scholarly journals A Blue-Purple Pigment-Producing Bacterium Isolated from the Vezelka River in the City of Belgorod

2021 ◽  
Vol 9 (1) ◽  
pp. 102
Author(s):  
Nikita S. Lyakhovchenko ◽  
Tatiana N. Abashina ◽  
Valentina N. Polivtseva ◽  
Vladislav Yu. Senchenkov ◽  
Daniil A. Pribylov ◽  
...  
Keyword(s):  
Ethanol Extract ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Inhibitory Influence ◽  
Purple Pigment ◽  
Biotechnological Processes ◽  
First Time ◽  
The City ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

Violacein is a biotechnologically significant secondary metabolite due to its antibacterial, antifungal, and other properties. Isolation, research, and identification of violacein producing strains are of interest for the development of biotechnological processes, in order to enhance the biosynthesis of this compound. The purpose of the present work was to study the properties of a newly isolated bacterium capable of synthesizing blue-purple pigment. An aboriginal bacterium was isolated from the coastal zone of the Vezelka River in the city of Belgorod. Based on chemical and spectrophotometric studies of the crude ethanol extract, the pigment was identified as violacein, and the isolate was assigned to the group of violacein-forming bacteria, which includes bacteria of the genera Chromobacterium, Iodobacter, Janthinobacterium, Duganella, Collimonas, and Massilia. Based on cultural, morphological, tinctorial, physiological, and biochemical properties, as well as analysis of the 16S rRNA gene sequence, the new isolated strain was assigned to the genus Janthinobacterium. The isolated strain is capable of suppressing the growth of a number of fungal and bacterial phytopathogens. For representatives of the genus Janthinobacterium, their inhibitory influence on cyanobacteria was shown for the first time.

Environmental DNA reveals cryptic diversity within the subterranean amphipod genus Pseudocrangonyx Akatsuka & Komai, 1922 (Amphipoda: Crangonyctoidea: Pseudocrangonyctidae) from central Japan

2020 ◽  
Vol 40 (4) ◽  
pp. 479-483
Author(s):  
Satoru Yonezawa ◽  
Takafumi Nakano ◽  
Naoyuki Nakahama ◽  
Ko Tomikawa ◽  
Yuji Isagi
Keyword(s):  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Lake Biwa ◽  
Detection Method ◽  
Environmental Dna ◽  
Rrna Gene ◽  
History Of ◽  
First Time ◽  
The City ◽  
The 16S Rrna Gene

Abstract An environmental DNA (eDNA) detection method confirms the presence of the subterranean amphipod genus PseudocrangonyxAkatsuka & Komai, 1922 in the city of Kyoto, Honshu, Japan for the first time in more than 90 years. Phylogenetic trees using partial sequences of the 16S rRNA gene of eDNA samples from Kyoto and specimens collected from various locations in Japan and Korea highlight that two genetically distinct taxonomic units inhabit Kyoto’s subterranean environments. Results reveal that the ranges of distinct phylogroups of Pseudocrangonyx widely overlap with each other around Lake Biwa in central western Honshu. The eDNA results increase our understanding of the species richness and complicated evolutionary history of these stygobitic amphipods.

scholarly journals Streptomyces fenghuangensis sp. nov., isolated from seawater

2011 ◽  
Vol 61 (12) ◽  
pp. 2811-2815 ◽  
Author(s):  
Honghui Zhu ◽  
Shumei Jiang ◽  
Qing Yao ◽  
Yonghong Wang ◽  
Meibiao Chen ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Substrate Mycelium ◽  
Physiological And Biochemical Characteristics ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

