nafion\uffe2\uff84\uffa2 resin pellets and size filtration. Chemical processing altered the surface chemistry of Nafion\uffe2\uff84\uffa2 particles and facilitated nutrient binding by titration of a defined liquid culture medium. Metabolic profiling determined non-metabolisable sugars and provided an inert refractive index matching substrate, which was added to the final nutrient titration. Inoculation and growth of the test strain allowed for downstream assessment of colonisation behaviours and community dynamicsin situby, for example, optical microscopy.Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.The soil microbiome determines the fate of belowground inputs of plant fixed carbon. The shifts in soil properties caused by changes in land use leads to modifications in microbiome structure and function, resulting in either loss or gain of soil organic carbon (SOC). Soil pH is the primary factor regulating microbiome characteristics leading to distinct pathways of microbial carbon cycling, but the underlying mechanisms remain understudied. Here, the taxa-trait relationships behind the variable fate of SOC were investigated across two temperate paired land use intensity contrasts with differing soil pH using metaproteomics, metabarcoding and a13C labelled litter decomposition experiment.13C incorporation into microbial biomass increased with land use intensification in low pH soils but decreased in high pH soils, impacting ecosystem carbon use efficiency (CUE) in opposing directions. Reduction in biosynthesis traits across land use intensity contrasts was due to increased abundance of proteins linked to resource acquisition and stress tolerance. These community-level trait trade-offs were underpinned by land use intensification-induced changes in dominant taxa with distinct traits. These trait changes alter the balance of decomposition and stabilisation of carbon in soil through divergent pH-controlled pathways. In low pH soils, land use intensification alleviates microbial abiotic stress resulting in increased CUE but promotes decomposition and SOC loss. In contrast, in high pH soils, land use intensification increases microbial physiological constraints and decreases CUE, leading to reduced necromass build-up and SOC stabilisation. We demonstrate how microbial CUE can be decoupled from SOC highlighting the need for its careful consideration in predicting or managing SOC storage for soil health and climate change mitigation.MicroRNAs (miRNAs) are a class of small non-coding RNAs that play important regulatory roles in plant genomes. While some miRNA genes are deeply conserved, the majority appear to be species-specific, raising the question of how they emerge and integrate into cellular regulatory networks. To address this question, we first performed a detailed annotation of miRNA genes in the closely related Arabidopsis halleri and A. lyrata, then evaluated their phylogenetic conservation across 87 plant species. We then characterized the process by which newly emerged miRNA genes progressively acquire the properties of \uffe2\uff80\uff9ccanonical\uffe2\uff80\uff9d miRNA genes, in terms of size and stability of the hairpin precursor, loading of their cleavage products into Argonaute proteins, and potential to regulate downstream target genes. Analysis of nucleotide polymorphism distribution along the hairpin sequence (stem, mature miRNA, terminal loop) revealed that the selective constraints on recently emerged miRNA genes were initially weak, gradually increasing toward evolutionarily conserved miRNA genes. Our results illustrate the rapid birth-and-death of miRNA genes in plant genomes, and provide a detailed picture of the evolutionary progression toward canonical miRNAs by which a small fraction of de novo formed miRNA genes eventually integrate into \uffe2\uff80\uff9ccore\uffe2\uff80\uff9d biological processes.Resource acquisition and growth yield are fundamental traits of microorganisms that have consequences for ecosystem functioning. However, there is a lack of empirical observations linking these traits. Using a landscape-scale survey of temperate near-neutral pH soils, we show tradeoffs in key community-level parameters linked to these traits. Increased investment into extracellular enzymes was associated with reduced growth yield; this reduction was linked more to carbon than nitrogen acquisition enzymes suggesting smaller stoichiometric constraints on community metabolism in examined soils.The whipwormTrichuris trichiurais a soil-transmitted helminth that dwells in the epithelium of the caecum and proximal colon of their hosts causing the human disease, trichuriasis. Trichuriasis is characterized by colitis attributed to the inflammatory response elicited by the parasite while tunnelling through intestinal epithelial cells (IECs).
The IL-10 family of receptors, comprising combinations of subunits IL-10R\uffce\uffb1, IL-10R\uffce\uffb2, IL-22R\uffce\uffb1 and IL-28R\uffce\uffb1, modulates intestinal inflammatory responses. Here we carefully dissected the role of these subunits in the resistance of mice to infection withT. muris,a mouse model of the human whipwormT. trichiura.Our findings demonstrate that whilst IL-22R\uffce\uffb1 and IL-28R\uffce\uffb1 are dispensable in the host response to whipworms, IL-10 signalling through IL-10R\uffce\uffb1 and IL-10R\uffce\uffb2 is essential to control caecal pathology, worm expulsion and survival duringT. murisinfections. We show that deficiency of IL-10, IL-10R\uffce\uffb1 and IL-10R\uffce\uffb2 results in dysbiosis of the caecal microbiota characterised by expanded populations of opportunistic bacteria of the families Enterococcaceae and Enterobacteriaceae. Moreover, breakdown of the epithelial barrier after whipworm infection in IL-10, IL-10R\uffce\uffb1 and IL-10R\uffce\uffb2-deficient mice, allows the translocation of these opportunistic pathogens or their excretory products to the liver causing organ failure and lethal disease. Importantly, bone marrow chimera experiments indicate that signalling through IL-10R\uffce\uffb1 and IL-10R\uffce\uffb2 in haematopoietic cells, but not IECs, is crucial to control worm expulsion and immunopathology. These findings are supported by worm expulsion upon infection of conditional mutant mice for the IL-10R\uffce\uffb1 on IECs. Our findings emphasize the pivotal role of systemic IL-10R\uffce\uffb1 signalling on immune cells in promoting microbiota homeostasis and maintaining the intestinal epithelial barrier, thus preventing immunopathology during whipworms infections.
