Chemometric analysis reveals links in the formation of fragrant bio-molecules during agarwood (Aquilaria malaccensis) and fungal interactions

Enzyme Activity of Culturable Fungi and Bacteria Isolated from Traditional Agarwood Fermentation Basin Indicate Temporally Significant Lignocellulosic and Lipid Substrate Modulations

Agarwood oil is one of the costliest essential oils used in perfumery, medicine and aroma. Production of the oil traditionally involves a soaking/fermentation step. Studies have indicated a definite role of the diverse microorganisms growing during the open soaking step, and in the emergent aroma of the essential oil. However, the temporal nature of fermentation and a key functional aspect i.e., the enzymatic properties of the microbes from the fermentation basin have not been studied yet. A total of 20 bacteria and 14 fungi isolated from fermentation basins located in Assam, India, at different soaking periods classified as early (0-20 days), medium (20-40 days) and late (40-60 days) clearly pointed towards an early fungal domination followed by succession of bacteria. The physico-chemical transformations of the wood are controlled by enzymatic properties (cellulase, xylanase, amylase and lipase) of the isolates. The results indicated a strong lignocellulosic substrate modulation potential in the four isolates, viz- Purpureocillium lilacinum (0.354 mg/mL), Mucor circinelloides (0.331 mg/mL), Penicillium citrinum (0.324 mg/mL) and Bacillus megaterium (0.152 mg/mL). The highest culturable abundance (CFU/mL) was found in M. circinelloides (2 × 109) among fungi and B. megaterium (4.5 × 109) among bacteria. The highest cellulase activity was shown by P. lilacinum (0.354 mg/mL) while xylanase and lipase by M. circinelloides (0.873 and 0.128 mg/mL). An interesting revelation was that a substantial proportion of the isolates (70% bacteria and 78% fungi) were positive for lipase activity. This is the first report on the "culturable microbiome" of the agarwood fermentation basin from a temporal and functional bioactivity perspective.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-024-01257-y.

Anatomical, chemical and endophytic fungal diversity of a Qi-Nan clone of Aquilaria sinensis (Lour.) Spreng with different induction times

Recently, some new Qi-Nan clones of Aquilaria sinensis (Lour.) Spreng which intensively produces high-quality agarwood have been identified and propagated through grafting techniques. Previous studies have primarily focused on ordinary A. sinensis and the differences in composition when compared to Qi-Nan and ordinary A. sinensis. There are few studies on the formation mechanism of Qi-Nan agarwood and the dynamic changes in components and endophytic fungi during the induction process. In this paper, the characteristics, chemical composition, and changes in endophytic fungi of Qi-Nan agarwood induced after 1 year, 2 years, and 3 years were studied, and Qi-Nan white wood was used as the control. The results showed that the yield of Qi-Nan agarwood continued to increase with the induction time over a period of 3 years, while the content of alcohol extract from Qi-Nan agarwood reached its peak at two years. During the formation of agarwood, starch and soluble sugars in xylem rays and interxylary phloem are consumed and reduced. Most of the oily substances in agarwood were filled in xylem ray cells and interxylary phloem, and a small amount was filled in xylem vessels. The main components of Qi-Nan agarwood are also chromones and sesquiterpenes. With an increasing induction time, the content of sesquiterpenes increased, while the content of chromones decreased. The most abundant chromones in Qi-Nan agarwood were 2-(2-Phenethyl) chromone, 2-[2-(3-Methoxy-4-hydroxyphenyl) ethyl] chromone, and2-[2-(4-Methoxyphenyl) ethyl] chromone. Significant differences were observed in the species of the endophytic fungi found in Qi-Nan agarwood at different induction times. A total of 4 phyla, 73 orders, and 448 genera were found in Qi-Nan agarwood dominated by Ascomycota and Basidiomycota. Different induction times had a significant effect on the diversity of the endophytic fungal community in Qi-Nan. After the induction of agarwood formation, the diversity of Qi-Nan endophytic fungi decreased. Correlation analysis showed that there was a significant positive correlation between endophytic fungi and the yield, alcohol extract content, sesquiterpene content, and chromone content of Qi-Nan agarwood, which indicated that endophytic fungi play a role in promoting the formation of Qi-Nan agarwood. Qi-Nan agarwood produced at different induction times exhibited strong antioxidant capacity. DPPH free radical scavenging activity and reactive oxygen species clearance activity were significantly positively correlated with the content of sesquiterpenes and chromones in Qi-Nan agarwood.

