About

Paul Falkowski is a professor at Rutgers University within the Department of Marine and Coastal Sciences. His research focuses on microbial oceanography, particularly microbial ecophysiology, host-virus interactions, virology, molecular evolution, and ecosystem processes. His work merges physiology, biochemistry, and genome-enabled omics approaches to elucidate the molecular and cellular mechanisms that shape microbial interactions, their success in the oceans, and their influence on natural biogeochemical cycles. Falkowski's research emphasizes understanding how microbial arms races are regulated, especially between algal hosts and viruses, and how specific microbial genes influence responses to environmental stress, ultimately affecting ocean ecology and biogeochemistry. He is involved in NSF-funded projects assessing the impact of viruses on Earth's carbon cycle and how ocean conditions influence these processes.

Research topics

• Biology
• Environmental chemistry
• Chemistry
• Astrobiology
• Physics
• Aeronautics
• Mathematics
• Botany
• Optics
• Aerospace engineering
• Philosophy
• Ecology
• Inorganic chemistry
• Linguistics
• Engineering ethics
• Engineering

Selected publications

• Anoxic photo-oxidation of Mn(II)-bearing carbonates on Mars and early Earth

  Proceedings of the National Academy of Sciences · 2026-05-11

  articleOpen access

  , catalyze oxidative transformations among redox-sensitive metals. Thus, the occurrence of Mn oxides, either observed or inferred from sedimentary geochemical data, has formed the basis for multiple hypotheses concerning the evolution of the atmospheric redox state on the early Earth and Mars. Here, using theory and experiments, we report that the band gap of common Ca/Mg carbonate minerals (including calcite, magnesite, and aragonite) is significantly lowered by trace incorporation (0.8 wt% or lower) of Mn(II) into their bulk structure or surface, conferring photochemical reactivity under ultraviolet conditions relevant to early Earth and Mars (200 to 400 nm). Moreover, we show that surface incorporation of Mn(II) reduces the fundamental band gap much more effectively (by >1 eV) than bulk incorporation. Our results suggest that photo-oxidation of Mn(II)-bearing carbonates could have occurred widely on planetary surfaces, resulting in the abiotic formation of manganese oxides without free molecular oxygen. Photochemically driven redox cycling of manganese could help sustain redox disequilibria for microbial metabolisms, but compromises the use of manganese oxides as oxygen barometers.

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• Novel insights into conserved biomineralization mechanisms revealed from a cold-water scleractinian coral skeletal proteome

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-27

  articleOpen access

  Stony corals exhibit striking morphological plasticity across diverse environments and trophic strategies, raising fundamental questions about the conservation of their biomineralization machinery. Here, we characterize the skeletal organic matrix (SOM) proteome of the cosmopolitan cold-water, asymbiotic coral Desmophyllum pertusum and compare it with published skeletal proteomes from a facultatively photosymbiotic temperate coral and an obligately photosymbiotic subtropical coral. Despite pronounced differences in habitat, symbiotic status, and skeletal micro-density, we observe convergence on a conserved biomineralization toolkit spanning these taxa. Comparative proteomics, genomics, and AI-based structural predictions reveal that this toolkit integrates acidic matrix proteins, carbonic anhydrases, adhesion and structural proteins, and signaling components with multiple export pathways, including secretion, vesicle-mediated trafficking, and cytoskeleton-associated transport. The current proteome expands the diversity of acidic proteins, suggesting roles not only in stabilizing amorphous calcium carbonate but also in proton buffering within intracellular and extracellular calcifying compartments. Together, these findings redefine coral biomineralization as a dynamic, coordinated network of cellular pathways rather than a static assemblage of matrix components. By establishing D. pertusum as a symbiont-free model system, this work provides a mechanistic framework for dissecting coral calcification across environments and for assessing the resilience of this conserved machinery to ongoing ocean change.

