RESUMO
In sugarcane, sequences related to the genus Sphingomonas have been widely detected by microbiome studies. In this work, the presence of bacteria of this genus was confirmed using culture-dependent and independent techniques. A collection of thirty isolates was obtained using semispecific cultivation conditions, and a specific PCR assay was applied to help confirm the isolates as belonging to the genus. A series of laboratory evaluations were carried out to identify potential properties among the isolates in the collection, which consequently allowed the identification of some most promising isolates for the development of new agricultural bioinputs. In a separate analysis, the culture-independent fluorescence in situ hybridization (FISH) methodology was applied to demonstrate the natural occurrence of Sphingomonas in different organs and tissues of sugarcane. The results showed the presence of bacteria of the genus in the spaces between cells (apoplast) of the culm parenchyma, in vessels in the region of the leaf vein, on the adaxial surface of the leaf blade, and on the root surface, sometimes close to the base of root hairs, which suggests extensive colonization on the host plant. In summary, the present study corroborates previous metagenomic amplicon sequencing results that indicated a high occurrence of Sphingomonas associated with sugarcane. This is the first study that uses approaches other than amplicon sequencing to confirm the occurrence of the genus in sugarcane and, at the same time, demonstrates potentially beneficial activities to be explored by sugarcane cultivation.
Assuntos
Hibridização in Situ Fluorescente , Filogenia , RNA Ribossômico 16S , Saccharum , Sphingomonas , Saccharum/microbiologia , Sphingomonas/isolamento & purificação , Sphingomonas/classificação , Sphingomonas/genética , RNA Ribossômico 16S/genética , DNA Bacteriano/genética , Raízes de Plantas/microbiologia , Folhas de Planta/microbiologia , Análise de Sequência de DNARESUMO
Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.
Assuntos
Bactérias , Cavernas , Filogenia , RNA Ribossômico 16S , Cavernas/microbiologia , RNA Ribossômico 16S/genética , Bactérias/classificação , Bactérias/metabolismo , Bactérias/isolamento & purificação , Bactérias/genética , Dióxido de Silício/química , Microbiota , Venezuela , Sphingomonas/metabolismo , Sphingomonas/isolamento & purificação , Sphingomonas/classificação , Sphingomonas/genética , Biotecnologia/métodos , Anti-Infecciosos/metabolismo , Anti-Infecciosos/farmacologia , Microbiologia do Solo , DNA Bacteriano/genéticaRESUMO
Two novel strains of bacteria, CA1-15T and BIUV-7T, were isolated from soil samples gathered in Cheonan-si, Republic of Korea, and Inje-gun, Republic of Korea, respectively. These bacteria are Gram-negative, aerobic, and non-motile. Phylogenetic evaluations, using the sequence of the 16S rRNA gene, showed that strains CA1-15T and BIUV-7T belong to a distinctive clade within the family Sphingomonadaceae (order Sphingomonadales, class Alphaproteobacteria). The strains exhibited the highest similarity in their genetic makeup with representatives of the genus Sphingomonas. Strain CA1-15T was closely related to Sphingomonas echinoides NRRL B-3126T (97.8% similarity in 16S rRNA gene sequence), Sphingomonas oligophenolica JCM 12,082T (97.8%), Sphingomonas glacialis C16yT (97.6%) and Sphingomonas psychrolutea MDB1-AT (97.3%). Strain BIUV-7T was closely related to Sphingomonas nostoxanthinifaciens AK-PDB1-5T (97.0%), Sphingomonas vulcanisoli SN6-13T (96.3%), Sphingomonas naphthae DKC-5-1T (96.2%), and Sphingomonas prati W18RDT (95.7%). The optimal growth conditions for strains CA1-15T and BIUV-7T were determined to be at pH 7.0 and a temperature of 25 °C. Analysis of the cellular fatty acids of strain CA1-15T and BIUV-7T revealed that summed feature 8 (C18:1ω7c/C18:1ω6c) (60.4%), summed feature 8 (C18:1ω7c/C18:1ω6c) (62.9%) were the major component, respectively. Additionally, both strains exhibited ubiquinone Q-10 as their major respiratory quinone, and diphosphatidylglycerol (DPG), glycosphingolipid (SGL), and phosphatidylethanolamine (PE) as the major polar lipid. The genome of strain CA1-15T measures 4,133,944 bp, comprising 4,026 coding sequences (CDSs) and 46 tRNA genes. Similarly, the genome of strain BIUV-7T is 4,563,252 bp, characterized by 4,226 CDSs and 44 tRNA genes. The average nucleotide identity (ANI) analysis and digital DNA-DNA hybridization (dDDH) values between strain CA1-15T and other Sphingomonas species range from 73.2 to 79.9% and 19.4-22.9%, respectively. Comparatively, ANI and dDDH values between strain BIUV-7T and other Sphingomonas species are in the range of 72.9-76.5% and 19.3-20.9%, respectively. Based on the biochemical, chemotaxonomic, and phylogenetic analyses, it is evident that strains CA1-15T and BIUV-7T represent two novel bacterial species within the genus Sphingomonas. Accordingly, the names Sphingomonas immobilis sp. nov. and Sphingomonas natans sp. nov. are proposed. also, CA1-15T(= KCTC 92960T = NBRC 116547T) is the type strain of Sphingomonas immobilis and BIUV-7T(= KCTC 92961T = NBRC 116546T) is the type strain of Sphingomonas natans.
Assuntos
Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano , Ácidos Graxos , Filogenia , RNA Ribossômico 16S , Microbiologia do Solo , Sphingomonas , Sphingomonas/genética , Sphingomonas/isolamento & purificação , Sphingomonas/classificação , RNA Ribossômico 16S/genética , República da Coreia , Ácidos Graxos/análise , DNA Bacteriano/genética , Análise de Sequência de DNA , Fosfolipídeos/análiseRESUMO
An alpha-proteobacterial strain JXJ CY 53 T was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) collected from Lake Dianchi, China. JXJ CY 53 T was observed to be an aerobic, Gram-stain-negative, oval shaped, and mucus-secreting bacterium. It had C18:1ω7c and C16:0 as the major cellular fatty acids, Q-10 as the predominant ubiquinone, and sphingoglycolipid, diphosphatidylglycerol, phosphatidylcholine, and phosphatidylmethylethanolamine as the polar lipids. The G + C content of DNA was 65.85%. The bacterium had 16S rRNA gene sequence identities of 98.9% and 98.7% with Sphingomonas panni DSM 15761 T and Sphingomonas hankookensis KCTC 22579 T, respectively, while less than 97.4% identities with other members of the genus. Further taxonomic analysis indicated that JXJ CY 53 T represented a new member of Sphingomonas, and the species epithet was proposed as Sphingomonas lacusdianchii sp. nov. (type strain JXJ CY 53 T = KCTC 72813 T = CGMCC 1.17657 T). JXJ CY 53 T promoted the growth of MF-905 by providing bio-available phosphorus and nitrogen, plant hormones, vitamins, and carotenoids. It could modulate the relative abundances of nonculturable bacteria associated with MF-905 and influence the interactions of MF-905 and other bacteria isolated from the cyanobacterium, in addition to microcystin production characteristics. Meanwhile, MF-905 could provide JXJ CY 53 T dissolved organic carbon for growth, and control the growth of JXJ CY 53 T by secreting specific chemicals other than microcystins. Overall, these results suggest that the interactions between Microcystis and its attached bacteria are complex and dynamic, and may influence the growth characteristics of the cyanobacterium. This study provided new ideas to understand the interactions between Microcystis and its attached bacteria. KEY POINTS: ⢠A novel bacterium (JXJCY 53 T) was isolated from the cyanosphere of Microcystis sp. FACHB-905 (MF-905) ⢠JXJCY 53 T modulated the growth and microcystin production of MF-905 ⢠MF-905 could control the attached bacteria by specific chemicals other than microcystins (MCs).
