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2 • The Microbial World
INTRODUCTION
Microbes
For most of Earth’s history, life consisted solely of microscopic organisms and in many respects these microbes still dominate the Earth today1. Microbes include bacteria, archaea, fungi, protists, green algae, and plankton. Viruses are also sometimes considered to be microbes. The ~5 X 1030 microorganisms that inhabit our planet play an important role in the cycling of carbon, oxygen, nitrogen, phosphorus, sulfur and other elements which are essential to life2. Two important parts of the cycling process are called assimilation and decomposition. During assimilation, microbes convert inorganic elements into forms that are useable by other microbes, plants, and animals. During decomposition, microbes break down organic matter and recycle it so it can once again be made available to other organisms. Photosynthetic microorganisms were responsible for initially pumping oxygen into the atmosphere and today these microbes carry out almost 50% of all the photosynthesis on our planet3. Microbes can also change the weather and affect climate by sequestering CO2 and releasing small particles that aid cloud formation.
Microbes are easily the most abundant and diverse life form on the planet4. Although microbes cannot be seen with the unaided eye, there are so many of them that their combined weight is estimated to be more than all other organisms combined. Microbes can be found almost everywhere on the planet including soil, air, and water. They can be found in the upper reaches of our atmosphere and 6 km below the Earth’s surface. They live everywhere macroscopic organisms are present and they can survive extreme temperatures, pressures, and pH levels that other organisms cannot tolerate. They can be found growing in extremely cold places such as Antarctica and extremely hot places such as the volcanic pools at Yellowstone National Park and deep sea thermal vents where temperatures can reach 350˚C. Microbes are also found on and within larger organisms including humans. The number of microbes that live on and inside of the human body (~1014) exceeds the total number of human cells (~1013) by a factor of ten5,6. Microbes that live on or in humans can aid digestion, make vitamin K, help develop the immune system, fight off disease-causing microbes and detoxify harmful chemicals2. Studying microbes in the human gut will likely lead to new ways to diagnose, treat, and prevent disease7.
Human industries including agriculture, medicine, biotechnology and the food industry have greatly benefited from the use of microbes. In agriculture, certain crops are seeded with specific strains of nitrogen-fixing bacteria to increase yields. Additionally, a microbe that causes plant disease, Agrobacterium tumefaciens, has been used to create genetically modified crops that are more drought and pest resistant and have higher yields. In medicine, hundreds of drugs that are available today were originally derived from microbial sources and many of these drugs (especially antibiotics) are mass-produced for human use by microbes. Medical microbes are used to produce insulin, interferon, human growth hormone, vaccines and many other useful compounds. Biotechnology has used microbes to generate important chemicals, enzymes, and alternative fuels such as hydrogen, methane, and butanol4. Microbes are also used in bioremediation projects designed to clean up oil spills, gasoline leaks, sewage, and industrial discharges4. In the food industry, microbes are instrumental in making bread, cheese, yogurt, wine, and beer. Without microbes you could not have something as simple as a roast beef sandwich. This is because microbes produce the cheese, make the vinegar for the pickles, and help the bread to rise. In addition, microbes contribute to the beef by enabling cows to digest grass and other plant matter they depend on to survive.
Not all microbes are beneficial however. A minority of microbes are pathogens that cause a wide range of ailments, which effect humans, animals, and crops. This has led some to incorrectly fear all microbes. Such fears have led to the development and use of antimicrobial soaps and cleaners and the excessive use of antibiotics. Both of these practices select for resistant microbes and facilitate the evolution and spread of resistance genes. Excessive use of antimicrobials and antibiotics may counter-intuitively speed up the development of resistant pathogens and lead to the development of ‘superbugs’ for which there is no treatment. Many ‘superbugs’ already exist including the SMS-3-5 strain of E. coli that is tolerant of or resistant to high concentrations of 32 different antibiotics8!
