Extreme Limits of Microbial Life
Mostafa S. ElShahed, PhD
Last updated, Oct 7, 2007
Contents:
What are
the limits of microbial life?
So how many species of microorganisms are there?
How do you describe a new species?
How do you give a new microorganism its name?
How did we know that there are large numbers of “novel”
microorganisms in nature?
Where can we find novel microorganisms?
Why are there so many uncultured microorganisms?
Beside resources, why can’t we culture many groups of these
novel microorganisms?
What are the future trends in microbial diversity studies?
So what research am I currently working on?
What are the limits of microbial life?
Bacteria can live virtually everywhere. You will be surprised by the abilities of bacteria to survive and grow in extremely hostile environments (hostile or extreme by our measures, but for them it is just Home). The range of temperature supporting microbial growth ranges from the frozen Arctic and Antarctic lakes where temperature dips to –10oC, and microorganisms, among other things, produce antifreeze proteins and store them in the cell to prevent their cytoplasm from freezing (see http://www.thesecondlayer.com/marine/psychrophiles.html for a cool website), to undersea volcanoes and hydrothermal vents were temperature goes well above 100oC (Pressure keeps water from boiling in these places). A recent microorganism was isolated by a friend and colleague (Dr. Kazem Kashefi at Michigan State University) that can grow at 121oC overnight. This is the temperature we use to autoclave glassware!!! (http://www.geobacter.org/research/lexen.html)
Bacteria can grow in extremely salty conditions as well. Microorganisms can grow in a saturated (33%) NaCl solution. They can even be revived from salt crystals thousands of years old. Microorganisms can grow at the bottom of the Ocean, where pressure is unbelievably high (barophilic microorganisms). Finally microorganisms can grow in a wide range of pHs. Some organisms love to bath in acid (e.g. Genus Picrophilus grows at a pH 0.6) while alkaliphilic microorganisms have an upper pH limit of 11.
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Extremophiles: A. Strain 121 that grows at 121oC.
B. Picrophilus torridus that grows at pH of 0.6, and Halosarcina palida grows
at 30% NaCl concentration. Courtesy of http://en.wikipedia.org/wiki/Strain_121,
http://www.gwdg.de/~wliebl, and
my laboratory archives |
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Also, many microbiology students think that microorganisms
are present only in aerobic environments where air is available for respiration
(O2 reduction to H2O), but NO!! In absence of oxygen,
many microorganisms can grow by respiring other compounds such as sulfate,
nitrate, and Fe3+ to sulfide, nitrogen, and Fe3+. Other
microorganisms (fermentative microorganisms) use part of their substrate as a
reducing agent producing fermentation end products.
So how many species of microorganisms
are there?
It depends on how you look at it. If you mean how many species do scientists have in their laboratories and can grow and use in experiments then the number as of September 2007 is 8,394 species. If you mean how many species are present in nature, then the answer is at least 5 million, probably even more.
How do you describe a new species?
Like other living creatures, bacteria are described in a scientific genus and species name. For a microorganism to be OFFICIALLY recognized as a novel microbial species, a scientist must isolate it by itself in a pure culture, conduct experiments to show that it is different from its closest relatives previously described, send the culture to at least two official culture collections (so it would be available to other scientists), identify the DNA sequence of key genes in this microorganism and compare it to other microorganisms, and publish his findings in a scientific Journal (preferably in the International Journal of Systematic and Evolutionary Microbiology).
How do you give a new microorganism its
name?
There are guidelines for this process. For a new bacterium that belongs to a new genus, you need to come up with the genus name and a species name. In case you are wondering, YOU CANNOT NAME A MICROORGANISM AFTER YOURSELF! However, you could name it after a famous (preferably retired or dead) scientist who spent his or her life working on related microorganisms. You are also discouraged to name it after your hometown, village, country, or name it after a geographical location (e.g. a river or lake) where you isolated it. This is because bacteria, unlike most animals, do no appear to be restricted to a specific geographical habitat. A microorganism that grows in the Nile sediments can grow and will probably be present in sediments with similar characteristics (e.g. temperature, pH, etc.) in South America.
