Characterization of halophilic bacteria from environmental samples from the brackish water of Pulicat Lake, India

Biologia ◽  
2011 ◽  
Vol 66 (5) ◽  
Author(s):  
Harmesh Sahay ◽  
Surendra Singh ◽  
Rajeev Kaushik ◽  
Anil Saxena ◽  
Dilip Arora
Keyword(s):  
16S Rdna ◽  
Brackish Water ◽  
Phylogenetic Analyses ◽  
Halophilic Bacteria ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Gram Positive Bacteria ◽  
Nutrient Agar Medium

AbstractCulture dependent phenotypic characterization and 16S rDNA based phylogenetic analyses were applied to study the aerobic halophilic bacterial population present in the Pulicat brackish-water Lake of India. Five different media were employed for isolation of bacteria. A total of 198 morphotypes were recovered, purified and screened for salt tolerance in nutrient agar medium amended with 5–25% NaCl. Based on 16S rDNA restriction fragment length polymorphism analysis with three restriction endonucleases, 51 isolates tolerant to 5% or more NaCl were grouped into 29 clusters. Phylogenetic analysis using 16S rRNA gene sequences revealed that 29 strains could further be allocated into two clades: 19 to Firmicutes and 10 to γ-Proteobacteria. Firmicutes included low G+C Gram-positive bacteria related to family Bacillaceae, which included five genera Bacillus, Virgibacillus, Rummelibacillus, Alkalibacillus and Halobacillus. Another genera included in Firmicutes was Salimicrobium halophilum. In the γ-Proteobacteria group, all the isolates belonged to one genus Halomonas, represented by six different species Halomonas salina, H. shengliensis, H. salifodinae, H. pacifica, H. aquamarina and H. halophila. Most of the isolates exhibited cellulase, xylanase, amylase and protease activities.

scholarly journals Phenotypic characterization of Astragalus glycyphyllos symbionts and their phylogeny based on the 16S rDNA sequences and RFLP of 16S rRNA gene

2014 ◽  
Vol 105 (6) ◽  
pp. 1033-1048 ◽  
Author(s):  
Sebastian Gnat ◽  
Magdalena Wójcik ◽  
Sylwia Wdowiak-Wróbel ◽  
Michał Kalita ◽  
Aneta Ptaszyńska ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Astragalus Glycyphyllos Symbionts

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

scholarly journals Unraveling the Etiology of North American Grapevine Yellows (NAGY): Novel NAGY Phytoplasma Sequevars Related to ‘Candidatus Phytoplasma pruni’

Plant Disease ◽  
2015 ◽  
Vol 99 (8) ◽  
pp. 1087-1097 ◽  
Author(s):  
Robert E. Davis ◽  
Ellen L. Dally ◽  
Yan Zhao ◽  
Ing-Ming Lee ◽  
Wei Wei ◽  
...  
Keyword(s):  
16S Rdna ◽  
North American ◽  
Phylogenetic Analyses ◽  
New York State ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Vitis Vinifera L ◽  
Polymorphism Analysis ◽  
Ribosomal Protein Genes ◽  
Grapevine Yellows

North American grapevine yellows (NAGY) disease has sometimes been attributed to infection of Vitis vinifera L. by Prunus X-disease phytoplasma (‘Candidatus Phytoplasma pruni’) but this attribution may not be fully adequate. In this study, phytoplasma strains related to ‘Ca. Phytoplasma pruni’ were found in NAGY-diseased grapevines in Maryland, Pennsylvania, Virginia, Ohio, Missouri, and New York State. Based on restriction fragment length polymorphism analysis of 16S ribosomal RNA gene (16S rDNA) sequences, the strains (termed NAGYIII strains) were classified in group 16SrIII (X-disease group) but they contained a recognition site for the restriction endonuclease MseI that is not present in the 16S rDNA of ‘Ca. Phytoplasma pruni’. The 16S rDNA of the strains differed by three or four nucleotides from that of ‘Ca. Phytoplasma pruni’, indicating that they belonged to two novel 16S rDNA sequevars, designated NAGYIIIα and NAGYIIIβ. Both sequevars differed from ‘Ca. Phytoplasma pruni’ by a single base in each of three regions corresponding to species-unique (signature) sequences described for ‘Ca. Phytoplasma pruni’. Phylogenetic analyses of 16S rRNA genes and SecY proteins, and single-nucleotide polymorphism analyses of secY and ribosomal protein genes, further distinguished the two grapevine sequevar lineages from one another and from ‘Ca. Phytoplasma pruni’. The NAGYIIIα and NAGYIIIβ sequevars also differed from ‘Ca. Phytoplasma pruni’ in regions of the folded SecY protein that are predicted to be near or exposed at the outer surface of the phytoplasma membrane. No evidence indicated that diseased grapevines contained any phytoplasma strain conforming to ‘Ca. Phytoplasma pruni’ sensu stricto. Because the NAGYIII sequevars have not been reported in X-disease, a question is raised as to whether NAGYIII and Prunus X-disease are caused by different phytoplasma genotypes.

