/CRC AquaDiva /PUBLICATIONS /Peer-Reviewed

Data Portal
Peer-Reviewed Publications of the CRC AquaDiva

google scholar logo


Baumeister T.U.H., Ueberschaar N., Pohnert G. (2019) Gas-phase chemistry in the GC orbitrap mass spectrometer. Journal of the American Society for Mass Spectrometry 30(4): 573-580.

Behrendt T., Catao E.C.P., Bunk R., Yi Z., Schweer E., Kolb S., Kesselmeier J., Trumbore S. (2019) Microbial community responses determine how soil-atmosphere exchange of carbonyl sufide, carbon monooxide, and nitric oxide responds to soil moisture. SOIL 5: 121-135.

Fischer C., Leimer S., Roscher C., Ravenek J., de Kroon H., Kreutziger Y., Baade J., Beßler H., Eisenhauer N., Weigelt A., Mommer L., Lange M., Gleixner G., Wilcke W., Schröder B., Hildebrandt A. (2019) Plant species richness and functional groups have different effects on soil water content in a decade-long grassland experiment. Journal of Ecology 107(1): 127-141.

Frischbier N., Tiebel K, Tischer A., Wagner S. (2019) Small scale rainfall partitioning in a European beech forest ecosystem reveals heterogeneity of Leaf Area Index and its connectivity to hydro- and atmosphere. Geosciences 9(9): 393.

Hellrich J., Kampe B., Hahn U. (2019) The influence of down-sampling strategies on SVD word embedding stability. In: Proceedings of the 3rd Workshop on Evaluating Vector Space Representations for NLP (RepEval2019), pages 18-26; 06/06/2019; Minneapolis, Minnesota, USA; Association for Computational Linguistics.

Hermann M., Wegner C.-E., Taubert M., Geesink P., Lehmann K., Yan L., Lehmann R., Totsche K.U., Küsel K. (2019) Predominance of Cand. Patescibacteria in groundwater is caused by their preferential mobilization from soils and flourishing under oligotrophic conditions. Frontiers in Microbiology 10: article 1407.

Hölzer M., Marz M. (2019) De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. GigaScience 8(5): giz039.

Jing M., Heße F., Kumar R., Kolditz O., Attinger S. (2019) Influence of input and parameter uncertainty on the prediction of catchment-scale groundwater travel time distributions. Hydrology and Earth System Sciences 23: 171-190.

Kallies R., Hölzer M., Toscan R.B., da Rocha U.N., Anders J., Marz M., Chatzinotas A. (2019) Evaluation of sequencing library preparation protocols for viral metagenomic analysis from pristine aquifer groundwaters. Viruses 11(6): 484.

Kallies R., Kiesel B., Schmidt M., Ghanem N., Zopfi J., Hackermüller J., Harms H., Wick L.Y., Chatzinotas A. (2019) Complete genome sequence of Pseudoalteromonas virus vB_PspP-H6/1 that infects Pseudoalteromonas sp. strain H6. Marine Genomics, in press. Doi: 10.1016/j.margen.2019.03.002.

Knebl A., Domes R., Yan D., Popp J., Trumbore S., Frosch T. (2019) Fiber-enhanced Raman gas spectroscopy for 18O-13C-labelling experiments. Analytical Chemistry 91(12): 7562-7569.

Lazar C.S., Lehmann R., Stoll W., Rosenberger J., Totsche K.U., Küsel K. (2019) The endolithic bacterial diversity of shallow bedrock ecosystems. Science of the Total Environment 679: 35-44.

Metzger J.C., Schumacher J., Lange M., Hildebrandt A. (2019) Neighbourhood and stand structure affect stemflow generation in a heterogeneous deciduous temperate forest. HESS Discussions, preprint. Doi: 10.5194/hess-2019-336.

Moawed S., Algergawy A., Sarhan A., Eldosouky A. (2019) A framework for efficient matching of large-scale metadata models. Arabian Journal for Science and Engineering 44(4): 3117-3135.

Nawaz A., Purahong W., Herrmann M., Küsel K., Buscot F., Wubet T. (2019) DNA and RNA derived fungal communities in subsurface aquifers only partly overlap but react similarly to environmental factors. Microorganisms 7(9): 341.

Roth V.-N., Lange M., Simon C., Hertkorn N., Bucher S., Goodall T., Griffiths R.I., Mellado-Vázquez P.G., Mommer L., Oram N.J., Weigelt A., Dittmar T., Gleixner G. (2019) Persistence of dissolved organic matter explained by molecular changes during its passage through soil. Nature Geoscience. Doi: 10.1038/s41561-019-0417-4.

Schwab V., Nowak M.E., Trumbore S.E., Xu X., Gleixner G., Muhr J., Küsel K., Totsche K.U. (2019) Isolation of individual saturated fatty acid methyl esters derived from groundwater phospholipids by preparative-high pressure liquid chromatography for compound specific radiocarbon analyses. Water Resources Research 55(3): 2521-2531.

