Biodiversity of Trichoderma Community in the Tidal Flats and Wetland of Southeastern China

Diversity of Trichoderma species associated with the black rot disease of Gastrodia elata, including four new species

Introduction

Trichoderma species establish symbiotic relationships with plants through both parasitic and mutualistic mechanisms. While some Trichoderma species act as plant pathogenic fungi, others utilize various strategies to protect and enhance plant growth.

Methods

Phylogenetic positions of new species of Trichoderma were determined through multi-gene analysis relying on the internal transcribed spacer (ITS) regions of the ribosomal DNA, the translation elongation factor 1-α (tef1-α) gene, and the RNA polymerase II (rpb2) gene. Additionally, pathogenicity experiments were conducted, and the aggressiveness of each isolate was evaluated based on the area of the cross-section of the infected site.

Results

In this study, 13 Trichoderma species, including 9 known species and 4 new species, namely, T. delicatum, T. robustum, T. perfasciculatum, and T. subulatum were isolated from the diseased tubers of Gastrodia elata in Yunnan, China. Among the known species, T. hamatum had the highest frequency. T. delicatum belonged to the Koningii clade. T. robustum and T. perfasciculatum were assigned to the Virens clade. T. subulatum emerged as a new member of the Spirale clade. Pathogenicity experiments were conducted on the new species T. robustum, T. delicatum, and T. perfasciculatum, as well as the known species T. hamatum, T. atroviride, and T. harzianum. The infective abilities of different Trichoderma species on G. elata varied, indicating that Trichoderma was a pathogenic fungus causing black rot disease in G. elata.

Discussion

This study provided the morphological characteristics of new species and discussed the morphological differences with phylogenetically proximate species, laying the foundation for research aimed at preventing and managing diseases that affect G. elata.

Exploring Trichoderma Species in Industrial Wastewater: Morphological and Molecular Insights from Isolates

The genus Trichoderma holds economic significance due to its widespread distribution and diverse applications, including biological control, enzyme production, and various biotechnological uses. The accurate identification of Trichoderma species is crucial given their close association with human activities. Despite previous efforts in classification, a comprehensive analysis combining morphological and molecular approaches is necessary. This study focuses on the isolation of four Trichoderma species from industrial wastewater in Pakistan, expanding on the known diversity in the region; isolation involved collecting samples from industrial wastewater effluents at specific sites in Punjab, Pakistan. Trichoderma strains were cultured and purified on solid media, with subsequent biomass production for bisorptional activity. Morphological characterization included colony features and microscopic examinations. DNA extraction, polymerase chain reaction (PCR), and sequencing of the internal transcribed spacer (ITS) region were conducted for molecular analysis. Phylogenetic analysis was performed using the Maximum Likelihood Algorithm. The study identified three Trichoderma species, viz. T. citrinoviride, T. erinaceum, and T. longibrachiatum. Each species was characterized morphologically and supported by molecular-phylogenetic analysis. Illustrations of microscopic features and a phylogenetic tree based on the ITS-nrDNA region were recorded. T. citrinoviride and T. longibrachiatum, isolated from steel mill and tanneries wastewater, respectively, were differentiated based on morphological characteristics such as phialides and conidia. The combination of morphological and molecular techniques enhances the accuracy of species identification. The study highlights the significance of Trichoderma in industrial wastewater environments and underscores the need for continued research in this area. Future research should focus on exploring the ecological roles and potential applications of the newly identified Trichoderma species. Additionally, further investigations into the biotechnological potential of these species, including enzyme production and bioremediation capabilities, would contribute to their practical applications.

Genetic diversity and antagonistic properties of Trichoderma strains from the crop rhizospheres in southern Rajasthan, India

There are fewer studies on Trichoderma diversity in agricultural fields. The rhizosphere of 16 crops was analyzed for Trichoderma species in 7 districts of Rajasthan state of India. Based on DNA sequence of translation elongation factor 1α (tef-1α), and morphological characteristics, 60 isolates were identified as 11 species: Trichoderma brevicompactum, species in Harzianum clade identified as T. afroharzianum, T. inhamatum, T. lentiforme, T. camerunense, T. asperellum, T. asperelloides, T. erinaceum, T. atroviride, T. ghanense, and T. longibrachiatum. T. brevicompactum is the most commonly occurring strain followed by T. afroharzianum. No new species were described in this study. T. lentiforme, showed its first occurrence outside the South American continent. The morphological and cultural characteristics of the major species were observed, described, and illustrated in detail. The isolates were tested for their antagonistic effect against three soilborne plant pathogens fungi: Sclerotium rolfsii, Rhizoctonia solani, and Fusarium verticillioides in plate culture assays. One of the most potent strains was T. afroharzianum BThr29 having a maximum in vitro inhibition of S. rolfsii (76.6%), R. solani (84.8%), and F. verticillioides (85.7%). The potential strain T. afroharzianum BThr29 was also found to be efficient antagonists against soil borne pathogens in in vivo experiment. Such information on crop selectivity, antagonistic properties, and geographic distribution of Trichoderma species will be beneficial for developing efficient Trichoderma-based biocontrol agents.