scholarly journals The New Human Babesia sp. FR1 Is a European Member of the Babesia sp. MO1 Clade

Pathogens ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1433
Author(s):  
Claire Bonsergent ◽  
Marie-Charlotte de Carné ◽  
Nathalie de la Cotte ◽  
François Moussel ◽  
Véronique Perronne ◽  
...  
Keyword(s):  
Roe Deer ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Natural Host ◽  
Etiological Agent ◽  
Rrna Gene ◽  
Separate Species ◽  
Apical Membrane Antigen 1 ◽  
Babesia Divergens

In Europe, Babesia divergens is responsible for most of the severe cases of human babesiosis. In the present study, we describe a case of babesiosis in a splenectomized patient in France and report a detailed molecular characterization of the etiological agent, named Babesia sp. FR1, as well as of closely related Babesia divergens, Babesia capreoli and Babesia sp. MO1-like parasites. The analysis of the conserved 18S rRNA gene was supplemented with the analysis of more discriminant markers involved in the red blood cell invasion process: rap-1a (rhoptry-associated-protein 1) and ama-1 (apical-membrane-antigen 1). The rap-1a and ama-1 phylogenetic analyses were congruent, placing Babesia sp. FR1, the new European etiological agent, in the American cluster of Babesia sp. MO1-like parasites. Based on two additional markers, our analysis confirms the clear separation of B. divergens and B. capreoli. Babesia sp. MO1-like parasites should also be considered as a separate species, with the rabbit as its natural host, differing from those of B. divergens (cattle) and B. capreoli (roe deer). The natural host of Babesia sp. FR1 remains to be discovered.

Detection and Characterization of a Multi-drug and Multi-metal Resistant Enterobacterium Pantoea sp. from Tannery Wastewater after Secondary Treatment Process

2016 ◽  
Vol 2 (1 and 2) ◽  
pp. 37-42 ◽  
Author(s):  
Ashutosh Yadav ◽  
Abhay Raj ◽  
Ram Naresh Bharagava
Keyword(s):  
Toxic Metal ◽  
Tannery Wastewater ◽  
Contaminated Sites ◽  
Diffusion Method ◽  
Rrna Gene ◽  
Disk Diffusion Method ◽  
Gene Sequence Analysis ◽  
Nutrient Agar Medium ◽  
The 16S Rrna Gene

In this study, an enterobacterium was isolated from treated tannery wastewater and characterized as gram-negative, rod shaped, motile, and lactose fermenting bacterium. Further, based on the 16S rRNA gene sequence analysis, the bacterium was identified as Pantoea sp. with accession number The antibiotic and heavy KJ576899. metal resistant property of isolated bacterium was investigated by the disk diffusion method on Muller-Hinton and nutrient agar medium amended with the increasing concentrations of various toxic metal ions, respectively. Results showed that the isolated bacterium was sensitive for amikacin, ampicillin, cefepime, cetriaxone, chloramphenicol, levofloxacin, meropenem, nalidixic acid, piperacillin and tobramycin, resistant for aztreonam, carbenicillin, cefotaxime, ceftazidime, ciprofloxacin, cotrimoxazole, imepenam, moxifloxacin, streptomycin and tetracycline, but intermediate for amoxicillin and gentamicin. In addition, the bacterium also showed the Minimum Inhibitory Concentration (MIC) values of 250, 500, 160, 190, 600, 700, 500, 380, 600 and 350 μg ml-1 forCu, Cr, Cd, Co, Zn, Fe, Ni, Pb, Mo and As, respectively with a plasmid DNA of 33.5 kb. This multi-drug and multi-metal resistant bacterium can be used as a potential agent for the bioremediation of metal contaminated sites.

