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Cai et al. 2021 The pleiotropic functions of intracellular hydrophobins in aerial hyphae and fungal spores

HFB4::mRFP on the surface of Trichoderma guizhouense NJAU 4742

Cai F, Zhao Z, Gao R, Chen P, Ding M, Jiang S, et al. (2021) The pleiotropic functions of intracellular hydrophobins in aerial hyphae and fungal spores. PLoS Genet 17(11): e1009924. https://doi.org/10.1371/journal.pgen.1009924

Cai-et-al-PLoS-Genetics-2021Download
Animated 3D reconstructions of extracellular HFB-enriched matrices coating sporulating Trichoderma colonies.

Higher fungi can rapidly produce large numbers of spores suitable for aerial dispersal. The efficiency of the dispersal and spore resilience to abiotic stresses correlate with their hydrophobicity provided by the unique amphiphilic and superior surface-active proteins – hydrophobins (HFBs) – that self-assemble at hydrophobic/hydrophilic interfaces and thus modulate surface properties. Using the HFB-enriched mold Trichoderma (Hypocreales, Ascomycota) and the HFB-free yeast Pichia pastoris (Saccharomycetales, Ascomycota), we revealed that the rapid release of HFBs by aerial hyphae shortly prior to conidiation is associated with their intracellular accumulation in vacuoles and/or lipid-enriched organelles. The occasional internalization of the latter organelles in vacuoles can provide the hydrophobic/hydrophilic interface for the assembly of HFB layers and thus result in the formation of HFB-enriched vesicles and vacuolar multicisternal structures (VMSs) putatively lined up by HFBs. These HFB-enriched vesicles and VMSs can become fused in large tonoplast-like organelles or move to the periplasm for secretion. The tonoplast-like structures can contribute to the maintenance of turgor pressure in aerial hyphae supporting the erection of sporogenic structures (e.g., conidiophores) and provide intracellular force to squeeze out HFB-enriched vesicles and VMSs from the periplasm through the cell wall. We also show that the secretion of HFBs occurs prior to the conidiation and reveal that the even spore coating of HFBs deposited in the extracellular matrix requires microscopic water droplets that can be either guttated by the hyphae or obtained from the environment. Furthermore, we demonstrate that at least one HFB, HFB4 in T. guizhouense, is produced and secreted by wetted spores. We show that this protein possibly controls spore dormancy and contributes to the water sensing mechanism required for the detection of germination conditions. Thus, intracellular HFBs have a range of pleiotropic functions in aerial hyphae and spores and are essential for fungal development and fitness.

Cai et al., 2021 PLoS Genetics
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Publications of Komal Chenthamara

Peer-reviewed scientific articles

CAI Feng, GAO Renwai, ZHAO Zheng, DING Mingyue, JIANG Siqi, YAGTU Civan, ZHU Hong, ZHANG Jian, EBNER Thomas, MAYRHOFER-REINHARTSHUBER Michael, KAINZ Philipp, CHENTHAMARA Komal, AKCAPINAR Gunseli Bayram, SHEN Qirong, DRUZHININA Irina. Evolutionary compromises in fungal fitness: hydrophobins can hinder the adverse dispersal of conidiospores and challenge their survival. ISME Journal 14(10):1-15, July 2020

GAO Renwai, DING Mingyue, JIANG Siqi, ZHAO Zheng, CHENTHAMARA Komal, SHEN Qirong, CAI Feng, DRUZHININA Irina. The evolutionary and functional paradox of cerato- platanins in the mycoparasitic fungus Trichoderma: high diversity, stabilizing selection, and a minor role in biotic interactions. Applied Environmental Microbiology, April 2020

PÉREZ-LLANO Yordanis, RODRÍGUEZ-PUPO Eya Caridad, DRUZHININA Irina, CHENTHAMARA Komal, CAI Feng, GUNDE-CIMERMAN Nina, ZALAR Polona, GOSTINČAR Cene, KOSTANJŠEK Rok, FOLCH-MALLOL Jorge Luis, BATISTA-GARCÍA Ramón Alberto and SÁNCHEZ-CARBENTE María del Rayo. Stress Reshapes the Physiological Response of Halophile Fungi to Salinity. Cells, February 2020

HATVANI Lóránt, HOMA Mónika, CHENTHAMARA Komal, KOCSUBÉ Sándor, ATANASOVA Lea, MLINARIC-MISSONI Emilija, MANIKANDAN Palanisamy, REVATHI Rajaraman, DÓCZI Ilona, IVÁNYI Béla, BOGÁTS Gábor, NARENDRAN Venkatapathy, BÜCHNER Rita, VÁGVÖLGYI Csaba, DRUZHININA Irina, KREDICS László. Agricultural systems as potential sources of emerging human mycoses caused by Trichoderma. FEMS Microbiology letters, December 2019

KUBICEK Christian§, STEINDORFF Andrei§, CHENTHAMARA Komal, MANGANIELLO Gelsomina, BERNARD Henrissat, ZHANG Jian, CAI Feng, KOPCHINSKIY Alexey, KUBICEK Eva M, KUO Alan, BARONCELLI Riccardo, SARROCCO Sabrina, NORONHA Eliane Ferreira, VANNACCI Giovanni, SHEN Qirong, GRIGORIEV Igor and DRUZHININA Irina. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics, June 2019

ZHANG Jian, MIAO Youzhi, RAHIMI Mohammad Javad, ZHU Hong, STEINDORFF Andrei, SCHIESSLER Sabine, CAI Feng, PANG Guan, CHENTHAMARA Komal, XU Yu, KUBICEK Christian, SHEN Qirong, and DRUZHININA Irina. Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi. Environmental Microbiology, February 2019

DRUZHININA Irina, CHENTHAMARA Komal, ZHANG Jian, ATANASOVA Lea, YANG Dongqing, MIAO Youzhi, RAHIMI Mohammad, GRUJIC Marica, CAI Feng, POURMEHDI Shadi, ABU SALIM Kamariah, PRETZER Carina, KOPCHINSKIY Alexey, HENRISSAT Bernard, KUO Alan, HUNDLEY Hope, WANG Mei, AERTS Andrea, SALAMOV Asaf, LIPZEN Anna, LABUTTI Kurt, BARRY Kerrie, GRIGORIEV Igor, SHEN Qirong, and KUBICEK Christian. Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLOS Genetics, April 2018

QIN Yuan, PAN Xueyu, KUBICEK Christian, DRUZHININA Irina, CHENTHAMARA Komal, LABBÉ Jessy and YUAN Zhilin. Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth. Frontiers in Microbiology, February 2017

PRZYLUCKA Agnes, AKCAPINAR Gunseli Bayram, CHENTHAMARA Komal, CAI Feng, GRUJIC Marica, KARPENKO Juriy, LIVOI Miriam, SHEN Qirong, KUBICEK Christian, DRUZHININA Irina. HFB7 – A Novel Orphan Hydrophobin of the Harzianum and Virens Clades of Trichoderma, Is Involved in Response to Biotic and Abiotic Stresses. Fungal Genetics and Biology, May 2017

DE MAN Tom, STAJICH Jason, KUBICEK Christian, TEILING Clotilde, CHENTHAMARA Komal, ATANASOVA Lea, DRUZHININA Irina, LEVENKOVA Natasha, BIRNBAUM Stephanie, BARRIBEAU Seth, BOZICK Brooke, SUEN Garret, CURRIE Cameron, and GERARDO Nicole. Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. PNAS, Proceedings of the National Academy of Sciences, March 2016

YANG Dongqing, POMRANING Kyle, KOPCHINSKIY Alexey, AGHCHEH Razieh Karimi, ATANASOVA Lea, CHENTHAMARA Komal, BAKER Scott E., ZHANG Ruifu, SHEN Qirong, FREITAG Michael, KUBICEK Christian, and DRUZHININA Irina. Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei. American Society for Microbiology – Genome Announcements August 2015

Book chapters

CHENTHAMARA Komal, DRUZHININA Irina, RAHIMI Mohammad, GRUJIC Marica, and CAI Feng. “Ecological genomics and evolution of Trichoderma reesei”. Springer – Trichoderma reesei ‐ Methods and Protocols, January 2021

RAHIMI Mohammad, CAI Feng, GRUJIC Marica, CHENTHAMARA Komal, and DRUZHININA Irina. Molecular Identification of Trichoderma reesei”. Springer – Trichoderma reesei ‐ Methods and Protocols, January 2021

CHENTHAMARA Komal, DRUZHININA Irina. “Ecological Genomics of Mycotrophic Fungi”. Springer – THE MYCOTA, Environmental and Microbial Relationships, Volume IV, Third Edition, March 2016

List of first author conference papers (Scientific posters)

CHENTHAMARA Komal, STEINDORFF Andrei, GOJIC Vladimir, SHELEST Ekaterina, GRIGORIEV Igor, KUBICEK Christian, DRUZHININA Irina. “The comparative genomics of the most common Trichoderma species reveals the unique pattern of the ankyrin domain-containing proteins in orphomes of individual Trichoderma species”; Poster: Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, April 2019

CHENTHAMARA Komal, CAI Feng, VON ROTZ Sebastian, CERVENKA Isabella, SHEN Qirong, DRUZHININA Irina. “The enrichment in hydrophobin-encoding genes constitutes the main genomic hallmark of Trichoderma: the pattern search revealed a plethora of unknown genes absent in other hypocrealean fungi”; Poster: Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, April 2019

CHENTHAMARA Komal, GOJIC Vladimir, BAJTELA Robert, DRUZHININA Irina. “Decoding the expanded Ankyrin-Repeat gene family in Trichoderma”; Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, March 2018

CHENTHAMARA Komal, CAI Feng, PRZYLUCKA Agnieszka, SHEN Qirong, BAYRAM AKCAPINAR Günseli, DRUZHININA Irina.: “The origin and architecture of Trichoderma hydrophobome”; Poster: Joint Genome Institute User Meeting, Walnut Creek, San Francisco, USA, March 22, 2017, in “Abstract Book”, (2016), S.24

CHENTHAMARA Komal, CAI Feng, PRZYLUCKA Agnieszka, SHEN Qirong, BAYRAM AKCAPINAR Günseli, DRUZHININA Irina. “The origin and architecture of Trichoderma hydrophobome”; Short-talk and poster: Vienna young Scientists Symposium, TU WIEN, June 6, 2017; in “Abstract Book”, (2016), S90-91

DRUZHININA Irina, ATANASOVA Lea, CHENTHAMARA Komal, GRUJIC Marica, HENRISSAT Bernard, ZHANG Jian, SHEN Qirong, GRIGORIEV Igor, KUBICEK Christian. Horizontal gene transfers drove the mycoparasite Trichoderma to adapt to saprotrophy and cellulase production. Talk: 13th European Conference on Fungal Genetics, 3-6, April 2016, Paris, France; in “Abstract Book”, (2016), S.70.

