Functional analysis of non-ribosomal peptide synthetases (NRPSs) in Trichoderma virens reveals a polyketide synthase (PKS)/NRPS hybrid enzyme involved in the induced systemic resistance response in maize

Allochthonous Trichoderma Isolates Boost Atractylodes lancea Herb Quality at the Cost of Rhizome Growth

Atractylodes lancea is a perennial herb whose rhizome (AR) is a valuable traditional Chinese medicine with immense market demand. The cultivation of Atractylodes lancea faces outbreaks of root rot and deterioration in herb quality due to complex causes. Here, we investigated the effects of Trichoderma spp., well-known biocontrol agents and plant-growth-promoters, on ARs. We isolated Trichoderma strains from healthy ARs collected in different habitats and selected three T. harzianum strains (Th2, Th3 and Th4) with the strongest antagonizing effects on root rot pathogens (Fusarium spp.). We inoculated geo-authentic A. lancea plantlets with Th2, Th3 and Th4 and measured the biomass and quality of 70-day-old ARs. Th2 and Th3 promoted root rot resistance of A. lancea. Th2, Th3 and Th4 all boosted AR quality: the concentration of the four major medicinal compounds in ARs (atractylon, atractylodin, hinesol and β-eudesmol) each increased 1.6- to 18.2-fold. Meanwhile, however, the yield of ARs decreased by 0.58- to 0.27-fold. Overall, Th3 dramatically increased the quality of ARs at a relatively low cost, namely lower yield, showing great potential for practical application. Our results showed selectivity between A. lancea and allochthonous Trichoderma isolates, indicating the importance of selecting specific microbial patches for herb cultivation.

Microbial siderophores as molecular shuttles for metal cations: sources, sinks and application perspectives

Iron is one of the highly abundant elements on the earth's crust, an essential micronutrient for a majority of life forms, and exists in two frequent oxidation states such as ferrous (Fe2+) and ferric (Fe3+). These two oxidation states are interconvertible by redox reactions and form complexes with a wide range of siderophores. At neutral pH in soil, Fe2+ is highly soluble upto 100 mM but have less biological value, whereas Fe3+ is less soluble upto 10-9 M. This reduced bioavailability of Fe3+ induces competition among microorganisms. As many microorganisms need at least 10-6 M of Fe3+ form of iron for their growth, siderophores from these microbes readily withdraw Fe3+ iron from a variety of habitats for their survival. In this review, we bring into light the several recent investigations related to diverse chemistry of microbial siderophores, mechanisms of siderophore uptake, biosynthetic gene clusters in microbial genomes, various sources of heavy metal cations in soil, siderophore-binding protein receptors and commercialisation perspectives of siderophores. Besides, this review unearths the recent advancements in the characterisation of novel siderophores and its heavy metal complexes alongside the interaction kinetics with receptors.

The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum

The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography-mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana ('Aiptasia'). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host-endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian-dinoflagellate symbiosis.

Structure-activity correlations for peptaibols obtained from clade Longibrachiatum of Trichoderma: A combined experimental and computational approach

Integrated disease management and plant protection have been discussed with much fervor in the past decade due to the rising environmental concerns of using industrially produced pesticides. Members of the genus Trichoderma are a subject of considerable research today due to their several properties as biocontrol agents. In our study, the peptaibol production of Trichoderma longibrachiatum SZMC 1775, T. longibrachiatum f. bissettii SZMC 12546, T. reesei SZMC 22616, T. reesei SZMC 22614, T. saturnisporum SZMC 22606 and T. effusum SZMC 22611 were investigated to elucidate structure-activity relationships (SARs) between the properties of peptaibols and their 3D structures. The effects of peptaibol mixtures obtained from every Trichoderma strain were examined against nine commonly known bacteria. The lowest minimum inhibitory concentrations (MIC, mg ml^-1) were exerted by T. longibrachiatum f. bissettii SZMC 12546 against Gram-positive bacteria, which was also able to inhibit the plant pathogenic Gram-negative Rhizobium radiobacter. Accelerated molecular dynamics (aMD) simulations were performed in aqueous solvent to explore the folding dynamics of 12 selected peptaibol sequences. The most characteristic difference between the peptaibols from group A and B relies in the 'Gly-Leu-Aib-Pro' and 'Gly-Aib-Aib-Pro' motifs ('Aib' stands for α-aminoisobutyric acid), which imparted a significant effect on the folding dynamics in water and might be correlated with their expressed bioactivity. In our aMD simulation experiments, Group A peptaibols showed more restricted folding dynamics with well-folded helical conformations as the most stable representative structures. This structural stability and dynamics may contribute to their bioactivity against the selected bacterial species.

Trichopsistides A and B: Two Highly Oxygenated Pentacyclic Polyketides with Promising Inhibitory Effects on the NF-κB Signaling Pathway from the Fungus Trichoderma koningiopsis WZ-196

Two highly oxygenated pentacyclic polyketides with two new carbon skeletons, trichopsistide A (1) and trichopsistide B (2), were isolated from the plant endophyte Trichoderma koningiopsis WZ-196 derived from the leaf of Rubia podantha Diels. The structures of these polyketides with full configurations were determined by comprehensive spectroscopic analysis, computer-assisted structure elucidation software, computational calculation, and X-ray crystal diffraction. Among them, 1 represented the first example of an unprecedented 5/6/6/6/5 pentacyclic ketal-containing polyketide pyridine alkaloid, and 2 possessed a novel 6/6/6/6/5 pentacyclic ketal-containing polyketide scaffold fused with an α-pyrone. The plausible biosynthetic route for 1 and 2 was also proposed. Moreover, biological activity assays showed that 1 and 2 possessed inhibitory effects on the NF-κB signaling pathway with IC₅₀ values of 14.77 and 8.58 μM, respectively. Furthermore, 1 and 2 could also inhibit the expression of IκBα and p65 phosphorylation, decrease the expression of MCP-1, E-selectin, and IL-8 at the mRNA level, and inhibit the TNF-α-induced nuclear translocation of p65.

