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72 results for “monoculture”
qPCR raw datasets on the assessments of cover crop monocultures and mixtures improving the rhizosphere bacterial abundance and functionality through rerooting
<p>Quantitative PCR (qPCR) raw data includes the source data that corresponds to the the counts of 16S rRNA gene copies per gram of soil for different variations, as discussed in the research article - "Cover crop monocultures and mixtures improve the rhizosphere bacterial abundance and functionality through rerooting". The copy number of the 16S rRNA gene per gram of soil was quantified by SYBR® Green-based qPCR using a 7500 Fast Real-Time PCR System (Applied Biosystems™, Thermo Fisher Scientific, Waltham, MA, USA). Aliquots of the same DNA extract utilized in amplicon sequencing were used in qPCR. Dilutions of template DNA were used to compensate for the effect of PCR inhibitors in the samples. Each sample was analyzed in triplicate. A PCR amplicon of the <i>Escherichia coli</i> V3 region was used as standard. Each reaction of 20 µL contained 1 µL of template DNA, the forward primer 341F (Muyzer et al., 1993), the reverse primer 518R (Muyzer et al., 1993), and Luna® Universal qPCR Master Mix (NEB). Reaction conditions were an initial denaturation for 1 min at 95 °C, followed by 40 cycles of denaturation at 95 °C for 15 s and extension at 60 °C for 30 s. The melting curve was recorded in the temperature range of 60 °C to 95 °C. The 16S rRNA gene copy numbers per gram of soil were calculated using the standard curve method and then normalized against the standard (Adelowo et al., 2018). The average efficiency value was 100.77 ± 3.15 %. The absolute copy numbers for each bacterial phylum were calculated by multiplying the qPCR values by the relative abundance values in percent obtained from the 16S rRNA gene sequencing analyses.</p>
Scanned images of monocultures and mixtures of six grassland plant species roots, and of simulated fine roots
<p>Soil core samples were taken from a multi-species grassland experiment with field plots of monocultures and mixtures of six grassland plant species: <em>Lolium perenne</em> L. (PRG),<em> Phleum pratense</em> L. (TIM), <em>Trifolium pratense</em> L. (RC), <em>Trifolium repens</em> L. (WC), <em>Cichorium intybus </em>L. (CHIC), and <em>Plantago lanceolata </em>L.. The multi-species plots had a two species mixture with <em>Trifolium repens </em>L. and<em> Lolium perenne</em> L. (PRGWC), and a 6 species mixture with all species mentioned above. The cores were separated into soil depths of 0-10 cm, 10-15 cm and 15-20 cm and the roots separated from the soil.</p> <p>A ground-truth image set was created to simulate fine roots using fishing line. The fishing line used was a clear copolymer monofilament (Greys<sup>TM</sup> Greylon Tippet Material 3 lb), measured using a scanning electron microscope (Hitachi SU8200) to be 0.14 mm in diameter. The fishing line was used in its clear colour or coloured black using a permanent marker to simulate unstained and stained fine roots respectively. The fishing line was cut into lengths of 30 cm or 5 cm. </p> <p>Roots and fishing line were scanned using an Epson Perfection V800 flatbed scanner at 600 dpi. </p> <p>The Roots ZIP file contains a folder for the scanned root images and the Line zip file contains a folder with the scanned fishing line. The excel spreadsheet describes the naming convention for the images.</p> <p>Further details about the root sampling and image acquisition can be found in the publication that analyses these images: <a href="https://doi.org/10.1002/ppj2.20034">https://doi.org/10.1002/ppj2.20034</a></p>
Metadata for Confocal Laser Scanning Microscopy Images of Monoculture and Mixed-Species Biofilms Formed by Bacterial Isolates of Dairy Origin
<p>In a project conducted by ILVO (Belgium), a wide variety of bacterial species were recovered from the surface of a dairy pasteurizer after cleaning and disinfection (C&D). The biofilm-forming ability of these bacteria was determined in both single-species and various mixed-culture combinations. Some work related to this study has been published in Frontiers: "Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries". Bacterial species were mixed in different combinations to assess the community biofilm mass and growth dynamics of individual species. ILVO and the University of Copenhagen conducted experiments aimed at revealing the structural characteristics and spatial organization of bacterial species within different mixed-species biofilms. In our research, we employed oligonucleotide FISH probes, each conjugated with a unique fluorescent dye: Cy5 for <em>Stenotrophomonas rhizophila</em> (B68), Cy3 for <em>Bacillus licheniformis</em> (B65), and FAM for <em>Microbacterium lacticum</em> (B30). C1 combination refers to a combination containing B68 and B30. </p> <p><span>Images of the biofilms formed on the coupons were captured using a confocal laser scanning microscope (LSM 800, Zeiss) with a Plan-Apochromat 63x/1.4 oil-immersion objective. Z-stacks were recorded to obtain three-dimensional (3D) images. Standard images were made with an image size of 1024 × 1024 pixels, corresponding to physical dimensions of 101.4 × 101.4 μm for each image. For each image, two separate channels were applied to detect any dual-species combination using a flexible detector (GaAsP-PMT) in the LSM 800 system. Representative 3D views of images were generated using the 3D model function in the ZEN system 3.7.