A novel selective growth medium-PCR assay to isolate and detect Sphingomonas in environmental samples

Modulation of Terpenoid Indole Alkaloid Biosynthesis in Catharanthus roseus by Sphingomonas Sp Y503 via the CrMAPKKK1-CrMAPKK1/CrMAPKK2-CrMPK3 Signaling Cascade

Catharanthus roseus is a highly relevant model for investigating plant defense mechanisms and the biosynthesis of therapeutically valuable compounds, including terpenoid indole alkaloids (TIAs). It has been demonstrated that beneficial microbial interactions can regulate TIA biosynthesis in C. roseus, highlighting the need to fully comprehend the molecular mechanisms involved to efficiently implement eco-friendly strategies. This study explores the effects of a novel microbial strain, Y503, identified as Sphingomonas sp., on TIA production and the underlying mechanisms in C. roseus. Through bioinformatics analysis, we have identified 17 MAPKKKs, 7 MAPKKs, and 13 MAPKs within the C. roseus genome. Further investigation has verified the presence of the MAPK module (CrMAPKKK1-CrMAPKK1/CrMAPKK2-CrMPK3) mediating Y503 in regulating TIA biosynthesis in C. roseus. This study provides foundational information for strengthening the plant defense system in C. roseus through advantageous microbial interactions, which could contribute to the sustainable cultivation of medicinal plants such as C. roseus.

Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential

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.

Diversity of bacteria of the genus Sphingomonas associated with sugarcane (Saccharum spp.) culm apoplast fluid and their agrotechnological potential

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.

Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.

The perfluoroalkyl substances influenced the distribution of bacterial communities and their functions from source water to tap water

Perfluoroalkyl substances (PFASs) and antibiotic resistance genes (ARGs) in drinking water are environmental issues that require special attention. The objective of this study was to know the effects of PFASs on microbial communities and their functional genes from source water to tap water. PFASs were detected by mass-labeled internal standards method, and the microbial communities and functional genes were analyzed by metagenomics. Our results indicated that the concentration of total PFASs in the water ranged from 47.7 to 171.4 ng/L, with perfluorobutanoic acid (PFBA) and perfluorooctanoic acid (PFOA) being the dominant types. The PFASs concentration decreased slowly from source to tap water in some months. PFBA, PFOA, perfluorooctane sulfonic acid (PFOS) and perfluorohexanoic acid (PFHxA) influenced the functional genes related to two-component system, bacterial secretion system and flagellar assembly of Aquabacterium, Methylobacterium, and Curvibacter, which contributed significantly to macB and evgS. Therefore, the bacterial communities enhanced adaptation to fluctuating environments by upregulating some functional genes under the PFASs stress, with concomitant changes in the expression of ARGs. Moreover, PFASs also promoted the expression of functional genes associated with human diseases, such as shigellosis and tuberculosis, which increased the risk of human pathogenicity. The bench scale experiment results also suggested that PFOA and PFOS in drinking water can promote the ARGs proliferation and induce microbial risk. Therefore, it is necessary to take measures to prevent the risks caused by PFASs and ARGs in drinking water.

Does nest occupancy by birds influence the microbial composition?

Nest microbiota plays a vital role in the breeding and development of birds, which not only provides protection to bird hosts but also negatively affects the host. At present, it is unclear whether the composition of the microbes in the nests is affected by nesting. For this reason, we hung artificial nest boxes to simulate the natural nesting environment and combined 16S rRNA and ITS high-throughput sequencing technology to further study the differences in microbial composition and richness between used nests and control nests of Japanese tits (Parus minor). The study found that the bacteria in used nests and control nests showed significant differences at the phylum level (p < 0.05). It is also worth noting that the predominant bacteria in used nests were Proteobacteria (51.37%), Actinobacteria (29.72%), Bacteroidetes (6.59%), and Firmicutes (3.82%), while the predominant bacteria in control nests were Proteobacteria (93.70%), Bacteroidetes (2.33%), and Acidobacteria (2.06%). Both used nests and control nests showed similar fungi at the phylum level, which consisted mainly of Ascomycota and Basidiomycota, although significant differences were found in their relative abundance between both groups. The results of alpha diversity analysis showed significant differences in bacteria between the two groups and not in fungi. However, the beta diversity analysis showed significant differences between both bacteria and fungi. In summary, our results showed that the used nests had a higher abundance of beneficial microbiota and a lower presence of pathogenic microbiota. Therefore, we speculate that birds will change the characteristics of the nest microbial composition in the process of nest breeding to ensure their smooth reproductive development.

Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield

Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.

Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus

Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages-particularly those targeting phyllosphere-associated bacteria-remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.