Assuntos
Composição de Bases , DNA Bacteriano , Ácidos Graxos , Filogenia , RNA Ribossômico 16S , Sphingomonas , Sphingomonas/metabolismo , Sphingomonas/genética , Sphingomonas/isolamento & purificação , Sphingomonas/classificação , RNA Ribossômico 16S/genética , China , Ácidos Graxos/metabolismo , DNA Bacteriano/genética , Fosfolipídeos/análise , Microcystis/genética , Microcystis/metabolismo , Microcystis/crescimento & desenvolvimento , Lagos/microbiologia , Análise de Sequência de DNA , Técnicas de Tipagem Bacteriana , Simbiose , UbiquinonaRESUMO
Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R2 = 0.465) and clade composition (R2 = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.
Assuntos
Mudança Climática , Microbiologia do Solo , Sphingomonas , Sphingomonas/genética , Sphingomonas/classificação , Sphingomonas/metabolismo , Sphingomonas/isolamento & purificação , California , Ecossistema , Filogenia , Microbiota/genética , Metagenômica , PradariaRESUMO
In an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Based on the 16S rRNA gene sequence, phylogenetic analysis identified the ISS strains as Sphingomonas sanguinis (n = 2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as Sphingomonas paucimobilis. Metagenomic sequence analyses of different ISS locations identified 23 Sphingomonas species. An abundance of shotgun metagenomic reads were detected for S. sanguinis in the location from where the ISS strains were isolated. A complete metagenome-assembled genome was generated from the shotgun reads metagenome, and its comparison with the whole-genome sequences (WGS) of the ISS S. sanguinis isolates revealed that they were highly similar. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with the WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well-characterized Sphingomonas sp. LK11, an arid desert strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, indole-3-acetic acid, was further confirmed in the ISS strains using liquid chromatography-mass spectrometry. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, and oxidative and osmotic stress resistance, appear to be present in these space-related S. sanguinis and S. paucimobilis strains. Characterizing these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future. IMPORTANCESphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the ISS, which are capable of producing the phytohormone indole-3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, and oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology-related applications.
Assuntos
Genômica , Desenvolvimento Vegetal/fisiologia , Sphingomonas/genética , Sphingomonas/isolamento & purificação , Sphingomonas/fisiologia , Ácidos Indolacéticos , Metagenoma , Metagenômica , Filogenia , Desenvolvimento Vegetal/genética , Reguladores de Crescimento de Plantas/genética , RNA Ribossômico 16S , Astronave , Sphingomonas/classificação , Sequenciamento Completo do GenomaRESUMO
Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner's 2A (R2A) agar. The isolates were found to grow at 4-45 °C (optimum, 28-30 °C), at pH 6.0-7.0 (optimum, 7.0) and with 0-1.5â% (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria-Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17â:â1 ω6c, summed feature 8 (C18â:â1 ω7c and/or C18â:â1 ω6c) and C16â:â0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6â%, and 100.0â% average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas, and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3â%). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2â%, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).
