Homologous npdGI Genes in 2,4-Dinitrophenol- and 4-Nitrophenol-Degrading Rhodococcus spp

ABSTRACT Rhodococcus (opacus) erythropolis HL PM-1 grows on 2,4,6-trinitrophenol or 2,4-dinitrophenol (2,4-DNP) as a sole nitrogen source. The NADPH-dependent F420 reductase (NDFR; encoded by npdG) and the hydride transferase II (HTII; encoded by npdI) of the strain were previously shown to convert both nitrophenols to their respective hydride Meisenheimer complexes. In the present study, npdG and npdI were amplified from six 2,4-DNP degrading Rhodococcus spp. The genes showed sequence similarities of 86 to 99% to the respective npd genes of strain HL PM-1. Heterologous expression of the npdG and npdI genes showed that they were involved in 2,4-DNP degradation. Sequence analyses of both the NDFRs and the HTIIs revealed conserved domains which may be involved in binding of NADPH or F420. Phylogenetic analyses of the NDFRs showed that they represent a new group in the family of F420-dependent NADPH reductases. Phylogenetic analyses of the HTIIs revealed that they form an additional group in the family of F420-dependent glucose-6-phosphate dehydrogenases and F420-dependent N 5,N 10-methylenetetrahydromethanopterin reductases. Thus, the NDFRs and the HTIIs may each represent a novel group of F420-dependent enzymes involved in catabolism.

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Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004959 ◽

2021 ◽

Vol 71 (8) ◽

Author(s):

Shan Jiang ◽

Feng-Bai Lian ◽

You-Yang Sun ◽

Xiao-Kui Zhang ◽

Zong-Jun Du

Keyword(s):

Type Species ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

Gene Sequences ◽

Unidentified Phospholipid ◽

Respiratory Quinone ◽

Content Type ◽

Link Type ◽

The Family ◽

Sequence Similarities

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1 ω7c / C18 : 1 ω6c; 60.7 %), summed feature 3 (C16 : 1 ω7c/C16 : 1 ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).

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Purification of arginase from Aspergillus nidulans.

Acta Biochimica Polonica ◽

10.18388/abp.1994_4700 ◽

1994 ◽

Vol 41 (4) ◽

pp. 467-471 ◽

Cited By ~ 4

Author(s):

A Dzikowska ◽

J P Le Caer ◽

P Jonczyk ◽

P Wëgleński

Keyword(s):

Saccharomyces Cerevisiae ◽

Neurospora Crassa ◽

Molecular Mass ◽

Nitrogen Source ◽

Aspergillus Nidulans ◽

Sole Nitrogen Source ◽

Mass Ratio ◽

Conserved Domains ◽

Native Molecular Mass ◽

High Degree

Arginase (EC 3.5.3.1) of Aspergillus nidulans, the enzyme which enables the fungus to use arginine as the sole nitrogen source was purified to homogeneity. Molecular mass of the purified arginase subunit is 40 kDa and is similar to that reported for the Neurospora crassa (38.3 kDa) and Saccharomyces cerevisiae (39 kDa) enzymes. The native molecular mass of arginase is 125 kDa. The subunit/native molecular mass ratio suggests a trimeric form of the protein. The arginase protein was cleaved and partially sequenced. Two out of the six polypeptides sequenced show a high degree of homology to conserved domains in arginases from other species.

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Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.022327-0 ◽

2011 ◽

Vol 61 (4) ◽

pp. 742-746 ◽

Cited By ~ 23

Author(s):

Onuma Kaewkla ◽

Christopher M. M. Franco

Keyword(s):

Sequence Similarity ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

Spore Surface ◽

Biochemical Tests ◽

Liquid Culture Medium ◽

Endophytic Actinobacterium ◽

The Family ◽

The Media ◽

Sequence Similarities

A novel strain, designated EUM 374T, was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374T grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095T and Pseudonocardia spinosispora LM 141T, respectively, and 93–96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374T from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374T ( = DSM 45351T = ACM 5285T).