</span></p> <p>Biofilms were grown in BHI for 24 h on plastic coupons. The samples were imaged at different time points: 6h, 12h, 18h and 24h. Each samples had three replicates and for each replicate imaging was performed from 3-6 different positions. </p> <p>Details of the oligonucleotide probes are given below:</p> <table> <tbody> <tr> <td> <p><strong><span>Name of the species</span></strong></p> </td> <td> <p><strong><span>Sequences</span></strong></p> </td> <td> <p><strong><span>Max. excitation</span></strong></p> </td> <td> <p><strong><span>Max. emission</span></strong></p> </td> <td> <p><strong><span>Fluorophores</span></strong></p> </td> </tr> <tr> <td> <p><em><span>S. rhizophila</span></em><span> B68<span> </span></span></p> </td> <td> <p><span>GGGCCTTTACCCCGCCA</span></p> </td> <td> <p><span>649 nm</span></p> </td> <td> <p><span>670 nm</span></p> </td> <td> <p><span>Cy5</span></p> </td> </tr> <tr> <td> <p><em><span>B. licheniformis</span></em><span> B65</span></p> </td> <td> <p><span>ACCGCCTGCGCGCGCTT</span></p> </td> <td> <p><span>550 nm</span></p> </td> <td> <p><span>570 nm</span></p> </td> <td> <p><span>Cy3</span></p> </td> </tr> <tr> <td> <p><em><span>M. lacticum</span></em><span> B30</span></p> </td> <td> <p><span>CCCCACCCTTTCGCTCC</span></p> </td> <td> <p><span>495 nm</span></p> </td> <td> <p><span>520 nm</span></p> </td> <td> <p><span>FAM</span></p> </td> </tr> </tbody> </table>
VCF files of common grassland plants from wild collected seeds of 19 common European grassland species with up to 4 consecutive generations grown in monoculture for seed production for restoration
<p>A growing number of restoration projects require large amounts of seeds. As harvesting natural populations cannot cover the demand, wild plants are often propagated in large-scale monocultures. There are concerns that this cultivation process may cause genetic drift and unintended selection, which would alter the genetic properties of the cultivated populations and reduce their genetic diversity. Such changes could reduce the pre-existing adaptation of restored populations, and limit their adaptability to environmental change.</p> <p>We used single nucleotide polymorphism (SNP) markers and a pool-sequencing approach to test for genetic differentiation and changes in gene diversity during cultivation in 19 wild grassland species, comparing the source populations and up to four consecutive cultivation generations. We then linked the magnitudes of genetic changes to the species' breeding systems and seed dormancy, to understand the roles of these traits in genetic change.</p> <p>The propagation changed the genetic composition of the cultivated generations only moderately. The genetic differentiation we observed as a consequence of cultivation was much lower than the natural genetic differentiation between different source regions. The propagated generations harbored even higher gene diversity than wild-collected seeds. Genetic change was stronger in self-compatible than in self-incompatible species, probably as a result of increased outcrossing in the monocultures.</p> <p><em>Synthesis and applications</em>: Our study indicates that large-scale seed production maintains the genetic integrity of natural populations. Increased genetic diversity may be indicative of increased adaptive potential of propagated seeds, which would make them especially suitable for ecological restoration. Yet, it remains to be tested whether these patterns observed on the level of molecular markers will be mirrored also in plant phenotypes. Further, we used seeds produced in Germany and Austria, where the seed production is regulated and certified. Whether other seed production systems perform equally well remains to be tested.</p>
Figure 5 in Impact of rainforest conversion into monoculture plantation systems on pseudoscorpion density, diversity and trophic niches
Figure 5. Stable isotope values of pseudoscorpion species in different land-use systems; means with standard deviation. Dashed horizontal lines represent estimated trophic level boundaries; trophic level 1 (plant material) not shown. Decomposers feeding on detritus (trophic level 2) were assumed to be enriched in 15N by 1.7 ‰ compared to leaf litter, each following trophic level was assumed to span 3.4 ‰ (Post 2002; Potapov et al. 2019a). For abbreviations see Table 1.
Figure 3 in Impact of rainforest conversion into monoculture plantation systems on pseudoscorpion density, diversity and trophic niches
Figure 3. Bootstrap species accumulation curve based on the number of adult individuals in the studied land-use systems.
Figure 4 in Impact of rainforest conversion into monoculture plantation systems on pseudoscorpion density, diversity and trophic niches
Figure 4. Venn diagram of the species composition in the three land-use systems studied (rainforest, rubber, oil palm) in the Bukit Duabelas (left) and Harapan landscape (right). Landscape-specific species are underlined in red. The riparian-specific species in Harapan is underlined in cyan. For abbreviations see Table 1.