Assuntos
Filogenia , Microbiologia do Solo , Sphingomonas , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Clima Desértico , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonas/classificação , Sphingomonas/isolamento & purificaçãoRESUMO
Species belonging to the genus Sphingomonas have been isolated from environments such as soil, water and plant tissues. Many strains are known for their capability of degrading aromatic molecules and producing extracellular polymers. A Gram-stain-negative, strictly aerobic, motile, red-pigmented, oxidase-negative, catalase-positive, rod-shaped strain, designated DH-S5T, has been isolated from pork steak packed under CO2-enriched modified atmosphere. Cell diameters were 1.5×0.9 µm. Growth optima were at 30 °C and at pH 6.0. Phylogenetic analyses based on both complete 16S rRNA gene sequence and whole-genome sequence data revealed that strain DH-S5T belongs to the genus Sphingomonas, being closely related to Sphingomonas alpina DSM 22537T (97.4â% gene sequence similarity), followed by Sphingomonas qilianensis X1T (97.4â%) and Sphingomonas hylomeconis GZJT-2T (97.3â%). The DNA G+C content was 64.4 mol%. The digital DNA-DNA hybridization value between the isolate strain and S. alpina DSM 22537T was 21.0â% with an average nucleotide identity value of 77.03â%. Strain DH-S5T contained Q-10 as the ubiquinone and major fatty acids were C18â:â1 cis 11 (39.3â%) and C16â:â1 cis 9 (12.5â%), as well as C16â:â0 (12.1â%) and C14â:â0 2-OH (11.4â%). As for polar lipids, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, dimethylphosphatidylethanolamine and sphingoglycolipid could be detected, alongside traces of monomethylphosphatidylethanolamine. Based on its phenotypic, chemotaxonomic and phylogenetic characteristics, strain DH-S5T (=DSM 110829T=LMG 31606T) is classified as a representative of the genus Sphingomonas, for which the name Sphingomonas aliaeris sp. nov. is proposed.
Assuntos
Filogenia , Carne de Porco , Sphingomonas , Animais , Atmosfera , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Microbiologia de Alimentos , Alemanha , Fosfolipídeos/química , Pigmentação , Carne de Porco/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingomonas/classificação , Sphingomonas/isolamento & purificação , SuínosRESUMO
Sphingomonas sp. Shah is a bacterium that was first isolated from mammalian cell cultures. According to ribotyping data it is very much homologous to the clinically important pathogen Sphingomonas paucimobilis, which has generated pseudo-outbreaks. Using a tissue culture system, Sphingomonas sp. Shah was discovered to induce apoptosis in human lung epithelial carcinoma. Apoptosis of infected cells was determined by numerous criteria including (1) visual alterations in cellular morphology, (2) initiation of nuclear marginalization and chromatin compaction condensation, (3) the attendance of a high percentage of cells with subG1 DNA content, and (4) caspase-3 activation. In the current study we demonstrate the induction of apoptosis in mammalian lung epithelial cells upon infection with Sphingomonas sp. Shah and provide insight into the molecular processes triggering apoptosis.
Assuntos
Apoptose/fisiologia , Meios de Cultura , Pulmão/citologia , Sphingomonas/isolamento & purificação , Células A549 , Apoptose/genética , Células Epiteliais/citologia , Genes Bacterianos , Humanos , Filogenia , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Sphingomonas/classificação , Sphingomonas/genética , Sphingomonas/fisiologiaRESUMO
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).
Assuntos
Nocardioides/classificação , Nocardioides/isolamento & purificação , Sphingomonas/classificação , Sphingomonas/isolamento & purificação , Animais , Composição de Bases , DNA Bacteriano/genética , DNA Bacteriano/metabolismo , Peixes/microbiologia , Intestinos/microbiologia , Nocardioides/genética , Nocardioides/metabolismo , Fosfolipídeos/metabolismo , Filogenia , República da Coreia , Sphingomonas/genética , Sphingomonas/metabolismoRESUMO
INTRODUCTION AND OBJECTIVE: Ixodes ricinus (I. ricinus) and Dermacentor reticulatus (D. reticulatus) are the most common ticks in Poland. These ticks contain many bacteria, which compose a microbiome with potential impact on humans. The aim of the study was to discover the microbiome of ticks in Poland. MATERIAL AND METHODS: Ticks were collected in The Protected Landscape Area of the Bug and Nurzec Valley, Poland, in 2016-2018 by flagging. They were cleaned in 70% ethanol and damaged in mortar with PBS (without Ca2+ and Mg2+ ions). DNA was extracted from the homogenates with spin columns kits, and used as a matrix in end-point PCR for bacterial 16S rRNA fragments amplifications, and further for next generation sequencing (NGS) by ILLUMINA. RESULTS: In 22 ticks (3 I. ricinus and 19 D. reticulatus) 38 microorganisms were detected. The most common were Francisella hispaniensis and Francisella novicida. In 17 ticks, Sphingomonas oligophenolica, and in 12 Rickettsia aeshlimanii were found. In 2, I. ricinus specific DNA of Borrelia americana and Borrelia carolinensis were found. In one female, D. reticulatus Anaplasma phagocytophilum and Anaplasma centrale were found. Pseudomonas lutea and Ps. moraviensis were detected in 9 and 8 ticks, respectively. CONCLUSIONS: Polish ticks microbiome contains not only well-known tick-borne pathogens, but also other pathogenic microorganisms. For the first time in Poland, Borrelia americana and Borrelia carolinensis in I. ricinus collected from the environment were detected. The dominant pathogenic microorganisms for humans were Francisella spp. and Rickettsia spp., and non-pathogenic - Sphingomonas oligophenolica. Knowledge of a tick microbiome might be useful in tick-borne biocontrol and tick-borne diseases prevention.
