Spatio-temporal variation in the root-associated microbiota of orchard-grown apple trees
Maximilian Fernando Becker, Manfred Hellmann, Claudia Knief
Environmental microbiome 17 (1), 1-21, 2022

Topographic attributes override impacts of agronomic practices on prokaryotic community structure
Mitra Ghotbi, Ademir Durrer, Katharina Frindte, William R Horwath, Jorge L Mazza Rodrigues, Isaac Danso, Claudia Knief
Applied Soil Ecology 175, 104446, 2022

Root-rhizosphere-soil interactions in biopores
Anna S Wendel, Sara L Bauke, Wulf Amelung, Claudia Knief
Plant and Soil, 1-25, 2022

Microbial potential for denitrification in the hyperarid Atacama Desert soils
Di Wu, Mehmet Senbayram, Ghazal Moradi, Ramona Mörchen, Claudia Knief, Erwin Klumpp, Davey L Jones, Reinhard Well, Ruirui Chen, Roland Bol
Soil Biology and Biochemistry 157, 108248, 2021

Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota
Michael Bonkowski, Mika Tarkka, Bahar S Razavi, Hannes Schmidt, Evgenia Blagodatskaya, Robert Koller, Peng Yu, Claudia Knief, Frank Hochholdinger, Doris Vetterlein
Frontiers in microbiology 12, 619499, 2021

Wet sieving versus dry crushing: Soil microaggregates reveal different physical structure, bacterial diversity and organic matter composition in a clay gradient
Vincent JMNL Felde, Steffen A Schweizer, Danh Biesgen, Angela Ulbrich, Daniel Uteau, Claudia Knief, Markus Graf‐Rosenfellner, Ingrid Kögel‐Knabner, Stephan Peth
European Journal of Soil Science 72 (2), 810-828, 2021

Influence of Physical-Chemical Soil Parameters on Microbiota Composition and Diversity in a Deep Hyperarid Core of the Atacama Desert
Bárbara Fuentes, Alessandra Choque, Francisco Gómez, Jaime Alarcón, Eduardo Castro-Nallar, Franko Arenas, Daniel Contreras, Ramona Mörchen, Wulf Amelung, Claudia Knief, Ghazal Moradi, Erwin Klumpp, Claudia P Saavedra, Jörg Prietzel, Wantana Klysubun, Francisco Remonsellez, Roland Bol
Frontiers in microbiology 12, 794743, 2021

Rhizosphere Spatiotemporal Organisation
Mika T Tarkka, Michael Bonkowski, Tida Ge, Claudia Knief, Bahar S Razavi, Doris Vetterlein
Frontiers in Plant Science 12, 795136, 2021

Bridging microbial functional traits with localized process rates at soil interfaces
Evgenia Blagodatskaya, Mika Tarkka, Claudia Knief, Robert Koller, Stephan Peth, Volker Schmidt, Sandra Spielvogel, Daniel Uteau, Matthias Weber, Bahar S Razavi
Frontiers in microbiology 12, 625697, 2021

Differential impact of plant secondary metabolites on the soil microbiota
Vadim Schütz, Katharina Frindte, Jiaxin Cui, Pengfan Zhang, Stéphane Hacquard, Paul Schulze-Lefert, Claudia Knief, Margot Schulz, Peter Dörmann
Frontiers in microbiology, 12, 666010, 2021

D Biesgen, K Frindte, S Maarastawi, C Knief (2020) Clay content modulates differences in bacterial community structure in soil aggregates of different size , Geoderma 376, 114544

K Frindte, E Lehndorff, SVlaminck, K Werner, M Kehl, F Khormali, C Knief (2020) Evidence for signatures of ancient microbial life in paleosols, Scientific reports 10 (1), 1-11

TJ Dunai, M Melles, D Quandt,C Knief, W Amelung (2020) Whitepaper: Earth–Evolution at the dry limit, Global and Planetary Change193, 103275

