Saturday, March 07, 2015

Microbes encourage us to rethink the foundations of biology

2 linked bacteria from Benomar et al
Bacteria are by far the most numerous living creatures on earth, and continue to hold many surprises.

A fascinating review in Science of a book called The  Philosophy of Microbiology  by a philosopher of biology called Maureen O'Malley draws attention to many of the ways in which our thinking about microbes has changed and has to change further.  The reviewer says the book
makes a case for the special significance of microbes by describing four of their unique features:
  • their biomass and diversity,
  • ability to impact planetary processes,
  • influence on the major evolutionary transitions, and 
  • tendency to coexist in mutually beneficial relationships with other organisms. 
Of course the relationships are not always mutually beneficial - but in the great majority of cases they are. Indeed microbes certainly made the earth inhabitable for higher animals by generating enough oxygen, almost certainly are the origin of mirochondria, and our microbiomes in our gut and other places play a significant role in our continued health.

This article in Nature gives a summary of much of what is known about gut microbiomes.

There are also a couple of fascinating papers referred to in Nature about different species of microbes cooperating in unexpected ways.
  • Benomar et al show that "Nutritional stress induces exchange of cell material and energetic coupling between bacterial species" They "demonstrate the formation of an artificial consortium between two anaerobic bacteria, Clostridium acetobutylicum (Gram-positive) and Desulfovibrio vulgaris Hildenborough (Gram-negative, sulfate-reducing) in which physical interactions between the two partners induce emergent properties. Molecular and cellular approaches show that tight cell–cell interactions are associated with an exchange of molecules, including proteins, which allows the growth of one partner (D. vulgaris) in spite of the shortage of nutrients. This physical interaction induces changes in expression of two genes ...with concomitant changes in the distribution of metabolic fluxes, and allows a substantial increase in ​hydrogen production without requiring genetic engineering.
  • A separate study mutated E. coli and Acinetobacter baylyi so that they could not produce certain essential amino acids. When grown in a medium lacking the amino acid it required, E. coli formed nanotubes up to 14 micrometres long to connect with and share the cytoplasm of nearby A. baylyi, which was producing the amino acid. In return, E. coli provided A. baylyi with the amino acid it needed. These bacteria function as interconnected entities rather than individuals, the authors suggest.
Astonishing stuff. And further confirmation that the new synthesis Denis Noble and colleagues seek is so essential. "Selfish Genes" simply don't hack it here!

PS I sent this to Denis who was kind about the post, and I was delighted to hear that he was at an event to celebrate 350 years of Proceedings of the Royal Society, where they had picked 33 papers published over the last 350 years and DiFrancesco and Noble (1985) ‘A model of cardiac electrical activity incorporating ionic pumps and concentration changes’ was one of the papers featured!

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