Microbial Ecology and Biotechnology

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  1. Published

    How to disentangle microbially functional complexity: an insight from the network analysis of C, N, P and S cycling genes

    Zheng, B., Zhao, Y., Bi, Q., Zhou, G., Wang, H., Hao, X. & Ding, K., 2019, In: Science Bulletin. 64, 16, p. 1129-1131

    Research output: Contribution to journal › Editorial › Research

  2. Published

    Human health risk assessment (HHRA) for environmental development and transfer of antibiotic resistance

    Ashbolt, N. J., Amézquita, A., Backhaus, T., Borriello, P., Brandt, Kristian Koefoed, Collignon, P., Coors, A., Finley, R., Gaze, W. H., Heberer, T., Lawrence, J. R., Larsson, D. G. J., McEwen, S. A., Ryan, J. J., Schönfeld, J., Silley, P., Snape, J. R., Van den Eede, C. & Topp, E., 2013, In: Environmental Health Perspectives. 121, 9, p. 993-1001 9 p.

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

  3. Published

    Hydraulically active biopores stimulate pesticide mineralization in agricultural subsoil

    Badawi, N., Johnsen, A. R., Brandt, Kristian Koefoed, Sørensen, Jan & Aamand, J., 2013, In: Soil Biology & Biochemistry. 57, p. 533-541 9 p.

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

  4. Published

    Hyphae colonizing bacteria associated with Penicillium bilaii

    Ghodsalavi, B., 2015, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen.

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

  5. Published

    Identification and Characterization of a β-N-Acetylhexosaminidase with a Biosynthetic Activity from the Marine Bacterium Paraglaciecola hydrolytica S66T

    Visnapuu, T., Teze, D., Kjeldsen, C., Lie, A., Duus, J. Ø., André-Miral, C., Pedersen, L. H., Stougaard, P. & Svensson, B., 2020, In: International Journal of Molecular Sciences (Online). 21, 2, 22 p.

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

  6. Published

    Identification and Functional Characterisation of Two Oat UDP-Glucosyltransferases Involved in Deoxynivalenol Detoxification

    Khairullina, A., Renhuldt, N. T., Wiesenberger, G., Bentzer, J., Collinge, David B., Adam, G. & Bülow, L., 2022, In: Toxins. 14, 7, 16 p., 446.

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

  7. Published

    Identification of Root-Associated Bacteria That Influence Plant Physiology, Increase Seed Germination, or Promote Growth of the Christmas Tree Species Abies nordmanniana

    Garcia-Lemos, A. M., Grosskinsky, D. K., Akhtar, S. S., Nicolaisen, Mette Haubjerg, Roitsch, Thomas Georg, Nybroe, O. & Veierskov, Bjarke, 2020, In: Frontiers in Microbiology. 11, 15 p., 566613.

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

  8. Published

    Identification of two endophytic fungi that control Septoria tritici blotch in the field, using a structured screening approach

    Latz, Meike, Jensen, Birgit, Collinge, David B. & Jørgensen, Hans Jørgen Lyngs, 2020, In: Biological Control. 141, p. 1-8 104128.

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

  9. Published

    Imaging Gene Expression Dynamics in Pseudomonas fluorescens In5 during Interactions with the Fungus Fusarium graminearum PH-1

    Hennessy, Rosanna Catherine, Stougaard, P. & Olsson, S., 20 Jun 2019, In: Bio-protocol. 9, 12, 14 p., e3264.

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

  10. Published

    Imaging transcription during microbe-microbe interactions

    Hennessy, Rosanna Catherine, Olsson, S. & Stougaard, P., 13 Nov 2017, p. 79-79.

    Research output: Contribution to conference › Poster › Research › peer-review

  11. Published

    Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios

    Braga, L. P. P., Spor, A., Kot, Witold, Breuil, M., Hansen, Lars Hestbjerg, Setubal, J. C. & Philippot, L., 2020, In: Microbiome. 8, 1, 14 p., 52.