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• Coupling of excitation energy to photochemistry in natural marine phytoplankton communities under iron stress

  Proceedings of the National Academy of Sciences · 2025-07-29 · 2 citations

  articleOpen accessSenior authorCorresponding

  Oxygenic photosynthesis requires excitation energy transfer from light-harvesting complexes (LHCs) to reaction centers (RCs) to drive photochemical redox chemistry. The effective absorption cross section of RCs dynamically responds to the light environment on time scales of seconds to days, allowing rapid acclimations to changes in spectral irradiance and photoprotection under high light, thereby optimizing light absorption for photochemistry. Although energy coupling between LHC-RCs has been studied for decades in laboratory cultures, it remains poorly understood in real-world conditions, where it is potentially influenced by nutrients. In the oceans, one of the most critical micronutrients for photosynthesis is iron (Fe). To investigate the effects of Fe stress on the energetic coupling between LHC-RCs in natural phytoplankton assemblages in the Southern Atlantic Ocean, we assessed photophysiological responses using a pair of custom-built fluorometers measuring chlorophyll-a variable fluorescence and picosecond fluorescence lifetimes. Detailed analysis based on the functional absorption cross section of the oxygen-evolving complex, quantum yield of photochemistry, energetic connectivity of RCs, and the average lifetime of in vivo chlorophyll fluorescence suggested that between 10 and 25% of LHCs remain uncoupled from RCs and do not effectively contribute to photochemical charge separation. Addition of Fe to samples under trace metal-clean on-board incubations indicates relatively rapid recoupling (< 24 h) of antennae to photochemistry, followed by biophysical stabilization of recoupled complexes. Our findings highlight the crucial role of micronutrients in controlling the excitation energy transfer from LHCs to RCs in marine phytoplankton and the overall primary productivity in the real-world oceans.

  PublisherDOI

• On the emergence of metabolism: the evolution of proteins that powered life

  Philosophical Transactions of the Royal Society B Biological Sciences · 2025-08-07 · 2 citations

  reviewOpen accessSenior authorCorresponding

  Life is far from thermodynamic equilibrium. Hence, life must extract energy from the environment. On Earth, that energy is driven by networks of metabolic reactions in all cells which ultimately move electrons and protons (i.e. hydrogen atoms) across the planet. The origin of metabolism required the emergence and evolution of proteins. Proteins are nanometre-scale chemical machines-i.e. literal nanomachines which physically move. These nanomachines enable living systems to perform essential biochemical tasks from replication to metabolism; the latter being the engines of life. In all extant life on Earth, a small set of these nanomachines, called oxidoreductases, couple chemical energy from the environment with core redox reactions including photosynthesis, respiration and nitrogen fixation. The origins and emergence of complex life have been intimately tied with evolution of oxidoreductases. Here, using structure-based analyses, we describe the evolution of the protein catalysts in three biological epochs. First, thermodynamically driven polymerization reactions generated simple metal-binding peptides with specific sequences that catalysed core metabolic reactions. Second, these catalysts were incorporated in small structural 'folds'. In the third epoch, these folds served as building blocks for extant, complex nanomachines.This article is part of the discussion meeting issue 'Chance and purpose in the evolution of biospheres'.

  PublisherDOI

• Stability of the marine nitrogen cycle over the past 165 million years

  Nature Communications · 2025-10-09 · 3 citations

  articleOpen accessSenior author

  Abstract Nitrogen and phosphorus are the two macro-nutrients that limit biological productivity in the ocean. While the supply of P depends on geological processes, N is biologically supplied from an inexhaustible atmospheric source, but can be limited by micro-nutrients, especially iron. Here we present a record of N and C isotopes over the past 165 Ma in marine sediments to address feedbacks between the N-cycle and productivity. Over most of the last 165 Myr, the fixed N averaged +3.2‰, (−2 and +9‰), but higher in distal areas of the ocean due to limited vertical mixing. Using an isotope box model and a coupled climate model we show that this is caused by winds that induce upwelling changing due to continental meander. Upwelling along low latitude east-west orientated Tethyan coastlines results in low δ 15 N, while upwelling along narrow N-S coastlines as it does today, results in high δ 15 N due to denitrification.

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• Designing Peptide Fossils That Model the Evolution of the Bacterial Ferredoxin Fold

