Rhizobiome diversity of field-collected hyperaccumulating Noccaea sp.

Hyperaccumulating plants are able to (hyper)accumulate high concentrations of metal(loid)s in their above-ground tissues without any signs of toxicity. Studies on the root-associated microbiome have been previously conducted in relation to hyperaccumulators, yet much remains unknown about the interactions between hyperaccumulating hosts and their microbiomes, as well as the dynamics within these microbial communities. Here, we assess the impact of the plant host on shaping microbial communities of three naturally occurring populations of Noccaea species in Slovenia: Noccaea praecox and co-occurring N. caerulescens from the non-metalliferous site and N. praecox from the metalliferous site. We investigated the effect of metal enrichment on microbial communities and explored the interactions within microbial groups and their environment. The abundance of bacterial phyla was more homogeneous than fungal classes across all three Noccaea populations and across the three root-associated compartments (roots, rhizosphere, and bulk soil). While most fungal and bacterial Operational Taxonomic Units (OTUs) were found at both sites, the metalliferous site comprised more unique OTUs in the root and rhizosphere compartments than the non-metalliferous site. In contrast to fungi, bacteria exhibited differentially significant abundance between the metalliferous and non-metalliferous sites as well as statistically significant correlations with most of the soil parameters. Results revealed N. caerulescens had the highest number of negative correlations between the bacterial phyla, whereas the population from the metalliferous site had the fewest. This decrease was accompanied by a big perturbation in the bacterial community at the metalliferous site, indicating increased selection between the bacterial taxa and the formation of potentially less stable rhizobiomes. These findings provide fundamentals for future research on the dynamics between hyperaccumulators and their associated microbiome.

Endophyte-based fungal elicitors for enhanced production of valepotriates and sesquiterpenoids in leaf cell suspension cultures of Valeriana jatamansi Jones.

AIMS: The immense therapeutic value of Valeriana jatamansi is attributed to the presence of bioactive secondary metabolites (valepotriates and sesquiterpenoids). Its over-exploitation in wild habitats resulted in extensive depletion, necessitating alternative approaches to produce its therapeutic metabolites. This study sought to assess the ability of endophytes of V. jatamansi to boost the biosynthesis of secondary metabolites in the leaf-cell suspension (LCS) culture of V. jatamansi. METHODS AND RESULTS: A total of 11 fungal endophytes were isolated from the rhizomes of V. jatamansi. Isolated endophytes were found to belong to phylum Ascomycota, Basidiomycota, and Mucoromycota. Supplementation of extracts of endophyte Phaeosphaeriaceae sp. VRzFB, Mucor griseocyanus VRzFD, Penicillium raistrickii VRzFK, and Penicillium sajarovii VRzFL in the LCS culture of V. jatamansi increased the fresh cell biomass by 19.6%-39.1% and dry cell biomass by 23.4%-37.8%. Most of the endophytes' extract could increase the content of valepotriates (26.5%-76.5% valtrate and 40.5%-77.9% acevaltrate) and sesquiterpenoids (19.9%-61.1% hydroxyl valerenic acid) in LCS culture. However, only two endophytes, Irpex lacteus VRzFI and Fusarium oxysporum VRzFF, could increase the sesquiterpenoids acetoxy valerenic acid (36.9%-55.3%). In contrast, some endophytes' extracts caused negative or no significant effect on the cell biomass and targeted metabolites. Increased secondary metabolites were corroborated with increased expression of iridoid biosynthesis genes in LCS culture. Production of H2O2 and lipid peroxidation was also varied with different endophytes indicating the modulation of cellular oxidative stress due to endophyte elicitors. CONCLUSIONS: The results suggest the distinct effect of different fungal endophytes-extract on LCS culture, and endophytes can serve as biotic elicitors for increasing the secondary metabolite production in plant in vitro systems.

Metabolome-driven microbiome assembly determining the health of ginger crop (Zingiber officinale L. Roscoe) against rhizome rot.

