Insights on mining the pangenome of Sphingobacterium thalpophilum NMS02 S296 from the resistant banana cultivar Pisang lilin confirms the antifungal action against Fusarium oxysporum f. sp. cubense

Introduction

Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), poses a significant global threat to banana cultivation. Conventional methods of disease management are increasingly challenged, thus making it necessary to explore alternative strategies. Bacterial endophytes, particularly from resistant genotypes, are gaining attention as potential biocontrol agents. Sphingobacterium thalpophilum, isolated from the resistant banana cultivar Pisang lilin (JALHSB010000001-JALHSB010000029), presents an intriguing prospect for combating Fusarium wilt. However, its underlying biocontrol mechanisms remain poorly understood. This study aimed to elucidate the antifungal efficacy of S. thalpophilum NMS02 S296 against Foc and explore its biocontrol mechanisms at the genomic level.

Methods

Whole genome sequencing of S. thalpophilum NMS02 S296 was conducted using next-generation sequencing technologies and bioinformatics analyses were performed to identify genes associated with antifungal properties. In vitro assays were used to assess the inhibitory effects of the bacterial isolate on the mycelial growth of Foc. To explore the biomolecules responsible for the observed antagonistic activity, metabolites diffused into the agar at the zone of inhibition between Foc S16 and S. thalpophilum NMS02 S296 were extracted and identified.

Results

Whole genome sequencing revealed an array of genes encoding antifungal enzymes and secondary metabolites in S. thalpophilum NMS02 S296. In vitro experiments demonstrated significant inhibition of Foc mycelial growth by the bacterial endophyte. Comparative genomic analysis highlighted unique genomic features in S. thalpophilum linked to its biocontrol potential, setting it apart from other bacterial species.

Discussion

The study underscores the remarkable antifungal efficacy of S. thalpophilum NMS02 S296 against Fusarium wilt. The genetic basis for its biocontrol potential was elucidated through whole genome sequencing, shedding light on the mechanisms behind its antifungal activity. This study advanced our understanding of bacterial endophytes as biocontrol agents and offers a promising avenue for plant growth promotion towards sustainable strategies to mitigate Fusarium wilt in banana cultivation.

An unusual cause of pyrexia of unknown origin with sepsis: A diagnostic challenge

Sphingobacterium species are ubiquitous and are abundant in nature and rarely involved in causing human infections. A 62-year-old man presented with recurrent episodes of high fever up to 40 ​°C accompanied by rigors, sweating, and malaise for the past 4 weeks. After a thorough workup, only elevated C-reactive protein with a leucocytosis was evident. Blood culture showed growth of Gram-negative bacilli which was identified as spingobacterium spiritivorum. Although S. spiritivorum is rare, with limited cases reported in the literature, it must be considered as a causative organism in patients with persistent fevers with sepsis.

Sphingobacterium lumbrici sp. nov., a novel bacterium isolated from wormcast of Eisenia foetida

A novel Gram-stain-negative, rod-shaped, non-motile, yellowish bacterium, designated strain 1.3611^T, was isolated from the wormcast of Eisenia foetida. The strain grew optimally at 30-37 ℃, at pH 7.0 and with 0-1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain 1.3611^T showed the highest degree of 16S rRNA gene sequence similarity to Sphingobacterium olei HAL-9^T (97.0 %), followed by Sphingobacterium alkalisoli Y3L14^T (95.8 %). The respiratory quinone of strain 1.3611^T was menaquinone-7 (MK-7) and its major cellular fatty acids were iso-C_15 : 0 (41.3 %), summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c, 22.1 %) and iso-C_17 : 0 3-OH (16.2 %). The major polar lipids were sphingophospholipid, phosphatidylethanolamine, four unidentified glycolipids, two unidentified phospholipids and five unidentified polar lipids. The genomic DNA G+C content was 39.0 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genomes of strain 1.3611^T and S. olei HAL-9^T were 37.9 and 88.9 %, respectively. According to the phenotypic and chemotaxonomic phylogenetic results, strain 1.3611^T should represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium lumbrici sp. nov. is proposed, with strain 1.3611^T (=KCTC 62980^T=CCTCC AB 2018349^T) as the type strain.

Sphingomonas corticis sp. nov., and Sphingobacterium corticibacterium sp. nov., from bark canker

Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7^T and 30C10-4-7^T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7^T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418^T, and strain 30C10-4-7^T shows highest sequence similarity to Sphingobacterium arenae H-12^T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7^T is a novel member different from recognized species in the genus Sphingomonas. The main fatty acids and respiratory quinone detected in strain 36D10-4-7^T are C_18 : 1  ω7c and/or C_18 : 1  ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7^T, the major fatty acids and menaquinone are iso-C_15 : 0, C_16 : 1  ω7c and/or C_16 : 1  ω6c and iso-C_17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium. The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7^T=CFCC 13112^T=KCTC 52799^T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7^T=CFCC 13069^T=KCTC 52797^T) are proposed.