Fungal-Bacterial Combinations in Plant Health under Stress: Physiological and Biochemical Characteristics of the Filamentous Fungus Serendipita indica and the Actinobacterium Zhihengliuella sp. ISTPL4 under In Vitro Arsenic Stress

Fungal-bacterial combinations have a significant role in increasing and improving plant health under various stress conditions. Metabolites secreted by fungi and bacteria play an important role in this process. Our study emphasizes the significance of secondary metabolites secreted by the fungus Serendipita indica alone and by an actinobacterium Zhihengliuella sp. ISTPL4 under normal growth conditions and arsenic (As) stress condition. Here, we evaluated the arsenic tolerance ability of S. indica alone and in combination with Z. sp. ISTPL4 under in vitro conditions. The growth of S. indica and Z. sp. ISTPL4 was measured in varying concentrations of arsenic and the effect of arsenic on spore size and morphology of S. indica was determined using confocal microscopy and scanning electron microscopy. The metabolomics study indicated that S. indica alone in normal growth conditions and under As stress released pentadecanoic acid, glycerol tricaprylate, L-proline and cyclo(L-prolyl-L-valine). Similarly, d-Ribose, 2-deoxy-bis(thioheptyl)-dithioacetal were secreted by a combination of S. indica and Z. sp. ISTPL4. Confocal studies revealed that spore size of S. indica decreased by 18% at 1.9 mM and by 15% when in combination with Z. sp. ISTPL4 at a 2.4 mM concentration of As. Arsenic above this concentration resulted in spore degeneration and hyphae fragmentation. Scanning electron microscopy (SEM) results indicated an increased spore size of S. indica in the presence of Z. sp. ISTPL4 (18 ± 0.75 µm) compared to S. indica alone (14 ± 0.24 µm) under normal growth conditions. Our study concluded that the suggested combination of microbial consortium can be used to increase sustainable agriculture by combating biotic as well as abiotic stress. This is because the metabolites released by the microbial combination display antifungal and antibacterial properties. The metabolites, besides evading stress, also confer other survival strategies. Therefore, the choice of consortia and combination partners is important and can help in developing strategies for coping with As stress.

Progressive Vertical and Horizontal Phytocompound Changes during Agarwood Formation in Aquilaria sinensis after Geotrichum candidum Injection

(1) Background: Agarwood is an aromatic resin produced by the host tree through an immunological response against biotic and abiotic stress. The aim was, first, to use the fungus Geotrichum candidum to stimulate compound changes in Aquilaria sinensis horizontally (color formation) and vertically (cutting layers) after injection with it. (2) Methods: Horizontal and vertical sections were collected and separated five months after injection with the fungal broth. Two grams of dry powder was mixed with 20 mL methanol for 3 h at room temperature, and the solution was vibrated in an ultrasonic cleaner bath at 40 °C for 1 h. After vacuum drying, a concentration of 10 mg/mL of the tested samples in methanol was prepared for reversed-phase high-performance liquid chromatography (RP-HPLC), gas chromatography/mass spectrometry (GC/MS), and thin-layer chromatography (TLC) analysis. (3) Results: The horizontal changes in the compounds and their concentrations were associated with color. Compared to the normal (N) group, G. candidum injection stimulated more compounds at RT 27-42 in the white (W) group, brown (BR) group, and black (B) group. Furthermore, a significant increase in fatty acids was observed in the W group, implying an early plant response after G. candidum injection. In the BR group, the compounds were more similar to commercial agarwood (Out group). In the B group, alkaloids were the main compounds. Vertical changes in the main compounds were not observed, although the compound level varied. A TLC analysis determined the main compounds in the BR group at 254 nm and in the B group at 365 nm. Higher fatty acid levels were found in L6 and L5 and were correlated with higher terpenoid and sesquiterpene levels, suggesting that these compounds were possibly the first stage of agarwood formation. A GC/MS analysis demonstrated that the main compound groups were almost identical to the BR parts. (4) Conclusions: The injection of G. candidum led A. sinensis to synthesize different phytochemicals horizontally, not vertically, in the BR group.

