New model reveals adaptations of world's most abundant ocean microbe

November 15, 2016

Researchers from David Karl's laboratory at the University of Hawai'i at Mānoa (UHM) and from Professor Jens Nielsen's laboratory at Chalmers University of Technology in Göteborg, Sweden, developed a computer model which takes into account hundreds of genes, chemical reactions, and compounds required for the survival of Prochlorococcus, the most abundant photosynthetic microbe on the planet. They found that Prochlorococcus has made extensive alterations to its metabolism as a way to reduce its dependence on phosphorus, an element that is essential and often growth-limiting in the ocean.

Revolutionary developments in gene sequencing technology have allowed scientists to catalog and investigate the genetic diversity and metabolic capability of life on Earth--from E. coli bacteria to humans, and much in between. Ocean monitoring and advances in oceanographic sensors have enabled a more detailed look than ever before at the environmental conditions that are both the consequence of microbial activity and act as stressors on the growth of microbes in the ocean.

This new metabolic model represents a window to the inner workings that enable microbes to dominate Earth's chemical and biological cycles, thrive in the harshest conditions, and make the planet habitable--a black box, in a sense.

Microbes are known to employ three basic strategies to compete for limiting elemental resources: cell quotas may be adjusted, stressed cells may synthesize molecules to make more efficient use of available resources, and cells may access alternatives or more costly sources of the nutrient.

In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan Prochlorococcus thrives by adopting all three strategies and a fourth, previously unknown strategy.

"By generating the first detailed model of metabolism for an ecologically important marine microbe, we found that Prochlorococcus has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, thus relieving intracellular demands" said John Casey, an oceanography doctoral candidate in the UHM School of Ocean and Earth Science and Technology and lead author of the recently published study.

Prochlorococcus has an extremely minimal genome. If it were to lose the function of any one metabolic gene, its survival would be nearly a coin toss. To their surprise, Casey and co-authors discovered that the world's most abundant microbe has performed, through a process called "genome streamlining"--the concerted loss of frivolous genes over evolutionary time--a comprehensive re-design of the core metabolic pathways in response to the persistent limitation of phosphorus.

"The dramatic and widespread change in the metabolic network is really a shock," said Casey. "However, we're seeing that these changes provide a substantial growth advantage for this ubiquitous microbe in phosphorus-limited regions of the ocean, so it seems that where there's a will there's a way."

The computer model is built from an enormous library of genetic data compiled from researchers around the world, and the results are validated with data from numerous laboratory culture experiments and field studies.

"We're interested in the underlying principles guiding metabolism and physiology in marine microbes, and that is going to require a deep understanding of not only the 1-dimensional genetic code, but also the 4-dimensional product it codes for," said Casey. "So we're looking to a systems-level approach to incorporate a great variety of physiological and 'omics studies all in one computational structure, with the hope that we can start to learn from the design and interactions of these complex systems."

In the future, the researchers plan to expand the model to include more representatives of the marine microbial community and to look deeper into micro-diversity within the Prochloroccocus genus.

"This will allow us to simulate marine microbial community metabolism at an unprecedented level of detail; embedding these fine-scale simulations within global ocean circulation models promises to deliver insights into how microbial assemblages interact with their environment and amongst each other," said Casey.
This work was funded by the National Science Foundation (NSF) through the competitive Graduate Research Fellowship Program which provided Casey with three years of research support. A portion of this work was made possible through Casey's acceptance into NSF's Graduate Research Opportunities Worldwide (GROW) program which expands opportunities for U.S. graduate students to engage in international research collaboration. GROW is open to only active awardees of the Graduate Research Fellowship Program. Additional funding was provided by the Simons Foundation, the Swedish Research Council, and the Gordon and Betty Moore Foundation.

University of Hawaii at Manoa

Related Metabolism Articles from Brightsurf:

Early trauma influences metabolism across generations
A study by the Brain Research Institute at UZH reveals that early trauma leads to changes in blood metabolites - similarly in mice and humans.

Cannabinoids decrease the metabolism of glucose in the brain
What happens when THC acts on the glial cells named astrocytes ?

New role of arginine metabolism in plant morphogenesis identified
A research team led by ExCELLS/NIBB found that arginine metabolism has a vital role in regulating gametophore shoot formation in the moss Physcomitrium patens.

Watching changes in plant metabolism -- live
Almost all life on Earth, e.g. our food and health, depend on metabolism in plants.

redHUMAN: Deciphering links between genes and metabolism
Scientists at EPFL have developed a new method that simplifies the processing of genetic-metabolic data by picking up changes in metabolism, a hallmark of numerous diseases like cancer and Alzheimer's.

Lipid metabolism controls brain development
A lipid metabolism enzyme controls brain stem cell activity and lifelong brain development.

Inhibition of sphingolipid metabolism and neurodegenerative diseases
Disrupting the production of a class of lipids known as sphingolipids in neurons improved symptoms of neurodegeneration and increased survival in a mouse model.

Viruses don't have a metabolism; but some have the building blocks for one
'Giant viruses' are many times larger than typical viruses and have more complex genomes.

New metabolism discovered in bacteria
Microbiologists at Goethe University Frankfurt have discovered how the bacterium Acetobacterium woodii uses hydrogen in a kind of cycle to conserve energy.

Protein controls fat metabolism
A protein in the cell envelope influences the rate of fatty acid uptake in cells.

Read More: Metabolism News and Metabolism Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to