About

Sallie (Penny) W. Chisholm is an MIT Institute Professor who studies the biology, ecology, and evolution of the most abundant marine phytoplankton species to understand the forces that shape microbial ecosystems. Her research focuses on the cyanobacterium Prochlorococcus, which is the smallest and most abundant microbe in ocean ecosystems, sometimes accounting for half of the total photosynthetic biomass. She uses this model system to study life across all scales, from the genome to the ecosystem, with the goal of understanding how ocean microbes influence global biogeochemical cycles. Her work has significantly contributed to our understanding of microbial ecology and evolution in marine environments.

Research topics

• Biology
• Ecology
• Botany
• Oceanography
• Genetics

Selected publications

• Priming the pump: enhanced nitrite release in response to a nitrate pulse by nitrogen-limited <i>Prochlorococcus</i>

  Critical Insights in Microbiology · 2026-03-15

  articleSenior author
  PublisherDOI

• Uptake of <i>Prochlorococcus</i> ‐derived metabolites by <i>Alteromonas macleodii</i> <scp>MIT1002</scp> shows high levels of substrate specificity

  Limnology and Oceanography Letters · 2026-02-17

  articleOpen access

  Abstract Seawater contains small biomolecules, or metabolites, that are highly labile components of dissolved organic matter (DOM). Marine microbes interact by exchanging metabolites, thus shaping marine microbial ecology, DOM composition, and global carbon cycling. To better constrain one set of microbe‐metabolite interactions, we cultured the marine gammaproteobacterium Alteromonas macleodii MIT1002 on a range of compounds excreted by a sympatric cyanobacterium, Prochlorococcus . Alteromonas macleodii MIT1002 could metabolize the branched‐chain amino acids leucine, isoleucine, and valine, as well as 3‐methyl‐2‐oxobutanoic acid (a branched‐chain ketoacid intermediate of valine metabolism), but not thymidine, kynurenine, 4‐hydroxybenzoic acid, nor the other branched‐chain ketoacids. The utilization of branched‐chain amino acids indicates that A. macleodii MIT1002 can metabolize each corresponding ketoacid, suggesting that transporter specificity underlies the observed substrate specificity for 3‐methyl‐2‐oxobutanoic acid. These experiments show that even subtle changes in chemical structure can result in different microbial interactions and different fates for dissolved metabolites.

  PublisherOA PDFDOI

• Biofilm formation and dynamics in the marine cyanobacterium <i>Prochlorococcus</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-05

  preprintOpen accessSenior author

  Summary The picocyanobacterium Prochlorococcus is responsible for ∼10% of annual marine carbon fixation and plays a role in the global carbon budget. While these phototrophs are primarily considered free-living and neutrally buoyant in the euphotic zone, we observe that they can form biofilms on diverse substrates. This trait is conserved across Prochlorococcus ecotypes, and populations continuously transition between planktonic and biofilm states via a non-genetic heritable mechanism. Throughout their growth, cells in biofilms retain a reversible, dynamic attachment state, and measurements of growth, photosynthesis, and respiration rates reveal that cells in biofilms exude more organic carbon than their planktonic counterparts. Estimates of the fraction of Prochlorococcus cells attached to particles in the ocean reveal that a significant adherent population exists throughout the euphotic and mesopelagic zones. This work describes a new dimension of Prochlorococcus ’s ecological niche and suggests a role in carbon export to the deep sea.

  PublisherOA PDFDOI

• Uptake of Prochlorococcus-derived metabolites by <i>Alteromonas macleodii</i> MIT1002 shows high levels of substrate specificity