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

  12. Published

    Impacts of biochar materials on copper speciation, bioavailability, and toxicity in chromated copper arsenate polluted soil

    Tang, Yinqi, Wang, Chen, Holm, Peter Engelund, Hansen, Hans Chr. Bruun & Brandt, Kristian Koefoed, 2023, In: Journal of Hazardous Materials. 459, 14 p., 132067.

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

  13. Published

    Impacts of dietary copper on the swine gut microbiome and antibiotic resistome

    Brinck, J. E., Lassen, Simon Bo, Forouzandeh, A., Pan, T., Wang, Y. Z., Monteiro, A., Blavi, L., Solà-Oriol, D., Stein, H. H., Su, J. Q. & Brandt, Kristian Koefoed, 2023, In: Science of the Total Environment. 857, 11 p., 159609.

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

  14. Published

    Impaired skeletal muscle hypertrophy signaling and amino acid deprivation response in Apoe knockout mice with an unhealthy lipoprotein distribution

    Agergaard, J., Zillmer, M. C. F., Castro-Mejía, J. L., Mertz, K., Kot, Witold, Højfeldt, Grith Stougaard, van Hall, Gerrit, Nielsen, Dennis Sandris, Schjerling, Peter & Holm, Lars Morten, 2021, In: Scientific Reports. 11, 15 p., 16423.

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

  15. Published

    Improved cultivation and metagenomics as new tools for bioprospecting in cold environments

    Vester, J. K., Glaring, M. A. & Stougaard, P., 2015, In: Extremophiles. 19, 1, p. 17-29 13 p.

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

  16. Published

    Improving Griffith's protocol for co-extraction of microbial DNA and RNA in adsorptive soils

    Paulin, M. M., Nicolaisen, Mette Haubjerg, Jacobsen, C. S., Gimsing, A. L., Sørensen, Jan & Bælum, J., 2013, In: Soil Biology & Biochemistry. 63, p. 37-49 13 p.

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

  17. Published

    Improving diversity in cultures of bacteria from an extreme environment

    Vester, J. K., Glaring, M. A. & Stougaard, P., 2013, In: Canadian Journal of Microbiology. 59, 8, p. 581-586 6 p.

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

  18. Published

    In vitro characterization of the Ac locus in white clover (Trifolium repens L.)

    Collinge, David B. & Hughes, M. A., 1 Oct 1982, In: Archives of Biochemistry and Biophysics. 218, 1, p. 38-45 8 p.

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

  19. Published

    Induced resistance in sugar beet against Cercospora beticola: Induction by dichloroisonicotinic acid is independent of chitinase and β-1,3-glucanase transcript accumulation

    Nielsen, K. K., Bojsen, K., Collinge, David B. & Mikkelsen, Jens D., 1 Jan 1994, In: Physiological and Molecular Plant Pathology. 45, 2, p. 89-99 11 p.

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

  20. Published

    Induction, purification and characterization of chitinase isolated from pea leaves inoculated with Ascochyta pisi

    Vad, K., Mikkelsen, Jens D. & Collinge, David B., 1 Apr 1991, In: Planta. 184, 1, p. 24-29 6 p.

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

  21. Published

    Influence of Environmental Factors on Occurrence of Cyanobacteria and Abundance of Saxitoxin-Producing Cyanobacteria in a Subtropical Drinking Water Reservoir in Brazil

    Moraes, M. A. B., Rodrigues, R. A. M., Schlüter, L., Podduturi, Raju, Jørgensen, Niels O. G. & Calijuri, M. C., 2021, In: Water. 13, 12, p. 1716

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

  22. Published

    Influence of Environmental Stressors on the Physiology of Pollutant Degrading Bacteria: From the Test Tube to the Environment

    Svenningsen, N. B., 2015, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen. 133 p.

