Mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long-term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist....
Microbial communities harbor almost unimaginable complexity at all levels of organization. Vast genomic diversity is present even within a single taxon. Diverse genomes across taxa encode complex regulatory programs that modulate physiological traits from chemotaxis to metabolic processes. From these traits emerge interactions between taxa that depend on abiotic factors. Together, these...
Microbial growth relies on the presence of several nutrients, including elemental nutrients such as carbon and nitrogen, as well as complex nutrients like vitamins and amino acids. Evidence from biogeochemistry, especially in aquatic environments, suggests that multiple nutrients may be simultaneously rare in nature and therefore limit growth. However, we poorly understand how this...
Communities of interacting microbes perform fundamental processes on Earth. These processes arise from a dense network of interactions between individual cells. Most microbial communities are spatially structured systems, where cells move little, thus interactions occur mostly between cells close in space. Therefore, the spatial arrangement of different species can affect the processes that...
Bacteria derived from polymicrobial urinary tract infections (UTIs) together with commensal urinary residents can be viewed as small ecosystems. By measuring pair-wise interactions we obtained a unique insight in the ecological interactions of these microbiome members. We find that many of these bacterial interactions affect the immediate tolerance to antibiotics, as well as their ability to...
Jeroen Meijer, Paulien Hogeweg, Paul Rainey, Bas Dutilh.
Bacteriophages are important players in shaping microbial communities, yet their abundance and dynamics in highly diverse, natural environments remain poorly understood. In particular, many different genotypes of a single phage can be present, but their relevance for viral dynamics and ecological interactions is not currently known....
In this talk I'll provide a survey of studies from my research program all aimed to thinking about higher-order interactions in microbial and social systems. In doing so, I propose the question of whether the science of interactions is truly headed towards being a generalizable physics, that would apply to microbial communities and other sets of actors and parcels of information.
Microbial communities provide an excellent study system to explore the integration of ecology and evolution. At one end of the spectrum, the composition of microbial communities (assessed at broad taxonomic levels) dramatically shifts in response to environmental changes. At the other end, laboratory studies demonstrate the potential for rapid evolution in response to the similar environmental...
A longstanding question in Ecology is which drivers are responsible for the difference in abundance of species within a community. While some species are relatively abundant, many others are rare. Theoretical models have been useful to investigate the drivers of community dynamics. In particular, models that consider the death, birth, and immigration of individuals have been used extensively....
In many natural environments, microorganisms self-assemble around heterogeneously distributed resource patches. The growth and collapse of populations on resource patches can unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of biological interactions and nutrient fluxes. Despite the potential importance of patch-level dynamics for...
Microbes affect global nutrient cycles, the development of our immune system, and resource acquisition and stress responses of multicellular organisms. In a rapidly changing world, we would like to predict the ecological and evolutionary trajectories of populations and communities. Recent efforts have shown that microbial community assembly is often fairly predictable at a functional level,...
Bacteria have the potential for rapid evolution thanks to short generation times, large population sizes, and mechanisms for generating genetic variation. But in the wild they live in open communities made up of hundreds of species and exposed to a constant rain of potential new colonists. This talk discusses the potential consequences of natural diversity for bacterial evolution and outlines...
Understanding how microbial traits affect the evolution and functioning of microbial communities is fundamental for improving the management of harmful microorganisms, while promoting those that are beneficial. Decades of evolutionary ecology research has focused on examining microbial cooperation, diversity, productivity and virulence but with one crucial limitation. The traits under...
Multispecies bacterial communities often perform functions arising from the interactions among their members. These community functions can, in principle, be improved via directed evolution. Yet, current selection methods for improved community function have shown limited success. One reason for this limited success might be that methods of community selection rely on the assumption that...
Mutualisms, or interactions between species where both provide a net fitness benefit to each other, are numerous and ecologically relevant. Presumably, these interactions affect the evolution of both species, possibly resulting in coevolution where evolutionary changes in one causes selection for changes in the other species. However, rigorous studies of coevolution in mutualisms have been...
Predation drives the microbial world, but trophic interactions among microbes are poorly understood. One charismatic predator, the social soil bacterium Myxococcus xanthus, is a model system for studying cooperation and aggregative multicellularity. It has been studied in bi-trophic but never tri-trophic systems, despite the proposed importance for interactions with predators in the evolution...
We analyze properties of experimental microbial time series, from plankton and the human microbiome, and investigate whether stochastic generalized Lotka-Volterra (gLV) models could reproduce those properties. We show that this is the case when the noise term is large and a linear function of the species abundance, while the strength of the self-interactions varies over multiple orders of...
Stressful water-limited soils are typically covered by scattered plant patches that generate a mosaic of low-productive habitats, which are almost devoid of plants and comparatively driven by abiotic filters, interspersed with high-productive habitats comparatively driven by biotic interactions. Such ecosystems provide an ideal setting to disentangle which processes dominate the community...
Microbial communities are incredibly diverse. Molecular techniques such as ‘omics’ have uncovered a vast number of microbial ‘species’ in communities from natural environments. Yet, the ecological and evolutionary processes originating this diversity remain understudied. This study investigated the ecological and evolutionary forces by which new bacterial ‘species’ emerge and coexist in...
