Introduction

What is Microbial Diversity?

“Diverse” is defined as:

differing from one another, or composed of distinct or unlike elements or qualities

So in what ways can we consider microbes to be diverse or differing from one another or
composed of distinct or unlike elements or qualities?

Diversity can be considered in many ways and also relative to the development of microbiology

Diversity Index Example

Morphology Shape Rods, cocci, spirals, filaments, squares, stars, and most irregular forms
Size From less than 1µm to greater than 500 µm
Structure Procaryote Gram positive form, Gram negative form, Archae form
External Features Flagella, pili, stalks, capsules, sheaths
Internal Features Spores, mesosomes, gas vesicles, crystals
Ecological Habitat Freshwater, Marine, soil, deep subsurface
Tolerance Psychrophile, mesophile, thermophile, pH conditions
Behavioral Motility and taxis Gliding, flagella
Symbiosis Phototaxis, aerotaxis, chemotaxis
Root nodules
Metabolic Source of carbon Chemoautotrophs (carbon from CO2, energy from light)
and energy Chemoheterotrophs (carbon and energy from organic molecules)
Photoautotrophs (carbon from CO2 molecules, energy from light)
Photoheterotrophs (carbon from organic molecules, energy from light)
Genetic Similarity among genes, evolutionary linkages
(A similar summary was constructed by J. Brown from the North Carolina State University. The web site for this summary is
http://www.mbio.ncsu.edu/JWB/MB409/home.html)

Traditionally, diversity of the microbes focused on Morphology, Structure, and Metabolism with
lesser emphasis on Ecological , Behavioral, and Genetic aspects.
• Review reasons for this.

Today, diversity focuses on three areas: Ecological, Metabolic, and Genetic.

• Review reasons for this and the consequences….what will the future of microbiology look
like (The following is edited from http://www.asmusa.org/pasrc/microbia.htm)
Microbial Diversity Research Priorities
A Working Document for Multi-Agency Consideration

The Unseen National Resource:

Microbial diversity is an unseen national resource that deserves greater attention. Too small to be
seen no longer means too small to be studied or valued. Microbial diversity encompasses the
spectrum of variability among all types of microorganisms (bacteria, fungi, viruses and many
more) in the natural world and as altered by human intervention.
Microorganisms are essential for the earth to function. They play many roles both on land and in
water, including being the first to colonize and ameliorate effects of naturally occurring and
man-made disturbed environments. The nation has committed to protecting the environment, and
has included ecological diversity in this goal (National Science and Technology Council, 1994).
Because microorganisms are small, they are least known, and this gap in knowledge is
particularly apparent for bacteria and other procaryotic organisms. Current evidence suggests
there exists perhaps 300,000 to 1 million species of procaryotes on earth yet only 3,100 bacteria
are described in Bergey's Manual. Learning more about these microorganisms will be of value
for the following reasons:

• microorganisms are important sources of knowledge about the strategies and limits of life,

• microorganisms are of critical importance to the sustainability of life on our planet,

• the untapped diversity of microorganisms is a resource for new genes and organisms of
value to biotechnology,

• diversity patterns of microorganisms can be used for monitoring and predicting

environmental change,

• microorganisms play a role in conservation and restoration biology of higher organisms, and

• microbial communities are excellent models for understanding biological interactions and
evolutionary history.