An actinomycete, designated strain GIMN4.003T, was isolated from seawater collected in Sanya, China. It produced white aerial mycelium and yellow substrate mycelium on Gause’s synthetic agar medium no. 1. The substrate mycelium colour was not sensitive to pH. Scanning electron microscopy observations revealed that GIMN4.003T produced straight to flexuous spore chains of rough to warty spores. ll-Diaminopimelic acid was present in the cell-wall hydrolysate. Based on chemotaxonomy and morphological features, strain GIMN4.003T was identified as a member of the genus Streptomyces. Melanin was not produced. No antimicrobial activity was detected against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Penicillium citrinum or Candida albicans. Analysis of the 16S rRNA gene sequence revealed that the highest sequence similarity was to Streptomyces radiopugnans R97T (99.0 %). However, DNA relatedness between GIMN4.003T and S. radiopugnans DSM 41901T was low (41.24±1.47 %). Furthermore, the morphological, physiological and biochemical characteristics of strain GIMN4.003T were different from those of S. radiopugnans DSM 41901T and the type strains of other closely related Streptomyces species. On the basis of its physiological and molecular properties, it is evident that strain GIMN4.003T ( = CCTCCM 208215T  = NRRL B-24801T) represents the type strain of a novel species within the genus Streptomyces, for which the name Streptomyces fenghuangensis sp. nov. is proposed.

scholarly journals Marinobacter salsuginis sp. nov., isolated from the brine–seawater interface of the Shaban Deep, Red Sea

2007 ◽  
Vol 57 (5) ◽  
pp. 1035-1040 ◽  
Author(s):  
André Antunes ◽  
Luis França ◽  
Fred A. Rainey ◽  
Robert Huber ◽  
M. Fernanda Nobre ◽  
...  
Keyword(s):  
Red Sea ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gram Negative Bacteria ◽  
Respiratory Quinone ◽  
Physiological And Biochemical Characteristics ◽  
Major Respiratory Quinone ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

Two moderately halophilic Gram-negative bacteria were isolated from a sample taken from the brine–seawater interface of the Shaban Deep in the Red Sea. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms represent a novel species of the genus Marinobacter. Cells of the new isolates formed non-pigmented colonies and were motile by means of a single polar flagellum. Strains SD-14BT and SD-14C grew optimally at 35–37 °C, in 5 % NaCl and at pH 7.5–8.0. The organisms were aerobic, but reduced nitrate to nitrogen under anaerobic conditions. Acid was produced from only a few carbohydrates. Ubiquinone 9 was the major respiratory quinone. The major fatty acids of strains SD-14BT and SD-14C were C16 : 0, C18 : 1 ω9c, summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c) and C12 : 0 3-OH. The DNA G+C contents were 55.9 and 55.7 mol%, respectively. On the basis of the phylogenetic analyses and physiological and biochemical characteristics, it is proposed that strains SD-14BT and SD-14C represent a novel species of the genus Marinobacter, with the name Marinobacter salsuginis sp. nov. The type strain is strain SD-14BT (=DSM 18347T=LMG 23697T).

scholarly journals Emended descriptions of the genus Lewinella and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica, and description of Lewinella lutea sp. nov. and Lewinella marina sp. nov.

2007 ◽  
Vol 57 (12) ◽  
pp. 2946-2951 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yukiyo Fukunaga ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
Type Strain ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
The Pacific ◽  
Marine Sediment Sample ◽  
Pacific Coast Of Japan ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
Physiological And Biochemical Properties

Two strains, MKG-38T and FYK2402M69T, were isolated from a marine sediment sample and a sea snail, respectively, both collected on the Pacific coast of Japan. Phylogeny of these new isolates based on 16S rRNA gene sequences indicated that they are members of the genus Lewinella. Morphological, physiological and biochemical properties of these two isolates, together with the type strains of the three previously described species of the genus Lewinella, were characterized. The new isolates were Gram-negative, aerobic, rod-shaped, chemo-organotrophic and able to degrade starch and CM-cellulose. A comparative polyphasic study showed that these two isolates represent two novel species of the genus Lewinella, for which the names Lewinella marina sp. nov. (type strain, MKG-38T=NBRC 102633T=NCIMB 14312T) and Lewinella lutea sp. nov. (type strain, FYK2402M69T=NBRC 102634T=NCIMB 14313T) are proposed. Emended descriptions of the genus Lewinella (Sly et al. 1998) and of Lewinella cohaerens, Lewinella nigricans and Lewinella persica are also proposed.