Author summaryThe human gut is home to millions of bacteria, collectively called the microbiota, and also to parasites that include whipworms. The interactions between gut cells, the microbiota and whipworms define conditions for balanced parasitism. Cells lining the gut host whipworms but also interact with gut immune cells to deploy measures that control or expel whipworms whilst maintaining a barrier to prevent microbial translocation. Whipworms affect the composition of the microbiota, which in turn impacts the condition of the gut lining and the way in which immune cells are activated. In order to avoid tissue damage and disease, these interactions are tightly regulated. Here we show that signalling through a member of the IL-10 receptor family, IL-10R\uffce\uffb1, in gut immune cells is critical for regulating of these interactions. Lack of this receptor on gut immune cells results in persistence of whipworms in the gut accompanied by an uncontrolled inflammation that destroys the gut lining. This tissue damage is accompanied by the overgrowth of members of the microbiota that act as opportunistic pathogens. Furthermore, the destruction of the gut barrier allows these bacteria to reach the liver where they cause organ failure and fatal disease.Winemakers have long used copper as a fungicide on grapevine. However, the potential of copper to accumulate on soil and affect the biota poses a challenge to achieving sustainable agriculture. One recently developed option is the use of biocontrol agents to replace or complement traditional methods. In the present study, a field experiment was conducted in South Africa in which the leaves in two blocks of a vineyard were periodically treated with either copper sulphate or sprayed withLactobacillus plantarumMW-1 as a biocontrol agent. This study evaluated the impact of the two treatments on the bacterial and fungal communities as they changed during the growing season. To do this, NGS was combined with quantitative strain-specific and community qPCRs. The results revealed the progression of the microbial communities throughout the season and how the different treatments affected the microbiota. Bacteria appeared to be relatively stable at the different time points, with the only taxa that systematically changed between treatments beingLactobacillaceae, which included reads from the biocontrol agent. Cells ofLactobacillus plantarumMW-1 were only detected on treated leaves using strain-specific qPCR, with its amount spanning from 103to 105cells/leaves. Conversely the fungal community was largely shaped by a succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the number of ITS copies was also comparable. In this regards, the two treatments seemed to affect the microbial community similarly, revealing the potential of this biocontrol strain as a promising alternative among sustainable fungicide treatments, although further investigation is required.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "0303 health sciences", "03 medical and health sciences", "15. Life on land", "6. Clean water", "12. Responsible consumption"], "contacts": [{"organization": "Alex, Gobbi, Ifigeneia, Kyrkou, Elisa, Filippi, Lea, Ellegaard-Jensen, Hestbjerg, Hansen Lars,", "roles": ["creator"]}]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/523977v1.full.pdf"}, {"href": "https://doi.org/10.1101/523977"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/523977", "name": "item", "description": "10.1101/523977", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/523977"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-01-18T00:00:00Z"}}, {"id": "10.1101/688010", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:42Z", "type": "Journal Article", "created": "2019-07-02", "title": "High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation", "description": "ABSTRACTBy developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation. Specifically, high-throughput phenotyping of 530 knockout mouse lines identified 140 monogenic \uffe2\uff80\uff9chits\uffe2\uff80\uff9d (>25%), most of which had never hitherto been implicated in immunology. Furthermore, they were conspicuously enriched in genes for which humans show poor tolerance to loss-of-function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with one another and with specific physiologic traits. By limiting the freedom of individual immune parameters, such linkages impose genetically regulated \uffe2\uff80\uff9cimmunological structures\uffe2\uff80\uff9d, whose integrity was found to be associated with immunocompetence. Hence, our findings provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.An important step in metagenomics studies is to identify which species are present in a sample as well as to compare samples from different environments. Here we introduce MicroWineBar, a graphical tool for analyzing and comparing metagenomics samples. MicroWineBar can visualize the abundances of metagenomics samples in line and bar graphs, as well as analyse the richness and diversity. For a PCA as well as a differential abundance analysis, the abundance data is treated as compositional data and center log-ratio transformed. We use MicroWineBar to analyse two different years of wine fermentation as well as data from a human microbiome study of colorectal cancer. Importantly, MicroWineBar does not require any programming skills, is intuitive and user friendly. MicroWineBar is available athttps://github.com/klincke/MicroWineBarand as a python package from the Python Package Index.
", "keywords": ["0301 basic medicine", "03 medical and health sciences", "0206 medical engineering", "02 engineering and technology"], "contacts": [{"organization": "Klincke, Franziska, Abel-Kistrup, Martin, Saerens, Sofie Maria Gilberte, Rasmussen, Simon,", "roles": ["creator"]}]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/742684v1.full.pdf"}, {"href": "https://doi.org/10.1101/742684"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/742684", "name": "item", "description": "10.1101/742684", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/742684"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-21T00:00:00Z"}}, {"id": "10.1101/531145", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-03T16:19:42Z", "type": "Report", "created": "2019-01-27", "title": "Ecological niche differentiation in soil cyanobacterial communities across the globe", "description": "AbstractCyanobacteria are key organisms in the evolution of life on Earth, but their distribution and environmental preferences in terrestrial ecosystems remain poorly understood. This lack of knowledge is particularly evident for two recently discovered non-photosynthetic cyanobacterial classes, Melainabacteria and Sericytochromatia, limiting our capacity to predict how these organisms and the important ecosystem functions they perform will respond to ongoing global change. Here, we conducted a global field survey covering a wide range of vegetation types and climatic conditions to identify the environmental factors associated with the distribution of soil cyanobacterial communities. Network analyses revealed three major clusters of cyanobacterial phylotypes, each one dominated by members of one of the extant classes of Cyanobacteria (Oxyphotobacteria, Melainabacteria and Sericytochromatia), suggesting that species within these taxonomic groups share similar environmental preferences. Melainabacteria appear mostly in acidic and humid ecosystems, especially forests, Oxyphotobacteria are prevalent in arid and semiarid areas, and Sericytochromatia are common in hyperarid oligotrophic environments. We used this information to construct a global atlas of soil cyanobacteria. Our results provide novel insights into the ecology and biogeography of soil cyanobacteria and highlight how their global distribution could change in response to increased aridity, a landmark feature of climate change in terrestrial ecosystems worldwide.
