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ABSTRACT A large annual carbon flux occurs through the surface ocean’s labile dissolved organic carbon (DOC) pool, with influx dominated by phytoplankton-derived metabolites and outflux by heterotrophic bacterioplankton uptake. We addressed the dynamics of this carbon flow between microbial primary and secondary producers through analysis of theThalassiosira pseudonanaCCMP1335 endometabolome, a proxy for the labile DOC released upon phytoplankton lysis, as temperature and bacterial presence were altered. Diatom strains acclimated at one of three different temperatures (14°C, 20°C, or 28°C) were cultured either axenically or with the bacteriumRuegeria pomeroyiDSS-3, and their endometabolites analyzed by NMR. Median concentration variation between conditions was ~1.5-fold across all identified endometabolites. Those with roles as osmolytes varied most, exhibiting concentration differences up to 170-fold across conditions with the largest variations triggered by the presence/absence of the heterotrophic bacterium. Differential expression observed for diatom metabolite synthesis pathways suggested changes in synthesis rates as a mechanism for endometabolome remodeling. Consistent with expectations of high turnover by heterotrophic bacteria, endometabolite mean lifetimes in a DOC pool 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 highly variable 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, suggests that the chemical composition of phytoplankton intracellular pools released during lysis shift with ocean conditions. As phytoplankton cell lysis is one of the largest sources of labile dissolved compounds in the ocean, dynamic compositional changes in the metabolites released to heterotrophic bacteria have implications for the fate of surface ocean carbon. 

Abstract Marine biogeochemical cycles are built on interactions between surface ocean microbes, particularly those connecting phytoplankton primary producers to heterotrophic bacteria. Details of these associations are not well understood, especially in the case of direct influences of bacteria on phytoplankton physiology. Here we catalogue how the presence of three marine bacteria (Ruegeria pomeroyiDSS‐3,Stenotrophomonassp. SKA14 andPolaribacter dokdonensisMED152) individually and uniquely impact gene expression of the picoeukaryotic algaMicromonas commodaRCC 299. We find a dramatic transcriptomic remodelling byM. commodaafter 8 h in co‐culture, followed by an increase in cell numbers by 56 h compared with the axenic cultures. Some aspects of the algal transcriptomic response are conserved across all three bacterial co‐cultures, including an unexpected reduction in relative expression of photosynthesis and carbon fixation pathways. Expression differences restricted to a single bacterium are also observed, with the FlavobacteriiaP. dokdonensisuniquely eliciting changes in relative expression of algal genes involved in biotin biosynthesis and the acquisition and assimilation of nitrogen. This study reveals thatM. commodahas rapid and extensive responses to heterotrophic bacteria in ways that are generalizable, as well as in a taxon specific manner, with implications for the diversity of phytoplankton‐bacteria interactions ongoing in the surface ocean. 

The global ocean is a profoundly important ecosystem that regulates Earth’s climate and is responsible for nearly half of the oxygen we breathe. Oceanographic concepts and marine microbial ecology are often excluded from undergraduate curricula despite their significance. Specifically, phytoplankton in the surface ocean fix atmospheric CO2 into organic molecules, which are released into the water where they serve as substrates for heterotrophic bacteria. Upon release, bacteria use transporter proteins to move these substrates across their membranes for metabolism inside their cells. However, the substrate preference and specificity of many microbial transporters in the ocean remains unknown. To address these curricular and scientific gaps, we developed the Ocean Genes course-based undergraduate research experience (CURE). In this five-session CURE lesson, students perform growth assays with a mutant library of the ecologically relevant marine bacterium Ruegeria pomeroyi DSS-3 on different carbon sources. The scientific goal of their investigation is to identify the substrate specificity of the bacterium’s 126 transporter genes, most of which remain uncharacterized despite their critical role in the food web that underpins global carbon cycles. Through this lesson, students develop their skills in interpreting scientific literature, performing microbiological techniques, analyzing data using relevant statistical tests, interpreting experimental results, and making arguments from evidence. This lesson aims to broaden engagement of undergraduate students with authentic marine science research. In doing so, the Ocean Genes CURE offers a novel avenue to increase diversity in the marine science and expand ocean literacy of undergraduate students. 

