\n

\n \n 2024\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Assessing the response of an urban stream ecosystem to salinization under different flow regimes.\n \n \n \n \n\n\n \n Madge Pimentel, I.; Baikova, D.; Buchner, D.; Burfeid Castellanos, A.; David, G. M.; Deep, A.; Doliwa, A.; Hadžiomerović, U.; Mayombo, N. A. S.; Prati, S.; Spyra, M. A.; Vermiert, A.; Beisser, D.; Dunthorn, M.; Piggott, J. J.; Sures, B.; Tiegs, S. D.; Leese, F.; and Beermann, A. J.\n\n\n \n\n\n\n Science of The Total Environment, 926: 171849. Mar 2024.\n \n\n\n\n
\n\n\n\n \n \n $\"Assessing$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n

\n

@Article{MADGEPIMENTEL2024171849,\n  author   = {Iris {Madge Pimentel} and Daria Baikova and Dominik Buchner and Andrea {Burfeid Castellanos} and Gwendoline M. David and Aman Deep and Annemie Doliwa and Una Hadžiomerović and Ntambwe A. Serge Mayombo and Sebastian Prati and Marzena Agata Spyra and Anna-Maria Vermiert and Daniela Beisser and Micah Dunthorn and Jeremy J. Piggott and Bernd Sures and Scott D. Tiegs and Florian Leese and Arne J. Beermann},\n  journal  = {Science of The Total Environment},\n  title    = {Assessing the response of an urban stream ecosystem to salinization under different flow regimes},\n  year     = {2024},\n  issn     = {0048-9697},\n  month    = {Mar},\n  pages    = {171849},\n  volume   = {926},\n  abstract = {Urban streams are exposed to a variety of anthropogenic stressors. Freshwater salinization is a key stressor in these ecosystems that is predicted to be further exacerbated by climate change, which causes simultaneous changes in flow parameters, potentially resulting in non-additive effects on aquatic ecosystems. However, the effects of salinization and flow velocity on urban streams are still poorly understood as multiple-stressor experiments are often conducted at pristine rather than urban sites. Therefore, we conducted a mesocosm experiment at the Boye River, a recently restored stream located in a highly urbanized area in Western Germany, and applied recurrent pulses of salinity along a gradient (NaCl, 9 h daily of +0 to +2.5 mS/cm) in combination with normal and reduced current velocities (20 cm/s vs. 10 cm/s). Using a comprehensive assessment across multiple organism groups (macroinvertebrates, eukaryotic algae, fungi, parasites) and ecosystem functions (primary production, organic-matter decomposition), we show that flow velocity reduction has a pervasive impact, causing community shifts for almost all assessed organism groups (except fungi) and inhibiting organic-matter decomposition. Salinization affected only dynamic components of community assembly by enhancing invertebrate emigration via drift and reducing fungal reproduction. We caution that the comparatively small impact of salt in our study can be due to legacy effects from past salt pollution by coal mining activities >30 years ago. Nevertheless, our results suggest that urban stream management should prioritize the continuity of a minimum discharge to maintain ecosystem integrity. Our study exemplifies a holistic approach for the assessment of multiple-stressor impacts on streams, which is needed to inform the establishment of a salinity threshold above which mitigation actions must be taken.},\n  doi      = {https://doi.org/10.1016/j.scitotenv.2024.171849},\n  keywords = {Macroinvertebrates, Algae, Fungi, Parasites, Organic-matter decomposition, Primary production},\n  url      = {https://www.sciencedirect.com/science/article/pii/S0048969724019922},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2023\n \n \n (5)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release.\n \n \n \n \n\n\n \n Vos, M.; Hering, D.; Gessner, M. O.; Leese, F.; Schäfer, R. B.; Tollrian, R.; Boenigk, J.; Haase, P.; Meckenstock, R.; Baikova, D.; Bayat, H.; Beermann, A.; Beisser, D.; Beszteri, B.; Birk, S.; Boden, L.; Brauer, V.; Brauns, M.; Buchner, D.; Burfeid-Castellanos, A.; David, G.; Deep, A.; Doliwa, A.; Dunthorn, M.; Enß, J.; Escobar-Sierra, C.; Feld, C. K.; Fohrer, N.; Grabner, D.; Hadziomerovic, U.; Jähnig, S. C.; Jochmann, M.; Khaliq, S.; Kiesel, J.; Kuppels, A.; Lampert, K. P.; Le, T. Y.; Lorenz, A. W.; Madariaga, G. M.; Meyer, B.; Pantel, J. H.; Pimentel, I. M.; Mayombo, N. S.; Nguyen, H. H.; Peters, K.; Pfeifer, S. M.; Prati, S.; Probst, A. J.; Reiner, D.; Rolauffs, P.; Schlenker, A.; Schmidt, T. C.; Shah, M.; Sieber, G.; Stach, T. L.; Tielke, A.; Vermiert, A.; Weiss, M.; Weitere, M.; and Sures, B.\n\n\n \n\n\n\n Science of The Total Environment, 872: 162196. May 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@Article{Vos2023,\n  author    = {Matthijs Vos and Daniel Hering and Mark O. Gessner and Florian Leese and Ralf B. Sch\\"{a}fer and Ralph Tollrian and Jens Boenigk and Peter Haase and Rainer Meckenstock and Daria Baikova and Helena Bayat and Arne Beermann and Daniela Beisser and B{\\'{a}}nk Beszteri and Sebastian Birk and Lisa Boden and Verena Brauer and Mario Brauns and Dominik Buchner and Andrea Burfeid-Castellanos and Gwendoline David and Aman Deep and Annemie Doliwa and Micah Dunthorn and Julian En{\\ss} and Camilo Escobar-Sierra and Christian K. Feld and Nicola Fohrer and Daniel Grabner and Una Hadziomerovic and Sonja C. J\\"{a}hnig and Maik Jochmann and Shaista Khaliq and Jens Kiesel and Annabel Kuppels and Kathrin P. Lampert and T.T. Yen Le and Armin W. Lorenz and Graciela Medina Madariaga and Benjamin Meyer and Jelena H. Pantel and Iris Madge Pimentel and Ntambwe Serge Mayombo and Hong Hanh Nguyen and Kristin Peters and Svenja M. Pfeifer and Sebastian Prati and Alexander J. Probst and Dominik Reiner and Peter Rolauffs and Alexandra Schlenker and Torsten C. Schmidt and Manan Shah and Guido Sieber and Tom Lennard Stach and Ann-Kathrin Tielke and Anna-Maria Vermiert and Martina Weiss and Markus Weitere and Bernd Sures},\n  journal   = {Science of The Total Environment},\n  title     = {The Asymmetric Response Concept explains ecological consequences of multiple stressor exposure and release},\n  year      = {2023},\n  month     = may,\n  pages     = {162196},\n  volume    = {872},\n  abstract  = {Our capacity to predict trajectories of ecosystem degradation and recovery is limited, especially when impairments are caused by multiple stressors. Recovery may be fast or slow and either complete or partial, sometimes result in novel ecosystem states or even fail completely. Here, we introduce the Asymmetric Response Concept (ARC) that provides a basis for exploring and predicting the pace and magnitude of ecological responses to, and release from, multiple stressors. The ARC holds that three key mechanisms govern population, community and ecosystem trajectories. Stress tolerance is the main mechanism determining responses to increasing stressor intensity, whereas dispersal and biotic interactions predominantly govern responses to the release from stressors. The shifting importance of these mechanisms creates asymmetries between the ecological trajectories that follow increasing and decreasing stressor intensities. This recognition helps to understand multiple stressor impacts and to predict which measures will restore communities that are resistant to restoration.},\n  doi       = {10.1016/j.scitotenv.2023.162196},\n  publisher = {Elsevier {BV}},\n  url       = {https://doi.org/10.1016/j.scitotenv.2023.162196},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Chemoproteomics Reveals the Pan-HER Kinase Inhibitor Neratinib To Target an Arabidopsis Epoxide Hydrolase Related to Phytohormone Signaling.\n \n \n \n \n\n\n \n Ninck, S.; Halder, V.; Krahn, J. H.; Beisser, D.; Resch, S.; Dodds, I.; Scholtysik, R.; Bormann, J.; Sewald, L.; Gupta, M. D.; Heilmann, G.; Bhandari, D. D.; Morimoto, K.; Buscaill, P.; Hause, B.; van der Hoorn, R. A. L.; Kaschani, F.; and Kaiser, M.\n\n\n \n\n\n\n ACS Chemical Biology, 18(5): 1076–1088. Apr 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Chemoproteomics$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@Article{Ninck2023,\n  author    = {Sabrina Ninck and Vivek Halder and Jan H. Krahn and Daniela Beisser and Sarah Resch and Isobel Dodds and Ren{\\'{e}} Scholtysik and Jenny Bormann and Leonard Sewald and Mainak D. Gupta and Geronimo Heilmann and Deepak D. Bhandari and Kyoko Morimoto and Pierre Buscaill and Bettina Hause and Renier A. L. van der Hoorn and Farnusch Kaschani and Markus Kaiser},\n  journal   = {{ACS} Chemical Biology},\n  title     = {Chemoproteomics Reveals the Pan-{HER} Kinase Inhibitor Neratinib To Target an Arabidopsis Epoxide Hydrolase Related to Phytohormone Signaling},\n  year      = {2023},\n  month     = {Apr},\n  number    = {5},\n  pages     = {1076--1088},\n  volume    = {18},\n  abstract  = {Plant phytohormone pathways are regulated by an intricate network of signaling components and modulators, many of which still remain unknown. Here, we report a forward chemical genetics approach for the identification of functional SA agonists in Arabidopsis thaliana that revealed Neratinib (Ner), a covalent pan-HER kinase inhibitor drug in humans, as a modulator of SA signaling. Instead of a protein kinase, chemoproteomics unveiled that Ner covalently modifies a surface-exposed cysteine residue of Arabidopsis epoxide hydrolase isoform 7 (AtEH7), thereby triggering its allosteric inhibition. Physiologically, the Ner application induces jasmonate metabolism in an AtEH7-dependent manner as an early response. In addition, it modulates PATHOGENESIS RELATED 1 (PR1) expression as a hallmark of SA signaling activation as a later effect. AtEH7, however, is not the exclusive target for this physiological readout induced by Ner. Although the underlying molecular mechanisms of AtEH7-dependent modulation of jasmonate signaling and Ner-induced PR1-dependent activation of SA signaling and thus defense response regulation remain unknown, our present work illustrates the powerful combination of forward chemical genetics and chemical proteomics for identifying novel phytohormone signaling modulatory factors. It also suggests that marginally explored metabolic enzymes such as epoxide hydrolases may have further physiological roles in modulating signaling.},\n  doi       = {10.1021/acschembio.2c00322},\n  publisher = {American Chemical Society ({ACS})},\n  url       = {https://doi.org/10.1021/acschembio.2c00322},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater.\n \n \n \n \n\n\n \n Sieber, G.; Drees, F.; Shah, M.; Stach, T. L.; Hohrenk-Danzouma, L.; Bock, C.; Vosough, M.; Schumann, M.; Sures, B.; Probst, A. J.; Schmidt, T. C.; Beisser, D.; and Boenigk, J.\n\n\n \n\n\n\n Science of The Total Environment, 903: 167457. Sep 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Exploring$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@Article{Sieber2023,\n  author    = {Guido Sieber and Felix Drees and Manan Shah and Tom L. Stach and Lotta Hohrenk-Danzouma and Christina Bock and Maryam Vosough and Mark Schumann and Bernd Sures and Alexander J. Probst and Torsten C. Schmidt and Daniela Beisser and Jens Boenigk},\n  journal   = {Science of The Total Environment},\n  title     = {Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater},\n  year      = {2023},\n  month     = {Sep},\n  pages     = {167457},\n  volume    = {903},\n  abstract  = {Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters. We aimed at assessing the impact of introducing 33 % treated wastewater into a triplicated large-scale mesocosm setup during a 10-day exposure period. Discharge of treated wastewater significantly altered the chemical signature as well as the microeukaryotic and prokaryotic diversity of the mesocosms. Non-target screening, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding detected these changes with significant covariation of the detected pattern between methods.\n\nThe 18S V9 rRNA gene metabarcoding exhibited superior sensitivity immediately following the introduction of treated wastewater and remained one of the top-performing methods throughout the study. Full-length 16S rRNA gene metabarcoding demonstrated sensitivity only in the initial hour, but became insignificant thereafter. The non-target screening approach was effective throughout the experiment and in contrast to the metabarcoding methods the signal to noise ratio remained similar during the experiment resulting in an increasing relative strength of this method. Based on our findings, we conclude that all methods employed for monitoring environmental disturbances from various sources are suitable. The distinguishing factor of these methods is their ability to detect unknown pollutants and organisms, which sets them apart from previously utilized approaches and allows for a more comprehensive perspective. Given their diverse strengths, particularly in terms of temporal resolution, these methods are best suited as complementary approaches.},\n  doi       = {10.1016/j.scitotenv.2023.167457},\n  publisher = {Elsevier {BV}},\n  url       = {https://doi.org/10.1016/j.scitotenv.2023.167457},\n}\n\n

