scholarly journals Caldicoprobacter oshimai gen. nov., sp. nov., an anaerobic, xylanolytic, extremely thermophilic bacterium isolated from sheep faeces, and proposal of Caldicoprobacteraceae fam. nov.

2010 ◽  
Vol 60 (1) ◽  
pp. 67-71 ◽  
Author(s):  
Hiroshi Yokoyama ◽  
Isaac D. Wagner ◽  
Juergen Wiegel
Keyword(s):  
Cell Wall ◽  
Potato Starch ◽  
Single Layer ◽  
Thermophilic Bacterium ◽  
Wall Structure ◽  
Rrna Gene ◽  
Fermentation Products ◽  
University Of Georgia ◽  
Casamino Acids ◽  
The University

An obligately anaerobic, xylanolytic, extremely thermophilic bacterium, strain JW/HY-331T, was isolated from sheep faeces collected from a farm at the University of Georgia, USA. Cells of strain JW/HY-331T stained Gram-positive and were catalase-negative, non-motile rods. Single terminal endospores (0.4–0.6 μm in diameter) swelled the mother cell. Growth ranges were 44–77 °C (optimum 70 °C at pH70 °C 7.2) and pH70 °C 5.9–8.6 (optimum 7.2 at 70 °C). Salt tolerance was 0–2.0 % (w/v) NaCl. No growth was observed at or below 42 °C or at or above 79 °C or at pH70 °C 5.7 and below or 8.9 and above. In the presence of 0.3 % yeast extract and 0.1 % tryptone, strain JW/HY-331T utilized xylose, glucose, galactose, cellobiose, raffinose and xylan as carbon and energy sources, but not dextran, soluble potato starch, CM-cellulose, cellulose powder, casein or Casamino acids. Fermentation products from glucose were lactate, acetate, ethanol, CO2 and H2. The G+C content of the genomic DNA was 45.4 mol% (HPLC). Major cellular fatty acids were iso-C17 : 0, iso-C15 : 0 and anteiso-C17 : 0. No respiratory quinones were detected. The cell-wall structure was a single layer (Gram-type positive) of the peptidoglycan type A1γ; the cell-wall sugars were galactose and mannose. Based on 16S rRNA gene sequence analysis, ‘Catabacter hongkongensis’ HKU16 (85.4 % similarity), Caloramator fervidus ATCC 43204T (84.2 %) and Caloranaerobacter azorensis MV1087T (83.4 %) were the closest relatives, but they were only distantly related to strain JW/HY-331T. On the basis of physiological, chemotaxonomic and phylogenetic data, isolate JW/HY-331T (=DSM 21659T =ATCC BAA-1711T) is proposed as the type strain of Caldicoprobacter oshimai gen. nov., sp. nov., placed in Caldicoprobacteraceae fam. nov. within the order Clostridiales of the phylum Firmicutes.

The maturation of cell wall structure during germination of Bacillus polymyxa spores

1970 ◽  
Vol 16 (9) ◽  
pp. 883-887 ◽  
Author(s):  
R. G. E. Murray ◽  
Myrtle M. Hall ◽  
J. Marak
Keyword(s):  
Cell Wall ◽  
Intermediate Layer ◽  
Single Layer ◽  
Regular Structure ◽  
Wall Structure ◽  
Bacillus Polymyxa ◽  
Rectangular Array ◽  
Crack Open ◽  
Freeze Etching ◽  
Primordial Cell

Sections of germinating spores of Bacillus polymyxa show that the primordial cell wall consists of a single layer. The intermediate layer and an outer rectangular array of macromolecules found on vegetative cells do not appear until the spore coats crack open about 60 min after initiation of germination. The initial areas of the new components appear in patches under the cracks in the coats. Within 10 min the wall is completed and takes on the profile seen in the vegetative cell. Negative staining and freeze-etching techniques show the regular structure to be identical with that previously shown for mature cells, although the subunits are more readily visible in negatively stained preparations.

scholarly journals Alkaliphilus halophilus sp. nov., a strictly anaerobic and halophilic bacterium isolated from a saline lake, and emended description of the genus Alkaliphilus

2010 ◽  
Vol 60 (12) ◽  
pp. 2898-2902 ◽  
Author(s):  
Xiao-Yue Wu ◽  
Kong-Lan Shi ◽  
Xue-Wei Xu ◽  
Min Wu ◽  
Aharon Oren ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Saline Lake ◽  
Salt Lake ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Fermentation Products ◽  
Substrate Utilization Pattern ◽  
Emended Description ◽  
Casamino Acids

