scholarly journals Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov., moderately halophilic bacteria isolated from a deep-sea methane cold seep

2007 ◽  
Vol 57 (6) ◽  
pp. 1243-1249 ◽  
Author(s):  
Ngoc-Phuc Hua ◽  
Atsuko Kanekiyo ◽  
Katsunori Fujikura ◽  
Hisato Yasuda ◽  
Takeshi Naganuma
Keyword(s):  
Deep Sea ◽  
Sequence Similarity ◽  
Halophilic Bacteria ◽  
Cold Seep ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
High Sequence Similarity ◽  
Moderately Halophilic ◽  
Type Strains ◽  
Moderately Halophilic Bacteria

Two Gram-positive, rod-shaped, moderately halophilic bacteria were isolated from a deep-sea carbonate rock at a methane cold seep in Kuroshima Knoll, Japan. These bacteria, strains IS-Hb4T and IS-Hb7T, were spore-forming and non-motile. They were able to grow at temperatures as low as 9 °C and hydrostatic pressures up to 30 MPa. Based on high sequence similarity of their 16S rRNA genes to those of type strains of the genus Halobacillus, from 96.4 % (strain IS-Hb7T to Halobacillus halophilus NCIMB 9251T) to 99.4 % (strain IS-Hb4T to Halobacillus dabanensis D-8T), the strains were shown to belong to this genus. DNA–DNA relatedness values of 49.5 % and 1.0–33.0 %, respectively, were determined between strains IS-Hb4T and IS-Hb7T and between these strains and other Halobacillus type strains. Both strains showed the major menaquinone MK7 and l-orn–d-Asp cell-wall peptidoglycan type. Straight-chain C16 : 0, unsaturated C16 : 1 ω7c alcohol and C18 : 1 ω7c and cyclopropane C19 : 0 cyc fatty acids were predominant in both strains. The DNA G+C contents of IS-Hb4T and IS-Hb7T were respectively 43.3 and 42.1 mol%. Physiological and biochemical analyses combined with DNA–DNA hybridization results allowed us to place strains IS-Hb4T (=JCM 14154T=DSM 18394T) and IS-Hb7T (=JCM 14155T=DSM 18393T) in the genus Halobacillus as the respective type strains of the novel species Halobacillus profundi sp. nov. and Halobacillus kuroshimensis sp. nov.

Aquisalimonas asiatica gen. nov., sp. nov., a moderately halophilic bacterium isolated from an alkaline, saline lake in Inner Mongolia, China

2007 ◽  
Vol 57 (5) ◽  
pp. 1137-1142 ◽  
Author(s):  
M. C. Márquez ◽  
I. J. Carrasco ◽  
Y. Xue ◽  
Y. Ma ◽  
D. A. Cowan ◽  
...  
Keyword(s):  
Inner Mongolia ◽  
Type Strain ◽  
Sequence Similarity ◽  
Halophilic Bacterium ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strictly Aerobic ◽  
Moderately Halophilic ◽  
Hybridization Data ◽  
Moderately Halophilic Bacterium

Two novel moderately halophilic, Gram-negative rods (strains CG12T and CG13) were isolated from Lake Chagannor in Inner Mongolia Autonomous Region, China. They were strictly aerobic and motile. They grew at pH 6.0–10.8 (optimally at pH 7.5–8.5), at 20–50 °C (optimally at 37 °C) and at salinities of 1–20 % (w/v) total salts (optimally at 7–10 %, w/v). Phylogenetic analysis of the two strains, based on a comparison of their 16S rRNA genes, led to their classification within the class Gammaproteobacteria, the closest recognized type strain being Alkalispirillum mobile DSM 12769T, with which they were found to share 94.4–94.6 % sequence similarity. On the basis of DNA–DNA hybridization data (showing 100 and 99 % relatedness for each other), the two isolates were found to be members of the same species. The DNA G+C contents of strains CG12T and CG13 were found to be 63.6 and 64.0 mol%, respectively. The major cellular fatty acids of strain CG12T, selected as the representative strain, were C18 : 1 ω7c, C16 : 0 and C12 : 0, and its polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, a phosphoglycolipid and six unidentified phospholipids. On the basis of the polyphasic evidence from this study, strains CG12T and CG13 represent a novel genus and species, for which the name Aquisalimonas asiatica gen. nov., sp. nov. is proposed. The type strain of Aquisalimonas asiatica is CG12T (=CCM 7368T=CECT 7151T=CGMCC 1.6291T=DSM 18102T).