Assuntos
Dermacentor/microbiologia , Ixodes/microbiologia , Microbiota , Spirochaetales/genética , Animais , Francisella/classificação , Francisella/genética , Francisella/isolamento & purificação , Genoma Bacteriano , Metagenômica , Polônia , Pseudomonas/classificação , Pseudomonas/isolamento & purificação , Sphingomonas/classificação , Sphingomonas/genética , Sphingomonas/isolamento & purificação , Spirochaetales/classificação , Spirochaetales/isolamento & purificaçãoRESUMO
A novel bacterial strain, designated MAH-20T, was isolated from a soil sample of a tomato garden. Cells of strain MAH-20T were Gram-stain negative, aerobic, motile, and rod-shaped. The colonies were light brown colored, smooth, spherical, and 0.2-0.7 mm in diameter when grown on Luria-Bertani agar for 2 days. Strain MAH-20T grows at 15-40 °C (optimum growth temperature 30-32 °C), at pH 5.0-10.0 (optimum growth pH 7.0) and at 0-2.0% NaCl. The strain showed positive activity for both oxidase and catalase tests. Cells were able to hydrolyze starch, DNA, urea, gelatin, L-arginine, and Tween 20. According to the 16S rRNA gene sequence similarity, the strain MAH-20T was identified as a new member of the genus Sphingomonas and had the close sequence similarity with Sphingomonas changbaiensis V2M44T (98.9%) and Sphingomonas tabacisoli X1-8T (98.1%). The genomic ANI value between strain MAH-20T and S. changbaiensis NBRC 104936T was 84.4%. The novel strain MAH-20T has a draft genome size of 3,350,026 bp (25 contigs), annotated with 3210 protein-coding genes, 46 tRNA, and 3 rRNA genes. The genomic DNA G + C content of isolate was 67.3 mol%, the predominant quinone was ubiquinone 10 and the major fatty acids were C16:0, C17:1 ω6c and summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c). On the basis of DNA-DNA hybridization results, phenotypic, genotypic, and chemotaxonomic data, the isolated strain MAH-20T represents a novel species, for which the name Sphingomonas horti sp. nov. is proposed, with MAH-20T as the type strain (= KACC 19746T = CGMCC1.13658T).
