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Pushing the limits of C3 intrinsic water use efficiency in Mediterranean semiarid steppes: responses of a drought-avoider perennial grass to climate aridification
<ol> <li>Intrinsic water use efficiency (WUEi) reflects the trade-off between photosynthetic carbon gain and water loss through stomatal conductance and is key for understanding dryland plant responses to climate change. <em>Stipa tenacissima</em> is a perennial tussock C<sub>3</sub> grass with an opportunistic, drought-avoiding water use strategy that dominates arid and semiarid steppes across the western Mediterranean region. However, its ecophysiological responses to aridification and woody shrub encroachment, a major land-use change in drylands worldwide, are not well understood.</li> <li>We investigated the variations in leaf stable isotopes (δ<sup>18</sup>O, δ<sup>13</sup>C, δ<sup>15</sup>N), nutrient concentrations (N, P, K), and culm water content and isotopic composition (δ<sup>18</sup>O, δ<sup>2</sup>H) of paired pure-grass and shrub-encroached <em>S. tenacissima</em> steppes along a 350 km aridity gradient in Spain (10 sites, 160 individuals). </li> <li>Culm water isotopes revealed that <em>S. tenacissima</em> is a shallow-rooted grass that depends heavily on recent rainwater for water uptake, which may render it vulnerable to increasingly irregular rainfall combined with faster topsoil drying under climate warming and aridification. With increasing aridity, <em>S. tenacissima</em> enhanced leaf-level WUEi through more stringent stomatal regulation of plant water flux and carbon assimilation (higher δ<sup>13</sup>C and δ<sup>18</sup>O), reaching exceptionally high δ<sup>13</sup>C values (-23 to -21‰) at the most arid steppes. Foliar N concentration was remarkably low across sites regardless of woody shrub encroachment, evidencing severe water and N co-limitation of photosynthesis and productivity. Shrub encroachment decreased leaf P and K but did not affect <em>S. tenacissima</em> water status. Perennial grass cover decreased markedly with both declining winter rainfall and shrub encroachment suggesting population- rather than individual-level responses of <em>S. tenacissima</em> to these changes.</li> <li>The fundamental physiological constraints of photosynthetic C<sub>3</sub> metabolism combined with low foliar N content may hamper the ability of <em>S. tenacissima</em> and other drought-avoider species with shallow roots to achieve further adaptive improvements in WUEi under increasing climatic stress. A drought-avoiding water use strategy based on early stomatal closure and photosynthesis suppression during prolonged rainless periods may thus compromise the capacity of <em>S. tenacissima</em> steppes to maintain perennial grass cover, sustain productivity and cope with ongoing climate aridification at the drier parts of their current distribution. </li> </ol>
Environmental context shapes the relationship between grass consumption and body size in African herbivore communities
<p>Though herbivore grass dependence has been shown to increase with body size across herbivore species, it is unclear whether this relationship holds at the community level. Here we evaluate whether grass consumption scales positively with body size within African large mammalian herbivore communities and how this relationship varies with environmental context. We used stable carbon isotope and community occurrence data to investigate how grass dependence scales with body size within 23 savanna herbivore communities throughout eastern and central Africa. We found that dietary grass fraction increased with body size for the majority of herbivore communities considered, especially when complete community data were available. However, the slope of this relationship varied, and rainfall seasonality and elephant presence were key drivers of the variation—grass dependence increased less strongly with body size where rainfall was more seasonal and where elephants were present. We found also that the dependence of the herbivore community as a whole on grass peaked at intermediate woody cover. Intraspecific diet variation contributed to these community-level patterns: common hippopotamus (<em>Hippopotamus amphibius</em>) and giraffe (<em>Giraffa camelopardalis</em>) ate less grass where rainfall was more seasonal, whereas Cape buffalo (<em>Syncerus caffer</em>) and savanna elephant (<em>Loxodonta africana</em>)<strong> </strong>grass consumption were parabolically related to woody cover. Our results indicate that general rules appear to govern herbivore community assembly, though some aspects of herbivore foraging behavior depend upon local environmental context.</p>
