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Eichfeld R, Mahdi LK, De Quattro C, Armbruster L, Endeshaw AB, Miyauchi S, Hellmann MJ, Cord-Landwehr S, Grigoriev I, Peterson D, Singan V, Lail K, Savage E, Ng V, Langen G, Moerschbacher BM, Zuccaro A (2023) Time-resolved transcriptomics reveal a mechanism of host niche defense: beneficial root endophytes deploy a host-protective antimicrobial GH18-CBM5 chitinase. BioRxiv doi: 10.1101/2023.12.29.572992

Hofmann D, Thiele B, Siebers M, Rahmati M, Schütz V, Jeong S, Cui J, Bigler L, Held F, Wu B, Babic N, Kovacic F, Hamacher J, Hölzl G, Dörmann P, Schulz M (2023) Implications of Below-Ground Allelopathic Interactions of Camelina sativa and Microorganisms for Phosphate Availability and Habitat Maintenance. Plants doi 10.3390/plants12152815

Ranner JL, Schalk S, Martyniak C, Parniske M, Gutjahr C, Stark TD, Dawid C (2023) Primary and Secondary Metabolites in Lotus japonicus. Journal of Agricultural and Food Chemistry doi: 10.1021/acs.jafc.3c02709

Pfeilmeier S, Werz A, Ote M, Bortfeld-Miller M, Kirner P, Keppler A, Hemmerle L, Gäbelein CG, Pestalozzi CM, Vorholt JA (2023) Dysbiosis of a leaf microbiome is caused by enzyme secretion of opportunistic Xanthomonas strain. BioRxiv doi: 10.1101/2023.05.09.539948

Ordon J, Thouin J, Nakano RT, Ma KW, Zhang P, Huettel B, Garrido-Oter R, Schulze-Lefert P (2023) Simultaneous tracking of near-isogenic bacterial strains in synthetic Arabidopsis microbiota by chromosomally-integrated barcodes. BioRxiv doi: 10.1101/2023.04.20.537712

Koprivova A, Schwier M, Volz V, Kopriva S (2023) Shoot-root interaction in control of camalexin exudation in Arabidopsis. Journal of Experimental Botany doi: 10.1093/jxb/erad031


Lundberg DS, de Pedro Jové R, Ayutthaya PPN, Karasov TL, Shalev O, Poersch K, Ding W, Bollmann-Giolai A, Bezrukov I, Weigel D (2022) Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere. Proceedings of the National Academy of Sciences doi: 10.1073/pnas.2211881119

Eccleston L, Brambilla A, Vlot AC (2022) New molecules in plant defence against pathogens. Essays in Biochemistry doi: 10.1042/EBC20210076

Girel S, Schütz V, Bigler L, Dörmann P, Schulz M (2022) Bioactive Nitrosylated and Nitrated N-(2-hydroxyphenyl)acetamides and Derived Oligomers: An Alternative Pathway to 2-Amidophenol-Derived Phytotoxic Metabolites. Molecules doi: 10.3390/molecules27154786

Chandrasekar B, Wanke A, Wawra S, Saake P, Mahdi L, Charura N, Neidert M, Poschmann G, Malisic M, Thiele M, Stühler K, Dama M, Pauly M, Zuccaro A (2022) Fungi hijack a ubiquitous plant apoplastic endoglucanase to release a ROS scavenging β-glucan decasaccharide to subvert immune responses. The Plant Cell doi: 10.1093/plcell/koac114

Koprivova A, Kopriva S (2022) Plant secondary metabolites altering root microbiome composition and function. Current Opinion in Plant Biology doi: 10.1016/j.pbi.2022.102227

Türksoy GM, Carron R, Koprivova A, Kopriva S, Wippel K, Andersen TG (2022) Modulation of Arabidopsis growth by volatile organic compounds from a root-derived bacterial community. BioRxiv doi: 10.1101/2022.04.12.488003

Shalev O, Karasov TL, Lundberg DS, Ashkenazy H, Ayutthaya PPN, Weigel D (2022) Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant. Nature Ecology & Evolution doi: 10.1038/s41559-022-01673-7

