Sphingomonas rustica sp. nov. and Sphingomonas agrestis sp. nov., novel carotenoid-producing bacterial species isolated from farm soil

Two yellow-pigmented novel strains, designated HF-S3T and HF-S4T, were isolated from farm soil in Paju, Republic of Korea. Cells of the two strains are characteristically Gram-stain-negative, facultatively anaerobic, catalase- and oxidase-positive, non-motile and rod-shaped. Strain HF-S3T grew at 10-37 °C, while HF-S4T grew at 15-35 °C. Both strains grew at pH 5.0-12.0 and in NaCl concentrations (w/v) of 0-2.0%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that HF-S3T and HF-S4T belong to the genus Sphingomonas, with HF-S3T exhibiting 97.7, 97.6 and 97.4% similarity to Sphingomonas cannabina DM2-R-LB4T, Sphingomonas leidyi DSM 4733T and Sphingomonas canadensis FWC47T, respectively. Strain HF-S4T displayed 97.9, 97.7 and 97.6% similarity to Sphingomonas psychrotolerans Cra20T, Sphingomonas gei ZFGT-11T and Sphingomonas naasensis KIS18-15T, respectively. The DNA G+C contents of HF-S3T and HF-S4T were 67.0 and 66.5 mol%, respectively. The digital DNA-DNA hybridization and average nucleotide identity values among the novel and related type strains were 20.2-28.2% and 75.9-84.3%, respectively. They all contained C14:0 2-OH and C16:0, summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) as the major fatty acids and ubiquinone-10 as the predominant respiratory quinone. Strains HF-S3T and HF-S4T were found to produce carotenoid-type pigments. Based on polyphasic taxonomic analysis, the new isolates ostensibly represent two novel species of the genus Sphingomonas, with the proposed names Sphingomonas rustica sp. nov. and Sphingomonas agrestis sp. nov. for strains HF-S3T and HF-S4T, respectively. The S. rustica and S. agrestis type strains are HF-S3T (=KACC 23554T =TBRC 18352T) and HF-S4T (=KACC 23386T =TBRC 17899T), respectively.

Multi-scale analysis of acidophilic microbial consortium biofilm's tolerance of lithium and cobalt ions in bioleaching

Metal ions stress will inhibit the oxidation capacity of iron and sulfur of an acidophilic microbial consortium (AMC), which leads to reduced bioleaching efficiency. This work explored the impacts of Li+ and Co2+ on the composition and function of AMC biofilms with a multi-scale approach. At the reactor scale, the results indicated that the oxidative activity, the adsorption capacity, and the biofilm formation ability of AMC on pyrite surfaces decreased under 500 mM Li+ and 500 mM Co2+. At the biofilm scale, the electrochemical measurements showed that Li+ and Co2+ inhibited the charge transfer between the pyrite working electrode and the biofilm, and decreased the corrosion current density of the pyrite working electrode. At the cell scale, the content of proteins in extracellular polymers substrate (EPS) increased as the concentrations of metal ions increased. Moreover, the adsorption capacity of EPS for Li+ and Co2+ increased. At the microbial consortium scale, a BugBase phenotype analysis showed that under 500 mM Li+ and 500 mM Co2+, the antioxidant stress capacity and the content of mobile gene elements in AMC increased. The results in this work can provide useful data and theoretical support for the regulation strategy of the bioleaching of spent lithium-ion batteries to recover valuable metals.

Delignified porous wood as biofilm support for 1,4-dioxane-degrading bacterial consortium

Delignified porous wood samples were used as carriers for biofilm formation of a bacterial consortium with the ability to degrade 1,4-dioxane (DX). The delignification treatment of the natural wood resulted in higher porosity, formation of macropores, increase in surface roughness and hydrophilicity of the treated wood pieces. These superior properties of two types of treated carriers (respectively, A and B) compared to the untreated wood resulted in 2.19 ± 0.52- and 2.66 ± 0.23-fold higher growth of biofilm. Moreover, analysis of the fatty acid profiles indicated an increase in proportion of the saturated fatty acids during the biofilm formation, characterising an enhancement in rigidity and hydrophobicity of the biofilms. DX initial concentration of 100 mg/L was completely degraded (detection limit 0.01 mg/L) in 24 and 32 h using the treated A and B woods, while only 25.84 ± 5.95% was removed after 32 h using the untreated wood. However, fitting the DX biodegradation data to the Monod model showed a lower maximum specific growth rate for biofilm (0.0276 ± 0.0018 1/h) versus planktonic (0.0382 ± 0.0024 1/h), because of gradual accumulation of inactive cells in the biofilm. Findings of this study can contribute to the knowledge of biofilm formation regarding the physical/chemical properties of biofilm carriers and be helpful to the ongoing research on bioremediation of DX.

A novel UV-resistant bacterium Sphingomonas endolithica sp. nov., and genomic analysis, isolated from the north slope of Mount Everest

Gram-stain-negative, aerobic, rod-shaped, non-motile bacterium strain ZFBP2030T was isolated from a rock on the North slope of Mount Everest. This strain contained a unique ubiquinone-10 (Q-10) as a predominant respiratory quinone. Among the tested fatty acids, the strain contained summed feature 8, C14:0 2OH, and C16:0, as major cellular fatty acids. The polar lipid profile contained phosphatidyl glycerol, phosphatidyl ethanolamine, three unidentified phospholipids, two unidentified aminolipids, and six unidentified lipids. The cell-wall peptidoglycan was a meso-diaminopimelic acid, and cell-wall sugars were ribose and galactose. Phylogenetic analyses based on 16S rRNA gene sequence revealed that strain ZFBP2030T was a member of the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas aliaeris DH-S5T (97.9%), Sphingomonas alpina DSM 22537T (97.3%) and Sphingomonas hylomeconis CCTCC AB 2013304T (97.0%). The 16S rRNA gene sequence similarity between ZFBP2030T and other typical strains was less than 97.0%. The average amino acid identity values, average nucleotide identity, and digital DNA-DNA hybridization values between strain ZFBP2030T and its highest sequence similarity strains were 56.9-79.9%, 65.1-82.2%, and 19.3-25.8%, respectively. The whole-genome size of the novel strain ZFBP2030T was 4.1 Mbp, annotated with 3838 protein-coding genes and 54 RNA genes. Moreover, DNA G + C content was 64.7 mol%. Stress-related functions predicted in the subsystem classification of the strain ZFBP2030T genome included osmotic, oxidative, cold/heat shock, detoxification, and periplasmic stress responses. The overall results of this study clearly showed that strain ZFBP2030T is a novel species of the genus Sphingomonas, for which the name Sphingomonas endolithica sp. nov. is proposed. The type of strain is ZFBP2030T (= EE 013T = GDMCC 1.3123T = JCM 35386T).

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.