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Gryllotalpicola reticulitermitis sp. nov., isolated from a termite gut

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.062984-0 ◽

2015 ◽

Vol 65 (Pt_1) ◽

pp. 85-89 ◽

Cited By ~ 12

Author(s):

Hao Fang ◽

Wanyu Lv ◽

Zhou Huang ◽

Shuang-Jiang Liu ◽

Hong Yang

Keyword(s):

Type Strain ◽

Phylogenetic Analyses ◽

Cellular Fatty Acid ◽

Rrna Gene ◽

Polar Lipid Profile ◽

Content Type ◽

Link Type ◽

Light Yellow ◽

The Family ◽

Sequence Similarities

Strain TS-56T was isolated from the gut of a wood-feeding termite, Reticulitermes chinensis Snyder. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain represented a member of the genus Gryllotalpicola of the family Microbacteriaceae , with sequence similarities to other species of the genus ranging from 96.6 % to 97.8 %. The isolate was Gram-stain-positive, non-motile, with light yellow colonies and irregular short rod-shaped cells (0.4–0.6 µm in diameter, 0.6–1.0 µm in length). Growth of TS-56T occurred at 20–35 °C (optimum, 30 °C) and at pH 4.0–8.0 (optimum, pH 5.0). The peptidoglycan of TS-56T contained ornithine, glutamic acid, alanine, homoserine and glycine. The acyl type was acetyl. The most abundant cellular fatty acid of TS-56T was cyclohexyl-C17 : 0 (88.79 %). The respiratory menaquinone was MK-11. The polar lipid profile contained disphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and two unknown glycolipids. DNA of the type strain had a G+C content of 67.4 mol%. On the basis of the phylogenetic properties and phenotypic distinctiveness, TS-56T represents a novel species of the genus Gryllotalpicola , for which the name Gryllotalpicola reticulitermitis sp. nov. is proposed. The type strain is TS-56T ( = CGMCC 1.10363T = NBRC 109838T).

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Pontirhabdus pectinivorans gen. nov., sp. nov., isolated from seawater

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.027441-0 ◽

2011 ◽

Vol 61 (10) ◽

pp. 2475-2481 ◽

Cited By ~ 16

Author(s):

Hana Yi ◽

Jang-Cheon Cho ◽

Jongsik Chun

Keyword(s):

Phylogenetic Analyses ◽

Gliding Motility ◽

Phenotypic Traits ◽

Rrna Gene ◽

The Novel ◽

16S Rrna Gene Sequences ◽

The Family ◽

Phyletic Line ◽

Taxonomic Approach ◽

Sequence Similarities

A yellow-coloured, rod-shaped, Gram-reaction-negative and aerobic bacterial strain, designated JC2675T, was isolated from a seawater sample from Jeju Island, Korea. The isolate required sea salts for growth. Gliding motility was observed. Flexirubin-type pigments were absent. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2675T represented a distinct phyletic line that reflected a novel generic status within the family Flavobacteraceae with relatively low gene sequence similarities (<95.7 %) to other recognized genera. The predominant isoprenoid quinone (MK-6) and DNA G+C content (30 mol%) were consistent with the assignment of the novel strain to the family Flavobacteriaceae, but overall phenotypic traits demonstrated that the novel strain was not closely affiliated with any previously described genus. Based on data from a study using a polyphasic taxonomic approach, it is proposed that strain JC2675T represents a new genus and novel species belonging to the family Flavobacteriaceae, for which the name Pontirhabdus pectinivorans gen. nov., sp. nov. is proposed. The type strain of the type species is JC2675T ( = KACC 14153T = JCM 17107T).

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Snuella lapsa gen. nov., sp. nov., isolated from tidal flat sediment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.027458-0 ◽

2011 ◽

Vol 61 (10) ◽

pp. 2469-2474 ◽

Cited By ~ 11

Author(s):

Hana Yi ◽

Jongsik Chun

Keyword(s):

Tidal Flat ◽

Phylogenetic Analyses ◽

Gliding Motility ◽

Phenotypic Traits ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Tidal Flat Sediment ◽