Ma KW, Ordon J, Schulze-Lefert P (2022) Gnotobiotic Plant Systems for Reconstitution and Functional Studies of the Root Microbiota. Current Protocols doi: 10.1002/cpz1.362

Vanacore A, Vitiello G, Wanke A, Cavasso D, Clifton L, Mahdi L, Campanero-Rhodes MA, Solís D, Wuhrer M, Nicolardi S, Molinaro A, Marchetti R, Zuccaro A, Paduano L, Silipo A (2022) Lipopolysaccharide O-antigen molecular and supramolecular modifications of plant root microbiota are pivotal for host recognition. Carbodhydrate Polymers doi: 10.1016/j.carbpol.2021.118839

Crosbie DB, Mahmoudi M, Radl V, Brachmann A, Schloter M, Kemen E, Marín M (2022) Microbiome profiling reveals that Pseudomonas antagonises parasitic nodule colonisation of cheater rhizobia in Lotus. New Phytologist doi: 10.1111/nph.17988

Laschke L, Schütz V, Schackow O, Sicker D, Hennig L, Hofmann D, Dörmann P, Schulz M (2022) Survival of Plants during Short-Term BOA-OH Exposure: ROS Related Gene Expression and Detoxification Reactions are Accompanied with Fast Membrane Lipid Repair in Root Tips. Journal of Chemical Ecology doi: 10.1007/s10886-021-01337-z


Siani R, Stabl G, Gutjahr C, Schloter M, Radl V (2021) Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations. Microbial Genomics doi: 10.1099/mgen.0.000666

Jung JH, Reis F, Richards CL, Bossdorf O (2021) Understanding plant microbiomes requires a genotype x environment framework. American Journal of Botany doi: 10.1002/ajb2.1742

Wippel K, Tao K, Niu Y, Zgadzaj R, Kiel N, Guan R, Dahms E, Zhang P, Jensen DB, Logemann E, Radutoiu S, Schulze-Lefert P, Garrido-Oter R (2021) Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. Nature Microbiology doi: 10.1038/s41564-021-00941-9

Pfeilmeier S, Petti GC, Bortfeld-Miller M, Daniel B, Field CM, Sunagawa S, Vorholt JA (2021) The plant NADPH oxidase RBOHD is required for microbiota homeostasis in leaves. Nature Microbiology doi: 10.1038/s41564-021-00929-5

Maier BA, Kiefer P, Field CF, Hemmerle L, Bortfeld-Miller M, Emmenegger B, Schäfer M, Pfeilmeier S, Sunagawa S, Vogel CM, Vorholt JA (2021) A general non-self-response as part of plant immunity. Nature Plants doi: 10.1038/s41477-021-00913-1

Liu Y, Balcke GU, Porzel A, Mahdi LK, Scherr-Henning A, Bathe U, Zuccaro A, Tissier A (2021) A barley gene cluster for the biosynthesis of diterpenoid phytoalexins. BioRxiv doi: 10.1101/2021.05.21.445084

Hucklenbroich J, Gigolashvili T, Koprivova A, Spohr P, Nezamivand Chegini M, Klau GW, Kopriva S, Nakano RT (2021) Rhizobiales commensal bacteria promote Arabidopsis thaliana root growth via host sulfated peptide pathway. BioRxiv doi: 10.1101/2021.05.25.444716

Shimasaki T, Masuda S, Garrido-Oter R, Kawasaki T, Aoki Y, Shibata A, Suda W, Shirasu K, Yazaki K, Nakano RT, Sugiyama A (2021) Tobacco Root Endophytic Arthrobacter Harbors Genomic Features Enabling the Catabolism of Host-Specific Plant Specialized Metabolites. mBio in press

Dunken N, Mahdi L, Häusler ER, Zuccaro A (2021) Monitoring Cell Death via Ion leakage and PAM Fluorometry. Chapter in MiMB (Methods in Molecular Biology), Humana Press, Springer Nature in press

Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S (2021) Genetic determinants of endophytism in the Arabidopsis root mycobiome. BioRxiv doi: 10.1101/2021.04.28.441743

Shalev O, Karasov T, Lundberg DS, Ashkenazy H, Weigel D (2021) Protective host-dependent antagonism among Pseudomonas in the Arabidopsis phyllosphere. BioRxiv doi: 10.1101/2021.04.08.438928