CHENTHAMARA Komal, ATANASOVA Lea, YANG Dongqing, ZHANG Jian, KOPCHINSKIY Alexey, GRIGORIEV Igor, KUBICEK Christian, SHEN Qirong, DRUZHININA Irina. Phylogenomics of Trichoderma. Poster: ECFG12- 12th European conference on fungal genetics, Seville, Spain; 23.3.-27.3. 2014. S: 184

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Dipl. Ing. Dr. Tech. Komal Chenthamara

Email: komal.chenthamara@gmail.com

Research Gate Profile

Linkedin Profile

List of Publications

Professional Experience

2020 – currentExternal lab member at FungiG – research group of Irina S. Druzhinina and Feng Cai in China
2019 – 2020In statutory maternal protection and then maternity leave
2015 – 2018Project Assistant (FWF) (PhD student)
 E166-05-2 – Research Group for Microbiology and Applied Genomics, Research Area Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Gumpendorfer Str. 1a, 1060 Vienna, Austria

Education

2018Doctoral programme, TU Wien (mit auszeichnung bestanden), Ph.D. Thesis (November 16, 2018): “Using comparative genomics to link phenotypes to genotypes of the mycotrophic fungus Trichoderma“
2015Masters in Biotechnology and Bioanalytics, TU Wien, Vienna, Austria. Master Thesis: “Evolution of mycoparasitism in Hypocreales through phylogenomic approach”
2011 – 2012B2 level -German, Österreichische Orient Gesellschaft, Vienna, Austria
2006 – 2010Bachelor of Technology (B-Tech) in Biotechnology, SRM University, Chennai, Tamil Nadu, India

Special Trainings

2018Trainee at the Bioinformatics unit (BIU), German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
2018Fungal Genomics Workshop, The DOE JGI Genomics of Energy and Environment Meeting, San Francisco, California, USA
2017Fungal Genomics Workshop, The DOE JGI Genomics of Energy and Environment Meeting, Walnut Creek, California, USA
KBase Workshop, The DOE JGI Genomics of Energy and Environment Meeting, Walnut Creek, California, USA
2013Intern in Research Group for Microbiology and Applied Genomics, TU Wien, TU Wien, Vienna, Austria
2013Training in Communication, BEST, Board of European Students of Technology, Vienna, Austria
2013Training in Time Management, BEST, Board of European Students of Technology, Vienna, Austria
2012Intern in Research Group for Bioprocess Technology, TU Wien, Vienna, Austria
2009IELTS (International English Language Testing System), Chennai, Tamil Nadu, India

Prizes and Awards

2017TU Wien Christiana HÖRBIGER Preis – Preis zur Förderung der internationalen Mobilität von Nachwuchswissenschaftler_innen
2016TU Wien Short-term grants for participation in conferences for PhD-students

Skills

Microbiological techniques and microscopy: axenic cultures, microbial diagnostics by DNA barcoding, fungal morphology, microbial cultivations, and phenotype microarrays. Basic molecular biological techniques for fungi and bacteria.

Molecular evolutionary analyses such as multiloci phylogenetics, phylogenomics, lateral gene transfer tests (T-Rex, Notung), natural selection pressure analyses, DNA barcoding, and protein modeling.

Basic skills in genomics (sequence similarity search, manual gene annotation), basic skills in the analyses of NGS data

Descriptive and multivariate exploratory statistical techniques(Statistica, Tableau, UpSet)

Bitmap and vector graphic skills for illustrations (CorelDraw, Affinity Designer)

Experience with citation tools like Zotero and EndNote

Experience with WorkFlow softwares like Geneious, CLC Bio

Experience with GitHub

Experience with Microsoft 365 and Acrobat

Curator of TUCIM (TU Wien Collection of Industrial Microorganisms)- A collection of over 7350 species and their respective DNAs.

Responsible for the introduction of lab techniques to new group members

Responsible for safety-training of all group members

Organized regular group meetings

Member of Journal club, – an initiative of young PostDoc researchers and Ph.D. students. A gathering dedicated to the discussion of the most paradigm-changing scientific discoveries in biotechnology and applied microbiology

Teaching Experience

2016 – 2018Lecturer for the course 166.648 “Biology and genetics of industrial microorganisms”, master Program Technical Chemistry (Biotechnology and Bioanalytics), TU Wien 
2016 – 2018Teaching Assistant for the mandatory course 166.231 “Applied Bioinformatics Lab”, master Program Technical Chemistry Biotechnology and Bioanalytics, TU Wien
2015 – 2018Tutor for mandatory laboratory course 166.222 “Biochemistry and Biotechnology”, bachelor program Technical Chemistry, TU Wien
2014Assistant for the mandatory laboratory course 166.193 “Microbiology”, master Program Technical Chemistry Biotechnology and Bioanalytics, TU Wien

Language Skills

English                                                         Fluent

German                                                       Basic

Hindi and Malayalam                           Mother-tongues

Interests / Hobbies

Reading comics

DIY skin and hair care

Baking

List of Publications

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Rigorosum of Feng Cai in the TU Wien

The public oral online examination (Rigorosum*) of

Feng Cai for the Ph. D. degree of the Vienna University of Technology (TU Wien)

is scheduled for

February 24, 11:00 a.m. (Vienna) or 06:00 p.m. (Nanjing).

Rigorosum Committee:

Prof. Dr. Robert L. Mach, TU Wien, Austria, the Head

Prof. Dr. Irina S. Druzhinina, TU Wien, Austria and NJAU, China, the Examiner, and Ph.D. Advisor

Prof. Dr. Oded Yarden, University of Jerusalem, Israel, the Examiner

Referees:

Prof. Dr. Oded Yarden, University of Jerusalem, Israel

Prof. Dr. Christian P. Kubicek, TU Wien, Austria

The examination will consist of the presentation (25 min) followed by questions (5 min) and the oral examination by the Committee members (30 min).

The electronic version of the cumulative Ph. D. Thesis “RESOLVING THE CONUNDRUM OF TRICHODERMA TAXONOMY: HOW ECOLOGICAL GENETICS COUPLED WITH EVOLUTIONARY ANALYSIS ENHANCES THE POLYPHASIC SPECIES CONCEPT IN FUNGI” can be viewed here

Cai-Feng-TU-Wien-PhD- thesis-electronicDownload

* Rigorosum (rigorous examination) is the final examination for obtaining a doctoral degree. In addition to the topic of the dissertation, other subjects are usually examined.

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Curriculum Vitae

Irina S. Druzhinina, Ph.D.

Irina-S-Druzhinina-CV-2021Download

PROFESSIONAL ADDRESS

Nanjing Agricultural University, College of Resources and Environmental Sciences.

FungiG Fungal Genomics Laboratory www.FungiG.org

Weigang NO. 1, Nanjing, P.R. China, 210095 Tel +86 15 996344211 Email: Irina.druzhinina@njau.edu.cn

CURRENT POSITIONS

Professor (Full), Research Group Leader

Editor, Applied and Environmental Microbiology, ASM

QUALIFICATIONS

  • 1981 – 1991 Gymnasium with emphasis on Mathematics & Physics, school-leaving certificate with honor, Moscow, Russia
  • 1991 – 1996 Lomonosov’s Moscow State University, Faculty of Biology, Dept. of Mycology & Algology, Russia. Diploma with honor degree: Botany and Ecology, Mycology and Algology
  • 1996 – 1997 Post-graduate course (Philosophy, Mycology, Genetics of Populations) at the Lomonosov’s Moscow University, Russia
  • 1998 Ratification of Master’s degree in University of Vienna, Austria
  • 1998 – 2001 PhD study in the Institute of Botany, University of Vienna, Austria, Doctor of natural sciences, specialization on Botany, University of Vienna, Austria
  • 2001 PhD degree (Doctor of natural science) University of Vienna, Austria
  • 2011 Habilitation on Microbiology (“Privatdozentin”) TU Wien, Vienna, Austria