\n

\n\n\n

\n Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters. We aimed at assessing the impact of introducing 33 % treated wastewater into a triplicated large-scale mesocosm setup during a 10-day exposure period. Discharge of treated wastewater significantly altered the chemical signature as well as the microeukaryotic and prokaryotic diversity of the mesocosms. Non-target screening, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding detected these changes with significant covariation of the detected pattern between methods. The 18S V9 rRNA gene metabarcoding exhibited superior sensitivity immediately following the introduction of treated wastewater and remained one of the top-performing methods throughout the study. Full-length 16S rRNA gene metabarcoding demonstrated sensitivity only in the initial hour, but became insignificant thereafter. The non-target screening approach was effective throughout the experiment and in contrast to the metabarcoding methods the signal to noise ratio remained similar during the experiment resulting in an increasing relative strength of this method. Based on our findings, we conclude that all methods employed for monitoring environmental disturbances from various sources are suitable. The distinguishing factor of these methods is their ability to detect unknown pollutants and organisms, which sets them apart from previously utilized approaches and allows for a more comprehensive perspective. Given their diverse strengths, particularly in terms of temporal resolution, these methods are best suited as complementary approaches.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Differences in pigment composition and concentration between phototrophic, mixotrophic, and heterotrophic Chrysophyceae.\n \n \n \n \n\n\n \n Boenigk, J.; Beisser, D.; Franke, L.; Klar, L.; Ilic, M.; and Fink, P.\n\n\n \n\n\n\n Fottea, 23(2): 223–234. Oct 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Differences$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{fot-202302-0008,\n  author   = {Boenigk, Jens and Beisser, Daniela and Franke, Luise and Klar, Lea and Ilic, Maja and Fink, Patrick},\n  journal  = {Fottea},\n  title    = {Differences in pigment composition and concentration between phototrophic, mixotrophic, and heterotrophic Chrysophyceae},\n  year     = {2023},\n  issn     = {18025439},\n  month    = {Oct},\n  number   = {2},\n  pages    = {223--234},\n  volume   = {23},\n  abstract = {The presence of distinct pigments is characteristic of different algal groups while the relative concentration of these pigments may vary with light conditions. Here we investigate the pigment pattern of 35 strains of Chrysophyceae by means of high-performance liquid chromatography. We further investigated shifts in pigment concentrations between light and dark conditions and the conservation of these pigment patterns in heterotrophic, mixotrophic, and phototrophic taxa. We did not find chlorophyll in heterotrophic strains but carotenoids were present in all taxa. In phototrophs and mixotrophs, we confirm the presence of the chlorophylls-a, c<sub>1</sub>, and c<sub>2</sub> as well as of fucoxanthin. We provide evidence for the violaxanthin cycle as the dominant xanthophyll cycle. Moreover, we found pigments of the diadinoxanthin cycle in low concentrations. While pigment concentrations were regulated depending on light availability in photosynthetic taxa, they were unaffected by light in heterotrophic taxa.},\n  doi      = {10.5507/fot.2023.001},\n  keywords = {carotenoids; chlorophylls; Chrysophyceae; light adaptation; pigments; trophic mode},\n  url      = {https://fottea.czechphycology.cz/artkey/fot-202302-0008.php},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Natrix2 – Improved amplicon workflow with novel Oxford Nanopore Technologies support and enhancements in clustering, classification and taxonomic databases.\n \n \n \n \n\n\n \n Deep, A.; Bludau, D.; Welzel, M.; Clemens, S.; Heider, D.; Boenigk, J.; and Beisser, D.\n\n\n \n\n\n\n Metabarcoding and Metagenomics, 7: e109389. Oct 2023.\n \n\n\n\n
\n\n\n\n \n \n $\"Natrix2$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@Article{10.3897/mbmg.7.109389,\n  author    = {Aman Deep and Dana Bludau and Marius Welzel and Sandra Clemens and Dominik Heider and Jens Boenigk and Daniela Beisser},\n  journal   = {Metabarcoding and Metagenomics},\n  title     = {Natrix2 – Improved amplicon workflow with novel Oxford Nanopore Technologies support and enhancements in clustering, classification and taxonomic databases},\n  year      = {2023},\n  month     = {Oct},\n  pages     = {e109389},\n  volume    = {7},\n  abstract  = {Sequencing of amplified DNA is the first step towards the generation of Amplicon Sequence Variants (ASVs) or Operational Taxonomic Units (OTUs) for biodiversity assessment and comparative analyses of environmental communities and microbiomes. Notably, the rapid advancements in sequencing technologies have paved the way for the growing utilization of third-generation long-read approaches in recent years. These sequence data imply increasing read lengths, higher error rates, and altered sequencing chemistry. Likewise, methods for amplicon classification and reference databases have progressed, leading to the expansion of taxonomic application areas and higher classification accuracy. With Natrix, a user-friendly and reducible workflow solution, processing of prokaryotic and eukaryotic environmental Illumina sequences using 16S or 18S is possible. Here, we present an updated version of the pipeline, Natrix2, which incorporates VSEARCH as an alternative clustering method with better performance for 16S metabarcoding approaches and mothur for taxonomic classification on further databases, including PR2, UNITE and SILVA. Additionally, Natrix2 includes the handling of Nanopore reads, which entails initial error correction and refinement of reads using Medaka and Racon to subsequently determine their taxonomic classification.},\n  doi       = {10.3897/mbmg.7.109389},\n  eprint    = {https://doi.org/10.3897/mbmg.7.109389},\n  publisher = {Pensoft Publishers},\n  url       = {https://doi.org/10.3897/mbmg.7.109389},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2022\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution.\n \n \n \n \n\n\n \n Frantal, D.; Agatha, S.; Beisser, D.; Boenigk, J.; Darienko, T.; Dirren-Pitsch, G.; Filker, S.; Gruber, M.; Kammerlander, B.; Nachbaur, L.; Scheffel, U.; Stoeck, T.; Qian, K.; Weißenbacher, B.; Pröschold, T.; and Sonntag, B.\n\n\n \n\n\n\n Frontiers in Microbiology, 12. Feb 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Molecular$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Frantal2022,\n  author    = {Daniela Frantal and Sabine Agatha and Daniela Beisser and Jens Boenigk and Tatyana Darienko and Gianna Dirren-Pitsch and Sabine Filker and Michael Gruber and Barbara Kammerlander and Laura Nachbaur and Ulrike Scheffel and Thorsten Stoeck and Kuimei Qian and Birgit Wei{\\ss}enbacher and Thomas Pr\\"{o}schold and Bettina Sonntag},\n  journal   = {Frontiers in Microbiology},\n  title     = {Molecular Data Reveal a Cryptic Diversity in the Genus Urotricha (Alveolata, Ciliophora, Prostomatida), a Key Player in Freshwater Lakes, With Remarks on Morphology, Food Preferences, and Distribution},\n  year      = {2022},\n  month     = {Feb},\n  volume    = {12},\n  abstract  = {Species of the ciliate genus Urotricha are key players in freshwater plankton communities. In the pelagial of lakes, about 20 urotrich species occur throughout an annual cycle, some of which play a pivotal role in aquatic food webs. For example, during the phytoplankton spring bloom, they consume a remarkable proportion of the algal production. In ecological studies, urotrich ciliates are usually merely identified to genus rank and grouped into size classes. This is unsatisfying considering the distinct autecological properties of individual species and their specific spatial and temporal distribution patterns. As a basis for future research, we characterized in detail four common urotrich morphotypes, i.e., specimens identified as U. furcata and tentatively as U. agilis, U. pseudofurcata, and U. castalia, using state-of-the-art methods. We used an integrative polyphasic approach, in which morphological studies (in vivo observation, silver staining methods, scanning electron microscopy) were linked with a molecular approach exploiting four different gene fragments as taxonomic DNA barcodes with different resolution potential (SSU rDNA, ITS-1, ITS-2, hypervariable V4 and V9 regions of the SSU rDNA). We shed light on the diversity of urotrich ciliates as well as on their global distribution patterns, and annual cycles. Additionally, we coupled individual species occurrences and environmental parameters, and subsequently modeled the distribution and occurrence, using logistic regressions. Furthermore, for one strain putatively identified as U. castalia, we ascertained the optimal cultivation media and food preferences. Thereby, our comprehensive view on these important freshwater ciliates that frequently occur in environmental high throughput sequencing datasets worldwide will allow future studies to better exploit protistan plankton data from lakes.},\n  doi       = {10.3389/fmicb.2021.787290},\n  keywords  = {paper},\n  publisher = {Frontiers Media {SA}},\n  url       = {https://doi.org/10.3389/fmicb.2021.787290},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n The relationship between land cover and microbial community composition in European lakes.\n \n \n \n \n\n\n \n Sperlea, T.; Schenk, J. P.; Dreßler, H.; Beisser, D.; Hattab, G.; Boenigk, J.; and Heider, D.\n\n\n \n\n\n\n Science of The Total Environment, 825: 153732. Jun 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"The$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Sperlea2022,\n  author    = {Theodor Sperlea and Jan Philip Schenk and Hagen Dre{\\ss}ler and Daniela Beisser and Georges Hattab and Jens Boenigk and Dominik Heider},\n  journal   = {Science of The Total Environment},\n  title     = {The relationship between land cover and microbial community composition in European lakes},\n  year      = {2022},\n  month     = {Jun},\n  pages     = {153732},\n  volume    = {825},\n  abstract  = {Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.},\n  doi       = {10.1016/j.scitotenv.2022.153732},\n  keywords  = {paper},\n  publisher = {Elsevier {BV}},\n  url       = {https://doi.org/10.1016/j.scitotenv.2022.153732},\n}\n\n

\n

\n\n\n

\n Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion.\n \n \n \n \n\n\n \n Sieber, G.; Beisser, D.; Rothenberger, J. L.; Shah, M.; Schumann, M.; Sures, B.; and Boenigk, J.\n\n\n \n\n\n\n Scientific Reports, 12(1): 18684. Nov 2022.\n \n\n\n\n
\n\n\n\n \n \n $\"Microbial$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n\n\n\n