Significance statementCyanobacteria have shaped the history of life on Earth and can be important photosynthesizers and nitrogen fixers in terrestrial ecosystems worldwide. The recent discovery of two non-photosynthetic classes has advanced our understanding of their evolution, but their distribution and environmental preferences remain poorly described. Using a global survey conducted across 237 locations on six continents, we identified three main groups of soil cyanobacteria with contrasting environmental preferences: acidic and humid ecosystems, arid and semiarid areas, and hyperarid oligotrophic ecosystems. We then constructed the first global atlas of soil cyanobacteria, an important advance in our understanding of the ecology and biogeography of these functionally important organisms.Bacteria of Lactobacillus sp. are very useful to humans. However, the biology and genomic diversity of their (bacterio)phage enemies remains understudied. Knowledge on Lactobacillus phage diversity should broaden to develop efficient phage control strategies. To this end, organic waste samples were screened for phages against two wine-related Lactobacillus plantarum strains. Isolates were shotgun sequenced and compared against the phage database and each other by phylogenetics and comparative genomics. The new isolates had only three distant relatives from the database, but displayed a high overall degree of genomic similarity amongst them. The latter allowed for the use of one isolate as a representative to conduct transmission electron microscopy and structural protein sequencing, and to study phage adsorption and growth kinetics. The microscopy and proteomics tests confirmed the observed diversity of the new isolates and supported their classification to the family Siphoviridae and the proposal of the new phage genus \uffe2\uff80\uff9cSilenusvirus\uffe2\uff80\uff9d.
", "keywords": ["0301 basic medicine", "0303 health sciences", "FRAMESHIFT", "Denmark", "BACTERIOPHAGES", "PROTEIN", "Wine", "Genome", " Viral", "Viral Plaque Assay", "SEQUENCE", "CLASSIFICATION", "Article", "12. Responsible consumption", "Microscopy", " Electron", "Waste Disposal Facilities", "03 medical and health sciences", "Bacteriolysis", "Species Specificity", "DNA", " Viral", "Bacteriophages", "Adsorption", "Phylogeny", "Lactobacillus plantarum"]}, "links": [{"href": "https://www.biorxiv.org/content/10.1101/728261v1.full.pdf"}, {"href": "https://doi.org/10.1101/728261"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Scientific%20Reports", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/728261", "name": "item", "description": "10.1101/728261", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/728261"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-08-07T00:00:00Z"}}, {"id": "10.1103/physrevb.107.035431", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-03T16:19:43Z", "type": "Journal Article", "created": "2023-01-24", "title": "Evolution of the edge states and corner states in a multilayer honeycomb valley-Hall topological metamaterial", "description": "The valley-Hall effect provides topological protection to a broad class of defects in valley-Hall photonic topological metamaterials. Unveiling precisely how such protection is achieved and its implications in practical implementations is paramount to move from fundamental science to applications. To this end, we investigate a honeycomb valley-Hall topological metamaterial and monitor the evolution of the topological valley-Hall edge states and higher-order corner states under different perturbation \u03b4R. The evolutions of the edge states of the armchair and zigzag interfaces are demonstrated, respectively. By adjusting the geometric parameters and introducing disturbances to break the inversion symmetry, we achieve the edge states with different modes including the conventional crossed edge state and the specific gapped edge state. It is found that the edge states of topological valley kinking will gradually separate with the increase of \u03b4R, and finally a complete gap between the edge states appears. The gap has rarely been reported previously in topological materials fabricated by printed circuit board technology. In addition, the higher-order topological corner states can also be observed in the proposed topological metamaterial. The higher-order topological phase is theoretically characterized by nontrivial bulk polarization and the Wannier centers. Our results show that the corner state localization becomes stronger with the increase of \u03b4R. It is expected that our results will provide a platform for the realization of optical topological insulators.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "530"]}, "links": [{"href": "https://doi.org/10.1103/physrevb.107.035431"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Physical%20Review%20B", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1103/physrevb.107.035431", "name": "item", "description": "10.1103/physrevb.107.035431", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1103/physrevb.107.035431"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2023-01-24T00:00:00Z"}}, {"id": "10.1104/pp.19.00818", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:43Z", "type": "Journal Article", "created": "2019-09-30", "title": "SnRK2 Protein Kinases and mRNA Decapping Machinery Control Root Development and Response to Salt", "description": "SNF1-RELATED PROTEIN KINASES 2 (SnRK2) are important components of early osmotic and salt stress signaling pathways in plants. The Arabidopsis (Arabidopsis thaliana) SnRK2 family comprises the abscisic acid (ABA)-activated protein kinases SnRK2.2, SnRK2.3, SnRK2.6, SnRK2.7, and SnRK2.8, and the ABA-independent subclass 1 protein kinases SnRK2.1, SnRK2.4, SnRK2.5, SnRK2.9, and SnRK2.10. ABA-independent SnRK2s act at the posttranscriptional level via phosphorylation of VARICOSE (VCS), a member of the mRNA decapping complex, that catalyzes the first step of 5'mRNA decay. Here, we identified VCS and VARICOSE RELATED (VCR) as interactors and phosphorylation