Allometric relationships and trade-offs in eleven common Mediterranean-climate grasses
<p>Release for EA final submission</p>
Nitrogen and phosphorus availability alter tree-grass competition intensity in savannas
<p>Plant essential macronutrients like nitrogen (N) and phosphorus (P) can limit savanna tree growth and are important determinants of savanna vegetation dynamics, along with rainfall, fire, and herbivory. How nitrogen and phosphorus shape tree-grass competition and their coexistence remain unclear, hindering our ability to predict how savannas may respond to altered nutrient cycling.</p> <p>Here, we evaluate (1) if trees and grasses respond differently to N vs. P availability, or (2) if grasses are more competitive in low nutrient environments while trees are more competitive in high nutrient environments. To do this, we grew saplings of 6 tree and 1 grass species from Kruger National Park, South Africa, for 16 weeks under fully factorial nutrient and competition treatments (with/without competitors, low/high rate of N supply, and low/high rate of P supply) under a watering regime designed to mimic wet season rainfall in a mesic savanna.</p> <p>Trees and grasses foraged most aggressively for nitrogen and allocated biomass differently depending on nitrogen availability. Overall, tree growth decreased in competition with grass, even in high nutrient environments where they grew faster. Grasses were always better belowground competitors, utilizing aggressive nutrient foraging strategies, including high root phosphatase activity in response to nitrogen and large root biomass allocation.</p> <p><em>Synthesis:</em> In low nutrient environments (e.g., on nutrient-poor sandy soils), nutrients may limit tree growth. Nutrient rich environments enable tree growth, but grasses continue to compete effectively with trees. Understanding what this means for ecosystem responses to nutrient availability is not trivial, especially in the context of fire and herbivory. However, it is clear that soil nutrients likely affect tree and grass growth and competition in savannas, which suggests that future changes in nutrient cycling, such as N deposition, may have important effects on savanna vegetation.</p>
Data from: Nitrogen niche partitioning between tropical legumes and grasses conditionally weakens under elevated CO2
<p>Plant community biodiversity can be maintained, at least partially, by shifts in species interactions between facilitation and competition for resources as environmental conditions change. These interactions also drive ecosystem functioning, including productivity, and can promote over-yielding- an ecosystem service prioritized in agro-ecosystems, such as pastures, that occurs when multiple species together are more productive than the component species alone. Importantly, species interactions that can result in over-yielding may shift in response to rising CO<sub>2</sub> concentrations and changes in resource availability, and the consequences these shifts have on production is uncertain especially in the context of tropical mixed-species grasslands.</p> <p>We examined the relative performance of two species pairs of tropical pasture grasses and legumes growing in monoculture and mixtures in a glasshouse experiment manipulating CO<sub>2</sub>. We investigated how over-yielding can arise from nitrogen (N) niche partitioning and biotic facilitation using stable isotopes to differentiate soil N from biological N fixation (BNF) within N acquisition into aboveground biomass for these two-species mixtures.</p> <p>We found that N niche partitioning in species-level use of soil N vs. BNF drove species interactions in mixtures. Importantly partitioning and overyielding were generally reduced under elevated CO<sub>2</sub>. However, this finding was mixture-dependent based on biomass of dominant species in mixtures and the strength of selection effects for the dominant species.</p> <p>This study demonstrates that rising atmospheric CO<sub>2</sub> may alter niche partitioning between co-occurring species, with negative implications for the over-yielding benefits predicted for legume-grass mixtures in working landscapes with tropical species. Furthermore, these changes in inter-species interactions may have consequences for grassland composition that are not yet considered in larger-scale projections for impacts of climate change and species distributions. </p>
