Geomicrobiology Workshop

Geomicrobiology Workshop Course summary: Lecturers: This is an introductory course to geomicrobiology. The course will Gordon Southam (The University of Queensland, Australia) - Web cover bacterial process affecting minerals and tools to study these Emma Gagen (The University of Queensland, Australia) - Web processes (microscopy, microorganism isolation and DNA Guilherme Oliveira (ITV, Belém, PA) - Web sequencing). We will also cover how these natural processes can Ivan Nancucheo (ITV, Belém, PA) - Web be applied in the industry for bioleaching and bioremediation. The Rafael Valadares (ITV, Belém, PA) - Web course will be based lectures and problem solving. Sara Cuadros (Fiocruz, Belo Horizonte, MG) - Web Total hours: 30 (24 in class + 3 extra class work). Felipe Hilario (CDM, Santa Luzia, MG) - Web Date: Public: 22-24 Feb/2016 Vale operations ITV Professional MSc students Venue: Students and post-docs from industry and academia Auditorium ITV-DS, Belém, PA Google Maps Registration: If you would like to register please send an email to: [email protected] and include the following information: CV or link to it Current position Short text with your motivation to participate Course schedule: Time Day 1 Day 2 Day 3 8:30 – 9:00 Welcome - - Fundamental bacterial processes affecting Genes involved in geomicrobiological 9:00-10:30 Bioleaching (Hilario) metals & minerals (Southam) processes (Cuadros) 10:30-11:00 Interval Interval Interval Bacteria in natural systems; limits of life, Metagenomics approaches to geomicrobiology Bioremediation of heavy metals 11:00-12:00 microenvironments and biofilms (Gagen) (Oliveira) (Nancucheo) 12:00-13:00 Lunch Lunch Lunch Challenge 1: Bioremediation of iron mines; 13:00-14:30 Microscopy tools (Southam) Challenge 2: In situ bioleaching canga formation 14:30-15:00 Interval Interval Interval Discussion of challenge 1 (Cuadros, Gagen, Discussion of challenge 2 Bacterial diversity and culturing bacteria 15:00-17:00 Hilario, Nancucheo, Oliveira, Southam, (Cuadros, Gagen, Hilario, (Gagen) Valadares) Nancucheo, Oliveira, Southam) Recommended reading: Sharpton. An introduction to the analysis of shotgun metagenomic data. Front Plant Sci. 2014; 5: 209 Link Wooley et al. A Primer on Metagenomics. PLoS Comput Biol 6(2): e1000667. Link Gagen et al. The geomicrobiology of supergene metal eposits. ELEMENTS, v. 11, p. (5): 305-310. Link Gagen Minerals as Substrates for Life: The Prokaryotic View. ELEMENTS, v. 8, p. (2): 101-106. Link Southam et al. The biogeochemistry of gold. ELEMENTS, October 2009, v. 5, p. (5): 303-307. Link Southam et. al. The geomicrobiology of ore deposits. Economic Geology, v. 100 no. 6 p. 1067-1084. Link .

