WordCloud (based on CRC 1076 AquaDiva publications)

Publications of CRC 1076 AquaDiva

AquaDiva researchers published more than 200 papers overall so far.
WordCloud (based on CRC 1076 AquaDiva publications)
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Early View Expand entry

Demir G., Michalzik B., Filipzik J., Metzger J. and Hildebrandt A. (2022) Spatial variation of grassland canopy affects soil wetting patterns and preferential flow. Authorea Preprints. DOI: 10.22541/au.164970545.54927607/v1


2022 Expand entry

Akinyede R., Taubert M., Schrumpf M., Trumbore S., Küsel K. (2022a) Dark CO2 fixation in temperate beech and pine forest soils. Soil Biology and Biochemistry 165.
DOI: 10.1016/j.soilbio.2021.108526

Akinyede R., Taubert M., Schrumpf M., Trumbore S., Küsel K. (2022b) Temperature sensitivity of dark CO2 fixation in temperate forest soils. Biogeosciences Discussions.
DOI: 10.5194/bg-2022-90

Azemtsop Matanfack G., Taubert M., Reilly-Schott V., Küsel K., Rösch P., Popp J. (2022) Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D2O Labeling. Anal. Chem. DOI: 10.1021/acs.analchem.1c04097.

Blohm A., Kumar S., Knebl A., Herrmann M., Küsel K., Popp J., Frosch T. (2022) Activity and electron donor preference of two denitrifying bacterial strains identified by Raman gas spectroscopy. Analytical and Bioanalytical Chemistry 414, 601-611. DOI:10.1007/s00216-021-03541-y

Castro-Morales K., Canning A., Körtzinger A., Göckede M., Küsel K., Overholt W.A., Wichard T., Redlich S., Arzberger S., Kolle O., Zimov N. (2022a) Effects of reversal of water flow in an Arctic floodplain river on fluvial emissions of CO2 and CH4. Journal of Geophysical Research: Biogeosciences 127. DOI: 10.1029/2021JG006485.

Castro-Morales K., Canning A., Arzberger S., Overholt W.A., Küsel K., Kolle O., Göckede M., Zimov N. and Körtzinger A. (2022b) Highest methane concentrations in an Arctic river linked to local terrestrial inputs. Biogeosciences, Vol. 19, issue 21, 5059-5077
Doi: 10.5194/bg-19-5059-2022.

Demir G., Friesen J., Filipzik J., Michalzik B., Hildebrandt A. (2022) A Method Proposal for Throughfall Measurement in Grassland at Plot Scale in Temperate Climate: ‘Interception Tubes’. Front. Earth Sci., 10. DOI: 10.3389/feart.2022.799419  

Geesink P., Taubert M., Jehmlich N., von Bergen M., Küsel K. (2022) Bacterial Necromass Is Rapidly Metabolized by Heterotrophic Bacteria and Supports Multiple Trophic Levels of the Groundwater Microbiome. ASM Journals, Microbiology Spectrum. Online ahead of print. DOI: 10.1128/spectrum.00437-22.

Khurana S., Heße F., Hildebrandt A., Thullner M. (2022) Predicting the impact of spatial heterogeneity on microbially mediated nutrient cycling in the subsurface. Biogeosciences 19(3): 665-688. DOI: 10.5194/bg-19-665-2022.

Khurana S., Heße F., Hildebrandt A., & Thullner M. (2022) Should we worry about surficial dynamics when assessing nutrient cycling in the groundwater? Frontiers in Water, 4. DOI: 10.3389/frwa.2022.780297.

Kraus D., Böke J.S., Ehrhardt E., Henkel T. (2022) Multispectral imaging flow cytometry for process monitoring in microalgae biotechnology. Micro and Nano Engineering, 15, 100125. DOI: 10.1016/j.mne.2022.100125.

Overholt W.A., Trumbore S., Xu X., Bornemann T.L.V., Probst A.J., Krüger M., Herrmann M., Thamdrup B., Bristow L.A., Taubert M., Schwab V.F., Hölzer M., Marz M., Küsel K. (2022) Carbon fixation rates in groundwater similar to those in oligotrophic marine systems. Nat. Geosci. DOI: 10.1038/s41561-022-00968-5

Potthast K., Tischer A., Herrmann M., Weinhold A., Küsel K., van Dam N.M., Michalzik B. (2022) Woolly beech aphid infestation reduces soil organic carbon availability and alters phyllosphere and rhizosphere bacterial microbiomes. Plant and Soil, 473, 639–657. DOI: 10.1007/s11104-022-05317-4.

Sanchez-Arcos C., Ueberschaar N., Pohnert G. (2022) Aquifer system and depth specific chemical patterns in fractured-rock groundwater from the Critical Zone revealed by untargeted LC-MS-based metabolomics. Water Research, 219, 118566. DOI: 10.1016/j.watres.2022.118566

Savio D., Derx J., Lang R.-P., Kirschner A.K.T., Sommer R., Blaschke A.P., Küsel K., Farnleitner A.H. (2022) From groundwater to drinking water - Microbiology of karstic water resources. In: Tockner K., Mehner T. (eds.) Encyclopedia of Inland Waters 2nd edition. Vol. 3, pp. 560-579. Elsevier, Oxford. DOI: 10.1016/B978-0-12-819166-8.00181-X

Schroeter S.A., Eveillard D., Chaffron S., Zoppi J., Kampe B., Lohmann P., Jehmlich N., von Bergen M., Sanchez-Arcos C., Pohnert G., Taubert M., Küsel K., Gleixner G. (2022). Microbial community functioning during plant litter decomposition. Scientific reports, 12(1), 7451. DOI:10.1038/s41598-022-11485-1

Stolze K., Barnes A.D., Eisenhauer N., Totsche K.U. (2022) Depth-differentiated, multivariate control of biopore number under different land-use practices. Geoderma, 418, 115852. DOI:  10.1016/j.geoderma.2022.115852.