The Family ◽

Phyletic Line ◽

Sequence Similarities

A yellow-coloured, rod-shaped, Gram-reaction-negative, aerobic bacterial strain, designated JC2132T, was isolated from a tidal flat sediment sample from Ganghwa Island, Korea. The isolate required sea salts for growth. Cells produced non-diffusible carotenoid pigments, but flexirubin-type pigments were absent. Gliding motility was observed. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2132T represented a distinct phyletic line that reflected a novel generic status within the family Flavobacteriaceae with relatively low sequence similarities (<95 %) to members of other genera with validly published names. The predominant isoprenoid quinone (MK-6) and DNA G+C content (35 mol%) were consistent with assignment of the isolate to the family Flavobacteriaceae, but overall phenotypic traits demonstrated that strain JC2132T was not closely affiliated with any previously described genera. Based on taxonomic data obtained using a polyphasic approach, it is proposed that strain JC2132T represents a novel species in a new genus belonging to the family Flavobacteriaceae, for which the name Snuella lapsa gen. nov., sp. nov. is proposed; the type strain of the type species is JC2132T ( = KACC 14152T = JCM 17111T).

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Molecular confirmation and description of the larval morphology of Thalassocaris lucida (Dana, 1852) (Decapoda, Caridea, Pandaloidea)

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315419000791 ◽

2019 ◽

Vol 99 (8) ◽

pp. 1797-1805 ◽

Cited By ~ 1

Author(s):

José María Landeira ◽

Chien-Hui Yang ◽

Tomoyuki Komai ◽

Tin-Yam Chan ◽

Kaori Wakabayashi

Keyword(s):

Ribosomal Rna ◽

Gene Sequence ◽

Phylogenetic Analyses ◽

Larval Morphology ◽

Family Status ◽

Larval Stages ◽

The Family ◽

16S Ribosomal Rna Gene ◽

Distinct Features ◽

Sequence Similarities

AbstractThe morphology of the zoeal stages IX and XI of the shrimp Thalassocaris lucida is described and illustrated in detail from plankton specimens identified by barcoding of the mitochondrial 16S ribosomal RNA gene (sequence similarities 99.4–99.6%). The present study confirms the larval morphology of Thalassocaris, that shows distinct features within Pandaloidea: (1) carapace broad and dorsoventrally flattened, (2) coxal endite of maxilla with only one lobe, (3) basis of third maxilliped with a distal globose lobe. On the other hand, the funnel-shaped eyes, and the development with long series of larval stages of Thalassocaris indicate affinities with some genera of Pandalidae which corroborates the results of recent phylogenetic analyses in abandoning the family status of Thalassocarididae.

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Ultrastructural and molecular delineation of the Chytridiaceae (Chytridiales)

Canadian Journal of Botany ◽

10.1139/b05-115 ◽

2005 ◽

Vol 83 (12) ◽

pp. 1561-1573 ◽

Cited By ~ 32

Author(s):

Peter M. Letcher ◽

Martha J. Powell ◽

James G. Chambers ◽

Joyce E. Longcore ◽

Perry F. Churchill ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Large Subunit ◽

Taxonomic Revision ◽

Small Subunit ◽

Developmental Morphology ◽

Sequence Analyses ◽

Bayesian Analyses ◽

Molecular Sequence ◽

Small Subunit Rdna ◽

The Family

The Chytridiomycota is in need of taxonomic revision, especially the largest order, the Chytridiales. We analyzed 25 isolates in, or allied to, the Chytridium clade of this order. Isolates were selected based on one or more of the following criteria: (i) having a large subunit molecular sequence similar to that of the type of the genus Chytriomyces, (ii) having specific zoospore morphology, and (iii) currently classified as a species in the genus Chytriomyces . We examined ultrastructural characters and partial sequences of large subunit and small subunit rDNA and generated a phylogenetic hypothesis using maximum parsimony and Bayesian analyses. The sequence analyses strongly supported the Chytridiaceae, Phlyctochytrium, and Chytriomyces angularis clades, and each clade had a specific zoospore type. Developmental morphology of the thallus did not mirror the DNA-based phylogeny. Based on the results of phylogenetic analyses of sequences and ultrastructural characters, we emend the Chytridiaceae by including exogenous and polycentric development and define the family on the basis of a single zoospore type. Species identified as being in the genus Chytriomyces occur in several separate, well-supported clades along with species currently classified in seven other genera ( Asterophlyctis , Entophlyctis , Obelidium , Physocladia , Podochytrium , Rhizoclosmatium , and Siphonaria ), indicating that Chytriomyces as currently defined is polyphyletic.

