Using Biogeocementation to Reduce Physical Instability and Wind Erosion of Mine Tailings
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A Moderately Boron-Tolerant Candidatus Novel Soil Bacterium Lysinibacillus Pakistanensis Sp
Pak. J. Bot., 45(SI): 41-50, January 2013. A MODERATELY BORON-TOLERANT CANDIDATUS NOVEL SOIL BACTERIUM LYSINIBACILLUS PAKISTANENSIS SP. NOV. CAND., ISOLATED FROM SOYBEAN (GLYCINE MAX L.) RHIZOSPHERE RIFAT HAYAT1,2,3*, IFTIKHAR AHMED2*, JAYOUNG PAEK4, MUHAMMAD EHSAN1, 2, MUHAMMAD IQBAL2 AND YOUNG H. CHANG4* 1Department of Soil Science & SWC, PMAS Arid Agriculture University, Rawalpindi, 46300, Pakistan 2Plant Biotechnology Program, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Park Road, Islamabad-45500, Pakistan 3Institute of Molecular and Cellular Biosciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan 4Korean Collection of Type Cultures, Biological Resource Center, KRIBB, 52 Oeundong, Daejeon 305-806, Republic of Korea *Correspondence E-mail: [email protected]; [email protected]; [email protected] Abstract A Gram-positive, motile, rod-shaped, endospore-forming and moderately boron (B) tolerant novel candidatus strain, designated as NCCP-54T, was isolated from rhizospheric soil of soybean (Glycine max L.) sampled from the experimental area of Research Farm, PMAS Arid Agriculture University, Rawalpindi, Pakistan. To delineate its taxonomic position, the strain was subject to polyphasic characterization. Cells of the strain NCCP-54T can grow at 10-45○C (optimum at 28○C) at pH ranges of 6.5-9.0 (optimum at pH 7.0) and in 0-6% NaCl (w/v) in tryptic soya agar medium. It can also tolerate 150 mM boric acid in agar medium; however, optimum growth occurs in the absence of boric acid. Based on 16S rRNA gene sequence analysis, strain NCCP-54T showed highest similarity to Lysinibacillus xylanilyticus KCTC13423T (99.1%), Lysinibacillus fusiformis KCTC3454T (98.5%), Lysinibacillus boronitolerans KCTC13709T (98.4%), Lysinibacillus parviboronicapiens KCTC13154T (97.8%), and Lysinibacillus sphaericus KCTC3346T (97.5%) and less than 97% with other closely related taxa. -
Catalogue of Bacteria Shapes
We first tried to use the most general shape associated with each genus, which are often consistent across species (spp.) (first choice for shape). If there was documented species variability, either the most common species (second choice for shape) or well known species (third choice for shape) is shown. Corynebacterium: pleomorphic bacilli. Due to their snapping type of division, cells often lie in clusters resembling chinese letters (https://microbewiki.kenyon.edu/index.php/Corynebacterium) Shown is Corynebacterium diphtheriae Figure 1. Stained Corynebacterium cells. The "barred" appearance is due to the presence of polyphosphate inclusions called metachromatic granules. Note also the characteristic "Chinese-letter" arrangement of cells. (http:// textbookofbacteriology.net/diphtheria.html) Lactobacillus: Lactobacilli are rod-shaped, Gram-positive, fermentative, organotrophs. They are usually straight, although they can form spiral or coccobacillary forms under certain conditions. (https://microbewiki.kenyon.edu/index.php/ Lactobacillus) Porphyromonas: A genus of small anaerobic gram-negative nonmotile cocci and usually short rods thatproduce smooth, gray to black pigmented colonies the size of which varies with the species. (http:// medical-dictionary.thefreedictionary.com/Porphyromonas) Shown: Porphyromonas gingivalis Moraxella: Moraxella is a genus of Gram-negative bacteria in the Moraxellaceae family. It is named after the Swiss ophthalmologist Victor Morax. The organisms are short rods, coccobacilli or, as in the case of Moraxella catarrhalis, diplococci in morphology (https://en.wikipedia.org/wiki/Moraxella). *This one could be changed to a diplococcus shape because of moraxella catarrhalis, but i think the short rods are fair given the number of other moraxella with them. Jeotgalicoccus: Jeotgalicoccus is a genus of Gram-positive, facultatively anaerobic, and halotolerant to halophilicbacteria. -
Bacillus Safensis FO-36B and Bacillus Pumilus SAFR-032: a Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates
