/CRC AquaDiva /PUBLICATIONS /Peer-Reviewed

Data Portal
Peer-Reviewed Publications of the CRC AquaDiva

Below, you can find a complete list of all AquaDiva publications.


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.

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.

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

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.


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. In: Proceedings of the ODBASE 2017 (Springer) - 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.

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.

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.

Klan F., Faessler E., Algergawy A., König-Ries B., Hahn U. (2017) Integrated Semantic Search on Structured and Unstructured Data in the ADOnIS System. In: Proceedings of the 2nd International Workshop on Semantics for Biodiversity at ISWC 2017, 10/22/2017. Vienna, Austria.

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.

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.

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.


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.

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.

Fäßler E., Klan F., Algergawy A., König-Ries B., Hahn U. (2016) Selecting and tailoring ontologies with JOYCE. Conference Paper in: EKAW 2016 Satellite Events, LNAI 10180, P. Ciancarini et al. (eds.): pp. 114-118, 2017.

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.

Heße F., Zink M., Kumar R., Samaniego L., Attinger S. (2016) Spatially distributed characterization of soil dynamics using travel-time distributions. Hydrol Earth Syst Sci 21: 549-570. Doi: 10.5194/hess-21-549-2017.

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.

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