Trichoderma spp. Genes Involved in the Biocontrol Activity Against Rhizoctonia solani

Rhizoctonia solani is a pathogen that causes considerable harm to plants worldwide. In the absence of hosts, R. solani survives in the soil by forming sclerotia, and management methods, such as cultivar breeding, crop rotations, and fungicide sprays, are insufficient and/or inefficient in controlling R. solani. One of the most challenging problems facing agriculture in the twenty-first century besides with the impact of global warming. Environmentally friendly techniques of crop production and improved agricultural practices are essential for long-term food security. Trichoderma spp. could serve as an excellent example of a model fungus to enhance crop productivity in a sustainable way. Among biocontrol mechanisms, mycoparasitism, competition, and antibiosis are the fundamental mechanisms by which Trichoderma spp. defend against R. solani, thereby preventing or obstructing its proliferation. Additionally, Trichoderma spp. induce a mixed induced systemic resistance (ISR) or systemic acquired resistance (SAR) in plants against R. solani, known as Trichoderma-ISR. Stimulation of every biocontrol mechanism involves Trichoderma spp. genes responsible for encoding secondary metabolites, siderophores, signaling molecules, enzymes for cell wall degradation, and plant growth regulators. Rhizoctonia solani biological control through genes of Trichoderma spp. is summarized in this paper. It also gives information on the Trichoderma-ISR in plants against R. solani. Nonetheless, fast-paced current research on Trichoderma spp. is required to properly utilize their true potential against diseases caused by R. solani.

Functional and Genomic Analysis of Rouxiella badensis SER3 as a Novel Biocontrol Agent of Fungal Pathogens

In recent decades, various bacterial species have been characterized as biocontrol agents for plant crop diseases; however, only a few genera have been predominantly reported in the literature. Therefore, the identification of new antagonists against phytopathogens is essential for boosting sustainable food production systems. In this study, we evaluated the role of strain SER3 from the recently discovered Rouxiella badensis as a biocontrol agent. SER3 was isolated from the phyllosphere of decaying strawberry fruit (Fragaria × ananassa) and showed different grades of antagonism against 20 fungal pathogens of berries, based on confrontation assays, due to the action of its diffusible and volatile compounds. These fungal pathogens were isolated from decayed strawberry, blackberry, and blueberry fruit and were characterized through internal transcribed spacer (ITS) sequencing and homology searches, exhibiting similarity with well-known postharvest pathogens such as Botrytis, Fusarium, Geotrichum, Mucor, Penicillium, Alternaria, and Botryosphaeria. Koch’s postulates were confirmed for most pathogens by reinfecting berry fruit. SER3 showed good capacity to inhibit the growth of Botrytis cinerea and Fusarium brachygibbosum in strawberry fruit, affecting mycelial development. To gain better understanding of the genetic and metabolic capacities of the SER3 strain, its draft genome was determined and was found to comprise a single chromosome of 5.08 Mb, 52.8% G + C content, and 4,545 protein-coding genes. Phylogenetic analysis indicated that the SER3 strain is affiliated with the R. badensis species, with an average nucleotide identity >96% and a genome-to-genome distance >70%. A comparison of the genomic properties of R. badensis SER3 and other close bacterial relatives showed several genes with potential functions in biocontrol activities, such as those encoding siderophores, non-ribosomal peptide synthetases, and polyketide synthases. This is the first study to demonstrate a novel role of the recently discovered R. badensis species (and any other species of the genus Rouxiella) as a biocontrol agent against postharvest fungal pathogens.

Identification of non-ribosomal peptide synthetase in Ganoderma boninense Pat. that was expressed during the interaction with oil palm

Basal stem rot (BSR) of oil palm is a disastrous disease caused by a white-rot fungus Ganoderma boninense Pat. Non-ribosomal peptides (NRPs) synthesized by non-ribosomal peptide synthetases (NRPSs) are a group of secondary metabolites that act as fungal virulent factors during pathogenesis in the host. In this study, we aimed to isolate NRPS gene of G. boninense strain UPMGB001 and investigate the role of this gene during G. boninense-oil palm interaction. The isolated NRPS DNA fragment of 8322 bp was used to predict the putative peptide sequence of different domains and showed similarity with G. sinense (85%) at conserved motifs of three main NRPS domains. Phylogenetic analysis of NRPS peptide sequences demonstrated that NRPS of G. boninense belongs to the type VI siderophore family. The roots of 6-month-old oil palm seedlings were artificially inoculated for studying NRPS gene expression and disease severity in the greenhouse. The correlation between high disease severity (50%) and high expression (67-fold) of G. boninense NRPS gene at 4 months after inoculation and above indicated that this gene played a significant role in the advancement of BSR disease. Overall, these findings increase our knowledge on the gene structure of NRPS in G. boninense and its involvement in BSR pathogenesis as an effector gene.

Screening and evaluation of laccase produced by different Trichoderma species along with their phylogenetic relationship

Laccases have high biotechnological potential in industries since they catalyze the oxidation of many chemical compounds. The production of laccases by fungi has been extensively studied due to their secretion of enzymes and rapid growth using cheap substrates. Trichoderma; the versatile fungal genus includes species of great biotechnological value and considered as a magnificent industrial cell factory of enzymes. In this study, 10 Trichoderma species were screened for laccase enzyme production by submerged cultivation. The studied species were identified by internal transcribed spacer (ITS) gene sequences. Guaiacol (0.04%) as an enzyme substrate in plate medium was used for the selection of maximum laccase-enriched Trichoderma species by formation of visual color halo intensity. This activity was evaluated by liquid submersion (flask medium) also. The absorbance of laccase contained broth was measured by a spectrophotometer (450 nm). The highest laccase production was obtained by T. atroviride (2.62 U/mL). Trichoderma cremeum and T. longipile showed medium laccase potency, while T. beinartii exhibited weak laccase secretion ability. Laccase from T. atroviride was purified by SDS-PAGE and the molecular weight was determined (57 kDa). The laccase was confirmed by their respective amino acid sequences, and the phylogenetic tree was constructed for further analysis.