A novel strictly anaerobic, halophilic and fermentative strain, designated E2RT, was isolated from sediments of Xiaokule salt lake in Xinjiang Province, China. Cells were straight to slightly curved, Gram-stain-positive rods that were motile by means of flagella and formed endospores. Strain E2RT was moderately halophilic and grew optimally in the presence of 7.5 % NaCl, at pH 8.0 and at 32 °C. Substrates used include yeast extract, Casamino acids, tryptone, fructose, sucrose, xylose, ribose, lactate and tartrate. Thiosulfate could be used as an accessory electron acceptor and stimulated growth. The main fermentation products from fructose were formate and acetate. The predominant fatty acids were iso-C15 : 0, iso-C15 : 1 F and iso-C13 : 0. 16S rRNA gene sequence analyses revealed that strain E2RT was related most closely to members of the genus Alkaliphilus (95.5–91.1 % similarity). The G+C content of strain E2RT was 28.5 mol%. Strain E2RT could be differentiated from its closest relatives based on its halophilic nature and its lower DNA G+C content. It could also be differentiated based on its substrate utilization pattern and relatively high levels of iso-C15 : 0. On the basis of these data, strain E2RT is considered to represent a novel species of the genus Alkaliphilus, for which the name Alkaliphilus halophilus sp. nov. is proposed. The type strain is E2RT (=CGMCC 1.5124T =JCM 16124T). An emended description of the genus Alkaliphilus is also provided.

scholarly journals Phenylobacterium lituiforme sp. nov., a moderately thermophilic bacterium from a subsurface aquifer, and emended description of the genus Phenylobacterium

2004 ◽  
Vol 54 (6) ◽  
pp. 2141-2146 ◽  
Author(s):  
Sungwan Kanso ◽  
Bharat K. C. Patel
Keyword(s):  
Yeast Extract ◽  
Optimal Growth ◽  
Thermophilic Bacterium ◽  
Wall Structure ◽  
Rrna Gene ◽  
Thin Sections ◽  
Gram Negative ◽  
Moderately Thermophilic ◽  
Registration Number ◽  
Flowing Waters

A facultative anaerobic bacterium, strain FaiI3T, was isolated from samples collected from the free-flowing waters of a bore well (Fairlea Bore, registration number 3768) which taps into the Australian Great Artesian Basin subsurface thermal aquifer. Strain FaiI3T developed yellow to pale-yellow colonies (0·5–1·5 mm) after 48 h. The non-spore forming rods (0·5×1–3 μm) were slightly curved, occurred singly and as pairs and were motile with a single polar flagellum. Cells tended to form clumps in liquid medium and rosettes were commonly observed. The cells stained Gram-negative and electron micrographs of thin sections revealed a multi-layered complex Gram-negative cell wall structure. Strain FaiI3T grew optimally at 40–41 °C, with growth observed at 45 °C but not at 50 °C. The pH growth range was between pH 6 and 9 and optimal growth occurred between pH 6 and 6·5. Strain FaiI3T grew best with yeast extract as the sole carbon and energy source. Peptone, yeast extract, acetate, xylose, sucrose, glucose, glycerol, succinate, butyrate, lactate, fumarate, citrate, l-phenylalanine, cellobiose and gelatin supported growth but maltose, fructose, glycine, ethanol, benzoate and oxalate did not. Tyrosine was produced from l-phenylalanine. Strain FaiI3T was catalase-positive and oxidase-negative and did not hydrolyse starch. Growth was inhibited by neomycin, tetracycline, streptomycin, chloramphenicol, ampicillin, vancomycin and spectinomycin. The G+C content was determined to be 66·5±0·5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain FaiI3T was assigned as a novel species of the genus Phenylobacterium, Phenylobacterium lituiforme sp. nov. in the order Caulobacterales, subclass α-Proteobacteria, class Proteobacteria. The type strain is FaiI3T (=ATCC BAA-294T=DSM 14363T).

scholarly journals Genomic Characterization of Candidate Division LCP-89 Reveals an Atypical Cell Wall Structure, Microcompartment Production, and Dual Respiratory and Fermentative Capacities

