Coliforms and operational definitions

Recently, I was talking about coliforms with my colleagues from the lab. ‘Coliforms’ is the name given to a group of bacteria that usually serve as indicators of fecal contamination in water and food samples, because most coliforms come from the intestinal flora of animals. For this reason, water and food that contain too high levels of coliforms are deemed unfit for human consumption (the US EPA recommends a limit of 10 or less per liter in drinking water). The most famous coliform, Escherichia coli, is a commensal in our intestine, although some pathogenic strains exist as well (for instance O157:H7, involved in deadly outbreaks in the US and Europe). Coliforms behave similarly as fecal pathogenic bacteria, notably regarding their survival in water. We can thus assume that a sample devoid of coliforms will also be free of fecal pathogens. Commercially-available tests for coliforms, such as the culture medium CHROMagar ECC, also permits us to differentiate between total coliforms and fecal coliforms (mostly E. coli), simply based on the coloration of the bacterial colonies on agar plates.

Macroscopic fungi

In the lab I have only dealt with microscopic fungi, such as yeasts, but a couple of weeks ago I had the privilege to accompany a group of UC Davis students and staff on a mushroom hunting trip! This excursion was led by the very knowledgeable mycologist Dr. Mike Davis, author of the Field Guide to Mushrooms of Western North America, and Professor of Plant Pathology at UCD.

Fungi are curious organisms, neither animal nor plant, with unique chemical traits such as the presence of chitin in the wall of their cells. My beloved Brock Biology of Microorganims reminds me that there are three major groups of fungi: the molds (the type you don't want in your household); the yeasts, which we commonly use to ferment sugars; and finally the mushrooms, or macroscopic fungi.

Mother of vinegar

Mother of vinegar from a wine vinegar pot

I'm currently visiting my parents in Switzerland, in a lovely region located between the lake Léman (lake Geneva) and the mountains of Jura (see Nyon région tourisme). On that occasion my father gave me a tour of his vinegar pots, and even fished out the mother of vinegar from inside the pot so that I could take a picture. Have a look at this biofilm of acetic acid bacteria: it's a large and thick disc with the color of a liver!

As their name implies, these bacteria transform alcohol, for instance from wine, into acetic acid. From what I read during a quick overview of the literature, common acetic acid bacteria include species of the genera Acetobacter and Gluconobacter. 

Bacteria, Archaea, bacteria, or prokaryotes?

In this blog, I use the term ‘bacteria’ (with a lower case), as a generic term equivalent to prokaryotes (that is, Bacteria and Archaea). In this I follow the example of the Brock Biology of Microorganisms, a reference textbook in microbiology (and a wonderful read, by the way).

If you are not familiar with these denominations, here is a brief recap:

How many bacteria out there?

At first sight, it seems a very difficult question to answer. How can we possibly estimate such a number? Well, William Whitman, David Coleman and William Wiebe - all from the University of Georgia, USA - have provided us with a very exciting proposition in a 1998 article published in the Proceedings of the National Academy of Sciences of the USA.

And the astonishing number is: ~5 x 10³⁰ bacteria!

~5,000,000,000,000,000,000,000,000,000,000

Our own 7,000,000,000 suddenly seem less impressive.
 

Whitman and his colleagues noted that the actual total number of bacterial cells had never been assessed, ‘because an estimation of the number of prokaryotes would seem to require endless cataloging of numerous habitats’. It certainly seemed to me that way, but they ended up with a convincing estimation after looking for representative habitats in both aqueous and terrestrial environments. What is striking is that many habitats that show very high densities of bacteria, such as, say, animals’ gut (up to 10¹¹ per g of human colon), account for a negligible fraction of the total. The main crowd is apparently to be found in subsurface sediments and terrestrial subsurface (probably >95%). Hence, what is directly accessible to us (plants, animals, soil, oceans, lakes, etc.) represents a mere 5% of the total bacterial environment. Talking about the tip of the iceberg…