Assuntos
Microbiologia do Solo , Sphingomonas/classificação , Composição de Bases , Ácidos Graxos/análise , Jardins , Solanum lycopersicum/microbiologia , Filogenia , RNA Ribossômico 16S/genética , Especificidade da Espécie , Sphingomonas/genéticaRESUMO
The novel bacterial strain C33T was isolated from a freshwater sample collected from the Hapcheon-Changnyeong barrage. The Gram-negative, motile, yellow-pigmented strain C33T was characterized as a rod-shaped and strictly aerobic bacterium. A 16S-rRNA phylogenetic analysis revealed that this strain was most closely related to Sphingomonas changbaiensis V2M44T, Sphingomonas tabacisoli X1-8T, and Sphingomonas flavalba ZLT-5T with 97.1, 97.0, and 95.0â% 16S-rRNA sequence similarities, respectively. The genomic DNA GC content of strain C33T was estimated at 65.0 mol%. The average nucleotide identity of strain C33T relative to S. changbaiensis V2M44T and S. flavalba ZLT-5T was found to be 77.0 and 75.6%, with average amino-acid identities of 69.9, and 66.7%, and the digital DNA-DNA hybridization values of 21.3 and 17.7â%, respectively. The cells grew at 19-37 °C and pH 6-9 with 0-0.5â% (w/v) NaCl (optimum: 28 °C, pH 6.5, and 0â% NaCl). The major component identified in the polyamine pattern was sym-homospermidine, and the main ubiquinone was Q-10. The predominant polar lipids characterized were diphophatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, and sphingoglycolipid. Iso-C15â:â0, C15â:â0 anteiso, and summed feature 3 (C16â:â1 ω6c and/or C16â:â1 ω7c) were found to be the primary cellular fatty acids in strain C33T. Based on these genotypic and phenotypic characteristics, strain C33T was classified as a novel species of the genus Sphingomonas; and the name Sphingomonas changnyeongensis sp. nov. is proposed (=KACC 21511T=JCM 33880T).
Assuntos
Filogenia , Rios/microbiologia , Sphingomonas/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , República da Coreia , Análise de Sequência de DNA , Espermidina/análogos & derivados , Espermidina/química , Sphingomonas/isolamento & purificaçãoRESUMO
A novel bacterial strain, designated CSW-10T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed yellow-coloured colonies. Optimal growth occurred at 30 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CSW-10T formed a phylogenetic lineage in the genus Sphingomonas. The 16S rRNA gene sequence similarity indicated that strain CSW-10T was most closely related to Sphingomonas fonticola TNR-2T (97.6%). Strain CSW-10T showed 69.8-70.7% average nucleotide identity and 19.0-23.0% digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. The major fatty acids of strain CSW-10T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C17:1 ω6c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized sphingoglycolipid, five uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamines were homospermidine and spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-10T was 62.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CSW-10T should represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lacunae sp. nov. is proposed. The type strain is CSW-10T (=BCRC 81190T =LMG 31340T).
Assuntos
Filogenia , Lagoas/microbiologia , Sphingomonas/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Água Doce/microbiologia , Hibridização de Ácido Nucleico , Fosfolipídeos/química , Pigmentação , Poliaminas/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/química , Sphingomonas/isolamento & purificação , Taiwan , Ubiquinona/análogos & derivados , Ubiquinona/químicaRESUMO
In this study, two endophytic bacterial strains designated JS21-1T and S6-262T isolated from leaves of Elaeis guineensis and stem tissues of Jatropha curcas respectively, were subjected for polyphasic taxonomic approach. On R2A medium, colonies of strains JS21-1T and S6-262T are orange and yellow, respectively. Phylogenetic analyses using 16S rRNA gene sequencing and whole-genome sequences placed the strains in distinct clades but within the genus Sphingomonas. The DNA G + C content of JS21-1T and S6-262T were 67.31 and 66.95%, respectively. Furthermore, the average nucleotide identity and digital DNA-DNA hybridization values of strains JS21-1T and S6-262T with phylogenetically related Sphingomonas species were lower than 95% and 70% respectively. The chemotaxonomic studies indicated that the major cellular fatty acids of the strain JS21-1T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, and C14:0 2OH; strain S6-262T possessed summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c). The major quinone was Q10, and the unique polyamine observed was homospermidine. The polar lipid profile comprised of mixture of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and certain uncharacterised phospholipids and lipids. Based on this polyphasic evidence, strains JS21-1T and S6-262T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas palmae sp. nov. and Sphingomonas gellani sp. nov. are proposed, respectively. The type strain of Sphingomonas palmae sp. nov. is JS21-1T (= DSM 27348T = KACC 17591T) and the type strain of Sphingomonas gellani sp. nov. is S6-262T (= DSM 27346T = âKACC 17594T).