  JACS Au · 2025-11-03 · 1 citations

  articleOpen access

  Electron transfer coupled to redox chemistry is at the heart of metabolism. The proteins responsible for moving electrons (protein electron carriers) must have emerged at the origin of life. The small iron-sulfur-binding bacterial ferredoxins were likely among these first proteins. Embedded within the ferredoxin sequence and structure is a symmetry that points to an ancient gene duplication event. Little is understood about the nature of ferredoxins prior to this duplication event or what environmental factors may have driven the selection for more complex forms. The deep-time molecular history of ferredoxins goes back billions of years and cannot be reconstructed by phylogenetic analyses based on amino acid sequences. Here, we use structure-guided protein design to model a fossil half-ferredoxin stage in the evolution of this fold, the semidoxins, and their symmetric full-length counterparts, the symdoxins. Semidoxin designs homodimerize, exhibiting structural, thermodynamic, and electrochemical behaviors in most cases identical to cognate symdoxins. However, the semi- and symdoxin fossil stages behave differently when incorporated into an in vivo electron transfer complementation assay. Both can support bacterial growth dependent on protein expression. Growth rates of bacteria expressing the semidoxins are much more sensitive to oxygen than those of bacteria expressing symdoxins. Motivated by the in vivo functionality of designed semidoxins, we identified putative naturally occurring semidoxins in extant anaerobic microorganisms. This is consistent with the observed in vivo oxygen sensitivity of the semidoxin designs. One natural semidoxin is shown to be folded and redox active. However, it exists as a mixture of monomers and dimers, suggesting a potential connection between semidoxins and even simpler single iron-sulfur cluster-binding peptides.

  PublisherDOI

• Tracing Antarctic snow's chemical and biological properties in the air-polar ocean exchange

  2025-01-01

  article
  PublisherDOI

• A Tribute to Richard W. Eppley

  Oceanography · 2024-01-01

  articleOpen access1st authorCorresponding

  Richard W. Eppley (1931–2023), better known as “Dick,” was a tour de force in biological oceanography. Most of his research life was at Scripps Institution of Oceanography (Scripps), where he studied marine phytoplankton and their roles in biogeochemical processes. Over the course of his career, he influenced many people, not only in science but also as exemplar of integrity and fundamental curiosity about the ocean. His formidable contributions to phytoplankton physiology and biological oceanography were appreciatively reviewed shortly after his retirement (Weiler et al., 1990), and with added perspective after his death (Cullen and Eppley, 2024). What follows are tributes from several of his former students, postdocs, and colleagues.

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• Zvy Dubinsky (1934–2024)

