Project description:In the surface ocean, carbon is fixed by phytoplankton and respired by the entire marine community at an astonishingly high rate. At any point in time, the difference between these two processes yields a carbon pool in surface particles that is a combination of both freshly fixed and partially degraded material. On a molecular level, we have a limited knowledge of the small molecules, or metabolites, within this pool. Specific metabolites have been shown to be responsible for fueling respiration, maintaining organismal interactions, and transferring energy throughout the microbial community. Metabolomics, or the direct observation and quantification of the small molecules that are the result of cellular activity, provides an important lens through which we can begin to assess the standing stocks of small compounds that likely fuel a great deal of heterotrophic activity in the surface ocean. Here we describe community metabolomes of particulate material into the North Pacific Ocean and compare the metabolomes to a variety of phytoplankton grown in the lab. Using both targeted and untargeted metabolomics, we identify metabolites in the particulate carbon pool and explore their latitudinal and phylogenetic distributions. This analysis reveals several compounds that have not been previously recognized as abundant components of the marine organic carbon pool. We found that the community metabolome showed distinct differences between the regimes that likely reflects the phytoplankton community present. The community metabolome in surface waters of the subtropical domain was remarkably consistent even when sampled weeks apart, while the northern regions showed a patichier and less reproducible community metabolome. Some individual compounds showed distinct patterns between oceanographic regimes, including homarine, an abundant molecule that can contribute up to 4\% of the total particulate carbon pool in marine surface waters. Glutamic acid and glutamine showed opposite patterns in the oceanographic regimes, suggesting differences in community-level nitrogen assimilation in these different regimes. Overall, this study offers a new perspective into particulate carbon composition in oceanographic research, reveals important carbon pools that may fuel the microbial loop, and suggests an altered community-level nitrogen assimilation capacity over the North Pacific transition zone.

Project description:In the surface ocean, carbon is fixed by phytoplankton and respired by the entire marine community at an astonishingly high rate. At any point in time, the difference between these two processes yields a carbon pool in surface particles that is a combination of both freshly fixed and partially degraded material. On a molecular level, we have a limited knowledge of the small molecules, or metabolites, within this pool. Specific metabolites have been shown to be responsible for fueling respiration, maintaining organismal interactions, and transferring energy throughout the microbial community. Metabolomics, or the direct observation and quantification of the small molecules that are the result of cellular activity, provides an important lens through which we can begin to assess the standing stocks of small compounds that likely fuel a great deal of heterotrophic activity in the surface ocean. Here we describe community metabolomes of particulate material into the North Pacific Ocean and compare the metabolomes to a variety of phytoplankton grown in the lab. Using both targeted and untargeted metabolomics, we identify metabolites in the particulate carbon pool and explore their latitudinal and phylogenetic distributions. This analysis reveals several compounds that have not been previously recognized as abundant components of the marine organic carbon pool. We found that the community metabolome showed distinct differences between the regimes that likely reflects the phytoplankton community present. The community metabolome in surface waters of the subtropical domain was remarkably consistent even when sampled weeks apart, while the northern regions showed a patchier and less reproducible community metabolome. Some individual compounds showed distinct patterns between oceanographic regimes, including homarine, an abundant molecule that can contribute up to 4% of the total particulate carbon pool in marine surface waters. Glutamic acid and glutamine showed opposite patterns in the oceanographic regimes, suggesting differences in community-level nitrogen assimilation in these different regimes. Overall, this study offers a new perspective into particulate carbon composition in oceanographic research, reveals important carbon pools that may fuel the microbial loop, and suggests an altered community-level nitrogen assimilation capacity over the North Pacific transition zone.

