Guang-Da Feng

Burkholderia dabaoshanensis sp. nov., a heavy-metal-tolerant bacteria isolated from Dabaoshan mining area soil in China.

Heavy-metal-tolerant bacteria, GIMN1.004T, was isolated from mine soils of Dabaoshan in South China, which were acidic (pH 2–4) and polluted with heavy metals. The isolation was Gram-negative, aerobic, non-spore-forming, and rod-shaped bacteria having a cellular width of 0.5−0.6 µm and a length of 1.3−1.8 µm. They showed a normal growth pattern at pH 4.0–9.0 in a temperature ranging from 5°C to 40°C.The organism contained ubiquinone Q-8 as the predominant isoprenoid quinine, and C16∶0, summed feature 8 (C18∶1 ω7c and C18∶1 ω6c), C18∶0, summed feature 3 (C16∶1 ω7c or iso-C15∶0 2-OH), C17∶0 cyclo, C18∶1 ω9c, C19∶0 cyclo ω8c, C14∶0 as major fatty acid. These profiles were similar to those reported for Burkholderia species. The DNA G+C % of this strain was 61.6%. Based on the similarity to 16S rRNA gene sequence, GIMN1.004T was considered to be in the genus Burkholderia. The similarities of 16S rRNA gene sequence between strain GIMN1.004T and members of the genus Burkholderia were 96−99.4%, indicating that this novel strain was phylogenetically related to members of that genus. The novel strain showed the highest sequence similarities to Burkholderia soli DSM 18235T (99.4%); Levels of DNA-DNA hybridization with DSM 18235T was 25%. Physiological and biochemical tests including cell wall composition analysis, differentiated phenotype of this strain from that closely related Burkholderia species. The isolation had great tolerance to cadmium with MIC of 22 mmol/L, and adsorbability of 144.94 mg/g cadmium,and it was found to exhibit antibiotic resistance characteristics. The adsorptive mechanism of GIMN1.004T for cadmium depended on the action of the amide,carboxy and phosphate of cell surface and producing low-molecular-weight (LMW ) organic acids to complex or chelated Cd2+.Therefore, the strain GIMN1.004T represented a new cadmium resistance species, which was tentatively named as Burkholderia dabaoshanensis sp. nov. The strain type is GIMN1.004T ( = CCTCC M 209109T =  NRRL B-59553T ).

Lysobacter mobilis sp. nov., isolated from abandoned lead-zinc ore.

An aerobic and Gram-stain-negative bacterial strain, designated 9NM-14(T), was isolated from abandoned lead-zinc ore from Meizhou, Guangdong Province, south China. Strain 9NM-14(T) was motile by means of a single polar flagellum. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain 9NM-14(T) was affiliated with the genus Lysobacter and was most closely related to Lysobacter xinjiangensis RCML-52(T) and Lysobacter bugurensis ZLD-29(T) (97.4 % and 96.3 % 16S rRNA gene sequence similarity, respectively). The DNA-DNA relatedness value between strain 9NM-14(T) and L. xinjiangensis RCML-52(T) was 30.1±7.6 %. The major respiratory quinone was unbiquinone 8 (Q-8) and the major cellular fatty acids consisted of iso-C17 : 1ω9c (29.1 %), iso-C15 : 0 (28.9 %), iso-C17 : 0 (9.4 %), iso-C16 : 0 (8.6 %), iso-C11 : 0 3-OH (6.9 %) and iso-C11 : 0 (5.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminolipid and five unidentified phospholipids. The genomic DNA G+C content of strain 9NM-14(T) was 70.7±0.1 mol%. On the basis of the data from this polyphasic taxonomic study, strain 9NM-14(T) should be assigned to a novel species of the genus Lysobacter, for which the name Lysobacter mobilis sp. nov. is proposed. The type strain is 9NM-14(T) ( = GIMCC 1.659(T) = CCTCC AB 2014273(T) = DSM 27574(T)).

Massilia putida sp. nov., a dimethyl disulfide-producing bacterium isolated from wolfram mine tailing.

A heavy metal-resistant and dimethyl disulfide-producing bacterial strain, designated 6NM-7T, was isolated from wolfram mine tailing, Dayu County, Jiangxi Province, PR China. Strain 6NM-7T was aerobic, Gram-stain-negative and motile by means of a single polar flagellum. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain 6NM-7T was affiliated with the genus Massilia and was closely related to Massilia norwichensis LMG 28164T (98.8 % 16S rRNA gene sequence similarity), Massilia kyonggiensis KACC 17471T (98.4 %), Massilia niastensis KACC 12599T (97.8 %), Massilia tieshanensis KACC 14940T (97.3 %), Massilia haematophila KACC 13771T (97.2 %), Massilia namucuonensis CGMCC 1.11014T (97.1 %) and Massilia aerilata KACC 12505T (97.1 %). The DNA-DNA relatedness values between strain 6NM-7T and its closely related type strains were all below 70 %. The major respiratory quinone was unbiquinone 8 (Q-8) and the major cellular fatty acids consisted of C16 : 0 (33.2 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 21.8 %), C17 : 0 cyclo (20.8 %), C18 : 1ω7c (7.4 %) and C10 : 0 3-OH (5.8 %). The major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The genomic DNA G+C content of strain 6NM-7T was 66.8 ± 0.6 mol%. On the basis of the results of this polyphasic taxonomic study, strain 6NM-7T should be assigned to a novel species of the genus Massilia, for which the name Massilia putida sp. nov. is proposed. The type strain is 6NM-7T ( = DSM 27523T = KCTC 42761T).

Acinetobacter guangdongensis sp. nov., isolated from abandoned lead-zinc ore.

