Nocardioides ginkgobilobae sp. nov., an endophytic actinobacterium isolated from the root of the living fossil Ginkgo biloba L

High-throughput sequencing-based analysis of the composition and diversity of the endophyte community in roots of Stellera chamaejasme

Stellera chamaejasme (S. chamaejasme) is an important medicinal plant with heat-clearing, detoxifying, swelling and anti-inflammatory effects. At the same time, it is also one of the iconic plants of natural grassland degradation in northwest China, playing a key role in the invasion process. Plant endophytes live in healthy plant tissues and can synthesize substances needed for plant growth, induce disease resistance in host plants, and enhance plant resistance to environmental stress. Therefore, studying the root endophytes of S. chamaejasme is of great significance for mining beneficial microbial resources and biological prevention and control of S. chamaejasme. This study used Illumina MiSeq high-throughput sequencing technology to analyze the composition and diversity of endophytes in the roots of S. chamaejasme in different alpine grasslands (BGC, NMC and XGYZ) in Tibet. Research results show that the main phylum of endophytic fungi in the roots of S. chamaejasme in different regions is Ascomycota, and the main phyla of endophytic bacteria are Actinobacteria, Proteobacteria and Firmicutes (Bacteroidota). Overall, the endophyte diversity of the NMC samples was significantly higher than that of the other two sample sites. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) results showed significant differences in the composition of endophytic bacterial and fungal communities among BGC, NMC and XGYZ samples. Co-occurrence network analysis of endophytes showed that there were positive correlations between fungi and some negative correlations between bacteria, and the co-occurrence network of bacteria was more complex than that of fungi. In short, this study provides a vital reference for further exploring and utilizing the endophyte resources of S. chamaejasme and an in-depth understanding of the ecological functions of S. chamaejasme endophytes.

Description and genomic characterization of Nocardioides bruguierae sp. nov., isolated from Bruguiera gymnorhiza

Strains BSK12Z-3^T and BSK12Z-4, two Gram-stain-positive, aerobic, non-spore-forming strains, were isolated from Shankou Mangrove Nature Reserve, Guangxi Zhuang Autonomous Region, China. The diagnostic diamino acid in the cell-wall peptidoglycan of strain BSK12Z-3^T was LL-diaminopimelic acid and MK-8(H₄) was the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phospholipid (PL). The major fatty acids was iso-C_16:0. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the two strains fell within the genus Nocardioides, appearing most closely related to Nocardioides ginkgobilobae KCTC 39594^T (97.5-97.6 % sequence similarity) and Nocardioides marinus DSM 18248^T (97.4-97.6 %). Genome-based phylogenetic analysis confirmed that strains BSK12Z-3^T and BSK12Z-4 formed a distinct phylogenetic cluster within the genus Nocardioides. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of strains BSK12Z-3^T, BSK12Z-4 with their most related species N. marinus DSM18248^T were within the ranges of 77.2-77.3 % and 21.3-21.4 %, respectively, clearly indicated that strains BSK12Z-3^T, BSK12Z-4 represented novel species. Strains BSK12Z-3^T and BSK12Z-4 exhibited 99.9 % 16S rRNA gene sequence similarity. The ANI and dDDH values between the two strains were 97.8 % and 81.1 %, respectively, suggesting that they belong to the same species. However, DNA fingerprinting discriminated that they were not from one clonal origin. Based on phylogenomic and phylogenetic analyses coupled with phenotypic and chemotaxonomic characterizatons, strains BSK12Z-3^T and BSK12Z-4 could be classified as a novel species of the genus Nocardioides, for which the name Nocardioides bruguierae sp. nov., is proposed. The type strain is BSK12Z-3^T (=CGMCC 4.7709^T = JCM 34554^T).