2019 ◽  
Vol 85 (10) ◽  
Author(s):  
Noha H. Youssef ◽  
Ibrahim F. Farag ◽  
C. Ryan Hahn ◽  
Jessica Jarett ◽  
Eric Becraft ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Structural Features ◽  
Wall Structure ◽  
Rrna Gene ◽  
Atypical Cell ◽  
Wide Range ◽  
Candidate Division

ABSTRACTRecent experimental and bioinformatic advances enable the recovery of genomes belonging to yet-uncultured microbial lineages directly from environmental samples. Here, we report on the recovery and characterization of single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) representing candidate phylum LCP-89, previously defined based on 16S rRNA gene sequences. Analysis of LCP-89 genomes recovered from Zodletone Spring, an anoxic spring in Oklahoma, predicts slow-growing, rod-shaped organisms. LCP-89 genomes contain genes for cell wall lipopolysaccharide (LPS) production but lack the entire machinery for peptidoglycan biosynthesis, suggesting an atypical cell wall structure. The genomes, however, encode S-layer homology domain-containing proteins, as well as machinery for the biosynthesis of CMP-legionaminate, inferring the possession of an S-layer glycoprotein. A nearly complete chemotaxis machinery coupled to the absence of flagellar synthesis and assembly genes argues for the utilization of alternative types of motility. A strict anaerobic lifestyle is predicted, with dual respiratory (nitrite ammonification) and fermentative capacities. Predicted substrates include a wide range of sugars and sugar alcohols and a few amino acids. The capability of rhamnose metabolism is confirmed by the identification of bacterial microcompartment genes to sequester the toxic intermediates generated. Comparative genomic analysis identified differences in oxygen sensitivities, respiratory capabilities, substrate utilization preferences, and fermentation end products between LCP-89 genomes and those belonging to its four sister phyla (Calditrichota, SM32-31, AABM5-125-24, and KSB1) within the broader FCB (Fibrobacteres-Chlorobi-Bacteroidetes) superphylum. Our results provide a detailed characterization of members of the candidate division LCP-89 and highlight the importance of reconciling 16S rRNA-based and genome-based phylogenies.IMPORTANCEOur understanding of the metabolic capacities, physiological preferences, and ecological roles of yet-uncultured microbial phyla is expanding rapidly. Two distinct approaches are currently being utilized for characterizing microbial communities in nature: amplicon-based 16S rRNA gene surveys for community characterization and metagenomics/single-cell genomics for detailed metabolic reconstruction. The occurrence of multiple yet-uncultured bacterial phyla has been documented using 16S rRNA surveys, and obtaining genome representatives of these yet-uncultured lineages is critical to our understanding of the role of yet-uncultured organisms in nature. This study provides a genomics-based analysis highlighting the structural features and metabolic capacities of a yet-uncultured bacterial phylum (LCP-89) previously identified in 16S rRNA surveys for which no prior genomes have been described. Our analysis identifies several interesting structural features for members of this phylum, e.g., lack of peptidoglycan biosynthetic machinery and the ability to form bacterial microcompartments. Predicted metabolic capabilities include degradation of a wide range of sugars, anaerobic respiratory capacity, and fermentative capacities. In addition to the detailed structural and metabolic analysis provided for candidate division LCP-89, this effort represents an additional step toward a unified scheme for microbial taxonomy by reconciling 16S rRNA gene-based and genomics-based taxonomic outlines.

scholarly journals Thermocrinis minervae sp. nov., a hydrogen- and sulfur-oxidizing, thermophilic member of the Aquificales from a Costa Rican terrestrial hot spring

2010 ◽  
Vol 60 (2) ◽  
pp. 338-343 ◽  
Author(s):  
Sara L. Caldwell ◽  
Yitai Liu ◽  
Isabel Ferrera ◽  
Terry Beveridge ◽  
Anna-Louise Reysenbach
Keyword(s):  
Hot Spring ◽  
Sequence Similarity ◽  
Thermophilic Bacterium ◽  
Costa Rican ◽  
Close Relative ◽  
Rrna Gene ◽  
Sulfur Oxidizing ◽  
Casamino Acids ◽  
Terrestrial Hot Spring ◽  
The 16S Rrna Gene

