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opencc-by-4.0Dec 2019View details →

In silico Database for Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1)

Modern methods of mass spectrometry have emerged recently allowing reliable, fast and cost-effective identification of pathogenic microorganisms. For example, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has revolutionized the way pathogenic microorganisms are identified in today’s routine clinical microbiology. Furthermore, recent years have witnessed also substantial progress in the development of liquid chromatography-mass spectrometry (LC-MS) based proteomics for microbiological applications. In this context, we introduce a new concept for microbial identification by mass spectrometry. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC-MS measurements. MS1 data are then extracted and systematically tested against in silico libraries of peptide mass data. The first version of such a database has been computed from UniProt Knowledgebase [Swiss-Prot and TrEMBL] and contains more than 12,000 strain-specific synthetic mass profiles. The database is stored in the pkf data format which is interpretable by the MicrobeMS software package (requires MicrobeMS version 0.82, or later). For details see the following preprint: Lasch, P. Schneider, A. Blumenscheit, C. and Doellinger, J. “Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data”. bioRxiv preprint, http://dx.doi.org/10.1101/870089.

opencc-by-4.0Mar 2023View details →

Version 4.2 (20230306) of the MALDI-ToF Mass Spectrometry Database for Identification and Classification of Highly Pathogenic Microorganisms from the Robert Koch-Institute (RKI)