targets of SnRK2.5, SnRK2.6, and SnRK2.10. All three protein kinases phosphorylated Ser-645 and Ser-1156 of VCS, whereas SnRK2.6 and SnRK2.10 also phosphorylated VCS Ser-692 and Ser-680 of VCR. We showed that subclass 1 SnRK2s, VCS, and 5' EXORIBONUCLEASE 4 (XRN4) are involved in regulating root growth under control conditions as well as modulating root system architecture in response to salt stress. Our results suggest interesting patterns of redundancy within subclass 1 SnRK2 protein kinases, with SnRK2.1, SnRK2.5, and SnRK2.9 controlling root growth under nonstress conditions and SnRK2.4 and SnRK2.10 acting mostly in response to salinity. We propose that subclass 1 SnRK2s function in root development under salt stress by affecting the transcript levels of aquaporins, as well as CYP79B2, an enzyme involved in auxin biosynthesis.", "keywords": ["0301 basic medicine", "570", "Arabidopsis", "Protein Serine-Threonine Kinases", "03 medical and health sciences", "HYPEROSMOTIC STRESS", "Life Science", "RNA", " Messenger", "TRITICUM-AESTIVUM L.", "Phosphorylation", "DIFFERENT PHOSPHORYLATION MECHANISMS", "Plant Proteins", "580", "0303 health sciences", "IDENTIFICATION", "Arabidopsis Proteins", "Biology and Life Sciences", "ABSCISIC-ACID", "ARABIDOPSIS", "GENE", "FAMILY", "OSMOTIC STRESSES", "Exoribonucleases", "Salts", "DECAY", "Protein Kinases", "Signal Transduction"]}, "links": [{"href": "https://doi.org/10.1104/pp.19.00818"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1104/pp.19.00818", "name": "item", "description": "10.1104/pp.19.00818", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1104/pp.19.00818"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-09-30T00:00:00Z"}}, {"id": "10.1104/pp.76.1.244", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:43Z", "type": "Journal Article", "created": "2008-12-13", "title": "Effects Of Water-Stress On Photosynthesis And Carbon Partitioning In Soybean (Glycine-Max [L] Merr) Plants Grown In The Field At Different Co2 Levels", "description": "The effects of water stress and CO(2) enrichment on photosynthesis, assimilate export, and sucrose-P synthase activity were examined in field grown soybean plants. In general, leaves of plants grown in CO(2)-enriched atmospheres (300 microliters per liter above unenriched control, which was 349 +/- 12 microliters per liter between 0500 and 1900 hours EST over the entire season) had higher carbon exchange rates (CER) compared to plants grown at ambient CO(2), but similar rates of export and similar activities of sucrose-P synthase. On most sample dates, essentially all of the extra carbon fixed as a result of CO(2) enrichment was partitioned into starch. CO(2)-enriched plants had lower transpiration rates and therefore had a higher water use efficiency (milligrams CO(2) fixed per gram H(2)O transpired) per unit leaf area compared to nonenriched plants. Water stress reduced CER in nonenriched plants to a greater extent than in CO(2)-enriched plants. As CER declined, stomatal resistance increased, but this was not the primary cause of the decrease in assimilation because internal CO(2) concentration remained relatively constant. Export of assimilates was less affected by water stress than was CER. When CERs were low as a result of the imposed stress, export was supported by mobilization of reserves (mainly starch). Export rate and leaf sucrose concentration were related in a curvilinear manner. When sucrose concentration was above about 12 milligrams per square decimeter, obtained with nonstressed plants at high CO(2), there was no significant increase in export rate. Assimilate export rate was also correlated positively with SPS activity and the quantitative relationship varied with CER. Thus, export rate was a function of both CER and carbon partitioning.", "keywords": ["2. Zero hunger", "0106 biological sciences", "0301 basic medicine", "03 medical and health sciences", "01 natural sciences", "6. Clean water"], "contacts": [{"organization": "Hugo H. Rogers, Steven C. Huber, Fred L. Mowry,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1104/pp.76.1.244"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1104/pp.76.1.244", "name": "item", "description": "10.1104/pp.76.1.244", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1104/pp.76.1.244"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1984-09-01T00:00:00Z"}}, {"id": "10.1105/tpc.20.00318", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:43Z", "type": "Journal Article", "created": "2020-10-10", "title": "ARADEEPOPSIS, an Automated Workflow for Top-View Plant Phenomics using Semantic Segmentation of Leaf States", "description": "Linking plant phenotype to genotype is a common goal to both plant breeders and geneticists. However, collecting phenotypic data for large numbers of plants remain a bottleneck. Plant phenotyping is mostly image based and therefore requires rapid and robust extraction of phenotypic measurements from image data. However, because segmentation tools usually rely on color information, they are sensitive to background or plant color deviations. We have developed a versatile, fully open-source pipeline to extract phenotypic measurements from plant images in an unsupervised manner. ARADEEPOPSIS (https://github.com/Gregor-Mendel-Institute/aradeepopsis) uses semantic segmentation of top-view images to classify leaf tissue into three categories: healthy, anthocyanin rich, and senescent. This makes it particularly powerful at quantitative phenotyping of different developmental stages, mutants with aberrant leaf color and/or phenotype, and plants growing in stressful conditions. On a panel of 210 natural Arabidopsis (Arabidopsis thaliana) accessions, we were able to not only accurately segment images of phenotypically diverse genotypes but also to identify known loci related to anthocyanin production and early necrosis in genome-wide association analyses. Our pipeline accurately processed images of diverse origin, quality, and background composition, and of a distantly related Brassicaceae. ARADEEPOPSIS