bioRxiv preprint doi: https://doi.org/10.1101/283937; this version posted April 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: A Whole Genome 2 Comparison of Two Spacecraft Assembly Facility Isolates 3 Madhan R Tirumalai1, Victor G. Stepanov1, Andrea Wünsche1, Saied Montazari1, 4 Racquel O. Gonzalez1, Kasturi Venkateswaran2, George. E. Fox1§ 5 1Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001. 6 2 Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California 7 Institute of Technology, Pasadena, CA, 91109. 8 9 §Corresponding author: 10 Dr. George E. Fox 11 Dept. Biology & Biochemistry 12 University of Houston, Houston, TX 77204-5001 13 713-743-8363; 713-743-8351 (FAX); email: [email protected] 14 15 Email addresses: 16 MRT: [email protected] 17 VGS: [email protected] 18 AW: [email protected] 19 SM: [email protected] 20 ROG: [email protected] 21 KV: [email protected] 22 GEF: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/283937; this version posted April 24, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Keywords: Planetary protection, Bacillus endospores, extreme radiation resistance, peroxide 24 resistance, genome comparison, phage insertions 25 26 Background 27 Microbial persistence in built environments such as spacecraft cleanroom facilities [1-3] is often 28 characterized by their unusual resistances to different physical and chemical factors [1, 4-7]. -
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative
CALIFORNIA STATE UNIVERSITY, NORTHRIDGE Comparative Genomics and Epigenomics of Sporosarcina ureae A thesis submitted in partial fulfillment of the requirement for the degree of Master of Science in Biology By Andrew Oliver August 2016 The thesis of Andrew Oliver is approved by: _________________________________________ ____________ Sean Murray, Ph.D. Date _________________________________________ ____________ Gilberto Flores, Ph.D. Date _________________________________________ ____________ Kerry Cooper, Ph.D., Chair Date California State University, Northridge ii Acknowledgments First and foremost, a special thanks to my advisor, Dr. Kerry Cooper, for his advice and, above all, his patience. If I can be half the scientist you are someday, I would be thrilled. I would like to also thank everyone in the Cooper lab, especially my colleagues Courtney Sams and Tabitha Bayangnos. It was a privilege to work along side you. More thanks to my committee members, Dr. Gilberto Flores and Dr. Sean Murray. Dr. Flores, you were instrumental in guiding me to ask the right questions regarding bacterial taxonomy. Dr. Murray, your contributions to my graduate studies would make this section run on for pages. I thank you for taking me under your wing from the beginning. Acknowledgement and thanks to the Baresi lab, especially Dr. Larry Baresi and Tania Kurbessoian for their partnership in this research. Also to Bernardine Pregerson for all the work that lays at the foundation of this study. This research would not be what it is without the help of my childhood friend, Matthew Kay. You wrote programs, taught me coding languages, and challenged me to go digging for answers to very difficult questions. -
Access to Electronic Thesis
Access to Electronic Thesis Author: Khalid Salim Al-Abri Thesis title: USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS Qualification: PhD This electronic thesis is protected by the Copyright, Designs and Patents Act 1988. No reproduction is permitted without consent of the author. It is also protected by the Creative Commons Licence allowing Attributions-Non-commercial-No derivatives. If this electronic thesis has been edited by the author it will be indicated as such on the title page and in the text. USE OF MOLECULAR APPROACHES TO STUDY THE OCCURRENCE OF EXTREMOPHILES AND EXTREMODURES IN NON-EXTREME ENVIRONMENTS By Khalid Salim Al-Abri Msc., University of Sultan Qaboos, Muscat, Oman Mphil, University of Sheffield, England Thesis submitted in partial fulfillment for the requirements of the Degree of Doctor of Philosophy in the Department of Molecular Biology and Biotechnology, University of Sheffield, England 2011 Introductory Pages I DEDICATION To the memory of my father, loving mother, wife “Muneera” and son “Anas”, brothers and sisters. Introductory Pages II ACKNOWLEDGEMENTS Above all, I thank Allah for helping me in completing this project. I wish to express my thanks to my supervisor Professor Milton Wainwright, for his guidance, supervision, support, understanding and help in this project. In addition, he also stood beside me in all difficulties that faced me during study. My thanks are due to Dr. D. J. Gilmour for his co-supervision, technical assistance, his time and understanding that made some of my laboratory work easier. In the Ministry of Regional Municipalities and Water Resources, I am particularly grateful to Engineer Said Al Alawi, Director General of Health Control, for allowing me to carry out my PhD study at the University of Sheffield. -
