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Student Resources
(animations, interactive exercises, links)

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Introduction

The resources presented at this website will help students and practitioners find additional information, and follow evolving research trends on particular topics. Like any exciting field of science, microbial diversity is an international enterprise. Consequently, many of the resources encourage international exploration, and provide opportunities for contacts that should nurture international collaborations. Finally, the interactive exercises are meant to inspire the generation of new ideas that make this a personal endeavor and to encourage ambitious career goals in microbial diversity. These resources will be updated regularly. The author welcomes suggestions to include new websites, exercises, and recent research advances. Please send suggestions to the author at oaogunse@uci.edu

General Resources

Interactive Phylogenetic Tree: A Phylogenetic Tree of the Prokaryotes

Physicists have their grails: the origin of the universe, and the universal theory of all physical phenomena. In biology, there are also at least two grails: the origin of life, and the universal tree of life. Like all objects of extended and difficult quests, the paths toward their discovery are tortuous and intriguing. Frequently, there are philosophical disagreements regarding the very existence of the grail and on how cold or hot particular paths are. Excursions into the similarity of molecular signatures carried by all living organisms have generated great optimism that a universal tree of life is both feasible and meaningful. However, there are debates over the appropriate molecules to use for constructing such a tree (see Chapter 5). There are also debates over the interpretation of trees because horizontal genetic exchange events appear to be rampant, and phylogenetic signals can be degraded over time. Nevertheless, a good picture of the universal phylogenetic tree is emerging. It is not perfect, nor is it likely ever to be, given the dynamic nature of evolution. The tree presented here for the domain Prokarya was constructed on the basis of large combined protein sequence data sets. Brown and colleagues (2001) constructed the robust tree by using large combined alignments of 23 orthologous proteins that are conserved across 45 “species” belonging to the Archaea, Bacteria, and Eukarya. The combination of protein data sets reduces the variability inherent in constructing such trees with the sequence of amino acids from individual protein molecules. This particular tree agrees with other lines of evidence indicating that the spirochetes and thermophiles are the earliest evolved lineages of prokaryotes. Without doubt, there will be more refinements to the tree as we discover more about microbial diversity, especially from the silent majority that have not been cultivated nor observed in any other way. The universal phylogenetic tree will likely have to await consensus on a universal “microbial group theory” that encompasses seen and unseen microorganisms.

 

Microbiology Video Library: http://www-micro.msb.le.ac.uk/video/index.html

The microbiology video library was developed by Dr. Alan Cann of the University of Leicester in England . This resource covers more than 300 topics, and includes high quality video documentary as well as commentary on many prokaryotes and some microscopic eukaryotes discussed in this book. The site is linked to the department of microbiology and immunology at the University of Leicester . The website also includes online tutorial and guidance on laboratory experiments.

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Chapter 1

Extract of Interview conducted by David Morrison for NASA.
For the full interview please visit http://nai.arc.nasa.gov/news_stories/news_detail.cfm?ID=274

In a 1977 publication with colleague Ralph Wolff, [Carl] Woese showed that a previously little-known group of microbes called the archaebacteria were actually more closely related to the eucarya than to the other, true bacteria. Plotted on the tree of life, these obscure microbes occupy a large space, distinct from that of both the eukarya and the bacteria. Based on these discoveries, Woese in 1990 proposed the now-accepted division of life in a paper entitled “Towards a natural system of organisms: Proposals for the domains of Archeae, Bacteria, and Eucarya.” In spite of their name, the archaea are not older than the bacteria. But they are an ancient lineage, many of whose members avoid oxygen (they are anaerobes) and seek high temperatures (they are thermophiles).

The tree of life developed by Woese and his collaborators deserves careful study by astrobiologists. It tells us some surprising things. The wide spread in the various microbial species, which is roughly proportional to the passage of time, shows us the tremendous range of evolutionary change that has taken place within the microbial world. Contrary to the ideas of conventional biology, life did not lie quiescent on Earth for the three billion years that proceeded the burst of evolution that constitutes the “Cambrian explosion” 600 million years ago. The great physiological diversity we associate with plants and animals represents a rather small change as measured by these RNA sequences. In fact, the three kingdoms of plants, animals, and fungi are confined to a few outlying twigs in the much greater tree of microbial life.