Establishment of an unfed strain of Paramecium bursaria and analysis of associated bacterial communities controlling its proliferation

The ciliate Paramecium bursaria harbors several hundred symbiotic algae in its cell and is widely used as an experimental model for studying symbiosis between eukaryotic cells. Currently, various types of bacteria and eukaryotic microorganisms are used as food for culturing P. bursaria; thus, the cultivation conditions are not uniform among researchers. To unify cultivation conditions, we established cloned, unfed strains that can be cultured using only sterile medium without exogenous food. The proliferation of these unfed strains was suppressed in the presence of antibiotics, suggesting that bacteria are required for the proliferation of the unfed strains. Indeed, several kinds of bacteria, such as Burkholderiales, Rhizobiales, Rhodospirillales, and Sphingomonadales, which are able to fix atmospheric nitrogen and/or degrade chemical pollutants, were detected in the unfed strains. The genetic background of the individually cloned, unfed strains were the same, but the proliferation curves of the individual P. bursaria strains were very diverse. Therefore, we selected multiple actively and poorly proliferating individual strains and compared the bacterial composition among the individual strains using 16S rDNA sequencing. The results showed that the bacterial composition among actively proliferating P. bursaria strains was highly homologous but different to poorly proliferating strains. Using unfed strains, the cultivation conditions applied in different laboratories can be unified, and symbiosis research on P. bursaria will make great progress.

Sphingomonas liriopis sp. nov., Sphingomonas donggukensis sp. nov., and Sphingomonas tagetis sp. nov., isolated from Liriope platyphylla fruit, soil, and Tagetes patula roots

Three bacterial strains, designated RP10^T, RMG20^T, and MG17^T, were isolated from Liriope platyphylla fruit (strain RP10^T), soil (RMG20^T), and Tagetes patula roots (MG17^T) collected in Goyang, Republic of Korea. The 16S rRNA gene sequences revealed that strains RP10^T, RMG20^T, and MG17^T were closely related to Sphingomonas melonis DSM 14444 ^T (highest similarity of the strain RP10^T), Sphingomonas asaccharolytica DSM 10564 ^T (strain RMG20^T), and Sphingomonas suaedae JCM 33850 ^T (strain MG17^T) with 98.0-99.0% highest sequence similarity. The 16S rRNA gene sequences similarity between strains RP10^T, RMG20^T, and MG17^T was 96.6-97.4%. Strains RP10^T, RMG20^T, MG17^T_, and the closely related type strains have digital DNA-DNA hybridization and average nucleotide identity values of 19.4-65.3% and 74.0-95.7%, respectively. Based on phylogenetic, biochemical, chemotaxonomic, and phenotypic data, strains RP10^T, RMG20^T, and MG17^T are considered to represent novel species of the genus Sphingomonas, for which the name Sphingomonas liriopis sp. nov. (type strain RP10^T = KACC 22357 ^T = TBRC 15161 ^T), Sphingomonas donggukensis sp. nov. (type strain RMG20^T = KACC 22358 ^T = TBRC 15162 ^T), and Sphingomonas tagetis sp. nov. (type strain MG17^T = KACC 22355 ^T = TBRC 15160 ^T), are proposed.

Sphingomonas cannabina sp. nov., isolated from Cannabis sativa L. 'Cheungsam'

A Gram-negative, aerobic, rod-shaped bacterium, designated DM2-R-LB4^T was isolated from Cannabis sativa L. 'Cheungsam' in Andong, Republic of Korea. The strain DM2-R-LB4^T grew at temperatures of 15-45 °C (optimum, 30-37 °C), pH of 5.5-9 (optimum, 8.0), and 0-2 % (w/v) NaCl concentration (optimum, 0%). Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strain DM2-R-LB4^T is related to species of the genus Sphingomonas, and shared 97.8 and 97.5% similarity to Sphingomonas kyenggiensis KCTC 42244^T and Sphingomonas leidyi DSM 4733^T, respectively. The DNA G+C content was 67.9 mol% and genome analysis of the strain DM2-R-LB4^T revealed that the genome size was 4 386 171 bp and contained 4 009 predicted protein-coding genes. The average nucleotide identity (ANI) values between strain DM2-R-LB4^T and S. kyenggiensis KCTC 42244^T, and S. leidyi DSM 4733^T was 76.8 and 76.7 %, respectively, while the values of digital DNA-DNA hybridization (dDDH) were 20.7 and 20.6 %, respectively. C_14 : 0 2-OH, C_16 : 0, and summed feature 8 (C_18 : 1 ω6c and/or C_18 : 1 ω7c) were the major fatty acids (>10 %) in the strain DM2-R-LB4^T. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), sphingoglycolipid (SGL), glycolipid (GL), phospholipid (PL), and two unidentified polar lipids (L1 and L2). Ubiquinone-10 (Q-10) was the only respiratory quinone. The polyamine pattern was found to contain homospermidine, putrescine, and spermidine. The results of phylogenetic anlayses, polyphasic studies, revealed that strain DM2-R-LB4^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas cannabina sp. nov., is proposed. The type strain is DM2-R-LB4^T (=KCTC 92075^T = GDMCC 1.3018^T).

Sphingomonas baiyangensis sp. nov., isolated from water in Baiyang Lake

A novel Gram-stain-negative, short-rod-shaped, orange-pigmented bacterial strain, designated L-1–4 w-11T, was isolated from Baiyang Lake in China. The strain grew at 15–35 °C (optimum 30 °C) and pH 7–8 (optimum pH 7) in TSA medium. The predominant polar lipids of strain L-1–4 w-11T were sphingoglycolipid, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified glycolipid and three unidentified lipids; the major cellular fatty acids were C17 : 1ω6c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c); and the major respiratory quinone was ubiquinone 10 (Q-10). Strain L-1–4 w-11T showed the highest 16S rRNA gene sequence similarity to Sphingomonas japonica JCM 15438T (98.3 %) and S. spermidinifaciens GDMCC 1.657T (98.0 %). The draft genome size of strain L-1–4 w-11T was 3.3 Mbp, and the G+C content was 67.8 mol%. Digital DNA–DNA hydridization and average nucleotide identity values between the genome sequences of strain L-1–4 w-11T and S. spermidinifaciens GDMCC 1.657T (76.9 and 21.0 %), S. japonica JCM 15438T (76.0 and 19.9 %) and S. paucimobilis CGMCC 1.12825T (72.8 and 19.6 %) were far below the thresholds for prokaryotic conspecific assignment. With the evidence from the phylogenetic, chemotaxonomic and genotypic analyses, we propose that strain L-1–4 w-11T represents a novel Sphingomonas species with the name S. baiyangensis sp. nov. The type strain is L-1–4 w-11T (=CGMCC 1.13572T=JCM 33962T).

