Full-Text (PDF)
Total Page:16
File Type:pdf, Size:1020Kb

Load more
Recommended publications
-
Archaea, Bacteria and Termite, Nitrogen Fixation and Sustainable Plants Production
Sun W et al . (2021) Notulae Botanicae Horti Agrobotanici Cluj-Napoca Volume 49, Issue 2, Article number 12172 Notulae Botanicae Horti AcademicPres DOI:10.15835/nbha49212172 Agrobotanici Cluj-Napoca Re view Article Archaea, bacteria and termite, nitrogen fixation and sustainable plants production Wenli SUN 1a , Mohamad H. SHAHRAJABIAN 1a , Qi CHENG 1,2 * 1Chinese Academy of Agricultural Sciences, Biotechnology Research Institute, Beijing 100081, China; [email protected] ; [email protected] 2Hebei Agricultural University, College of Life Sciences, Baoding, Hebei, 071000, China; Global Alliance of HeBAU-CLS&HeQiS for BioAl-Manufacturing, Baoding, Hebei 071000, China; [email protected] (*corresponding author) a,b These authors contributed equally to the work Abstract Certain bacteria and archaea are responsible for biological nitrogen fixation. Metabolic pathways usually are common between archaea and bacteria. Diazotrophs are categorized into two main groups namely: root- nodule bacteria and plant growth-promoting rhizobacteria. Diazotrophs include free living bacteria, such as Azospirillum , Cupriavidus , and some sulfate reducing bacteria, and symbiotic diazotrophs such Rhizobium and Frankia . Three types of nitrogenase are iron and molybdenum (Fe/Mo), iron and vanadium (Fe/V) or iron only (Fe). The Mo-nitrogenase have a higher specific activity which is expressed better when Molybdenum is available. The best hosts for Rhizobium legumiosarum are Pisum , Vicia , Lathyrus and Lens ; Trifolium for Rhizobium trifolii ; Phaseolus vulgaris , Prunus angustifolia for Rhizobium phaseoli ; Medicago, Melilotus and Trigonella for Rhizobium meliloti ; Lupinus and Ornithopus for Lupini, and Glycine max for Rhizobium japonicum . Termites have significant key role in soil ecology, transporting and mixing soil. Termite gut microbes supply the enzymes required to degrade plant polymers, synthesize amino acids, recycle nitrogenous waste and fix atmospheric nitrogen. -
Desulfuribacillus Alkaliarsenatis Gen. Nov. Sp. Nov., a Deep-Lineage
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Extremophiles (2012) 16:597–605 DOI 10.1007/s00792-012-0459-7 ORIGINAL PAPER Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes D. Y. Sorokin • T. P. Tourova • M. V. Sukhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 3 May 2012 / Published online: 24 May 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract An anaerobic enrichment culture inoculated possible within a pH range from 9 to 10.5 (optimum at pH with a sample of sediments from soda lakes of the Kulunda 10) and a salt concentration at pH 10 from 0.2 to 2 M total Steppe with elemental sulfur as electron acceptor and for- Na? (optimum at 0.6 M). According to the phylogenetic mate as electron donor at pH 10 and moderate salinity analysis, strain AHT28 represents a deep independent inoculated with sediments from soda lakes in Kulunda lineage within the order Bacillales with a maximum of Steppe (Altai, Russia) resulted in the domination of a 90 % 16S rRNA gene similarity to its closest cultured Gram-positive, spore-forming bacterium strain AHT28. representatives. On the basis of its distinct phenotype and The isolate is an obligate anaerobe capable of respiratory phylogeny, the novel haloalkaliphilic anaerobe is suggested growth using elemental sulfur, thiosulfate (incomplete as a new genus and species, Desulfuribacillus alkaliar- T T reduction) and arsenate as electron acceptor with H2, for- senatis (type strain AHT28 = DSM24608 = UNIQEM mate, pyruvate and lactate as electron donor. -
Antonie Van Leeuwenhoek Journal of Microbiology