PROFESSIONAL LIFE

  • 2002 Postdoc Researcher in the Institute of Risk Research, University of Vienna, Vienna, Austria
  • 2002 – 2003 Postdoc Researcher in the Institute of Chemical Engineering, TU Wien, Vienna, Austria
  • 2002 – 2007 Scientific secretary of the International Subcommission on Trichoderma and Hypocrea of IUMS, International Commission on Taxonomy of Fungi (ICTF)
  • 2003 – 2014 University assistant in the Institute of Chemical Engineering, TU Wien, Vienna, Austria
  • since 2003 Leader of the Project Group Fungal Diversity and Evolution
  • since 2002 Responsible curator of the TU Collection of Industrial Microorganisms (TUCIM), TU Wien
  • 2003 Training on Phenotype Microarrays, ECORC, Ottawa, Canada
  • 2004 Training on Molecular Evolution, Woods Hole, USA
  • since 2007 Chair of the International Subcommission on Trichoderma and Hypocrea, www.ISTH.info
  • 2008 – Maternity leave, 10 months
  • 2009 – 2010 Principal investigator for industrial project “Pest management”, BASF, Germany
  • 2008 – 2009 Principal investigator for industrial project “BioDiesel production from microalgae”, TUMA pumpen, Austria
  • 2010 – 2015 Project manager in the Austrian Centre of Industrial Biotechnology (ACIB), strategic project “Targeting Enzymes to Polymers”
  • May 2011 Habilitation on Microbiology (“Privatdozentin”)
  • 2011 – 2018 Leader of the Microbiology Research Group (FG), Institute of Chemical Engineering (ICEBE), TU Wien, Austria
  • 2011 – 2013 Lecturer for TVFA (TU Wien) Seminar SCHIMMELPILZE IN GEBÄUDEN
  • 2012 – 2018 Key Researcher in the Austrian Centre of Industrial Biotechnology (ACIB)
  • 2013 – 2014 Project Group Leader in the Austrian Centre of Industrial Biotechnology (ACIB)
  • 2013 – 2016 Acting head (Bereichsleiterin) of the Research Division Biotechnology and Microbiology, ICEBE, TU Wien, Austria
  • 2014 – 2016 Assistant Professor, ICEBE, TU Wien, Austria
  • 2015 “Leadership in science”, hfp consulting, UK
  • 2016 – 2018 Associate Professor (Laufbahnstelle), ICEBE, TU Wien, Austria
  • 2017 – 2018 Guest Professor FH Campus Wien
  • 2018 – Honored guest Professor, Nanjing Agricultural University, Nanjing, China
  • 2018 – 2023 – Editor in the Applied and Environmental Microbiology, ASM
  • Since 2019 – Professor, Research group leader, Nanjing Agricultural University, Nanjing, China

RESEARCH KEYWORDS

Fungal genomics, fungal communities, genetics, molecular evolution and phylogeny, horizontal gene transfer in fungi, fungal diversity, metagenomics, surface-active proteins, hydrophobins, Trichoderma, mycoparasitism, microbial diversity, DNA BarCoding, phenotype profiles, microbial ecophysiology, heterologous protein production, proteomics, microbial ecology, fungal – bacterial interactions, biological control of fungal pests, plant growth promotion, tropical ecology, insect microbiomes, biological degradation of synthetic polymers

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Book chapters by Irina S. Druzhinina

Chen, P., Pang, G., Cai, F., Druzhinina I.S., Genetic improvement of Trichoderma strains for biotechnology. De Vries, R., Mäkelä, M.R., eds. Encyclopedia of Mycology, Elsevier, ISBN: 9780128199909 (in press)

Chenthamara, K., Rahimi, M., Grujic, M., Druzhinina, I. S. and Cai, F. Trichoderma reesei – Methods and Protocols: Ecological genomics and evolution of Trichoderma reesei, Mach-Aigner, A., and Martzy, R., eds. Methods in Molecular Biology, Springer Nature (in press)

Rahimi, M., Cai, F., Grujic, M., Chenthamara, K., and Druzhinina, I. S. Trichoderma reesei – Methods and Protocols: Molecular identification of Trichoderma reesei. Mach-Aigner, A. and Martzy, R., eds. Methods in Molecular Biology, Springer Nature (in press)

Cai, F., Kubicek, C. P., and Druzhinina, I. S. Biofuels and Biodiesel: Genetic transformation of Trichoderma spp. Chhandak B., ed. Methods in Molecular Biology, Springer Nature (in press)

Marik T, Szekeres A, Andersson MA, Salkinoja-Salonen M, Tyagi C, Leitgeb B, Vágvölgyi C, Druzhinina IS, Kredics L Bioactive Peptaibols of Forest-Derived Trichoderma Isolates from Section Longibrachiatum. In: Soil Biological Communities and Ecosystem Resilience Lukac M, Grenni P, Gamboni M (eds), 2017. Springer International Publishing, Cham, pp 277-290

Chenthamara K, Druzhinina IS (2016) 12 Ecological Genomics of Mycotrophic Fungi. In: Druzhinina IS, Kubicek CP (eds) Mycota IV Environmental and Microbial Relationships. Springer International Publishing, Cham, pp 215-246

Kubicek CP and Druzhinina IS. Trichoderma Mycoses and Mycotoxins. In Paterson RRM, Lima N (eds.): Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi. CRC Press, 2015. ISBN 9781466559868 – CAT# K15868

Hatvani L, Vagvölgyi C, Kredics L, Druzhinina I. DNA Barcode for Species Identification in Trichoderma. In: Gupta VK, Schmoll M, Herrera‐Estrella A, Upadhyay RS, Druzhinina IS and Tuohy M (eds.) Biotechnology and Biology of Trichoderma. 2014. Elsevier BV, Amsterdam, the Netherlands.

Kredic L, Hatvani L, Naeimi S, Körmöczi P, Manczinger L, Vagvölgyi C, Druzhinina I. Biodiversity of the Genus Hypocrea/Trichoderma in Different Habitats. In: Gupta VK, Schmoll M, Herrera‐Estrella A, Upadhyay RS, Druzhinina IS and Tuohy M (eds.) Biotechnology and Biology of Trichoderma. 2014. Elsevier BV, Amsterdam, the Netherlands.

Seidl-Seiboth V, Ihrmark K, Druzhinina I, Karlsson M. Molecular Evolution of Trichoderma Chitinases. In: Gupta VK, Schmoll M, Herrera‐Estrella A, Upadhyay RS, Druzhinina IS and Tuohy M (eds.) Biotechnology and Biology of Trichoderma. 2014. Elsevier BV, Amsterdam, the Netherlands.

Schmoll M, Seiboth B, Druzhinina I, Kubicek CP. Genomics Analysis of Biocontrol Species and Industrial Enzyme Producers from the Genus Trichoderma. In: Nowrousian M (ed.) Fungal Genomics, 2nd Edition, The Mycota XIII. Springer-Verlag Berlin Heidelberg 2014

Kubicek CP and Druzhinina IS 2013 Trichoderma – genomic aspects of biocontrol and biomass degradation In: Genomics of Soil- and Plant-Associated Fungi Soil Biology Volume 36, 2013, pp 127-156

Kubicek CP. And Druzhinina IS. 2013 Trichoderma and mycotoxins. In: R.R. M. Paterson (ed.) Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi of Humans. CRC Press, http://www.crcpress.com/product/isbn/9781466559868

Atanasova L, Druzhinina IS, Jaklitsch WM. 2013 Two hundered Trichoderma species recognized based on molecular phylogeny. In: Mukherjee PK, Sigh US, Horwitz BA, Schmoll M, Mukherjee M (eds.) Trichoderma: Biology and Applications. . CABI of Nosworthy Way, Wallingford, Oxon, UK.

Druzhinina IS and Kubicek CP. 2013. Ecological genomics of Trichoderma. In: F. Martinn (ed.) Ecological genomics of fungi.  Wiley-Blackwell, Oxford, UK, in press.

dela Cruz TEE, Schulz BE and IS Druzhinina (2010) Polyphasic approach to the taxonomy of the marine Dendriphiella species from different geographic locations. In Gupta VK et al (eds.) “Fungal Biochemistry and Biotechnology, LAP LAMBERT Academic Publishing AG & Co. KG, Germany

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Peer-reviewed articles of Irina S. Druzhinina

A complete list of publications may also be found at https://www.researchgate.net/profile/Irina_Druzhinina/contributions

Cai, F., Zhao, Z., Gao R., Ding, M., Jiang, S., Gao, Q., Chenthamara, K., Grujic, M., Bayram-Akcapinar, G., Shen, Q., and Druzhinina, I. S. Intracellular hydrophobin vesicles modulate the architecture and longevity of fungal colonies. (preprint) doi: 10.1101/2020.08.18.255406

Cai F, Druzhinina IS (2020) In honor of John Bissett: Authoritative guidelines on molecular identification of Trichoderma. Fungal Diversity. (in press) doi: 10.1007/s13225-020-00464-4

Cai F, Gao R, Zhao Z, Ding M, Jiang S, Yagtu C, Zhu H, Zhang J, Ebner T, Mayrhofer-Reinhartshuber M, Kainz P, Chenthamara K, Akcapinar GB, Shen Q, Druzhinina IS (2020) Evolutionary compromises in fungal fitness: hydrophobins can hinder the adverse dispersal of conidiospores and challenge their survival. The ISME Journal 14 (10):2610-2624. doi:10.1038/s41396-020-0709-0

Ding MY, Chen W, Ma XC, Lv BW, Jiang SQ, Yu YN, Rahimi MJ, Gao RW, Zhao Z, Cai F, Druzhinina IS (2020) Emerging salt marshes as a source of Trichoderma arenarium sp. nov. and other fungal bio effectors for bio saline agriculture. Journal of Applied Microbiology :jam.14751. doi:10.1111/jam.14751

Gao R, Ding M, Jiang S, Zhao Z, Chenthamara K, Shen Q, Cai F, Druzhinina IS (2020) The Evolutionary and Functional Paradox of Cerato-platanins in Fungi. Appl Environ Microb 86 (13):e00696-00620, /aem/00686/00613/AEM.00696-00620.atom. doi:10.1128/AEM.00696-20