Agarwood-The Fragrant Molecules of a Wounded Tree

Agarwood, popularly known as oudh or gaharu, is a fragrant resinous wood of high commercial value, traded worldwide and primarily used for its distinctive fragrance in incense, perfumes, and medicine. This fragrant wood is created when Aquilaria trees are wounded and infected by fungi, producing resin as a defense mechanism. The depletion of natural agarwood caused by overharvesting amidst increasing demand has caused this fragrant defensive resin of endangered Aquilaria to become a rare and valuable commodity. Given that instances of natural infection are quite low, artificial induction, including biological inoculation, is being conducted to induce agarwood formation. A long-term investigation could unravel insights contributing toward Aquilaria being sustainably cultivated. This review will look at the different methods of induction, including physical, chemical, and biological, and compare the production, yield, and quality of such treatments with naturally formed agarwood. Pharmaceutical properties and medicinal benefits of fragrance-associated compounds such as chromones and terpenoids are also discussed.

Effects of various artificial agarwood-induction techniques on the metabolome of Aquilaria sinensis

BACKGROUND

Agarwood is a highly sought-after resinous wood for uses in medicine, incense, and perfume production. To overcome challenges associated with agarwood production in Aquilaria sinensis, several artificial agarwood-induction treatments have been developed. However, the effects of these techniques on the metabolome of the treated wood samples are unknown. Therefore, the present study was conducted to evaluate the effects of four treatments: fire drill treatment (F), fire drill + brine treatment (FS), cold drill treatment (D) and cold drill + brine treatment (DS)) on ethanol-extracted oil content and metabolome profiles of treated wood samples from A. sinensis.

RESULTS

The ethanol-extracted oil content obtained from the four treatments differed significantly (F < D < DS < FS). A total of 712 metabolites composed mostly of alkaloids, amino acids and derivatives, flavonoids, lipids, phenolic acids, organic acids, nucleotides and derivatives, and terpenoids were detected. In pairwise comparisons, 302, 155, 271 and 363 differentially accumulated metabolites (DAM) were detected in F_vs_FS, D_vs_DS, F_vs_D and FS_vs_DS, respectively. The DAMs were enriched in flavonoid/flavone and flavonol biosynthesis, sesquiterpenoid and triterpenoid biosynthesis. Generally, addition of brine to either fire or cold drill treatments reduced the abundance of most of the metabolites.

CONCLUSION

The results from this study offer valuable insights into synthetically-induced agarwood production in A. sinensis.

Utilization of starch effluent from a textile industry as a fungal growth supplement for enhanced α-amylase production for industrial application

Desizing process in textile industry produces large volume of starch effluent. This carbon-rich waste can be used for resource recovery, such as the production of industrially useful enzymes. The present work assesses the usability of starch effluent from textile industry as an additional carbon source for enhanced production of α-amylase during solid-state fermentation (SSF) of agro-wastes by Trichoderma reesei. A significant increase (p ≤ 0.05) in α-amylase activity (25.48 ± 1.12 U mL^-1) was observed with supplementation of starch effluent in SSF. Partial purification of α-amylase by 80% ammonium sulphate precipitation produced a yield of 58.39% enzyme with purification fold of 1.89. The enzyme was thermally stable at 40 °C with 90% residual activity after 5 h and 70% residual activity at 50 °C after 3 h. Using Michaelis-Menten kinetics analysis, the estimated K_m and V_max values for the partially purified α-amylase were found to be 2.55 mg mL^-1 and 53.47 U mg^-1, respectively. For the rapid assessment of the industrial application, desizing of the fabric was attempted. The cotton fabric was efficiently desized using α-amylase (at a concentration of 1% on the weight of fabric basis) at 80 °C. The present work demonstrates starch effluent from desizing process as a resource for the production of amylase. The amylase can further be used in the desizing process. With in-depth research, the work may lead to the development of a closed-loop, waste-recycling process for the textile industry.

Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum

Agarwood, one of the precious woods in the globe, is produced by Aquilaria plant species during an upshot of wounding and infection. Produced as a defence response, the dark, fragrant resin gets secreted in the plant's duramen, which is impregnated with fragrant molecules with the due course. Agarwood has gained worldwide popularity due to its high aromatic oil, fragrance, and pharmaceutical value, which makes it highly solicited by numerous industries. Predominant chemical constituents of agarwood, sesquiterpenoids, and 2-(2-phenylethyl) chromones have been scrutinized to comprehend the scientific nature of the fragrant wood and develop novel products. However, the genes involved in the biosynthesis of these aromatic compounds are still not comprehensively studied in Aquilaria. In this study, publicly available genomic and transcriptomics data of Aquilaria agallochum were integrated to identify putative functional terpene synthase genes (TPSs). The in silico study enabled us to identify ninety-six TPSs, of which thirty-nine full-length genes were systematically classified into TPS-a, TPS-b, TPS-c, TPS-e, TPS-f, and TPS-g subfamilies based on their gene structure, conserve motif, and phylogenetic comparison with TPSs from other plant species. Analysis of the cis-regulatory elements present upstream of AaTPSs revealed their association with hormone, stress and light responses. In silico expression studies detected their up-regulation in stress induced tissue. This study provides a basic understanding of terpene synthase gene repertoire in Aquilaria agallochum and unlatches opportunities for the biochemical characterization and biotechnological exploration of these genes.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01040-z.