Lundberg DS, de Pedro Jové R, Pramoj Na Ayutthaya P, Karasov TL, Shalev O, Poersch K, Ding W, Bollmann-Giolai A, Bezrukov I, Weigel D (2021) Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere. BioRxiv doi: 10.1101/2021.04.06.438366

Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E (2021) Shaping the leaf microbiota: plant–microbe–microbe interactions. Journal of Experimental Botany Vol: 72, Issue 1 doi: 10.1093/jxb/eraa417

Mahdi LK, Miyauchi S, Uhlmann C, Garrido-Oter R, Langen G, Wawra S, Niu Y, Robertson-Albertyn S, Bulgarelli D, Parker JE, Zuccaro A (2021) The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. ISME Journal doi:10.1038/s41396-021-01138-y

Zhang P, Spaepen S, Bai Y, Hacquard S, Garrido-Oter R (2021) Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities. ISME Communications doi: 10.1038/s43705-021-00077-1

Sommer A, Wenig M, Knappe C, Kublik S, Fösel B, Schloter M, Vlot AC (2021) Induced systemic resistance impacts the phyllosphere microbiome through plant-microbe-microbe interactions. BioRxiv doi: 10.1101/2021.01.13.426583

Schandry N, Jandrasits K, Garrido-Oter R, Becker C (2021) Plant-derived benzoxazinoids act as antibiotics and shape bacterial communities. BioRxiv doi: 10.1101/2021.01.12.425818

Vlot AC, Sales JH, Lenk M, Bauer K, Brambilla A, Sommer A, Chen Y, Wenig M, Nayem S (2021) Systemic propagation of immunity in plants. New Phytologist doi: 10.1111/nph.16953

Hou S, Thiergart T, Vannier N, Mesny F, Ziegler J, Pickel B, Hacquard S (2021) A microbiota-root-shoot circuit favours Arabidopsis growth over defence under suboptimal light. Nature Plants in press

Schütz V, Frindte K, Cui J, Zhang P, Hacquard S, Schulze-Lefert P, Knief C, Schulz M, Dörmann P (2021) Differential Impact of Plant Secondary Metabolites on the Soil Microbiota. Frontiers in Microbiology doi: 10.3389/fmicb.2021.666010

Yu P, He X, Baer M, Beirinckx S, Tian T, Moya YAT, Zhang X, Deichmann M, Frey FP, Bresgen V, Li C, Razavi BS, Schaaf G, von Wirén N, Su Z, Bucher M, Tsuda K, Goormachtig S, Chen X, Hochholdinger F (2021) Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation. Nature Plants doi: 10.1038/s41477-021-00897-y

Ma KW, Niu Y, Yong J, Ordon J, Copeland C, Emonet A, Geldner N, Guan R, Stolze SC, Nakagami H, Garrido-Oter R, Schulze-Lefert P (2021) Coordination of microbe-host homeostasis by crosstalk with plant innate immunity. Nature Plants doi: 10.1038/s41477-021-00920-2

Kremer JM, Sohrabi R, Paasch BC, Rhodes D, Thireault C, Schulze-Lefert P, Tiedje JM, He SY (2021) Peat-based gnotobiotic plant growth systems for Arabidopsis microbiome research. Nature Protocols doi: 10.1038/s41596-021-00504-6

Winkelmüller TM, Entila R, Anver S, Piasecka A, Song B, Dahms E, Sakakibara H, Gan X, Kulak K, Sawikowska A, Krajewski P, Tsiantis M, Garrido-Oter R, Fukushima K, Schulze-Lefert P, Laurent S, Bednarek P, Tsuda K (2021) Gene expression evolution in pattern-triggered immunity within Arabidopsis thaliana and across Brassicaceae species. The Plant Cell doi: 10.1093/plcell/koab073

Eitzen K, Sengupta P, Kroll S, Kemen E, Doehlemann G (2021) A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme. eLife 10:e65306 

Zhang J, Liu YX, Guo X, QinY, Garrido-Oter R, Schulze-Lefert P, Bai Y (2021) High-throughput cultivation and identification of bacteria from the plant root microbiota. Nature Protocols doi: 10.1038/s41596-020-00444-7