Taubert M., Overholt W.A., Heinze B., Azemtsop Matanfak G., Houhou R., Jehmlich N., von Bergen M., Rösch P., Popp J., Küsel K. (2022) Bolstering fitness via CO2 fixation and organic carbon uptake: mixotrophs in modern groundwater. The ISME Journal, 2021-12-07. DOI: 10.1038/s41396-021-01163-x.

Xiong B.J., Kleinsteuber S., Sträuber H., Dusny C., Harms H., Wick L.Y. (2022) Impact of Fungal Hyphae on Growth and Dispersal of Obligate Anaerobic Bacteria in Aerated Habitats. mBio;13(3):e0076922. DOI: 10.1128/mbio.00769-22

Xiong B.J., Stanley C.E., Dusny C., Schlosser D., Harms H., Wick L.Y. (2022) pH Distribution along Growing Fungal Hyphae at Microscale. J Fungi 8(6):599. DOI: 10.3390/jof8060599.

You X., Kallies R., Hild K., Hildebrandt A., Harms H., Chatzinotas A., Wick L.Y. (2022) Transport of marine tracer phage particles in soil. Science of The Total Environment 814: 152704. DOI: 10.1016/j.scitotenv.2021.152704.

You X., Klose N., Kallies R., Harms H., Chatzinotas A., Wick L.Y. (2022) Mycelia-assisted isolation of non-host bacteria able to co-transport phages. Viruses 14(2): 195. DOI: 10.3390/v14020195.

Zerfaß C., Lehmann R., Ueberschaar N., Sanchez-Arcos C., Totsche K.U. and Pohnert G. (2022) Groundwater metabolome responds to recharge in fractured sedimentary strata. Water Research 223: 118998. DOI: 10.1016/j.watres.2022.118998

2021 Expand entry

Abdelmageed N., Algergawy A., Samuel S. (2021) BiodivOnto: Towards a core ontology for biodiversity. In: Verborgh R., Dimou A., Hogan A., d'Amato C., Tiddi I., Bröring A., Mayer S., Ongenae F., Tommasini R., Alam M. (eds.) The Semantic Web: ESWC 2021 Satellite Events. ESWC 2021, 06/06/2021-06/10/2021, virtual event. Lecture Notes in Computer Science, vol 12739. Springer, Cham. DOI: 10.1007/978-3-030-80418-3_1.

Abdelmageed N., Algergawy A., Samuel S., König-Ries B. (2021) A data-driven approach for core biodiversity ontology development. In: Sanfilippo E.M., Kutz O., Troquard N., Hahmann T., Masolo C., Hoehndorf R., Vita R. (eds.) Proceedings of the 3rd International Workshop on Semantics for Biodiversity (S4BioDiv 2021) [held at the Joint Ontology Workshops (JOWO 2021), co-located with the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021) and the 12th International Conference on Biomedical Ontologies (ICBO 2021): Episode VII The Bolzano Summer of Knowledge]. 09/11/2021 - 09/18/2021, Bolzano, Italy. CEUR Workshop Proceedings Vol-2969.

Achilles F., Tischer A., Bernhardt-Römermann M., Heinze M., Reinhardt F., Makeschin F., Michalzik B. (2021) European beech leads to more bioactive humus forms but stronger mineral soil acidification as Norway spruce and Scots pine - Results of a repeated site assessment after 63 and 82 years of forest conversion in Central Germany. Forest Ecology and Management 483: 118769. DOI: 10.1016/j.foreco.2020.118769.

Algergawy A., Hamed H., König-Ries B. (2021) Towards scientific data synthesis using deep learning and semantic web. In: Verborgh R., Dimou A., Hogan A., d'Amato C., Tiddi I., Bröring A., Mayer S., Ongenae F., Tommasini R., Alam M. (eds.) The Semantic Web: ESWC 2021 Satellite Events. ESWC 2021, 06/06/2021-06/10/2021, virtual event. Lecture Notes in Computer Science, vol 12739. Springer, Cham. DOI: 10.1007/978-3-030-80418-3_10.

Azemtsop Matanfack G., Pistiki A., Rösch P., Popp J. (2021) Raman 18O-labeling of bacteria in visible and deep UV-ranges. Journal of Biophotonics 14(6):e202100013. DOI: 10.1002/jbio.202100013.

Azemtsop Matanfack G., Pistiki A., Rösch P., Popp J. (2021) Raman stable isotope probing of bacteria in visible and deep UV-ranges. Life 11(10): 1003. DOI: 10.3390/life11101003.

Brunzel M., Dirauf M., Sahn M., Czaplewska J.A., Fritz N., Weber C., Nischang I., Schubert U.S. (2021) On the identification and quantification of proton-initiated species in the synthesis of poly(2-alkyl-2-oxazoline)s by high resolution liquid chromatography. Journal of Chromatography A 1653: 462364.
DOI: 10.1016/j.chroma.2021.462364.

Carrasco Flores D., Fricke M., Vesp V., Desirò D., Kniewasser A., Hölzer M., Marz M., Mittag M. (2021) A marine Chlamydomonas sp. emerging as an algal model. Journal of Phycology 57(1): 54-69. DOI: 10.1111/jpy.13083.

Chamanara J., Gaikwad J., Gerlach R., Algergawy A., Ostrowski A., König-Ries B. (2021) BEXIS2: A FAIR-aligned data management system for biodiversity, ecology and environmental data. Biodiversity Data Journal 9: e72901. DOI: 10.3897/BDJ.9.e72901.

Ehrle A., Kolle O., Tischer A., Trumbore S.E., Michalzik B. (2021) Effects of mound building Lasius flavus on organic carbon and nutrient fluxes in soils of temperate grassland ecosystems. Pedobiologia 84: 150701. DOI: 10.1016/j.pedobi.2020.150701.

