Sphingopyxis Species Isolated from Sand Filter Biofilm at an Australian Drinking Water Treatment Works

Three strains isolated by geosmin enrichment from a sand filter in an Australian drinking water treatment works were genome sequenced to identify their taxonomic placement, and a bench-scale batch experiment confirmed their geosmin-degrading capability. Using the average nucleotide identity based on the MUMmer algorithm (ANIm), pairwise digital DNA-DNA hybridization (dDDH), and phylogenomic analyses, the strains were identified as Sphingopyxis species.

Evaluation of the degradation capacity of WWTP sludge enrichment cultures towards several organic UV filters and the isolation of octocrylene-degrading microorganisms

Organic UV filters are present in wastewater treatment plants (WWTPs) due to the use of these compounds in many personal care products (PCPs) and their subsequent release into the wastewater system from showering/bathing. Once in the wastewater system, organic UV filters generally partition into the solid phase but might also undergo other processes, such as degradation by microorganisms. To further understand the fate of organic UV filters in WWTPs, the degradation of 7 UV filters by WWTP sludge was investigated The UV filters 2-ethylhexyl salicylate (ES), homosalate (HS), butyl methoxydibenzoylmethane (BM) and octocrylene (OC) were degraded after 20-60 days. The rest of the filters tested, namely, bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT) and diethylhexyl butamido triazone (DBT), did not degrade even after 120 days of incubation. The microbial community from the microcosms degrading ES, HS, OC and BM was transferred every 30 days into new microcosms to enrich for microorganisms capable of utilizing the individual UV filters for growth. The enrichment cultures continued to degrade throughout 20 transfers. The microbial community was clearly different between the enrichments degrading ES, HS, OC and BM, meaning that the microbial community was strongly influenced by the UV filter present. Furthermore, several strains were isolated from OC-degrading cultures and two of these strains, Gordonia sp. strain OC_S5 and Sphingopyxis sp. strain OC_4D, degraded OC with and without other carbon sources present. These experiments show that several organic UV filters can be degraded by a specific set of microorganisms. The lack of degradation observed for BEMT, MBBT and DBT is probably due to limited bioavailability. Indeed, this is the first biodegradation study of these filters, in addition to being the first description of ES and HS degradation in microcosm experiments.

Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping

Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 μg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.

The genus Sphingopyxis: Systematics, ecology, and bioremediation potential - A review

The genus Sphingopyxis was first reported in the year 2001. Phylogenetically, Sphingopyxis is well delineated from other genera Sphingobium, Sphingomonas and Novosphingobium of sphingomonads group, family Sphingomonadaceae of Proteobacteria. To date (at the time of writing), the genus Sphingopyxis comprises of twenty validly published species available in List of Prokaryotic Names with Standing in Nomenclature. Sphingopyxis spp. have been isolated from diverse niches including, agricultural soil, marine and fresh water, caves, activated sludge, thermal spring, oil and pesticide contaminated soil, and heavy metal contaminated sites. Sphingopyxis species have drawn considerable attention not only for their ability to survive under extreme environments, but also for their potential to degrade number of xenobiotics and other environmental contaminants that impose serious threat to human health. At present, genome sequence of both cultivable and non-cultivable strains (metagenome assembled genome) are available in the public databases (NCBI) and genome wide studies confirms the presence of mobile genetic elements and plethora of degradation genes and pathways making them a potential candidate for bioremediation. Beside genome wide predictions there are number of experimental evidences confirm the degradation potential of bacteria belonging to genus Sphingopyxis and also the production of different secondary metabolites that help them interact and survive in their ecological niches. This review provides detailed information on ecology, general characteristic and the significant implications of Sphingopyxis species in environmental management along with the bio-synthetic potential.

Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

The class Alphaproteobacteria is comprised of a diverse assemblage of Gram-negative bacteria that includes organisms of varying morphologies, physiologies and habitat preferences many of which are of clinical and ecological importance. Alphaproteobacteria classification has proved to be difficult, not least when taxonomic decisions rested heavily on a limited number of phenotypic features and interpretation of poorly resolved 16S rRNA gene trees. Despite progress in recent years regarding the classification of bacteria assigned to the class, there remains a need to further clarify taxonomic relationships. Here, draft genome sequences of a collection of genomes of more than 1000 Alphaproteobacteria and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa recognized as problematic long ago but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera and of a variety of genera to other families. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which are confirmed as valuable taxonomic markers. Similarly, analysis of the gene content was shown to provide valuable taxonomic insights in the class. Significant incongruities between 16S rRNA gene and whole genome trees were not found in the class. The incongruities that became obvious when comparing the results of the present study with existing classifications appeared to be caused mainly by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. Another probable cause of misclassifications in the past is the partially low overall fit of phenotypic characters to the sequence-based tree. Even though a significant degree of phylogenetic conservation was detected in all characters investigated, the overall fit to the tree varied considerably.

Comparative genomics of Sphingopyxis spp. unravelled functional attributes

Members of genus Sphingopyxis are known to thrive in diverse environments. Genomes of 21 Sphingopyxis strains were selected. Phylogenetic analysis was performed using GGDC, AAI and core-SNP showed agreement at sub-species level. Based on our results, we propose that both S. baekryungensis DSM16222 and Sphingopyxis sp. LPB0140 strains should not be included under genus Sphingopyxis. Core-analysis revealed, 1422 genes were shared which included essential pathways and genes for conferring adaptation against stress environment. Polyhydroxybutyrate degradation, anaerobic respiration, type IV secretion were notable abundant pathways and exopolysaccharide, hyaluronic acid production and toxin-antitoxin system were differentially present families. Interestingly, genome of S. witflariensis DSM14551, Sphingopyxis sp. MG and Sphingopyxis sp. FD7 provided a hint of probable pathogenic abilities. Protein-Protein Interactome depicted that membrane proteins and stress response has close integration with core-proteins while aromatic compounds degradation and virulence ability formed a separate network. Thus, these should be considered as strain specific attributes.

Genomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis

Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxislindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.

Description of novel members of the family Sphingomonadaceae: Aquisediminimonas profunda gen. nov., sp. nov., and Aquisediminimonas sediminicola sp. nov., isolated from freshwater sediment

Two Gram-stain-negative bacterial strains, DS48-3^T and CH68-4^T, were isolated from freshwater sediment taken from the Daechung Reservoir, Republic of Korea. Cells of strains DS48-3^T and CH68-4^T were aerobic, non-motile, non-spore-forming and rod-shaped. Strain DS48-3^T was isolated from a sediment surface sample at a depth of 48 m from the Daechung Reservoir and was most closely related to the genus Sphingopyxis according to 16S rRNA gene sequence analysis (94.5-95.9 % similarity). Strain CH68-4^T was isolated from the very bottom of a 67-cm-long sediment core collected from Daechung Reservoir at a water depth of 17 m and was most closely related to the genus Sphingopyxis (16S rRNA gene sequence similarity of 93.7-95.0 %). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the two strains formed a separate lineage within the order Sphingomonadales showing similarity values below 95.9 % with their closest phylogenetic neighbours, and sharing 97.3 % similarity with each other. The combined genotypic and phenotypic data showed that strains DS48-3^T and CH68-4^T could be distinguished from all genera within the family Sphingomonadaceae and represented two distinct species of a novel genus, Aquisediminimonas profunda gen. nov., sp. nov. (type strain DS48-3^T=KCTC 52068^T=CCTCC AB 2018061^T) and Aquisediminimonas sediminicola sp. nov. (type strain CH68-4^T=KCTC 62205^T=CCTCC AB 2018062^T).