\n

@Article{Sieber2022,\n  author   = {Sieber, G. and Beisser, D. and Rothenberger, J. L. and Shah, M. and Schumann, M. and Sures, B. and Boenigk, J.},\n  journal  = {Scientific Reports},\n  title    = {Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion},\n  year     = {2022},\n  issn     = {2045-2322},\n  month    = {Nov},\n  number   = {1},\n  pages    = {18684},\n  volume   = {12},\n  abstract = {Aquatic environments serve as a sink for anthropogenic discharges. A significant part of the discharge is tire wear, which is increasingly being released into the environment, causing environmental disasters due to their longevity and the large number of pollutants they contain. Main components of tires are plastic and zinc, which therefore can be used as substitutes for tire abrasion to study the effect on microbial life. We investigate environmentally realistic concentrations of plastic and zinc on a freshwater microeukaryotic community using high-throughput sequencing of the 18S V9 region over a 14-day exposure period. Apart from a generally unchanged diversity upon exposure to zinc and nanoplastics, a change in community structure due to zinc is evident, but not due to nanoplastics. Evidently, nanoplastic particles hardly affect the community, but zinc exposure results in drastic functional abundance shifts concerning the trophic mode. Phototrophic microorganisms were almost completely diminished initially, but photosynthesis recovered. However, the dominant taxa performing photosynthesis changed from bacillariophytes to chlorophytes. While phototrophic organisms are decreasing in the presence of zinc, the mixotrophic fraction initially benefitted and the heterotrophic fraction were benefitting throughout the exposure period. In contrast to lasting changes in taxon composition, the functional community composition is initially strongly imbalanced after application of zinc but returns to the original state.},\n  day      = {04},\n  doi      = {10.1038/s41598-022-22906-6},\n  url      = {https://doi.org/10.1038/s41598-022-22906-6},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2021\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates.\n \n \n \n \n\n\n \n Majda, S.; Beisser, D.; and Boenigk, J.\n\n\n \n\n\n\n Communications Biology, 4(1): 328. Mar 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Nutrient-driven$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Majda2021,\n  author    = {Stephan Majda and Daniela Beisser and Jens Boenigk},\n  journal   = {Communications Biology},\n  title     = {Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates},\n  year      = {2021},\n  month     = {Mar},\n  number    = {1},\n  pages     = {328},\n  volume    = {4},\n  abstract  = {Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation. We sequenced the genomes of 16 chrysophyte strains and compared them in terms of size, function, and sequence characteristics in relation to photo-, mixo- and heterotrophic nutrition. All strains were sequenced with Illumina and partly with PacBio. Heterotrophic taxa have reduced genomes and a higher GC content of up to 59% as compared to phototrophic taxa. Heterotrophs have a large pan genome, but a small core genome, indicating a differential specialization of the distinct lineages. The pan genome of mixotrophs and heterotrophs taken together but not the pan genome of the mixotrophs alone covers the complete functionality of the phototrophic strains indicating a random reduction of genes. The observed ploidy ranges from di- to tetraploidy and was found to be independent of taxonomy or trophic mode. Our results substantiate an evolution driven by nutrient and carbon limitation.},\n  doi       = {10.1038/s42003-021-01781-3},\n  keywords  = {paper},\n  publisher = {Springer Science and Business Media {LLC}},\n  url       = {https://doi.org/10.1038/s42003-021-01781-3},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n A multi-omics study on quantifying antimicrobial resistance in European freshwater lakes.\n \n \n \n \n\n\n \n Spänig, S.; Eick, L.; Nuy, J. K.; Beisser, D.; Ip, M.; Heider, D.; and Boenigk, J.\n\n\n \n\n\n\n Environment International, 157: 106821. Dec 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"A$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Spaenig2021,\n  author   = {Sebastian Spänig and Lisa Eick and Julia K. Nuy and Daniela Beisser and Margaret Ip and Dominik Heider and Jens Boenigk},\n  journal  = {Environment International},\n  title    = {A multi-omics study on quantifying antimicrobial resistance in European freshwater lakes},\n  year     = {2021},\n  issn     = {0160-4120},\n  month    = {Dec},\n  pages    = {106821},\n  volume   = {157},\n  abstract = {The surveillance of wastewater for the Covid-19 virus during this unprecedented pandemic and mapped to the distribution and magnitude of the infected in the population near real-time exemplifies the importance of tracking rapidly changing trends of pathogens or public health problems at a large scale. The rising trends of antimicrobial resistance (AMR) with multidrug-resistant pathogens from the environmental water have similarly gained much attention in recent years. Wastewater-based epidemiology from water samples has shown that a wide range of AMR-related genes is frequently detected. Albeit sewage is treated before release and thus, the abundance of pathogens should be significantly reduced or even pathogen-free, several studies indicated the contrary. Pathogens are still measurable in the released water, ultimately entering freshwaters, such as rivers and lakes. Furthermore, socio-economic and environmental factors, such as chemical industries and animal farming nearby, impact the presence of AMR. Many bacterial species from the environment are intrinsically resistant and also contribute to the resistome of freshwater lakes. This study collected the most extensive standardized freshwater data set from hundreds of European lakes and conducted a comprehensive multi-omics analysis on antimicrobial resistance from these freshwater lakes. Our research shows that genes encoding for AMR against tetracyclines, cephalosporins, and quinolones were commonly identified, while for some, such as sulfonamides, resistance was less frequently present. We provide an estimation of the characteristic resistance of AMR in European lakes, which can be used as a comprehensive resistome dataset to facilitate and monitor temporal changes in the development of AMR in European freshwater lakes.},\n  doi      = {https://doi.org/10.1016/j.envint.2021.106821},\n  keywords = {paper},\n  url      = {https://www.sciencedirect.com/science/article/pii/S0160412021004463},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework.\n \n \n \n \n\n\n \n Sperlea, T.; Kreuder, N.; Beisser, D.; Hattab, G.; Boenigk, J.; and Heider, D.\n\n\n \n\n\n\n Molecular Ecology. Mar 2021.\n \n\n\n\n
\n\n\n\n \n \n $\"Quantification$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Sperlea2021,\n  author   = {Sperlea, Theodor and Kreuder, Nico and Beisser, Daniela and Hattab, Georges and Boenigk, Jens and Heider, Dominik},\n  journal  = {Molecular Ecology},\n  title    = {Quantification of the covariation of lake microbiomes and environmental variables using a machine learning-based framework},\n  year     = {2021},\n  month    = {Mar},\n  abstract = {It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators. We apply the framework to a data set containing operational taxonomic units (OTUs) as well as more than twenty physicochemical and geographic variables measured in a large-scale survey of European lakes. While a large part of variation (up to 61\\%) in many environmental variables can be explained by microbial community composition, some variables do not show significant covariation with the microbial lake community. Moreover, we have identified OTUs that act as “multitask” bioindicators, i.e., that are indicative for multiple environmental variables, and thus could be candidates for lake water monitoring schemes. Our results represent, for the first time, a quantification of the covariation of the lake microbiome and a wide array of environmental variables for lake ecosystems. Building on the results and methodology presented here, it will be possible to identify microbial taxa and processes that are essential for functioning and stability of lake ecosystems.},\n  doi      = {https://doi.org/10.1111/mec.15872},\n  eprint   = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.15872},\n  keywords = {paper},\n  url      = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.15872},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2020\n \n \n (6)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Factors shaping community patterns of protists and bacteria on a European scale.\n \n \n \n \n\n\n \n Bock, C.; Jensen, M.; Forster, D.; Marks, S.; Nuy, J.; Psenner, R.; Beisser, D.; and Boenigk, J.\n\n\n \n\n\n\n Environmental Microbiology, 22(6): 2243-2260. Mar 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Factors$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Bock2020,\n  author   = {Bock, Christina and Jensen, Manfred and Forster, Dominik and Marks, Sabina and Nuy, Julia and Psenner, Roland and Beisser, Daniela and Boenigk, Jens},\n  journal  = {Environmental Microbiology},\n  title    = {Factors shaping community patterns of protists and bacteria on a European scale},\n  year     = {2020},\n  month    = {Mar},\n  number   = {6},\n  pages    = {2243-2260},\n  volume   = {22},\n  abstract = {Summary Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high-throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross-domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.},\n  doi      = {https://doi.org/10.1111/1462-2920.14992},\n  eprint   = {https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.14992},\n  keywords = {paper},\n  url      = {https://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.14992},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Propionate supplementation promotes the expansion of peripheral regulatory T-Cells in patients with end-stage renal disease.\n \n \n \n \n\n\n \n Meyer, F.; Seibert, F. S.; Nienen, M.; Welzel, M.; Beisser, D.; Bauer, F.; Rohn, B.; Westhoff, T. H.; Stervbo, U.; and Babel, N.\n\n\n \n\n\n\n Journal of Nephrology, 33(4): 817–827. Mar 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Propionate$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Meyer2020,\n  author   = {Meyer, Fabian and Seibert, Felix S. and Nienen, Mikalai and Welzel, Marius and Beisser, Daniela and Bauer, Frederic and Rohn, Benjamin and Westhoff, Timm H. and Stervbo, Ulrik and Babel, Nina},\n  journal  = {Journal of Nephrology},\n  title    = {Propionate supplementation promotes the expansion of peripheral regulatory T-Cells in patients with end-stage renal disease},\n  year     = {2020},\n  issn     = {1724-6059},\n  month    = {Mar},\n  number   = {4},\n  pages    = {817--827},\n  volume   = {33},\n  abstract = {Patients with end-stage renal disease (ESRD) suffer from a progressively increasing low-grade systemic inflammation, which is associated with higher morbidity and mortality. Regulatory T cells (Tregs) play an important role in regulation of the inflammatory process. Previously, it has been demonstrated that short-chain fatty acids reduce inflammation in the central nervous system in a murine model of multiple sclerosis through an increase in tissue infiltrating Tregs. Here, we evaluated the effect of the short-chain fatty acid propionate on the chronic inflammatory state and T-cell composition in ESRD patients. Analyzing ESRD patients and healthy blood donors before, during, and 60?days after the propionate supplementation by multiparametric flow cytometry we observed a gradual and significant expansion in the frequencies of CD25highCD127- Tregs in both groups. Phenotypic characterization suggests that polarization of na{\\"i}ve T cells towards Tregs is responsible for the observed expansion. In line with this, we observed a significant reduction of inflammatory marker CRP under propionate supplementation. Of interest, the observed anti-inflammatory surroundings did not affect the protective pathogen-specific immunity as demonstrated by the stable frequencies of effector/memory T cells specific for tetanus/diphtheria recall antigens. Collectively, our data suggest that dietary supplements with propionate have a beneficial effect on the elevated systemic inflammation of ESRD patients. The effect can be achieved through an expansion of circulating Tregs without affecting the protective pathogen-reactive immunity.},\n  doi      = {10.1007/s40620-019-00694-z},\n  keywords = {paper},\n  url      = {https://doi.org/10.1007/s40620-019-00694-z},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Functional screening identifies aryl hydrocarbon receptor as suppressor of lung cancer metastasis.\n \n \n \n \n\n\n \n Nothdurft, S.; Thumser-Henner, C.; Breitenbücher, F.; Okimoto, R. A.; Dorsch, M.; Opitz, C. A.; Sadik, A.; Esser, C.; Hölzel, M.; Asthana, S.; Forster, J.; Beisser, D.; Kalmbach, S.; Grüner, B. M.; Bivona, T. G.; Schramm, A.; and Schuler, M.\n\n\n \n\n\n\n Oncogenesis, 9(11): 102. Nov 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Functional$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Nothdurft2020,\n  author    = {Silke Nothdurft and Clotilde Thumser-Henner and Frank Breitenb\\"{u}cher and Ross A. Okimoto and Madeleine Dorsch and Christiane A. Opitz and Ahmed Sadik and Charlotte Esser and Michael H\\"{o}lzel and Saurabh Asthana and Jan Forster and Daniela Beisser and Sophie Kalmbach and Barbara M. Gr\\"{u}ner and Trever G. Bivona and Alexander Schramm and Martin Schuler},\n  journal   = {Oncogenesis},\n  title     = {Functional screening identifies aryl hydrocarbon receptor as suppressor of lung cancer metastasis},\n  year      = {2020},\n  month     = {Nov},\n  number    = {11},\n  pages     = {102},\n  volume    = {9},\n  abstract  = {Lung cancer mortality largely results from metastasis. Despite curative surgery many patients with early-stage non-small cell lung cancer ultimately succumb to metastatic relapse. Current risk reduction strategies based on cytotoxic chemotherapy and radiation have only modest activity. Against this background, we functionally screened for novel metastasis modulators using a barcoded shRNA library and an orthotopic lung cancer model. We identified aryl hydrocarbon receptor (AHR), a sensor of xenobiotic chemicals and transcription factor, as suppressor of lung cancer metastasis. Knockdown of endogenous AHR induces epithelial–mesenchymal transition signatures, increases invasiveness of lung cancer cells in vitro and metastasis formation in vivo. Low intratumoral AHR expression associates with inferior outcome of patients with resected lung adenocarcinomas. Mechanistically, AHR triggers ATF4 signaling and represses matrix metalloproteinase activity, both counteracting metastatic programs. These findings link the xenobiotic defense system with control of lung cancer progression. AHR-regulated pathways are promising targets for innovative anti-metastatic strategies.},\n  doi       = {10.1038/s41389-020-00286-8},\n  keywords  = {paper},\n  publisher = {Springer Science and Business Media {LLC}},\n  url       = {https://doi.org/10.1038/s41389-020-00286-8},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients.\n \n \n \n \n\n\n \n Nuy, J. K.; Hoetzinger, M.; Hahn, M. W.; Beisser, D.; and Boenigk, J.\n\n\n \n\n\n\n Frontiers in Microbiology, 11: 154. Feb 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Ecological$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Nuy2020,\n  author   = {Nuy, Julia K. and Hoetzinger, Matthias and Hahn, Martin W. and Beisser, Daniela and Boenigk, Jens},\n  journal  = {Frontiers in Microbiology},\n  title    = {Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients},\n  year     = {2020},\n  issn     = {1664-302X},\n  month    = {Feb},\n  pages    = {154},\n  volume   = {11},\n  abstract = {Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising large genetic and taxonomic diversities, with species adapted to physico-chemically distinct types of freshwater systems. The relative importance of environmental drivers, i.e., physico-chemistry, presence of microeukaryotes and geographic position for the diversity and prevalence has not been investigated for both taxa before. Here, we present the first pan-European study on this topic, comprising 255 freshwater lakes. We investigated Limnohabitans and Polynucleobacter using an amplicon sequencing approach of partial 16S rRNA genes along environmental gradients. We show that physico-chemical factors had the greatest impact on both genera. Analyses on environmental gradients revealed an exceptionally broad ecological spectrum of operational taxonomic units (OTUs). Despite the coarse resolution of the genetic marker, we found OTUs with contrasting environmental preferences within Polynucleobacter and Limnohabitans subclusters. Such an ecological differentiation has been characterized for PnecC and LimC before but was so far unknown for less well studied subclusters such as PnecA and PnecB. Richness and abundance of OTUs are geographically clustered, suggesting that geographic diversity patterns are attributable to region-specific physico-chemical characteristics (e.g., pH and temperature) rather than latitudinal gradients or lake sizes.