A visiting researcher working on the taxonomy and identification of Trichoderma
Kai Dou
Peijie Chen
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.
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
Siqi Jiang
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
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.
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
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
Druzhinina et al. 2018 Massive lateral transfer of genes encoding plant cell wall-degrading enzymes to the mycoparasitic fungus Trichoderma from its plant-associated hosts
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
Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma. A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.
Zhang et al. 2019. Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi: The role of hydrogen peroxide in fungal wars. Environmental Microbiology.
Zhang, J., Miao, Y., Rahimi, M.J., Zhu, H., Steindorff, A., Schiessler, S., Cai, F., Pang, G., Chenthamara, K., Xu, Y., Kubicek, C.P., Shen, Q.*, Druzhinina, I.S.*, 2019. Guttation capsules containing hydrogen peroxide: an evolutionarily conserved NADPH oxidase gains a role in wars between related fungi: The role of hydrogen peroxide in fungal wars. Environmental Microbiology.
When resources are limited, the hypocrealean fungus Trichoderma guizhouense can overgrow another hypocrealean fungus Fusarium oxysporum, cause sporadic cell death and arrest growth. A transcriptomic analysis of this interaction shows that T. guizhouense undergoes a succession of metabolic stresses while F. oxysporum responded relatively neutrally but used the constitutive expression of several toxin-encoding genes as a protective strategy. Because of these toxins, T. guizhouense cannot approach it is potential host on the substrate surface and attacks F. oxysporum from above. The success of T. guizhouense is secured by the excessive production of hydrogen peroxide (H2 O2 ), which is stored in microscopic bag-like guttation droplets hanging on the contacting hyphae. The deletion of NADPH oxidase nox1 and its regulator, nor1 in T. guizhouense led to a substantial decrease in H2 O2 formation with concomitant loss of antagonistic activity. We envision the role of NOX proteins in the antagonism of T. guizhouense as an example of metabolic exaptation evolved in this fungus because the primary function of these ancient proteins was probably not linked to interfungal relationships. In support of this, F. oxysporum showed almost no transcriptional response to T. guizhouense Δnox1 strain indicating the role of NOX/H2 O2 in signalling and fungal communication.
Kubicek et al. 2019. Evolution and comparative genomics of the most common Trichoderma species. BMC Genomics 20.
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 specieshttps://pubmed.ncbi.nlm.nih.gov/31189469/. BMC Genomics 20.
Background
The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood.
Results
We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function.
Conclusions
Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.
Jiang et al. 2019 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
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.
Coastal saline soil is an important reserve land resource that has high potential for agricultural utilization. The present study adopted a high-throughput absolute quantification 16S rRNA sequencing method to investigate the effect of four different fertilization regimes (namely 100% of bio-organic fertilizer, 70% of bio-organic fertilizer +30% of chemical fertilizer, 30% of bio-organic fertilizer +70% of chemical fertilizer, and 100% of chemical fertilizer) on bacterial community assembly in a tomato cultivated saline soil. The results from the field experiment showed that a combination of 70% bio-organic fertilizer plus 30% of chemical fertilizer was the optimal dose to develop tomato cultivation (for improving yield and fruit quality) in this coastal tidal zone. The pot experiment gave the similar results on tomato growth and indicated the application of 70% bio-organic fertilizer plus 30% of chemical fertilizer as the best treatment to active the soil microbiome. The input of nutrients by fertilizers increased the total abundance of bacteria (to >3 fold compared to the initial soil) and simultaneously led to a significant loss of bacterial diversity in soil. The predominant phyla including Proteobacteria, Bacteroidetes and Firmicutes were the main contributors in the microbiome shift especially shown by their remarkable enrichment in the soil that treated by 70% of bio-organic fertilizer and those by the 100% chemical fertilizer. The RDA and Pearson correlation analyses indicated that the soil nutrient availability, especially available P and K, and soil salinity were the key environmental factors that shaped the bacterial community in this ecosystem, though the organic matter content and soil pH also played important roles in microbiome assembly.
Keywords: Absolute quantification 16S-seq; Bio-organic fertilizer; Coastal mud flat; Microbiome; Tomato cultivation.
Fungi around us: Penicillium digitatum
Marcet-Houben et al., 2012 “Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus” BMC Genomics