Data for: Shifts in grasses diversity patterns between two contrasting 40-year climate periods in tropical dry islands
<p><span>Grasses are one of the most successful and dispersed plant families worldwide and their environmental and economic values are widely acknowledged. They dominate the landscape of Cabo Verde, the southernmost and driest archipelago of Macaronesia, and are relevant natural resources for local populations, but a comprehensive evaluation of their distribution patterns is still lacking. In this study, we aim to evaluate the potential effects of climate changes using the long-term data concerning grass distribution in Cabo Verde and the widely recognized climatic variability of this archipelago, which entails a huge irregularity in spatial and temporal rainfall. We identified two contrasting climatic periods (wet, from 1929 to 1968, and dry, from 1969 to 2007) and gathered all the information available from the bibliography, herbaria and fieldwork concerning spontaneous grass species recorded in Cabo Verde during those two periods, which amounted to 107 taxa. This information was then used to disclose the patterns of grass diversity as related to climatic and topographic variables (altitude and windward vs leeward aspects). Different altitudinal shifts in the distribution patterns of grass species assemblages and an assemblage specific to the wet period were revealed by comparing the two climatic periods. The role of exposure in delimiting the altitudinal distribution of the various assemblages was highlighted; the trade winds clearly determine the distribution of grass assemblages. We detected shifts in the distribution of grass assemblages according to the climatic periods (related to the macroclimate) and local topographic factors (associated with mesoclimates). Also, functional traits (i.e., annuals vs. perennials, C3 vs. C4 grasses, and tropical vs. temperate species) were found to vary between wet and dry periods, as well as with altitude and with slope aspect. Understanding species distributions and the role of the climatic variability of Cabo Verde is crucial to predict how climate change will affect them and thus to support effective management and conservation actions.</span></p>
Dataset for the SFmodel, applied in Evapotranspiration dynamics and partitioning in a grassed vineyard: ecophysiological and computational modelling approaches
<p>Dataset used for the SFmodel, applied in the work "Evapotranspiration dynamics and partitioning in a grassed vineyard: ecophysiological and computational modelling approaches".</p> <p>For units and nomenclature of the variables refer to Units_and_Nomenclature_for_SFmodel_in_Evapotranspiration_dynamics_and_partitioning_in_a_grassed_vineyard.pdf. </p>
Dataset for Evapotranspiration dynamics and partitioning in a grassed vineyard: ecophysiological and computational modelling approaches
<p>Data sets of the work "Evapotranspiration dynamics and partitioning in a grassed vineyard: ecophysiological and computational modelling approaches".</p> <p>You will find all data files needed for this work, organised by the figures of the paper. For the codes, refer to Flavio Bastos Campos. (2024). flaviobastoscampos/ET_dynamics_and_partitioning_vineyard: v2024.1 (v2024.1). Zenodo. <a href="https://doi.org/10.5281/zenodo.10864169" target="_blank" rel="nofollow noopener">https://doi.org/10.5281/zenodo.10864169</a>. </p>
Fig. 8 in The first record of the Far Eastern grass-carrying wasp Isodontia nigella (F. Smith, 1856) (Hymenoptera: Sphecidae: Sphecinae) from the Crimea
Fig. 8. Opened nests of Isodontia nigella (F. Smith, 1856) in reed canes. Scale bar = 1 cm.