Frankenbacteriosis targeting interactions between pathogen and symbiont to control infection in the tick vector

Tick microbiota can be targeted for the control of tick-borne diseases such as human granulocytic anaplasmosis (HGA) caused by model pathogen, Anaplasma phagocytophilum. Frankenbacteriosis is inspired by Frankenstein and defined here as paratransgenesis of tick symbiotic/commensal bacteria to mimic and compete with tick-borne pathogens. Interactions between A. phagocytophilum and symbiotic Sphingomonas identified by metaproteomics analysis in Ixodes scapularis midgut showed competition between both bacteria. Consequently, Sphingomonas was selected for frankenbacteriosis for the control of A. phagocytophilum infection and transmission. The results showed that Franken Sphingomonas producing A. phagocytophilum major surface protein 4 (MSP4) mimic pathogen and reduce infection in ticks by competition and interaction with cell receptor components of infection. Franken Sphingomonas-MSP4 transovarial and trans-stadial transmission suggests that tick larvae with genetically modified Franken Sphingomonas-MSP4 could be produced in the laboratory and released in the field to compete and replace the wildtype populations with associated reduction in pathogen infection/transmission and HGA disease risks.

Intratumor Microbiome Analysis Identifies Positive Association Between Megasphaera and Survival of Chinese Patients With Pancreatic Ductal Adenocarcinomas

Human tumors harbor a plethora of microbiota. It has been shown that the composition and diversity of intratumor microbiome are significantly associated with the survival of patients with pancreatic ductal adenocarcinoma (PDAC). However, the association in Chinese patients as well as the effect of different microorganisms on inhibiting tumor growth are unclear. In this study, we collected tumor samples resected from long-term and short-term PDAC survivors and performed 16S rRNA amplicon sequencing. We found that the microbiome in samples with different survival time were significantly different, and the differential bacterial composition was associated with the metabolic pathways in the tumor microenvironment. Furthermore, administration of Megasphaera, one of the differential bacteria, induced a better tumor growth inhibition effect when combined with the immune checkpoint inhibitor anti-programmed cell death-1 (anti-PD-1) treatment in mice bearing 4T1 tumor. These results indicate that specific intratumor microbiome can enhance the anti-tumor effect in the host, laying a foundation for further clarifying the underlying detailed mechanism.

Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H218O-based DNA-Stable isotope probing and metagenomics

The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H₂¹⁸O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.

Enhanced fluoroglucocorticoid removal from groundwater in a bio-electrochemical system with polyaniline-loaded activated carbon three-dimensional electrodes: Performance and mechanisms

This study aimed to investigate the removal performance and mechanisms of dexamethasone (DEX), a representative fluoroglucocorticoid (FGC), from micro-polluted oligotrophic groundwater in a bio-electrochemical system amended with polyaniline-loaded activated carbon (PANI@AC) as three-dimensional particle electrodes (BES-3D). The BES-3D achieved a DEX removal efficiency of 95.7%, which was 39.0% and 14.1% higher than that of a single biological system (SBIO) and two-dimensional bio-electrochemical system (BES-2D), respectively. The preliminary metabolic mechanism of defluorination accounted for 53.5%, 41.1%, and 16.3% in BES-3D, BES-2D, and SBIO, respectively, which was accompanied by demethylation, side-chain fracture, and hydroxyl oxidation for ketone formation and final-ring opening. The main mechanism by which removal was improved in BES-3D was the enrichment of functional microbes and enhancement of the expression of dehalogenation genes. The relative abundance of functional microbes with electron transfer ability and reductive dehalogenating genera, i.e., Pseudomonas, Methylotenera, Desulfuromonas, Sphingomonas, and Microbacterium, in BES-3D was 3.7-6.1 times higher and the copy number of functional genes was 1.9 times higher than those of SBIO, which contributed to the high DEX removal.

Cultivation and characterization of snowbound microorganisms from the South Pole

Little is known about microbial ecosystems of interior Antarctica, if indeed such ecosystems exist. Although considerable research has assessed microorganisms indigenous to coastal regions of Antarctica, particularly their lakes, ponds, and soils, to our knowledge only one characterized bacterium, a strain of Pseudomonas, has been isolated from South Pole ice or snow. Metagenomic community analyses described in this work and elsewhere reveal that a diversity of bacteria exists in inland polar snows, yet attempts to culture and characterize these microbes from this extreme environment have been few to date. In this molecular and culture-dependent investigation of the microbiology of inland Antarctica, we enriched and isolated two new strains of bacteria and one strain of yeast (Fungi) from South Pole snow samples. The bacteria were of the genera Methylobacterium and Sphingomonas, and the yeast grouped with species of Naganishia (class Tremellocytes). In addition to phylogenetic analyses, characterization of these isolates included determinations of cell morphology, growth as a function of temperature, salinity tolerance, and carbon and energy source versatility. All organisms were found to be cold-adapted, and the yeast strain additionally showed considerable halotolerance. These descriptions expand our understanding of the diversity and metabolic activities of snowbound microorganisms of interior Antarctica.

Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench

A Gram-stain-negative, short rod-shaped, yellow bacterium (strain LMO-1^T) was isolated from deep-sea sediment of the Mariana Trench, Challenger Deep. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LMO-1^T belonged to genus Sphingomonas, with the highest sequence similarity to Sphingomonas formosensis CC-Nfb-2^T (96.3 %), followed by Sphingomonas prati W18RD^T (96.1 %), Sphingomonas arantia 6P^T (96.0 %) and Sphingomonas montana W16RD^T (95.9 %). The predominant polar lipids were phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol and phosphatidylcholine. The main cellular fatty acids were summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c), C_16 : 0 and C_14 : 0 2-OH. The major polyamine was sym-homospermidine and the predominant isoprenoid quinone was ubiquinone-10. The genome DNA G+C content of strain LMO-1^T was 69.2 mol%. The average nucleotide identity and DNA-DNA hybridization values between strain LMO-1^T and CC-Nfb-2^T were 75.9 and 20.5 %, respectively. Based on these data, LMO-1^T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas profundi sp. nov. is proposed. The type strain is LMO-1^T (=MCCC 1K04066^T=JCM 33666^T).

Enhanced reductive defluorination and inhibited infiltration of fluoroglucocorticoids in a river receiving reclaimed water amended by nano zero-valent iron-modified biochar: Performance and mechanisms

The main aim of this study was to investigate the effect of a nano zero-valent iron-modified biochar-amended composite riverbed (nZVI@BC-R) on inhibited infiltration and enhanced biodegradation of fluoroglucocorticoids (FGCs) in a river receiving reclaimed water. The results demonstrated that the removal efficiency of triamcinolone acetonide (TA), a representative FGC, increased from 38.40% and 77.91% to 91.60% in the nZVI@BC-R compared with that of a natural soil riverbed (S-R) and biochar-amended soil riverbed (BC-R). The main removal mechanismwas attributedto adsorption and biodegradation, of which the contribution rates were 32.2% and 59.4% in nZVI@BC-R, 18.9% and 19.5% in S-R, and 24.4% and 53.5% in BC-R, respectively. The removal process could be described by a two-compartment, first-order dynamic model with decay rate constants for adsorption and biodegradation of 4.02700, 22.44400, and 29.07300 d-1 and 0.00286, 0.01562, and 0.03484 d-1 in the S-R, BC-R and nZVI@BC-R, respectively. The mechanism of defluorination accounted for 42.2% of biodegradation in the nZVI@BC-R, which was accompanied by side-chain rupture, oxidation, and ringopening. Functional microbes with iron oxidizing ability and reductive dehalogenating genera, namely Pseudoxanthomonas, Pedobacter, and Bosea, contributed to the high removal rate of TA, particularly in the nZVI@BC-R. Overall, the nZVI@BC-R provided an effective method to inhibit glucocorticoids infiltration into groundwater.

Isolation and characterization of Sphingomonadaceae from fouled membranes

Membrane filtration systems are widely applied for the production of clean drinking water. However, the accumulation of particles on synthetic membranes leads to fouling. Biological fouling (i.e., biofouling) of reverse osmosis and nanofiltration membranes is difficult to control by existing cleaning procedures. Improved strategies are therefore needed. The bacterial diversity on fouled membranes has been studied, especially to identify bacteria with specialized functions and to develop targeted approaches against these microbes. Previous studies have shown that Sphingomonadaceae are initial membrane colonizers that remain dominant while the biofilm develops. Here, we characterized 21 Sphingomonadaceae isolates, obtained from six different fouled membranes, to determine which physiological traits could contribute to colonization of membrane surfaces. Their growth conditions ranged from temperatures between 8 and 42 oC, salinity between 0.0 and 5.0% w/v NaCl, pH from 4 and 10, and all isolates were able to metabolize a wide range of substrates. The results presented here show that Sphingomonadaceae membrane isolates share many features that are uncommon for other members of the Sphingomonadaceae family: all membrane isolates are motile and their tolerance for different temperatures, salt concentrations, and pH is high. Although relative abundance is an indicator of fitness for a whole group, for the Sphingomonadaceae it does not reveal the specific physiological traits that are required for membrane colonization. This study, therefore, adds to more fundamental insights in membrane biofouling.

Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta)

A polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539^T) isolated from the chopped tuber of taro (Colocasia esculanta) in Taiwan. Strain CC-MHH0539^T was able to grow at 15-30 °C (optimum, 25 °C), at pH 6.0-9.0 (optimum, 7.0) and with 0-1 % (w/v) NaCl. Strain CC-MHH0539^T showed highest 16S rRNA gene sequence similarity to Sphingomonas laterariae LNB2^T (96.8 %), Sphingobium boeckii 469^T (96.5 %), Sphingomonas faucium E62-3^T (96.4 %) and Sphingosinicella vermicomposti YC7378^T (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539^T was found to cluster mainly with the clade that accommodated members of the genus Sphingomonas. The dominant cellular fatty acids were C16 : 0, C16 : 1ω5c, C14 : 0 2-OH, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglycolipids and two unidentified phospholipids were detected in strain CC-MHH0539^T. The DNA G+C content was 69.5 mol%. The respiratory quinone system and predominant polyamine was ubiquinone 10 (Q-10) and sym-homospermidine, respectively, which is in line with Sphingomonas representatives. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, strain CC-MHH0539^T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas colocasiae sp. nov. is proposed. The type strain is CC-MHH0539^T (=BCRC 80933^T=JCM 31229^T).

The first characterized phage against a member of the ecologically important sphingomonads reveals high dissimilarity against all other known phages

This study describes the first molecular characterization of a bacteriophage infecting a member of the environmentally important Sphingomonadaceae family. Both bacteriophage Lacusarx and its host Sphingobium sp. IP1 were isolated from activated sludge from a wastewater treatment plant. Genome sequencing revealed that the phage genes display little similarity to other known phages, despite a remarkable conservation of the synteny in which the functional genes occur among distantly related phages. Phylogenetic analyses confirmed that Lacusarx represents a hitherto undescribed genus of phages. A classical lysis cassette could not be identified in Lacusarx, suggesting that the genes encoding endolysin, holin, and spanin are host-specific and not found in phages infecting other bacteria. The virus harbors 24 tRNA genes corresponding to 18 different amino acids and furthermore has a significantly different codon usage than its host. Proteomic analysis of Lacusarx revealed the protein components of the phage particle. A lysogeny test indicated that Lacusarx is not a temperate phage.

Biofilm forming ability of Sphingomonas paucimobilis isolated from community drinking water systems on plumbing materials used in water distribution

Sphingomonas paucimobilis, an oligotroph, is well recognized for its potential for biofilm formation. The present study explored the biofilm forming ability of a strain isolated from municipal drinking water on plumbing materials. The intensity of biofilm formation of this strain on different plumbing materials was examined by using 1 × 1 cm² pieces of six different pipe materials, i.e. polyvinyl chloride (PVC), polypropylene (PP), polyethylene (PE), aluminium (Al), copper (Cu) and rubber (R) and observing by staining with the chemical chromophore, Calcofluor. To understand whether biofilm formation occurs under flow through conditions, a laboratory-scale simulated distribution system, comprised of the above materials was fabricated. Biofilm samples were collected from the designed system at different biofilm ages (10, 40 and 90 hours old) and enumerated. The results indicated that the biofilm formation occurred on all plumbing materials with Cu and R as exceptions. The intensity of biofilm formation was found to be maximum on PVC followed by PP and PE. We also demonstrated the chemical chromophore (Calcofluor) successfully for rapid and easy visual detection of biofilms, validated by scanning electron microscope (SEM) analysis of the plumbing materials. Chlorination has little effect in preventing biofilm development.

Sphingomonas carri sp. nov., isolated from a car air-conditioning system

A Gram-stain-negative, yellow-pigmented bacterial strain, designated PR0302^T, was isolated from a car evaporator core collected in Korea. The cells were strictly aerobic, non-spore-forming and rod-shaped. The strain grew at 15-37 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, 7.0) and in the presence of 0-1 % (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Sphingomonas(97.04-91.22 % 16S rRNA gene sequence similarities) and showed the highest sequence similarity of 97.04 % to Sphingomonas kyeonggiensis THG-DT81^T. It contained C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C14 : 0 2-OH as the predominant fatty acids and Q-10 as the major ubiquinone. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The major polyamine was sym-homospermidine. The serine palmitoyl transferase gene (spt) was detected and sphingolipid synthesis was confirmed. The mean DNA G+C content of the strain was 67.8±0.5 mol%. DNA-DNA relatedness between strain PR0302^T and closely related type strains of Sphingomonas species was less than 30 %. The low levels of DNA-DNA relatedness identified strain PR0302^T as a member of a novel species in the genus Sphingomonas. Based on phenotypic, genotypic and chemotaxonomic data, strain PR0302^T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas carri sp. nov. is proposed. The type strain is PR0302^T (=KACC 18487^T=NBRC 111532^T).

