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Post Archive
2017 (0)2012 (1)2011 (51)
August (1)

Wednesday Micro Hits
Wednesday, August 17, 2011
July (1)

Is it worth getting an education?
Thursday, July 7, 2011
June (2)

Miscellany
Tuesday, June 28, 2011

It Gets Better
Thursday, June 2, 2011
May (4)

Wednesday Micro Hits
Wednesday, May 11, 2011

My first experience with science writing (Part 1 of 2)
Tuesday, May 10, 2011

This is why we get vaccinated
Thursday, May 5, 2011

Monday Morning Jam
Monday, May 2, 2011
April (2)

Saturday Morning Serenade
Saturday, April 23, 2011

So long, farewell ...
Friday, April 1, 2011
March (10)

Stay Tuned ...
Thursday, March 31, 2011

From the Union of Concerned Scientists
Tuesday, March 15, 2011

Week 23 - Hockey Pool
Monday, March 14, 2011

March Madness
Monday, March 14, 2011

Saturday Morning Serenade
Saturday, March 12, 2011

What a bargain!
Wednesday, March 9, 2011

Wednesday Micro Hits
Wednesday, March 9, 2011

Technique Overload
Monday, March 7, 2011

Saturday Morning Serenade
Saturday, March 5, 2011

Et tu FDA?
Wednesday, March 2, 2011
February (10)

Saturday Morning Serenade - A Hip Edition
Saturday, February 26, 2011

Saturday Morning Serenade
Saturday, February 19, 2011

Wednesday Micro Hits (on Thursday!)
Thursday, February 17, 2011

HR1
Wednesday, February 16, 2011

Happy Valentine's Day
Monday, February 14, 2011

Saturday Morning Serenade
Saturday, February 12, 2011

The GOP War on Science
Wednesday, February 9, 2011

Wednesday Micro Hits
Wednesday, February 9, 2011

People, how about some ...
Tuesday, February 8, 2011

Saturday Morning Serenade
Saturday, February 5, 2011
January (21)

Saturday Morning Serenade
Saturday, January 29, 2011

Sacrifice
Friday, January 28, 2011

Are you married to your reagents?
Thursday, January 27, 2011

Wednesday Micro Hits
Wednesday, January 26, 2011

Common Sense Tip #1
Tuesday, January 25, 2011

Saturday Morning Serenade
Saturday, January 22, 2011

From the Baby Boomers, a Big "Screw You"
Friday, January 21, 2011

Student Worker - More Student or More Worker?
Friday, January 21, 2011

Wednesday Micro Hits
Wednesday, January 19, 2011

Saturday Morning Serenade
Saturday, January 15, 2011

Holy moly!
Friday, January 14, 2011

Thursday Pondering
Thursday, January 13, 2011

The Electronic Office
Thursday, January 13, 2011

Wednesday Micro Hits
Wednesday, January 12, 2011

Saturday Morning Serenade
Saturday, January 8, 2011

The Plug - January Edition
Friday, January 7, 2011

Bits 'N Pieces
Thursday, January 6, 2011

Latest Manuscript Review
Wednesday, January 5, 2011

The $4 gallon of gas
Wednesday, January 5, 2011

Our slowly shrinking (and dying) planet
Tuesday, January 4, 2011

It's 2011 already? For reals?
Monday, January 3, 2011
2010 (46)
December (9)

Saturday Morning Serenade
Saturday, December 11, 2010

The State of Microbiology
Thursday, December 9, 2010

Wednesday Micro Hits
Wednesday, December 8, 2010

2010 blogging meme
Tuesday, December 7, 2010

The Environmental Impact of the Christmas Season
Tuesday, December 7, 2010

Music Snobbery
Thursday, December 2, 2010

Phantom Power
Thursday, December 2, 2010

What's Your Name?
Wednesday, December 1, 2010

Wednesday Micro Hits
Wednesday, December 1, 2010
November (8)