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Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.017707-0 ◽

2010 ◽

Vol 60 (9) ◽

pp. 2061-2065 ◽

Cited By ~ 15

Author(s):

Yochan Joung ◽

Jaeho Song ◽

Kiyoung Lee ◽

Hyun-Myung Oh ◽

Kiseong Joh ◽

...

Keyword(s):

Sequence Similarity ◽

Phylogenetic Analyses ◽

The Yellow Sea ◽

Rrna Gene ◽

Strictly Aerobic ◽

Elizabethkingia Meningoseptica ◽

The Family ◽

Novel Genus And Species ◽

Phyletic Line ◽

Sequence Similarities

A Gram-negative, non-motile, non-gliding, strictly aerobic, pale yellow colony-forming, rod-shaped bacterial strain, designated HM0024T, was isolated from coastal seawater of the Yellow Sea and subjected to a polyphasic taxonomy study. Based on 16S rRNA gene sequence similarities, strain HM0024T was most closely related to Chryseobacterium balustinum LMG 8329T (94.4 %), Chryseobacterium scophthalmum LMG 13028T (94.4 %), Chryseobacterium piscium LMG 23089T (94.3 %) and Elizabethkingia meningoseptica ATCC 13253T (94.0 %) and shared less than 92 % sequence similarity with other members of the family Flavobacteriaceae. Phylogenetic analyses showed that strain HM0024T formed an independent phyletic line of descent within the family Flavobacteriaceae. The DNA G+C content of the strain was 29.6 mol% and its major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1 ω7c and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The major isoprenoid quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and several aminolipids. Strain HM0024T was differentiated from phylogenetically related members of the family by having lower DNA G+C content, larger proportions of summed feature 3, anteiso-C15 : 0 and iso-C16 : 0 3-OH and particular phenotypic characteristics. On the basis of phenotypic and phylogenetic data, strain HM0024T is classified as a representative of a novel genus and species, for which the name Soonwooa buanensis gen. nov., sp. nov. is proposed. The type strain of Soonwooa buanensis is HM0024T (=KCTC 22689T =CECT 7503T).

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Rheinheimera aestuari sp. nov., a marine bacterium isolated from coastal sediment

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.000312 ◽

2015 ◽

Vol 65 (Pt_8) ◽

pp. 2640-2645 ◽

Cited By ~ 11

Author(s):

Kyunghwa Baek ◽

Che Ok Jeon

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Analyses ◽

Coastal Sediment ◽

Rrna Gene ◽

Strictly Aerobic ◽

The Family ◽

Optimum Ph ◽

Type Strains ◽

Sequence Similarities

A Gram-stain-negative, strictly aerobic, non-pigmented, motile bacterium with a single polar flagellum, designated H29T, was isolated from coastal sediment of Jeju Island, South Korea. Cells were non-spore-forming rods showing catalase- and oxidase-positive reactions. Growth of strain H29T was observed at 10–40 °C (optimum, 20–25 °C) and pH 6.0–9.0 (optimum, pH 7.0–8.0), and in the presence of 1–4 % (w/v) NaCl (optimum, 2–3 %). Strain H29T contained C16 : 0, iso-C15 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c) as the major fatty acids and ubiquinone-8 (Q-8) as the sole isoprenoid quinone. Phosphatidylethanolamine and phosphatidylglycerol were identified as the major polar lipids. The G+C content of the genomic DNA was 46.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain H29T formed a phyletic lineage with Rheinheimera hassiensis E48T within the genus Rheinheimera of the family Chromatiaceae. Strain H29T was most closely related to Rheinheimera pacifica KMM 1406T, Rheinheimera muenzenbergensis E49T, Rheinheimera hassiensis E48T and Rheinheimera baltica OSBAC1T with 97.8 %, 97.6 %, 97.4 % and 97.2 % 16S rRNA gene sequence similarities, respectively. However, DNA–DNA hybridization values of strain H29T with type strains of these species were lower than 70 %. On the basis of the phenotypic, chemotaxonomic and molecular properties, strain H29T represents a novel species of the genus Rheinheimera, for which the name Rheinheimera aestuarii sp. nov. is proposed. The type strain is H29T ( = KACC 18251T = JCM 30404T).

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