Monitoring of biofilm aging in a Sphingomonas sp. strain from public drinking water sites through changes in capacitance

This study reports the applicability of a capacitance-based technique for evaluating the biofilm progression of Sphingomonas sp. One hundred and forty isolates of Sphingomonas were screened from public drinking water sites, and one potential strain with biofilm-forming ability was used for the study. The biofilm production by this strain was established in microtiter plates and aluminum coupons. The standard biofilm-forming strain Sphingomonas terrae MTCC 7766 was used for comparison. Changes in biofilm were analyzed by energy-dispersive X-ray spectroscopy (EDX) and scanning electron microscope (SEM). Capacitance values were measured at 1, 100 and 200 kHz frequency; however, 1 kHz was selected since resulted in reproducible values, which could be correlated to biofilm age measured as dry weight over a time of 96 h (4 days) depicting the biofilm growth/progression over time. The EDX, SEM and capacitance values obtained in parallel indicated the related physiological profile usually displayed by biofilms upon growth, suggesting authenticity to the observed capacitance profile. The results of this study demonstrated the feasibility of a capacitance-based method for analyzing biofilm development/progression by Sphingomonas sp. and suggested a simple approach for developing an online system to detect biofilms by this opportunistic pathogen of concern in drinking water.

Draft Genome Sequence of Sphingomonas sp. Strain Sph1(2015), Isolated from a Fouled Membrane Filter Used To Produce Drinking Water

We report here the high-quality draft genome sequence of Sphingomonas sp. strain Sph1(2015), isolated from a fouled reverse osmosis membrane used for the production of high-quality drinking water. The draft sequence provides insights into the modus operandi of this strain to form biofilms on membrane surfaces. This knowledge offers tools to develop novel antifouling strategies.

Sphingomonas from petroleum-contaminated soils in Shenfu, China and their PAHs degradation abilities

Members of the Sphingomonas genus are often isolated from petroleum-contaminated soils due to their unique abilities to degrade polycyclic aromatic hydrocarbons (PAHs), which are important for in situ bioremediation. In this study, a combined phenotypic and genotypic approach using streptomycin-containing medium and Sphingomonas-specific PCR was developed to isolate and identify culturable Sphingomonas strains present in petroleum-contaminated soils in the Shenfu wastewater irrigation zone. Of the 15 soil samples examined, 12 soils yielded yellow streptomycin-resistant colonies. The largest number of yellow colony-forming units (CFUs) could reach 10⁵ CFUs g⁻¹ soil. The number of yellow CFUs had a significant positive correlation (p < 0.05) with the ratio of PAHs to total petroleum hydrocarbons (TPH), indicating that Sphingomonas may play a key role in degrading the PAH fraction of the petroleum contaminants at this site. Sixty yellow colonies were selected randomly and analyzed by colony PCR using Sphingomonas-specific primers, out of which 48 isolates had PCR-positive signals. The 48 positive amplicons generated 8 distinct restriction fragment length polymorphism (RFLP) patterns, and 7 out of 8 phylotypes were identified as Sphingomonas by 16S rRNA gene sequencing of the representative strains. Within these 7 Sphingomonas strains, 6 strains were capable of using fluorene as the sole carbon source, while 2 strains were phenanthrene-degrading Sphingomonas. To the best of our knowledge, this is the first report to evaluate the relationship between PAHs contamination levels and culturable Sphingomonas in environmental samples.

Isolation and characterisation of a Sphingomonas strain able to degrade the fungicide ortho-phenylphenol

BACKGROUND

Ortho-phenylphenol (OPP) is a fungicide used in fruit packaging plants for the control of fungal infestations during storage. Its application leads to the production of large wastewater volumes which according to the European legislation should be treated on site. In spite of this, no efficient treatment systems are currently available, and the development of biological systems based on tailored-made pesticide-degrading inocula for the treatment of these wastewaters is an appealing solution.

RESULTS

Enrichment cultures from a soil collected from a wastewater disposal site resulted in the isolation of a pure Sphingomonas haloaromaticamans strain P3 able to degrade rapidly OPP and use it as an energy source. Its degrading capacity was dependent on the external supply of amino acids or on the presence of other bacteria that did not contribute to fungicide degradation. The isolated S. haloaromaticamans strain was able to metabolise up to 150 mg L(-1) of OPP within 7 days, in a wide range of pH (4.5-9) and temperatures (4-37 °C), and in the presence of other pesticides (thiabendazole and diphenylamine) co-used in the fruit packaging industry.