Study on biocharacteristics and puruvate production of moderately halophilic bacteria isolated from dunalliella tertiolecta’s culture medium

2018 ◽  
Vol 40 (4) ◽  
Author(s):  
Hoang Thi Lan Anh ◽  
Luu Thi Tam ◽  
Dang Diem Hong
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Culture Medium ◽  
Sequence Similarity ◽  
Halophilic Bacteria ◽  
Rrna Gene ◽  
Wild Type ◽  
Moderately Halophilic ◽  
Moderately Halophilic Bacteria

A moderately halophilic bacteria designed strain D34 was isolated from the culture medium of green microalga Dunaliella tertiolecta. The isolate was Gram-negative, aerobic, rod-shaped, approximately 0.45–0.60 mm wide and 1.25–5.10 mm long, occuring singly, non-motile, and flagellum- less. Colonies on solid media are cream, circular, and smooth. This strain was able to produce exopolysaccharide, poly hydroxybutyrate, oxidase and catalase positive. Growth occurred in a temparature range of 20–40°C, a salts concentration of 0.1–25% (w/v), and pH range 6–12. The major fatty acids were C16:0 (35.59%), C16:1w-7 (20.54%), C18: 1w-7 (30.14%), and C12:0 (10.03% of total fatty acids). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain D34 belonged to the genus Halomonas. The highest levels of 16S rRNA gene sequence similarity were found between the strain D34 and H. aquamarina (sequence similarity 98.6 %).Pyruvate, a central intermediate in metabolism processes in all organisms, is widely used for the synthesis of various chemicals and polymers as well as ingredient or additive in food, cosmetics, and pharmaceuticals. In this study, pyruvate production by strain D34 following changes in culture medium, glucose and nitrate concentrations and culture temperature were also studied. In 84 hours of batch- cultivation, pyruvate production by wild-type Halomonas sp. D34 reached 37.24 g/L at 37°C with 20% glucose and 30 g/L sodium nitrate adding to SOT medium. These data provided evidences for pyruvate production using novel wild-type strains. 

Cultivation and characterization of symbiotic bacteria from the gut of Reticulitermes chinensis

2016 ◽  
Vol 1 (1) ◽  
pp. 3 ◽  
Author(s):  
Hao Fang ◽  
Wen Chen ◽  
Baojun Wang ◽  
Xiaojuan Li ◽  
Shuang-Jiang Liu ◽  
...  
Keyword(s):  
Cellulose Degradation ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Symbiotic Bacteria ◽  
Nitrogen Recycling ◽  
Bacterial Strains ◽  
High Sequence Similarity

The complex symbiotic relationship between wood-feeding termites and microorganisms inhabiting their intestinal tracts is a fascinating phenomenon in nature. To understand the physiological functions of symbiotic micro-organisms, bacteria were isolated from the gut homogenate of Reticulitermes chinensis with different media and culture conditions. Under aerobic conditions, 105 bacterial strains were isolated with 1/5 LB medium, 1/3 TSB medium and a modified basal mineral medium, MM-4. Most dominant isolates were bacteria in the genera Bacillus (27.6%) and Lactococcus (21.9%). Under anaerobic conditions, 60 bacterial strains were isolated with 1/5 LB medium, 1/3 TSB medium and a modified Peptone-Yeast medium. The predominant isolates were bacteria in the genus Enterobacter (41.7%) and Citrobacter (33.3%). Many of these bacterial isolates shared high sequence similarity (>98%) in 16S rRNA genes to bacterial clones obtained from the same termite and the other wood-feeding termites or cockroaches. Several bacterial species such as Deinococcus and Gryllotalpicola were isolated from termite gut for the first time. Characterization of these isolates showed that (i) most of Enterobacteriaceae and Lactococcus strains were able to hydrolyze uric acid; and (ii) many of the Bacillus and Streptomyces strains presented endo-β-1,4-glucanase activity. The preliminary results of this work gave us hints of possible functions of symbiotic bacteria in nitrogen recycling and cellulose degradation in the gut of wood-feeding termites

scholarly journals The Complete Chloroplast Genome of the Vulnerable Oreocharis esquirolii (Gesneriaceae): Structural Features, Comparative and Phylogenetic Analysis

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1692
Author(s):  
Li Gu ◽  
Ting Su ◽  
Ming-Tai An ◽  
Guo-Xiong Hu
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Similarity ◽  
Single Copy ◽  
Structural Features ◽  
Rrna Genes ◽  
Trna Genes ◽  
Sequencing Data ◽  
High Sequence Similarity ◽  
Plastid Genomes ◽  
Cp Genome

