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Creators/Authors contains: "Aluwihare, Lihini I."

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  1. Abstract

    A targeted method for the quantification of bioavailable amide N found in marine DON (bDON) is presented. The method utilizes mild acid hydrolysis to convert amide N found in proteins andN‐acetyl amino polysaccharides to primary amine containing products that are measured using a highly sensitive (nanomolar range and precision) fluorometric technique with addition ofO‐phthaldialdehyde. We find amidic bDON concentrations ranging from 0.08 to 1.82 μM N within waters from the upper 300 m in the southern California Current, Southern California Bight, and subtropical North Pacific representing 15–33% of bulk DON concentrations. Bioassay experiments from the North Pacific revealed consumption of ~20% of the in situ bDON within 5 days. The method represents a simple and rapid tool for the quantification of bioavailable DON concentrations in seawater with improved analytical precision over traditional estimates of bulk DON concentrations.

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    Free, publicly-accessible full text available April 25, 2025
  2. Free, publicly-accessible full text available May 14, 2025
  3. Abstract

    Iron is an essential nutrient for all microorganisms of the marine environment. Iron limitation of primary production has been well documented across a significant portion of the global surface ocean, but much less is known regarding the potential for iron limitation of the marine heterotrophic microbial community. In this work, we characterize the transcriptomic response of the heterotrophic bacterial community to iron additions in the California Current System, an eastern boundary upwelling system, to detect in situ iron stress of heterotrophic bacteria. Changes in gene expression in response to iron availability by heterotrophic bacteria were detected under conditions of high productivity when carbon limitation was relieved but when iron availability remained low. The ratio of particulate organic carbon to dissolved iron emerged as a biogeochemical proxy for iron limitation of heterotrophic bacteria in this system. Iron stress was characterized by high expression levels of iron transport pathways and decreased expression of iron-containing enzymes involved in carbon metabolism, where a majority of the heterotrophic bacterial iron requirement resides. Expression of iron stress biomarkers, as identified in the iron-addition experiments, was also detected insitu. These results suggest iron availability will impact the processing of organic matter by heterotrophic bacteria with potential consequences for the marine biological carbon pump.

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  4. Abstract

    Coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, yet there has been relatively little research on the implications for reef water column microbiology and biogeochemistry. A mesocosm heating experiment and bottle incubation compared how unbleached and bleached corals alter dissolved organic matter (DOM) exudation in response to thermal stress and subsequent effects on microbial growth and community structure in the water column. Thermal stress of healthy corals tripled DOM flux relative to ambient corals. DOM exudates from stressed corals (heated and/or previously bleached) were compositionally distinct from healthy corals and significantly increased growth of bacterioplankton, enriching copiotrophs and putative pathogens. Together these results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend into the water column, with altered coral DOM exudation driving microbial feedbacks that influence how coral reefs respond to and recover from mass bleaching events.

