skip to main content

Title: Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy

The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-d-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.

more » « less
Award ID(s):
Author(s) / Creator(s):
; ; ; ; ; ;
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
The ISME Journal
Medium: X Size: p. 762-773
["p. 762-773"]
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract

    Phytoplankton-derived metabolites fuel a large fraction of heterotrophic bacterial production in the global ocean, yet methodological challenges have limited our understanding of the organic molecules transferred between these microbial groups. In an experimental bloom study consisting of three heterotrophic marine bacteria growing together with the diatom Thalassiosira pseudonana, we concurrently measured diatom endometabolites (i.e., potential exometabolite supply) by nuclear magnetic resonance (NMR) spectroscopy and bacterial gene expression (i.e., potential exometabolite uptake) by metatranscriptomic sequencing. Twenty-two diatom endometabolites were annotated, with nine increasing in internal concentration in the late stage of the bloom, eight decreasing, and five showing no variation through the bloom progression. Some metabolite changes could be linked to shifts in diatom gene expression, as well as to shifts in bacterial community composition and their expression of substrate uptake and catabolism genes. Yet an overall low match indicated that endometabolome concentration was not a good predictor of exometabolite availability, and that complex physiological and ecological interactions underlie metabolite exchange. Six diatom endometabolites accumulated to higher concentrations in the bacterial co-cultures compared to axenic cultures, suggesting a bacterial influence on rates of synthesis or release of glutamate, arginine, leucine, 2,3-dihydroxypropane-1-sulfonate, glucose, and glycerol-3-phosphate. Better understanding of phytoplankton metabolite production, release, and transfer to assembled bacterial communities is key to untangling this nearly invisible yet pivotal step in ocean carbon cycling.

    more » « less
  2. Abstract

    The Arctic Ocean is more susceptible to ocean acidification than other marine environments due to its weaker buffering capacity, while its cold surface water with relatively low salinity promotes atmospheric CO2uptake. We studied how sea‐ice microbial communities in the central Arctic Ocean may be affected by changes in the carbonate system expected as a consequence of ocean acidification. In a series of four experiments during late summer 2018 aboard the icebreakerOden, we addressed microbial growth, production of dissolved organic carbon (DOC) and extracellular polymeric substances (EPS), photosynthetic activity, and bacterial assemblage structure as sea‐ice microbial communities were exposed to elevated partial pressures of CO2(pCO2). We incubated intact, bottom ice‐core sections and dislodged, under‐ice algal aggregates (dominated byMelosira arctica) in separate experiments under approximately 400, 650, 1000, and 2000 μatm pCO2for 10 d under different nutrient regimes. The results indicate that the growth of sea‐ice algae and bacteria was unaffected by these higher pCO2levels, and concentrations of DOC and EPS were unaffected by a shifted inorganic C/N balance, resulting from the CO2enrichment. These central Arctic sea‐ice microbial communities thus appear to be largely insensitive to short‐term pCO2perturbations. Given the natural, seasonally driven fluctuations in the carbonate system of sea ice, its resident microorganisms may be sufficiently tolerant of large variations in pCO2and thus less vulnerable than pelagic communities to the impacts of ocean acidification, increasing the ecological importance of sea‐ice microorganisms even as the loss of Arctic sea ice continues.

    more » « less
  3. null (Ed.)
    Primary productivity occurs throughout the deep euphotic zone of the oligotrophic South Pacific Gyre (SPG), fueled largely by the regeneration of nutrients and thus recycling of organic matter. We investigated the heterotrophic capabilities of the SPG’s bacterial communities by examining their ability to process polysaccharides, an important component of marine organic matter. We focused on the initial step of organic matter degradation by measuring the activities of extracellular enzymes that hydrolyze six different polysaccharides to smaller sizes. This process can occur by two distinct mechanisms: “selfish uptake,” in which initial hydrolysis is coupled to transport of large polysaccharide fragments into the periplasmic space of bacteria, with little to no loss of hydrolysis products to the external environment, and “external hydrolysis,” in which low molecular weight (LMW) hydrolysis products are produced in the external environment. Given the oligotrophic nature of the SPG, we did not expect high enzymatic activity; however, we found that all six polysaccharides were hydrolyzed externally and taken up selfishly in the central SPG, observations that may be linked to a comparatively high abundance of diatoms at the depth and location sampled (75 m). At the edge of the gyre and close to the center of the gyre, four of six polysaccharides were externally hydrolyzed, and a lower fraction of the bacterial community showed selfish uptake. One polysaccharide (fucoidan) was selfishly taken up without measurable external hydrolysis at two stations. Additional incubations of central gyre water from depths of 1,250 and 2,800 m with laminarin (an abundant polysaccharide in the ocean) led to extreme growth of opportunistic bacteria ( Alteromonas) , as tracked by cell counts and next generation sequencing of the bacterial communities. These Alteromonas appear to concurrently selfishly take up laminarin and release LMW hydrolysis products. Overall, extracellular enzyme activities in the SPG were similar to activities in non-oligotrophic regions, and a considerable fraction of the community was capable of selfish uptake at all three stations. A diverse set of bacteria responded to and are potentially important for the recycling of organic matter in the SPG. 
    more » « less
  4. Abstract