Schwab V., Nowak M.E., Elder C.D., Trumbore S.E., Xu X., Gleixner G., Lehmann R., Pohnert G., Muhr J., Küsel K. (2019) 14C-free carbon is a major contributor to cellular biomass in geochemically distinct groundwater of shallow sedimentary aquifers. Water Resources Research 55(3): 2104-2121.

Sieburg A., Knebl A., Jacob J.M., Frosch T. (2019) Characterization of fuel gases with fiber-enhanced Raman Spectroscopy. Analytical and Bioanalytical Chemistry. Doi: 10.1007/s00216-019-02145-x.

Simon C., Osterholz H., Koschinsky A., Dittmar T. (2019) Riverine mixing at the molecular scale - An ultrahigh-resolution mass spectrometry study on dissolved organic matter and selected metals in the Amazon confluence zone (Manaus, Brazil). Organic Geochemistry 129: 45-62.

Taubert M., Stähly J., Kolb S., Küsel K. (2019) Divergent microbial communities in groundwater and overlying soils exhibit functional redundancy for plant-polysaccharide degradation. PLOS ONE 14(3): e0212937.

Thullner M., Regnier P. (2019) Microbial controls on the biogeochemical dynamics in the subsurface. Reviews in Mineralogy and Geochemistry 85(1): 265-302.

Tischer A., Sehl L., Meyer U.-N., Kleinebecker T., Klaus V., Hamer U. (2019) Land-use intensity shapes kinetics of extracellular enzymes in rhizosphere soil of agricultural grassland plant species. Plant and Soil 437(1-2): 215-239.

Viehweger A., Krautwurst S., Lamkiewicz K., Madhugiri R., Ziebuhr J., Hölzer M., Marz M. (2019) Direct RNA nanopore sequencing of full-lenth coronavirus genomes provides novel insights into structural variants and enables modification analysis. Genome Research 29(9): 1545-1554. (Preprint: bioRxiv 483693)

Wegner C.-E., Gaspar M., Geesink P., Herrmann M., Marz M., Küsel K. (2019) Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of elements of nitrogen, sulfur and carbon. Applied and Environmental Microbiology 85(5): e02346-18.


Baumeister T.U.H., Ueberschaar N., Schmidt-Heck W., Mohr F., Deicke M., Wichard T., Guthke R., Pohnert G. (2018) DeltaMS: a tool to track isotopologues in GC- and LC-MS data. Metabolomics 14: 41.

Benk S., Li Y., Roth V.-N., Gleixner G. (2018) Lignin dimers as potential markers for 14C-young terrestrial dissolved organic matter in the Critical Zone. Frontiers in Earth Science 6: article 168.

Bocklitz T., Meyer T., Schmitt M., Rimke I., Hoffmann F., von Eggeling F., Ernst G., Guntinas-Lichius O., Popp J. (2018) Invited Article: Comparison of hyperspectral coherent Raman scattering microscopies for biomedical applications. APL Photonics 3: 092404.

Bourtsoukidis E., Behrendt T., Yanez-Serrano A.M., Hellén H., Diamantopoulos E., Catao E., Ashworth K., Pozzer A., Quesada C.A., Martins D.L., Sá M., Araujo A., Brito J., Artaxo P., Kesselmeier J., Lelieveld J., Williams J. (2018) Strong sesquiterpene emissions from Amazonian soils. Nature Communications 9: article 2226.

Brunzel M., Majdanski T.C., Vitz J., Nischang I., Schubert U.S. (2018) Fast screening of diol impurities in methoxy poly(ethylene glycol)s (mPEG)s by liquid chromatography on monolithic silica rods. Polymers 10(12): 1395.

Carlyle-Moses D.E., Iida S., Germer S., Llorens P., Michalzik B., Nanko K., Tischer A., Levia D.F. (2018) Expressing stemflow commensurate with its ecohydrological importance. Advances in Water Resources 121: 472-479.

Deveau A., Bonito G., Uehling J., Paoletti M., Becker M., Bindschedler S., Hacquard S., Hervé V., Labbé J., Lastovetsky O.A., Mieszkin S., Millet L.J., Vajna B., Junier P., Bonfante P., Krom B.P., Olsson S., van Elsas J.D., Wick L.Y. (2018) Bacterial-fungal interactions: ecology, mechanisms and challenges. FEMS Microbiology Reviews 42(3): 335-352.

Ding S., Kohlhepp B., Trumbore S., Küsel K., Totsche K.U., Pohnert G., Gleixner G., Schwab V.F. (2018) In situ production of core and intact bacterial and archaeal tetraether lipids in groundwater. Organic Geochemistry 126: 1-12.