Figure 2 in Impact of rainforest conversion into monoculture plantation systems on pseudoscorpion density, diversity and trophic niches
Figure 2. Density of pseudoscorpions in litter and soil of the three land-use systems studied (rainforest, rubber, oil palm) in the Bukit Duabelas and Harapan landscape. Each data point represents one sampling plot (three pooled subplot samples). Only non-riparian sites are shown.
Figure 1 in Impact of rainforest conversion into monoculture plantation systems on pseudoscorpion density, diversity and trophic niches
Figure 1. Four species of pseudoscorpions found at the study sites. From left to right: Atemnidae sp.1, Lagynochthonius sp.1, Atemnidae sp.2, Hya minuta.
Figure 4 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 4. Mean (¡SE) number of food items per stomach in each habitat. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation.
Figure 5 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 5. Rarefaction curves of Physalaemus lisei diet, relating taxonomic richness to the number of individuals in each habitat. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation. The vertical lines comprise the 95% confidence intervals.
Figure 3 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 3. Diet composition of Physalaemus lisei (black bars) in relation to the taxonomic composition of pitfall traps (white bars). Dotted line delimits the feeding niche of P. lisei.
Figure 2 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 2. Body mass (g) distribution of Physalaemus lisei captured in the São Francisco de Paula National Forest, southern Brazil. (A) Temporal variation in body mass (g) distribution between October 2003 and April 2005; (B) among-habitat variation in body mass distribution. Horizontal line represents the median; the box delimits the first and third quartile; the vertical lines delimit the maximum and minimum values, except for the outliers that are represented by asterisks. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation.
Figure 1 in Ecologically-sustainable tree monocultures contribute to conservation of an Araucaria Forest endemic frog
Figure 1. Number of individuals of Physalaemus lisei captured in the São Francisco de Paula National Forest, southern Brazil. (A) Temporal dynamic between October 2003 and April 2005; (B) among-habitat variation in the mean (¡SE) number of captures. FO, Araucaria Forest; PA, Araucaria angustifolia plantation; PP, Pinus plantation; PE, Eucalyptus plantation.
VCF files of common grassland plants from wild collected seeds of 19 common European grassland species with up to 4 consecutive generations grown in monoculture for seed production for restoration
Open the record for dataset details and reuse information.
Multicolor flow cytometry of monocultures and co-cultures of Bacteroides species
<p>Dataset of FCS (Flow Cytometry Standard) files, along with meta-data, related to a flow cytometry analysis of monocultures and co-cultures of <em>Bacteroides </em>species under several different conditions. </p> <p><strong>Data Collection. </strong>This<strong> </strong>dataset accompanies a journal artcle which was published in <em>Frontiers in Microbiology</em> (<a href="https://doi.org/10.3389/fmicb.2022.910390">https://doi.org/10.3389/fmicb.2022.910390</a>). The "Methods and Materials" section in this article fully describes the biological nature of these samples and how the samples were processed for flow analysis and analyzed with flow cytometry. </p> <p><strong>Data Organization. </strong>Dataset includes 1832 samples. See mapping.xlsx and mapping_key.xlsx for list of samples and their meta-data. Folders are formatted as {run_data}_{time_point} and contains only samples belonging to either a run performed on 2018/07/17 or 2018/07/21 for time points of either 0, 24, 48, 72, or 102 hours. </p> <p><strong>Data Analysis. </strong>Code used for manipulating and analyzing these samples is publicly available (<a href="https://github.com/firasmidani/BacteroidesFlowCytometry">https://github.com/firasmidani/BacteroidesFlowCytometry</a>).</p> <p><strong>Data Integrity</strong>. "hardac-hashes.txt" stores the MD5 hashes of the original folders created by the authors prior to uploading data to Zenodo.</p>
Data from: Multispecies forest plantations outyield monocultures across a broad range of conditions
<p>Data from: Multispecies forest plantations outyield monocultures across a broad range of conditions (doi: 10.1126/science.abm6363).</p>
Summary data for "Young mixed planted forests store more carbon than monocultures: a meta-analysis"
<p>This is the dataset used in "Young mixed planted forests store more carbon than monocultures: a meta-analysis" published in Frontiers in Forests & Global Change. </p><p>The dataset contains carbon or biomass data for mixed and monoculture planted forests from 21 sites with a global coverage. We provide summary data necessary to conduct a meta-analysis: mean, standard deviation, and sample size, for each unique mixed and monoculture treatment at each study site. We indicate whether the values provided are aboveground carbon or biomass.</p><p>For each treatment we also provide the species richness, age and species. We provide the longitude, latitude and country for each study site.</p><p>Our study also assessed the effect of study design (experiment vs existing plantation), species origin (native vs non-native/mixed), and presence of nitrogen fixer in the mixture (N fixer present vs absent), we record the value of each of these factors. Finally, we categorised a subset of monocultures as commercial species monocultures based on the species use in that location. </p>
Data from: Legacy effects of alfalfa monocultures or annual crop/alfalfa mixtures on subsequent corn yield and quality
Open the record for dataset details and reuse information.
Data from: Yield, growth, and labor demands of growing maize, beans, and squash in monoculture versus the Three Sisters
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