CONCLUSION

Overall, the OPP-degrading bacterium isolated showed high potential for use in future biodepuration treatment systems and bioremediation strategies.

Sphingomonas arantia sp. nov., isolated from Hoh Xil basin, China

A Gram-negative, rod-shaped, non-motile, non-spore forming, aerobic, orange-pigmented bacterium, designated strain 6P(T), was isolated from a soil sample collected from the Hoh Xil basin, China. Strain 6P(T) grew optimally at 25 °C, pH 7.0-7.5 and NaCl concentration of 0-1 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6P(T) belongs to the genus Sphingomonas, with high sequence similarity (97.1 %) to Sphingomonas fennica. The DNA-DNA hybridization homology with S. fennica DSM 13665(T) was 45.3 %. The DNA G+C content of the novel strain is 65.3 mol%. The isolate contained Q-10 as the only respiratory quinone. The major polar lipids are diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and sphingoglycolipid (SGL). C18:1 ω7c and C16:1 ω7c are the major fatty acids. On the basis of the polyphasic evidence presented, strain 6P(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas arantia sp. nov. is proposed. The type strain is 6P(T) (=CGMCC 1.12702(T) = JCM 19855(T)).

Sphingosinicella cucumeris sp. nov., isolated from soil of a cucumber garden

A novel bacterial strain, THG-sc1(T), was isolated from a soil sample of a cucumber garden and was characterised by using a polyphasic approach. Cells were observed to be Gram-stain negative, non-motile and rod-shaped. The strain was found to be aerobic, catalase and oxidase positive, esculin and starch negative, and to have an optimum growth temperature and pH of 28 °C and 7.5, respectively. On the basis of 16S rRNA gene sequence analysis, strain THG-sc1(T) was found to belong to the genus Sphingosinicella and to be closely related to Sphingosinicella vermicomposti KCTC 22446(T), followed by Sphingosinicella xenopeptidilytica DSM 17130(T) and Sphingosinicella microcystinivorans KCTC 12019(T). The DNA G+C content was determined to be 60.8 mol% and the predominant respiratory quinone was identified as ubiquinone-10. The major polyamine was found to be sym-homospermidine. The major polar lipids were identified as sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid. The major fatty acids were identified as C(18:1)ω7c, C(16:0) and summed feature 3 (C(16:1)ω7c and/or iso-C(15:0) 2-OH, as defined by MIDI). The results of the genotypic analysis, in combination with chemotaxonomic and physiological data, demonstrated that strain THG-sc1(T) represents a novel species within the genus Sphingosinicella, for which the name Sphingosinicella cucumeris is proposed. The type strain is THG-sc1(T) (=KACC 18279(T) = CCTCC AB 2015120(T)).

Endophytic bacterial community of grapevine leaves influenced by sampling date and phytoplasma infection process

BACKGROUND

Endophytic bacteria benefit host plant directly or indirectly, e.g. by biocontrol of the pathogens. Up to now, their interactions with the host and with other microorganisms are poorly understood. Consequently, a crucial step for improving the knowledge of those relationships is to determine if pathogens or plant growing season influence endophytic bacterial diversity and dynamic.

RESULTS

Four healthy, four phytoplasma diseased and four recovered (symptomatic plants that spontaneously regain a healthy condition) grapevine plants were sampled monthly from June to October 2010 in a vineyard in north-western Italy. Metagenomic DNA was extracted from sterilized leaves and the endophytic bacterial community dynamic and diversity were analyzed by taxon specific real-time PCR, Length-Heterogeneity PCR and genus-specific PCR. These analyses revealed that both sampling date and phytoplasma infection influenced the endophytic bacterial composition. Interestingly, in June, when the plants are symptomless and the pathogen is undetectable (i) the endophytic bacterial community associated with diseased grapevines was different from those in the other sampling dates, when the phytoplasmas are detectable inside samples; (ii) the microbial community associated with recovered plants differs from that living inside healthy and diseased plants. Interestingly, LH-PCR database identified bacteria previously reported as biocontrol agents in the examined grapevines. Of these, Burkholderia, Methylobacterium and Pantoea dynamic was influenced by the phytoplasma infection process and seasonality.

CONCLUSION

Results indicated that endophytic bacterial community composition in grapevine is correlated to both phytoplasma infection and sampling date. For the first time, data underlined that, in diseased plants, the pathogen infection process can decrease the impact of seasonality on community dynamic. Moreover, based on experimental evidences, it was reasonable to hypothesize that after recovery the restructured microbial community could maintain the main structure between seasons.

