Sphingobacterium caeni sp. nov., isolated from activated sludge

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2260-2264 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Qing Chen ◽  
Jian He ◽  
Shun-Peng Li
Keyword(s):  
Phylogenetic Analysis ◽  
Activated Sludge ◽  
Dna Hybridization ◽  
Type Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach ◽  
Ph Range

The taxonomic status of a bacterium, strain DC-8T, isolated from activated sludge, was determined using a polyphasic taxonomic approach. The cells of strain DC-8T were Gram-negative, non-motile, non-spore-forming and rod-shaped. The isolate grew at temperature range of 10–40 °C (optimum 30–35 °C), pH range of 5.0–10.0 (optimum 6.5–8.0) and NaCl concentrations of 0–5 % (optimum 0–1 %). The predominant menaquinone of strain DC-8T was MK-7 and major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 39.7 %), iso-C15 : 0 (33.7 %) and C16 : 0 (5.2 %). The DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain DC-8T was a member of the genus Sphingobacterium . Strain DC-8T shared the highest similarity with Sphingobacterium siyangense SY1T (98.4 %), Sphingobacterium multivorum IAM 14316T (98.3 %), Sphingobacterium canadense CR11T (98.0 %) and Sphingobacterium detergens 6.2ST (97.9 %) and shared less than 97 % similarity with other members of the genus Sphingobacterium . DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain DC-8T and its closest phylogenetic neighbours were below 70 %. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain DC-8T was clearly distinguished from all recognized species of the genus Sphingobacterium and should be classified as a representative of a novel species of the genus Sphingobacterium , for which the name Sphingobacterium caeni sp. nov. is proposed. The type strain is DC-8T ( = CCTCC AB 2012020T = KACC 16850T).

scholarly journals Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide–degrading bacterium isolated from activated sludge

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2573-2578 ◽  
Author(s):  
Qing Chen ◽  
Jun Zhang ◽  
Cheng-Hong Wang ◽  
Jin Jiang ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Activated Sludge ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Sequence Similarities

Strain BUT-14T, a Gram-reaction-negative, non-spore-forming, ellipse-shaped bacterium, was isolated from activated sludge of a chloroacetamide-herbicides-manufacturing wastewater treatment facility. The strain was able to degrade more than 90 % of butachlor, acetochlor and alachlor (100 mg l−1) within 5 days of incubation. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-14T was a member of the genus Novosphingobium and showed the highest sequence similarities to Novosphingobium soli DSM 22821T (97.9 %), N. naphthalenivorans KACC 15258T (97.4 %), N. pentaromativorans JCM 12182T (97.4 %) and N. barchaimii DSM 25411T (97.1 %) and lower (<97 %) sequence similarities to all other species of the genus Novosphingobium . Chemotaxonomic analysis revealed that strain BUT-14T possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine and C18 : 1ω7c (46.9 %), C17 : 1ω6c (17.9 %), summed feature 3, C14 : 0 2-OH (4.4 %), C15 : 0 2-OH (3.1 %) and C16 : 0 (5.51 %) as the major fatty acids. The polar lipids included lipid, glycolipid, phosphatidylglycerol, phospholipid, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phospatidyldimethylethanolamine. Strain BUT-14T showed low DNA–DNA relatedness with N. soli DSM 22821T (41.5±2.9 %), N. naphthalenivorans JCM 12182T (49.2±4.2 %), N. pentaromativorans KACC 12295T (53.2±1.9 %) and N. barchaimii DSM 25411 (51.2±4.5 %). The DNA G+C content was 66±0.3 mol%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic data and DNA–DNA hybridization supports the suggestion that strain BUT-14T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-14T ( = CCTCC AB 2013086T = KACC 17147T = JCM 19923T).

Rhizobium paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis)

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3823-3828 ◽  
Author(s):  
Chokchai Kittiwongwattana ◽  
Chitti Thawai
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Low Levels ◽  
Sequence Similarity Analysis ◽  
Ph Range

A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus Rhizobium . Its closest relatives were Rhizobium borbori DN316T (97.6 %), Rhizobium oryzae Alt 505T (97.3 %) and Rhizobium pseudoryzae J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and R. borbori DN316T, R. oryzae Alt505T and R. pseudoryzae J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium , for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).