For more information on microbes please see:
Intimate Strangers: Unseen Life on Earth Video
http://www.microbeworld.org/index.php?Itemid=194&id=259&option=com_content&view=article
Understanding Microbial Life
http://www.lifeworksfoundation.com/news/microbe-ecology-film.php
Soil Microbes
www.agron.iastate.edu/~loynachan/mov/
Size and abundance of microorganisms
www.pmbio.icbm.de/mikrobiologischer-garten/eng/index.php3
Microbes in the News
www.microbeworld.org
MANGA/ANIME Microbes
Search microbe theater on microbeworld.org or
www.youtube.com/show/moyashimon?s=1
http://en.wikipedia.org/wiki/Moyashimon
Online Textbook of Bacteriology
http://textbookofbacteriology.net/index.html
Metagenomics
The majority of life’s diversity lies in the microbial world. Historically, scientists have studied microbes by collecting samples from the environment and growing them in nutrient rich media. They would then examine cultures of specific organisms in isolation. Unfortunately, <1% of all microorganisms on Earth can be cultivated in this manner4,9. Only about 5,000 species of bacteria have been classified but scientists think there are probably several million species out there. Many of these unculturable microbes depend on each other to survive and thus cannot live in isolation. For these reasons, existing genomics data on microorganisms has historically been highly biased to organisms that we can easily culture. While much has been learned using this paradigm for studying the microbial world, it has left us with an incredibly incomplete understanding of microbial species and the communities in which they live.
Fast, cheap sequencing technologies and the ability to obtain DNA samples from a variety of microbial habitats has given rise to the new science of metagenomics. Metagenomics is the study of all the DNA in a given environmental sample (also known as the metagenome). Metagenomics has given rise to metatranscriptomics and metaproteomics that examine all the RNA transcripts and proteins present, respectively, in an environmental sample. Metagenomics can indicate what an organism is capable of doing (i.e. what genes it has) while metatranscriptomics and metaproteomics will tell us what the organism is actually doing at any given time (i.e. what RNAs and proteins are being expressed). Importantly, these techniques do not require microbes to be cultured, so scientists can get a better picture of the microbial diversity of an area while simultaneously studying thousands or millions of species in their natural habitat. The ultimate goal is to understand how different members of the microbial community can interact, change, and perform complex functions4. Metagenomics has been used to study the microbes present in the ocean, soils, sewage, coral reefs, whale carcasses, thermal vents, hot springs, and microbial communities associated with humans, termites, aphids, and worms.
The National Research Council has recently concluded that the emerging field of metagenomics promises to revolutionize research in microbiology and will likely contribute to research in nearly all biological fields4,10. Metagenomics will likely yield many practical applications in life sciences, earth sciences, medicine, alternative energy, environmental remediation, biotechnology, agriculture, biodefense, and microbial forensics11.
“We are in the midst of the fastest growing revolution in molecular biology, perhaps in all of life science, and it only seems to be accelerating” -JC Wooley1.
Minnesota Mississippi Metagenomics Project
“The Mississippi is well worth reading about. It is not a commonplace river, but on the contrary is in all ways remarkable.” –from Life on the Mississippi by Mark Twain
Out of all of the rivers on Earth, the Mississippi is one of the largest and most important. It serves as a transportation system and provides drinking water to >50 cities (~18 million people). It also is an important habitat for fish and wildlife, a source of recreation for millions of people, and an important source of nutrients for the Gulf of Mexico. Despite the importance of the river, we know little about its most common inhabitants: the Mississippi microbes.
The College of Biological Sciences was recently awarded a grant to study the metagenome of the Mississippi river in Minnesota, putting the University of Minnesota on the forefront of metagenomics research. The goal of the Minnesota Mississippi Metagenome Project (M3P) is to understand the function and diversity of microbial life in the Mississippi River and how humans impact it. The overarching hypothesis is that humans do impact the structure and function of the microbial community and that this impact is magnified downstream as the Mississippi accumulates water and pollutants from its tributaries and confluences. The M3P project seeks to understand how the microbial community changes with time (e.g. over days, years and seasons), space (e.g. different locations and depths), and environmental conditions such as water pH and temperature. It also seeks to determine how the input of chemical pollutants, pesticides, pharmaceuticals, and nutrients from run-off or sewage affects microbial diversity and function. Furthermore, it seeks to understand the levels and the source of pathogens and fecal bacteria in the river so that sources of these organisms can be identified and corrected. In addition to understanding what microbes live in the river and how they are affected by human activity, another goal of this project is to screen this resource for interesting biological activities such as cellulose-degrading enzymes important for biofuel production or proteins involved in antibiotic resistance.