A look at the new tree of life should also caution us against calling any of these microbes “primitive.” All of the species alive today have followed a long evolutionary trajectory from their early common ancestors.

While the tree of life can provide rich insights into evolution, it is important to remember that it shows only the genetic relationships among species extant today. There are no extinct species on this tree of life, since we cannot extract 16s mRNA from fossils. Thus in spite of similarity in presentation, this is not an evolutionary tree in the traditional sense of showing our descent from previous species. We can learn who our relatives are from this tree, but not necessarily how we got to be where we are today. This tree is complementary to the traditional tree that shows evolutionary lineages derived from fossils.

The pioneering work done by Woese and his collaborators is today being supplemented by other ways of comparing the genomes of different species. The revolution in genomic technology now allows numerous other sections of both DNA and RNA to be sequenced and compared. Each of these techniques is yielding its own tree of life, generally similar to that based on 16s mRNA, but not identical. In fact, we have reached the stage where entire genomes can be compared.

Woese continues his work in the microbiology labs at the University of Illinois in Champaign-Urbana. In 1996 he was part of team that sequenced the first archaeon, and much of his current work is related to efforts to define the “last common ancestor”, if there really was such a thing. He calls himself today an evolutionary biologist. The ultimate objective of taxonomy, the classification of organisms and their relationships, is to better understand the evolutionary process through which life has expanded over the past 4 billion years to create our living world.

 

Interview with Andrew Knoll on Biodiversity:
http://nai.arc.nasa.gov/video_archive/andy_knoll.cfm?Movie=Knoll_1.mov#movie

Andrew H. Knoll is professor of biology in the department of Earth and Planetary Studies at Harvard University . He directs the paleobotany laboratory, where members study the relationships between the evolution of life and the evolution of Earth surface environments. The laboratory focuses on Archean and Proterozoic paleontology, carbonate sedimentology, and biogeochemistry. In this 15-piece video documentary, Professor Knoll shares his thoughts on the future of evolution. In the preface to the documentary, Daniella Scalice of NASA writes: "One of the three major questions which Astrobiology seeks to answer is "What is the Future of Life?" Toward that goal, we need to consider not only how Earth- based life might survive in space or on some other planet, but also, and perhaps more importantly, we need to plan for the future and survival of life on our home planet. According to Andrew Knoll and conservation biologist Norman Myers, that future hangs in the balance. They published a colloquium paper in Proceedings of the National Academy of Sciences entitled, "The Biotic Crisis and the Future of Evolution." The paper was first presented at the National Academy of Sciences Colloquium, "The Future of Evolution," in March 2000." "The looming crisis of mass extinctions threatens to disrupt basic evolutionary processes, the consequences of which are wholly unpredictable."

In this August 2001 interview, Dr. Knoll shared his perspective on the subject - calling the issues into scientific consciousness, and reminding us all of why we need to value and protect diversity not only for our own sake, but for that of the planet and of future generations as well.

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Chapter 2

"A picture is worth a thousand words" is an old adage that is especially pertinent for describing human understanding of the microbial world. Microscopy remains the quintessential instrument of the microbiological sciences, and there are several lines of research focused on improving the resolution and comprehensiveness of microscopic observations. The following websites each offer access to cutting-edge information on the development of microscopy. They include web-sites dedicated to instrumentation and photographic documentation of known organisms. In principle, this is a constantly emerging field, and readers should expect regular updates of the information presented.