Biological management of coffee wilt disease (Fusarium xylarioides) using antagonistic Trichoderma isolates

Coffee wilt disease (CWD) is a serious threat to the food security of small-scale farmers in Ethiopia, causing significant reductions in coffee yield. Currently, there are no effective control measures available against the causative agent of CWD, Fusarium xylarioides. The main objective of this study was therefore to develop, formulate, and evaluate a range of biofungicides against F. xylarioides, derived from Trichoderma species and tested under in vitro, greenhouse, and field conditions. In total, 175 Trichoderma isolates were screened as microbial biocontrol agents against F. xylarioides. The efficacy of two biofungicide formulations, wettable powder and water dispensable granules, were tested on the susceptible Geisha coffee variety in three different agro-ecological zones in southwestern Ethiopia over three years. The greenhouse experiments were set up using a complete block design, while in the field a randomized complete block design was used, with twice yearly applications of biofungicide. The test pathogen spore suspension was applied to the coffee seedlings by soil drenching, and the subsequent incidence and severity of CWD evaluated annually. The mycelial growth inhibition profiles of the Trichoderma isolates against F. xylarioides ranged from 44.5% to 84.8%. In vitro experiments revealed that T. asperelloides AU71, T. asperellum AU131 and T. longibrachiatum AU158 reduced the mycelial growth of F. xylarioides by over 80%. The greenhouse study indicated that wettable powder (WP) of T. asperellum AU131 had the highest biocontrol efficacy (84.3%), followed by T. longibrachiatum AU158 (77.9%) and T. asperelloides AU71 (71.2%); they also had a significant positive impact on plant growth. The pathogen-treated control plants had a disease severity index of 100% across all the field experiments, and of 76.7% in the greenhouse experiments. In comparison to untreated controls, the annual and cumulative disease incidence over the three years of the study period varied from 46.2 to 90%, 51.6 to 84.5%, and 58.2 to 91%, at the Teppi, Gera and Jimma field experimental locations. Overall, the greenhouse and field experiments and in vitro assays support the biocontrol potential of Trichoderma isolates, and T. asperellum AU131 and T. longibrachiatum AU158 in particular are recommended for the management of CWD under field conditions.

Endophytic Fungi Associated with Coffee Leaves in China Exhibited In Vitro Antagonism against Fungal and Bacterial Pathogens

Coffee endophytes have been studied for almost 74 years, and several studies have demonstrated coffee-endophytic fungi with antibacterial and antifungal potential for human and plant pathogens. In this study, we isolated and identified a total of 235 strains of endophytic fungi from coffee leaf tissues collected in four coffee plantations in Pu’er city, Yunnan province, China. Molecular identification was carried out using maximum likelihood phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS1-5.8S rDNA-ITS2) sequences, while the colonization rate and the isolation frequency were also calculated. Two pathogenic fungi (Alternaria alternata and Penicillium digitatum) and two pathogenic bacteria (Pseudomonas syringae and Salmonella enterica subsp. enterica) were used for screening the antagonistic activities of 61 strains of coffee-endophytic fungi by a dual-culture test assay while maximum likelihood phylogenetic analysis confirmed their natural classification. This is the first study of coffee-leaf-endophytic fungal diversity in China, and the results revealed that coffee-endophytic fungi from this study belong to the Ascomycota, distributed among two classes, 10 orders, and 17 families. Concurrently, endophytic fungi isolates distributed in Arthrinium, Biscogniauxia, Daldinia, Diaporthe, and Nigrospora showed strong antagonistic activities against the pathogens. For the pathogens Alternaria alternata and Pseudomonas syringae, Nigrospora XCE-7 showed the best inhibitory effects with inhibition rates of 71.76% and 61.11%, respectively. For the pathogen Penicillium digitatum, Daldinia ME-9 showed the best inhibitory effect with a 74.67% inhibition rate, while Biscogniauxia PTE-7 and Daldinia T5E-1-3 showed the best inhibitory effect with a rate of 60.42% against the pathogen Salmonella enterica subsp. enterica. Overall, our study shows the diversity of coffee endophytes in four coffee-growing areas in Pu’er city, Yunnan province, China, and their potential use as biological control agents against two fungal and two bacterial pathogens.

