Development and application of millifluidic technologies to the study of microbial population biology

Working with LCMD and MilliDrop Instruments, LGE is at the forefront of the development of new applications for droplet technologies in microbiology and evolution. Initial foci of investigation include the relationship between microbial population density and growth dynamics, interactions between populations of pyoverdin-producing and non-producing populations, and phage-bacteria co-evolution.

Maxime Ardré, Steven Quistad and Guilhem Doulcier are working on this

Ecological scaffolding and the major evolutionary transitions

Life is hierarchically structured, with replicating entities nested within higher order self-replicating structures. Take, for example, multicellular life: the multicellular entity replicates, as do the cells that comprise the organism. Inside cells are mitochondria that also have capacity for autonomous replication; the same is true of chromosomes within the nucleus, and of genes that comprise chromosomes. Such hierarchical structure reflects a series of major evolutionary transitions in which lower order self-replicating entities have been subsumed within higher order structures. Typically this involves the lower level entity “giving up its right to autonomous replication” and with this “sacrifice” comes enslavement to the “needs” of the higher order “corporate body”. Posed in these terms it is difficult to see how evolutionary transitions unfold; how selection might shift levels and why life is hierarchically structured.

Necessary for progress is clarity concerning what needs to be explained: the evolution of Darwinian Individuality those properties of entities (variation, reproduction and heredity) that ensure participation in the process of evolution by natural selection. There has been a tendency to assume these properties as pre-existing, but they are not: they are derived and require evolutionary explanation. Pressing to the heart of the problem, the challenge is to explain how Darwinian properties emerge from non-Darwinian entities by non-Darwinian means. This challenge permeates each evolutionary transition including the emergence of life from matter.

Solutions to this seemingly unsolvable problem arise once ecology is considered and thus possibilities for Darwinian properties to be exogenously imposed. Such ideas underpin on-going work on the evolutionary transition to multicellularity and also the construction of symbiotic communities. A major motivation for development of millifluidic technologies stems from the realisation that droplets themselves can become units of selection in their own right. This has driven theoretical developments that guide operation of selection over longer time scales, investigations into the emergence of heredity, reproduction and new opportunities for top-down engineering of microbial communities, with applications in biotechnology, medicine and agriculture.

Guilhem Doulcier is working on this, but much has been done in recent times by Philippe Remigi and Daniel Rexin (on the evolution of multicellularity) with the experiment now continuing at the MPI for Evolutionary Biology; work on ecological scaffolding and the evolution of reproduction is in collaboration with Andrew Black at the University of Adelaide and Pierrick Bourrat at Macquarie.

See publication in Nature Ecology & Evolution (2020) here.

The evolution of heredity

In major evolutionary transitions of the egalitarian type, the primary challenge is to explain how alignment of reproductive interests of the ancestral partners came into being given destabilising effects wrought by individual-level selection. One possible explanation involves growth of partner types under ecological conditions (specific population structures) that result in collectives of types being units of selection.

Our focus is on development of mathematical descriptions of evolution within this meta population structure and subsequent testing of ideas using millifluidic devices.

Guilhem Doulcier worked on this in collaboration with Silvia De Monte (EEM, IBENS), and Amaury Lambert (SMILE, UPMC). The work was funded by the Programme Origines et Conditions d’Apparition de la Vie PSL Research University, Paris. (ANR-10-IDEX-0001-02)

See publication in eLife (2020) here.

Lateral gene transfer and impacts on the ecological and evolutionary dynamics of microbial communities

Although the mechanics of horizontal gene transfer are well understood, its operation, impact and dynamic at the level of communities is unknown. In a year-long selection experiment we have followed "adaptation" of microbial communities to a new carbon source in the presence and absence of horizontal gene transfer. Current efforts focus on dissecting the evolutionary response using metagenomic approaches incorporating chromosome conformational capture and whole genome resequencing, and stable isotope analysis.

Steven Quistad worked on this and much more happens here.

See publications in Philosophical Transactions of the Royal Society (2020) here and here.

Biophysics of microbial mat formation

At the heart of many Rainey lab experimental analyses of evolution in real time are a class of genotype that builds a complex self-supporting mat at the air-liquid interface of static broth microcosms. New quantitative optical scanning approaches have been developed by LGE to study the dynamics of mat formation, and to unravel hitherto unstudied dimensions of the genotype-to-phenotype map.

Maxime Ardré is working on this.

See publication in Journal of Bacteriology (2019) here.

Phage in droplets

Phage drive the evolution of bacteria through antagonistic coevolution and by promoting transfer of genetic material between bacteria. This project seeks to understand the mechanism behind a phage-induced growth phenotype using and Evolution Machine, developed by Millidrop Instruments.

Steven Quistad is working on this

The biophysics of diffusible products

Bacteria produce and secrete a range of molecules many of which affect interactions with neighbouring cells. A particularly well-studied example is the water soluble iron-chelating agent pyoverdin. Development of new millifluidic technologies in combination with microscopy and genetics allows enhanced understanding — and quantification of — the physical basis of microbial interactions.

Clara Moreno-Fenoll and Maxime Ardré are working on this with Clara focused on the mechanistic basis of pyoverdin privatisation

Building hybrid microbe-machine ecosystems

The interface between artificial intelligence and factors governing the establishment of biological complexity is largely unexplored. LGE is home to a new programme in which machines manipulate microbial systems, monitor their responses at microscopic scale, processes the resulting response, and then further impose new stimuli to control pattern formation. Ultimately we seek an artificial intelligence that will co-evolve with a given microbial community.