Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Mechanisms and Flux Measurements of Microbial Processing of Photosynthetically Fixed Algal Carbon Using Isotope Tracing and Secondary Ion Mass Spectrometry


Xavier Mayali1* (, Peter K. Weber1, Nana Ankrah2, Hyu Kim3, Vanessa Brisson1, Usha Lingappa4, Sunnyjoy Dupuis4, Christina Ramon1, Joaquin Martinez5, Sabeeha Merchant4, Cullen Buie3, Rhona Stuart1


1Lawrence Livermore National Laboratory; 2State University of New York–Plattsburgh; 3Massachusetts Institute of Technology–Boston; 4University of California–Berkeley; Laboratory for Ocean Science



Algal and plant systems have the unrivaled advantage of converting solar energy and CO2 into useful organic molecules. Their growth and efficiency are largely shaped by the microbial communities in and around them. The μBiospheres Science Focus Area seeks to understand phototroph-heterotroph interactions that shape productivity, robustness, the balance of resource fluxes, and the functionality of the surrounding microbiome. Researchers hypothesize that different microbial associates not only have differential effects on host productivity but can change an entire system’s resource economy. This approach encompasses single-cell analyses, quantitative isotope tracing of elemental exchanges, omics measurements, and multiscale modeling to characterize microscale impacts on system-scale processes. Researchers aim to uncover crosscutting principles that regulate these interactions and their resource allocation consequences to develop a general predictive framework for system-level impacts of microbial partnerships.


Photosynthetic carbon (C) fixation by algae and cyanobacteria represents half of the global C fixation on Earth and holds promise as a strategy for nonfossil fuel-based generation of biofuels. Loss of fixed C as dissolved organic matter (DOM) through exudation, lysis, and as viral progeny after infection represent critical fluxes that become a source of biomass for the algal microbiome. Using four different experimental systems, researchers used stable isotope tracing with 13C and nitrogen-15 (15N) labeling combined with single-cell resolution isotope analysis by nanoSIMS to investigate mechanisms and fluxes of algal organic C into the algal microbiome.

The first two experimental systems examine the model biofuel-producing diatom Phaeodactylum tricornutum and bacterial isolates that grow using P. tricornutum fixed C. Using a porous microplate that cocultivates bacteia near a constant source of algal DOM, the team tested whether the isolates compete for the algal DOM. Researchers found that the presence of some bacterial strains inhibited the uptake of algal-derived C by Marinobacter, a common algal-associated bacterium, while others did not. This suggests that niche partitioning and competition directly influence C from algae to bacteria.

In the second experimental system, researchers are examining how oxidative stress, which is prevalent in high-biomass and high-light ecosystems, impacts the transfer of algal C and N into heterotrophic bacteria. The team aimed to compare bacteria that relieve oxidative stress versus those that do not, and thus used two photoheterotrophic bacteria (one mutualistic and the other commensal under oxidative stress). Researchers quantified the transfer of algal C and N into the bacteria with and without and addition of hydrogen peroxide, and found that the non-mutualist incorporated more C and N under oxidative stress, whereas the mutualist did not change its uptake.

The third experimental system used the alga Chlamydomonas reinhardtii and the vitamin producing soil bacterium Mesorhizobium japonicum, previously used as a model for vitamin exchange for fixed C. The team unexpectedly found little algal-derived C being exchanged from alga to bacterium, and the modest amounts could be explained by a low level of algal cell lysis, suggesting this bacterium grows using algal lysate rather than exudate.

For the fourth experimental system, the team aimed to examine the flux of algal derived C into bacteria using algal viruses as a mechanism. Researchers isotope-labeled a giant virus infecting the alga Emiliania huxleyii and added this isotope-labeled viral fraction to a complex aquatic microbial community. Viral particles in the presence of the microbial community decreased faster than without cells, and this corresponded to increased isotope labeling into bacteria and eukaryotic protist cells, demonstrating another mechanism for algal-derived C feeding the microbial loop.

The direct isotope measurements in these four experimental algal systems have demonstrated the capabilities to measure fluxes from algae to bacteria, and the team found they are impacted by mechanisms (cell lysis, exudation, and viral particles) and environmental factors (oxidative stress, competition by other bacteria).

Funding Information

Part of this work was performed under the auspices of the DOE at Lawrence Livermore National Laboratory (LLNL) under contract no. DE-AC52- 07NA27344 and supported by the Genome Sciences Program of the BER program under the LLNL μBiospheres SFA, FWP SCW1039.