Jacoby RP, Koprivova A, Kopriva S (2021) Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. Journal of Experimental Botany doi: 101093/jxb/eraa424

Chen L, Schwier M, Krumbach J, Kopriva S, Jacoby RP (2021) Metabolomics in plant-microbe interactions in the roots. Advances in Botanical Research Vol. 98: Plant Metabolomics. Elsevier in press


Lundberg DS, Na Ayutthaya, PP, Strauß A, Shirsekar G, Lo WS, Lahaye T, Weigel D (2020) Host-associated microbe PCR (hamPCR): accessing new biology through convenient measurement of both microbial load and community composition. BioRxiv doi: 10.1101/2020.05.19.103937

Nobori T*, Wang Y*, Wu J, Stolze SC, Tsuda Y, Finkemeier I, Nakagami H, Tsuda K (2020) Multidimensional gene regulatory landscape of a bacterial pathogen in plants. Nature Plants doi: 10.1038/s41477-020-0746-8 *indicates joint first authors

Regalado J​*, Lundberg DS​*, Deusch O, Kersten S, Karasov TL​, Poersch K, Shirsekar G, Weigel D (2020) Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves. ISME Journal doi: 10.1038/s41396-020-0665-8 *indicates joint first authors

Karasov TL, Neumann M, Duque-Jaramillo A, Kersten S, Bezrukov I, Schröppel B, Symeonidi E,  Lundberg DS, Regalado J, Shirsekar G, Bergelson J, Weigel D (2020) The relationship between microbial population size and disease in the Arabidopsis thaliana phyllosphere. bioRxiv doi: 10.1101/828814v2

Jacoby RP, Chen L, Schwier M, Koprivova A, Kopriva S (2020) Recent advances in the role of plant metabolites in shaping the root microbiome. F1000Res. 2020; 9: F1000 Faculty Rev-151

Koprivova A, Schmalenberger A, Kopriva S (2020) Sulfatase Assay to Determine Influence of Plants on Microbial Activitiy in Soil. Bio-protocol doi: 10.21769/BioProtoc.3490

Thiergart T, Durán P, Ellis T, Vannier N, Garrido-Oter R, Roux F, Alonso-Blanco C, Ågren J, Schulze-Lefert P, Hacquard S (2020) Root microbiota assembly and adaptive differentiation among European Arabidopsis populations. Nature Ecology & Evolution 4:122-131, doi:10.1038/s41559-019-1063-3

Kabdullayeva T, Crosbie DB, Marín M (2020) Mesorhizobium norvegicum sp. nov., a rhizobium isolated from a Lotus corniculatus root nodule in Norway. International Journal of Systematic and Evolutionary Microbiology doi: 10.1099/ijsem.0.003769. PMID: 31626582.


Rodriguez PA, Rothballer M, Chowdhury SP, Nussbaumer T, Gutjahr C, Falter-Braun P (2019) Systems Biology of Plant-Microbiome Interactions. Molecular Plant doi: 10.1016/j.molp.2019.05.006

Thiergart T, Zgadzaj R, Bozsóki Z, Garrido-Oter R, Radutoiu S, Schulze-Lefert P (2019) Lotus japonicus Symbiosis Genes Impact Microbial Interactions between Symbionts and Multikingdom Commensal Communities. mBio doi: 10.1128/mBio.01833-19

Koprivova A, Schuck S, Jacoby R, Klinkhammer I, Welter B, Leson L, Martyn A, Nauen J, Grabenhorst N, Mandelkow JF, Zuccaro A, Zeier J, Kopriva S (2019) Root-specific camalexin biosynthesis controls the plant growth promoting effects of multiple bacterial strains. PNAS doi: 10.1073/pnas.1818604116

Sarkar D, Rovenich H, Jeena G, Nizam S, Tissier A, Balcke GU, Mahdi L, Bonkowski M, Langen G, Zuccaro A (2019) The inconspicuous gatekeeper: endophytic Serendipita vermifera acts as extended plant protection barrier in the rhizosphere. New Phytologist doi: 10.1111/nph.15904

Nobori T, Tsuda K (2019) The plant immune system in heterogeneous environments. Current Opinion in Plant Biology doi: 10.1016/j.pbi.2019.02.003