(Version 20230306, btmsp files modified May 31, 2023, additional taxonomic information added Dec 27, 2024) Version 4.2 (20230306) of the RKI MALDI-ToF mass spectra database represents the third update of the original database (version 20161027, <a href="http://doi.org/10.5281/zenodo.163517">https://doi.org/10.5281/zenodo.163517</a>). The RKI Database v.4.2 now contains a total of 11055 MALDI-ToF mass spectra from 1601 microbial strains of highly pathogenic (i.e. biosafety level 3, BSL-3) bacteria such as Bacillus anthracis, Brucella melitensis, Yersinia pestis, Burkholderia mallei / pseudomallei and Francisella tularensis as well as a selection of spectra of their close and distant relatives. The database can be used as a reference for the diagnosis of BSL-3 bacteria using proprietary and free software packages for MALDI-ToF MS-based microbial identification. The spectral data are provided as a zip archive (<a href="https://zenodo.org/records/14562231/files/zenodo%20db%20230306.zip?download=1&preview=1">zenodo db 230306.zip</a>) containing the original mass spectra in their native data format (Bruker Daltonics). Please refer to the pdf file (<a href="https://zenodo.org/records/14562231/files/230306-ZENODO-Metadata.pdf?download=1&preview=1">230306-ZENODO-Metadata.pdf</a>) for information on cultivation conditions, sample preparation and details of the spectra acquisition. Please do not try to print this document (>1600 pages!). Version 20230306 of the RKI database contains for the first time files in the btmsp format (e.g.  <a href="https://zenodo.org/records/14562231/files/2023-May-23-Bacillus-RKI-Database-568.btmsp?download=1&preview=1">2023-May-23-Bacillus-RKI-Database-568.btmsp </a> <a href="https://zenodo.org/api/files/35e90a0c-653d-4ba4-bf93-50b2bd80d073/2023-May-23-Bacillus-RKI-Database-570.btmsp"> </a>and others). These files were generated using the MALDI Biotyper software (Bruker Daltonics) and contain a total of 1601 main spectra (msp) from the BSL-3 database in the proprietary data format of the MALDI Biotyper software. *.btmsp files can be imported and used for identification with this software solution. Please refer to the manufacturer's manual for details on importing btmsp files. Note that the btmsp file available in database version 4 is broken and cannot be imported. The pkf files (<a href="https://zenodo.org/records/14562231/files/230306_ZENODO_30Peaks_0.75.pkf?download=1&preview=1">230306_ZENODO_30Peaks_0.75.pkf</a>, <a href="https://zenodo.org/records/14562231/files/230306_ZENODO_45Peaks_0.75.pkf?download=1&preview=1">230306_ZENODO_45Peaks_0.75.pkf</a>) represent two versions of the MS peak list data in a Matlab compatible format. The latter data can be imported into MicrobeMS, a free Matlab-based software solution developed at the RKI. MicrobeMS can be used for the identification of microorganisms by MALDI-ToF MS and is available at <a href="https://wiki-ms.microbe-ms.com">https://wiki-ms.microbe-ms.com</a>. The Excel file <a href="https://zenodo.org/records/14562231/files/Taxonomy%20information%20-%20RKI%20MALDI-ToF%20MS%20database%20of%20HPB%20at%20ZENODO%20v.4.xlsx?download=1&preview=1">Taxonomy information - RKI MALDI-ToF MS database of HPB at ZENODO v.4.xlsx</a> contains additional taxonomic information such as a detailed list of bacterial MALDI-ToF mass spectra (sheet #1), overviews on the number of spectra per strain, species or bacterial genus (sheet #2), numbers of strains per species, or genus (sheet #3), etc. The RKI mass spectrometry database is updated regularly. The author would like to thank the following individuals for providing microbial strains and species or mass spectra thereof. Without their help, this work would not have been possible. <ul> <li>Wolfgang Beyer - University of Hohenheim, Faculty of Agricultural Sciences, Stuttgart, Germany</li> <li>Guido Werner - Robert Koch-Institute, Nosocomial Pathogens and Antibiotic Resistances (FG13), Wernigerode, Germany</li> <li>Alejandra Bosch - CINDEFI, CONICET-CCT La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina</li> <li>Michal Drevinek - National Institute for Nuclear, Biological and Chemical Protection, Milin, Czech Republic</li> <li>Roland Grunow, Daniela Jacob, Silke Klee, Susann Dupke and Holger Scholz - Robert Koch-Institute, Highly Pathogenic Microorganisms (ZBS2), Berlin, Germany</li> <li>Jörg Rau - Chemisches und Veterinäruntersuchungsamt Stuttgart, Fellbach, Germany</li> <li>Jens Jacob - Robert Koch-Institute, Hospital Hygiene, Infection Prevention and Control (FG14), Berlin, Germany</li> <li>Martin Mielke - Robert Koch-Institute, Department 1 - Infectious Diseases, Berlin, Germany</li> <li>Monika Ehling-Schulz - Functional Microbiology, Institute of Microbiology, University of Veterinary Medicine, Vienna, Austria</li> <li>Armand Paauw - Department of Medical Microbiology, CBRN protection, Universitair Medisch Centrum Utrecht, TNO, Rijswijk, The Netherlands</li> <li>Herbert Tomaso – Friedrich-Löffler-Institut (FLI), Federal Research Institute for Animal Health, Jena, Germany</li> <li>Gabriel Karner - Karner Düngerproduktion GmbH, Research & Development, Neulengbach, Austria</li> <li>Rainer Borriss - Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany</li> <li>Le Thi Thanh Tam - Division of Plant Pathology and Phyto-Immunology, Plant Protection Research Institute, Hanoi, Socialist Republic of Vietnam</li> <li>Xuewen Gao - College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Integrated Management of Crop Diseases and Pests, Nanjing, People’s Republic of China</li> </ul> For a detailed description of the database see: Lasch, P., Beyer, W., Bosch, A. et al. A MALDI-ToF mass spectrometry database for identification and classification of highly pathogenic bacteria. Sci Data 12, 187 (2025). <a href="https://doi.org/10.1038/s41597-025-04504-z">https://doi.org/10.1038/s41597-025-04504-z</a>

opencc-by-4.0Sep 2022View details →

Dimethylsulfoniopropionate-derived compound concentrations, volatile organic compound concentrations, and microorganism abundances around two corals and a seaweed in the reefs of Moorea (French Polynesia)