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

  23. Published

    Influence of mussel shell on As and Cr competitive and non-competitive sorption-desorption kinetics in a mine soil: stirred flow chamber experiments

    Fernandez Calviño, D., Garrido-Rodríguez, B., Cutillas-Barreiro, L., Araújo-Nespereira, P., Arias-Estevez, M., Fernandez-Sanjurjo, M. J., álvarez-Rodríguez, E. & Núnez-Delgado, A., 2014, In: Geoderma. 232-234, p. 300-308 9 p.

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

  24. Published

    Influence of two-phase anaerobic digestion on fate of selected antibiotic resistance genes and class I integrons in municipal wastewater sludge

    Wu, Y., Cui, E., Zuo, Y., Cheng, W., Rensing, C. G. T. & Chen, H., 2016, In: Bioresource Technology. 211, p. 414-421 8 p.

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

  25. Published

    Influence of vintage, geographic location and cultivar on the structure of microbial communities associated with the grapevine rhizosphere in vineyards of San Juan Province, Argentina

    Aguilar, M. O., Gobbi, Alex, Browne, Patrick Denis, Ellegaard-Jensen, L., Hansen, Lars Hestbjerg, Semorile, L. & Pistorio, M., 2020, In: PLoS ONE. 15, 12, 19 p., 0243848.

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

  26. Published

    Inoculation of tomato (Solanum lycopersicum) roots with growth promoting Pseudomonas strains induces distinct local and systemic metabolic biosignatures

    Mekureyaw, M. F., Beierholm, A. E., Nybroe, O. & Roitsch, Thomas Georg, 2022, In: Physiological and Molecular Plant Pathology. 117, 10 p., 101757.

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

  27. Published

    Insights into abundance, adaptation and activity of prokaryotes in arctic and Antarctic environments

    Holmberg, S. M. & Jørgensen, Niels O. G., 2023, In: Polar Biology. 46, p. 381-396

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

  28. Published

    Insights into mixed contaminants interactions and its implication for heavy metals and metalloids mobility, bioavailability and risk assessment

    Cipullo, S., Snapir, B., Tardif, S., Campo, P., Prpich, G. & Coulon, F., 2018, In: Science of the Total Environment. 645, p. 662-673

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

  29. Published

    Insights into the circular: The cryptic plasmidome and its derived antibiotic resistome in the urban water systems

    Yu, Z., He, Wanli, Klincke, F., Madsen, Jonas Stenløkke, Kot, Witold, Hansen, Lars Hestbjerg, Quintela-Baluja, M., Balboa, S., Dechesne, A., Smets, B., Nesme, Joseph & Sørensen, Søren Johannes, 2024, In: Environment International. 183, 12 p., 108351.

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

  30. Published

    Insights into the community structure and lifestyle of the fungal root endophytes of tomato by combining amplicon sequencing and isolation approaches with phytohormone profiling

    Manzotti, A., Bergna, A., Burow, Meike, Jørgensen, Hans Jørgen Lyngs, Cernava, T., Berg, G., Collinge, David B. & Jensen, Birgit, 2020, In: FEMS Microbiology Ecology. 96, 5, 16 p., fiaa052.

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

  31. Published

    Insights on strain 115 plant growth-promoting bacteria traits and its contribution in lead stress alleviation in pea (Pisum sativum L.) plants

    Chamekh, Anissa, Kharbech, O., Fersi, C., Driss Limam, R., Brandt, Kristian Koefoed, Djebali, W. & Chouari, R., 2023, In: Archives of Microbiology. 205, 12 p., 1.

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

  32. Published

    Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea

    Karlsson, M., Durling, M. B., Choi, J., Kosawang, C., Lackner, G., Tzelepis, G. D., Nygren, K., Dubey, M. K., Kamou, N., Levasseur, A., Zapparata, A., Wang, J., Amby, D. B., Jensen, B., Sarrocco, S., Panteris, E., Lagopodi, A. L., Pöggeler, S., Vannacci, G., Collinge, D. B. & 4 others, Hoffmeister, D., Henrissat, B., Lee, Y. & Jensen, Dan Funck, 2015, In: Genome Biology and Evolution. 7, 2, p. 465-480 16 p.

