Proteomic analysis reflects an environmental alkalinization-coupled pH-dependent mechanism of regulating lignocellulases in Trichoderma guizhouense NJAU4742

Parascedosporium putredinis NO1 tailors its secretome for different lignocellulosic substrates

Parascedosporium putredinis NO1 is a plant biomass-degrading ascomycete with a propensity to target the most recalcitrant components of lignocellulose. Here we applied proteomics and activity-based protein profiling (ABPP) to investigate the ability of P. putredinis NO1 to tailor its secretome for growth on different lignocellulosic substrates. Proteomic analysis of soluble and insoluble culture fractions following the growth of P. putredinis NO1 on six lignocellulosic substrates highlights the adaptability of the response of the P. putredinis NO1 secretome to different substrates. Differences in protein abundance profiles were maintained and observed across substrates after bioinformatic filtering of the data to remove intracellular protein contamination to identify the components of the secretome more accurately. These differences across substrates extended to carbohydrate-active enzymes (CAZymes) at both class and family levels. Investigation of abundant activities in the secretomes for each substrate revealed similar variation but also a high abundance of "unknown" proteins in all conditions investigated. Fluorescence-based and chemical proteomic ABPP of secreted cellulases, xylanases, and β-glucosidases applied to secretomes from multiple growth substrates for the first time confirmed highly adaptive time- and substrate-dependent glycoside hydrolase production by this fungus. P. putredinis NO1 is a promising new candidate for the identification of enzymes suited to the degradation of recalcitrant lignocellulosic feedstocks. The investigation of proteomes from the biomass bound and culture supernatant fractions provides a more complete picture of a fungal lignocellulose-degrading response. An in-depth understanding of this varied response will enhance efforts toward the development of tailored enzyme systems for use in biorefining.IMPORTANCEThe ability of the lignocellulose-degrading fungus Parascedosporium putredinis NO1 to tailor its secreted enzymes to different sources of plant biomass was revealed here. Through a combination of proteomic, bioinformatic, and fluorescent labeling techniques, remarkable variation was demonstrated in the secreted enzyme response for this ascomycete when grown on multiple lignocellulosic substrates. The maintenance of this variation over time when exploring hydrolytic polysaccharide-active enzymes through fluorescent labeling, suggests that this variation results from an actively tailored secretome response based on substrate. Understanding the tailored secretomes of wood-degrading fungi, especially from underexplored and poorly represented families, will be important for the development of effective substrate-tailored treatments for the conversion and valorization of lignocellulose.

Intracellular kynurenine promotes acetaldehyde accumulation, further inducing the apoptosis in soil beneficial fungi Trichoderma guizhouense NJAU4742 under acid stress

In this study, the growth of fungi Trichoderma guizhouense NJAU4742 was significantly inhibited under acid stress, and the genes related to acid stress were identified based on transcriptome analysis. Four genes including tna1, adh2/4, and bna3 were significantly up-regulated. Meanwhile, intracellular hydrogen ions accumulated under acid stress, and ATP synthesis was induced to transport hydrogen ions to maintain hydrogen ion balance. The enhancement of glycolysis pathway was also detected, and a large amount of pyruvic acid from glycolysis was accumulated due to the activity limitation of PDH enzymes. Finally, acetaldehyde accumulated, resulting in the induction of adh2/4. In order to cope with stress caused by acetaldehyde, cells enhanced the synthesis of NAD⁺ by increasing the expression of tna1 and bna3 genes. NAD⁺ effectively improved the antioxidant capacity of cells, but the NAD⁺ supplement pathway mediated by bna3 could also cause the accumulation of kynurenine (KYN), which was an inducer of apoptosis. In addition, KYN had a specific promoting effect on acetaldehyde synthesis by improving the expression of eno2 gene, which led to the extremely high intracellular acetaldehyde in the cell under acidic stress. Our findings provided a route to better understand the response of filamentous fungi under acid stress.