These data belong in the paper:  M. Masdeu-Navarro, J-F. Mangot, L. Xue, M. Cabrera-Brufau, S.G. Gardner, D.J. Kieber, J.M. González, R. Simó (2022). Spatial and diel patterns of volatile organic compounds, DMSP-derived compopunds and planktonic microorganisms around a tropical scleractinian coral colony. Frontiers in Marine Science. Concentrations of DMSP, acrylate, DMSO, DMS, DMDS, COS, CS2, isoprene, CH3I, CH2ClI, CH2Br2 and CHBr3 in seawater samples around colonies of the corals Acropora pulchra and Pocillopora sp., and the brown seaweed Turbinaria ornata. Abundances of high-DNA and low-DNA bacteria, Prochlorococcus, Synechococcus, picoeukaryotes and nanoeukaryotes in the same samples, as determined by flow cytometry. All samples were collected in April 2018 in the coral reefs of Mo'orea, French Polynesia.  The upper set of data contains concentrations at the distance of 0.5 cm from the coral polyps on the branch tips or verrucae, as well as from the seaweed thalli (samples IN), and 2 m away, downcurrent (samples OUT). The second set of data corresponds to A. pulchra only, and contains seawater samples IN, OUT and AL, the latter being sampled at 0.5 cm from the base of the dead branches colonized by a turf alga. IN, OUT and AL samples were collected over an entire diel cycle, every 6 hours for a period of 30 hours.

opencc-by-4.0Aug 2023View details →

Dataset of scientific article "Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms"

Dataset for journal paper entitled "Variability in Arsenic Methylation Efficiency across Aerobic and Anaerobic Microorganisms" (DOI: 10.1021/acs.est.0c03908). Partial publication's abstract: "Microbially-mediated methylation of arsenic (As) plays an important role in the As biogeochemical cycle, particularly in rice paddy soils where methylated As, generated microbially, is translocated into rice grains. The presence of the arsenite (As(III)) methyltransferase gene (arsM) in soil microbes has been used as an indication of their capacity for As methylation. Here, we evaluate the ability of seven microorganisms encoding active ArsM enzymes to methylate As. Amongst those, only the aerobic species were efficient methylators. The anaerobic microorganisms presented high resistance to As exposure, presumably through their efficient As(III) efflux, but methylated As poorly. The only exception were methanogens, for which efficient As methylation was seemingly an artifact of membrane disruption." The files deposited include: the flow cytometry data and fluorescence microscopy pictures used to assess membrane disruption of the methanogen Methanosarcina mazei, for experimental details please refer to publication, and the supporting information of the publication. Files: <ol> <li>Figure 3_flowcytometry files.zip: flow cytometry measurements reported in Figure 3 of publication. Measurements were performed with a 5-laser LSRII SORP flow cytometer. SYBR Green I (SG) (Invitrogen) was excited by the Blue laser (488 nm) and detected using a 530/30 band pass filter. propidium iodide (PI) (Sigma) was excited by the YG laser (561 nm) and detected using a 610/20 band pass filter. 30’000 events per sample were analyzed into four populations (no fluorescence, SG, SG/PI, or PI). Cells could be assigned to the membrane-compromised population, based on the gating of double-stained and single-stained controls of glutaraldehyde- fixed and ethanol-permeabilized cells. Cytometric data were acquired and analyzed using BD TM FACSDiva software v. 8.0.1 (BD Biosciences, CA, USA). The files consist of the reports generated by BD TM FACSDiva software in .jpg format.</li> <li>Figure S14_fluorescence microscopy files.zip: Fluorescence microscopy pictures in .lsm format of single-stained SG control (SG), single-stained PI control (PI), double-stained control (SG/PI), 16-days sample (16 days) and 20-day sample (20 days) of a Methanosarcina mazei culture grown with 10 μM As(III) as initial concentration. The pictures are published as Figure S14 of the publication. The pictures were taken using Zeiss LSM 700 in the upright configuration equipped with a Plan-Apochromat 63x/1.40 oil immersion objective. For more details please refer to supplementary information in publicaiton. Recommended software for .lsm format included in .zip file.</li> <li>SI_tables_Viacava_et_al_for_publication: file in .xlsx format including the tables: Accession numbers for As(III)-efflux and ArsM proteins and genes; primers used in preparing mutants of C. pasteurianum; growth curves and growth rates values for all sampled cultures; relative abundance of flow-cytometry populations; ICP-MS settings for As analysis; primers for arsM gene amplifications; primers for RT-qPCR of C. pasteurianum; HPLC-ICP-MS spectrum values ; values of arsM and acr3 expression in C. pasteurianum WT and Δacr3; and concentration of total soluble arsenic and soluble arsenic species in filtered medium from all sampled cultures.</li> <li>SI_Viacava_et_al_for_publication: file in .pdf format including: <ol> <li>Materials and methods: total arsenic and arsenic speciation analysis; cloning the arsM genes and gene expression in E. coli AW3110 (DE3); growth conditions of C. pasteurianum H0D0R4, strain used for genetic modification; isolation of the Δacr3 and ΔpyrE::Δacr3 mutants; arsenic methylation by C. pasteurianum Δacr3; transcription of arsM in C. pasteurianum WT and Δacr3; and membrane-integrity assessment of M. mazei cells using flow cytometry.</li> <li>Figures: growth rate of each individual species; abiotic control growth curves; total soluble anaerobic bacterium culture; soluble arsenic species in filtered medium from anaerobic bacterial cultures grown with 50 μM As(III); soluble arsenic species in filtered medium and volatile arsenic species from an A. rosenii culture; soluble arsenic in filtered medium from S. vietnamensis, M. mazei and M. acetivorans cultures; soluble arsenic species in abiotic controls; spiked HPLC-ICP-MS spectra; growth and concentration of soluble arsenic species in ArsM-expressing E. coli AW3110 (DE3); fluorescence microscopy pictures of flow cytometry controls from the membrane-integrity assessment from a M. mazei culture grown with 50 μM As(III); expression of arsM and acr3 in C. pasteurianum WT and Δacr3 mutant; and alignment of ArsM proteins.</li> </ol> </li> <li>README.txt: .txt file with this description text.</li> </ol>