Hoenigsberger M, Pretzer C, Rahimi MJ, Kopchinskiy AG, Parich A, Laciny A, Metscher B, Chan CM, Lim LBL, Salim KA, Zettel H, Druzhinina IS, Schuhmacher R (2020) Strong antimicrobial and low insecticidal activity of mandibular gland reservoir content in Bornean “exploding ants” Colobopsis explodens Laciny & Zettel, 2018 (Hymenoptera: Formicidae). doi:10.25849/ MYRMECOL.NEWS_030:201

Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL (2020) Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 11 (1):14. doi:10.1186/s43008-020-00033-z

Pérez-Llano Y, Rodríguez-Pupo EC, Druzhinina IS, Chenthamara K, Cai F, Gunde-Cimerman N, Zalar P, Gostinčar C, Kostanjšek R, Folch-Mallol JL, Batista-García RA, Sánchez-Carbente MdR (2020) Stress Reshapes the Physiological Response of Halophile Fungi to Salinity. Cells 9 (3):525. doi:10.3390/cells9030525

Wijayawardene N, Hyde KD, Dai DQ, Tang LZ, Aptroot A, CastanedaRuiz RF, Druzhinina IS, Cai F, Ekanayaka AH, Erdogdu M (2020) A dynamic portal for a community-driven, continuously updated classification of Fungi and fungus-like organisms: outlineoffungi.org. Mycosphere 11 (1):1514-1526. doi:10.5943/mycosphere/11/1/11

Grujić M, Dojnov B, Potočnik I, Atanasova L, Duduk B, Srebotnik E, Druzhinina IS, Kubicek CP, Vujčić Z (2019) Superior cellulolytic activity of Trichoderma guizhouense on raw wheat straw. World Journal of Microbiology and Biotechnology 35 (12):194. doi:10.1007/s11274-019-2774-y

Hatvani L, Homa M, Chenthamara K, Cai F, Kocsubé S, Atanasova L, Mlinaric-Missoni E, Manikandan P, Revathi R, Dóczi I, Bogáts G, Narendran V, Büchner R, Vágvölgyi C, Druzhinina IS, Kredics L (2019) Agricultural systems as potential sources of emerging human mycoses caused by Trichoderma: a successful, common phylotype of Trichoderma longibrachiatum in the frontline. FEMS Microbiology Letters 366 (21):fnz246. doi:10.1093/femsle/fnz246

Hoenigsberger M, Kopchinskiy A, Bueschl C, Parich A, Laciny A, Zettel H, Salim K, Lim L, Druzhinina I, Schuhmacher R (2019) Volatiles from the Mandibular Gland Reservoir Content of Colobopsis explodens Laciny and Zettel, 2018, Worker Ants (Hymenoptera: Formicidae). Molecules 24 (19):3468. doi:10.3390/molecules24193468

Kubicek CP, Steindorff AS, Chenthamara K, Manganiello G, Henrissat B, Zhang J, Cai F, Kopchinskiy AG, Kubicek EM, Kuo A, Baroncelli R, Sarrocco S, Noronha EF, Vannacci G, Shen Q, Grigoriev IV, Druzhinina IS (2019) Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 20 (1):485. doi:10.1186/s12864-019-5680-7

Laciny A, Nemeschkal HL, Zettel H, Metscher B, Druzhinina IS (2019) Caste-specific morphological modularity in the ant tribe Camponotini (Hymenoptera, Formicidae). BMC Zoology 4 (1):9. doi:10.1186/s40850-019-0048-7

Marik T, Tyagi C, Balázs D, Urbán P, Szepesi Á, Bakacsy L, Endre G, Rakk D, Szekeres A, Andersson MA, Salonen H, Druzhinina IS, Vágvölgyi C, Kredics L (2019) Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma. Front Microbiol 10:1434. doi:10.3389/fmicb.2019.01434

Zhang J, Miao Y, Rahimi MJ, Zhu H, Steindorff A, Schiessler S, Cai F, Pang G, Chenthamara K, Xu Y, Kubicek CP, Shen Q, Druzhinina IS (2019) Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi. Environmental Microbiology 21 (8):2644-2658. doi:10.1111/1462-2920.14575

Chadha S, Mehetre ST, Bansal R, Kuo A, Aerts A, Grigoriev IV, Druzhinina IS, Mukherjee PK (2018) Genome-wide analysis of cytochrome P450s of Trichoderma spp.: annotation and evolutionary relationships. Fungal Biology and Biotechnology 5 (1):12. doi:10.1186/s40694-018-0056-3

Druzhinina IS, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, Rahimi MJ, Grujic M, Cai F, Pourmehdi S, Salim KA, Pretzer C, Kopchinskiy AG, Henrissat B, Kuo A, Hundley H, Wang M, Aerts A, Salamov A, Lipzen A, LaButti K, Barry K, Grigoriev IV, Shen Q, Kubicek CP (2018) Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLOS Genetics 14 (4):e1007322. doi:10.1371/journal.pgen.1007322

du Plessis IL, Druzhinina IS, Atanasova L, Yarden O, Jacobs K (2018) The diversity of Trichoderma species from soil in South Africa, with five new additions. Mycologia 110 (3):559-583. doi:10.1080/00275514.2018.1463059

Hoenigsberger M, Kopchinskiy AG, Parich A, Hiller K, Laciny A, Zettel H, Lim LBL, Salim KA, Druzhinina IS, Schuhmacher R (2018) Isolation of Mandibular Gland Reservoir Contents from Bornean ‘Exploding Ants’ (Formicidae) for Volatilome Analysis by GC-MS and Metabolite Detector. JoVE (138):57652. doi:10.3791/57652

Kamravamanesh D, Kovacs T, Pflügl S, Druzhinina I, Kroll P, Lackner M, Herwig C (2018) Increased poly-β-hydroxybutyrate production from carbon dioxide in randomly mutated cells of cyanobacterial strain Synechocystis sp. PCC 6714: Mutant generation and characterization. Bioresource Technology 266:34-44. doi:10.1016/j.biortech.2018.06.057

Laciny A, Zettel H, Kopchinskiy A, Pretzer C, Pal A, Abu Salim K, Javad Rahimi M, Hoenigsberger M, Lim L, Jaitrong W, Druzhinina IS (2018) Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group. Zookeys 751:1-40. doi:10.3897/zookeys.751.22661

Zettel H, Laciny A, Weeyawat J, Syaukani S, Kopchinskiy A, Druzhinina IS (2018) Evidence of predation in two species of the Colobopsis cylindrica group (Hymenoptera: Formicidae: Camponotini). Asian Myrmecology 10: e010011 (1-11) doi:10.20362/AM.010011

Druzhinina IS, Kubicek CP (2017) Genetic engineering of Trichoderma reesei cellulases and their production. Microb Biotechnol 10 (6):1485-1499. doi:10.1111/1751-7915.12726

Gaskell J, Kersten P, Larrondo LF, Canessa P, Martinez D, Hibbett D, Schmoll M, Kubicek CP, Martinez AT, Yadav J, Master E, Magnuson JK, Yaver D, Berka R, Lail K, Chen C, LaButti K, Nolan M, Lipzen A, Aerts A, Riley R, Barry K, Henrissat B, Blanchette R, Grigoriev IV, Cullen D (2017) Draft genome sequence of a monokaryotic model brown-rot fungus Postia (Rhodonia) placenta SB12. Genomics Data 14:21-23. doi:10.1016/j.gdata.2017.08.003

Laciny A, Zettel H, Metscher B, Kamariah AS, Kopchinskiy A, Druzhinina IS (2017) Morphological variation and mermithism in female castes of Colobopsis sp. nrSA, a Bornean “exploding ant” of the Colobopsis cylindrica group (Hymenoptera: Formicidae). Myrmecological News 24:91-106

Marik T, Urbán P, Tyagi C, Szekeres A, Leitgeb B, Vágvölgyi M, Manczinger L, Druzhinina IS, Vágvölgyi C, Kredics L (2017) Diversity Profile and Dynamics of Peptaibols Produced by Green Mould Trichoderma Species in Interactions with Their Hosts Agaricus bisporus and Pleurotus ostreatus. Chem Biodiversity 14 (6):e1700033. doi:10.1002/cbdv.201700033

Miao Y, Li P, Li G, Liu D, Druzhinina IS, Kubicek CP, Shen Q, Zhang R (2017) Two degradation strategies for overcoming the recalcitrance of natural lignocellulosic xylan by polysaccharides-binding GH10 and GH11 xylanases of filamentous fungi: Lignocellulosic xylan degradation strategies. Environmental Microbiology 19 (3):1054-1064. doi:10.1111/1462-2920.13614

Pretzer C, Druzhinina IS, Amaro C, Benediktsdóttir E, Hedenström I, Hervio‐Heath D, Huhulescu S, Schets FM, Farnleitner AH, Kirschner AKT (2017) High genetic diversity of Vibrio cholerae in the European lake Neusiedler See is associated with intensive recombination in the reed habitat and the long‐distance transfer of strains. Environmental Microbiology 19 (1):328-344. doi:10.1111/1462-2920.13612

Przylucka A, Akcapinar GB, Bonazza K, Mello-de-Sousa TM, Mach-Aigner AR, Lobanov V, Grothe H, Kubicek CP, Reimhult E, Druzhinina IS (2017) Comparative physiochemical analysis of hydrophobins produced in Escherichia coli and Pichia pastoris. Colloids and Surfaces B: Biointerfaces 159:913-923. doi:10.1016/j.colsurfb.2017.08.058

Przylucka A, Akcapinar GB, Chenthamara K, Cai F, Grujic M, Karpenko J, Livoi M, Shen Q, Kubicek CP, Druzhinina IS (2017) HFB7 – A novel orphan hydrophobin of the Harzianum and Virens clades of Trichoderma, is involved in response to biotic and abiotic stresses. Fungal Genetics and Biology 102:63-76. doi:10.1016/j.fgb.2017.01.002