Fäßler E., Hahn U. (2018) Annotation Data Manaement with JeDIS. ACM Symposium on Document Engineering 2018 (DocEng '18), August 28-31, 2018, Halifax, NS, Canada. ACM, New York, NY, USA, Article 4, 4 pages.

Fricke M., Gerst R., Ibrahim B., Niepmann M., Marz M. (2018) Global importance of RNA secondary structures in protein-coding sequences. Bioinformatics, bty678. Doi: 10.1093/bioinformatics/bty678.

Geesink P., Tyc O., Küsel K., Taubert M., van de Velde C., Kumar S., Garbeva P. (2018) Growth promotion and inhibition induced by interactions of groundwater bacteria. FEMS Microbiology Ecology, fiy164. Doi: 10.1093/femsec/fiy164

Gerst R., Hölzer M. (2018) PCAGO: An interactive web service to analyze RNA-Seq data with principal component analysis. preprint

Ghanem N., Trost M., Sánchez Fontanet L., Harms H., Chatzinotas A., Wick L.Y. (2018) Changes of the specific infectivity of tracer phages during transport in porous media. Environ Sci Technol 52(6): 3486-3492.

Guderle M., Bachmann D., Milcu A., Gockele A., Bechmann M., Fischer C., Roscher C., Landais D., Ravel O., Devidal S., Roy J., Gessler A., Buchmann N., Weigelt A., Hildebrandt A. (2018) Dynamic niche partitioning in root water uptake facilitates water use in more diverse grassland plant communities. Functional Ecology 32: 214-227.

Huang J., Hartmann H., Hellén H., Wisthaler A., Perreca E., Weinhold A., Rücker A., van Dam N.M., Gershenzon J., Trumbore S., Behrendt T. (2018) New perspectives on CO2, temperature, and light effects on BVOC emissions using online measurements by PTR-MS and cavity ring-down spectroscopy. Environmental Science & Technology 52(23): 13811-13823.

Jing M., Heße F., Kumar R., Wang W., Fischer T., Walther M., Zink M., Zech A., Samaniego L., Kolditz O., Attinger S. (2018) Improved regional-scale groundwater representation by the coupling of the mesoscale Hydrologic Model (mHM v5.7) to the groundwater model OpenGeoSys (OGS). Geoscientific Model Development 11(5): 1989-2007.

Knebl A., Yan D., Popp J., Frosch T. (2018) Fiber enhanced Raman gas spectroscopy. Trends in Analytical Chemistry 103: 230-238.

Kumar S., Herrmann M., Blohm A., Hilke I., Frosch T., Trumbore S.E., Küsel K. (2018) Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiology Ecology: fiy141.

Majdanski T.C., Vitz J., Meier A., Brunzel M., Schubert S., Nischang I., Schubert U.S. (2018) "Green" ethers as solvent alternatives for anionic ring-opening polymerizations of ethylene oxide (EO): In-situ kinetic and advanced characterization studies. Polymer 159: 86-94.

Nawaz A., Purahong W., Lehmann R., Herrmann M., Totsche K.U., Küsel K., Wubet T., Buscot F. (2018) First insights into the living groundwater mycobiome of the terrestrial biogeosphere. Water Research 145: 50-61.

Simon C., Roth V.-N., Dittmar T., Gleixner G. (2018) Molecular signals of heterogeneous terrestrial environments identified in dissolved organic matter: a comparative analysis of orbitrap and ion cyclotron resonance mass spectrometers. Frontiers in Earth Science 6: article 138.

Taubert M., Stöckel S., Geesink P., Girnus S., Jehmlich N., von Bergen M., Rösch P., Popp J., Küsel K. (2018) Tracking active groundwater microbes with D2O labelling to understand their ecosystem function. Environmental Microbiology  20: 369-384.

Zhang L., Lehmann K., Totsche K. U., Lueders T. (2018) Selective successional transport of bacterial populations from rooted agricultural topsoil to deeper layers upon extreme precipitation events. Soil Biology and Biochemistry 124: 168-178.


Abdelreheim M., Klan F., Soliman T. (2017) Towards personalized support for ontology selection. In: Proceedings of the 29th GI-Workshop Grundlagen von Datenbanken, 05/30/2017 - 06/02/2017.  Blankenburg/Harz, Germany.

Amara J., Bouaziz B., Algergawy A. (2017) A Deep Learning-based Approach for Banana Leaf Diseases Classification. In: BTW 2017 - Workshopband, Lecture Notes in Informatics (LNI), Gesellschaft für Informatik, Bonn 2017, B. Mitschang et al. (ed.). 17th Conference on Database Systems for Business, Technology, and Web; 03/06/2017 - 03/10/2017; Stuttgart, Germany.

Babalou S., Algergawy A., König-Ries B. (2017) An Ontology-based Scientific Data Integration Workflow. In: Proceedings of the 29th GI-Workshop Grundlagen von Datenbanken, 05/30/2017 - 06/02/2017.  Blankenburg/Harz, Germany.