opencc-by-4.0Oct 2023View details →

Data presented in figure 2 of "Evidence of nitrate based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific"

Data collected at the Maïdo observatory between April 24th and April 29th 2018 used in the calculation of statistics presented in Figure 2 of "Evidence of nitrate based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific". Data were obtained by an API-ToF-MS; molecular clusters are grouped by family as described in Chamba et al. 2023. Data were first filtered based on SO2 mixing ratios to exclude the periods when the station was under the influence of the volcanic plume of the Piton de la Fournaise. Hourly averages of the signals of interest were then calculated and only the data corresponding to the periods during which the station was in the free troposphere were considered.

opencc-by-4.0Apr 2020View details →

Supplement of manuscript "microorganisms-746193"

This folder contains analysis data from the study submitted as manuscript (Manuscript ID microorganisms-746193): TITLE: Functional genomics differentiate inherent and environmentally influenced traits in dinoflagellate and diatom communities AUTHORS: Stephanie Elferink, <a href="mailto:Stephanie.westphal@awi.de"> Stephanie.westphal@awi.de</a>, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research   Uwe John, <a href="mailto:Uwe.John@awi.de"> Uwe.John@awi.de</a>, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, and Helmholtz Institute for Functional Marine Biodiversity Stefan Neuhaus, <a href="mailto:Stephan.neuhaus@awi.de">Stephan.neuhaus@awi.de</a>, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research   Sylke Wohlrab, <a href="mailto:Sylke.wohlrab@awi.de"> Sylke.wohlrab@awi.de</a>, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, and Helmholtz Institute for Functional Marine Biodiversity JOURNAL: MDPI - microorganisms MS-ID: microorganisms-746193 HOWTO: Sequences identified as Alveloates or Stramenopiles (description in manuscript) had been were classified more accurately by PhyloAssigner version 6.166 (https://github.com/jungbluth/phyloassigner, Vergin et al., 2013, DOI:10.1038/ismej.2013.32) with a phylogenetic placement onto reference trees based on 18S/28S concatenated alignments, according to Elferink et al. 2017 (DOI: 10.1016/j.dsr.2016.11.002). CONTENT: reference databases: - Alveolata_SSU-LSU-concat_310715_636.phyloassignerdb - Stramenopiles_SSU_LSU_concat_030815_1777.phyloassignerdb query sequence files: - Alveolata_seqtab_SIGN_dada2.fasta - Alveolata_seqtab_SIGN_dada2.fasta created output folder including the taxonomic annotation: - Alveolata_seqtab_SIGN_dada2.place.out - Stramenopiles_seqtab_SIGN_dada2.place.out text file containing the used commands: - commands

opencc-by-4.0Jan 2023View details →

Updated list of QPS-recommended microorganisms for safety risk assessments carried out by EFSA

