ENVIRONMENTAL MICROBIOLOGY

BIOL/CEE/CSES/ENSC 4164


WEEKLY CURRENT EVENTS FOR 2010 - WEEKS 1 AND 2

Antarctica
Did you know that Antarctica is almost 1.5 times larger than the U.S. and, while only a small portion of the land is not ice covered, the ice over the landmass averages almost two miles thick. This represents 90% of the ice and 70% of the freshwater on the planet. Guess what?

The ice is melting, faster than predicted just a few years ago. This is not good news.

As glaciers and ice worldwide are melting, there is a rush in the scientific community to intensively sample the ice as glaciers can be thousands to millions of years old and they contain gasses, dust, and pollen that can tell a lot about conditions on the planet when the ice was formed. In addition, the melting ice contains ANCIENT MICROBES that were also trapped when the ice was formed. So far, microbes from 100,000 years old to eight million years old have been recovered from melting ice around the world. What if one of these was a human pathogen and modern humankind had no immunity against it? Sounds like a good topic for a SciFi channel movie to me.

So what types of microbes have been recovered from frozen ice? Lots of different types of microbes have been recovered, and in much larger numbers than expected. A whole new world of microbes is being released around the globe by melting ice. Let's hope they're friendly.

Since the topic for Weeks 1 and 2 deals with unusual habitats, it is only fitting to compliment it with a selection of UNUSUAL MICROBES, such as microbes that are square, are unusually large or small, or give birth to live young, or eat other bacteria, are magnetic, or are multicellular. The microbial world is much more diverse than you might think.

Here is a new take on microbes. Scientists with the Institute of Tibetan Plateau Research (ITP), Chinese Academy of Sciences, and coworkers recently reported that MICROBES deposited in ice and snow might tell how our climate has been changing. The discovery might bring about a new indicator for climate change, which is by nature different from all previous physical or chemical benchmarks.

There are as many signs of global warming in the Arctic as there are in the Antarctic, and many Arctic signs are more dramatic. The ice in the Arctic is meting faster than anyone predicted and the consequences of this are very serious. Arctic sea ice may well have reached its lowest volumes ever, as summer ICE COVERAGE of the Arctic Sea in 2008 was close to last year's (2007) record lows, with thinner ice overall.

Lastly, how does global warming actually impact you in the near future? Here's the answer: WARS caused by climate change. The prospect of global wars driven by climate change is not something often discussed publicly by our political leaders. But according to one of America's top military analysts, governments in the US and UK are already being briefed by their own military strategists about how to prepare for a world of mass famine, floods of refugees and even nuclear conflicts over resources.

Many countries are just one crop failure away from famine. Global warming will cause extended droughts and crop failures in many countries - count on it, and wars will result from this - in your lifetime. You can bet on this, its a sure thing.

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 3

Microbes in the Deep Earth Subsurface
As we discussed in class, we now know the deep earth subsurface holds an amazing number and diversity of different microbes. I have added three links to good web articles on this topic that you should read over. As an example of what the scientific community thinks about these microbes, here is a quote from the above link: "An attempt to estimate the total carbon in terrestrial and intra-terrestrial environments was made recently. These calculations indicate that the total amount of carbon in the intra-terrestrial organisms appears to equal that of all terrestrial and marine plants. Although subject to a great deal of uncertainty, the estimates suggest that the biomass of intra-terrestrial life is very large. A wealth of microbial life may exist deep inside Earth with many new species, representing novel microorganisms with unique physiological and biochemical features that await exploration".

Microbes thrive far below ground and these populations are living off of energy that is independent of photosynthesis. Here are two great quotes from this link:
"Evidence suggests that the microbes have been trapped for 80 million years, and possibly as long as 160 million years", says the author. "This means that these species of bacteria may have become locked within the rock while the thunderous footsteps of dinosaurs were resounding overhead".
"The discoveries not only redefine how scientists view the modern Earth, they also raise intriguing questions about the origin of life and the possibility that microbes survive today beneath the surface of Mars and other planets".

Rock-eating microbes are also found under the seafloor. Here is a quote from the third article.
"It's like walking into a tropical rainforest for the first time and beginning to identify and count the birds," said Tom Davies, manager of the Ocean Drilling Program (ODP) at Texas A&M. "This type of microbiology is a new science field for ODP. Such research raises questions about the presence of life in extreme environments on this planet and possibly other planets."

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 4

Soil Aggregates
Aggregates are the fundamental soil habitat for microbes (as biofilms are in water). Bacteria and fungi are both involved in soil aggregation and this website has a nice summary and overview of the role that microbes play in soil aggregation and why aggregates are important.

Soils and the Aggregation Process
This a "soils" website that will serve as a review or primer (if you have never had a soils course) that explains soil structure, texture, porosity, and how they all fit together to make up the material we call soil. There is a good section in the same material on aggregation and its importance to crop productivity.

Aggregate Formation
The way that soil particles and cations/anions and microbes fit together is a very complicated process that results in an aggregate. Some parts of the process are well understood, some are not. This site is a chapter summary from USDA that describes the importance of microbes in soil aggregation.

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 5

Aquatic Habitats - Microbes in the Ocean
This link is a good example of material related to one of the major aquatic habitats, the water column. In the open ocean, microbes are also be found in more aerobic habitats on suspended sediments, on biofilms covering kelp and aquatic plants, and in mats associated usually with beds of algae. The aquatic habitat becomes more anaerobic with depth, giving rise to unique microbe communities on the Ocean Floor and, surprisingly, in the depths of some caves.

