16S rRNA and Multilocus Phylogenetic Analysis of the Iron Oxidizing Acidophiles of the Acidiferrobacteraceae Family

2017 ◽  
Vol 262 ◽  
pp. 339-343 ◽  
Author(s):  
Francisco Issotta ◽  
Paulo C. Covarrubias ◽  
Ana Moya-Beltrán ◽  
Sören Bellenberg ◽  
Christian Thyssen ◽  
...  
Keyword(s):  
Draft Genome ◽  
Phylogenetic Reconstruction ◽  
Taxonomic Status ◽  
Genomic Diversity ◽  
Evolutionary Information ◽  
Comparative Genomic ◽  
The Family ◽  
Sulfur Oxidizer ◽  
Acid Waters ◽  
Type Strains

The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains three genera of chemolithoautotrophs: Sulfuricaulis (2016), Sulfurifustis (2015) and Acidiferrobacter (2011). While the two former are neutrophilic sulfur oxidizers isolated from lake sediments in Japan, the latter is an extremely acidophilic, moderately osmophilic, thermotolerant iron/sulfur oxidizer known to occur in macroscopic streamers in Rio Tinto, Spain and in acid waters worldwide. The type strains of both Sulfuricaulis limnicola (HA5T) and Sulfurifustis variabilis (skN76T) have been sequenced, and the draft genome of the ZJ isolate of Acidiferrobacter thiooxydans (MDCF01) has recently been deposited in public databases. Despite this fact, little evidence on the genomic diversity and evolution of this group has been presented so far. Using comparative genomic analyses and phylogenetic reconstruction strategies, we explored the evolutionary information contained in the available genome sequences to shed light on the taxonomic status of a novel isolate of the genus Acidiferrobacter (SP-III/3; DSM 27195).

Draft genome sequence of multidrug-resistant Bradyrhizobium sp. BL isolated from a sewage treatment plant in China

2019 ◽  
Author(s):  
Peng Bao ◽  
Guo-Xiang Li ◽  
Yu-Qin He ◽  
Yi Dai
Keyword(s):  
Antibiotic Resistance ◽  
Municipal Wastewater ◽  
Draft Genome ◽  
Sewage Treatment Plant ◽  
Treatment Plant ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Municipal Wastewater Treatment ◽  
Total Size ◽  
Bradyrhizobium Sp

Abstract The genus Bradyrhizobium is considered to be widespread and abundant group of symbiotic bacteria in many plant-soil ecosystems. However, the ecological versatility of this phylogenetic group remains highly understudied in man-made ecosystems, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this genus for human health, we analyzed the high quality draft genome of Bradyrhizobium strain BL, isolated from a municipal wastewater treatment plant in Ningbo, China. The Bradyrhizobium sp. BL draft genome has a total size of 7,718,431 bp with an overall G + C content of 46.43%. From a total of 7236 predicted sequences, 7176 and 60 are protein and RNA coding sequences, respectively. Moreover, 63.51% of the predicted genes were assigned into to Clusters of Orthologous Groups (COG) functional categories. The Bradyrhizobium sp. BL genome contains various defense mechanisms against antibiotics that up to predicted 60 antibiotic resistance coding genes. The Bradyrhizobium sp. BL genome contains 237 termed virulence factors coding genes which show its potential pathogenicity. This study provides important insights into the genomic diversity of the genus Bradyrhizobium and provides a foundation for future comparative genomic studies that will generate a better understanding of the antibiotic resistance process.

scholarly journals Leekyejoonella antrihumi gen. nov., sp. nov., a new member of the family Dermacoccaceae isolated from a cave soil

2020 ◽  
Vol 70 (5) ◽  
pp. 3340-3347 ◽  
Author(s):  
Soon Dong Lee ◽  
In Seop Kim ◽  
Peter Schumann ◽  
Gwanpil Song
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Rrna Gene ◽  
The Novel ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