Paracoccus huijuniae sp. nov., an amide pesticide-degrading bacterium isolated from activated sludge of a wastewater biotreatment system

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1132-1137 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Soon-Wo Kwon ◽  
Jian He ◽  
Shun-Gui Zhou ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Type Species ◽  
Amide Bond ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A facultatively anaerobic, non-spore-forming, non-motile, catalase- and oxidase-positive, Gram-reaction-negative, coccoid to short rod-shaped strain, designated FLN-7T, was isolated from activated sludge of a wastewater biotreatment facility. The strain was able to hydrolyse amide pesticides (e.g. diflubenzuron, propanil, chlorpropham and dimethoate) through amide bond cleavage. Strain FLN-7T grew at 4–42 °C (optimum 28 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–5.0 % (w/v) NaCl (optimum 1.0 %). The major respiratory quinone was ubiquinone-10. The major cellular fatty acid was C18 : 1ω7c. The genomic DNA G+C content of strain FLN-7T was 66.4±0.5 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain FLN-7T was a member of the genus Paracoccus and showed highest 16S rRNA gene sequence similarities with Paracoccus aminovorans JCM 7685T (99.2 %), P. denitrificans DSM 413T (97.8 %), P. yeei CDC G1212T (97.3 %) and P. thiocyanatus THI 011T (97.1 %). Strain FLN-7T showed low DNA–DNA relatedness with P. aminovorans KACC 12261T (36.5±3.4 %), P. denitrificans KACC 12251T (30.5±2.6 %), P. yeei CCUG 46822T (26.2±2.4 %) and P. thiocyanatus KACC 13901T (15.5±0.9 %). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain FLN-7T was clearly distinguished from all recognized species of the genus Paracoccus and should be classified in a novel species, for which the name Paracoccus huijuniae sp. nov. is proposed. The type strain is FLN-7T ( = KACC 16242T  = ACCC 05690T).

Luteimonas huabeiensis sp. nov., isolated from stratum water

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3352-3357 ◽  
Author(s):  
Gang Wu ◽  
Yang Liu ◽  
Qing Li ◽  
Huijing Du ◽  
Jing You ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical Characteristics ◽  
Taxonomic Approach ◽  
Type Strains ◽  
Physiological And Biochemical

A yellow-coloured bacterial strain, designated HB2T, isolated from stratum water was investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a member of the genus Luteimonas , its three closest neighbours being Luteimonas aquatica BCRC 17731T (97.5 % similarity), Luteimonas marina JCM 12488T (97.3 %) and Luteimonas aestuarii DSM 19680T (96.9 %). Strain HB2T could clearly be distinguished from these type strains based on phylogenetic analysis, DNA–DNA hybridization, fatty acid composition and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain HB2T represents a novel species of the genus Luteimonas , for which the name Luteimonas huabeiensis sp. nov. is proposed. The type strain is HB2T ( = DSM 26429T = CICC 11005sT).

Comamonas jiangduensis sp. nov., a biosurfactant-producing bacterium isolated from agricultural soil

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2168-2173 ◽  
Author(s):  
Li-Na Sun ◽  
Jun Zhang ◽  
Qing Chen ◽  
Jian He ◽  
Qin-Fen Li ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Type Species ◽  
Agricultural Soil ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Sequence Similarities