 

Microscopy Bulleting Board, "a World Wide Web resource designed specifically for the microscopist." The goal of this site is to provide both the commercial and non-commercial microscopy communities with a forum for information exchange.
http://www.microscopy-online.com/

 

WWW Virtual Library - Microscopy: http://www.ou.edu/research/electron/www-vl/

 

The Microscopy Society of America is a non-profit organization dedicated to the promotion and advancement of the knowledge of the science and practice of all microscopical imaging, analysis and diffraction techniques useful for elucidating the ultrastructure and function of materials in diverse areas of biological, material, medical and physical sciences: http://www.msa.microscopy.com/

 

Veteran microscopist Dennis Kunkel's images of the microbial world are visually stunning and technically accurate. The collection of images is extensive and regularly updated: http://www.denniskunkel.com/

 

Microscopy Analysis is an academic journal published by Wiley. It is the premier international journal for users of microscopical, analytical and imaging equipment: http://www.microscopy-analysis.com/

 

A microscopy enthusiast website based in the United Kingdom : http://www.microscopy-uk.org.uk/

 

Lance Ladic at the University of British Columbia , Canada hosts this excellent website dedicated to 3D-laser Scanning Confocal Microscopy. The site includes links to other sites with animations and demonstration programs on various aspects of confocal microscopy: http://www.cs.ubc.ca/spider/ladic/confocal.html

 

Molecular Expressions website at Florida State University . The site features acclaimed photo galleries that explore the fascinating world of optical microscopy, including one of the Web's largest collections of color photographs taken through an optical microscope (photomicrographs). The photographs are available for licensing to commercial, private, and non-profit institutions: http://micro.magnet.fsu.edu/index.html

 

Journal of Electron Microscopy , published by Oxford University Press. This is the official journal of the Japanese Society of Microscopy, the second largest society of microscopy in the world. The journal is an international forum open to all scientists in the field of advanced electron microscopy and new scanning probe microscopy. Six issues are published per year, and papers cover the application of advanced microscopy in diverse fields. Articles cover theories, methods, techniques, and instrumentation, as well as their applications to life and material sciences: http://jmicro.oupjournals.org/

 

IBM's website on Scanning Tunneling Microscopy, includes an image gallery and tutorials on techniques: http://www.almaden.ibm.com/vis/stm/stm.html

 

Microscopy Society of America's alternative peer-reviewed journal Microscopy Today : http://www.microscopy-today.com/

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Chapter 3

Winogradsky Column: The Winogradsky column is probably the best known demonstration project in microbial ecology, valued because of the simplicity of its construction, its reproducibility, and the profound nature of the information that the column provides. The Quick Time Movie created by Daniella Scalice for NASA is a valuable source of practical information on how to build a Winogradsky column and how to interpret the observations. Beyond reproducing the typical observations of the column, a more rewarding experience can be obtained by experimenting with different sources of nutrients, stressors, and environmental conditions to gather data on how these changes influence the microbial diversity at various layers of the column. Additional websites are provided for access to other groups working systematically with Winogradsky columns.

 

NASA Quest Video: How to Build a Winogradsky Column: http://quest.arc.nasa.gov/projects/astrobiology/fieldwork/lessons/demo.html

 

Jane Orbuch's hotlist on Winogradsky column features several links to soil profiles and other variations: http://www.kn.pacbell.com/wired/fil/pages/listwindograja.html

 

Jim Deacon's "The Microbial World" segment on Winogradsky columns: http://helios.bto.ed.ac.uk/bto/microbes/winograd.htm

 

The Marine Biological Laboratory's website on microbiological methods and biochemical reactions within the Winogradsky column. Also includes a link to the Microbial Diversity course at MBL: http://ecosystems.mbl.edu/SES/MicrobialMethods/Winogradsky/default.htm

 

John Lennox's site at Pennsylvania State University offers some tips on Winogradsky column and other topics in environmental microbiology: http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/winogradsky.html

 

Frances Vandervoort's entry on Winogradsky column at the Access Excellence web host site: http://www.accessexcellence.org/AE/AEPC/WWC/1991/microbial.html