Sphingomonas folii sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov., isolated from citrus phyllosphere

Three novel Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RHCKR7T, RRHST34T and RHCKR47T, were isolated from phyllosphere of healthy citrus collected in Renhua County, Guangdong Province, PR China. Phylogenetic analyses showed that they belonged to the genus Sphingomonas , among which both strains RHCKR7T and RRHST34T showed a close relationship with Sphingomonas yunnanensis YIM 003T with 16S rRNA gene similarity of 99.0 and 99.1%, respectively, and the similarity between the two novel strains was 99.2%, meanwhile strain RHCKR47T was most closely related to Sphingomonas palmae KACC 17591T (99.5%). Genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between closely related novel strains RHCKR7T and RRHST34T were 90.43 and 40.80 %, respectively, and their most closely related type strain, S. yunnanensis YIM 003T, showed 90.43 % ANI and 40.7 % dDDH with RHCKR7T and 90.21 % and 42.9 % with RRHST34T, respectively, and the corresponding values between strain RHCKR47T and S. palmae KACC 17591T were 85.53 % and 29.30%, respectively. They all took C14 : 0 2-OH and summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) as the major fatty acids, and ubiquinone 10 as the predominant respiratory quinone. The major polar lipids contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipids. sym-Homospermidine was the major polyamine. Based on phenotypic, genotypic and chemotaxonomic analyses, the new isolates should be considered as representing three novel species of the genus Sphingomonas , for which the names Sphingomonas folli sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov. are proposed with RHCKR7T (=GDMCC 1.2663T=JCM 34794T), RRHST34T (=GDMCC 1.2665T=JCM 34796T) and RHCKR47T (=GDMCC 1.2664T=JCM 34795T) as the type strains, respectively.

Sphingomonas psychrotolerans sp. nov., isolated from root surface of Leontopodium leontopodioides in the Tianshan Mountains, Xinjiang, China

A novel rod-shaped, Gram-stain-negative, aerobic bacterial strain, designated Cra20T, was isolated from the root surface of Leontopodium leontopodioides collected in the Tianshan Mountains, Xinjiang, PR China. Phylogenetic analysis based on 16S rRNA gene sequences, indicated that strain Cra20T was affiliated with the genus Sphingomonas , and was most closely related to Sphingomonas gei ZFGT-11T (99.0 %), Sphingomonas naasensis KIS18-15T (97.8%) and Sphingomonas kyeonggiensis THG-DT81T (97.2 %). The average nucleotide identity values between strain Cra20T, S. gei ZFGT-11T, S. naasensis KIS18-15T and S. kyeonggiensis THG-DT81T were 86.2, 84.2 and 78.2 %, respectively. The genomic DNA G+C content of strain Cra20T was 65.6 mol% (whole genome sequence), and Q-10 was the predominant ubiquinone. The major cellular fatty acids of strain Cra20T were summed feature 8 (comprising C18 : 1  ω6c and/or C18 : 1  ω7c, 67.3 %) and C14 : 0 2-OH (6.4 %). On the basis of genotypic, phenotypic and biochemical data, strain Cra20T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas psychrotolerans sp. nov. is proposed. The type strain is Cra20T (=CGMCC 1.15510T=NBRC 112697T).

Sphingomonas quercus sp. nov., Isolated from Rhizosphere Soil of Quercus mongolica

Strain XMGL2^T, isolated from rhizosphere soil of Quercus mongolica in China, was characterized using a polyphasic taxonomic approach. Cells were Gram-negative, aerobic, non-spore-forming, and rod-shaped. Growth occurred at 20-37 °C (optimum, 28 °C), pH 5.0-10.0 (optimum, pH 6.0), and with 0-1% NaCl (optimum, 1%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain XMGL2^T was related to members of the genus Sphingomonas and had the highest 16S rRNA gene sequence identity to Sphingomonas oleivorans FW-11 ^T (96.4%). The average nucleotide identity and digital DNA-DNA hybridization values between strain XMGL2^T and the closely related taxa Sphingomonas oleivorans FW-11 ^T and Sphingomonas fennica K101^T were 75.3/19.8% and 75.8/20.2%, respectively. The major cellular fatty acids were C_18:1 ω7c, C_14:0 2-OH, and C_16:0. The major isoprenoid quinone was Q-10 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycophospholipid and an unidentified phospholipid. The genomic DNA G + C content was 67.9%. Based on the phenotypic and genotypic properties and phylogenetic inference, strain XMGL2^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas quercus sp. nov. is proposed. The type strain is XMGL2^T (= JCM 34441 ^T = GDMCC 1.2153 ^T).

Sphingomonas arenae sp. nov., isolated from desert soil

Two bacterial strains, designated as SYSU D00720T and SYSU D00722, were isolated from a desert sandy soil sample collected from Gurbantunggut Desert in Xinjiang, north-west China. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped, oxidase-positive and catalase-negative. Colonies were circular, opaque, convex, smooth, orange on Reasoner's 2A (R2A) agar. The isolates were found to grow at 4-45 °C (optimum, 28-30 °C), at pH 6.0-7.0 (optimum, 7.0) and with 0-1.5 % (w/v) NaCl (optimum, 0%). Growth was observed on R2A agar, Luria-Bertani agar and nutrient agar, but not on trypticase soy agar. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid, two unidentified aminolipids, one unidentified glycolipid, one unidentified aminoglycolipid, one unidentified aminophospholipid, one unidentified phospholipid and two unidentified lipids. The main fatty acids (>10%) were C17 : 1  ω6c, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. The major respiratory quinone was ubiquinone-10 and the major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.0 mol%. Strains SYSU D00720T and SYSU D00722 were nearly identical with a 16S rRNA gene sequence similarity of 99.6 %, and 100.0 % average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values. Phylogenetic analyses clearly demonstrated that these two strains belonged to the same species of the genus Sphingomonas, and had highest sequence similarity to Sphingomonas lutea KCTC 23642T (97.3 %). The ANI, AAI and dDDH values of strains SYSU D00720T and SYSU D00722 to S. lutea KCTC 23642T were both 73.2, 69.9 and 19.2 %, respectively. Based on phylogenetic, phenotypic and chemotaxonomic distinctiveness, strains SYSU D00720T and SYSU D00722 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas arenae sp. nov. is proposed. The type strain is SYSU D00720T (=MCCC 1K05154T=NBRC 115061T).

Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish)

A polyphasic taxonomic approach was used to characterize three novel bacterial strains, designated as HDW12AT, HDW-15BT, and HDW15CT, isolated from the intestine of fish species Odontobutis interrupta or Siniperca scherzeri. All isolates were obligate aerobic, non-motile bacteria, and grew optimally at 30°C. Phylogenetic analysis based on 16S rRNA sequences revealed that strain HDW12AT was a member of the genus Nocardioides, and closely related to Nocardioides allogilvus CFH 30205T (98.9% sequence identities). Furthermore, strains HDW15BT and HDW15CT were members of the genus Sphingomonas, and closely related to Sphingomonas lutea JS5T and Sphingomonas sediminicola Dae 20T (97.1% and 97.9% sequence identities), respectively. Strain HDW12AT contained MK-8 (H4), and strains HDW15BT and HDW15CT contained Q-10 as the respiratory quinone. Major polar lipid components of strain HDW12AT were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylinositol, and those of strains HDW15BT and HDW15CT were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The G + C content of strains HDW12AT, HDW15BT, and HDW15CT were 69.7, 63.3, and 65.5%, respectively. The results of phylogenetic, phenotypic, chemotaxonomic, and genotypic analyses suggest that strain HDW12AT represents a novel species within the genus Nocardioides, and strains HDW15BT and HDW15CT represent two novel species within the genus Sphingomonas. We propose the names Nocardioides piscis for strain HDW12AT (= KACC 21336T = KCTC 49321T = JCM 33670T), Sphingomonas piscis for strain HDW15BT (= KACC 21341T = KCTC 72588T = JCM 33738T), and Sphingomonas sinipercae for strain HDW15CT (= KACC 21342T = KCTC 72589T = JCM 33739T).

