Genomic-based taxonomic classification of the order Sphingomonadales

The order Sphingomonadales strains are globally distributed in various biomes and are renowned for their biodegradable and biosynthesis capabilities. At present, it consists of 4 families and 49 genera making it the third largest order within the class Alphaproteobacteria. However, their taxonomy remains complex, especially due to polyphyly in the family Sphingomonadaceae. In this study, we collected 429 Sphingomonadales type strain genomes, reconstructed robust phylogenomic relationships, and proposed delineation thresholds at the genus and family levels based on average amino acid identities (AAI) and evolutionary distances (ED). Based on the maximum-likelihood and Bayesian phylogenomic trees reconstructed by two molecular sets determined by orthologous sequence identity and the Genome Taxonomy Database, the consensus degree values were all higher than 90%, revealing that those phylogenomic trees had similar topological structures. By confirming monophyletic taxa and determining stable nodes, we reclassified the order Sphingomonadales into thirteen families including nine novel ones. AAI calculations indicated that the average intra-family AAI values ranged from 0.62 to 0.84, while inter-family ones were 0.51 to 0.60. ED summaries demonstrated that the average and median intra-family ED values were 0.16 to 0.57, and inter-family ones ranged from 0.50 to 1.22. Comparisons of AAI and ED values calculated by using genomic and phylogenetic analyses supported that those 13 families were significantly separated with p values < 2.2×10-16. Thus, it was speculated that the AAI and ED thresholds for distinguishing different families were <0.6 and >0.5, respectively. Additionally, we reclassified 163 species into new genera with their phylogenetic topologies, according to the previous genus AAI and ED boundaries of 0.7 and 0.4. Our study is the first genomic-based study of the order Sphingomonadales and will promote further insights into the evolution of this order.

Sphingomonas flavescens sp. nov., isolated from soil

An aerobic bacterium, designated as PT-12T, was isolated from soil collected from agriculture field, and its taxonomic position was validated through a comprehensive polyphasic methodology. The strain was identified as Gram-stain-negative, non-motile, rod-shaped, and catalase- and oxidase-positive. The yellow-colored colonies showed growth ability at temperature range of 18-37 °C, NaCl content of 0-1.0% (w/v), and at a pH of 6.0-8.0. The 16S rRNA gene and phylogenetic analysis showed that strain PT-12T affiliated with the genus Sphingomonas in the family Sphingomonadaceae, and displayed the highest 16S rRNA nucleotide sequence similarity with Sphingomonas limnosediminicola 03SUJ6T (98.4%). The genome size of strain PT-12T was 2,656,862 bp and the DNA G + C content estimated from genome was 63.5%. The highest values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were observed between strain PT-12T and Sphingomonas segetis YJ09T, accounting to 76.2% and 20.2%, respectively. In addition, both ANI and dDDH values between strain PT-12T and other phylogenetically related neighbors ranged between 69.6% and 76.2% and 18.4% and 20.2%, respectively. Chemotaxonomic features exhibited Q-10 as the only ubiquinone; homospermidine as the major polyamine; summed feature 8 (C18:1ω7c and/or C18:1ω6c), C16:0, and 10-methyl C18:0 as the notable fatty acids; and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, and sphingoglycolipid as dominating polar lipids. Overall, the comprehensive polyphasic data supported that strain PT-12T represents a novel bacterial species within the genus Sphingomonas. Accordingly, we propose the name Sphingomonas flavescens sp. nov. The type strain is PT-12T (= KCTC 92114T = NBRC 115717T).

