227 research outputs found
Script from "Comparing Quantile Regression Spline analyses and Supervised Machine Learning for environmental quality assessment at coastal marine aquaculture installations"
No full textThis zip archive contains data and R code used in the manuscript 'Comparing Quantile Regression Spline analyses and Supervised Machine Learning for environmental quality assessment at coastal marine aquaculture installations' by Kleopatra Leontidou, Verena Rubel, Thorsten Stoeck.
It contains a data folder with the datasets used for Quantile Regression Spline analyses and Supervised Machine Learning, R code for the Quantile Regression Splines Analysis and for the production of the figures shown in the results section and R code for the Supervised Machine Learning analysis.
Description of data files:
Two 'asv table' datasets were used (Norway_asvtable.csv, Scotland_asvtable.csv), one of which included all samples from seven Norwegian salmon farms (n = 138) and one including all samples (n=92) from seven Scottish salmon farms. The 'asv table' datasets include as rows the Amplicon Sequence Variants (ASVs), as columns the samples (corresponding to the Sample column in the 'metadata' datasets) and as cell values the number of sequence reads.
The 'metadata' datasets (Norway_metadata.csv, Scotland_metadata.csv) include as rows the samples and as columns information about the samples.
The data folder includes also data from Supervised Machine Learning analysis (table_of_predictions_relab_norway.csv, table_of_predictions_relab_scotland.csv,
varimp_mean_nor.csv, varimp_mean_sco.csv).
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Benthic protists: the under-charted majority
No full textForster, Dominik ... et al.-- 11 pages, 6 figures, 1 table, supplementary data http://femsec.oxfordjournals.org/content/suppl/2016/06/05/fiw120.DC1Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribedThis work was supported by the European Commission and is part of the EU-FP7 ERA-net program BiodivERsA, under the project BioMarKs [2008-6530]. Dominik Forster was supported by a graduate scholarship of Stipendienstiftung Rheinland-Pfalz. Micah Dunthorn and Frédéric Mahé were supported by the Deutsche Forschungsgemeinschaft [grant #DU1319/1-1]. Thorsten Stoeck was supported by the Deutsche Forschungsgemeinschaft [grant #STO414/11-1]. Daniel Vaulot was supported by the European Union [grants MicroB3/FP7-287589, MaCuMBA/FP7-KBBE-2012-6-311975]Peer Reviewe
Figure 1 in Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information
No full textFigure 1. Morphology and infraciliature of Psammomitra retractilis (F–J, from Song & Warren, 1996). A, B, F, individuals in extended states to show the typical body shapes. Arrowheads in (A) mark the long, dominant membranelles. C, lateral view of a contracted specimen. D, posterior part, to demonstrate the long dorsal cilia. E, anterior part. Arrowheads indicate the long membranelles, whereas arrows mark the dorsal cilia. G, H, dorsal and lateral views of contracted cells. I, J, ventral and dorsal views to show the infraciliature and macronuclear nodules. Scale bars: A, C, D, F = 40 Mm; E = 30 Mm.Published as part of Yi, Zhenzhen, Song, Weibo, Stoeck, Thorsten, Al-Rasheid, Khaled A. S., Al-Khedhairy, Abdulaziz A., Gong, Jun, Ma, Hongwei & Chen, Zigui, 2009, Phylogenetic analyses suggest that Psammomitra (Ciliophora, Urostylida) should represent an urostylid family, based on small subunit rRNA and alpha-tubulin gene sequence information, pp. 227-236 in Zoological Journal of the Linnean Society 157 (2) on page 229, DOI: 10.1111/j.1096-3642.2008.00524.x, http://zenodo.org/record/544376
Marine microbes and climate change - a Qatari prospective
No full textOverwhelming scientific evidence has emphasized that climate change is a serious global threat driven by human activity and requires a global response. The importance of marine microbial diversity and the involvement of microbes in processes such as the carbon and nitrogen cycles, production and consumption of greenhouse gasses such as carbon dioxide and methane has been highlighted in the past. Qatari marine environment is unique with an unusual harsh and arid climate, which influences sea salinity and temperature, thus influencing the water density and currents. Of economic importance, these waters are heavily influenced through anthropogenic use. Thus, Qatar's marine flora including the exotic phytoplankton and zooplankton species have adapted and developed a tolerance for extreme conditions. However, despite their relevance for ecosystem functioning, little is known about smaller size classes of organisms (bacteria, archaea, protists, fungi) in coastal habitats, their diversity, their distribution, biological interactions and how they cope with environmental changes. Therefore, a QNRF funded study, a first step towards an understanding and protection of the Qatari marine biosphere, established a baseline of microbial life in the waters surrounding Qatar, in order to monitor and react to the effect of global changes in these waters. Our multi-collaboration project established a comprehensive understanding of microbial biodiversity in Qatari coastal waters using the culture and metagenomic approaches. Results will be presented and the future perspectives discussed.Acknowledgement: This Research was supported by grant (NPRP-6-647-1-127) from the Qatar National Research Fund (a member of Qatar Foundation) to Rashmi Fotedar, Teun Boekhout, Jack. W. Fell, and Thorsten Stoeck.</jats:p
Mining environmental high-throughput sequence data sets to identify divergent amplicon clusters for phylogenetic reconstruction and morphotype visualization
No full textCotterillia bromelicola nov. gen., nov. spec., a gonostomatid ciliate (Ciliophora, Hypotricha) from tank bromeliads (Bromeliaceae) with de novo originating dorsal kineties
No full textMassively Parallel Tag Sequencing Unveils the Complexity of Marine Protistan Communities in Oxygen-Depleted Habitats
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Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments
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