VJ Felde, SA Schweizer, D Biesgen, A Ulbrich, D Uteau, C Knief, M Graf‐Rosenfellner, I Kögel‐Knabner, S Peth (2020) Wet sieving versus dry crushing: Soil microaggregates reveal different physical structure, bacterial diversity and organic matter composition in a clay gradient, European Journal of Soil Science,

K Frindte, SA Zoche, C Knief (2020) Development of a distinct microbial community upon first season crop change in soils of long-term managed maize and rice fields, Frontiers in Microbiology 11, 2749

C Knief, R Bol, W Amelung, S Kusch, K Frindte, E Eckmeier, A Jaeschke, T, Dunai, B Fuentes, R Mörchen, T Schütte, A Lücke, E Klumpp, K Kaiser, J Rethemeyer (2020) Tracing elevational changes in microbial life and organic carbon sources in soils of the Atacama Desert, Global and Planetary Change 184, 103078)

V Sentek, G Braun, M Braun, Z Sebesvari, F G Renaud, M Herbst, K Frindte, W Amelung (2020) Salinity-independent dissipation of antibiotics from flooded tropical soil: a microcosm study, Scientific reports 10, 14088 

Krause, L., Biesgen, D., Treder, A., Schweizer, S. A., Klumpp, E., Knief, C., Siebers, N. (2019) Initial microaggregate formation: association of microorganisms to montmorillonite-goethite aggregates under wetting and drying cycles. Geoderma. in press

Frindte, K., Pape, R., Werner, K., Löffler, J., Knief, C. (2019) Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients. ISME J. in press

Maarastawi, S. A., Frindte, K., Bodelier, P. L. E., Knief, C. (2019) Rice straw serves as additional carbon source for rhizosphere microorganisms and reduces root exudate consumption. Soil Biol. Biochem. 135: 235-238.

Knief, C. (2019) Diversity of methane-cycling microorganisms in soils and their relation to oxygen. In: Methylotrophs and methylotroph communities. Editor: L. Chistoserdova. Caister Academic Press, Poole, U.K. P. 23 – 56.

Sickel, W., Van de Weyer, A.-L., Bemm, F., Schultz, J., Keller, A. (2019) Venus flytrap microbiota withstand harsh conditions during prey digestion. FEMS Microbiol. Ecol. 95: fiz010.

Fuhrmann, I., Maarastawi, S., Neumann, J., Amelung, W., Frindte, K., Knief, C.,Lehndorff, E., Wassmann, R., Siemens, J. (2018) Preferential flow pathways in paddy rice soils as hot spots for nutrient cycling. Geoderma 337: 549-606.

Dedysh, S.N., Knief, C. (2018) Diversity and phylogeny of described aerobic methanotrophs. In: Methane biocatalysis: paving the way to sustainability. Editor: Marina Kalyuzhnaya, Springer Publishing. 67: 4507-4514
Jones, D. L., Olivera-Ardid, S., Klumpp, E., Knief, C., Hill, P. W., Lehndorff, E., Bol, R. (2018) Moisture activation and carbon use efficiency of soil microbial communities along an aridity gradient in the Atacama Desert. Soil. Biol. Biochem. 117: 68-71.
Keller, A., Brandel, A., Becker, M. C., Balles, R., Abdelmohsen, U. R., Ankenbrand, M. J., & Sickel, W. (2018). Wild bees and their nests host Paenibacillus bacteria with functional potential of avail. Microbiome, 6(1), 229.
Maarastawi, S. A., Frindte, K., Geer, R., Kröber, E., Knief, C. (2018) Temporal dynamics and compartment specific rice straw degradation in bulk soil and the rhizosphere of maize. Soil Biol. Biochem 127: 220-212.

Maarastawi, S. A., Frindte, K., Linnartz, M., Knief, C. (2018) Crop rotation and straw application impact microbial communities in Italian and Philippine soils and the rhizosphere of Zea mays. Front. Microbiol. 9: 1295.