BACKGROUND: Plant-associated microorganisms can be found in various plant niches and collectively comprise the plant microbiome. The plant microbiome assemblages have been extensively studied, primarily in model species. However, a deep understanding of the microbiome assembly associated with plant health is still needed. Ginger rhizome rot has been variously attributed to multiple individual causal agents. Due to its global relevance, we used ginger and rhizome rot as a model to elucidate the metabolome-driven microbiome assembly associated with plant health. RESULTS: Our study thoroughly examined the biodiversity of soilborne and endophytic microbiota in healthy and diseased ginger plants, highlighting the impact of bacterial and fungal microbes on plant health and the specific metabolites contributing to a healthy microbial community. Metabarcoding allowed for an in-depth analysis of the associated microbial community. Dominant genera represented each microbial taxon at the niche level. According to linear discriminant analysis effect size, bacterial species belonging to Sphingomonas, Quadrisphaera, Methylobacterium-Methylorubrum, Bacillus, as well as the fungal genera Pseudaleuria, Lophotrichus, Pseudogymnoascus, Gymnoascus, Mortierella, and Eleutherascus were associated with plant health. Bacterial dysbiosis related to rhizome rot was due to the relative enrichment of Pectobacterium, Alcaligenes, Klebsiella, and Enterobacter. Similarly, an imbalance in the fungal community was caused by the enrichment of Gibellulopsis, Pyxidiophorales, and Plectosphaerella. Untargeted metabolomics analysis revealed several metabolites that drive microbiome assembly closely related to plant health in diverse microbial niches. At the same time, 6-({[3,4-dihydroxy-4-(hydroxymethyl)oxolan-2-yl]oxy}methyl)oxane-2,3,4,5-tetrol was present at the level of the entire healthy ginger plant. Lipids and lipid-like molecules were the most significant proportion of highly abundant metabolites associated with ginger plant health versus rhizome rot disease. CONCLUSIONS: Our research significantly improves our understanding of metabolome-driven microbiome structure to address crop protection impacts. The microbiome assembly rather than a particular microbe's occurrence drove ginger plant health. Most microbial species and metabolites have yet to be previously identified in ginger plants. The indigenous microbial communities and metabolites described can support future strategies to induce plant disease resistance. They provide a foundation for further exploring pathogens, biocontrol agents, and plant growth promoters associated with economically important crops. Video Abstract.

Fungal endophytes Fusarium solani SGGF14 and Alternaria tenuissima SGGF21 enhance the glycyrrhizin production by modulating its key biosynthetic genes in licorice (Glycyrrhiza glabra L.).

AIMS: To identify promising fungal endophytes that are able to produce glycyrrhizin and enhance it in licorice and the mechanisms involved. METHODS AND RESULTS: Fifteen fungal endophytes were isolated from Glycyrrhiza glabra L. rhizomes among which SGGF14 and SGGF21 isolates were found to produce glycyrrhizin by 4.29 and 2.58 µg g-1 dry weight in the first generation of their culture. These isolates were identified as Fusarium solani and Alternaria tenuissima, respectively, based on morphological characteristics and sequence analysis of internal transcribed spacer, TEF1, ATPase, and CAL regions. Subsequently, G. glabra plants were inoculated with these fungal isolates to examine their effect on glycyrrhizin production, plant growth parameters and the expression of key genes involved in glycyrrhizin pathway: SQS1, SQS2, bAS, CAS, LUS, CYP88D6, and CYP72A154. Endophytes were able to enhance glycyrrhizin content by 133%-171% in the plants. Natural control (NC) plants, harboring all natural endophytes, had better growth compared to SGGF14- and SGGF21-inoculated and endophyte-free (EF) plants. Expression of SQS1, SQS2, CYP88D6, and CYP72A154 was upregulated by inoculation with endophytes. LUS and CAS were downregulated after endophyte inoculation. Expression of bAS was higher in SGGF21-inoculated plants when compared with NC, EF, and SGGF14-inoculated plants. CONCLUSIONS: Two selected fungal endophytes of G. glabra can produce glycyrrhizin and enhance glycyrrhizin content in planta by modulating the expression of key genes in glycyrrhizin biosynthetic pathway.

Soil fungal community structure and function response to rhizoma perennial peanut cultivars.

BACKGROUND: Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars. RESULTS: This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars. CONCLUSIONS: Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.

Heat Stress and Microbial Stress Induced Defensive Phenol Accumulation in Medicinal Plant Sparganium stoloniferum.