Biocementation Mediated by Stimulated Ureolytic Microbes from Brahmaputra Riverbank for Mitigation of Soil Erosion
Biocementation Mediated By Stimulated Ureolytic Microbes From Brahmaputra Riverbank For Mitigation of Soil Erosion Anant Aishwarya Dubey Indian Institute of Technology Guwahati K Ravi Indian Institute of Technology Guwahati Abhijit Mukherjee Curtin University Lingaraj Sahoo Indian Institute of Technology Guwahati Abiala Moses Akindele Mountain top University Navdeep Kaur Dhami ( [email protected] ) Curtin University Research Article Keywords: Riverbank erosion, Microbially induced carbonate precipitation (MICP), Sporosarcina pasteurii, Pseudogracilibacillus auburnensis Posted Date: February 26th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-235959/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published at Scientic Reports on July 27th, 2021. See the published version at https://doi.org/10.1038/s41598-021-94614-6. Page 1/24 Abstract Riverbank erosion is a global problem with signicant socio-economic impacts. Microbially induced carbonate precipitation (MICP) has recently emerged as a promising technology for improving the mechanical properties of soils. The presented study investigates the potential of native calcifying bacterial communities of the Brahmaputra riverbank for the rst time via biostimulation and explores its effect on the mitigation of soil erosion. The ureolytic and calcium carbonate cementation ability of the enriched cultures were investigated with reference to the standard calcifying culture of Sporosarcina pasteurii (ATCC 11859). 16S rRNA analysis revealed Firmicutes to be the most predominant calcifying class with Sporosarcina pasteurii and Pseudogracilibacillus auburnensis as the prevalent strains. The morphological and mineralogical characterization of carbonate crystals conrmed the calcite precipitation potential of these communities. -
Beneficial Factors for Biomineralization by Ureolytic Bacterium Sporosarcina Pasteurii
Ma et al. Microb Cell Fact (2020) 19:12 https://doi.org/10.1186/s12934-020-1281-z Microbial Cell Factories RESEARCH Open Access Benefcial factors for biomineralization by ureolytic bacterium Sporosarcina pasteurii Liang Ma, Ai‑Ping Pang, Yongsheng Luo, Xiaolin Lu* and Fengming Lin* Abstract Background: The ureolytic bacterium Sporosarcina pasteurii is well‑known for its capability of microbially induced calcite precipitation (MICP), representing a great potential in constructional engineering and material applications. However, the molecular mechanism for its biomineralization remains unresolved, as few studies were carried out. Results: The addition of urea into the culture medium provided an alkaline environment that is suitable for S. pasteurii. As compared to S. pasteurii cultivated without urea, S. pasteurii grown with urea showed faster growth and urease production, better shape, more negative surface charge and higher biomineralization ability. To survive the unfavorable growth environment due to the absence of urea, S. pasteurii up‑regulated the expression of genes involved in urease production, ATPase synthesis and fagella, possibly occupying resources that can be deployed for MICP. As compared to non‑mineralizing bacteria, S. pasteurii exhibited more negative cell surface charge for binding calcium ions and more robust cell structure as nucleation sites. During MICP process, the genes for ATPase synthesis in S. pasteurii was up‑regulated while genes for urease production were unchanged. Interestingly, genes involved in fagella were down‑regulated during MICP, which might lead to poor mobility of S. pasteurii. Meanwhile, genes in fatty acid degradation pathway were inhibited to maintain the intact cell structure found in calcite precipitation. Both weak mobility and intact cell structure are advantageous for S. -
Product Sheet Info