is deployable on most operating systems and high-performance computing environments and can be used independently of bioinformatics expertise and resources.", "keywords": ["0301 basic medicine", "0303 health sciences", "Genotype", "Large-Scale Biology Articles", "Arabidopsis", "Computational Biology", "Semantics", "Workflow", "Plant Leaves", "03 medical and health sciences", "Phenotype", "Image Processing", " Computer-Assisted", "Phenomics", "Software", "Genome-Wide Association Study"]}, "links": [{"href": "https://doi.org/10.1105/tpc.20.00318"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/The%20Plant%20Cell", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1105/tpc.20.00318", "name": "item", "description": "10.1105/tpc.20.00318", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1105/tpc.20.00318"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-10-09T00:00:00Z"}}, {"id": "10.1104/pp.18.01546", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:43Z", "type": "Journal Article", "created": "2019-06-04", "title": "Abscisic Acid Coordinates Dose-Dependent Developmental and Hydraulic Responses of Roots to Water Deficit.", "description": "Root water uptake is influenced by root system architecture, which is determined by root growth and branching and the hydraulics of root cells and tissues. The phytohormone abscisic acid (ABA) plays a major role in the adaptation of plants to water deficit (WD). Here we addressed at the whole-root level in Arabidopsis (Arabidopsis thaliana) the regulatory role of ABA in mechanisms that determine root hydraulic architecture. Root system architecture and root hydraulic conductivity (Lpr) were analyzed in hydroponically grown plants subjected to varying degrees of WD induced by various polyethylene glycol (PEG) concentrations. The majority of root traits investigated, including first- and second-order lateral root production and elongation and whole-root hydraulics, had a bell-shaped dependency on WD, displaying stimulation under mild WD conditions (25 g PEG L-1) and repression under more severe conditions. These traits also showed a bell-shaped dependency on exogenous ABA, and their regulation by WD was attenuated in genotypes altered in ABA biosynthesis and response. Thus, we propose that ABA acts as a coordinator and an integrator of most root responses to mild and moderate WD, whereas responses to strong WD (150 g PEG L-1) are largely ABA independent. We also found that roots exhibit different growth responses to both WD and ABA depending on their rank and age. Taken together, our results give further insights into the coordinated water acquisition strategies of roots deployed in relation to WD intensity.", "keywords": ["580", "2. Zero hunger", "0301 basic medicine", "0303 health sciences", "[SDV]Life Sciences [q-bio]", "Water", "15. Life on land", "Plant Roots", "6. Clean water", "Polyethylene Glycols", "[SDV] Life Sciences [q-bio]", "03 medical and health sciences", "Gene Expression Regulation", " Plant", "[SDV.BV]Life Sciences [q-bio]/Vegetal Biology", "[SDV.BV] Life Sciences [q-bio]/Vegetal Biology", "Abscisic Acid"]}, "links": [{"href": "https://hal.science/hal-02139355/file/Rosales-A.M.-et%20al-PostPrint-PlantPhysiol-2019.pdf"}, {"href": "https://doi.org/10.1104/pp.18.01546"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1104/pp.18.01546", "name": "item", "description": "10.1104/pp.18.01546", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1104/pp.18.01546"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-04T00:00:00Z"}}, {"id": "10.1104/pp.19.01464", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:43Z", "type": "Journal Article", "created": "2020-03-04", "title": "How Plants Sense and Respond to Stressful Environments", "description": "Plants are exposed to an ever-changing environment to which they have to adjust accordingly. Their response is tightly regulated by complex signaling pathways that all start with stimulus perception. Here, we give an overview of the latest developments in the perception of various abiotic stresses, including drought, salinity, flooding, and temperature stress. We discuss whether proposed perception mechanisms are true sensors, which is well established for some abiotic factors but not yet fully elucidated for others. In addition, we review the downstream cellular responses, many of which are shared by various stresses but result in stress-specific physiological and developmental output. New sensing mechanisms have been identified, including heat sensing by the photoreceptor phytochrome B, salt sensing by glycosylinositol phosphorylceramide sphingolipids, and drought sensing by the specific calcium influx channel OSCA1. The simultaneous occurrence of multiple stress conditions shows characteristic downstream signaling signatures that were previously considered general signaling responses. The integration of sensing of multiple stress conditions and subsequent signaling responses is a promising venue for future research to improve the understanding of plant abiotic stress perception.", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "Stress", " Physiological", "Life Science", "Calcium", "Environment", "Plants", "15. Life on land", "Reactive Oxygen Species", "Signal Transduction"]}, "links": [{"href": "https://doi.org/10.1104/pp.19.01464"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1104/pp.19.01464", "name": "item", "description": "10.1104/pp.19.01464", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1104/pp.19.01464"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-04T00:00:00Z"}}, {"id": "10.1104/pp.89.4.1060", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:43Z", "type": "Journal Article", "created": "2008-12-13", "title": "Mild Water-Stress Effects On Carbon-Reduction-Cycle Intermediates, Ribulose Bisphosphate Carboxylase Activity, And Spatial Homogeneity Of Photosynthesis In Intact Leaves", "description": "We have examined the effect of mild water stress on photosynthetic chloroplast reactions of intact Phaseolus vulgaris leaves by measuring two parameters