Caulobacter endophyticus sp. nov., an endophytic bacterium harboring three lasso peptide biosynthetic gene clusters and producing indoleacetic acid isolated from maize root

A novel Gram-stain-negative, aerobic and rod-shaped bacterium with a single polar flagellum or a stalk at the end of the cell, was isolated from maize roots in the Fangshan District of Beijing, People's Republic of China. The new strain designated 774^T produced indole acetic acid (IAA). The 16S rRNA gene sequence analysis indicated that strain 774^T belongs to the genus Caulobacter and is closely related to Caulobacter flavus RHGG3^T, Caulobacter zeae 410^Tand Caulobacter radices 695^T, all with sequence similarities of 99.9%. The genome size of strain774^T was 5.4 Mb, comprising 5042 predicted genes with a DNA G+C content of 68.7%.Three striking lasso peptide biosynthetic gene clusters and two IAA synthesis genes belonging to the TPM pathway were also found in the genome of strain 774^T. The average nucleotide identity values and digital DNA-DNA hybridization values of the strain774^T with its closely phylogenetic neighbours were less than 91.5% and 45.0%, respectively, indicating a new Caulobacter species. The major fatty acids of strain774^T were identified as C16: 0 (27.7%), summed feature 3 (C16: 1ω6c and/or C16: 1ω7c) (12.6%) and summed feature 8 (C18: 1ω7c and/or C18: 1ω6c) (42.9%).The major polar lipids consisted of phosphatidyl-glycerol and glycolipids. The predominant ubiquinone was identified as Quinone 10. Based on the polyphasic characterization, strain 774^T represents a novel species of the genus Caulobacter, for which the name Caulobacter endophyticus sp. nov. is proposed with 774^T (= CGMCC 1.16558^T = DSM 106777^T) as the type strain.

Thermaurantiacus tibetensis gen. nov., sp. nov., a novel moderately thermophilic bacterium isolated from hot spring microbial mat in Tibet

Two bacterial strains SYSU G02173^T and SYSU G03142 were isolated from hot springs in Tibet, China. Based on the results of nearly full-length 16S rRNA gene sequences and phylogenetic analyses, strains SYSU G02173^T and SYSU G03142 were assigned to the family Sphingosinicellaceae, and were closest to Sandaracinobacter sibiricus RB16-17 ^T (96.04% and 96.12% similarity, respectively). Cells of the both new strains were observed to be motile rod-shape, Gram-staining negative. Growth occurred at pH 6-8 (optimal: pH 7.0) and 37-55 °C (optimal: 45 °C) with 0-1.0% (w/v) NaCl in T4 broth. The cells were found to be positive for oxidase and catalase activities. The major respiratory ubiquinone was Q-8. The major fatty acids were identified as summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), C_16:0, C_14:0 2-OH. The major polar lipids were found to consist of sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified phospholipid, one unidentified glycolipid, three unidentified aminolipids and two unidentified polar lipids. The DNA G + C contents of strains SYSU G02173^T and SYSU G03142 were 71.8%. The average nucleotide identity (ANI) value between strain SYSU G02173^T and SYSU G03142 was 99.98%. The amino acid identity (AAI) values between them and their closely related species were below 66.14%. The isolates are characterized by aerobic growth, a yellow endocellular pigment and a higher optimum growth temperature. The results showed that strains SYSU G02173^T and SYSU G03142 represent a novel species of a novel genus in the family Sphingomonadaceae, and thus the name Thermaurantiacus tibetensis (type strain SYSU G02173^T = KCTC 72052 ^T = CGMCC 1.16680 ^T) is proposed.

Competitive Exclusion and Metabolic Dependency among Microorganisms Structure the Cellulose Economy of an Agricultural Soil

Microorganisms that degrade cellulose utilize extracellular reactions that yield free by-products which can promote interactions with noncellulolytic organisms. We hypothesized that these interactions determine the ecological and physiological traits governing the fate of cellulosic carbon (C) in soil. We performed comparative genomics with genome bins from a shotgun metagenomic-stable isotope probing experiment to characterize the attributes of cellulolytic and noncellulolytic taxa accessing ¹³C from cellulose. We hypothesized that cellulolytic taxa would exhibit competitive traits that limit access, while noncellulolytic taxa would display greater metabolic dependency, such as signatures of adaptive gene loss. We tested our hypotheses by evaluating genomic traits indicative of competitive exclusion or metabolic dependency, such as antibiotic production, growth rate, surface attachment, biomass degrading potential, and auxotrophy. The most ¹³C-enriched taxa were cellulolytic Cellvibrio (Gammaproteobacteria) and Chaetomium (Ascomycota), which exhibited a strategy of self-sufficiency (prototrophy), rapid growth, and competitive exclusion via antibiotic production. Auxotrophy was more prevalent in cellulolytic Actinobacteria than in cellulolytic Proteobacteria, demonstrating differences in dependency among cellulose degraders. Noncellulolytic taxa that accessed ¹³C from cellulose (Planctomycetales, Verrucomicrobia, and Vampirovibrionales) were also more dependent, as indicated by patterns of auxotrophy and ¹³C labeling (i.e., partial labeling or labeling at later stages). Major ¹³C-labeled cellulolytic microbes (e.g., Sorangium, Actinomycetales, Rhizobiales, and Caulobacteraceae) possessed adaptations for surface colonization (e.g., gliding motility, hyphae, attachment structures) signifying the importance of surface ecology in decomposing particulate organic matter. Our results demonstrated that access to cellulosic C was accompanied by ecological trade-offs characterized by differing degrees of metabolic dependency and competitive exclusion.

Sphingomonas lacunae sp. nov., isolated from a freshwater pond

A novel bacterial strain, designated CSW-10^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed yellow-coloured colonies. Optimal growth occurred at 30 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CSW-10^T formed a phylogenetic lineage in the genus Sphingomonas. The 16S rRNA gene sequence similarity indicated that strain CSW-10^T was most closely related to Sphingomonas fonticola TNR-2^T (97.6%). Strain CSW-10^T showed 69.8-70.7% average nucleotide identity and 19.0-23.0% digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. The major fatty acids of strain CSW-10^T were summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) and C_17:1 ω6c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized sphingoglycolipid, five uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamines were homospermidine and spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-10^T was 62.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CSW-10^T should represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lacunae sp. nov. is proposed. The type strain is CSW-10^T (=BCRC 81190^T =LMG 31340^T).