Product Information Sheet for HM-331 Sporosarcina sp., Strain 2681 Incubation: Temperature: 37°C Atmosphere: Aerobic Catalog No. HM-331 Propagation: 1. Keep vial frozen until ready for use, then thaw. For research use only. Not for human use. 2. Transfer the entire thawed aliquot into a single tube of broth. Contributor: 3. Use several drops of the suspension to inoculate an Kimberlee A. Musser, Ph.D., Chief, Bacterial Diseases, agar slant and/or plate. Division of Infectious Diseases, Wadsworth Center, New York 4. Incubate the tubes and plate at 37°C for 48 hours. State Department of Health, Albany, New York Citation: Manufacturer: NIH Biodefense and Emerging Infections Acknowledgment for publications should read “The following reagent was obtained through the NIH Biodefense and Research Resource Repository Emerging Infections Research Resources Repository, NIAID, NIH as part of the Human Microbiome Project: Sporosarcina Product Description: sp., Strain 2681, HM-331.” Bacteria Classification: Planococcaceae, Sporosarcina Species: Sporosarcina sp. Biosafety Level: 2 Strain: 2681 Original Source: Sporosarcina sp., strain 2681 was isolated Appropriate safety procedures should always be used with 1 this material. Laboratory safety is discussed in the following from human blood. Comments: Sporosarcina sp., strain 2681 is a reference publication: U.S. Department of Health and Human Services, Public Health Service, Centers for Disease Control and genome for The Human Microbiome Project (HMP). HMP Prevention, and National Institutes of Health. Biosafety in is an initiative to identify and characterize human microbial flora. The complete genome of Sporosarcina sp., strain Microbiological and Biomedical Laboratories. 5th ed. Washington, DC: U.S. Government Printing Office, 2007; see 2681 is currently being sequenced at the Human Genome www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm. -
A Low-Tech Bioreactor System for the Enrichment and Production of Ureolytic Microbes
Polish Journal of Microbiology 2018, Vol. 67, No 1, 59–65 ORIGINAL PAPER A Low-Tech Bioreactor System for the Enrichment and Production of Ureolytic Microbes MASATAKA AOKI1*, TAKUYA NOMA1, HIROSHI YONEMITSU2, NOBUO ARAKI3, TAKASHI YAMAGUCHI4 and KAZUYUKI HAYASHI1 1 Department of Civil Engineering, National Institute of Technology, Wakayama College, Gobo, Wakayama, Japan 2 Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College, Gobo, Wakayama, Japan 3 Department of Civil Engineering, National Institute of Technology, Nagaoka College, Nagaoka, Niigata, Japan 4 Department of Science of Technology Innovation, Nagaoka University of Technology, Nagaoka, Niigata, Japan Submitted 16 May 2017, revised 15 September 2017, accepted 27 September 2017 Abstract Ureolysis-driven microbially induced carbonate precipitation (MICP) has recently received attention for its poten- tial biotechnological applications. However, information on the enrichment and production of ureolytic microbes by using bioreactor systems is limited. Here, we report a low-tech down-flow hanging sponge (DHS) bioreac- tor system for the enrichment and production of ureolytic microbes. Using this bioreactor system and a yeast extract-based medium containing 0.17 M urea, ureolytic microbes with high potential urease activity (> 10 µmol urea hydrolyzed per min per ml of enrichment culture) were repeatedly enriched under non-sterile conditions. In addition, the ureolytic enrichment obtained in this study showed in vitro calcium carbonate precipitation. Fluorescence in situ hybridization analysis showed the existence of bacteria of the phylum Firmicutes in the bio- reactor system. Our data demonstrate that this DHS bioreactor system is a useful system for the enrichment and production of ureolytic microbes for MICP applications. -
Influence of Elevation in Structuring the Gut Bacterial Communities of Apis Cerana
Journal of Entomology and Zoology Studies 2017; 5(3): 434-440 E-ISSN: 2320-7078 P-ISSN: 2349-6800 Influence of elevation in structuring the gut JEZS 2017; 5(3): 434-440 © 2017 JEZS bacterial communities of Apis cerana Fab Received: 04-03-2017 Accepted: 04-04-2017 S Sudhagar S Sudhagar, PV Rami Reddy and G Nagalakshmi (A). Ph.D. Scholar, Department of Biotechnology, Jain Abstract University, Bengaluru, India (B). Division of Entomology and Apis cerana F., a native honey bee of India, is an important crop pollinator and also managed for honey Nematology, ICAR-Indian production and other bee products. In present study, 13 population samples were collected from different Institute of Horticultural agro climatic regions of South India, with varied elevation ranging from 1 to 2268 m Mean Sea Level Research, Bengaluru - 560089, (MSL). The research work was carried out at the Division of India Entomology and Nematology, ICAR-Indian Institute of Horticultural Research (IIHR), Bengaluru during 2014-16 to understand