Panax notoginseng-microbiota interactions: From plant cultivation to medicinal application

BACKGROUND

Microbiomes and their host plants are closely linked with each other; for example, the microbiome affects plant growth, fitness, nutrient uptake, stress tolerance and pathogen resistance, whereas the host plant supports the photosynthetically carbon-rich nutrition of the microbiome. The importance of the microbiome in plant‒soil ecosystems is unquestioned and has expanded to influence the medicinal application of some herbal plants via the gut microbiota.

PURPOSE

Herbal plant-microbiome interactions may provide novel knowledge to enhance the robustness of herbal plant crop performance and medicinal applications, which requires a systematic review and preceding discussion.

STUDY DESIGN AND METHODS

The interactions between Panax notoginseng and microorganisms (from soil to host) were reviewed from the literature. The terms "Panax notoginseng" and "microbiota" were used in combination with the keywords "microbiota/microbes", "bacteria/bacterium" or "fungi/fungus" or "endophyte", as well as our targeted bioactive phytochemicals, including saponins and ginsenosides.

RESULT

Our study focuses on the famous medicinal herb Panax notoginseng F. H. Chen and proposes that the microbiota is a crucial participant not only in the cultivation of this herbal plant but also in its medicinal application. We also summarize and discuss how these plant‒microbe co-associations shape the assembly of plant-related microbiomes and produce bioactive phytochemicals, as well as influence beneficial herbal traits, such as herbal plant health and pharmacology. In addition, we also highlight future directions.

CONCLUSION

The rhizosphere and endophytic microbiome of Panax notoginseng are indirectly or directly involved in plant health, biomass production, and the synthesis/biotransformation of plant secondary metabolites. Harnessing the microbiome to improve the quality of traditional Chinese medicine and improve the value of medicinal plants for human health is highly promising.

Unveiling the genomic potential of a novel thermostable glycoside hydrolases producing Neobacillus sedimentimangrovi UE25

Genetic and enzymatic potential of Neobacillus sedimentimangrovi has not been assembled to date. Here, we report a high-quality genome assembly of thermophilic bacterium Neobacillus sedimentimangrovi UE25 using Illumina Hi-seq 2500. The strain was isolated from a crocodile pond Manghopir, Karachi, Pakistan. QUAST quality parameters showed 37.75% GC content and exhibited the genome into 110 contigs, with a total size of 3,230,777 bases. Genome of N. sedimentimangrovi UE25 harbors phage mediated DNA through horizontal gene exchange from the phages, symbiotic and pathogenic bacteria. Most of the phage genome encodes for hypothetical proteins, protease, and phage assembly proteins. Gene clusters encoding the intrinsic resistance to glycopeptides, isoniazid, rifamycin, elfamycin, macrolide, aminoglycosides, tetracycline and fluoroquinolone were identified into the genome. Since, the strain has been reported for the production of many industrially important thermostable enzymes, therefore, the genomic data of thermostable enzymes might be helpful to employ this species in commercial sectors. Probing genes of multiple thermostable glycoside hydrolase enzymes especially xylanases of N. sedimentimangrovi UE25 showed genetic diversity among the genes and confer the industrial importance of this microorganism. Furthermore, the genome of N. sedimentimangrovi will greatly improve our understanding of its genetics and evolution.

Neobacillus rhizosphaerae sp. nov., isolated from the rhizosphere, and reclassification of Bacillus dielmonensis as Neobacillus dielmonensis comb. nov

A Gram-stain-positive, facultative anaerobic endospore-forming bacterium, which originated from roots/rhizosphere of maize (Zea mays), was investigated for its taxonomic position. On the basis of 16S rRNA gene sequence similarities, strain JJ-3T was grouped together with Neobacillus species showing the highest similarities to Neobacillus bataviensis (98.8 %) and the three species Neobacillus dendrensis, Neobacillus soli and Neobacillus cucumis (all 98.6 %). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were lower than 98.5 %. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the JJ-3T genome assembly and those of the other Neobacillus type strains were <83, <85 and <27 %, respectively. Chemotaxonomic features supported the grouping of the strain to the genus Neobacillus, e.g. the major fatty acids were C15 : 0 anteiso and C15 : 0 iso, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major quinone was menaquinone MK-7. Physiological and biochemical test results were slightly different from those of the most closely related species. For this reason, JJ-3T represents a novel species of the genus Neobacillus , for which we propose the name Neobacillus rhizosphaerae sp. nov., with JJ-3T (= CIP 111895T=LMG 32087T=DSM 111784T=CCM 9084T) as the type strain. We also propose to reclassify Bacillus dielmonensis as Neobacillus dielmonensis comb. nov. based mainly on the results of phylogenomic and conserved signature indel analyses.

Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., isolated from maize root rhizosphere

A facultative anaerobic, Gram-stain-positive, endospore-forming bacterium, isolated from the rhizosphere of maize roots (Zea mays), was taxonomically studied. Based on 16S rRNA gene sequence similarity comparisons, strain JJ-79T clustered only loosely with Neobacillus species and showed the highest similarity to Neobacillus soli (97.9%). The 16S rRNA gene sequence similarities to the sequences of the type strains of other Neobacillus species were 97.5 % and below. Chemotaxonomic features supported the grouping of the strain to the Neobacillus group, e.g. the major fatty acids were C15 : 0 anteiso, C15 : 0 iso and C16 : 0, the polar lipid profile contained the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid, the major quinone was menaquinone MK-7, and major compound in the polyamine pattern was spermidine. However, the JJ-79T genome assembly did not share most of the 11 conserved signature indels that are indicative of the genus Neobacillus . The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between the JJ-79T genome assembly and those of the closest relative Bacillaceae type strains were <71, <71 and <25 %, respectively. Physiological and biochemical test results were also different from those of the most closely related Bacillaceae species. As a consequence, JJ-79T represents a novel genus for which we propose the name Pseudoneobacillus rhizosphaerae gen. nov., sp. nov., with JJ-79T (=CIP 111885T=CCM 9045T) as the type strain.

Neobacillus rhizophilus sp. nov. and Neobacillus citreus sp. nov., isolated from the citrus rhizosphere soil

Two Gram-staining positive strains, FJAT-49825^T and FJAT-50051^T were isolated from a citrus rhizosphere soil sample. Strains FJAT-49825^T and FJAT-50051^T showed the highest 16S rRNA gene sequence similarity with the type strain of Neobacillus cucumis (98.4-98.5%). The 16S rRNA gene sequence similarity between strains FJAT-49825^T and FJAT-50051^T was 99.8%. Strain FJAT-49825^T optimally grew at 35 °C, pH 6.0 in the absence of NaCl while strain FJAT-50051^T grew at 40 °C, pH 7.0 and in presence of 2% NaCl (w/v). Both strains contained meso-2,6-diaminopimelic acid as the cell-wall diamino acid. The respiratory quinone of strains FJAT-49825^T and FJAT-50051^T was MK-7. The polar lipids of strain FJAT-49825^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminolipid and unidentified lipid whereas strain FJAT-50051^T polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified phospholipid and unidentified lipid. The major fatty acids (> 10%) in both strains were iso-C_15:0 and anteiso-C_15:0. The genomic DNA G + C content of strains FJAT-49825^T and FJAT-50051^T were 40.8 and 41.1%, respectively. The average nucleotide identity and digital DNA-DNA hybridization value between strains FJAT-49825^T and FJAT-50051^T and with other members of the genus Neobacillus were lower than the cut-off value (95-96/70%) for interspecies identity. Based on the results, strains FJAT-49825^T and FJAT-50051^T represent two novel species of the genus Neobacillus, for which the names Neobacillus rhizophilus sp. nov. and Neobacillus citreus sp. nov. are proposed. The type strains are FJAT-49825^T (= GDMCC 1.2592^T = JCM 34834^T) and FJAT-50051^T (= GDMCC 1.2593^T = JCM 34835^T).

Neobacillus kokaensis sp. nov., isolated from soil

A Gram-stain-variable, motile, aerobic, spore-forming, rod-shaped bacterium, designated as strain LOB 377T, was isolated from soil sampled in Koka County (now Konan City), in Shiga Prefecture, Japan. To determine its taxonomic position, the bacterium was evaluated by a polyphasic approach based on genomic, phenotypic and chemotaxonomic tests. From phylogenetic analysis based on 16S rRNA gene sequences, strain LOB 377T (LC570960) was revealed to have the highest similarity to the type strain of Neobacillus mesonae FJAT-13985T (9.1 %). The average nucleotide identity and digital DNA–DNA hybridization values between both strains based on whole genome sequences were 84.1 and 42.8 %, respectively, which were below the recommended thresholds. The strain grew at 15–45 °C (optimum, 25–37 °C), at pH 5.5–9.5 (optimum, pH 6.5–8.5) and with 1.0–2.0 % (w/v) NaCl. Cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid. The major menaquinone was menaquinone-7. Predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and C16 : 1 ω11c. The polar lipids were phosphatidylglycerol, unidentified phospholipid and unidentified aminophospholipid. The DNA G+C content was 40.5 mol%. According to the genomic, phenotypic and chemotaxonomic results, strain LOB 377T represents a novel species in the genus Neobacillus , for which the name Neobacillus kokaensis sp. nov. is proposed. The type strain is LOB 377T (=ATCC 31382T=NBRC 114637T=DSM 113418T).

