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10 results for “microbial oil”
Supplementary data for Model-driven engineering of Cutaneotrichosporon oleaginosus ATCC 20509 for improved microbial oil production
<p>Supplementary data corresponding to manuscript named Model-driven engineering of <em>Cutaneotrichosporon oleaginosus</em> ATCC 20509 for improved microbial oil production. </p> <p>The Supplementary material document contains supplementary figures and tables. The content of the figures and tables are indicated below. </p> <ul> <li>Figure S1. Plasmid map of pUC57NAT containing pGpd, nourseothricin acyltransferase gene and tGpd.</li> <li>Figure S2. Plasmid maps of overexpression targets containing TEF1α promoter, ATP-citrate lyase gene, TEF1α terminator, TPI1 promoter, Acetyl-CoA carboxylase gene, TPI1, YAT1 promoter, threonine synthase gene, YAT1 terminator and ENO1 promoter, hydroxymethylglutaryl-CoA synthase gene, ENO1 terminator.</li> <li>Table S2. Nucleotide sequences of promoters, genes, and terminators from <em>C. oleaginosus.</em></li> <li>Figure S3. Calibration curve of glycerol for calculating the glycerol concentration of medium.</li> <li>Figure S4. Volcano plots displaying differentially expressed genes and fold change (log2) in expression levels in WT, Δ9 and Δ12 strains at low lipid accumulation vs high lipid accumulation conditions.</li> <li>Figure S5. Flux distribution graphs of selected reactions for overexpression in C. oleaginosus.</li> <li>Figure S6. Colony PCR products were run on 1 % agarose gel. The colony PCR was performed for WT, ACL, ACC and TS transformants.</li> <li>Table S4. qPCR outputs, CT: The threshold cycle.</li> <li>Table S5. Fatty acid profile of C. oleaginosus grown at minimal medium with or without supplement (biotin, thiamine, threonine, serine, and aspartate) at 96h.</li> <li>Table S6. Lipid content, dry cell weight, and lipid weight of WT, ACL, ACC, TS, and HMGS <em>C. oleaginosus</em> at various C/N ratio minimal medium.</li> <li>Table S7. Fatty acid profile of WT, ACL, ACC, HMGS, and TS grown at C/N30, 120, 175, 200, and 300 minimal medium at 96h.</li> <li>Figure S7. Quadratic regression analysis on lipid accumulation, biomass and lipid content of wild-type, ACL, ACC, and TS C. oleaginosus at C/N 30, 120, 175, 200, 300.</li> <li>Table S8. Regression equations, statistics of regression equations for lipid content, biomass, and lipid content of wild-type, ACL, ACC, and TS.</li> <li>Table S9. Calculated optimum C/N ratios and responses (lipid content, biomass, and total lipid) by using built regression models for wild-type, ACL, ACC, and TS.</li> </ul> <p>Authors: </p> <p>Zeynep Efsun Duman-Özdamar<sup>a,b,c</sup>, Mattijs K. Julsing<sup>c</sup>, Janine A.C. Verbokkem<sup>c</sup>, Emil Wolbert<sup>c</sup>, Vitor A.P. Martins dos Santos<sup>a,b,d</sup>, Jeroen Hugenholtz<sup>e,f</sup>, Maria Suarez-Diez<sup>b*</sup></p> <p><sup>a</sup>Bioprocess Engineering, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands</p> <p><sup>b</sup>Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE, Wageningen, the Netherlands</p> <p><sup>c</sup>Wageningen Food & Biobased Research, Wageningen University & Research, 6708 WE, Wageningen, The Netherlands</p> <p><sup>d</sup>LifeGlimmer GmbH, Berlin, 12163, Germany</p> <p><sup>e</sup>Faculty of Science Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands</p> <p><sup>f</sup>NoPalm Ingredients BV, 6709 PA Wageningen, The Netherlands</p>
Soil microbial communities from tropical forest and oil palm
