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ABSTRACT The marine cyanobacteriumProchlorococcusnumerically dominates the phytoplankton communities in all lower latitude, open ocean environments. Having lost the catalase gene,Prochlorococcusis highly susceptible to exogenous hydrogen peroxide (H₂O₂) produced at the ocean’s surface. Protection by H₂O₂-scavenging heterotrophic “helper” bacteria has been demonstrated in laboratory cultures and implicated as an important mechanism ofProchlorococcussurvival in the ocean. Importantly, some other phytoplankton can also scavenge H₂O₂, suggesting these competing microbes may inadvertently protectProchlorococcus. In this study, we assessed the ability of co-occurring phytoplankton, the cyanobacteriumSynechococcusand picoeukaryotesMicromonasandOstreococcus, to protectProchlorococcusfrom H₂O₂exposure when cocultured at ecologically relevant abundances. All three genera could significantly degrade H₂O₂and diminishProchlorococcusmortality during H₂O₂exposures simulating photochemical production and rainfall events. We suggest that these phytoplankton groups contribute significantly to the H₂O₂microbial sink of the open ocean, thus complicating their relationships with and perhaps contributing to the evolutionary history ofProchlorococcus.IMPORTANCEThe marine cyanobacteriumProchlorococcusis the most abundant photosynthetic organism on the planet and is crucially involved in microbial community dynamics and biogeochemical cycling in most tropical and subtropical ocean waters. This success is due, in part, to the detoxification of the reactive oxygen species hydrogen peroxide (H₂O₂) performed by “helper” organisms. Earlier work identified heterotrophic bacteria as helpers, and here, we demonstrate that rival cyanobacteria and picoeukaryotic phytoplankton can also contribute to the survival ofProchlorococcusduring exposure to H₂O₂. Whereas heterotrophic bacteria helper organisms can benefit directly from promoting the survival of carbon-fixingProchlorococcuscells, phytoplankton helpers may suffer a twofold injury: production of H₂O₂degrading enzymes constrains already limited resources in oligotrophic environments, and the activity of these enzymes bolsters the abundance of their numerically dominant competitor. These findings build toward a better understanding of the intricate dynamics and interactions that shape microbial community structure in the open ocean. 

ABSTRACT The fastest replicating bacteriumVibrio natriegensis a rising workhorse for molecular and biotechnological research with established tools for efficient genetic manipulation. Here, we expand on the capabilities of multiplex genome editing by natural transformation (MuGENT) by identifying a neutral insertion site and showing how two selectable markers can be swapped at this site for sequential rounds of natural transformation. Second, we demonstrated that MuGENT can be used for complementation by gene insertion at an ectopic chromosomal locus. Additionally, we developed a robust method to cure the competence plasmid required to induce natural transformation. Finally, we demonstrated the ability of MuGENT to create massive deletions; the 280 kb deletion created in this study is one of the largest artificial deletions constructed in a single round of targeted mutagenesis of a bacterium. These methods each advance the genetic potential ofV. natriegensand collectively expand upon its utility as an emerging model organism for synthetic biology. IMPORTANCEVibrio natriegensis an emerging model organism for molecular and biotechnological applications. Its fast growth, metabolic versatility, and ease of genetic manipulation provide an ideal platform for synthetic biology. Here, we develop and apply novel methods that expand the genetic capabilities of theV. natriegensmodel system. Prior studies developed a method to manipulate multiple regions of the chromosome in a single step. Here, we provide new resources that diversify the utility of this method. We also provide a technique to remove the required genetic tools from the cell once the manipulation is performed, thus establishing “clean” derivative cells. Finally, we show the full extent of this technique’s capability by generating one of the largest chromosomal deletions reported in the literature. Collectively, these new tools will be beneficial broadly to theVibriocommunity and specifically to the advancement ofV. natriegensas a model system. 

Abstract Marine microorganisms play a critical role in regulating atmospheric CO₂concentration via the biological carbon pump. Deposition of continental mineral dust on the sea surface increases carbon sequestration but the interaction between minerals and marine microorganisms is not well understood. We discovered that the interaction of clay minerals with dissolved organic matter and a γ-proteobacterium in seawater increases Transparent Exopolymer Particle (TEP) concentration, leading to organoclay floc formation. To explore this observation further, we conducted a microcosm experiment using surface seawater collected from the Spring 2023 phytoplankton bloom in the Gulf of Maine. Unfiltered (natural community) and filtered (200 μm and 3 μm) seawater was sprayed with clay (20 mg L^− 1and 60 mg L^− 1) and incubated. All clay treatments led to a tenfold increase in TEP concentration. 16S rRNA gene amplicon sequence analyses of seawater and settled organoclay flocs showed the dominance of α-proteobacteria, γ-proteobacteria, and Bacteroidota. The initial seawater phytoplankton community was dominated by dinoflagellates followed by a haptophyte (Phaeocystissp.) and diatoms. Following clay addition, dinoflagellate cell abundance declined sharply while diatom cell abundance increased. By analyzing organoclay flocs for 18S rRNA we confirmed that dinoflagellates were removed in the flocs. The clay amendment removed as much as 50% of phytoplankton organic carbon. We then explored the fate of organoclay flocs at the next trophic level by feeding clay and phytoplankton (Rhodomonas salina) toCalanus finmarchicus. The copepod ingestedR. salinaand organoclay flocs and egested denser fecal pellets with 1.8- to 3.6- fold higher sinking velocity compared to controls. Fecal pellet density enhancement could facilitate carbon sequestration through zooplankton diel vertical migration. These findings provide insights into how atmospheric dust-derived clay minerals interact with marine microorganisms to enhance the biological carbon pump, facilitating the burial of organic carbon at depths where it is less likely to exchange with the atmosphere. 

