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 1^th, 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:

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.
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.
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.

October 12, 2020January 30, 2022

Peijie Chen

Chen-Peijie-CURRICULUM-VITAE-February-2022 Download

Hi there, I am Peijie Chen, and I have started my PhD project in September 2020 in Fungal Genomics Group. I have been curious about winemaking since I was a child, and the mechanism behind this is even more fascinating. From genes to proteins (enzymes), simple ATCG permutations and combinations create unlimited possibilities. This also gives us the possibility of manipulating genes to obtain ideal microorganisms. I am now working on genetic engineering of Aureobasidium spp. and Trichoderma spp. for better CAZyme production so that we can achieve high utilization of massive plant biomass and better renewable resources production.

Here are my recent publications:

Jiang, G., Chen, P., Bao, Y., Wang, X., Yang, T., Mei, X., Banerjee, S., Wei, Z., Xu, Y., Shen, Q. 2021. Isolation of a novel psychrotrophic fungus for efficient low-temperature composting. Bioresource Technology. 331: 0960-8524.

Chen, P, Pang, G, Cai, F, Druzhinina, I. S. 2021. Strain Improvement and Genetic Engineering of Trichoderma for Industrial Applications. Zaragoza O., and Casadevall A., eds. Encyclopedia of Mycology, Elsevier pp 505-517.

Cai, F., Zhao, Z., Gao, R., Chen, P., Ding, M., Jiang, S, Fu, Z., Xu, P., Chenthamara, K., Akcapinar, G. B., Shen, Q., Druzhinina, I. S. 2021. The pleiotropic functions of intracellular hydrophobins in aerial hyphae and fungal spores. Plos Genetics. 17.11 (2021): e1009924.

Zhao, Z., Cai, F., Gao, R., Ding, M., Jiang, S., Chen, P., Pang, G., Chenthamara, K., Shen, Q., Akcapinar, G. B., Druzhinina, I. S. 2021. At least three families of hyphosphere small secreted cysteine-rich proteins can optimize surface properties to a moderately hydrophilic state suitable for fungal attachment. Environmental Microbiology. 1462-2920.

October 12, 2020October 12, 2020

Zheng Zhao

My name is Zhao Zheng. I am a Ph.D. student in FungiG. My primary research is focused on the production and application of fungal surface-active proteins hydrophobins (HFBs) and cerato-platanins (CPs). These are amphiphilic small secreted cysteine-rich proteins that are only found in filamentous fungi, including Trichoderma, Aspergillus, and some other common molds. HFBs have shown numerous remarkable functions, such as contributing to spore surfaces’ hydrophobicity and their subsequent dispersal, fungal stress resistance. To humankind, HFBs can also be made into antifoaming agents and used as drug carriers for targeted medicine. Gene mutation can change protein characters and even biological function. Therefore, besides the research work on the production of HFBs and such other proteins by eukaryotic cell factories (yeast and filamentous fungi), my other research interest is protein engineering, which allows me to explore the possibility of artificial design in improving one designated protein function.

Besides doing research, I like street dance. I especially enjoy Popping. My goal is to be the one who can dance the most in the scientific circles and do the best in the street dance.

My recent publication:

Zhao, Z., Cai, F., Gao, R., Ding, M., Jiang, S., Chen, P.J, Chenthamara, K., Shen, Q., Bayram Akcapinar, G., Druzhinina, I.S. Hyphosphere SSCPs optimize surface properties to a moderately hydrophilic state suitable for fungal attachment, in preparation

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., Bayram-Akcapinar, G., Shen, Q., and Druzhinina, I. S. 2020 Evolutionary compromises in fungal fitness: hydrophobins hinder the adverse dispersal of spores and challenge their survival, The ISME J 14, 2610–2624 (2020). https://doi.org/10.1038/s41396-020-0709-0

Ding, M., Chen, W., Gao, R., Jiang, S., Zhao, Z., Cai, F., and Druzhinina, I. S. Emerging salt marshes as a source of Trichoderma arenerea sp. nov. and other fungal bioeffectors for biosaline agriculture, Journal of Applied Microbiology, doi: 10.1111/jam.14751.

