Root Endophytes and Ginkgo biloba Are Likely to Share and Compensate Secondary Metabolic Processes, and Potentially Exchange Genetic Information by LTR-RTs

Microbial inheritance through seed: a clouded area needs to be enlightened

Seed endophytes are actively used by the mother plant as both reservoir and vector of beneficial microbes. During seed dormancy endophytes experience significant physiochemical changes and only competent endophytes could colonise successfully in seeds and some of them act as obligate endophyte that are transmitted vertically across generations. The adaptive nature of endophytes allows them to switch lifestyles depending on environment and host conditions. In this review, instead of providing broad discussion on applicability of endophytes in plant growth improvement, the fundamental nature of endophytes, their survival strategies under stress conditions, transmittance, etc. have been broadly highlighted by collaborating recent discoveries and theories. We have also tried to differentiate endophyte with their pathogenic counterpart and their survival mechanism during seed dormancy stages. Critical analyses of physio-biochemical changes in seeds during maturation and parallel modifications of life styles of seed endophytes along with pathogens will enlighten the shaded part of seed-microbiome interactions. The mutualistic interrelations as well as their shipment towards pathogenic behaviour under stress are being discussed acutely. Finally, importances of conservation of seed microbiome to maintain seed quality and vigour have been pointed out. Throughout the manuscript, the knowledge gap on seed-microbiota have been mentioned, thus, in future, studies on these areas could help us to understand properly the actual role of endophytes for the betterment of maintaining seed quality and vigour.

Endophytic Pseudomonas fluorescens relieves intraspecific allelopathy of Atractylodes lancea by reducing ethylene transportation

BACKGROUND

Endophytes play an important role in promoting plant growth. To date, although many reports provided insight into the function of endophytes in their hosts, few reports focus on their impact on nearby plants. Intraspecific allelopathy in plant community is common and presents a notable challenge to medicinal plant yield and productivity. Atractylodes lancea is a perennial herb that has relatively low yields due to intraspecific allelopathy. The bacterial endophyte Pseudomonas fluorescens ALEB7B has previously been found to increase essential oil content of A. lancea, but the role of ALEB7B in A. lancea allelopathy is still unknown.

RESULTS

Noninoculated A. lancea exhibited growth retardation when it was grown in a community, which was related to ethylene-induced intraspecific allelopathy. Further experiment showed that exposing A. lancea to volatile from noninoculated A. lancea or same concentration of ethylene reduced growth of A. lancea. P. fluorescens-inoculated plants showed reduced ethylene emission and relieved growth retardation on neighboring noninoculated A. lancea. Moreover, P. fluorescens inoculation had little allelopathic effect when receivers were treated with ethylene receptor inhibitor or when emitters were treated with ethylene production inhibitor. Transcriptomic analysis revealed that endophyte ALEB7B altered transcriptional response associated with ethylene response and essential oil production in neighboring A. lancea.

CONCLUSIONS

Our results demonstrated that the bacterial endophyte ALEB7B provides fitness benefits for both hosts and neighbors. The allelopathic effect on nearby plants can be alleviated by altering airborne signals, such as ethylene, in endophytic bacteria.

The inhibitory effects of endophytic metabolites on glycated proteins under non-communicable disease conditions: A review

Protein glycation in human body is closely linked to the onset/progression of diabetes associated complications. These glycated proteins are commonly known as advanced glycation end products (AGEs). Recent literature has also highlighted the involvement of AGEs in other non-communicable diseases (NCDs) such as cardiovascular, cancer, and Alzheimer's diseases and explored the impact of plant metabolites on AGEs formation. However, the significance of endophytic metabolites against AGEs has recently garnered attention but has not been thoroughly summarized thus far. Therefore, the objective of this review is to provide a comprehensive overview of the importance of endophytic metabolites in combating AGEs under NCDs conditions. Additionally, this review aims to elucidate the processes of AGEs formation, absorption, metabolism, and their harmful effects. Collectively, endophytic metabolites play a crucial role in modulating signaling pathways and enhancing the digestibility properties of gut microbiota (GM) by targeting on AGEs/RAGE (receptor for AGEs) axis. Furthermore, these metabolites exhibit anti-AGEs activities similar to those derived from host plants, but at a lower cost and higher production rate. The use of endophytes as a source of such metabolites offers a risk-free and sustainable approach that holds substantial potential for the treatment and management of NCDs.

