Isolation of endophytic bacteria from the medicinal, forestal and ornamental tree Handroanthus impetiginosus

Insight into endophytic microbiota-driven geographical and bioactive signatures toward a novel quality assessment model for Codonopsis Radix

Codonopsis Radix, a medicinal and dietary herb in traditional Chinese medicine, largely owes its pharmacological efficacy to both intrinsic phytochemistry and symbiotic interactions with plant-associated microbes. Here, we deciphered the geo-environmental regulation of Codonopsis Radix's endophytic microbiota across four major production regions using 16S rRNA/ITS sequencing and bioactive compound profiling. Results demonstrated that the planting environment significantly shaped the endophytic community of Codonopsis Radix, where Bifidobacteriaceae and Muribaculaceae exhibited the strongest correlations with its bioactive components. Monolobus and Bradyrhizobium not only exhibit distinct associations with Lobetyolin and Atractylenolide III respectively, but also demonstrate significant correlations with the key biosynthetic pathways of these compounds. Leveraging machine learning, we developed the first microbiota-driven quality assessment model, achieving 100.0% and 85.7% prediction accuracies for Lobetyolin and Atractylenolide III respectively, using Random Forest algorithms. This dual-metric framework-integrating microbial signatures with chemical profiles-establishes a novel paradigm for Codonopsis Radix quality control, bridging ecological insights with precision agriculture. Our findings illuminate the microbiota's role as a biosynthetic orchestrator in geoherbalism, offering actionable strategies for sustainable cultivation and standardized production of Codonopsis Radix.

Diversity and Correlation Analysis of Endophytes and Top Metabolites in Phlomoides rotata Roots from High-Altitude Habitats

Phlomoides rotata, a traditional medicinal plant, always grows on the Tibetan Plateau at a high altitude of 3100-5200 m. The major active ingredients in P. rotata were used in medicines due to their diverse pharmacological effects, including hemostatic, anti-inflammatory, antitumor, immuno-modulatory, and antioxidant activities. This study screened 15 top endophytic genus through the analysis of OTUs and the top 30 metabolites with relatively high content in P. rotata roots from four different habitats (HN, GL, YS, and CD regions) in Qinghai Province. Twelve physicochemical indicators were measured and analyzed in the rhizosphere soils of P. rotata habitats. The results indicated that the top 30 metabolites compounds included 7 amino acids, 5 sugars and alcohols, 4 phenylpropanoids, 3 Organic acids, and 3 Alkaloids. Four endophytic bacteria (Acidibacter, Sphingomonas, Variovorax, and Sphingobium) and three endophytic fungi (Tetracladium, Cadophora, and Minimelanolocus) were dominant genera in P. rotata roots from four habitats. There were 109 positive significant correlations and 57 negative correlations between OTUs of endophytic bacteria and contents of top 30 metabolites, and 59 positive significant correlations and 58 negative correlations between OTUs of endophytic fungus and contents of top 30 metabolites. The OTUs of Acidibacter were significantly positively correlated with the content of 5 soil physicochemical indicators (total phosphorus, amylase, sucrase, total potassium, or soil organic carbon) and significantly negatively correlated with the content of acid protease. OTUs of Tetracladium or Cadophora showed a positive correlation with the content of total phosphorus and a negative correlation with that of alkaline phosphatase. This study provides a theoretical basis for the study of the correlation between endophytes and metabolites in P. rotata roots.

Invisible Inhabitants of Plants and a Sustainable Planet: Diversity of Bacterial Endophytes and their Potential in Sustainable Agriculture

Uncontrolled usage of chemical fertilizers, climate change due to global warming, and the ever-increasing demand for food have necessitated sustainable agricultural practices. Removal of ever-increasing environmental pollutants, treatment of life-threatening diseases, and control of drug-resistant pathogens are also the need of the present time to maintain the health and hygiene of nature, as well as human beings. Research on plant-microbe interactions is paving the way to ameliorate all these sustainably. Diverse bacterial endophytes inhabiting the internal tissues of different parts of the plants promote the growth and development of their hosts by different mechanisms, such as through nutrient acquisition, phytohormone production and modulation, protection from biotic or abiotic challenges, assisting in flowering and root development, etc. Notwithstanding, efficient exploitation of endophytes in human welfare is hindered due to scarce knowledge of the molecular aspects of their interactions, community dynamics, in-planta activities, and their actual functional potential. Modern "-omics-based" technologies and genetic manipulation tools have empowered scientists to explore the diversity, dynamics, roles, and functional potential of endophytes, ultimately empowering humans to better use them in sustainable agricultural practices, especially in future harsh environmental conditions. In this review, we have discussed the diversity of bacterial endophytes, factors (biotic as well as abiotic) affecting their diversity, and their various plant growth-promoting activities. Recent developments and technological advancements for future research, such as "-omics-based" technologies, genetic engineering, genome editing, and genome engineering tools, targeting optimal utilization of the endophytes in sustainable agricultural practices, or other purposes, have also been discussed.

