Kingdoms or domains?

I view taxonomy – the classification of organisms – at the same time as the most useless and the most useful science. Useless because we know that all life forms are related to one another, and therefore the categories that we create to separate them are arbitrary (with the exception of the distinction at the species level). Most useful, since naming and organizing things seem necessary if we are to claim any knowledge. And isn't it a true pleasure (I almost dare to write "bliss") to point at a plant, a mushroom or an animal (if the latter doesn't move too fast) and be able to name it? 

I learned my share of taxonomy as a student, but I also forgot quite a bunch… At least I remember that I got a good grade at my zoology exam (I had to talk about the subphylum Chelicerata!), based on a course by one of the best professors I ever had, Peter Vogel. 

Taxonomy, which is part of Systematics (the study of biological diversity), proposes a hierarchy from the most particular to the most general: Species, Genera, Families, Orders, Classes, Phyla… (In the classic evolutionary taxonomy, classification is mostly based on morphology, while modern molecular systematics compares the sequence of amino acids in proteins or of nucleotides in nucleic acids.) But, what about higher (more global) levels of classification? 

Unwanted guests

Microbial contaminants (three species) on a plate

Microbiologists use Petri dishes, filled with a variety of agar media, to grow microbes. Even a small lab can produce hundreds of plates every week… And it is quite common to store in the fridge those of these plates that are not directly inoculated for a future use. Thus, when you open a microbiologist's fridge, you may find columns of Petri plates labeled with the medium and antibiotics they contain, waiting to be covered with a suspension of microbes.

Sometimes, when you store them for long periods, you can have the disagreeable surprise to find unwanted guests on your plates, that is, contaminant microbes!

Back from ASM General Meeting

I'm just back from the 112^th general meeting of the American Society for Microbiology, which took place from June 16 to 19 in San Francisco. The general meeting is huge: thousands of microbiologists from all over the US and abroad, representing all fields of microbiology; hundreds of talks and more than 3,000 posters presented; about 200 biotech companies showing their products. 

That is something to see! It's great to feel part of this large community of microbiologists. We are one big family, even though we work on topics as varied as human health, environmental ecosystems, agriculture, food safety, biotechnology, etc.

The endosymbiotic theory of Lynn Margulis

Published by Basic Books

Lynn Margulis passed away last November, sadly. She was renowned for the endosymbiotic theory of evolution, which is now part of biology textbooks. She had a wonderful insight: the mitochondria and chloroplasts that are found in eukaryotic cells were, in distant past, free-living bacteria. Thanks to at least two distinct endosymbiosis events, they were incorporated—and not digested—in the eukaryotic ancestor. They became responsible of key functions within the new association, namely respiration and photosynthesis. These symbionts persisted until at some point they were indistinguishable from their host, and all merged to become one new organism, a eukaryotic cell. 

Recently I found a copy of her book Symbiotic Planet (1998) in my usual second-hand bookshop in Davis. It is a short book in which Margulis deals with the scientific idea that has occupied her during most of her career: the serial endosymbiosis theory (or SET). The author sums up the book as follows (p.33):

In short, I believe that most evolutionary novelty arose, and still arises, directly from symbiosis.

Filamentous bacteria under the microscope

Filamentous bacteria from soil, seen with phase contrast microscopy.

It's pretty easy to isolate soil bacteria: take a scoop of soil, mix it with some water, then plate the liquid on a Petri dish and incubate it overnight at 25-30 °C. Voilà. 

The isolated bacterial species will vary with the conditions (type of medium, temperature); here I found many filamentous bacteria on the plate. They look a little bit like filamentous fungi (since they also form a mycelium), but usually you can easily tell them apart (with a microscope) because of their smaller diameter. 

The Human Zoo by Desmond Morris

Back in the days when I was a biology student in Lausanne I had a great time reading Desmond Morris' best seller The Naked Ape (1967), in which the British zoologist discusses what sort of curious social animals we are—and he does so with a lot of wit and humor.  

The Human Zoo (1969) is his follow-up book, thus when I found a copy of it in a second-hand bookshop I happily bought it (probably equally motivated by the lovely vintage yellow cover!). Newer editions are available, as you can see in the author's bibliography.

The Human Zoo still deals with the human animal, but this time the focus is on the social ties that we develop between each other and the sort of society in which we live. The underlying question is: How beings used to living in tribes of at most hundreds of individuals can cope with our modern society and its super-tribes of millions? The city, writes Morris, is not a concrete jungle, it is a human zoo. In the modern life and its crowded places, we tend to behave as animals in captivity.

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.