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298 results for “plant richness”
Plant richness of the terrestrial ecoregions of the world with a mean aridity index lower than 0.65
<p>Data used to compose the <strong>Figure 1</strong> and the <strong>Table S1</strong> of the paper <strong>Biogeography of Global Drylands</strong>, by Maestre <em>et al</em>. (2021).</p>
Species cover, community biomass, and richness in global grasslands from NutNet (2007–2023): Dominant species predict plant richness and biomass in global grasslands
The Nutrient Network (NutNet) is a globally coordinated research initiative designed to investigate the impacts of human-driven alterations in nutrient availability and consumer presence on grassland ecosystems. Data were collected from over 130 herbaceous-dominated sites worldwide, spanning diverse environmental conditions from desert grasslands to arctic tundra. Standardized methodologies were employed across all sites to enable direct comparisons of productivity, diversity, and ecosystem responses. Experimental treatments included nutrient additions to assess co-limitation of plant growth by multiple nutrients, as well as grazer manipulations to examine their role in regulating biomass, species diversity, and community composition. By compiling these cross-site data, NutNet aims to enhance our understanding of productivity-diversity relationships and provide new insights into the ecological consequences of anthropogenic changes to nutrient cycles and food webs at a global scale.
Species richness of vascular plants and bryophytes in nine grassland sites (Europe and California collected in 2013-2016)
We sampled vascular plants (VP) and bryophytes (non-vascular plant; NVP) 1×1 m experimental plots in nine sites belonging to the Nutrient Network. Three sites were in California, two in Finland and UK and one in Germany and Switzerland. The data were collected to compare the responses of NVPs and VPs to nutrient addition and grazing exclusion treatments. The NVP and VP cover sampling was conducted in March-August 2016, except for heron.uk and rook.uk, which had been sampled for VPs in 2013. NVPs were mostly identified to species, but in absence of necessary diagnostic characters (capsules, other reproductive organs, distinctive gametophytic features), some specimens were identified at morphospecies group, subgenus, or genus level. We calculated three plant diversity indices for NVPs, VPs and total (NVPs and VPs combined) in each plot. First, species richness (S) is the number of species per 1 m2 for NVPs and VPs. For plots having no NVPs, NVP richness is zero. Second, for plots having at least one NVP, we calculated Inverse Simpson’s index of diversity (referred to as species diversity), which is equivalent to the Probability of Interspecific Encounter or Effective Number of Species (ENSPIE). Third, we calculated Simpson’s evenness (E = ENSPIE/S; referred to as evenness), which was expected to reflect changes in species’ dominance. We also sampled aboveground plant biomass at peak biomass of vascular plants (in May- August, depending on local site level characteristics) by clipping at ground level and removing all aboveground vegetation (live and dead) from two 0.1 × 1 m strips, sorting the current year’s VP and NVP biomass from the previous year’s biomass (dead litter), drying the biomass to a constant mass at 60 °C, and weighing it to the nearest 0.01 g. Except for two sites (heron.uk and rook.uk), we also measured photosynthetically active radiation (PAR) at the ground surface and above grassland canopy at time of peak biomass and calculated the proportion of tra
PRP02 Plant diversity, richness, and plant species cover in konza prairie restoration heterogeneity plots, since 1998
The experiment is a randomized complete block design with four whole plot hetereogeneity treatments replicated within each of four blocks (n=16 whole plots). The whole plot treatments were created using different combinations of soil depth and nutrient manipulations. The control plots contained no depth or nutrient manipulations. The maximum hetereogeneity plots contained three 2 m x 8 m vertical strips assigned to ambient, enriched and reduced N treatments and four 2 m x 6 m horizontal strips assigned to deep and shallow soil to result in six treatment combinations. The maximum heterogeneity plots are a split-block design. Every plot contained 12 subplots (2 m x 2 m) for sampling. Prior to sowing, all of the plots were excavatedto a depth of approximately 25 cm. Natural limestone slabs were laid in strips assigned to the shallow soil treatment. The soil from all plots was then replaced, leveled, and disked (2-3 cm deep). In February 1998, we incorporated sawdust (49% C; C:N ratio=122) into the strips assigned to the reduced-N treatment. The average C concentration and bulk density in the surface 15 cm following long-term cultivation was 1.5% and 1.2 g cm-3, respectively. Sawdust was tilled into the soil at a rate of 5.5 kg dry wt./m2 to achieve a C concentration representative of native prairie soil (approx. 3% C). Surface applications of granular sugar were initiated in 2004 at a rate of 200 g sucrose m-2 (84.22 g C/m2) 3-4 times each growing season. Strips assigned to the enriched-N treatment were fertilized with 5 g N m2/y (applied as ammonium-nitrate) in July of the first growing season and early June of each subsequent years.