ABSTRACT Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a “top 10” list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy. 

Abstract It has been proposed that microbial predator and prey densities are related through sublinear power laws. We revisited previously published biomass and abundance data and fitted Power‐law Biomass Scaling Relationships (PBSRs) between marine microzooplankton predators (Z) and phytoplankton prey (P), and marine viral predators (V) and bacterial prey (B). We analysed them assuming an error structure given by Type II regression models which, in contrast to the conventional Type I regression model, accounts for errors in both the independent and the dependent variables. We found that the data support linear relationships, in contrast to the sublinear relationships reported by previous authors. The scaling exponent yields an expected value of 1 with some spread in different datasets that was well‐described with a Gaussian distribution. Our results suggest that the ratiosZ/P, andV/Bare on average invariant, in contrast to the hypothesis that they systematically decrease with increasingPand B, respectively, as previously thought. 

Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements with single-cell resolution and flow cytometry, we quantified the flux of viral C and N into virovorous protists and bacteria and compared the loss of viruses due to abiotic vs biotic factors. We found that some protists can obtain most of their C and N requirements from viral particles and that viral C and N get incorporated into bacterial biomass. We found that bacteria and protists were responsible for increasing the daily removal rate of viruses by 33% to 85%, respectively, compared to abiotic processes alone. Our laboratory incubation experiments showed that abiotic processes removed roughly 50% of the viruses within a week, and adding biotic processes led to a removal of 83% to 91%. Our data provide direct evidence for the transfer of viral C and N back into the microbial loop through protist grazing and bacterial breakdown, representing a globally significant flux that needs to be investigated further to better understand and predictably model the C and N cycles of the hydrosphere. 

Abstract. Recent meta-analyses suggest that microzooplankton biomass density scales linearly with phytoplankton biomass density, suggesting a simple, general rule may underpin trophic structure in the global ocean. Here, we use a set of highly simplified food web models, solved within a global general circulation model, to examine the core drivers of linear predator–prey scaling. We examine a parallel food chain model which assumes microzooplankton grazers feed on distinct size classes of phytoplankton and contrast this with a diamond food web model allowing shared microzooplankton predation on a range of phytoplankton size classes. Within these two contrasting model structures, we also evaluate the impact of fixed vs. density-dependent microzooplankton mortality. We find that the observed relationship between microzooplankton predators and prey can be reproduced with density-dependent mortality on the highest predator, regardless of choices made about plankton food web structure. Our findings point to the importance of parameterizing mortality of the highest predator for simple food web models to recapitulate trophic structure in the global ocean. 

ABSTRACT The marine cyanobacterium Prochlorococcus numerically dominates the phytoplankton community of the nutrient-limited open ocean, establishing itself as the most abundant photosynthetic organism on Earth. This ecological success has been attributed to lower cell quotas for limiting nutrients, superior resource acquisition, and other advantages associated with cell size reduction and genome streamlining. In this study, we tested the prediction that Prochlorococcus outcompetes its rivals for scarce nutrients and that this advantage leads to its numerical success in nutrient-limited waters. Strains of Prochlorococcus and its sister genus Synechococcus grew well in both mono- and cocultures when nutrients were replete. However, in nitrogen-limited medium, Prochlorococcus outgrew Synechococcus but only when heterotrophic bacteria were also present. In the nitrogen-limited medium, the heterotroph Alteromonas macleodii outcompeted Synechococcus for nitrogen but only if stimulated by the exudate released by Prochlorococcus or if a proxy organic carbon source was provided. Genetic analysis of Alteromonas suggested that it outcompetes Synechococcus for nitrate and/or nitrite, during which cocultured Prochlorococcus grows on ammonia or other available nitrogen species. We propose that Prochlorococcus can stimulate antagonism between heterotrophic bacteria and potential phytoplankton competitors through a metabolic cross-feeding interaction, and this stimulation could contribute to the numerical success of Prochlorococcus in nutrient-limited regions of the ocean. IMPORTANCE In nutrient-poor habitats, competition for limited resources is thought to select for organisms with an enhanced ability to scavenge nutrients and utilize them efficiently. Such adaptations characterize the cyanobacterium Prochlorococcus , the most abundant photosynthetic organism in the nutrient-limited open ocean. In this study, the competitive superiority of Prochlorococcus over a rival cyanobacterium, Synechococcus , was captured in laboratory culture. Critically, this outcome was achieved only when key aspects of the open ocean were simulated: a limited supply of nitrogen and the presence of heterotrophic bacteria. The results indicate that Prochlorococcus promotes its numerical dominance over Synechococcus by energizing the heterotroph’s ability to outcompete Synechococcus for available nitrogen. This study demonstrates how interactions between trophic groups can influence interactions within trophic groups and how these interactions likely contribute to the success of the most abundant photosynthetic microorganism.