},\n  doi      = {10.3389/fmicb.2020.00154},\n  keywords = {paper},\n  url      = {https://www.frontiersin.org/article/10.3389/fmicb.2020.00154},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Protistan and fungal diversity in soils and freshwater lakes are substantially different.\n \n \n \n \n\n\n \n Sieber, G.; Beisser, D.; Bock, C.; and Boenigk, J.\n\n\n \n\n\n\n Scientific Reports, 10(1). Nov 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Protistan$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Sieber2020,\n  author    = {G. Sieber and D. Beisser and C. Bock and J. Boenigk},\n  journal   = {Scientific Reports},\n  title     = {Protistan and fungal diversity in soils and freshwater lakes are substantially different},\n  year      = {2020},\n  month     = {Nov},\n  number    = {1},\n  volume    = {10},\n  abstract  = {Freshwater and soil habitats hold rich microbial communities. Here we address commonalities and differences between both habitat types. While freshwater and soil habitats differ considerably in habitat characteristics organismic exchange may be high and microbial communities may even be inoculated by organisms from the respective other habitat. We analyze diversity pattern and the overlap of taxa of eukaryotic microbial communities in freshwater and soil based on Illumina HiSeq high-throughput sequencing of the amplicon V9 diversity. We analyzed corresponding freshwater and soil samples from 30 locations, i.e. samples from different lakes across Germany and soil samples from the respective catchment areas. Aside from principle differences in the community composition of soils and freshwater, in particular with respect to the relative contribution of fungi and algae, soil habitats have a higher richness. Nevertheless, community similarity between different soil sites is considerably lower as compared to the similarity between different freshwater sites. We show that the overlap of organisms co-occurring in freshwater and soil habitats is surprisingly low. Even though closely related taxa occur in both habitats distinct OTUs were mostly habitat–specific and most OTUs occur exclusively in either soil or freshwater. The distribution pattern of the few co-occurring lineages indicates that even most of these are presumably rather habitat-specific. Their presence in both habitat types seems to be based on a stochastic drift of particularly abundant but habitat-specific taxa rather than on established populations in both types of habitats.},\n  doi       = {10.1038/s41598-020-77045-7},\n  keywords  = {paper},\n  publisher = {Springer Science and Business Media {LLC}},\n  url       = {https://doi.org/10.1038/s41598-020-77045-7},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads.\n \n \n \n \n\n\n \n Welzel, M.; Lange, A.; Heider, D.; Schwarz, M.; Freisleben, B.; Jensen, M.; Boenigk, J.; and Beisser, D.\n\n\n \n\n\n\n BMC Bioinformatics, 21(1). Nov 2020.\n \n\n\n\n
\n\n\n\n \n \n $\"Natrix:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Welzel2020,\n  author    = {Marius Welzel and Anja Lange and Dominik Heider and Michael Schwarz and Bernd Freisleben and Manfred Jensen and Jens Boenigk and Daniela Beisser},\n  journal   = {{BMC} Bioinformatics},\n  title     = {Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads},\n  year      = {2020},\n  month     = {Nov},\n  number    = {1},\n  volume    = {21},\n  abstract  = {Background\nSequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system.\n\nResults\nWe present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix) or as a Docker container on DockerHub (https://hub.docker.com/r/mw55/natrix).\n\nConclusion\nNatrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data.},\n  doi       = {10.1186/s12859-020-03852-4},\n  keywords  = {paper},\n  publisher = {Springer Science and Business Media {LLC}},\n  url       = {https://doi.org/10.1186/s12859-020-03852-4},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2019\n \n \n (4)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Interaction-specific changes in the transcriptome of Polynucleobacter asymbioticus caused by varying protistan communities.\n \n \n \n \n\n\n \n Beisser, D.; Bock, C.; Hahn, M. W.; Vos, M.; Sures, B.; Rahmann, S.; and Boenigk, J.\n\n\n \n\n\n\n Frontiers in Microbiology, 10: 1498. Jul 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Interaction-specific$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Beisser2019,\n  author   = {Beisser, Daniela and Bock, Christina and Hahn, Martin W. and Vos, Matthijs and Sures, Bernd and Rahmann, Sven and Boenigk, Jens},\n  journal  = {Frontiers in Microbiology},\n  title    = {Interaction-specific changes in the transcriptome of Polynucleobacter asymbioticus caused by varying protistan communities},\n  year     = {2019},\n  issn     = {1664-302X},\n  month    = {Jul},\n  pages    = {1498},\n  volume   = {10},\n  abstract = {We studied the impact of protist grazing and exudation on the growth and transcriptomic response of the prokaryotic prey species \\textit{Polynucleobacter asymbioticus}.\nDifferent single- and multi-species communities of chrysophytes were used to determine a species-specific response to the predators and the effect of chrysophyte diversity.\nWe sequenced the mRNA of \\textit{Pn. asymbioticus} in communities with three single chrysophyte species (\\textit{Chlorochromonas danica}, \\textit{Poterioochromonas malhamensis} and \\textit{Poteriospumella lacustris}) and all combinations.\nThe molecular responses of \\textit{Pn. asymbioticus} significantly changed in the presence of predators with different trophic modes and combinations of species.\nIn the single-species samples we observed significant differences related to the relative importance of grazing and exudation in the protist-bacteria interaction, i.e. to the presence of either the heterotrophic \\textit{Ps. lacustris} or the mixotrophic \\textit{C. danica}.\nWhen grazing dominates the interaction, as in the presence of \\textit{Ps. lacustris}, genes acting in stress response are up-regulated. \nFurther genes associated with transcription and translation are down-regulated indicating a reduced growth of \\textit{Pn. asymbioticus}. \nIn contrast, when the potential use of algal exudates dominates the interaction, genes affiliated with iron transport are up-regulated. \nRapid phototrophic growth of chrysophytes, with a high demand on soluble iron, could thus lead to iron-limitation and cause changes in the iron metabolism of \\textit{Pn. asymbioticus}.\nAdditionally, we observe a benefit for \\textit{Pn. asymbioticus} from a more diverse protistan community, which could be due to shifts in the relative importance of phototrophy in the mixotrophic chrysophytes when competing for food with other species.\nOur study highlights the importance of biotic interactions and the specificity of such interactions, in particular the differential effect of grazing and algal exudation in the interaction of bacteria with mixotrophic protists.},\n  doi      = {10.3389/fmicb.2019.01498},\n  keywords = {paper},\n  url      = {https://www.frontiersin.org/article/10.3389/fmicb.2019.01498},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations.\n \n \n \n \n\n\n \n Bock, C.; Zimmermann, S.; Beisser, D.; Dinglinger, S.; Engelskirchen, S.; Giesemann, P.; Klink, S.; Olefeld, J. L.; Rahmann, S.; Vos, M.; Boenigk, J.; and Sures, B.\n\n\n \n\n\n\n Environmental Pollution, 244: 314–322. Jan 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Silver$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Bock2018,\n  author   = {Christina Bock and Sonja Zimmermann and Daniela Beisser and Sarah-Maria Dinglinger and Simone Engelskirchen and Philipp Giesemann and Saskia Klink and Jana Laura Olefeld and Sven Rahmann and Matthijs Vos and Jens Boenigk and Bernd Sures},\n  journal  = {Environmental Pollution},\n  title    = {Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations},\n  year     = {2019},\n  issn     = {0269-7491},\n  month    = {Jan},\n  pages    = {314--322},\n  volume   = {244},\n  abstract = {Silver ions are among the predominant anthropogenic introduced pollutants in aquatic systems. As silver has effects on species at all trophic levels the community composition in aquatic habitats can be changed as a result of silver stress. The response of planktonic protists to environmental stressors is particularly important as they act both as producers and consumers in complex planktonic communities. Chrysomonad flagellates are of major interest, since this group includes heterotrophic, mixotrophic and phototrophic taxa, and therefore allows analysis of silver stress in organisms with contrasting nutritional strategies independent of a potential taxonomic bias. In a series of lab experiments, we compared the response of different trophic chrysophyte strains to low (5 μg L−1), medium (10 μg L−1) and high (20 μg L−1) nominal Ag concentrations in combination with changes in temperature and light intensity (phototrophs), temperature and food concentration (heterotrophs), or a combination of the above settings (mixotrophs). All tested strains were negatively affected by silver in their growth rates. The phototrophic strains reacted strongly to silver stress, whereas light intensity and temperature had only minor effects on growth rates. For heterotrophic strains, high food concentration toned down the effect of silver, whereas temperatures outside the growth optimum had a combined stress effect. The mixotrophic strains reacted differently depending on whether their nutritional mode was dominated by heterotrophy or by phototrophy. The precise response pattern across all variables was uniquely different for every single species we tested. The present work contributes to a deeper understanding of the effects of environmental stressors on complex planktonic communities. It indicates that silver will negatively impact planktonic communities and may create shifts in their composition and functioning.},\n  doi      = {https://doi.org/10.1016/j.envpol.2018.09.146},\n  keywords = {paper},\n  url      = {http://www.sciencedirect.com/science/article/pii/S0269749118321018},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data.\n \n \n \n \n\n\n \n Kraus, D.; Chi, J.; Boenigk, J.; Beisser, D.; Graupner, N.; and Dunthorn, M.\n\n\n \n\n\n\n PeerJ, 6: e5894. Jan 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Putatively$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Kraus2019,\n  author   = {Kraus, Diana and Chi, Jingyun and Boenigk, Jens and Beisser, Daniela and Graupner, Nadine and Dunthorn, Micah},\n  journal  = {PeerJ},\n  title    = {Putatively asexual chrysophytes have meiotic genes: evidence from transcriptomic data},\n  year     = {2019},\n  issn     = {2167-8359},\n  month    = {Jan},\n  pages    = {e5894},\n  volume   = {6},\n  abstract = {Chrysophytes are a large group of heterotrophic, phototrophic, or even mixotrophic protists that are abundant in aquatic as well as terrestrial environments. Although much is known about chrysophyte biology and ecology, it is unknown if they are sexual or not. Here we use available transcriptomes of 18 isolates of 15 putatively asexual species to inventory the presence of genes used in meiosis. Since we were able to detect a set of nine meiosis-specific and 29 meiosis-related genes shared by the chrysophytes, we conclude that they are secretively sexual and therefore should be investigated further using genome sequencing to uncover any missed genes from the transcriptomes.},\n  doi      = {10.7717/peerj.5894},\n  keywords = {paper},\n  url      = {https://doi.org/10.7717/peerj.5894},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae).\n \n \n \n \n\n\n \n Majda, S.; Boenigk, J.; and Beisser, D.\n\n\n \n\n\n\n Genome Biology and Evolution, 11(9): 2492–2504. Sep 2019.\n \n\n\n\n
\n\n\n\n \n \n $\"Intraspecific$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Majda2019,\n  author   = {Majda, Stephan and Boenigk, Jens and Beisser, Daniela},\n  journal  = {Genome Biology and Evolution},\n  title    = {{Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae)}},\n  year     = {2019},\n  issn     = {1759-6653},\n  month    = {Sep},\n  number   = {9},\n  pages    = {2492--2504},\n  volume   = {11},\n  abstract = {{Species delimitation in protists is still a challenge, attributable to the fact that protists are small, difficult to observe and many taxa are poor in morphological characters, whereas most current phylogenetic approaches only use few marker genes to measure genetic diversity. To address this problem, we assess genome-level divergence and microevolution in strains of the protist Poteriospumella lacustris, one of the first free-living, nonmodel organisms to study genome-wide intraspecific variation.Poteriospumella lacustris is a freshwater protist belonging to the Chrysophyceae with an assumed worldwide distribution. We examined three strains from different geographic regions (New Zealand, China, and Austria) by sequencing their genomes with the Illumina and PacBio platforms.The assembled genomes were small with 49–55 Mb but gene-rich with 16,000–19,000 genes, of which ∼8,000 genes could be assigned to functional categories. At least 68\\\\% of these genes were shared by all three species. Genetic variation occurred predominantly in genes presumably involved in ecological niche adaptation. Most surprisingly, we detected differences in genome ploidy between the strains (diploidy, triploidy, and tetraploidy).In analyzing intraspecific variation, several mechanisms of diversification were identified including SNPs, change of ploidy and genome size reduction.}},\n  doi      = {10.1093/gbe/evz171},\n  eprint   = {https://academic.oup.com/gbe/article-pdf/11/9/2492/29966922/evz171.pdf},\n  keywords = {paper},\n  url      = {https://doi.org/10.1093/gbe/evz171},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2018\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Geographic distance and mountain ranges structure freshwater protist communities on a European scalе.\n \n \n \n \n\n\n \n Boenigk, J.; Wodniok, S.; Bock, C.; Beisser, D.; Hempel, C.; Grossmann, L.; Lange, A.; and Jensen, M.\n\n\n \n\n\n\n Metabarcoding and Metagenomics, 2: e21519. Jan 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Geographic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Boenigk2018,\n  author    = {Jens Boenigk and Sabina Wodniok and Christina Bock and Daniela Beisser and Christopher Hempel and Lars Grossmann and Anja Lange and Manfred Jensen},\n  journal   = {Metabarcoding and Metagenomics},\n  title     = {Geographic distance and mountain ranges structure freshwater protist communities on a {E}uropean scalе},\n  year      = {2018},\n  month     = {Jan},\n  pages     = {e21519},\n  volume    = {2},\n  abstract  = {Protists influence ecosystems by modulating microbial population size, diversity, metabolic outputs and gene flow. In this study we used eukaryotic ribosomal amplicon diversity from 218 European freshwater lakes sampled in August 2012 to assess the effect of mountain ranges as biogeographic barriers on spatial patterns and microbial community structure in European freshwaters. The diversity of microbial communities as reflected by amplicon clusters suggested that the eukaryotic microbial inventory of lakes was well-sampled at the European and at the local scale. Our pan-European diversity analysis indicated that biodiversity and richness of high mountain lakes differed from that of lowland lakes. Further, the taxon inventory of high-mountain lakes strongly contributed to beta-diversity despite a low taxon inventory. Even though ecological factors, in general, strongly affect protist community pattern, we show that geographic distance and geographic barriers significantly contribute to community composition particularly for high mountain regions which presumably act as biogeographic islands. However, community composition in lowland lakes was also affected by geographic distance but less pronounced as in high mountain regions. In consequence protist populations are locally structured into distinct biogeographic provinces and community analyses revealed biogeographic patterns also for lowland lakes whereby European mountain ranges act as dispersal barriers in particular for short to intermediate distances whereas the effect of mountain ranges levels off on larger scale.},\n  doi       = {10.3897/mbmg.2.21519},\n  keywords  = {paper},\n  publisher = {Pensoft Publishers},\n  url       = {https://doi.org/10.3897/mbmg.2.21519},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Bioconda: sustainable and comprehensive software distribution for the life sciences.\n \n \n \n \n\n\n \n Grüning, B.; Dale, R.; Sjödin, A.; Chapman, B. A.; Rowe, J.; Tomkins-Tinch, C. H.; Valieris, R.; ...; Beisser, D.; ...; and Köster, J.\n\n\n \n\n\n\n Nature Methods, 15(7): 475–476. Jul 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Bioconda:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Groening2018,\n  author    = {Bj\\"{o}rn Gr\\"{u}ning and Ryan Dale and Andreas Sj\\"{o}din and Brad A. Chapman and Jillian Rowe and Christopher H. Tomkins-Tinch and Renan Valieris and ... and Daniela Beisser and ... and Johannes K\\"{o}ster},\n  journal   = {Nature Methods},\n  title     = {Bioconda: sustainable and comprehensive software distribution for the life sciences},\n  year      = {2018},\n  month     = {Jul},\n  number    = {7},\n  pages     = {475--476},\n  volume    = {15},\n  doi       = {10.1038/s41592-018-0046-7},\n  keywords  = {paper},\n  publisher = {Springer Nature},\n  url       = {https://doi.org/10.1038/s41592-018-0046-7},\n}\n\n