Sphingomonas parva sp. nov., isolated from soil in Jeju Island

A Gram staining-negative, yellow-colored, rod-shaped, non-motile and aerobic, designated strain 17J27-24^T was isolated from a soil sample in Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 17J27-24^T was related to the members of the family Sphingomonadaceae and formed a distinct monophyletic cluster within the genus Sphingomonas with Sphingomonas deserti (98.3% 16S rRNA gene sequence similarity). Growth was observed at 30 °C (optimum), at pH 7.0 (optimum), and in the absence of NaCl (%). The predominant cellular fatty acids were summed feature 8 (18:1 ω7c and/or 18:1 ω6c) and C_17:1 ω6c. The major respiratory quinone was Q10. The polar lipids profile comprised of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and sphingoglycolipid (SGL). The DNA G + C content was 77.8 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between 17J27-24^T and its phylogenetically closest Sphingomonas deserti (KCTC 62411^T) were below the established cut-off < 94% (ANI) and < 70% (dDDH) for species delineation. Moreover, the results of the polyphasic approach confirmed that strain 17J27-24^T represents a novel species of the genus Sphingomonas within the family Sphingomonadaceae, for which the name Sphingomonas parva sp. nov. is proposed. The type strain of this species is 17J27-24^T (= KCTC 62208^T = JCM 3896^T). An emended description of the species Sphingomonas parva is provided.

Sphingomonas segetis sp. nov., isolated from spinach farming field soil

A Gram-stain-negative bacterium, designated strain YJ09^T, was isolated from spinach farming field soil at Shinan in the Republic of Korea. Cells of strain YJ09^T were found to be strictly aerobic, non-motile, non-spore-forming creamy-yellow rods which can grow at 20-37 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0-8.0) and at salinities of 0-0.5 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain YJ09^T belongs to the genus Sphingomonas with high sequence similarities to Sphingomonas parvus GP20-2 ^T (98.0 %), Sphingomonas agri HKS-06^T (97.7 %) and Sphingomonas lutea JS5^T (97.4 %). The results of phylogenetic analysis indicated that strain YJ09^T formed a distinct phyletic line in the genus Sphingomonas and the results of DNA-DNA relatedness studies demonstrated that strain YJ09^T could be separated from its closest relatives in the genus Sphingomonas. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unidentified glycolipids, an unidentified phospholipid and sphingoglycolipid. The predominant ubiquinone and polyamine components were Q-10 and spermidine, respectively. The major fatty acids were C_18:1  ω7c, C_{16  : 0} and C_16:1  ω7c and/or iso-C_15 : 0 2-OH. The DNA G+C content of this novel isolate was 65.9 mol%. On the basis of phenotypic, chemotaxonomic properties and phylogenetic analyses in this study, strain YJ09^T is considered to represent a novel species in the genus Sphingomonas, for which the name Sphingomonas segetis sp. nov. is proposed. The type strain is YJ09^T (=KACC 19551^T=NBRC 113247^T).

Sphingomonas montanisoli sp. nov., isolated from mountain soil

A soil bacterium, designated ZX9611T, was isolated from Taihang Mountain in Henan province, PR China. The strain was Gram-stain-negative and strictly aerobic. The cells were motile, rod-shaped and formed light pink-colored colonies. The 16S rRNA gene sequence of ZX9611T shared the highest similarities with those of Sphingomonas crocodyli CCP-7T (97.0%), Sphingomonas jatrophae S5-249T (96.6%) and Sphingomonas starnbergensis 382T (95.9%). Phylogenetic analyses based on 16S rRNA gene sequences demonstrated that ZX9611T clustered with S. crocodyli CCP-7T, S. jatrophae S5-249T and S. starnbergensis 382T. The average nucleotide identity (ANI) values between ZX9611T and two type strains ( S. crocodyli BCRC 81096T and S. jatrophae DSM 27345T) were 88.3 and 68.6% respectively. ZX9611T exhibited genome-sequence-based digital DNA–DNA hybridization (dDDH) values of 53.3 % and 15.3 %, compared with S. crocodyli BCRC 81096T and S . jatrophae DSM 27345T, respectively. ZX9611T had a genome size of 4.12 Mb and an average DNA G+C content of 64.8 %. ZX9611T had major fatty acids (>5 %) including summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), and the major polyamine was sym-homospermidine. The only respiratory quinone was ubiquinone-10. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. On the basis of phenotypic, chemotaxonomic and phylogenetic characteristics, strain ZX9611T represents a novel species of genus Sphingomonas, for which the name Sphingomonas montanisoli sp. nov. is proposed. The type strain is ZX9611T (=KCTC 72622T=CCTCC AB 2019350T).

Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov., isolated from a wastewater treatment plant

Two Gram-stain-negative, aerobic, motile and rod-shaped bacteria, one designated as strain AXB^T, capable of degrading estrogens, and another, YL23^T, capable of degrading estrogen and bisphenol A, were isolated from activated sludge in Xiamen City, PR China. The optimum temperature and pH of both strains were 25-35 °C and pH 7.0-8.0. While strain AXB^T could tolerate 3 % (w/v) NaCl, YL23^T could only grow between 0-1 % (w/v) NaCl. They contained ubiquinone-10 as the major quinone, spermidine as the major polyamine, summed feature 8 (comprising C_18:1ω6c and/or C_18:1ω7c) as the major fatty acids and diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid as the major polar lipids. The DNA G+C contents of strains AXB^T and YL23^T were 63.6 and 63.7 mol%, respectively. Based on the results of 16S rRNA gene sequence analysis, strains AXB^T and YL23^T belonged to the genus Sphingobium. Strain AXB^T was most closely related to Sphingobium chlorophenolicum NBRC 16172^T (97.5 %) and Sphingobium chungbukense DJ77^T (97.2 %), and strain YL23^T was most closely related to S. chlorophenolicum NBRC 16172^T (97.4 %) and S. quisquiliarum P25^T (97.1 %). Average nucleotide identity values between these two strains and S. chlorophenolicum NBRC 16172^T, S. chungbukense DJ77^T, Sphingobium chinhatense IP26^T, Sphingobium quisquiliarum P25^T and Sphingobium japonicum UT26S^T were from 80.7 to 85.8 %. In conclusion, strains AXB^T and YL23^T represent novel species of the genus Sphingobium, for which the names Sphingobium estronivorans sp. nov. and Sphingobium bisphenolivorans sp. nov. are proposed, respectively. The type strains of S. estronivorans and S. bisphenolivorans are AXB^T (=MCCC 1K01232^T=DSM 102173^T) and YL23^T (=MCCC 1K02300^T=DSM 102172^T), respectively.

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.