An approach based on the heat stress and microbial stress model of the medicinal plant Sparganium stoloniferum was proposed to elucidate the regulation and mechanism of bioactive phenol accumulation. This method integrates LC-MS/MS analysis, 16S rRNA sequencing, RT-qPCR, and molecular assays to investigate the regulation of phenolic metabolite biosynthesis in S. stoloniferum rhizome (SL) under stress. Previous research has shown that the metabolites and genes involved in phenol biosynthesis correlate to the upregulation of genes involved in plant-pathogen interactions. High-temperature and the presence of Pseudomonas bacteria were observed alongside SL growth. Under conditions of heat stress or Pseudomonas bacteria stress, both the metabolites and genes involved in phenol biosynthesis were upregulated. The regulation of phenol content and phenol biosynthesis gene expression suggests that phenol-based chemical defense of SL is stimulated under stress. Furthermore, the rapid accumulation of phenolic substances relied on the consumption of amino acids. Three defensive proteins, namely Ss4CL, SsC4H, and SsF3'5'H, were identified and verified to elucidate phenol biosynthesis in SL. Overall, this study enhances our understanding of the phenol-based chemical defense of SL, indicating that bioactive phenol substances result from SL's responses to the environment and providing new insights for growing the high-phenol-content medicinal herb SL.

Endophytic fungi of Panax sokpayensis produce bioactive ginsenoside Compound K in flask fermentation.

Endophytes of Panax have the potential to produce their host plant secondary metabolites, ginsenosides. Panax sokpayensis, an endemic traditional medicinal plant of the Sikkim Himalayas was explored for the isolation of endophytic fungi. In the present study, we have isolated 35 endophytic fungal cultures from the rhizome of P. sokpayensis and screened for ginsenosides production by HPLC by comparing the peak retention time with that of standard ginsenosides. The HPLC analysis revealed that out of 35 isolates, the mycelial extracts of four fungal endophytes (PSRF52, PSRF53, PSRF49 and PSRF58) exhibited peaks with a similar retention time of the standard ginsenoside, Compound K (CK). LC-ESI-MS/MS analysis led to the confirmation of ginsenoside CK production by the four fungal endophytes which showed a compound with m/z 639.6278, similar to that of standard ginsenoside CK with yield in potato dextrose broth flask fermentation ranging from 0.0019 to 0.0386 mg/g of mycelial mass in dry weight basis. The four prospective fungal endophyte isolates were identified as Thermothielavioides terrestris PSRF52, Aspergillus sp. PSRF49, Rutstroemiaceae sp. strain PSRF53, and Phaeosphaeriaceae sp. strain PSRF58 based on ITS sequencing. The present finding highlights the need for further study on growth optimization and other culture parameters to exploit the endophytes as an alternative source for ginsenoside CK production.

Plant growth-promoting and biocontrol traits of endophytic Bacillus licheniformis against soft rot causing Pythium myriotylum in ginger plant.

Bacterial endophytes from plants harbor diverse metabolites that play major roles in biocontrol and improve plant growth. In this study, a total of 12 endophytic bacteria were isolated from the ginger rhizome. The strain K3 was highly effective in preventing mycelia growth of Pythium myriotylum (78.5 ± 1.5% inhibition) in dual culture. The cell-free extract (2.5%) of endophyte K3 inhibited 76.3 ± 4.8% mycelia growth, and 92.4 ± 4.2% inhibition was observed at a 5% sample concentration. The secondary metabolites produced by Bacillus licheniformis K3 showed maximum activity against Pseudomonas syringae (24 ± 1 mm zone of inhibition) and Xanthomonas campestris (28 ± 3 mm zone of inhibition). The strain K3 produced 28.3 ± 1.7 IU mL-1 protease, 28.3 ± 1.7 IU mL-1 cellulase, and 2.04 ± 0.13 IU mL-1 chitinase, respectively. The ginger rhizome treated with K3 in the greenhouse registered 53.8 ± 1.4% soft rot incidence, and the streptomycin-treated pot registered 78.3 ± 1.7% disease incidence. The selected endophyte K3 improved ascorbate peroxidase (1.37 ± 0.009 µmole ASC min-1 mg-1 protein), catalase (8.7 ± 0.28 µmole min-1 mg-1 protein), and phenylalanine ammonia-lyase (26.2 ± 0.99 Umg-1) in the greenhouse. In addition, K3 treatment in the field trial improved rhizome yield (730 ± 18.4 g) after 180 days (p < 0.01). The shoot length was 46 ± 8.3 cm in K3-treated plants, and it was about 31% higher than the control treatment (p < 0.01). The lytic enzyme-producing and growth-promoting endophyte is useful in sustainable crop production through the management of biotic stress.

Antagonistic potential of rhizobacterial isolates against fungal pathogens causing rhizome rot in turmeric.