Antonie van Leeuwenhoek Journal of Microbiology Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients --Manuscript Draft-- Manuscript Number: ANTO-D-15-00548R1 Full Title: Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients Article Type: Original Article Keywords: Kroppenstedtia species, Kroppenstedtia pulmonis, Kroppenstedtia sanguinis, polyphasic taxonomy, 16S rRNA gene, thermoactinomycetes Corresponding Author: Melissa E Bell, MS Centers for Disease Control and Prevention Atlanta, Georgia UNITED STATES Corresponding Author Secondary Information: Corresponding Author's Institution: Centers for Disease Control and Prevention Corresponding Author's Secondary Institution: First Author: Melissa E Bell, MS First Author Secondary Information: Order of Authors: Melissa E Bell, MS Brent A. Lasker, PhD Hans-Peter Klenk, PhD Lesley Hoyles, PhD Catherine Spröer Peter Schumann June Brown Order of Authors Secondary Information: Funding Information: Abstract: Three human clinical strains (W9323T, X0209T and X0394) isolated from lung biopsy, blood and cerebral spinal fluid, respectively, were characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequences showed the three strains belonged to two novel branches within the genus Kroppenstedtia: 16S rRNA gene sequence analysis of W9323T showed closest sequence similarity to Kroppenstedtia eburnea JFMB-ATE T (95.3 %), Kroppenstedtia guangzhouensis GD02T (94.7 %) and strain X0209T (94.6 %); sequence analysis of strain X0209T showed closest sequence similarity to K. eburnea JFMB-ATE T (96.4 %) and K. guangzhouensis GD02T (96.0 %). Strains X0209T and X0394 were 99.9 % similar to each other by 16S rRNA gene sequence analysis. The DNA-DNA relatedness was 94.6 %, confirming that X0209T and X0394 belong to the same species. -
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure Authors: Suzanne L. Ishaq, Stephen P. Johnson, Zach J. Miller, Erik A. Lehnhoff, Sarah Olivo, Carl J. Yeoman, and Fabian D. Menalled The final publication is available at Springer via http://dx.doi.org/10.1007/s00248-016-0861-2. Ishaq, Suzanne L. , Stephen P. Johnson, Zach J. Miller, Erik A. Lehnhoff, Sarah Olivo, Carl J. Yeoman, and Fabian D. Menalled. "Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure." Microbial Ecology 73, no. 2 (February 2017): 417-434. DOI: 10.1007/s00248-016-0861-2. Made available through Montana State University’s ScholarWorks scholarworks.montana.edu Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure 1,2 & 2 & 3 & 4 & Suzanne L. Ishaq Stephen P. Johnson Zach J. Miller Erik A. Lehnhoff 1 1 2 Sarah Olivo & Carl J. Yeoman & Fabian D. Menalled 1 Department of Animal and Range Sciences, Montana State University, P.O. Box 172900, Bozeman, MT 59717, USA 2 Department of Land Resources and Environmental Sciences, Montana State University, P.O. Box 173120, Bozeman, MT 59717, USA 3 Western Agriculture Research Center, Montana State University, Bozeman, MT, USA 4 Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, USA Abstract Farming practices affect the soil microbial commu- then individual farm. Living inoculum-treated soil had greater nity, which in turn impacts crop growth and crop-weed inter- species richness and was more diverse than sterile inoculum- actions. -
Melghirimyces Thermohalophilus Sp. Nov., a Thermoactinomycete Isolated from an Algerian Salt Lake
International Journal of Systematic and Evolutionary Microbiology (2013), 63, 1717–1722 DOI 10.1099/ijs.0.043760-0 Melghirimyces thermohalophilus sp. nov., a thermoactinomycete isolated from an Algerian salt lake Ammara Nariman Addou,1,2 Peter Schumann,3 Cathrin Spro¨er,3 Amel Bouanane-Darenfed,2 Samia Amarouche-Yala,4 Hocine Hacene,2 Jean-Luc Cayol1 and Marie-Laure Fardeau1 Correspondence 1Aix-Marseille Universite´, Universite´ du Sud Toulon-Var, CNRS/INSU, IRD, MIO, UM 110, 13288 Marie-Laure Fardeau Marseille Cedex 09, France [email protected] 2Laboratoire de Biologie Cellulaire et Mole´culaire (e´quipe de Microbiologie), Universite´ des sciences et de la technologie, Houari Boume´die`nne, Bab Ezzouar, Algiers, Algeria 3Leibniz Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany 4Centre de Recherche Nucle´aire d’Alger (CRNA), Algeria A novel filamentous bacterium, designated Nari11AT, was isolated from soil collected from a salt lake named Chott Melghir, located in north-eastern Algeria. The strain is an aerobic, halophilic, thermotolerant, Gram-stain-positive bacterium, growing at NaCl concentrations between 5 and 20 % (w/v) and at 43–60 6C and pH 5.0–10.0. The major fatty acids were iso-C15 : 0, anteiso- C15 : 0 and iso-C17 : 0. The DNA G+C content was 53.4 mol%. LL-Diaminopimelic acid was the diamino acid of the peptidoglycan. The major menaquinone was MK-7, but MK-6 and MK-8 were also present in trace amounts. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and three unidentified phospholipids. -