A novel Gram-stain-positive, actinobacterial strain, designated C5-26T, was isolated from soil from a natural cave in Jeju, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The organism was aerobic, and cells were non-spore-forming, non-motile cocci that occurred singly, in pairs, in triplets, in tetrads, in short chains or in irregular clusters. Colonies of the cells were circular, convex, entire and white. The peptidoglycan type was A4α with an l-Ser–d-Asp interpeptide bridge. The whole-cell sugars comprised glucose, rhamnose, mannose, arabinose, galactose and ribose. The major menaquinone was MK-8(H4). The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid. The major fatty acids were iso-C16 : 0 and iso-C16 : 1 h. The size of the draft genome was 5.32 Mbp with depth of coverage of 161×. The G+C content of the genomic DNA was 67.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel isolate belonged to the family Dermacoccaceae and formed a distinct subcluster at the base of the radiation of the genus Luteipulveratus . Highest sequence similarities of the novel isolate were found to the type strains of Luteipulveratus halotolerans (96.2 %), Branchiibius hedensis (95.4 %), Luteipulveratus mongoliensis (95.4 %) and Branchiibius cervicis (95.3 %). The whole genome-based phylogeny supported the novelty of the isolate at the genus level in the family Dermacoccaceae . On the basis of data from this polyphasic study, strain C5-26T (=KCTC 39632T=DSM 108676T) represents a novel species of a new genus in the family Dermacoccaceae , for which the name Leekyejoonella antrihumi gen. nov., sp. nov. is proposed.

scholarly journals Draft Genome Sequences of Chryseobacterium lactis NCTC11390T Isolated from Milk, Chryseobacterium oncorhynchi 701B-08T from Rainbow Trout, and Chryseobacterium viscerum 687B-08T from Diseased Fish

2018 ◽  
Vol 6 (26) ◽  
Author(s):  
Jin-Ju Jeong ◽  
Ye Ji Lee ◽  
Duleepa Pathiraja ◽  
Byeonghyeok Park ◽  
In-Geol Choi ◽  
...  
Keyword(s):  
Growth Promotion ◽  
Bacterial Species ◽  
Draft Genome ◽  
Genome Sequences ◽  
Free Living ◽  
Gram Negative ◽  
Content Type ◽  
The Family ◽  
Diseased Fish ◽  
Type Strains

The genus Chryseobacterium, belonging to the family Flavobacteriaceae, contains Gram-negative, yellow-pigmented, rod-shaped, and non-spore-forming bacterial species, which may be free living or parasitic. Here, we report draft genome sequences of type strains of three species of Chryseobacterium containing genes related to biological control and plant growth promotion.

scholarly journals Draft Genome Sequences of Chryseobacterium artocarpi UTM-3 T and Chryseobacterium contaminans C26 T , Isolated from Rhizospheres, and Chryseobacterium arthrosphaerae CC-VM-7 T , Isolated from the Feces of a Pill Millipede: TABLE 1 

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Jin-Ju Jeong ◽  
Byeonghyeok Park ◽  
Ji Yeon Oh ◽  
Mohamed Mannaa ◽  
Yoo Jun Kim ◽  
...  
Keyword(s):  
Plant Growth ◽  
Plant Growth Promotion ◽  
Growth Promotion ◽  
Draft Genome ◽  
Stress Adaptation ◽  
Genome Sequences ◽  
The Family ◽  
Type Strains

Species of the genus Chryseobacterium belonging to the family Flavobacteriaceae are nonmotile, yellow-pigmented, and rod-shaped bacteria, some of which were frequently isolated from soil or plant-related materials. Here, we present draft genome sequences of three type strains of Chryseobacterium , which contain genes related to plant growth promotion, colonization, or stress adaptation.

scholarly journals Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3507-3510 ◽  
Author(s):  
Christopher A. Dunlap
Keyword(s):  
Dna Hybridization ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Sequencing Analysis ◽  
Emended Description ◽  
Type Strains

‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

scholarly journals Draft Genome Sequences of Type Strains of Adlercreutzia muris and Ellagibacter urolithinifaciens, Belonging to the Family Eggerthellaceae

2019 ◽  
Vol 8 (47) ◽  
Author(s):  
Nicolas Danylec ◽  
Dominic A. Stoll ◽  
Melanie Huch
Keyword(s):  
Draft Genome ◽  
Genome Sequences ◽  
The Family ◽  
Type Strains

Here, we report the annotated draft genome sequences of two type strains belonging to the family Eggerthellaceae within the class Coriobacteriia (phylum Actinobacteria), Adlercreutzia muris WCA-131-CoC-2 (= DSM 29508 = KCTC 15543) and Ellagibacter urolithinifaciens CEBAS 4A (= CCUG 70284 = DSM 104140).