Climatic adaptation and phylogenetic history shape the intra-specific variation of CSR strategies in a widespread grass
<p>Data and R script for the paper entitled "Climatic adaptation and phylogenetic history shape the intra-specific variation of CSR strategies in a widespread grass".</p>
Effects of Grass Cover on the Overland Soil Erosion Mechanism under Simulated Rainfall
<p><span>Grass cover has a complex influence on overland soil erosion. This study quantified the impact of grass cover on overland soil erosion using a dimensionless water flow path index. It systematically analyzed the response mechanism among overland soil erosion, slope gradient, rainfall intensity, and hydrodynamic parameters, aiming to identify the optimal hydrodynamic parameters capable of characterizing overland soil erosion. A predictive model for soil erosion was constructed based on general dimensionless water flow intensity parameters, comprehensively evaluating the mechanism of soil erosion on grass-covered overland under simulated rainfall conditions. The results indicate that the model constructed using dimensionless parameters exhibits strong adaptability and can be effectively validated in other experiments.</span></p>
Above and belowground plant traits of dominant dune grasses from Duck, Outer Banks, USA
<p>We examined above and belowground traits among four prominent dune grasses of the Atlantic and Gulf Coasts of North America: <i>Ammophila breviligulata</i>, <i>Panicum amarum</i>, <i>Spartina patens</i>, and <i>Uniola paniculata</i>. Whole plant samples of each species were collected from the foredune at the US Army Engineer Research and Development Center's Field Research Facility in Duck, North Carolina, USA and quantified for several above and belowground traits (e.g., stem height, rhizome number and length, root surface area by diameter class, root tensile strength, mycorrhizal percent infection).</p>
Local male breeding density affects extra‐pair paternity in a south temperate population of grass wrens Cistothorus platensis
<p>Demographic factors can affect the frequency of extra-pair paternity (EPP) in birds, as the distribution and availability of potential mates in both space and time influence the rate of encounters between females and males. Over three breeding seasons, we intensively studied the breeding system of a south temperate population of grass wrens <i>Cistothorus platensis</i> by genotyping 73 broods (319 nestlings) and estimating EPP rates for those broods. Using five different radii (80, 160, 240, 320, and 400 m) around each nest with assigned paternity, we examined the effects of local breeding synchrony, male breeding density, and adult sex ratio (ASR) on the EPP rate. The majority of extra-pair offspring (~80%) were sired by neighboring males. Neither local breeding synchrony nor ASR consistently explained the EPP rate variation as their effects were only statistically significant within 320 m and 400 m. However, the EPP rate increased as the local male breeding density increased within every radius category, strongly suggesting that neighboring male abundance might play an important role in the extra-pair mating behavior in this species. Our study also highlights the relevance of using a local scale approach when studying mating behavior.</p>
Fire, grazers and browsers interact with grass competition to determine tree establishment in an African savanna
<p>In savanna ecosystems, fire and herbivory alter the competitive relationship between trees and grasses. Mechanistically, grazing herbivores favor trees by removing grass, which reduces tree-grass competition and limits fire. Conversely, browsing herbivores consume trees and limit their recovery from fire. Herbivore feeding decisions are in turn shaped by risk-resource trade-offs that potentially determine the spatial patterns of herbivory. Identifying the dominant mechanistic pathways by which fire and herbivores control tree cover remains challenging, but is essential for understanding savanna dynamics. We used an experiment in the Serengeti ecosystem and a simple simulation driven by experimental results to address two main aims: (1) determine the importance of direct and indirect effects of grass, fire and herbivory on seedling establishment; and (2) establish whether predators determine the spatial pattern of successful seedling establishment via effects on mesoherbivore distribution. We transplanted tree seedlings into plots with a factorial combination of grass and herbivores (present/absent) across a lion kill-risk gradient in the Serengeti, burning half of the plots near the end of the experiment. Ungrazed grass limited tree seedling survival directly via competition, indirectly via fire, and by slowing seedling growth, which drove higher seedling mortality during fires. These effects restricted seedling establishment to below 18% and, in conjunction with browsing, resulted in seedling establishment dropping below 5%. In the absence of browsing and fire, grazing drove a 7.5-fold increase in seedling establishment. Lion predation risk had no observable impact on herbivore effects on seedling establishment. The severe negative effects of grass on seedling mortality suggests that regional patterns of tree cover and fire may overestimate the role of fire in limiting tree cover, with regular fires representing a proxy for the competitive effects of grass.</p>