Copy Link

Recommended publications

Student Handbook
A Handbook for Geology Students 1 Contents Why study Geology? ............................................................................................. 3 Job Prospects and Salaries .................................................................................. 7 Why Appalachian Geology? ................................................................................ 10 Geology Faculty and Staff ................................................................................... 13 Financial Support in the Department ................................................................... 23 Geology Department Awards and Honors .......................................................... 26 Opportunities and Requirements ........................................................................ 28 Degree Programs in Geology ............................................................................. 35 Geology Courses ................................................................................................ 44 Field Camp ......................................................................................................... 51 2 Why study Geology? Geology is the multi-disciplinary science that studies the earth and its history. We live on a dynamic planet that is constantly changing. Our ability to survive as a civilization and as a species is intricately linked to the geologic processes that shape our earth, form its natural resources and allow it to recover from the abuse that our society heaps upon it. Geology is important because
[Show full text]
Geological Sciences 1
Geological Sciences 1 GEOLOGICAL SCIENCES Certificates • Geophysics - Graduate Certificate (catalog.colorado.edu/graduate/ With one of the most successful graduate programs in the nation, colleges-schools/arts-sciences/programs-study/geological-sciences/ the Department of Geological Sciences has enjoyed a reputation of geophysics-graduate-certificate/) excellence for more than 100 years. Our doctoral program is ranked • Hydrologic Sciences - Graduate Certificate (catalog.colorado.edu/ among the top 10 percent of U.S. geology programs by the National graduate/colleges-schools/arts-sciences/programs-study/geological- Research Council, and CU Boulder is ranked as one of the top two sciences/hydrologic-sciences-graduate-certificate/) universities in the world for geosciences by U.S. News and World Report. Graduate students have an opportunity to work with over 35 tenured Faculty and tenure-track faculty who support a wide range of interdisciplinary While many faculty teach both undergraduate and graduate students, research programs in such areas as: cosmochemistry and planetary some instruct students at the undergraduate level only. For more geology; Earth science education; economic and energy resources; information, contact the faculty member's home department. geobiology and astrobiology; geochemistry; geochronology and Abbott, Lon D. (https://experts.colorado.edu/display/fisid_145044/) thermochronology; geodynamics, geophysics, and remote sensing; Senior Instructor; PhD, University of California, Santa Cruz geomorphology and cryosphere; global change; hydrology; natural hazards; paleoclimate and paleoceanography; paleontology and Anderson, Robert S. (https://experts.colorado.edu/display/fisid_130117/) paleobiology; petrology and mineralogy; sedimentology and stratigraphy; Distinguished Professor; PhD, University of Washington and structure and tectonics. Arthurs, Leilani A. (https://experts.colorado.edu/display/fisid_145087/) The graduate degrees offered include Master of Science (MS) and Doctor Assistant Professor; PhD, University of Notre Dame of Philosophy (PhD).
[Show full text]
Geomicrobiological Processes in Extreme Environments: a Review
202 Articles by Hailiang Dong1, 2 and Bingsong Yu1,3 Geomicrobiological processes in extreme environments: A review 1 Geomicrobiology Laboratory, China University of Geosciences, Beijing, 100083, China. 2 Department of Geology, Miami University, Oxford, OH, 45056, USA. Email: [email protected] 3 School of Earth Sciences, China University of Geosciences, Beijing, 100083, China. The last decade has seen an extraordinary growth of and Mancinelli, 2001). These unique conditions have selected Geomicrobiology. Microorganisms have been studied in unique microorganisms and novel metabolic functions. Readers are directed to recent review papers (Kieft and Phelps, 1997; Pedersen, numerous extreme environments on Earth, ranging from 1997; Krumholz, 2000; Pedersen, 2000; Rothschild and crystalline rocks from the deep subsurface, ancient Mancinelli, 2001; Amend and Teske, 2005; Fredrickson and Balk- sedimentary rocks and hypersaline lakes, to dry deserts will, 2006). A recent study suggests the importance of pressure in the origination of life and biomolecules (Sharma et al., 2002). In and deep-ocean hydrothermal vent systems. In light of this short review and in light of some most recent developments, this recent progress, we review several currently active we focus on two specific aspects: novel metabolic functions and research frontiers: deep continental subsurface micro- energy sources. biology, microbial ecology in saline lakes, microbial Some metabolic functions of continental subsurface formation of dolomite, geomicrobiology in dry deserts, microorganisms fossil DNA and its use in recovery of paleoenviron- Because of the unique geochemical, hydrological, and geological mental conditions, and geomicrobiology of oceans. conditions of the deep subsurface, microorganisms from these envi- Throughout this article we emphasize geomicrobiological ronments are different from surface organisms in their metabolic processes in these extreme environments.
