scholarly journals Porticoccus hydrocarbonoclasticus sp. nov., an Aromatic Hydrocarbon-Degrading Bacterium Identified in Laboratory Cultures of Marine Phytoplankton

2011 ◽  
Vol 78 (3) ◽  
pp. 628-637 ◽  
Author(s):  
Tony Gutierrez ◽  
Peter D. Nichols ◽  
William B. Whitman ◽  
Michael D. Aitken
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Marine Phytoplankton ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sequence Comparisons ◽  
Content Type ◽  
Degrading Bacterium ◽  
Laboratory Cultures

ABSTRACTA marine bacterium, designated strain MCTG13d, was isolated from a laboratory culture of the dinoflagellateLingulodinium polyedrumCCAP1121/2 by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. Based on 16S rRNA gene sequence comparisons, the strain was most closely related toPorticoccus litoralisIMCC2115T(96.5%) and to members of the generaMicrobulbifer(91.4 to 93.7%) andMarinimicrobium(90.4 to 92.0%). Phylogenetic trees showed that the strain clustered in a distinct phyletic line in the classGammaproteobacteriafor whichP. litoralisis presently the sole cultured representative. The strain was strictly aerobic, rod shaped, Gram negative, and halophilic. Notably, it was able to utilize hydrocarbons as sole sources of carbon and energy, whereas sugars did not serve as growth substrates. The predominant isoprenoid quinone of strain MCTG13d was Q-8, and the dominant fatty acids were C16:1ω7c, C18:1ω7c, and C16:0. DNA G+C content for the isolate was 54.9 ± 0.42 mol%. Quantitative PCR primers targeting the 16S rRNA gene of this strain showed that this organism was common in other laboratory cultures of marine phytoplankton. On the basis of phenotypic and genotypic characteristics, strain MCTG13d represents a novel species ofPorticoccus, for which the namePorticoccus hydrocarbonoclasticussp. nov. is proposed. The discovery of this highly specialized hydrocarbon-degrading bacterium living in association with marine phytoplankton suggests that phytoplankton represent a previously unrecognized biotope of novel bacterial taxa that degrade hydrocarbons in the ocean.

scholarly journals Flavihumibacter cheonanensis sp. nov., isolated from sediment of a shallow stream

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3235-3239 ◽  
Author(s):  
Wan-Hoe Kim ◽  
Siwon Lee ◽  
Tae-Young Ahn
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Taxonomic Approach ◽  
Shallow Stream

A Gram-reaction-positive, rod-shaped, strictly aerobic and non-motile bacterial strain, designated WS16T, was isolated from the sediment of a shallow stream located in Cheonan, Korea. The strain grew optimally at 28 °C, at pH 7.0 and in the absence of NaCl. Phylogenetic trees based on 16S rRNA gene sequences suggested that the isolate belonged to the genus Flavihumibacter of the phylum Bacteroidetes . Comparative 16S rRNA gene sequence analysis showed that strain WS16T was related most closely to Flavihumibacter petaseus T41T (96.8 % similarity). The isolate contained MK-7 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 and iso-C17 : 0 3-OH as the major fatty acids. The genomic DNA G+C content of the isolate was 45.9 mol%. The results of a polyphasic taxonomic approach indicated that strain WS16T represents a novel species of the genus Flavihumibacter , for which the name Flavihumibacter cheonanensis sp. nov. is proposed. The type strain is WS16T ( = KACC 17467T = JCM 19322T).