Interactions of glycosphingolipids and lipopolysaccharides with silica and polyamide surfaces: adsorption and viscoelastic properties

Bacterial outer membrane components play a critical role in bacteria-surface interactions (adhesion and repulsion). Sphingomonas species (spp.) differ from other Gram-negative bacteria in that they lack lipopolysaccharides (LPSs) in their outer membrane. Instead, Sphingomonas spp. outer membrane consists of glycosphingolipids (GSLs). To delineate the properties of the outer membrane of Sphingomonas spp. and to explain the adhesion of these cells to surfaces, we employed a single-component-based approach of comparing GSL vesicles to LPS vesicles. This is the first study to report the formation of vesicles containing 100% GSL. Significant physicochemical differences between GSL and LPS vesicles are reported. Composition-dependent vesicle adherence to different surfaces using quartz crystal microbalance with dissipation monitoring (QCM-D) technology was observed, where higher GSL content resulted in higher mass accumulation on the sensor. Additionally, the presence of 10% GSL and above was found to promote the relative rigidity of the vesicle obtaining viscoelastic ratio of 30-70% higher than that of pure LPS vesicles.

Description of a Gram-negative bacterium, Sphingomonas guangdongensis sp. nov

A Gram-stain-negative bacterial strain, designated 9NM-8T, was isolated from an abandoned lead-zinc ore in Mei county, Meizhou, Guangdong province, PR China. The isolate was orange-pigmented, aerobic, oxidase- and catalase-positive, motile with lophotrichous flagella and rod-shaped. Strain 9NM-8T grew optimally at pH 7.0 and 30 °C and in the absence of NaCl on R2A agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 9NM-8T belongs to the genus Sphingomonas , with highest sequence similarities to Sphingomonas azotifigens KACC 14484T (96.1 %), Sphingomonas trueperi DSM 7225T (96.0 %) and Sphingomonas pituitosa DSM 13101T (95.6 %). Strain 9NM-8T contained Q-10 as the predominant ubiquinone. The major fatty acids included C18 : 1ω7c, C16 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and 11-methyl C18 : 1ω7c. The DNA G+C content was 69.6±1.3 mol%. The major component in the polyamine pattern was sym-homospermidine and the polar lipid profile contained sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and two unidentified phospholipids. Based on comparative analysis of physiological, chemotaxonomic and phylogenetic characteristics, strain 9NM-8T should be considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas guangdongensis sp. nov. is proposed. The type strain is 9NM-8T ( = GIMCC 1.653T = CGMCC 1.12672T = DSM 27570T).

Impacts of different salinities on bacterial biofilm communities in fresh water

Natural and anthropogenic salinization continuously impacts inland aquatic ecosystems. Associated bacterial biofilms respond rapidly to environmental conditions and are potential bioindicators for changes in water quality. This study evaluates the effects of different salinity concentrations (0.3‰–10‰) on bacterial biofilms communities grown in fresh water from Lake Bosten. Bacterial communities associated with biofilms were analyzed using terminal restriction fragment length polymorphism and clone library analyses of 16S rRNA genes. Results indicated that the attached bacterial community composition (ABCC) changed over several weeks of biofilm growth, but all followed similar bacterial successional trends in the different salinity groups. Detailed analysis showed the following. (i) ABCC did not differ (P > 0.05) in the low-salinity groups (0.3‰–3.5‰), which may be related to the lower osmotic pressure and the shorter time scale (weeks) of their present habitats. (ii) There were significant differences between the oligosaline (3.5‰) and saline (10‰) groups (P < 0.05). In particular, genus Flavobacterium became dominant in attached bacterial communities in the saline groups. The higher abundance of genus Flavobacterium was possibly due to the biological and metabolic characteristics of the bacteria. (iii) Some bacterial taxa can maintain the higher abundance within attached bacteria in the entire process of biofilms growth, such as the genera Hydrogenophaga and Methyloversatilis in Betaproteobacteria and the family Sphingomonadaceae in Alphaproteobacteria. These data suggested that the bacterial successional trends within biofilms seem almost unaffected by salinity (0.3‰–10‰), but ABCC in saline groups (10‰) are notably changed.