Metagenomic Analysis of a Complex Community Present in Pond Sediment

The metagenomic profiling of complex communities is gaining immense interest across the scientific community. A complex community present in the pond sediment of a water body located close to a hexachlorocyclohexane (HCH) production site of the Indian Pesticide Limited (IPL) (Chinhat, Lucknow) was selected in an attempt to identify and analyze the unique microbial diversity and functional profile of the site. In this study, we supplement the metagenomic study of pond sediment with a variety of binning approaches along with an in depth functional analysis. Our results improve the understanding of ecology, in terms of community dynamics. The findings are crucial with respect to the mechanisms such as those involving the lin group of genes that are known to be implicated in the HCH degradation pathway or the Type VI secretory system (T6SS) and its effector molecules. Metagenomic studies using the comparative genomics approach involving the isolates from adjacent HCH contaminated soils have contributed significantly towards improving our understanding of unexplored concepts, while simultaneously uncovering the novel mechanisms of microbial ecology.

Mercury remediation potential of a mercury resistant strain Sphingopyxis sp. SE2 isolated from contaminated soil

A mercury resistant bacterial strain SE2 was isolated from contaminated soil. The 16s rRNA gene sequencing confirms the strain as Sphingopyxis belongs to the Sphingomonadaceae family of the α-Proteobacteria group. The isolate showed high resistance to mercury with estimated concentrations of Hg that caused 50% reduction in growth (EC₅₀) of 5.97 and 6.22mg/L and minimum inhibitory concentrations (MICs) of 32.19 and 34.95mg/L in minimal and rich media, respectively. The qualitative detection of volatilized mercury and the presence of mercuric reductase enzyme proved that the strain SE2 can potentially remediate mercury. ICP-QQQ-MS analysis of the remaining mercury in experimental broths indicated that a maximum of 44% mercury was volatilized within 6hr by live SE2 culture. Furthermore a small quantity (23%) of mercury was accumulated in live cell pellets. While no volatilization was caused by dead cells, sorption of mercury was confirmed. The mercuric reductase gene merA was amplified and sequenced. Homology was observed among the amino acid sequences of mercuric reductase enzyme of different organisms from α-Proteobacteria and ascomycota groups.

Sphingopyxis flava sp. nov., isolated from a hexachlorocyclohexane (HCH)-contaminated soil

A Gram-negative-staining, aerobic, non-motile, non-spore-forming, rod-shaped and yellow-pigmented bacterium, designated R11HT, was isolated from a soil sample collected from a hexachlorocyclohexane dumpsite located at Ummari village, Lucknow, Uttar Pradesh, India. The 16S rRNA gene sequence similarity between strain R11HT and the type strains of species of genus Sphingopyxis with validly published names ranged from 93.75 to 97.85 %. Strain R11HT showed the highest 16S rRNA gene sequence similarity to Sphingopyxis indica DS15T (97.85 %), followed by Sphingopyxis soli JCM15910T (97.79 %), Sphingopyxis ginsengisoli KCTC 12582T (97.77 %) and Sphingopyxis panaciterrulae KCTC 22112T (97.34 %). The DNA G+C content of strain R11HT was 63.5 mol%. DNA–DNA relatedness between strain R11HT and its closest phylogenetic neighbours was well below the threshold value of 70 %, which suggested that strain R11HT represents a novel species of the genus Sphingopyxis. The major polar lipids of strain R11HT were sphingoglycolipid and other lipids commonly reported in this genus, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylmonomethylethanolamine. Spermidine was detected as the major polyamine. The chemotaxonomic markers in strain R11HT confirmed its classification in the genus Sphingopyxis, i.e. Q-10 as the major ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C14 : 0 2-OH as the predominant fatty acids. Results obtained from DNA–DNA hybridization and chemotaxonomic and phenotypic analyses clearly distinguished strain R11HT from its closest phylogenetic neighbours. Thus, strain R11HT represents a novel species of the genus Sphingopyxis, for which the name Sphingopyxis flava sp. nov. is proposed. The type strain is R11HT ( = DSM 28472T = MCC 2778T).

Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil

Strain RK1(T), a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium was isolated from a hexachlorocyclohexane (HCH) dumpsite, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RK1(T) belongs to the family Sphingobacteriaceae and showed highest sequence similarity to Parapedobacter koreensis Jip14(T) (95.63%). The major cellular fatty acids of strain RK1(T) were iso-C15:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), iso-C17:0 3-OH, summed feature 9 (10-methyl C16:0 and/or iso-C17:1ω9c), iso-C15:0 3-OH and C16 : 0. The major respiratory pigment and polyamine of RK1(T) were menaquinone (MK-7) and homospermidine, respectively. The main polar lipids were phosphatidylethanolamine and sphingolipid. The G+C content of the DNA was 44.5 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly demonstrated that strain RK1(T) represents a novel species of the genus Parapedobacter, for which the name Parapedobacter indicus sp. nov. is proposed. The type strain is RK1(T) ( = DSM 28470(T) =MCC 2546(T)).

Draft Genome Sequence of Hexachlorohexane (HCH)-Degrading Sphingobium lucknowense Strain F2T, Isolated from an HCH Dumpsite

Sphingobium lucknowense F2^T, isolated from the hexachlorocylcohexane (HCH) dumpsite located in Ummari village, Lucknow, India, rapidly degrades HCH isomers. Here we report the draft genome of strain F2 (4.4 Mbp), consisting of 4,910 protein coding genes with an average G+C content of 64.3%.

Pseudoxanthomonas wuyuanensis sp. nov., isolated from saline-alkali soil

A bacterium, designated XC21-2(T), was isolated from a saline-alkaline soil sample from China. Cells were Gram-stain-negative, rod-shaped and motile and grew optimally at 35-37 °C, pH 6.0-7.0 and in the presence of 0.5% (w/v) NaCl. Growth occurred in the range pH 5.5-9.0 and in the presence of up to 4 % (w/v) NaCl. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized amino-group-containing polar lipid. The major quinone was ubiquinone 8 (Q-8) and the G+C content of the genomic DNA was 66.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XC21-2(T) formed a tight phylogenetic lineage with Pseudoxanthomonas dokdonensis KCTC 12543(T) within the genus Pseudoxanthomonas and was most closely related to P. dokdonensis KCTC 12543(T) and P. mexicana ATCC 700993(T), with 97.9 and 97.5 % 16S rRNA gene sequence similarity, respectively. On the basis of the unique physiological profile of the isolate and its phylogenetic divergence from known species, strain XC21-2(T) represents a novel species within the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas wuyuanensis sp. nov. is proposed. The type strain is XC21-2(T) ( = CGMCC 1.10978(T) = KCTC 23877(T)).

Sphingopyxis italica sp. nov., isolated from Roman catacombs

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71T, was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71T belongs to the genus Sphingopyxis , and that it shows the greatest sequence similarity with Sphingopyxis chilensis DSM 14889T (98.72 %), Sphingopyxis taejonensis DSM 15583T (98.65 %), Sphingopyxis ginsengisoli LMG 23390T (98.16 %), Sphingopyxis panaciterrae KCTC 12580T (98.09 %), Sphingopyxis alaskensis DSM 13593T (98.09 %), Sphingopyxis witflariensis DSM 14551T (98.09 %), Sphingopyxis bauzanensis DSM 22271T (98.02 %), Sphingopyxis granuli KCTC 12209T (97.73 %), Sphingopyxis macrogoltabida KACC 10927T (97.49 %), Sphingopyxis ummariensis DSM 24316T (97.37 %) and Sphingopyxis panaciterrulae KCTC 22112T (97.09 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C14 : 0 2-OH and C16 : 0. The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus Sphingopyxis . However, a polyphasic approach using physiological tests, DNA base ratios, DNA–DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71T belongs to a novel species within the genus Sphingopyxis , for which the name Sphingopyxis italica sp. nov. is proposed. The type strain is SC13E-S71T ( = DSM 25229T = CECT 8016T).