Qin Y, Pan X, Kubicek C, Druzhinina I, Chenthamara K, Labbé J, Yuan Z (2017) Diverse Plant-Associated Pleosporalean Fungi from Saline Areas: Ecological Tolerance and Nitrogen-Status Dependent Effects on Plant Growth. Front Microbiol 8. doi:10.3389/fmicb.2017.00158

Davidson DW, Kopchinskiy A, Salim KA, Grujic M, Lim L, Mei CC, Jones TH, Casamatta D, Atanasova L, Druzhinina IS (2016) Nutrition of Borneo’s ‘exploding’ ants (Hymenoptera: Formicidae: Colobopsis ): a preliminary assessment. Biotropica 48 (4):518-527. doi:10.1111/btp.12323

de Man TJB, Stajich JE, Kubicek CP, Teiling C, Chenthamara K, Atanasova L, Druzhinina IS, Levenkova N, Birnbaum SSL, Barribeau SM, Bozick BA, Suen G, Currie CR, Gerardo NM (2016) Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proceedings of the National Academy of Sciences 113 (13):3567-3572. doi:10.1073/pnas.1518501113

Druzhinina IS, Kopchinskiy AG, Kubicek EM, Kubicek CP (2016) A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness. Biotechnology for Biofuels 9 (1):75. doi:10.1186/s13068-016-0488-z

Druzhinina IS, Kubicek CP (2016) Familiar Stranger. Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes In: Advances in Applied Microbiology, Adv Appl Microbiol. 2016;95:69-147.doi: 10.1016/bs.aambs.2016.02.001.

Druzhinina IS, Kubicek EM, Kubicek CP (2016) Several steps of lateral gene transfer followed by events of ‘birth-and-death’ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster. BMC Evolutionary Biology 16 (1):269. doi:10.1186/s12862-016-0834-6

Laciny A, Zettel H, Druzhinina I (2016) Workers, soldiers, and gynes – morphometric characterization and description of the female castes of Camponotus singularis (Smith, 1858) (Hymenoptera, Formicidae). DEZ 63 (2):183-193. doi:10.3897/dez.63.9435

Qin Y, Druzhinina IS, Pan X, Yuan Z (2016) Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture. Biotechnology Advances 34 (7):1245-1259. doi:10.1016/j.biotechadv.2016.08.005

Yuan Z, Druzhinina IS, Labbé J, Redman R, Qin Y, Rodriguez R, Zhang C, Tuskan GA, Lin F (2016) Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity. Scientific Reports: 2016 Aug 30;6:32467. doi: 10.1038/srep32467.

Zhang N, Yang D, Kendall JRA, Borriss R, Druzhinina IS, Kubicek CP, Shen Q, Zhang R (2016) Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats. Front Microbiol 7. doi:10.3389/fmicb.2016.02039

Bonazza K, Gaderer R, Neudl S, Przylucka A, Allmaier G, Druzhinina IS, Grothe H, Friedbacher G, Seidl-Seiboth V (2015) The fungal cerato-platanin protein EPL1 forms highly ordered layers at hydrophobic/hydrophilic interfaces. Soft Matter 11 (9):1723-1732. doi:10.1039/C4SM02389G

Ribitsch D, Herrero Acero E, Przylucka A, Zitzenbacher S, Marold A, Gamerith C, Tscheließnig R, Jungbauer A, Rennhofer H, Lichtenegger H, Amenitsch H, Bonazza K, Kubicek CP, Druzhinina IS, Guebitz GM (2015) Enhanced Cutinase-Catalyzed Hydrolysis of Polyethylene Terephthalate by Covalent Fusion to Hydrophobins. Appl Environ Microb 81 (11):3586-3592. doi:10.1128/AEM.04111-14

Yang D, Pomraning K, Kopchinskiy A, Karimi Aghcheh R, Atanasova L, Chenthamara K, Baker SE, Zhang R, Shen Q, Freitag M, Kubicek CP, Druzhinina IS (2015) Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei. Genome Announcements 3 (4):e00885-00815. doi:10.1128/genomeA.00885-15

Zhang J, Akcapinar GB, Atanasova L, Rahimi MJ, Przylucka A, Yang D, Kubicek CP, Zhang R, Shen Q, Druzhinina IS (2015) The neutral metallopeptidase NMP1 of Trichoderma guizhouense is required for mycotrophy and selfdefence. Environmental Microbiology: https://doi.org/10.1111/1462-2920.12966

Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Dueñas FJ, Held B, Canessa P, Larrondo LF, Schmoll M, Druzhinina IS, Kubicek CP, Gaskell JA, Kersten P, St. John F, Glasner J, Sabat G, Splinter BonDurant S, Syed K, Yadav J, Mgbeahuruike AC, Kovalchuk A, Asiegbu FO, Lackner G, Hoffmeister D, Rencoret J, Gutiérrez A, Sun H, Lindquist E, Barry K, Riley R, Grigoriev IV, Henrissat B, Kües U, Berka RM, Martínez AT, Covert SF, Blanchette RA, Cullen D (2014) Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood. PLoS Genetics 10 (12):e1004759. doi:10.1371/journal.pgen.1004759

Karimi Aghcheh R, Németh Z, Atanasova L, Fekete E, Paholcsek M, Sándor E, Aquino B, Druzhinina IS, Karaffa L, Kubicek CP (2014) The VELVET A Orthologue VEL1 of Trichoderma reesei Regulates Fungal Development and Is Essential for Cellulase Gene Expression. PLoS ONE 9 (11):e112799. doi:10.1371/journal.pone.0112799

Pfliegler WP, Atanasova L, Karanyicz E, Sipiczki M, Bond U, Druzhinina IS, Sterflinger K, Lopandic K (2014) Generation of New Genotypic and Phenotypic Features in Artificial and Natural Yeast Hybrids.12

Agneheh RK, Druzhinina IS, Kubicek CP (2013) The Putative Protein Methyltransferase LAE1 of Trichoderma atroviride Is a Key Regulator of Asexual Development and Mycoparasitism. PLoS ONE 8 (6):e67144. doi:10.1371/journal.pone.0067144

Atanasova L, Crom SL, Gruber S, Coulpier F, Seidl-Seiboth V, Kubicek CP, Druzhinina IS (2013) Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC Genomics 14 (1):121. doi:10.1186/1471-2164-14-121

Atanasova L, Knox BP, Kubicek CP, Druzhinina IS, Baker SE (2013) The Polyketide Synthase Gene pks4 of Trichoderma reesei Provides Pigmentation and Stress Resistance. Eukaryotic Cell 12 (11):1499-1508. doi:10.1128/EC.00103-13

Erper I, Turkkan M, Atanasova L, Druzhinina IS, Karaca GH, CebI-KilIcoglu M (2013) Integrated assessment of the mycoparasitic and phytostimulating properties of Trichoderma strains against Rhizoctonia solani. Bulgarian Journal of Agricultural Science 19(4):737-743

Espino-Rammer L, Ribitsch D, Przylucka A, Marold A, Greimel KJ, Herrero Acero E, Guebitz GM, Kubicek CP, Druzhinina IS (2013) Two Novel Class II Hydrophobins from Trichoderma spp. Stimulate Enzymatic Hydrolysis of Poly(Ethylene Terephthalate) when Expressed as Fusion Proteins. Appl Environ Microb 79 (14):4230-4238. doi:10.1128/AEM.01132-13

Karaffa L, Coulier L, Fekete E, Overkamp KM, Druzhinina IS, Mikus M, Seiboth B, Novák L, Punt PJ, Kubicek CP (2013) The intracellular galactoglycome in Trichoderma reesei during growth on lactose. Applied Microbiology and Biotechnology 97 (12):5447-5456. doi:10.1007/s00253-012-4667-y

Lehner SM, Atanasova L, Neumann NKN, Krska R, Lemmens M, Druzhinina IS, Schuhmacher R (2013) Isotope-Assisted Screening for Iron-Containing Metabolites Reveals a High Degree of Diversity among Known and Unknown Siderophores Produced by Trichoderma spp. Appl Environ Microb 79 (1):18-31. doi:10.1128/AEM.02339-12

López-Quintero CA, Atanasova L, Franco-Molano AE, Gams W, Komon-Zelazowska M, Theelen B, Müller WH, Boekhout T, Druzhinina I (2013) DNA barcoding survey of Trichoderma diversity in soil and litter of the Colombian lowland Amazonian rainforest reveals Trichoderma strigosellum sp. nov. and other species. Antonie van Leeuwenhoek 104 (5):657-674. doi:10.1007/s10482-013-9975-4

Mulaw T, Druzhinina I, Kubicek C, Atanasova L (2013) Novel Endophytic Trichoderma spp. Isolated from Healthy Coffea arabica Roots are Capable of Controlling Coffee Tracheomycosis. Diversity 5 (4):750-766. doi:10.3390/d5040750

Pummer BG, Atanasova L, Bauer H, Bernardi J, Druzhinina IS, Fröhlich-Nowoisky J, Grothe H (2013) Spores of many common airborne fungi reveal no ice nucleation activity in oil immersion freezing experiments. Biogeosciences 10 (12):8083-8091. doi:10.5194/bg-10-8083-2013

Degenkolb T, Karimi Aghcheh R, Dieckmann R, Neuhof T, Baker SE, Druzhinina IS, Kubicek CP, Brückner H, von Döhren H (2012) The Production of Multiple Small Peptaibol Families by Single 14-Module Peptide Synthetases in Trichoderma/Hypocrea. Chem Biodiversity 9 (3):499-535. doi:10.1002/cbdv.201100212