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-11 · 2 citations

  preprintOpen access

  Abstract Seawater contains an abundance of small biomolecules, or metabolites, that are highly labile components of dissolved organic matter (DOM). Marine microbes interact by exchanging metabolites, thus shaping marine microbial ecology, DOM composition, and global carbon cycling. To better constrain one set of microbe-metabolite interactions, we cultured the marine gammaproteobacterium Alteromonas macleodii MIT1002 on a range of compounds excreted by a sympatric cyanobacterium, Prochlorococcus . Alteromonas could assimilate the branched chain amino acids leucine, isoleucine, and valine, as well as 3-methyl-2-oxobutanoic acid (a branched chain ketoacid intermediate of valine metabolism), but not thymidine, kynurenine, 4-hydroxybenzoic acid, or the other branched chain ketoacids. The assimilation of branched chain amino acids indicates that Alteromonas can metabolically process each corresponding ketoacid, suggesting that transporter specificity underlies the observed substrate specificity for 3-methyl-2-oxobutanoic acid. These experiments show that even subtle changes in chemical structure can result in different microbial interactions and different fates for dissolved metabolites. Significance Statement Microbial interactions with dissolved organic matter are important controls on the marine carbon cycle. Dissolved organic matter is often considered in bulk, which leaves the specificity and nature of these interactions poorly constrained. Here we show that microbe-molecule interactions can be highly specific, distinguishing between molecules that are structurally and biochemically similar. This implies that small changes in this pool of carbon could have large impacts for the overall system function, and that measuring this pool of carbon with molecular-level resolution is important to characterizing microbe-molecule interactions. We further explore the mechanism underlying the observed substrate specificity and suggest that it is caused by transporter selectivity, meaning the ability of these microbes to selectively uptake specific dissolved organic molecules.

  PublisherOA PDFDOI

• The shared and distinct roles of <i>Prochlorococcus</i> and co-occurring heterotrophic bacteria in regulating community dynamics

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-26

  preprintOpen accessSenior author

  Abstract Prochlorococcus is the world’s most abundant photosynthetic organism with over 10 27 cells distributed across much of Earth’s oceans, and is collectively responsible for almost 10% of marine carbon fixation. Naturally co-occurring heterotrophic bacteria at roughly 10 5 -10 6 cells mL -1 in the oceans have been shown to increase Prochlorococcus fitness and productivity. Despite this massive scale, our understanding of these globally important interactions remains limited, with past research largely focused on single Prochlorococcus -heterotroph pairings involving only a few species. In this study, we extend this perspective by using synthetic communities containing multiple diverse heterotrophic strains isolated from Prochlorococcus enrichment cultures. Specifically, we isolated the four most abundant co-occurring heterotroph species and examined both individual Prochlorococcus –heterotroph interactions and interactions within a synthetic community comprising Prochlorococcus and all four heterotrophs. Using absolute quantification of RNA, DNA, and cell counts over the course of Prochlorococcus growth curves, we find that Prochlorococcus has a modest, species-independent transcriptional response to heterotrophs, whereas each heterotroph displays a markedly different transcriptional response to the community and fulfills distinct metabolic roles. Transcriptional analyses reveal several potential crossfeeding interactions and indicate that community dynamics are influenced not only by metabolic activity but also antagonistic mechanisms, defense responses, and coordinated group behaviors. By pairing synthetic community approaches with absolute abundance measurements, we can gain deeper insight into the forces that shape microbial community assembly in the oceans and their role in driving the global carbon cycle.

  PublisherOA PDFDOI

• Priming the pump: Enhanced nitrite release in response to a nitrate pulse by nitrogen-limited <i>Prochlorococcus</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-13

  preprintOpen accessSenior author

  Abstract Prochlorococcus is a diverse and widespread cyanobacterium with significant contributions to the marine nitrogen and carbon cycles. Some Prochlorococcus reduce and divert up to 20-30% of the nitrate that they take up to external pools of nitrite. Given that nitrite is a central intermediate of the nitrogen cycle and Prochlorococcus is highly abundant in nitrogen-limited waters, our goal was to advance our understanding of nitrite cycling in the context of nitrogen limitation. Here we observe that nitrate-limited Prochlorococcus have cell-specific nitrite production rates that are approximately a magnitude higher than nitrogen-replete Prochlorococcus when challenged with a pulse of nitrate. Nitrite production rates are unchanged or depressed during light and cold shocks, suggesting that nitrate is not used as an alternative electron acceptor to mitigate the impacts of excess photochemically generated electrons. These results suggest that in regions where phytoplankton growth is limited by nitrogen, Prochlorococcus cells could be primed to transform substantial quantities of nitrate into extracellular pools of nitrite during episodic upwellings of nitrate-rich water. Given that nitrite is an important intermediate in the nitrogen cycle, these results have ramifications for our understanding of nitrogen cycling in nitrogen-limited open ocean ecosystems.