Names are usually in Latin (although some have used old
Greek, German, and other languages), and should describe the characteristics of
a microorganism. For example we recently isolated a halophilic microorganism
that is well adapted to grow at different salt levels so we gave it the genus
name Haladaptatus (meaning: a halophilic
microorganism that can adapt). Unlike its relatives, it can survive even at
very low salt concentrations so we gave it the species name Paucihalophilus
(Pauci: little, halophilus: salt loving.
Meaning that it likes little salt).
A Picture of Haladaptatus Paucihalophilus is below:
However, it is now absolutely evident that the 8,394 microorganisms that are present in culture collections represent a very tiny fraction of the microorganisms present in nature. Microorganisms that are not yet available in pure cultures are called “novel”, “uncultured”, or “ not yet cultured”.
How did we know that there are large
numbers of “novel” microorganisms in nature?
There are now procedures that identify the presence of microorganism in a specific place without the need to culture them. These methods are thus called “culture-independent”. In these methods, you do not see the microorganisms but only observe evidence of their existence (like current methods used to identify the presence of planets outside our solar system). The most commonly used method is called “16S rRNA gene analysis” and is devised by a great scientist that I had the chance to train in his laboratory back in 2001. His Name is Dr. Norman Pace at the University of Colorado.
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Dr. Norman Pace http://pacelab.colorado.edu/PI_NormPace_new.html |
Every microorganism has a genome containing a few thousand different genes. This DNA blueprint differs between different microorganisms (e.g. those who grow respiring sulfate will have some genes that those who grow respiring oxygen don’t have). However, few genes that are essential for common cellular processes are present in all microorganisms. Since all microorganisms must have ribosomes for protein synthesis, then all microorganisms should have the genes coding for the synthesis of ribosomes. However, the DNA sequence of these ribosomal genes differs between different species. By sequencing the DNA of the 16S rRNA gene (the gene that codes for the synthesis of the small ribosomal subunit in bacteria) of a new microorganism and analyzing the sequence, one could identify what group (e.g. genus) to which this microorganism belongs.
Now imagine doing that not for a pure culture, but for a gram of soil that contains thousands of different species and analyze the DNA sequences of the many different microorganisms present in soil. This way, without culturing, you can identify what kinds of microorganisms are present in soil and how similar or different these microorganisms are from pure cultures available in culture collections (i.e. whether some of these microorganisms are novel or not). Remember, this technique just tells you who is there, but not gives you a pure culture of the microorganism.
The application of this technique has caused a revolution in our understanding of microbial diversity. It turned out that almost in all environments tested, there are way many novel groups of microorganisms. The level of difference between the 16S rRNA gene sequence of these microorganisms and those we have in pure culture suggests that many of these novel microorganisms not only belong to novel species and genera (pl. of genus), but to novel classes, families or even phyla.
Bacteria are classified into phyla, classes, orders, families, genera, and species. Before 1987 we thought that only 12 bacteria phyla are present in nature. Now scientists have collectively identified at least 103 bacteria phyla, many of which are identified by the culture-independent analysis described above and have no pure culture representatives (these are called candidate phyla). I had the honor to identify and name 2 of them and am currently working on identifying 5 more phyla
Where can we find novel microorganisms?
Again, you would think that these novel microorganisms are
hiding in hard to reach, less accessible environments. The answer is NO!!!
Novel microorganisms are present everywhere, from soil to wastewater to river
sediments, to—yes—extreme environments such as hydrothermal vents in the bottom
of the Ocean. In short it is often not necessary to go far to find a new
bacterium.
Why are there so many uncultured
microorganisms?