Herrmann M, Geesink P, Richter R, Küsel K (2021) Canopy position has a stronger effect than tree species identity on phyllosphere bacterial diversity in a floodplain hardwood forest. Microbial Ecology 81: 157-168. DOI: 10.1007/s00248-020-01565-y.

Houhou R., Rösch P., Popp J., Bocklitz T. (2021) Comparison of functional and discrete data analysis regimes for Raman spectra. Analytical and Bioanalytical Chemistry, 413, 5633–5644. DOI: 10.1007/s00216-021-03360-1.

Houhou R., Bocklitz T. (2021) Trends in artificial intelligence, machine learning, and chemometrics applied to chemical data. Analytical Science Advances, 2(3-2), 128–141. DOI: 10.1002/ansa.202000162.

Hölzer M., Marz M. (2021) PoSeiDon: a Nextflow pipeline for the detection of evolutionary recombination events and positive selection. Bioinformatics 37(7): 1018-1020. DOI: 10.1093/bioinformatics/btaa695.

Jing M., Kumar R., Attinger S., Li Q., Lu C., Heße F. (2021). Assessing the contribution of groundwater to catchment travel time distributions through integrating conceptual flux tracking with explicit Lagrangian particle tracking. Advances in Water Resources 149: 103849. DOI: 10.1016/j.advwatres.2021.103849.

Krüger M., Potthast K., Michalzik B., Tischer A., Küsel K., Deckner F.F.K., Herrmann M. (2021) Drought and rewetting events enhance nitrate leaching and seepage-mediated translocation of microbes from beech forest soils. Soil Biology and Biochemistry 154: 108153. DOI: 10.1016/j.soilbio.2021.108153.

Lehmann K., Lehmann R., Totsche K.U. (2021) Event-driven dynamics of the total mobile inventory in undisturbed soil account for significant fluxes of particulate organic carbon. Sci Total Environ 756: 143774. DOI: 10.1016/j.scitotenv.2020.143774.

Löffler F., Wesp V., König-Ries B., Klan F. (2021) Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs? PLoS ONE 16(3): e024609. DOI: 10.1371/journal.pone.0246099.

Metzger J.C., Filipzik J., Michalzik B., Hildebrandt A. (2021) Stemflow infiltration hotspots create soil microsites near tree stems in an unmanaged mixed beech forest. Frontiers in Forests and Global Change 4, 701293. DOI: 10.3389/ffgc.2021.701293.

Mock F., Viehweger A., Barth E., Marz M. (2021) VIDHOP, viral host prediction with Deep Learning. Bioinformatics 37(3): 318-325.
DOI: 10.1093/bioinformatics/btaa705.

Potthast K.Meyer S.Tischer A., Gleixner G., Sieburg A., Frosch T., Michalzik B. (2021) Grasshopper herbivory immediately affects element cycling but not export rates in an N-limited grassland system. Ecosphere 12(3): e03449. DOI: 10.1002/ecs2.3449

Ritschel T., Lehmann K., Brunzel M., Vitz J., Nischang I., Schubert U.S., Totsche K.U. (2021) Well-defined poly(ethylene glycol) polymers as non-conventional reactive tracers of colloidal transport in porous media. Journal of Colloid and Interface Science 584, 592-601. DOI: 10.1016/j.jcis.2020.09.056.

Samuel S., Algergawy A., König-Ries B. (2021) Towards an ontology network for the reproducibility of scientific studies. In: Sanfilippo E.M., Kutz O., Troquard N., Hahmann T., Masolo C., Hoehndorf R., Vita R. (eds.) Proceedings of the Joint Ontology Workshops 2021 [co-located with the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021) and the 12th International Conference on Biomedical Ontologies (ICBO 2021): Episode VII The Bolzano Summer of Knowledge]. 09/11/2021 - 09/18/2021, Bolzano, Italy. CEUR Workshop Proceedings Vol-2969.

Simon C., Petras D., Roth V.-N., Dührkop K., Böcker S., Dorrestein P., Gleixner G. (2021) Mass difference matching crystallizes hidden molecular structures of dissolved organic matter from ultrahigh-resolution tandem mass spectra. Preprint ChemRxiv 10.33774/chemrxiv-2021-cxxt1. Cambridge: Cambridge Open Engage.

Simon C., Pimentel T.P., Monteiro M.T.F., Candido L.A., Gastmans D., Geilmann H., da Costa Oliveira R., Rocha J.B., Pires E., Quesada C.A., Forsberg B.R., Ferreira S.J.F., da Cunha H.B., Gleixner G. (2021) Molecular links between whitesand ecosystems and blackwater formation in the Rio Negro watershed. Geochimica et Cosmochimica Acta 311: 274-291. DOI: 10.1016/j.gca.2021.06.036.

Starke R., Schäpe S.S., Jehmlich N., von Bergen M. (2021) Protein stable isotope probing with H218O differentiated cold stress response at permissive temperatures from general growth at optimal conditions in Escherichia coli K12. Rapid communications in Mass Spectrometry 35(1): e8941. DOI: 10.1002/rcm.8941.

Ueberschaar N., Lehmann K., Meyer S., Zerfaß C., Michalzik B., Totsche K.U., Pohnert G. (2021) Soil solution analysis with untargeted GC-MS - A case study with different lysimeter types. Front Earth Sci 8: 563379. DOI: 10.3389/feart.2020.563379.

Van Damme R., Hölzer M., Viehweger A., Müller B., Bongcam-Rudloff E., Brandt C. (2021) Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN). PLoS Computational Biology 17(2): e1008716. DOI: 10.1371/journal.pcbi.1008716.

