When and Why a Microbial Community Might Collapse

When and Why a Microbial Community Might Collapse

3 Bullets:

  • It takes too much energy to adapt to frequent environmental changes, which can cause a microbial community to collapse.
  • A microbial community that is inept at regulating its genes, however, is more resilient to frequent environmental changes.
  • ISB researchers developed a framework to quantify microbial community resilience that could be applied to identify environmental tipping points related to climate change and ocean acidification.

Microbial communities are critical to the survival of all ecosystems, from the soil to the oceans to our guts, and are essential to a large number of processes and industries, including fermentation, sewage treatment, bioremediation, and biofuel production. For example, microbial communities directly impact fisheries by playing an essential role in sequestering, mineralizing and recycling more than 60 billion tons of carbon each year. Understanding how microbial communities respond to environmental changes, such as global warming and ocean acidification, and anthropological factors, such as pesticide use and water contamination, will be critical to understanding how ecosystems function and will guide future conservation efforts and industrial research.

Researchers at Institute for Systems Biology have developed a framework for assessing the “health” of a microbial community through a stress test that enables them to ask when and why microbial communities collapse under different environmental conditions. The study, published on March 20, 2017, in the journal Molecular Systems Biology, determined that while microbes are equipped to respond to environmental changes, when pushed to the extreme under rapidly fluctuating conditions, the energetic cost of adapting becomes a burden and is unsustainable, leading to collapse. This framework will be invaluable for observing the behavior of microbial communities under simulations of current and projected environmental conditions, allowing scientists to make predictions about the future of our ecosystems and, more importantly, identify ways to protect those ecosystems.

Title: Mechanism for microbial population collapse in a fluctuating resource environment
Journal: Molecular Systems Biology
Authors: Serdar Turkarslan, Arjun V Raman, Anne W Thompson, Christina E Arens, Mark A Gillespie, Frederick von Netzer, Kristina L Hillesland, Sergey Stolyar, Adrian López García de Lomana, David J Reiss, Drew Gorman-Lewis, Grant M Zane, Jeffrey A Ranish, Judy D Wall, David A Stahl, and Nitin S Baliga
Link: msb.embopress.org/content/13/3/919

Acknowledgements
This material by ENIGMA‐Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Scientific Focus Area Program at Lawrence Berkeley National Laboratory, is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Biological & Environmental Research under contract number DE‐AC02‐05CH11231. JAR and MAG are supported by National Institute of General Medical Sciences Center for Systems Biology Award Number 2P50 GM076547. We thank Lisa Jones of the Fred Hutch Proteomics Resource for assistance with MS runs.

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii.

Biotechnol Biofuels. 2015 Dec 2;8:207. doi: 10.1186/s13068-015-0391-z. eCollection 2015.

López García de Lomana A1, Schäuble S2, Valenzuela J1, Imam S1, Carter W1, Bilgin DD3, Yohn CB3, Turkarslan S1, Reiss DJ1, Orellana MV4, Price ND5, Baliga NS6.

Author information
Abstract
BACKGROUND:
Algae accumulate lipids to endure different kinds of environmental stresses including macronutrient starvation. Although this response has been extensively studied, an in depth understanding of the transcriptional regulatory network (TRN) that controls the transition into lipid accumulation remains elusive. In this study, we used a systems biology approach to elucidate the transcriptional program that coordinates the nitrogen starvation-induced metabolic readjustments that drive lipid accumulation in Chlamydomonas reinhardtii.
RESULTS:
We demonstrate that nitrogen starvation triggered differential regulation of 2147 transcripts, which were co-regulated in 215 distinct modules and temporally ordered as 31 transcriptional waves. An early-stage response was triggered within 12 min that initiated growth arrest through activation of key signaling pathways, while simultaneously preparing the intracellular environment for later stages by modulating transport processes and ubiquitin-mediated protein degradation. Subsequently, central metabolism and carbon fixation were remodeled to trigger the accumulation of triacylglycerols. Further analysis revealed that these waves of genome-wide transcriptional events were coordinated by a regulatory program orchestrated by at least 17 transcriptional regulators, many of which had not been previously implicated in this process. We demonstrate that the TRN coordinates transcriptional downregulation of 57 metabolic enzymes across a period of nearly 4 h to drive an increase in lipid content per unit biomass. Notably, this TRN appears to also drive lipid accumulation during sulfur starvation, while phosphorus starvation induces a different regulatory program. The TRN model described here is available as a community-wide web-resource at http://networks.systemsbiology.net/chlamy-portal.
CONCLUSIONS:
In this work, we have uncovered a comprehensive mechanistic model of the TRN controlling the transition from N starvation to lipid accumulation. The program coordinates sequentially ordered transcriptional waves that simultaneously arrest growth and lead to lipid accumulation. This study has generated predictive tools that will aid in devising strategies for the rational manipulation of regulatory and metabolic networks for better biofuel and biomass production.

Diatom Portal

Diatom Portal

http://networks.systemsbiology.net/diatom-portal

The Diatom Portal is a new resource for the diatom community. It's aim is not only to provide a repository for experimental and computational results, but to be used as an interface to existing resources. Our hope is to continue expanding this resource for many diatoms including T. pseudonana.

References

in preperation

MTB Network Portal

MTB Network Portal

http://networks.systemsbiology.net/mtb

The MTB Network Portal serves as a portal for computational modeling program to generate an integrated, predictive gene regulatory network model of host/pathogen interactions.

References