  Limnology and Oceanography Bulletin · 2024-10-29

  articleOpen access

  Professor Zvy Dubinsky passed away on 25 March 2024. Zvy was a long-time member of ASLO, a distinguished colleague, and friend of many (Fig. 1). Zvy left behind a legacy of excellent and ground-breaking science, generations of students, and extensive networks of colleagues around the world, many of whom became close friends. Zvy was also a devoted husband to Maya, father, grandfather of four, and great-grandfather of four. Born in Barcelona in 1934, Zvy emigrated as a child to Israel where he trained as a teacher and worked for several years in developing an advanced, modern biology curriculum for high schools. In his mid-30s, he returned to study for a M.Sc. in biology at Bar-Ilan University (BIU), Israel where he investigated “The influence of select environmental factors on the abundance and composition of algal populations from Lake Kinneret (Israel)” and then continued to complete his Ph.D. (under Tom Berman's supervision) on “Light as an ecological factor in Lake Kinneret phytoplankton dynamics.” After a postdoctoral fellowship at Queens College, New York, USA, where he focused on algal lipid physiology, biochemistry, and the potential of algae in biofuel production, Zvy accepted a faculty position at the Department of Life Sciences at BIU where he developed a laboratory focusing on biophysical, physiological, and ecological aspects of aquatic photosynthesis. He markedly advanced the research study in the fields of phytoplankton photoacclimation and their interactions with the underwater light field, and helped develop the application of photoacoustics to directly determine photosynthetic quantum yields of any benthic phototroph. For his extensive publication list and highly cited papers, see https://scholar.google.co.il/citations?hl=en&user=0zUQYWIAAAAJ. “I first met Zvy in 1977. I had just begun my research career at Brookhaven National Laboratory, where I could explore any aspect of research that interested me. At that time I was fascinated with how single celled algae could acclimate to irradiance. When their growth light was low, cells made more photosynthetic pigments, and when light was high, the converse. Zvy told me that corals could also photoacclimate. I had no idea what corals were. We wrote a proposal together to the NSF/BSF, about photoacclimation in corals. Amazingly, it was funded. It led to the most interesting collaboration I have had in science. Zvy taught me how corals lived. I saw corals for the first time in my life in Nabeq in the Sinai—where Israel had made the area a National Park. I was blown away. We worked every evening from about 8 in the evening until 2 in the morning in a Bedouin coffee shop, with our portable generators making electricity for our tabletop centrifuges, the lights for our microscopes, and our spectrophotometers. The camels ate the paper coming out of the spectrophotometers (seriously).” “His continued interest in phytoplankton photosynthesis encouraged me to invite him to a cruise on the then newly built German ice-breaking vessel Polarstern during the Austral spring of 1988, within the framework of the European Polarstern Study (EPOS). Our project on this expedition was to study the carbon and energy balance in the phytoplankton of the Southern Ocean which, with water temperatures consistently below 0°C, is the coldest part of the World Ocean. We were able to show that because respiration is more temperature-sensitive than photosynthesis, the energy balance in phytoplankton can be positive, even when radiant energy supply for photosynthesis is extremely low, owing to deep water column mixing.” With a flourishing scientific career Zvy planned and worked on >100 research projects, including ~25 international research projects funded by a variety of competitive sources including the prestigious FP7 ERC Advanced Career Grant under which he was the Project Principal Investigator for CoralWarm (www.coralwarm.eu) which explored the impacts of anthropogenic eutrophication on coral reefs. His research also diverged to more applied projects and he established the “Algal Biotechnology Center (BIU)” initiating research on biodiesel and natural products from microalgae. “The idea behind the project was to contribute to the peace process in the Middle East, in addition to supporting science. At the time of the project, this looked rather promising. In addition to German and Israeli scientists, researchers from Jordan, Egypt, and Palestine participated. One of the Palestinian participants was Mutas Qutob who had studied at Bar Ilan University and subsequently became Professor at the Palestinian Al-Quds University in Jerusalem.” Zvy's prolific work resulted in ~270 scientific publications (https://scholar.google.co.il/citations?hl=en&user=0zUQYWIAAAAJ) and edited books, invitations to lecture around the world, and prestigious acknowledgment of his work via numerous international editorial and advisory positions to both industry and government translating research into policy. Zvy was also a dedicated and talented teacher. He mentored ~90 graduate students (including myself - I. Berman-Frank) and postdoctoral fellows, established a new program in ecology at BIU based on hands-on desert and coral reef studies in the field, taught a wide variety of courses from plant physiology and ecology to marine photosynthesis and ecophysiology, bioenergetics, and “Man and the Biosphere.” This last course became one of the most popular courses taught at BIU annually attracting >100 students from all faculties. Zvy also headed the M.B.A. program in Management of Natural Resources, Energy and Water at the Netanya Academic College (Israel), and a M.Sc. program in Marine Science at Ruppin College/Faculty of Marine Sciences (Israel). “When I first met Zvy in the late 90s as an undergraduate student in biology, I was immediately captivated by his distinctive academic style. He was teaching an introductory course on marine biology, and his lectures were brimming with energy. He had a unique way of intertwining solar energy with the coral reef ecosystem and photosynthesis, explaining these complex topics with such patience and passion that I was inspired to learn more and more from him. His stories of fieldwork and global exploration ignited in me a desire to follow in his footsteps. Zvy was a true renaissance man, with passions extending beyond biology to nature, photography, art, and philosophy. During my Ph.D. thesis under his guidance, I came to know him much more deeply as I traveled with him to Japan, Europe, and other magical places. I admired his peaceful way of living, his wisdom in addressing both big and small questions, and his remarkable ability to connect people with the nature he cherished so much.” Zvy organized many international symposia, workshops and seminars. One of the most notable was the co-founding of the Group of Aquatic Primary Productivity (GAP) workshops to which he contributed from 1980 to 2008. GAP workshops brought together freshwater and marine scientists to plan and work together, running experiments with state-of-the-science equipment and methodologies, analyzing data, and publishing the results in peer-reviewed journals. “I was introduced to Zvy on the occasion of the International Limnology Congress at Kyoto in 1980 by Tom Berman, whom I had met in a similar fashion in Leningrad in 1972. This was the starting point of my lifelong collaboration with Zvy. During the Kyoto Congress, Tom, Zvy, and I decided to establish the Group on Aquatic Productivity (GAP), whose format from the very beginning was organizing hands-on meetings, focusing on topics related to measuring aquatic primary production. During the early planning phase of GAP Paul Falkowski joined GAP, which substantially added to the scientific clout of the group. In 1982, the very first GAP meeting took place at Konstanz (see photo; Fig. 3). I am happy that by now, 10 GAP-meetings have taken place.” One of these meetings was the 8th GAP in Eilat, Israel with Zvy helping me (I. Berman-Frank) co-chair a workshop with ~100 participants and 7 experimental groups from ~20 countries. After a very successful Gala evening at the underwater observatory, Zvy unfortunately had a bicycle accident on the way back to his hotel room and spent the night in the emergency room. This did not deter him from participating throughout the workshop, weaving more international connections, and helping with all aspects of the workshop and the subsequent ~30 publications in a special issue of Aquatic Microbial Ecology and Theme Section in Aquatic Biology. Zvy was also a talented photographer with the flair and ability to record nature and people through the lens of the camera. This led to several exhibitions including joint exhibitions with Max von Tilzer with the last one titled “Ripples and Patterns” showing in Konstanz, Jerusalem, and at the German Embassy in Tel Aviv (Fig. 4). “Our families became extremely close. Indeed, when I came home from Brookhaven, Zvy would often call me about a new idea, or to meet with him and Maya (Zvy's wife) for lunch, or to walk along a beach. Zvy taught me to appreciate the sea. But, more than that—he projected love for the world.” Oren Levy adds, and his sentiments are echoed by many of us – Zvy's students, colleagues, and friends: His (Zvy's) legacy will live on in the hearts of those he touched and in the countless contributions he made to the field of marine biology.

