The Vital Question, by Nick Lane - Part 2

Mitochondrion. Source: US NIH

" So what about sex, or the nucleus, or phagocytosis? [...] If each of these traits arose by natural selection – which they undoubtedly did – and all of the adaptive steps offered some small advantage – which they undoubtedly did – then we should see multiple origins of eukaryotic traits in bacteria. But we don't. This is little short of an evolutionary 'scandal'. "
Nick Lane – The Vital Question (2015)

In my previous post I commented on the first part of Nick Lane's book, which deals with the proton-motive force and the origin of life. This second post focuses on the second half of the book, which explores the origin of complex life (i.e. eukaryotic cells).

If the first half of the book was equally part history of the field and part new hypotheses, the second half leans clearly more towards hypothetical ideas – albeit including many facts, and backed with rigorous thinking. Lane's big idea is the following. Most traits that differentiate eukaryotes from prokaryotes (cell and genome sizes, nucleus, introns, sexual reproduction) ultimately follow from a single and singular event: the endosymbiosis event that created mitochondria. For Lane, the organelles that power respiration in all eukaryotic cells are the one special ingredient that permitted the development of cellular complexity.

The Vital Question, by Nick Lane

“In the end, respiration and burning are equivalent; the slight delay in the middle is what we know as life.”

This quote, from Nick Lane’s book The Vital Question (2015), is both poetic and true, which is the mark of great popular science writing. What Lane’s book attempts to do (and in my opinion succeeds in doing) is to radically change our perspective on life by showing us the crucial role played by energy. 

Lane is a biochemist at University College London and already the author of three books. I think there’s something to be said about popular science written by scientists, as opposed to science journalists, in the sense that they can sometimes achieve much more than educating. For example, they can fundamentally change our understanding of some topics (that certainly happened to me on some occasions). Actually, reading The Vital Question reminded me of reading Richard Dawkins’ The Selfish Gene many years ago, and Lane’s book did for me with biochemistry what Dawkins did with genetics and evolutionary theory: it opened a window into a fascinating new landscape. 

Cooperation shapes the spatial patterns of bacterial organization

Cooperative bacterial strains colonizing a surface

Bacteria colonize surfaces in all environments. That could be the surfaces of soil aggregates, of rocks in a stream bed, of plant leaves, of animal skin, or that could be the surface of your showerhead... On such surfaces microbes establish complex communities ('biofilms') that can contain many different interacting species. These various species are usually not randomly distributed in the biofilm, but rather organized depending on their environmental preferences (for example some like well-aerated areas, others not so much...) and on the type of interactions that they have with each other. This can result in complex patterns of organization that manifest at the microscopic scale and up to the millimeter scale. Such patterns are not trivial, as they can sustain microbial activity and functions that would not be possible in a well-mixed environment, which has importance for biotechnology applications as well.

In a new study published this month, we examined the role of cooperation in shaping spatial patterns of bacterial organization on wet surfaces. The paper is available online and is entitled 'Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces'. Our idea was that a feeding dependency between two partners would directly control their distribution in space, hence imposing a specific pattern. We used a simple model system made of two bacterial strains that could grow using the chemical compound toluene (a hydrocarbon), but only when they were working together as a 'team' (a bacterial consortium in the jargon).

Symplasmata: a curious case of multicellularity in bacteria

Cells in a symplasmatum and surrounded by a capsule,
seen with transmission electron microscopy.

'Curiouser and curiouser’, famously said Lewis Carrol’s Alice, as she was experiencing some very peculiar events in Wonderland. I have sometimes felt like Alice when I was studying the curious behavior of the bacterium Pantoea agglomerans [1], during my time in the Lab Leveau at UC Davis.

At first sight, Pantoea agglomerans looks quite ordinary. It grows as rods a few micrometers long, it can swim with flagella and it feeds on all sorts of sugars. It belongs to the family Enterobacteriaceae, and thus it is a distant cousin of E. coli. You can find P. agglomerans in all sorts of environments, but it is particularly good at colonizing the surface of plants, and in certain cases it competes with pathogens and thus keeps its plant host healthy (that is, it can serve as a biocontrol agent). Because it is a very good leaf colonizer, we have used it in many studies of bacterial life in the ‘phyllosphere’ (the aerial surfaces of plants), such as the one described in this previous post. 

Now here’s what special, and actually seemingly unique, about Pantoea bacteria. Under certain conditions, instead of dividing and spreading as individual cells, the bacteria stay close together and form an aggregate containing up to hundreds of tightly packed cells. Aggregation is not uncommon in bacteria but, in the case of Pantoea, cells are constrained by a fibrillar layer, and surrounded by a thick capsule made of polysaccharides, which indicates some level of cooperation and resources sharing (see image on top of the post). The resulting sausage-shaped structures are called symplasmata [2]. Interestingly, the species name 'agglomerans' (forming into a ball), which was coined by the great Dutch microbiologist and botanist Martinus Beijerinck in a paper dating from 1888, probably refers to the species' ability to form symplasmata [3]. Although symplasmata have been known for a very long time, their importance and function in the environment is still a mystery. We have observed symplasmata on bean leaf surfaces, and others have described them attached to the roots of rice plants (Achouak et al., 1994). What is their ecological role? Does it benefit the plant as well? We do not know yet. 