Methyl jasmonate and crude extracts of Fusarium solani elicit agarwood compounds in shoot culture of Aquilaria malaccensis Lamk

Agarwood forms in the heartwood of trees in the family Thymelaeaceae in response to wounding, infection, or other stresses. Its formation is random and takes decades in natural populations, which are harvested for their aromatic compounds. This harvest has led to declining population, and many agarwood producing trees are considered endangered. Therefore, an alternative source would be desirable. We established an in vitro shoot culture method for one agarwood species, Aquillaria malaccensis. Agarwood production was elicited by introducing methyl jasmonate (MeJA) and crude extracts of Fusarium solani into the liquid culture medium. A high concentration of MeJA resulted in necrotic shoot tissue, while application of the crude extracts had no effect on growth of the shoots. Interestingly, gas chromatography-mass spectrometry (GC-MS) analysis of MeJA-treated shoots revealed the presence of several agarwood compounds, including sesquiterpenes and chromone derivative. In addition, GC-MS analysis of shoot-treated with the extracts revealed the presence of alkanes, aromatic compounds, and fatty acid derivatives. It may be that different elicitors induce the production of different compounds in A. malaccensis in vitro shoot cultures and could be used to manipulate the accumulation of different products in culture.

Fusarium solani induces the formation of agarwood in Gyrinops versteegii (Gilg.) Domke branches

Agarwood is a resinous wood produced by some members of plant family Thymelaeaceae under certain conditions. Agarwood is highly prized, but its formation requires a long-time process in nature. Therefore, various induction techniques have been explored to hasten the process. In this study, we induced agarwood in Gyrinops versteegii, one of the most abundant agarwood-producing trees in Indonesia. We used 12 trees and wounded four branches on each tree through an injection process. We used two strains of the endophytic fungi Fusarium solani isolated from Gorontalo and Jambi Provinces. After 3 months, the inoculated wood had an extensive resinous zone, when compared to wounded control wood. Gas chromatographic-mass spectrometric analysis of the inoculated samples revealed the presence of several sesquiterpenes characteristic of agarwood. These included alloaromadendrene, β-eudesmol and β-selinene as well as the chromone derivatives 2-(2-phenylethyl) chromen-4-one, 6-methoxy-2-(2-phenylethyl) chromen-4-one, and 6,7-dimethoxy-2-(2-phenylethyl) chromen-4-one. We conclude that this method successfully induced agarwood to form in a matter of months and could be used to enhance the success of agarwood cultivation.

The Scent of Stress: Evidence From the Unique Fragrance of Agarwood

Agarwood (Aquilaria spp.) fragrance and its origin in stress make it probably the most suitable model to study stress-induced aroma. Production being confined only to certain small pockets of South and Southeast Asia, agarwood is arguably the costliest wood in the world. Formation of fragrant agarwood resin is the outcome of complex biotic, abiotic, and physical stress on the Aquilaria trees. The intricate mechanism by which some 150 odd fragrant molecules that constitute agarwood aroma is formed is still not clearly understood. The present review therefore aims to bring to focus this less known but highly valuable stress-induced aroma from Asia. Discussions on agarwood species, occurrence, distribution, formation, and products have been included as foundation. Although global trade in agarwood and its products is estimated at US$6 billion to US$8 billion, no reliable data are readily available in literature. Therefore, an effort has been made to review the current status of agarwood trade. The element of stress and its correlation to agarwood aroma is discussed in the subsequent sections. Natural agarwood formation as well as technologies and interventions in agarwood induction are stress-based (natural and artificial injury, insect and fungal attack, chemical induction). The molecular triggers are gradually coming to light as new studies are implicating jasmonate, LOX signaling, and other stress reaction routes as the source of agarwood aroma. This review therefore has strived to compile the information that is scattered across scientific as well as other authentic literature and update the reader on the current status. More information about the specific roles of other vital stressors like insects, abiotic, and genetic factors is eagerly awaited from ongoing and future research to further understand the unique fragrance of agarwood.