Assuntos
Produtos Agrícolas/microbiologia , Endófitos/classificação , Endófitos/isolamento & purificação , Sphingomonas/classificação , Sphingomonas/isolamento & purificação , Técnicas de Tipagem Bacteriana , Benzoquinonas/análise , DNA Bacteriano/genética , Endófitos/genética , Ácidos Graxos/análise , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Espermidina/análogos & derivados , Espermidina/análise , Sphingomonas/genéticaRESUMO
Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7T and 30C10-4-7T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7T shows 98.0â% sequence similarity to Sphingomonas adhaesiva DSM 7418T, and strain 30C10-4-7T shows highest sequence similarity to Sphingobacterium arenae H-12T (95.6â%). Average nucleotide identity analysis indicates that strain 36D10-4-7T is a novel member different from recognized species in the genus Sphingomonas. The main fatty acids and respiratory quinone detected in strain 36D10-4-7T are C18â:â1 ω7c and/or C18â:â1 ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7T, the major fatty acids and menaquinone are iso-C15â:â0, C16â:â1 ω7c and/or C16â:â1 ω6c and iso-C17â:â0 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 36D10-4-7T=CFCC 13112T=KCTC 52799T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7T=CFCC 13069T=KCTC 52797T) are proposed.
Assuntos
Filogenia , Casca de Planta/microbiologia , Doenças das Plantas/microbiologia , Populus/microbiologia , Sphingobacterium/classificação , Sphingomonas/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sphingobacterium/isolamento & purificação , Sphingomonas/isolamento & purificação , Ubiquinona/análogos & derivados , Ubiquinona/químicaRESUMO
A Gram-stain-negative, aerobic, motile strain, HHU CXWT, was isolated from hair of a healthy 21-year-old female student of Hohai University, Nanjing, China. The 16S rRNA gene sequence analysis indicated that HHU CXWT represents a member of the genus Sphingomonas with the highest sequence similarity (97.6%) to the type strain S. aquatilis JSS7T. HHU CXWT grew at 4-35 °C and pH 6-8, with optimum growth at 28 °C and pH 7. Tolerance to NaCl was up to 2% (w/v) with optimum growth in 0.5-1.0% NaCl. The major fatty acids were C16:0, C17:1ω6c, C18:1ω7c11-methyl, summed feature 3 (C16:1ω7c and/or C16:1ω6c), and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The predominant isoprenoid quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), sphingoglycolipid (SGL), phosphatidylinositol mannosides (PIM), and an unidentified glycolipid (GL). The DNA G + C content was 67.1%. The average nucleotide identity (ANI) values and digital DNA-DNA hybridization (dDDH) between HHU CXWT and closely related members of the genus Sphingomonas were all below the cut-off level (95-96% and 70%, respectively) for species delineation. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, HHU CXWT represents a novel species of the genus Sphingomonas, for which the name Sphingomonas hominis sp. nov. is proposed. The type strain is HHU CXWT (= KCTC 72946T = CGMCC 1.17504T = MCCC 1K04223T).
