Microbiology

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  1. 2017
  2. Published

    Adaptation of root growth to increased ambient temperature requires auxin and ethylene coordination in Arabidopsis

    Fei, Q., Wei, S., Zhou, Z., Gao, H. & Li, X., 2017, In: Plant Cell Reports. 36, 9, p. 1507-1518 12 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  3. Published

    A novel baiting microcosm approach used to identify the bacterial community associated with Penicillium bilaii hyphae in soil

    Ghodsalavi, B., Svenningsen, N. B., Hao, X., Olsson, S., Nicolaisen, Mette Haubjerg, Al-Soud, W. A., Sørensen, Søren Johannes & Nybroe, O., 27 Oct 2017, In: PLOS ONE. 12, 10, 14 p., e0187116.

    Research output: Contribution to journal › Journal article › Research › peer-review

  4. Published

    Whole-genome sequence of Pseudomonas fluorescens EK007-RG4, a promising biocontrol agent against a broad range of bacteria, including the fire blight bacterium Erwinia amylovora

    Habibi, R., Tarighi, S., Behravan, J., Taheri, P., Kjøller, Annelise Helene, Brejnrod, A. D., Madsen, Jonas Stenløkke & Sørensen, Søren Johannes, 2017, In: Genome Announcements. 5, 13, 2 p., e00026-17.

    Research output: Contribution to journal › Journal article › Research › peer-review

  5. Published

    Distinct gene expression profile of Xanthomonas retroflexus engaged in synergistic multispecies biofilm formation

    Hansen, L. B. S., Ren, D., Burmølle, Mette & Sørensen, Søren Johannes, 2017, In: The ISME Journal. 11, 1, p. 300-303 4 p.

    Research output: Contribution to journal › Letter › Research › peer-review

  6. Published

    Bacterial resistance to arsenic protects against protist killing

    Hao, X., Li, Xuan Ji, Pal, C., Hobman, J., Larsson, D. G. J., Saquib, Q., Alwathnani, H. A., Rosen, B. P., Zhu, Y. & Rensing, C., Apr 2017, In: BioMetals. 30, 2, p. 307-311 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  7. Published

    A meta-proteomics approach to study the interspecies interactions affecting microbial biofilm development in a model community

    Herschend, J., Damholt, Z. B. V., Marquard, A. M., Svensson, B., Sørensen, Søren Johannes, Hägglund, Per Mårten & Burmølle, Mette, 28 Nov 2017, In: Scientific Reports. 7, 13 p., 16483.

    Research output: Contribution to journal › Journal article › Research › peer-review

  8. Published

    Response of the bacterial community in an on-farm biopurification system, to which diverse pesticides are introduced over an agricultural season

    Holmsgaard, P. N., Dealtry, S., Dunon, V., Heuer, H., Hansen, Lars Hestbjerg, Springael, D., Smalla, K., Riber, Leise & Sørensen, Søren Johannes, Oct 2017, In: Environmental Pollution. 229, p. 854-862 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  9. Published

    Long-term and realistic global change manipulations had low impact on diversity of soil biota in temperate heathland

    Holmstrup, M., Damgaard, C., Schmidt, Inger Kappel, Arndal, M. F., Beier, Claus, Mikkelsen, T. N., Ambus, Per Lennart, Larsen, Klaus Steenberg, Pilegaard, K., Michelsen, Anders, Andresen, L. C., Haugwitz, M. S., Bergmark, L., Priemé, Anders, Zaitsev, A. S., Georgieva, S., Dam, M., Vestergård, M. & Christensen, Søren, 2017, In: Scientific Reports. 7, 11 p., 41388.

    Research output: Contribution to journal › Journal article › Research › peer-review

  10. Published

    Comparative genomic analysis reveals ecological differentiation in the genus Carnobacterium

    Iskandar, C. F., Borges, F., Taminiau, B., Daube, G., Zagorec, M., Remenant, B., Leisner, Jørgen, Hansen, M. A., Sørensen, Søren Johannes, Mangavel, C., Cailliez-Grimal, C. & Revol-Junelles, A., 2017, In: Frontiers in Microbiology. 8, 14 p., 357.