Sphingopyxis indica sp. nov., isolated from a high dose point hexachlorocyclohexane (HCH)-contaminated dumpsite

A Gram-stain-negative, aerobic, non-motile, non-spore-forming, rod-shaped and light-yellow-pigmented bacterium, designated DS15T, was isolated from a soil sample collected from a hexachlorocyclohexane dumpsite in Lucknow, Uttar Pradesh, India. Strain DS15T showed highest 16S rRNA gene sequence similarity to Sphingopyxis panaciterrulae DCY34T (98.7 %) and Sphingopyxis soli BL03T (98.0 %). The 16S rRNA gene sequence similarity between strain DS15T and species of genus Sphingopyxis with validly published names ranged from 92.5 % to 98.7 %. The DNA G+C content of strain DS15T was 67.5 mol%. The chemotaxonomic markers in strain DS15T were consistent with its classification in the genus Sphingopyxis , i.e. Q-10 as the major ubiquinone and summed feature 8 (C18 : 1ω7c/C18 : 1ω9c), C17 : 1ω6c, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C14 : 0 2-OH, C15 : 0 2-OH, C16 : 0 and C17 : 1ω8c as the predominant fatty acids. The major polar lipids of strain DS15T were phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidylglycerol (PG) and sphingoglycolipids (SGL) and spermidine was detected as the major polyamine. Phylogenetic analysis, DNA–DNA hybridization, and chemotaxonomic and phenotypic analysis support the conclusion that strain DS15T represents a novel species within the genus Sphingopyxis , for which the name Sphingopyxis indica is proposed. The type strain is DS15T ( = MTCC 9455T = CCM 7542T = MCC 2023T).

Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis

Two yellow-pigmented, Gram-reaction-negative strains, designated 01SU5-PT and 03SU3-PT, were isolated from the freshwater of Woopo wetland, Republic of Korea. Both strains were aerobic, non-motile and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Sphingopyxis , showing the highest level of sequence similarity with respect to Sphingopyxis witflariensis W-50T (95.4–95.7 %). The two novel isolates shared 99.4 % sequence similarity. DNA–DNA hybridization between the isolates and the type strain of S. witflariensis clearly suggested that strains 01SU5-PT and 03SU3-PT represent two separate novel species in the genus Sphingopyxis . The two strains displayed different fingerprints after PCR analysis using the repetitive primers BOX, ERIC and REP. Several phenotypic characteristics served to differentiate these two isolates from recognized members of the genus Sphingopyxis . The data from the polyphasic study presented here indicated that strains 01SU5-PT and 03SU3-PT should be classified as representing novel species in the genus Sphingopyxis , for which the names Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., respectively, are proposed. The type strain of Sphingopyxis rigui sp. nov. is 01SU5-PT ( = KCTC 23326T = JCM 17509T) and the type strain of Sphingopyxis wooponensis sp. nov. is 03SU3-PT ( = KCTC 23340T = JCM 17547T).

Sphingomonas indica sp. nov., isolated from hexachlorocyclohexane (HCH)-contaminated soil