Microbial Depolymerization of Epoxy Resins: A Novel Approach to a Complex Challenge

The objective of this project is evaluating the potential of microbes (fungi and bacteria) for the depolymerization of epoxy, aiming at the development of a circular management of natural resources for epoxy in a long-term prospective. For depolymerization, epoxy samples were incubated for 1, 3, 6 and 9 months in soil microcosms inoculated with Ganoderma adspersum. Contact angle data revealed a reduction in the hydrophobicity induced by the fungus. Environmental scanning electron microscopy on epoxy samples incubated for more than 3 years in microbiological water revealed abundant microbiota. This comprised microbes of different sizes and shapes. The fungi Trichoderma harzianum and Aspergillus calidoustus, as well as the bacteria Variovorax sp. and Methyloversatilis discipulorum, were isolated from this environment. Altogether, these results suggest that microbes are able to colonize epoxy surfaces and, most probably, also partially depolymerize them. This could open promising opportunities for the study of new metabolisms potentially able depolymerize epoxy materials.

Isolation of Polysaccharides from Trichoderma harzianum with Antioxidant, Anticancer, and Enzyme Inhibition Properties

In this work, a total of six polysaccharides were isolated from culture filtrate (EPS1, EPS2) and mycelia (IPS1-IPS4) of Trichoderma harzianum. The HPLC analysis results showed that EPS1, EPS2, IPS1, and IPS2 were composed of mannose, ribose, glucose, galactose, and arabinose. The FT-IR, 1H, and 13C NMR chemical shifts confirmed that the signals in EPS1 mainly consist of (1→4)-linked α-d-glucopyranose. EPS1 and IPS1 showed a smooth and clean surface, while EPS2, IPS2, and IPS3 exhibited a microporous structure. Among polysaccharides, EPS1 displayed higher ABTS+ (47.09 ± 2.25% and DPPH (26.44 ± 0.12%) scavenging activities, as well as higher α-amylase (69.30 ± 1.28%) and α-glucosidase (68.22 ± 0.64%) inhibition activity than the other polysaccharides. EPS1 exhibited high cytotoxicity to MDA-MB293 cells, with an IC50 of 0.437 mg/mL, and this was also confirmed by cell staining and FACS assays. These results report the physicochemical and bioactive properties of polysaccharides from T. harzianum.

Biodiversity of Trichoderma from grassland and forest ecosystems in Northern Xinjiang, China

Trichoderma spp., a cosmopolitan fungal genus, has remarkable economic value in industry and agriculture. The resources of Trichoderma spp. in the grassland and forest ecosystems of northern Xinjiang were explored in this study. A total of 634 soil samples was collected, and 312 strains assigned to 23 species of Trichoderma spp. were identified. T. harzianum was the dominant species with 28.2% from all isolates. The principal components analysis indicated that ecosystem was the most dominant impact factor among longitude, latitude, altitude and ecosystems for the species diversities of Trichoderma spp. with the decreasing trend from the north to the south of northern Xinjiang (e.g., from Altay, followed by Yili, Changji, Bayingolin and finally Urumqi). Overall, Trichoderma spp. were more frequently encountered in forest ecosystems (coniferous forest and coniferous and broadleaf mixed forest) than in grassland ecosystems (desert steppe and temperate steppe). Frequency of Trichoderma spp. was significantly decreased along with increased altitude and only a few strains were isolated from altitudes above 3000 m. The results provided essential information on Trichoderma occurrence and distribution, which should benefit the application of Trichoderma in agriculture.

El-Meihy R. Phylogenetic Diversity of Trichoderma Strains and Their Antagonistic Potential against Soil-Borne Pathogens under Stress Conditions

Trichoderma species are known as excellent biocontrol agents against soil-borne pathogens that cause considerable crop losses. Eight strains of Trichoderma were isolated from five Egyptian regions. They identified based on translation elongation factor-1α (TEF1) sequencing as four different Trichoderma species: Trichoderma asperellum, Trichoderma harzianum, Trichoderma viride, and Trichoderma longibrachiatum. Optimal growth conditions (temperature and media), and the phosphate solubilization capability of Trichoderma strains were evaluated in vitro. Further, the ability of these strains to antagonize Fusarium solani, Macrophomina phaseolina, and Fusarium graminearum was also evaluated. The results revealed that Trichoderma harzianum (Th6) exhibited the highest antagonistic ability against F. solani, M. phaseolina and F. graminearum with inhibition rates of 71.42%, 72.97%, and 84.61%, respectively. Trichoderma viride (Tv8) exhibited the lowest antagonism against the same pathogens with inhibition rates of 50%, 64% and 69.23%, respectively. Simple-sequence repeats (SSRs) and random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic variability of the Trichoderma strains. The results revealed that of 45 RAPD amplified bands, 36 bands (80%) were polymorphic and of SSRs amplified 36 bands, 31 bands (86.11%) were polymorphic. The amplification of calmodulin and β-1,3-endoglucanase was noted at 500 bp and 230 bp, respectively. Data indicated that T. viride (Tv8) had the highest phosphate solubilization index (10.0 mm), while T. harzianum (Th6) had the lowest phosphate solubilization index (4.0 mm). In conclusion, T. harzianum (Th6) had the highest antagonistic activity in dual culture assay along with the growth rate; while T. viride (Tv8) had the highest phosphate solubilization activity. There are still gaps in obtaining new formulations, selecting potent Trichoderma strains to confirm disease control in planta. For improving Trichoderma recommendation in the organic agricultural system and sustaining the fertility of the soil, the field application of highly antagonistic biocontrol agents in different types of soil and plant species will be the first approach toward bio-pesticide treatments along with bio-fertilizer inoculation. Furthermore, secondary metabolites will be investigated for the most promising strains with the combination of different pathogens and application timing.

