Sphingomonas cannabina sp. nov., isolated from Cannabis sativa L. ‘Cheungsam’

Jeon, Doeun; Jiang, Lingmin; Peng, Yuxin; Seo, Ji Min; Li, Zhun; Park, Seung-Hwan; Jeong, Rae‐Dong; Park, Soon Ju; Jeong, Jae Cheol; Lee, Ji-Young

doi:10.1099/ijsem.0.005566

Cited by 5 publications

(4 citation statements)

References 37 publications

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“…Sphingomonas is highly abundant in hemp plants ( Barnett et al 2020, Tang et al 2022) and in some cases speci cally the phyllosphere 56 . Recently, a potentially novel strain of Sphingomonas was isolated from Cannabis sativa 57 . Highlighting the potential for this dominant genera to play a relationship in CBD-producing genotypes but further research is required.…”

Section: Discussionmentioning

confidence: 99%

Microbiome Diversity and Variations in Industrial Hemp Genotypes

Ahmad,

Coffman,

Ray

et al. 2024

Preprint

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Microorganisms like bacteria and fungi are crucial for host medicinal plant growth and development. However, environmental factors and host genotypes can influence microbiome composition and diversity in plants such as industrial hemp (Cannabis sativa L.), which can help us understand how they cope with climatic stresses and pathogenic attacks. We evaluated the endophytic and rhizosphere microbial communities of two cannabidiol (CBD; Sweet Sensi and Cherry Wine) and two fibers (American Victory and Unknown). The four hemp varieties showed significant variation in microbiome diversity. The roots had significantly abundant fungal and bacterial endophyte diversity indices, whereas the stem had higher fungal than bacterial diversity. Interestingly, the soil system showed no significant diversity variation across CBD vs. fiber genotypes. In fungal phyla, Ascomycota, Basidiomycota, and Mucuromycota were significantly more abundant in root and stem than leaves in CBD-rich genotypes compared to fiber-rich genotypes. The highly abundant bacterial phyla were Proteobacteria, Acidobacteria, and Actinobacteria. We found 16 and 11 core-microbiome bacterial and fungal species across genotypes, respectively. Sphingomonas, Pseudomonas, and Bacillus were the core bacterial microbiome of fiber genotypes with high abundance compared to CBD genotypes. Contrarily, Microbacterium, and Rhizobium were significantly higher in CBD than fiber. The Alternaria and Gibberella formed core-fungal microbiome of fiber-genotype than CBD. Contrarily, Penicillium, and Nigrospora were significantly more abundant in CBD than fiber genotypes. In conclusion, specific hemp genotypes recruit specialized microbial communities. Utilizing the core-microbiome species can help to maintain and improve the growth of hemp plants and to target specialized traits of the genotype.

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Section: Discussionmentioning

confidence: 99%

Microbiome Diversity and Variations in Industrial Hemp Genotypes

Ahmad,

Coffman,

Ray

et al. 2024

Preprint

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“…We used the BBL™ Gram Stain Kit (BD, USA) for Gram-staining. The shape and size of the bacterial strains was observed by a scanning electron microscope (Regulus 8,100, Hitachi; Jeon et al, 2022 ). Motility was observed by using a hanging-drop technique, and gliding activity was observed by growing the strain on low-nutrient media composed of sea water and 0.7% (w/v) agar ( Tittsler and Sandholzer, 1936 ).…”

Section: Methodsmentioning

confidence: 99%

Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides

Muhammad,

Avila,

Nedashkovskaya

et al. 2023

Front. Microbiol.

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Three novel strains designated ABR2-5T, BKB1-1T, and WSW4-B4T belonging to the genus Reichenbachiella of the phylum Bacteroidota were isolated from algae and mud samples collected in the West Sea, Korea. All three strains were enriched for genes encoding up to 216 carbohydrate-active enzymes (CAZymes), which participate in the degradation of agar, alginate, carrageenan, laminarin, and starch. The 16S rRNA sequence similarities among the three novel isolates were 94.0%–94.7%, and against all three existing species in the genus Reichenbachiella they were 93.6%–97.2%. The genome sizes of the strains ABR2-5T, BKB1-1T, and WSW4-B4T were 5.5, 4.4, and 5.0 Mb, respectively, and the GC content ranged from 41.1%–42.0%. The average nucleotide identity and the digital DNA–DNA hybridization values of each novel strain within the isolates and all existing species in the genus Reichenbachiella were in a range of 69.2%–75.5% and 17.7–18.9%, respectively, supporting the creation of three new species. The three novel strains exhibited a distinctive fatty acid profile characterized by elevated levels of iso-C15:0 (37.7%–47.4%) and C16:1 ω5c (14.4%–22.9%). Specifically, strain ABR2-5T displayed an additional higher proportion of C16:0 (13.0%). The polar lipids were phosphatidylethanolamine, unidentified lipids, aminolipids, and glycolipids. Menaquinone-7 was identified as the respiratory quinone of the isolates. A comparative genome analysis was performed using the KEGG, RAST, antiSMASH, CRISPRCasFinder, dbCAN, and dbCAN-PUL servers and CRISPRcasIdentifier software. The results revealed that the isolates harbored many key genes involved in central metabolism for the synthesis of essential amino acids and vitamins, hydrolytic enzymes, carotenoid pigments, and antimicrobial compounds. The KEGG analysis showed that the three isolates possessed a complete pathway of dissimilatory nitrate reduction to ammonium (DNRA), which is involved in the conservation of bioavailable nitrogen within the ecosystem. Moreover, all the strains possessed genes that participated in the metabolism of heavy metals, including arsenic, copper, cobalt, ferrous, and manganese. All three isolated strains contain the class 2 type II subtype C1 CRISPR-Cas system in their genomes. The distinguished phenotypic, chemotaxonomic, and genomic characteristics led us to propose that the three strains represent three novel species in the genus Reichenbachiella: R. ulvae sp. nov. (ABR2-5T = KCTC 82990T = JCM 35839T), R. agarivorans sp. nov. (BKB1-1T = KCTC 82964T = JCM 35840T), and R. carrageenanivorans sp. nov. (WSW4-B4T = KCTC 82706T = JCM 35841T).

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“…A BBL™ Gram staining kit (BD, USA) was used to perform Gram staining. The morphology and size of bacterial cells were determined using a scanning electron microscope (SEM) (Regulus 8100, Hitachi) [26]. All isolates were checked for gliding motility through the hanging-drop technique and using soft agar media [27].…”

Section: Physical Biochemical and Chemotaxonomic Analysismentioning

confidence: 99%

Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov

Muhammad,

Avila,

Kim

2024

Preprint

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Background The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2T, ABR2-2, and BDSF4-3T) were isolated from the West Sea, Republic of Korea. Results To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2T and BDSF4-3T, and the six reference strains were 70.5–76.5% for ANI and 18.1–25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3–6), Cu2+ (0.2–0.4), Ni2+ (3–5), Zn2+ (2–4), Mn2+ (20–50), and Hg2+ (0.3). Conclusions Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2T = KCTC 82989T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3T = KCTC 82973T = InaCC B1619T).

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Sphingomonas cannabina sp. nov., isolated from Cannabis sativa L. ‘Cheungsam’

Cited by 5 publications

References 37 publications

Microbiome Diversity and Variations in Industrial Hemp Genotypes

Microbiome Diversity and Variations in Industrial Hemp Genotypes

Three novel marine species of the genus Reichenbachiella exhibiting degradation of complex polysaccharides

Comparative genome analysis of the genus Marivirga and proposal of two novel marine species: Marivirga arenosa sp. nov., and Marivirga salinae sp. nov

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