Project description:The fraction of dissolved dimethylsulfoniopropionate (DMSPd) converted by marine bacterioplankton into the climate-active gas dimethylsulfide (DMS) varies widely in the ocean, with the factors that determine this value still largely unknown. One current hypothesis is that the ratio of DMS formation:DMSP demethylation is determined by DMSP availability, with 'availability' in both an absolute sense (i.e., concentration in seawater) and in a relative sense (i.e., proportionally to other labile organic S compounds) being proposed as the critical factor. We investigated these models during an experimentally-induced phytoplankton bloom using an environmental microarray targeting DMSP-related gene expression in the Roseobacter group, a taxon of marine bacteria known to play an important role in the surface ocean sulfur cycle. The array consisted of 1,578 probes to 431 genes, including those previously linked to DMSP degradation as well as core genes common in sequenced Roseobacter genomes. The prevailing pattern of Roseobacter gene expression showed depletion of DMSP-related transcripts during the peak of the bloom, despite the fact that absolute concentrations and flux of DMSP-related compounds were increasing. A likely interpretation is that DMSPd was assimilated by Roseobacter populations in proportion to its relative abundance in the organic matter pool (the “relative sense” hypothesis), and that it is not taken up in preference to other sources of labile organic sulfur or carbon produced during the bloom. The relative investment of the Roseobacter community in DMSP demethylation did not predict the fractional conversion of DMSP to DMS, however, suggesting a complex regulatory process that may involve multiple fates of DMSPd. DMSP-related gene expression in the Roseobacter group was investigated using an environmental microarray. Coastal seawater from the Gulf of Mexico was collected and dispensed into 20-L microcosms. Two replicate cubitainers were amended with nutrients (N and P) to stimulate phytoplankton bloom, while two untreated cubitainers served as controls. The microcosms were incubated at 27ºC in a temperature-controlled incubator on a 12 h light/dark cycle for total of 7 days. Ten RNA samples (Day 0: 2 conditions with 1 biological replicate each; Days 2 and 4: 2 conditions with 2 biological replicates each) were prepared for microarray hybridization. After total RNA extraction, rRNAs were removed and mRNA transcripts were amplified and labeled with Alexa Fluor 647. Two technical replicates were hybridized from each RNA sample. The microarray was designed based on selected Ruegeria pomeroyi DSS-3 genes and their orthologs in 12 other sequenced Roseobacter genomes. Probes were designed from the orthologs using the Hierarchical Probe Design (HPD) algorithm.

Project description:Marine phytoplankton are a diverse group of photoautotrophic organisms and key mediators in the global carbon cycle. Phytoplankton physiology and biomass accumulation are closely tied to mixed layer depth, but the intracellular metabolic pathways activated in response to changing mixed layer depths remain unexplored. Here, metatranscriptomics was used to characterize the phytoplankton community response to a mixed layer shallowing from 233 meters to 5 meters over the course of two days during the late spring in the Northwest Atlantic. Most phytoplankton genera downregulated core photosynthesis, carbon storage, and carbon fixation genes as the system transitioned from a deep to a shallow mixed layer and shifted towards catabolism of stored carbon ic pathways supportive of rapid cell growth. In contrast, phytoplankton genera exhibited divergent transcriptional strategies for photosystem light harvesting complex genes during this transition. Active infection, taken as the ratio of virus to host transcripts, increased in the Bacillariophyta (diatom) phylum and decreased in the Chlorophyta (green algae) phylum upon mixed layer shallowing. A conceptual model is proposed to provide ecophysiological context for our findings, in which light limitation during deep mixing induces populations into a transcriptional state which maximizes interrupts the oscillating levels of transcripts related to photosynthesis, carbon storage, and carbon fixation found in shallow mixed layers with relatively higher growth rates. We propose that upon sensing high light levels during mixed layer shallowing, phytoplankton resume diel oscillation of core sets of genes enabling photoprotection, biosynthesis and cell replication. Our findings highlight the shared and unique transcriptional response strategies within phytoplankton communities acclimating to the dynamic light environment associated with transient deep mixing and shallowing events during the annual North Atlantic bloom.

Dataset Information

GNPS Metabolomics Workbench ST001372 - GNPS Patterns in metabolite pools show that phytoplankton leave a taxon-specific signature on particulate carbon: North Pacific Subtropical Gyre depth profile

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