of ribulose bisphosphate (RuBP) carboxylase activity and the pool sizes of RuBP, 3-phosphoglycerate (PGA), triose phosphates, hexose monophosphates, and ATP. We also tested for patchy stomatal closure by feeding (14)CO(2). The k(cat) of RuBP carboxylase (moles CO(2) fixed per mole enzyme per second) which could be measured after incubating the enzyme with CO(2) and Mg(2+) was unchanged by water stress. The ratio of activity before and after incubation with CO(2) and Mg(2+) (the carbamylation state) was slightly reduced by severe stress but not by mild stress. Likewise, the concentration of RuBP was slightly reduced by severe stress but not by mild stress. The concentration of PGA was markedly reduced by both mild and severe water stress. The concentration of triose phosphates did not decline as much as PGA. We found that photosynthesis in water stressed leaves occurred in patches. The patchiness of photosynthesis during water stress may lead to an underestimation of the effect of stomatal closure. We conclude that reductions in whole leaf photosynthesis caused by mild water stress are primarily the result of stomatal closure and that there is no indication of damage to chloroplast reactions.", "keywords": ["0106 biological sciences", "0301 basic medicine", "03 medical and health sciences", "01 natural sciences", "6. Clean water"]}, "links": [{"href": "https://doi.org/10.1104/pp.89.4.1060"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Physiology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1104/pp.89.4.1060", "name": "item", "description": "10.1104/pp.89.4.1060", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1104/pp.89.4.1060"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "1989-04-01T00:00:00Z"}}, {"id": "10.1109/iceea.2010.5596085", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:44Z", "type": "Journal Article", "created": "2010-10-08", "title": "Phosphorus Limitation On CoOrganisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.The worldwide distribution of microinvertebrates on glaciers, the coldest biome, is poorly known. Owing to their tolerance to hostile conditions, small size and dispersal abilities, nematodes, tardigrades and rotifers are considered cosmopolitan and together inhabit various ecosystems. In this study, we investigated their global distribution in cryoconite holes \uffe2\uff80\uff93 a type of freshwater reservoir forming directly in the glacial ice that creates biodiversity hotspots on glaciers. We analysed cryoconite samples (using classical microscopic observations and environmental DNA metabarcoding) from 42 glaciers located around the world (the Arctic, Subarctic, Scandinavia, the Alps, the Caucasus, Siberia, Central Asia, Africa, South America and Antarctica), as well as using literature data. Samples from Antarctic, Karakoram and the Alps were analysed using next\uffe2\uff80\uff90generation sequencing (NGS) and classical observations under microscopes, while all other samples were analysed by microscope alone. Three general outcomes were found: (1) tardigrades and rotifers represented the most common invertebrates in cryoconite holes; (2) tardigrades and rotifers often coexisted together, with one or the other dominating, but the dominant taxon varied by region or by glacier; (3) nematodes \uffe2\uff80\uff93 the most abundant, hyperdiverse and widespread metazoans on Earth, including in environments surrounding and seeding glacial surfaces \uffe2\uff80\uff93 were consistently absent from cryoconite holes. Despite the general similarity of environmental conditions in cryoconite holes, the distribution of tardigrades and rotifers differed among glaciers, but not in any predictable way, suggesting that their distribution mostly depended on the random dispersal, extreme changes of supraglacial zone or competition. Although nematodes have been found in supraglacial habitats, cryoconite hole environments seem not to provide the necessary conditions for their growth and reproduction. Lack of physiological adaptations to permanently low temperatures (~0\uffc2\uffb0C) and competition for different food resources in the cryoconite hole environment may explain the absence of nematodes in cryoconite holes.
", "keywords": ["0301 basic medicine", "0303 health sciences", "03 medical and health sciences", "550", "13. Climate action", "[SDE]Environmental Sciences", "500", "distribution; ecological selection; extremophiles; glaciers; Nematoda; psychrophiles; Rotifera; Tardigrada;", "15. Life on land", "ecological selection; extremophiles; distribution; glaciers; Nematoda; psychrophiles; Rotifera; Tardigrada"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/793600/4/Zawierucha%202020%20J%20Zool%20submitted%20manuscript.pdf"}, {"href": "https://air.unimi.it/bitstream/2434/793600/5/jzo.12832.pdf"}, {"href": "https://zslpublications.onlinelibrary.wiley.com/doi/pdf/10.1111/jzo.12832"}, {"href": "https://doi.org/10.1111/jzo.12832"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Zoology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/jzo.12832", "name": "item", "description": "10.1111/jzo.12832", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/jzo.12832"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-09-19T00:00:00Z"}}, {"id": "10.1111/1365-2435.14512", "type": "Feature", "geometry": null, "properties": {"updated": "2026-04-03T16:19:47Z", "type": "Journal Article", "created": "2024-02-07", "title": "Trait\u2010based mechanistic approach highlights global patterns and losses of herbivore biomass functional diversity", "description": "Abstract
Mammalian herbivores play a pivotal role in Earth System processes by affecting biogeochemical cycles and ecosystem functioning, potentially leading to significant repercussions on atmosphere\uffe2\uff80\uff93biosphere feedbacks. Global dynamic models of mammalian populations can improve our understanding of their ecological role at large scales and the consequences of their extinctions. However, such models are still lacking and mammals are poorly integrated in Earth System Science.