Cultivable bacterial flora of Indian oil reservoir: isolation, identification and characterization of the biotechnological potential

Biologia ◽  
2015 ◽  
Vol 70 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Neha Saxena ◽  
Soham Pore ◽  
Preeti Arora ◽  
Neelam Kapse ◽  
Anupama Engineer ◽  
...  
Keyword(s):  
Oil And Gas ◽  
Produced Water ◽  
Phylogenetic Analyses ◽  
Bacterial Flora ◽  
Oil Reservoirs ◽  
Rrna Gene ◽  
Oil Reservoir ◽  
Biotechnological Potential ◽  
Taxonomic Novelty

Abstract‘Produced water’ is a term used in oil industry to describe water produced along with oil and gas from oil reservoir. Microorganisms have been frequently isolated from produced water/oil reservoirs; however, there is paucity of information regarding the diversity and characterization of bacterial flora from Indian oil reservoirs. The present investigation was undertaken to study bacterial diversity associated with Indian oil reservoirs and to investigate their potential as a source of industrially valuable enzymes. A total of 103 strains were isolated from five oil reservoirs. PCR-based DNA fingerprinting grouped these strains into 72 genovars. These isolates were identified using morphological, phenotypical and phylogenetic analyses. Most of these isolates were thermophiles (growing at 45◦C or higher), halotolerant (growth at 5% salinity) and were distributed through a variety of genera including but not limited to Bacillus, Chelatococcus, Paenibacillus and Pseudomonas species. The 16S rRNA gene sequence of several strains shared less than 97% homology with the reference sequences in the GenBank database indicating taxonomic novelty of these strains. Assessment of the biotechnological potential of 72 genovars revealed that majority of strains produce one or many of the valuable enzymes including amylase, cellulase, xylanase, pectinase, inulinase, protease, alcohol dehydrogenase and urease. Most of the isolates also degraded crude oil or petroleum hydrocarbons. The vast pool of phenotypic, genetic and functional diversity of the strains retrieved in this study suggested oil reservoirs as yet largely untapped and potent source of taxonomically novel and biotechnologically valuable microorganisms.

scholarly journals Phenotypic characterization of Sodalis praecaptivus sp. nov., a close non-insect-associated member of the Sodalis-allied lineage of insect endosymbionts

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1400-1405 ◽  
Author(s):  
Abhishek Chari ◽  
Kelly F. Oakeson ◽  
Shinichiro Enomoto ◽  
D. Grant Jackson ◽  
Mark A. Fisher ◽  
...  
Keyword(s):  
Novel Species ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Sodalis Glossinidius ◽  
Large Gene ◽  
Close Relationship ◽  
Metabolic Properties ◽  
Insect Symbionts ◽  
The 16S Rrna Gene

A Gram-stain-negative bacterium, isolated from a human wound was previously found to share an unprecedentedly close relationship with Sodalis glossinidius and other members of the Sodalis-allied clade of insect symbionts. This relationship was inferred from sequence analysis of the 16S rRNA gene and genomic comparisons and suggested the strain belonged to a novel species. Biochemical and genetic analyses supported this suggestion and demonstrated that the organism has a wide repertoire of metabolic properties, which is consistent with the presence of a relatively large gene inventory. Among members of the Sodalis-allied clade, this is the first representative that has sufficient metabolic capabilities to sustain growth in minimal media. On the basis of the results of this study, we propose that this organism be classified as a representative of a novel species, Sodalis praecaptivus sp. nov. (type strain HST = DSM 27494T = ATCC BAA-2554T).

Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean

2007 ◽  
Vol 57 (8) ◽  
pp. 1815-1818 ◽  
Author(s):  
Kiyoung Lee ◽  
Yoe-Jin Choo ◽  
Stephen J. Giovannoni ◽  
Jang-Cheon Cho
Keyword(s):  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Sargasso Sea ◽  
Bacterial Strains ◽  
Ruegeria Pomeroyi ◽  
Distinct Line ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Gram-negative, facultatively aerobic, chemoheterotrophic, short rod-shaped marine bacterial strains HTCC2662T and HTCC2663, isolated from the Sargasso Sea by using a dilution-to-extinction culturing method, were investigated to determine their taxonomic position. Characterization of the two strains by phenotypic and phylogenetic analyses revealed that they belonged to the same species. The DNA G+C content of strain HTCC2662T was 58.4 mol% and the predominant cellular fatty acids were C18 : 1 ω7c (52.5 %), C16 : 0 2-OH (13.5 %) and C18 : 1 11-methyl ω7c (12.2 %). Phylogenetic analysis of the 16S rRNA gene sequences showed that the strains represented a distinct line of descent within the genus Ruegeria, with highest sequence similarities to Ruegeria atlantica DSM 5823T (97.2 %), Ruegeria lacuscaerulensis DSM 11314T (96.5 %) and Ruegeria pomeroyi DSM 15171T (95.6 %). Several phenotypic characteristics, including facultatively requiring NaCl and oxygen for growth, together with the cellular fatty acid composition, differentiated strain HTCC2662T from other members of the genus Ruegeria. Based on phenotypic, chemotaxonomic and phylogenetic traits, it is suggested that strains HTCC2662T and HTCC2663 represent a novel species of the genus Ruegeria, for which the name Ruegeria pelagia sp. nov. is proposed. The type strain is HTCC2662T (=KCCM 42378T=NBRC 102038T).

