Nocardioides ferulae sp. nov., isolated from root of an endangered medicinal plant Ferula songorica Pall. ex Spreng

GC/MS Fatty Acid Profile of Marine-Derived Actinomycetes from Extreme Environments: Chemotaxonomic Insights and Biotechnological Potential

This study investigated the fatty acids (FA) profile of 54 actinomycete strains isolated from marine sediments collected off the Portugal continental coast, specifically from the Estremadura Spur pockmarks field, by GC/MS. Fatty acid methyl esters (FAMEs) were prepared from the ethyl acetate lipidic extracts of these strains and analyzed by gas chromatography-mass spectrometry (GC/MS), with FA identification performed using the NIST library. The identified FAs varied from C12:0 to C20:0, where 32 distinct FAs were identified, including 7 branched-chain fatty acids (BCFAs), 9 odd-chain fatty acids (OCFAs), 8 monounsaturated fatty acids (MUFAs), 6 saturated fatty acids (SFAs), 1 polyunsaturated fatty acid (PUFA), and 1 cyclic chain fatty acid (CCFA). The average expressed content was BCFA (47.54%), MUFA (28.49%), OCFA (26.93%), and SFA (22.16%), of which i-C16:0, C18:1ω9, and C16:0 were predominant, while PUFA (3.58%) and CCFA (0.41%) were identified as minor components. The identified BCFA were i-C16:0, a-C15:0, i-C15:0, i-C15:1ω6, a-C16:0, a-C14:0, and i-C17:0, which include combined branching and unsaturation and branching and odd. SFAs were present in all species, with C16:0 and C18:0 being the most representative. Rare OCFAs C19:1ω9, C17:1ω7, C15:0, and C17:0 were expressed. PUFA C18:1ω9 was detected; within this class, omega families ω9, ω7, ω6, and ω5 were identified, and no ω3 was detected. The only CCFA was benzene-butanoic acid (benzene-C4:0). These findings highlight the metabolic versatility of actinomycetes, providing valuable insights into microbial chemotaxonomy and offering promising biochemical leads for the development of biofuel, nutraceutical, and antifungal agents. Furthermore, these results underline the diversity and biotechnological potential of FAs in actinomycetes, uncovering their potential to be used as microbial cell factories, and paving the way for innovations in biofuels, pharmaceuticals, and eco-friendly industrial products.

Nocardioides xinjiangensis sp. nov., a novel species isolated from desert soil

Two novel strains, SYSU D00514T and SYSU D00778, were isolated from desert soil in the Gurbantunggut Desert, Xinjiang Uygur Autonomous Regions, PR China. SYSU D00514T and SYSU D00778 were aerobic, Gram-stain-positive, rod-shaped, catalase-positive and oxidase-negative. SYSU D00514T grew at temperatures ranging from 4 to 37 °C (optimum, 28-30 °C), at pH 6.0-8.0 (optimum, 7.0), and tolerated NaCl concentrations from 0 to 7.5% (optimum, 0.5% w/v). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains SYSU D00514T and SYSU D00778 were closely related to the members of the genus Nocardioides. Two isolates were most closely related to Nocardioides alpinus Cr7-14 T (98.05% and 98.19%). The G + C content of the genomic DNA of strains SYSU D00514T and SYSU D00778 were both 72.8%. Strain SYSU D00514T and the type strains of the genus Nocardioides in the analysis had average nucleotide identity values of 76.8-85.8% as well as digital DNA-DNA hybridization values between 19.5% and 28.0%. The predominant cellular fatty acids of strain SYSU D00514T were C17:1 ω8c, C18:1 ω9c and iso-C16:0. For strain SYSU D00514T, the major polar lipids encompassed diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, an unidentified aminophospholipid and two unidentified aminolipids. The main respiratory quinone of strain SYSU D00514T was MK-8 (H4). Based on the results of polyphasic taxonomic experiments, we propose that strains SYSU D00514T and SYSU D00778 represent a novel species of the genus Nocardioides, with the name Nocardioides xinjiangensis. The type strain is SYSU D00514T (= CGMCC 1.18622 T = MCCC 1K05001T = KCTC 49488 T).