Babalou S., Algergawy A., König-Ries B. (2017) A Particle Swarm-based Approach for Semantic Similarity Computation. Conference Paper. In: Panetto H. et al. (eds) On the Move to Meaningful Internet Systems. OTM 2017 Conferences. OTM 2017. Lecture Notes in Computer Science, vol 10574. Springer, Cham. (Proceedings of the 16th International Conference on Ontologies, DataBases, and Applications of Semantics, 10/24/2017 - 10/25/2017. Rhodes, Greece)

Crecelius A.C., Michalzik B., Potthast A., Meyer S., Schubert U.S. (2017) Tracing the fate and transport of secondary plant metabolites in a laboratory mesocosm experiment by employing mass spectrometric imaging. Anal Bioanal Chem 409(15): 3807-3820.

Crecelius A.C., Vitz J., Näthe K., Meyer S., Michalzik B., Schubert U.S. (2017) Effect of ecosystem type and fire on chemistry of WEOM as measured by LDI-TOF-MS and NMR. Talanta 162: 589-596.

Dalla Valle N., Potthast K., Meyer S., Michalzik B., Hildebrandt A., Wutzler T. (2017) Modeling macropore seepage fluxes from soil water content series by inversion of a dual permeability model. Hydrology and Earth System Sciences Discussions (preprint). doi: 10.5194/hess-2017-336.

Fäßler E., Hahn U. (2017) SEMEDICO: A comprehensive semantic search engine for the life sciences. Proceedings of the 55th Annual Meeting of the Association for Computational Linguistics (ACL 2017)- System Demonstrations, pages 91-96. Vancouver, Canada, July 30 - August 4, 2017. Doi: 10.18653/v1/P17-4016.

Fäßler E., Klan F., Algergawy A., König-Ries B., Hahn U. (2017) Selecting and tailoring ontologies with JOYCE. Conference Paper. In: Ciancarini P. et al. (eds.) Knowledge Engineering and Knowledge Management. EKAW 2016 Lecture Notes in Computer Science, vol 10180: pp. 114-118. Springer, Cham.

Friedmann R.C., Kalkhof S., Doppelt-Azeroual O., Mueller S.A., Chovancová M., von Bergen M., Schwikowski B. (2017) Common and phylogenetically widespread coding for peptides by bacterial small RNAs. BMC Genomics 18: 553.

Guo Y., Stärk H. J., Hause G., Schmidt M., Harms H., Wick L.Y. (2017) Heterogenic response of Prokaryotes toward silver nanoparticles and ions is facilitated by phenotypes and attachment of silver aggregates to cell surfaces. Cytometry Part A 91(8): 775-784.

Herrmann M., Opitz S., Harzer R., Totsche K. U., Küsel K. (2017) Attached and suspended denitrifier communities in pristine limestone aquifers harbor high fractions of potential authotrophs oxidizing resduced iron and sulfur compounds. Microb Ecol 74(2): 264-277.

Heße F., Zink M., Kumar R., Samaniego L., Attinger S. (2017) Spatially distributed characterization of soil-moisture dynamics using travel-time distributions. Hydrol Earth Syst Sci 21: 549-570. Doi: 10.5194/hess-21-549-2017.

Jochum T., Fastnacht A., Trumbore S.E., Popp J., Frosch T. (2017) Direct Raman spectroscopic measurements of biological nitrogen fixation under natural conditions: An analytical approach for studying nitrogenase activity. Anal Chem 89(2): 1117-1122.

Kallies R., Kiesel B., Schmidt M., Kacza J., Ghanem N., Narr A., Zopfi J., Wick L.Y., Hackermüller J., Harms H., Chatzinotas A. (2017) Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. Stand Genomic Sci 12: 20. Doi: 10.1186/s40793-017-0235-5.

Kallies R., Kiesel B., Zopfi J., Wick L. Y. (2017) Complete genome sequence of Alteromonas virus vB_AspP-H4/4. Genome Announc. 5(43): e00914-17.

Klan F., Faessler E., Algergawy A., König-Ries B., Hahn U. (2017) Integrated Semantic Search on Structured and Unstructured Data in the ADOnIS System. Research Paper. In: Algergawy A., Karam N., Klan F., Jonquet C. (eds.) Proceedings of the 2nd International Workshop on Semantics for Biodiversity co-located with 16th International Semantic Web Conference (ISWC 2017), 10/22/2017. Vienna, Austria. CEUR Workshop Proceedings Vol-1933.

Kohlhepp B., Lehmann R., Seeber P., Küsel K., Trumbore S., Totsche K.U. (2017) Aquifer configuration and geostructural links control the groundwater quality in thin-bedded carbonate-siliciclastic alternations of the Hainich CZE, central Germany. Hydrology and Earth System Sciences 21(12): 6091-6116. Doi: 10.5194/hess-21-6091-2017.