GRASS GIS Location for South-East US urban growth case study
<p>GRASS GIS Location containing data prepared for a FUTURES urban growth modeling case study for the South East United States (NC, SC, TN, GA, AL, FL). Contains NLCD 2001-2019 (land cover for all years; 2001 and 2019 impervious descriptor), county boundaries, USGS DEM, PAD-US protected areas.</p>
South-East US historical and projected population per county for FUTURES urban growth modeling in GRASS GIS
<p>South East US historical (2001-2019) and projected (2020-2100) population per county for 6 states (NC, SC, TN, GA, AL, FL). Historical data come from The National Vital Statistics System (https://seer.cancer.gov/popdata/download.html) and future data are projected by Hauer 2019 (https://doi.org/10.1038/sdata.2019.5) for SSP2 scenario. Data are formatted for r.futures.demand module, which is a GRASS GIS addon for computing future land demand for FUTURES urban growth model. </p>
Grazing lawns and overgrazing in frequently grazed grass communities
<p>Frequent grazing can establish high forage value grazing lawns supporting high grazer densities, but can also produce overgrazed grass communities with unpalatable or low grass basal cover, supporting few grazers. Attempts to create grazing lawns via concentrated grazing, with a goal to increase grazer numbers, are thus risky without knowing how environmental conditions influence the likelihood of each outcome.</p> <p>We collected grass species and trait data from 33 frequently grazed grass communities across eastern South Africa (28 sites) and the Serengeti National Park, Tanzania (5 sites), covering wide rainfall (336–987 mm.yr-1) and soil (e.g. 44–93% sand) gradients. We identified four grass growth forms using hierarchical clustering on principal components analyses of trait data, and assessed trait-environment and growth form-environment relationships using fourth corner and principal components analyses.</p> <p>We distinguished two palatable grass growth forms that both attract yet resist grazers, and comprise grazing lawns: 1) 'lateral attractors' that spread vegetatively via stolons and rhizomes, and 2) 'tufted attractors' that form isolated tufts, and may have alternate tall growth forms. By contrast, 3) tough, upright, tufted 'resisters', and 4) 'avoiders' with sparse architectures or that grow appressed to the soil surface, are of little forage value and avoided by grazers.</p> <p>Grazing lawns occurred across a wide range of conditions, typically comprising lateral attractor grasses in drier, sandy environments, and tufted attractor grasses in wetter, low-sand environments. Resisters occurred on clay-rich soils in mesic areas, while avoiders were widespread but scarce.</p> <p>While grazing lawns can be established under most conditions, monitoring their composition and cover is important, as the potential for overgrazing seems as widely relevant. Tufted attractor-dominated lawns appear somewhat more vulnerable to degradation than lateral attractor-dominated lawns. Increased avoider or resister abundance both reduce forage value, although resisters may provide better soil protection.</p>
Supplementary data for: Hybridisation has shaped a recent radiation of grass-feeding aphids
<p><strong>Orthogroups and species tree</strong></p> <p>Proteomes included in the analysis: proteomes.tar.gz<br> Orthogroups: Orthogroups.txt<br> Gene counts per orthogroup, per species: Orthogroups.GeneCount.tsv<br> Single copy conserved orthogroups used for species tree: Orthogroups_SingleCopyOrthologues.txt<br> Protein alignment used for species tree reconstruction: SpeciesTreeAlignment.fa<br> Species tree: SpeciesTree_rooted.txt</p> <p><strong>Whole genome alignment of <em>S. avenae</em>, <em>S. miscanthi,</em> <em>M. dirhodum</em> and <em>A. pisum</em></strong></p> <p>Cactus whole genome alignment (hal format): Siave_Simis_Medir_Acpis.hal.gz</p> <p><strong>Haplotype divergence analysis (whole genome sequences)</strong></p> <p>VCF files of HapCUT2 phased variants for <em>S. miscanthi </em>Langfang-1 chromosomes (Simis_v2 assembly scaffolds 1 to 9):<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_1.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_2.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_3.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_4.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_5.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_6.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_7.