Aliidiomarina indica sp. nov., isolated from deep seawater

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Lei Song ◽  
Hongcan Liu ◽  
Ying Huang ◽  
Xin Dai ◽  
Yuguang Zhou
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sea Water ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, rod-shaped bacterial strain, designated SW123T, was isolated from a deep-sea water sample collected from the Indian Ocean. Strain SW123T was strictly aerobic, catalase- and oxidase-positive. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 and summed feature 9 (comprising C16 : 0-methyl or iso-C17 : 1 ω9c). Ubiquinone-8 was the sole respiratory quinone. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content was 49.4 mol%. 16S rRNA gene sequence analysis showed that strain SW123T was closely related to Aliidiomarina shirensis AIST (96.7 % sequence similarity), Aliidiomarina iranensis GBPy7T (96.3%), Aliidiomarina haloalkalitolerans AK5T (96.0%) and Aliidiomarina celeris F3105T (95.9%). Phylogenetic trees based on 16S rRNA gene sequences showed that strain SW123T represented a novel member of the genus Aliidiomarina , forming a distinct cluster with A. celeris F3105T. On the basis of phylogenetic inference and phenotypic characteristics, we propose that strain SW123T represents a novel species of the genus Aliidiomarina , with the name Aliidiomarina indica sp. nov. The type strain is SW123T (=CGMCC1.16169T=KCTC 82234T).

scholarly journals Polycyclovorans algicola gen. nov., sp. nov., an Aromatic-Hydrocarbon-Degrading Marine Bacterium Found Associated with Laboratory Cultures of Marine Phytoplankton

2012 ◽  
Vol 79 (1) ◽  
pp. 205-214 ◽  
Author(s):  
Tony Gutierrez ◽  
David H. Green ◽  
Peter D. Nichols ◽  
William B. Whitman ◽  
Kirk T. Semple ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Aromatic Hydrocarbon ◽  
Skeletonema Costatum ◽  
Marine Phytoplankton ◽  
Marine Diatom ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Degrading Bacteria

ABSTRACTA strictly aerobic, halotolerant, rod-shaped bacterium, designated strain TG408, was isolated from a laboratory culture of the marine diatomSkeletonema costatum(CCAP1077/1C) by enrichment with polycyclic aromatic hydrocarbons (PAHs) as the sole carbon source. 16S rRNA gene sequence analysis placed this organism within the orderXanthomonadalesof the classGammaproteobacteria. Its closest relatives included representatives of theHydrocarboniphaga-Nevskia-Sinobacterclade (<92% sequence similarity) in the familySinobacteraceae. The strain exhibited a narrow nutritional spectrum, preferring to utilize aliphatic and aromatic hydrocarbon compounds and small organic acids. Notably, it displayed versatility in degrading two- and three-ring PAHs. Moreover, catechol 2,3-dioxygenase activity was detected in lysates, indicating that this strain utilizes themeta-cleavage pathway for aromatic compound degradation. Cells produced surface blebs and contained a single polar flagellum. The predominant isoprenoid quinone of strain TG408 was Q-8, and the dominant fatty acids were C16:0, C16:1ω7c, and C18:1ω7c. The G+C content of the isolate's DNA was 64.3 mol% ± 0.34 mol%. On the basis of distinct phenotypic and genotypic characteristics, strain TG408 represents a novel genus and species in the classGammaproteobacteriafor which the namePolycyclovorans algicolagen. nov., sp. nov., is proposed. Quantitative PCR primers targeting the 16S rRNA gene of this strain were developed and used to show that this organism is found associated with other species of marine phytoplankton. Phytoplankton may be a natural biotope in the ocean where new species of hydrocarbon-degrading bacteria await discovery and which contribute significantly to natural remediation processes.

scholarly journals Sphingorhabdus arenilitoris sp. nov., isolated from a coastal sand, and reclassification of Sphingopyxis rigui as Sphingorhabdus rigui comb. nov. and Sphingopyxis wooponensis as Sphingorhabdus wooponensis comb. nov.