Evolutionary analysis and structural characterization of Aquilaria sinensis sesquiterpene synthase in agarwood formation: A computational study

Agarwood originating from Aquilaria sinensis contains sesquiterpenoids that have tremendous commercial value in the pharmaceutical and fragrance industries. Aquilaria sinensis sesquiterpene synthase (AsSTS) is the key enzyme in the agarwood biosynthesis pathway, and its activity directly affects the chemical composition of agarwood; however, its role in species evolution remains unclear. In this study, we performed an evolutionary analysis based on 68 plant sesquiterpene synthase (STS) genes and further structural characterization of the gene encoding AsSTS to explore its molecular evolution. The phylogenetic tree indicated that these STS genes included three subfamilies. Additionally, 23 positively selected sites were detected, and no influence of recombination was found. Furthermore, the protein structure of AsSTS was characterized using primary sequence and structural analyses as having a functional active site lid domain, a substrate binding site, two post-translational modification sites and four conserved motifs. Finally, most virtual mutations of positively selected sites could be stabilized against thermal denaturation by a decrease in free energy, and three virtual mutations (D403R, G470Q and S538K) were shown to play important roles in the function and stability of AsSTS. The molecular evolutionary analysis of plant STSs provides essential clues for further experimental site-directed mutagenesis and molecular modification of AsSTS.

iTRAQ-Based Quantitative Proteomic Analysis of Chemically Induced Aquilaria sinensis Provides Insights into Agarwood Formation Mechanism

Agarwood is a precious traditional Chinese medicine with a variety of pharmacological effects. Although efforts have been made in elucidating the mechanism of agarwood formation, little progress is obtained till now. Therefore, the molecular mechanism of agarwood formation needs to be further explored using different biological approaches. In this study, the quantitative proteomic analysis using iTRAQ technology combined with transcriptomic and metabolomic analyses on chemically induced Aquilaria sinensis is performed to elucidate the agarwood formation mechanism by formic acid stimulus. Data are available via ProteomeXchange with identifier PXD007586; 1884 proteins are detected, 504 differential proteins that show at least twofold differences in their expression levels are selected based on GO annotations, KEGG, STRING analysis, and quantitative RT-PCR analysis. The results indicate that sesquiterpene synthase, germin-like protein, pathogenesis-related protein, 6-phosphogluconate dehydrogenase, lipoyl synthase, and superoxide dismutase play important roles in the agarwood formation, suggesting that the proteins related to the plant defensive response, the removal of peroxide, the disease-resistance, the biosythesis of glycan, fatty acids, and sesquiterpene are crucial for agarwood formation.

α-Glucosidase Inhibition and Antibacterial Activity of Secondary Metabolites from the Ecuadorian Species Clinopodium taxifolium (Kunth) Govaerts

The phytochemical investigation of both volatile and fixed metabolites of Clinopodium taxifolium (Kunth) Govaerts (Lamiaceae) was performed for the first time. It allowed the isolation and characterization of the essential oil and six known compounds: carvacrol (1), squalane (2), uvaol (3), erythrodiol (4), ursolic acid (5), and salvigenin (6). Their structures were identified and characterized by Nuclear Magnetic Resonance (NMR) and Gas Chromatography coupled to Mass Spectroscopy (GC-MS), and corroborated by literature. The essential oil of the leaves was obtained by hydrodistillation in two different periods and analyzed by GC-MS and GC coupled to Flame Ionization Detector (GC-FID). A total of 54 compounds were detected, of which 42 were identified (including trace constituents). The major constituents were carvacrol methyl ether (18.9-23.2%), carvacrol (13.8-16.3%) and, carvacryl acetate (11.4-4.8%). The antibacterial activities were determined as Minimum Inhibition Concentration (MIC) against Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae, Proteus vulgaris, Pseudomonas aeruginosa and Micrococcus luteus. The hexane and methanol extracts exhibited activity only against Klebsiella pneumoniae (250 and 500 μg/mL respectively), while the ethyl acetate extract was inactive. The hypoglycemic activity was evaluated by the in vitro inhibition of α-glucosidase. The ethyl acetate (EtOAc) extract showed strong inhibitory activity with IC50 = 24.88 µg/mL, however methanolic and hexanic extracts showed weak activity. As a pure compound, only ursolic acid showed a strong inhibitory activity, with IC50 = 72.71 μM.