Fungal Diversity in Intertidal Mudflats and Abandoned Solar Salterns as a Source for Biological Resources

Intertidal zones are unique environments that are known to be ecological hot spots. In this study, sediments were collected from mudflats and decommissioned salterns on three islands in the Yellow Sea of South Korea. The diversity analysis targeted both isolates and unculturable fungi via Illumina sequencing, and the natural recovery of the abandoned salterns was assessed. The phylogeny and bioactivities of the fungal isolates were investigated. The community analysis showed that the abandoned saltern in Yongyudo has not recovered to a mudflat, while the other salterns have almost recovered. The results suggested that a period of more than 35 years may be required to return abandoned salterns to mudflats via natural restoration. Gigasporales sp. and Umbelopsis sp. were selected as the indicators of mudflats. Among the 53 isolates, 18 appeared to be candidate novel species, and 28 exhibited bioactivity. Phoma sp., Cladosporium sphaerospermum, Penicillium sp. and Pseudeurotium bakeri, and Aspergillus urmiensis showed antioxidant, tyrosinase inhibition, antifungal, and quorum-sensing inhibition activities, respectively, which has not been reported previously. This study provides reliable fungal diversity information for mudflats and abandoned salterns and shows that they are highly valuable for bioprospecting not only for novel microorganisms but also for novel bioactive compounds.

Trichoderma cyanodichotomus sp. nov., a new soil-inhabiting species with a potential for biological control

During a biodiversity survey of Trichoderma (Ascomycota, Hypocreales, Hypocreaceae) in coastal and lake wetlands of China, a new species, Trichoderma cyanodichotomus, was isolated from Dongting Lake wetland of Hunan province. The strain TW21990-1 was characterized as having two types of conidia and producing a distinct blue–green pigment on potato dextrose agar and cornmeal dextrose agar. The taxonomic position was analyzed using three molecular markers, internal transcribed spacer rDNA, translation elongation factor 1-alpha, and RNA polymerase II subunit B, revealing less than 95.0% homology with all known Trichoderma species. The combined phylogenetic tree further identified T. cyanodichotomus as an independent subgroup belonging to Section Pachybasium, with no close relatives. In vitro antagonistic activity by dual-culture assay exhibited broad inhibition against various plant pathogens, including Botryosphaeria dothidea, Pythium aphanidermatum, Rhizoctonia solani, and Verticillium dahliae. In addition, TW21990-1 demonstrated moderate hydrolase activity of cellulase, chitinase, β-1,3-glucanase, and protease, which might be involved in mycoparasitism. Greenhouse experiments showed strong biocontrol effects against tomato damping-off incited by P. aphanidermatum, together with increased seedling height and weight gain. The identification of T. cyanodichotomus will provide useful information for sufficient utilization of fungal resources.

Effect of Trichoderma harzianum on maize rhizosphere microbiome and biocontrol of Fusarium Stalk rot

Fusarium stalk rot (FSR) caused by Fusarium graminearum (FG) significantly affects the productivity of maize grain crops. Application of agrochemicals to control the disease is harmful to environment. In this regard, use of biocontrol agent (BCA) is an alternative to agrochemicals. Although Trichoderma species are known as BCA, the selection of host-pathogen specific Trichoderma is essential for the successful field application. Hence, we screened a total of 100 Trichoderma isolates against FG, selected Trichoderma harzianum (CCTCC-RW0024) for greenhouse experiments and studied its effect on changes of maize rhizosphere microbiome and biocontrol of FSR. The strain CCTCC-RW0024 displayed high antagonistic activity (96.30%), disease reduction (86.66%), biocontrol-related enzyme and gene expression. The root colonization of the strain was confirmed by eGFP tagging and qRT-PCR analysis. Pyrosequencing revealed that exogenous inoculation of the strain in maize rhizosphere increased the plant growth promoting acidobacteria (18.4%), decreased 66% of FG, and also increased the plant growth. In addition, metabolites of this strain could interact with pathogenicity related transcriptional cofactor FgSWi6, thereby contributing to its inhibition. It is concluded that T. harzianum strain CCTCC-RW0024 is a potential BCA against FSR.