A thermophilic bacterium, designated strain CR11T, was isolated from a filamentous sample collected from a terrestrial hot spring on the south-western foothills of the Rincón volcano in Costa Rica. The Gram-negative cells are approximately 2.4–3.9 μm long and 0.5–0.6 μm wide and are motile rods with polar flagella. Strain CR11T grows between 65 and 85 °C (optimum 75 °C, doubling time 4.5 h) and between pH 4.8 and 7.8 (optimum pH 5.9–6.5). The isolate grows chemolithotrophically with S0, or H2 as the electron donor and with O2 (up to 16 %, v/v) as the sole electron acceptor. The isolate can grow on mannose, glucose, maltose, succinate, peptone, Casamino acids, starch, citrate and yeast extract in the presence of oxygen (4 %) and S0. Growth occurs only at NaCl concentrations below 0.4 % (w/v). The G+C content of strain CR11T is 40.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence places the strain as a close relative of Thermocrinis ruber OC 1/4T (95.7 % sequence similarity). Based on phylogenetic and physiological characteristics, we propose the name Thermocrinis minervae sp. nov., with CR11T (=DSM 19557T =ATCC BAA-1533T) as the type strain.

scholarly journals Natranaerobius thermophilus gen. nov., sp. nov., a halophilic, alkalithermophilic bacterium from soda lakes of the Wadi An Natrun, Egypt, and proposal of Natranaerobiaceae fam. nov. and Natranaerobiales ord. nov.

2007 ◽  
Vol 57 (11) ◽  
pp. 2507-2512 ◽  
Author(s):  
Noha M. Mesbah ◽  
David B. Hedrick ◽  
Aaron D. Peacock ◽  
Manfred Rohde ◽  
Juergen Wiegel
Keyword(s):  
Soda Lakes ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Characteristics ◽  
Fermentation Products ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Novel Genus And Species ◽  
Casamino Acids ◽  
Uncultivated Bacteria

Novel halophilic, alkalithermophilic, Gram-type-positive bacterial strains were isolated from sediment of alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Cells of strain JW/NM-WN-LFT were rod-shaped, non-spore-forming and non-motile. Strain JW/NM-WN-LFT grew (at pH55 °C 9.5) between 35 and 56 °C, with an optimum at 53 °C. The pH55 °C range for growth was 8.3–10.6, with an optimum at pH55 °C 9.5 and no growth at pH55 °C 8.2 or below, or at pH55 °C 10.8 or above. At the optimum pH and temperature, the strain grew in the Na+ range of 3.1–4.9 M (1.5–3.3 M added NaCl) and optimally between 3.3 and 3.9 M Na+ (1.7–2.3 M added NaCl). Strain JW/NM-WN-LFT utilized fructose, cellobiose, ribose, trehalose, trimethylamine, pyruvate, Casamino acids, acetate, xylose and peptone as carbon and energy sources. Fumarate (20 mM), S2O3 2− (20 mM), NO3 − (20 mM) and iron(III) citrate (20 mM) were utilized as electron acceptors. During growth on sucrose, the isolate produced acetate and formate as major fermentation products. Main cellular fatty acids were iso-branched 15 : 0, i17 : 0 dimethylacetal and 16 : 0 dimethylacetal. The G+C content of genomic DNA was 40.4 mol% (HPLC). On the basis of genotypic and phenotypic characteristics, it is proposed that strain JW/NM-WN-LFT represents a novel genus and species, Natranaerobius thermophilus gen. nov., sp. nov. The type strain is JW/NM-WN-LFT (=DSM 18059T=ATCC BAA-1301T). Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class ‘Clostridia’ and clusters with uncultivated bacteria and unidentified strains retrieved from alkaline, hypersaline environments. The phylogenetic data suggest that the lineage represents a novel family, Natranaerobiaceae fam. nov., and order, Natranaerobiales ord. nov.

scholarly journals Microbacter margulisiae gen. nov., sp. nov., a propionigenic bacterium isolated from sediments of an acid rock drainage pond

2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 3936-3942 ◽  
Author(s):  
Irene Sánchez-Andrea ◽  
Jose Luis Sanz ◽  
Alfons J. M. Stams
Keyword(s):  
Acid Rock Drainage ◽  
Sequence Similarity ◽  
Wall Structure ◽  
Rrna Gene ◽  
Acid Rock ◽  
Fermentation Products ◽  
Content Type ◽  
Optimum Growth Temperature ◽  
Tinto River ◽  
Link Type