Druzhinina IS, Komoń-Zelazowska M, Ismaiel A, Jaklitsch W, Mullaw T, Samuels GJ, Kubicek CP (2012) Molecular phylogeny and species delimitation in the section Longibrachiatum of Trichoderma. Fungal Genetics and Biology 49 (5):358-368. doi:10.1016/j.fgb.2012.02.004

Druzhinina IS, Shelest E, Kubicek CP (2012) Novel traits of Trichoderma predicted through the analysis of its secretome. FEMS Microbiology Letters 337 (1):1-9. doi:10.1111/j.1574-6968.2012.02665.x

Friedl MA, Druzhinina IS (2012) Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other’s development. Microbiology 158 (1):69-83. doi:10.1099/mic.0.052555-0

Mukherjee PK, Buensanteai N, Moran-Diez ME, Druzhinina IS, Kenerley CM (2012) Functional analysis of non-ribosomal peptide synthetases (NRPSs) in Trichoderma virens reveals a polyketide synthase (PKS)/NRPS hybrid enzyme involved in the induced systemic resistance response in maize. Microbiology 158 (1):155-165. doi:10.1099/mic.0.052159-0

Samuels GJ, Ismaiel A, Mulaw TB, Szakacs G, Druzhinina IS, Kubicek CP, Jaklitsch WM (2012) The Longibrachiatum Clade of Trichoderma: a revision with new species. Fungal Diversity 55 (1):77-108. doi:10.1007/s13225-012-0152-2

Druzhinina IS, Seidl-Seiboth V, Herrera-Estrella A, Horwitz BA, Kenerley CM, Monte E, Mukherjee PK, Zeilinger S, Grigoriev IV, Kubicek CP (2011) Trichoderma: the genomics of opportunistic success. Nature Reviews Microbiology 9 (10):749-759. doi:10.1038/nrmicro2637

Gal-Hemed I, Atanasova L, Komon-Zelazowska M, Druzhinina IS, Viterbo A, Yarden O (2011) Marine Isolates of Trichoderma spp. as Potential Halotolerant Agents of Biological Control for Arid-Zone Agriculture. Appl Environ Microb 77 (15):5100-5109. doi:10.1128/AEM.00541-11

Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Döhren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gómez-Rodríguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernández-Oñate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lübeck M, Lübeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV (2011) Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biology 12 (4):R40. doi:10.1186/gb-2011-12-4-r40

Atanasova L, Druzhinina IS (2010) Global nutrient profiling by Phenotype MicroArrays: a tool complementing genomic and proteomic studies in conidial fungi. J Zhejiang Univ Sci B 11 (3):151-168. doi:10.1631/jzus.B1000007

Atanasova L, Jaklitsch WM, Komoń-Zelazowska M, Kubicek CP, Druzhinina IS (2010) Clonal Species Trichoderma parareesei sp. nov. Likely Resembles the Ancestor of the Cellulase Producer Hypocrea jecorina/T. reesei. Appl Environ Microb 76 (21):7259-7267. doi:10.1128/AEM.01184-10

Druzhinina IS, Komoń-Zelazowska M, Atanasova L, Seidl V, Kubicek CP (2010) Evolution and Ecophysiology of the Industrial Producer Hypocrea jecorina (Anamorph Trichoderma reesei) and a New Sympatric Agamospecies Related to It. PLoS ONE 5 (2):e9191. doi:10.1371/journal.pone.0009191

Druzhinina IS, Kubicek CP, Komon-Zelazowska M, Belayneh Mulaw T, Bissett J (2010) The Trichoderma harzianum demon: complex speciation history resulting in coexistence of hypothetical biological species, recent agamospecies and numerous relict lineages. BMC Evolutionary Biology 10 (1):94. doi:10.1186/1471-2148-10-94

Mulaw TB, C.P. K, Druzhinina IS (2010) The Rhizosphere of Coffea Arabica in Its Native Highland Forests of Ethiopia Provides a Niche for a Distinguished Diversity of Trichoderma. Diversity 2(4)

Paz Z, Komon-Zelazowska M, Druzhinina IS, Aveskamp MM, Shnaiderman A, Aluma Y, Carmeli S, Ilan M, Yarden O (2010) Diversity and potential antifungal properties of fungi associated with a Mediterranean sponge. Fungal Diversity 42 (1):17-26. doi:10.1007/s13225-010-0020-x

Kemptner J, Marchetti-Deschmann M, Mach R, Druzhinina IS, Kubicek CP, Allmaier G (2009) Evaluation of matrix-assisted laser desorption/ionization (MALDI) preparation techniques for surface characterization of intact Fusarium spores by MALDI linear time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 23 (6):877-884. doi:10.1002/rcm.3949

Kredics Ls, Kocsubé Sn, Nagy Ls, Komoń-Zelazowska M, Manczinger Ls, Sajben E, Nagy A, Vágvölgyi C, Kubicek CP, Druzhinina IS, Hatvani Lrn (2009) Molecular identification of Trichoderma species associated with Pleurotus ostreatus and natural substrates of the oyster mushroom. FEMS Microbiology Letters 300 (1):58-67. doi:10.1111/j.1574-6968.2009.01765.x

Le Crom S, Schackwitz W, Pennacchio L, Magnuson JK, Culley DE, Collett JR, Martin J, Druzhinina IS, Mathis H, Monot F, Seiboth B, Cherry B, Rey M, Berka R, Kubicek CP, Baker SE, Margeot A (2009) Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing. Proceedings of the National Academy of Sciences 106 (38):16151-16156. doi:10.1073/pnas.0905848106

Migheli Q, Balmas V, Komoñ-Zelazowska M, Scherm B, Fiori S, Kopchinskiy AG, Kubicek CP, Druzhinina IS (2009) Soils of a Mediterranean hot spot of biodiversity and endemism (Sardinia, Tyrrhenian Islands) are inhabited by pan-European, invasive species of Hypocrea/Trichoderma. Environmental Microbiology 11 (1):35-46. doi:10.1111/j.1462-2920.2008.01736.x

Mikus M, Hatvani Lrn, Neuhof T, Komoń-Zelazowska M, Dieckmann R, Schwecke T, Druzhinina IS, von D�hren H, Kubicek CP (2009) Differential Regulation and Posttranslational Processing of the Class II Hydrophobin Genes from the Biocontrol Fungus Hypocrea atroviridis. Appl Environ Microb 75 (10):3222-3229. doi:10.1128/AEM.01764-08

Zachow C, Berg C, Müller H, Meincke R, Komon-Zelazowska M, Druzhinina IS, Kubicek CP, Berg G (2009) Fungal diversity in the rhizosphere of endemic plant species of Tenerife (Canary Islands): relationship to vegetation zones and environmental factors. The ISME Journal 3 (1):79-92. doi:10.1038/ismej.2008.87

Brunner K, Omann M, Pucher ME, Delic M, Lehner SM, Domnanich P, Kratochwill K, Druzhinina I, Denk D, Zeilinger S (2008) Trichoderma G protein-coupled receptors: functional characterisation of a cAMP receptor-like protein from Trichoderma atroviride. Current Genetics 54 (6):283-299. doi:10.1007/s00294-008-0217-7

Druzhinina IS, Komoń-Zelazowska M, Kredics L, Hatvani L, Antal Z, Belayneh T, Kubicek CP (2008) Alternative reproductive strategies of Hypocrea orientalis and genetically close but clonal Trichoderma longibrachiatum, both capable of causing invasive mycoses of humans. Microbiology 154 (11):3447-3459. doi:10.1099/mic.0.2008/021196-0

Friedl MA, Kubicek CP, Druzhinina IS (2008) Carbon Source Dependence and Photostimulation of Conidiation in Hypocrea atroviridis. Appl Environ Microb 74 (1):245-250. doi:10.1128/AEM.02068-07

Friedl MA, Schmoll M, Kubicek CP, Druzhinina IS (2008) Photostimulation of Hypocrea atroviridis growth occurs due to a cross-talk of carbon metabolism, blue light receptors and response to oxidative stress. Microbiology 154(Pt 4):1229-41

Jaklitsch WM, Kubicek CP, Druzhinina IS (2008) Three European species of Hypocrea with reddish brown stromata and green ascospores. Mycologia 100 (5):796-815. doi:10.3852/08-039

Kubicek CP, Baker SE, Gamauf C, Kenerley CM, Druzhinina IS (2008) Purifying selection and birth-and-death evolution in the class II hydrophobin gene families of the ascomycete Trichoderma/Hypocrea. BMC Evolutionary Biology 8 (1):4. doi:10.1186/1471-2148-8-4

Kubicek CP, Komon-Zelazowska M, Druzhinina IS (2008) Fungal genus Hypocrea/Trichoderma: from barcodes to biodiversity. J Zhejiang Univ Sci B 9 (10):753-763. doi:10.1631/jzus.B0860015

Seidl V, Gamauf C, Druzhinina IS, Seiboth B, Hartl L, Kubicek CP (2008) The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome. BMC Genomics 9 (1):327. doi:10.1186/1471-2164-9-327

Váczy KZ, Sándor E, Karaffa L, Fekete E, Fekete É, Árnyasi M, Czeglédi L, Kövics GJ, Druzhinina IS, Kubicek CP (2008) Sexual Recombination in the Botrytis cinerea Populations in Hungarian Vineyards. Phytopathology 98 (12):1312-1319. doi:10.1094/PHYTO-98-12-1312

Druzhinina IS, LaFe K, Willinger B, Komoń-Zelazowska M, Ammirati J, Kubicek CP, Rogers JD (2007) An Unknown Hypocreaceae Species Isolated from Human Lung Tissue of a Patient with Non-Fatal Pulmonary Fibrosis. Clinical Microbiology Newsletter 29 (23):180-184. doi:10.1016/j.clinmicnews.2007.11.002