Structural, mechanistic and regulatory studies of serine palmitoyltransferase

SLs (sphingolipids) are composed of fatty acids and a polar head group derived from L-serine. SLs are essential components of all eukaryotic and many prokaryotic membranes but S1P (sphingosine 1-phosphate) is also a potent signalling molecule. Recent efforts have sought to inventory the large and chemically complex family of SLs (LIPID MAPS Consortium). Detailed understanding of SL metabolism may lead to therapeutic agents specifically directed at SL targets. We have studied the enzymes involved in SL biosynthesis; later stages are species-specific, but all core SLs are synthesized from the condensation of L-serine and a fatty acid thioester such as palmitoyl-CoA that is catalysed by SPT (serine palmitoyltransferase). SPT is a PLP (pyridoxal 5'-phosphate)-dependent enzyme that forms 3-KDS (3-ketodihydrosphingosine) through a decarboxylative Claisen-like condensation reaction. Eukaryotic SPTs are membrane-bound multi-subunit enzymes, whereas bacterial enzymes are cytoplasmic homodimers. We use bacterial SPTs (e.g. from Sphingomonas) to probe their structure and mechanism. Mutations in human SPT cause a neuropathy [HSAN1 (hereditary sensory and autonomic neuropathy type 1)], a rare SL metabolic disease. How these mutations perturb SPT activity is subtle and bacterial SPT mimics of HSAN1 mutants affect the enzyme activity and structure of the SPT dimer. We have also explored SPT inhibition using various inhibitors (e.g. cycloserine). A number of new subunits and regulatory proteins that have a direct impact on the activity of eukaryotic SPTs have recently been discovered. Knowledge gained from bacterial SPTs sheds some light on the more complex mammalian systems. In the present paper, we review historical aspects of the area and highlight recent key developments.

Sphingomonas formosensis sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from agricultural soil

In the present study, a yellow-pigmented, Gram-negative, short rod-shaped novel bacterium that was capable of degrading a wide range of polycyclic aromatic hydrocarbons (naphthalene, phenanthrene and pyrene) was isolated from agricultural soil located in Yunlin County, Taiwan. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus Sphingomonas as an independent lineage adjacent to a subclade containing Sphingomonas fennica K101(T), Sphingomonas histidinilytica UM2(T), Sphingomonas wittichii RW1(T) and Sphingomonas haloaromaticamans A175(T). 16S rRNA gene sequence analysis of strain CC-Nfb-2(T) showed highest sequence similarity to S. fennica K101(T) (96.2%), S. histidinilytica UM2(T) (96.1%), S. wittichii RW1(T) (95.9%), S. haloaromaticamans A175(T) (95.7%), and Sphingobium ummariense RL-3(T) (94.7%); lower sequence similarities were observed with strains of all other Sphingomonas species. The strain contained phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and diphosphatidylglycerol. The predominant fatty acids were summed feature 8 (C(18:1)ω7c and/or C(18:1)ω6c) C(16:0) and 11-methyl C(18:1)ω7c; C(14:0) 2-OH was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus Sphingomonas. The serine palmitoyl transferase gene (spt) was also detected and sphingolipid synthesis was confirmed. The predominant isoprenoid quinone system was ubiquinone (Q-10) and the isolate contained sym-homospermidine as the major polyamine. The DNA G+C content of the isolate was 62.8±0.8 mol%. On the basis of chemotaxonomic, phenotypic and phylogenetic data, strain CC-Nfb-2(T) represents a novel species within the genus Sphingomonas, for which the name Sphingomonas formosensis sp. nov. is proposed; the type strain is CC-Nfb-2(T) (=BCRC 80272(T)=DSM 24164(T)).

Diversity and antibiotic resistance patterns of Sphingomonadaceae isolates from drinking water

Sphingomonadaceae (n = 86) were isolated from a drinking water treatment plant (n = 6), tap water (n = 55), cup fillers for dental chairs (n = 21), and a water demineralization filter (n = 4). The bacterial isolates were identified based on analysis of the 16S rRNA gene sequence, and intraspecies variation was assessed on the basis of atpD gene sequence analysis. The isolates were identified as members of the genera Sphingomonas (n = 27), Sphingobium (n = 28), Novosphingobium (n = 12), Sphingopyxis (n = 7), and Blastomonas (n = 12). The patterns of susceptibility to five classes of antibiotics were analyzed and compared for the different sites of isolation and taxonomic groups. Colistin resistance was observed to be intrinsic (92%). The highest antibiotic resistance prevalence values were observed in members of the genera Sphingomonas and Sphingobium and for beta-lactams, ciprofloxacin, and cotrimoxazole. In tap water and in water from dental chairs, antibiotic resistance was more prevalent than in the other samples, mainly due to the predominance of isolates of the genera Sphingomonas and Sphingobium. These two genera presented distinct patterns of association with antibiotic resistance, suggesting different paths of resistance development. Antibiotic resistance patterns were often related to the species rather than to the site or strain, suggesting the importance of vertical resistance transmission in these bacteria. This is the first study demonstrating that members of the family Sphingomonadaceae are potential reservoirs of antibiotic resistance in drinking water.