Oreocharis esquirolii, a member of Gesneriaceae, is known as Thamnocharis esquirolii, which has been regarded a synonym of the former. The species is endemic to Guizhou, southwestern China, and is evaluated as vulnerable (VU) under the International Union for Conservation of Nature (IUCN) criteria. Until now, the sequence and genome information of O. esquirolii remains unknown. In this study, we assembled and characterized the complete chloroplast (cp) genome of O. esquirolii using Illumina sequencing data for the first time. The total length of the cp genome was 154,069 bp with a typical quadripartite structure consisting of a pair of inverted repeats (IRs) of 25,392 bp separated by a large single copy region (LSC) of 85,156 bp and a small single copy region (SSC) of18,129 bp. The genome comprised 114 unique genes with 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Thirty-one repeat sequences and 74 simple sequence repeats (SSRs) were identified. Genome alignment across five plastid genomes of Gesneriaceae indicated a high sequence similarity. Four highly variable sites (rps16-trnQ, trnS-trnG, ndhF-rpl32, and ycf 1) were identified. Phylogenetic analysis indicated that O. esquirolii grouped together with O. mileensis, supporting resurrection of the name Oreocharis esquirolii from Thamnocharisesquirolii. The complete cp genome sequence will contribute to further studies in molecular identification, genetic diversity, and phylogeny.

scholarly journals Novosphingobium gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2831-2837 ◽  
Author(s):  
Peter Kämpfer ◽  
Karin Martin ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
Gossypium Hirsutum ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
High Sequence Similarity ◽  
Polar Lipid Profile ◽  
Gene Sequence Analysis ◽  
Bacterium Strain ◽  
Type Strains ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, non-spore-forming bacterium (strain JM-1396T) producing a yellow pigment, was isolated from the healthy internal stem tissue of post-harvest cotton (Gossypium hirsutum, cultivar ‘DES-119’) grown at the Plant Breeding Unit at the E. V. Smith Research Center in Tallassee (Macon county), AL, USA. 16S rRNA gene sequence analysis of strain JM-1396T showed high sequence similarity values to the type strains of Novosphingobium mathurense, Novosphingobium panipatense (both 98.6 %) and Novosphingobium barchaimii (98.5 %); sequence similarities to all other type strains of species of the genus Novosphingobium were below 98.3 %. DNA–DNA pairing experiments of the DNA of strain JM-1396T and N. mathurense SM117T, N. panipatense SM16T and N. barchaimii DSM 25411T showed low relatedness values of 8 % (reciprocal 7 %), 24 % (reciprocal 26 %) and 19 % (reciprocal 25 %), respectively. Ubiquinone Q-10 was detected as the dominant quinone; the fatty acids C18 : 1ω7c (71.0 %) and the typical 2-hydroxy fatty acid, C14 : 0 2-OH (11.7 %), were detected as typical components. The polar lipid profile contained the diagnostic lipids diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. The polyamine pattern contained the major compound spermidine and only minor amounts of other polyamines. All these data revealed that strain JM-1396T represents a novel species of the genus Novosphingobium. For this reason we propose the name Novosphingobium gossypii sp. nov. with the type strain JM-1396T ( = LMG 28605T = CCM 8569T = CIP 110884T).

scholarly journals Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts

2007 ◽  
Vol 57 (12) ◽  
pp. 2908-2911 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Seon-Young Lee ◽  
Byung-Yong Kim ◽  
Hyung-Jun Noh ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Phylogenetic Affiliation ◽  
Dna Reassociation ◽  
Compost Facility

Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145T and HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145T and HC148T and comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genus Ureibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existing Ureibacillus species were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains of Ureibacillus species ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type was l-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145T and HC148T were 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145T and HC148T represent members of the genus Ureibacillus, for which the names Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., respectively, are proposed. The type strain of U. composti is HC145T (=KACC 11361T =DSM 17951T) and the type strain of U. thermophilus is HC148T (=KACC 11362T =DSM 17952T).

scholarly journals Opening a next-generation black box: ecological trends for hundreds of species-like taxa uncovered within a single bacterial >99% 16S rRNA operational taxonomic unit

2021 ◽  
Author(s):  
Martin Hahn ◽  
Andrea Huemer ◽  
Alexandra Pitt ◽  
Matthias Hoetzinger
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Taxon Richness ◽  
Large Set ◽  
Free Living ◽  
Environmental Distribution ◽  
Living Bacteria