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

  33. Published

    Integrating bioinformatics in the teaching and redesign of the course Applied Microbiology

    Hennessy, Rosanna Catherine, 2020, Improving University Science Teaching and Learning: Pedagogical Projects 2020. Christiansen, F. V. & Arias, A. A. (eds.). Department of Science Education, University of Copenhagen, Vol. 15. p. 147-167 21 p. (Improving University Science Teaching and Learning - Pedagogical Projects, Vol. 15).

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

  34. Published

    Inter-laboratory testing of the effect of DNA blocking reagent G2 on DNA extraction from low-biomass clay samples

    Jacobsen, C. S., Nielsen, T. K., Vester, J. K., Stougaard, P., Nielsen, J. L., Voriskova, J., Winding, A., Baldrian, P., Liu, B., Frostegard, A., Pedersen, D., Tveit, A. T., Svenning, M. M., Tebbe, C. C., Ovreas, L., Jakobsen, P. B., Blazewicz, S. J., Hubablek, V., Bertilsson, S., Hansen, L. H. & 4 others, Cary, S. C., Holben, W. E., Ekelund, Flemming & Bælum, J., 2018, In: Scientific Reports. 8, p. 1-6 6 p., 5711.

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

  35. Published

    Inter-vendor variance of enteric eukaryotic DNA viruses in specific pathogen free C57BL/6N mice

    Rasmussen, Torben Sølbeck, Jakobsen, Rasmus Riemer, Castro-Mejía, J. L., Kot, Witold, Thomsen, Allan Randrup, Vogensen, Finn Kvist, Nielsen, Dennis Sandris & Hansen, Axel Kornerup, 2021, In: Research in Veterinary Science. 136, p. 1-5 5 p.

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

  36. Published

    Interaction between endophytic Proteobacteria strains and Serendipita indica enhances biocontrol activity against fungal pathogens

    del Barrio-Duque, A., Samad, A., Nybroe, O., Antonielli, L., Sessitsch, A. & Compant, S., 2020, In: Plant and Soil. 451, 1-2, p. 277-305 29 p.

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

  37. Published

    Interaction between pH and Cu toxicity on fungal and bacterial performance in soil

    Fernandez Calviño, D. & Baath, E., 2016, In: Soil Biology & Biochemistry. 96, p. 20-29 10 p.

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

  38. Published

    Interaction of the psychrotroph Pseudomonas fluorescens In5 with phytopathogens in cold soils

    Hennessy, Rosanna Catherine, Olsson, S. & Stougaard, P., 2017, p. 17-17.

    Research output: Contribution to conference › Conference abstract for conference › Research › peer-review

  39. Published

    Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition

    Hansen, Søren Blikdal, Bozzi, D., Mak, Sarah Siu Tze, Clausen, C. G., Nielsen, Tue Kjærgaard, Kodama, M., Hansen, Lars Hestbjerg, Gilbert, M Thomas P & Limborg, Morten Tønsberg, 2023, In: Genomics. 115, 3, 9 p., 110629.

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

  40. Published

    Inulin and milk mineral fortification of a pork sausage exhibits distinct effects on the microbiome and biochemical activity in the gut of healthy rats

    Thøgersen, R., Castro-Mejía, J. L., Sundekilde, U. K., Hansen, Lars Hestbjerg, Gray, N., Kuhnle, G., Jørgensen, Niklas Rye, Hansen, Axel Kornerup, Nielsen, Dennis Sandris & Bertram, H. C., 2020, In: Food Chemistry. 331, 10 p., 127291.

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

  41. Published

    Isolate-Specific Effect of Entomopathogenic Endophytic Fungi on Population Growth of Two-Spotted Spider Mite (Tetranychus urticae Koch) and Levels of Steroidal Glycoalkaloids in Tomato

    Rasool, S., Cárdenas, Pablo D., Pattison, David, Jensen, Birgit & Meyling, Nicolai Vitt, 2021, In: Journal of Chemical Ecology. 47, 4-5, p. 476–488 13 p.