The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications

This review provides a comprehensive overview of the key aspects of the natural metabolite production by endophytic fungi, which has attracted significant attention due to its diverse biological activities and wide range of applications. Synthesized by various fungal species, these metabolites encompass compounds with therapeutic, agricultural, and commercial significance. We delved into strategies and advancements aimed at optimizing fungal metabolite production. Fungal cultivation, especially by Aspergillus, Penicillium, and Fusarium, plays a pivotal role in metabolite biosynthesis, and researchers have explored both submerged and solid-state cultivation processes to harness the full potential of fungal species. Nutrient optimization, pH, and temperature control are critical factors in ensuring high yields of the targeted bioactive metabolites especially for scaling up processes. Analytical methods that includes High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS), are indispensable for the identification and quantification of the compounds. Moreover, genetic engineering and metabolic pathway manipulation have emerged as powerful tools to enhance metabolite production and develop novel fungal strains with increased yields. Regulation and control mechanisms at the genetic, epigenetic, and metabolic levels are explored to fine-tune the biosynthesis of fungal metabolites. Ongoing research aims to overcome the complexity of the steps involved to ensure the efficient production and utilization of fungal metabolites.

Isolation of endophytes from Dioscorea nipponica Makino for stimulating diosgenin production and plant growth

KEY MESSAGE

Both bacterial and fungal endophytes exhibited one or more plant growth-promoting (PGP) traits. Among these strains, the Paenibacillus peoriae SYbr421 strain demonstrated the greatest activity in the direct biotransformation of tuber powder from D. nipponica into diosgenin. Endophytes play crucial roles in shaping active metabolites within plants, significantly influencing both the quality and yield of host plants. Dioscorea nipponica Makino accumulates abundant steroidal saponins, which can be hydrolyzed to produce diosgenin. However, our understanding of the associated endophytes and their contributions to plant growth and diosgenin production is limited. The present study aimed to assess the PGP ability and potential of diosgenin biotransformation by endophytes isolates associated with D. nipponica for the efficient improvement of plant growth and development of a clean and effective approach for producing the valuable drug diosgenin. Eighteen bacterial endophytes were classified into six genera through sequencing and phylogenetic analysis of the 16S rDNA gene. Similarly, 12 fungal endophytes were categorized into 5 genera based on sequencing and phylogenetic analysis of the ITS rDNA gene. Pure culture experiments revealed that 30 isolated endophytic strains exhibited one or more PGP traits, such as nitrogen fixation, phosphate solubilization, siderophore synthesis, and IAA production. One strain of endophytic bacteria, P. peoriae SYbr421, effectively directly biotransformed the saponin components in D. nipponica. Moreover, a high yield of diosgenin (3.50%) was obtained at an inoculum size of 4% after 6 days of fermentation. Thus, SYbr421 could be used for a cleaner and more eco-friendly diosgenin production process. In addition, based on the assessment of growth-promoting isolates and seed germination results, the strains SYbr421, SYfr1321, and SYfl221 were selected for greenhouse experiments. The results revealed that the inoculation of these promising isolates significantly increased the plant height and fresh weight of the leaves and roots compared to the control plants. These findings underscore the importance of preparing PGP bioinoculants from selected isolates as an additional option for sustainable diosgenin production.