Too, C. C., Keller, A., Sickel, W., Lee, S. M., & Yule, C. M. (2018). Microbial community structure in a Malaysian tropical peat swamp forest: the influence of tree species and depth. Frontiers in microbiology, 9:2859. doi: 10.3389/fmicb.2018.02859
Totsche, K. U., Amelung, W., Gerzabek, M. H., Guggenberger, G., Klumpp, E., Knief, C., Lehndorff, E., Mikutta, R., Peth, S., Prechtel, A., Ray, N., Kögel-Knabner, I. (2018) Microaggregates in soils. J. Plant Nutr. Soil Sci. 191: 104-136

Frindte, K., Maarastawi, S.A., Lipski, A., Hamacher, J., Knief, C. (2017) Characterization of the first rice paddy cluster I isolate, Methyloterricola oryzae gen. nov., sp. nov. and amended description of Methylomagnum ishizawai. Int. J. Syst. Evol. Microbiol. In press

Kolb, S., Horn, M. A., Murrell, C., Knief, C. (2017) Impact of microorganisms on consumption of atmospheric trace gases. Front.Microbiol. 8: 1856.

Frindte, K., Kalyuzhnaya, M.G., Bringel, F., Dunfield, P.F., Jetten, M.S.M., Khmelenina, V.N., Klotz, M.G., Murrell, J.C., Op den Camp, H.J.M., Sakai, Y., Semrau, J.D., Shapiro, N., DiSpirito, A.A., Stein, L.Y., Svenning, M.M., Trotsenko, Y.A., Vuilleumier, S., Woyke, T., Knief, C. (2017) Draft genome sequences of two gammaproteobacterial methanotrophs isolated from rice ecosystems. Genome Announc. 5:e00526-17.

Wurzbacher, C., Fuchs, A., Attermayer, K., Frindte, K., Grossart, H. P., Hupfer, M., Casper, P., Monaghan, M. T. (2017) Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment. Microbiome 5: 41.

Flynn, J. D., Hirayama, H., Sakai, Y., Dunfield, P. F., Klotz, M., Knief, C., Op den Camp, H. J. M., Jetten, M., Khmelenina, V. N., Trotsenko, Y. A., Murrell, J. C., Semrau, J. D., Svenning, M. M., Stein, L. Y., Kyrpides, N., Shapiro, N. Woyke, T., Bringel, F., Vuilleumier, S., DiSpirito, A. A., Kalyuzhnaya, M. G. (2016) Draft genome sequences of gammaproteobacterial methanotrophs isolated from marine ecosystems. Genome Announc. 4: e01629-15

Frindte K, Allgaier M, Grossart H-P, Eckert W. 2016. Redox stability regulates community structure of active microbes at the sediment-water interface. Environ Microbiol Rep. 8: 798–804.

Ueda Y, Frindte K, Knief C, Ashrafuzzaman M, Frei M. 2016. Effects of elevated tropospheric ozone concentration on the bacterial community in the phyllosphere and rhizoplane of rice. PLoS One 11: e0163178.

Knief, C. (2015) Diversity and habitat preferences of cultivated and uncultivated aerobic methanotrophic bacteria evaluated based on pmoA as molecular marker. Front. Microbiol. 6: 1346

Attermeyer, K., Tittel, J., Allgaier, M., Frindte, K., Wurzbacher, C., Hilt, S., Kamjunke, N., Grossart, HP (2015) Effects of light and autochthonous carbon additions on microbial turnover of allochthonous organic carbon and community composition. Microb. Ecol. 69: 361–371.

Frindte, K., Allgaier, M., Grossart, H.-P., and Eckert, W. (2015) Microbial response to experimentally controlled redox transitions at the sediment water interface. PLoS One 10: e0143428.