The study aims to select potent bacterial antagonists to be used as biocontrol agents against rhizome rot disease in turmeric (Curcuma longa L.). A total of 48 bacterial isolates were isolated from the rhizosphere of turmeric. These isolates were screened for their in vitro antagonism against Fusarium solani FS-01 and Pythium aphanidermatum (ITCC 7908). Production of volatile organic compounds and chitinase activity were also performed. Among the tested isolates, two bacterial isolates (IJ2 and IJ10) showed the highest inhibitory activity against these fungal pathogens. GC/MS analysis of the crude extract produced by Pseudomonas sp. IJ2 and B. subtilis IJ10 was found to contain many bioactive compounds with antifungal and antimicrobial activities. The rhizome treatment with these isolates exhibited the lowest percent disease severity with high biocontrol efficacy against the tested pathogens. These isolates with promising antagonistic potential, therefore, can be used as biocontrol agents against rhizome rot in turmeric.

A positive response of ginger root zone and rhizome development to suitable sowing depth.

Sowing depth significantly affects ginger (Zingiber officinale Roscoe) yields, and sowing depth can affect rhizosphere community structure through root exudates. However, the relationship between the reaction process in root zone and ginger rhizome development is unclear. In this study, we investigated the rhizome and root development and rhizosphere environment at different sowing depths (2 cm (SD2), 5 cm (SD5), and 10 cm (SD10)). It was found that SD10 significantly increased ginger yield, which is related to the development of vascular bundles and the expression of aquaporin. PLS-PM analysis found that root length, root absorption capacity, and soil enzymes have the strongest correlation with yield, while root diameter is negatively correlated with yield. Under SD10, the increase of auxin and ethylene content together with the expression of ARF7, LBD16, and PIN1 promoted the development of lateral roots. In addition, SD10 increased the secretion of root organic acids, amino acids, and carbohydrates, which in turn promoted the development of rhizosphere bacteria. The promotion of SD10 on nitrogen cycle and nitrogen fixation ability in turn promoted the development of ginger.

Plant growth-promoting activities of bacterial endophytes isolated from the medicinal plant Pairs polyphylla var. yunnanensis.

Pairs polyphylla var. yunnanensis (Paris L.) is a valuable medicinal plant used in traditional Chinese medicine. The market demand for P. polyphylla has increased over time, but it has slow growth and a low natural propagation rate. Endophytic bacteria are bioactive microorganisms that form a mutualistic relationship with host plants in long-term coordinated evolution, and they can promote the growth and accumulation of effective components in host plants. The aims of this study were to identify endophytic bacteria of P. polyphylla and to characterize their properties in promoting plant growth. A total of 10 endophytic bacteria were isolated from rhizomes of P. polyphylla. The isolated endophytes exhibited a variable capacity for indole acetic acid production, phosphate solubilization and nitrogen fixation. To investigate the effects of the endophytes on plant growth, four endophyte strains, G5, J2, G20, and Y2, were selected to compare their ability to promote plant growth. The results indicated that microbial endophytes isolated from P. polyphylla rhizomes play a vital role in improving P. polyphylla plant growth and could be used as inoculants to establish a sustainable crop production system.

Latent Pathogenic Fungi in the Medicinal Plant Houttuynia cordata Thunb. Are Modulated by Secondary Metabolites and Colonizing Microbiota Originating from Soil.

Latent pathogenic fungi (LPFs) affect plant growth, but some of them may stably colonize plants. LPFs were isolated from healthy Houttuynia cordata rhizomes to reveal this mechanism and identified as Ilyonectria liriodendri, an unidentified fungal sp., and Penicillium citrinum. Sterile H. cordata seedlings were cultivated in sterile or non-sterile soils and inoculated with the LPFs, followed by the plants' analysis. The in vitro antifungal activity of H. cordata rhizome crude extracts on LPF were determined. The effect of inoculation of sterile seedlings by LPFs on the concentrations of rhizome phenolics was evaluated. The rates of in vitro growth inhibition amongst LPFs were determined. The LPFs had a strong negative effect on H. cordata in sterile soil; microbiota in non-sterile soil eliminated such influence. There was an interactive inhibition among LPFs; the secondary metabolites also regulated their colonization in H. cordata rhizomes. LPFs changed the accumulation of phenolics in H. cordata. The results provide that colonization of LPFs in rhizomes was regulated by the colonizing microbiota of H. cordata, the secondary metabolites in the H. cordata rhizomes, and the mutual inhibition and competition between the different latent pathogens.