Saturday Morning Serenade
Saturday, November 27, 2010

Awakening from the food coma ...
Friday, November 26, 2010

Wednesday Micro Hits
Wednesday, November 24, 2010

Donor's Choose Final Followup (Recipes #3 and #4)
Tuesday, November 23, 2010

A Monday Mess
Monday, November 22, 2010

Saturday Morning Serenade
Saturday, November 6, 2010

Wednesday Micro Hits (Peer-Review Edition)
Wednesday, November 3, 2010

Day 2 of the ASA-CSSA-SSSA Meeting (#ACSMtg)
Wednesday, November 3, 2010
October (29)

ASA-CSSA-SSSA Meeting - Day 1
Sunday, October 31, 2010

Stayin' Alive
Sunday, October 31, 2010

Saturday Morning Serenade
Saturday, October 30, 2010

Wednesday Micro Hits (Vol. 4)
Wednesday, October 27, 2010

ASA-CSSA-SSSA Early Career Program
Monday, October 25, 2010

Saturday Morning Serenade
Saturday, October 23, 2010

Wednesday Micro Hits (Vol. 3)
Wednesday, October 20, 2010

Donor's Choose - Family Recipe Number 1
Sunday, October 17, 2010

Making Good on Donor's Choose Bribe - Comfort Food Recipe 1
Saturday, October 16, 2010

Saturday Morning Serenade
Saturday, October 16, 2010

Friday Wrap-Up and Random Thoughts (Vol. 2)
Friday, October 15, 2010

First I Begged, Now I Bribe
Thursday, October 14, 2010

Finding Out Things The Hard Way(TM)
Wednesday, October 13, 2010

Wednesday Micro Hits (Vol 2)
Wednesday, October 13, 2010

Here's where I start begging ...
Tuesday, October 12, 2010

#UnK3rn3d: Life Outside the Lab?
Tuesday, October 12, 2010

First fleas, now frogs?
Tuesday, October 12, 2010

No Fleas Please
Monday, October 11, 2010

My next Research Blogging article has been chosen ...
Sunday, October 10, 2010

Saturday Morning Serenade
Saturday, October 9, 2010

Donor's Choose
Friday, October 8, 2010

Friday Wrap-up and Random Thoughts
Friday, October 8, 2010

RB: Waste Not, Want Not.
Thursday, October 7, 2010

Research Blogging
Wednesday, October 6, 2010

Wednesday Micro Hits
Wednesday, October 6, 2010

What if I were not a microbiologist ...
Tuesday, October 5, 2010

TJ's Tips on Manuscript Review
Monday, October 4, 2010

Chinese plagiarism and the death of English-language journals
Friday, October 1, 2010

Allow Me a Formal Introduction
Friday, October 1, 2010
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Blogger Profile

Thomas Joseph

It's a Micro World after all is a blog dedicated to discussing pretty much whatever I feel like. When I delve into scientific matters it will primarily be discussing microbiology (agricultural, bioenergy, and environmental focus). Otherwise, I'll probably ramble on about sports and life.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Awesome Stuff
Thursday, December 9, 2010

So, this press release that I forwarded to some people at work today generated some interesting email discussion. Me and my colleagues do a fair amount of work on animal waste and their byproducts, and when I say "waste" I mean it literally ... poop and pee, on a massive scale. We do a lot of work with CAFO's (Concentrated Animal Feeding Operations), so there are lots of animals (thousands if not tens of thousands) in a small area. If the waste is not handled or treated properly, it can have some dire environmental -- as well as animal and human health -- impacts. So, my job (and the job of my colleagues) is to find ways to improve on current waste treatment systems, which often leads us to cooperate with municipalities (and nations) to draw from their own applications (with reciprocation when they draw from us as well).

However that is really just a tangent to what we discusses this morning over a few emails. You see, the press release talks about a group of organisms called the PVC (Planctomycetes, Verrucomicrobiae, and Chlamydiae) which this research consortium have call "the missing link" between microbial life and eukaryotic life.

“Our analysis shows that PVC [Planctomycetes, Verrucomicrobiae, Chlamydiae] bacteria, members of which are commonly found in today’s sewage treatment plants or acid bogs, represent an intermediate type of cell structure. They are slightly bigger than other known bacteria, and they also divide more slowly.”

