Schreier, J. E. | bioRxiv Science

bioRxiv2025

Dynamic Reworking of Marine Diatom Endometabolomes

A large annual carbon flux occurs through the oceans labile dissolved organic carbon (DOC) pool, with carbon influx dominated by phytoplankton-derived metabolites and outflux by heterotrophic bacterioplankton uptake. We addressed the dynamics of this flux between marine primary and secondary producers through analysis of the Thalassiosira pseudonana CCMP1335 endometabolome, a proxy for labile DOC release during phytoplankton excretion and mortality. Diatom strains acclimated at one of three different temperatures (14{degrees}C, 20{degrees}C, or 28{degrees}C) were then cultured either axenically or with the bacterium Ruegeria pomeroyi DSS-3, and their endometabolites analyzed by NMR. Osmolytes were by far the most dynamic, exhibiting concentration differences up to 150-fold between conditions; median concentration variation across identified endometabolites was [~]1.5-fold. Differential expression of diatom metabolic pathways suggested changes in synthesis rates as a mechanism for endometabolome remodeling. Consistent with expectations of high turnover, endometabolite mean lifetimes prior to bacterial uptake were <2 h to 12 h. ImportanceThe role of labile DOC in the transfer of marine carbon between phytoplankton and heterotrophic bacteria was first recognized 40 years ago, yet the identity and dynamics of phytoplankton metabolites entering the labile DOC pool are still poorly known. Using metabolome and transcriptome profiling, we found dynamic composition and concentration of diatom endometabolites, depending on growth conditions and arising over time frames as short as a single growth cycle. This strong response to external conditions, both biotic and abiotic, has implications for downstream processing and fate of ocean carbon by heterotrophic bacteria.

ecology↗

bioRxiv2023

Interspecies interactions determine growth dynamics of biopolymer degrading populations in microbial communities.

Microbial communities perform essential ecosystem functions such as the remineralization of organic carbon that exists as biopolymers. The first step in mineralization is performed by biopolymer degraders, which harbor enzymes that can break down polymers into constituent oligo- or monomeric forms. The released nutrients not only allow degraders to grow, but also promote growth of cells that either consume the breakdown products, i.e., exploiters, or consume metabolites released by the degraders, i.e., scavengers. It is currently not clear how such remineralizing communities assemble at the microscale - how interactions between the different guilds influence their growth and spatial distribution, and hence the development and dynamics of the community. Here we address this knowledge gap by studying marine microbial communities that grow on the abundant marine biopolymer alginate. We used batch growth assays and microfluidics coupled to time-lapse microscopy to quantitatively investigate growth and spatial distribution of single cells. We found that the presence of exploiters or scavengers alters the spatial distribution of degrader cells. In general, exploiters and scavengers - which we collectively refer to as consumer cells - slowed down the growth of degrader cells. In addition, coexistence with consumers altered the production of the extracellular enzymes that breakdown polymers by degrader cells. Our findings reveal that ecological interactions by non-degrading community members have a profound impact on the functions of microbial communities that remineralize carbon biopolymers in nature. ImportanceBiopolymers are the most abundant source of carbon on the planet and their breakdown by microbial degraders releases metabolic products that allow cross-feeding cells to grow and fuel the assembly of microbial communities. While it is known that the growth of degraders can facilitate growth of downstream cross-feeders in microbial communities, it has remained generally unclear if and how cross-feeders influence growth of degraders. Bridging this knowledge gap is important because degraders primarily drive the remineralization of carbon, a central process in the carbon cycle. We found that the presence cross-feeders can influence the growth of degraders by altering their spatial distribution as well as extracellular breakdown enzyme activity. Our study sheds light on the role of microbial interactions in shaping the rate of carbon remineralization in nature.

microbiology↗