Inactivation of CbrAB two-component system hampers root colonization in rhizospheric strain of Pseudomonas aeruginosa PGPR2.

Two-component systems (TCS) are one of the signal transduction mechanisms, which sense physiological/biological restraints and respond to changing environmental conditions by regulating the gene expression. Previously, by employing a forward genetic screen (INSeq), we identified that cbrA gene is essential for the fitness of Pseudomonas aeruginosa PGPR2 during root colonization. Here, we report the functional characterization of cbrAB TCS in PGPR2 during root colonization. We constructed insertion mutants in cbrA and its cognate response regulator cbrB. Genetic characterization revealed drastic down-regultion of sRNA crcZ gene in both mutant strains which play a critical role in carbon catabolite repression (CCR). The mutant strains displayed 10-fold decreased root colonization efficiency when compared to the wild-type strain. On the other hand, mutant strains formed higher biofilm on the abiotic surface, and the expression of pelB and pslA genes involved in biofilm matrix formation was up-regulated. In contrast, the expression of algD, responsible for alginate production, and its associated sigma factor algU was significantly down-regulated in mutant strains. We further analyzed the transcript levels of rsmA, controlled by the algU sigma factor, and found that the expression of rsmA was hampered in both mutants. The ability of mutant strains to swim and swarm was significantly hindered. Also, the expression of genes associated with type III secretion system (T3SS) was dysregulated in mutant strains. Taken together, regulation of gene expression by CbrAB TCS is intricate, and we confirm its role beyond carbon and nitrogen assimilation.

Endophytic fungi stimulate the concentration of medicinal secondary metabolites in houttuynia cordata thunb.

Endophytic fungi usually establish a symbiotic relationship with the host plant and affect its growth. In order to evaluate the impact of endophytic fungi on the Chinese herbal medicinal plant Houttuynia cordata Thunb., three endophytes isolated from the rhizomes of H. cordata, namely Ilyonectria liriodendra (IL), unidentified fungal sp. (UF), and Penicillium citrinum (PC), were co-cultured individually with H. cordata in sterile soil for 60 days. Analysis of the results showed that the endophytes stimulated the host plant in different ways: IL increased the growth of rhizomes and the accumulation of most of the phenolics and volatiles, UF promoted the accumulation of the medicinal compounds afzelin, decanal, 2-undecanone, and borneol without influencing host plant growth, and PC increased the fresh weight, total leaf area and height of the plants, as well as the growth of the rhizomes, but had only a small effect on the concentration of major secondary metabolites. Our results proved that the endophytic fungi had potential practical value in terms of the production of Chinese herbal medicines, having the ability to improve the yield and accumulation of medicinal metabolites.

Rhizomal Reclassification of Living Organisms.

Living organisms interact with each other during their lifetime, leading to genomes rearrangement and sequences transfer. These well-known phenomena give these organisms mosaic genomes, which challenge their classification. Moreover, many findings occurred between the IXXth and XXIst century, especially the discovery of giant viruses and candidate phyla radiation (CPR). Here, we tried to provide an updated classification, which integrates 216 representative genomes of the current described organisms. The reclassification was expressed through a genetic network based on the total genomic content, not on a single gene to represent the tree of life. This rhizomal exploration represents, more accurately, the evolutionary relationships among the studied species. Our analyses show a separated branch named fifth TRUC (Things Resisting Uncompleted Classifications). This taxon groups CPRs together, independently from Bacteria, Archaea (which regrouped also Nanoarchaeota and Asgard members), Eukarya, and the giant viruses (recognized recently as fourth TRUC). Finally, the broadening of analysis methods will lead to the discovery of new organisms, which justify the importance of updating the classification at every opportunity. In this perspective, our pragmatic representation could be adjusted along with the progress of evolutionary studies.

Role of biochar, compost and plant growth promoting rhizobacteria in the management of tomato early blight disease.