“The structure of PVC suggests that it is an ancestor of a ‘missing link’ cell which connected prokaryotic to eukaryotic cells along an evolutionary path all those billions of years ago,” says Dr Damien P Devos, European Molecular Biology Laboratory, Heidelberg, Germany, the other scientist involved in the findings.

Now, the Planctomycetes are definitely a weird class of bugs, because they have intracellular compartments. Environmentally, they are fairly common, as are the Verrucomicrobiae ... our lab has detected numerous clones of each in both wastewater treatment systems (WWTS) and soils (agricultural as well as non-ag). Since they are relatively new kids on the block (identification wise) large numbers of them have not been isolated and studied in-depth, but that is now being rectified. Application-wise, research on Planctomycetes is steadily picking up steam, especially due to research on ANAMMOX (Anaerobic Ammonia Oxidation) (doi: 10.1016/j.resmic.2005.01.011, PDF, 7 pages). So here we have several classes of organisms found in WWTS and soils, several of which may have good applications outside of their environment. There is a lot of research potential involving these bugs, and it's a very exciting time.

As to the question I was asked ... one of my colleagues asked me if we could take these organisms and move them from one system to another. Unfortunately there is no simple yes or no answer to this question. There are a number of factors which will determine whether these organisms can establish residence in a new environment. A lot of research seems to indicate that no, you cannot take Organism X from Environment A and introduce it to Environment B. My response was as follows: Studies which have looked at trying to place organisms from one locale to another have had mixed results. Usually organisms cannot be transferred individually but as a community because they work in tandem with other organisms to get the nutrients they need. You disrupt those linkages and the organisms don't fare well.

I followed that up with the problem microbiologists now face: Microbiology has long been a culture-based system ... you isolate your organism and you study the heck out of it. You then move to the next organism and study the heck out of that one. Rarely do you mix the two to see how they interact with each other in mixed culture. Yes, it does happen, but even a decade or so ago, microbiology/molecular biology PhD projects were based on "one gene/one function" projects.

Plus, our tools can sort of suck when it comes to figuring out massive communities: Usually 16S studies tell us what is there, but they don't provide us with any biochemical data. Studies which might give us biochemical data sometimes cannot be tracked back to an identifiable (or currently isolatable) organism.

Yes, things are progressing in this area, just look at the rise of all the -omic disciplines, but they're still in their infancy. So in summary, there is still plenty to be done in the world of microbiology ... we've literally only scratched the surface of what we potentially can know. Even more interesting is that research in application sciences (even wastewater) can lead to interesting basic science discoveries describing evolution.

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Blog Comments

Genomic Repairman
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Micro was kind of boring in college and now getting out and finding out way more about all the new stuff happening in this field, its amazing.


Thomas Joseph
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In college I called my micro classes "bug parades" because the teachers literally threw species after species at you. Memorizing biochemical profiles was the staple of my clinical micro courses, and site of isolation was the primary determining factor of what biochemical tests you would typically run ... so it could get monotonous. Yet, it was the most hands on discipline in clinical laboratory science which is why I was pulled to it. The clinical side and research side are two different beasts, and the application sciences side is a 180 degree turn yet again ... very exciting stuff, and as we move more towards the -omics side of things ... we're going to have a lot of cool stuff to publish for sure!


Suzy
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I loved the Bug Parade :-)

I met the woman who basically wrote the book on Chlamydia, Karin Everett. She knows everything about Chlamydia in the environment- she identified and reclassified many of the new species in the Bergey's manual. I had no idea they were so abundant in the environment.


Genomic Repairman
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Dude don't even remind how much time I spent looking in Bergey's manual.


Thomas Joseph
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I used Koneman's Diagnostic Microbiology (4th Edition) text.


Genomic Repairman
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We only had three copies of Bergey's on campus and you had to stay in a certain section of the library to check them out.  This became a bitch near exam time when a few hundred of us needed to work out the identification of our microbes.


Evie
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Dude! This is a great post! I'm all excited about it and interested in this now! Very cool stuff.

I love that you think there is value is looking at these things in a group and not just on their own. I think that isolation concept is present across the board. For me, its a bit different, but same principle, engineers worry about making their part work great, but little to no emphasis is put on integrating the parts and making sure they fit well and work together. I too am a fan of working on a system level, not just isolated parts.

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