scholarly journals KARAKTERISASI FITOPLASMA PENYEBAB PENYAKIT LAYU KELAPA DI PULAU DERAWAN MENGGUNAKAN RFLP IN SILICO

2018 ◽  
Vol 17 (2) ◽  
pp. 105
Author(s):  
Agus Eko Prasetyo ◽  
Kikin Hamzah Mutaqin ◽  
Giyanto .
Keyword(s):  
Nested Pcr ◽  
In Silico ◽  
Bacterial Species ◽  
Rflp Analysis ◽  
Wilt Disease ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Gram Positive Bacteria ◽  
Pcr Method

Characterization of phytoplasmas associated with coconut wilt disease in Derawan Island using in silico RFLP. Coconutwilt disease has been reported in Derawan Island that resulted in eradication up to 10% of the total cultivated palms. Theobjective of this study was to detect and characterize phytoplasmas associated with coconut wilt disease in Derawan islandusing nested PCR technique and in silico RFLP based on 16S rRNA gene sequences. Detection of phytoplasmas was performedusing nested PCR method, cloning of nPCR products, sequencing, and analysis of sequencing results using in silico RFLP.The results revealed that phytoplasmas could not be detected by PCR using P1/P7 primer pairs however it could be amplifiedby nested PCR using R16F2n/R16R2 primer pairs resulting amplicon at about 1.25 kb. In silico RFLP analysis indicated thatphytoplasmas associated with coconut wilt disease in Derawan Island belong to 16SrII (witches broom phytoplasma). PCRproduct of the nPCR need to be sequenced because the R16F2n/R16R2 primer will also amplify the other bacterial species, mainly from Gram positive bacteria.

scholarly journals Taxono-genomics description of Olsenella lakotia SW165T sp. nov., a new anaerobic bacterium isolated from the cecum of feral chicken

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1103
Author(s):  
Supapit Wongkuna ◽  
Sudeep Ghimire ◽  
Tavan Janvilisri ◽  
Kinchel Doerner ◽  
Surang Chankhamhaengdecha ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Fatty Acid Production ◽  
Gram Staining ◽  
Biochemical Assays ◽  
A Genome ◽  
Culture Identification

Background: The microbial community residing in the animal gastrointestinal tract play a crucial role in host health. Because of the high complexity of gut microbes, many microbes remain unclassified. Deciphering the role of each bacteria in health and diseases is only possible after its culture, identification, and characterization. During the culturomics study of feral chicken cecal sample, we cultured a possible novel strain SW165T. Methods: For the possible novel strain SW165T, phenotypic characterization was performed using colony morphology, Gram staining, growth in different temperature and pH and motility. Biochemical assays included carbon source utilization, enzymatic activity, cellular fatty acids and short chain fatty acid production. 16S rRNA sequencing and whole genome sequencing and comparison was performed for genetic analysis. Results: This strain was isolated from cecal content of feral chickens in Brookings, South Dakota, USA. Phylogenetic analyses based on 16S rRNA gene sequence revealed that the closest valid neighbor was Olsenella profusa DSM 13989T (96.33% similarity) within the family Atopobiaceae. Cells were Gram-strain-positive and obligately anaerobic bacilli in chains. The optimum temperature and pH for the growth of the microorganism were 37-45oC and pH 6.0-7.5 respectively.  This strain produced acetic acid as the primary fermentation product. Major fatty acids were C12:0, C14:0, C14:0 DMA and summed feature 1 (C13:1 at 12-13 and C14:0 aldehyde). Strain SW165T exhibited a genome size of 2.43 Mbp with a G+C content of 67.59 mol%, which is the second highest G+C content among members of the genus Olsenella. The digital DNA-DNA hybridization and OrthoANI values between SW165T and DSM 13989T were only 17.6 ± 5.3 and 74.35%, respectively. Conclusion: Based on the phenotypic, biochemical, and genomic analyses, we propose the new species of the genus Olsenella, and name it Olsenella lakotia SW165T sp. nov., (=DSM 107283 =CCOS 1887) as the type strain.

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