Gao, R., Ding, M., Jiang, S., Zhao, Z., Chenthamara, K., Shen, Q. Cai, F., Druzhinina I.S. 2020. The evolutionary and functional paradox of cerato-platanins in the mycoparasitic fungi Applied and Environmental Microbiology 86:e00696-20

October 12, 2020January 30, 2022

Siqi Jiang

Jian-Siqi-CURRICULUM-VITAE-February-2022 Download

Siqi Jiang, a FungiG Ph.D. student researching the green mold disease in mushroom farms caused by Trichoderma. We have recently found a new Trichoderma species that is associated with one of the very common edible mushrooms. As it was my first sampling trip for Trichoderma diversity, I find this discovery fascinating and exciting. I want to explore the fungal ability to degrade petroleum-based synthetic polymers (plastic) in my other research direction. In my opinion, fungi are magical. They have very different morphology and life history compared to other organisms that I studied before. They can help humans and can also be dangerous. Today’s plastic pollution is worrying. Some fungi can deal with plastic. I hope to use enzymes produced by fungi to degrade plastics effectively and alleviate “white pollution”. I think we also do not understand the interactions within fungal communities. For example, the fungal wars between the mycoparasitic Trichoderma and such hosts as mushrooms and plant-pathogenic fungi have remarkable differences even though the basic scenario is the same: the hosts try to defend against Trichoderma invasion while Trichoderma breaks through. My goal is to figure out the molecular mechanisms of these interactions.

My recent publications:

Jiang S, Yu Y, Gao R, Wang H, Zhang J, Li R, Long X, Shen Q, Chen W, & Cai F. 2019. High-throughput absolute quantification sequencing reveals the effect of different fertilizer applications on bacterial communities in a tomato cultivated coastal saline soil. The Science of the total environment, 687, 601–609.

Cai F, Zhao Z, Gao R, Chen P, Ding M, Jiang S, Fu Z, Xu P, Chenthamara K, Shen Q, Bayram Akcapinar G, Druzhinina IS 2021 The pleiotropic functions of Intracellular hydrophobins in aerial hyphae and fungal spores. PLoS Genetics 17(11): e1009924. https://doi.org/10.1371/journal.pgen.1009924

Daly P, Cai F, Kubicek CP, Jiang S, Grujic M, Rahimi MJ, Sheteiwy MS, Giles R, Riaz A, de Vries RP, Bayram Akcapinar G, Wei L, Druzhinina IS 2021 From lignocellulose to plastics: knowledge transfer on the degradation approaches by fungi. Biotechnology Advances, DOI: 10.1016/j.biotechadv.2021.107770

Zhao Z, Cai F, Gao R, Ding M, Jiang S, Chen P J, Pang G, Chenthamara K, Shen Q, Bayram-Akcapinar G, Druzhinina S I. 2021 At least three families of hyphosphere small secreted cysteine-rich proteins can optimize surface properties to a moderately hydrophilic state suitable for fungal attachment. Environmental Microbiology. doi: 10.1111/1462-2920.15413

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 130: 179–195. 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. Applied and Environmental Microbiology 86 (13):e00696-00620. doi:10.1128/AEM.00696-20

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

October 12, 2020October 12, 2020

Ming Yue Ding

I’m Mingyue Ding, a PhD student. My fascination in microbiology started from the book of Ed Yong “I Contain Multitudes: The Microbes Within Us and a Grander View of Life”, about the amazing partnerships between microbes and animals. What made me more interested in microorganisms was that I studied many different species of the filamentous fungus Trichoderma during my master research. Only a few mutations in DNA Barcodes corresponded to the huge differences in morphology, nutrition, and fitness. Some Trichoderma spp. even showed the characteristics of environmental opportunistic fungi, which inspired my strong curiosity. I want to continue researching the diversity of fungivorous hypocrealean fungi such as Trichoderma and Escovopsis and reveal at the genomic level why some of themare cosmopolitan, while others are limited in some specific local habitats.

My recent publications:

Ding, M., Chen, W., Gao, R., Jiang, S., Zhao, Z., Cai, F., and Druzhinina, I. S. Emerging salt marshes as a source of Trichoderma arenerea sp. nov. and other fungal bioeffectors for biosaline agriculture, Journal of Applied Microbiology, doi: 10.1111/jam.14751.

October 10, 2020October 12, 2020

Renwei Gao

I am a FungiG Ph.D. student interested in the genetic engineering and functional genetics of fungi. I feel fascinated by how wonderful the eukaryotic cell is. Although it is the result of evolution, it follows a particular rule as if it is arranged. My primary research is focused on the surface-active small secreted cysteine-rich proteins (saSSCPs) in Trichoderma, such as cerato-platanins and HFBs.

My recent publications:

Gao, R., Ding, M., Jiang, S., Zhao, Z., Chenthamara, K., Shen, Q. Cai, F., Druzhinina I.S. 2020. The evolutionary and functional paradox of cerato-platanins in the mycoparasitic fungi. Applied and Environmental Microbiology 86:e00696-20

Jiang S-Q, Yu Y-N, Gao R-W, Wang H, Zhang J, Li R, Long X-H, Shen Q-R, Chen W, Cai F: High-throughput absolute quantification sequencing reveals the effect of different fertilizer applications on bacterial community in a tomato cultivated coastal saline soil. Science of The Total Environment 2019, 687:601-609.