Plant richness survey of mainland, barrier island and back-barrier hammock island locations around Sapelo Island and St. Simons Island, Georgia, in June-July 2005
I conducted a plant richness survey of 59 sites around Sapelo Island and St. Simons Island, Georgia, in June-July 2005. Sites were chosen to include a range of mainland, barrier island, and back-barrier hammock island locations. All sites were dominated by salt marsh plant species, primarily Spartina alterniflora. To provide a general indication of the salinity conditions prevailing at each site, I measured salinity of the nearest body of water with a refractometer on the date that the site was sampled. Plant richness was documented along a single 5.0m wide transect at each site. Each transect began at the lower elevational limit of vegetation and continued perpendicular to the water's edge to the shrub community at the upper marsh border. Plant presence was noted in a series of nested subplots within a 1.0m x 5.0m plot at each meter along the transect. The results posted here are sites, position, salinity, and the site pool, or species encountered at the site.
Plant richness survey of mainland and barrier island locations along the Texas Gulf Coast in April and May 2005
I conducted a plant richness survey of 49 sites on the Texas Gulf Coast in the Spring (April-May) of 2005. Sites were chosen to include a range of mainland and barrier island locations. All sites were dominated by salt marsh plant species, primarily Spartina alterniflora. To provide a general indication of the salinity conditions prevailing at each site, I measured salinity of the nearest body of water with a refractometer on the date that the site was sampled. Plant richness was documented along a single 5.0m wide transect at each site. Each transect began at the lower elevational limit of vegetation and continued perpendicular to the water’s edge to the shrub community at the upper marsh border. Plant presence was noted in a series of nested subplots within a 1.0m x 5.0m plot at each meter along the transect. The results posted here are sites, position, salinity, and the site pool, or species encountered at the site. This data set is a companion to PLT-GCET-0608, which provides similar data for sites around Sapelo Island, Georgia.
Annotation of Phytozome V12 protein plant sequences using the ragp pipeline for hydroxyproline-rich glycoprotein mining
<p>Hydroxyproline aware annotation of hydroxyproline-rich glycoprotein (HRGP) sequences was performed on sequence data from 62 plant proteomes obtained from Phytozome database (<a href="https://phytozome.jgi.doe.gov/pz/portal.html">https://phytozome.jgi.doe.gov/pz/portal.html</a>, version 12) using the ragp R package (<a href="https://github.com/missuse/ragp">https://github.com/missuse/ragp</a>, version 0.3.0.0001). </p> <p>In each archive a single comma separated value table (.csv) is present along with a README.txt file describing the contents of the corresponding .csv file. The archives are:</p> <p>- phytozome_V12.tar.gz - sequences from 62 plant proteomes (phytozome V12) with a total of 2797062 protein sequences.</p> <p>- phytozome_V12_phobius.tar.gz -<strong> </strong> Signal peptide prediction using Phobius (<a href="http://phobius.sbc.su.se/">http://phobius.sbc.su.se/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_signalp.tar.gz -<strong> </strong> Signal peptide prediction using SignalP 4.1 (<a href="http://www.cbs.dtu.dk/services/SignalP-4.1/">http://www.cbs.dtu.dk/services/SignalP-4.1/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_targetp.tar.gz - Signal peptide prediction using TargetP 1.1 (<a href="http://www.cbs.dtu.dk/services/TargetP/">http://www.cbs.dtu.dk/services/TargetP/</a>) on sequences present in phytozome_V12.tar.gz.</p> <p>- phytozome_V12_predict_hyp.tar.gz - Probability of proline hydroxylation for each proline from 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1).</p> <p>- phytozome_V12_maab.tar.gz - Motif and amino acid bias (MAAB) classification of hydroxyproline-rich glycoproteins performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). The number of predicted hydroxyprolines in each sequence is also indicated (based on predictions provided in phytozome_V12_predict_hyp.tar.gz).</p> <p>- phytozome_V12_scan_ag.tar.gz. - Hydroxyproline aware arabinogalactan motif scan performed on 266135 protein sequences which were predicted to be secreted by a majority vote (using Phobius, SignalP 4.1 and TargetP 1.1). Hydroxyproline predictions are provided in phytozome_V12_predict_hyp.tar.gz. </p> <p>- phytozome_V12_scan_ag_hmmscan.tar.gz - Detection of domains in a subset of protein sequences which were found to contain arabinogalactan motifs (a subset of phytozome_V12_scan_ag.tar.gz).</p> <p>The list of the 62 plant species is provided in phytozome_V12.tar.gz README.txt.</p> <p>For questions contact mdragicevic@ibiss.bg.ac.rs.</p> <p> </p> <p> </p>