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Chapter 4

The death of Francis Crick on July 28th 2004 marked the passing of one of the faces intimately associated with the advent of empirical reductionism in genetics and molecular biology. In less than fifty years since the discovery of the molecular structure of DNA by Francis Crick and James Watson, the entire genomes of several microorganisms have been sequenced, and the cloning of several phenotypes across taxonomic boundaries has been accomplished. Furthermore, the immense diversity inherent in genotypes is better understood, even if much more needs to be learnt about how this potential diversity is interpreted under various environmental conditions. The following websites link readers to active research sites. They will increase molecular-level knowledge of microbial diversity, and the information can be used to gain an understanding of the relationships among various groups of organisms. A good place to start is The National Center for Biotechnology Information, where carefully selected keywords can be used to retrieve a tremendous array of information on genomics and proteomics, submitted by scientists all over the world. http://www.ncbi.nlm.nih.gov/

 

Nature Publishing Company's Genome Gateway provides access to all microbial genomes that have been completely sequenced and published in Nature magazine: http://www.nature.com/genomics/

 

The United States Department of Energy Genomes-to-Life Initiative: http://www.doegenomestolife.org/index.shtml

 

The quintessential proteomics website. Includes access to protein sequence databases and tools for comparative assessment (Expert Protein Analysis System): http://au.expasy.org/

 

A company that specializes in the identification of microorganisms by means of comparing fatty acid profiles: http://www.midi-inc.com/

 

Lipid Molecular Structure Database at Ohio State University : http://www.lipidat.chemistry.ohio-state.edu/

 

Lipid Bank in Japan : http://lipidbank.jp/

 

Ribosomal RNA Database: http://www.psb.ugent.be/rRNA/

 

Small RNA Database: http://mbcr.bcm.tmc.edu/smallRNA/smallrna.html

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Chapter 5

Several computer software programs have been developed to organize large molecular sequence data into meaningful phylogenetic trees. These programs are constantly undergoing improvement, and as such, it is advisable to be on the lookout for software updates. Other web-based resources facilitate online comparison of molecular sequence data, including alignments and ultimate construction of phylogenetic trees.

 

TreeBASE, "A relational database designed to manage and explore information on phylogenetic relationships." The searchable database currently includes more than 1825 authors, 1001 studies, 2646 trees, and 40336 taxa. http://www.treebase.org/treebase/

 

The Tree of Life Web Project: http://tolweb.org/tree/phylogeny.html

 

Phylogenetic Tree Prediction: http://www.genebee.msu.su/services/phtree_reduced.html

 

"Phylodendron" - The phylogenetic tree printer: http://iubio.bio.indiana.edu/treeapp/treeprint-form.html

 

PHYLIP Software Homepage: http://evolution.genetics.washington.edu/phylip.html

 

Phylogenetic tree of prokaryotes: http://www2.unil.ch/comparativegenometrics/phylo_tree.html

 

PUZZLE Software: http://www.tree-puzzle.de/

 

TreeEdit - Software for Organizing Trees for PAUP Software: http://evolve.zoo.ox.ac.uk/software.html?id=TreeEdit

 

TreeView Software: http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/

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Chapter 6

The NASA and European Space Agency (ESA) both focus on space exploration and have played a role in the emergence of astrobiology. Together, these agencies and astrobiology have shed light on the co-evolution of life and the environment. Rapid developments in chemical analysis of space components are also fueling the re-evaluation of panspermia theories. The following websites and interactive videos provide a rich context for beginning the exploration of microbial diversity as a core discipline of environmental evolution and astrobiology. In addition, interviews with astrobiologists David Des Marais and Teresa Longazo of NASA are provided to demonstrate that careers in this field may be launched from different disciplines.

