scholarly journals Thermostable and Alkalistable Xylanases Produced by the Thermophilic Bacterium Anoxybacillus flavithermus TWXYL3

2012 ◽  
Vol 2012 ◽  
pp. 1-8 ◽  
Author(s):  
Joshua T. Ellis ◽  
Timothy S. Magnuson
Keyword(s):  
Hydrothermal System ◽  
Xylanase Activity ◽  
Electrophoretic Analysis ◽  
Economic Incentive ◽  
Thermophilic Bacterium ◽  
Rrna Gene ◽  
Ph Optimum ◽  
Anoxybacillus Flavithermus ◽  
The 16S Rrna Gene ◽  
Alvord Basin

With the rising cost and finite supply of fossil energy, there is an increasing economic incentive for the development of clean, efficient, and renewable domestic energy. The activities of microorganisms offer the potential conversion of lignocellulosic materials into fermentable sugars, usable for downstream fermentation processes. Strain TWXYL3, a thermophilic facultative anaerobe, was discovered in the Alvord Basin hydrothermal system in Oregon, USA. Phylogenetic analysis of strain TWXYL3 showed it to be 99% similar to the 16S rRNA gene of Anoxybacillus flavithermus WL (FJ950739). A. flavithermus TWXYL3 was shown to secrete a large multisubunit thermostable xylanase complex into the growth medium. Xylanase induction was achieved by resuspending the isolate in a selective xylan-containing medium. Extracellular xylanase activity showed a temperature optimum of 65°C and retained thermostability up to 85°C. Extracellular xylanase activity showed a bimodal pH optimum, with maxima at pH 6 and pH 8. Electrophoretic analysis of the extracellular xylanase shows 5 distinct proteins with xylanase activity. Strain TWXYL3 is the first xylanolytic isolate obtained from the Alvord Basin hydrothermal system and represents a new model system for development of processes where lignocellulosics are converted to biofuel precursors.

scholarly journals Microbacterium natoriense sp. nov., a novel d-aminoacylase-producing bacterium isolated from soil in Natori, Japan

2005 ◽  
Vol 55 (2) ◽  
pp. 661-665 ◽  
Author(s):  
Jian Liu ◽  
Toru Nakayama ◽  
Hisashi Hemmi ◽  
Yu Asano ◽  
Naoki Tsuruoka ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
Positive Bacterium ◽  
Ph Optimum ◽  
Bacterium Strain ◽  
Low Levels ◽  
Type Strains ◽  
The 16S Rrna Gene

A rod-shaped, Gram-positive bacterium, strain TNJL143-2T, having N-acyl-d-amino acid amidohydrolase (d-aminoacylase) activity, was isolated from a soil sample from Natori, Japan. It was a non-spore-forming, strictly aerobic bacterium without motility, showing a temperature optimum for growth of 30 °C and a pH optimum for growth of 5–7. The 16S rRNA gene sequence of the strain showed the highest similarities to members of the genus Microbacterium, in particular, Microbacterium aerolatum, Microbacterium foliorum and Microbacterium phyllosphaerae. The chemotaxonomic characteristics, including the compositions of cellular menaquinones, cellular fatty acids and cell-wall amino acids, were consistent with those described for the genus Microbacterium. The G+C content of the genomic DNA was determined as 69·1 mol%. DNA–DNA hybridization studies using type strains of M. aerolatum, M. foliorum and M. phyllosphaerae showed only low levels of relatedness (11–12 %). On the basis of these phenotypic and genotypic results, a novel species, Microbacterium natoriense sp. nov., is proposed, with TNJL143-2T (=JCM 12611T=ATCC BAA-1032T) as the type strain.

scholarly journals Biogenic Mineral Production by a Novel Arsenic-Metabolizing Thermophilic Bacterium from the Alvord Basin, Oregon

2007 ◽  
Vol 73 (18) ◽  
pp. 5928-5936 ◽  
Author(s):  
Rhesa N. Ledbetter ◽  
Stephanie A. Connon ◽  
Andrew L. Neal ◽  
Alice Dohnalkova ◽  
Timothy S. Magnuson
Keyword(s):  
Reductase Activity ◽  
Morphological Characteristics ◽  
Sulfide Mineral ◽  
Thermophilic Bacterium ◽  
Arsenate Reductase ◽  
Rrna Gene ◽  
Organic Substrates ◽  
Arsenic Sulfide ◽  
16S Rrna Gene Analysis ◽  
Alvord Basin