    Research output: Contribution to journal › Journal article › Research › peer-review

  11. Published

    Deciphering conjugative plasmid permissiveness in wastewater microbiomes

    Jacquiod, S. J. A., Brejnrod, A. D., Milani, S. M., Abu Al-Soud, W., Sørensen, Søren Johannes & Riber, Leise, Jul 2017, In: Molecular Ecology. 26, 13, p. 3556-3571 16 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  12. Published

    Autogenic succession and deterministic recovery following disturbance in soil bacterial communities

    Jurburg, S. D., Nunes, I. M., Stegen, J. C., Le Roux, X., Priemé, Anders, Sørensen, Søren Johannes & Salles, J. F., 6 Apr 2017, In: Scientific Reports. 7, 11 p., 45691.

    Research output: Contribution to journal › Journal article › Research › peer-review

  13. Published

    Legacy Effects on the Recovery of Soil Bacterial Communities from Extreme Temperature Perturbation

    Jurburg, S. D., Nunes, I. M., Brejnrod, A. D., Jacquiod, S. J. A., Priemé, Anders, Sørensen, Søren Johannes, Van Elsas, J. D. & Salles, J. F., 2017, In: Frontiers in Microbiology. 8, 13 p., 1832.

    Research output: Contribution to journal › Journal article › Research › peer-review

  14. Published

    Plasmids, viruses, and other circular elements in rat gut

    Jørgensen, T. S., Hansen, M. A., Xu, Z., Tabak, M. A., Sørensen, Søren Johannes & Hansen, Lars Hestbjerg, 2017, Cold Spring Harbor Laboratory Press, 30 p.

    Research output: Working paper › Research

  15. Published

    Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner

    Klümper, U., Dechesne, A., Riber, Leise, Brandt, Kristian Koefoed, Gülay, A., Sørensen, Søren Johannes & Smets, B. F., 2017, In: The ISME Journal. 11, 1, p. 152-165 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  16. Published

    Hot spots of N2O emission move with the seasonally mobile oxic-anoxic interface in drained organic soils

    Lee, A. J., Winther, M. N., Priemé, Anders, Blunier, Thomas & Christensen, Søren Tvorup, 1 Dec 2017, In: Soil Biology & Biochemistry. 115, p. 178-186 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  17. Published

    Interplay of Bacterial Interactions and Spatial Organisation in Multispecies Biofilms

    Liu, W., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  18. Published

    Low-abundant species facilitates specific spatial organization that promotes multispecies biofilm formation

    Liu, W., Russel, J., Røder, Henriette Lyng, Madsen, Jonas Stenløkke, Burmølle, Mette & Sørensen, Søren Johannes, 2017, In: Environmental Microbiology. 19, 7, p. 2893-2905 13 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  19. Published

    Partial drying accelerates bacterial growth recovery to rewetting

    Meisner, A., Leizeaga, A., Rousk, J. & Bååth, E., Sep 2017, In: Soil Biology & Biochemistry. 112, p. 269-276 8 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  20. Published

    Metagenomic analysis of dairy bacteriophages: extraction method and pilot study on whey samples derived from using undefined and defined mesophilic starter cultures

    Muhammed, Musemma Kedir, Kot, Witold, Neve, H., Mahony, J., Castro Mejia, J. L., Krych, Lukasz, Hansen, L. H., Nielsen, Dennis Sandris, Sørensen, Søren Johannes, Heller, K. J., van Sinderen, D. & Vogensen, Finn Kvist, 2017, In: Applied and Environmental Microbiology. 83, 19, 15 p., e00888-17.

