A view of microbial life in soil

Image source

All soils teem with microscopic life that is invisible to the naked eye, and for that reason often overlooked. Yet, microorganisms are an essential component of all soils, and through their metabolic activity (mineral weathering, production and recycling of organic matter, and more) soil microbes actually play a major role in soil formation, development, and fertility.

The images presented here show diverse microorganisms inhabiting a pasture soil. I sampled this soil on the Uetliberg, in Zürich, Switzerland, in 2018. Samples were chemically fixed and observed with scanning electron microscopy. Post-acquisition pseudocoloring was applied to the images - in other words, colors were added to the original black and white images to facilitate visualization of the microbes and soil particles. (The pseudocolors do not represent the real colors of the samples.)

All images are courtesy of the Soil and Terrestrial Environmental Physics group of Dani Or at ETH Zurich. SEM image acquisition and coloring by Anne Greet Bittermann, ETH Zurich - ScopeM.

We do not know the precise identity of these microbes (we would need DNA sequencing for that), but given their shape and size some level of characterization is possible. Most of them are bacteria, which are the most abundant cellular organisms in all soils.

 

Self-organization of bacterial populations

Fluorescent bacteria in glass microchannels

In many environments, hundreds, sometimes thousands of different microbial species coexist as mixtures of cells of various sizes and shapes. For example, each human being teems with their very own and unique microbial mixture (trillions of cells), as the human microbiome project unveiled a few years ago. Microbial diversity in soil is equally – possibly even more – astounding, with a gram of rich soil capable to host thousands to millions of distinct bacterial and archaeal species, as well as hundreds of fungal and protistan species. A recent study in the magazine Nature highlights the results of the earth microbiome project, which aims at revealing the extent of  microbial diversity on our planet.


Yet, despite this wealth of diversity, microbial communities are not simply soups of species – there is order hiding behind this curtain of complexity. Actually, the more we look, the more we find patterns of microbial organization in the natural world. Some patterns are obvious and have been known for a long time, such as the distinct layers of microorganisms visible with the naked eye in sections of microbial mats. The vast majority of patterns, however, reveal themselves only at the scale of individual microbes, that is, at the microscopic scale. See, for example, the beautiful arrangements revealed in  the lab of Jessica Mark Welch at the University of Chicago. 

Microbial populations are thus often spatially organized at small scale, and in a very defined and refined way. But how does it work? Obviously, microbes don't organize following some kind of blueprint that is imposed on the community!... But what then? Part of the answer seems to reside in so-called self-organization processes. With such processes, patterns emerge from the individual behavior of cells that can only sense the conditions in their local environment and react accordingly. This in appearance simple process at the individual level can lead to seemingly complex patterns of organization at larger scale. Think of bird murmuration, or of how ants can form bridges with their own bodies! I also discussed spatial patterns of bacterial organization triggered by metabolic cooperation in a previous post.

In a recent paper whose lead author is my colleague Benedict Borer, we examined some of the basic processes that can lead to bacterial spatial self-organization. (In that study we were specifically interested in pore networks that mimic the spatial structure of soil aggregates, but the processes that matter here are valid in other kinds of environments as well.) The idea is as follows. In a given habitat, bacterial populations with distinct metabolic capabilities and food preferences would spontaneously arrange in space in order to optimize their use of the available resources. We thought there must be two necessary conditions for that. First, that the bacterial cells have some level of motility (which could be flagellar motility, such as swimming, or simply movement provide by growth and cell division). Second, that gradients of carbon and nutrients are present in the habitat (i.e. there must be some spatial heterogeneity for the microbes to respond to).  


We chose to work with two bacterial species that differ on their ability to respire: one is a strict aerobe (Pseudomonas putida), which only respires using oxygen as final electron acceptor, while the other (Pseudomonas veronii) is a facultative anaerobe that can respire with oxygen but also with nitrate as final electron acceptor. Both species are motile thanks to flagella that they can use to swim within liquid films. To facilitate observation, the two species were each tagged with a distinct fluorescent protein (green or red). The two bacterial populations were inoculated into micrometric pore networks with various structures,  and which allowed us to create gradients of oxygen (coming from the periphery of the network) and of carbon source (citrate, coming from the center of the network). Although initially well-mixed in the center of the network, after a week of incubation the two bacterial species segregated in the network to form two distinct and coexisting populations (see figure below). One grew preferentially where the oxygen was more abundant (the obligate aerobe), while the other could occupy the anoxic niche at the center of the network, which also contained more carbon.
 

The two bacterial populations, initially well-mixed, grow and segregate in the pore network as function of their respiration metabolism. From Borer et al., 2018

Interestingly, this spatial organization did not occur when carbon source and oxygen were provided together (i.e., there was no counter-gradients of oxygen and carbon). Another intriguing result was that the coexistence of the two species, as seen in the figure, could not been achieved in well-mixed liquid environments (vials or flasks), because one of the species would always win over and dominate the community (see below). This illustrates how the habitat spatial structure can help limit competition and maintain species coexistence.

Experimental and modeling results show competitive exclusion in homogeneous cultures (a) and coexistence in structured pore networks (b). The percentage corresponds to the connectivity in the network (100% is highest connectivity).

Admittedly, our system is artificial and our community only composed of two species... Yet,  the basic mechanisms that we observed most probably also apply to more complex environments and could participate to the final structure of the community. Bacteria have a remarkable faculty of optimizing their distribution and activity in complex habitats, which we could demonstrate with our simple mathematical and experimental models.
 

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.