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

Ginkgo biloba is a pharmaceutical resource for terpenes and flavonoids. However, few insights discussed endophytes' role in Ginkgo, and whether genetic exchange happens between Ginkgo and endophytes remains unclear. Herein, functional gene profiles and repetitive sequences were analyzed to focus on these issues. A total of 25 endophyte strains were isolated from the Ginkgo root and distributed in 16 genera of 6 phyla. Significant morphological diversities lead to the diversity in the COG functional classification. KEGG mapping revealed that endophytic bacteria and fungi potentially synthesize chalcone, while endophytic fungi might also promote flavonoid derivatization. Both bacteria and fungi may facilitate the lignin synthesis. Aspergillus sp. Gbtc_1 exhibited the feasibility of regulating alcohols to lignans. Although Ginkgo and the endophytes have not observed the critical levopimaradiene synthase in ginkgolides synthesis, the upstream pathways of terpenoid precursors are likely intact. The MVK genes in Ginkgo may have alternative non-homologous copies or be compensated by endophytes in long-term symbiosis. Cellulomonas sp. Gbtc_1 became the only bacteria to harbor both MEP and MVA pathways. Endophytes may perform the mutual transformation of IPP and DMAPP in the root. Ginkgo and bacteria may lead to the synthesis and derivatization of the carotenoid pathway. The isoquinoline alkaloid biosynthesis seemed lost in the Ginkgo root community, but L-dopa is more probably converted into dopamine as an essential signal-transduction substance. So, endophytes may participate in the secondary metabolism of the Ginkgo in a shared or complementary manner. Moreover, a few endophytic sequences predicted as Ty3/Gypsy and Ty1/Copia superfamilies exhibited extremely high similarity to those of Ginkgo. CDSs in such endophytic LTR-RT sequences were also highly homologous to one Ginkgo CDS. Therefore, LTR-RTs may be a rare unit flowing between the Ginkgo host and endophytes to exchange genetic information. Collectively, this research effectively expanded the insight on the symbiotic relationship between the Ginkgo host and the endophytes in the root.

Nocardioides cynanchi sp. nov., isolated from soil of rhizosphere of Cynanchum wilfordii

A novel actinobacterial strain, SB3-45^T, was isolated from soil of Cynanchum wilfordii rhizosphere, Jaecheon-si, Chungcheongbuk-do, Republic of Korea. Strain SB3-45^T, was Gram-stain-positive, aerobic and coccoid to short rod-shaped bacterium. Growth occurred at 4-37 °C (optimum 28 °C), pH 5-8 (optimum pH 7) and 0-2.5 % NaCl (optimum 0%). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain SB3-45^T belonged to the genus Nocardioides and was closely related to Nocardioides opuntiae OS-21^T (96.2%) and Nocardioides panacihumi Gsoil 616^T (95.9%). ll-DAP as the diamino acid in the peptidoglycan and the menaquinone MK-8(H₄) as the predominant isoprenoid quinone were detected. The polar lipids of strain SB3-45^T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and unidentified phospholipid. The major cellular fatty acids (>5%) of strain SB3-45^T were iso-C_16 : 0, C_18 : 1 ω9c and C_17 : 0. Based on phylogenetic, physiological and chemotaxonomic characteristics, strain SB3-45^T represents a novel species of the genus Nocardioides, for which the name Nocardioides cynanchi sp.nov. is proposed. The type strain is SB3-45^T (=KCTC 49133^T=NBRC 114107^T).

Nocardioides jishulii sp. nov.,isolated from faeces of Tibetan gazelle (Procapra picticaudata)

Two novel Gram-stain-positive, irregular rod-shaped bacterial strains, dk3136^T and dk3543, were isolated from the faeces of Tibetan gazelle (Procapra picticaudata) in the Qinghai-Tibet Plateau of PR China. The cells were aerobic, oxidase-negative and catalase-positive. Colonies were yellowish, circular without any observable aerial mycelium after culturing at 28 ℃ for 3 days on brain-heart infusion (BHI) agar with 5 % sheep blood. The cells grew optimally at 28 °C, pH 7.5 and with 1 % (w/v) NaCl on BHI agar supplemented with 5 % sheep blood. Phylogenetic analysis of the 16S rRNA gene sequences revealed that their nearest phylogenetic relative was Nocardioides solisilvae Ka25^T (97.9 % similarity). The results of 16S rRNA gene sequence and phylogenetic/phylogenomic analyses illustrated that N. solisilvae Ka25^T, Nocardioides gilvus XZ17^T, Nocardioides houyundeii 78^T and Nocardioides daphniae D287^T were their nearest phylogenetic neighbours. The DNA G+C contents of strains dk3136^T and dk3543 were 70.3 mol% and 70.4 mol%, respectively. Their genomes exhibit lower than threshold (95-96 %) average nucleotide identity to known species of the genus Nocardioides. ll-2,6-diaminopimelic acid was the diagnostic diamino acid and MK-8(H₄) was the predominant respiratory quinone. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The two strains had C_18 : 1 ω9c, iso-C_16 : 0 and C_17 : 1 ω8c as the major fatty acids, and rhamnose and galactose as the main whole-cell sugars. On the basis of the results of our genotypic, phenotypic and biochemical analyses, we conclude that strains dk3136^T and dk3543 represent a novel species in genus Nocardioides, for which the name Nocardioides jishulii sp. nov. is proposed. The type strain is dk3136^T (=CGMCC 4.7570^T=JCM 33496^T=KCTC 49314^T).

Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau

Two novel Gram-stain-positive, irregular rod-shaped actinomycetes, S-1144^T and 4053, were isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau, PR China. Cells were aerobic, catalase-positive and oxidase-negative. Colonies on Reasoner's 2A agar were light yellow, circular, shiny, smooth and convex after 2 days of incubation. The isolates grew optimally at 25 °C, pH 7.5 and with 0 % (w/v) NaCl. The results of polyphasic analyses indicated that strain S-1144^T belonged to the genus Nocardioides and its close phylogenetic neighbours (16S rRNA gene sequence similarity) were Nocardioides litoris DSM 103718^T (98.4 %), Nocardioides rubriscoriae DSM 23986^T (98.2%) and Nocardioides plantarum DSM 11054^T (97.8 %). The genome of strain S-1144^T showed less than 70 % digital DNA-DNA hybridization and < 95-96 % average nucleotide identity values to the above reference strains. The DNA G+C content of strain S-1144^T was 73.5 mol%. MK-8(H₄) was the predominant respiratory quinone (96.0 %) and llLL-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipid profile of strain S-1144^T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C_16 : 0, C_17 : 1  ω8c, C_17 : 0 and C_18 : 1  ω9c. On the basis of obtained data, strain S-1144^T represented a novel species of the genus Nocardioides, for which the name Nocardioides dongxiaopingii sp. nov. is proposed. The type strain is S-1144^T (=CGMCC 4.7568^T=JCM 33469^T).

Nocardioides zhouii sp. nov., isolated from the Hailuogou Glacier in China

A novel Gram-stain-positive, non-motile, rod-shaped, non-spore-forming bacterium, designated HLT2-9^T, was isolated from the ice tongue surface of Hailuogou Glacier in Sichuan Province, PR China. Colonies of cells were cream yellow, convex and round. Growth occurred at 0-27 °C (optimum, 20 °C), pH 7.0-10.0 (pH 7.0) and in the presence of 0-2.0 % (w/v) NaCl (0 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HLT2-9^T belonged to the genus Nocardioides. The highest level of sequence similarities were found to Nocardioides glacieisoli CGMCC1.11097^T (99.24 %), Nocardioides oleivorans CGMCC 4.6882^T (98.54 %) and Nocardioides ganghwensis CGMCC 4.6875^T (98.54 %). However, the low average nucleotide identity (85.6-87.9 %) and digital DNA-DNA hybridization values (26.4-30.2 %) of strain HLT2-9^T to its three closest relatives demonstrated that it represents a novel species of the genus Nocardioides. The major cellular fatty acids of strain HLT2-9^T were C17 : 1ω8c and iso-C16 : 0. Strain HLT2-9^T contained ll-2,6-diaminopimelic acid as the diamino acid in the cell-wall peptidoglycan. The predominant menaquinone is MK-8(H4). The G+C content of the genomic DNA was 70.65 mol%. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, a novel species Nocardioideszhouii sp. nov. is proposed, with HLT2-9^T (=CGMCC 1.11084^T=NBRC 109783^T) as the type strain.

Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces

In the present study, we describe two novel Gram-stain-positive, irregular rod-shaped bacterial strains, 78^T and 601, that had been isolated from the faeces of Tibetan antelopes at the Hoh Xil Nature Reserve, Qinghai-Tibet Plateau, China. The cells were aerobic, oxidase-negative and catalase-positive. When cultured on brain-heart infusion agar supplemented with 5 % sheep blood, colonies were cream in colour, circular, smooth and convex. Phylogenetic analysis based on the full-length 16S rRNA sequences revealed that type strain 78^T and strain 601 belong to the genus Nocardioides, sharing the highest similarity to Nocardioides solisilvae JCM 31492^T (98.3 %), Nocardioides gilvus XZ17^T (97.4 %) and Nocardioides daejeonensis JCM 16922^T (97.4 %). The average nucleotide identity values between the two novel strains and the three closely related type strains of the genus Nocardioides were lower than the 95-96 % threshold. The DNA G+C content of strains 78^T and 601 were 71.2 and 71.3 mol% respectively. MK-8 (H4) was the predominant respiratory quinone and ll-2,6-diaminopimelic acid was the diagnostic diamino acid in its cell-wall peptidoglycan. Its polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and an unidentified lipid. The main whole-cell sugars were rhamnose, xylose and galactose and the major fatty acids (>10 %) were C17 : 1ω8c, iso-C16 : 0 and C18 : 1ω9c. These data supported the affiliation of strains 78^T and 601 to genus Nocardioides. Based on evidence collected from the phenotypic, genotypic and phylogenetic analyses, we propose a novel species named Nocardioideshouyundeii sp. nov. The type strain is 78^T (=CGMCC 4.7461^T=DSM 106424^T).

Nocardioides astragali sp. nov., isolated from a nodule of wild Astragalus chrysopterus in northwestern China

A Gram-positive, non-motile, rod-shaped bacterial strain, designated HH06^T, was isolated from a nodule of Astragalus chrysopterus in northwestern China. Phylogenetic analysis of the 16S rRNA gene sequence showed that the strain is closely related to Nocardioides alpinus Cr7-14^T and Nocardioides furvisabuli DSM 18445^T with 98.5 and 98.1% similiarity, respectively. Growth was observed at 4–28 °C in R2A medium (optimum at 25 °C), at 10–30 °C in YMA and LB medium (optimum in both at 28 °C) and at pH 5.0–10.0 in R2A medium (optimum at pH 7.0–8.0). The cell wall peptidoglycan was found to contain LL-diaminopimelic acid as the principal diamino acid and MK-8(H4) was identified as the predominant menaquinone. The major polar lipids were identified as phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, two unidentified glycolipids and two unidentified polar lipids. The major fatty acids were identified as iso-C_16:0 (32.8%) and C_18:1ω9c (15.1%). The DNA G+C content of strain HH06^T was determined to be 71.4 mol%. Based on phenotypic, chemotaxonomic, phylogenetic properties and DNA–DNA relatedness, it is concluded that strain HH06^T represents a novel species of the genus Nocardioides, for which the name Nocardioides astragali sp. nov. is proposed. The type strain is HH06^T (= CGMCC 4.7327^T = NBRC 112322^T).

Diversity of cultivable bacterial endophytes in Paullinia cupana and their potential for plant growth promotion and phytopathogen control

Endophytic bacteria occupy the same niche of phytopathogens and may produce metabolites that induce the host plant systemic resistance and growth. Host and environmental variables often determine the endophytic community's structure and composition. In this study, we addressed whether the plant genotype, organ, and geographic location influence the structure, composition, and functionality of endophytic bacterial communities in Paullinia cupana. To characterize the communities and identify strains with potential application in agriculture, we analyzed two P. cupana genotypes cultivated in two cities of the State of Amazonas, Brazil. Endophytic bacteria were isolated from surface-disinfested root, leaf, and seed tissues through the fragmentation and maceration techniques. The colonization rate, number of bacteria, richness, diversity, and functional traits were determined. The plant growth-promoting ability of selected bacterial strains was assessed in Sorghum bicolor. We identified 95 bacterial species distributed in 29 genera and 3 phyla (Proteobacteria, Actinobacteria, and Firmicutes). The colonization rate, richness, diversity, and species composition varied across the plant organs; the last parameter also varied across the plant genotype and location. Some strains exhibited relevant plant growth-promoting traits and antagonistic traits against the main phytopathogens of P. cupana, but they were not separated by functional traits. The main bacterial strains with plant growth-promoting traits induced S. bicolor growth. Altogether, our findings open opportunities to study the application of isolated endophytic bacterial strains in the bioprospection of processes and products.

Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala

A Gram-staining-positive, aerobic non-spore-forming and short-rod-shaped endophytic actinomycete was isolated from a branch of Sonneratia apetala, designated strain BGMRC0092T and investigated in detail data to determine its taxonomic position. On the basis of the 16S rRNA gene sequence analysis, the results of the phylogenetic analyses indicated that BGMRC0092T was most closely related to Nocardioides alpinus Cr7-14T (96.9 %), Nocardioides oleivorans DSM16090T (96.4 %) and Nocardiodes exalbidus RC825T (96.3 %). The predominant cellular fatty acids of BGMRC0092T were iso-C16 : 0 and C18 : 1ω8c. The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were composed of galactose, mannose, rhamnose and xylose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, one unknown phospholipid and three unknown polar lipids. The DNA G+C content was 69.3 mol%. On the basis of phenotypic and chemotaxonomic characteristics and the results of phylogenetic analysis, BGMRC0092T represents a novel species of the genus Nocardioides, for which the name Nocardioides sonneratiae sp. nov. is proposed. The type strain is Nocardioides sonneratiae BGMRC0092T (=KCTC 39565T=NBRC 110251 T=DSM 100390T).

Nocardioides thalensis sp. nov., isolated from a desert

A novel actinobacterial strain, designated NCCP-696T, was isolated from the Thal desert in Punjab, Pakistan, and characterized by using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NCCP-696T belongs to the genus Nocardioides and showed the highest level of sequence similarity with respect to Nocardioides panacisoliGsoil 346T (98.2 %) and less than 96.4 % to the strains of other species of the genus Nocardioides. Cells of strain NCCP-696T were Gram-positive, aerobic, non-motile rods and formed cream-coloured colonies. The strain was positive for oxidase and catalase. Growth occurred at 20-42 °C (optimum 30-37 °C) at pH 5.5-9.0 (optimum pH 7.0) and with 0-4 % NaCl (optimum 0-2 %, w/v). Strain NCCP-696T contained Iso-C16 : 0, C18 : 1ω9c, C17 : 1ω8c and C17 : 0 as the predominant fatty acids and was found to have LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan. The polar lipid profile consisted of phosphatidylinositol, phosphatidylglycerol and one unknown phospholipid. The major menaquinone was MK-8(H4) (98.7 %) while a minor amount (1.3 %) of MK-9(H2) was also detected. The DNA G+C content of the genomic DNA was 71.6 mol%. The DNA-DNA hybridization value of the isolate against the closely related type strain Nocardioides panacisoliGsoil 346T was 56.3±1.4. On the basis of the phylogenetic inference, chemotaxonomic characteristics and phenotypic data, strain NCCP-696T should be classified as a novel species, for which the name Nocardioides thalensis sp. nov. is proposed. The type strain is NCCP-696T (=DSM 103833T=CCTCC AB 2016296T).

Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave

A novel actinobacterial strain, designated YIM A1136T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-staining-positive and rod-shaped. Colonies of the strain were circular, convex, opaque and yellowish-white in colour. On the basis of 16S rRNA gene sequence analysis, strain YIM A1136T was most closely related to the type strains Nocardioides ganghwensis JC2055T (98.3 % sequence similarity), Nocardioides exalbidus RC825T (98.2 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides hwasunensis HFW-21T (98.0 %), Nocardioides oleivorans DSM 16090T (97.9 %) and Nocardioides furvisabuli SBS-26T (97.8 %) and is therefore considered to represent a member of the genus Nocardioides. DNA-DNA hybridization values between strain YIM A1136T and related type strains of the genus Nocardioides were less than 70 %. ll-Diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose, rhamnose and ribose. The major isoprenoid quinone was MK-8(H4), while the major fatty acids (>10 %) were C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The genomic DNA G+C content was 71.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain YIM A1136T merits representation of a novel species of the genus Nocardioides, for which the name Nocardioides cavernae sp. nov. is proposed. The type strain is YIM A1136T (=KCTC 39551T=DSM 29950T).