\n

\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics.\n \n \n \n \n\n\n \n Graupner, N.; Jensen, M.; Bock, C.; Marks, S.; Rahmann, S.; Beisser, D.; and Boenigk, J.\n\n\n \n\n\n\n FEMS Microbiology Ecology, 94(4): fiy039. Apr 2018.\n \n\n\n\n
\n\n\n\n \n \n $\"Evolution$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Graupner2018,\n  author   = {Graupner, Nadine and Jensen, Manfred and Bock, Christina and Marks, Sabina and Rahmann, Sven and Beisser, Daniela and Boenigk, Jens},\n  journal  = {FEMS Microbiology Ecology},\n  title    = {Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics},\n  year     = {2018},\n  month    = {Apr},\n  number   = {4},\n  pages    = {fiy039},\n  volume   = {94},\n  abstract = {Shifts in the nutritional mode between phototrophy, mixotrophy and heterotrophy are a widespread phenomenon in the evolution of eukaryotic diversity. The transition between nutritional modes is particularly pronounced in chrysophytes and occurred independently several times through parallel evolution. Thus, chrysophytes provide a unique opportunity for studying the molecular basis of nutritional diversification and of the accompanying pathway reduction and degradation of plastid structures. In order to analyze the succession in switching the nutritional mode from mixotrophy to heterotrophy, we compared the transcriptome of the mixotrophic Poterioochromonas malhamensis with the transcriptomes of three obligate heterotrophic species of Ochromonadales. We used the transcriptome of P. malhamensis as a reference for plastid reduction in the heterotrophic taxa. The analyzed heterotrophic taxa were in different stages of plastid reduction. We investigated the reduction of several photosynthesis related pathways e.g. the xanthophyll cycle, the mevalonate pathway, the shikimate pathway and the tryptophan biosynthesis as well as the reduction of plastid structures and postulate a presumable succession of pathway reduction and degradation of accompanying structures.},\n  doi      = {10.1093/femsec/fiy039},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1093/femsec/fiy039},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2017\n \n \n (5)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes.\n \n \n \n \n\n\n \n Beisser, D.; Graupner, N.; Bock, C.; Wodniok, S.; Grossmann, L.; Vos, M.; Sures, B.; Rahmann, S.; and Boenigk, J.\n\n\n \n\n\n\n PeerJ, 5: e2832. Jan 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Comprehensive$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Beisser2017a,\n  author   = {Beisser, Daniela and Graupner, Nadine and Bock, Christina and Wodniok, Sabina and Grossmann, Lars and Vos, Matthijs and Sures, Bernd and Rahmann, Sven and Boenigk, Jens},\n  journal  = {PeerJ},\n  title    = {Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes},\n  year     = {2017},\n  issn     = {2167-8359},\n  month    = {Jan},\n  pages    = {e2832},\n  volume   = {5},\n  abstract = {Background: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes. Results: We sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.\nConclusions: Our study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.},\n  doi      = {10.7717/peerj.2832},\n  keywords = {paper},\n  url      = {https://doi.org/10.7717/peerj.2832},\n}\n\n

\n

\n\n\n

\n Background: Chrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes. Results: We sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae. Conclusions: Our study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.\n

\n\n\n

\n \n\n \n \n \n \n \n \n TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms.\n \n \n \n \n\n\n \n Beisser, D.; Graupner, N.; Grossmann, L.; Timm, H.; Boenigk, J.; and Rahmann, S.\n\n\n \n\n\n\n BMC Genomics, 18(1): 787. Oct 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"TaxMapper:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Beisser2017,\n  author    = {Daniela Beisser and Nadine Graupner and Lars Grossmann and Henning Timm and Jens Boenigk and Sven Rahmann},\n  journal   = {BMC Genomics},\n  title     = {TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms},\n  year      = {2017},\n  month     = {Oct},\n  number    = {1},\n  pages     = {787},\n  volume    = {18},\n  abstract  = {Background: High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.\nResults: From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample.\nConclusions: TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapperand as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html.},\n  doi       = {10.1186/s12864-017-4168-6},\n  keywords  = {paper},\n  publisher = {Springer Nature},\n  url       = {https://doi.org/10.1186/s12864-017-4168-6},\n}\n\n