 

NASA Astrobiology Institute: http://nai.arc.nasa.gov/

 

Carnegie Institution of Washington astrobiology program: http://astrobiology.ciw.edu/

 

A website dedicated to theories on panspermia and the origin of life: http://www.panspermia.org/

 

The Planetary Society: http://www.planetary.org/html/society/society.html

 

Astrobiology Magazine: http://www.astrobio.net/news/index.php

 

Astrobiology at the Marine Biological Laboratory: http://www.mbl.edu/Astrobiology/

 

European Space Agency : http://www.spaceflight.esa.int/users/virtualinstitutes/exobio/index.html

 

Astrobiology Society of Britain : http://www.astrobiologysociety.org/

 

Centro de Astrobiologia (CAB) The CAB was the first astrobiology center outside the USA to be associated with the NASA Astrobiology Institute (NAI). In 1999, CAB was an Acting Associate International Member of NAI. The membership was formalized in 2000: http://www.cab.inta.es/

 

The Groupement de Recherche en Exobiologie (GdRE), France was created by the Centre National de la Recherche Scientifique (CNRS) in 1999, and is a French federation of research laboratories working in Exo/Astrobiology. http://www.lisa.univ-paris12.fr/GDRexobio/exobio.html

 

Australia Center for Astrobiology: http://aca.mq.edu.au/

 

Microbial Mat. Gallery

Stardust Commentary

Interview with astrobiologist David Des Marais: http://nai.arc.nasa.gov/video_archive/desmarais.cfm

 

Interview with astrobioloist Teresa Longazo: http://nai.arc.nasa.gov/video_archive/longazo.cfm

 

Organelle Genome Database: http://megasun.bch.umontreal.ca/welcome.html

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Chapter 7

The investigation of global biogeochemical cycles provides unparalleled opportunity to understand the integrated function of diverse groups of microorganisms in both environmental change and homeostasis. Carbon and nitrogen are key elemental components of all known organisms, and therefore are actively cycled through microorganisms. In certain cases, such as nitrogen fixation, the action of a small number of taxonomic groups is critical. The following websites and interactive files provide important microbiological context for carbon and nitrogen cycles, and the linkage of these cycles to Earth system science. The Hadley Center in the United Kingdom is at the forefront of research on climate change and carbon cycle experiments. Similarly, NASA is at the forefront of research on these important cycles through the "Earth Science Enterprise" program and the Office of Biological and Physical Research.

 

General Carbon Cycle Information: http://earthobservatory.nasa.gov/Library/CarbonCycle/

 

Methane Hydrate Stocks and Energy at the USGS Screening Room: http://visualmedia.usgs.gov/screeningroom/

 

Climate and Carbon Cycling Modeling: http://eed.llnl.gov/cccm/hiresolu.html

 

Hadley Center (UK) Carbon Cycle Experiments: http://www.met-office.gov.uk/research/hadleycentre/models/carbon_cycle/results_trans.html

 

Earth Science Enterprise at NASA: http://www.earth.nasa.gov/Introduction/index.html

 

The Office of Biological and Physical Research: http://spaceresearch.nasa.gov/

 

Interactive Nitrogen Cycle (Powerpoint "View Show" format)

 

Carbon dioxide cycling NASA video

 

Global Methane Cycling NASA interactive video

 

Ozone destruction by nitrogen oxides NASA interactive video

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Chapter 8

This chapter continues the discussion on the influences of microbial diversity on the global geochemical cycles. Here we focus on sulfur, phosphorus, and some trace elements, including metals. The treatment of individual element cycles separately should not lead to the erroneous assumption that these cycles are independent in nature. In fact, they are intimately linked. Thus, the "iron fertilization" experiment has enjoyed considerable publicity because iron limits carbon assimilation in parts of the oceans, and the threat of global warming is encouraging research into all opportunities for carbon sequestration.

 

Chlorine release in Antarctica - NASA interactive video

Global Phytoplankton - NASA interactive video

Sulfur Dioxide Release fromMount Pinatumbo - NASA interactive video

 

"Living on Earth" radio program on iron fertilization: http://www.loe.org/series/iron_fertilization/

 

Planktos Foundation: http://www.planktos.com/main.htm

 

Department of Energy Carbon Sequestration Program: http://cdiac2.esd.ornl.gov/ (See also http://www.fe.doe.gov/programs/sequestration/

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Chapter 9

Microbial Ecology is the discipline that counts among its specific foci the interactions among prokaryotes. This is a relatively mature topic in the assessment of microbial diversity, but there are still many surprises, and the stakes are high for applied research. For example, quorum sensing and the role of antibiotics in nature are extremely important topics for agriculture, public health, and industrial manufacturing systems.

