Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions

Potential of Trichoderma virens HZA14 in Controlling Verticillium Wilt Disease of Eggplant and Analysis of Its Genes Responsible for Microsclerotial Degradation

Verticillium dahliae is a soilborne fungal pathogen that causes vascular wilt diseases in a wide range of economically important crops, including eggplant. Trichoderma spp. are effective biological control agents that suppress a wide range of plant pathogens through a variety of mechanisms, including mycoparasitism. However, the molecular mechanisms of mycoparasitism of Trichoderma spp. in the degradation of microsclerotia of V. dahliae are not yet fully understood. In this study, the ability of 15 isolates of Trichoderma to degrade microsclerotia of V. dahliae was evaluated using a dual culture method. After 15 days, isolate HZA14 showed the greatest potential for microsclerotial degradation. The culture filtrate of isolate HZA14 also significantly inhibited the mycelial growth and conidia germination of V. dahliae at different dilutions. Moreover, this study showed that T. virens produced siderophores and indole-3-acetic acid (IAA). In disease control tests, T. virens HZA14 reduced disease severity in eggplant seedlings by up to 2.77%, resulting in a control efficacy of 96.59% at 30 days after inoculation. Additionally, inoculation with an HZA14 isolate increased stem and root length and fresh and dry weight, demonstrating plant growth promotion efficacy. To further investigate the mycoparasitism mechanism of T. virens HZA14, transcriptomics sequencing and real-time fluorescence quantitative PCR (RT-qPCR) were used to identify the differentially expressed genes (DEGs) of T. virens HZA14 at 3, 6, 9, 12, and 15 days of the interaction with microsclerotia of V. dahliae. In contrast to the control group, the mycoparasitic process of T. virens HZA14 exhibited differential gene expression, with 1197, 1758, 1936, and 1914 genes being up-regulated and 1191, 1963, 2050, and 2114 genes being down-regulated, respectively. Among these genes, enzymes associated with the degradation of microsclerotia, such as endochitinase A1, endochitinase 3, endo-1,3-beta-glucanase, alpha-N-acetylglucosaminidase, laccase-1, and peroxidase were predicted based on bioinformatics analysis. The RT-qPCR results confirmed the RNA-sequencing data, showing that the expression trend of the genes was consistent. These results provide important information for understanding molecular mechanisms of microsclerotial degradation and integrated management of Verticillium wilt in eggplant and other crops.

Multiomics provides insights into the succession of microbiota and metabolite during plant leaf fermentation

The quality of fermented plant products is closely related to microbial metabolism. Here, the associations of bacterial communities, metabolites, and functional genes were explored using multi-omics techniques based on plant leaf fermentation systems. The results showed significant changes in the structure of the microbial community, with a significant decrease in Firmicutes and a significant increase in Proteobacteria. In addition, the concentration of metabolites with antibacterial, antioxidant and aroma properties increased significantly, enhancing the quality of the fermented plant leaves. Integrated macrogenomic and metabolomic analyses indicated that amino acid metabolism could be key metabolic pathway affecting fermentation quality. Actinobacteria, Proteobacteria, Firmicutes were actively involved in tyrosine metabolism (ko00350) and phenylalanine metabolism (ko00360), and are presumed to be the major groups responsible for synthesizing growth and flavor compounds. This study emphasized the important role of microorganisms in the changes of metabolites during the fermentation of plant leaves.

Analysis of the Properties of 44 ABC Transporter Genes from Biocontrol Agent Trichoderma asperellum ACCC30536 and Their Responses to Pathogenic Alternaria alternata Toxin Stress