\n

\n\n\n

\n Background: High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task. Results: From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample. Conclusions: TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapperand as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Quantitative proteomics reveals ecophysiological effects of light and silver stress on the mixotrophic protist Poterioochromonas malhamensis.\n \n \n \n \n\n\n \n Beisser, D.; Kaschani, F.; Graupner, N.; Grossmann, L.; Jensen, M.; Ninck, S.; Schulz, F.; Rahmann, S.; Boenigk, J.; and Kaiser, M.\n\n\n \n\n\n\n PLOS ONE, 12(1): 1–20. Jan 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Quantitative$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Beisser2017b,\n  author    = {Beisser, Daniela and Kaschani, Farnusch and Graupner, Nadine and Grossmann, Lars and Jensen, Manfred and Ninck, Sabrina and Schulz, Florian and Rahmann, Sven and Boenigk, Jens and Kaiser, Markus},\n  journal   = {PLOS ONE},\n  title     = {Quantitative proteomics reveals ecophysiological effects of light and silver stress on the mixotrophic protist {P}oterioochromonas malhamensis},\n  year      = {2017},\n  month     = {Jan},\n  number    = {1},\n  pages     = {1--20},\n  volume    = {12},\n  abstract  = {Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct interference with the silver ions, mainly affecting energy supply.},\n  doi       = {10.1371/journal.pone.0168183},\n  keywords  = {paper},\n  publisher = {Public Library of Science},\n  url       = {http://dx.doi.org/10.1371%2Fjournal.pone.0168183},\n}\n\n