The Mosaic Architecture of NRPS-PKS in the Arbuscular Mycorrhizal Fungus Gigaspora margarita Shows a Domain With Bacterial Signature

As obligate biotrophic symbionts, arbuscular mycorrhizal fungi (AMF) live in association with most land plants. Among them, Gigaspora margarita has been deeply investigated because of its peculiar features, i.e., the presence of an intracellular microbiota with endobacteria and viruses. The genome sequencing of this fungus revealed the presence of some hybrid non-ribosomal peptide synthases-polyketide synthases (NRPS-PKS) that have been rarely identified in AMF. The aim of this study is to describe the architecture of these NRPS-PKS sequences and to understand whether they are present in other fungal taxa related to G. margarita. A phylogenetic analysis shows that the ketoacyl synthase (KS) domain of one G. margarita NRPS-PKS clusters with prokaryotic sequences. Since horizontal gene transfer (HGT) has often been advocated as a relevant evolutionary mechanism for the spread of secondary metabolite genes, we hypothesized that a similar event could have interested the KS domain of the PKS module. The bacterial endosymbiont of G. margarita, Candidatus Glomeribacter gigasporarum (CaGg), was the first candidate as a donor, since it possesses a large biosynthetic cluster involving an NRPS-PKS. However, bioinformatics analyses do not confirm the hypothesis of a direct HGT from the endobacterium to the fungal host: indeed, endobacterial and fungal sequences show a different evolution and potentially different donors. Lastly, by amplifying a NRPS-PKS conserved fragment and mining the sequenced AMF genomes, we demonstrate that, irrespective of the presence of CaGg, G. margarita, and some other related Gigasporaceae possess such a sequence.

Divergence of Beauvericin Synthase Gene among Fusarium and Trichoderma Species

Beauvericin (BEA) is a cyclodepsipeptide mycotoxin, showing insecticidal, antibiotic and antimicrobial activities, as well as inducing apoptosis of cancer cell lines. BEA can be produced by multiple fungal species, including saprotrophs, plant, insect and human pathogens, particularly belonging to Fusarium, Beauveria and Isaria genera. The ability of Trichoderma species to produce BEA was until now uncertain. Biosynthesis of BEA is governed by a non-ribosomal peptide synthase (NRPS), known as beauvericin synthase (BEAS), which appears to present considerable divergence among different fungal species. In the present study we compared the production of beauvericin among Fusarium and Trichoderma strains using UPLC methods. BEAS fragments were sequenced and analyzed to examine the level of the gene’s divergence between these two genera and confirm the presence of active BEAS copy in Trichoderma. Seventeen strains of twelve species were studied and phylogenetic analysis showed distinctive grouping of Fusarium and Trichoderma strains. The highest producers of beauvericin were F. proliferatum and F. nygamai. Trichoderma strains of three species (T. atroviride, T. viride, T. koningiopsis) were minor BEA producers. The study showed beauvericin production by Fusarium and Trichoderma species and high variance of the non-ribosomal peptide synthase gene among fungal species from the Hypocreales order.

Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping

Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large-scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome-wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re-sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p < .001) between strains, indicating a polygenic inheritance. Twenty-one strains produced culture filtrates with higher (p ≤ .05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p ≤ .05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10-10) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p ≤ .001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p < .001) nematicidal activity and reduced (p ≤ .05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5.

Strong preference for the integration of transforming DNA via homologous recombination in Trichoderma atroviride

Trichoderma species play important roles in nature as plant growth promotors and antagonists of phytopathogenic fungi, and are used as models to study photomorphogenesis. Molecular tools have been implemented to manipulate and improve these fungi. However, instability of transformants or very low frequency of homologous recombination has been reported. Here, we report the fate of transforming DNA, demonstrating that it can follow two different fates. When a vector contains sequences also present in the Trichodermaatroviride genome, it mainly integrates by homologous recombination generating stable recombinant strains. In contrast, vectors with no sequence homology to the T. atroviride genome generate unstable transformants, losing the transforming DNA in the first generation of conidia produced without selection where, surprisingly, the vector behaves as autoreplicative. Integration by homologous recombination was demonstrated when transformants were generated with a truncated version of the blr2 gene, resulting in insertional mutants with phenotypes identical to those of knockout mutants. Our results indicate that T. atroviride is highly efficient in integrating DNA by homologous recombination and that plasmid vectors with no sequence homology to the genome are maintained for several generations in T. atroviride if kept under selective pressure even though they lacked fungal autonomous replication sequences.

Genomic and transcriptomic insights into Raffaelea lauricola pathogenesis

BACKGROUND

Laurel wilt caused by Raffaelea lauricola is a lethal vascular disease of North American members of the Lauraceae plant family. This fungus and its primary ambrosia beetle vector Xyleborus glabratus originated from Asia; however, there is no report of laurel wilt causing widespread mortality on native Lauraceae trees in Asia. To gain insight into why R. lauricola is a tree-killing plant pathogen in North America, we generated and compared high quality draft genome assemblies of R. lauricola and its closely related non-pathogenic species R. aguacate.