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_8.hap.phased.VCF.gz<br> Langfang1.Hapcut2_PB_plus_HiC.scaffold_9.hap.phased.VCF.gz</p> <p>VCF files of HapCUT2 phased variants for <em>S. avenae </em>JIC1<em> </em>chromosomes (Siave_v2.1 assembly scaffolds 1 to 9):<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_1.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_2.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_3.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_4.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_5.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_6.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_7.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_8.hap.phased.VCF.gz<br> JIC1.Hapcut2_IL_plus_HiC.scaffold_9.hap.phased.VCF.gz</p> <p>Haplotype resolved assemblies of <em>S. avenae</em> JIC1 and <em>S. miscanthi </em>Langfang-1 based on HapCUT2 phasing results:<br> JIC1_H1.Hapcut2.fa<br> JIC1_H2.Hapcut2.fa<br> Langfang1_H1.Hapcut2.fa<br> Langfang1_H2.Hapcut2.fa</p> <p>SibeliaZ whole genome alignment of <em>S. avenae </em>JIC1 and <em>S. miscanthi </em>Langfang-1 haplotypes: alignment.filtered.ordered.stranded.sorted.maf</p> <p><strong>Filtered VCF files used for population genomics analysis</strong></p> <p><em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1 and Langfang1 WGS samples variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.vcf<br> <em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1 and Langfang1 WGS samples phased variant calls: freebayes.q30_dp2_biallelic.mm_75.indv_max_30pc_missing.recode.fix_mis.beagle.vcf<br> <em>S. avenae</em> and <em>S. miscanthi</em> GBS samples + JIC1, Langfang1 and <em>M. dirhodum </em>WGS samples variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.vcf<br> <em>S. avenae</em> and <em>S. miscanthi </em>GBS samples + JIC1, Langfang1 and <em>M. dirhodum</em> WGS samples phased variant calls: with_Medir.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf<br> <em>S. miscanthi </em>GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.vcf<br> <em>S. miscanthi </em>GBS samples + JIC1 and Langfang1 WGS samples variant calls: China_plus_JIC1.merged.q30_dp2_biallelic.mm_90.recode.fix_mis.beagle.vcf</p> <p><strong>SNAPP phylogenetic analysis configuration file and trees</strong></p> <p>SNAPP configuration file: snapp.xml<br> SNAPP log file: ut.log<br> SNAPP posterior sample of trees: ut.trees<br> SNAPP maximum clade credibility tree with 10% burn in: ut.trees.max_cred_burn_10pc</p> <p> </p> <p> </p>
Differential methylation patterns in apomictic vs. sexual genotypes of the diplosporous grass Eragrostis curvula.
<p>Methylation is an epigenetic mechanism where a methyl group take place over the C5 of cytosine or C6 of adenine repressing or de-repressing genes depending on the context, position (coding or non-coding) and species. Eragrostis curvula is a forage grass that reproduces by apomixis. Increases of the frequency of sexual pistils in facultative genotypes of this grass has been associated to epigenetic changes triggered by different biotic and abiotic stresses. The aim of the present study was to associate differences in the reproductive mode with specific methylated regions and genes contrasting full apomictic, facultative and sexual genotypes using the methylation sensitive technique MCSeEd. The distribution of the differentially methylated positions over the genes shows a peak around the start and stop codon boundaries, hence regulating gene expression mainly through the incorporation of methyl groups on these positions. The main pathways being regulated were ubiquitin and auxins. The methylation pathway itself was also found to be self-regulated since ROS1 and ROS4, the main demethylating genes were found differentially methylated among the different genotypes. Even more, this work allowed us to detect genes regulated by methylation that were previously found differentially expressed in the comparisons between apomictic and sexual genotypes.</p>
Data from: Drought mitigates negative effects of natural microbiomes in grasses
<p><strong>Abstract:</strong> Research suggests that soil microbes, specifically arbuscular mycorrhizal fungi (AMFs), can help mitigate plant drought stress, but their beneficial effects on grasses are unclear. Here we test the hypothesis that soil microbes alleviate drought's negative effects on grass growth. In a greenhouse experiment, we used natural microbial inocula and eight grass species from various positions along an ecological succession gradient. Under normal watering, live soil communities decreased grass biomass, indicating a net pathogenic effect. However, this negative effect was reduced under drought compared to well-watered conditions. Amplicon sequencing revealed a significant impact of drought on rhizosphere microbial communities, particularly fungi. However, we found no evidence linking AMFs to drought stress alleviation in grasses. Our study suggests that drought reduces the negative effects of soil microbes on grass performance, regardless of successional positions. Our results also indicate that the beneficial effects of AMFs under drought are not universal, and soil biota's role in shaping plant-soil feedbacks may be less pronounced under drought conditions.