ATP-binding cassette (ABC) transporters are involved in transporting multiple substrates, such as toxins, and may be important for the survival of Trichoderma when encountering biotic toxins. In this study, genome searching revealed that there are 44 ABC transporters encoded in the genome of Trichoderma asperellum. These ABC transporters were divided into six types based on three-dimensional (3D) structure prediction, of which four, represented by 39 ABCs, are involved in transport and the remaining two, represented by 5 ABCs, are involved in regulating translation. The characteristics of nucleotide-binding domain (NBD) are important in the identification of ABC proteins. Even though the 3D structures of the 79 NBDs in the 44 ABCs are similar, multiple sequence alignment showed they can be divided into three classes. In total, 794 motifs were found in the promoter regions of the 44 ABC genes, of which 541 were cis-regulators related to stress responses. To characterize how their ABCs respond when T. asperellum interact with fungi or plants, T. asperellum was cultivated in either minimal media (MM) control, C-hungry, N-hungry, or poplar medium (PdPap) to simulate normal conditions, competition with pathogens, interaction with pathogens, and interaction with plants, respectively. The results show that 17 of 39 transport ABCs are highly expressed in at least one condition, whereas four of the five translation-regulating ABCs are highly expressed in at least one condition. Of these 21 highly expressed ABCs, 6 were chosen for RT-qPCR expression under the toxin stress of phytopathogen Alternaria alternata, and the results show ABC01, ABC04, ABC05, and ABC31 were highly expressed and may be involved in pathogen interaction and detoxifying toxins from A. alternata.

Antagonistic potential of Trichoderma as a biocontrol agent against Sclerotinia asari

In the present study, the inhibitory potential of 14 Trichoderma strains (isolated from Asarum rhizosphere) was investigated against Sclerotinia asari using the plate dilution method. The activity of antioxidant enzymes viz; catalase (CAT), peroxidase (POD), superoxide dismutase (SOD), and malondialdehyde (MDA) in S. asari treated with the two Trichoderma strains was also evaluated. Untargeted metabolomic analysis by using LC/MS analysis was carried out to determine differential metabolites in T. hamatum (A26) and T. koningiopsis (B30) groups. Moreover, transcriptome analysis of S. asari during the inhibition of S. asari by B30, and A26 compared with the control (CK) was performed. Results indicated that inhibition rates of T. koningiopsis B30, and T. hamatum A26 were highest compared to other strains. Similarly, non-volatile metabolites extracted from the B30 strain showed a 100% inhibition of S. asari. The activity of CAT, SOD, and POD decreased after treatment with A26 and B30 strains while increasing MDA content of S. asari. Antifungal activity of differential metabolites like abamectin, eplerenone, behenic acid, lauric acid, josamycin, erythromycin, and minocycline exhibited the highest inhibition of S. asari. Transcriptome analysis showed that differentially expressed genes were involved in many metabolic pathways which subsequently contributed toward antifungal activity of Trichoderma. These findings suggested that both Trichoderma strains (B30 and A26) could be effectively used as biocontrol agents against Sclerotinia disease of Asarum.

Early transcriptomic response of the mycoparasite Sphaerodes mycoparasitica to the mycotoxigenic Fusarium graminearum 3-ADON, the cause of Fusarium head blight

Mycoparasites are an assemblage of biotrophic and necrotrophic fungi that occur on plant pathogenic fungal hosts. Biotrophic mycoparasites are often overlooked in transcriptomic-based biocontrol studies. Sphaerodes mycoparasitica (S.m.) is a specific biotrophic mycoparasite of plant pathogenic Fusarium graminearum (F.g.), a devastating Fusarium head blight (FHB) disease in small-grain cereals. To understand the biotrophic mycoparasitism comprehensively, we performed Illumina RNA-Seq transcriptomic study on the fungus–fungus interaction in vitro. The aim is to identify the transcript-level mechanism related to the biotrophic S.m. mycoparasitism, particularly its ability to effectively control the F.g. 3-ADON chemotype. A shift in the transcriptomic profile of the mycoparasite was triggered in response to its interaction with F.g. during recognition (1.5 days) and colonization (3.5 days) steps. RNA-Seq analysis revealed ~ 30% of annotated transcripts with "function unknown". Further, 14 differentially expressed genes functionally linked to the biotrophic mycoparasitism were validated by quantitative real-time PCR (qPCR). The gene expression patterns of the filamentous haemagglutinin/adhesin/attachment factor as well as cell wall-degrading glucanases and chitinases were upregulated by host interaction. Besides, mycoparasitism-associated antioxidant resistance genes encoding ATP-binding cassette (ABC) transporter(s) and glutathione synthetase(s) were upregulated. However, the thioredoxin reductase was downregulated which infers that this antioxidant gene can be used as a resistance marker to assess S.m. antifungal and antimycotoxigenic activities. The interactive transcriptome of S. mycoparasitica provides new insights into specific mycoparasitism and will contribute to future research in controlling FHB.