<div> <h1>Description</h1> <p>A study examining the impact of selective logging and forest conversion to oil palm on soil microbial community composition. Soil samples were collected from old growth forest, selectively logged forest and oil palm plantations. Soil bacterial, protistan and fungal community composition were measured and summarised by calculating richness. </p> <h1>Projects</h1> <p> This dataset was collected as part of the following projects: </p><ul> <li><a href="https://safeproject.net/projects/project_view/124">https://safeproject.net/projects/project_view/124</a> </li> </ul> <p></p> <h1>Funding</h1> <p> These data were collected as part of research funded by: </p> <ul> <li>UK NERC-funded Biodiversity And Land-use Impacts on Tropical Ecosystem Function (BALI) consortium (Standard grant , NE/K016377/1 ) </li> </ul> <p></p> <p>This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.</p> <h1>Permits</h1> <p>These data were collected under permit from the following authorities:</p> <ul> <li>Sabah Biodiversity Centre ( Research licence JKM/MBS.1000-2/2 JLD.5 (20))</li> <li>Sabah Biodiversity Centre ( Export licence JKM/MBS.1000-2/3 JLD.2 (70))</li> </ul> <p></p> <h1>Files</h1> <p>This dataset consists of 1 file: SAFE_Dataset_Richness.xlsx</p> <h2>SAFE_Dataset_Richness.xlsx</h2> <p>This file contains dataset metadata and 1 data tables:</p> <h3>Soil_Microbial_Communities</h3> <ul> <li>Worksheet: Soil_Microbial_Communities</li> <li>Description: Summary richness statistics from bacterial 16S, protistan 18S and fungal ITS biomarker microbial sequencing from DNA extracted from soils</li> <li>Number of fields: 10</li> <li>Number of data rows: 225</li> <ul> <li>PlotName: Plot name corresponding to the GEM Carbon plot where soils were sampled (type: id)</li> <li>ForestType: Old-growth, Logged or Oil palm (type: categorical)</li> <li>ForestPlotsCode: Plot name as listed in ForestPlots database (type: id)</li> <li>Replicate: replicate identifier for which soil core taken from each subplot (type: replicate)</li> <li>location_name: Name of subplot where soils were collected (type: location)</li> <li>Bacteria_Richness: Number of observed bacterial taxa from sequencing of 16S marker genes from soil samples (type: numeric)</li> <li>Protist_Richness: Number of observed protistan taxa from sequencing of 18S marker genes from soil samples (type: numeric)</li> <li>Fungal_Richness: Number of observed fungal taxa from sequencing of 16S marker genes from soil samples (type: numeric)</li> <li>EcM_Fungal_Richness: Number of observed Ectomycorrhizal fungal taxa from sequencing of ITS marker genes from soil samples (type: numeric)</li> <li>AMF_Fungal_Richness: Number of observed Arbuscular Mycorrhizal fungal taxa from sequencing of ITS marker genes from soil samples (type: numeric)</li> </ul> </ul> <h1>Extents</h1> <ul> <li>Date range: 2014-10-01 to 2018-09-01</li> <li>Latitudinal extent: 4.64° to 4.954°</li> <li>Longitudinal extent: 116.95° to 117.796°</li> </ul> </div>
Soil and litter chemistry, soil microbial communities and litter decomposition from tropical forest and oil palm
<b>Description: </b><p>A study examining the interactions between soil chemistry, litter chemistry and soil microbial decomposers as controls on rates of litter decomposition across a tropical land use disturbance gradient. Co-located soil and litter samples were collected from old growth forest, moderately logged forest, heavily logged forest and oil palm plantations. Soil and litter were chemically characterised and soil bacterial and fungal community composition and abundance were measured. These were then combined in fully factorial ex-situ microcosms and measured litter decomposition rates at 3 time points during different stages of decomposition.</p><p><b>Project: </b>This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/124"><b>Biodiversity and land-use impacts on tropical ecosystem function (BALI): Quantifying biogeochemistry across forest disturbance gradients in Sabah</b></a></p><p><b>Funding: </b>These data were collected as part of research funded by: </p><ul><li>UK NERC-funded Biodiversity And Land-use Impacts on Tropical Ecosystem Function (BALI) consortium (Standard grant, NE/K016377/1)</li></ul><p>This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.