Complete Genome Sequence of Sphingobacterium psychroaquaticum Strain SJ-25, an Aerobic Bacterium Capable of Suppressing Fungal Pathogens

Using antagonistic bacterium is an effective method to control plant disease by fungal pathogens. An aerobic bacterium designated SJ-25, capable of suppressing Fusarium graminearum, Exserohilum turcicum, Pythium aphanidermatum, and Cochliobolus sativus, was isolated from farmland soil. The phylogenetic analysis revealed that strain SJ-25 belongs to the species of Sphingobacterium psychroaquaticum. The genome of strain SJ-25 consists of a 4,396,535-bp chromosome with a G+C content of 41.7 mol%; including 3696 CDS, 64 tRNA genes and six rRNA operons. Genomic analysis revealed that its genome contains multiple genes responsible for biosynthesis of siderophore, methyl 4-hydroxybenzoate, chitinase, giving strain SJ-25 the antagonistic ability on fungi pathogen. Strain SJ-25 harbors sets genes responsible for production of 2, 3-butanediol and salicylic acid, which could elicit the induced systemic resistance of the host plant. This genome sequence could be used as a basis material for further exploration of antagonistic mechanisms on fungi, widening our understanding of the ecological role of the genus Sphingobacterium in farmland ecosystem.

Sphingobacterium praediipecoris sp. nov. isolated from effluent of a dairy manure treatment plant

A novel Gram-reaction-negative, rod-shaped, non-motile bacterium, designated as strain G2-10^T was isolated from effluent of a dairy manure treatment plant. Growth occurred at 20-40 °C (optimum at 25-30 °C), pH 7.0-8.0 (optimum at pH 7.0). The range of NaCl concentration for growth was between 0% and 3% (w/v) (optimum 0-1%, w/v). Comparison of 16S rRNA gene sequence indicated that strain G2-10^T was moderately related to the type strains of Sphingobacterium nematocida M-SX103^T and Sphingobacterium suaedae T47^T with a pair-wise sequence similarity of 94.3% and 94.0%, respectively. The major fatty acid constituents of strain G2-10^T were identified as iso-C_15:0 (37.6%), summed feature 3 (consisting of C_16:1ω7c and/or C_16:1ω6c, 29.6%) and iso-C_17:0 3-OH (15.2%). Phosphatidylethanolamine was the major polar lipids of strain G2-10^T. Sphingophospholipids were present. The isoprenoid quinone was composed of only MK-7. The DNA G + C content of strain G2-10^T was found to be 42.5 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain G2-10^T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium praediipecoris is proposed. The type strain is G2-10^T (= KCTC 52880^T = NBRC 112848^T).

Sphingobacterium tabacisoli sp. nov., isolated from a tobacco field soil sample

A Gram-staining-negative, non-motile and rod-shaped bacterium, designated strain h337T, was isolated from an arable soil sample of a tobacco field in Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10-35 °C, at pH 6.0-9.0 and in the presence of up to 3 % (w/v) NaCl, with optimal growth at 30 °C, pH 7.0 and with 1-2 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The cellular polar lipids contained phosphatidylethanolamine, sphingophospholipid, four unidentified phospholipids, five unidentified lipids and three unidentified aminophospholipids. The genomic DNA G+C content was 41.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain h337T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain h337T was most closely related to 'Sphingobacteriumyamdrokense' 3-0-1 (98.8 %) and Sphingobacteriumyanglingense CCNWSP36-1T (98.5 %) and shared less than 97 % similarity with other species of the genus Sphingobacterium. DNA-DNA hybridization data indicated that the isolate represented a novel genomic species belonging to the genus Sphingobacterium. The characteristics determined in this polyphasic taxonomic study indicated that strain h337T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium tabacisoli sp. nov. (type strain h337T=KCTC 52298T=CCTCC AB 2017155T) is proposed.

Sphingobacterium spiritivorum bacteremia due to cellulitis in an elderly man with chronic obstructive pulmonary disease and congestive heart failure: a case report

Background

Sphingobacterium spiritivorum is a glucose non-fermenting Gram-negative rod, formerly classified as one of the Flavobacterium species. It is characterized by a large number of cellular membrane sphingophospholipids. Sphingobacterium species are ubiquitous and isolated from natural environments, such as soil and water. However, they rarely cause infections in humans. Only a limited number of cases have been reported in elderly and immunocompromised patients with underlying diseases and predisposing factors.

Case presentation

An 80-year-old Japanese man with chronic obstructive pulmonary disease and congestive heart failure visited the Kariya Toyota General Hospital, Aichi, Japan with the chief complaint of fever accompanied by chills and left leg pain. At initial presentation, he was distressed and dyspneic. He was febrile (38.8 °C), and his left foot was swollen with reddening and tenderness. We diagnosed him as having cellulitis, and he was hospitalized for antibiotic therapy. Initially, he was treated with intravenously administered cefazolin, but after the isolation of a glucose non-fermenting Gram-negative rod from blood cultures, we decided to switch cefazolin to intravenously administered meropenem on day 4, considering the antibiotic resistance of the causative organism. The causative organism was identified as S. spiritivorum on day 6. His condition gradually stabilized after admission. Meropenem was switched to orally administered levofloxacin on day 12. He was discharged on day 16 and treated successfully without any complications.