Kuhlisch C., Deicke M., Ueberschaar N., Wichard T., Pohnert G. (2017) A fast and direct liquid chromatography-mass spectrometry method to detect and quantify polyunsaturated aldehydes and polar oxylipins in diatoms. Limnol Oceanogr Methods 15(1): 70-79.

Kumar S., Herrmann M., Thamdrup B., Schwab V.F., Geesink P., Trumbore S.E., Totsche K.U., Küsel K. (2017) Nitrogen loss from pristine carbonate-rock aquifers of the Hainich Critical Zone Exploratory (Germany) is primarily driven by chemolithoautotrophic anammox processes. Frontiers in Microbiology 8: 1951.

Lazar C.S., Baker B.J., Seitz K., Teske A.P. (2017) Genomic reconstruction of multiple lineages of uncultered benthic archaea suggests distinct biogeochemical roles and ecological niches. The ISME Journal 11: 1118-1129.

Lazar C.S., Stoll W., Lehmann R., Herrmann M., Schwab V.F., Akob D.M., Nawaz A., Wubet T., Buscot F., Totsche K.U., Küsel K. (2017) Archaeal diversity and CO2 fixers in carbonate-/siliciclastic-rock groundwater ecosystems. Archaea 2017: article ID 2136287. Doi: 10.1155/2017/2136287.

Löffler F., Pfaff C-T., Karam N., Fichtmüller D., Klan F. (2017) What do biodiversity scholars search for? Identifying high-level entities for biological metadata. Poster Paper. In: Algergawy A., Karam N., Klan F., Jonquet C. (eds.) Proceedings of the 2nd International Workshop on Semantics for Biodiversity co-located with 16th International Semantic Web Conference (ISWC 2017), 10/22/2017. Vienna, Austria. CEUR Workshop Proceedings Vol-1933.

Metzger J.C., Wutzler T., Dalla Valle N., Filipzik J., Grauer C., Lehmann R., Roggenbuck M., Schelhorn D., Weckmüller J., Küsel K., Totsche K.U., Trumbore S., Hildebrandt A. (2017) Vegetation impacts soil water content patterns by shaping canopy water fluxes and soil properties. Hydrological Processes 31(22): 3783-3795.

Mori J.F., Ueberschaar N., Lu S., Cooper R.E., Pohnert G., Küsel K. (2017) Sticking together: Inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling. The ISME Journal 11: 1075-1086.

Narr A., Nawaz A., Wick L. Y., Harms H., Chatzinotas A. (2017) Soil viral communities vary temporally and along a land use transect as revealed by virus-like particle counting and a modified community fingerprinting approach (fRAPD). Front Microbiol 8: article 1975.

Nowak M., Schwab V.F., Lazar C.S., Behrendt T., Kohlhepp B., Totsche K.U., Küsel K., Trumbore S.E. (2017) Carbon isotopes of dissolved inorganic carbon reflect utilization of different carbon sources by microbial communities in two limestone aquifer assemblages. Hydrology and Earth System Sciences 21: 4283-4300. Doi: 10.5194/hess-21-4283-2017.

Potthast K., Meyer S., Crecelius A.C., Schubert U.S., Tischer A., Michalzik B. (2017) Land-use and fire drive temporal patterns of soil solution chemistry and nutrient fluxes. Science of The Total Environment 605-606: 514-526.

Samir S., Sarhan A., Algergawy A. (2017) Context-based web service discovery framework with QoS considerations. In: IEEE Xplore Digital Library for the 11th International Conference on Research Challenges in Information Science (RCIS_2017), May 10-12, 2017.  Brighton, UK. Doi: 10.1109/RCIS.2017.7956531.

Schwab V.F., Herrmann M., Roth V.-N., Gleixner G., Lehmann R., Pohnert G., Trumbore S.E., Küsel K., Totsche K.U. (2017) Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches. Biogeosciences 14: 2697-2714. Doi: 10.5194/bg-14-2697-2017.

Shehab E., Algergawy A., Sarhan A. (2017) Accelerating relational database operations using both CPU and GPU co-processor. Computers & Electrical Engineering 57: 69-80.

Sieburg A., Jochum T., Trumbore S.E., Popp J., Frosch T. (2017) Onsite cavity enhanced Raman spectrometry for the investigation of gas exchange processes in the Earth's critical zone. Analyst 142: 3360-3369.

Starke R., Müller M., Gaspar M., Marz M., Küsel K., Totsche K.U., von Bergen M., Jehmlich N. (2017) Candidate Brocadiales dominates C, N and S cycling in anoxic groundwater of a pristine limestone-fracture aquifer. Journal of Proteomics 152: 153-160.