Osawa, A., Kaseya, Y., Koue, N., Schrader, J., Knief, C., Vorholt, J. A. Sandmann, G., Shindo, K. (2015) 4-[2-O-11Z-Octadecenoyl-β-glucopyranosyl]-4,4′-diapolycopene-4,4′-dioic acid and 4-[2-O-9Z-hexadecenoyl-β-glucopyranosyl]-4,4′-diapolycopene-4,4′-dioic acid: New C30-carotenoids produced by Methylobacterium. Tetrahedon Letters 56: 2791-2794.

Sharp, C. E., Smirnova, A. V., Kalyuzhnaya, M. G., Bringel, F., Hirayama, H., Jetten, M. S. M., Khmelenina, V. N., Klotz, M. G., Knief, C., Kyrpides, N., Op den Camp, H. J. M., Reshetnikov, A. S., Sakai, Y., Shapiro, N., Trotsenko, Y. A., Vuilleumier, S., Woyke, T., Dunfield, P. F. (2015) Draft genome sequence of the moderately halophilic methanotroph, Methylohalobius crimeensis strain 10Ki. Genome Announc. 3: e00644-15

Hamilton, R., Kits, K. D., Ramonovskaya, V. A., Rozova, O. N., Yurimoto, H., Iguchi, H., Khmelenina, V. N., Sakai, Y., Dunfield, P. F., Klotz, M. G., Knief, C., op den Camp, H. J. M., Jetten, M. S. M., Bringel, F., Vuilleumier, S., Svenning, M. M., Shaprio, N., Woyke, T., Trotsenko, Y. A., Stein, L. Y., Kalyuzhnaya, M. G. (2015) Draft genomes of gammaproteobacterial methanotrophs isolated from terrestrial ecosystems. Genome Announc. 3: e00515-15

Wannicke, N., Frindte, K., Gust, G., Liskow, I., Wacker, A., Meyer, A., and Grossart, H.-P. (2015) Measuring bacterial activity and community composition at high hydrostatic pressure using a novel experimental approach: a pilot study. FEMS Microbiol. Ecol. 69: 361-371.

Knief, C. (2014) Analysis of plant microbe interactions in the era of next generation sequencing technologies. Front. Plant Sci. 5: 216

Khmelenina, V.N., Beck, D.A., Munk, C., Davenport, K., Daligault, H., Erkkila, T., Goodwin, L., Gu, W., Lo, C.C., Scholz, M., Teshima, H., Xu, Y., Chain, P., Bringel, F., Vuilleumier, S., Dispirito, A., Dunfield, P., Jetten, M.S., Klotz, M.G., Knief, C., Murrell, J.C., Op den Camp, H.J., Sakai, Y., Semrau, J., Svenning, M., Stein, L.Y., Trotsenko, Y.A., Kalyuzhnaya, M.G. (2013) Draft genome sequence of Methylomicrobium buryatense strain 5G, a haloalkaline-tolerant methanotrophic bacterium. Genome Announc. 1: e00053-13.

Marx, C. J., Bringel, F., Chistoserdova, L., Moulin, L., Ul Haque, M. F., Fleischman, D. E., Gruffaz, C., Jourand, P., Knief, C., Lee, M.-C., Muller, E. E. L., Nadalig, T., Peyraud, R., Roselli, S., Russ, L., Goodwin, L. A., Ivanova, N., Kyrpides, N., Lajus, A., Land, M., Médigue, C., Mikahilova, N., Nolan, M., Woyke, T., Stolyar, S., Vorholt J. A., Vuilleumier, S. (2012) Complete genome sequences of six strains of the genus Methylobacterium. J. Bacteriol. 194: 4746-4748.

Knief, C., Delmotte, N., Chaffron, S., Stark, M., Innerebner, G., Wassmann, R., von Mering, C. Vorholt, J. A. (2012) Metaproteomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6: 1378-1390.

Knief, C., Dengler, V., Bodelier, P. L. E., Vorholt, J. A. (2012) Characterization of Methylobacterium strains isolated from the phyllosphere and description of Methylobacterium longum sp. nov. Antonie van Leeuwenhoek 101: 169-183.