We developed a mechanistic global model of terrestrial herbivore populations simulated with 37 functional groups defined through the analysis of eco\uffe2\uff80\uff90physiological traits across all extant herbivores (2599 species). We coupled this model with a global vegetation model to predict herbivores' maximum potential biomass in pre\uffe2\uff80\uff90industrial and at present\uffe2\uff80\uff90day and to study the environmental drivers explaining the distribution of herbivore biomass. Present\uffe2\uff80\uff90day biomass was estimated by accounting for anthropogenic activity causing habitat and range losses.
We show that natural ecosystems could have sustained a potential wild herbivore wet biomass of 330 Mt (95% CI: 245\uffe2\uff80\uff93417), comprised of 193 Mt (95% CI: 177\uffe2\uff80\uff93208) by large species (body mass >1\uffe2\uff80\uff9310\uffe2\uff80\uff89kg, depending on functional group) and 138 Mt (95% CI: 68\uffe2\uff80\uff93209) by small species. We estimate that the remaining present\uffe2\uff80\uff90day large herbivores biomass is 82 Mt (95% CI: 32\uffe2\uff80\uff93133), reduced by 57% due to anthropogenic activity; consequently, small herbivores currently dominate global herbivore biomass with 98 Mt (95% CI: 91\uffe2\uff80\uff93106, \uffe2\uff88\uff9229%). Losses vary greatly across climatic zones and functional groups, suggesting that size is not the only discriminant feature of biomass decline.
Actual evapotranspiration is the most important driver of total, large and small herbivore biomass and explains 64%, 59% and 49% of its variation, respectively. Distribution of modelled and observed large herbivores' biomass suggested a high dependency on energy and water with more biomass in hot and wet areas. These results challenge the notion that large herbivore biomass peaks primarily in ecosystems with intermediate precipitation levels such as savannas.
Outside Africa and the Tropics, pre\uffe2\uff80\uff90industrial biomass hotspots occur in areas today dominated by humans; this could undermine the recovery of larger species biomass in certain areas. Our herbivore biomass estimates provide a quantitative benchmark for setting conservation and rewilding goals at large spatial scales. The herbivore model and functional classification create new opportunities to integrate mammals into Earth System Science and models.
Read the free Plain Language Summary for this article on the Journal blog.
Soil microbes provide multiple ecosystem functions such as nutrient cycling, decomposition and climate regulation. However, we lack a quantitative understanding of the relative importance of microbial richness and composition in controlling multifunctionality. This knowledge gap limits our capacity to understand the influence of biotic attributes in the provision of services and functions on which humans depend.
We used two independent approaches (i.e. experimental and observational), and applied statistical modelling to identify the role and relative importance of bacterial richness and composition in driving multifunctionality (here defined as seven measures of respiration and enzyme activities). In the observational study, we measured soil microbial communities and functions in both tree\uffe2\uff80\uff90 and bare soil\uffe2\uff80\uff90dominated microsites at 22 locations across a 1,200\uffc2\uffa0km transect in southeastern Australia. In the experimental study we used soils from two of those locations and developed gradients of bacterial diversity and composition through inoculation of sterilized soils.
Microbial richness and the relative abundance of Gammaproteobacteria, Actinobacteria, and Bacteroidetes were positively related to multifunctionality in both the observational and experimental approaches; however, only Bacteroidetes was consistently selected as a key predictor of multifunctionality across all experimental approaches and statistical models used here. Moreover, our results, from two different approaches, provide evidence that microbial richness and composition are both important, yet independent, drivers of multiple ecosystem functions.
Overall, our findings advance our understanding of the mechanisms underpinning relationships between microbial diversity and ecosystem functionality in terrestrial ecosystems, and further suggest that information on microbial richness and composition needs to be considered when formulating sustainable management and conservation policies, and when predicting the effects of global change on ecosystem functions.
A plain language summary is available for this article.
Biotic interactions are highly affected by species traits and micro\uffe2\uff80\uff90environmental variability. Research on facilitation has primarily focused on how nurse species alleviate abiotic stress for beneficiary species, while the impact of the micro\uffe2\uff80\uff90environmental variability generated by nurse plants in shaping facilitation outcomes is poorly understood. This study has two objectives: (i) To evaluate which traits define beneficiary species and (ii) to evaluate whether nurse and non\uffe2\uff80\uff90nurse species differ in their ability to reduce abiotic stress and its variability under their canopy.
We sampled recruits in two arid and stressful environments to assess (i) which species accumulate more juveniles beneath their canopy controlling for their coverage (nurse vs. non\uffe2\uff80\uff90nurse species) and (ii) which species benefited from facilitation by determining whether they tend to recruit more beneath other species or on the bare ground (beneficiary/non\uffe2\uff80\uff90beneficiary). First, we compared how nurse and non\uffe2\uff80\uff90nurse species modify the physical and chemical microenvironments underneath their canopy, both in terms of magnitude and variation. Second, we compared root growth, water retention and nutrient accumulation in juvenile plants of beneficiary and non\uffe2\uff80\uff90beneficiary species.
We found that facilitation is enhanced by species that provide a more homogeneous microenvironment rather than an intense reduction of microenvironmental stress under their canopy. In addition, the juveniles of beneficiary species invest more in root development, accumulate Ca and S in their shoot tissues, and show a higher water content than non\uffe2\uff80\uff90beneficiary species.
Our findings indicate that the homogeneity of microenvironments plays a crucial role in facilitative interactions, and the juveniles of beneficiary species show a less conservative strategy, investing more in resource acquisition than juveniles of non\uffe2\uff80\uff90beneficiary species.
Read the free Plain Language Summary for this article on the Journal blog.
Organic farming (OF) enhances top soil organic carbon (SOC) stocks in croplands compared with conventional farming (CF), which can contribute to sequester C. As farming system differences in the amount of C inputs to soil (e.g. fertilization and crop residues) are not enough to explain such increase, shifts in crop residue traits important for soil C losses such as litter decomposition may also play a role.