A novel biosurfactant-producing strain, designated YW1T, was isolated from agricultural soil. Its taxonomic position was investigated using a polyphasic approach. The cells were short rods, Gram-negative, non-sporulating and motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YW1T was a member of the genus Comamonas , and showed highest sequence similarities to Comamonas aquatica LMG 2370T (98.5 %), Comamonas kerstersii LMG 3475T (97.7 %) and Comamonas terrigena LMG 1253T (97.7 %). Furthermore, DNA–DNA hybridization experiments against these three strains gave results that were clearly lower than 70 % DNA–DNA similarity, and consequently confirmed that this new strain does not belong to a previously described species of the genus Comamonas . The major respiratory quinone was ubiquinone-8. The major fatty acids (>5 %) were C16 : 0 (30.1 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 25.4 %), summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c; 15.3 %), C17 : 0 cyclo (7.4 %) and C14 : 0 (5.8 %). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, unknown phospholipids and unknown lipids. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain YW1T was clearly distinguishable from all species of the genus Comamonas with validly published names and should be classified as a representative of a novel species of the genus Comamonas , for which the name Comamonas jiangduensis sp. nov. is proposed. The type strain is YW1T ( = CCTCC AB 2012033T = KACC 16697T).

scholarly journals Streptosporangium jomthongense sp. nov., an actinomycete isolated from rhizospheric soil and emendation of the genus Streptosporangium

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2400-2406 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Watanalai Panbangred ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain 30EHST, was isolated from the rhizospheric soil under an elephant ear plant (Caladium bicolor) in Jomthong district, Bangkok, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 30EHST fell within the cluster of the genus Streptosporangium . Chemical composition analysis confirmed that the strain represented a member of the genus Streptosporangium even though this strain produced a tightly packed single spore on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain 30EHST was most closely related to Streptosporangium fragile NBRC 14311T (98.1 %), Streptosporangium carneum NBRC 15562T (97.8 %) and Streptosporangium violaceochromogenes NBRC 15560T (97.4 %). The DNA–DNA hybridization relatedness values between strain 30EHST and the above three strains were below 70 %. Based on combined data for phylogenetic analysis, DNA–DNA hybridization relatedness and physiological characteristics, it was concluded that strain 30EHST should be classified as representing a novel species of the genus Streptosporangium . We propose the name Streptosporangium jomthongense sp. nov., with the type strain 30EHST ( = BCC 53154T = NBRC 110047T). An emended description of the genus Streptosporangium is also proposed.

scholarly journals Reclassification of Clostridium diolis Biebl and Spröer 2003 as a later heterotypic synonym of Clostridium beijerinckii Donker 1926 (Approved Lists 1980) emend. Keis et al. 2001

2020 ◽  
Vol 70 (4) ◽  
pp. 2463-2466 ◽  
Author(s):  
Hisami Kobayashi ◽  
Yasuhiro Tanizawa ◽  
Mitsuo Sakamoto ◽  
Yasukazu Nakamura ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Type Species ◽  
Taxonomic Status ◽  
Clostridium Beijerinckii ◽  
Rrna Gene ◽  
High Similarity ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Clostridium diolis shares high similarity based on 16S rRNA gene sequences and fatty acid composition with Clostridium beijerinckii . In this study, the taxonomic status of C. diolis was clarified using genomic and phenotypic approaches. High similarity was detected among C. diolis DSM 15410T, C. beijerinckii DSM 791T and NCTC 13035T, showing average nucleotide identity on blast and in silico DNA–DNA hybridization values over 97 and 85 %, respectively. Results of investigations for substrate utilization and enzyme activity displayed no striking differences between C. diolis DSM 15410T and C. beijerinckii JCM 1390T. Based on the results, we propose the reclassification of Clostridium diolis as a later heterotypic synonym of Clostridium beijerinckii . The type strain is ATCC 25752T (=CIP 104308T=DSM 791T=JCM 1390T=LMG 5716T=NCTC 13035T).