Nocardioides potassii sp. nov., isolated from weathered potash tailings soil

A Gram-positive, aerobic actinomycete, designated strain KLBMP 9356^T, was isolated from weathered potash tailings soil sampled in Xuzhou, Jiangsu Province, PR China. The colonies were cream-coloured, convex and rounded. The optimal growth conditions of strain KLBMP 9356^T were 1 % (w/v) NaCl, 28 °C and pH 7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KLBMP 9356^T showed the highest similarity to Nocardioides zhouii CGMCC 1.11084^T (98.9 %) and Nocardioides glacieisoli CGMCC 1.11097^T (98.7 %). Results from two tree-making algorithms supported the position that strain KLBMP 9356^T forms a stable clade with N. zhouii CGMCC 1.11084^T and N. glacieisoli CGMCC 1.11097^T. Strain KLBMP 9356^T exhibited low digital DNA-DNA hybridization values with N. zhouii CGMCC 1.11084T (27.6 %) and N. glacieisoli CGMCC 1.11097^T (31.4 %). The average nucleotide identity values between strain KLBMP 9356^T and N. zhouii CGMCC 1.11084^T and N. glacieisoli CGMCC 1.11097^T were 83.8% and 85.9%, respectively. The peptidoglycan in the cell wall of the novel strain was ll-2,6-diaminopimelic acid and the predominant menaquinone was MK-8(H₄). The major fatty acids (>10 %) were C_17:1ω8c and C_18:1ω9c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, lyso-phospatidylglycerol and phosphatidylinositol. The genomic DNA G+C content was 71.6 mol%. Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain KLBMP 9356^T represents a novel species of the genus Nocardioides, for which the name Nocardioides potassii sp. nov. is proposed. The type strain is KLBMP 9356^T (=CGMCC 4.7738^T=NBRC 115493^T).

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Introduction

The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).

Methods

In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes.

Results and discussion

Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.

Endophytic bacterial and fungal community compositions in different organs of ginseng (Panax ginseng)

Panax ginseng (Panax ginseng C. A. Mey.) is a perennial herb of the genus ginseng, which is used as medicine with dried roots and rhizomes. With the deepening of research on ginseng, the chemical components and pharmacological effects of ginseng have gradually been discovered. Endophytes are beneficial to host plants. However, the composition of endophytes in different organs from ginseng is poorly elucidated. The report of ginsenoside production by endophytic microbes isolated from Panax sp., motivated us to explore the endophytic microbial diversity related to the roots, stems, and leaves. In this study, the V5-V7 variable region of endophytic bacteria 16S rRNA gene and V1 variable region of endophytic fungi ITS gene in different organs were analyzed by high-throughput sequencing. The diversity and abundance of endophytic microbes in the three organs are different and are affected by the organs. For example, the most abundant endophytic bacterial genus in roots was Mycobacterium, while, the stems and leaves were Ochrobactrum. Similarly, the fungal endophytes, Coniothyrium and Cladosporium, were also found in high abundance in stems, in comparison to roots and leaves. The Shannon index shows that the diversity of endophytic bacteria in roots is the highest, and the richness of endophytic bacterial was root > stem (p < 0.05). Principal coordinate analysis showed that there were obvious microbial differences among the three groups, and the endophytic bacterial composition of the leaves was closer to that of the roots. This study provides an important reference for the study of endophytic microorganisms in ginseng.

Nocardioides donggukensis sp. nov. and Hyunsoonleella aquatilis sp. nov., isolated from Jeongbang Waterfall on Jeju Island

Two bacterial strains, designated MJB4^T and SJ7^T, were isolated from water samples collected from Jeongbang Falls on Jeju Island, Republic of Korea. Phylogenetic analysis of 16S rRNA gene sequences indicated that the two strains belonged to the genera Nocardioides and Hyunsoonleella, owing to their high similarities to Nocardioides jensenii DSM 29641^T (97.5 %) and Hyunsoonleella rubra FA042 ^T (96.3 %), respectively. These values are much lower than the gold standard for bacterial species (98.7 %). The average nucleotide identity values between strains MJB4^T, SJ7^T and the reference strains, Nocardioides jensenii DSM 29641^T, Nocardioides daejeonensis MJ31^T and Hyunsoonleella flava T58^T were 77.2, 75.9 and 75.4 %, respectively. Strains MJB4^T and SJ7^T and the type strains of the species involved in system incidence have average nucleotide identity and average amino acid threshold values of 60.1-82.6 % for the species boundary (95-96 %), which confirms that strains MJB4^T and SJ7^T represent two new species of genus Nocardioides and Hyunsoonleella, respectively. Based on phylogenetic and phenotypic data, strains MJB4^T and SJ7^T are considered to represent novel species of the genus Nocardioides and Hyunsoonleella, respectively, for which the names Nocardioides donggukensis sp. nov. (type strain MJB4^T=KACC 21724^T=NBRC 114402^T) and Hyunsoonleella aquatilis sp. nov., (type strain SJ7^T=KACC 21715^T=NBRC 114486^T) have been proposed.

Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) and leaves of dandelion (Taraxacum officinale), respectively, on the Qinghai-Tibet Plateau

In the present study, four bacterial strains, two (S-713^T and 406) isolated from faecal samples of Tibetan antelopes and the other two (S-531^T and 1598) from leaves of dandelion collected on the Qinghai-Tibet Plateau of PR China, were analysed using a polyphasic approach. All four isolates were aerobic, rod-shaped, non-motile, oxidase-negative, Gram-stain-positive and catalase-positive. According to four phylogenetic trees, strain pairs S-713^T/406 and S-531^T/1598 form two independent branches belonging to the genus Nocardioides, and are closest to Nocardioides lianchengensis, Nocardioides dokdonensis, Nocardioides salarius, Nocardioides marinisabuli, Nocardioides psychrotolerans and Nocardioides szechwanensis. Although sharing MK8-(H₄) as their major isoprenoid quinone, strains S-713^T and S-531^T contained C_18 : 1  ω9c (24.64 and 16.34 %) and iso-C_16 : 0 (9.74 and 29.38 %), respectively, as their main fatty acids, with remarkable differences in their biochemical profiles but only slight ones in their optimal growth conditions. The chromosomes of strains S-713^T and S-531^T were 4 207 844 bp (G+C content, 73.0 mol%) and 4 809 817 bp (G+C content, 72.5 mol%), respectively. Collectively, the two strain pairs represent two separate novel species of the genus Nocardioides, for which the names Nocardioides dongkuii sp. nov. and Nocardioides lijunqiniae sp. nov. are proposed, with S-713^T (=JCM 33698^T=CGMCC 4.7660^T) and S-531^T (=JCM 33468^T=CGMCC 4.7659^T) as the respective type strains.

Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish)

A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW-15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).

Targeted 16S rRNA gene and ITS2 amplicon sequencing of leaf and spike tissues of Piper longum identifies new candidates for bioprospecting of bioactive compounds

Piper longum (also known as Indian long pepper) is widely used in Ayurvedic, Siddha and Unani medicine systems. The principle bioactive compound of this plant is piperine, which mainly accumulates in the fruits called spikes. The report of piperine production by endophytic microbes isolated from Piper sp., motivated us to investigate the endophytic microbial diversity associated with the spikes vis-à-vis leaves (which contain negligible levels of piperine). This is the first report to use metagenomics approach to unravel the endophytic microbial diversity in P. longum. Our results indicate that 2, 56, 631 bacterial OTUs and 1090 fungal OTUs were picked cumulatively from both the tissues. Although bacterial and fungal endophytes occupy the same niche, remarkable differences exist in their diversity and abundance. For instance, the most abundant bacterial genera in spikes were Nocardioides and Pseudonocardia (Phylum Actinobacteria; reported to produce bioactive compounds); while, in leaves were Larkinella and Hymenobacter (Phylum Bacteriodetes). Likewise, the fungal endophytes, Periconia, Cladosporium and Coniothyrium (which have been earlier reported to produce commercially important metabolites including piperine), were also present in high abundance in spikes, in comparison to leaves. Further, the results of PICRUSt analysis reveal the high metabolic potential of spike-associated bacteria for secondary metabolism, namely biosynthesis of alkaloids (including pyridine/piperidine), terpenes, flavonoids and antibiotics. Therefore, our findings indicate that the endophytes abundant or unique in spikes could be explored for bioprospecting of novel/commercially important metabolites; an approach that has both ecological and economical benefits.