To assess whether crop residue (leaf and root) traits determined SOC sequestration responses to OF, we coupled a global meta\uffe2\uff80\uff90analysis with field measurements across a European\uffe2\uff80\uff90wide network of sites. In the meta\uffe2\uff80\uff90analysis, we related crop species averages of leaf N, leaf\uffe2\uff80\uff90dry matter content, fine\uffe2\uff80\uff90root C and N, with SOC stocks and sequestration responses in OF vs. CF. Across six European sites, we measured the management\uffe2\uff80\uff90induced changes in SOC stocks and leaf litter traits after long\uffe2\uff80\uff90term ecological intensive (e.g. OF) vs. CF comparisons.
Our global meta\uffe2\uff80\uff90analysis showed that the positive OF\uffe2\uff80\uff90effects on soil respiration, SOC stocks, and SOC sequestration rates were significant even in organic farms with low manure application rates. Although fertilization intensity was the main driver of OF\uffe2\uff80\uff90effects on SOC, leaf and root N concentrations also played a significant role. Across the six European sites, changes towards higher leaf litter N in CF also promoted lower SOC stocks.
Our results highlight that crop species displaying traits indicative of resource\uffe2\uff80\uff90acquisitive strategies (e.g. high leaf and root N) increase the difference in SOC between OF and CF. Indeed, changes towards higher crop residue decomposability was related with decreased SOC stocks under CF across European sites.
Synthesis and applications. Our study emphasizes that, with management, changes in crop residue traits contribute to the positive effects of organic farming (OF) on soil carbon sequestration. These results provide a clear message to land managers: the choice of crop species, and more importantly their functional traits (e.g. leave and root nitrogen), should be considered in addition to management practices and climate, when evaluating the potential of OF for climate change mitigation.
", "keywords": ["SOC sequestration", "0301 basic medicine", "Organic farming", "Resource economics traits", "Soil Science", "Ecological intensification", "[SDV.SA.SDS]Life Sciences [q-bio]/Agricultural sciences/Soil study", "Markvetenskap", "630", "Soil quality", "climate change mitigation", "Climate change mitigation", "03 medical and health sciences", "ecological intensification", "organic farming", "[SDE.ES] Environmental Sciences/Environment and Society", "Crop residue", "soil carbon stocks", "'Organics' in general", "[SDE.ES]Environmental Sciences/Environment and Society", "[SDV.SA.SDS] Life Sciences [q-bio]/Agricultural sciences/Soil study", "580", "2. Zero hunger", "leaf nitrogen", "04 agricultural and veterinary sciences", "15. Life on land", "resource economics traits", "meta-analysis", "[SDE.BE] Environmental Sciences/Biodiversity and Ecology", "Meta-analysis", "crop residue", "13. Climate action", "crop traits", "0401 agriculture", " forestry", " and fisheries", "[SDE.BE]Environmental Sciences/Biodiversity and Ecology", "Leaf nitrogen", "Soil carbon stocks"]}, "links": [{"href": "https://doi.org/10.1111/1365-2664.13113"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Applied%20Ecology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/1365-2664.13113", "name": "item", "description": "10.1111/1365-2664.13113", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/1365-2664.13113"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-15T00:00:00Z"}}, {"id": "10.1111/1365-2664.14641", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-04-03T16:19:47Z", "type": "Journal Article", "created": "2024-04-25", "title": "Heathland management affects soil response to drought", "description": "Abstract
Drought can affect ecosystem functioning by altering plant\uffe2\uff80\uff93soil interactions, posing a significant threat to vulnerable ecosystems like heathlands. In heathlands, ongoing nitrogen deposition increases the dominance of fast\uffe2\uff80\uff90growing grasses over the slow\uffe2\uff80\uff90growing shrub Calluna vulgaris. These changes above\uffe2\uff80\uff90ground can influence soil dynamics and heathlands' responses to drought. Here, we assessed whether the legacy effects of drought on heathland soils depended on mowing times as a management practice commonly used to regenerate Calluna and decrease the abundance of fast\uffe2\uff80\uff90growing grasses.
Using a long\uffe2\uff80\uff90term field experiment, we investigated if soil response to drought differed under Calluna and grasses, as well as under Calluna plants of different growth stages through different mowing times. We hypothesized that drought would decrease soil C and nutrient pools underneath grasses and younger Calluna plants through its impact on soil microbial communities.
Our results show that long\uffe2\uff80\uff90term drought decreased soil C but only underneath grasses and old Calluna, while under young Calluna, soil C increased under drought when compared to control conditions. Bacterial and fungal community composition differed between drought and control and were affected by the growth stage of Calluna but not by plant growth strategies. Furthermore, drought and Calluna growth stage\uffe2\uff80\uff90induced changes in bacterial communities directly affected total soil C and indirectly by reducing microbial C, which was positively related to total soil C.
Synthesis and applications. Understanding ecosystem response to drought is crucial for maintaining biodiversity and mitigating climate change feedbacks. Heathlands are threatened by high nitrogen deposition, a lack of management and an increasing frequency of drought. Our results emphasize the importance of frequent mowing (decadal) as a management practice that promotes a younger and more Calluna\uffe2\uff80\uff90dominated plant community for reducing soil C losses under future climate change\uffe2\uff80\uff90induced drought conditions. The active management of heathlands is essential not only for keeping above\uffe2\uff80\uff90ground vegetation dynamics, but also for maintaining below\uffe2\uff80\uff90ground soil nutrient and carbon pools.