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2551-2557 ◽  
Author(s):  
Ja-Min Park ◽  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Hyangmi Kim ◽  
Jung-Sook Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Coastal Sand ◽  
Type Strains

A Gram-stain-negative, strictly aerobic, non-flagellated and rod-shaped bacterial strain, designated GJR-7T, was isolated from coastal sand of the South Sea of South Korea. Strain GJR-7T grew optimally at 30 °C, at pH 7.0–7.5 and without NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain GJR-7T clustered with the type strains of Sphingopyxis wooponensis , Sphingopyxis rigui and Sphingorhabdus planktonica , with which it exhibited 16S rRNA gene sequence similarity values of 96.0–96.3 %. Sequence similarities to the type strains of other recognized species were less than 95.5 %. Strain GJR-7T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, 11-methyl C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) or C14 : 0 2-OH. The major polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and one unidentified glycolipid. The DNA G+C content of strain GJR-7T was 55.5 mol%. Differential phenotypic properties, together with phylogenetic distinctiveness, revealed that strain GJR-7T is separated from the type strains of Sphingopyxis wooponensis , Sphingopyxis rigui and Sphingorhabdus planktonica . On the basis of the data presented, strain GJR-7T is considered to represent a novel species of the genus Sphingorhabdus , for which the name Sphingorhabdus arenilitoris sp. nov. is proposed. The type strain is GJR-7T ( = KCTC 42051T = CECT 8531T). It is also proposed that Sphingopyxis wooponensis and Sphingopyxis rigui should be reclassified as members of the genus Sphingorhabdus .

scholarly journals Bacillus salinus sp. nov., isolated from commercial solar salt

2020 ◽  
Vol 70 (4) ◽  
pp. 2696-2702 ◽  
Author(s):  
Heeyoung Kang ◽  
Jinkyeong Kang ◽  
Inseong Cha ◽  
Haneul Kim ◽  
Yochan Joung ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Polar Lipids ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

Two strains of Gram-stain-positive, strictly aerobic, motile, spore-forming, rod-shaped, moderately halotolerant bacteria, designated as HMF5848T and HME7618, were isolated from salt/brine and subjected to a polyphasic taxonomic investigation. Growth of both yellow-coloured strains occurred in the presence of 1–9 % NaCl (w/v; optimum, 2–3 %), at 15–45 °C (optimum, 37 °C) and pH 6–9 (optimum, pH 7). The major fatty acids were iso-C15 : 0, iso-C16 : 0 and anteiso-C15 : 0. The cell-wall peptidoglycan was meso-diaminopimelic acid. The only respiratory quinone was menaquinone-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, four unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. DNA G+C content was 37.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strains HMF5848T and HME7618 clustered with Bacillus luteolus YIM 93174T. Strains HMF5848T showed the highest 16S rRNA gene sequence similarities to Bacillus humi LMG 22167T (96.1 %), Bacillus isabeliae CVS-8T (96.0 %) and Bacillus luteolus YIM 93174T (96.0 %). The values of in silico DNA–DNA hybridization and average nucleotide identity between strains HMF5848T and B. humi DSM 16318T were 25.8 and 69.7 %, respectively. On the basis of phylogenetic, physiological and chemotaxonomic properties, strain HMF5848T represents a novel species, Bacillus salinus sp. nov. The type strain is HMF5848T (=KCTC 43010T=CECT 9695T).

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

scholarly journals Sphingopyxis italica sp. nov., isolated from Roman catacombs

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2565-2569 ◽  
Author(s):  
Cynthia Alias-Villegas ◽  
Valme Jurado ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Dna Base ◽  
Physiological Tests

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

Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov., isolated from forest soil

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Hye Su Jung ◽  
Byung Hee Chun ◽  
Hyung Min Kim ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Forest Soil ◽  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type

Two Gram-stain-negative, yellow-pigmented and strictly aerobic bacteria, designated strains SE-s27T and SE-s28T, were isolated from forest soil. Both strains were non-motile rods that were catalase-positive and oxidase-negative and grew optimally at 25–30 °C, pH 8.0 and with 0 % (w/v) NaCl. Strain SE-s28T produced flexirubin-type pigments, but strain SE-s27T did not produce them. Both strains contained menaquinone-6 as the sole respiratory quinone and phosphatidylethanolamine as a major polar lipid. As the major cellular fatty acids (>10 %), SE-s27T contained iso-C15 : 1 and iso-C15 : 1G, whereas SE-s28T contained iso-C15 : 0 and summed feature 3 comprising C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH. The DNA G+C contents of strains SE-s27T and SE-s28T were 33.1 and 44.3 mol%, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that SE-s27T and SE-s28T formed respective distinct phylogenetic lineages within the genus Flavobacterium . Strains SE-s27T and SE-s28T were most closely related to Flavobacterium macrobrachii an-8T and Flavobacterium piscinae ICH-30T with 98.0 and 94.5 % 16S rRNA gene sequence similarities, respectively. In conclusion, strains SE-s27T and SE-s28T represent novel species of the genus Flavobacterium , for which the names Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov. are proposed. The type strains of F. solisilvae and F. silvaticum are SE-s27T (=KACC 18802T=JCM 31544T) and SE-s28T (=KACC 18803T=JCM 31545T), respectively.