RESULTS

Relative to R. aguacate, the R. lauricola genome uniquely encodes several small-secreted proteins that are associated with virulence in other pathogens and is enriched in secondary metabolite biosynthetic clusters, particularly polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS) and PKS-NRPS anchored gene clusters. The two species also exhibit significant differences in secreted proteins including CAZymes that are associated with polysaccharide binding including the chitin binding CBM50 (LysM) domain. Transcriptomic comparisons of inoculated redbay trees and in vitro-grown fungal cultures further revealed a number of secreted protein genes, secondary metabolite clusters and alternative sulfur uptake and assimilation pathways that are coordinately up-regulated during infection.

CONCLUSIONS

Through these comparative analyses we have identified potential adaptations of R. lauricola that may enable it to colonize and cause disease on susceptible hosts. How these adaptations have interacted with co-evolved hosts in Asia, where little to no disease occurs, and non-co-evolved hosts in North America, where lethal wilt occurs, requires additional functional analysis of genes and pathways.

Deletion of the Trichoderma virens NRPS, Tex7, induces accumulation of the anti-cancer compound heptelidic acid

The anticancer antibiotic heptelidic acid is a sesquiterpene lactone produced by the beneficial plant fungus Trichoderma virens. This species has been separated into two strains, referred to as P and Q, based on its biosynthesis of secondary metabolites; notably, only P-strains were reported to produce heptelidic acid. While characterizing a Q-strain of T. virens containing a directed mutation in the non-ribosomal peptide synthetase encoding gene Tex7, the appearance of an unknown compound in anomalously large quantities was visualized by TLC. Using a combination of HPLC, LC-MS/MS, and NMR spectroscopy, this compound was identified as heptelidic acid. This discovery alters the strain classification structure of T. virens. Additionally, the Tex7 mutants inhibited growth of maize seedlings, while retaining the ability to induce systemic resistance against the foliar fungal pathogen, Cochliobolus heterostrophus.

Beneficial effects of Trichoderma secondary metabolites on crops

Selected microbial strains used as active ingredients of biopesticides for agricultural management practices (e.g., IPM, Integrated Pest Management) are known for their ability to control phytopathogens, promote plant growth, and/or induce disease resistance. Microbes belonging to the Trichoderma genus are considered as an appropriate example of beneficial microbes and are model organisms to study plant-microbe interactions. Several Trichoderma strains are marketed as biocontrol agents and are known to increase plant growth, stress tolerance, and nutrient availability. These effects have sometimes been related to the production of effector metabolites that beneficial microbes produce during the interaction with plant and other microbes. Secondary metabolites (SMs) comprise different classes of natural compounds with low molecular weight and having numerous biological roles, especially in the interactions among organisms. Metabolomic analysis of the interactions between plants, phytopathogens, and beneficial fungi aided in the identification of several bioactive fungal SMs that positively affect plant metabolism. Some of these compounds showed direct activity against phytopathogens, but also increased disease resistance by triggering the plant defence system, and/or enhanced vegetative growth. A new generation of bioformulations based on microbial metabolites and living consortia responsible for the desired beneficial effects on crops may overcome the difficulties associated with the use of a single living microbial strain.

Trichoderma: The "Secrets" of a Multitalented Biocontrol Agent

The plant-Trichoderma-pathogen triangle is a complicated web of numerous processes. Trichoderma spp. are avirulent opportunistic plant symbionts. In addition to being successful plant symbiotic organisms, Trichoderma spp. also behave as a low cost, effective and ecofriendly biocontrol agent. They can set themselves up in various patho-systems, have minimal impact on the soil equilibrium and do not impair useful organisms that contribute to the control of pathogens. This symbiotic association in plants leads to the acquisition of plant resistance to pathogens, improves developmental processes and yields and promotes absorption of nutrient and fertilizer use efficiency. Among other biocontrol mechanisms, antibiosis, competition and mycoparasitism are among the main features through which microorganisms, including Thrichoderma, react to the presence of other competitive pathogenic organisms, thereby preventing or obstructing their development. Stimulation of every process involves the biosynthesis of targeted metabolites like plant growth regulators, enzymes, siderophores, antibiotics, etc. This review summarizes the biological control activity exerted by Trichoderma spp. and sheds light on the recent progress in pinpointing the ecological significance of Trichoderma at the biochemical and molecular level in the rhizosphere as well as the benefits of symbiosis to the plant host in terms of physiological and biochemical mechanisms. From an applicative point of view, the evidence provided herein strongly supports the possibility to use Trichoderma as a safe, ecofriendly and effective biocontrol agent for different crop species.

Bioactive Secondary Metabolites from Trichoderma spp. against Phytopathogenic Fungi

Phytopathogenic fungi, causing significant economic and production losses, are becoming a serious threat to global food security. Due to an increase in fungal resistance and the hazardous effects of chemical fungicides to human and environmental health, scientists are now engaged to explore alternate non-chemical and ecofriendly management strategies. The use of biocontrol agents and their secondary metabolites (SMs) is one of the potential approaches used today. Trichoderma spp. are well known biocontrol agents used globally. Many Trichoderma species are the most prominent producers of SMs with antimicrobial activity against phytopathogenic fungi. Detailed information about these secondary metabolites, when grouped together, enhances the understanding of their efficient utilization and further exploration of new bioactive compounds for the management of plant pathogenic fungi. The current literature provides the information about SMs of Trichoderma spp. in a different context. In this review, we summarize and group different antifungal SMs of Trichoderma spp. against phytopathogenic fungi along with a comprehensive overview of some aspects related to their chemistry and biosynthesis. Moreover, a brief overview of the biosynthesis pathway, action mechanism, and different approaches for the analysis of SMs and the factors affecting the regulation of SMs in Trichoderma is also discussed.