Voigt E., Rall B.C., Chatzinotas A., Brose U., Rosenbaum B. (2021) Phage strategies facilitate bacterial coexistence under environmental variability. PeerJ 9:e12194
Doi: 10.7717/peerj.12194

Wegner C.-E., Westermann M., Steiniger F., Gorniak L., Budhraja R., Adrian L., Küsel K. (2021) Extracellular and intracellular lanthanide accumulation in the methylotrophic Beijerinckiaceae bacterium RH AL1. Applied and Environmental Microbiology 87(13): e03144-20. DOI: 10.1128/AEM.03144-20.

Xenophontos C., Taubert M., Harpole W.S., Küsel K. (2021) Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities. FEMS Microbiology Ecology 97 (3), fiab017. DOI: 10.1093/femsec/fiab017. Selected as Editor´s Choice March 2021.

Yan L., Hermans S.M., Totsche K.U., Lehmann R., Herrmann M., Küsel K. (2021) Groundwater bacterial communities evolve over time in response to recharge. Water Research 201: 117290. DOI: 10.1016/j.watres.2021.117290.

You X., Kallies R., Kühn I., Schmidt M., Harms H., Chatzinotas A., Wick L. (2021) Phage co-transport with hyphal-riding bacteria fuels bacterial invasion in a water-unsaturated microbial model system. The ISME Journal, 2021-12-13. DOI: 10.1038/s41396-021-01155-x.

2020 Expand entry

Akinyede R., Taubert M. , Schrumpf M., Trumbore S., Küsel K. (2020) Rates of dark CO2 fixation are driven by microbial biomass in a temperate forest soil. Soil Biology and Biochemistry 150: 107950. DOI: 10.1016/j.soilbio.2020.107950.

Algergawy A., Babalou S., Klan F., König-Ries B. (2020) Ontology modularization with OAPT. Journal on Data Semantics 9: 53-83. DOI: 10.1007/s13740-020-00114-7

Algergawy A., Stangneth R., Heger T., Jeschke J.M., König-Ries B. (2020) Towards a core ontology for hierarchies of hypotheses in invasion biology. In: Harth A. et al. (eds) The Semantic Web: ESWC 2020 Satellite Events. ESWC 2020. Lecture Notes in Computer Science, vol 12124. Springer, Cham.
DOI: 10.1007/978-3-030-62327-2_1.

Azemtsop Matanfack G., Rüger J., Stiebing C., Schmitt M., Popp J. (2020) Imaging the invisible - Bioorthogonal Raman probes for imaging of cells and tissues. Journal of Biophotonics 13(9): e202000129. DOI: 10.1002/jbio.202000129.

Azemtsop Matanfack G., Taubert M., Guo S., Houhou R., Bocklitz T., Küsel K., Rösch P., PoppJ. (2020) Influence of carbon sources on quantification of deuterium incorporation in heterotrophic bacteria: A Raman-stable isotope labeling approach. Anal. Chem. 92(16): 11429-11437. DOI: 10.1021/acs.analchem.0c02443.

Blohm A., Sieburg A., Popp J.,Frosch T. (2020) 6 - Detection of gas molecules by means of spectrometric and spectroscopic methods. In: Baia L., Pap Z., Hernadi K., Baia M. (eds) Micro and Nano Technologies, Advanced Nanostructures for Environmental Health, pp. 251-294. Elsevier, Amsterdam, The Netherlands.
DOI: 10.1016/B978-0-12-815882-1.00006-9.

Frosch Ta., Knebl A., Frosch T. (2020) Recent advances in nano-photonic techniques for pharmaceutical drug monitoring with emphasis on Raman spectroscopy. Nanophotonics 9(1): 19-37. DOI: 10.1515/nanoph-2019-0401.

Geesink P., Wegner C.-E., Probst A.J., Herrmann M., Dam H.T., Kaster A.-K., Küsel K. (2020) Genome-inferred spatio-temporal resolution of an uncultivated Roizmanbacterium reveals its ecological preferences in oligotrophic groundwater. Environmental Microbiology 22(2): 726-737. DOI: 10.1111.1462-2920.14865.

Hawkes J.A., D'Andrilli J., Agar J.N., Barrow M.P., Berg S.M., Catalán N., Chen H., Chu R.K., Cole R.B., Dittmar T., Gavard R., Gleixner G., Hatcher P.G., He C., Hess N.J., Hutchins R.H.S., Ijaz A., Jones H.E., Kew W., Khaksari M., Palacio Lozano D.C., Lv J., Mazzoleni L.R., Noriega‐Ortega B.E., Osterholz H., Radoman N., Remucal C.K., Schmitt N.D., Schum S.K., Shi Q., Simon C., Singer G., Sleighter R.L., Stubbins A., Thomas M.J., Tolic N., Zhang S., Zito P., Podgorski D.C. (2020) An international laboratory comparison of dissolved organic matter composition by high resolution mass spectrometry: Are we getting the same answer? Limnol Oceanogr Methods 18(6): 235-258. DOI: 10.1002/lom3.10364.

Herrmann M., Geesink P., Yan L., Lehmann R., Totsche K.U., Küsel K. (2020) Complex food webs coincide with high genetic potential for chemolithoautotrophy in fractured bedrock groundwater. Water Research 170: 115306. DOI: 10.1016/j.watres.2019.115306.

Hildebrandt A. (2020) Root-water relations and interactions in mixed forest settings. In: Levia D., Carlyle-Moses D., Iida S., Michalzik B., Nanko K., Tischer A. (eds) Forest-Water Interactions. Ecological Studies (Analysis and Synthesis) 240. Pp. 319-348. Springer, Cham, Switzerland. DOI: 10.1007/978-3-030-26086-6_14.

Houhou R., Barman P., Schmitt M., Meyer T., Popp J., Bocklitz T. (2020) Deep learning as phase retrieval tool for CARS spectra. Optics Express 28(14): 21002-21024. DOI: 10.1364/OE.390413.