Transcriptome Profiling Provides Insights Into Potential Antagonistic Mechanisms Involved in Chaetomium globosum Against Bipolaris sorokiniana

Chaetomium globosum Kunze is recognized as a potential biocontrol fungus against spot blotch of wheat caused by Bipolaris sorokiniana. Its molecular mechanism of biocontrol activity and the biosynthetic pathways involved have not been yet elucidated. Here, global transcriptome profiling of C. globosum strain Cg2 during interaction with B. sorokiniana isolate BS112 using RNA-seq was performed in order to gain insights into the potential mechanisms of antagonism. The Illumina HiSeq platform (2 × 150 bp) yielded an average of 20-22 million reads with 50-58% GC. De novo assembly generated 45,582 transcripts with 27,957 unigenes. Transcriptome analysis displayed distinct expression profiles in the interaction (Cg2-BS112), out of which 6,109 unique differentially expressed genes were present. The predominant transcripts classified as genes involved in "catalytic activity" constituted 45.06%, of which 10.02% were associated with "hydrolytic activity" (GO:0008152), and similarly, in the biological process, 29.18% of transcripts were involved in "metabolic activity" (GO:0004096 and GO:0006979). Heat map and cluster categorization suggested an increase in the expression levels of genes encoding secondary metabolites like polyketide synthase (GO:0009058), S-hydroxymethyl glutathione dehydrogenase (GO:0006069), terpene cyclase (EC 4.2.3.-), aminotran_1_2 domain-containing protein (GO:0009058), and other hydrolytic CAZYmes such as the glycosyl hydrolase (GH) family (GH 13, GH 2, GH 31, and GH 81; GO:0005975), cellulase domain-containing protein, chitinases, β-1, 3-glucanases (GO:0004565), glucan endo-1,3-beta-glucanase (GO:0052861), and proteases (GO:0004177). The obtained RNA-seq data were validated by RT-qPCR using 20 randomly chosen genes, showing consistency with the RNA-seq results. The present work is worldwide the first effort to unravel the biocontrol mechanism of C. globosum against B. sorokiniana. It generated a novel dataset for further studies and facilitated improvement of the gene annotation models in the C. globosum draft genome.

Antiproliferative and Antimicrobial Activities of Secondary Metabolites and Phylogenetic Study of Endophytic Trichoderma Species From Vinca Plants

Endophytic fungi have been recognized as a potential source of bioactive secondary metabolites. The endophytic Trichoderma species were isolated from Vinca plants (Vinca major, Vinca herbacea, and Vinca minor), found in Iran and screened for antimicrobial and anti-proliferative activity. Based on morphological and phylogenetic analyses, four fungal species were identified: T. asperellum, T. brevicompactum, T. koningiopsis, and T. longibrachiatum. In addition, endophytic fungi bioactivity of methanol and ethyl acetate extracts (7.8–250 μgml⁻¹) were assessed against a panel of pathogenic fungi and bacteria and IC₈₀ was calculated. Data showed that both methanol and ethyl acetate extracts from all endophytic isolates had significant cytotoxic effects against the model target fungus Pyricularia oryzae. Further research indicated that they had significant antimicrobial bioactivity against the human pathogenic bacteria Staphylococcus aureus and Escherichia coli, and plant pathogenic bacteria Ralstonia solanacearum and Clavibacter michiganensis as well. According to the bioactivity results, crude ethyl acetate extract of T. koningiopsis VM115 isolate was determined for TLC and GC-MS analysis. An antifungal compound was isolated from ethyl acetate extract of T. koningiopsis VM115 based on bioassay guided fractionation. The ¹H-NMR and ¹³C-NMR spectroscopic data showed that the compound was trichodermin, which exhibited strong fungicidal effects against P. oryzae, Aspergillus fumigatus, and Botrytis cinera with MICs of 31.25 μg ml⁻¹ through in vitro antifungal tests. GC-MS analysis identified six classes of volatile compound produced by T. koningiopsis VM115 (alcohols, esters, pyrones (lactones), acids, furanes and lipids). 6-n-pentyl-6H-pyran-2-one (6PP) was identified as one of the most abundant metabolites in this research. These results indicate that the fungal endophytes from Vinca plants had antibacterial and cytotoxic activities; evidence that endophytes are a good source of biological activity and compounds. This work is the first report of Trichodermin production by T. koningiopsis species.