The presence of these novel, yet uncultured microorganisms
in all environment is due to several reasons: First the adaptability of
microorganisms to grow everywhere provides for an unlimited habitats for microorganisms,
novel or not. Second the large and complex nature of microbial communities. For
example, a gram of soil could contain 10,000 to 20,000 different microbial
species. If you remember, there is only 8,394 different microbial species
officially described and given a species name. If you realize that the
microbial communities differ between different kinds of soil, and that soil is
only one of thousand different habitats that microorganisms can live in, you
can start to gauge the level of natural diversity within the microbial world.
Finally, it is important to remember that to describe a new
species, considerable effort, money, and time are needed (one year on average
in my laboratory). On the other hand a single study using culture-independent
analysis generates a large number of 16S rRNA gene sequences each representing
a microorganism (novel or not). A recent study we conducted generated 13,000
sequences from a single gram of soil. The study and analysis took us one year,
the same time needed for identifying a single microorganism. So clearly, the
pace of describing new species is much faster than the pace of discovery of
uncultured microorganisms, resulting in the accumulation of a lot of data of
uncultured microorganisms.
Also, unfortunately, the field of taxonomy and description
of new microbial species are not very popular among microbiologists nowadays:
Many scientists prefer to research other areas of microbiology rather than
spend their career giving names to bacteria.
Beside resources, why can’t we culture
many groups of these novel microorganisms?
Many reasons exist. Lack of resources and scientists
interested in isolating new microorganisms is only one of them. Another
important reason is that our lack of knowledge regarding the preferred mode of
growth of many of these microorganisms is preventing us culturing them.
Therefore, in spite of being present in a common and accessible environment,
they still cannot be cultured. Remember, you cannot culture a microorganism
unless you know what food and conditions it prefers (e.g. whether it likes to
grow on nutrient agar, sugar, amino acids, whether it likes aerobic,
microaerophlic, or anaerobic conditions, or whether it is phototrophic,
heterotrophic, or autotrophic etc.).
Finally, when you grow these microorganisms is the
laboratory, you use rich media that have no resemblance to the environment from
which these cultures live. Many of these environments are very oligotrophic
(i.e. poor in nutrients) environments, and these microorganisms have adapted
themselves on living at these low nutrient levels. When you try to grow them on
a rich media, their metabolic pathways become overwhelmed and they can produce
too much by-products that can accumulate to toxic levels. So remember: TOO MUCH
FOOD CAN KILL SOME MICROORGANISMS.
What are the future trends in
microbial diversity studies?
This is a very exciting time to be studying microbial
diversity. We now realize that there are so many things that we do not know and
are starting to think of new ways to tackle it. One of the new approaches is
metagenomics: Similar to sequencing the genome of a microorganism, you try to
sequence DNA derived from a complex community. By identifying the genomes or
pieces of the genomes that belong to a novel group of microorganism, you can
start to understand how they live and what do they do in the environment.
Another interesting area of research is to use new ways to isolate
microorganisms. For example, you can try to grow them in simulated natural
environments or new types of food. You can also use sophisticated technologies
to try to capture single cell from these uncultured groups of microorganism and
try to grow it and propagate it to a pure culture.
So what research am I currently working
on?
Generally, we work on isolation, characterization and naming
of microorganisms. We also do a lot of research using “culture-independent 16S
rRNA gene analysis” to discover novel groups of microorganisms in this
environment, as well as metagenomic analysis to study the genomes of novel
groups of microorganisms.
I currently do my research in two environments. One of them
(Zodletone spring in Oklahoma) is kind of extreme because parts of the spring
have no oxygen at all, so only anaerobic microorganisms can grow in. Also,
other parts of Zodletone spring have high salt concentrations so many different
groups of halophiles (salt loving microorganisms) are present in this
environment. Read about it at:
http://faculty-staff.ou.edu/K/Lee.R.Krumholz-1/nsfzodletonepage03.html
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Mostafa Elshahed sampling at Zodletone spring, Oklahoma |
Also, we look at the microorganisms present in soil. We
recently identified 5 new bacterial phyla that are present in Oklahoma soil,
proving, like I said earlier, that novel groups of microorganisms are present
in extreme as well as non-extreme environments.