Research
Adapted from Goldford et al. (2018).
Microbial community assembly
I am currently conducting experiments with natural soil microbial communities to understand how microbial communities assemble in simple environments. Some of the questions I am asking are: Why is there taxonomic variability in microbial community assembly? What is the effect of migration on community assembly and dynamics? What is the role of species interactions in shaping the emergent properties of these multi-species communities (e.g. function and stability)?
To address these questions, I am combining two approaches: top-down assembly of microbial communities (and perform 16S sequencing to see who is there) and bottom-up reconstitution of microbial communities (by isolating key species members and then asking how do they interact in duos, trios, ..). See also Goldford et al (2018).
I am currently conducting experiments with natural soil microbial communities to understand how microbial communities assemble in simple environments. Some of the questions I am asking are: Why is there taxonomic variability in microbial community assembly? What is the effect of migration on community assembly and dynamics? What is the role of species interactions in shaping the emergent properties of these multi-species communities (e.g. function and stability)?
To address these questions, I am combining two approaches: top-down assembly of microbial communities (and perform 16S sequencing to see who is there) and bottom-up reconstitution of microbial communities (by isolating key species members and then asking how do they interact in duos, trios, ..). See also Goldford et al (2018).
From Estrela et al. 2021 (Cell Systems).
Which descriptive features of microbial communities are reproducible and predictable, which are not, and why? Here we address this question by experimentally studying parallelism and convergence in microbial community assembly in replicate glucose-limited habitats. We show that the previously observed family-level convergence in these habitats reflects a reproducible metabolic organization, where the ratio of the dominant metabolic groups can be explained from a simple resource-partitioning model. In turn, taxonomic divergence among replicate communities arises from multistability in population dynamics. Multistability can also lead to alternative functional states in closed ecosystems but not in metacommunities (Estrela et al. 2021).
Adapted from Estrela et al. 2012 (i) and from Estrela & Brown 2013; Estrela et al. 2015 (ii).
Metabolic interactions and consequences for microbial community functional and spatial relationships
How do metabolic interactions between species (cross-feeding, detoxification) shape their emergent functional and spatial relationships? We have shown that a single mechanism of metabolic exchange - food for detoxification of metabolic waste products- can generate a diverse array of ecological relationships, depending on the properties of the metabolic by-products exchanged (Estrela et al. 2012). In addition, using an individual-based model of biofilm growth, we showed that under competitive interactions microbial species tend to segregate while under mutualistic interactions they tend to mix (Estrela & Brown 2013).
I am also interested in applying fundamental principles of microbial interactions to real world problems, especially health and disease. Applying our findings to the challenge of antibiotic resistance, we recently showed that the ecological and spatial relationships between bacterial species impact how communities respond to antibiotics. In particular, we showed that competition between antibiotic-resistant and sensitive bacteria leads to the 'competitive release' of the resistant type whereas mutualism leads to a ‘mutualistic suppression' where both species are harmed by antibiotics. In addition, these effects may be magnified or dampened, respectively, in structured environments because competitors tend to segregate while mutualists tend to mix as they grow (Estrela & Brown 2018).
How do metabolic interactions between species (cross-feeding, detoxification) shape their emergent functional and spatial relationships? We have shown that a single mechanism of metabolic exchange - food for detoxification of metabolic waste products- can generate a diverse array of ecological relationships, depending on the properties of the metabolic by-products exchanged (Estrela et al. 2012). In addition, using an individual-based model of biofilm growth, we showed that under competitive interactions microbial species tend to segregate while under mutualistic interactions they tend to mix (Estrela & Brown 2013).
I am also interested in applying fundamental principles of microbial interactions to real world problems, especially health and disease. Applying our findings to the challenge of antibiotic resistance, we recently showed that the ecological and spatial relationships between bacterial species impact how communities respond to antibiotics. In particular, we showed that competition between antibiotic-resistant and sensitive bacteria leads to the 'competitive release' of the resistant type whereas mutualism leads to a ‘mutualistic suppression' where both species are harmed by antibiotics. In addition, these effects may be magnified or dampened, respectively, in structured environments because competitors tend to segregate while mutualists tend to mix as they grow (Estrela & Brown 2018).
|
Evolution of microbial dependencies and host-microbe dependencies
Why and how do some species lose functions that leave them dependent on other species? We showed that whether full autonomy, one-way dependency or mutual dependency arises depends on the interplay between costs, essentiality and privatization level of the function (Estrela et al. 2015). In some cases, such dependencies can be so strong that 'individuals' (or organisms) eventually lose their own 'individuality' and merge together, forming a symbiotic organism. I am interested in why and how this happens. That is, why do different species come together to form a single, fully integrated organism (defined as a major egalitarian transition)? What are the evolutionary paths to symbiotic organismality? We have proposed that classifying host-symbiont associations into two interconnected continuum axes: a symbiont’s dependency for dispersal into new hosts (symbiont mode of transmission) and interdependency for reproduction, growth and survival (dependency for nutrients/services) can help us better understand and predict the evolutionary path to symbiotic organismality (Estrela et al. 2016). |
Adapted from Estrela et al (2015).
Adapted from Estrela et al (2016).
|