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  5. Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples. 
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  6. Francois Morel (Ed.)
    Marine dissolved organic matter (DOM) is a major reservoir that links global carbon, nitrogen, and phosphorus. DOM is also important for marine sulfur biogeochemistry as the largest water column reservoir of organic sulfur. Dissolved organic sulfur (DOS) can originate from phytoplankton-derived biomolecules in the surface ocean or from abiotically “sulfurized” organic matter diffusing from sulfidic sediments. These sources differ in 34S/32S isotope ratios (δ34S values), with phytoplankton-produced DOS tracking marine sulfate (21‰) and sulfurized DOS mirroring sedimentary porewater sulfide (∼0 to –10‰). We measured the δ34S values of solid-phase extracted (SPE) DOM from marine water columns and porewater from sulfidic sediments. Marine DOM_SPE δ34S values ranged from 14.9‰ to 19.9‰ and C:S ratios from 153 to 303, with lower δ34S values corresponding to higher C:S ratios. Marine DOM_SPE samples showed consistent trends with depth: δ34S values decreased, C:S ratios increased, and δ13C values were constant. Porewater DOM_SPE was 34S-depleted (∼-0.6‰) and sulfur-rich (C:S ∼37) compared with water column samples. We interpret these trends as reflecting at most 20% (and on average ∼8%) contribution of abiotic sulfurized sources to marine DOS_SPE and conclude that sulfurized porewater is not a main component of oceanic DOS and DOM. We hypothesize that heterogeneity in δ34S values and C:S ratios reflects the combination of sulfurized porewater inputs and preferential microbial scavenging of sulfur relative to carbon without isotope fractionation. Our findings strengthen links between oceanic sulfur and carbon cycling, supporting a realization that organic sulfur, not just sulfate, is important to marine biogeochemistry. 
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  7. 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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  8. null (Ed.)
    The rapidly advancing field of metabolomics encompasses a diverse suite of powerful analytical and bioinformatic tools that can help to reveal the diversity and activity of chemical compounds in individual organisms, species interactions, and entire ecosystems. In this perspective we use examples from studies of coral reefs to illustrate ways in which metabolomics has been and can be applied to understand coastal ecosystems. Examples of new insights that can be provided by metabolomics include resolving metabolite exchange between plants, animals and their microbiota, identifying the relevant metabolite exchanges associated with the onset and maintenance of diverse, microbial mutualisms characterizing unknown molecules that act as cues in coral, reproduction, or defining the suites of compounds involved in coral-algal competition and microbialization of algal-dominated ecosystems. Here we outline sampling, analytical and informatic methods that marine biologists and ecologists can apply to understand the role of chemical processes in ecosystems, with a focus on open access data analysis workflows and democratized databases. Finally, we demonstrate how these metabolomics tools and bioinformatics approaches can provide scientists the opportunity to map detailed metabolic inventories and dynamics for a holistic view of the relationships among reef organisms, their symbionts and their surrounding marine environment. 
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  9. Abstract

    In eastern boundary current systems, strong coastal upwelling brings deep, nutrient‐rich waters to the surface ocean, supporting a productive food web. The nitrate load in water masses that supply the region can be impacted by a variety of climate‐related processes that subsequently modulate primary productivity. In this study, two coastal upwelling regimes along central and southern California were sampled seasonally for nitrogen and oxygen stable isotopes of nitrate (i.e., nitrate isotopes) over several years (2010–2016) on 14 California Cooperative Oceanic Fisheries Investigations (CalCOFI) cruises. Seasonal, interannual, and spatial variations in euphotic zone nitrate isotopes were largely driven by the extent of nitrate utilization, sometimes linked to iron limitation of diatom productivity. Pronounced isotopic enrichment developed with the El Niño conditions in late 2015 and early 2016 which likely resulted from increased nitrate utilization linked to reduced nitrate supply to the euphotic zone. Differential enrichment of nitrogen and oxygen isotopes was observed in the surface ocean, suggesting that phytoplankton increased their reliance on locally nitrified (recycled) nitrate during warmer and more stratified periods. Overall, nitrate isotopes effectively differentiated important euphotic zone processes such as nitrate assimilation and nitrification, while archiving the influence of disparate controls such as iron limitation and climatic events through their effects on nitrate utilization and isotopic fractionation.

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  10. Abstract

    The >5,000‐year radiocarbon age (14C‐age) of much of the 630 ± 30 Pg C oceanic dissolved organic carbon (DOC) reservoir remains an enigma in the marine carbon cycle. The fact that DOC is significantly older than dissolved inorganic carbon at every depth in the ocean forms the basis of our current framing of the marine DOC cycle, where some component persists over multiple cycles of ocean mixing. As a result,14C‐depleted, aged DOC is hypothesized to be present as a uniform reservoir with a constant14C signature and concentration throughout the water column. However, key requirements of this model, including direct observations of DOC with similar14C signatures in the surface and deep ocean, have never been met. Despite decades of research, the distribution of Δ14C values in marine DOC remains a mystery. Here, we applied a thermal fractionation method to compare operationally defined refractory DOC (RDOC) from different depths in the North Pacific Ocean. We found that RDOC shares chemical characteristics (as recorded by OC bond strength) throughout the water column but does not share the same14C signature. Our results support one part of the current paradigm—that RDOC is comprised of structurally related components throughout the ocean that form a “background” reservoir. However, in contrast to the current paradigm, our results are consistent with a vertical concentration gradient and a vertical and inter‐ocean Δ14C gradient for RDOC. The observed Δ14C gradient is compatible with the potential addition of pre‐aged DOC to the upper ocean.

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