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

  42. Published

    Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, "Silenusvirus"

    Kyrkou, I., Carstens, Alexander Byth, Ellegaard-Jensen, L., Kot, Witold, Zervas, A., Djurhuus, Amaru Miranda, Neve, H., Franz, C. M. A. P., Hansen, M. & Hansen, Lars Hestbjerg, 2020, In: Scientific Reports. 10, 1, 10 p., 8763.

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

  43. Published

    Isothiazolinone inhibition of soil microbial activity persists despite biocide dissipation

    Fernández-Calviño, D., Rousk, J., Bååth, E., Bollmann, U. E., Bester, K. & Brandt, Kristian Koefoed, 2023, In: Soil Biology and Biochemistry. 178, 9 p., 108957.

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

  44. Published

    Kinetics of tetracycline, oxytetracycline, and chlortetracycline adsorption and desorption on two acid soils

    Fernandez Calviño, D., Bermúdez-Couso, A., Arias-Estévez, M., Nóvoa-Muñoz, J. C., Fernández-Sanjurjo, M. J., Álvarez-Rodríguez, E. & Núñez-Delgado, A., 2015, In: Environmental Science and Pollution Research. 22, 1, p. 425-433 9 p.

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

  45. Published

    Large-scale phenomics identifies primary and fine-tuning roles for CRKs in responses related to oxidative stress

    Bourdais, G., Burdiak, P., Gauthier, A., Nitsch, L., Salojärvi, J., Rayapuram, C., Idänheimo, N., Hunter, K., Kimura, S., Merilo, E., Vaattovaara, A., Oracz, K., Kaufholdt, D., Pallon, A., Anggoro, D. T., Glów, D., Lowe, J., Zhou, J., Mohammadi, O., Puukko, T. & 13 others, Albert, A., Lang, H., Ernst, D., Kollist, H., Brosché, M., Durner, J., Borst, J. W., Collinge, David B., Karpinski, S., Lyngkjær, M. F., Robatzek, S., Wrzaczek, M. & Kangasjärvi, J., 2015, In: P L o S Genetics. 11, 7, 36 p., e1005373.

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

  46. Published

    Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community

    Cyriaque, V., Madsen, Jonas Stenløkke, Fievez, L., Leroy, B., Hansen, Lars Hestbjerg, Bureau, F., Sørensen, Søren Johannes & Wattiez, R., 2021, In: Frontiers in Microbiology. 12, 14 p., 655903.

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

  47. Published

    Limited impacts of high doses of dietary copper on the gut bacterial metal resistome explain negligible co-selection of antibiotic resistance

    Forouzandeh, A., Lassen, Simon Bo, Brinck, J. E., Zhou, Y. Y., Zhu, J., Solà-Oriol, D., Monteiro, A., Hao, X., Su, J. Q., Stein, H. H., Pérez, J. F. & Brandt, Kristian Koefoed, 2023, In: Science of the Total Environment. 889, 11 p., 164183.

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

  48. Published

    Limited recovery of soil microbial activity after transient exposure to gasoline vapors

    Modrzynski, J. J., Christensen, Jan H., Mayer, P. & Brandt, Kristian Koefoed, 2016, In: Environmental Pollution. 216, p. 826-835 10 p.

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

  49. Published

    Linking bioavailability and toxicity changes of complex chemicals mixture to support decision making for remediation endpoint of contaminated soils

    Cipullo, S., Negrin, I., Claveau, L., Snapir, B., Tardif, S., Pulleyblank, C., Prpich, G., Campo, P. & Coulon, F., 10 Feb 2019, In: Science of the Total Environment. 650, Part 2, p. 2150-2163 14 p.

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

  50. Published

    Lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms

    Bonnichsen, L., Svenningsen, N. B., Rybtke, Morten Levin, de Bruijn, I., Raaijmakers, J. M., Tolker-Nielsen, Tim & Nybroe, O., 2015, In: Microbiology. 161, 12, p. 2289-2297 9 p.

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

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