[Show full text]
MICR 423: Geomicrobiology Fall 2018 3 Credit Hours
MICR 423: Geomicrobiology Fall 2018 3 Credit Hours Course description. This course will focus on the role that microorganisms play in fundamental geological processes. Topics will include an outline of the present understanding of microbial involvement of weathering of rocks, formation and transformation of soils and sediments, genesis and degradation of minerals. Elemental cycles will also be covered with emphasis on the interrelationships between the various geochemical cycles and the microbial trophic groups involved. Prerequisite: MICR 301 and Chemistry 210 and 21l. Recommended: GEOL 220, 221 or 222. Lecture. Life Science II, Room 430, 9:35 – 10:50 Tues and Thurs Course Goals. At the end of this course you will be able to: • Intelligently converse with microbiologists, geologists, environmental scientists and engineers about the role microorganisms play in the cycling of elements • Be familiar with a variety of techniques to identify and characterize microorganisms in any environment • Relate microbial physiology, genetics, cell structure, and metabolism to the effect, role, or signature that microbes imprint on their surroundings Instructor Office Office Hours Dr. Scott Hamilton-Brehm Life Science III, Rm 1009 M 10-12 pm or by 453-3818 appointment [email protected] Strongly suggested textbooks: • BROCK BIOLOGY OF MICROORGANISMS, 15th edition, 2017, Michael T. Madigan, Kelly S. Bender, Daniel H. Buckley, Matthew W. Sattley, and David A. Stahl (Benjamin Cummings/Pearson). • Hall BG. Phylogenetic trees made easy: a how-to manual. 2008. Final Course Grading scale Grade Points Percentage A 900 - 1000 90-100% B 800 - 899 80-89% C 700 - 799 70-79% D 600 - 699 60-69% F 0 - 599 0-59% Lecture Grades.
[Show full text]
Need for Seismic Hydrology Research with a Geomicrobiological Focus
sustainability Communication Need for Seismic Hydrology Research with a Geomicrobiological Focus Heejung Kim Department of Geology, Kangwon National University, Chuncheon 24341, Korea; [email protected] Abstract: Earthquakes cause deformation in previously stable groundwater environments, resulting in changes to the hydrogeological characteristics. The changes to hydrological processes follow- ing large-scale earthquakes have been investigated through many physicochemical studies, but understanding of the associated geomicrobiological responses remains limited. To complement the understanding of earthquakes gathered using hydrogeochemical approaches, studies on the effects of the Earth’s deep crustal fluids on microbial community structures can be applied. These studies could help establish the degree of resilience and sustainability of the underground ecosystem following an earthquake. Furthermore, investigations on changes in the microbial community structure of the Earth’s deep crustal fluids before and after an earthquake can be used to predict an earthquake. The results derived from studies that merge hydrogeochemical and geomicrobiological changes in the deep crustal fluids due to the effect of stress on rock characteristics within a fault zone can be used to correlate these factors with earthquake occurrences. In addition, an earthquake risk evaluation method may be developed based on the observable characteristics of fault-zone aquifers. Keywords: earthquake; seismic hydrology; groundwater; hydrogeochemistry; geomicrobiology Citation: Kim, H. Need for Seismic Many studies on the reaction of the Earth’s deep crustal fluids before and after earth- Hydrology Research with a quakes have been conducted worldwide, including in countries with a high frequency Geomicrobiological Focus. of earthquakes. Seismic hydrology is the study of earthquake prediction by analyzing Sustainability 2021, 13, 8704.