Endophytic actinobacteria of a halophytic desert plant Pteropyrum olivieri: promising growth enhancers of sunflower

In the present study, 40 actinobacterial isolates were obtained from the roots of a desert plant, Pteropyrum olivieri and tested for extracellular hydrolytic enzyme activities, hydrogen cyanide, and siderophore production. Based on these activities, three isolates designated UTMC 2482, UTMC 2483, and UTMC 3136 were selected with an aim of developing bio-fertilizing agent to improve the growth of sunflower plants under normal conditions. The selected isolates showed 98.2, 98.4, and 100% similarities in the 16S rRNA gene sequences to Streptomyces chromofuscus, Streptomyces ambofaciens, and Streptomyces gardneri, respectively. These isolates exhibited indole acetic acid production while UTMC 2483 was found to produce 1-aminocyclopropane-1-carboxylate deaminase, as well. Sunflower seeds soaked in the bacterial spore suspensions increased the tolerance of sunflower seedlings to the stresses of salinity and water deficiency up to 270 mM of NaCl and - 2Mpa of PEG6000, respectively. Under normal conditions, inoculation with individual isolates and their consortia enhanced the yield (plant length, weight, and flower diameter) and biochemical contents (i.e. chlorophyll, protein, and oil) up to 5.3, 1.7, and 2.4 times higher than that of un-inoculated plants, significantly (p < 0.05) in greenhouse and field experiments. This is the first study demonstrating that endophytic actinobacteria from the desert plant, P. olivieri, have profound bio-fertilizing effects on the growth of sunflower.

Nocardioides convexus sp. nov. and Nocardioides anomalus sp. nov., isolated from soil and mineral water

Two bacterial strains designated as W3-2-3^T and HKS04^T were isolated from mineral water and a soil sample, respectively, in the Republic of Korea. The 16S rRNA genes of the two strains shared a sequence similarity of 93.5 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains W3-2-3^T and HKS04^T formed a distinct lineage within the genus Nocardioides of the family Nocardioidaceae (order Propionibacteriales). The closely related species of strain W3-2-3^T were Nocardioides albidus (98.9 %), Nocardioides caeni (98.8 %), Nocardioides kongjuensis (98.6 %), Nocardioides aromaticivorans (98.5 %), Nocardioides nitrophenolicus (98.4 %), Nocardioides flava (98.2 %) and Nocardioides ginsengisoli (98.1 %). The closest species of strain HKS04^T was Nocardioides halotolerans (98.7 %). The genome sizes of strains W3-2-3^T and HKS04^T were 4741198 and 5 120341 bp, respectively. The genomic DNA G+C contents of strains W3-2-3^T and HKS04^T were 73.3 and 72.1 mol%, respectively. The main fatty acids of strain W3-2-3^T were C_17:1 ω6c and iso-C_16:0 and those of strain HKS04^T were iso-C_16:0 and iso-C_16:0 H. The main polar lipids of both strains were diphosphatidylglycerol and phosphatidylglycerol and the predominant respiratory quinone was MK-8(H₄), supporting the affiliation of these strains with the genus Nocardioides. Based on the results of biochemical, chemotaxonomic and phylogenetic analyses, two novel species, Nocardioides convexus W3-2-3^T (KACC 21211^T=LMG 31251^T) and Nocardioides anomalus HKS04^T (KACC 18879^T=LMG 31249^T), are proposed.

Nocardioides vastitatis sp. nov., isolated from Taklamakan desert soil

A Gram-stain-positive, aerobic, non-motile, rod-shaped actinobacterium, designated strain 21Sc5-5^T, was isolated from a soil sample collected in the Taklamakan desert in Xinjiang Uygur Autonomous Region, PR China and investigated by using a polyphasic approach. Strain 21Sc5-5^T grew at 10-37 °C (optimum, 28-30 °C), pH 6.0-9.0 (optimum, pH 7.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain 21Sc5-5^T formed a distinct lineage within the genus Nocardioides and had the highest similarity to Nocardioides albidus THG-S11.7^T (97.30 %), followed by Nocardioides kongjuensis A2-4^T (97.22 %), Nocardioides nitrophenolicus NSP 41^T (97.15 %) and Nocardioides caeni MN8^T (97.15 %). The results of chemotaxonomic analyses showed that the isolate possessed ll-diaminopimelic acid as the diagnostic diamino acid of the peptidoglycan and MK-8(H₄) as the predominant menaquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid and three unidentified lipids. The major fatty acids were iso-C_16 : 0 and 10-methyl C_18 : 0. The genome length of strain 21Sc5-5^T was 4.67 Mb containing 372 contigs and with a DNA G+C content of 70.4 mol%. On the basis of data from phylogenetic, phenotypic and chemotaxonomic analyses, strain 21Sc5-5^T represents a novel species of the genus Nocardioides, for which the name Nocardioides vastitatis sp. nov. is proposed. The type strain is 21Sc5-5^T (=JCM 33365^T=CGMCC 4.7608^T).