The individual role of biochar, compost and PGPR has been widely studied in increasing the productivity of plants by inducing resistance against phyto-pathogens. However, the knowledge on combined effect of biochar and PGPR on plant health and management of foliar pathogens is still at juvenile stage. The effect of green waste biochar (GWB) and wood biochar (WB), together with compost (Comp) and plant growth promoting rhizobacteria (PGPR; Bacillus subtilis) was examined on tomato (Solanum lycopersicum L.) physiology and Alternaria solani development both in vivo and in vitro. Tomato plants were raised in potting mixture modified with only compost (Comp) at application rate of 20% (v/v), and along with WB and GWB at application rate of 3 and 6% (v/v), each separately, in combination with or without B. subtilis. In comparison with WB amended soil substrate, percentage disease index was significantly reduced in GWB amended treatments (Comp + 6%GWB and Comp + 3%GWB; 48.21 and 35.6%, respectively). Whereas, in the presence of B. subtilis disease suppression was also maximum (up to 80%) in the substrate containing GWB. Tomato plant growth and physiological parameters were significantly higher in treatment containing GWB (6%) alone as well as in combination with PGPR. Alternaria solani mycelial growth inhibition was less than 50% in comp, WB and GWB amended growth media, whereas B. subtilis induced maximum inhibition (55.75%). Conclusively, the variable impact of WB, GWB and subsequently their concentrations in the soil substrate was evident on early blight development and plant physiology. To our knowledge, this is the first report implying biochar in synergism with PGPR to hinder the early blight development in tomatoes.

Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures.

Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.

Structural variability and differentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis).

The plant microbiota play a key role in plant productivity, nutrient uptake, resistance to stress and flowering. The flowering of moso bamboo has been a focus of study. The mechanism of flowering is related to nutrient uptake, temperature, hormone balance and regulation of key genes. However, the connection between microbiota of moso bamboo and its flowering is unknown. In this study, samples of rhizosphere soil, rhizomes, roots and leaves of flowering and nonflowering plants were collected, and 16S rRNA amplicon Illumina sequencing was utilized to separate the bacterial communities associated with different flowering stages of moso bamboo. We identified 5442 OTUs, and the number of rhizosphere soil OTUs was much higher than those of other samples. Principal component analysis (PCA) and hierarchical clustering (Bray Curtis dis) analysis revealed that the bacterial microorganisms related to rhizosphere soil and endophytic tissues of moso bamboo differed significantly from those in bulk soil and rhizobacterial and endosphere microbiomes. In addition, the PCA analyses of root and rhizosphere soil revealed different structures of microbial communities between bamboo that is flowering and not flowering. Through the analysis of core microorganisms, it was found that Flavobacterium, Bacillus and Stenotrophomonas played an important role in the absorption of N elements, which may affect the flowering time of moso bamboo. Our results delineate the complex host-microbe interactions of this plant. We also discuss the potential influence of bacterial microbiome in flowering, which can provide a basis for the development and utilization of moso bamboo.

Plant Beneficial Features and Application of Paraburkholderia sp. NhPBG1 Isolated from Pitcher of Nepenthes hamblack.

Pitchers are the unique structures of carnivorous plants used for the trapping of insects and other small invertebrates. The digestion of captured prey here is assisted by the bacteria, which have been associated with pitchers. These bacterial communities can therefore expect to have a variety of plant beneficial functions. In this study, the bacterial isolate NhPBG1 from the pitcher of Nepenthes hamblack was screened for activity against Pythium aphanidermatum, Rhizoctonia solani, Fusarium oxysporum, and Colletotrichum accutatum and was found to have the inhibitory activity towards all the tested phytopathogens. Interestingly, the isolate was found to have hyper-inhibitory effect against P. aphanidermatum. Further to this, the isolate was also shown to be positive for plant beneficial traits such as indole-3-acetic acid (IAA) and ammonia production, phosphate, potassium and zinc solubilization, nitrogen fixation, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. BLAST analysis of the 16S rDNA sequence of NhPBG1 has identified it as Paraburkholderia sp. Also, the Zingiber officinale rhizome pre-treated with NhPBG1 was found to get protected from P. aphanidermatum induced infection, whereas the control showed symptoms of infection. This was further confirmed by the microscopic evaluation of the presence of fungal mycelia in the tissues of control. However, the mycelial invasion could not be detected in the NhPBG1 treated rhizome. The metabolite profiling of NhPBG1 by GC-MS has identified variety of general metabolites, while the antifungal compounds pyocyanin and 1-hydroxyphenazine could be identified by the LC-MS/MS analysis.

Sampling Microbiomes Associated with Different Plant Compartments.

The microbiome is known to influence plant fitness and differs significantly between plant compartments. To characterize the communities associated with different plant compartments, it is necessary to separate plant tissues in a manner that is suitable for microbiome analysis. Here, we describe a standardized protocol for sampling the microbiomes associated with bulk soil, the apical and basal ectorhizosphere, the apical and ectorhizosphere, the rhizome, pseudostem, and leaves of Musa spp. The approach can easily be modified for work with other plants.