Jing M., Kumar R., Heße F., Thober S., Rakovec O., Samaniego L., Attinger S. (2020) Assessing the response of groundwater quantity and travel time distribution to 1.5, 2, and 3 °C global warming in a mesoscale central German basin. Hydrol. Earth Syst. Sci. 24(3): 1511-1526. DOI: 10.5194/hess-24-1511-2020.

Kampe B., Duan T., Hahn U. (2020) Allgemeine Musikalische Zeitung as a searchable online corpus. In: Calzolari N. et al. (eds) Proceedings of the 12th Conference on Language Resoiurces and Evaluation (LREC 2020), pp. 969-976, 05/11/2020-05/16/2020, Marseille, France.

Karam N., Khiat A., Algergawy A., Sattler M., Weiland C., Schmidt M. (2020) Matching biodiversity and ecology ontologies: challenges and evaluation results. The Knowledge Engineering Review 35: E9. DOI: 10.1017/S0269888920000132.

Knebl A., Domes R., Wolf S., Domes C., Popp J., Frosch T. (2020) Fiber-enhanced Raman gas spectroscopy for the study of microbial methanogenesis. Anal. Chem. 92(18): 12564-12571. DOI: 10.1021/acs.analchem.0c02507.

Lehmann R. and Totsche K.U. (2020) Multi-directional flow dynamics shape groundwater quality in sloping bedrock strata. Journal of Hydrology 580: 124291.
DOI: 10.1016/j.jhydrol.2019.124291.

Lehnert A.-S., Behrendt T., Rücker A., Pohnert G., Trumbore S. (2020) SIFT-MS optimization for atmospheric trace gas measurements at varying humidity. Atmos. Meas. Tech. 13: 3507-3520. DOI: 10.5194/amt-13-3507-2020.

Lehnert A.-S., Perreca E., Gershenzon J., Pohnert G., Trumbore S.E. (2020) Simultaneous real-time measurement of isoprene and 2-methyl-3-buten-2-ol emissions from trees using SIFT-MS. Frontiers in Plant Science 11: 578204. DOI: 10.3389/fpls.2020.578204.

Lohmann P., Benk S., Gleixner G., Potthast K., Michalzik B., Jehmlich N., von Bergen M. (2020) Seasonal patterns of dominant microbes involved in central nutrient cycles in the subsurface. Microorganisms 8(11): 1694. DOI: 10.3390/microorganisms8111694.

Lohmann P., Schäpe S.S., Haange S.-B., Oliphant K., Allen-Vercoe E., Jehmlich N., von Bergen M. (2020) Function is what counts: how microbial community complexity affects species, proteome and phathway coverage in metaproteomics. Expert Review of Proteomics 17(2): 163-173. DOI: 10.1080/14789450.2020.1738931.

Mostajo N.F., Lataretu M., Krautwurst S., Mock F., Desirò D., Lamkiewicz K., Collatz M., Schoen A., Weber F., Marz M., Hölzer M. (2020) A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes. NAR Genomics and Bioinformatics 2(1): lqz006.
DOI: 10.1093/nargab/lqz006.

Overholt W.A., Hölzer M., Geesink P., Diezel C., Marz M., Küsel K. (2020) Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system. Environmental Microbiology 22(9): 4000-4013. DOI: 10.1111/1462-2920.15186.

Pour M.A.N., Algergawy A., Amini R., Faria D., Fundulaki I., Harrow I., Hertling S., Jiménez-Ruiz E., Jonquet C., Karam N., Khiat A., Laadhar A., Lambrix P., Li H., Li Y., Hitzler P., Paulheim H., Pesquita C., Saveta T., Shvaiko P., Splendiani A., Thiéblin É., Trojahn C., Vatascinová J., Yaman B., Zamazal O., Zhou L. (2020) Results of the Ontology Alignment Evaluation Initiative 2020. In: Shvaiko P., Euzenat J., Jiménez-Ruiz E., Hassanzadeh O., Trojahn C. (eds) Proceedings of the 15th International Workshop on Ontology Matching co-located with the 19th International Semantic Web Conference (ISWC 2020), 11/02/2020, virtual conference (originally planned to be in Athens, Greece). CEUR Proceedings Vol-2788.

Reimann, L., Schwäble, A., Fricke, A.L., Mühlhäuser, W.W.D., Leber, Y., Lohanadan, K., Puchinger, M.G., Schäuble, S., Fäßler, E., Wiese, H., Reichenbach, C., Knapp, B., Peikert, C.D., Drepper, F., Hahn, U., Kreutz, C., van der Ven, P.F.M., Radziwill, G., Djinović-Carugo, K., Fürst, D.O., and Warscheid, B. (2020). Phosphoproteomics identifies dual-site phosphorylation in an extended basophilic motif regulating FILIP1-mediated degradation of filamin-C. Communications Biology 3, 253.
DOI: 10.1038/s42003-020-0982-5.

Starke R., Oliphant K., Jehmlich N., Schäpe S.S., Sachsenberg T., Kohlbacher O., Allen-Vercoe E., von Bergen M. (2020) Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. Journal of Proteomics 222: 103791. DOI: 10.1016/j.jprot.2020.103791.

Tischer A., Michalzik B., Lotze R. (2020) Non-uniform but highly preferential stemflow routing along bark surfaces and actual smaller infiltration areas than previously assumed: A case study on European beech (Fagus sylvatica L.) and sycamore maple (Acer pseudoplatanus L.). ECO Letter - Ecohydrology 13(6): e2230.
DOI: 10.1002/eco.2230.

Van Stan, II J.T., Hildebrandt A., Friesen J., Metzger J.C., Yankine S.A. (2020) Spatial variability and temporal stability of local net precipitation patterns. In: Van Stan, II J.T., Gutmann E., Friesen J. (eds) Precipitation Partitioning by Vegetation. Springer, Cham, Switzerland. DOI: 10.1007/978-3-030-29702-2_6.

