With respect to the postscript

http://download.bioon.com.cn/view/upload/201112/19191116_6450.pdf

--bks

If you already know that the organism inside the cell is an endosymbiont, you can perform an in situ stain against the conserved segments of the bacterial ribosome and only the bacteria will show up

Mark Martin wants me to tell this story. I told a friend who is a science reporter some years ago and he wrote about it.

When I was a surgery resident at LA County Hospital in 1967, our surgery chief, named Clarence J Berne, was convinced that normal flora were better adapted to the colon and would quickly replace antibiotic resistant strains. Of course, we knew nothing of C. difficile but resistant Staph was a worry and we knew there were strains of Klebsiella that were resistant to all antibiotics. What we would do is to test the stool of newly admitted patients for elective surgery who had been on antibiotics and get sensitivities. Of course, the lab hated this and would give us an argument about testing stool !

At his private practice at Good Samaritan Hospital in LA, he kept a pure culture of E. coli that was sensitive to every antibiotic. We weren't that lucky at County so we would collect some fresh stool from a new admission for a hernia repair or something similar. As long as they had not been on antibiotics they would do.

If a new admission patient had resistant organisms, usually KA or E. coli, in the stool, we would mix up a malted milk shake with the E.coli culture added. At County the addition was fresh stool. Of course, there was no mention of the addition.

We would check the stool again a couple of days later and the stool would almost always be purely sensitive organisms.

I don't think Bradley has had a malted milk shake since I told him the story. Saving the patient's own stool is a new wrinkle to me and sounds better but the other worked just fine.

When I was in graduate school, I used to sneak over to the medical school so I could watch Dr. Falkow's lectures: funny, wise, and irreverent. I will never look at a gelatin capsule in quite the same way. That should have been on "Dirty Jobs"! Thank you, Dr. Falkow, for a great essay.

Might there be a continuum from endosymbiont to organelle? ... are there some that are difficult to classify one way or the other? (asking out of ignorance)

Hi Elio, don't feel bad about not knowing much, or indeed, anything about glomalin. I retired from medical practice and started ranching cattle in my retirement. As a physician, if I am to be effective, It is mandatory to understand the anatomy and physiology of the human body. As a manager of grasslands I felt it was mandatory to at least understand how nature works. I was fortunate to be mentored by a soil scientist from a local university, who included glomalin in my Soil Science Crash Course. Lucky me. Since then I have found that no one knows anything about this amazing glycoprotein. Its amazing to me that with all the argument about CO2 and climate change, noone cares about Glomalin. Sara Wright showed that increasing atmospheric CO2 dramatically increased mycorrhizal fungi and therefore the laying down of glomalin. Good to read your blog.

If the eukaryotic cell can fulfill its life cycle without the organelle, it's an endosymbiont.

--bks

I think that the presence of evolutionary echoes of independence is the key point. Peptidoglycan is not present in all bacteria (or among the archaea at all). Metabolic pathways can be co-opted and harnessed, blurring distinctions. I guess I would be inclined to stick with evidence of the "organelle/endosymbiont" having some kind of genetic blueprint: some DNA or RNA. And I guess we can add "compartmentalization" to the Venn diagram of this conundrum.

Prokaryotic surface features including peptidoglycan, (lipo)teichoic acids, and capsular protieins/peptides

Is there some sort of "extracellular soil proteome" published?
Thanks for the interesting post.

From a person to a planet, it's the little known small things that matter. I've been reading Tom Lovejoy and Allan Savory on restoring the soil to help solve carbon sequestration. Altering terrain has unhealthful consequences for human health and survival on a once bountiful planet. Love the symmetry. Thanks for this very interesting read.

Lovely work, Elio! This really makes me wonder about the people who want to grow plants in the soil of other planets---the amendments necessary may be more complex than we would normally envision.

Soil microbiology is fascinating. In my microbiology course, I enjoy having students sniff plates of Streptomyces. At least one of them will exclaim that it smells like dirt. "No so!," I reply. "Dirt smells like Streptomyces."

Honestly, microbes are at the center of everything. And how much time do we spend in the undergraduate curriculum on the topic? Sigh.

Elio sometimes asks if the eukaryotes have added anything substantially to the art of living. Mayby one answer would be alchemy? Among the living, only postbacterial eukaryots – like humans – seem to master the art of nucleosynthesis. Some consortia of them are even able to create elements that have never existed, like antihydrogen.

Well, at least everyone now knows what to get me for my birthday!

Seriously, a wonderful post, Gemma. Even though it isn't my background, I always try to emphasize to my students the role that microbes play in elemental cycling other than carbon and nitrogen. Even metals! And microbial respiration is nothing if not diverse. Great job!

My biggest question was how does PLE prevent phage infection? Quite curious!

One of my favorite things to do with students is show T4 infection under a phase contrast scope to really dramatically demonstrate how very little simple things like a 151 AA long protein can have massive complex effects and give a visceral sense for the majestic brutality of lytic phage infection. Where just a couple of minutes into infection, T4 produces enough Ndd to drag the entire nucleoid mass to the sides of the cell - visible in real time.

Ndd, the Bacteriophage T4 Protein That Disrupts the Escherichia coli Nucleoid, Has a DNA Binding Activity: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC107561/

I have long been a proponent of "microbial literacy" both on and off campus, to the point I was labeled a "microbial supremacist" (what started as a mild semi-humorous insult during a department meeting has become my motto). I gave my freshman students copies of Margaret's Perspectives article a few weeks ago, and they wrote some amazing responses to it...it is clear that students are ready and waiting for this paradigm shift. At the same time, I have been bemused by some of the, um, uninformed verbiage I have read or heard from non-microbiologists. Only education and outreach can change that.