RECOMMENDATIONS FOR MICROBIAL DIVERSITY RESEARCH

National Institutes of Health/Department of Energy/National Science Foundation

Microbial Genome Studies
Determination of the course of evolution, e.g., the way in which elements of genes
developed; the genetic basis of diversity; the mechanism by which microbial metabolic
pathways overlap for different organisms; and access to the large and as yet untapped
gene pool resident in the microbial world.
Definition of the entire repertoire of organisms in specialized niches and, ultimately, the
mechanisms by which they interact in the larger "organism," i.e., ecology, and
Analysis of organisms responsible for bioremediation and geochemical cycles of the
planet; these organisms may prove useful for special purposes in the future, possibly for
global environmental protection or food production.
To determine the course of evolution of pathogens, and the way in which metabolism
overlaps for different pathogens;
To define the repertoire of natural commensal microbes as well as their pathogenic
relatives, and ultimately the way they interact in the ecology of health and disease in the
human body; and
To analyze the capacities of pathogens to interact with environmental conditions and host
genes at the level of specific virulence mechanisms and recognition signals and of
metabolic routes.
Culture Collections
Integral to studies in microbial genome research is the accumulation, analysis and
communication of information about genomes, and the collection, definition and preservation of
genetic stocks allowing comparison of genetic diversity to be made and subsequently utilized in
applied research.
National Science Foundation/Department of the Interior
Training of scientists with expertise in phylogeny, taxonomy, and physiology of
environmental microorganisms so that diversity can be more efficiently recognized and
characterized. The nation has very little remaining expertise in the identification and
characterization of microbial groups.
Create, maintain, and integrate databases of microbial information including molecular,
phenotypic, chemical, taxonomic, metabolic, and ecological information. Such databases
are essential if new biodiversity discoveries are to be efficiently compared to what is
already known. This may require support of centers, systems or laboratories, whose
function is to characterize new organisms rapidly, collect and curate diverse isolates and
maintain and disseminate data on them.
Support research on new methods and strategies for cultivation and isolation of
microorganisms, and for rapid characterization of the projected large number of
undiscovered organisms.
Support research that will identify sites of new diversity. This will lead to an
understanding of the pattern of microbial diversity on earth and of the ecological and
evolutionary mechanisms that could have contributed to localized diversity.
Foster Multidisciplinary involvement in microbial biodiversity research. Scientists with
expertise in molecular biology, computer science, chemistry, device engineering, optical
sciences, and macroecology are expected to be particularly important contributors.
Culture collections are key repositories of biodiversity as microbiology moves into an
ever more powerful era, integrating genome science with ecology, systematics, molecular
evolution and microbial chemistry. Innovative research in information management
(databases, information processing technology, information networks, etc.), rapid
identification techniques, and large volume handling (strains, vector, genetic material,
etc.), will be needed.
Department of Agriculture
Microbial Biocontrol A program, is needed to support research in microorganisms that
promote plant growth by interfering with (controlling) pathogens and pests. For most
weeds, insect pests, nematodes and microbial pathogens of plants, alternative control
measures are either not known, not yet developed, or are less effective or not
economically feasible than are currently available pesticides. There is a compelling need
for discovery and identification of microbial biocontrol agents, an assessment of their
efficacy, development of delivery systems, and policy analyses and changes to encourage
their use in public and private sectors. The studies collectively would include new
developments in molecular ecology in natural and managed environments, where it is
now possible to identify and track specific genes or traits fulfilling a particular function
without necessarily isolating or culturing source microorganisms. Additionally, studies
are needed to discover and classify diverse insect as well as plant viruses. These could be
useful respectively, as natural insecticides and in weed-control, cutting down on the
release of organo-phosphates into the environment.
Microbial Genome Studies A program is needed to study the molecular nature of
genomes of at least representative microorganisms in order to understand and manage
pathogenesis, biocontrol, and bioremediation (e.g. nitrate pollution), develop rapid
detection and monitoring techniques, and identify candidate genes for transfer of
desirable properties. Research should also focus on microbial diversity related to
emerging pathogens, which are becoming increasingly important to plant health, food
security and food safety. Emphasis should be on increased understanding of interactions
between agriculturally and environmentally important microbes and higher organisms,
for example, crop, forest and urban systems.
Microbial Collections. These collections, although they may represent limited diversity,
are critical as reference cultures for comparative analyses for both basic science and
commerce. Individual organisms in such collections are potentially useful and may also
provide a source of a useful gene sequence or product. Also, collections are a repository
for cultures used in published literature or as commercial products (e.g. patent deposits).
Environmental Protection Agency
Microorganisms are sensitive indicators of environmental quality. Their responsiveness to
environmental change and their rapid reproductive capacities result in population changes that
alter relative numbers and types of microorganisms; thus indices of microbial diversity are a
sensitive measure for the environmental state of a given habitat or ecosystem. By determining
the diversity of microorganisms at selected sites using conventional and modern molecular
approaches the agency can establish baselines against which changes in environmental quality
can be measured. Microbial diversity measurement can be a sensitive and suitable index of
environmental status and trends. Measurement of microbial diversity could be predictive of
changes in populations that have resulted in serious threats to human, plant and animal health
such as the outbreak of Cryptosporidium infections in Milwaukee. They also would permit
detection of impact from chemical pollution and recovery of impacted biological communities.
Department of Defense
The U.S. Department of Defense has two reasons to initiate and expand programs in microbial
diversity. The first is an extension of health programs aimed at protecting American forces,
including defending against potential uses of biological warfare. Since diverse microorganisms
can cause disease and could potentially be used as biological weapons, establishing an inventory
of organisms and their distributions can aid in protecting troops against infectious diseases.
Knowing what is likely to be present can lead to rapid diagnosis and treatment as well. The
second reason for interest in microbial diversity by the Department of Defense concerns the
numerous sites that the military has polluted and must now clean up and the various ordinances
that must be destroyed. Biodegradation and bioremediation are potentially attractive means of
achieving cleanup and destructions of unwanted materials. Given the specific compounds, e.g.
nitroaromatics, microorganisms will be needed if biodegradation is employed.
Department of Commerce
To support microbial diversity research and education in oceanographic, shellfish and
aquaculture industries, it is recommended that the Department of Commerce through the
National Oceanic and Atmospheric Administration and associated agencies, e.g. Food and Drug
Administration, undertake the classification and study of diverse aquatic plants: microbe
interactions, as well as virus-host relationships as they exist in natural environments. Specific
examples of this involve blue-green algae and cyanophages, as well as Vibrio species including
Vibrio vulnificus and their resident bacteriophages. Recent dangers associated with V. vulnificus
contaminated oysters have had a serious negative impact on the national shellfish industry, while
algal blooms have been associated with massive fish kills in aquaculture ponds.

So about this course……

OK…..so great, all of this is important and Rah Rah….I wanna be a microbiologist because the
future for the science looks really cool and I might get a job and actually get out of debt (yeah,
right.)…..but how does all of this crap fit into this course?

This course is an extension of your introductory microbiology education. Your introductory

course(s) focused much attention on organisms that are common in your environment, health
related, well studied, or simply easy to deal with in the lab. Collectively, they represent a very
small fraction of the world that is Microbiology. In this course we want to focus on introducing
you to the organisms that are also common in your environment but may not be so easy to deal
with in the lab, not so easy to grow, and may have little clinical importance yet play significant
roles in shaping our environment.

We will take a broad taxonomic approach when looking at organisms…we will discuss the
metabolic features, the ecology, and the behavior of the groups. In many ways this will be a
traditional approach to examining these organisms but we will recognize more modern (genetic
based) approaches where organisms may be looked at by grouping them according to
evolutionary similarity. In many cases, but not all, modern molecular approaches to grouping of
organisms confirms the more traditional approaches and in others, modern approaches to
grouping organisms remain at odds with traditional approaches because genetic phylogeny may
not reflect physiological similarity.