In this talk we'll explore three different approaches to understanding and prediction in microbiomes. First, we'll explore commonalities between microbial community dynamics and several other complex systems, identifying where general lessons and constraints can inform our interpretation of community patterns. Second, we'll survey a range of mechanistic models, where these have given insights,...
To understand the organization and dynamics of microbial communities is a fundamental challenge in current biology. To tackle this challenge, the construction of computational models of interacting microbes is an indispensable tool. There is, however, still a chasm between ecologically motivated descriptions of microbial growth used in typical ecosystems simulations, and the detailed metabolic...
Predation shapes biological evolution at multiple scales, from genomes and organisms to entire ecosystems. Albeit traditionally studied in larger organisms, predation also pervades the microbial world: nematodes and protists ingest prey whole via phagocytosis; many Bdellovibrio-and-like organisms (BALOs) invade their prey and reproduce in a virus-like fashion; and group-hunting myxobacteria...
Research on consumer-resource dynamics is vast and has been addressed in both theoretical and empirical studies. A primary goal in this research agenda is to understand how mascroscopic descriptions of trophic interactions relate to the individual processes that define the consumer-resource interaction in the first place. Despite decades of studies, there is still no clear agreement on the...
Soil bacteria are critical for sustaining ecosystem functions and services. Recent studies show that soil bacterial communities are susceptible to climate change, particularly to extreme climatic events. Yet, we know little about the biotic mechanisms through which extreme climatic events, such as heat waves, restructure soil bacterial communities. Previous studies indicate that slower growing...
Glacial retreats represent a unique opportunity to study primary successional processes. The new exposed rock is a new material for the assembly of a new ecosystem. Soil formation after glacial retreat is strongly influenced by plant colonization, but this colonization depends on nutrient availability. An ongoing project in the forefront of the last Venezuelan glacier has established a...
Plants are associated with a diverse microbiome consisting of bacteria, fungi, and protists that play a crucial role in establishing a stable microbial community that contributes to the health of their host under atypical environmental stresses. Although these microbial communities are co-evolved with plants in either beneficial, commensal, or pathogenic lifestyles, how each member cooperates...
Multilevel selection in host-associated microbiomes has important implications for understanding the origin and evolution of these complex associations. To date, we do not have a clear understanding of the different levels that can affect selection on microbial communities. There is evidence that the higher level of selection provided to the microbiome by the host has a significant impact on...
The gut microbiota is now well established as a mediator of human health and disease with a central role in a myriad of host functions beyond digestion, including immune modulation, metabolic regulation and neurological signalling. Compositional changes in these bacterial communities have been causally linked to a multitude of diseases including obesity, inflammatory bowel disease, cancer,...
The microbial ecosystem is full of narrow constrictions that microorganisms need to learn to navigate in order to survive. Here, we study a Nature example of a "microorganism billiard": a system composed of a population of microorganisms packed in a closed space, with only a few narrow apertures to escape from. This situation occurs when the marine parasite Parvilucifera sinerae infects and...
Oceanographers can now collect flow cytometry data in real time while onboard a moving ship, which provides them with fine-scale information about the distribution of phytoplankton across thousands of kilometers. This presents an exciting opportunity to learn new insights about the microbial ecology of the ocean. We present a set of novel statistical models to estimate the time-varying...
In this talk, I will address some timely questions in theoretical ecology by discussing the Generalized Lotka-Volterra model in the presence of many randomly interacting species and finite demographic fluctuations. Leveraging on disordered systems’ techniques, I will unveil a rich, eventually hierarchical, organization of the equilibria and relate the slowing down of dynamical correlators to...
In the very recent years, an increasing amount of interest has been devoted to the study of models of ecosystems defined on sparse random graphs.
In this scenario both network topology and interactions nature play a relevant role in establishing the ecosystem properties.
In particular, differently from what usually happens in dense random matrices, the spectra of locally tree-like graphs...
This talk aims at opening a debate on i) how to address important challenges in predicting microbial community dynamics and ii) how to leverage state-of-the-art ecology to control microbial community dynamics.
I will begin with a brief overview of the dynamics of natural communities in terms of stability in composition and functions, fluctuations, and response to perturbations. Next, I will...
Collectives of microbes exhibit functions that individual species cannot, such as degrading waste, producing vitamins, and creating biofuels, which can benefit humans. To improve these functions, researchers suggest using artificial selection on collectives to choose the best-performing ones for the next generation. However, this method has shown that there is a limitation to improving the...
Photosynthetic organisms, such as land plants and algae, release organic compounds to the surrounding environment, which create a niche for colonization by heterotrophic microbes. These microbes consume photosynthates and assemble into complex communities, often providing their host with beneficial services in exchange, such as pathogen protection, or enhanced nutrient mobilization. While...
Microbes are ubiquitous and play key roles in ecosystem functions. In nature, most microbes live in spatially structured multi-species communities. In such communities, cells live in close proximity and engage in a variety of metabolic interactions with neighbours. The overall metabolic potential of a microbial community is determined by the activities of individual cells and the interactions...
The enormous diversity of heterotrophic bacteria in the environment begs the question to what degree their metabolic niches can be understood in terms of a small number of simplified metabolic categories. Here, we show that, despite high variability at all levels of taxonomy, the catabolic niches of heterotrophic bacteria can be understood in terms of their preference for either glycolytic...
There is a clear need for robust tools for prediction and inference of ecological dynamics that do not depend on precisely knowing how ecosystems work. Data-driven methods such as empirical dynamic modeling (EDM) allow us to learn dynamics with minimal assumptions. Here, I will introduce the basic ideas of EDM and then discuss two recently developed approaches to incorporating external driving...
Seasonality in the conditions for life is a ubiquitous phenomenon in the grand majority of biomes at the Earth’s surface. In aquatic environments, reasonably predictable temporal dynamics in physicochemical conditions of for example temperature and nutrients along with biotic variables set the stage for successional changes in planktonic food webs. This is frequently first noted as changes in...
Marine diazotrophs convert atmospheric nitrogen gas into bioavailable nitrogen that can fuel up to 50% of the primary productivity in oligotrophic subtropical and tropical seas. Despite their importance, little is known about their global biogeography and diversity since global studies have been hampered by scarce data observations. This limitation prevents us from understanding the link...
We all know that activities and interactions of microbes in the wild underpin the biogeochemical cycles that support earth’s biomes, and the modern climate that we love so well. As in other ecosystems, in the oceans these activities can be difficult to measure particularly in connection with molecular mechanisms or in a manner that identifies the key members responsible for an activity....