Groundwater microbial communities and their connection to hydrochemical environment in Golmud, Northwest China

Groundwater microbial community normally co-varies with the associated geochemical transect in some hydrogeological sections along flowpath. However, in hydrogeological section with similar geochemical transect (e.g., salinity, ion compositions) how microbial community in groundwater varies are poorly understood. In this study, groundwater samples were collected at six boreholes vertically and horizontally along a generalized groundwater flowpath in the Golmud area, Qaidam Basin, northwest China. High-throughput sequencing and multivariate statistical analysis were applied to explore the underlying relationships between microbial community structure and hydrogeochemical environment. The result showed that microbial communities changed considerably at both horizontal and vertical scales, although the groundwater samples were of relatively stable ionic compositions and hydrochemical types. The dominant bacterial phyla in groundwater varied from Alphaproteobacteria, Betaproteobacteria and Flavobacteriia in 'phreatic and phreatic-like' groundwater in the recharge area to Gammaproteobacteria in the confined groundwater in the lacustrine plain. At both vertical and horizontal scale, Gammaproteobacteria increased while Alpha- and Betaproteobacteria decreased as the function of distance. Genera Roseateles, Aquabacterium, Sphingomonas, Acinetobacter, Acidovorax and Flavobacterium presented in phreatic groundwater, while Pseudomonas, Hydrogenophaga and Perlucidibaca presented in confined groundwater. Spatial distribution of microbial community was highly affected by the pH (for 'phreatic and phreatic-like' groundwater) and ORP (for confined groundwater) of groundwater that had similar salinity or ion compositions. This research extends our knowledge about microbial communities' variation along groundwater flowpath in studied area and similar arid or semi-arid areas.

Sphingomonas paeninsulae sp. nov., isolated from soil sampled at Fildes Peninsula, Antarctica

Strain YZ-8^T, isolated from soil sampled at Fildes Peninsula, Antarctica, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain YZ-8^T grewoptimally at pH 7.0 and 20 °C. Tolerance to NaCl was up to 0.3 % (w/v) with optimum growth in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YZ-8^T belonged to the family Sphingomonas. Strain YZ-8^T showed the highest sequence similarities to Sphingomonas molluscorum KMM 3882^T (94.4 %), Sphingomonas oligophenolica JCM 12082^T (94.4 %), Sphingomonas gotjawalisoli SN6-9^T (94.3 %) and Sphingomonas aquatica W1-2-1^T (94.3 %). The predominant respiratory isoprenoid quinone and polyamine components were identified as ubiquinone Q-10 and sym-homospermidine, respectively. In addition, carotenoid were also found. The polar lipid profile of the strain YZ-8^T was found to contain one phosphatidylethanolamine, an unidentified phospholipid, one diphosphatidylglycerol, one phosphatidylglycerol, two sphingophosphonolipids, one phosphatidylcholine and two unidentified alkali-stable lipids. The G+C content of the genomic DNA was determined to be 58.8 mol%. The main fatty acids were summed feature 8 (comprising C_18 : 1ω7c and/or C_18 : 1ω6c; 35.4 %), summed feature 3 (comprising C_16 : 1ω7c and/or C_16 : 1ω6c; 32.6 %) and C_14 : 0 2-OH (7.7 %). On the basis of the evidence presented in this study, a novel species of the genus Sphingomonas, Sphingomonaspaeninsulae sp. nov., is proposed, with the type strain YZ-8^T (=CCTCC AB 2017137^T=LMG 31027^T).

Sphingomonas crocodyli sp. nov., isolated from a crocodile pond

Strain CCP-7^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CCP-7^T formed a phylogenetic lineage in the genus Sphingomonas. Strain CCP-7^T was most closely related to Sphingomonas starnbergensis 382^T and Sphingomonas naphthae DKC-5-1^T with 96.2 % 16S rRNA gene sequence similarity. Strain CCP-7^T showed 65.5-76.7 % average nucleotide identity and 20.2-22.5 % digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. Cells were Gram-stain-negative, aerobic, motile, rod-shaped and formed light orange-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acid of strain CCP-7^T was C18 : 1ω7c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, three uncharacterized sphingoglycolipids, two uncharacterized phospholipids and six uncharacterized lipids. The predominant polyamine was homospermidine. The only isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CCP-7^T was 64.5 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CCP-7^T should be classified in a novel species of the genus Sphingomonas, for which the name Sphingomonas crocodyli sp. nov. is proposed. The type strain is CCP-7^T (=BCRC 81096^T=LMG 30311^T=KCTC 62190^T).

Description of Sphingomonas mesophila sp. nov., isolated from Gastrodia elata Blume

A Gram-staining-negative, strictly aerobic, non-motile strain, SYSUP0001^T, was isolated from tubers of Gastrodia elata Blume. The 16S rRNA gene sequence result indicated that SYSUP0001^T represents a member of the genus Sphingomonas, with the highest sequence similarity (97.7 %) to the type strain of Sphingomonasginsengisoli. SYSUP0001^T grew at 14-37 °C and pH 6-8, with optimum growth at 28 °C and pH 7. Tolerance to NaCl was up to 3 % (w/v) with optimum growth in the absence of NaCl. The respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, Summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), and C16 : 0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), sphingoglycolipid (SGL), phosphatidylcholine (PC) and four unidentified polar lipids (L). The DNA G+C content was 67.5 %. The average nucleotide identity (ANI) values between SYSUP0001^T and closely related members of the genus Sphingomonas were below the cut-off level (95-96 %) for species delineation. On the basis of the phenotypic, phylogenetic and chemotaxonomic characterizations, SYSUP0001^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasmesophila sp. nov. is proposed. The type strain is SYSUP0001^T (=KCTC 62179 ^T=CGMCC 1.16462^T).

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 deserti sp. nov., isolated from Mu Us Sandy Land soil

A Gram-stain-negative, rod-shaped bacterium, designated as strain GL-C-18^T, was isolated from soil sample collected at Mu Us Sandy Land, China, and its taxonomic position was investigated using a polyphasic approach. Growth was observed in the presence of 0-1 % (w/v) NaCl (optimum, 0 %), pH 6.0-9.0 (optimum, pH 7.0-8.0) and 20-37 °C. On the basis of 16S rRNA gene sequence similarity, strain GL-C-18^T belonged to the family Sphingomonadaceae and was most closely related to Sphingosinicella vermicomposti YC7378^T (95.7 %), Sphingomonas oligophenolica S213^T (95.0 %) and Sphingobium boeckii 301^T (94.8 %). The draft genome of strain GL-C-18^T was 6.09 Mb, and the G+C content was 66.0 %. The average nucleotide identity value to Sphingosinicella vermicomposti YC7378^T was 83.7 %. The predominant respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16:0 and C14 : 0 2OH. The main polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain GL-C-18^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasdeserti sp. nov. is proposed. The type strain is GL-C-18^T (=ACCC 60076^T=KCTC 62411^T).

Sphingomonas turrisvirgatae sp. nov., an agar-degrading species isolated from freshwater

A yellow pigmented and agar-pitting colony was isolated from a water sample obtained from a drainage ditch within a disused system of constructed wetlands. The strain was purified and named MCT13^T. This rod-shaped, Gram-negative, oxidase- and catalase-positive, aerobic, non-spore-forming, and non-motile strain formed round colonies and grew optimally at pH 7.5±0.2, at 28-30 °C on LB agar, with 0-0.5 % NaCl. The 16S rRNA gene sequence analysis placed the MCT13^T isolate within the Sphingomonas (sensu stricto) cluster. The DNA G+C content was 65.3 %. The only observed ubiquinone was Q10. The major fatty acids included C17 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. The major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major polyamine was spermidine. The 16S rRNA gene phylogenetic analysis performed on the whole sequence, showed the closest relative of MCT13^T to be Sphingomonas koreensis (98.52 %); however, there are several genotypic and phenotypic differences between the novel isolate and the type strain JSS26^T of S. koreensis. On the basis of these results, strain MCT13^T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas turrisvirgatae sp. nov. is proposed. The type strain is MCT13^T (=DSM 105457^T=BAC RE RSCIC 7^T).