Wick L.Y.  (2020) Bioavailability as a microbial system property: Lessons learned from biodegradation in the mycosphere: In: Ortega-Calvo J.J., Parsons J.R. (eds) The Handbook of Environmental Chemistry. Springer, Berlin, Heidelberg. DOI: 10.1007/698_2020_568.

Yan L., Herrmann M., Kampe B., Lehmann R., Totsche K.U., Küsel K. (2020) Environmental selection shapes the formation of near-surface groundwater microbiomes. Water Research 170: 115341. DOI: 10.1016/j.watres.2019.115341.

2019 Expand entry

Algergawy A., Faria D., Ferrara A., Fundulaki I., Harrow I., Hertling S., Jiménez-Ruiz E., Karam N., Khiat A., Lambrix P., Li H., Montanelli S., Paulheim H., Pesquita C., Saveta T., Shvaiko P., Splendiani A., Thiéblin É., Trojahn C., Vatascinová J., Zamazal O., Zhou L. (2019) Results of the Ontology Alignment Evaluation Initiative 2019. In: Shvaiko P., Euzenat J., Jiménez-Ruiz E., Hassanzadeh O., Trojahn C. (eds) Proceedings of the 14th International Workshop on Ontology Matching co-located with the 18th International Semantic Web Conference (ISWC 2019), 10/26/2019, Auckland, New Zealand. CEUR Proceedings Vol-2536.

Algergawy A., König-Ries B. (2019) Partitioning of BioPortal ontologies: An empirical study. In: Cornet R., Waagmester A. (eds.) Proceedings of the 12th International Conference on Semantic Web Applications and Tools for healthcare and Life Sciences (SWAT4HCLS), 12/10/2019-12/11/2019, Edinburgh, UK. CEUR Proceedings Vol-2849.

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. DOI: 10.1007/s13361-018-2117-5.

Behrendt T., Agam N., Horn M.A. (2019) Microbial nitric oxide, nitrous oxide, and nitrous acid emissions from drylands. In: D'Odorico P., Porporato A., Wilkinson Runyan C. (eds) Dryland Ecohydrology. Springer, Cham, Switzerland. DOI: 10.1007/978-3-030-23269-6_13.

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. DOI: 10.5194/soil-5-121-2019.

Benk S.A., Yan L., Lehmann R., Roth V.-N., Schwab V.F., Totsche K.U., Küsel K., Gleixner G. (2019) Fueling diversity in the subsurface: Composition and age of dissolved organic matter in the Critical Zone. Frontiers in Earth Science 7: 296. DOI: 10.3389/feart.2019.00296.

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. DOI: 10.1111/1365-2745.13046.

Fricke M., Gerst R., Ibrahim B., Niepmann M., Marz M. (2019) Global importance of RNA secondary structures in protein-coding sequences. Bioinformatics 35(4): 579-583, bty678. DOI: 10.1093/bioinformatics/bty678.

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. DOI: 10.3390/geosciences9090393.

Gerst R., Hölzer M. (2019) PCAGO: An interactive tool to analyze RNA-Seq data with principal component analysis. BioRxiv preprint DOI: 10.1101/433078.

Ghanem N., Stanley C.E., Harms H., Chatzinotas A., Wick L.Y. (2019) Mycelial effects on phage retention during transport in a microfluidic platform. Environmental Science and Technology 53(20): 11755-11763. DOI: 10.1021/acs.est.9b03502.

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. arXiv:1808.06810v2.

Herrmann 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.
DOI: 10.3389/fmicb.2019.01407.

Hölzer M., Marz M. (2019) De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. GigaScience 8(5): giz039. DOI: 10.1093/gigascience/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 & Earth System Sciences 23(1): 171-190. DOI: 10.5194/hess-23-171-2019.

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. DOI: 10.3390/v11060484.

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 47: 100667. 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. DOI: 10.1021/acs.analchem.8b05684.

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. DOI: 10.1016/j.scitotenv.2019.04.281.

Metzger J.C., Schumacher J., Lange M., Hildebrandt A. (2019) Neighbourhood and stand structure affect stemflow generation in a heterogeneous deciduous temperate forest. HESS 23: 4433-4452. DOI: 10.5194/hess-23-4433-2019.

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. DOI: 10.1007/s13369-018-3443-4.

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. DOI: 10.3390/microorganisms7090341.

Peter S., Hölzer M., Lamkiewicz K., Peroni di Fenizio P., Al Hwaeer H., Marz M., Schuster S., Dittrich P., Ibrahim B. (2019) Structure and hierarchy of influenza virus models revealed by reaction network analysis. Viruses 11(5): 449. DOI: 10.3390/v11050449.

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 12: 755-761.
DOI: 10.1038/s41561-019-0417-4.

Schmidt R., Ulanova D., Wick L.Y., Bode H.B., Garbeva P. (2019) Microbe-driven chemical ecology: past, present and future. The ISME Journal 13: 2656-2663.
DOI: 10.1038/s41396-019-0469-x.

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. DOI: 10.1029/2017WR022067.

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. DOI: 10.1029/2018WR024076.

Sharafeldeen D., Algergawy A., König-Ries B. (2019) Species Association Knowledge Graph Construction - A Demo Paper. In: Cornet R., Waagmester A. (eds.) Proceedings of the 12th International Conference on Semantic Web Applications and Tools for healthcare and Life Sciences (SWAT4HCLS), 12/10/2019-12/11/2019, Edinburgh, UK. CEUR Proceedings Vol-2849.

Sharafeldeen D., Algergawy A., König-Ries B. (2019) Towards knowledge graph construction using semantic data mining. In: Indrawan-Santiago M., Pardede E., Salvadori I.L., Steinbauer M., Khalil I., Anderst-Kotsis G. (eds) Proceedings of the 21st International Conference on Information Integration and Web-based Applications & Services (iiWAS2019), pp. 323-329. DOI: 10.1145/3366030.3366035.