ABSTRACT The Alvord Basin in southeast Oregon contains a variety of hydrothermal features which have never been microbiologically characterized. A sampling of Murky Pot (61°C; pH 7.1) led to the isolation of a novel arsenic-metabolizing organism (YeAs) which produces an arsenic sulfide mineral known as β-realgar, a mineral that has not previously been observed as a product of bacterial arsenic metabolism. YeAs was grown on a freshwater medium and utilized a variety of organic substrates, particularly carbohydrates and organic acids. The temperature range for growth was 37 to 75°C (optimum, 55°C), and the pH range for growth was 6.0 to 8.0 (optimum, pH 7.0 to 7.5). No growth was observed when YeAs was grown under aerobic conditions. The doubling time when the organism was grown with yeast extract and As(V) was 0.71 h. Microscopic examination revealed Gram stain-indeterminate, non-spore-forming, nonmotile, rod-shaped cells, with dimensions ranging from 0.1 to 0.2 μm wide by 3 to 10 μm long. Arsenic sulfide mineralization of cell walls and extracellular arsenic sulfide particulate deposition were observed with electron microscopy and elemental analysis. 16S rRNA gene analysis placed YeAs in the family Clostridiaceae and indicated that the organism is most closely related to the Caloramator and Thermobrachium species. The G+C content was 35%. YeAs showed no detectable respiratory arsenate reductase but did display significant detoxification arsenate reductase activity. The phylogenetic, physiological, and morphological characteristics of YeAs demonstrate that it is an anaerobic, moderately thermophilic, arsenic-reducing bacterium. This organism and its associated metabolism could have major implications in the search for innovative methods for arsenic waste management and in the search for novel biogenic mineral signatures.

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 Thermoanaerobacter sulfurigignens sp. nov., an anaerobic thermophilic bacterium that reduces 1 M thiosulfate to elemental sulfur and tolerates 90 mM sulfite

2007 ◽  
Vol 57 (7) ◽  
pp. 1429-1434 ◽  
Author(s):  
Yong-Jin Lee ◽  
Mona Dashti ◽  
Alexander Prange ◽  
Fred A. Rainey ◽  
Manfred Rohde ◽  
...  
Keyword(s):  
Elemental Sulfur ◽  
Thermophilic Bacteria ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Thermophilic Bacterium ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Sulfur Globules ◽  
The 16S Rrna Gene ◽  
White Island

Two anaerobic thermophilic bacteria, designated strains JW/SL824 and JW/SL-NZ826T, were isolated from an acidic volcanic steam outlet on White Island, New Zealand. Cells were rod-shaped, spore-forming, motile and Gram-stain negative, but contained Gram-type positive cell wall. Strain JW/SL-NZ826T utilized various carbohydrates including xylose and glucose. The fermentation end products produced from glucose in the absence of thiosulfate were lactate, ethanol, acetate, CO2 and H2. The temperature range for growth was 34–72 °C, with an optimum at 63–67 °C. The pH60 °C range for growth was 4.0–8.0, with an optimum at 5.0–6.5. The doubling time of strain JW/SL-NZ826T under optimal growth conditions was 2.4 h. The DNA G+C content was 34–35 mol% (HPLC). The two strains reduced up to 1 M thiosulfate to elemental sulfur without sulfide formation, which is a trend typically observed among species belonging to the genus Thermoanaerobacterium. Sulfur globules containing short and long sulfur chains but no S8-ring sulfur were produced inside and outside the cells. Up to 90 mM sulfite was tolerated. This tolerance is assumed to be an adaptation to the geochemistry of the environment of White Island. The 16S rRNA gene sequence analysis, however, indicated that the two strains belonged to the genus Thermoanaerobacter, with similarities in the range 95.6–92.7 %. Therefore, strains JW/SL-NZ824 and JW/SL-NZ826T represent a novel taxon, for which the name Thermoanaerobacter sulfurigignens sp. nov. is proposed, with strain JW/SL-NZ826T (=ATCC 700320T=DSM 17917T) as the type strain. Based on this and previous studies, an emended description of the genus Thermoanaerobacter is given.

scholarly journals Anoxybacillus voinovskiensis sp. nov., a moderately thermophilic bacterium from a hot spring in Kamchatka

2004 ◽  
Vol 54 (4) ◽  
pp. 1239-1242 ◽  
Author(s):  
Isao Yumoto ◽  
Kikue Hirota ◽  
Tomoo Kawahara ◽  
Yoshinobu Nodasaka ◽  
Hidetoshi Okuyama ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Hot Spring ◽  
16S Rrna Gene Sequencing ◽  
Thermophilic Bacterium ◽  
Rrna Gene ◽  
Moderately Thermophilic ◽  
Hybridization Data ◽  
Facultative Aerobe ◽  
Anoxybacillus Flavithermus ◽  
Rrna Gene Sequencing

A novel moderately thermophilic bacterium, strain TH13T, was isolated from a hot spring in Kamchatka. It was found to be a Gram-positive, facultative aerobe; the straight, non-motile rods grew at 30–64 °C (optimum 54 °C). The isolate was positive for catalase and oxidase tests and reduced nitrate to nitrite, but was negative for H2S production and growth in more than 3 % NaCl (w/v). The isolate grew at pH 7–8, but not at pH values higher than 9. The DNA G+C content was 43·9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain TH13T was a member of the genus Anoxybacillus. DNA–DNA hybridization revealed a low relatedness (less than 30·2 %) between the isolate and its close phylogenetic neighbours Anoxybacillus pushchinoensis and Anoxybacillus flavithermus. On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA hybridization data, it was concluded that the isolate merited classification as a novel species, for which the name Anoxybacillus voinovskiensis sp. nov. is proposed. The type strain of this species is TH13T (=NCIMB 13956T=JCM 12111T).