    Research output: Contribution to journal › Journal article › Research › peer-review

  21. Published

    Arctic Soil Microbial Sensitivity to Seasonal Dynamics and Climate Change

    Priemé, Anders, Blok, D., Haugwitz, M. S., Voriskova, J. & Elberling, Bo, 2017, Microbial Biomass: A Paradigm Shift in Terrestrial Biogeochemistry. Tate, K. R. (ed.). World Scientific, p. 275-307

    Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

  22. Published

    Human milk oligosaccharide effects on intestinal function and inflammation after preterm birth in pigs

    Rasmussen, S. O., Martin, L., Østergaard, M. V., Rudloff, S., Roggenbuck, M., Nguyen, Duc Ninh, Sangild, Per Torp & Bering, S. B., 2017, In: The Journal of Nutritional Biochemistry. 40, p. 141-154 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  23. Published

    Antagonism correlates with metabolic similarity in diverse bacteria

    Russel, J., Røder, Henriette Lyng, Madsen, Jonas Stenløkke, Burmølle, Mette & Sørensen, Søren Johannes, 3 Oct 2017, In: Proceedings of the National Academy of Science of the United States of America. 114, 40, p. 10684-10688 5 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  24. Published

    Co-existence in multispecies biofilm communities

    Røder, Henriette Lyng, 2017, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  25. Published

    Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome

    Santos, S. S., Nunes, I. M., Nielsen, Tue Kjærgaard, Jacquiod, S. J. A., Hansen, L. H. & Winding, A., Jul 2017, In: Protist. 168, 3, p. 283-293 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  26. Published

    Living in the cold: Microbial community and function dynamics in Arctic soils at changing temperature

    Schostag, M. D., 2017, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  27. Published

    Critical Assessment of Metagenome Interpretation: a benchmark of metagenomics software

    Sczyrba, A., Hofmann, P., Belmann, P., Koslicki, D., Janssen, S., Dröge, J., Gregor, I., Majda, S., Fiedler, J., Dahms, E., Bremges, A., Fritz, A., Garrido-Oter, R., Jørgensen, T. S., Shapiro, N., Blood, P. D., Gurevich, A., Bai, Y., Turaev, D., DeMaere, M. Z. & 47 others, Chikhi, R., Nagarajan, N., Quince, C., Meyer, F., Balvociute, M., Hansen, L. H., Sørensen, Søren Johannes, Chia, B. K. H., Denis, B., Froula, J. L., Wang, Z., Egan, R., Kang, D. D., Cook, J. J., Deltel, C., Beckstette, M., Lemaitre, C., Peterlongo, P., Rizk, G., Lavenier, D., Wu, Y., Singer, S. W., Jain, C., Strous, M., Klingenberg, H., Meinicke, P., Barton, M. D., Lingner, T., Lin, H., Liao, Y., Silva, G. G. Z., Cuevas, D. A., Edwards, R. A., Saha, S., Piro, V. C., Renard, B. Y., Pop, M., Klenk, H., Göker, M., Kyrpides, N. C., Woyke, T., Vorholt, J. A., Schulze-Lefert, P., Rubin, E. M., Darling, A. E., Rattei, T. & McHardy, A. C., 2017, In: Nature Methods. 14, 11, p. 1063-1071 9 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  28. Published

    An alternative anionic bio-sustainable anti-fungal agent: investigation of its mode of action on the fungal cell membrane

    Stenbæk, J., Löf, D., Falkman, P., Jensen, B. & Cárdenas, M., 1 Jul 2017, In: Journal of Colloid and Interface Science. 497, p. 242-248 7 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  29. Published

    Eosinophilic airway inflammation in asthmatic patients is associated with an altered airway microbiome

    Sverrild, Asger, Kiilerich, P., Brejnrod, A. D., Pedersen, R., Porsbjerg, Celeste Michala, Bergqvist, A., Erjefält, J. S., Kristiansen, Karsten & Backer, Vibeke, Aug 2017, In: Journal of Allergy and Clinical Immunology. 140, 2, p. 407-417 e11.