Knief, C., Delmotte, N., Vorholt, J. A. (2011) Bacterial adaptation to life in association with plants – A proteomic perspective from culture to in situ conditions. Proteomics 11: 3086-3105.

Innerebner, G., Knief, C., Vorholt, J. A. (2011) Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77: 3202-3210.

Knief, C., Frances, L., Vorholt, J. A. (2010) Competitiveness of diverse Methylobacteriumstrains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. Microb. Ecol. 60: 440-452.

Knief, C., Ramette, A., Frances, L., Alonso-Blanco, C., Vorholt, J. A. (2010) Site and plant species are important determinants of the Methylobacterium community composition in the phyllosphere. ISME J. 4: 719-728.

Delmotte,N., Ahrens,C. H., Knief, C., Qeli, E., Koch, M., Fischer, H-M., Vorholt, J. A., Hennecke, H., Pessi, G. (2010) An integrated proteomics and transcriptomics reference dataset provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules. Proteomics 10: 1391-1400.

Delmotte, N., Knief, C., Chaffron, S., Innerebner, G., Roschitzki, B., Schlapbach, R., von Mering, C. Vorholt, J. A. (2009) Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. U S A 106: 16428-16433.

Knief, C., Frances, L. Cantet, F., Vorholt, J. A. (2008) Cultivation-independent characterization of Methylobacterium populations in the plant phyllosphere by automated ribosomal intergenic spacer analysis (ARISA). Appl. Environ. Microbiol. 74: 2218 – 2228.

Knief, C., Kolb, S., Bodelier, P. L. E., Lipski, A., and Dunfield P. F. (2006) The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environ. Microbiol. 8: 321 – 333.

Sy, A., Timmers, A. C. J., Knief, C., and Vorholt, J. A. (2005) Methylotrophic metabolism provides advantage for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl. Environ. Microbiol. 71: 7245 – 7252.

Knief, C., and Dunfield, P. F. (2005) Response and adaptation of methanotrophic bacteria to low methane concentrations. Environ. Microbiol. 7: 1307 – 1317.

Dedysh, S. N., Knief, C., and Dunfield, P. F. (2005) Methylocella species are facultatively methanotrophic. J. Bacteriol. 187: 4665 – 4670.

Knief, C., Vanitchung, S., Harvey, N. W., Conrad, R., Dunfield, P. F., and Chidthaisong, A. (2005) Diversity of methanotrophic bacteria in tropical upland soils under different land uses. Appl. Environ. Microbiol. 71: 3826 – 3831.

Kolb, S., Knief, C., Dunfield, P. F., and Conrad, R. (2005) Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environ. Microbiol. 7: 1150 – 1161.

Jaatinen, K., Knief, C., Dunfield, P. F., Yrjäla, K., and Fritze, H. (2004) Methanotrophic bacteria in boreal forest soil after fire. FEMS Microbiol. Ecol. 50: 195 – 202.

Knief, C., Lipski, A., and Dunfield P. F. (2003) Diversity and activity of methanotrophic bacteria in different upland soils. Appl. Environ. Microbiol. 69: 6703 – 6714.

Kolb, S., Knief, C., Stubner, S., and Conrad, R. (2003) Quantitative detection of methanotrophs in soil by novel pmoA-targeted real-time PCR assays. Appl. Environ. Microbiol. 69: 2423 – 2429.

Knief, C., Altendorf, K., and Lipski, A. (2003) Linking autotrophic activity in envrionmental samples with specific bacterial taxa by detection of 13C-labelled fatty acids. Environ. Microbiol. 5: 1155 – 1167.
Alexandrino, M., Knief, C., and Lipski, A. (2001) Stable-isotope-based labeling of styrene-degrading microorganisms in biofilters. Appl. Environ. Microbiol. 67: 4796 – 4804.

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