The European Food Safety Authority (EFSA) asked the Panel on Biological Hazards (BIOHAZ) to deliver a scientific Opinion on the maintenance of the list of qualified presumption of safety (QPS) biological agents. The QPS approach was developed by the EFSA Scientific Committee to provide a harmonised generic pre-evaluation to support safety risk assessments of biological agents intentionally introduced into the food and feed chain, in support of the concerned scientific Panels and Units in the frame of market authorisations. The taxonomic identity, body of knowledge, the safety concerns in relation to pathogenicity and virulence, and the safety for the environment of those microbiological agents are assessed. Safety concerns identified for a respective taxonomic unit (TU) are, where possible and reasonable in number, reflected as ‘qualifications’ that are assessed at the strain level by the EFSA’s scientific Panels. The “list of microorganisms with QPS status” first established in 2007, has been revised and updated annually until 2014 via QPS Opinions; since 2014 the updates are carried out and published every 3 years. If new information is retrieved from extended literature searches (ELS) that would change the QPS status of a TU or its qualifications, this is also published in the Panel Statement covering the previous 6-months period. The ELS protocol can be found at <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzenodo.org%2Fdoi%2F10.5281%2Fzenodo.3607188&data=05%7C02%7C%7Ca719c81b95134433fddc08dc112814e1%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C638404111040390688%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=FaY3tbLnn%2BB%2BDu3PrtEzJR0zPa14z%2FpoKWUBBOaHk34%3D&reserved=0">https://zenodo.org/doi/10.5281/zenodo.3607188</a> and the Search strategies are available at: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.5281%2Fzenodo.3607193&data=02%7C01%7C%7Ca3e4d3a851c84defc2a008d7aa44f9e5%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637165085527347066&sdata=tCzKMQLR2I%2BZBr%2F0sOXPDoPitdjQyqKdlVqDqwigA%2Bo%3D&reserved=0">https://doi.org/</a><a href="https://doi.org/10.5281/zenodo.3607192">10.5281/zenodo.3607192</a>.   The QPS Panel Statement also includes the evaluation of microbiological agents notified to EFSA within the 6-month period for an assessment for feed additives, food enzymes, food additives and flavourings, and novel foods or plant protection products for a possible QPS status. The new QPS status recommendations are incorporated into the 2022 updated “list of microorganisms with QPS status” is available in this upload. The list of “Microbiological agents as notified to EFSA” from 2007, in the context of technical dossiers to EFSA Units, for intentional use in feed and/or food or as sources of food and feed additives, enzymes and plant protection products (PPPs) for safety assessment can be found at <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.5281%2Fzenodo.3607184&data=02%7C01%7C%7Ca3e4d3a851c84defc2a008d7aa44f9e5%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637165085527357024&sdata=%2Fe7qiRXiuKQi%2FBvK5S%2F7undYHv7ibxBlLEHPcSlRz24%3D&reserved=0">https://doi.org/10.5281/zenodo.</a><a href="https://doi.org/10.5281/zenodo.3607183">3607183</a>.   