Identification of Differentially Expressed Genes in Trichoderma koningii IABT1252 During Its Interaction with Sclerotium rolfsii

Sclerotium rolfsii, a soil-borne fungal pathogen, infects more than 500 crop species and causes stem rot/collar rot/seed rot/southern blight/wilt in a wide variety of crops which results in significant yield loses. Presently, antagonistic microbes are gaining more importance in managing plant pathogens because they control the pathogen in an environment-friendly manner. Trichoderma is an antagonistic fungi and most popularly used biocontrol agent against phytopathogenic fungi. It is predominantly used to treat soil and seed for the control of Sclerotium rolfsii infestation. In this study, the Trichoderma koningii IABT1252 that performed better in controlling groundnut seed/ seedling rot caused by S. rolfsii in pot experiments were selected to know the molecular basis for the control. Differentially expressed genes in Trichoderma at two different stages of interaction (prior to contact and after contact with S. rolfsii) were identified. In both the stages, some of the differentially expressed genes included ones coding for hydrolytic enzymes, secondary metabolite biosynthesis, transcription factors, signaling proteins, transporter proteins, and proteins involved in mycoparasitic process of Trichoderma.

Deletion of the Nonribosomal Peptide Synthetase Gene nps1 in the Fungus Clonostachys rosea Attenuates Antagonism and Biocontrol of Plant Pathogenic Fusarium and Nematodes

Secondary metabolites produced by biological control agents may influence the outcome of their interactions with plant pathogenic microorganisms and plants. In the present study, we investigated the role of the nonribosomal peptide synthetase gene nps1 expressed by the biocontrol fungus Clonostachys rosea. A gene expression analysis showed that nps1 was induced during confrontations with the plant pathogenic fungus Botrytis cinerea. Gene deletion strains of nps1 displayed increased growth rates and conidiation. However, the nematicidal activity of culture filtrates from C. rosea Δnps1 strains was significantly weaker than that from wild-type filtrates (P ≤ 0.001); after 24 h of incubation with culture filtrates from nps1 deletion strains, only 13 to 33% of a mixed community of nematodes were dead compared with 42% of nematodes incubated with wild-type culture filtrates. The Δnps1 strains also showed reduced biocontrol efficacy during pot experiments, thus failing to protect wheat seedlings from foot rot disease caused by the plant pathogenic fungus Fusarium graminearum. Furthermore, C. rosea Δnps1 strains were not able to reduce populations of plant-parasitic nematodes in soil or in roots of wheat as efficiently as the wild-type strain. Both C. rosea wild-type and Δnps1 strains increased the dry shoot weight and shoot length of wheat by 20 and 13%, respectively. We showed that NPS1, a putative nonribosomal peptide synthetase encoded by nps1, is a biocontrol factor, presumably by producing a hitherto unknown nonribosomal peptide compound with antifungal and nematicidal properties that contributes to the biocontrol properties of C. rosea.

Trichoderma/pathogen/plant interaction in pre-harvest food security

Large losses before crop harvesting are caused by plant pathogens, such as viruses, bacteria, oomycetes, fungi, and nematodes. Among these, fungi are the major cause of losses in agriculture worldwide. Plant pathogens are still controlled through application of agrochemicals, causing human disease and impacting environmental and food security. Biological control provides a safe alternative for the control of fungal plant pathogens, because of the ability of biocontrol agents to establish in the ecosystem. Some Trichoderma spp. are considered potential agents in the control of fungal plant diseases. They can interact directly with roots, increasing plant growth, resistance to diseases, and tolerance to abiotic stress. Furthermore, Trichoderma can directly kill fungal plant pathogens by antibiosis, as well as via mycoparasitism strategies. In this review, we will discuss the interactions between Trichoderma/fungal pathogens/plants during the pre-harvest of crops. In addition, we will highlight how these interactions can influence crop production and food security. Finally, we will describe the future of crop production using antimicrobial peptides, plants carrying pathogen-derived resistance, and plantibodies.

Trichoderma as a Model to Study Effector-Like Molecules

Plants are capable of perceiving microorganisms by coordinating processes to establish different forms of plant–microbe relationships. Plant colonization is governed in fungal and bacterial systems by secreted effector molecules, suppressing plant defense responses and modulating plant physiology to promote either virulence or compatibility. Proteins, secondary metabolites, and small RNAs have been described as effector molecules that use different mechanisms to establish the interaction. Effector molecules have been studied in more detail due to their involvement in harmful interactions, leading to a negative impact on agriculture. Recently, research groups have started to study the effectors in symbiotic interactions. Interestingly, most symbiotic effectors are members of the same families present in phytopathogens. Nevertheless, the quantity and ratio of secreted effectors depends on the microorganism and the host, suggesting a complex mechanism of recognition between the plant and their associated microorganisms. Fungi belonging to Trichoderma genus interact with plants by inducing their defense system and promoting plant growth. Research suggests that some of these effects are associated with effector molecules that Trichoderma delivers during the association with the plant. In this review, we will focus on the main findings concerning the effector molecules reported in Trichoderma spp. and their role during the interaction with plants, mainly in the molecular dialogue that takes place between them.

Differential expression analysis of Trichoderma virens RNA reveals a dynamic transcriptome during colonization of Zea mays roots

Background

Trichoderma spp. are majorly composed of plant-beneficial symbionts widely used in agriculture as bio-control agents. Studying the mechanisms behind Trichoderma-derived plant benefits has yielded tangible bio-industrial products. To better take advantage of this fungal-plant symbiosis it is necessary to obtain detailed knowledge of which genes Trichoderma utilizes during interaction with its plant host. In this study, we explored the transcriptional activity undergone by T. virens during two phases of symbiosis with maize; recognition of roots and after ingress into the root cortex.

