Publications and Preprints
You can find our full publication list on Google Scholar. Please reach out if you need access to a paper and we'll send you a copy.
Bold denotes Jabre Lab members and affiliates.
2026
Willem H. van de Poll, Rebecca Zitoun, Loay J. Jabre, Marieke M. Bos, Anna C. Koek, Wen-Hsuan Liao, Sharyn Ossebaar, Patrick Laan, Erin M. Bertrand, Rob Middag
High-latitude North Atlantic currents (60°–70°N) exhibit contrasting nutrient stoichiometries, but the spatial extent of post-spring bloom iron (Fe) and nitrogen (N) stress on phytoplankton around Iceland remains poorly constrained. Here we pair in situ biogeochemical characteristics with 72 h Fe and N addition experiments in the East Greenland Current (EGC), Irminger Current (IC), Atlantic Current (AC), and East Icelandic Current (EIC) regions. Dissolved iron (dFe) was elevated in the EGC region and depleted in Atlantic surface waters. Unlike dFe, surface nitrate in the EGC region was depleted and elevated in Atlantic waters. Chlorophyll a (Chl a) and particulate organic carbon standing stocks in the diatom and chlorophyte enriched EGC were ~ 40% lower than in the haptophyte dominated Atlantic waters. Changes in photophysiology during the incubation experiments revealed widespread Fe stress in the IC and in most of the AC stations. Notably, 80% of the experiments with nutrient stoichiometry suggesting Fe limitation (dFe < 0.2 nmol L−1, N > 0.6 μmol L−1) revealed Fe stress. In contrast, 30% of the experiments with nutrient stoichiometry suggesting N limitation (N < 0.6 μmol L−1, dFe > 0.2 nmol L−1) showed N stress, mainly in the EGC region. The EIC showed depleted concentrations of nitrate and dFe at the surface. Here, one incubation experiment revealed responses of combined N and Fe stress. The strong summertime density differences between the EGC and Atlantic water masses most likely limits the ability of advected dFe from Greenland and the Arctic to fertilize the Fe-depleted Atlantic waters.
Loay J. Jabre, Elden Rowland, J. Scott P. McCain, Erin Bertrand
Fragilariopsis cylindrus is a key diatom in the Southern Ocean, where low iron and manganese availability constrain primary production and biogeochemical activity. The molecular mechanisms used by polar diatoms, including F. cylindrus, to cope with trace metal limitations remain largely unexplored. Here we present phenotypic characterizations and proteomic profiles of F. cylindrus grown under controlled iron (low, medium, high) and manganese (low, high) conditions that reflect those observed in the Southern Ocean. Using data-independent acquisition mass spectrometry, we measured over 8000 unique proteins capturing diverse metabolic responses, including those related to photosynthesis, elemental transport, and intracellular trafficking. We confirm consistent expression of canonical iron stress proteins (e.g., phytotransferrin) under low iron, and identify additional candidate biomarkers for iron and manganese stress that could be explored in future laboratory and field experiments. Our data also support the notion that one flavodoxin isoform in F. cylindrus is iron responsive and one is not, and show that PsaE, a protein associated with the iron-rich photosystem-I, is upregulated under low iron. Altogether, this dataset is among the most comprehensive proteomic characterizations of trace metal physiology in polar diatoms to date, providing a foundation for connecting molecular responses to trace metal availability and ocean biogeochemistry.
2025
Ziyue Zheng, Loay J. Jabre, Matthew McIlvin, Mak A. Saito, Sangwon Hyun
Intracellular compartmentalization of proteins underpins their function and the metabolic processes they sustain. Various mass spectrometry-based proteomics methods (subcellular spatial proteomics) now allow high throughput subcellular protein localization. Yet, the curation, analysis and interpretation of these data remain challenging, particularly in non-model organisms where establishing reliable marker proteins is difficult, and in contexts where experimental replication and subcellular fractionation are constrained. Here, we develop FSPmix, a semi-supervised functional clustering method implemented as an open-source R package, which leverages partial annotations from a subset of marker proteins to predict protein subcellular localization from subcellular spatial proteomics data. This method explicitly assumes that protein signatures vary smoothly across subcellular fractions, enabling more robust inference under low signal-to-noise data regimes. We applied FSPmix to a subcellular proteomics dataset from a marine diatom, allowing us to assign probabilistic localizations to proteins and uncover potentially new protein functions. Altogether, this work lays the foundation for more robust statistical analysis and interpretation of subcellular proteomics datasets, particularly in understudied organisms.​
Loay J. Jabre, Elden Rowland, Charlotte Eich, Mathijs van Manen, Corina Brussaard, Rob Middag, Erin Bertrand
Metabolic processes underpinning ocean biogeochemistry are powered by molecular machines, proteins, that require various elements to function. Yet, the allocation of elements to these proteins, and subsequent implications for biogeochemical processes, remain poorly characterized. Here we integrate elemental measurements with metaproteomics to quantitatively examine elemental use in Southern Ocean microbial proteins and metabolic processes. We demonstrate that iron availability influences elemental allocation, including decreased iron allocation to photosynthesis and compensatory incorporation of non-iron metals into metalloproteins under iron scarcity. Manganese was primarily allocated to photosynthesis in iron-replete conditions, and reallocated to other metabolic roles under low iron.
Photosystem I:II protein mass ratios impacted both iron and manganese allocation, and appeared to be driven by iron availability. Approximately half of biogenic copper was found in plastocyanin, likely substituting for iron-containing cytochromes in photosynthesis. Moreover, biogenic nitrogen to phosphorus ratios were decoupled from ribosomal abundance, contrary to prevailing assumptions about ribosomal influence on stoichiometric regulation in the ocean. Instead, our results suggest that community composition and intracellular storage are important regulators of N:P in the Southern Ocean. Together, our findings identify key molecular mechanisms that modulate elemental demand and limitation, and provide a foundation for quantitatively connecting molecular measurements with biogeochemical models.
J. Scott P. McCain, Loay J. Jabre, Elden Rowland, Jinyoung Jung, Youngju Lee, Tae-Wan Kim, Corina Brussaard, Rob Middag, Erin Bertrand
Elemental stoichiometry of biomass is a focal point that connects different biogeochemical cycles. Yet, the mechanistic underpinnings of elemental stoichiometry are poorly quantified in many cases. We combined targeted and untargeted metaproteomics, Bayesian statistical modelling, and geochemical measurements to quantify the contribution of specific proteins to metal stoichiometry in natural populations of Southern Ocean diatoms. Our analyses indicate that a substantial amount of non-photosynthetic manganese (Mn) in diatoms in an Antarctic polynya can be attributed to superoxide dismutases (∼0.7 µmol Mn: mol Carbon; ∼20% of the total cellular Mn quota). We then used cultures and proteomic profiling of the key polar diatom Fragilariopsis cylindrus to identify environmental controls on superoxide dismutases, and discovered that iron concentration has little influence on the abundance of two Mn superoxide dismutases, while Mn limitation induces the depletion of these Mn superoxide dismutases and an accompanying increase of nickel superoxide dismutase. Overall, we combined metaproteomic approaches to quantify proteomic composition and connected these measurements to metal-to-carbon ratios and their responses to metal availability. Because metal quotas are key parameters in some biogeochemical models, our approach provides a direct mechanism for informing ecosystem-scale models with molecular measurements.