I am always struck by the comment by the late Carl Woese (and other microbiologists) that if bacteria and archaea vanished overnight, the entire biosphere would collapse and result in a dead planet. Yet if all eukaryotes vanished, sure, the biosphere would undergo some wild adjustments...but this would remain a world brimming with life. Yes, when folks write about microbiology, they sometimes suffer from eukaryocentrism, from oxycentrism, and (for some microbiologists) colicentrism. The microbial world is vast, various, and incredibly diverse. For example, when I show my students how microbes control many elemental cycles on our planet (and that the only source of bioavailable nitrogen---other than volcanoes and lightning strikes---is prokaryotic), it strikes them how central matters microbial are to the world around us. And how little that is part of their curriculum, to be frank.

There is no doubt that microbes are the basis and very base of the biosphere of our living planet.

I remain hopeful we change that. Perhaps ASM would sponsor a colloquium about the centrality of the microbial world to Planet Earth (should it be called "Planet Microbe"?)for non-microbiologists, with a view toward reforming first year biology course curricula (both high school and college). I gave a talk about this at the ASM General Meeting last year, and attendees were disturbed by some of the things I found in textbooks and even review books for the Biology subject test for the GRE (did you know, for example, that bacteria do not have a cytoskeleton...despite review papers on this topic that are nearly ten years old?). Again, we need to promote microbial literacy, and Margaret's Perspectives essay can only help us, I think.

I appreciated Fred Neidhardt's title for his talk. I am reminded of the late science fiction author Isaac Asimov's description of ou solar system as consisting of "Jupiter...plus debris." I would suggest that our biosphere is mostly microbial, plus contaminants. To me, there is no question "whose" planet this is! There is a saying about the late Frank Sinatra: "It's Frank's world; we just live in it."

I think it is clear-cut (and backed up with data) that Earth is actually a microbial world, and we just live in it.

Great job, again, Elio. I will be blogging about this paper later this week, but you have said it far more elegantly and eloquently than I could! Kudos from a fellow microbial supremacist!

"A formidable challenge" for the virus or for one of us to figure out Euux?

FIV is so prevalent in cats who live closely together in the wild that if it were easy for a like virus to go airborne it likly would have. Thus it might be difficultl and also, after learning to floatit would have to find some new receptor sites.

Maybe, the virus doesn't think it's worth all the trouble considering how much fun its current mode of infection is. Both cats and humans are more likely to give up breathing than sex.

Query --an FIV-positive mom cat had 4 kittens two of whom tested positive and two negative. How come all four kittens didn't acquire the virus?

Elio, love this blog! Our worldwide cohort depend on more and more information about who we really are: a supra organism with a meta genome that can be altered and cause great suffering. So bring it! Dr. McFall-Ngai sent me the PDF. Loved the interdomain communication section. She says it’s time we stop trifling with our microbiota ;)
Our cohort certainly feels the same way. The microbiota profoundly affect our immune, circulatory, neuro, digestive, and many more systems. And enjoyed these topics: human-associated bacteria exchange genes at a rate that is 25-fold higher than those not living in host-associated host environments; and up to one third of an animal’s small molecules in the blood (its metabolome) are of microbial origin.

Fantastic, Elio. It's like you have a listening device in my classroom. During my last review session, a freshman asked: "So we talk a lot about the nucleus and mitosis and meiosis...how do bacteria package up their DNA? I mean, it's huge compared to the bacterial cell, right?"

I wanted to give him a dollar. My class is pretty eukaryocentric (that's the curriculum), but I do slip in some Microbial Pride here and there. Thanks again!

http://tvtropes.org/pmwiki/pmwiki.php/Main/DrillTank

Hi, everybody,

Thanks for the comments.

I agree that a diversity of styles and schedules would serve the broadest group,of students. And it is certainly true that' "total commitment" is needed to do a block of microbiology. While I do not think it would work well for many married or parenting students, every once in a while some such person graduates from Colorado College. Many of our students with jobs are employed by the College, which is a particularly understanding employer!

It sounds like I would really enjoy talking more with all of you about teaching!

-Phoebe

Do the swimmers have "helmets" on their leading edges to help them batter through?

Anyone want to bet on when quarks will be smashed into smaller constituent particles?

"Parasite Gal," a pathologist at Mayo Clinic, puts up a quiz each week in which she invites the readers to guess the parasite (usually based on pictures from her microscope). Her clinical identification is given at the end of the week:
http://parasitewonders.blogspot.com/

Protists and bacteria make frequent appearances but Diphyllobothrium was featured a few weeks ago:
http://parasitewonders.blogspot.com/2013/02/case-of-week-246.html

--bks

Block formats are great for lab activities. I taught a block microbiology class for k-12 teachers one summer - it was great because each student cared for a culture of their own like a pet and they used their own cultures for the lab activities.

I think you may have that info reversed. Sexual differentiation begins in the human stage as gametocytes form from the otherwise asexual schizogonus replicating parasites, but sex is completed within the mosquito (once the flagella come out ;).

Elio replies:

You are right but I was not totally off, being that the sexual cycle starts with gametogenesis in the human and is complete by conjugation of gametes in the mosquito. Can we split the difference? Sex can be complicated, no?

I enjoy reading write-up. Hope i can discover a lot more articles like this one. Thanks for posting.

Cool article Heather, thanks.

Phoebe, that is a nice post! I know many CC alums, and they loved the structure. A diversity of approaches is probably best, given the diversity of the student styles we face. Best wishes!

Is there any place on Earth where you wouldn't spot microbes if you looked closely enough? Imagine, further, packing stain reservoirs, polarizers, ultraviolet illumination, and what-have-you. Doesn't NASA have any laboratory biologists on staff?