Category Archives: archaea
Is the government telling women not to drink? How many microbes in the human body?
Posted by alcohol, archaea, Bacteria, brain, CDC, Centers for Disease Control and Prevention, contraception, drinking, FASD, featured, fetal alcohol spectrum disorders, fungi, health care, media criticism, medically unexplained symptoms, microbes, Microbiology, On Science Blogs, Palaeomerycidae, Politics, psychology, Research, united states, women
inTwisted Tree of Life Award #16: Nature & Authors doing taxonomic alchemy converting an archaeon to a bacterium
I got pointed to this by Uri Gophna (in an email and in a comment on my blog)(all see this on Twitter) Sure - some people debate the structure of the tree of life. But I am pretty certain the authors here (Siddhesh S. Kamat, Howard J. Williams, Lawrence J. Dangott, Mrinmoy Chakrabarti & Frank M. Raushel) are not trying to make a statement about monophyly of bacteria or just what archaea are. They just made what seems to be a colossal screw up. And Nature not only let them, but added to it with things like their "Editors Summary":
Novel bacterial biosynthesis of methane
Aerobic marine organisms produce significant quantities of the potent greenhouse gas methane, much of it via the cleavage of the highly unreactive carbon–phosphorus bonds of alkylphosphonates. In this study the authors explore the mechanism of PhnJ, an unusual radical S-adenosyl-L-methionine (SAM) enzyme that appears to use a cysteine-based thiyl radical to help catalyse the conversion of the alkylphosphonate substrate to methane and ribose-1,2-cyclic phosphate-5-phosphate. This reaction, not previously encountered in biological chemistry, establishes a novel mechanism for cleaving carbon–phosphorus bonds to form methane and phosphate via a covalent thiophosphate intermediate.
And for this taxonomic alchemy (converting an archaeon to a bacterium) I am awarding them and Nature my coveted "Twisted Tree of Life Award #16".
UPDATE 5/28 7AM
I love the ad that came up while I was writing this post and searching for some information. I think Nature could use the services from this ad:
Worth a read: Jim Staley on a "Universal Species Concept" and the history of microbial species concepts
- Discovery of microorganisms,
- Advent of pure cultures and phenotypic features,
- Introduction of molecular analyses and
- Gene sequencing and genomics.
Posted by archaea, Bacteria, James Staley, Microbiology, number of species, phylogenomics, species
inRIP Carl Woese: Collecting posts / notes / other information about my main science hero here
My tribute to Carl Woese 12/30/12 |
News stories about Woese's passing
- Champaign/Urbana News-Gazette Visionary UI biologist Carl Woese, 84, dies
- U. of I. News: Renowned microbiologist Carl R. Woese dies at age 84
- University professor of microbiology dies at 84 years old
- Chicago Sun Times: Revolutionary U of I biologist Carl R. Woese dies
- NY Times: Carl Woese Dies at 84; Discovered Life's 'Third Domain'
- Wired: Carl Woese, (R)evolutionary Biologist
- Huff Post: Evolution Scientist Carl Woese Dies: 'The Most Important Evolution Scientist of the 20th Century'
- Carl Woese Dies | The Daily Scan | GenomeWeb
- Chicago Tribune: Carl R. Woese, microbiologist and professor at U. of I., 1928-2012
- January 2013 Reading in detail Carl Woese's 1998 "Manifesto on Microbial Genomics" for the first time ...
- April 2010 Most important paper ever in microbiology? Woese & Fox, 1977, discovery of archaea
- October 2010: Here's hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine ...
- September 2012: Some arguments for why Carl Woese (and probably Norm Pace) deserves a Nobel Prize
- Notes from a talk by Woese in 1993
- Evolution pumpkins - from Darwin to Woese
Storification of Tweets and other posts about his passing
Other posts worth reading about Woese's passing
- So long, and thanks for all the Archaea » Pharyngula
- Prof. Carl Woese – 1928-2012 | C.W. Schadt | Microbial Ecology Lab
- A Sad Post: RIP Carl Woese! - Creatures Great AND Small ...
- T. taxus: Carl Woese 1928-2012
- Carl Woese - NASA Astrobiology: Life in the Universe
- Honoring a scientific revolutionary from Rob Dunn
- In Memoriam Carl Woese from Karl Fogel's blog
- Carl Woese dead at 84 - The Panda's Thumb
- RIP Carl Woese: Evolutionary Pioneer from the DailyKos
- From Larry Smarr
- Reposting of a Woese interview in LaborJournal.De
- El árbol que plantó Carl R. Woese
- Archaea Are More Wonderful Than You Know
- A sad loss for Microbiology
- Curiosidades de la Microbiología: Carl Woese 1928-2012
- The new biology of Carl Woese
Miscellaneous
My graduate student Russell Neches used a laser to etch a picture of Carl Woese on a piece of toast. |
- Carl Woese - Wikipedia, the free encyclopedia
- Carl R Woese - The School of Molecular and Cellular Biology ...
- Phenomenal history / discussion of Woese's work: Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life
- 2007 Science article by Virginia Morell
Posted by archaea, Carl Woese, Evolution, microbial diversity, Microbiology, rRNA, tree of life
inWelcome to the Microbial Earth Project
Map of type strains. |
There are some 10,000 described type strains of bacteria and archaea. Not really a lot given that there are probably millions upon millions of species of bacteria and archaea. But it is what we have available to us in terms of the formally described and accepted species for which there is an available cultured strain.
At this site you can do things like "Adopt a Type Strain" or view a cool "Map of the type strains".
The Steering Committee for the project is
- Jonathan Eisen (University of California, Davis)
- George Garrity (Names for Life, USA)
- Philip Hugenholtz (Australian Centre for Ecogenomics Research, Australia)
- Hans-Peter Klenk (DSMZ, Germany)
- Nikos C. Kyrpides (DOE-Joint Genome Institute, USA)
- William B. Whitman (University of Georgia)
- Tanja Woyke (DOE-Joint Genome Institute, USA)
Posted by archaea, Bacteria, genomes, JGI, microbes, microbial earth project, Nikos Kyrpides
inGet the genomes of up to 12 type strains of bacteria and/or archaea sequenced, for free
Genomic Sequencing of
The Community Sequencing Program (CSP) Quarterly Microbial call of the DOE Joint Genomes Institute provides a great opportunity to obtain draft genomic sequences of the type strains of bacterial and archaeal species. The type strains may also include proposed species prior to publication. Type strains must be relevant to DOE mission areas, such as bioenergy, biogeochemistry, bioremediation, carbon cycling, and phylogenetic diversity. However, strains of human pathogens and human associated species are not eligible. Proposals for genome sequencing of type strains can be submitted through the CSP Quarterly Microbial call, whose deadline is December 17, 2012, with approval usually being completed within one month. Up to 12 strains can be included in each proposal. Proposals for larger numbers of strains need to be submitted to the CSP annual call in the spring. If you cannot make the December call, Quarterly calls are also scheduled for March 25, June 17, and September 23, 2013.
Proposals may be completed on-line at: http://proposals.jgi-psf.org/proposals. You will need to register and sign in to this server. Once on the server, follow the links to the “CSP Quarterly Microbial/Metagenome”. All strains will have to have been deposited in a culture collection, including proposed type strains prior to publication. If a culture collection ID is not available, you can attach a copy of the Certification of Availability. Once approved, you will need to provide 5-10 µg of high molecular weight DNA.
For questions, contact Barny Whitman, University of Georgia (whitman@uga.edu).