scholarly journals A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

2020 ◽  
Vol 8 (6) ◽  
pp. 936 ◽  
Author(s):  
Claudia Leoni ◽  
Mariateresa Volpicella ◽  
Bruno Fosso ◽  
Caterina Manzari ◽  
Elisabetta Piancone ◽  
...  
Keyword(s):  
Ecological Model ◽  
Salinity Range ◽  
Rrna Gene ◽  
Hypervariable Regions ◽  
Cell Counts ◽  
Precious Resource ◽  
Catalyzed Reporter Deposition ◽  
Card Fish ◽  
The 16S Rrna Gene

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters.

scholarly journals A Novel Microbial Zearalenone Transformation through Phosphorylation

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 294
Author(s):  
Yan Zhu ◽  
Pascal Drouin ◽  
Dion Lepp ◽  
Xiu-Zhen Li ◽  
Honghui Zhu ◽  
...  
Keyword(s):  
Microbial Transformation ◽  
Acid Tolerance ◽  
Transformation Product ◽  
The United States ◽  
Corn Silage ◽  
Rrna Gene ◽  
Bacillus Spp ◽  
High Concentrations ◽  
The 16S Rrna Gene ◽  
Bacillus Strains

Zearalenone (ZEA) is a mycotoxin widely occurring in many agricultural commodities. In this study, a purified bacterial isolate, Bacillus sp. S62-W, obtained from one of 104 corn silage samples from various silos located in the United States, exhibited activity to transform the mycotoxin ZEA. A novel microbial transformation product, ZEA-14-phosphate, was detected, purified, and identified by HPLC, LC-MS, and NMR analyses. The isolate has been identified as belonging to the genus Bacillus according to phylogenetic analysis of the 16S rRNA gene and whole genome alignments. The isolate showed high efficacy in transforming ZEA to ZEA-14-phosphate (100% transformation within 24 h) and possessed advantages of acid tolerance (work at pH = 4.0), working under a broad range of temperatures (22–42 °C), and a capability of transforming ZEA at high concentrations (up to 200 µg/mL). In addition, 23 Bacillus strains of various species were tested for their ZEA phosphorylation activity. Thirteen of the Bacillus strains showed phosphorylation functionality at an efficacy of between 20.3% and 99.4% after 24 h incubation, suggesting the metabolism pathway is widely conserved in Bacillus spp. This study established a new transformation system for potential application of controlling ZEA although the metabolism and toxicity of ZEA-14-phosphate requires further investigation.

scholarly journals A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

scholarly journals Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Sesilje Weiss ◽  
David Taggart ◽  
Ian Smith ◽  
Kristofer M. Helgen ◽  
Raphael Eisenhofer
Keyword(s):  
Microbial Community ◽  
Reproductive Cycle ◽  
Tammar Wallaby ◽  
The Body ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Birth Canal ◽  
Gram Positive Bacteria ◽  
Rigorous Framework ◽  
The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

scholarly journals New Chitosan-Degrading Strains That Produce Chitosanases Similar to ChoA of Mitsuaria chitosanitabida

2005 ◽  
Vol 71 (9) ◽  
pp. 5138-5144 ◽  
Author(s):  
ChoongSoo Yun ◽  
Daiki Amakata ◽  
Yasuhiro Matsuo ◽  
Hideyuki Matsuda ◽  
Makoto Kawamukai
Keyword(s):  
Southern Hybridization ◽  
Glycosyl Hydrolase ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Glycosyl Hydrolase Family ◽  
Broad Variety ◽  
Hydrolase Family ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

ABSTRACT The betaproteobacterium Mitsuaria chitosanitabida (formerly Matsuebacter chitosanotabidus) 3001 produces a chitosanase (ChoA) that is classified in glycosyl hydrolase family 80. While many chitosanase genes have been isolated from various bacteria to date, they show limited homology to the M. chitosanitabida 3001 chitosanase gene (choA). To investigate the phylogenetic distribution of chitosanases analogous to ChoA in nature, we identified 67 chitosan-degrading strains by screening and investigated their physiological and biological characteristics. We then searched for similarities to ChoA by Western blotting and Southern hybridization and selected 11 strains whose chitosanases showed the most similarity to ChoA. PCR amplification and sequencing of the chitosanase genes from these strains revealed high deduced amino acid sequence similarities to ChoA ranging from 77% to 99%. Analysis of the 16S rRNA gene sequences of the 11 selected strains indicated that they are widely distributed in the β and γ subclasses of Proteobacteria and the Flavobacterium group. These observations suggest that the ChoA-like chitosanases that belong to family 80 occur widely in a broad variety of bacteria.

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