Hatvani L, Antal Z, Manczinger L, Szekeres A, Druzhinina IS, Kubicek CP, Nagy A, Nagy E, Vágvölgyi C, Kredics L (2007) Green Mold Diseases of Agaricus and Pleurotus spp. Are Caused by Related but Phylogenetically Different Trichoderma Species. Phytopathology 97 (4):532-537. doi:10.1094/PHYTO-97-4-0532

Komoń-Zelazowska M, Bissett J, Zafari D, Hatvani L, Manczinger L, Woo S, Lorito M, Kredics L, Kubicek CP, Druzhinina IS (2007) Genetically Closely Related but Phenotypically Divergent Trichoderma Species Cause Green Mold Disease in Oyster Mushroom Farms Worldwide. Appl Environ Microb 73 (22):7415-7426. doi:10.1128/AEM.01059-07

Komon-Zelazowska M, Neuhof T, Dieckmann R, von Döhren H, Herrera-Estrella A, Kubicek CP, Druzhinina IS (2007) Formation of Atroviridin by Hypocrea atroviridis Is Conidiation Associated and Positively Regulated by Blue Light and the G Protein GNA3. Eukaryotic Cell 6 (12):2332-2342. doi:10.1128/EC.00143-07

Kubicek CP, Komoń-Zelazowska M, Sándor E, Druzhinina IS (2007) Facts and Challenges in the Understanding of the Biosynthesis of Peptaibols by Trichoderma. Chem Biodiversity 4 (6):1068-1082. doi:10.1002/cbdv.200790097

Nagy V, Seidl V, Szakacs G, Komoń-Zelazowska M, Kubicek CP, Druzhinina IS (2007) Application of DNA Bar Codes for Screening of Industrially Important Fungi: the Haplotype of Trichoderma harzianum Sensu Stricto Indicates Superior Chitinase Formation. Appl Environ Microb 73 (21):7048-7058. doi:10.1128/AEM.00995-07

Neuhof T, Dieckmann R, Druzhinina IS, Kubicek CP, Nakari-Setälä T, Penttilä M, von Döhren H (2007) Direct identification of hydrophobins and their processing in Trichoderma using intact-cell MALDI-TOF MS: Trichoderma hydrophobins. FEBS Journal 274 (3):841-852. doi:10.1111/j.1742-4658.2007.05636.x

Neuhof T, Dieckmann R, Druzhinina IS, Kubicek CP, von Döhren H (2007) Intact-cell MALDI-TOF mass spectrometry analysis of peptaibol formation by the genus Trichoderma/Hypocrea: can molecular phylogeny of species predict peptaibol structures? Microbiology 153 (10):3417-3437. doi:10.1099/mic.0.2007/006692-0

Schuster A, Kubicek CP, Friedl MA, Druzhinina IS, Schmoll M (2007) Impact of light on Hypocrea jecorina and the multiple cellular roles of ENVOY in this process. BMC Genomics 8 (1):449. doi:10.1186/1471-2164-8-449

Zhang C-l, Liu S-p, Lin F-c, Kubicek CP, Druzhinina IS (2007) Trichoderma taxi sp. nov., an endophytic fungus from Chinese yew Taxus mairei. FEMS Microbiology Letters 270 (1):90-96. doi:10.1111/j.1574-6968.2007.00659.x

Dela Cruz TEE, Schulz BE, Kubicek CP, Druzhinina IS (2006) Carbon source utilization by the marine Dendryphiella species D. arenaria and D. salina. FEMS Microbiology Ecology 58 (3):343-353. doi:10.1111/j.1574-6941.2006.00184.x

Druzhinina IS, Kopchinskiy AG, Kubicek CP (2006) The first 100 Trichoderma species characterized by molecular data. Mycoscience 47 (2):55-64. doi:10.1007/S10267-006-0279-7

Druzhinina IS, Schmoll M, Seiboth B, Kubicek CP (2006) Global Carbon Utilization Profiles of Wild-Type, Mutant, and Transformant Strains of Hypocrea jecorina. Appl Environ Microb 72 (3):2126-2133. doi:10.1128/AEM.72.3.2126-2133.2006

Jaklitsch WM, Komon M, Kubicek CP, Druzhinina IS (2006) Hypocrea crystalligena sp. nov., a common European species with a white-spored Trichoderma anamorph. Mycologia 98(3):499-513

Jaklitsch WM, Komon M, Kubicek CP, Druzhinina IS (2006) Hypocrea voglmayrii sp. nov. from the Austrian Alps represents a new phylogenetic clade in Hypocrea/Trichoderma. Mycologia 97(6):1365-78

Jaklitsch WM, Samuels GJ, Dodd SL, Lu B-S, Druzhinina IS (2006) Hypocrea rufa/Trichoderma viride: a reassessment, and description of five closely related species with and without warted conidia. Studies in Mycology 56:135-177. doi:10.3114/sim.2006.56.04

Samuels GJ, Dodd SL, Lu B-S, Petrini O, Schroers H-J, Druzhinina IS (2006) The Trichoderma koningii aggregate species. Studies in Mycology 56:67-133. doi:10.3114/sim.2006.56.03

Seidl V, Druzhinina IS, Kubicek CP (2006) A screening system for carbon sources enhancing β-N-acetylglucosaminidase formation in Hypocrea atroviridis (Trichoderma atroviride). Microbiology 152 (7):2003-2012. doi:10.1099/mic.0.28897-0

Druzhinina I, Kubicek CP (2005) Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters? J Zhejiang Univ Sci B (2):100-112. doi:10.1631/jzus.2005.B0100

Druzhinina IS, Kopchinskiy AG, Komoń M, Bissett J, Szakacs G, Kubicek CP (2005) An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genetics and Biology 42 (10):813-828. doi:10.1016/j.fgb.2005.06.007

Kopchinskiy A, Komoń M, Kubicek CP, Druzhinina IS (2005) TrichoBlast: A Multilocus Database for Trichoderma and Hypocrea Identifications. Mycol Res 109 (6):658-660. doi:10.1017/S0953756205233397

Zhang C-l, Druzhinina IS, Kubicek CP, Xu T (2005) Trichoderma biodiversity in China: Evidence for a North to South distribution of species in East Asia. FEMS Microbiology Letters 251 (2):251-257. doi:10.1016/j.femsle.2005.08.034

Druzhinina I, Palma-Oliveira JM (2004) Radioactive contamination of wild mushrooms: a cross-cultural risk perception study. Journal of Environmental Radioactivity 74 (1-3):83-90. doi:10.1016/j.jenvrad.2004.01.025

Druzhinina IS, Chaverri P, Fallah P, Kubicek CP, Samuels GJ (2004) Hypocrea flaviconidia, a new species from Costa Rica with yellow conidia. Studies in Mycology, 50:401–407.

Gherbawy Y, Druzhinina I, Shaban GM, Wuczkowsky M, Yaser M, El-Naghy MA, Prillinger H-J, Kubicek CP (2004) Trichoderma populations from alkaline agricultural soil in the Nile valley, Egypt, consist of only two species. Mycol Prog 3 (3):211-218. doi:10.1007/s11557-006-0091-y

Kraus GF, Druzhinina I, Gams W, Bissett J, Zafari D, Szakacs G, Koptchinski A, Prillinger H, Zare R, Kubicek CP (2004) Trichoderma brevicompactum sp. nov. Mycologia 96 (5):1059-1073. doi:10.1080/15572536.2005.11832905

Lu B, Druzhinina IS, Fallah P, Chaverri P, Gradinger C, Kubicek CP, Samuels GJ (2004) Hypocrea/Trichoderma species with pachybasium-like conidiophores: teleomorphs for T. minutisporum and T. polysporum and their newly discovered relatives. Mycologia 96(2):310-42

Pail M, Peterbauer T, Seiboth B, Hametner C, Druzhinina I, Kubicek CP (2004) The metabolic role and evolution of l-arabinitol 4-dehydrogenase of Hypocrea jecorina. Eur J Biochem 271 (10):1864-1872. doi:10.1111/j.1432-1033.2004.04088.x

Bissett J, Szakacs G, Nolan CA, Druzhinina I, Gradinger C, Kubicek CP (2003) New species of Trichoderma from Asia. Can J Bot 81 (6):570-586. doi:10.1139/b03-051

Kubicek CP, Bissett J, Druzhinina I, Kullnig-Gradinger C, Szakacs G (2003) Genetic and metabolic diversity of Trichoderma: a case study on South-East Asian isolates. Fungal Genetics and Biology 38 (3):310-319. doi:10.1016/S1087-1845(02)00583-2

Wuczkowski M, Druzhinina I, Gherbawy Y, Klug B, Prillinger H, Kubicek CP (2003) Species pattern and genetic diversity of Trichoderma in a mid-European, primeval floodplain-forest. Microbiological Research 158 (2):125-133. doi:10.1078/0944-5013-00193

Druzhinina IS, Insarova ID, Shnyreva AV, D’Yakov YT, Altukhov YP (1997) Homokaryotic mycelial pellets of basidiomycetes: Application to genetic analysis. Russian Journal of Genetics 33 (5):521-526

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Christian P. Kubicek

Christian P. Kubicek, Vienna, 2018

Christian P. Kubicek is a retired Professor for Biotechnology and Microbiology at the University of Technology in Vienna (Austria). His scientific work concentrated on both basic and applied research on filamentous fungi with most emphasis on those from the genus Trichoderma and Aspergillus. These studies comprised enzymology and protein chemistry, metabolic regulation, microbial ecology, functional gene characterization, and all “omics” approaches towards the improvement of fungal strains used in industry and agriculture by science-driven strategies. His work is documented in more than 300 original papers in peer-reviewed journals, as well as many patents and books, and was distinguished by several international honors.