The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles

Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.

Diversity of Endophytes of Actinidia arguta in Different Seasons

The seasonal changes in environmental conditions can alter the growth states of host plants, thereby affecting the living environment of endophytes and forming different endophytic communities. This study employs Illumina MiSeq next-generation sequencing to analyze the 16SrRNA and ITS rDNA of endophytes in 24 samples of Actinidia arguta stem tissues across different seasons. The results revealed a high richness and diversity of endophytes in Actinidia arguta, with significant seasonal variations in microbial community richness. This study identified 897 genera across 36 phyla for bacteria and 251 genera across 8 phyla for fungi. Notably, 69 bacterial genera and 19 fungal genera significantly contributed to the differences in community structure across seasons. A distinctive feature of coexistence in the endophytic community, both specific and conservative across different seasons, was observed. The bacterial community in winter demonstrated significantly higher richness and diversity compared to the other seasons. Environmental factors likely influence the optimal timing for endophyte colonization. Solar radiation, temperature, precipitation, and relative humidity significantly impact the diversity of endophytic bacteria and fungi. In addition, seasonal variations show significant differences in the nutritional modes of fungal endophytes and the degradation, ligninolysis, and ureolysis functions of bacterial endophytes. This study elucidates the potential role of endophytes in assisting Actinidia arguta in adapting to seasonal changes and provides a theoretical basis for further exploration of functional microbial strains.

Cultivable Endophyte Resources in Medicinal Plants and Effects on Hosts

With the increasing demand for medicinal plants and the increasing shortage of resources, improving the quality and yield of medicinal plants and making more effective use of medicinal plants has become an urgent problem to be solved. During the growth of medicinal plants, various adversities can lead to nutrient loss and yield decline. Using traditional chemical pesticides to control the stress resistance of plants will cause serious pollution to the environment and even endanger human health. Therefore, it is necessary to find suitable pesticide substitutes from natural ingredients. As an important part of the microecology of medicinal plants, endophytes can promote the growth of medicinal plants, improve the stress tolerance of hosts, and promote the accumulation of active components of hosts. Endophytes have a more positive and direct impact on the host and can metabolize rich medicinal ingredients, so researchers pay attention to them. This paper reviews the research in the past five years, aiming to provide ideas for improving the quality of medicinal plants, developing more microbial resources, exploring more medicinal natural products, and providing help for the development of research on medicinal plants and endophytes.

Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery

Bacterial communities have been identified as functional key members in soil ecology. A deep relation with these communities maintains forest coverture. Trees harbor particular bacteriomes in the rhizosphere, endosphere, or phyllosphere, different from bulk-soil representatives. Moreover, the plant microbiome appears to be specific for the plant-hosting species, varies through season, and responsive to several environmental factors. This work reports the changes in bacterial communities associated with dominant pioneer trees [Tabebuia rosea and Handroanthus chrysanthus [(Bignoniaceae)] during tropical forest recovery chronosequence in the Mayan forest in Campeche, Mexico. Massive 16S sequencing approach leads to identifying phylotypes associated with rhizosphere, bulk-soil, or recovery stage. Lotka-Volterra interactome modeling suggests the presence of putative regulatory roles of some phylotypes over the rest of the community. Our results may indicate that bacterial communities associated with pioneer trees may establish more complex regulatory networks than those found in bulk-soil. Moreover, modeled regulatory networks predicted from rhizosphere samples resulted in a higher number of nodes and interactions than those found in the analysis of bulk-soil samples.

Beneficial Relationships Between Endophytic Bacteria and Medicinal Plants

Plants benefit extensively from endophytic bacteria, which live in host plant tissues exerting no harmful effects. Bacterial endophytes promote the growth of host plants and enhance their resistance toward various pathogens and environmental stresses. They can also regulate the synthesis of secondary metabolites with significant medicinal properties and produce various biological effects. This review summarizes recent studies on the relationships between bacterial endophytes and medicinal plants. Endophytic bacteria have numerous applications in agriculture, medicine, and other industries: improving plant growth, promoting resistance toward both biotic and abiotic stresses, and producing metabolites with medicinal potential. Their distribution and population structure are affected by their host plant's genetic characteristics and health and by the ecology of the surrounding environment. Understanding bacterial endophytes can help us use them more effectively and apply them to medicinal plants to improve yield and quality.