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Abstract Horizontal gene transfer (HGT) is a fundamental ecological and evolutionary process involving the movement of genetic material across taxa within a single generation. While traditionally studied at the level of individual genes with encoded adaptive functions, recent advances in genomics and metagenomics highlight the need for a broader, integrative framework. Here, we expand the concept of the “ecology of DNA transfer,” which conceptualizes HGT as a multi-layered process spanning the genome, cell, and ecological context. We further explore how the fate and expression of transferred DNA vary over evolutionary timescales, from recently acquired, transcriptionally silenced sequences to ancient, fully integrated genes. Together, this framework underscores HGT as a dynamic, context-dependent process shaped by interactions across biological scales. 

Horizontal gene transfer (HGT) generates genetic variation in populations across all domains of life; however, most studies focus on individual transfers and functional information derived therefrom. This is useful but does not consider DNA transfer more broadly, that is, nongene transfers, donor–recipient dynamics, or trends and background levels that may help infer ecological information. Here, we review the mechanistic underpinnings of DNA transfer, literature from diverse fields that addresses HGT on a community basis and the associated methodological challenges, and propose a framework for conceptualizing the process of DNA transfer, highlighting DNA mobility as a feature of community ecology and DNA itself as a public good. These ideas coalesce to support DNA transfer as a fundamental ecological phenomenon that remains largely unmeasured. 

Marine diatoms are an important group of phytoplankton that can shape marine ecosystems and global carbon cycling. When stressed, either physiologically or by grazing, diatoms release oxidized, lipid-derived signals known as oxylipins. Diatom-derived oxylipins are proposed to serve as defense and signaling chemicals that affect multiple components of marine ecosystems. Therefore, to elucidate the diversity of diatom-derived oxylipins produced during stress, we profiled the spectrum of dissolved lipids of five diatom species in culture under silicon limitation and across growth phases using ultra-high performance liquid chromatography coupled with high-resolution accurate mass spectrometry. In this study, we present evidence that physiological changes associated with Si-limitation elicit the extracellular release of linear oxygenated fatty acids (LOFAs) across five diatom species. For diatoms like Skeletonema japonicum and Pseudo-nitzschia multiseries, silicon limitation induced a distinct lipidomic signature driven by oxylipins known to be allelopathic. While their lipoxygenases were found to be different, S. japonicum and P. multiseries had the most similar dissolved lipidomes, suggesting alternative controls on oxylipin biosynthesis. Consequently, elevated oxylipin concentrations with silicon stress, estimated up to 5.91 µM, pose implications for diatoms at sea, potentially affecting ecosystems and biogeochemistry. 

Abstract As chloroplast‐stealing or “kleptoplastidic” lineages become more reliant on stolen machinery, they also tend to become more specialized on the prey from which they acquire this machinery. For example, the ciliateMesodinium rubrumobtains > 95% of its carbon from photosynthesis, and specializes on plastids from theTeleaulaxclade of cryptophytes. However,M. rubrumis sometimes observed in nature containing plastids from other cryptophyte species. Here, we report on substantial ingestion of the blue‐green cryptophyteHemiselmis pacificabyM. rubrum, leading to organelle retention and transient increases inM. rubrum's growth rate. However, microscopy data suggest thatH. pacificaorganelles do not experience the same rearrangement and integration asTeleaulax amphioxeia's. We measuredM. rubrum's functional response, quantified the magnitude and duration of growth benefits, and estimated kleptoplastid photosynthetic rates. Our results suggest that a lack of discrimination betweenH. pacificaand the preferred preyT. amphioxeia(perhaps due to similarities in cryptophyte size and swimming behavior) may result inH. pacificaingestion Thus, while blue‐green cryptophytes may represent a negligible prey source in natural environments, they may helpM. rubrumsurvive whenTeleaulaxare unavailable. Furthermore, these results represent a useful tool for manipulatingM. rubrum's cell biology and photophysiology. 