The Genus Geobacillus
The Genus Geobacillus Introduction and Strain Catalog polymyxa macerans popilliae brevis Paenibacillus pantothenticus agri Virgibacillus laterosporus Brevibacillus cycloheptanicus Alicyclobacillus salexigens acidocaldarius Salibacillus marismortui halotolerans acidoterrestris Gracilibacillus thermoaerophilus Aneurinibacillus subtilis migulanus Bacillus cereus Geobacillus Ureibacillus kaustophilus badius stearothermophilus subterraneus halophilus thermosphaericus terreneus Bacillus Genetic Stock Center Catalog of Strains 7th Edition, Volume 3 Bacillus Genetic Stock Center Catalog of Strains, Seventh Edition Volume 3: The Genus Geobacillus © 2001 Permission is given to copy this material or portions of it freely, provided that no alterations are made and that this copyright page is included. Daniel R. Zeigler, Ph.D. The Bacillus Genetic Stock Center Department of Biochemistry The Ohio State University 484 West Twelfth Avenue Columbus, Ohio 43210 Disclaimer: The information in this catalog is believed to be correct. Due to the dynamic nature of the scientific process and to normal human limitations in dealing with such a large amount of data, however, some undetected errors may persist. Users bear the responsibility of verifying any important data before making a significant investment of time or other physical or financial resources. Cover: Phylogenetic tree of the genus Bacillus and closely related genera, including the new genus Geobacillus (Nazina, 2001). 16S rRNA gene sequences were obtained from GenBank for the species represented on the tree. After they were manually trimmed to the same length, they were aligned with ClustalW to create a Phylip distance matrix. The Neighbor program from the Phylip suite was used to generate a UPGMA tree, which was visualized with TreeView32. I used MacroMedia Freehand and Microsoft Image Composer to edit the tree image. -
Mechanisms of Action of the Duodenal-Jejunal Bypass Sleeve
Mechanisms of action of the duodenal-jejunal bypass sleeve Jessica Jade McMaster BSc, MDietSt A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2019 Faculty of Medicine ABSTRACT The prevalence of obesity and related comorbidities, such as type 2 diabetes mellitus (T2DM) have reached epidemic proportions globally. Weight loss improves morbidity and mortality in people with obesity and T2DM. However, effective long-term obesity treatments are limited. Lifestyle modification is the first line treatment, but long-term data suggest a return to baseline weight after successful weight loss. In contrast, bariatric surgery causes permanent anatomical changes in the gastrointestinal tract (GIT) to facilitate weight loss. This is the most effective long-term treatment for obesity and T2DM. However, compared to the large number of eligible individuals, very few patients undergo bariatric surgery. Minimally invasive treatment options have been developed to fill the treatment gap between conservative and surgical measures. One treatment option is the duodenal-jejunal bypass sleeve (DJBS; EndoBarrier®; GI Dynamics, Lexington, MA, USA). This is a 60 cm impermeable sleeve device, which is placed endoscopically into the duodenal bulb, extending to the jejunum and left in place for up to 48 weeks. The device separates bile and pancreatic secretions from chyme, reducing the contact of ingested food with the small intestinal mucosa. Significant weight loss and improvements in glycaemic control have been reported after DJBS treatment, but little is known about the mechanisms of action of the device. The device dwells in the GIT, but the impact of implantation on gastrointestinal function has undergone limited investigation. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants. -
CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations. -
Characterization and Identification of Some Aerobic Spore- Forming Bacteria Isolated from Saline Habitat, West Coastal Region, Saudi Arabia