Assuntos
Cabelo/microbiologia , Sphingomonas/isolamento & purificação , Técnicas de Tipagem Bacteriana , Feminino , Genômica/métodos , Humanos , Tipagem de Sequências Multilocus , Fenótipo , Filogenia , RNA Ribossômico 16S/genética , Sphingomonas/química , Sphingomonas/classificação , Sphingomonas/genética , Adulto JovemRESUMO
A strain LZ1, which showed efficient asymmetric reduction of 3,5-bis(trifluoromethyl) acetophenone to enantiopure (S)-[3,5-bis(trifluoromethyl)phenyl]ethanol, which is the key intermediate for the synthesis of a receptor antagonist and antidepressant, was isolated from a soil sample. Based on its morphological, 16S rDNA sequence, and phylogenetic analysis, the strain LZ1 was identified to be Sphingomonas sp. LZ1. To our knowledge, this is the first reported case of the species Sphingomonas exhibiting stricter S-enantioselectivity and its use for the asymmetric reduction of 3,5-bis(trifluoromethyl) acetophenone. Some key reaction parameters involved in the bioreduction catalyzed by whole cells of Sphingomonas sp. LZ1 were subsequently optimized, and the optimized conditions for the synthesis of (S)-[3,5-bis(trifluoromethyl)phenyl]ethanol were determined to be as follows: phosphate buffer pH 7.5, 70 mM of 3,5-bis(trifluoromethyl) acetophenone, 30 g/L of glucose as a co-substrate, 300 g (wet weight)/L of resting cell as the biocatalyst, and a reaction for 24 h at 30°C and 180 rpm. Under the above conditions, a best yield of 94% and an excellent enantiomeric excess of 99.6% were obtained, respectively. Sphingomonas sp. LZ1 could also asymmetrically reduce a variety of prochiral ketones to their corresponding optical alcohols with excellent enantioselectivity. These results indicated that Sphingomonas sp. LZ1 had a remarkable capacity to reduce 3,5-bis(trifluoromethyl)acetophenone to its corresponding (S)-[3,5-bis(trifluoromethyl)phenyl]ethanol, and might be a new potential biocatalyst for the production of valuable chiral alcohols in industry.
Assuntos
Álcoois/metabolismo , Sphingomonas/classificação , Sphingomonas/metabolismo , Acetofenonas/química , Acetofenonas/metabolismo , Álcoois/química , Biocatálise , Concentração de Íons de Hidrogênio , Cetonas/química , Cetonas/metabolismo , Filogenia , RNA Ribossômico 16S/genética , Sphingomonas/genética , Sphingomonas/isolamento & purificação , Estereoisomerismo , Especificidade por Substrato , TemperaturaRESUMO
A Gram staining-negative, yellow-colored, rod-shaped, non-motile and aerobic, designated strain 17J27-24T was isolated from a soil sample in Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 17J27-24T was related to the members of the family Sphingomonadaceae and formed a distinct monophyletic cluster within the genus Sphingomonas with Sphingomonas deserti (98.3% 16S rRNA gene sequence similarity). Growth was observed at 30 °C (optimum), at pH 7.0 (optimum), and in the absence of NaCl (%). The predominant cellular fatty acids were summed feature 8 (18:1 ω7c and/or 18:1 ω6c) and C17:1 ω6c. The major respiratory quinone was Q10. The polar lipids profile comprised of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and sphingoglycolipid (SGL). The DNA G + C content was 77.8 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between 17J27-24T and its phylogenetically closest Sphingomonas deserti (KCTC 62411T) were below the established cut-off < 94% (ANI) and < 70% (dDDH) for species delineation. Moreover, the results of the polyphasic approach confirmed that strain 17J27-24T represents a novel species of the genus Sphingomonas within the family Sphingomonadaceae, for which the name Sphingomonas parva sp. nov. is proposed. The type strain of this species is 17J27-24T (= KCTC 62208T = JCM 3896T). An emended description of the species Sphingomonas parva is provided.
Assuntos
Filogenia , Microbiologia do Solo , Sphingomonas/classificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/análise , Hibridização de Ácido Nucleico , Quinonas/análise , RNA Ribossômico 16S/genética , República da Coreia , Especificidade da Espécie , Sphingomonas/genéticaRESUMO
A Gram-stain-negative bacterium, designated strain YJ09T, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09T were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5â% (w/v) NaCl (optimum, 0â% NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09T belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 T (98.0â%), Sphingomonas agri HKS-06T (97.7â%) and Sphingomonas lutea JS5T (97.4â%). The results of phylogenetic analysis indicated that strain YJ09T formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09T could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C18:1 ω7c, C16â :â0 and C16:1 ω7c and/or iso-C15â:â0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09T is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09T (=KACC 19551T=NBRC 113247T).