[Show full text]
Area of Study
DEPARTMENT OF EARTHDEPARTMENT SCIENCES OF THE GRADUATE SCHOOL | MONTANA STATE UNIVERSITY AreaEarth ofSciences Study DEGREES OFFERED • M.S. in Earth Sciences FirstThe Departmentgraph of Earth Sciences at Montana State University has a faculty of 13 earth • Ph.D. in Earth Sciences scientists, geologists and geographers. The Master of Science and Doctor of Philosophy in Earth • Ph.D. in Ecology and TextSciences programs have around 45 active graduate students and stress independent thesis Environmental Science research with some supporting course work. Faculty expertise and research in the department spans a large majority of the subfields of Earth Sciences. Our geography faculty includes specialties from settlement geography to bioclimatology, from international urban geography to GIS to snow science. The interests of our geology faculty range from petrogenesis to paleobiology to structural geology, and from dinosaur taphonomy and stratigraphy to geomorphology. Our geobiology faculty have research interests in vertebrate paleontology, paleoecology, biogeography, paleoclimatology and geomicrobiology. Program strengths are in basin analysis and energy resources, dinosaur paleontology, geography of the northern Rocky Mountains, architecture and composition of the lithosphere, snow science and cryospheric processes, and climate change. ADMISSION Applicants should a GPA of 3.0 or higher, GRE scores better than the 50th percentile and a strong academic background in Earth Sciences (geography, geology or geobiology). Foreign students must have a TOEFL score better than 550 for the paper test and 231 for the computer test. The department does not accept general applicants to our graduate program. An applicant should identify a major advisor from the list of faculty, contact that individual, and Department Address: determine whether there is space available in that advisor’s program.
[Show full text]
Geomicrobiology: Interactions Between Microbes and Minerals, Comes at a Very Opportune Time
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Hemeroteca Cientifica Catalana INTERNATL MICROBIOL (1998) 1:241–242 241 © Springer-Verlag Ibérica 1998 BOOK REVIEWS a few chapters are devoid of typographical mistakes which Geomicrobiology: Interactions between in some case have resulted in factual errors. Nealson and Microbes and Minerals Stahl state that freshwater environments typically contain JILLIAN F. BANFIELD, KENNETH H. NEALSON (eds) 100 to 250 mM of sulfate while marine systems contain 1997. Mineralogical Society of America, Washington, DC. micromolar amounts (just the opposite is true). Bazylinski (Series: Reviews in Mineralogy, vol. 35) and Moskowitz have inadvertently created a new subgroup 448 pp. Paperback, $32. of Proteobacteria. The volume I received also included an ISBN 0-93995045-6 insert correcting a figure in chapter 11, earlier versions did not. Suffice it to say reediting would greatly enhance the The recent controversy over nanofossils in a Martian utility of this text. Despite its shortcomings, it is a good meteorite and reports of bacteria growing in basalt have once primer for the novice and an important volume for the again brought the study of geomicrobiology into the seasoned veteran. headlines. Thus, Geomicrobiology: Interactions Between Microbes and Minerals, comes at a very opportune time. The book, a byproduct of a short course of the same title hosted John F. Stolz by the Mineralogical Society of America last fall, provides Duquesne University, Pittsburgh, Pennsylvania an in depth look at a fascinating subject. Containing 13 chapters it begins with a review for non-specialists on microorganisms and biogeochemical cycles and concludes with the evolution of the carbon cycle.
[Show full text]
Geomicrobiology and Microbial Geochemistry
Geomicrobiology and Microbial Geochemistry 1Gregory K Druschel and 2Andreas Kappler 1Department of Earth Sciences, Indiana University Purdue University Indianapolis 723 W. Michigan St., Indianapolis, IN 46202, USA. E-mail: [email protected] 2Center for Applied Geoscience (ZAG), Eberhard-Karls-University Tuebingen, Sigwartstrasse 10, 72076 Tuebingen, Germany Geomicrobiology and Microbial Geochemistry (GMG) investigates the interaction between Earth and environmental systems and microbial life. Microbes shape their geochemical surroundings through their metabolism and growth needs, exerting control on every facet of redox, metal, organic, nutrient, and trace element geochemical and mineralogical components. Conversely, geochemical surroundings dictate what metabolisms are possible. Microbial evolution has occurred in concert with changing geosphere conditions – microbes have driven major shifts in the chemistry of oceans, continents, and atmosphere just as key changes in physical and chemical surroundings affects microbial communities (Knoll, 2003a,b). If one wishes to understand element cycling in any system containing water, including the role of microbes is critical to the story. Development of Geomicrobiology and Microbial Geochemistry As part of the broader disciplines of geobiology or biogeochemistry, the developing field of GMG has crucial overlaps with fields of biology addressing microbes, but is specifically focused on combined approaches to bring chemical, biological, AND geological perspectives together to characterize the role of microbes in environmental and geological processes (Fig. 1). Geobiochemistry turns this perspective toward establishing the role of geology Figure 1: To understand biogeochemical cycles of elements and the evolution of life on Earth, the interplay in the development of organismal biochemical of various aspects of biology, chemistry and geology must processes over time (Boyd and Shock, this issue).