Neobacillus endophyticus sp. nov., an endophytic bacterium isolated from Selaginella involvens roots

A Gram-stain-positive, facultatively anaerobic, rod-shaped, endospore-forming, oxidase-positive, and catalase-negative strain designated as BRMEA1^T was isolated from the surface-sterilized Selaginella involvens roots. Growth of strain BRMEA1^T was found to occur at pH 6.0-8.0 (optimum, pH 7.0), 15-50 °C (optimum, 25-30 °C) and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BRMEA1^T formed a lineage within the genus Neobacillus (family Bacillaceae) and showed the highest sequence similarity to Neobacillus drentensis DSM 15600^T (98.3 %) and Neobacillus fumarioli KCTC 13885^T (98.2 %), and less than 98.2 % 16S rRNA gene sequence similarity to the other members of the genus Neobacillus. Whole-genome analysis of strain BRMEA1^T comprised a circular chromosome (5 632 809 bp in size) with 38.5 mol% G+C content. Digital DNA-DNA hybridization analyses revealed that strain BRMEA1^T showed 20.5 and 22.0% genomic DNA relatedness with the closest species, N. drentensis DSM 15600^T and N. fumarioli KCTC 13885^T, respectively. The whole-genome sequence of strain BRMEA1^T showed the presence of 11 specific conserved signature indels for the genus Neobacillus. The major cellular fatty acids (>10 %) of strain BRMEA1^T were found to be iso-C_15 : 0 and anteiso-C_15 : 0, while the major polar lipids were found to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Polyphasic analysis results revealed that BRMEA1^T represents a novel species of the genus Neobacillus, with the proposed name Neobacillus endophyticus sp. nov. The type strain is BRMEA1^T (=KCTC 43208^T=CCTCC AB 2020071^T).

Neobacillus sedimentimangrovi sp. nov., a Thermophilic Bacterium Isolated from Mangrove Sediment

Two Gram-stain positive, rod-shaped, endospore-forming, aerobic, thermophilic strains, designated FJAT-2464^T and FJAT-52740, were isolated from the sediment collected from Zhangjiang Estuary Mangrove National Nature Reserve in Fujian Province, China. The 16S rRNA gene sequence similarity between strains FJAT-2464^T and FJAT-52740 was 100%. The result suggests that strains FJAT-2464^T and FJAT-52740 belong to the same genome species, hence only FJAT-2464^T was considered for further analysis. Strain FJAT-2464^T showed the highest 16S rRNA gene sequence similarities to the type strains of Neobacillus thermocopriae SgZ-7^T (99.9%), Neobacillus cucumis AP-6^T (97.6%) and Neobacillus drentensis LMG 21831^T (97.5%). Growth was observed at 25-65 °C (optimum 60 °C), pH 7.0-8.0 (optimum 8.0) with NaCl tolerance up to 1.0% (w/v) (optimum without NaCl %). The cell-wall peptidoglycan contained meso-diaminopimelic acid and MK-7 was the only respiratory quinone. The major fatty acids were iso-C_15:0 and anteiso-C_15:0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified aminophospholipid and unidentified lipids. The average nucleotide identity and digital DNA-DNA hybridization values between strain FJAT-2464^T and the most closely related strain N. thermocopriae SgZ-7^T was below the threshold value for species delineation. Based on the above results, strain FJAT-2464^T represents a novel species of the genus Neobacillus, for which the name Neobacillus sedimentimangrovi sp. nov. is proposed. The type strain is FJAT-2464^T (= MCCC 1K04406^T = KCTC 43264^T).

Bacillus alkalicellulosilyticus sp. nov., isolated from extremely alkaline bauxite residue (red mud) site

A Gram-stain-negative, rod-shaped, facultatively anaerobic, motile and spore-forming strain designated FJAT-44921^T was isolated from red mud collected from Chiping County, Shandong Province, China. The 16S rRNA gene sequence result showed that strain FJAT-44921^T shared a low sequence identity (96.6%) with the members of the genus Bacillus. Growth was observed at pH 8.0-10.0 (optimum pH 9.0), 10-40 °C (optimum 20-25 °C) with 0-8% (v/w %) NaCl (optimum 4-6 v/w %). FJAT-44921^T consists of MK-7 as the isoprenoid quinone and meso-2,6-diaminopimelic acid as the cell-wall diamino acid. The predominant fatty acids were anteiso-C_15:0, iso-C_15:0, C_16:0, and anteiso-C_17:0. The polar lipids were diphosphatidylglycerol, phosphatidyl glycerol, phosphatidylmethylethanolamine, unidentified phospholipid, and unidentified aminophospholipid. The genomic DNA G + C content was 37.3 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between FJAT-44921^T and other closely related Bacillus members were lower than the recognized threshold values of ANI (95-96%) and dDDH (70%) recommended as the criterion for interspecies identity. The type strain is FJAT-44921^T (=CCTCC AB 2016196^T =DSM 104630^T).