Useful links on EFSA QPS EFSA topic on QPS: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.efsa.europa.eu%2Fen%2Ftopics%2Ftopic%2Fqualified-presumption-safety-qps&data=02%7C01%7C%7Ca3e4d3a851c84defc2a008d7aa44f9e5%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637165085527366985&sdata=TlcglouTWhBY24K5ApAoawNpADKgyl%2FefxVUEbxjQo0%3D&reserved=0">https://www.efsa.europa.eu/en/topics/topic/qualified-presumption-safety-qps</a> Link to the virtual issue on QPS on Wiley Online Library: <a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fefsa.onlinelibrary.wiley.com%2Fdoi%2Ftoc%2F10.1002%2F(ISSN)1831-4732.QPS&data=02%7C01%7C%7C7f88eba744034d83233b08d7a8cd3c1c%7C406a174be31548bdaa0acdaddc44250b%7C1%7C0%7C637163471731831002&sdata=AiprIUek%2B%2But46VabBGk0IMIgLR98CDmxoINYPkKBbs%3D&reserved=0">https://efsa.onlinelibrary.wiley.com/doi/toc/10.1002/(ISSN)1831-4732.QPS</a> Versions history: Versions 1 and 2 were substituted by version 3 – all are associated with the QPS Panel statement EFSA 7: suitability of taxonomic units notified to EFSA until September 2017: <a href="https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2018.5131">https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2018.5131</a>   Version 4 is associated with the QPS Panel statement EFSA 8: suitability of taxonomic units notified to EFSA until March 2018: <a href="https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2018.5315">https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2018.5315</a>   Versions 5 and 6 were substituted by version 7 – all are associated with the QPS Panel statement EFSA 9: suitability of taxonomic units notified to EFSA until September 2018: <a href="https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5555">https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5555</a>   Version 8 is associated with the QPS Panel statement EFSA 10: suitability of taxonomic units notified to EFSA until March 2019: <a href="https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5753">https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5753</a>   Version 9 is associated with the QPS Panel statement EFSA 11: suitability of taxonomic units notified to EFSA until September  2019: <a href="https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2020.5965">https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2020.5965</a> and with the Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA (2017-2019):  <a href="https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2020.5966">https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2020.5966</a>   Version 10: updates version 9 following the update of the qualification of Bacillus velezensis as: ‘absence of toxigenic potential and absence of aminoglycoside production ability’ - applied in the QPS Statement part 11 (ON-5965) and in the 2019 Scientific Opinion (ON-5966). Version 11: updates version 10 following the addition of the Bacillus circulans ‘for production purposes only’ - applied in the QPS Statement part 13 (ON-6377) and in the 2019 Scientific Opinion (ON-5966). Version 12 updates version 11 following the addition of the Bacillus paralicheniformis with the qualifications 'absence of toxigenic activity’ and ‘absence of genetic information to synthesize bacitracin'; and adding Schizochytrium limacinum, which is a synomym for Aurantiochytrium limacinum, - applied in the QPS Statement part 14 (ON-6689) and in the 2019 Scientific Opinion (ON-5966). Version 13 updates version 12 following the addition of Haematococcus lacustris synonym Haematococcus pluvialis, recommended for QPS status with the qualification ‘for production purposes only’. Some other changes related to taxonomy and qualifications are described in the QPS Statement part 15 (ON-7045). Version 14, update of version 13, is related to QPS Statement part 16 (ON-7408). Version 15  is related to QPS Statement part 17 (ON-7746). Version 16  is related to QPS Statement part 18 (ON-8092). Version 17 is related to QPS Statement part 19 (ON-8517). Version 18 is also related to QPS Statement part 19 (ON-8517) with a small correction. Version 19 and 20 are related to QPS Statement part 20 (ON-8882). Version 21 is related to QPS Statement part 21 (ON-9169) Version 22 is related to QPS Statement part 22 (ON-9510)     Note: As of January 2022 the updated list is provided only as excel file format.

