Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems.

@article{Goyal2018DiversitySA,
  title={Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems.},
  author={Akshit Goyal and Sergei Maslov},
  journal={Physical review letters},
  year={2018},
  volume={120 15},
  pages={
          158102
        }
}
Microbial ecosystems are remarkably diverse, stable, and usually consist of a mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real ecosystem data, specifically species abundance and prevalence distributions. Resource competition and metabolic commensalism drive the stochastic ecosystem assembly in our model. We demonstrate that even when supplied with just one resource, ecosystems can exhibit high… 

Figures from this paper

Laws of diversity and variation in microbial communities
TLDR
It is shown that a mathematical model based on environmental stochasticity quantitatively predicts the three macroecological laws, as well as non-stationary properties of community dynamics.
Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities
TLDR
This work shows that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a “resource-limited” regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species’ consumption preferences.
Enzyme regulation and mutation in a model serial-dilution ecosystem.
TLDR
This paper makes explicit, using a simple serial-dilutions framework, the conflicting ways that microbial adaptation and evolution can affect community diversity.
Emergent Diversity and Persistent Turnover in Evolving Microbial Cross-Feeding Networks
TLDR
This work studies how complex cross-feeding networks of microbial species may develop from a simple initial community given some elemental evolutionary mechanisms of resource-dependent speciation and extinctions using a network flow model and finds that even in stable environments, the system is subject to persisting turnover, indicating an ongoing co-evolution.
Nutrient levels and trade-offs control diversity in a serial dilution ecosystem
TLDR
It is demonstrated theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.
Microbial metabolically cohesive consortia and ecosystem functioning
TLDR
It is argued that the ability to identify MeCoCos would open new avenues to link the species-, community-, and ecosystem-level properties, with consequences for the understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild.
Macroecological laws describe variation and diversity in microbial communities
  • J. Grilli
  • Environmental Science
    Nature communications
  • 2020
TLDR
It is shown that a mathematical model based on environmental stochasticity, the Stochastic logistic model, quantitatively predicts the three macroecological laws, as well as non-stationary properties of community dynamics.
Metabolically cohesive microbial consortia and ecosystem functioning
TLDR
It is argued that the ability to identify MeCoCos would open new avenues to link the species-, community- and ecosystem-level properties, with consequences for the understanding of microbial ecology and evolution, and an improved ability to predict ecosystem functioning in the wild.
A simple linear relationship between resource availability and microbial community diversity
Microbial community diversity is pivotal for the functioning of our planet, but its drivers are still unclear, in particular the role of resource number and identity. To fill this gap, we studied the
Nutrient levels and trade-offs control diversity in a model seasonal ecosystem.
TLDR
It is demonstrated that in serial dilution culture, metabolic trade-offs allow for arbitrarily high diversity, and it is found that, unlike the chemostat case, diversity depends on the amount of nutrient supplied to the community.
...
...

References

SHOWING 1-10 OF 66 REFERENCES
Metabolic Trade-Offs Promote Diversity in a Model Ecosystem.
TLDR
This model spontaneously reproduces several notable features of natural ecosystems, including keystone species and population dynamics and abundances characteristic of neutral theory, despite an underlying non-neutral competition for resources.
Microbial diversity arising from thermodynamic constraints
TLDR
It is shown that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products, and this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy.
Chemical warfare between microbes promotes biodiversity
TLDR
It is suggested that antibiotic interactions within microbial communities may be very effective in maintaining diversity, based on a spatially explicit game theoretical model with multiply cyclic dominance structures.
Estimating prokaryotic diversity and its limits
TLDR
It is evident that local and global prokaryotic diversity can be understood through species abundance curves and purely experimental approaches to solving this conundrum will be fruitless.
Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems
TLDR
The analysis leads to a reciprocal relationship between bacterial diversity and viruses, in which coexistence of competing bacterial species is ensured by the presence of viruses that ‘‘kill the winner,’’ whereas the differences in substrate affinity between the coexisting bacterial species determine viral abundance.
Diversity, stability and resilience of the human gut microbiota
TLDR
Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
Metabolic trade-offs and the maintenance of the fittest and the flattest
TLDR
The possibility of a new general mechanism of stable diversity maintenance, one that stems from metabolic and physiological trade-offs, is demonstrated and predicted, which predicts the enigmatic richness of metabolic strategies in clonal bacteria and questions the safety of lethal mutagenesis as an antimicrobial treatment.
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
TLDR
The approach presented here lays the foundation for a reverse-ecology framework for addressing key questions concerning the assembly of host-associated communities and for informing clinical efforts to manipulate the microbiome.
Cooperation and Competition in the Evolution of ATP-Producing Pathways
TLDR
It is shown that ATP production with a low rate and high yield can be viewed as a form of cooperative resource use and may evolve in spatially structured environments and argued that the high ATP yield of respiration may have facilitated the evolutionary transition from unicellular to undifferentiated multicellular organisms.
Using network analysis to explore co-occurrence patterns in soil microbial communities
TLDR
The potential of exploring inter-taxa correlations to gain a more integrated understanding of microbial community structure and the ecological rules guiding community assembly is demonstrated.
...
...