Biofilms
This is an ASM website deals with biofilms; click on topic 1 on the left, "A Biofilm Primer" that describes how biofilms form and the activities that occur within. The biofilm is the most common and metabolically active of all aquatic habitats. Biofilms are also extensively found in Sewage Treatment Plants.

Microbial Mats
Mats are also very common in aquatic habitats, and pay special attention at this link to the pages on "How do Microbial Mats Work?" and What Are Stromatolites?" Biological mats are also found in Extreme Environments such as most of the thermal features in YNP.

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 6

The topic for week 6 is the pathogenic microbes spread by the fecal-oral route. These include bacteria, viruses, and protozoa; and there are many more when one moves from the temperate to the tropical zones around the world. Here are some of the major "bad characters":

THE "BIG 5" BACTERIA
Camplyobacter
The Cholera Vibrio
Shigellosis
Salmonellosis
ETEC

THE "BIG 3" PROTOZOA
Amebiasis
Cryptosporidiosis
Giardiasis

A FEW OF THE 120+ ENTERIC VIRUSES
Rotavirus
Viral Meningitis
Norovirus
Non-polio enterovirus
HMFD

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 7

The topic for week 7 is Microbial Source Tracking (MST). Since this is a new area of research, there is a lot available on the web. Here are a few of the more interesting sites:

Class MST Website
This is the best site on the internet, of course, because it's our class site, linked under Microbial Applications on our class homepage. There are a few others at least worth mentioning.

USGS Website
This is a very high quality website, based on the stringent review that anything posted by USGS is subjected to.

Source Molecular
This MST website is from a company in Florida that is one of several around the country that have entered the MST field from a commercial standpoint.

European Union
Here is an excellent site of course, since it is maintained by a friend of mine, where MST is explained based on the approach taken by the European Union member countries.

EPA
The EPA produced an MST Guide Document a few years ago, and it can be accessed and downloaded here.

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 9

The topic for week 9 is using soils and wetlands for waste treatment. While this is an old concept, it is considered a new area of research mainly due to innovative engineering techniques that allow better dispersion and contact of wastes within the treatment medium. There is a lot available on the web, but this is a highly regulated topic so many of the better sites are maintained by the EPA. Here are links to a few of the agency's process design manuals for the different types of applications:

Land Treatment of Municipal Wastewater Effluents

Fact Sheet that Outlines the Main Types of Land-Based Treatment Systems

Constructed Wetlands and Aquatic Plant Systems for Municipal Wastewater Treatment

Primer for Municipal Wastewater Treatment Systems
This link leads to an excellent EPA website that will take you on a tour of a modern wastewater treatment plant and explains the processes that occur at each step and how they all fit together to make the system work.

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 10

The topic for week 10 is anaerobes. In describing anaerobes in the environment, the concept of communities or guilds is used rather than describing individual genera or species. We will take this same approach in class. If you need a quick overview of Anaerobic Metabolism, try this link. Here are a few other useful links on anaerobes.

Gram Negative and Gram Positive Anaerobes
Although this is a medical website, it has a good description (but no images) of the main gram negative and gram positive anaerobes. Be sure to read over the section on Clostridium. Another good site for Clostridium is our class webpage on individual microbes.

Purple Non-Sulfur Photosynthetic Bacteria
This site describes one of three main groups of anaerobic photosynthetic bacteria that we covered in lecture. This is an excellent site and also contains descriptions for isolation and some very good pictures of these pigment-producing bacteria, as well as info on their taxonomy.

Anaerobes and Bioremediation
Anaerobes are important in many bioremediation approaches, as oxygen is typically lacking in the subsurface. This link gives an overview of some of the uses for anaerobes in this capacity.

The Microbial Biorealm
This is an excellent student-edited online microbiology resource that should be useful for anyone interested in microbes. For our current discussion on anaerobes, go to this site and scroll down in the left column (Bacteria) and read over the information provided by the links to:
Bifidobacterium
Bacteroides
Chlorobium
Clostridium
Desulfosarcina
Fusobacterium
Thermodesulfobacterium

Scroll down in the center column (Archaea) and read over the information provided by the links to:
Desulfurococcus
Methanococcus

There are also good sources on our class webpages for Desulfovibrio and Methanobacterium.

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 11

The topic for week 11 is methodology. Between the four chapters in the textbook (10, 11, 12, 13) and our class webpages on methods, this topic is sufficiently covered. So, I'm going to take the easy route this week and just use the topics in the chapters plus our class webpage.

Class Webpage on Methods

The single best reference on methods for working with soil is:
Methods of Soil Analysis. Part 2, 1994. Microbiological and Biochemical Properties. Editors - R. W. Weaver, Scott Angle, Peter Bottomley, and David Bezdiecek. Soil Science Society of America Press, Book No 5.

WEEKLY CURRENT EVENTS FOR 2010 - WEEK 12

The topic for week 12 is biological nitrogen fixation. This process accounts for 98%+ of the nitrogen that is transferred from the planet's atmosphere into the biomass. It is a very widespread characteristic among procaryotic microbes and is the most heavily studied of all global microbial processes. We have excellent class webpages on:
Rhizobium
Bradyrhizobium
Nitrogen Fixation

In addition to the class webpages, here are a couple more interesting and very useful websites on nitrogen fixation:

An excellent primer on Nitrogen Fixation, both the legumes and everything else.
This site has three sections, the N-fixers, the process itself, and the ecology of the fixers and the process. Read over all three of the sections.

Symbiotic Nitrogen Fixation
This site covers the symbiotic process, the most heavily examined of any of the nitrogen fixation relationships. This site also has a link to a very excellent site on the nitrogen cycle.


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