  PublisherOA PDFDOI

• Proteomic characterization of a foraminiferal test’s organic matrix

  Proceedings of the National Academy of Sciences · 2024-12-06 · 3 citations

  articleOpen accessSenior authorCorresponding

  Foraminifera are unicellular protists capable of precipitating calcite tests, which fossilize and preserve geochemical signatures of past environmental conditions dating back to the Cambrian period. The biomineralization mechanisms responsible for the mineral structures, which are key to interpreting palaeoceanographic signals, are poorly understood. Here, we present an extensive analysis of the test-bound proteins. Using liquid chromatography–tandem mass spectrometry, we identify 373 test-bound proteins in the large benthic foraminifer Amphistegina lobifera , the majority of which are highly acidic and rich in negatively charged residues. We detect proteins involved in vesicle formation and active Ca 2+ trafficking, but in contrast, do not find similar proteins involved in Mg 2+ transport. Considering findings from this study and previous ones, we propose a dual ion transport model involving seawater vacuolization, followed by the active release of Ca 2+ from the initial vacuoles and subsequent uptake into newly formed Ca-rich vesicles that consequently enrich the calcification fluid. We further speculate that Mg 2+ passively leaks through the membrane from the remaining Mg-rich vesicles, into the calcifying fluid, at much lower concentrations than in seawater. This hypothesis could not only explain the low Mg/Ca ratio in foraminiferal tests compared to inorganic calcite, but could possibly also account for its elevated sensitivity to temperature compared with inorganically precipitated CaCO 3 .

  PublisherOA PDFDOI

Recent grants

• Collaborative Research: Impacts of Eddies and Mixing on Plankton Community Structure and Biogeochemical Cycling in the Sargasso Sea

  NSF · $378k · 2003–2007

• Ocean Acidification: Mechanisms of Coral Biomineralization

  NSF · $1.4M · 2014–2018

• Understanding how global warming will select for zooxanthellae phenotypes

  NSF · $607k · 2009–2013

• Ocean Acidification-Category 1: The Molecular Basis of Ocean Acidification Effects on Calcification in Zooxanthellate Corals

  NSF · $1.9M · 2010–2014

• EAGER: Environmental signals in a marine diatom

  NSF · $298k · 2016–2017

Frequent coauthors

• Ken O. Buesseler

  Woods Hole Oceanographic Institution

  62 shared

• Maxim Y. Gorbunov

  Rutgers, The State University of New Jersey

  56 shared

• Miriam Katz

  New York Medical College

  51 shared

• Oscar Schofield

  Rutgers, The State University of New Jersey

  43 shared

• Vikas Nanda

  Johnson University

  38 shared

• Zbigniew Kolber

  38 shared

• Cabell S. Davis

  Woods Hole Oceanographic Institution

  37 shared

• David A. Siegel

  37 shared

Education

• Ph.D., Marine Microbiology

  University of California, Santa Barbara

  1989

• M.S., Marine Microbiology

  University of California, Santa Barbara

  1984

• B.S., Marine Biology

  University of California, Santa Barbara

  1982

Awards & honors

• Bennett L. Smith Chair in Business and Natural Resources
• Board of Governors Professor
• Founding Director of the Rutgers Energy Institute
• Elected to the National Academy of Science (2007)