Dataset Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere
<p>This dataset is related to the paper "<strong>Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial <em>Pseudomonas </em>in the wheat rhizosphere</strong>" (Garrido-Sanz et al., 2023, doi: 10.1186/s40168-023-01660-5) and contains the data obtained from bacterial competition asays and plant-growth measurements.</p> <p>Sequencing data used in this study has been deposited in the NCBI Sequence Read Archive (RSA) under the BioProject accession number <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA948847">PRJNA948847</a>.</p> <p>The R script used to analyze the data generated in the paper is available at <a href="https://github.com/dgarrs/Pprotegens_proliferation_NatComs">GitHub </a>and <a href="https://doi.org/10.5281/zenodo.8322086">Zenodo</a>.</p>
Projected climate and canopy change lead to thermophilization and homogenization of forest floor vegetation in a hotspot of plant species richness, Berchtesgaden National Park, Bavaria, Germany
Mountain forests are plant diversity hotspots, but changing climate and increasing forest disturbances will likely lead to far-reaching plant community change. Projecting future change, however, is challenging for forest understory plants, which respond to forest structure and composition as well as climate. Here, we jointly assessed effects of both climate and forest change, including wind and bark beetle disturbances, using the process-based simulation model iLand in a protected landscape in the northern Alps (Berchtesgaden National Park, Germany), asking: (1) How do understory plant communities respond to 21st-century change in a topographically complex mountain landscape, representing a hotspot of plant species richness? (2) How important are climatic changes (i.e., direct climate effects) versus forest structure and composition changes (i.e., indirect climate effects and recovery from past land use) in driving understory responses at landscape scales? Stacked individual species distribution models fit with climate, forest, and soil predictors (248 species currently present in the landscape, derived from 150 field plots stratified by elevation and forest development, overall AUC = 0.86) were driven with projected climate (RCP4.5 and RCP8.5) and modeled forest variables to predict plant community change. Nearly all species persisted in the landscape in 2050, but on average 8% of the species pool was lost by the end of the century. By 2100, landscape mean species richness and understory cover declined (-13% and -8%, respectively), warm-adapted species increasingly dominated plant communities (i.e., thermophilization, +12%), and plot-level turnover was high (62%). Subalpine forests experienced the greatest richness declines (-16%), most thermophilization (+17%), and highest turnover (67%), resulting in plant community homogenization across elevation zones. Climate rather than forest change was the dominant driver of understory responses. The magnitude of unabated 2
Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes
Data associated with "Plant community richness and foliar fungicides impact soil Streptomyces inhibition, resistance, and resource use phenotypes" (DOI: 10.3389/fmicb.2024.1452534). These data include soil resource measurements and various phenotypic measurements of associated Streptomyces isolates/populations. Specifically, these data note population level inhibition phenotypes according to Herr's Assays, isolate level antibiotic resistance phenotypes against 9 standard antibiotics, and isolate level resource use phenotypes quantified with Biolog SF-P2 96 well plates.
Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning, though their relationship has not been properly evaluated. We tested whether the genetic and species levels of biodiversity co-vary, using a large-scale and multi-species approach. We chose the high-mountain flora of the Alps and the Carpathians as study systems and demonstrate that species richness and genetic diversity are not correlated. Species richness thus cannot act as a surrogate for genetic diversity. Our results have important consequences for implementing the CBD when designing conservation strategies.