opencc-by-4.0Jun 2024View details →

Crosswalks IUCLID 6 v9 EU PPP Microorganisms - active substance application (product) to Data Requirements

The Excel file provides detailed crosswalks from the current Table of Content (ToC) for Microbial Plant Protection Product (PPP) dossier in <a href="https://iuclid6.echa.europa.eu/it/home">IUCLID 6 v.9</a> to Commission Regulation (EU) 283/2013 and Commission Regulation (EU) 284/2013 as amended by Commission Regulation (EU) 2022/1439 & Commission Regulation (EU) 2022/1440. There are two worksheets: <ul> <li>ACTIVE SUBSTANCE (283-2013): mapping between the current IUCLID working context "EU PPP Microorganisms - active substance information" to the Commission Regulation (EU) No 283/2013  as amended by Commission Regulation (EU) 2022/1439.</li> <li>PRODUCT (284-2013): mapping between the the current IUCLID  working context "EU PPP Microorganisms - active substance application (product)" to the Commission Regulation (EU) No 284/2013 as amended by Commission Regulation (EU) 2022/1440.</li> </ul> The spreadsheets contain the following columns: <ul> <li>Data Requirements Section (Commission Reguation (EU) 2022/1439 or 2022/1440): the name of the ToC section (in accordance with the new data requirements).</li> <li>IUCLID section: the name of the ToC section in IUCLID.</li> <li>Endpoint study record: name of the document template used to report individual studies of the section. These usually correspond to <a href="https://www.oecd.org/en/topics/sub-issues/assessment-of-chemicals/harmonised-templates.html">OECD Harmonised Templates (OHT)</a>. </li> <li>Endpoint summary: name of the document template used to report the summary information for the section endpoints.</li> <li>Other IUCLID document: name of any other document template in IUCLID used to report information of the section.  </li> <li>OHT: number of the OECD Harmonised Template used in the section.</li> <li>Additional context: fulI IUCLID paths indicating the section of the respective document where information needs to be provided and/or specific values to be indicated. </li> </ul> Note: in cases where an IUCLID document is not included in the updated ToC this will be found in a specific section 'Documents applicable to the former data requirements' which can be found at the end of the dataset. Version 5 includes changes in the table of contents of <a href="https://iuclid6.echa.europa.eu/it/home">IUCLID 6 v9</a>.

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Disentangling the multiple drivers of ecological adaptation in a microorganism

The survival and reproduction of living organisms depend on their ability to achieve an adequate balance between energy intake and energy expenditure. Multiple quantities contribute to this energetic balance, such as the feeding rate, and the allocation of available energy to growth, maintenance, movement, and reproduction. Given that many of these quantities scale in a predictable way with the size of the organism and with environmental parameters, it should be possible to predict how organisms may adapt to novel environmental conditions in terms of adjusting their morphology, physiology, and behaviour. In a series of experiments, we adapted axenic experimental populations of the ciliate Tetrahymena pyriformis to different environmental conditions of temperature (15°C, 20°C and 25°C) and resource levels (50%, 100%, and 200% of a standard protein solution). We measured population growth, metabolic rate (from respiration), cell size, and movement speed (from video-tracking). On a very short time scale, movement speed and metabolic rate increased with environmental temperature in a way that can be predicted from simple physical scaling relations such as the Boltzmann-Arrhenius equation and the `viscous drag' impacting movement. However, soon after the introduction of Tetrahymena into a novel environment, all the measured quantities were further modulated in a direction that likely provided better biological fitness in the new environment. Changes in cell size played a central role in mediating these adaptations: in small organisms with short generation times, cell size regulations can be a fast and effective way to mediate environmental adaptation by simultaneously affecting multiple phenotypic traits, such as metabolic rate and the energetic costs of movement.