scholarly journals Aliiglaciecola aliphaticivorans sp. nov., an aliphatic hydrocarbon-degrading bacterium, isolated from a sea-tidal flat and emended description of the genus Aliiglaciecola Jean et al. 2013

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1550-1555 ◽  
Author(s):  
Hyun Mi Jin ◽  
Hye Im Jeong ◽  
Che Ok Jeon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Molecular Features ◽  
Degrading Bacterium ◽  
Emended Description

A Gram-stain-negative heterotrophic bacterium, designated GSD6T, capable of growth on aliphatic hydrocarbons as a sole carbon and energy source, was isolated from sea-tidal flat sediment of the Yellow Sea, South Korea. Cells were facultatively aerobic, catalase- and oxidase-positive, motile rods with a single polar flagellum. Growth of strain GSD6T was observed at 4–37 °C (optimum 30 °C), at pH 5.5–9.0 (optimum pH 6.5–7.5) and in the presence of 1–9 % (w/v) NaCl (optimum 2 %). Strain GSD6T contained ubiquinone-8 (Q-8) as the sole isoprenoid quinone and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C18 : 1ω7c, C17 : 0 10-methyl and C17 : 1ω8c as the major fatty acids. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 44.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSD6T formed a phylogenetic lineage with members of the genus Aliiglaciecola . Strain GSD6T was most closely related to Aliiglaciecola lipolytica E3T with a 16S rRNA gene sequence similarity of 97.4 %, but their DNA–DNA hybridization value was 39.1±7.1 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain GSD6T represents a novel species of the genus Aliiglaciecola , for which the name Aliiglaciecola aliphaticivorans sp. nov. is proposed. The type strain is GSD6T ( = KACC 18129T = JCM 30133T). An emended description of the genus Aliiglaciecola is also proposed.

Flavobacterium enshiense sp. nov., isolated from soil, and emended descriptions of the genus Flavobacterium and Flavobacterium cauense , Flavobacterium saliperosum and Flavobacterium suncheonense

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 886-892 ◽  
Author(s):  
Kun Dong ◽  
Fang Chen ◽  
Yan Du ◽  
Gejiao Wang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
The City

A Gram-negative, strictly aerobic, yellow-pigmented rod, designated DK69T, was isolated from soil collected from the waste liquid treatment facility of Bafeng Pharmaceutical Company in the city of Enshi, Hubei Province, China. Phylogenetic analysis based on 16S rRNA gene sequences placed strain DK69T in the genus Flavobacterium of the family Flavobacteriaceae . The highest 16S rRNA gene sequence similarities were found with Flavobacterium cauense R2A-7T (96.9 %), Flavobacterium saliperosum AS 1.3801T (96.3 %) and Flavobacterium suncheonense GH29-5T (95.7 %). The major fatty acids (≥5 %) were iso-C15 : 0, iso-C17 : 1ω9c, C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The major respiratory quinone was menaquinone-6. The genomic DNA G+C content was 34.4 mol%. Strain DK69T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium enshiense sp. nov. is proposed. The type strain is DK69T ( = CCTCC AB 2011144T  = KCTC 23775T). Emended descriptions of the genus Flavobacterium and Flavobacterium cauense , Flavobacterium saliperosum and Flavobacterium suncheonense are also proposed.

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