Bacillus miscanthi sp. nov., a alkaliphilic bacterium from the rhizosphere of Miscanthus sacchariflorus

A novel bacterial strain, designated AK13^T (=KACC 21401^T=DSM 109981^T), was isolated from the rhizosphere of Miscanthus sacchariflorus. Strain AK13^T was found to be an aerobic, Gram-stain-positive, endospore-forming and rod-shaped bacterium. It formed yellow circular colonies with smooth convex surfaces. The genomic DNA G+C content of strain AK13^T was estimated to be 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that this strain was most closely related to Bacillus lehensis MLB2^T (99.4 %), Bacillus oshimensis K11^T (98.8 %) and Bacillus patagoniensis PAT 05^T (96.6 %). The average nucleotide identity values between strain AK13^T and B. lehensis MLB2^T, B. oshimensis K11^T and B. patagoniensis PAT 05^T were 90.93, 91.05 and 71.87 %, respectively, with the digital DNA-DNA hybridization values of 42.7, 42.6 and 18.8 %, respectively. Cells grew at 5-40 °C (optimum, 28-35 °C), pH 6.5-13 (optimum, pH 8-9) and in the presence of 0-13.0 % (w/v) NaCl (optimum, 1 %). The cell wall of strain AK13^T contained meso-diaminopimelic acid, and the major isoprenoid quinone was MK-7. Results of fatty acid methyl ester analysis revealed that iso-C_{15 : 0} was the predominant cellular fatty acid. Two-dimensional thin-layer chromatography analysis indicated that the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and glycolipid. The genotypic and phenotypic characteristics suggested that strain AK13^T represented a novel species of the genus Bacillus, and thus the name Bacillus miscanthi sp. nov. is proposed.

A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov

The genus Bacillus, harbouring 293 species/subspecies, constitutes a phylogenetically incoherent group. In the absence of reliable means for grouping known Bacillus species into distinct clades, restricting the placement of new species into this genus has proven difficult. To clarify the evolutionary relationships among Bacillus species, 352 available genome sequences from the family Bacillaceae were used to perform comprehensive phylogenomic and comparative genomic analyses. Four phylogenetic trees were reconstructed based on multiple datasets of proteins including 1172 core Bacillaceae proteins, 87 proteins conserved within the phylum Firmicutes, GyrA-GyrB-RpoB-RpoC proteins, and UvrD-PolA proteins. All trees exhibited nearly identical branching of Bacillus species and consistently displayed six novel monophyletic clades encompassing 5-23 Bacillus species (denoted as the Simplex, Firmus, Jeotgali, Niacini, Fastidiosus and Alcalophilus clades), interspersed with other Bacillaceae species. Species from these clades also generally grouped together in 16S rRNA gene trees. In parallel, our comparative genomic analyses of Bacillus species led to the identification of 36 molecular markers comprising conserved signature indels in protein sequences that are specifically shared by the species from these six observed clades, thus reliably demarcating these clades based on multiple molecular synapomorphies. Based on the strong evidence from multiple lines of investigations supporting the existence of these six distinct 'Bacillus' clades, we propose the transfer of species from these clades into six novel Bacillaceae genera viz. Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. These results represent an important step towards clarifying the phylogeny/taxonomy of the genus Bacillus.

Bacillus salacetis sp. nov., a slightly halophilic bacterium from Thai shrimp paste (Ka-pi)

A Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4^T, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4^T grew at pH 6.0-9.0 (optimum, 7.5), at 20-40 °C (37 °C) and in 0-15 % (w/v) NaCl (1-3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C15 : 0 and anteiso-C15 : 0 as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4^T belonged to the genus Bacillus and was closely related to Bacillus vietnamensis JCM 11124^T, Bacillus marisflavi JCM 11544^T, Bacillus aquimaris JCM 11545^T and Bacillusoryzaecorticis JCM 19602^T, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4^T was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4^T were 70.0 and 84.3 %, respectively, and the digital DNA-DNA hybridization value was 20 % in comparison with the draft genome of B. vietnamensis JCM 11124^T. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus Bacillus and the name Bacillus salacetis sp. nov. is proposed. The type strain is SKP7-4^T (=JCM 33205^T=KCTC 43014^T=TISTR 2596^T).