Principles of Microbial Diversity, by James Brown

Published by ASM Press

A new textbook on microbial diversity has just been published by ASM Press. Principles of Microbial Diversity is a relatively thin textbook (392 pages) that is intended for undergraduate students who need to follow a course on microbial diversity, hence filling a gap in the available teaching material. His author is James W. Brown, a professor at North Carolina State University.

The book is pleasant to read and richly illustrated by hundreds of micrographs. But what is quite original, and to me very justified, is the author's perspective, which is, in James Brown's own words in the preface, "phylogenetic and organismal, from the Carl Woese school".  I applaud that! Woese, as I discussed in a previous post, revolutionized biology by showing that we had until then totally ignored a whole distinct domain of life, the Archaea. This discovery was made through the careful analysis of the sequence of 16S rRNA gene (not an easy feat in the days of Woese's work). Because of this pedagogical and scientifical choice, Brown's book dedicates lots of pages to introduce phylogenetic concepts. Notably, he gives a didactic and useful explanation of how to construct a phylogenetic tree (Chapter 3). Brown explains his focus as follows (p. 351):

"In this book, the vantage point from which all of microbial diversity is viewed is the phylogenetic perspective. Other perspectives are possible and are very useful. Medical microbiology views the microbial world from the perspective of its influence on microbe-human interactions and human health. Environmental microbiology views the microbial world from the perspective of biogeochemical processes and ecosystems. […] However, the organizing principle of biology is evolutionary theory. The phylogenetic perspective is the view of biological diversity as the outcome of evolutionary history. This perspective is not exclusive of any other perspective on microbiology, but instead enriches these other perspectives."

Brown's textbook contribution is very welcome, and should find a place in each university's library.

Example of book photo. The eukaryote Arcella. Source: Wikimedia Commons

References:

• Brown, J. W. (2015) Principles of Microbial Diversity. ASM Press, Washington DC. 392 pages.

Mining soil for new antibiotics

Methicillin-resistant Staph aureus. Photo NIAID

The beginning of 2015 brought (potentially) good news for medicine: the discovery of a new antibiotic - teixobactin - isolated from soil bacteria. This result was published in Nature on January 22. (Unfortunately the whole text is not visible without payment or subscription.) Many newspapers and news outlets covered the story in early January, for instance the Guardian, and the New York Times. Teixobactin is a small peptide that acts as an inhibitor of cell wall synthesis in Gram-positive bacteria, which means it can kill pathogens like drug-resistant Staphylococcus aureus (often referred to as MRSA, or methicillin-resistant S. aureus).

The issue at stake here is, of course, the increasing prevalence of antibiotic-resistant bacteria worldwide, a situation well summarized in an article at Swissinfo.ch. We have thus seen a dramatic increase in resistant strains of, for instance, S. aureus, Escherichia coli and Klebsiella pneumoniae. Who or what is to blame? Most probably the overuse of antibiotics, not only in humans but also in animals. It is frightening to know that some pathogenic strains can survive our entire arsenal of antibiotics, while new potent drugs are extremely hard to find. Some simple solutions have helped mitigate the problem, notably more effective and systematic hand disinfection by hopital personnel, but this will not prevent all cases of infection. New antimicrobials are clearly needed, but where to find them?

The Logic of Life, by François Jacob

The Logic of Life (La logique du vivant) opens with the following quote by the French philosopher and Enlightenment figure Denis Diderot:

"Do you see this egg? It's with it that we overturn all theological schools and all temples on Earth".

[All translations in this post are mine.]

The choice of a 18th century thinker for the epigraph prefigures a lot of this book, which was published by the late Nobel laureate François Jacob in 1970. The book—subtitled "a history of heredity"—thus proves to be of great erudition and cites the original work of, among many names, Paré, Montaigne, Paracelse, Descartes, Galilée, Harvey, Réaumur, Buffon, Redi, Leibniz, D'Holbach, La Mettrie, Lamarck, Linné, Geoffroy Saint-Hilaire... and I haven't even mentioned the 20th century references yet! Excusez du peu!

This story of heredity truly is a huge endeavor, spanning about four centuries of philosophical and scientific attempts to understand what kind of stuff we're made of. Articulated in long chapters that correspond to conceptual milestones ("visible structure", "organization", "time", "gene", "molecule", and "integron"), the book follows the chronological development of our biological knowledge (which was part of "natural philosophy") with plenty of referenced sources and with a quality of writing that is hardly matched today.