Conclusions

Although S. spiritivorum is rare, with limited cases isolated from cellulitis, it should be considered as a causative organism in elderly and immunocompromised patients with cellulitis. Blood cultures are the key to correct diagnosis and appropriate treatment.

Sphingobacterium humi sp. nov., isolated from soil

A Gram-stain-negative, facultatively aerobic bacterium, designated strain D1^T, was isolated from soil in South Korea. Cells of strain D1^T were non-motile rods with oxidase- and catalase-positive activities. Growth was observed at 15-40 °C (optimum, 30-37 °C), at pH 5.5-9.0 (optimum, pH 7.0-8.0) and in the presence of 0.0-5.0 % (w/v) NaCl (optimum, 0.0-1.0 %). The only respiratory quinone detected was menaquinone 7 (MK-7), and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) were identified as the major fatty acids. Phosphatidylethanolamine was the major polar lipid, and two unidentified glycophospholipids and four unidentified lipids were also detected as minor polar lipids. Sphingolipids, a typical chemotaxonomic feature of the genus Sphingobacterium, were detected. The G+C content of the genomic DNA was 43.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D1^T formed a phyletic lineage with Sphingobacterium hotanense XH4^T within the genus Sphingobacterium. Strain D1^T was most closely related to S. hotanense XH4^T (98.1 % 16S rRNA gene sequence similarity) and Sphingobacterium cellulitidis R-53603^T (97.2 %), and the DNA-DNA relatedness level between strain D1^T and the type strain of S. cellulitidis was 43.1±0.7 %. Based on the phenotypic, chemotaxonomic and molecular features, strain D1^T clearly represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium humi sp. nov. is proposed. The type strain is D1^T (=KACC 18595^T=JCM 31225^T).

Arenimonas soli sp. nov., isolated from saline-alkaline soil

A Gram-staining-negative, non-motile, aerobic bacterial strain, designated Y3L17T, was isolated from the saline-alkaline soil of a farmland, Hangjin Banner, Inner Mongolia, northern China. Y3L17T could grow at 15-45 °C (optimum 35 °C), pH 6.0-10.0 (optimum pH 8.0) and with 0-4 % (w/v) NaCl (optimum 0 %). The results of phylogenetic analysis based on the 16S rRNA gene and gyrB gene sequences revealed that Y3L17T tightly clustered with strains of members of the genus Arenimonas, sharing the highest 16S rRNA gene similarities with Arenimonas aestuarii S2-21T (99.5 %) and Arenimonas donghaensis HO3-R19T (98.2 %), and lower similarities (<97 %) with all the other type strains of species of this genus. However, Y3L17T shared only 92.62 % gyrB gene similarities with A. aestuarii S2-21T. The DNA-DNA hybridization values of Y3L17T with A. aestuariiS2-21T and A. donghaensis HO3-R19T were 20.1±2.5 and 18.2±3.2 %, respectively. Y3L17T contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, five unknown phospholipids and one unknown lipid as the major polar lipids. Ubiquinone-8 (Q-8) was the predominant respiratory quinone, while iso-C15 : 0, iso-C17 : 0ω9c and iso-C11 : 0 3-OH were the major cellular fatty acids. Its genomic DNA G+C content was 65.4 mol%. On the basis of its phenotypic, phylogenetic and genotypic characteristics, Y3L17T represents a novel species within the genus Arenimonas, for which the name Arenimonas soli sp. nov. is proposed, the type strain is Y3L17T (=CGMCC 1.15905T =KCTC 52420T).

Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil

A Gram-staining-negative, non-motile, non-spore-forming bacterium designated Y3L14T was isolated from the saline-alkaline soil of a farmland, Inner Mongolia, northern China. Strain Y3L14T could grow at 10-40 °C (optimally at 30 °C), pH 6.0-10.0 (optimally at pH 8.0), and in the presence of 0-6.0 % (w/v) NaCl (optimally with 0-2.0 %). Phylogenetic analysis based on the 16S rRNA gene and DNA gyrase subunit B (gyrB) gene sequences revealed that strain Y3L14T clustered with strains belonging to the genus Sphingobacterium, sharing the highest 16S rRNA gene sequence similarity with Sphingobacterium lactis WCC 4512T (94.99 %). Its major cellular fatty acids contained iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone-7 (MK-7) was the only isoprenoid quinone. Strain Y3L14T contained phosphatidylethanolamine, sphingophospholipid, two unknown phospholipids and three unknown lipids as the major polar lipids. The genomic DNA G+C content of strain Y3L14T was 36.0 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y3L14T represents a novel species within the genus Sphingobacterium, for which Sphingobacterium alkalisoli sp. nov. is proposed; the type strain is Y3L14T (=CGMCC 1.15782T=KCTC 52379T).