scholarly journals Streptomyces graminifolii sp. nov., isolated from bamboo (Sasa borealis) litter

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2517-2521 ◽  
Author(s):  
Hyo-Jin Lee ◽  
Kyung-Sook Whang
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Morphological Properties ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

The taxonomic position of strain JL-22T, isolated from litter of a bamboo (Sasa borealis) forest, was determined using a polyphasic approach. The organism had phenotypic and morphological properties consistent with it being a member of the genus Streptomyces . Phylogenetic analysis of the 16S rRNA gene sequence showed that strain JL-22T was closely related to Streptomyces prunicolor NRRL B-12281T (99.2 %), Streptomyces galilaeus JCM 4757T (99.0 %) and Streptomyces chartreusis NBRC 12753T (99.0 %). However, the results of DNA–DNA hybridization and physiological and biochemical tests showed that strain JL-22T could be differentiated from its closest phylogenetic relatives both genotypically and phenotypically. Based on phenotypic and genotypic data, strain JL-22T represents a novel species of the genus Streptomyces , for which the name Streptomyces graminifolii sp. nov. is proposed. The type strain is JL-22T ( = KACC 17180T = NBRC 109806T).

scholarly journals Polaromonas hydrogenivorans sp. nov., a psychrotolerant hydrogen-oxidizing bacterium from Alaskan soil

2007 ◽  
Vol 57 (3) ◽  
pp. 616-619 ◽  
Author(s):  
Maria Sizova ◽  
Nicolai Panikov
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Organic Substrates ◽  
The Novel ◽  
Membrane Phospholipids ◽  
Wide Range ◽  
Physiological And Biochemical ◽  
Physiological And Biochemical Properties

Psychrotolerant (0–25 °C), chemolithotrophic Gram-negative cocci were isolated from Alaskan forest soil. The novel isolate was found to grow autotrophically on H2 : CO2 mixtures and to switch to heterotrophic growth on media containing organic substrates. The novel strain utilized a wide range of organic acids, some simple sugars and alcohols. Naphthalene vapour did not support growth. On the basis of 16S rRNA gene sequence similarity, the novel strain is affiliated to the genus Polaromonas, of the class Betaproteobacteria, and is related to Polaromonas naphthalenivorans (99.6 % gene sequence similarity), Polaromonas aquatica (97.4 %) and Polaromonas vacuolata (96.1 %). The membrane phospholipids contained 16 : 1ω7c/16 : 1ω6c, 16 : 0 and 18 : 1ω7c, similar to the fatty acids found for P. naphthalenivorans, P. aquatica and P. vacuolata. On the basis of DNA–DNA hybridization, physiological and biochemical properties, the hydrogen-oxidizing mixotrophic isolate represents a novel species, for which the name Polaromonas hydrogenivorans sp. nov. is proposed. The type strain is DSM 17735T (=NRRL B-41369T).

scholarly journals Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha)

2020 ◽  
Vol 96 (4) ◽  
Author(s):  
César Ruiz ◽  
Marcela Villegas-Plazas ◽  
Olivier P Thomas ◽  
Howard Junca ◽  
Thierry Pérez
Keyword(s):  
Extreme Environments ◽  
Amplicon Sequencing ◽  
Sponge Species ◽  
Rrna Gene ◽  
Microbiome Composition ◽  
16S Amplicon Sequencing ◽  
Ecological Success ◽  
Specific Community ◽  
First Time ◽  
The 16S Rrna Gene

ABSTRACT The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.

scholarly journals Dynamics and Heterogeneity of Microbial Communities in Urban Water Environments

2020 ◽  
Author(s):  
Yanqing Lian ◽  
Lisha Zhen ◽  
Xi Chen ◽  
Yang Li ◽  
Xiaona Li
Keyword(s):  
Microbial Communities ◽  
Urban Areas ◽  
Pathogenic Bacteria ◽  
Temporal Dynamics ◽  
Statistical Analyses ◽  
Polluted Water ◽  
Outer Side ◽  
Rrna Gene ◽  
The City ◽  
The 16S Rrna Gene