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Fig. 14. a in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 14. a) Spirostomum teres numbers plot [cells mL–1] against autotrophic, APP vs. heterotrophic picoplankton, HPP [cells mL–1], and all analysed APP/HPP data plot, b) Species occurrence in habitats, in which S. teres was found (in the logarithmic scale of APP).

Fig. 15. a in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 15. a) Spirostomum teres numbers plot [cells mL–1] against Photosynthetically Active Radiation, PAR [%] vs. autotrophic picoplankton, APP [cells mL–1], and analysed PAR/APP data plot; blue bubbles mark the samples from the event of incomplete mixing (January); b) Species occurrence in habitats, in which S. teres was found (in the logarithmic scale of PAR).

Fig. 5 in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 5. Representative Spirostomum teres sampling profiles in Lake La Preciosa (a to c) and Lake de La Cruz (d to f). a, d, g) T [°C], Dissolved oxygen, DO [mg L–1], and Photosynthetically active radiation PAR [%]; b, e, h) numbers of APP [cells mL–1] (not analysed in de La Cruz) and of Spirostomum teres [cells L–1]; c) turbidity [NTU]; f, I) chlorophyll a, Chl a [µg L–1], phycoerythrin, PE [µg L–1], and phycocyanin, PC [ng L–1].

Fig. 2 in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 2. Heterotrophic (HPP) and autotrophic picoplankton (APP) in Lake Alchichica (based on Peštová et al. 2008, Macek et al. 2009, Hernández-Avilés et al. 2010, Bautista-Reyes and Macek 2012, Sánchez-Medina et al. 2016, Pájares et al. 2017, and this study).

Fig. 6 in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 6. Spirostomum teres: a) Lake Alchichica (8/8/2011, 30 m), b) Lake La Preciosa (2/9/2011, 20.5 m and c) Lake de La Cruz (25/6/2010, 11.25 m. Protargol stain (QPS). 1 ≡ 10 µm.

Fig. 10 in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 10. Feeding experiments with FLB in Lake Alchichica (a, b), La Preciosa (c, d) and Lake de la Cruz (e, f). Triple DAPI/FITC/CY3 set (a, b); DAPI set (c, e), Chlorophyll a / FITC set. Arrow: Just filled vacuole. 1 ≡ 10 µm.

Fig. 9 in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 9. Lake Alchichica Spirostomum teres with apparent purple sulphur bacteria in Protargol stain a) 4/12/2012, 36.5 m; b) 19/11/14, 38 m, and in infrared autofluorescence b) 19/11/14, 38 m. 1 ≡ 10 µm.

Fig. 4 in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 4. Representative early- (a to h) and late-stratification (i to p) of Spirostomum teres in Lake Alchichica. a, e, i, m) Temperature, T [°C], Dissolved oxygen, DO [mg L–1], and Photosynthetically active radiation PAR [%]; b, f, j, n) numbers of heterotrophic-, HPP [cells mL–1] and autotrophic picoplankton, APP [cells mL–1], and Spirostomum teres [cells L–1]; c, g, k, o) nitrites, NO –, nitrates NO – and ammonium, 2 3 NH [µmol L–1]; d, h, l, p) chlorophyll a, Chl a [µg L–1], phycoerythrin, PE [µg L–1], and phycocyanin, PC [ng L–1].

Fig. 13. a in Spirostomum teres: A Long Term Study of an Anoxic-Hypolimnion Population Feeding upon Photosynthesizing Microorganisms

Fig. 13. a) Spirostomum teres numbers plot [cells mL–1] against dissolved oxygen, DO [mg L–1] vs. nitrite nitrogen NO – [µmolL–1], and all 2 analysed DO/nutrients data plot, b) Species occurrence in habitats, in which S. teres was found (in the logarithmic scale of nitrite nitrogen concentration).