Isolation and Characterization of Sphingomonas telluris, Sphingomonas caseinilyticus Isolated from Wet Land Soil

Two novel bacterial strains, designated as SM33^T and NSE70-1^T, were isolated from wet soil in South Korea. To get the taxonomic positions, the strains were characterized. The genomic information (both 16S rRNA gene and draft genome sequence analysis) show that both novel isolates (SM33^T and NSE70-1^T) belong to the genus Sphingomonas. SM33^T share the highest 16s rRNA gene similarity (98.2%) with Sphingomonas sediminicola Dae20^T. In addition, NSE70-1^T show 96.4% 16s rRNA gene similarity with Sphingomonas flava THG-MM5^T. The draft genome of strains SM33^T and NSE70-1^T consist of a circular chromosome of 3,033,485 and 2,778,408 base pairs with DNA G+C content of 63.9, and 62.5%, respectively. Strains SM33^T and NSE70-1^T possessed the ubiquinone Q-10 as the major quinone, and a fatty acid profile with C_16:0, C_18:1 2-OH_, C_16:1 ω7c/C_16:1 ω6c (summed feature 3) and C_18:1 ω7c/C_18:1 ω6c (summed feature 8) as major fatty acids. The major polar lipids of SM33^T and NSE70-1^T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine, respectively. Moreover, genomic, physiological, and biochemical results allowed the phenotypic and genotypic differentiation of strains SM33^T and NSE70-1^T from their closest and other species of the genus Sphingomonas with validly published names. Therefore, the SM33^T and NSE70-1^T represent novel species of the genus Sphingomonas, for which the name Sphingomonas telluris sp. nov. (type strain SM33^T = KACC 22222^T = LMG 32193^T), and Sphingomonas caseinilyticus (type strain NSE70-1^T = KACC 22411^T = LMG 32495^T).

Characterization of four novel bacterial species of the genus Sphingomonas, Sphingomonas anseongensis, Sphingomonas alba, Sphingomonas brevis and Sphingomonas hankyongi sp.nov., isolated from wet land

Four novel bacterial strains, designated as RG327^T, SE158^T, RB56-2^T and SE220^T, were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus Sphingomonas. The draft genomes of RG327^T, SE158^T, RB56-2^T and SE220^T consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C_16 : 0, C_17 : 1ω6c, C_18 : 1 2-OH_, summed feature 3 (C_16 : 1ω7c/C_16 : 1ω6c) and summed feature 8 (C_18 : 1ω7c/C_18 : 1ω6c) as the major fatty acids, supporting the affiliation of strains RG327^T, SE158^T, RB56-2^T and SE220^T to the genus Sphingomonas. The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA-DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327^T, SE158^T, RB56-2^T and SE220^T from other species of the genus Sphingomonas with validly published names and indicated that they represented novel species of the genus Sphingomonas, for which the names Sphingomonas anseongensis sp. nov. (RG327^T = KACC 22409^T = LMG 32497^T), Sphingomonas alba sp. nov. (SE158^T = KACC 224408^T = LMG 324498^T), Sphingomonas brevis (RB56-2^T = KACC 22410^T = LMG 32496^T) and Sphingomonas hankyongi sp. nov., (SE220^T = KACC 22406^T = LMG 32499^T) are proposed.

Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production

The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.

Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3^T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11^T (97.0 %), Sphingomonas edaphi DAC4^T (96.8 %), Sphingomonas xanthus AE3^T (96.5 %) and Sphingomonas oryziterrae YC6722^T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3^T grew at 7-50 °C (optimum, 30-35 °C), pH 5.0-8.0 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C_18 : 1 ω6c and/or C_18 : 1 ω7c) and C_18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3^T and its reference strains with publicly available genomes were 17.9-18.9 %, 72.0-75.3 % and 63.3-76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas. The type strain is sand1-3^T (=KCTC 82358^T=NBRC 114538^T).

Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of Ginkgo biloba

Strain HMF7854^T, isolated from a ginkgo tree, was an orange-pigmented, Gram-stain-negative, motile by means of a single flagellum, strictly aerobic, rod-shaped bacterium. The isolate grew optimally on Reasoner's 2A agar at 30 °C, pH 7.0-8.0 and 0 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain HMF7854^T belonged to the genus Sphingomonas and was most closely related to Sphingomonasagri HKS-06^T (96.8 % sequence similarity). The major fatty acids were C_17 : 1 ω6c, summed feature 8 (C_18 : 1ω7c and/or C_18 : 1ω6c), summed feature 3 (C_16 : 1ω7c and/or C_16 : 1ω6c) and C_16 : 0. The predominant isoprenoid quinone was ubiquinone-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified lipids and two unidentified glycolipids. The genomic DNA G+C content was 68.4 mol%. Thus, based on its phylogenetic, phenotypic and chemotaxonomic data, strain HMF7854^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasginkgonis sp. nov. is proposed. The type strain of the species is strain HMF7854^T (=KCTC 62461^T=NBRC 113337^T).

Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth

Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.

Sphingomonas lacus sp. nov., an astaxanthin-dideoxyglycoside-producing species isolated from soil near a pond

Taxonomic studies were performed on an astaxanthin-dideoxyglycoside-producing strain, designated PB304T, isolated from soil near a pond in Daejeon city, South Korea. Cells of strain PB304T were Gram-staining-negative, strictly aerobic, orange-coloured and motile, and occurred as single or paired short chains. PB304T did not contain bacteriochlorophyll a. 16S rRNA gene sequence analysis revealed that strain PB304T was closely related to ‘Sphingomonas humi’ KCTC 12341 (98.7 %), Sphingomonas kaistensis KCTC 12344T (97.9 %), Sphingomonas astaxanthinifaciens DSM 22298T (97.6 %) and Sphingomonas ginsengisoli KCTC 12630T (97.5 %). Analysis of pufLM gene sequences revealed strain PB304T to be closely related to ‘S. humi’ KCTC 12341 (88.1 %). The major cellular fatty acids were C16 : 0, summed feature 4 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c), and summed feature 7 (comprising C18 : 1ω7c/ω9t/ω12t). Ubiquinone 10 (Q-10) was the sole quinone identified, and the major pigment was astaxanthin dideoxyglycoside. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The polyamine was spermidine. The DNA–DNA relatedness values of strain PB304T with respect to its closest phylogenetic neighbours were 57.1 % for ‘S. humi’ KCTC 12341, 51.2 % for Sphingomonas kaistensis KCTC 12334T, 50.6 % for Sphingomonas astaxanthinifaciens DSM 22298T and 50.2 % for Sphingomonas ginsengisoli KCTC 12630T. The DNA G+C content of strain PB304T was 66.6 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain PB304T is concluded to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lacus is proposed. The type strain is PB304T ( = KCTC 32458T = CECT 8383T).

Sphingomonas panaciterrae sp. nov., a plant growth-promoting bacterium isolated from soil of a ginseng field

Strain DCY91(T), a Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, was isolated from soil of ginseng field in Gyeonggi province, South Korea. Strain DCY91(T) shared the highest 16S rRNA gene sequence similarity with Sphingomonas mucosissima DSM 17494(T) (98.55%), Sphingomonas dokdonensis KACC 17420(T) (98.11%) and Sphingomonas xinjiangensis DSM 26736(T) (96.68%). The strain DCY91(T) was found to able to grow best in trypticase soy agar at 28 °C, at pH 7 and at 0.5 % NaCl. Ubiquinone 10 was identified as the isoprenoid quinone. The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The major fatty acids of strain DCY91(T) were identified as unsaturated C18:1 ω7c and saturated C16:0. The major polyamine content was sym-homospermidine. The DNA G + C content was determined to be 65.8 mol% (HPLC). After 6 days of incubation, strain DCY91(T) produced 9.64 ± 1.73 and 33.73 ± 4.66 µg/ml indole-3-acetic acid, using media without L-tryptophan and supplemented with L-tryptophan, respectively. Strain DCY91(T) was also weakly solubilized phosphate and produced siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY91(T) is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas panaciterrae sp. nov. is proposed. The type strain is DCY91(T) (=KCTC 42346(T) =JCM 30807(T)).