Warnke M., Jacoby C., Jung T., Agne M., Mergelsberg M., Starke R., Jehmlich N., von Bergen M., Richnow H.-H., Brüls T., Boll M. (2017) A patchwork pathway for oxygenase-independent degradation of side chain containing steroids. Environmental Microbiology 19(11): 4684-4699.

Wutzler T., Zaehle S., Schrumpf M., Ahrens B., Reichstein M. (2017) Adaption of microbial resource allocation affects modelled long term soil organic matter and nutrient cycling. Soil Biology and Biochemistry 115: 322-336.


Algergawy A., Babalou S., Klan F., König-Ries B. (2016) OAPT: A tool for ontology analysis and partitioning (Demo paper). In: Proceedings of the 19th International Conference on Extending Database Technology (EDBT 2016). Bordeaux, France, March 15-18, 2016.

Algergawy A., Babalou S., König-Ries B. (2016) A new metric to evaluate ontology modularization. In: Proceedings of the 2nd International Workshop on Summarizing and Presenting Entities and Ontologies (SumPre 2016) co-located with the 13th Extended Semantic Web Conference (ESWC 2016), Anissaras, Greece, May 30, 2016; CEUR Workshop Proceedings 1605. Thalhamer A., Cheng G., Gunaratna K. (eds.); available online at http://ceur-ws.org/Vol-1605/.

Bastida F., Torres I.F., Moreno J.L., Baldrian P., Ondoño S., Ruiz-Navarro A., Hernández T., Richnow H.H., Starke R., García C., Jehmlich N. (2016) The active microbial diversity drives ecosystem multifunctionality and is physiologically related to carbon availability in Mediterranean semi-arid soils. Mol Ecol 25: 4660-4673.

Berthold T., Centler F., Hübschmann T., Remer R., Thullner M., Harms H., Wick L.Y. (2016) Mycelia as a focal point for horizontal gene transfer among soil bacteria. Scientific reports 6: 36390. Doi: 10.1038/srep36390.

Dalle Pezze P., Ruf S., Sonntag A., Langelaar-Makkinje M., Hall P., Heberle A., Razquin Navas P., van Eunen K., Toelle R., Schwarz J., Wiese H., Warscheid B., Deitersen J., Stork B., Fäßler E., Schäuble S., Hahn U., Horvatovich P., Shanley D., Thedieck K. (2016) A system study reveals concurrent activation of AMPK and mTor by amino acids. Nature Communications 7: #13254.

Ding S., Schwab V.F., Ueberschaar N., Roth V.-N., Lange M., Xu Y., Gleixner G., Pohnert G. (2016) Identification of novel 7-methyl and cyclopentanyl branched glycerol dialkyl glycerol tetraethers in lake sediments. Organic Geochemistry 102: 52-58.

European Commission, Joint Research Centre (2016) Global Soil Biodiversity Atlas - Earth Sciences Research - EU Bookshop: http://bookshop.europa.eu/en/global-soil-biodiversity-atlas-pbLBNA27236/. Contributors: Küsel K., Totsche K.U., Trumbore S.E., Buscot F.; Chapter III - Geographical and temporal distribution, p. 73.

Ghanem N., Kiesel B., Kallies R., Harms H., Chatzinotas A., Wick L.Y. (2016) Marine phages as tracers: Effects of size, morphology, and physico-chemical surface properties on transport in a porous medium. Environmental Science & Technology 50(23): 12816-12824.

Hahn U., Matthies F., Fäßler E., Hellrich J. (2016) UIMA-based JCorRe 2.0 goes GitHub and Maven Central: State-of-the-art software resource engineering and distribution of NLP pipelines. In: Proceedings of the 10th International Conference on Language Resources and Evaluation (LREC 2016). Portorož, Slovenia; pp. 2502-2509.

Hildebrandt A., Kleidon A., Bechmann M. (2016) A thermodynamic formulation of root water uptake. Hydrology and Earth System Sciences 20(8): 3441-3454.

Jehmlich N., Müller M., Meyer S., Tischer A., Richnow H.H., Potthast K., Michalzik B., von Bergen M. (2016) Proteome data on the microbial microbiome of grasshopper feces. Data in Brief 9: 1147-1154.

Küsel K., Totsche K.U., Trumbore S., Lehmann R., Steinhäuser* C., Herrmann M. (2016) How deep can surface signals be traced in the critical zone? Merging biodiversity with biogeochemistry research in a central German Muschelkalk landscape. Frontiers in Earth Science 4: 32.

Löffler F., Klan F. (2016) Does term expansion matter for the retrieval of biodiversity data? In: Joint Proceedings of the Posters and Demos Track of the 12th International Conference on Semantic Systems - SEMANTiCS2016, and the 1st International Workshop on Semantic Change & Evolving Semantics (SuCCESS'16) (Poster paper). Leipzig, Germany; available online at http://ceur-ws.org/Vol-1695/.

