Effect of Roof Material on Water Quality for Rainwater Harvesting Systems – Additional Physical, Chemical, and Microbiological Data
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(12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub
US 2005O289672A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2005/0289672 A1 Jefferson (43) Pub. Date: Dec. 29, 2005 (54) BIOLOGICAL GENE TRANSFER SYSTEM Publication Classification FOR EUKARYOTC CELLS (75) Inventor: Richard A. Jefferson, Canberra (AU) (51) Int. Cl. ............................. A01H 1700; C12N 15/82 (52) U.S. Cl. .............................................................. 800,294 Correspondence Address: CAROL NOTTENBURG 81432ND AVE 5 SEATTLE, WA 98144 (US) (57) ABSTRACT (73) Assignee: CAMBIA Appl. No.: 10/954,147 This invention relates generally to technologies for the (21) transfer of nucleic acids molecules to eukaryotic cells. In Filed: Sep. 28, 2004 particular non-pathogenic Species of bacteria that interact (22) with plant cells are used to transfer nucleic acid Sequences. Related U.S. Application Data The bacteria for transforming plants usually contain binary vectors, Such as a plasmid with a Vir region of a Tiplasmid (60) Provisional application No. 60/583,426, filed on Jun. and a plasmid with a T region containing a DNA sequence 28, 2004. of interest. pEHA105 244981 bp M3REW M13Fw f1 origin accA W pEHA105::pWBE58 (Km, Ap) moaa. Patent Application Publication Dec. 29, 2005 Sheet 1 of 24 US 2005/0289672 A1 FIGURE 1A CLASS ALPHAPROTEOBACTERIA ORDER Rhizobiales family Rhizobiaceae bgenus Rhizobium (includes former Agrobacterium) bgenus Chelatobacter bgenus Sinorhizobium Dunclassified Rhizobiaceae family Bartonellaceae bgenus Bartonella Dunclassified Bartonellaceae family Brucellaceae -
Stable-Isotope Probing Implicates Methylophaga Spp and Novel Gammaproteobacteria in Marine Methanol and Methylamine Metabolism
The ISME Journal (2007) 1, 480–491 & 2007 International Society for Microbial Ecology All rights reserved 1751-7362/07 $30.00 www.nature.com/ismej ORIGINAL ARTICLE Stable-isotope probing implicates Methylophaga spp and novel Gammaproteobacteria in marine methanol and methylamine metabolism Josh D Neufeld1, Hendrik Scha¨fer, Michael J Cox2, Rich Boden, Ian R McDonald3 and J Colin Murrell Department of Biological Sciences, University of Warwick, Coventry, UK The metabolism of one-carbon (C1) compounds in the marine environment affects global warming, seawater ecology and atmospheric chemistry. Despite their global significance, marine micro- organisms that consume C1 compounds in situ remain poorly characterized. Stable-isotope probing (SIP) is an ideal tool for linking the function and phylogeny of methylotrophic organisms by the metabolism and incorporation of stable-isotope-labelled substrates into nucleic acids. By combining DNA-SIP and time-series sampling, we characterized the organisms involved in the assimilation of methanol and methylamine in coastal sea water (Plymouth, UK). Labelled nucleic acids were analysed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA genes. In addition, we characterized the functional gene complement of labelled nucleic acids with an improved primer set targeting methanol dehydrogenase (mxaF) and newly designed primers for methylamine dehydrogenase (mauA). Predominant DGGE phylotypes, 16S rRNA, methanol and methylamine dehydrogenase gene sequences, and cultured isolates all implicated Methylophaga spp, moderately halophilic marine methylotrophs, in the consumption of both methanol and methylamine. Additionally, an mxaF sequence obtained from DNA extracted from sea water clustered with those detected in 13C-DNA, suggesting a predominance of Methylophaga spp among marine methylotrophs. -
The Methanol Dehydrogenase Gene, Mxaf, As a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments
The Methanol Dehydrogenase Gene, mxaF, as a Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Lau, Evan, Meredith C. Fisher, Paul A. Steudler, and Colleen Marie Cavanaugh. 2013. The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments. PLoS ONE 8(2): e56993. Published Version doi:10.1371/journal.pone.0056993 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11807572 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Open Access Policy Articles, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#OAP The Methanol Dehydrogenase Gene, mxaF,asa Functional and Phylogenetic Marker for Proteobacterial Methanotrophs in Natural Environments Evan Lau1,2*, Meredith C. Fisher2, Paul A. Steudler3, Colleen M. Cavanaugh2 1 Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, West Virginia, United States of America, 2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America, 3 The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America Abstract The mxaF gene, coding for the large (a) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. -
Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. -
Contents Topic 1. Introduction to Microbiology. the Subject and Tasks
Contents Topic 1. Introduction to microbiology. The subject and tasks of microbiology. A short historical essay………………………………………………………………5 Topic 2. Systematics and nomenclature of microorganisms……………………. 10 Topic 3. General characteristics of prokaryotic cells. Gram’s method ………...45 Topic 4. Principles of health protection and safety rules in the microbiological laboratory. Design, equipment, and working regimen of a microbiological laboratory………………………………………………………………………….162 Topic 5. Physiology of bacteria, fungi, viruses, mycoplasmas, rickettsia……...185 TOPIC 1. INTRODUCTION TO MICROBIOLOGY. THE SUBJECT AND TASKS OF MICROBIOLOGY. A SHORT HISTORICAL ESSAY. Contents 1. Subject, tasks and achievements of modern microbiology. 2. The role of microorganisms in human life. 3. Differentiation of microbiology in the industry. 4. Communication of microbiology with other sciences. 5. Periods in the development of microbiology. 6. The contribution of domestic scientists in the development of microbiology. 7. The value of microbiology in the system of training veterinarians. 8. Methods of studying microorganisms. Microbiology is a science, which study most shallow living creatures - microorganisms. Before inventing of microscope humanity was in dark about their existence. But during the centuries people could make use of processes vital activity of microbes for its needs. They could prepare a koumiss, alcohol, wine, vinegar, bread, and other products. During many centuries the nature of fermentations remained incomprehensible. Microbiology learns morphology, physiology, genetics and microorganisms systematization, their ecology and the other life forms. Specific Classes of Microorganisms Algae Protozoa Fungi (yeasts and molds) Bacteria Rickettsiae Viruses Prions The Microorganisms are extraordinarily widely spread in nature. They literally ubiquitous forward us from birth to our death. Daily, hourly we eat up thousands and thousands of microbes together with air, water, food. -
Universitá Di Bologna MICROBIAL ECOLOGY of BIOTECHNOLOGICAL PROCESSES
Alma Mater Studiorum – Universitá di Bologna Dottorato di Ricerca in Scienze Biochimiche e Biotecnologiche Ciclo XXVII Settore Concorsuale 03/D1 Settore Scientifico Disciplinare CHIM/11 MICROBIAL ECOLOGY OF BIOTECHNOLOGICAL PROCESSES Presentata da: Dott.ssa Serena Fraraccio Coordinatore Dottorato Relatore Chiar.mo Prof. Chiar.mo Prof. Fabio Fava Santi Mario Spampinato Correlatori Giulio Zanaroli, Ph.D. Assoc. Prof. Ondřej Uhlík, Ph.D. Esame finale anno 2015 Abstract The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater -
Occurrence Networks Among Spatially Close Bacterial Microbiota of Bark, Mosses and Lichens
Molecular Ecology (2017) doi: 10.1111/mec.14070 Differential sharing and distinct co-occurrence networks among spatially close bacterial microbiota of bark, mosses and lichens INES ALINE ASCHENBRENNER,* TOMISLAV CERNAVA,*† ARMIN ERLACHER,* GABRIELE BERG* and MARTIN GRUBE‡ *Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria, †ACIB GmbH, Petersgasse 14, 8010 Graz, Austria, ‡Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010 Graz, Austria Abstract Knowledge of bacterial community host-specificity has increased greatly in recent years. However, the intermicrobiome relationships of unrelated but spatially close organisms remain little understood. Trunks of trees covered by epiphytes represent complex habitats with a mosaic of ecological niches. In this context, we investigated the structure, diversity and interactions of microbiota associated with lichens, mosses and the bare tree bark. Comparative analysis revealed significant differences in the habitat-associated community structures. Corresponding co-occurrence analysis indi- cated that the lichen microbial network is less complex and less densely intercon- nected than the moss- and bark-associated networks. Several potential generalists and specialists were identified for the selected habitats. Generalists belonged mainly to Proteobacteria, with Sphingomonas as the most abundant genus. The generalists com- prise microorganisms with generally beneficial features, such as nitrogen fixation or other supporting functions, according to a metagenomic analysis. We argue that benefi- cial strains shared among hosts contribute to ecological stability of the host bio- coenoses. Keywords: amplicon sequencing, co-occurrence patterns, host microbe associations, metagenome, microbial ecology Received 21 March 2016; revision received 4 January 2017; accepted 6 February 2017 3.04 trillion trees (Crowther et al. -