Duhita G. Sant 1, Aysha L. Sezmis 1, Laura C. Woods 1 and Mike J. McDonald1* 1 School of Biological Sciences, Monash University, Monash, Australia * Correspondence should be addressed to: mike.mcdonald@monash.edu
Microbial communities comprised of many interacting species sustain all ecosystems and are essential for life. A major goal is to be able to intervene when microbiomes become...
Microbial communities in soil or the mammalian gut are constantly changing, as they first assemble and as species adapt to each other and to their environment. Being able to predict how these dynamics play out is crucial, as these communities greatly affect us and our environment. But since studying co-evolutionary dynamics in natural systems is extremely challenging, in my lab we study small...
Evolutionary dynamics can occur over similar time scales as ecological selection, meaning that there can be feedback between ecology and evolution. However, evidence of concordant eco-evolutionary selection often comes from in vitro studies, where there necessarily will be strong selection. Moreover, these studies have typically focussed on different focal traits meaning ecological and...
Reciprocal interactions such as cooperation, parasitism, altruism, etc are strongly affected by population mixing and modes of transmission. However, the effect of population mixing on the evolutionary dynamics of prey-predator interactions remains largely unexplored. Hence, in a laboratory evolution experiment, we propagated bacterial predator-prey communities in two distinct transfer...
Microbial ecosystems are composed of multiple species in constant metabolic exchange. A pervasive interaction in microbial communities is metabolic cross-feeding. The metabolic burden of producing costly metabolites is distributed between community members, in some cases for the benefit of all interacting partners. In particular, amino acid auxotrophies generate obligate metabolic...
Authors: Josie Elliott, Bridget Watson, Edze Westra, Tiffany Taylor
CRISPR-Cas is an adaptive bacterial defence system that offers protection against foreign DNA, including phages. This antiviral system allows bacteria to acquire resistance to new infections, providing a powerful weapon in the evolutionary arms races that exist between bacteria and their phage. Despite these systems being...
Discharging deeply-sourced groundwater can contain reduced inorganic sulfur compounds that sustain chemoautotrophic ecosystems, yet questions remain regarding the role of CPR bacteria within these complex subsurface communities. Here, we studied two sites where microbial biofilms grow in cold, sulfide-rich groundwater derived from deep crustal and meteoric sources. Profiling of biofilms and...
Managing and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium,...
City sewers shelter rich and diverse bacterial communities that are continuously exposed to antibiotic residues from human excreta, thus becoming a reservoir of resistance. Predicting the risk of antibiotic resistance evolution in city sewers thus requires a comprehensive understanding of the dynamics and evolution of wastewater bacterial communities. However, interactions between species...
Microbial communities comprise an astonishing diversity. Decomposing these often complex communities into small community modules holds the promise to elucidate the mechanisms behind the assembly and maintenance of this diversity. Among these, the apparent competition module, where two prey types compete and are preyed on by a shared predator, has received particular attention, often with a...
Hospital-built environments, and especially Intensive Care Units (ICUs), are hotspots for the emergence, transmission, and evolution of antimicrobial resistance (AMR). Most bacterial species able to acquire genes encoding resistance to antibiotics (ARGs), heavy metals (MRGs) or biocides (BcRGs) are colonizing opportunistic pathogens able to survive in abiotic systems (surfaces, medical...
The study of evolution has traditionally focused on the effects of selection on individuals. In recent years, attention has turned to the possibility of selection on communities. Yet much remains to be understood about the conditions necessary for selection to work on collectives. Previous theoretical works have shown that communities can evolve as units of selection provided that the...
Interspecific coevolutionary interactions can result in rapid biotic adaptation, but most studies have focused only on species pairs. Here, we (co)evolved five microbial species in replicate polycultures and monocultures for 10 weeks (~100 generations) and quantified local adaptation. Specifically, growth rate assays were used to determine adaptations of each species’ populations to (1) the...
Recent work from our lab showed that it is possible to use selfish genetic elements (SGEs) to link genes to community function. My project uses this same experimental approach and applies it to understand how horizontal gene transfer (HGT) might affect the establishment of the microbiome of the well-studied nematode Caenorhabditis elegans. To achieve this, I am experimentally evolving C....
Synthetic communities provide a proxy to reveal the ecological interaction between microbes, including metabolic cross feeding and inter-species signals that influence growth and differentiation. Among these laboratory communities, biofilm retains a spatially organized niche. We have recently demonstrated how metabolic interaction between Bacilli and Pseudomonads in biofilms is translated to...
Bacteria require a diverse set of metabolites to proliferate. While some bacteria fulfil their metabolic needs through de novo biosynthesis, others rely on uptake. Mechanisms enabling stable metabolite provisioning among free-living bacteria, i.e., in the absence of means for positive assortment, remain largely unclear. Particularly, since the production of ‘public goods’ bares the inherent...
Mobile genetic elements (MGEs) are integral members of microbial communities, interacting with cellular microbes as well as other mobile genetic elements (MGEs), and affecting the dynamics and evolution of cells, populations, and microbiomes. Conjugative plasmids are MGEs that can transfer themselves between bacteria, forming a major route for the transmission of diverse adaptive traits in...