Christian P. Kubicek pioneered and most advanced Trichoderma’s genomics by making the first and most significant comparative genomic studies for this genus (below). Being the first Chair of the International Commission on Trichoderma Taxonomy (now ICTT, that time ISTH), Christian was among the first scientists who implemented the DNA Barcoding and Genealogical Concordance Phylogenetic Species Recognition concept in Trichoderma taxonomy. Irina worked together with Christian for ten years from 2002 until his retirement in 2013. We highly appreciate the still ongoing cooperation with Christian on Trichoderma genetics, genomics and systems biology.

Selected publications:

Kubicek, C.P., Steindorff, A.S., Chenthamara, K., Manganiello, G., Henrissat, B., Zhang, J., Cai, F., Kopchinskiy, A.G., Kubicek, E.M., Kuo, A., Baroncelli, R., Sarrocco, S., Noronha, E.F., Vannacci, G., Shen, Q.*, Grigoriev, I.V., Druzhinina, I.S.*, 2019. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 20.

Druzhinina, I.S., V. Seidl-Seiboth, A. Herrera-Estrella, B.A. Horwitz, C.M. Kenerley, E. Monte, P.K. Mukherjee, S. Zeilinger, I.V. Grigoriev and C.P. Kubicek, Trichoderma: the genomics of opportunistic success (vol 9, pg 749, 2011). Nature Reviews Microbiology, 2011. 9(12): p. 896-896 doi: 10.1038/nrmicro2689. PubMed PMID: WOS:000297255800016.

Kubicek, C.P., A. Herrera-Estrella, V. Seidl-Seiboth, D.A. Martinez, I.S. Druzhinina, M. Thon, S. Zeilinger, S. Casas-Flores, B.A. Horwitz and P.K. Mukherjee, Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biology, 2011. 12(4): p. R40 doi.org/10.1186/gb-2011-12-4-r40.

Druzhinina IS, Chenthamara K, Zhang J, Atanasova L, Yang D, Miao Y, et al. (2018) Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts. PLoS Genet 14(4): e1007322. https://doi.org/10.1371/journal.pgen.1007322

Druzhinina, I.S., E.M. Kubicek and C.P. Kubicek, Several steps of lateral gene transfer followed by events of ‘birth-and-death’ evolution shaped a fungal sorbicillinoid biosynthetic gene cluster. BMC Evolutionary Biology, 2016. 16: p. 269. doi: 10.1186/s12862-016-0834-6. PubMed PMID: PMC5182515.

Druzhinina, I.S. and C.P. Kubicek, Genetic engineering of Trichoderma reesei cellulases and their production. Microb Biotechnol, 2017 doi: 10.1111/1751-7915.12726. PubMed PMID: 28557371.

de Man, T.J.B., J.E. Stajich, C.P. Kubicek, C. Teiling, K. Chenthamara, L. Atanasova, I.S. Druzhinina, N. Levenkova, S.S.L. Birnbaum, S.M. Barribeau, B.A. Bozick, G. Suen, C.R. Currie and N.M. Gerardo, Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture. Proceedings of the National Academy of Sciences of the United States of America, 2016. 113(13): p. 3567-3572 doi: 10.1073/pnas.1518501113.

Druzhinina, I.S. and C.P. Kubicek, Familiar Stranger: Ecological Genomics of the Model Saprotroph and Industrial Enzyme Producer Trichoderma reesei Breaks the Stereotypes. Advances in Applied Microbiology, 2016. 95: p. 69-147 doi: 10.1016/bs.aambs.2016.02.001.

Druzhinina, I.S., A.G. Kopchinskiy, E.M. Kubicek and C.P. Kubicek, A complete annotation of the chromosomes of the cellulase producer Trichoderma reesei provides insights in gene clusters, their expression and reveals genes required for fitness. Biotechnology for Biofuels, 2016. 9: p. 75 doi: 10.1186/s13068-016-0488-z.

Atanasova, L., S. Le Crom, S. Gruber, F. Coulpier, V. Seidl-Seiboth, C.P. Kubicek and I.S. Druzhinina, Comparative transcriptomics reveals different strategies of Trichoderma mycoparasitism. BMC genomics, 2013. 14(1): p. 121 doi: 10.1186/1471-2164-14-121.

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Siqiao Chen

Siqiao Chen

Siqiao Chen, a FungiG Ph.D. guest student researching the fungal-like bioeffectors used to control plant disease caused by Pythium spp. pathogen.

We studied the diversity of Trichoderma (Hypocreales, Ascomycota) – Pythium (Peronosporales, Oomycota) antagonistic interactions on a taxonomically-wide scale for a better understanding of the molecular mechanisms governing microbial dialogues in environmentally friendly control to Pythium diseases by next next-generation bioeffectors. For this purpose, we set a library of Trichoderma strains that represent the major taxonomic clades, and investigated their interactions with five species of causative plant diseases Pythium, and revealed that the ability to suppress Pythium is a generic property of Trichoderma as most species showed profound antagonism regardless of the partner identity. Furthermore, the soil-dwelling species, such as T. asperellum, T. atroviride and T. virens showed to be the most efficient. In contrast, canopy-associated and putatively strictly mycoparasitic species (T. minutisporum, T. parepimyces, and T. strictipile) were only moderately antagonistic to Pythium spp. These results suggest that the interactions with Pythium spp. benefit from the shared (core-genome) genetic traits of Trichoderma, such as hydrolytic enzymes that can degrade cellulose, one of the main polysaccharides of the water mold cell wall. Therefore, we harnessed exo-proteomics in combative interactions by liquid culture with Pythium mycelia to analyze the contribution of exo-emzymes (e.g. cellulases and proteases) to the antagonism. We also exploited the mutant of the highly cellulolytic species T. reesei lacking XYR1, which is the major transcriptional activator of cellulase gene expression to investigate the contribution of cellulases to the antagonism. The T. reesei △xyr1 mutant showed reduced antagonism levels to all of the five Pythium plant pathogens species analyzed compared to the wild-type. Still, the ability of Trichoderma to inhibit Pythium spp. was not abolished, suggesting other factors contributed to the antagonism. Our goal is to figure out the potential of Trichoderma bioeffectors to control diseases caused by Pythium plant pathogens, and molecular mechanisms of the multi-faceted nature of the antagonism.

CURRICULUM VITAE

Siqiao Chan,B.Sc.(Ag.)

Professional address:   Nanjing Agricultural University, Weigang 1th, Nanjing, 210095, Nanjing, Jiangsu, China

E-mail:              33315220@njau.edu.cn

Born on:            Aug/15/1996, Huizhou, Guangdong, China

Web links:         www.FungiG.org & ResearchGate

Education and trainings:

Sept/2019 ꟷPresent                                   Directly Ph.D. study, College of Resources and Environmental Sciences, Nanjing Agricultural University, and Plant Protection Institute, Jiangsu Academy of Agricultural Sciences, Nanjing, China. Supervisor: Prof. Dr. Qirong Shen Advisory board: Prof. Dr. Irina S. Druzhinina, Dr. Paul Daly.

Dec/2018 ꟷMar/2019                                Undergraduate graduation thesis. Supervisor: Prof. Dr. Irina S. Druzhinina and Dr. Feng Cai

Jul/2018 ꟷAug/2018                                 Academic Summer camp, Boston, USA

Sept/2015 ꟷJul/2019                                 B.S. in Agro-grassland science, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China

Research interests and skills:

Keywords:  Fungal-like bioeffectors to Pythium plant diseases, fungal cellulases, exo-proteomics, fungal wars, Trichoderma genetic engineering.

Microbiological techniques:  Axenic cultures, microbial diagnostics by DNA barcoding, fungal morphology, microbial cultivations, light, confocal, and scanning electron microscopy techniques.

Molecular biological techniques: Qualitative and quantitative nucleic acid manipulation techniques, protoplast transformation of Trichoderma and Pythium.

Proteomic and analytical techniques: Fungal exo-proteomics and basic proteomic assays, metaproteomic analysis

Fungal ecophysiology: BIOLOG phenotype microarrays, qualitative assays for enzymatic activity, dual confrontations of fungi, growth profiling.

Microbial metagenomics: Transcriptomics sequencing for fungi and Oomycota, absolute quantification technique, qPCR

Molecular evolution: Phylogenetics analyses, DNA barcoding of fungi and Oomycota

Other skills: Plant physiology, plant biochemical assays and nutrition

Publications:

  1. Daly, P., Chen, S., Xue, T., Li, J., Sheikh, T. M. M., Zhang, Q., Wang, X., Zhang, J., Fitzpatrick, D A., McGowan, J., Shi, X., Deng, S., Jiu, M., Zhou, D., Druzhinina, S I., Wei, L. (2021). Dual-Transcriptomic, Microscopic, and Biocontrol Analyses of the Interaction Between the Bioeffector Pythium oligandrum and the Pythium Soft-Rot of Ginger Pathogen Pythium myriotylum. Frontiers in microbiology, 12, 765872-765872.
  2. Xue, T., Wang L., Chen, S., Xie, W., Chen, Y., Zhang, J., Zhou, D., Wei, L. (2021).  Analysis of the Pathogenicity of Ginger-infecting Pythium myriotylum Isolates Towards Tobacco (Nicotiana tabacum). Acta Phytopathologica Sinica, submitted.
  3. Chen, S., Daly, P., Zhou, D., Li, J., Wang, X., Deng, S., Feng, H., Wang, C., Sheikh, T. M. M., Chen, Y., Xue, T., Cai, F., Kubicek, C P., Wei, L., Druzhinina S I. (2021). The use of mutant and engineered microbial agents for biological control of plant diseases caused by Pythium: achievements versus challenges, Fungal Biology Reviews, under review.