Lünsmann V., Kappelmeyer U., Benndorf R., Martinez-Lavanchy P.M., Taubert A., Adrian L., Duarte M., Pieper D.H., von Bergen M., Müller J.A., Heipieper H.J., Jehmlich N. (2016) In situ protein-SIP highlights Burkholderiaceae as key players degrading toluene by para ring hydroxylation in a constructed wetland model. Environ Microbiol 18(4): 1176-1186.

Lünsmann V., Kappelmeyer U., Taubert A., Nijenhuis I., von Bergen M., Heipieper H.J., Müller J.A., Jehmlich N. (2016) Aerobic toluene degraders in the rhizosphere of a constructed wetland model show diurnal polyhydroxyalkanoate metabolism. Appl Environ Microbiol 82(14): 4126-4132.

Malik A.A., Roth V.-N., Hébert M., Tremblay L., Dittmar T., Gleixner G. (2016) Linking molecular size, composition and carbon turnover of extractable soil microbial compounds. Soil Biology and Biochemistry 100: 66-73.

Malghani S., Reim A., von Fischer J., Conrad R., Kuebler K., Trumbore S.E. (2016) Soil methanotroph abundance and community composition are not influenced by substrate availability in laboratory incubations. Soil Biology and Biochemistry 101: 184-194.

Nawaz A., Purahong W., Lehmann R., Herrmann M., Küsel K., Totsche K.U., Buscot F., Wubet T. (2016) Superimposed pristine limestone aquifers with marked hydrochemical differences exhibit distinct fungal communities. Front Micobiol 7: 666.

Renner M., Hassler S.K., Blume T., Weiler M., Hildebrandt A., Guderle M., Schymanski S.J., Kleidon A. (2016) Dominant controls of transpiration along a hillslope transect inferred from ecohydrological measurements and thermodynamic limits. Hydrology and Earth System Sciences 20(5): 2063-2083.

Rughöft S., Herrmann M., Lazar C.S., Cesarz S., Levick S.R., Trumbore S.E., Küsel K. (2016) Community composition and abundance of bacterial, archaeal and nitrifying populations in savanna soils on contrasting bedrock material in Kruger National Park, South Africa. Frontiers Microbiology, Terrestrical Microbiology 7: 1954.

Seifert A.-G., Roth V.-N., Dittmar T., Gleixner G., Breuer L., Houska T., Marxsen J. (2016) Comparing molecular composition of dissolved organic matter in soil and stream water: Influence of land use and chemical characteristics. Science of the Total Environment 571: 142-152.

van Stan J., Lewis E.S., Hildebrandt A., Rebmann C., Friesen J. (2016) Impact of interacting bark structure and rainfall conditions on stemflow variability in a temperate beech-oak forest, central Germany. Hydrological Sciences Journal 61(11): 2071-2083.

Zech A., Müller S., Mai J., Heße F., Attinger S. (2016) Extending Theis' solution: Using transient pumping tests to estimate parameters of aquifer heterogeneity. Water Resour Res 52(8): 6156-6170.

Zimmermann A., Voss S., Metzger J.C., Hildebrandt A., Zimmermann B. (2016) Capturing heterogeneity: The role of a study area's extent for estimating  mean throughfall. Journal of Hydrology 542: 781-789.


Algergawy A., Babalou S., Kargar, M., Davarpanah, S. H. (2015) SeeCOnt: A new seeding-based clustering approach for ontology matching. In: Tadeusz M, Valduriez P, Bellatreche L (eds) Advances in Databases and Information Systems. Springer International Publishing; Switzerland; pp 245-258.

Algergawy A., Klan F. (2015) A sequence-based tree similarity search. In: 9th IEEE International Conference on Research Challenges in Information Science (RCIS 2015). Athens, Greece; pp. 121-126.

Fischer S., Hanf S., Frosch T., Gleixner G., Popp J., Trumbore S., Hartmann H. (2015) Pinus sylvestries switches respiration substrates under shading but not during drought. The New Phytologist 207(3): 542-550.

Fischer C., Tischer J., Roscher C., Eisenhauer N., Ravenek J., Gleixner G., Attinger S., Jensen B., de Kroon H., Mommer L., Scheu S., Hildebrandt A. (2015) Plant species diversity affects infiltration capacity in an experimental grassland through changes in soil properties. Plant Soil 397: 1-16.

Hanf S., Fischer S., Hartmann H., Trumbore S., Popp J., Frosch T. (2015) Online investigation of respiratory quotients in Pinus sylvestris and Picea abies during drought and shading by means of cavity-enhanced Raman gas spectroscopy. Analyst 140(13): 4473-448.

Herrmann M., Rusznyak A., Akob D.M., Schulze I., Opitz S., Totsche K.U., Küsel K. (2015) Large fractions of CO2-fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Applied and Environmental Microbiology 81(7): 2384-2394.