IOSR Journal of Pharmacy and Biological Sciences (IOSR-JPBS) e-ISSN:2278-3008, p-ISSN:2319-7676. Volume 12, Issue 2 Ver. II (Mar. - Apr.2017), PP 14-19 www.iosrjournals.org Characterization and Identification of Some Aerobic Spore- Forming Bacteria Isolated From Saline Habitat, West Coastal Region, Saudi Arabia 1* 1 2 1,3 Naheda Alshammari , Fatma Fahmy , Sahira Lari and Magda Aly 1Biology Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 2Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 3Botany Department, Faculty of Science, Kafr el-Sheikh University, Egypt Abstract: Ten isolates of aerobic endospore- forming moderately halophilic bacteria were isolated fromsaline habitat at the west coastal region near Jeddah. All isolates that were Gram positive, catalase positive andshowing different colony morphology and shapes were studied. They were mesophilic, neutralophilic, with temperature range 20-40°C and pH range 7-9. The isolates were separating into two distinct groups facultative anaerobic strictly aerobic. One isolate was identified as Paenibacillus dendritiformis, two isolates as Bacillus oleronius, two isolates as P. alvei, three isolates belong to B. subtilis and B. atrophaeus, and finally two isolates was identified as Bacillus sp. Furthermore, two aerobic endospore-forming cocci, isolated from salt-march soil in Germany were tested for their taxonomical status and used as reference isolates and these isolates belong to the species Halobacillus halophilus. Chemotaxonomic characteristics represented by cell wall analysis and fatty acid profiles of some selected isolates were studied to determine the differences between species. Keywords: Halobacillus, Bacillus, spore, mesophilic, physiological, morphological I. Introduction Aerobic spore-forming bacteria represent a major microflora in many natural biotopes and play an important role in ecosystem development. -
Reorganising the Order Bacillales Through Phylogenomics
Systematic and Applied Microbiology 42 (2019) 178–189 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Reorganising the order Bacillales through phylogenomics a,∗ b c Pieter De Maayer , Habibu Aliyu , Don A. Cowan a School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, South Africa b Technical Biology, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Germany c Centre for Microbial Ecology and Genomics, University of Pretoria, South Africa a r t i c l e i n f o a b s t r a c t Article history: Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant Received 7 August 2018 on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, Received in revised form these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in 21 September 2018 the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. Accepted 18 October 2018 However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome- Keywords: based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A Bacillales Lactobacillales suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of Bacillaceae eight families (and six family incertae sedis taxa) within the order Bacillales. -
Literature Review
ABSTRACT DEVINE, ANTHONY ANDREW. Examining Complex Microbial Communities Using the Terminal Restriction Fragment Length Polymorphism Method and Dedicated TRFLP Analysis Software. (Under the direction of Amy Michele Grunden). The purpose of this research was to develop a robust methodology that could be used to determine the composition of complex microbial communities found in a variety of environments. In an effort to profile these communities, a 16S rDNA directed, sequencing independent method, Terminal Restriction Fragment Length Polymorphism (TRFLP) was used to generate fragment profiles from genomic DNA isolated from each sample. A custom designed software package, In Silico©, was then used to match these terminal restriction fragments in the sample to patterns of 16S rDNA fragments in a custom database of reference patterns. Identifying these patterns allowed for inferences to be made about the structure of the microbial populations in the environments sampled. TRFLP was chosen as the method of identification since it is a high throughput, cost effective method for community profiling. A combination of this method and the In Silico© software was used to examine microbial communities associated with open air swine waste lagoon systems, the large intestine of the Trichechus manatus latirostrus, Florida manatee, and the microbial populations found in rumen fed fermentors. The community analysis methodology we developed and employed was able to not only detect large and diverse microbial populations within each sample, but was also