Sieburg A., Knebl A., Jacob J.M., Frosch T. (2019) Characterization of fuel gases with fiber-enhanced Raman Spectroscopy. Analytical and Bioanalytical Chemistry 411(28): 7399-7408. 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. DOI: 10.1016/j.orggeochem.2019.01.013.

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. DOI: 10.1371/journal.pone.0212937.

Thullner M., Regnier P. (2019) Microbial controls on the biogeochemical dynamics in the subsurface. Reviews in Mineralogy and Geochemistry 85(1): 265-302.
DOI: 10.2138/rmg.2019.85.9.

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. DOI: 10.1007/s11104-019-03970-w.

Udovenko V., Algergawy A. (2019) Entity extraction in the ecological domain - A practical guide. In: Meyer H., Ritter N., Thor A., Nicklas D., Heuer A., Klettke M. (eds) BTW 2019 - Workshopband, Lecture Notes in Informatics (LNI), Gesellschaft für Informatik, Bonn. Pp. 155-160.  DOI: 10.18420/btw2019-ws-16.

Viehweger A., Hölzer M., Brandt C. (2019) Addressing dereplication crisis: Taxonomy-free reduction of massive genome collections using embeddings of protein content. Preprint: bioRxiv 855262. DOI: 10.1101/855262.

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. DOI: 10.1101/gr.247064.118.

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. DOI: 10.1128/AEM.02346-18.

Wieczorek A.S., Schmidt O., Chatzinotas A., von Bergen M., Gorissen A., Kolb S. (2019) Ecological functions of agricultural soil bacteria and microeukaryotes in chitin degradation: a case study. Frontiers in Microbiology 10: 1293. DOI: 10.3389/fmicb.2019.01293

2018 Expand entry

Achich N., Algergawy A., Bouaziz B., König-Ries B. (2018) BioOntoVis: An Ontology Visualization Tool.  In: Cimiano P., Corby O. (eds) Proceedings of the EKAW 2018 Posters and Demonstrations Session co-located with 21st International Conference on Knowledge Engineering and Knowledge Management, 11/12/2018-11/16/2018, Nancy, France. CEUR Proceedings Vol-2262.

Algergawy A., Cheatham M., Faria D., Ferrara A., Fundulaki I., Harrow I., Hertling S., Jiménez-Ruiz E., Karam N., Khiat A., Lambrix P., Li H., Montanelli S., Paulheim H., Pesquita C., Saveta T., Schmidt D., Shvaiko P., Splendiani A., Thiéblin É., Trojahn C., Vatascinová J., Zamazal O., Zhou L. (2019) Results of the Ontology Alignment Evaluation Initiative 2018. In: Shvaiko P., Euzenat J., Jiménez-Ruiz E., Cheatham M., Hassanzadeh O. (eds) Proceedings of the 13th International Workshop on Ontology Matching co-located with the 17th International Semantic Web Conference (ISWC 2018), 10/8/2018, Monterey, CA, USA. CEUR Proceedings Vol-2288.

Algergawy A., Klan F., Fäßler E., Hamed H., Kampe B., Koenig-Ries B., Hahn U. (2018) ADOnIS: An ontology-based information system providing seamless integration of structured and unstructured data. 11th International Conference on Semantic Web Applications and Tools for Life Sciences (SWAT4HCLS), 12/3/2018-12/6/2018, Antwerp, Bergium. DOI: 10.6084/m9.figshare.7322024.v1.

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. DOI: 10.1007/s11306-018-1336-x.

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. DOI: 10.3389/feart.2018.00168.

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. DOI: 10.1063/1.5030159.

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.
DOI: 10.1038/s41467-018-04658-y.

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. DOI: 10.3390/polym10121395.

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. DOI: 10.1016/j.advwatres.2018.08.015.

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. DOI: 10.1093/femsre/fuy008.

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. DOI: 10.1016/j.orggeochem.2018.10.005.

Fäßler E., Hahn U. (2018) Annotation data management with JeDIS. DocEng '18: Proceedings of the ACM Symposium on Document Engineering 2018, August 28-31, 2018, Halifax, NS, Canada. Article no.: 42, pages 1-4. ACM, New York, NY, USA. DOI: 10.1145/3209280.3229102.

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.

Gerlach R., Ostrowski A., Gaikwad J., Algergawy A. (2018) Research data management in action - demonstrating the full range of features of the BEXIS 2 platform. In: Jitendra G., König-Ries B., Recknagel F. (eds) Proceedings of the 10th International Conference on Ecological Informatics: translating ecological data into knowledge and decisions in a rapidly changing world: ICEI2018, p. 288. DOI: 10.22032/dbt.37846. (And all other contributions in these proceedings by Algergawy A.)

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. DOI: 10.1021/acs.est.7b06271.

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. DOI: 10.1111/1365-2435.12948.

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. DOI: 10.1021/acs.est.8b01435.

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. DOI: 10.5194/gmd-11-1989-2018.

Knebl A., Yan D., Popp J., Frosch T. (2018) Fiber enhanced Raman gas spectroscopy. Trends in Analytical Chemistry 103: 230-238. DOI: 10.1016/j.trac.2017.12.001.

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:DOI: 10.1093/femsec/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. DOI: 10.1016/j.polymer.2018.09.049.

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. DOI: 10.1016/j.watres.2018.07.067.

Oleynik M., Fäßler E., Sasso A.M., Kappattanavar A., Bergner B., Freitas da Cruz H., Sachs J.-P., Datta S., Böttinger E. (2018) HPI-DHC at TREC 2018 Precision Medicine Track. In: The 27th Text REtrieval Conference (TREC 2018) Proceedings, 11/14/2018-11/16/2018, Gaithersburg, Md, USA.

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. DOI: 10.3389/feart.2018.00138.