</p><p></p><p><b>Permits: </b>These data were collected under permit from the following authorities:</p><ul><li>Sabah Biodiversity Centre (Research licence JKM/MBS.1000-2/2 JLD.5 (20))</li><li>Sabah Biodiversity Centre (Export licence JKM/MBS.1000-2/3 JLD.2 (70))</li></ul><p></p><p><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=3929632">here</a></p><p><b>Files: </b>This consists of 1 file: SAFE_Dataset.xlsx</p><p><b>SAFE_Dataset.xlsx</b></p><p>This file contains dataset metadata and 5 data tables:</p><ol><li><p><b>Soil_Properties</b> (described in worksheet Soil_Properties)</p><p>Description: Basic measured soil properties</p><p>Number of fields: 9</p><p>Number of data rows: 20</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>gravimetric moisture content</b>: Soil moisture content at the time of sample collection (Field type: numeric)</li><li><b>soil_pH</b>: Soil pH measured on fresh soils (Field type: numeric)</li><li><b>soil_N</b>: Total soil Nitrogen (Field type: numeric)</li><li><b>soil_C</b>: Total soil Carbon (Field type: numeric)</li><li><b>soil_C.N</b>: Soil carbon to nitrogen ratio (Field type: numeric)</li><li><b>soil_P</b>: soil inorganic phosphorus (Field type: numeric)</li></ul></li><li><p><b>Litter_Chemistry</b> (described in worksheet Litter_Chemistry)</p><p>Description: Litter chemistry data of mixed forest floor litter, collected, sorted to remove humified material, woody debris and dried</p><p>Number of fields: 20</p><p>Number of data rows: 40</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Pretreatment</b>: Whether the litter sample was sterilised by autoclaving or not (Field type: categorical)</li><li><b>leaf_K</b>: leaf potassium concentration (Field type: numeric)</li><li><b>leaf_Ca</b>: leaf Calcium concentration (Field type: numeric)</li><li><b>leaf_Mg</b>: leaf Magnesium concentration (Field type: numeric)</li><li><b>leaf_Al</b>: leaf aluminium concentration (Field type: numeric)</li><li><b>leaf_P</b>: leaf phosphorus concentrations (Field type: numeric)</li><li><b>solubles</b>: leaf soluble cell content (Field type: numeric)</li><li><b>hem_pro_cel_lig_rec</b>: leaf hemicellulose, proteins, cellulose, lignin and recalcitrant fibres (Field type: numeric)</li><li><b>hem_pro</b>: leaf hemicellulose and proteins (Field type: numeric)</li><li><b>cel_lig_rec</b>: leaf cellulose, lignin and recalcitrant fibres (Field type: numeric)</li><li><b>cel</b>: leaf cellulose (Field type: numeric)</li><li><b>lig_rec</b>: leaf lignin and recalcitrants (Field type: numeric)</li><li><b>leaf_N</b>: leaf nitrogen concentration (Field type: numeric)</li><li><b>leaf_C</b>: leaf carbon concentration (Field type: numeric)</li><li><b>c.n</b>: leaf carbon to nitrogen ration (Field type: numeric)</li><li><b>d13c</b>: leaf carbon stable isotope ratio (Field type: numeric)</li><li><b>d15n</b>: leaf nitrogen stable isotope ratio (Field type: numeric)</li></ul></li><li><p><b>PLFA_Concentrations</b> (described in worksheet PLFA_Concentrations)</p><p>Description: Phospolipid Fatty Acid (PLFA) concentrations as biomarkers of soil bacteria and fungi. Extracted from freeze dried soils prior to the microcosm experiment</p><p>Number of fields: 10</p><p>Number of data rows: 20</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Total_PLFA</b>: Total PLFA concentrations extracted from soil samples (Field type: numeric)</li><li><b>Fungal_PLFA</b>: Fungal PLFA biomarker concentrations extracted from soils (Field type: numeric)</li><li><b>Bacteria_PLFA</b>: Bacteria PLFA biomarkers extracted from soils (Field type: numeric)</li><li><b>Fungal:Bacteria</b>: Ratio of fungal to bacteria PLFAs (Field type: numeric)</li><li><b>Gram_Pos_PLFA</b>: Gram Positive PLFA Biomarker concentrations extracted from soil (Field type: numeric)</li><li><b>Gram_Neg_PLFA</b>: Gram Negative PLFA Biomarker concentrations extracted from soil (Field type: numeric)</li><li><b>GramPos:GramNeg</b>: Gram positive to Gram negative PLFA ratios (Field type: numeric)</li></ul></li><li><p><b>Soil_Microbial_Communities</b> (described in worksheet Soil_Microbial_Communities)</p><p>Description: Summary diversity statistics from bacterial 16S and fungal ITS biomarker microbial sequencing. DNA extracted from soils prior to microcosm experiment</p><p>Number of fields: 9</p><p>Number of data rows: 