Results

We present a model of T. virens – maize interaction wherein T. virens experiences global repression of transcription upon recognition of maize roots and then induces expression of a broad spectrum of genes during colonization of maize roots. The genes expressed indicate that, during colonization of maize roots, T. virens modulates biosynthesis of phytohormone-like compounds, secretes a plant-environment specific array of cell wall degrading enzymes and secondary metabolites, remodels both actin-based and cell membrane structures, and shifts metabolic activity. We also highlight transcription factors and signal transduction genes important in future research seeking to unravel the molecular mechanisms of T. virens activity in maize roots.

Conclusions

T. virens displays distinctly different transcriptional profiles between recognizing the presence of maize roots and active colonization of these roots. A though understanding of these processes will allow development of T. virens as a bio-control agent. Further, the publication of these datasets will target future research endeavors specifically to genes of interest when considering T. virens – maize symbiosis.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5651-z) contains supplementary material, which is available to authorized users.

Trichoderma as a Model to Study Effector-Like Molecules

Plants are capable of perceiving microorganisms by coordinating processes to establish different forms of plant-microbe relationships. Plant colonization is governed in fungal and bacterial systems by secreted effector molecules, suppressing plant defense responses and modulating plant physiology to promote either virulence or compatibility. Proteins, secondary metabolites, and small RNAs have been described as effector molecules that use different mechanisms to establish the interaction. Effector molecules have been studied in more detail due to their involvement in harmful interactions, leading to a negative impact on agriculture. Recently, research groups have started to study the effectors in symbiotic interactions. Interestingly, most symbiotic effectors are members of the same families present in phytopathogens. Nevertheless, the quantity and ratio of secreted effectors depends on the microorganism and the host, suggesting a complex mechanism of recognition between the plant and their associated microorganisms. Fungi belonging to Trichoderma genus interact with plants by inducing their defense system and promoting plant growth. Research suggests that some of these effects are associated with effector molecules that Trichoderma delivers during the association with the plant. In this review, we will focus on the main findings concerning the effector molecules reported in Trichoderma spp. and their role during the interaction with plants, mainly in the molecular dialogue that takes place between them.

Genomic characterization of Trichoderma atrobrunneum (T. harzianum species complex) ITEM 908: insight into the genetic endowment of a multi-target biocontrol strain

BACKGROUND

So far, biocontrol agent selection has been performed mainly by time consuming in vitro confrontation tests followed by extensive trials in greenhouse and field. An alternative approach is offered by application of high-throughput techniques, which allow extensive screening and comparison among strains for desired genetic traits. In the genus Trichoderma, the past assignments of particular features or strains to one species need to be reconsidered according to the recent taxonomic revisions. Here we present the genome of a biocontrol strain formerly known as Trichoderma harzianum ITEM 908, which exhibits both growth promoting capabilities and antagonism against different fungal pathogens, including Fusarium graminearum, Rhizoctonia solani, and the root-knot nematode Meloidogyne incognita. By genomic analysis of ITEM 908 we investigated the occurrence and the relevance of genes associated to biocontrol and stress tolerance, providing a basis for future investigation aiming to unravel the complex relationships between genomic endowment and exhibited activities of this strain.

RESULTS

The MLST analysis of ITS-TEF1 concatenated datasets reclassified ITEM 908 as T. atrobrunneum, a species recently described within the T. harzianum species complex and phylogenetically close to T. afroharzianum and T. guizhouense. Genomic analysis revealed the presence of a broad range of genes encoding for carbohydrate active enzymes (CAZYmes), proteins involved in secondary metabolites production, peptaboils, epidithiodioxopiperazines and siderophores potentially involved in parasitism, saprophytic degradation as well as in biocontrol and antagonistic activities. This abundance is comparable to other Trichoderma spp. in the T. harzianum species complex, but broader than in other biocontrol species and in the species T. reesei, known for its industrial application in cellulase production. Comparative analysis also demonstrated similar genomic organization of major secondary metabolites clusters, as in other Trichoderma species.

CONCLUSIONS

Reported data provide a contribution to a deeper understanding of the mode of action and identification of activity-specific genetic markers useful for selection and improvement of biocontrol strains. This work will also enlarge the availability of genomic data to perform comparative studies with the aim to correlate phenotypic differences with genetic diversity of Trichoderma species.

Draft genome sequence, disease-resistance genes, and phenotype of a Paenibacillus terrae strain (NK3-4) with the potential to control plant diseases

Paenibacillus terrae NK3-4 is a plant growth-promoting rhizobacterium that may be useful for controlling plant diseases. We conducted a genomic analysis and identified the genes mediating antimicrobial functions. Additionally, an extracellular antifungal protein component was isolated and identified. The draft genome sequence was assembled into 54 contigs, with 5 458 568 bp and a G+C content of 47%. Moreover, 4 690 015 bp encoded 5090 proteins, 7 rRNAs, and 54 tRNAs. Forty-four genes involved in antimicrobial functions were detected. They mainly encode 19 non-ribosomal peptide synthetases (NRPSs); one polyketide synthase/NRPSs hybrid enzyme; four Zn-dependent metalloproteases; three antilisterial bacteriocin subtilosin biosynthesis proteins (AlbA); four serine proteases; five pectate lyases; three beta-glucanases; and four 1,4-beta-xylanases. These include four novel NRPSs that have not been found in any species of Paenibacillus. Furthermore, five proteins exhibiting antifungal activity were identified from the antifungal extracellular protein component based on MS/MS and the strain NK3-4 predicted protein library. On the basis of these features, we propose that strain NK3-4 represents a promising biocontrol agent for protecting plant from diseases. The draft genome sequence described herein may provide the genetic basis for the characterization of the molecular mechanisms underlying the biocontrol functions. It may also facilitate the development of rational strategies for improving the strain.