Data from: Plant richness, land use and temperature differently shape invertebrate leaf-chewing herbivory on plant functional groups
<p class="MsoNormal">Nutrient demands of leaf-chewing invertebrate herbivores change with temperature, which causes shifts in herbivores' diets. Temperature may act differently on herbivore species, so that factors shaping herbivore species richness may modulate temperature effects on invertebrate herbivory among plant functional groups with different nutrient composition (C:N ratio low to high: legumes, non-leguminous forbs, grasses). Global warming urges a deeper understanding of temperature effects on herbivory among plant functional groups in different habitats and landscapes. This study obtained measures on proportional leaf area loss to leaf-chewing invertebrate herbivores ('herbivory') on three plant functional groups on 80 plots of open herbaceous vegetation adjacent to different habitat types (forest, grassland, arable field, settlement) along climate and land-use gradients in Bavaria, Germany. Herbivory was analysed with regard to habitat characteristics (habitat type, plant richness at species and family level, local mean temperature), landscape characteristics (proportion of grassland, landscape diversity; 0.2–3.0-km), climate (multi-annual mean temperature, 'MAT') and interactive effects of plant functional group, temperature and habitat or landscape characteristics. Herbivory on plant functional groups changed differently in response to plant richness (family level only) and habitat type, but not to differences in landscape characteristics and temperature – only on grassland plots, multi-annual mean temperature differentially affected herbivory among plant functional groups. Thus, abiotic and biotic factors can differently affect leaf-chewing herbivory on plant functional groups. Under current conditions, plant richness and habitat type more strongly affected herbivory among legumes, forbs and grasses than temperature and landscape-scale land use.</p>
Data and code from: Functional rarity of plants in German hay meadows - patterns on the species level and mismatches with community species richness
<p>Functional rarity (FR) - a feature combining a species' rarity with the distinctiveness of its traits - represents a promising tool to better understand the ecological importance of rare species and consequently to protect functional diversity more efficiently. Yet, we lack a systematic understanding of FR on both the species level (which species are functionally rare and why) and the community level (how is FR associated with biodiversity and environmental conditions). Here, we quantify FR for 218 plant species from German hay meadows on a local, regional, and national scale by combining data from 6500 vegetation relevés and 15 ecologically relevant traits. We investigate the association between rarity and trait distinctiveness on different spatial scales via correlation measures and show which traits lead to low or high trait distinctiveness via distance-based redundancy analysis. We test how species richness and FR are correlated and use boosted regression trees to determine environmental conditions driving species richness and FR. On the local scale, only rare species showed high trait distinctiveness while on larger spatial scales rare and common species showed high trait distinctiveness. As infrequent trait attributes (e.g., legumes, low clonality) led to higher trait distinctiveness, we argue that functionally rare species are either specialists or transients. While specialists occupy a particular niche in hay meadows leading to lower rarity on larger spatial scales, transients display distinct but maladaptive traits resulting in high rarity across all spatial scales. More functionally rare species than expected by chance occurred in species-poor communities indicating that they prefer environmental conditions differing from characteristic conditions of species-rich hay meadows. Finally, we argue that functionally rare species are not necessarily relevant for nature conservation, since many were transients from surrounding habitats. Yet, FR can facilitate our understanding of why species are rare in a habitat and under which conditions these species occur.</p>
Text-fig. 1. a: Po Plain and foothills of the Northern Apennine in Northern Italy (inset) with the location of Oriolo (black star) and other Early and Middle Pleistocene plant localities, Enza and Stirone. Red lines indicate the frontal thrust arcs (modified from Martinetto et al. 2015). b: The "La Salita" section, Oriolo and chronology of the two "Sabbie gialle" cycles based on large mammals and palaeomagnetic correlation (modified from Toniato et al. 2017; IMMS 2020* [Italian Mediterranean Marine Stages] updated from Cohen and Gibbars 2020; GTS 2021* [Global Time Scale] updated from Head et al. 2021). c: Quarry "La Salita", Oriolo, in 1987. Main unconformities (U) separating the two "Sabbie gialle" cycles and terrestrial deposits on top are shown. Leaf symbols indicate the positions of some of the layers rich in fossil leaves (photo by G. B. Vai, modified). d: Surroundings of Faenza with the location of Oriolo and adjacent coeval sites yielding plant macrofossils. in The Late Early Pleistocene Flora Of Oriolo, Faenza (Italy): Assembly Of The Modern Forest Biome