    Metabolite exchange within marine microbial communities transfers carbon and other major elements through global cycles and forms the basis of microbial interactions. Yet lack of gene annotations and concern about the quality of existing ones remain major impediments to revealing currencies of carbon flux. We employed an arrayed mutant library of the marine bacterium Ruegeria pomeroyi DSS-3 to experimentally annotate substrates of organic compound transporter systems, using mutant growth and compound drawdown analyses to link transporters to their cognate substrates. Mutant experiments verified substrates for thirteen R. pomeroyi transporters. Four were previously hypothesized based on gene expression data (taurine, glucose/xylose, isethionate, and cadaverine/putrescine/spermidine); five were previously hypothesized based on homology to experimentally annotated transporters in other bacteria (citrate, glycerol, N-acetylglucosamine, fumarate/malate/succinate, and dimethylsulfoniopropionate); and four had no previous annotations (thymidine, carnitine, cysteate, and 3-hydroxybutyrate). These bring the total number of experimentally-verified organic carbon influx transporters to 18 of 126 in the R. pomeroyi genome. In a longitudinal study of a coastal phytoplankton bloom, expression patterns of the experimentally annotated transporters linked them to different stages of the bloom, and also led to the hypothesis that citrate and 3-hydroxybutyrate were among the most highly available bacterial substrates. Improved functional annotation of the gatekeepers of organic carbon uptake is critical for deciphering carbon flux and fate in microbial ecosystems.

    more » « less
  5. Stabb, Eric V. (Ed.)
    ABSTRACT Dimethylsulfoniopropionate (DMSP), a key component of the global geochemical sulfur cycle, is a secondary metabolite produced in large quantities by marine phytoplankton and utilized as an osmoprotectant, thermoprotectant, and antioxidant. Marine bacteria can use two pathways to degrade and catabolize DMSP, a demethylation pathway and a cleavage pathway that produces the climate-active gas dimethylsulfide (DMS). Whether marine bacteria can also accumulate DMSP as an osmoprotectant to maintain the turgor pressure of the cell in response to changes in external osmolarity has received little attention. The marine halophile Vibrio parahaemolyticus contains at least six osmolyte transporters, namely four betaine carnitine choline transport (BCCT) carriers (BccT1 to BccT4) and two ATP-binding cassette (ABC) family ProU transporters. In this study, we showed that DMSP is used as an osmoprotectant by V. parahaemolyticus and by several other Vibrio species, including Vibrio cholerae and Vibrio vulnificus . Using a V. parahaemolyticus proU double mutant, we demonstrated that these ABC transporters are not required for DMSP uptake. However, a bccT null mutant lacking all four BCCTs had a growth defect compared to the wild type (WT) in high-salinity medium supplemented with DMSP. Using mutants possessing only one functional BCCT in growth pattern assays, we identified two BCCT family transporters, BccT1 and BccT2, that are carriers of DMSP. The only V. parahaemolyticus BccT homolog that V. cholerae and V. vulnificus possess is BccT3, and functional complementation in Escherichia coli MKH13 showed that V. cholerae VcBccT3 could transport DMSP. In V. vulnificus strains, we identified and characterized an additional BCCT family transporter, which we named BccT5, that was also a carrier for DMSP. IMPORTANCE DMSP is present in the marine environment, produced in large quantities by marine phytoplankton as an osmoprotectant, and is an important component of the global geochemical sulfur cycle. This algal osmolyte has not been previously investigated for its role in marine heterotrophic bacterial osmotic stress response. Vibrionaceae species are marine species, many of which are halophiles exemplified by V. parahaemolyticus , a species that possesses at least six transporters for the uptake of osmolytes. Here, we demonstrated that V. parahaemolyticus and other Vibrio species can accumulate DMSP as an osmoprotectant and show that several BCCT family transporters uptake DMSP. These studies suggest that DMSP is a significant bacterial osmoprotectant that may be important for understanding the fate of DMSP in the environment. DMSP is produced and present in coral mucus, and Vibrio species form part of the microbial communities associated with corals. The function of DMSP in these interactions is unclear, but it could be an important driver for these associations, allowing Vibrio proliferation. This work suggests that DMSP likely has a more important role in heterotrophic bacteria ecology than previously appreciated. 
    more » « less