10% to 5% to 1% - (Jun/28/2008 )

gerb - that's why the 16S info is so intriguing. The sequence never changes - neither in near term culture nor in extended from prehistoric terms. The rationale developed presumes that even a single base pair change disrupts protein synthesis so much that it is always lethal.

16S sequence changes all of the time. This is the basis for most bacterial systematics, after the pioneering work of Woese, who cataloged exactly these variations in 16S sequences. They change relatively little compared to other sequence, but are far from immutable.

There are indeed variable regions in 16s\S. Not sure if ohage434 is being obtuse or ignorant but the conserved regions of 16s rDNA (18s in fungi) is well known in microbiology to be the basis for modern microbial taxonomy as it is highly conserved and is the basis for microbial identification as practiced by Accugenix et al,

I am aware of the conserved nature of 16S (or more of 18S in fungi) but that is not what I wanted to discuss: What I wanted to know is: is there some sort of "definition" of a species (I learned it is 98 % sequence similarity to cut of a new spec., but in this forum I learned that this is not valid for all genera) in bacteria? With fungi I know the difficulty: I can define my isolate ("strain") very well, although it attenuates in culture very quickly too, but when it comes to the species a general definition is difficult, althoug the 18S rDNA is the same, as is the more variable ITS1-5.8S-ITS2 region.
But I was wondering if in bacteria, that have huge replication rates the 16S region changes as quickly as it attenuates; thinking about the billions of bacteria contained in one colony, the probability of a single bp mutation in 16S is quite high?

And other "problems" I have with bacterial diversity in soil is: (i) horizontal gene transfer (I know this happens in fungi too, but this would lead to another discussion)
(ii) DNA bound to soil particles that can be incorporated by bacteria


And as consequence: If one bacterium has taken up some DNA from any source, or mutated some way or the other and we can detect this: is there any evidence that this specific bacterium would be able to survive in soil or have we just amplified some "evolutionary experiment" that won't survive and we will not be able to test this hypothesis as we can not culture it????

Fascinating question gerb and one I'm not sure agreement exists as to an answer. Not my expertise so I can offer only disparate thoughts. I understand that some discuss that "species" could be an obsolete concept - seeing more of a vague continuum. Maybe there should be a chemical classification based only on sequences.

I've seen what to me is abuse of the species concept with the genus Malassezia. What until the 90's were 2 vague described spp. in the genus Pityrosporum became 7 species of genus Malassezia well described morphologically, physiologically and most important by 18S. Now there's up to 14 or so described with varying degrees of validity (some in non-refereed fora - genbank, vet journals, etc) based on minor reported differences in 18S. Since these apparently grow only on mammals and reasonably evolved to optimize association with individual host species (and prob. for specific body areas on hosts) minor differences could be more than just lab error but should taxonomy establish 3 or 4 (or more) unique species and on each mammal?

I also know DNA is more stable than prev considered so we have to be aware that presence doesn't mean vitality.

For bacteria - I know closely-related spp. can differ in as little as about one bp in 16S conserved region (staph epi vs. staph aureus) so I'm not sure how the colonial question works.

Looked up a good rev on free DNA and soil: http://www.sciencedirect.com/science/artic...9ca0425f4e5a09d

I see your point. Speaking for fungi the species debate could keep us discussing for years just thinking of Fusarium oxysporum which has more than 120 f.sp. mostly defined by the host plant but also confirmed by DNA work...there it seems that the oxysporum concept seems not to be a very good species (maybe because Fusarium is a morphologically difficult genus).....

But I would disagree on a complete chemical concept based on DNA; only because it is there it must never in the "life of a microbe" (could be the next discussion ) be expressed....and on the other hand DNA for something is not there but it is used (eg. RNA / protein uptake from hosts or alteration of the host). And maybe I am thinking to old fashioned here, but every life form has a certain place in the ecosystem, so just looking at the DNA will not help us to understand the diversity that is out there.....and in my eyes lots of these environmential DNA samplings are collecting stamps and putting them into an album. But this will not help you to send a letter if you know what I mean....its good to know that they are there but I am alwas the pragmatic asking what are they doing????

And maybe somebody can help me with my "how quick do bacterial species get another species when repeatedly cultivated" question???????

I'm with you (!!!) on degradation our science to simple chemical analysis. Life is not the sequence of base pairs but the expression of the information through all the filters, modifiers and nuances of systems (I hope) we'll never fully understand

To your question - I think the answer is that repeated cultivation does not drive unique speciation in bacteria or fungi. I suppose evolution does and that speaks more to the stability of bacterial/microbial taxonomy. That said, the USP requires no more than 3 transfers from the ATCC stock to ensure the validity of cultures for drug testing. This was not data-driven - it was based on perception.

gerb - consider that our basic technology for growth/recovery of microbes from our world changed little in over a century. Now it's a new world.

For the petri dish.

Petri, R.J. 1887. Eine kleine Modification des Koch'schen Platteverfahrens. Centralblatt fur Bakteriologie und Parasitenkunde 1:279-280.

In this paper, Julius Petri observes his innovation works for gelatin or agar - Frau and Herr Hesse;s innovation (that itself was never published).


Petri reportedly died in an asylum.

And this is where it went 100 years later.....

But back to the molecular approach: although it seems to be widely accepted that DNA based methods are biased too it is really making me angry to hear people talking about it as "the" solution for all problems environmential microbiology faced during the last decades of culturing approaches......

PCR provides another spectrum of organisms and probably a greater diversity but still does not tell anything about the state and importance of the organism itself....just because I sequence it very often it must not be abundant!

So true - I think folks have have tacitly accepted that the DNA signal is equivalent to a living bacterium. You could PCR your tap water and find signals of many bacteria not rececoverable by culture AND probably not there as viable bacteria.

Did some similar stuff in South America a while back and found DNA signals for E. coli, Pseudomonas aeruginosa, Salmonella, etc. in a commercial product made with "city" water. Most were not recoverable in culture , even on concentration - I'm sure they were present only as remnant DNA.