ABSTRACT Askenasiais a conspicuous ciliate in plankton assemblages of fresh and marine ecosystems; however, many aspects of its biology, taxonomy, and ecology remain enigmatic. Here we provide new information on the behavior, prey preferences, ultrastructure, and phylogenetic diversity of marineAskenasia, from perhaps the first ever cultures established for this genus.Askenasiaspp. have long been suspected of being predatory, i.e., feeding on other ciliates, and here we reveal that several isolates of marineA. cf.stellarishad high ingestion and growth rates on the ciliateMesodinium rubrum. This result supports numerous observations ofAskenasiaco‐occurring withM. rubrumin a variety of ecosystems. While we found no evidence of grazing on several other species of ciliates or photosynthetic flagellates,A. cf.stellarisprobably does ingest other small ciliates as prey. Using transmission electron microscopy imaging ofAskenasia, we show that the dikinetids of its equatorial ciliary belt resemble those found in Prostomatea ciliates, supporting phylogenetic analysis of partial 18S rRNA genes from twoA. cf.stellarisstrains. We also provide ultrastructural details of the contractile and food vacuoles inAskenasia. Our results suggest thatA. cf.stellariscan be an important predator ofM. rubrumin coastal marine ecosystems. 

Abstract Mixotrophic protists combine photosynthesis and phagotrophy to obtain energy and nutrients. Because mixotrophs can act as either primary producers or consumers, they have a complex role in marine food webs and biogeochemical cycles. Many mixotrophs are also phenotypically plastic and can adjust their metabolic investments in response to resource availability. Thus, a single species's ecological role may vary with environmental conditions. Here, we quantified how light and food availability impacted the growth rates, energy acquisition rates, and metabolic investment strategies of eight strains of the mixotrophic chrysophyte,Ochromonas. All eightOchromonasstrains photoacclimated by decreasing chlorophyll content as light intensity increased. Some strains were obligate phototrophs that required light for growth, while other strains showed stronger metabolic responses to prey availability. When prey availability was high, all eight strains exhibited accelerated growth rates and decreased their investments in both photosynthesis and phagotrophy. Photosynthesis and phagotrophy generally produced additive benefits: In low‐prey environments,Ochromonasgrowth rates increased to maximum, light‐saturated rates with increasing light but increased further with the addition of abundant bacterial prey. The additive benefits observed between photosynthesis and phagotrophy inOchromonassuggest that the two metabolic modes provide nonsubstitutable resources, which may explain why a tradeoff between phagotrophic and phototrophic investments emerged in some but not all strains. 

Protist plankton can be divided into three main groups: phytoplankton, zooplankton, and mixoplankton.In situmethods for studying phytoplankton and zooplankton are relatively straightforward since they generally target chlorophyll/photosynthesis or grazing activity, while the integration of both processes within a single cell makes mixoplankton inherently challenging to study. As a result, we understand less about mixoplankton physiology and their role in food webs, biogeochemical cycling, and ecosystems compared to phytoplankton and zooplankton. In this paper, we posit that by merging conventional techniques, such as microscopy and physiological data, with innovative methods likein situsingle-cell sorting and omics datasets, in conjunction with a diverse array of modeling approaches ranging from single-cell modeling to comprehensive Earth system models, we can propel mixoplankton research into the forefront of aquatic ecology. We present eight crucial research questions pertaining to mixoplankton and mixotrophy, and briefly outline a combination of existing methods and models that can be used to address each question. Our intent is to encourage more interdisciplinary research on mixoplankton, thereby expanding the scope of data acquisition and knowledge accumulation for this understudied yet critical component of aquatic ecosystems. 

Identifying mechanisms driving the substantial dissolution of biogenic CaCO₃(60 to 80%) in surface and mesopelagic waters of the global ocean is critical for constraining the surface ocean’s alkalinity and inorganic carbon budgets. We examine microzooplankton grazing on coccolithophores, photosynthetic calcifying algae responsible for a majority of open-ocean CaCO₃production, as a mechanism driving shallow dissolution. We show that microzooplankton grazing dissolves 92 ± 7% of ingested coccolith calcite, which may explain 50 to 100% of the observed CaCO₃dissolution in supersaturated surface waters. Microzooplankton grazing on coccolithophores is thus a substantial, previously unrecognized biological mechanism affecting the ballasting of organic carbon to deeper waters, the ecology and fitness of microzooplankton themselves due to buffering of food vacuole pH, and ultimately the continued ability of the surface ocean to take up atmospheric carbon dioxide.