20</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Bacteria_Richness</b>: Number of observed bacterial taxa from sequencing of 16S marker genes from soil samples (Field type: numeric)</li><li><b>Bacteria_Shannon</b>: Bacterial Shannon diversity from 16S Marker gene sequencing (Field type: numeric)</li><li><b>Fungal_Richness</b>: Number of observed fungal taxa from sequencing of 16S marker genes from soil samples (Field type: numeric)</li><li><b>Fungal_Shannon</b>: Fungal Shannon diversity from 16S Marker gene sequencing (Field type: numeric)</li><li><b>Saprotrophic_Fungal_Richness</b>: Number of observed saprotrophic fungal taxa from sequencing of 16S marker genes from soil samples (Field type: numeric)</li><li><b>Saprotrophic_Fungal_Shannon</b>: Saprotrophic Fungal Shannon diversity from 16S Marker gene sequencing (Field type: numeric)</li></ul></li><li><p><b>Ex_Situ_Litter_Decomposition</b> (described in worksheet Ex_Situ_Litter_Decomposition)</p><p>Description: Fully factorial litter decomposition experiment. 16 unique soil and litter combinations (4x4) were incubated in petri dishes at constant temperature and moisture and mass loss measured after 31, 105 and 398 days.</p><p>Number of fields: 8</p><p>Number of data rows: 240</p><p>Fields: </p><ul><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Soil_ID</b>: Soil ID indicating which land use soil was collected from (Field type: categorical)</li><li><b>Litter_Location</b>: Location of which GEM carbon plot the litter was collected from. Litter was collected from the 5 carbon subplots as per soil collection and homogenised into one composite sample per carbon plot (Field type: location)</li><li><b>Litter_ID</b>: Litter ID indicating which land use litter was collected from (Field type: categorical)</li><li><b>Experimental_Block</b>: Which experimental block the microcosm was assigned to. N= 5 (Field type: replicate)</li><li><b>Timepoint</b>: At what timepoint the litter was harvested from each microcosm (Field type: categorical)</li><li><b>Mass_Loss</b>: The mass loss of litter relative to the starting mass of 1g (Field type: numeric)</li><li><b>home_away</b>: Descriptor for whether the soil and litter combination in microcosm (Field type: categorical)</li></ul></li></ol><p><b>Date range: </b>2014-10-01 to 2018-09-01</p><p><b>Latitudinal extent: </b>4.6402 to 4.9539</p><p><b>Longitudinal extent: </b>117.4518 to 117.7942</p>
Simulation results for "Integration of Plant and Microbial Oil Processing at Oilcane Biorefineries for More Sustainable Biofuel Production" publication
<p>Simulation results for "Integration of Plant and Microbial Oil Processing at Oilcane Biorefineries for More Sustainable Biofuel Production" publication.</p>
Test of Isolate Acid Bacteria as Microbial Enchanced Oil Recovery in Ledok Field
<p>This material has presented on 2nd International Conference on Advanced Research in Engineering and Technology in October 25, 2023.</p>
Phytochemical Screening and Microbial Activity of Essential Oil from Aerial Parts of Murraya paniculata (L.) Orange Jasmine
<p>Phytochemical Screening and Microbial Activity of Essential Oil from Aerial Parts of Murraya paniculata (L.) Orange Jasmine </p>
Phytochemical Screening and Microbial Activity of Essential Oil from Aerial Parts of Murraya paniculata (L.) Orange Jasmine
<p>Phytochemical Screening and Microbial Activity of Essential Oil from <br>Aerial Parts of Murraya paniculata (L.) Orange Jasmine </p>
Data from: Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill
Open the record for dataset details and reuse information.
A metagenomic study revealing unexpectedly diverse functional groups in microbial communities of deep-ground oil
GEO Series GSE55293. Bacteria; uncultured bacterium. 9 samples. Type: Other.
Effects of Neolamarckia cadamba essential Oil on microbial transcription
GEO Series GSE241080. Nakaseomyces glabratus; Niallia circulans; Aspergillus flavus. 18 samples. Type: Expression profiling by high throughput sequencing.
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