Flavonoid Synthesis by Deinococcus sp. 43 Isolated from the Ginkgo Rhizosphere

Flavonoids are crucial in physiological and pharmaceutical processes, especially the treatment of cancer and the prevention of cardiovascular and cerebrovascular diseases. Flavonoid-producing plants and fungi have been extensively reported, but bacteria have been much less investigated as a source of flavonoid production. Deinococcus sp. 43, a spherical flavonoid-producing bacteria from the Ginkgo rhizosphere, was reported in this study. First, the whole genome of Deinococcus sp. 43 was sequenced and a series of flavonoid anabolic genes were annotated. Simultaneously, High Performance Liquid Chromatography (HPLC) results showed that Deinococcus sp. 43 was capable of producing flavonoids, with a maximum quercetin output of 2.9 mg/L. Moreover, the relative expression of key genes involved in flavonoid synthesis was determined to test the completeness of the flavonoid anabolic pathway. The results of LC-MS analysis demonstrated that the flavonoids produced by Deinococcus sp. 43 were significantly different between intracellular and extracellular environments. The concentration of multiple glycosylated flavonoids was substantially higher in extracellular than intracellular environments, while the majority of flavonoids obtained in intracellular environments were hydroxylated multiple times. Lastly, the flavonoid biosynthetic pathway of Deinococcus sp. 43 was constructed based on the genomic analysis and the detected flavonoids. In conclusion, this study represents the first comprehensive characterization of the flavonoid-producing pathway of Deinococcus. The findings demonstrate that the strain has excellent potential as a genetically engineered strain for the industrial production of flavonoids.

Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station

A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1T. The 16S sequence of the F6_2S_P_1T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1T are anteiso-C15:0 (51.7%), iso-C16:0 (23.1%), and iso-C15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1T (=NRRL B-65657T and DSMZ 115098T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1T and other members of this clade.

Plants as the Extended Phenotype of Endophytes-The Actual Source of Bioactive Compounds

For thousands of years, plants have been used for their medicinal properties. The industrial production of plant-beneficial compounds is facing many drawbacks, such as seasonal dependence and troublesome extraction and purification processes, which have led to many species being on the edge of extinction. As the demand for compounds applicable to, e.g., cancer treatment, is still growing, there is a need to develop sustainable production processes. The industrial potential of the endophytic microorganisms residing within plant tissues is undeniable, as they are often able to produce, in vitro, similar to or even the same compounds as their hosts. The peculiar conditions of the endophytic lifestyle raise questions about the molecular background of the biosynthesis of these bioactive compounds in planta, and the actual producer, whether it is the plant itself or its residents. Extending this knowledge is crucial to overcoming the current limitations in the implementation of endophytes for larger-scale production. In this review, we focus on the possible routes of the synthesis of host-specific compounds in planta by their endophytes.

Dynamic variation of Paris polyphylla root-associated microbiome assembly with planting years

P. polyphylla selectively enriches beneficial microorganisms to help their growth. Paris polyphylla (P. polyphylla) is an important perennial plant for Chinese traditional medicine. Uncovering the interaction between P. polyphylla and the related microorganisms would help to utilize and cultivate P. polyphylla. However, studies focusing on P. polyphylla and related microbes are scarce, especially on the assembly mechanisms and dynamics of the P. polyphylla microbiome. High-throughput sequencing of the 16S rRNA genes was implemented to investigate the diversity, community assembly process and molecular ecological network of the bacterial communities in three root compartments (bulk soil, rhizosphere, and root endosphere) across three years. Our results demonstrated that the composition and assembly process of the microbial community in different compartments varied greatly and were strongly affected by planting years. Bacterial diversity was reduced from bulk soils to rhizosphere soils to root endosphere and varied over time. Microorganisms benefit to plants was selectively enriched in P. polyphylla roots as was its core microbiome, including Pseudomonas, Rhizobium, Steroidobacter, Sphingobium and Agrobacterium. The network's complexity and the proportion of stochasticity in the community assembly process increased. Besides, nitrogen metabolism, carbon metabolism, phosphonate and phosphinate metabolism genes in bulk soils increased over time. These findings suggest that P. polyphylla exerts a selective effect to enrich the beneficial microorganisms and proves the sequential increasing selection pressure with P. polyphylla growth. Our work adds to the understanding of the dynamic processes of plant-associated microbial community assembly, guides the selection and application timing of P. polyphylla-associated microbial inoculants and is vital for sustainable agriculture.