the influence of habitat elevation on the gut colonizing bacterial communities of PV Rami Reddy A. cerana. By culturing and 16S rDNA sequencing the major bacterial isolates of the gut were identified. Division of Entomology and Forty six isolates of culturable bacteria belonging to phyla Proteobacteria and Firmicutes were identified. Nematology, ICAR-Indian Bacillus sp. (Firmicutes) was predominant among higher elevation populations, while Proteobacteria Institute of Horticultural (Serratia sp., Klebsiella sp. and Enterobacter sp.) was dominant bacterial phylotype in plain and coastal Research, Bengaluru - 560089, populations. From the results it was evident that variability existed in gut microbial communities among India populations inhabiting different elevations. -
Research Journal of Pharmaceutical, Biological and Chemical Sciences
ISSN: 0975-8585 Research Journal of Pharmaceutical, Biological and Chemical Sciences Florula of Larval and Imaginal Phases of the Volfartova Fly (Wohlfarthia magnifica) In the Conditions of the Steppe Zone of The Pavlodar Region. A A Bitkeyeva1* and L T Bulekbayeva2. 1Senior teacher, Master of Ecology, Pavlodar State University named after S. Toraygyrov, The Republic of Kazakhstan. 2Associate professor, Candidate of Biological Sciences, Pavlodar State Pedagogical Institute, Republic of Kazakhstan. ABSTRACT Groups of bacteria were found during research in a steppe zone of the Pavlodar region, belonging to 3 families: Baccilaceae, Micrococcaceae, Enterobacteriacea. 13 species of pathogenic and opportunistic bacteria are obtained and identified, which cause diseases. Reception of agents from flies of Wohlfartia magnifica family in region farms forces to pay attention to quite real possibility and contagion of various infections. It creates the menacing epidemiological and epizootiology situation on the adjacent to farms of populated places, as flies with excrements can infect forages and migrate on considerable distances. Keywords: bacteria, diseases, infections, larvaes, microorganisms, flies, sheep, pathogenic microorganisms, carriers. *Corresponding author July– August 2015 RJPBCS 6(4) Page No. 2069 ISSN: 0975-8585 INTRODUCTION Flies are known as carriers of causative agents of dangerous infectious and invasive diseases. Therefore, in the populated places and on the pastures, studying of microbal and helminthosis impurity of flies represents scientific and practical interest. Epidemiological value of flies was opened by E.N. Pavlovskiy and V.P. Derbeneva-Ukhova, they participate in distribution about 70 pathogenic microflora, and including agents of a tularemia, anthrax, diphtheria, cholera, plague, a crab hand, etc. [2; 8; 12]. -
Screening of Antagonistic Bacterial Isolates from Hives of Apis Cerana in Vietnam Against the Causal Agent of American Foulbrood
1202 Chiang Mai J. Sci. 2018; 45(3) Chiang Mai J. Sci. 2018; 45(3) : 1202-1213 http://epg.science.cmu.ac.th/ejournal/ Contributed Paper Screening of Antagonistic Bacterial Isolates from Hives of Apis cerana in Vietnam Against the Causal Agent of American Foulbrood of Honey Bees, Paenibacillus larvae Sasiprapa Krongdang [a,b], Jeffery S. Pettis [c], Geoffrey R. Williams [d] and Panuwan Chantawannakul* [a,e,f] [a] Bee Protection Laboratory, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand. [b] Interdisciplinary Program in Biotechnology, Graduate School, Chiang Mai University, Chiang Mai 50200, Thailand. [c] USDA-ARS, Bee Research Laboratory, Beltsville, MD, 20705, USA. [d] Department of Entomology & Plant Pathology, Auburn University, Auburn, AL, 36849, USA. [e] Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, 50200, Thailand. [f] International College of Digital Innovation, Chiang Mai University, 50200, Thailand. * Author for correspondence; e-mail: [email protected] Received: 15 February 2017 Accepted: 20 June 2017 ABSTRACT American foulbrood (AFB) is a virulent disease of honey bee brood caused by the Gram-positive, spore-forming bacterium; Paenibacillus larvae. In this study, we determined the potential of bacteria isolated from hives of Asian honey bees (Apis cerana) to act antagonistically against P. larvae. Isolates were sampled from different locations on the fronts of A. cerana hives in Vietnam. A total of 69 isolates were obtained through a culture-dependent method and 16S rRNA gene sequencing showed affiliation to the phyla Firmicutes and Actinobacteria. Out of 69 isolates, 15 showed strong inhibitory activity against P.