Tri11, tri3, and tri4 genes are required for trichodermin biosynthesis of Trichoderma brevicompactum

Trichoderma brevicompactum and T. arundinaceum both can synthesize trichodermin with strong antifungal activity and high biotechnological value. The two Trichoderma species have a tri cluster, which includes seven genes (tri14, tri12, tri11, tri10, tri3, tri4, and tri6) that encode transport and regulatory enzymes required for the biosynthesis of trichodermin. Here, we isolated T. brevicompactum 0248 transformants with disrupted tri11, tri4, or tri3 gene. We also described the effect of tri11, tri3, or tri4 deletion on the expression of other genes in the tri cluster. Targeted Δtri3 knockout mutant exhibited a sharp decline in the production of trichodermin, and trichodermol, which is a substrate for trichodermin production, accumulated. Thus, the results demonstrated that tri3 was responsible for the biosynthesis of trichodermin, and the tri3 gene-encoded enzyme catalyzed the acetylation reaction of the hydroxy group at C-4 of the trichodermin skeleton. In addition, tri4 and tri11 deletion mutants were generated to evaluate the roles of tri4 and tri11 in trichodermin biosynthesis, respectively. Deletion mutant strain Δtri4 or Δtri11 did not produce trichodermin in T. brevicompactum, indicating that tri4 and tri11 are essential for trichodermin biosynthesis. This is the first to report the function of tri3, tri4 and tri11 in T. brevicompactum, although the role of tri4 and tri11 has already been described for T. arundinaceum by Cardoza et al. (Appl Environ Microbiol 77:4867-4877, 2011).

Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma

Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process. In biocontrol agents (BCAs), the molecular response at translational level may represents noise-like response of absolute transcript level and an adaptive response to physiological and pathological situations representing subset of mRNAs population actively translated in a cell. The molecular responses of biocontrol are complex and involve multistage regulation of number of genes. The use of high-throughput techniques has led to rapid increase in volume of transcriptomics data of Trichoderma. In general, almost half of the variations of transcriptome and protein level are due to translational control. Thus, studies are required to integrate raw information from different “omics” approaches for accurate depiction of translational response of BCAs in interaction with plants and plant pathogens. The studies on translational status of only active mRNAs bridging with proteome data will help in accurate characterization of only a subset of mRNAs actively engaged in translation. This review highlights the associated bottlenecks and use of state-of-the-art procedures in addressing the gap to accelerate future accomplishment of biocontrol mechanisms.

De novo assembly of the Carcinus maenas transcriptome and characterization of innate immune system pathways

Background

The European shore crab, Carcinus maenas, is used widely in biomonitoring, ecotoxicology and for studies into host-pathogen interactions. It is also an important invasive species in numerous global locations. However, the genomic resources for this organism are still sparse, limiting research progress in these fields. To address this resource shortfall we produced a C. maenas transcriptome, enabled by the progress in next-generation sequencing technologies, and applied this to assemble information on the innate immune system in this species.

Results

We isolated and pooled RNA for twelve different tissues and organs from C. maenas individuals and sequenced the RNA using next generation sequencing on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome was generated encompassing 212,427 transcripts (153,699 loci). The transcripts were filtered, annotated and characterised using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including NCBI, Gene Ontology and KEGG). There were differential patterns of expression for between 1,223 and 2,741 transcripts across tissues and organs with over-represented Gene Ontology terms relating to their specific function. Based on sequence homology to immune system components in other organisms, we show both the presence of transcripts for a series of known pathogen recognition receptors and response proteins that form part of the innate immune system, and transcripts representing the RNAi, Toll-like receptor signalling, IMD and JAK/STAT pathways.

Conclusions

We have produced an assembled transcriptome for C. maenas that provides a significant molecular resource for wide ranging studies in this species. Analysis of the transcriptome has revealed the presence of a series of known targets and functional pathways that form part of their innate immune system and illustrate tissue specific differences in their expression patterns.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1667-1) contains supplementary material, which is available to authorized users.