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1. Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo‐alteration for freshwater microbes

   https://doi.org/10.1111/1462‐2920.15121  

   Nalven, Sarah G.; Ward, Collin P.; Payet, Jérôme P.; Cory, Rose M.; Kling, George W.; Sharpton, Thomas J.; Sullivan, Christopher M.; Crump, Byron C. (January 2020, Environmental Microbiology)

   Microbes and sunlight convert terrigenous dissolved organic matter (DOM) in surface waters to greenhouse gases. Prior studies show contrasting results about how biological and photochemical processes interact to contribute to the degradation of DOM. In this study, DOM leached from the organic layer of tundra soil was exposed to natural sunlight or kept in the dark, incubated in the dark with the natural microbial community, and analyzed for gene expression and DOM chemical composition. Microbial gene expression (metatranscriptomics) in light and dark treatments diverged substantially after 4 hours. Gene expression suggested that sunlight exposure of DOM initially stimulated microbial growth by (a) replacing the function of enzymes that degrade higher molecular weight DOM such as enzymes for aromatic carbon degradation, oxygenation, and decarboxylation, and (b) releasing low molecular weight compounds and inorganic nutrients from DOM. However, growth stimulation following sunlight exposure of DOM came at a cost. Sunlight depleted the pool of aromatic compounds that supported microbial growth in the dark treatment, ultimately causing slower growth in the light treatment over 5 days. These first measurements of microbial metatranscriptomic responses to photo-alteration of DOM provide a mechanistic explanation for how sunlight exposure of terrigenous DOM alters microbial processing and respiration of DOM. 

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2. Coral high molecular weight carbohydrates support opportunistic microbes in bacterioplankton from an algae-dominated reef

   https://doi.org/10.1128/msystems.00832-24  

   Thobor, Bianca M; Haas, Andreas F; Wild, Christian; Nelson, Craig E; Wegley_Kelly, Linda; Hehemann, Jan-Hendrik; Arts, Milou; Boer, Meine; Buck-Wiese, Hagen; Nguyen, Nguyen P; et al (November 2024, mSystems)

   Meyer, Julie L (Ed.)

   High molecular weight (HMW; >1 kDa) carbohydrates are a major component of dissolved organic matter (DOM) released by benthic primary producers. Despite shifts from coral to algae dominance on many reefs, little is known about the effects of exuded carbohydrates on bacterioplankton communities in reef waters. We compared the monosaccharide composition of HMW carbohydrates exuded by hard corals and brown macroalgae and investigated the response of the bacterioplankton community of an algae-dominated Caribbean reef to the respective HMW fractions. HMW coral exudates were compositionally distinct from the ambient, algae-dominated reef waters and similar to coral mucus (high in arabinose). They further selected for opportunistic bacterioplankton taxa commonly associated with coral stress (i.e.,Rhodobacteraceae,Phycisphaeraceae,Vibrionaceae, andFlavobacteriales) and significantly increased the predicted energy-, amino acid-, and carbohydrate-metabolism by 28%, 44%, and 111%, respectively. In contrast, HMW carbohydrates exuded by algae were similar to those in algae tissue extracts and reef water (high in fucose) and did not significantly alter the composition and predicted metabolism of the bacterioplankton community. These results confirm earlier findings of coral exudates supporting efficient trophic transfer, while algae exudates may have stimulated microbial respiration instead of biomass production, thereby supporting the microbialization of reefs. In contrast to previous studies, HMW coral and not algal exudates selected for opportunistic microbes, suggesting that a shift in the prevalent DOM composition and not the exudate type (i.e., coral vs algae)per se, may induce the rise of opportunistic microbial taxa. IMPORTANCEDissolved organic matter (DOM) released by benthic primary producers fuels coral reef food webs. Anthropogenic stressors cause shifts from coral to algae dominance on many reefs, and resulting alterations in the DOM pool can promote opportunistic microbes and potential coral pathogens in reef water. To better understand these DOM-induced effects on bacterioplankton communities, we compared the carbohydrate composition of coral- and macroalgae-DOM and analyzed the response of bacterioplankton from an algae-dominated reef to these DOM types. In line with the proposed microbialization of reefs, coral-DOM was efficiently utilized, promoting energy transfer to higher trophic levels, whereas macroalgae-DOM likely stimulated microbial respiration over biomass production. Contrary to earlier findings, coral- and not algal-DOM selected for opportunistic microbial taxa, indicating that a change in the prevalent DOM composition, and not DOM type, may promote the rise of opportunistic microbes. Presented results may also apply to other coastal marine ecosystems undergoing benthic community shifts. 