Potential biocontrol efficacy of Trichoderma atroviride with cellulase expression regulator ace1 gene knock-out

The biocontrol function of the repressor of cellulase expression I (ACE1) in Trichoderma atroviride was verified through constructing Δace1 mutant strain by Agrobacterium tumefaciens-mediated transformation. The activities of cell wall-degrading enzymes (cellulase, xylanase, chitinase, β-1,3-glucanase, and protease) in the supernatant of Δace1 mutant strain were distinctly higher than those of control strain, followed with the elevation of related genes transcript levels. Besides, the Δace1 mutant resulted in an elevating transcript level of xyr1, but no obvious change in the expression of cre1, which suggested that ACE1 was negative regulator of the xyr1 transcription, but not involved in cre1 transcription. On core polyketide synthases of four biosynthesis gene clusters for antibiotic secondary metabolites, only the transcription levels of encoding genes Try83179/TryH and Aza79482/AzaJ in Δace1 mutant strain were significantly higher than that in wild-type during antagonizing with pathogenic fungi Fusarium oxysporum and Rhizoctonia solani (with the inhibition rate of 30.7 and 19.8%, respectively). The biocontrol function of Δace1 mutant strain was remarkably enhanced. The results indicated that ACE1, indeed, acted as a repressor for cell wall-degrading enzymes and PKSs expression in T. atroviride, and the Δace1 mutant strain effectively made related enzymes activities improved with potential enhancement of biocontrol potency.

Isolation and Mass Production of Trichoderma

Members of the genus Trichoderma comprise the majority of commercial fungal biocontrol agents of plant diseases. As such, there is a wealth of information available on the analysis of their biocontrol potential and the mechanisms behind their superior abilities. This chapter aims to summarize the most common methods utilized within a Trichoderma biocontrol program for the isolation, identification, and mass propagation of individual strains.

Isolation of the antibiotic methyl (R,E)-3-(1-hydroxy-4-oxocyclopent-2-en-1-yl)-acrylate EA-2801 from Trichoderma atroviridae

The endophytic Trichoderma atroviridae UB-LMA was isolated as a symbiont of Taxus baccata and analyzed for its antimicrobial activity. By applying an original approach consisting of solid-state cultivation coupled with solid-phase extraction, a new methyl (R,E)-3-(1-hydroxy-4-oxocyclopent-2-en-1-yl)-acrylate derivative named EA-2801 (1) was isolated together with the previously reported isonitrin A and dermadin methyl ester. The chemical structure of 1 was determined by NMR and MS. Compound 1 showed antimicrobial activity against a panel of Gram-positive and -negative bacteria.

Total crude protein extract of Trichoderma spp. induces systemic resistance in pearl millet against the downy mildew pathogen

Several proteins and peptides of microbial origin are reported for their elicitor properties, which play a vital role in the development of local and systemic resistances in plants. In this study, the efficacy of total crude proteins (TCP) extracted from six different Trichoderma spp. (T. asperellum, T. harzianum, T. atroviride, T. virens, T. longibrachiatum, and T. brevicompactum) was evaluated for their ability to elicit defense responses in pearl millet against downy mildew disease. Priming of pearl millet seeds (with or without mannitol) with different concentrations of TCP from Trichoderma spp. does not affect the seed germination and seedling vigor significantly. Under greenhouse conditions, a varied level of disease protection was recorded with TCP of different Trichoderma spp., and furthermore, its efficacy was found increased when treated with mannitol. Total crude protein extracts of T. atroviride (75 µg/ml) with mannitol recorded significantly higher disease protection of 53.6% in comparison with respective controls. Furthermore, this observation was supported by elevated levels of peroxidase (7.7 U @ 36 h after inoculation) and lipoxygenase (29.5 U @ 48 h after inoculation) and hypersensitive necrotic spots (56% @ 24 h after inoculation). The present study illustrated the capability of TCP extracted from different Trichoderma spp. to elicit the disease resistance mechanism in pearl millet seedlings against Sclerospora graminicola.

Biologically Based Methods for Control of Fumonisin-Producing Fusarium Species and Reduction of the Fumonisins

Infection by the fumonisin-producing Fusarium spp. and subsequent fumonisin contamination of maize adversely affect international trade and economy with deleterious effects on human and animal health. In developed countries high standards of the major food suppliers and retailers are upheld and regulatory controls deter the importation and local marketing of fumonisin-contaminated food products. In developing countries regulatory measures are either lacking or poorly enforced, due to food insecurity, resulting in an increased mycotoxin exposure. The lack and poor accessibility of effective and environmentally safe control methods have led to an increased interest in practical and biological alternatives to reduce fumonisin intake. These include the application of natural resources, including plants, microbial cultures, genetic material thereof, or clay minerals pre- and post-harvest. Pre-harvest approaches include breeding for resistant maize cultivars, introduction of biocontrol microorganisms, application of phenolic plant extracts, and expression of antifungal proteins and fumonisin degrading enzymes in transgenic maize cultivars. Post-harvest approaches include the removal of fumonisins by natural clay adsorbents and enzymatic degradation of fumonisins through decarboxylation and deamination by recombinant carboxylesterase and aminotransferase enzymes. Although, the knowledge base on biological control methods has expanded, only a limited number of authorized decontamination products and methods are commercially available. As many studies detailed the use of natural compounds in vitro, concepts in reducing fumonisin contamination should be developed further for application in planta and in the field pre-harvest, post-harvest, and during storage and food-processing. In developed countries an integrated approach, involving good agricultural management practices, hazard analysis and critical control point (HACCP) production, and storage management, together with selected biologically based treatments, mild chemical and physical treatments could reduce fumonisin contamination effectively. In rural subsistence farming communities, simple, practical, and culturally acceptable hand-sorting, maize kernel washing, and dehulling intervention methods proved to be effective as a last line of defense for reducing fumonisin exposure. Biologically based methods for control of fumonisin-producing Fusarium spp. and decontamination of the fumonisins could have potential commercial application, while simple and practical intervention strategies could also impact positively on food safety and security, especially in rural populations reliant on maize as a dietary staple.