Heße F., Savoy H., Osorio-Murillo C.A., Sege J., Attinger S., Rubin Y. (2015) Characterizing the impact of roughness and connectivity features of aquifer conductivity using Bayesian inversion. Journal of Hydrology 531: 73-87.

Jochum T., Michalzik B., Bachmann** A., Popp J., Frosch T. (2015) Microbial respiration and natural attenuation of benzene-contaminated soils investigated by cavity-enhanced Raman multi-gas spectroscopy. Analyst 140: 3143-3149.

Jochum T., von Fischer J.C., Trumbore S., Popp J., Frosch T. (2015) Multigas leakage correction in static environmental chambers using sulfur hexafluoride and Raman spectroscopy. Anal Chem 87(21): 11137-11142.

Khattab A., Algergawy A., Sarhan A. (2015) MAG: A performance evaluation framework for database systems. Knowledge-Based Systems 85: 245-255.

Keiner R., Herrmann M., Küsel K., Popp J., Frosch T. (2015) Rapid monitoring of intermediate states and mass balance of nitrogen during denitrification by means of cavity enhanced Raman multi-gas sensing.  Analytica Chimica Acta 864: 39-47.

Keiner R., Gruselle M-C., Michalzik B., Popp J., Frosch T. (2015) Raman spectroscopic investigation of 13CO2 labeling and leaf dark respiration of Fagus sylvatica L. (European Beech). Analytical and Bioanalytical Chemistry 407: 1813-1817.

König-Ries B., Hahn U. (2015) Semantic technologies for consolidating structured data and unstructured documents in biodiversity research. In: Kolbe T.H., Bill R., Donaubauer A. (eds) Geoinformationssysteme 2015 - Beiträge zur 2. Münchner GI-Runde. Wichmann Verlag; Berlin, Germany.

Palatinszky M., Herbold C., Jehmlich N., Pogoda M., Han P., von Bergen M., Lagkouvardos I., Karst S.M., Galushko A., Koch H., Berry D., Daims H., Wagner M. (2015) Cyanate as an energy source for nitrifiers. Nature 524: 105-108.

Roth V.-N., Dittmar T., Gaupp R., Gleixner G. (2015) The molecular composition of dissolved organic matter in forest soils as a function of pH and temperature. PLoS ONE 10(3): e0119188.


Keiner R., Frosch T., Massad T., Trumbore S., Popp J. (2014) Enhanced Raman multigas sensing - a novel tool for control and analysis of 13CO2 labeling experiments in environmental research. Analyst 139(16): 3879-3884.

Opitz S., Küsel K., Spott O., Totsche K.U., Herrmann M. (2014) Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol 90(1): 39-53.

Roth V.N., Dittmar T., Gaupp R., Gleixner G. (2014) Ecosystem-specific composition of dissolved organic matter. Vadose Zone J 13(7). Doi: 10.2136/vzj2013.09.0162.


Frosch T., Keiner R., Michalzik B., Fischer B., Popp J. (2013) Investigation of gas exchange processes in peat bog ecosystems by means of innovative Raman gas spectroscopy. Anal Chem 85: 1295-1299.

Keiner R., Frosch T., Hanf S., Rusznyak A., Akob D.M., Küsel K., Popp J. (2013) Raman spectroscopy - an innovative and versatile tool to follow the respirational activity and carbonate biomineralization of important cave bacteria. Anal Chem 85: 8708

Risse-Buhl U., Herrmann M., Lange P., Akob D.M., Pizani N., Schönborn W., Totsche K.U., Küsel K. (2013) Phagotrophic protist diversity in the groundwater of a karstic aquifer - morphological and molecular analysis. J Euk Microbiol 60: 467

Previous publications

Akob D.M., Küsel K. (2011) Where microorganisms meet rocks in the Earth's Critical Zone. Biogeosciences 8: 3531-3543.

Kalbacher T., Delfs J.-O., Shao H., Wang W., Walther M., Samaniego L., Schneider C., Kumar R., Musolff A., Centler F., Sun F., Hildebrandt A., Liedl R., Borchardt D., Krebs P. and Kolditz O. (2011) The IWAS-ToolBox: software coupling for an integrated water resources management. Environ Earth Sci 65: 1367-1380.

Kalbacher T., Schneider C.L., Wang W., Hildebrandt A., Attinger S., Kolditz O. (2011) Modeling soil-coupled water uptake of multiple root systems with automatic time stepping. Vadose Zone J 10: 727.

Rusznyák A., Akob D.M., Nietzsche S., Eusterhues K., Totsche K.U., Neu T.R., Frosch T., Popp J., Keiner R., Geletneky J., Katzschmann L., Schulze E.-D., Küsel K. (2012) Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic Herrenberg Cave. Appl Environ Microbiol 78: 1157-1167.

* C. Steinhäuser is now C. Hess

** A. Bachmann is now A. Sieburg