Enriching the endophytic bacterial microbiota of Ginkgo roots

Bacterial endophytes of Ginkgo roots take part in the secondary metabolic processes of the fossil tree and contribute to plant growth, nutrient uptake, and systemic resistance. However, the diversity of bacterial endophytes in Ginkgo roots is highly underestimated due to the lack of successful isolates and enrichment collections. The resulting culture collection contains 455 unique bacterial isolates representing 8 classes, 20 orders, 42 families, and 67 genera from five phyla: Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Deinococcus-Thermus, using simply modified media (a mixed medium without any additional carbon sources [MM)] and two other mixed media with separately added starch [GM] and supplemented glucose [MSM]). A series of plant growth-promoting endophytes had multiple representatives within the culture collection. Moreover, we investigated the impact of refilling carbon sources on enrichment outcomes. Approximately 77% of the natural community of root-associated endophytes were predicted to have successfully cultivated the possibility based on a comparison of the 16S rRNA gene sequences between the enrichment collections and the Ginkgo root endophyte community. The rare or recalcitrant taxa in the root endosphere were mainly associated with Actinobacteria, Alphaproteobacteria, Blastocatellia, and Ktedonobacteria. By contrast, more operational taxonomic units (OTUs) (0.6% in the root endosphere) became significantly enriched in MM than in GM and MSM. We further found that the bacterial taxa of the root endosphere had strong metabolisms with the representative of aerobic chemoheterotrophy, while the functions of the enrichment collections were represented by the sulfur metabolism. In addition, the co-occurrence network analysis suggested that the substrate supplement could significantly impact bacterial interactions within the enrichment collections. Our results support the fact that it is better to use the enrichment to assess the cultivable potential and the interspecies interaction as well as to increase the detection/isolation of certain bacterial taxa. Taken together, this study will deepen our knowledge of the indoor endophytic culture and provide important insights into the substrate-driven enrichment.

The novel distribution of intracellular and extracellular flavonoids produced by Aspergillus sp. Gbtc 2, an endophytic fungus from Ginkgo biloba root

Here, we reported a Ginkgo endophyte, Aspergillus sp. Gbtc 2, isolated from the root tissue. Its flavonoid biosynthesis pathway was reconstructed, the effect of phenylalanine on the production of flavonoids was explored, and the flavonoid metabolites were identified with the high-resolution Liquid chromatography–mass spectrometry (LC–MS). Some essential genes were annotated to form the upstream of the complete biosynthesis pathway, indicating that Aspergillus sp. Gbtc 2 has the ability to synthesize the C6–C3–C6 flavonoid monomers. HPLC results showed that adding an appropriate amount of phenylalanine could promote the production of flavonoids by Aspergillus Gbtc 2. LC–MS results depicted a significant difference in many flavonoids between intracellularly and extracellularly. Most of the flavonoids gathered in the cell contained glycosylation groups, while almost all components with multiple hydroxyls showed much higher concentrations extracellularly than intracellularly; they likely have different biological functions. A variety of these substances can be mapped back to the pathway pattern of flavonoid biosynthesis and prove the ability of flavonoid production once again. This study expanded the information on flavonoid biosynthesis in Aspergillus and provided a solid theoretical basis for developing the fungi into genetically engineered strains undertaking flavonoid industrialized production.

Endophytic Bacterial Communities of Ginkgo biloba Leaves During Leaf Developmental Period

Plant-specialized secondary metabolites have ecological functions in mediating interactions between plants and their entophytes. In this study, high-throughput gene sequencing was used to analyze the composition and abundance of bacteria from Ginkgo leaves at five different sampling times. The results indicated that the bacterial community structure varied during leaf developmental stage. Bacterial diversity was observed to be the highest at T2 stage and the lowest at T1 stage. Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes were found as the dominant phyla. The major genera also showed consistency across sampling times, but there was a significant variation in their abundance, such as Bacillus, Lysinibacillus, and Staphylococcus. Significant correlations were observed between endophytic bacteria and flavonoids. Especially, Staphylococcus showed a significant positive correlation with quercetin, and changes in the abundance of Staphylococcus also showed a strong correlation with flavonoid content. In order to determine the effect of flavonoids on endophytic bacteria of Ginkgo leaves, an extracorporeal culture of related strains (a strain of Staphylococcus and a strain of Deinococcus) was performed, and it was found that the effect of flavonoids on them remained consistent. The predicted result of Tax4Fun2 revealed that flavonoids might lead to a lower abundance of endophytic microorganisms, which further proved the correlation between bacterial communities and flavonoids. This study provided the first insight into the bacterial community composition during the development of Ginkgo leaves and the correlation between the endophytic bacteria and flavonoids.