Microbiomes, Symbiosis & Evolution

Cross section of a marine tidal sediment showing oxic/suboxic (brown) and sulfidic (black) layers

Understanding the vital roles of microbes for our planet

We live in a microbial world. Microbes are the dominant form of life – the most abundant and diverse of all organisms. All other life depends on microbes and the functions they perform, such as oxygen production, nitrogen cycling and degradation of organic carbon. Because microbes are also the most ancient organisms, all other life evolved on a planet already teeming with complex microbial communities. The lives of modern plants and animals, including humans, are therefore intricately intertwined with those of the smallest organisms around them, and microbes are often key to the wellbeing of their larger hosts.

At CeMESS, we study microbial communities in a variety of natural and engineered ecosystems, to understand how they perform their functions and how they evolved to encode them. Specifically, we explore the evolution of mutualism and parasitism, the ecology and biology of marine symbioses, and the interaction of microorganisms with each other, with their predators and with plants. Finally, an important and growing topic is how microbial processes influence the health of humans and other organisms.

Selected host-microbe relationships:
Beneficial symbionts in animals
Intracellular microbes and pathogens
Microbe-plant interactions
Bacteria-virus (phage) dynamics in the wild
Microbiomes in biotechnology and industry, e.g., wastewater treatment
Selected microbiomes:
Soil microbiomes, e.g., grasslands and permafrost
Microbiomes of ocean waters and sediments
Human and animal microbiomes, e.g., gut and skin
Microbiomes in biotechnology and industry, e.g., wastewater treatment
Selected topics in microbial evolution:
Population genomics
Evolution of resistance in hosts and counter resistance in viruses
Horizontal gene transfer rates and bounds in the wild
Mobile genetic element

Microbiomes, microbial symbionts and pathogens

The term “microbiome” describes the microbes associated with a specific environment, such as ocean water, desert soil, or the human body. These communities are often highly diverse, consisting of eukaryotes, bacteria, archaea and viruses. Their interactions with each other and with their environment determine functions such as large-scale ecosystem processes and global nutrient cycles. Many of these functions can also be exploited as biological solutions to waste and pollution. Animal- and plant-associated microbiomes can include microbes that are highly specific and either benefit or harm their host. Beneficial symbionts may provide essential nutrients to their hosts, in exchange for an optimised environment. Bacterial pathogens on the other hand exploit their hosts, sometimes with fatal consequences.Yet, there is a fine line between the two. The molecular mechanisms underlying host-symbiont or host-pathogen interactions are often similar, and the outcome of these associations often depends on environmental conditions, as well as genetics and lifestyle of the host. We study a wide range of systems to elucidate general ecological mechanisms as well as system-specific interactions. Our ultimate goal is to translate fundamental knowledge into a better understanding of how global change will affect ecosystem services, and how we can influence the health of plants, animals and humans.

Measuring salinity while sampling seawater at Nahant, Massachusetts to study drivers of microbial population structure.

Microbial Evolution

The process of evolution underlies adaptation of organisms to everchanging environmental conditions. Because microbes have fast generation times, evolutionary change happens on shorter time scales than in plants and animals, making microbes important model systems to understand the causes and consequences of evolution in general terms. However, the modes of evolution also differ in bacteria and archaea from those in eukaryotes. Horizontal gene transfer between unrelated individuals can introduce entirely novel sets of genes to genomes, and it is such genes that may, for example, turn a harmless bacterium into a pathogen, allow a microbe to utilise a new nutrient, or introduce antibiotic resistance to entire communities of organisms. Because evolution in microbes is fast, it can happen on ecological timescales, thus influencing how populations and communities of organisms change under different conditions. We cover diverse topics in microbial evolution, ranging from reconstruction of evolutionary history of genes and pathways to how species and populations arise and change. This includes investigating how organisms adapt to each other, such as how resistance to viruses evolves in microbes in the wild. Finally, we use experimental evolution to explore to what extent outcomes of evolutionary processes are reproducible and predictable.