</p> <p><strong>Data sets description:</strong></p> <ul> <li>Plant biomass_final.xlsx: The experiment was performed in a climatised greenhouse at 16/8 h light/dark and 20/15 °C Day/night conditions. In each pot, three plants were planted in monocultures according to a full randomized block design with eight blocks, 2 watering levels (control, drought), 2 inoculum types (agricultural, late-successional), 2 microbial conditions (sterilized, live) and 8 grass species. Each block contained one replicate of the treatment groups for a total of 64 pots per block. During the first four weeks of the experiment, the soil moisture content of all pots was maintained at 15% (w/w) by watering 2 times per week the pots to compensate unequal losses. After four weeks, we applied the drought treatment where half of the pots were maintained at 7.5% (w/w) by watering the pots to weight for three weeks.<br>After seven weeks of plant growth, shoots were clipped, dried at 60 °C until constant weight, and weighed, whereas roots were first washed and then dried at 60 °C, and weighed to determine biomass.</li> <li>Bacteria data.xlsx: The raw 16S sequence reads were processed using Dada2 (v. 1.12) (Callahan et al. 2016) using default parameters. SILVA (v.132) database was used to classify bacteria. All reads not belonging to bacterial or fungal kingdoms were excluded from the datasets. The analysis was conducted excluding the samples that had "sterilized" microbial treatment (see sample data).</li> <li>Fungi data.xlsx: The raw ITS sequence reads were processed using Pipits (v. 2.3) pipeline (Gweon et al. 2015) using default parameters. The UNITE (v. 8.0;) database (Abarenkov et al. 2010) was used for the identification of fungi, and the ITSx extractor was used to extract fungal ITS regions. The classification of fungal operational taxonomic units (OTUs) into potential functions was done using FUNGuild (v.1.1.; (Nguyen et al. 2016) and the assignment was further curated using an in-house database (Hannula et al. 2017). The OTUs were grouped into saprotrophs, plant pathogens, plant endophytes and others (i.e., fungal/animal-plant pathogens). Multiple assignments were included in case of uncertain fungal guilds. All reads not belonging to fungal kingdoms were excluded from the datasets. When analyzing fungi, the genus Penicillum was identified as a suspected contaminant in some samples and thus it was excluded from the analysis. SILVA (v.132) database was used to classify bacteria whereas the UNITE (v. 8.0;) database (Abarenkov et al. 2010) was used for the identification of fungi, and the ITSx extractor was used to extract fungal ITS regions. The classification of fungal operational taxonomic units (OTUs) into potential functions was done using FUNGuild (v.1.1.; (Nguyen et al. 2016) and the assignment was further curated using an in-house database (Hannula et al. 2017). The OTUs were grouped into saprotrophs, plant pathogens, plant endophytes and others (i.e., fungal/animal-plant pathogens). Multiple assignments were included in case of uncertain fungal guilds. All reads not belonging to bacterial or fungal kingdoms were excluded from the datasets. When analyzing fungi, the genus Penicillum was identified as a suspected contaminant in some samples and thus it was excluded from the analysis. The classification of fungal operational taxonomic units (OTUs) into potential functions was done using FUNGuild (v.1.1.; (Nguyen et al. 2016) and the assignment was further curated using an in-house database (Hannula et al. 2017). The OTUs were grouped into saprotrophs, plant pathogens, plant endophytes and others (i.e., fungal/animal-plant pathogens). Multiple assignments were included in case of uncertain fungal guilds. All reads not belonging to bacterial or fungal kingdoms were excluded from the datasets. When analyzing fungi, the genus Penicillum was identified as a suspected contaminant in some samples and thus it was excluded from the analysis. The OTUs were grouped into saprotrophs, plant pathogens, plant endophytes and others (i.e., fungal/animal-plant pathogens). Multiple assignments were included in case of uncertain fungal guilds. All reads not belonging to bacterial or fungal kingdoms were excluded from the datasets. When analyzing fungi, the genus Penicillum was identified as a suspected contaminant in some samples and thus it was excluded from the analysis.<br>The genus Penicillum was identified as a suspected contaminant in some samples and thus it was excluded from the analysis. The analysis was conducted excluding the samples that had "sterilized" microbial treatment (see sample data).</li> </ul>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.