\n

\n\n\n

\n Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct interference with the silver ions, mainly affecting energy supply.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Functional and phylogenetic analysis of the core transcriptome of Ochromonadales.\n \n \n \n \n\n\n \n Graupner, N.; Boenigk, J.; Bock, C.; Jensen, M.; Marks, S.; Rahmann, S.; and Beisser, D.\n\n\n \n\n\n\n Metabarcoding and Metagenomics, 1: e19862. Sep 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Functional$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Graupner2017a,\n  author    = {Nadine Graupner and Jens Boenigk and Christina Bock and Manfred Jensen and Sabina Marks and Sven Rahmann and Daniela Beisser},\n  journal   = {Metabarcoding and Metagenomics},\n  title     = {Functional and phylogenetic analysis of the core transcriptome of {O}chromonadales},\n  year      = {2017},\n  month     = {Sep},\n  pages     = {e19862},\n  volume    = {1},\n  abstract  = {Background: Most protist lineages consist of members with diverging features e.g. different modes of nutrition and adaptations for life in different habitat types and climatic zones. The nutritional mode is particularly variable in chrysophytes and they are therefore an excellent model group to study the core genes and metabolic pathways of a functionally diverse lineage. The objective of our study is the identification of the joint genetic repertoire expressed in closely related chrysophytes as well as the extent of variation on species and strain level. Therefore, we investigated the transcriptomes of six strains belonging to four species of Ochromonadales. We performed analyses on metabolic pathway level as well as on sequence level.\nResults: We could identify 1,574 core genes shared between all six investigated strains of Ochromonadales. Most of these core genes were affiliated with the primary metabolism. Phylogenetic analysis of 166 protein-coding core genes supported a close relation of Poteriospumella lacustris and Poterioochromonas malhamensis and resolved for more than 50\\% of investigated genes the relationship of strains affiliated with the species P. lacustris. Further, we found diverging phylogenetic patterns for genes interacting with the environment.\nConclusions: In Ochromonadales, a functionally diverse lineage, the core transcriptome represents only a minor part of the individual transcriptomes. But this small fraction of genes comprises the basal metabolism essential for life in several protist lineages. Phylogenetic analyses of these genes indicate a similar degree of conservation as observed for genes coding for ribosomal proteins.},\n  doi       = {10.3897/mbmg.1.19862},\n  keywords  = {paper},\n  publisher = {Pensoft Publishers},\n  url       = {https://doi.org/10.3897/mbmg.1.19862},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Effects of short-term flooding on aquatic and terrestrial microeukaryotic communities: a mesocosm approach.\n \n \n \n \n\n\n \n Graupner, N.; Röhl, O.; Jensen, M.; Beisser, D.; Begerow, D.; and Boenigk, J.\n\n\n \n\n\n\n Aquatic Microbial Ecology, 80(3): 257–272. Dec 2017.\n \n\n\n\n
\n\n\n\n \n \n $\"Effects$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Graupner2017,\n  author    = {Nadine Graupner and Oliver R\\"{o}hl and Manfred Jensen and Daniela Beisser and Dominik Begerow and Jens Boenigk},\n  journal   = {Aquatic Microbial Ecology},\n  title     = {Effects of short-term flooding on aquatic and terrestrial microeukaryotic communities: a mesocosm approach},\n  year      = {2017},\n  month     = {Dec},\n  number    = {3},\n  pages     = {257--272},\n  volume    = {80},\n  abstract  = {Freshwater and soil are not strictly isolated habitats. In particular, floods may facilitate the exchange of organisms and nutrients. Flooding can have both a stimulating and a harmful effect on the organisms of the respective habitats. The effects of short-term flooding on microeukaryotic communities in the aquatic and terrestrial habitat have so far been scarcely studied. Here, we investigated the effect of a 24 h artificial inundation on the microeukaryotic community composition in AquaFlow mesocosm systems. We investigated the shift of community composition based on molecular amplicon diversity both on soil and water during flooding and for a period of 12 d after flooding. Community composition was, as expected, strongly different between soil and water. Flooding had a significant effect on the freshwater community, whereas the soil community was hardly affected. In particular, we observed a transfer of nutrients from the terrestrial habitat into the aquatic habitat and identified ~50 taxa that were transferred by the flooding event. This effect of flooding was, however, overlaid by shifts of the communities with time, presumably reflecting an acclimatization to the conditions in the AquaFlow systems.},\n  doi       = {10.3354/ame01853},\n  keywords  = {paper},\n  publisher = {Inter-Research Science Center},\n  url       = {https://doi.org/10.3354/ame01853},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2016\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Characterization of pancreatic glucagon-producing tumors and pituitary gland tumors in transgenic mice overexpressing MYCN in hGFAP-positive cells.\n \n \n \n \n\n\n \n Fielitz, K.; Althoff, K.; Preter, K. D.; Nonnekens, J.; Ohli, J.; Elges, S.; Hartmann, W.; Klöppel, G.; Knösel, T.; Schulte, M.; Klein-Hitpass, L.; Beisser, D.; Eyking, A.; Cario, E.; Schulte, J. H.; Wang, S.; Schramm, A.; and Schüller, U.\n\n\n \n\n\n\n Oncotarget, 7(46): 74415-74426. Oct 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Characterization$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Fielitz2016,\n  author   = {Kathrin Fielitz and Kristina Althoff and Katleen De Preter and Julie Nonnekens and Jasmin Ohli and Sandra Elges and Wolfgang Hartmann and G\\"{u}nter Kl\\"{o}ppel and Thomas Kn\\"{o}sel and Marc Schulte and Ludger Klein-Hitpass and Daniela Beisser and Annette Eyking and Elke Cario and Johannes H. Schulte and Shuang-Xi Wang and Alexander Schramm and Ulrich Sch\\"{u}ller},\n  journal  = {Oncotarget},\n  title    = {Characterization of pancreatic glucagon-producing tumors and pituitary gland tumors in transgenic mice overexpressing {MYCN} in h{GFAP}-positive cells},\n  year     = {2016},\n  month    = {Oct},\n  number   = {46},\n  pages    = {74415-74426},\n  volume   = {7},\n  abstract = {Amplification or overexpression of MYCN is involved in development and maintenance of multiple malignancies. A subset of these tumors originates from neural precursors, including the most aggressive forms of the childhood tumors, neuroblastoma and medulloblastoma. In order to model the spectrum of MYCN-driven neoplasms in mice, we transgenically overexpressed MYCN under the control of the human GFAP-promoter that, among other targets, drives expression in neural progenitor cells. However, LSL-MYCN;hGFAP-Cre double transgenic mice did neither develop neural crest tumors nor tumors of the central nervous system, but presented with neuroendocrine tumors of the pancreas and, less frequently, the pituitary gland. Pituitary tumors expressed chromogranin A and closely resembled human pituitary adenomas. Pancreatic tumors strongly produced and secreted glucagon, suggesting that they derived from glucagon- and GFAP-positive islet cells. Interestingly, 3 out of 9 human pancreatic neuroendocrine tumors expressed MYCN, supporting the similarity of the mouse tumors to the human system. Serial transplantations of mouse tumor cells into immunocompromised mice confirmed their fully transformed phenotype. MYCN-directed treatment by AuroraA- or Brd4-inhibitors resulted in significantly decreased cell proliferation in vitro and reduced tumor growth in vivo. In summary, we provide a novel mouse model for neuroendocrine tumors of the pancreas and pituitary gland that is dependent on MYCN expression and that may help to evaluate MYCN-directed therapies.},\n  doi      = {10.18632/oncotarget.12766},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.18632/oncotarget.12766},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Trade-off between taxon diversity and functional diversity in European lake ecosystems.\n \n \n \n \n\n\n \n Grossmann, L.; Beisser, D.; Bock, C.; Chatzinotas, A.; Jensen, M.; Preisfeld, A.; Psenner, R.; Rahmann, S.; Wodniok, S.; and Boenigk, J.\n\n\n \n\n\n\n Molecular Ecology, 25(23): 5876–5888. Oct 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Trade-off$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 2 downloads\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Grossmann2016,\n  author   = {Grossmann, Lars and Beisser, Daniela and Bock, Christina and Chatzinotas, Antonis and Jensen, Manfred and Preisfeld, Angelika and Psenner, Roland and Rahmann, Sven and Wodniok, Sabina and Boenigk, Jens},\n  journal  = {Molecular Ecology},\n  title    = {Trade-off between taxon diversity and functional diversity in European lake ecosystems},\n  year     = {2016},\n  month    = {Oct},\n  number   = {23},\n  pages    = {5876--5888},\n  volume   = {25},\n  abstract = {Abstract Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa.},\n  doi      = {10.1111/mec.13878},\n  eprint   = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.13878},\n  keywords = {paper},\n  url      = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.13878},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Epigenetic dynamics of monocyte-to-macrophage differentiation.\n \n \n \n \n\n\n \n Wallner, S.; Schröder, C.; Leitão, E.; Berulava, T.; Haak, C.; Beisser, D.; Rahmann, S.; Richter, A. S.; Manke, T.; Bönisch, U.; Arrigoni, L.; Fröhler, S.; Klironomos, F.; Chen, W.; Rajewsky, N.; Müller, F.; Ebert, P.; Lengauer, T.; Barann, M.; Rosenstiel, P.; Gasparoni, G.; Nordström, K.; Walter, J.; Brors, B.; Zipprich, G.; Felder, B.; Klein-Hitpass, L.; Attenberger, C.; Schmitz, G.; and Horsthemke, B.\n\n\n \n\n\n\n Epigenetics and Chromatin, 9(33): 33. Jul 2016.\n \n\n\n\n
\n\n\n\n \n \n $\"Epigenetic$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Wallner2016,\n  author   = {Stefan Wallner and Christopher Schr\\"{o}der and Elsa Leit{\\~{a}}o and Tea Berulava and Claudia Haak and Daniela Beisser and Sven Rahmann and Andreas S. Richter and Thomas Manke and Ulrike B\\"{o}nisch and Laura Arrigoni and Sebastian Fr\\"{o}hler and Filippos Klironomos and Wei Chen and Nikolaus Rajewsky and Fabian M\\"{u}ller and Peter Ebert and Thomas Lengauer and Matthias Barann and Philip Rosenstiel and Gilles Gasparoni and Karl Nordstr\\"{o}m and J\\"{o}rn Walter and Benedikt Brors and Gideon Zipprich and B\\"{a}rbel Felder and Ludger Klein-Hitpass and Corinna Attenberger and Gerd Schmitz and Bernhard Horsthemke},\n  journal  = {Epigenetics and Chromatin},\n  title    = {Epigenetic dynamics of monocyte-to-macrophage differentiation},\n  year     = {2016},\n  month    = {Jul},\n  number   = {33},\n  pages    = {33},\n  volume   = {9},\n  abstract = {Monocyte-to-macrophage differentiation involves major biochemical and structural changes. In order to elucidate the role of gene regulatory changes during this process, we used high-throughput sequencing to analyze the complete transcriptome and epigenome of human monocytes that were differentiated in vitro by addition of colony-stimulating factor 1 in serum-free medium. Numerous mRNAs and miRNAs were significantly up- or down-regulated. More than 100 discrete DNA regions, most often far away from transcription start sites, were rapidly demethylated by the ten eleven translocation enzymes, became nucleosome-free and gained histone marks indicative of active enhancers. These regions were unique for macrophages and associated with genes involved in the regulation of the actin cytoskeleton, phagocytosis and innate immune response. In summary, we have discovered a phagocytic gene network that is repressed by DNA methylation in monocytes and rapidly de-repressed after the onset of macrophage differentiation.},\n  doi      = {10.1186/s13072-016-0079-z},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1186/s13072-016-0079-z},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2015\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.\n \n \n \n \n\n\n \n El-Kebir, M.; Soueidan, H.; Hume, T.; Beisser, D.; Dittrich, M.; Müller, T.; Blin, G.; Heringa, J.; Nikolski, M.; Wessels, L. F. A.; and Klau, G. W.\n\n\n \n\n\n\n Bioinformatics, 31(19): 3147–3155. Oct 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"xHeinz:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{El-Kebir2015,\n  author   = {Mohammed El-Kebir and Hayssam Soueidan and Thomas Hume and Daniela Beisser and Marcus Dittrich and Tobias M\\"{u}ller and Guillaume Blin and Jaap Heringa and Macha Nikolski and Lodewyk F. A. Wessels and Gunnar W. Klau},\n  journal  = {Bioinformatics},\n  title    = {x{H}einz: an algorithm for mining cross-species network modules under a flexible conservation model},\n  year     = {2015},\n  month    = {Oct},\n  number   = {19},\n  pages    = {3147--3155},\n  volume   = {31},\n  abstract = {Integrative network analysis methods provide robust interpretations of differential high-throughput molecular profile measurements. They are often used in a biomedical context-to generate novel hypotheses about the underlying cellular processes or to derive biomarkers for classification and subtyping. The underlying molecular profiles are frequently measured and validated on animal or cellular models. Therefore the results are not immediately transferable to human. In particular, this is also the case in a study of the recently discovered interleukin-17 producing helper T cells (Th17), which are fundamental for anti-microbial immunity but also known to contribute to autoimmune diseases. We propose a mathematical model for finding active subnetwork modules that are conserved between two species. These are sets of genes, one for each species, which (i) induce a connected subnetwork in a species-specific interaction network, (ii) show overall differential behavior and (iii) contain a large number of orthologous genes. We propose a flexible notion of conservation, which turns out to be crucial for the quality of the resulting modules in terms of biological interpretability. We propose an algorithm that finds provably optimal or near-optimal conserved active modules in our model. We apply our algorithm to understand the mechanisms underlying Th17 T cell differentiation in both mouse and human. As a main biological result, we find that the key regulation of Th17 differentiation is conserved between human and mouse. xHeinz, an implementation of our algorithm, as well as all input data and results, are available at http://software.cwi.nl/xheinz and as a Galaxy service at http://services.cbib.u-bordeaux2.fr/galaxy in CBiB Tools.},\n  doi      = {10.1093/bioinformatics/btv316},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1093/bioinformatics/btv316},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Human TLR8 senses UR/URR motifs in bacterial and mitochondrial RNA.\n \n \n \n \n\n\n \n Krüger, A.; Oldenburg, M.; Chebrolu, C.; Beisser, D.; Kolter, J.; Sigmund, A. M.; Steinmann, J.; Schäfer, S.; Hochrein, H.; Rahmann, S.; Wagner, H.; Henneke, P.; Hornung, V.; Buer, J.; and Kirschning, C. J.\n\n\n \n\n\n\n EMBO Reports, 16(12): 1656–1663. Dec 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Human$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Kruger2015,\n  author   = {Anne Kr\\"{u}ger and Marina Oldenburg and Chiranjeevi Chebrolu and Daniela Beisser and Julia Kolter and Anna M. Sigmund and J\\"{o}rg Steinmann and Simon Sch\\"{a}fer and Hubertus Hochrein and Sven Rahmann and Hermann Wagner and Philipp Henneke and Veit Hornung and Jan Buer and Carsten J. Kirschning},\n  journal  = {EMBO Reports},\n  title    = {Human {T}{L}{R}8 senses {U}{R}/{U}{R}{R} motifs in bacterial and mitochondrial {R}{N}{A}},\n  year     = {2015},\n  month    = {Dec},\n  number   = {12},\n  pages    = {1656--1663},\n  volume   = {16},\n  abstract = {Toll-like receptor (TLR) 13 and TLR2 are the major sensors of Gram-positive bacteria in mice. TLR13 recognizes Sa19, a specific 23S ribosomal (r) RNA-derived fragment and bacterial modification of Sa19 ablates binding to TLR13, and to antibiotics such as erythromycin. Similarly, RNase A-treated Staphylococcus aureus activate human peripheral blood mononuclear cells (PBMCs) only via TLR2, implying single-stranded (ss) RNA as major stimulant. Here, we identify human TLR8 as functional TLR13 equivalent that promiscuously senses ssRNA. Accordingly, Sa19 and mitochondrial (mt) 16S rRNA sequence-derived oligoribonucleotides (ORNs) stimulate PBMCs in a MyD88-dependent manner. These ORNs, as well as S. aureus-, Escherichia coli-, and mt-RNA, also activate differentiated human monocytoid THP-1 cells, provided they express TLR8. Moreover, Unc93b1(-/-)- and Tlr8(-/-)-THP-1 cells are refractory, while endogenous and ectopically expressed TLR8 confers responsiveness in a UR/URR RNA ligand consensus motif-dependent manner. If TLR8 function is inhibited by suppression of lysosomal function, antibiotic treatment efficiently blocks bacteria-driven inflammatory responses in infected human whole blood cultures. Sepsis therapy might thus benefit from interfering with TLR8 function.},\n  doi      = {10.15252/embr.201540861},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.15252/embr.201540861},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Mutational dynamics between primary and relapse neuroblastomas.\n \n \n \n \n\n\n \n Schramm, A.; Köster, J.; Assenov, Y.; Althoff, K.; Peifer, M.; Mahlow, E.; Odersky, A.; Beisser, D.; Ernst, C.; Henssen, A. G; Stephan, H.; Schröder, C.; Heukamp, L.; Engesser, A.; Kahlert, Y.; Theissen, J.; Hero, B.; Roels, F.; Altmüller, J.; Nürnberg, P.; Astrahantseff, K.; Gloeckner, C.; Preter, K. D.; Plass, C.; Lee, S.; Lode, H. N; Henrich, K.; Gartlgruber, M.; Speleman, F.; Schmezer, P.; Westermann, F.; Rahmann, S.; Fischer, M.; Eggert, A.; and Schulte, J. H\n\n\n \n\n\n\n Nature Genetics, 47(8): 872–877. Aug 2015.\n \n\n\n\n
\n\n\n\n \n \n $\"Mutational$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Schramm2015,\n  author   = {Alexander Schramm and Johannes K\\"{o}ster and Yassen Assenov and Kristina Althoff and Martin Peifer and Ellen Mahlow and Andrea Odersky and Daniela Beisser and Corinna Ernst and Anton G Henssen and Harald Stephan and Christopher Schr\\"{o}der and Lukas Heukamp and Anne Engesser and Yvonne Kahlert and Jessica Theissen and Barbara Hero and Frederik Roels and Janine Altm\\"{u}ller and Peter N\\"{u}rnberg and Kathy Astrahantseff and Christian Gloeckner and Katleen De Preter and Christoph Plass and Sangkyun Lee and Holger N Lode and Kai-Oliver Henrich and Moritz Gartlgruber and Frank Speleman and Peter Schmezer and Frank Westermann and Sven Rahmann and Matthias Fischer and Angelika Eggert and Johannes H Schulte},\n  journal  = {Nature Genetics},\n  title    = {Mutational dynamics between primary and relapse neuroblastomas},\n  year     = {2015},\n  month    = {Aug},\n  number   = {8},\n  pages    = {872--877},\n  volume   = {47},\n  abstract = {Neuroblastoma is a malignancy of the developing sympathetic nervous system that is often lethal when relapse occurs. We here used whole-exome sequencing, mRNA expression profiling, array CGH and DNA methylation analysis to characterize 16 paired samples at diagnosis and relapse from individuals with neuroblastoma. The mutational burden significantly increased in relapsing tumors, accompanied by altered mutational signatures and reduced subclonal heterogeneity. Global allele frequencies at relapse indicated clonal mutation selection during disease progression. Promoter methylation patterns were consistent over disease course and were patient specific. Recurrent alterations at relapse included mutations in the putative CHD5 neuroblastoma tumor suppressor, chromosome 9p losses, DOCK8 mutations, inactivating mutations in PTPN14 and a relapse-specific activity pattern for the PTPN14 target YAP. Recurrent new mutations in HRAS, KRAS and genes mediating cell-cell interaction in 13 of 16 relapse tumors indicate disturbances in signaling pathways mediating mesenchymal transition. Our data shed light on genetic alteration frequency, identity and evolution in neuroblastoma.},\n  doi      = {10.1038/ng.3349},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1038/ng.3349},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2014\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure.\n \n \n \n \n\n\n \n Boenigk, J.; Beisser, D.; Zimmermann, S.; Bock, C.; Jakobi, J.; Grabner, D.; Grossmann, L.; Rahmann, S.; Barcikowski, S.; and Sures, B.\n\n\n \n\n\n\n PLOS ONE, 9(4): e95340. Aug 2014.\n \n\n\n\n
\n\n\n\n \n \n $\"Effects$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Boenigk2014,\n  author   = {Jens Boenigk and Daniela Beisser and Sonja Zimmermann and Christina Bock and Jurij Jakobi and Daniel Grabner and Lars Grossmann and Sven Rahmann and Stephan Barcikowski and Bernd Sures},\n  journal  = {PLOS ONE},\n  title    = {Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure},\n  year     = {2014},\n  month    = {Aug},\n  number   = {4},\n  pages    = {e95340},\n  volume   = {9},\n  abstract = {Among metal pollutants silver ions are one of the most toxic forms, and have thus been assigned to the highest toxicity class. Its toxicity to a wide range of microorganisms combined with its low toxicity to humans lead to the development of a wealth of silver-based products in many bactericidal applications accounting to more than 1000 nano-technology-based consumer products. Accordingly, silver is a widely distributed metal in the environment originating from its different forms of application as metal, salt and nanoparticle. A realistic assessment of silver nanoparticle toxicity in natural waters is, however, problematic and needs to be linked to experimental approaches. Here we apply metatranscriptome sequencing allowing for elucidating reactions of whole communities present in a water sample to stressors. We compared the toxicity of ionic silver and ligand-free silver nanoparticles by short term exposure on a natural community of aquatic microorganisms. We analyzed the effects of the treatments on metabolic pathways and species composition on the eukaryote metatranscriptome level in order to describe immediate molecular responses of organisms using a community approach. We found significant differences between the samples treated with 5 µg/L AgNO3 compared to the controls, but no significant differences in the samples treated with AgNP compared to the control samples. Statistical analysis yielded 126 genes (KO-IDs) with significant differential expression with a false discovery rate (FDR) <0.05 between the control (KO) and AgNO3 (NO3) groups. A KEGG pathway enrichment analysis showed significant results with a FDR below 0.05 for pathways related to photosynthesis. Our study therefore supports the view that ionic silver rather than silver nanoparticles are responsible for silver toxicity. Nevertheless, our results highlight the strength of metatranscriptome approaches for assessing metal toxicity on aquatic communities.},\n  doi      = {10.1371/journal.pone.0095340},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1371/journal.pone.0095340},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2012\n \n \n (3)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Robustness and accuracy of functional modules in integrated network analysis.\n \n \n \n \n\n\n \n Beisser, D.; Brunkhorst, S.; Dandekar, T.; Klau, G. W.; Dittrich, M. T.; and Müller, T.\n\n\n \n\n\n\n Bioinformatics, 28(14): 1887–1894. Jul 2012.\n \n\n\n\n
\n\n\n\n \n \n $\"Robustness$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Beisser2012,\n  author   = {Daniela Beisser and Stephan Brunkhorst and Thomas Dandekar and Gunnar W. Klau and Marcus T. Dittrich and Tobias M\\"{u}ller},\n  journal  = {Bioinformatics},\n  title    = {Robustness and accuracy of functional modules in integrated network analysis},\n  year     = {2012},\n  month    = {Jul},\n  number   = {14},\n  pages    = {1887--1894},\n  volume   = {28},\n  abstract = {High-throughput molecular data provide a wealth of information that can be integrated into network analysis. Several approaches exist that identify functional modules in the context of integrated biological networks. The objective of this study is 2-fold: first, to assess the accuracy and variability of identified modules and second, to develop an algorithm for deriving highly robust and accurate solutions. In a comparative simulation study accuracy and robustness of the proposed and established methodologies are validated, considering various sources of variation in the data. To assess this variation, we propose a jackknife resampling procedure resulting in an ensemble of optimal modules. A consensus approach summarizes the ensemble into one final module containing maximally robust nodes and edges. The resulting consensus module identifies and visualizes robust and variable regions by assigning support values to nodes and edges. Finally, the proposed approach is exemplified on two large gene expression studies: diffuse large B-cell lymphoma and acute lymphoblastic leukemia.},\n  doi      = {10.1093/bioinformatics/bts265},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1093/bioinformatics/bts265},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.\n \n \n \n \n\n\n \n Beisser, D.; Grohme, M. A; Kopka, J.; Frohme, M.; Schill, R. O; Hengherr, S.; Dandekar, T.; Klau, G. W; Dittrich, M.; and Müller, T.\n\n\n \n\n\n\n BMC Systems Biology, 6(72): 72. Jun 2012.\n \n\n\n\n
\n\n\n\n \n \n $\"Integrated$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Beisser2012a,\n  author   = {Daniela Beisser and Markus A Grohme and Joachim Kopka and Marcus Frohme and Ralph O Schill and Steffen Hengherr and Thomas Dandekar and Gunnar W Klau and Marcus Dittrich and Tobias M\\"{u}ller},\n  journal  = {BMC Systems Biology},\n  title    = {Integrated pathway modules using time-course metabolic profiles and {E}{S}{T} data from {M}ilnesium tardigradum},\n  year     = {2012},\n  month    = {Jun},\n  number   = {72},\n  pages    = {72},\n  volume   = {6},\n  abstract = {Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration. The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner.},\n  doi      = {10.1186/1752-0509-6-72},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1186/1752-0509-6-72},\n}\n\n