[Show full text]
Geomicrobiology
Newsletter of the Mineralogical Society of America Vol. 13, No.2, May 1997 • ICe GEOMICROBIOLOGY: INTERACTIONS BETWEEN MICROBES AND MINERALS The mineralogical and geochemical characteristics Topics to be covered in the short course include the of the crust, hydrosphere, and atmosphere have evolved links between evolution of the Earth and in parallel with evolution of microorganisms. microorganisms, new insights into microbial diversity in Microorganisms cause mineral precipitation and natural environments and the nature of early life forms, dissolution and control the distribution of elements in the structure, chemistry, and reactivity of mineral diverse environments at and below the surface of the surfaces, the metabolic roles of metals and mechanisms Earth. Conversely, mineralogical and geochemical used to modulate metal concentrations, microbial factors exert important controls on microbial evolution attachment to mineral surfaces and biofilm formation, and the structure of microbial communities. microbial precipitation and the characteristics of The Mineralogical Society of America is offering a biologically precipitated minerals, microbially-mediated Short Course on Geomicrobiology on October 18-19, mineral dissolution, and the impacts of microbial 1997 in Alta, Utah. This course precedes the processes on geochemical cycles in soils and sediments. Mineralogical Society of America - Geological Society Convenors of the Short Course are Jillian F. America Annual Meeting in Salt Lake City, Utah. Banfield (Department of Geology and Geophysics, The short course will teach geologists about the ways in University of Wisconsin-Madison) and Kenneth which microbial activity impacts what have traditionally Nealson (University of Wisconsin Great Lakes Institute, been considered inorganic processes and microbiologists University of Wisconsin - Milwaukee). Additional and other life scientists about the mineralogical and information and registration materials are included in geochemical aspects of biogeochemical systems.
[Show full text]
How the Continents Deform: the Evidence from Tectonic Geodesy*
ANRV374-EA37-11 ARI 23 March 2009 12:5 How the Continents Deform: The Evidence From Tectonic Geodesy∗ Wayne Thatcher U.S. Geological Survey, Menlo Park, California 94025; email: [email protected] Annu. Rev. Earth Planet. Sci. 2009. 37:237–62 Key Words First published online as a Review in Advance on GPS, tectonics, microplates, plate tectonics, continental dynamics January 20, 2009 The Annual Review of Earth and Planetary Sciences is Abstract online at earth.annualreviews.org Space geodesy now provides quantitative maps of the surface velocity ﬁeld This article’s doi: within tectonically active regions, supplying constraints on the spatial dis- 10.1146/annurev.earth.031208.100035 by University of California - San Diego on 01/13/14. For personal use only. tribution of deformation, the forces that drive it, and the brittle and ductile Copyright c 2009 by Annual Reviews. properties of continental lithosphere. Deformation is usefully described as All rights reserved Annu. Rev. Earth Planet. Sci. 2009.37:237-262. Downloaded from www.annualreviews.org relative motions among elastic blocks and is block-like because major faults 0084-6597/09/0530-0237$20.00 are weaker than adjacent intact crust. Despite similarities, continental block ∗The U.S. Government has the right to retain a kinematics differs from global plate tectonics: blocks are much smaller, typ- nonexclusive, royalty-free license in and to any ically ∼100–1000 km in size; departures from block rigidity are sometimes copyright covering this paper. measurable; and blocks evolve over ∼1–10 Ma timescales, particularly near their often geometrically irregular boundaries. Quantitatively relating defor- mation to the forces that drive it requires simplifying assumptions about the strength distribution in the lithosphere.