Text-fig. 1. a: Po Plain and foothills of the Northern Apennine in Northern Italy (inset) with the location of Oriolo (black star) and other Early and Middle Pleistocene plant localities, Enza and Stirone. Red lines indicate the frontal thrust arcs (modified from Martinetto et al. 2015). b: The "La Salita" section, Oriolo and chronology of the two "Sabbie gialle" cycles based on large mammals and palaeomagnetic correlation (modified from Toniato et al. 2017; IMMS 2020* [Italian Mediterranean Marine Stages] updated from Cohen and Gibbars 2020; GTS 2021* [Global Time Scale] updated from Head et al. 2021). c: Quarry "La Salita", Oriolo, in 1987. Main unconformities (U) separating the two "Sabbie gialle" cycles and terrestrial deposits on top are shown. Leaf symbols indicate the positions of some of the layers rich in fossil leaves (photo by G. B. Vai, modified). d: Surroundings of Faenza with the location of Oriolo and adjacent coeval sites yielding plant macrofossils.
Supplementary data from: Current and past climate co-shape community-level plant species richness in the Western Siberian Arctic
<p>The Arctic ecosystems and their species are exposed to amplified climate warming and, in some regions, to rapidly developing economic activities. We used macroecological modeling to estimate the community-level species richness across the Western Siberian tundra, with climate variables and anthropogenic influence identified as main explanatory factors. Our results reveal complex spatial patterns of community-level species richness in the Western Siberian Arctic. We show that climatic factors such as temperature (including paleotemperature) and precipitation are the main drivers of plant species richness in this area, and the role of relief is clearly secondary.</p> <p>Here we present a supplementing dataset to the analysis of our paper "Current and past climate co-shape community-level plant species richness in the Western Siberian Arctic"<strong> </strong>(<a href="https://doi.org/10.1002/ece3.11140">https://doi.org/10.1002/ece3.11140</a>). Our research is based on the Western Siberian part of the Russian Arctic Vegetation Archive (AVA-RUS, <a href="http://avarus.space">http://avarus.space</a>), with 1483 Braun-Blanquet plots observed from 2005-2018.</p> <p>The dataset contains geolocated species richness data along with sampled raster data on environmental and anthropogenic predictors used for modeling. The scripts are used for paleoclimatic data sampling; testing univariate predictive performance and limited collinearity for all predictors; fitting four different modes: random forest, gradient boosting machine, generalized linear model, and generalized additive model; their validation and projection. Detailed information regarding the data structure and the applied methods could be found in the paper.</p>
Midpoint attractor models resolve the mid-elevation peak in Himalayan plant species richness
<p>The midpoint attractor models (MPA) of species richness integrate a unimodal environmental favourability gradient and neutral effects forced by geometric constraints and thus extend ecologically neutral mid-domain model. However, both alternative MPA algorithms assume that underlying environmental favourability peaks within the modeling domain. Here, we used elevational distribution data for 1054 plant species occurring in NW Himalaya to explore species richness gradients and MPA performance in species groups defined by biogeography, taxonomy and life form. MPA models achieved an excellent fit, but the two MPA algorithms produced contrasting estimates of midpoint attractor location, especially for species groups with richness originating in lowlands. Therefore, we propose a modification of the MPA model accounting for the environmental favourability peak outside the study domain to reflect these situations. Biogeographic origin was more decisive for midpoint attractor location than taxonomic or life-form classification, indicating relatively low climatic niche conservatism in plants.</p>
Data from: Plant richness, land use and temperature differently shape invertebrate leaf-chewing herbivory on plant functional groups
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Midpoint attractor models resolve the mid-elevation peak in Himalayan plant species richness
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Environmental heterogeneity explains contrasting plant species richness between the South African Cape and southwestern Australia
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Supplementary data from: Current and past climate co-shape community-level plant species richness in the Western Siberian Arctic
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Allen Brain Atlas
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