Mycobacterium vicinigordonae sp. nov., a slow-growing scotochromogenic species isolated from sputum

2021 ◽  
Vol 71 (5) ◽  
Author(s):  
Guan Liu ◽  
Xia Yu ◽  
Jingjing Luo ◽  
Yanjie Hu ◽  
Lingling Dong ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Taxonomic Status ◽  
Mycolic Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Slow Growing ◽  
Chinese Male ◽  
Mycobacterial Strain

A slow-growing, scotochromogenic mycobacterial strain (24T) was isolated from the sputum of a Chinese male human. Phylogenetic analysis using the 16S rRNA gene assigned strain 24T to the Mycobacterium gordonae complex, which includes Mycobacterium gordonae and Mycobacterium paragordonae . The phenotypic characteristics, unique mycolic acid profile and the results of phylogenetic analysis based on hsp65 and rpoB sequences strongly supported the taxonomic status of strain 24T as a representative of a species distinct from the other members of the M. gordonae complex. The genomic G+C content of strain 24T was 65.40mol%. Genomic comparisons showed that strain 24T and M. gordonae ATCC 14470T had an average nucleotide identity (ANI) value of 81.00 % and a DNA–DNA hybridization (DDH) value of 22.80 %, while the ANI and DDH values between strain 24Tand M. paragordonae 49 061T were 80.98 and 22.80 %, respectively. In terms of phylogenetic, phenotypic and chemotaxonomic features, strain 24T is distinguishable from its closest phylogenetic relatives and represents a novel species of the genus Mycobacterium , therefore the name Mycobacterium vicinigordonae sp. nov. is proposed. The type strain is 24T (=CMCC 93559T=DSM 105979T).

Reclassification of Sphingobacterium antarcticum Shivaji et al. 1992 as Pedobacter antarcticus comb. nov. and Pedobacter piscium (Takeuchi and Yokota 1993) Steyn et al. 1998 as a later heterotypic synonym of Pedobacter antarcticus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 863-868 ◽  
Author(s):  
Maribel Farfán ◽  
María Jesús Montes ◽  
Ana M. Marqués
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
The Family

The taxonomic position of Sphingobacterium antarcticum has been revised by means of 16S rRNA gene sequences, DNA–DNA hybridization, and phenotypic and chemotaxonomic characteristics. All data previously reported, as well as the results of the present phylogenetic analysis, support that Sphingobacterium antarcticum is clearly a member of the genus Pedobacter , also affiliated with the family Sphingobacteriaceae . We propose that Sphingobacterium antarcticum (corrig. Shivaji et al. 1992) should be reclassified as Pedobacter antarcticus comb. nov.

Chryseobacterium carnipullorum sp. nov., isolated from raw chicken

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3243-3249 ◽  
Author(s):  
George Charimba ◽  
Piet Jooste ◽  
Jacobus Albertyn ◽  
Celia Hugo
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Processing Plant ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Taxonomic Approach ◽  
The 16S Rrna Gene

Three Gram-staining-negative, rod-shaped, non-spore-forming, non-motile, oxidase-positive, yellow pigmented and aerobic bacterial isolates designated 8_R23573, 9_R23581T and 10_R23577 were isolated from raw chicken at a broiler processing plant in Bloemfontein, South Africa. A polyphasic taxonomic approach was used to determine their exact taxonomic identities. Phylogenetic analysis of the 16S rRNA gene sequences showed that the three strains belonged to the genus Chryseobacterium , exhibiting the highest similarities to Chryseobacterium shigense DSM 17126T (98.6–99.2 %) and Chryseobacterium luteum DSM 18605T (98.3–98.7 %). The most abundant quinone was menaquinone MK-6 and the predominant cellular fatty acids were iso-15 : 0, iso-17 : 1ω9c, iso-17 : 0 3-OH and summed feature 3 (iso-16 : 1ω7c and/or iso-15 : 0 2-OH), which supported the affiliation of the strains to the genus Chryseobacterium . The DNA G+C contents of the strains were 36.9, 36.7 and 36.6 mol% respectively. The DNA–DNA hybridization results gave relatedness values ranging from 78.8 to 87.2 % among the three strains and 23.4 to 56.1 % to the two nearest phylogenetic neighbours C. shigense DSM 17126T and C. luteum LMG 23785T. On the basis of the data from this polyphasic study, the three strains are concluded to represent a novel species of the genus Chryseobacterium for which the name Chryseobacterium carnipullorum sp. nov. is proposed. The type strain is 9_R23581T ( = LMG 26732T = DSM 25581T).

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