A Gram-stain-negative, non-motile bacterial strain designated 1NM-4(T) was isolated from an abandoned lead-zinc ore mine site in Mei County, Meizhou, Guangdong Province, southern China. The isolate was light yellow, strictly aerobic, oxidase-negative and catalase-positive. Phylogenetic analyses based on 16S rRNA, rpoB and gyrB gene sequences, together with DNA-DNA hybridization values less than 70%, revealed that strain 1NM-4(T) belongs to the genus Acinetobacter and may represent a novel species. The major respiratory quinone was ubiquinone 9 (Q-9) and the major cellular fatty acids consisted of C18:1ω9c, summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0 and C12:0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain 1NM-4(T) was 47.17 ± 0.02 mol%. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain 1NM-4(T) should be assigned to a novel species of the genus Acinetobacter, for which the name Acinetobacter guangdongensis sp. nov. is proposed. The type strain is 1NM-4(T) ( = GIMCC 1.656(T) = CCTCC AB 2014199(T) = KCTC 42012(T)).

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

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

Sphingomonas spermidinifaciens sp. nov., a novel bacterium containing spermidine as the major polyamine, isolated from an abandoned lead–zinc mine and emended descriptions of the genus Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica

A yellow-pigmented bacterial strain, designated 9NM-10T, was isolated from an abandoned lead-zinc mine in Meizhou, Guangdong Province, China. Cells were strictly aerobic, Gram-stain-negative and motile with a polar monotrichous flagellum. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain 9NM-10T belongs to the genus Sphingomonas and was most closely related to Sphingomonas yantingensis JCM 19201T and Sphingomonas japonica JCM 15438T. DNA-DNA relatedness values between strain 9NM-10T and these two type strains were 43.6±1.3 and 35.4±0.9 %, respectively. It contained Q-10 as the predominant respiratory quinone and the major cellular fatty acids were C18 : 1ω7c, C16 : 0, C17 : 1ω6c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The genomic DNA G+C content of strain 9NM-10T was 68.7±0.2 mol%. The polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and three unidentified lipids. Strain 9NM-10T contained spermidine as the major polyamine. On the basis of phenotypic, phylogenetic and chemotaxonomic analyses, strain 9NM-10T is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas spermidinifaciens sp. nov. is proposed. The type strain is 9NM-10T (=GDMCC 1.657T=DSM 27571T). Descriptions of the genus of Sphingomonas and the species Sphingomonas yantingensis and Sphingomonas japonica were also emended in this study.

Deinococcus metalli sp. nov., isolated from an abandoned lead-zinc mine.

An aerobic, non-motile and Gram-staining-positive bacterial strain (1PNM-19T) was isolated from a lead-zinc ore in an abandoned mine and was investigated in a taxonomic study using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 1PNM-19T was affiliated to the genus Deinococcus and most closely related to Deinococcus aquatilis DSM 23025T and Deinococcus ficus DSM 19119T. The major respiratory quinone was determined to be menaquinone 8 (MK-8) and the major fatty acids contained summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. A complex polar lipid profile consisted of different unidentified glycolipids and polar lipids, two unidentified aminolipids, an unidentified phosphoglycolipid, phospholipid and aminophospholipid. The genomic DNA G+C content of strain 1PNM-19T was 71.7 ± 0.1 mol%. Based on data from this taxonomic study, strain 1PNM-19T represents a novel species of the genus Deinococcus, for which the name Deinococcus metalli sp. nov. is proposed. The type strain is 1PNM-19T ( = GIMCC 1.654T = CCTCC AB 2014198T = DSM 27521T).

Complete genome sequence of Streptomyces vietnamensis GIMV4.0001 T, a genetically manipulable producer of the benzoisochromanequinone antibiotic granaticin.

We report the complete genome sequence of Streptomyces vietnamensis GIMV4.0001(T), a new and genetically manipulable producer of the benzoisochromanequinone antibiotic granaticin, whose unique sugar attachment pattern in structure has drawn much attention among chemical and biochemical researchers. The genome of S. vietnamensis GIMV4.0001(T) consists of one linear chromosome (8,867,142 bp, 72.09% G+C content) and one linear megaplasmid named pSVL1 (286,635 bp, 69.04% G+C content), encoding a total of 7356 protein coding genes. Twenty-nine gene clusters for secondary metabolites were predicted on the chromosome.

Reclassification of Sphingopyxis contaminans as Sphingorhabdus contaminans comb. nov. and emended description of the genus Sphingorhabdus.

With the description of the genus Sphingorhabdus, the taxonomic position of Sphingopyxis contaminans was re-evaluated based on analyses of 16S rRNA gene sequences and phenotypic and chemotaxonomic characteristics. The results revealed that Sphingopyxis contaminans is clearly a member of the genus Sphingorhabdus and we proposed that Sphingopyxis contaminans(Subhash Y, Sasikala C, Ramana CV. Int J Syst Evol Microbiol 2014;64:2238-2243) should be reclassified as Sphingorhabduscontaminans comb. nov. An emended description of the genus Sphingorhabdus is also provided.

Erratum to: Acinetobacter refrigeratoris sp. nov., Isolated from a Domestic Refrigerator.

The original version of this article unfortunately contained an error in title. The etymology of species name was incorrect based on The International Code of Nomenclature of Prokaryotes. The correct epithet is refrigeratoris (re.fri.ge.ra.to’ris. N.L. gen. n. refrigeratoris of a refrigerator, from which the type strain was isolated). The correct title is ‘‘Acinetobacter refrigeratoris sp. nov., Isolated from a Domestic Refrigerator’’. In the species description, the deposition numbers of type strain in different Culture collection center are the same as the original paper.