  PublisherOA PDFDOI

• Transformation of plasmid DNA into <i>Prochlorococcus</i> via electroporation

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-21

  preprintOpen accessSenior authorCorresponding

  Abstract Prochlorococcus is the most numerically abundant photosynthetic organism in the oceans and plays a role in global carbon cycling. Despite its ecological significance and the availability of over a thousand assembled genomes, progress in understanding gene function has been limited by the lack of genetic tools. Here, we report a reproducible electroporation-based protocol to introduce replicative plasmids into two strains of Prochlorococcus representing different ecotypes: MIT9313 (low-light adapted) and MED4 (high-light adapted). Using plasmids carrying a spectinomycin resistance cassette, we achieved transformation in ~33% of MED4 and ~10% of MIT9313 attempts, with greatest success when electroporating cells in late exponential phase. Transformed cells stably retained plasmids and expressed resistance genes, demonstrating functional uptake and gene expression. We also delivered a modified 13 kb plasmid carrying a CRISPR-Cpf1 system into MED4. While no targeted edits were observed, cpf1 and specR were expressed, indicating successful delivery of large constructs and active transcription. These findings represent a key step toward genetic manipulation of Prochlorococcus , enabling future optimization of gene editing approaches and deeper functional analysis of its vast and largely uncharacterized pangenome.

  PublisherDOI

• ProSynTax: A curated protein dataset for taxonomic classification of <i>Prochlorococcus</i> and <i>Synechococcus</i> in metagenomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-25 · 2 citations

  preprintOpen accessSenior author

  ABSTRACT Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus , including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus . This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data – even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus .

  PublisherOA PDFDOI

• A curated protein dataset for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes

  Scientific Data · 2025-12-03

  articleOpen accessSenior author

  Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying classification workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.

  PublisherOA PDFDOI

• Global niche partitioning of purine and pyrimidine cross-feeding among ocean microbes

  Science Advances · 2025-01-03 · 12 citations

  articleOpen accessSenior author

  Cross-feeding involves microbes consuming exudates of other surrounding microbes, mediating elemental cycling. Characterizing the diversity of cross-feeding pathways in ocean microbes illuminates evolutionary forces driving self-organization of ocean ecosystems. Here, we uncover a purine and pyrimidine cross-feeding network in globally abundant groups. The cyanobacterium Prochlorococcus exudes both compound classes, which metabolic reconstructions suggest follows synchronous daily genome replication. Co-occurring heterotrophs differentiate into purine- and pyrimidine-using generalists or specialists that use compounds for different purposes. The most abundant heterotroph, SAR11, is a specialist that uses purines as sources of energy, carbon, and/or nitrogen, with subgroups differentiating along ocean-scale gradients in the supply of energy and nitrogen, in turn producing putative cryptic nitrogen cycles that link many microbes. Last, in an SAR11 subgroup that dominates where Prochlorococcus is abundant, adenine additions to cultures inhibit DNA synthesis, poising cells for replication. We argue that this subgroup uses inferred daily adenine pulses from Prochlorococcus to synchronize to the daily photosynthate supply from surrounding phytoplankton.

  PublisherDOI

Recent grants

• Membrane vesicles produced by marine bacteria: origins, distributions, and functions

  NSF · $599k · 2014–2019

• Nitrate Assimilation and the Ecology of Prochlorococcus: Features and Implications of Intraspecific Diversity in a Model Marine Phototroph

  NSF · $803k · 2012–2018

• NIH Grant P41RR002250

  NIH · $9.3M · 2014

• IOS EDGE: Development of genetic tools for the dominant phototroph in the sea

  NSF · $890k · 2017–2022

• Microevolution and population dynamics of Prochlorococcus cells in the ocean: Insights through single-cell genomics

  NSF · $300k · 2012–2014

Frequent coauthors

• Allison Coe

  Massachusetts Institute of Technology

  111 shared

• Steven J. Biller

  Wellesley College

  96 shared

• Jamie W. Becker

  Massachusetts Institute of Technology

  76 shared

• Paul M. Berube

  Massachusetts Institute of Technology

  72 shared

• Thomas Hackl

  67 shared

• Robert Olson

  BC Cancer Agency

  63 shared

• Matthew B. Sullivan

  The Ohio State University

  62 shared

• Jessie W Berta-Thompson

  Massachusetts Institute of Technology

  58 shared

Labs

• Chisholm LabPI

Education

• Ph.D., Biology

  State University of New York

  1974

• B.A., Biology/Chemistry

  Skidmore College

  1969

Awards & honors

• Crafoord Prize (2019)
• Ramon Margalef Prize in Ecology (2013)
• American Association for the Advancement of Science, Fellow…
• National Medal of Science (2011)
• National Academy of Sciences, Alexander Agassiz Medal (2010)