Caulobacter zeae sp. nov. and Caulobacter radicis sp. nov., novel endophytic bacteria isolated from maize root (Zea mays L.)

Four bacterial strains designated 410^T, 441, 695^T and 736 were isolated from maize root in Beijing, P. R. China. Based on 16S rRNA gene phylogeny, the four strains formed two clusters in the genus Caulobacter. Since strain 441 was a clonal variety of strain 410^T, only three strains were selected for further taxonomic studies. The whole genome average nucleotide identity (ANI) value between strains 410^T and 695^T was 94.65%, and both strains shared less than 92.10% ANI values with their close phylogenetic neighbors Caulobacter vibrioides DSM 9893^T, Caulobacter segnis ATCC 21756^T and Caulobacter flavus CGMCC 1.15093^T. Strains 410^T and 695^T contained Q-10 as the sole ubiquinone and their major fatty acids were C_{16:0, 11-methyl C18:1ω 0}, 11-methyl C_{18: 1}ω7c, summed feature 3 (C_{16:1ω7c and/or C16:1ω 1}ω7c and/or C_{16: 1}ω6c) and summed feature 8 (C_{18:1ω7c and/or C18:1ω 1}ω7c and/or C_{18: 1}ω6c). Their major polar lipids consisted of glycolipids and phosphatidylglycerol, and phenotypic tests differentiated them from their closest phylogenetic neighbors. Based on the results obtained, it is proposed that the three strains represent two novel species, for which the names Caulobacter zeae sp. nov. (type strain 410^T=CGMCC 1.15991=DSM 104304) and Caulobacter radicis sp. nov. (type strain 695^T=CGMCC 1.16556=DSM 106792) are proposed.

Sphingomonas tabacisoli sp. nov., a member of the genus Sphingomonas, isolated from rhizosphere soil of Nicotiana tabacum L

A Gram-staining-negative, aerobic, motile and rod-shaped bacterium, designated strain X1-8T, was isolated from rhizosphere soil of Nicotiana tabacum L. collected from the tobacco produce base located in Kunming, south-west PR China. Cells showed oxidase-negative and catalase-positive reactions and were motile by means of peritrichous flagella. Growth occurred at 25-40 °C and pH 6.0-8.0 with optimal growth at 30-35 °C, pH 7.0. The major respiratory lipoquinone was Q-10. C16 : 0 and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) were identified as major cellular fatty acids. The profile of polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, sphingoglycolipid, phosphatidylcholine and one unidentified glycolipid. The major polyamine was sym-homospermidine. The genomic DNA G+C content was 66.5 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that X1-8T should be affiliated to the genus Sphingomonasand formed a clade with most closely related species Sphingomonas changbaiensisNBRC 104936T. The results of 16S rRNA gene sequences similarity analysis indicated that X1-8T had the highest similarity with S. changbaiensisNBRC 104936T (98.4 %) and lower than 96.0 % with other species of the genus Sphingomonas. DNA-DNA hybridization data indicated that X1-8T represented a novel genomic species of the genus Sphingomonas. The characteristics determined in the polyphasic taxonomic study indicated that X1-8T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas tabacisoli sp. nov. (type strain X1-8T=KCTC 62032T=CGMCC 1.16275T) is proposed.

Sphingomonas aeria sp. nov., isolated from air

A Gram-negative, aerobic, non-spore-forming, non-motile, yellow-pigmented and rod-shaped bacterial strain, designated B093034^T, was isolated from air at the foot of Xiangshan mountain, located in Beijing, China. Cells of strain B093034^T were oxidase-negative and catalase-positive. Growth was observed at 4-41 °C, at pH 4.5-10.0 and at 0-7 % (w/v) NaCl. The isolate contained Q-10 as the predominant isoprenoid quinone, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C14 : 02-OH as the major fatty acids, sym-homospermidine as the major polyamine, and sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, aminolipid, two unidentified phospholipids and three unidentified polar lipids as the polar lipids. The DNA G+C content was 67.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B093034^T grouped with members of the genus Sphingomonas and was closely related to Sphingomonas sanguinis IFO 13937^T (96.49 % similarity), Sphingomonas pseudosanguinis G1-2^T (96.37 %), Sphingomonas ginsenosidimutansGsoil 1429^T (95.99 %) and Sphingomonas endophytica YIM 65583^T (95.78 %). On the basis of the polyphasic evidence presented here, strain B093034^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasaeria sp. nov. is proposed. The type strain is B093034^T (=CFCC 13949^T=LMG 30133^T).

Sphingomonas difficilis sp. nov., a difficultly cultivable bacterium that grows on solid but not in liquid medium, isolated from an abandoned lead-zinc mine

A difficult to cultivate bacterial strain, designated 1PNM-26^T, isolated from a lead-zinc mine, was investigated using a polyphasic taxonomic approach. The strain was able to grow on solid medium but not in liquid medium. Cells were Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped. It showed positive reactions for catalase and oxidase and hydrolysis of aesculin. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain 1PNM-26^T represents a member of the genus Sphingomonas and forms a stable cluster with Sphingomonas morindae KCTC 42183^T, Sphingomonas polyaromaticivorans JCM 16711^T and Sphingomonas oligoaromativorans NBRC 105508^T. The major fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. C14 : 0 2-OH was present as the major hydroxyl fatty acid. The major polyamine was sym-homospermidine, and ubiquinone 10 (Q-10) was the predominant respiratory quinone. The genomic DNA G+C content of strain 1PNM-26^T was determined to be 66.3±0.3 mol%, and the polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, an unidentified glycolipid, three unidentified aminolipids and three unidentified lipids. The phenotypic, phylogenetic and chemotaxonomic results strongly supported the hypothesis that strain 1PNM-26^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasdifficilis sp. nov. is proposed. The type strain is 1PNM-26^T (=GDMCC 1.664^T=KCTC 42758^T=DSM 27573^T).

Sphingomonas antarctica sp. nov., isolated from Antarctic tundra soil

Strain 200^T, isolated from a soil sample taken from Antarctic tundra soil around Zhongshan Station, was found to be a Gram-stain-negative, yellow-pigmented, catalase-positive, oxidase-negative, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain 200^T grew optimally at pH 7.0 and in the absence of NaCl on R2A. Its optimum growth temperature was 20 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 200^T belonged to the genus Sphingomonas. Strain 200^T showed the highest sequence similarities to Sphingomonas kyeonggiense THG-DT81^T (95.1 %) and Sphingomonas molluscorum KMM 3882^T (95.1 %). Chemotaxonomic analysis showed that strain 200^T had characteristics typical of members of the genus Sphingomonas. Ubiquinone 10 was the predominant respiratory quinone and sym-homospermidine was the polyamine. The major polar lipids were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The G+C content of the genomic DNA was determined to be 60.9 mol%. Strain 200^T contained C16 : 0 (31.6 %), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c, 22.7 %), summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 11.2 %), C18 : 0 (7.8 %) and C14 : 0 2OH (6.7 %) as the major cellular fatty acids. On the basis of phylogenetic analysis, and physiological and biochemical characterization, strain 200^T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonasantarctica sp. nov. is proposed. The type strain is 200^T (=CCTCC AB 2016064^T=KCTC 52488^T).

Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil

A novel Sphingomonas strain was isolated from a sample of desert soil collected near Jeddah in Saudi Arabia. A polyphasic approach was performed to characterize this strain, initially designated as G39^T. Cells of strain G39^T are motile, Gram-negative, catalase- and oxidase-positive. The strain is able to grow aerobically at 20-35 °C, pH 6.5-8 and tolerates up to 4 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the closest relative type strains of G39^T are Sphingomonas mucosissima DSM 17494^T (98.6 %), S. dokdonensis DSM 21029^T (98.4 %) and S. hankookensis DSM 23329^T (97.4 %). Furthermore, the average nucleotide identities between the draft genome sequence of strain G39^T and the genome sequences of all other available and related Sphingomonas species are significantly below the threshold of 94 %. The G+C content of the draft genome (3.12 Mbp) is 65.84 %. The prevalent (>5 %) cellular fatty acids of G39^T were C18 : 1ω7c, C16 : 1ω7c and/or C16 : 1ω6c, C14 : 0 2-OH and C16 : 0. The only detectable respiratory quinone was ubiquinone-10 and the polar lipids profile is composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, as well as unidentified lipids, phospholipids and glycolipids. The results of the conducted polyphasic approach confirmed that this isolate represents a novel species of the genus Sphingomonas, for which the name Sphingomonas jeddahensis sp. nov. is proposed. The type strain of this species is G39^T (=DSM 103790^T=LMG 29955^T).

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).

Caulobacter hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (Mugunghwa flower)

A Gram-stain-negative, smooth, bright yellow-pigmented, aerobic, catalase- and oxidase-positive and rod-shaped bacterial strain was isolated from rhizosphere of Hibiscus syriacus L. (Mugunghwa flower) located in Kyung Hee University, Yongin, Gyeonggi, South Korea. Cells were dimorphic, non-motile or non-stalked, and motile by means of peritrichous flagellum. The strain, named THG-AG3.4T, grew at 15-35 °C, at pH 6.5-9.0 and in the presence of 0-1.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain THG-AG3.4T was most closely related to Caulobacter segnis ATCC 21756T (98.64 % similarity), Caulobacter vibrioides CB51T (98.57 %) and Caulobacter henricii ATCC 15253T (97.41 %). The DNA G+C content of strain THG-AG3.4T was 64.0 mol%. In DNA-DNA hybridization, the DNA-DNA relatedness between strain THG-AG3.4T and its closest phylogenetic neighbour was below 55.0 %. The predominant isoprenoid quinone detected in strain THG-AG3.4T was ubiquinone-10 (Q-10). The major polar lipids were found to be an unidentified lipid, two unidentified phosphoglycolipids, five unidentified glycolipids, eight unidentified aminolipids and phosphatidylglycerol. The major fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). Thus, based on the report of the phenotypic, genotypic and phylogenetic characterization of strain THG-AG3.4T, it has been concluded that the isolate represents a novel species of the genus Caulobacter, for which the name Caulobacter hibisci sp. nov. is proposed. The type strain is THG-AG3.4T (=KACC 18849T=CCTCC AB 2016077T).

Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029

Sphingomonas mucosissima and Sphingomonas dokdonensis are Gram-negative chemoheterotrophic strictly aerobic rods or cocci. The genomes (3.453 Mb and 3.587 Mb, respectively) contain 3,279 and 3,329 predicted protein-encoding genes, respectively. The genome of S. dokdonensis harbors a 90-kb plasmid.

Sphingomonas gotjawalisoli sp. nov., isolated from soil of a lava forest

A bacterial strain, designated SN6-9T, was isolated from soil of the Gotjawal, lava forest, located in Jeju, Republic of Korea. Strain SN6-9T was Gram-stain-negative, motile, oxidase- and catalase-negative, yellow-pigmented and rod-shaped. It contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids, Q-10 as the predominant isoprenoid quinone, sym-homospermidine as the major polyamine and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and two unidentified phospholipids as the polar lipids. The DNA G+C content was 64.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a separate lineage in the genus Sphingomonas. Based on the results from this polyphasic taxonomic study, it is concluded that strain SN6-9T represents a novel species in the genus Sphingomonas. The name Sphingomonas gotjawalisoli sp. nov. is proposed; the type strain is SN6-9T (=KCTC 52405T=NRRL B-65395T).

Sphingomonas montana sp. nov., isolated from a soil sample from the Tanggula Mountain in the Qinghai Tibetan Plateau

An orange pigmented, Gram-staining negative, aerobic, motile, rod-shaped bacterium isolated from a soil from the Tanggula Mountain, China was studied using a polyphasic approach. Based on 16S rRNA gene sequence similarity, strain W16RD^T was found to be closely related to Sphingomonas prati DSM 103336^T (99%), Sphingomonas fennica DSM 13665^T (97.21%), followed by Sphingomonas laterariae DSM 25432^T (96.44%), Sphingomonas haloaromaticamans CGMCC 1.10206 ^T (96.36%) and Sphingomonas formosensis DSM 24164^T (96.06%). The strain was found to be catalase and oxidase positive and was found to grow optimally at temperatures of 20-25 °C, pH 8 and tolerated NaCl concentration up to 1% (w/v). The major fatty acids identified were summed feature eight comprising C_18:1 ω 7c and/or C_18:1 ω 6c (39.2%), summed feature three comprising of C_16:1 ω7c and/or C_16:1 ω6c (36.7%) and C_16:0 (7.0%). The polar lipids detected were phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, and three unidentified lipids. The strain possessed ubiquinone-10 (Q-10) as the predominant respiratory quinone. Along with other distinguishing characteristics, we also describe the draft genome of strain W16RD^T. The final assembled draft genome sequence is 3,722,743 bp with 3390 coding and 48 RNA (45 tRNA and 3 rRNA) genes. The DNA G+C content of the genomic DNA was determined to be 67%. The DNA-DNA relatedness value between the strain W16RD^T and its closest phylogenetic relatives S. prati DSM 103336^T, S. fennica DSM 13665^T, S. laterariae DSM 25432^T, and S. haloaromaticamans CGMCC 1.10206^T were 52.17, 47.60, 20.93 and 17.09% respectively. The strain W16RD^T could be distinguished genotypically and phenotypically from the recognized species belonging to the genus Sphingomonas and thus represents a novel species, for which the name Sphingomonas montana sp. nov. is proposed. The type strain is W16RD^T (=CGMCC 1.15646^T = DSM 103337^T).