 

Microbe Library (subscription required): http://www.microbelibrary.org/

 

The Quorum Sensing Site: http://www.nottingham.ac.uk/quorum/

 

Quorum Sensing Site in Switzerland: http://www.quorum-sensing.de/

 

Bacteriophage Ecology Group: http://www.phage.org/

 

Johns Hopkins Antibiotics Guide: http://www.hopkins-abxguide.org/

 

The Campaign to Prevent Antibiotics Overuse: http://www.keepantibioticsworking.com/pages/home.cfm

 

Alliance for the Prudent Use of Antibiotics: http://www.tufts.edu/med/apua/

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Chapter 10

Prokaryotes help to sustain the lifestyle of many large multicellular eukaryotes. Prokaryotic organisms also cause a lot of grief in the world of large multicellular eukaryotes. These interactions are as varied and numerous as the number of associations that have been documented. This chapter reveals only the "tip of the iceberg", and much more can be found in the literature or through the websites listed below.

 

Center for Biological Informatics: http://www.nbii.gov/issues/biodiversity/

 

International Center for Genetic Engineering and Biotechnology: http://www.icgeb.trieste.it/

 

Global Biodiversity Information Facility: http://www.gbif.org

 

USDA Integrated Taxonomic System: http://www.itis.usda.gov/

 

Agriculture Research Service Culture Collection: http://nrrl.ncaur.usda.gov/


1983 - Transatlantic dust and coral reefs - NASA interactive video

2000 - Transatlantic dust and coral reefs - NASA interactive video

Transatlantic dust and toxic algae - NASA interactive video

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Chapter 11

Microbial diversity and function is at the center of global environmental change and at the forefront of strategies to mitigate adverse effects of environmental change on human welfare. There are now numerous research programs and websites dedicated to tracking global environmental change events. Too few of them recognize the importance of microbial activity. Hopefully, this book will contribute to change current attitudes. Nevertheless, the websites and interactive programs listed below will provide additional information and opportunities to further pursue the linkages between microbial diversity and human and ecological health and welfare.

 

World Data Center on Microorganisms: http://wdcm.nig.ac.jp

 

Ozone Hole Interactive Video from NASA

 

Global Temperature Interactive Video from NASA

 

Global Water Cycle - NASA interactive video

 

International Human Dimensions Programme on Global Environmental Change: http://www.ihdp.uni-bonn.de/

 

National Institute for Global Environmental Change: http://nigec.ucdavis.edu/

 

Global Environmental Change (UK) http://www.gecko.ac.uk/

 

The Center for International Earth Science Information Network (CIESIN) at Columbia University : http://www.ciesin.org/index.html

 

Socioeconomic Data and Applications Center : http://sedac.ciesin.columbia.edu/

 

Global Environmental Change and Health at Johns Hopkins University : http://www.pbs.org/journeytoplanetearth/johnshopkins/

 

Global Environmental Change and Human Security: http://www.gechs.org/

 

Global Environmental Change and Health at the World Health Organization: http://www.who.int/globalchange/en/

 

U.S. Environmental Protection Agency Website on Global Warming: http://yosemite.epa.gov/oar/globalwarming.nsf/content/index.html

 

Global Environmental Change and Food Systems: http://www.gecafs.org/

 

Global Environment Facility: http://www.gefweb.org/

 

United Nations Environment Program: http://www.grida.no/climate/

 

Center for Health and the Global Environment at Harvard University : http://www.med.harvard.edu/chge/resources.html

 

International Institute for Applied System Analysis: http://www.iiasa.ac.at/

 

 

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