[Show full text]
Introduction to Geomicrobiology
ITGA01 18/7/06 18:06 Page iii Introduction to Geomicrobiology Kurt Konhauser ITGC03 18/7/06 18:11 Page 93 3 Cell surface reactivity and metal sorption One of the consequences of being extremely 3.1 The cell envelope small is that most microorganisms cannot out swim their surrounding aqueous environment. Instead they are subject to viscous forces that 3.1.1 Bacterial cell walls cause them to drag around a thin ﬁlm of bound water molecules at all times. The im- Bacterial surfaces are highly variable, but one plication of having a watery shell is that micro- common constituent amongst them is a unique organisms must rely on diffusional processes material called peptidoglycan, a polymer con- to extract essential solutes from their local sisting of a network of linear polysaccharide milieu and discard metabolic wastes. As a (or glycan) strands linked together by proteins result, there is a prime necessity for those cells (Schleifer and Kandler, 1972). The backbone to maintain a reactive hydrophilic interface. of the molecule is composed of two amine sugar To a large extent this is facilitated by having derivatives, N-acetylglucosamine and N-acetyl- outer surfaces with anionic organic ligands and muramic acid, that form an alternating, and high surface area:volume ratios that provide repeating, strand. Short peptide chains, with four a large contact area for chemical exchange. or ﬁve amino acids, are covalently bound to some Most microorganisms further enhance their of the N-acetylmuramic acid groups (Fig. 3.1). chances for survival by growing attached to They serve to enhance the stability of the submerged solids.
[Show full text]
Mixotrophic Magnetosome-Dependent Magnetoautotrophic Metabolism of Model Magnetototactic Bacterium Magnetospirillum Magneticum A
Mixotrophic Magnetosome-Dependent Magnetoautotrophic Metabolism of Model Magnetototactic Bacterium Magnetospirillum magneticum AMB-1 Dissertation Presented In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Eric Keith Mumper, BA Graduate Program in the School of Earth Sciences The Ohio State University 2019 Dissertation Committee: Steven K. Lower, Adviser Brian H. Lower Ratnasingham Sooryakumar Ann E. Cook Copyright by Eric Keith Mumper 2019 Abstract Magnetospirillum magneticum AMB-1 is a member of a phylogenetically diverse group of bacteria characterized by their ability to biomineralize magnetic minerals known collectively as magnetotactic bacteria (MTB).1,2,3 MTB produce chains of membrane- bound intracellular magnetic nanocrystals, collectively known as magnetosomes.1,2,3 The current scientific consensus is that magnetosomes are used by MTB to orient themselves in vertically stratified water columns in order to achieve optimal oxygen concentrations in a process known as magnetoaerotaxis.4,5 Biomineralization of magnetosomes is an energy intensive process which accounts for roughly 33% of the cell's metabolic budget.6 This high metabolic cost seems to contradict with the amount of time MTB cells spend aligned with external magnetic fields.5 Due to this apparent discrepancy, I examined the potential role the magnetosome may play in bacterial metabolism. Through analysis of comparative growth on a variety of media compositions both magnetic, wild type and non-magnetic, mutant strains of AMB-1, I discovered that cells grown under stress conditions exhibit an inversion of growth dynamics which indicates some advantage for magnetic cells. Non-magnetic, mutant cells display a direct relationship between external magnetic field strength and growth, indicating magnetic field dependence.
[Show full text]