    Research output: Contribution to journal › Journal article › Research › peer-review

  30. Published

    All together now: experimental multispecies biofilm model systems

    Tan, C. H., Lee, K. W. K., Burmølle, Mette, Kjelleberg, S. & Rice, S. A., Jan 2017, In: Environmental Microbiology. 19, 1, p. 42-53 12 p.

    Research output: Contribution to journal › Review › Research › peer-review

  31. Published

    A post-planktonic era of in vitro infectious models: issues and changes addressed by a clinically relevant wound like media

    Trivedi, Urvish, Madsen, Jonas Stenløkke, Rumbaugh, K. P., Wolcott, R. D., Burmølle, Mette & Sørensen, Søren Johannes, 2017, In: Critical Reviews in Microbiology. 43, 4, p. 453-465 12 p.

    Research output: Contribution to journal › Review › Research › peer-review

  32. Published

    Social dynamics & adaptive strategies of microbes

    Trivedi, Urvish, 2017, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  33. Published

    Continuous measurements of nitrous oxide isotopomers during incubation experiments

    Winther, M., Balslev-Harder, D., Christensen, S., Priemé, Anders, Elberling, Bo, Crosson, E. & Blunier, Thomas, 16 May 2017, 24 p. Copernicus/EGU.

    Research output: Other contribution › Research

  34. Published

    Effects of soil pre-treatment with Basamid© granules, Brassica juncea, Raphanus sativus, and Tagetes patula on bacterial and fungal communities at two apple replant disease sites

    Yim, B., Nitt, H., Wrede, A., Jacquiod, S. J. A., Sørensen, Søren Johannes, Winkelmann, T. & Smalla, K., 1 Sep 2017, In: Frontiers in Microbiology. 8, 15 p., 1604.

    Research output: Contribution to journal › Journal article › Research › peer-review

  35. Published

    Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period

    Zhu, Z., Noel, S. J., Difford, G. F., Abu Al-Soud, W., Brejnrod, A. D., Sørensen, Søren Johannes, Lassen, J., Løvendahl, P. & Højberg, O., 8 Nov 2017, In: PLoS ONE. 12, 11, 24 p., e0187858.

    Research output: Contribution to journal › Journal article › Research › peer-review

  36. 2016
  37. Published

    Supraglacial bacterial community structures vary across the Greenland ice sheet

    Cameron, K. A., Stibal, M., Zarsky, J. D., Gözdereliler, E., Schostag, M. D. & Jacobsen, C. S., 2016, In: F E M S Microbiology Ecology. 92, 2, 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  38. Published

    Exploring the complex response to linuron of bacterial communities from biopurification systems by means of cultivation-independent methods

    Dealtry, S., Nour, E. H., Holmsgaard, P. N., Ding, G. C., Weichelt, V., Dunon, V., Heuer, H., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Springael, D. & Smalla, K., 2016, In: F E M S Microbiology Ecology. 92, 2, 12 p., fiv157.

    Research output: Contribution to journal › Journal article › Research › peer-review

  39. Published

    Herbivory and dominance shifts among exotic and congeneric native plant species during plant community establishment

    Engelkes, T., Meisner, A., Morriën, E., Kostenko, O., van der Putten, W. H. & Macel, M., 2016, In: Oecologia. 180, 2, p. 507-517 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  40. Published

    High frequencies of antibiotic resistance genes in infants' meconium and early fecal samples

    Gosalbes, M. J., Vallès, Y., Jiménez-Hernández, N., Balle, C., Riva, P., Miravet-Verde, S., de Vries, Lisbeth Elvira, Llop, S., Agersø, Y., Sørensen, Søren Johannes, Ballester, F. & Francino, M. P., 2016, In: Journal of Developmental Origins of Health and Disease. 7, 01, p. 35-44 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  41. Published

    Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

    Gülay, A., Musovic, S., Albrechtsen, H., Abu Al-Soud, W., Sørensen, Søren Johannes & Smets, B. F., 2016, In: The ISME Journal. 10, 9, p. 2209-2222 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  42. Published