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3. Sea ice coverage and water depth influence dissolved organic matter composition in Arctic waters and generated aerosols

   https://doi.org/10.1525/elementa.2025.00074  

   Boschi, V; Remenapp, A; Grannas, A M; Troutman, A; Ribas-Ribas, M; Wurl, O; Mirrielees, J A; Kirpes, R M; Ault, A P; Pratt, K A; et al (April 2026, Elem Sci Anth)

   Arctic warming has resulted in record sea ice reduction, increasing the length and extent of photosynthetic microorganism blooms, which impact water chemistry through the production and cycling of organic carbon. Chemical species in surface waters can become aerosolized, affecting atmospheric chemistry, cloud dynamics, and ultimately, radiative budgets. A greater understanding of how Arctic water and aerosol chemistry change with sea ice coverage is pivotal in modeling ocean-atmosphere dynamics in a changing climate. As such, water samples were collected from the marginal ice zone (MIZ) to pack ice conditions in the high Arctic Ocean and added to a marine aerosol reference tank to generate and collect aerosols for further characterization. Water and aerosol dissolved organic matter (DOM) was isolated using PPL solid phase extraction resin and characterized using high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Analysis of seawater samples revealed that greater heteroatom (N, S, P) abundance was characteristic of the MIZ seawater DOM relative to pack ice seawater DOM. Greater phytoplankton and bacterial cell counts found in MIZ seawater suggests that greater microbial activity results in greater heteroatom assimilation into their biomass, as measured in the marine DOM characterized here. Surface water samples collected at approximately 100 µm and 1 m were chemically similar, containing DOM with more surface-active lipid- and protein-like compounds and devoid of more photo-labile, lignin-like/carboxylic-rich alicyclic material, which was abundant in deeper waters (3–8 m), indicating the strong influence of photochemical and biological processes on DOM chemistry. Aerosol DOM did not mirror water DOM chemistry, but rather certain compounds appeared to be preferentially aerosolized. Aerosol DOM was more aliphatic in character, less oxidized, with greater heteroatom content, proteins, carbohydrates, and unsaturated hydrocarbons relative to the source water. 

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4. The cycling of glycine betaine and homarine in marine microbial communities: Quantitative flux measurements and the role of competitive uptake inhibition

   https://doi.org/10.1002/lol2.70069  

   Sacks, Joshua S; Carlson, Laura T; Finch, Anna H; Ferrer‐González, Frank X; Boysen, Angela K; Heal, Katherine R; Karl, David M; White, Angelicque E; Sosa, Oscar A; Ingalls, Anitra E (January 2026, Limnology and Oceanography Letters)

   Abstract The flux of carbon through the labile dissolved organic matter (DOM) pool supports marine microbial communities and represents the fate of approximately half of marine net primary production (NPP). However, the behavior of individual chemical structures that make up labile DOM remain largely unknown. We performed 12 uptake kinetics and two uptake competition experiments on the abundant betaine osmolytes glycine betaine (GBT) and homarine. Combining uptake kinetics with dissolved metabolite measurements, we quantified fluxes through the DOM pool. Fluxes were correlated with particulate concentrations and ranged from 0.53 to 41 and 0.003 to 0.54 nmol L⁻¹ d⁻¹for GBT and homarine, respectively, equivalent to up to 1.2% of NPP. Turnover times of dissolved GBT and homarine ranged from 1 to 57 d. Betaines and sulfoniums such as dimethylsulfoniopropionate competitively inhibited homarine uptake. Our results quantify GBT and homarine cycling and suggest an important role for uptake competition in regulating dissolved metabolite concentrations and fluxes. 

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5. Distinguishing the molecular diversity, nutrient content, and energetic potential of exometabolomes produced by macroalgae and reef-building corals

   https://doi.org/10.1073/pnas.2110283119  

   Wegley_Kelly, Linda; Nelson, Craig E.; Petras, Daniel; Koester, Irina; Quinlan, Zachary A.; Arts, Milou G.I.; Nothias, Louis-Felix; Comstock, Jacqueline; White, Brandie M.; Hopmans, Ellen C.; et al (February 2022, Proceedings of the National Academy of Sciences)

   Metabolites exuded by primary producers comprise a significant fraction of marine dissolved organic matter, a poorly characterized, heterogenous mixture that dictates microbial metabolism and biogeochemical cycling. We present a foundational untargeted molecular analysis of exudates released by coral reef primary producers using liquid chromatography–tandem mass spectrometry to examine compounds produced by two coral species and three types of algae (macroalgae, turfing microalgae, and crustose coralline algae [CCA]) from Mo’orea, French Polynesia. Of 10,568 distinct ion features recovered from reef and mesocosm waters, 1,667 were exuded by producers; the majority (86%) were organism specific, reflecting a clear divide between coral and algal exometabolomes. These data allowed us to examine two tenets of coral reef ecology at the molecular level. First, stoichiometric analyses show a significantly reduced nominal carbon oxidation state of algal exometabolites than coral exometabolites, illustrating one ecological mechanism by which algal phase shifts engender fundamental changes in the biogeochemistry of reef biomes. Second, coral and algal exometabolomes were differentially enriched in organic macronutrients, revealing a mechanism for reef nutrient-recycling. Coral exometabolomes were enriched in diverse sources of nitrogen and phosphorus, including tyrosine derivatives, oleoyl-taurines, and acyl carnitines. Exometabolites of CCA and turf algae were significantly enriched in nitrogen with distinct signals from polyketide macrolactams and alkaloids, respectively. Macroalgal exometabolomes were dominated by nonnitrogenous compounds, including diverse prenol lipids and steroids. This study provides molecular-level insights into biogeochemical cycling on coral reefs and illustrates how changing benthic cover on reefs influences reef water chemistry with implications for microbial metabolism. 

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