Promotion of Plant Growth in Arid Zones by Selected Trichoderma spp. Strains with Adaptation Plasticity to Alkaline pH

Trichoderma species are filamentous fungi that support plant health and confer improved growth, disease resistance, and abiotic stress tolerance. The objective of this study is to describe the physiological characteristics of the abundance and structure of Trichoderma model strains from arid zones and evaluate and describe their possible adaptation and modulation in alkaline pH. The presence of biotic factors such as phytopathogens forces farmers to take more actions such as using pesticides. In addition, factors such as the lack of water worldwide lead to losses in agricultural production. Therefore, the search for biocontrol microorganisms that support drought opens the door to the search for variations in the molecular mechanisms involved in these phenomena. In our case, we isolated 11 tested Trichoderma fungal strains from samples collected both from the rhizosphere and roots from two endemic plants. We probed their molecular markers to obtain their identity and assessed their resistance to alkaline conditions, as well as their response to mycoparasitism, plant growth promotion, and drought stress. The findings were worthy of being analyzed in depth. Three fungal taxa/species were grouped by phylogenetic/phenotypic characteristics; three T. harzianum strains showed outstanding capabilities to adapt to alkalinity stress. They also showed antagonistic activity against three phytopathogenic fungi. Additionally, we provided evidence of significant growth promotion in Sorghum bicolor seedlings under endemic agriculture conditions and a reduction in drought damage with Trichoderma infection. Finally, beneficial fungi adapted to specific ambient niches use various molecular mechanisms to survive and modulate their metabolism.

Exploring the multi-level regulation of lignocellulases in the filamentous fungus Trichoderma guizhouense NJAU4742 from an omics perspective

Background

Filamentous fungi are highly efficient at deconstructing plant biomass by secreting a variety of enzymes, but the complex enzymatic regulation underlying this process is not conserved and remains unclear.

Results

In this study, cellulases and xylanases could specifically respond to Avicel- and xylan-induction, respectively, in lignocellulose-degrading strain Trichoderma guizhouense NJAU4742, however, the differentially regulated cellulases and xylanases were both under the absolute control of the same TgXyr1-mediated pathway. Further analysis showed that Avicel could specifically induce cellulase expression, which supported the existence of an unknown specific regulator of cellulases in strain NJAU4742. The xylanase secretion is very complex, GH10 endoxylanases could only be induced by Avicel, while, other major xylanases were significantly induced by both Avicel and xylan. For GH10 xylanases, an unknown specific regulator was also deduced to exist. Meanwhile, the post-transcriptional inhibition was subsequently suggested to stop the Avicel-induced xylanases secretion, which explained the specifically high xylanase activities when induced by xylan in strain NJAU4742. Additionally, an economical strategy used by strain NJAU4742 was proposed to sense the environmental lignocellulose under the carbon starvation condition, that only slightly activating 4 lignocellulose-degrading genes before largely secreting all 33 TgXyr1-controlled lignocellulases if confirming the existence of lignocellulose components.

Conclusions

This study, aiming to explore the unknown mechanisms of plant biomass-degrading enzymes regulation through the combined omics analysis, will open directions for in-depth understanding the complex carbon utilization in filamentous fungi.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01869-3.

Rapid and mass production of biopesticide Trichoderma Brev T069 from cassava peels using newly established solid-state fermentation bioreactor system

Converting agricultural waste into value-added biopesticides to replace chemical pesticides for plant protection is a good alternative for environmental sustainability and resource recycling. In this study, five tropical wastes (cassava peels, banana pseudostem, coconut shell, sugarcane bagasse, and pineapple peels) were screened as substrates for the rapid production of biopesticide Trichoderma Brev T069. Five single tests and a Box-Behnken design (BBD) with response surface methodology were used to optimize the culture conditions to improve the spore yield. The results showed that cassava peel was the optimal solid fermentation substrate, and the optimization enabled a spore yield of 9.31 × 10⁹ spores/g at 3rd day, which was equal to 93.19% of spore yield obtained at 5th day (9.99 × 10⁹ spores/g). A newly packed-bed bioreactor with agitation and ventilation system was developed and used to expand the production that 250 kg of biopesticide (2.89 × 10⁹ spores/g) could be available on the 3rd day. A pot experiment indicated that the biopesticide T. Brev T069 obtained under this production system, when applied at 1 × 10⁷ spores/g of soil had a 64.65% biocontrol efficiency on banana fusarium wilt. This study provides a practical solution for turning a tropical waste into an effective biopesticide which can prevent banana wilt disease, thereby helping to reduce disease management cost and overcome environmental hazards caused by synthetic pesticides.