Currently 40 L (~10 gallons) water samples are collected from 10 or more sites once per year so that the resulting metagenomes can be compared. The water samples are filtered to obtain organisms 0.45-5 µm in size. Metadata (“data about the data”) including location, time, season, current speed, temperature, pH, and levels of pollutants is also collected. The metagenomics data obtained will be used to educate the public, and help guide regulations and policies to protect this important resource.
The M3P project has produced and will continue to produce a huge abundance of data that will take decades to fully analyze. Because of this, there are opportunities for students to get involved and learn about cutting-edge research techniques being used to explore the microbial world. You could potentially be the first person ever to discover an important fact about the microbes in the Mississippi. For those interested in continuing exciting hands-on research in the new field of metagenomics, please consider taking one of the two metagenomics courses available: Biol 4950 Exploring Mississippi Metagenomics and Biol 4850 Introduction to Metagenomics. Ask your professor about who you can contact to contribute to this project while getting real lab experience.
Figure 1. M3P Project sampling sites. Pristine water samples from Lake Itasca will be compared to downstream water samples that are potentially impacted by human activities. Samples are also taken before and after confluences with major tributaries to understand their impact on the microbial population of the Mississippi river.
For more information please see:
http://www.cbs.umn.edu/main/news/inthefield/m3p.shtml
Where do river microbes come from?
Asking how microbes get into the Mississippi river is a bit like asking how rain-water gets there. Microbes are pretty much everywhere so they enter the river from a variety of sources. Many microbes enter the Mississippi at its headwaters near Lake Itasca. Other microbes flow in from the tributaries such as the Minnesota River, the Zumbro River, and the St. Croix. During rainstorms, microbes wash into the river from the surrounding landscapes along the length of the Mississippi. Humans also contribute to the microbes which flow into the Mississippi; run-off from cattle and swine ranches and (treated) nutrient rich sewage from sewage treatment plants enter the Mississippi river and alter the microbial landscape.
Microbial populations in aquatic environments are known to fluctuate temporally and spatially due to varied input sources12. Because the river is constantly flowing, free-swimming bacteria are inevitably swept along with the flow of the river towards the Gulf of Mexico. Some bacteria are more stationary by avoiding regions with strong currents or by anchoring themselves to rocks, fallen logs, or the river bottom. No one really knows how much the microbial populations change over time in the Mississippi. Metagenomics can help answer questions such as: Does the number and abundance of species remain fairly constant or do they change with the season? How do current, depth, temperature, light, and chemicals such as pollutants affect microbial ecosystems? How does human activity alter microbial populations? These are important questions as changes in the microbial populations may affect larger organisms such as clams, crayfish, insects, fish, birds, mammals, and people.
Metagenomics also has an important role to play in medicine and public health. Scientists are particularly interested in elucidating the sources and abundance of potentially harmful organisms such as E. coli and Salmonella that can sometimes cause human infections. Antibiotics are the prime line of defense against bacterial infections, but unfortunately more and more microbes are evolving resistance to these drugs largely due to the widespread use of antibiotics in medicine (for humans and pets) and in animal feed for cows, pigs, and poultry. Remember that all of these organisms have populations of microbes living in their guts. When these microbe populations are repeatedly exposed to antibiotics, those in the population that already are resistant will be favored (natural selection) and the population’s genetic makeup will change with time (evolution). Many resistant microbes are not harmful to their host, but it becomes a problem when they transfer their resistance genes to organisms that cause disease. Because the feces of these organisms contain intestinal microbes, and because animal waste frequently runs-off into rivers, there is an increasing concern that resistant microbes are being released into waterways humans depend on for drinking water, transportation, and recreation. Metagenomics and microbial source-tracking may be able to identify the source of some river microbes so that problems could be corrected before it is too late. This type of analysis can provide information about where antibiotic resistant bacteria may have come from. For example, you may find that organisms located at a specific sample site came from cattle, so you could compare samples from nearby cattle ranches with your sample to identify the source of contamination.
Classification of Microbes and other Organisms
You may think that by now, most of the species on Earth have been discovered and described. Surprisingly, recent estimates suggest that it would take an army of 303,000 taxonomists 1,200 years and $364 billion dollars to characterize Earth’s remaining undiscovered species, and that doesn’t even include microbes13! To date there are about 1.5 million organisms have been named and described and scientists speculate that millions more remain to be discovered and classified.