scholarly journals Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil

2011 ◽  
Vol 61 (11) ◽  
pp. 2654-2658 ◽  
Author(s):  
Sung-Heun Cho ◽  
Song-Hee Chae ◽  
Myoungho Cho ◽  
Tae-Ui Kim ◽  
Seri Choi ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
The Family ◽  
Type Strains ◽  
Sequence Similarities

A Gram-reaction-negative, yellow-pigmented, gliding, rod-shaped, aerobic bacterium (RA5-111T) was isolated from foreshore soil. The taxonomic status of the novel isolate was determined using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain RA5-111T could be assigned to the genus Gramella, with sequence similarities of 97.7, 97.3 and 96.2 % to the type strains of Gramella echinicola, Gramella portivictoriae and Gramella marina, respectively. Chemotaxonomic and phenotypic characteristics also supported the affiliation of strain RA5-111T with the genus Gramella. The genomic DNA G+C content was 39.1 mol%. The isolate contained MK-6 as the predominant menaquinone, iso-C15 : 0, iso-C17 : 0 3-OH and a summed feature (iso-C15 : 0 2-OH and/or C16 : 1ω7c) as major fatty acids, and phosphatidylethanolamine and unknown phospholipids as the polar lipids. DNA–DNA relatedness, phenotypic, genotypic and chemotaxonomic data clearly indicate that the isolate represents a novel species of the genus Gramella, for which the name Gramella gaetbulicola sp. nov. is proposed. The type strain is RA5-111T ( = KCTC 23022T  = JCM 16528T  = NBRC 106272T).

scholarly journals Draft Genome Sequences of Type Strains of Gordonibacter faecihominis, Paraeggerthella hongkongensis, Parvibacter caecicola, Slackia equolifaciens, Slackia faecicanis, and Slackia isoflavoniconvertens

2019 ◽  
Vol 8 (2) ◽  
Author(s):  
Nicolas Danylec ◽  
Dominic A. Stoll ◽  
Andreas Dötsch ◽  
Melanie Huch
Keyword(s):  
Draft Genome ◽  
Genome Sequences ◽  
Content Type ◽  
The Family ◽  
Type Strains

Here, we report the annotated draft genome sequences of six type strains of the family Eggerthellaceae, Gordonibacter faecihominis JCM 16058, Paraeggerthella hongkongensis DSM 16106, Parvibacter caecicola DSM 22242, Slackia equolifaciens DSM 24851, Slackia faecicanis DSM 17537, and Slackia isoflavoniconvertens DSM 22006.

Cuticular structures in the copulatory apparatus of Planorbis planorbis (Linnaeus, 1758) (Gastropoda: Pulmonata: Planorbidae)

2009 ◽  
Vol 18 (1) ◽  
pp. 11-16
Author(s):  
E.V. Soldatenko ◽  
A.A. Petrov
Keyword(s):  
Light Microscopy ◽  
Confocal Laser Scanning Microscopy ◽  
Laser Scanning ◽  
Taxonomic Status ◽  
Laser Scanning Microscopy ◽  
Confocal Laser Scanning ◽  
Confocal Laser ◽  
Copulatory Apparatus ◽  
The Family ◽  
Cuticular Structures

The morphology of the copulatory apparatus and associated cuticular structures in Planorbis planorbis was studied by light microscopy, SEM, TEM and confocal laser scanning microscopy. The significance of these cuticular structures for the taxonomic status of the species and for the systematics of the family Planorbidae in general is discussed.

scholarly journals Draft Genome Sequences of Three Flavobacterium psychrophilum Strains Isolated from Diseased Ayu (Plecoglossus altivelis altivelis) Caught at Three Sites in the Kagami River in Kochi, Japan

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
Hazuki Yamashita ◽  
Takayuki Wada ◽  
Yusuke Kato ◽  
Takuji Ikeda ◽  
Masayuki Imajoh
Keyword(s):  
Draft Genome ◽  
Psychrophilic Bacterium ◽  
Genome Sequences ◽  
Plecoglossus Altivelis ◽  
Gram Negative ◽  
Content Type ◽  
Flavobacterium Psychrophilum ◽  
Skin Ulcers ◽  
The Family

Flavobacterium psychrophilum is a Gram-negative, psychrophilic bacterium within the family Flavobacteriaceae. Here, we report the draft genome sequences of three F. psychrophilum strains isolated from skin ulcers of diseased ayu caught by tomozuri angling at three sites in the Kagami River in Japan.

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