Current knowledge on environmental distribution and taxon richness of free-living bacteria is mainly based on cultivation-independent investigations employing 16S rRNA gene sequencing methods. Yet, 16S rRNA genes are evolutionarily rather conserved, resulting in limited taxonomic and ecological resolutions provided by this marker. We used a faster evolving protein-encoding marker to reveal ecological patterns hidden within a single OTU defined by >99% 16S rRNA sequence similarity. The studied taxon, subcluster PnecC of the genus Polynucleobacter, represents a ubiquitous group of planktonic freshwater bacteria with cosmopolitan distribution, which is very frequently detected by diversity surveys of freshwater systems. Based on genome taxonomy and a large set of genome sequences, a sequence similarity threshold for delineation of species-like taxa could be established. In total, 600 species-like taxa were detected in 99 freshwater habitats scattered across three regions representing a latitudinal range of 3400 km (42°N to 71°N) and a pH gradient of 4.2 to 8.6. Besides the unexpectedly high richness, the increased taxonomic resolution revealed structuring of Polynucleobacter communities by a couple of macroecological trends, which was previously only demonstrated for phylogenetically much broader groups of bacteria. A unexpected pattern was the almost complete compositional separation of Polynucleobacter communities of Ca-rich and Ca-poor habitats, which strongly resembled the vicariance of plant species on silicate and limestone soils. The presented new cultivation-independent approach opened a window to an incredible, previously unseen diversity, and enables investigations aiming on deeper understanding of how environmental conditions shape bacterial communities and drive evolution of free-living bacteria.

scholarly journals Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla)

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2320-2325 ◽  
Author(s):  
Shih-Yao Lin ◽  
Asif Hameed ◽  
Cheng-Zhe Wen ◽  
You-Cheng Liu ◽  
Yi-Han Hsu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sea Urchins ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
The Novel ◽  
Moderate Amount ◽  
Polar Lipid Profile

A Gram-stain-negative, aerobic, rod-shaped, yellow-pigment-producing bacterium (designated strain CC-CZW007T) was isolated from seafood samples (sea urchins) at Penghu Island in Taiwan. Strain CC-CZW007T grew optimally at pH 7.0 and 30 °C in the presence of 3 % (w/v) NaCl. The novel strain shared highest 16S rRNA gene sequence similarity to Vitellibacter vladivostokensis JCM 11732T (96.8 %), Vitellibacter soesokkakensis KCTC 32536T (96.4 %), Vitellibacter nionensis KCTC 32420T (95.8 %) and Vitellibacter aestuarii JCM 15496T (95.6 %) and lower sequence similarity to members of other genera. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CZW007T with respect to other species of the genus Vitellibacter. The major fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. The polar lipid profile was composed of major amounts of phosphatidylethanolamine, unidentified lipids and aminolipids; a moderate amount of aminophospholipid was also detected. The DNA G+C content was 34.7 mol%. The predominant quinone system was menaquinone (MK-6). On the basis of polyphasic taxonomic evidence presented here, strain CC-CZW007T is proposed to represent a novel species within the genus Vitellibacter, for which the name Vitellibacter echinoideorum sp. nov. is proposed. The type strain is CC-CZW007T ( = BCRC 80886T = JCM 30378T).

scholarly journals Rhizobium azibense sp. nov., a nitrogen fixing bacterium isolated from root-nodules of Phaseolus vulgaris

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1501-1506 ◽  
Author(s):  
Bacem Mnasri ◽  
Tian Yan Liu ◽  
Sabrine Saidi ◽  
Wen Feng Chen ◽  
Wen Xin Chen ◽  
...  
Keyword(s):  
Type Species ◽  
Root Nodules ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Physiological Properties ◽  
Microbial Strains ◽  
Type Strains

Three microbial strains isolated from common beans, 23C2T (Tunisia), Gr42 (Spain) and IE4868 (Mexico), which have been identified previously as representing a genomic group closely related to Rhizobium gallicum , are further studied here. Their 16S rRNA genes showed 98.5–99 % similarity with Rhizobium loessense CCBAU 7190BT, R. gallicum R602spT, Rhizobium mongolense USDA 1844T and Rhizobium yanglingense CCBAU 71623T. Phylogenetic analysis based on recA, atpD, dnaK and thrC sequences showed that the novel strains were closely related and could be distinguished from the four type strains of the closely related species. Strains 23C2T, Gr42 and IE4868 could be also differentiated from their closest phylogenetic neighbours by their phenotypic and physiological properties and their fatty acid contents. All three strains harboured symbiotic genes specific to biovar gallicum. Levels of DNA–DNA relatedness between strain 23C2T and the type strains of R. loessense , R. mongolense , R. gallicum and R. yanglingense ranged from 58.1 to 61.5 %. The DNA G+C content of the genomic DNA of strain 23C2T was 59.52 %. On the basis of these data, strains 23C2T, Gr42 and IE4868 were considered to represent a novel species of the genus Rhizobium for which the name Rhizobium azibense is proposed. Strain 23C2T ( = CCBAU 101087T = HAMBI3541T) was designated as the type strain.

Sign in / Sign up

Export Citation Format

Share Document