A bacterial strain, designated Dd16T, was isolated from a hexachlorocyclohexane (HCH) dumpsite at Lucknow, India. Cells of strain Dd16T were Gram-stain-negative, non-motile, rod-shaped and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Sphingomonas in the family Sphingomonadaceae , as it showed highest sequence similarity to Sphingomonas asaccharolytica IFO 15499T (95.36 %), Sphingosinicella vermicomposti YC7378T (95.30), ‘Sphingomonas humi’ PB323 (95.20 %), Sphingomonas sanxanigenens NX02T (95.14 %) and Sphingomonas desiccabilis CP1DT (95.00 %). The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) C14 : 0 2-OH, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile of strain Dd16T also corresponded to those reported for species of the genus Sphingomonas (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and a sphingoglycolipid), again supporting its identification as a member of the genus Sphingomonas . The predominant respiratory quinone was ubiquinone Q10, and sym-homospermidine was the major polyamine observed. The total DNA G+C content of strain Dd16T was 65.8 mol%. The results obtained on the basis of phenotypic characteristics and phylogenetic analysis and after biochemical and physiological tests, clearly distinguished strain Dd16T from closely related members of the genus Sphingomonas . Thus, strain Dd16T represents a novel species of the genus Sphingomonas for which the name Sphingomonas indica sp. nov. is proposed. The type strain is Dd16T ( = DSM 25434T = CCM 7882T).

Flavobacterium ummariense sp. nov., isolated from hexachlorocyclohexane-contaminated soil, and emended description of Flavobacterium ceti Vela et al. 2007

A Gram-negative, strictly aerobic, yellow bacterial strain, designated DS-12T, was isolated from hexachlorocyclohexane-contaminated soil in Lucknow, Uttar Pradesh, India. Strain DS-12T showed the highest 16S rRNA gene sequence similarity with Flavobacterium ceti 454-2T (94.2 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DS-12T belonged to the genus Flavobacterium . Strain DS-12T produced flexirubin-type pigments. Gliding motility was not observed. The major fatty acids of strain DS-12T were iso-C15 : 0 (48.0 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 19.3 %), iso-C17 : 0 3-OH (8.5 %) and summed feature 3 (comprising one or more of C16 : 1ω7c, C16 : 1ω6c and iso-C15 : 0 2-OH; 7.2 %). The only respiratory quinone was menaquinone-6 and the major polyamine was homospermidine. Strain DS-12T contained phosphatidyldimethylethanolamine, phosphatidylserine, phosphatidylethanolamine, one unknown phospholipid and one unknown aminolipid. The DNA G+C content was 37.4 mol%. Phylogenetic inference and phenotypic properties indicated that strain DS-12T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium ummariense sp. nov. is proposed. The type strain is DS-12T ( = CCM 7847T  = MTCC 10766T). An emended description of Flavobacterium ceti is also given.

Novosphingobium lindaniclasticum sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite

A yellow-pigmented, Gram-negative, aerobic, non-motile, non-spore-forming, rod-shaped-bacterium, LE124(T), was isolated from a hexachlorocyclohexane (HCH) dumpsite located in Lucknow, India. The type strain LE124(T) grew well with hexachlorocyclohexane as a sole carbon source, degrading it within 24 h of incubation. Phylogenetic analysis of strain LE124(T) showed highest 16S rRNA gene sequence similarity to Novosphingobium barchaimii LL02(T) (98.5%), Novosphingobium panipatense SM16(T) (98.1%), Novosphingobium soli CC-TPE-1(T) (97.9%), Novosphingobium naphthalenivorans TUT562(T) (97.6%), Novosphingobium mathurense SM117(T) (97.5%) and Novosphingobium resinovorum NCIMB 8767(T) (97.5%) and lower sequence similarity (<97%) to all other members of the genus Novosphingobium. The DNA-DNA relatedness between strain LE124(T) and N. barchaimii LL02(T) and other related type strains was found to vary from 15% to 45% confirming that it represents a novel species. The genomic DNA G+C content of strain LE124(T) was 60.7 mol%. The predominant fatty acids were summed feature 8 (C18:1ω7c, 49.1%), summed feature 3 (C16:1ω7c/C16:1ω6c, 19.9%), C16:0 (6.7%), C17:1ω6c (4.9%) and a few hydroxyl fatty acids, C14:0 2-OH (9.4%) and C16:0 2-OH (2.1%). Polar lipids consisted mainly of phosphatidyldimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, sphingoglycolipid and some unidentified lipids. The major respiratory quinone was ubiquinone Q-10. Spermidine was the major polyamine observed. Phylogenetic analysis, DNA-DNA hybridization, chemotaxonomic and phenotypic analysis support the conclusion that strain LE124(T) represents a novel species within the genus Novosphingobium for which we propose the name Novosphingbium lindaniclasticum sp. nov. The type strain is LE124(T) (=CCM 7976(T)=DSM 25409(T)).

Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov

A previously undescribed aerobic, non-sporulating bacterium, strain G1A_585(T), was isolated from an oligotrophic freshwater lake in Bavaria, Germany. The rod-shaped cells were Gram-stain-negative and non-motile. Based on 16S rRNA gene sequence similarity, strain G1A_585(T) was a member of the family Sphingomonadaceae and shared <95.2 % similarity with type strains of all members of the most closely related genus, Sphingopyxis. Phyogenetically, the isolate shared a root with strains of three marine species, Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T). The polar lipids of strain G1A_585(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipids, three glycolipids and one unknown lipid. Ubiquinone-10 was the dominant quinone (93.1 %) and ubiquinone-9 (6.5 %) was also detected. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 38.2 %); C16 : 1ω7c (33.6 %) and C14 : 0 2-OH (17.8 %). The major polyamine was spermidine and traces of 1,3-diaminopropane, putrescine and spermine were also detected. The DNA G+C content of strain G1A_585(T) was 55.7 mol% and the isolate was oxidase- and catalase-positive. Based on the phylogenetic relationship, the low DNA G+C content compared with most other members of the genus Sphingopyxis and the presence of signature nucleotides in the 16S rRNA gene sequence, a novel species in a new genus and species, Sphingorhabdus planktonica gen. nov., sp. nov., is proposed; the type strain of Sphingorhabdus planktonica is G1A_585(T) ( = DSM 25081(T)  = LMG 26646(T)). Because Sphingopyxis flavimaris DSM 16223(T), Sphingopyxis marina DSM 22363(T) and Sphingopyxis litoris DSM 22379(T) form a phylogenetic group together with strain G1A_585(T) that is clearly separated from all other known Sphingopyxis strains and share signature nucleotides, these three Sphingopyxis strains are reclassified as members of the proposed novel genus Sphingorhabdus: Sphingorhabdus flavimaris comb. nov. (type strain SW-151(T) = DSM 16223(T) = KCTC 12232(T)), Sphingorhabdus marina comb. nov. (type strain FR1087(T) = DSM 22363(T) = IMSNU 14132(T) = KCTC 12763(T) = JCM 14161(T)) and Sphingorhabdus litoris comb. nov. (type strain FR1093(T) = DSM 22379(T) = IMSNU 14133(T) = KCTC 12764(T) = JCM 14162(T)).

Sphingobium lucknowense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from HCH-contaminated soil

A yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterium, designated F2(T), was isolated from an HCH dumpsite at Ummari village in Lucknow, India. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus Sphingobium. Its closest neighbour was Sphingobium japonicum UT26(T) (99.2% 16S rRNA gene sequence similarity). The DNA G+C content was 65.7 mol%. The polyamine profile showed the presence of spermidine. The respiratory pigment was ubiquinone Q-10. The predominant cellular fatty acids were C(16:0) (12.5%), C(14:0) 2-OH (8.1%), summed feature 3 (consisting of C(16:1)ω7c and/or C(16:1)ω6c; 5.8%) and summed feature 8 (consisting of C(18:1)ω7c and/or C(18:1)ω6c; 53.1%). The major polar lipids of strain F2(T) were phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid. DNA-DNA relatedness and biochemical and physiological characters clearly distinguished the isolate from its closest phylogenetic neighbours. Thus, strain F2(T) represents a novel species of the genus Sphingobium, for which the name Sphingobium lucknowense sp. nov. is proposed. The type strain is strain F2(T) (=MTCC 9456(T) =CCM 7544(T)).