Isolation and expression of two polyketide synthase genes from Trichoderma harzianum 88 during mycoparasitism

Metabolites of mycoparasitic fungal species such as Trichoderma harzianum 88 have important biological roles. In this study, two new ketoacyl synthase (KS) fragments were isolated from cultured Trichoderma harzianum 88 mycelia using degenerate primers and analysed using a phylogenetic tree. The gene fragments were determined to be present as single copies in Trichoderma harzianum 88 through southern blot analysis using digoxigenin-labelled KS gene fragments as probes. The complete sequence analysis in formation of pksT-1 (5669bp) and pksT-2 (7901bp) suggests that pksT-1 exhibited features of a non-reducing type I fungal PKS, whereas pksT-2 exhibited features of a highly reducing type I fungal PKS. Reverse transcription polymerase chain reaction indicated that the isolated genes are differentially regulated in Trichoderma harzianum 88 during challenge with three fungal plant pathogens, which suggests that they participate in the response of Trichoderma harzianum 88 to fungal plant pathogens. Furthermore, disruption of the pksT-2 encoding ketosynthase-acyltransferase domains through Agrobacterium-mediated gene transformation indicated that pksT-2 is a key factor for conidial pigmentation in Trichoderma harzianum 88.

Methods for the Evaluation of the Bioactivity and Biocontrol Potential of Species of Trichoderma

Members of the genus Trichoderma comprise the majority of commercial fungal biocontrol agents of plant diseases. As such, there is a wealth of information available on the analysis of their biocontrol potential and the mechanisms behind their superior abilities. This chapter aims to summarize the most common methods utilized within a Trichoderma biocontrol program for assessing the biological properties of individual strains.

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants

For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants.

Genome sequence of Trichoderma virens FT-333 from tropical marine climate

Environmental factors can cause changes in the content of the fungal genome during evolution. In this study, a fungus used as a biocontrol agent, Trichoderma virens FT-333 (from a tropical marine climate) has been isolated. The genome (38.6 Mbp; GC content, 49.43%) has a total of 12,751 proteins. Gene ontology terms (cellular component and molecular function) and KEGG analyses demonstrated the importance of the secretion function in FT-333. Compared to the other Trichoderma species, copy number of genes related to defense and nutrient utilization was variable.

A paralog of the proteinaceous elicitor SM1 is involved in colonization of maize roots by Trichoderma virens

The biocontrol agent, Trichoderma virens, has the ability to protect plants from pathogens by eliciting plant defense responses, involvement in mycoparasitism, or secreting antagonistic secondary metabolites. SM1, an elicitor of induced systemic resistance (ISR), was found to have three paralogs within the T. virens genome. The paralog sm2 is highly expressed in the presence of plant roots. Gene deletion mutants of sm2 were generated and the mutants were found to overproduce SM1. The ability to elicit ISR in maize against Colletotrichum graminicola was not compromised for the mutants compared to that of wild type isolate. However, the deletion strains had a significantly lowered ability to colonize maize roots. This appears to be the first report on the involvement of an effector-like protein in colonization of roots by Trichoderma.

Surveying the potential of secreted antimicrobial peptides to enhance plant disease resistance

Antimicrobial peptides (AMPs) are natural products found across diverse taxa as part of the innate immune system against pathogen attacks. Some AMPs are synthesized through the canonical gene expression machinery and are called ribosomal AMPs. Other AMPs are assembled by modular enzymes generating nonribosomal AMPs and harbor unusual structural diversity. Plants synthesize an array of AMPs, yet are still subject to many pathogen invasions. Crop breeding programs struggle to release new cultivars in which complete disease resistance is achieved, and usually such resistance becomes quickly overcome by the targeted pathogens which have a shorter generation time. AMPs could offer a solution by exploring not only plant-derived AMPs, related or unrelated to the crop of interest, but also non-plant AMPs produced by bacteria, fungi, oomycetes or animals. This review highlights some promising candidates within the plant kingdom and elsewhere, and offers some perspectives on how to identify and validate their bioactivities. Technological advances, particularly in mass spectrometry (MS) and nuclear magnetic resonance (NMR), have been instrumental in identifying and elucidating the structure of novel AMPs, especially nonribosomal peptides which cannot be identified through genomics approaches. The majority of non-plant AMPs showing potential for plant disease immunity are often tested using in vitro assays. The greatest challenge remains the functional validation of candidate AMPs in plants through transgenic experiments, particularly introducing nonribosomal AMPs into crops.

Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?

Endophytic microorganisms live inside plants for at least part of their life cycle. According to their life strategies, bacterial endophytes can be classified as “obligate” or “facultative”. Reports that members of the genus Micromonospora, Gram-positive Actinobacteria, are normal occupants of nitrogen-fixing nodules has opened up a question as to what is the ecological role of these bacteria in interactions with nitrogen-fixing plants and whether it is in a process of adaptation from a terrestrial to a facultative endophytic life. The aim of this work was to analyse the genome sequence of Micromonospora lupini Lupac 08 isolated from a nitrogen fixing nodule of the legume Lupinus angustifolius and to identify genomic traits that provide information on this new plant-microbe interaction. The genome of M. lupini contains a diverse array of genes that may help its survival in soil or in plant tissues, while the high number of putative plant degrading enzyme genes identified is quite surprising since this bacterium is not considered a plant-pathogen. Functionality of several of these genes was demonstrated in vitro, showing that Lupac 08 degraded carboxymethylcellulose, starch and xylan. In addition, the production of chitinases detected in vitro, indicates that strain Lupac 08 may also confer protection to the plant. Micromonospora species appears as new candidates in plant-microbe interactions with an important potential in agriculture and biotechnology. The current data strongly suggests that a beneficial effect is produced on the host-plant.