\n

\n\n\n

\n Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration. The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner.\n

\n\n\n

\n \n\n \n \n \n \n \n \n Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations.\n \n \n \n \n\n\n \n Förster, F.; Beisser, D.; Grohme, M. A.; Liang, C.; Mali, B.; Siegl, A. M.; Engelmann, J. C.; Shkumatov, A.; Schokraie, E.; Müller, T.; Schnölzer, M.; Schill, R. O.; Frohme, M.; and Dandekar, T.\n\n\n \n\n\n\n Bioinformatics and Biology Insights, 6: 69–96. Apr 2012.\n \n\n\n\n
\n\n\n\n \n \n $\"Transcriptome$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Forster2012,\n  author   = {Frank F\\"{o}rster and Daniela Beisser and Markus A. Grohme and Chunguang Liang and Brahim Mali and Alexander Matthias Siegl and Julia C. Engelmann and Alexander Shkumatov and Elham Schokraie and Tobias M\\"{u}ller and Martina Schn\\"{o}lzer and Ralph O. Schill and Marcus Frohme and Thomas Dandekar},\n  journal  = {Bioinformatics and Biology Insights},\n  title    = {Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations},\n  year     = {2012},\n  month    = {Apr},\n  pages    = {69--96},\n  volume   = {6},\n  abstract = {Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum. To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions. ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum. These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.},\n  doi      = {10.4137/bbi.s9150},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.4137/BBI.S9150},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2011\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Bioinformatics identifies tardigrade molecular adaptations including the DNA-j family and first steps towards dynamical modelling.\n \n \n \n \n\n\n \n Förster, F.; Beisser, D.; Frohme, M.; Schill, R. O.; and Dandekar, T.\n\n\n \n\n\n\n Journal of Zoological Systematics and Evolutionary Research, 49: 120–126. Apr 2011.\n \n\n\n\n
\n\n\n\n \n \n $\"Bioinformatics$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Foerster2011,\n  author    = {Frank F\\"{o}rster and Daniela Beisser and Marcus Frohme and Ralph O. Schill and Thomas Dandekar},\n  journal   = {Journal of Zoological Systematics and Evolutionary Research},\n  title     = {Bioinformatics identifies tardigrade molecular adaptations including the {DNA}-j family and first steps towards dynamical modelling},\n  year      = {2011},\n  month     = {Apr},\n  pages     = {120--126},\n  volume    = {49},\n  abstract  = {Tardigrades are an independent animal phylum with remarkable adaptation against cold, heat, radiation and vacuum, which they outlast in a dormant stage (tun). Growing data resources and new large-scale data (e.g. from large EST sequencing projects) allows to investigate tardigrade-specific adaptations. Bioinformatical analysis and methods follow the flow of genetic information from DNA to proteins, from sequences to protein clusters, from pathways and dynamics of adaptations. These methods include the usage of internal transcribed spacer 2 as a new phylogenetic marker. Next we present recent examples of bioinformatical analysis on tardigrades for these steps. This includes specific RNA stability motifs. Clustering of protein families reveals tardigrade-specific protein families and pathway analysis allows insights into mechanisms of oxidative stress tolerance, protein repair, protein turnover, DNA protection and stress-pathways. We focus in more detail on the diversity of DNA-j-like proteins that enhances the adaptation potential of Milnesium tardigradum. Finally, a sketch of adaptation dynamics in tardigrades is presented including techniques for dynamical modelling; yet, quantitative modelling requires far more data and detail.},\n  doi       = {10.1111/j.1439-0469.2010.00609.x},\n  keywords  = {paper},\n  publisher = {Wiley-Blackwell},\n  url       = {http://dx.doi.org/10.1111/j.1439-0469.2010.00609.x},\n}\n\n

\n

\n\n\n\n\n\n

\n

\n \n 2010\n \n \n (2)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n BioNet: an R-Package for the functional analysis of biological networks.\n \n \n \n \n\n\n \n Beisser, D.; Klau, G. W.; Dandekar, T.; Müller, T.; and Dittrich, M. T.\n\n\n \n\n\n\n Bioinformatics, 26(8): 1129–1130. Apr 2010.\n \n\n\n\n
\n\n\n\n \n \n $\"BioNet:$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Beisser2010,\n  author   = {Beisser, Daniela and Klau, Gunnar W. and Dandekar, Thomas and M\\"{u}ller, Tobias and Dittrich, Marcus T.},\n  journal  = {Bioinformatics},\n  title    = {Bio{N}et: an {R}-{P}ackage for the functional analysis of biological networks},\n  year     = {2010},\n  month    = {Apr},\n  number   = {8},\n  pages    = {1129--1130},\n  volume   = {26},\n  abstract = {Increasing quantity and quality of data in transcriptomics and interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules. The BioNet package provides an extensive framework for integrated network analysis in R. This includes the statistics for the integration of transcriptomic and functional data with biological networks, the scoring of nodes as well as methods for network search and visualization. The BioNet package and a tutorial are available from http://bionet.bioapps.biozentrum.uni-wuerzburg.de.},\n  doi      = {10.1093/bioinformatics/btq089},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1093/bioinformatics/btq089},\n}\n\n

\n

\n\n\n\n\n\n

\n\n\n

\n \n\n \n \n \n \n \n \n Functional modules in protein-protein interaction networks.\n \n \n \n \n\n\n \n Dittrich, M.; Beisser, D.; Klau, G.; and Müller, T.\n\n\n \n\n\n\n In Choi, S., editor(s), Systems Biology for Signaling Networks, pages 353–369. Springer New York, 2010.\n \n\n\n\n
\n\n\n\n \n \n $\"Functional$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@InCollection{Dittrich2010,\n  author    = {Marcus Dittrich and Daniela Beisser and Gunnar Klau and Tobias M\\"{u}ller},\n  booktitle = {Systems Biology for Signaling Networks},\n  publisher = {Springer New York},\n  title     = {Functional modules in protein-protein interaction networks},\n  year      = {2010},\n  editor    = {Sangdun Choi},\n  pages     = {353--369},\n  doi       = {10.1007/978-1-4419-5797-9},\n  keywords  = {bookchapter},\n  url       = {http://dx.doi.org/10.1007/978-1-4419-5797-9},\n}\n\n

\n

\n\n\n\n

\n\n\n\n\n\n

\n

\n \n 2009\n \n \n (1)\n \n \n

\n

\n \n \n

\n \n\n \n \n \n \n \n \n Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.\n \n \n \n \n\n\n \n Förster, F.; Liang, C.; Shkumatov, A.; Beisser, D.; Engelmann, J. C; Schnölzer, M.; Frohme, M.; Müller, T.; Schill, R. O; and Dandekar, T.\n\n\n \n\n\n\n BMC Genomics, 10(469): 469. Oct 2009.\n \n\n\n\n
\n\n\n\n \n \n $\"Tardigrade$ Paper\n \n \n\n \n \n doi\n \n \n\n \n link\n \n \n\n bibtex\n \n\n \n \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n \n \n \n \n \n\n\n\n

\n

@Article{Forster2009,\n  author   = {Frank F\\"{o}rster and Chuanguang Liang and Alexander Shkumatov and Daniela Beisser and Julia C Engelmann and Martina Schn\\"{o}lzer and Marcus Frohme and Tobias M\\"{u}ller and Ralph O Schill and Thomas Dandekar},\n  journal  = {BMC Genomics},\n  title    = {Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as {R}{N}{A} elements in tardigrades},\n  year     = {2009},\n  month    = {Oct},\n  number   = {469},\n  pages    = {469},\n  volume   = {10},\n  abstract = {Tardigrades represent an animal phylum with extraordinary resistance to environmental stress. To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data. Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.},\n  doi      = {10.1186/1471-2164-10-469},\n  keywords = {paper},\n  url      = {http://dx.doi.org/10.1186/1471-2164-10-469},\n}\n\n

\n

\n\n\n\n\n\n

\n