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. DOI: 10.1111/1462-2920.14010.

Wutzler T. (2018) Efficient treatment of model discrepancy by Gaussian Processes - Importance for imbalanced multiple constraint inversions.
Preprint arXiv: 1812.07801.

Youssef N., Algergawy A., Moawad I.F., EL-Horbaty ES.M. (2018) Combined features for content based image retrieval: A comparative study. In: Hassanien A., Tolba M., Shaalan K., Azar A. (eds) Proceedings of the International Conference on Advanced Intelligent Systems and Informatics 2018 (AISI 2018) Advances in Intelligent Systems and Computing, vol 845, pp. 634-643. Springer, Cham. DOI: 10.1007/978-3-319-99010-1_58.

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. DOI: 10.1016/j.soilbio.2018.06.012.

2017 Expand entry

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.

Algergawy A., Karam N., Klan F., Jonquet C. (2017) Proceedings of the 2nd International Workshop on Semantics for Biodiversity (S4BioDiv 2017) co-located with 16th International Semantic Web Conference (ISWC2017), 10/22/2017, Vienna, Austria. CEUR Workshop Proceedings Vol-1933.

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).

Babalou S., Algergawy A., Lantow B., König-Ries B. (2017) Why the mapping process in ontology integration deserves attention. In: Indrawan-Santiago M., Steinbauer M., Salvadori I.L., Khalil I., Anderst-Kotsis G. (eds) Proceedings of the 19st International Conference on Information Integration and Web-based Applications & Services (iiWAS2017), pp. 451-456. DOI: 10.1145/3151759.3151834.

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. DOI: 10.1007/s00216-017-0325-7.

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. DOI: 10.1016/j.talanta.2016.10.067.

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. DOI: 10.1186/s12864-017-3932-y. #

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. DOI: 10.1002/cyto.a.23055.

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. DOI: 10.1007/s00248-017-0950-x

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. DOI: 10.1021/acs.analchem.6b03101.

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.
DOI: 10.1128/genomeA.00914-17

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. DOI: 10.1002/lom3.10143.

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.
DOI: 10.3389/fmicb.2017.01951.

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. DOI: 10.1038/ismej.2016.189.

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. DOI: 10.1002/hyp.11274.

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. DOI: 10.1038/ismej.2016.186.

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. DOI: 10.3389/fmicb.2017.01975

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. DOI: 10.1016/j.scitotenv.2017.06.182.

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: 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. DOI: 10.1016/j.compeleceng.2016.12.014.

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. DOI: 10.1039/C7AN01149K.

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. DOI: 10.1016/j.jprot.2016.11.003.

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. DOI: 10.1111/1462-2920.13933.

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. DOI: 10.1016/j.soilbio.2017.08.031.

2016 Expand entry

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 Vol-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.
DOI: 10.1111/mec.13783.

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. DOI: 10.1038/ncomms13254.

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. DOI: 10.1016/j.orggeochem.2016.09.009.

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. DOI: 10.1021/acs.est.6b04236.

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. DOI: 10.5194/hess-20-3441-2016.

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. DOI: 10.1016/j.dib.2016.11.033.

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. DOI: 10.3389/feart.2016.00032.

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; CEUR Workshop Proceedings Vol-1695; 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. DOI: 10.1111/1462-2920.13133.

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. DOI: 10.1128/AEM.00493-16.

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. DOI: 10.1016/j.soilbio.2016.07.009.

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. DOI: 10.1016/j.soilbio.2016.05.019.

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. DOI: 10.3389/fmicb.2016.00666.

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. DOI: 10.5194/hess-20-2063-2016.

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. DOI: 10.3389/fmicb.2016.01638.

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. DOI: 10.1016/j.scitotenv.2016.07.033.

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. DOI: 10.1080/02626667.2015.1083104.

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. DOI: 10.1002/2015WR018509.

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. DOI: 10.1016/j.jhydrol.2016.09.047.

2015 Expand entry

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. DOI: 10.1109/RCIS.2015.7128871

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. DOI: 10.1007/s11104-014-2373-5.

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. DOI: 10.1111/nph.13452.

Guderle M., and Hildebrandt A. (2015). Using measured soil water contents to estimate evapotranspiration and root water uptake profiles - a comparative study. Hydrol Earch Sci 19: 409-425. DOI: 10.5194/hess-19-409-2015.

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. DOI DOI: 10.1039/C5AN00402K.

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.
DOI: 10.1128/AEM.03269-14.

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. https://doi.org/10.1016/j.jhydrol.2015.09.067.

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. DOI: 10.1039/C5AN00091B .

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. DOI: 10.1021/acs.analchem.5b03312.

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. DOI: 10.1021/acs.analchem.5b03312.

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. DOI: 10.1016/j.aca.2015.02.007.

Khattab A., Algergawy A., Sarhan A. (2015) MAG: A performance evaluation framework for database systems. Knowledge-Based Systems 85: 245-255.
DOI: 10.1016/j.knosys.2015.05.010.

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. DOI: 10.1038/nature14856.

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. DOI: 10.1371/journal.pone.0119188.

2014 Expand entry

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. DOI: 10.1039/C3AN01971C.

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.
DOI: 10.1111/1574-6941.12370.

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.

2013 Expand entry

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. DOI: 10.1021/ac3034163.

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: 8708-8714. DOI: 10.1021/ac401699d.

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: 467-479. DOI: 10.1111/jeu.12054.

Previous publications Expand entry

Akob D.M., Küsel K. (2011) Where microorganisms meet rocks in the Earth's Critical Zone. Biogeosciences 8: 3531-3543. DOI: 10.5194/bg-8-3531-2011.

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.
DOI: 10.1007/s12665-011-1270-y.

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. DOI: 10.2136/vzj2010.0099.

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.
DOI: 10.1128/AEM.06568-11.