Abstract Water samples for the 16S rRNA gene and water quality analyses were collected from around 155 kilometers of river segments surrounding the urban areas in Xi’an of China. Multiple statistical analyses showed the temporal dynamics of microbial communities and heterogeneity in their spatial distributions. The dynamic shifts of microbial communities in the Chan, Ba, and Feng Rivers from the Spring to the Summer seasons were apparent, but little in the Zao River. The heterogeneity of microbial distributions was more due to the influence of hydrologic conditions and various sources of inflows in the rivers. The LEfSe analysis showed the Chan and Zao Rivers, both were more impacted by the sewage effluents, were more differentially abundant with bacteria related to polluted water, but the Ba and Feng Rivers, both on the outer side of the city, were more abundant with microbial communities in soil and freshwater environments in August. Multiple statistical analyses indicated that environmental variables had a significant impact on microbial communities. The GIS-based spatial analysis not only showed heterogeneity of microbial community distributions along the rivers, more importantly, could help identify locations where pathogenic bacteria presented.

scholarly journals Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples

2007 ◽  
Vol 57 (5) ◽  
pp. 1007-1013 ◽  
Author(s):  
Corinne Teyssier ◽  
Hélène Marchandin ◽  
Hélène Jean-Pierre ◽  
Agnès Masnou ◽  
Ghislaine Dusart ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Family ◽  
Ochrobactrum Intermedium ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

Three novel Gram-negative, non-fermenting aerobic bacilli were isolated from human clinical samples. They shared more than 99.8 % of the 16S rRNA gene nucleotide positions. The strains were related to Ochrobactrum intermedium with about 97.48 % 16S rRNA gene sequence similarity. In 16S rRNA gene-, dnaK- and rpoB-based phylogenies, the strains were grouped in a lineage that was distinct from other Ochrobactrum species in the family Brucellaceae. Fatty acid composition, polar lipids, quinone system, DNA–DNA relatedness, genome organization, and physiological and biochemical data differentiated these isolates from recognized species of the genus Ochrobactrum. The three clinical strains therefore represent a novel species within the genus Ochrobactrum, for which the name Ochrobactrum pseudintermedium sp. nov., is proposed. The type strain is ADV31T (=CIP 109116T=DSM 17490T). The DNA G+C content of strain ADV31T was 54.5 mol%.

scholarly journals Molecular and serological detection of Ehrlichia canis in naturally exposed dogs in Iran: an analysis on associated risk factors

2014 ◽  
Vol 23 (1) ◽  
pp. 16-22 ◽  
Author(s):  
Nadi Maazi ◽  
Abdolali Malmasi ◽  
Parviz Shayan ◽  
Seyed Mahdi Nassiri ◽  
Taghi Zahraei Salehi ◽  
...  
Keyword(s):  
Risk Factors ◽  
Rural Areas ◽  
Ehrlichia Canis ◽  
Rrna Gene ◽  
Igg Antibodies ◽  
Serological Detection ◽  
Blood Samples ◽  
Associated Risk Factors ◽  
First Time ◽  
The 16S Rrna Gene

The general aim of this study, which was conducted for the first time in Iran, was to evaluate the seroprevalence and geographical distribution of Ehrlichia canis in a dog population in Iran, followed by molecular confirmation using PCR and sequencing. Blood samples were collected from 240 dogs in different areas of Alborz and Tehran Provinces and initially analyzed using the immunofluorescent antibody (IFA) test to detect anti-Ehrlichia canis IgG antibodies. Subsequently, nested PCR was performed based on a fragment of the 16S rRNA gene of E. canis on serologically positive samples. The results showed that 40/240 dogs (16.6%) presented anti-Ehrlichia canis IgG antibodies and that nine of the blood samples from the 40 seropositive dogs (22.5%) contained E. canis DNA, which was confirmed by sequencing. The seroprevalence of E. canis tended to be higher in purebred, one to three-year-old male dogs living in the Plain zone, in rural areas; however, this difference was not statistically significant.

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