The ocean’s temperature increase has fundamental implications for physiological rates and processes of marine microbes. In this study, a marine diatom Thalassiosira pseudonana CCMP1335 was acclimated for three months at temperatures below (14°C), equal to (20°C), and above (28°C). Heterotrophic bacterium Ruegeria pomeroyi DSS-3 was inoculated into cultures, and transporter expression was compared between temperatures. R. pomeroyi transporter expression leveraged as a biosensor of available diatom exometabolites indicated temperature-related substitution of diatom osmolytes dimethylsulfoniopropionate (DMSP), dihydroxypropanesulfonate (DHPS), and homarine (dominating carbon transfer at lower temperatures) with glycine betaine and choline (dominating at higher temperatures). T. pseudonana endometabolome pools and biosynthetic pathway expression indicated increased availability of amino acids and glycerol-3-phosphate at higher temperatures. Overall trends across datasets supported a greater importance of organic sulfur compounds in diatom-bacterial metabolite transfer at lower temperatures and greater importance of organic nitrogen compounds at higher temperatures. 

Marine biogeochemical cycles are built on interactions between surface ocean microbes, particularly those connecting phytoplankton primary producers to heterotrophic bacteria. However, direct influences of bacteria on phytoplankton physiology are poorly known. In this study, three marine bacteria (Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152) were co-cultured with green alga Micromonas commoda, and the phytoplankter's transcriptome was studied by RNASeq. The presence of each bacterium invoked transcriptomic remodeling by M. commoda after 8 h in co-culture. Some aspects of the algal transcriptomic response were conserved across all three bacteria, while others were restricted to a single bacterium. M. commoda had both rapid and extensive responses to heterotrophic bacteria. 

Abstract Dissolved primary production released into seawater by marine phytoplankton is a major source of carbon fueling heterotrophic bacterial production in the ocean. The composition of the organic compounds released by healthy phytoplankton is poorly known and difficult to assess with existing chemical methods. Here, expression of transporter and catabolic genes by three model marine bacteria ( Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, and Polaribacter dokdonensis MED152) was used as a biological sensor of metabolites released from the picoeukaryote Micromonas commoda RCC299. Bacterial expression responses indicated that the three species together recognized 38 picoeukaryote metabolites. This was consistent with the Micromonas expression of genes for starch metabolism and synthesis of peptidoglycan-like intermediates. A comparison of the hypothesized Micromonas exometabolite pool with that of the diatom Thalassiosira pseudonana CCMP1335, analyzed previously with the same biological sensor method, indicated that both phytoplankton released organic acids, nucleosides, and amino acids, but differed in polysaccharide and organic nitrogen release. Future ocean conditions are expected to favor picoeukaryotic phytoplankton over larger-celled microphytoplankton. Results from this study suggest that such a shift could alter the substrate pool available to heterotrophic bacterioplankton. 

These data are from three laboratory studies of co-cultured temperature-acclimated marine microbes and Ruegeria pomeroyi DSS-3. Model systems were established in which temperature-acclimated microbial strains were co-cultured with the heterotrophic bacterium Ruegeria pomeroyi. Cultures of the coccolithophore Emiliania huxleyi CCMP151 were pre-acclimated to three temperature treatments (15°, 20°, and 28° Celsius (C)). Cultures of the diatom Thalassiosira pseudonana CCMP1335 were pre-acclimated to 14°, 20°, and 28°C. Cultures of Synechococcus sp. WH8102 were pre-acclimated to 20°, 24°, and 28°C. The investigators characterized the transcriptomes of both the phytoplankter and heterotrophic bacterium at initial and late exponential growth at the three temperatures. 

Bacteria that assemble in phycospheres surrounding living phytoplankton cells metabolize a substantial proportion of ocean primary productivity. Yet the type and extent of interactions occurring among species that colonize these micron-scale “hot spot” environments are challenging to study. We identified genes that mediate bacterial interactions in phycosphere communities by culturing a transposon mutant library of copiotrophic bacterium Ruegeria pomeroyi DSS-3 with the diatom Thalassiosira pseudonana CCMP1335 as the sole source of organic matter in the presence or absence of other heterotrophic bacterial species. The function of genes having significant effects on R. pomeroyi fitness indicated explicit cell–cell interactions initiated in the multibacterial phycospheres. We found that R. pomeroyi simultaneously competed for shared substrates while increasing reliance on substrates that did not support the other species’ growth. Fitness outcomes also indicated that the bacterium competed for nitrogen in the forms of ammonium and amino acids; obtained purines, pyrimidines, and cofactors via crossfeeding; both initiated and defended antagonistic interactions; and sensed an environment with altered oxygen and superoxide levels. The large genomes characteristic of copiotrophic marine bacteria are hypothesized to enable responses to dynamic ecological challenges occurring at the scale of microns. Here, we discover >200 nonessential genes implicated in the management of fitness costs and benefits of membership in a globally significant bacterial community.