Bibliography
Bibliography Aa, K. and R.A. Olsen. 1996. The use of various substrates and substrate caulis Poindexter by a polyphasic analysis. Int. J. Syst. Evol. Microbiol. concentrations by a Hyphomicrobium sp. isolated from soil: effect on 51: 27–34. growth rate and growth yield. Microb. Ecol. 31: 67–76. Abram, D., J. Castro e Melo and D. Chou. 1974. Penetration of Bdellovibrio Aalen, R.B. and W.B. Gundersen. 1985. Polypeptides encoded by cryptic bacteriovorus into host cells. J. Bacteriol. 118: 663–680. plasmids from Neisseria gonorrhoeae. Plasmid 14: 209–216. Abramochkina, F.N., L.V. Bezrukova, A.V. Koshelev, V.F. Gal’chenko and Aamand, J., T. Ahl and E. Spieck. 1996. Monoclonal antibodies recog- M.V. Ivanov. 1987. Microbial methane oxidation in a fresh-water res- nizing nitrite oxidoreductase of Nitrobacter hamburgensis, N. winograd- ervoir. Mikrobiologiya 56: 464–471. skyi, and N. vulgaris. Appl. Environ. Microbiol. 62: 2352–2355. Achenbach, L.A., U. Michaelidou, R.A. Bruce, J. Fryman and J.D. Coates. Aarestrup, F.M., E.M. Nielsen, M. Madsen and J. Engberg. 1997. Anti- 2001. Dechloromonas agitata gen. nov., sp. nov. and Dechlorosoma suillum microbial susceptibility patterns of thermophilic Campylobacter spp. gen. nov., sp. nov., two novel environmentally dominant from humans, pigs, cattle, and broilers in Denmark. Antimicrob. (per)chlorate-reducing bacteria and their phylogenetic position. Int. Agents Chemother. 41: 2244–2250. J. Syst. Evol. Microbiol. 51: 527–533. Abadie, M. 1967. Formations intracytoplasmique du type “me´some” chez Achouak, W., R. Christen, M. Barakat, M.H. Martel and T. Heulin. 1999. Chondromyces crocatus Berkeley et Curtis. -
Appendix 1. New and Emended Taxa Described Since Publication of Volume One, Second Edition of the Systematics
188 THE REVISED ROAD MAP TO THE MANUAL Appendix 1. New and emended taxa described since publication of Volume One, Second Edition of the Systematics Acrocarpospora corrugata (Williams and Sharples 1976) Tamura et Basonyms and synonyms1 al. 2000a, 1170VP Bacillus thermodenitrificans (ex Klaushofer and Hollaus 1970) Man- Actinocorallia aurantiaca (Lavrova and Preobrazhenskaya 1975) achini et al. 2000, 1336VP Zhang et al. 2001, 381VP Blastomonas ursincola (Yurkov et al. 1997) Hiraishi et al. 2000a, VP 1117VP Actinocorallia glomerata (Itoh et al. 1996) Zhang et al. 2001, 381 Actinocorallia libanotica (Meyer 1981) Zhang et al. 2001, 381VP Cellulophaga uliginosa (ZoBell and Upham 1944) Bowman 2000, VP 1867VP Actinocorallia longicatena (Itoh et al. 1996) Zhang et al. 2001, 381 Dehalospirillum Scholz-Muramatsu et al. 2002, 1915VP (Effective Actinomadura viridilutea (Agre and Guzeva 1975) Zhang et al. VP publication: Scholz-Muramatsu et al., 1995) 2001, 381 Dehalospirillum multivorans Scholz-Muramatsu et al. 2002, 1915VP Agreia pratensis (Behrendt et al. 2002) Schumann et al. 2003, VP (Effective publication: Scholz-Muramatsu et al., 1995) 2043 Desulfotomaculum auripigmentum Newman et al. 2000, 1415VP (Ef- Alcanivorax jadensis (Bruns and Berthe-Corti 1999) Ferna´ndez- VP fective publication: Newman et al., 1997) Martı´nez et al. 2003, 337 Enterococcus porcinusVP Teixeira et al. 2001 pro synon. Enterococcus Alistipes putredinis (Weinberg et al. 1937) Rautio et al. 2003b, VP villorum Vancanneyt et al. 2001b, 1742VP De Graef et al., 2003 1701 (Effective publication: Rautio et al., 2003a) Hongia koreensis Lee et al. 2000d, 197VP Anaerococcus hydrogenalis (Ezaki et al. 1990) Ezaki et al. 2001, VP Mycobacterium bovis subsp. caprae (Aranaz et al. -
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology
Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2017 Supplementary Information (SI) Methane-driven microbial fuel cells recover energy and mitigate dissolved methane emissions from anaerobic effluents Siming Chen* and Adam L. Smith*† *Astani Department of Civil and Environmental Engineering, University of Southern California, 3620 South Vermont Avenue, Los Angeles, CA 90089, USA †Corresponding author (Adam L. Smith) Phone: +1 213.740.0473 Email: [email protected] SI Figures Lane # Sample 1 DNA ladder 2 Primary effluent Figure S1. Gel electrophoresis of Geobacter 16S rRNA gene PCR products (top) and pmoA PCR products (bottom) of reverse transcribed RNA extracts (cDNA) after being treated by Invitrogen DNA-free kit. Bands for Geobacter and pmoA (faint) are shown in lane 2 and demonstrate that the inoculum contained both Geobacter and methanotrophs Lane # Sample Lane # Sample 1 DNA ladder 11 DNA ladder Reactor A Anode Reactor A 2 12 biofilm Anode biofilm Reactor A Reactor A 3 13 Cathode biofilm Cathode biofilm Reactor B Anode Reactor B 4 14 biofilm Anode biofilm Reactor B Reactor B 5 15 Cathode biofilm Cathode biofilm Reactor A Anode Primary 6 16 biofilm effluent Reactor A Reactor A 7 17 Cathode biofilm Anode biofilm Reactor B Anode Reactor A 8 18 biofilm Cathode biofilm Reactor B 9 19 Positive control Cathode biofilm 10 DNA ladder 20 DNA ladder Figure S2. Gel electrophoresis of 16S rRNA gene PCR products of RNA extracts after being treated by Invitrogen DNA-free kit. Figure S3. 2 cycles of voltage production while MFCs were operated in fed-batch mode on acetate containing media. -
Nitrogen Removal at the Expense of Methane Generation THESIS
The Wetland Dilemma: Nitrogen Removal at the Expense of Methane Generation THESIS Presented in Partial Fulfillment of the Requirements for the Degree Master of Science in the Graduate School of The Ohio State University By Michael R Brooker Graduate Program in Environmental Science The Ohio State University 2013 Master's Examination Committee: Paula Mouser, Advisor, Gil Bohrer, Jay Martin Copyrighted by Michael R Brooker 2013 Abstract Wetlands in the United States were subject to draining or dredging leading to substantial losses prior to gaining legal protection. Combined with increased fertilization and drainage tile use on agricultural fields, drainage basins have been affected by increased nutrient loads. Nitrogen introduction to large water bodies contributes to the development of hypoxic conditions and harming the ecosystem. To solve this issue, reconstruction of wetlands has been suggested as they are known nutrient sinks. However, wetlands also produce large amounts of the greenhouse gas, methane, giving rise to a dilemma: are the benefits worth the harm? Essentially, denitrification is the initial process which ultimately leads to the conditions necessary for methanogenesis, both being the result of microbial metabolisms present within the sediments. The potential for methane production from sediments collected at three distinct wetland biomes was investigated. Further processing investigated the methanogenic abilities of the upper and lower fifteen centimeter layers from the two hydric soils. Environmental indicators including effect of temperature and nutrient availability was ii investigated pertaining to their effect on microbial-source carbon cycling in an incubation experiment. Sediments collected from the same sites were analyzed for their microbial community in order to explain spatial variations of biogeochemical processes. -
Abundance, Viability and Diversity of the Indigenous Microbial
RESEARCH/REVIEW ARTICLE Abundance, viability and diversity of the indigenous microbial populations at different depths of the NEEM Greenland ice core Vanya Miteva,1 Kaitlyn Rinehold,1 Todd Sowers,2 Aswathy Sebastian3 & Jean Brenchley1 1 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 432 South Frear Building, University Park, PA 16802, USA 2 Department of Geosciences, Earth and Environment Systems Institute, The Pennsylvania State University, 2217 EES Building, 317a, University Park, PA 16802, USA 3 Bioinformatics Consulting Center, The Pennsylvania State University, 502B Wartik, University Park, PA 16802, USA Keywords Abstract Greenland; NEEM ice core; indigenous microbial diversity; isolates; Illumina MiSeq. The 2537-m-deep North Greenland Eemian Ice Drilling (NEEM) core provided a first-time opportunity to perform extensive microbiological analyses on Correspondence selected, recently drilled ice core samples representing different depths, ages, Vanya Miteva, Department of Biochemistry ice structures, deposition climates and ionic compositions. Here, we applied and Molecular Biology, The Pennsylvania cultivation, small subunit (SSU) rRNA gene clone library construction and State University, 432 South Frear Illumina next-generation sequencing (NGS) targeting the V4ÁV5 region, to Building, University Park, PA 16802, USA. examine the microbial abundance, viability and diversity in five deconta- E-mail: [email protected] minated NEEM samples from selected depths (101.2, 633.05, 643.5, 1729.75 and 2051.5 m)