A novel anaerobic propionigenic bacterium, strain ADRIT, was isolated from sediment of an acid rock drainage environment (Tinto River, Spain). Cells were small (0.4–0.6×1–1.7 µm), non-motile and non-spore-forming rods. Cells possessed a Gram-negative cell-wall structure and were vancomycin-resistant. Strain ADRIT utilized yeast extract and various sugars as substrates and formed propionate, lactate and acetate as major fermentation products. The optimum growth temperature was 30 °C and the optimum pH for growth was pH 6.5, but strain ADRIT was able to grow at a pH as low as 3.0. Oxidase, indole formation, and urease and catalase activities were negative. Aesculin and gelatin were hydrolysed. The predominant cellular fatty acids of strain ADRIT were anteiso-C15 : 0 (30.3 %), iso-C15 : 0 (29.2 %) and iso-C17 : 0 3-OH (14.9 %). Major menaquinones were MK-8 (52 %) and MK-9 (48 %). The genomic DNA G+C content was 39.9 mol%. Phylogenetically, strain ADRIT was affiliated to the family Porphyromonadaceae of the phylum Bacteroidetes . The most closely related cultured species were Paludibacter propionicigenes with 16S rRNA gene sequence similarity of 87.5 % and several species of the genus Dysgonomonas (similarities of 83.5–85.4 % to the type strains). Based on the distinctive ecological, phenotypic and phylogenetic characteristics of strain ADRIT, a novel genus and species, Microbacter margulisiae gen. nov., sp. nov., is proposed. The type strain is ADRIT ( = JCM 19374T = DSM 27471T).

scholarly journals Tilted cellulose arrangement as a novel mechanism for hygroscopic coiling in the stork's bill awn

2011 ◽  
Vol 9 (69) ◽  
pp. 640-647 ◽  
Author(s):  
Yael Abraham ◽  
Carmen Tamburu ◽  
Eugenia Klein ◽  
John W. C. Dunlop ◽  
Peter Fratzl ◽  
...  
Keyword(s):  
Cell Wall ◽  
Simple Model ◽  
Single Layer ◽  
Cellulose Microfibrils ◽  
Wall Structure ◽  
Environmental Humidity ◽  
A Cell ◽  
Dispersal Unit ◽  
Bilayered Structure ◽  
Isotropic Foam

The sessile nature of plants demands the development of seed-dispersal mechanisms to establish new growing loci. Dispersal strategies of many species involve drying of the dispersal unit, which induces directed contraction and movement based on changing environmental humidity. The majority of researched hygroscopic dispersal mechanisms are based on a bilayered structure. Here, we investigate the motility of the stork's bill ( Erodium ) seeds that relies on the tightening and loosening of a helical awn to propel itself across the surface into a safe germination place. We show that this movement is based on a specialized single layer consisting of a mechanically uniform tissue. A cell wall structure with cellulose microfibrils arranged in an unusually tilted helix causes each cell to spiral. These cells generate a macroscopic coil by spiralling collectively. A simple model made from a thread embedded in an isotropic foam matrix shows that this cellulose arrangement is indeed sufficient to induce the spiralling of the cells.

Crystalline order to a resolution of 4.7 A in the sheath of Methanospirilium hungatii: A cross-beta structure

1984 ◽  
Vol 42 ◽  
pp. 214-215
Author(s):  
Murray Stewart ◽  
T.J. Beveridge ◽  
D. Sprott
Keyword(s):  
Cell Wall ◽  
Single Layer ◽  
Uranyl Acetate ◽  
Optical Diffraction ◽  
Tube Axis ◽  
Basic Subunit ◽  
Beta Structure ◽  
Diffraction Patterns ◽  
Protein Treatment ◽  
General Appearance

The archaebacterium Methanospirillum hungatii has a sheath as part of its cell wall which is composed mainly of protein. Treatment with dithiothreitol or NaOH released the intact sheaths and electron micrographs of this material negatively stained with uranyl acetate showed flattened hollow tubes, about 0.5 μm diameter and several microns long, in which the patterns from the top and bottom were superimposed. Single layers, derived from broken tubes, were also seen and were more simply analysed. Figure 1 shows the general appearance of a single layer. There was a faint axial periodicity at 28.5 A, which was stronger at irregular multiples of 28.5 A (3 and 4 times were most common), and fine striations were also seen at about 3° to the tube axis. Low angle electron diffraction patterns (not shown) and optical diffraction patterns (Fig. 2) from these layers showed a complex meridian (as a result of the irregular nature of the repeat along the tube axis) which showed a clear maximum at 28.5 A, consistent with the basic subunit spacing.

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