In the development of medicinally important Orchidaceae, the extent of fungal endophytes specificity is not presently very clear. Limited study has been available on natural products formed and its role on plant growth, defence mechanism by endophytes, and to characterize the chief treasure of bioactive molecules. Therefore, this review article presents an evaluation of the endophytes associated with Orchidaceae for physiology, metabolism, and genomics which have prominently contributed to the resurgence of novel metabolite research increasing our considerate of multifaceted mechanisms regulatory appearance of biosynthetic gene groups encoding diverse metabolites. Additionally, we presented the comprehensive recent development of bio-strategies for the cultivation of endophytes from Orchidaceae and integration of bioengineered ‘Genomics with metabolism’ approaches with emphases collective omics as powerful approach to discover novel metabolite compounds. The Orchidaceae-fungal endophytes' biodynamics for sustainable development of bioproducts and its applications are supported in large-scale biosynthesis of industrially and pharmaceutical important biomolecules. Graphical abstract

Dendrobium are tropical orchid plants that host diverse endophytic fungi. The role of these fungi is not currently well understood in Dendrobium plants. We morphologically and molecularly identified these fungal endophytes, and created an efficient system for evaluating the pathogenicity and symptoms of endophytic fungi on Dendrobium nobile and Dendrobium officinale though in vitro co-culturing. ReThe colony morphological traits of Dendrobium myco-endophytes (DMEs) were recorded for their identification. Molecular identification revealed the presence of Colletotrichum tropicicola, Fusarium keratoplasticum, Fusarium oxysporum, Fusarium solani, and Trichoderma longibrachiatum. The pathogenicity results revealed that T. longibrachiatum produced the least pathogenic effects against D. nobile protocorms. In seedlings, T. longibrachiatum showed the least pathogenic effects against D. officinale seedlings after seven days. C. tropicicola produced highly pathogenic effects against both Dendrobium seedlings. The results of histological examination of infected tissues revealed that F. keratoplasticum and T. longibrachiatum fulfill Koch’s postulates for the existence of endophytes inside the living tissues. The DMEs are cross-transmitted inside the host plant cells, playing an important role in plant host development, resistance, and alkaloids stimulation.

Dendrobium nobile is the only plant that could produce the natural bioactive dendrobine. No other source of dendrobine has been found to date except from D. nobile and via chemical synthesis. In this study, we aimed to examine the potential fungal endophyte isolated from D. nobile stem segments using the molecular method and to detect dendrobine compound through high-performance liquid chromatography (HPLC), gas chromatography–mass spectrometry (GC-MS), and liquid chromatography with tandem mass spectrometry (LC-MS/MS) and their metabolite for their antibacterial activity. The potential dendrobine producer strain was recognized as Trichoderma longibrachiatum based on molecular DNA sequencing and GenBank databases. The T. longibrachiatum MD33 produced dendrobine and other compounds in a potato dextrose medium (PDM), as confirmed by HPLC retention time peak analysis. The HPLC results revealed that T. longibrachiatum MD33 biomass showed a peak retention time of 5.28 ± 0.2 min, similar to wild D. nobile stem dendrobine (5.32 ± 0.2 min) and standard chemical reference dendrobine (5.30 ± 0.2 min), indicating the presence of dendrobine in the fungal biomass. Results of GC-MS and LC-MS analysis revealed that T. longibrachiatum MD33 produced the same molecular weight (263 in GC-MS and 264.195 in LC-MS) of dendrobine as compared with standard chemical reference dendrobine and D. nobile dendrobine. Antibacterial activity data revealed that T. longibrachiatum MD33 produced the strongest bactericidal activity against Bacillus subtilis, Bacillus mycoides, and Staphylococcus species, and the diameter of the bacterial growth inhibition zone was 12 ± 0.2, 9 ± 0.2, and 8 ± 0.2 mm, respectively. To the best of our knowledge, this was the first study to investigate T. longibrachiatum as a dendrobine producer, and the results revealed that T. longibrachiatum was directly involved in the potential production of a similar bioactive compound to D. nobile (dendrobine). In addition, the T. longibrachiatum metabolite exhibited potent antibacterial activity and can be a potential strain for medical and industrial purposes.

Bacillus mucilaginosusandBacillus edaphicuswere reclassified based on their 16S rRNA andgyrBgene sequences, DNA–DNA hybridization, fatty acid methyl esters and other taxonomic characteristics. Phylogenetic analysis based on 16S rRNA andgyrBgene sequences indicated that strains ofB. mucilaginosusandB. edaphicuswere members of the genusPaenibacillus, with over 90.4 % and 70.3 % sequence similarity, respectively. Their DNA G+C contents were 54.5–56.8 mol%. The DNA–DNA relatedness values ofB. edaphicusVKPM B-7517^TwithB. mucilaginosusKNP414 andB. mucilaginosusCGMCC 1.236 were 89.2 % and 88.7 %, respectively. The major isoprenoid quinone ofB. mucilaginosusandB. edaphicuswas MK-7 (94.1–95.7 %). The peptidoglycan type was A1γ(meso-diaminopimelic acid) and the major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C_15 : 0, C_16 : 1ω11cand C_16 : 0. Phenotypic features and fatty acid profiles supported the similarity ofB. mucilaginosusandB. edaphicustoPaenibacillus validusCCTCC 95016^Tand confirmed their relationship with members of the genusPaenibacillus. Therefore, it is proposed thatBacillus mucilaginosusandBacillus edaphicusbe transferred to the genusPaenibacillusasPaenibacillus mucilaginosuscomb. nov. (type strain HSCC 1605^T=VKPM B-7519^T=VKM B-1480D^T=CIP 105815^T=KCTC 3870^T) andPaenibacillus edaphicuscomb. nov. (type strain VKPM B-7517^T=DSM 12974^T=CIP 105814^T), respectively.