Dynamic carbon flux network of a diverse marine microbial community
Open Access
- 25 September 2021
- journal article
- research article
- Published by Oxford University Press (OUP) in ISME Communications
- Vol. 1 (1), 1-10
- https://doi.org/10.1038/s43705-021-00055-7
Abstract
The functioning of microbial ecosystems has important consequences from global climate to human health, but quantitative mechanistic understanding remains elusive. The components of microbial ecosystems can now be observed at high resolution, but interactions still have to be inferred e.g., a time-series may show a bloom of bacteria X followed by virus Y suggesting they interact. Existing inference approaches are mostly empirical, like correlation networks, which are not mechanistically constrained and do not provide quantitative mass fluxes, and thus have limited utility. We developed an inference method, where a mechanistic model with hundreds of species and thousands of parameters is calibrated to time series data. The large scale, nonlinearity and feedbacks pose a challenging optimization problem, which is overcome using a novel procedure that mimics natural speciation or diversification e.g., stepwise increase of bacteria species. The method allows for curation using species-level information from e.g., physiological experiments or genome sequences. The product is a mass-balancing, mechanistically-constrained, quantitative representation of the ecosystem. We apply the method to characterize phytoplankton—heterotrophic bacteria interactions via dissolved organic matter in a marine system. The resulting model predicts quantitative fluxes for each interaction and time point (e.g., 0.16 µmolC/L/d of chrysolaminarin to Polaribacter on April 16, 2009). At the system level, the flux network shows a strong correlation between the abundance of bacteria species and their carbon flux during blooms, with copiotrophs being relatively more important than oligotrophs. However, oligotrophs, like SAR11, are unexpectedly high carbon processors for weeks into blooms, due to their higher biomass. The fraction of exudates (vs. grazing/death products) in the DOM pool decreases during blooms, and they are preferentially consumed by oligotrophs. In addition, functional similarity of phytoplankton i.e., what they produce, decouples their association with heterotrophs. The methodology is applicable to other microbial ecosystems, like human microbiome or wastewater treatment plants.Keywords
This publication has 42 references indexed in Scilit:
- Coherent dynamics and association networks among lake bacterioplankton taxaThe ISME Journal, 2011
- Dormancy contributes to the maintenance of microbial diversityProceedings of the National Academy of Sciences of the United States of America, 2010
- Agent‐based modeling of the complex life cycle of a cyanobacterium (Anabaena) in a shallow reservoirLimnology and Oceanography, 2008
- Modelling functional groups of phytoplankton in three lakes of different trophic stateEcological Modelling, 2008
- Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factorsBioinformatics, 2006
- Algae acquire vitamin B12 through a symbiotic relationship with bacteriaNature, 2005
- Biomass Production and Assimilation of Dissolved Organic Matter by SAR11 Bacteria in the Northwest Atlantic OceanApplied and Environmental Microbiology, 2005
- Covariance of bacterioplankton composition and environmental variables in a temperate delta systemAquatic Microbial Ecology, 2003
- Bacterial uptake of dissolved free and combined amino acids in estuarine watersLimnology and Oceanography, 1989
- The Paradox of the PlanktonThe American Naturalist, 1961