    A role for copper in protozoan grazing - two billion years selecting for bacterial copper resistance

    Hao, X., Lüthje, F. L., Rønn, Regin, German, N. A., Li, Xuan Ji, Huang, F., Kisaka, J., Huffman, D., Alwathnani, H. A., Zhu, Y. & Rensing, C., 2016, In: Molecular Microbiology. 102, 4, p. 628-641 14 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  43. Published

    Local diversity of heathland Cercozoa explored by in-depth sequencing

    Harder, Christoffer Bugge, Rønn, Regin, Brejnrod, A. D., Bass, D., Abu Al-Soud, W. & Ekelund, Flemming, 2016, In: The ISME Journal. 10, 10, p. 2488-2497 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  44. Published

    The legacy of climate change effects: previous drought increases short-term litter decomposition rates in a temperate mixed grass- and shrubland

    Haugwitz, M. S., Michelsen, Anders & Priemé, Anders, 2016, In: Plant and Soil. 408, 1, p. 183-193 11 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  45. Published

    Draft genome sequences of two Kocuria isolates, K. salsicia G1 and K. rhizophila G2, isolated from a slaughterhouse in Denmark

    Herschend, J., Raghupathi, P. K., Røder, Henriette Lyng, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Genome Announcements. 4, 2, 2 p., e00075-16.

    Research output: Contribution to journal › Journal article › Research › peer-review

  46. Published

    Genome sequence of Arthrobacter antarcticus strain W2, isolated from a slaughterhouse

    Herschend, J., Raghupathi, P. K., Røder, Henriette Lyng, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Genome Announcements. 4, 2, 2 p., e00073-16.

    Research output: Contribution to journal › Journal article › Research › peer-review

  47. Published

    Genome sequence of Kocuria palustris strain W4

    Herschend, J., Raghupathi, P. K., Røder, Henriette Lyng, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Genome Announcements. 4, 2, 1 p., e00074-16.

    Research output: Contribution to journal › Journal article › Research › peer-review

  48. Published

    Unravelling the mechanisms of bacterial interactions in model communities

    Herschend, J., 2016, Department of Biology, Faculty of Science, University of Copenhagen.

    Research output: Book/Report › Ph.D. thesis › Research

  49. Published

    Metagenomes provide valuable comparative information on soil microeukaryotes

    Jacquiod, S. J. A., Stenbæk, J., Santos, S. S., Winding, A., Sørensen, Søren Johannes & Priemé, Anders, 2016, In: Research in Microbiology. 167, 5, p. 436-450 15 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  50. Published

    Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients

    Jitwasinkul, T., Suriyaphol, P., Tangphatsornruang, S., Hansen, M. A., Hansen, Lars Hestbjerg, Sørensen, Søren Johannes, Permpikul, C., Rongrungruang, Y. & Tribuddharat, C., 2016, In: Journal of Global Antimicrobial Resistance. 6, p. 57-66 10 p.

    Research output: Contribution to journal › Journal article › Research › peer-review

  51. Published

    Impact of Sample Type and DNA Isolation Procedure on Genomic Inference of Microbiome Composition

    Knudsen, B. E., Bergmark, L., Munk, P., Lukjancenko, O., Priemé, Anders, Aarestrup, F. M. & Pamp, S. J., 2016, In: mSystems. 1, 5, p. 1-15 e00095-16.

    Research output: Contribution to journal › Journal article › Research › peer-review

  52. Published

    Interspecific bacterial interactions are reflected in multispecies biofilm spatial organization

    Liu, W., Røder, Henriette Lyng, Madsen, Jonas Stenløkke, Bjarnsholt, Thomas, Sørensen, Søren Johannes & Burmølle, Mette, 2016, In: Frontiers in Microbiology. 7, 8 p., 1366.

    Research output: Contribution to journal › Review › Research › peer-review

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