Metabolic trade-offs constrain the cell size ratio in a nitrogen-fixing symbiosis.

Biological dinitrogen (N2) fixation is a key metabolic process exclusively performed by prokaryotes, some of which are symbiotic with eukaryotes. Species of the marine haptophyte algae Braarudosphaera bigelowii harbor the N2-fixing endosymbiotic cyanobacteria UCYN-A, which might be evolving organelle-like characteristics. We found that the size ratio between UCYN-A and their hosts is strikingly conserved across sublineages/species, which is consistent with the size relationships of organelles in this symbiosis and other species. Metabolic modeling showed that this size relationship maximizes the coordinated growth rate based on trade-offs between resource acquisition and exchange. Our findings show that the size relationships of N2-fixing endosymbionts and organelles in unicellular eukaryotes are constrained by predictable metabolic underpinnings and that UCYN-A is, in many regards, functioning like a hypothetical N2-fixing organelle (or nitroplast).

Flexible B12 ecophysiology of Phaeocystis antarctica due to a fusion B12-independent methionine synthase with widespread homologues.

Coastal Antarctic marine ecosystems are significant in carbon cycling because of their intense seasonal phytoplankton blooms. Southern Ocean algae are primarily limited by light and iron (Fe) and can be co-limited by cobalamin (vitamin B12). Micronutrient limitation controls productivity and shapes the composition of blooms which are typically dominated by either diatoms or the haptophyte Phaeocystis antarctica. However, the vitamin requirements and ecophysiology of the keystone species P. antarctica remain poorly characterized. Using cultures, physiological analysis, and comparative omics, we examined the response of P. antarctica to a matrix of Fe-B12 conditions. We show that P. antarctica is not auxotrophic for B12, as previously suggested, and identify mechanisms underlying its B12 response in cultures of predominantly solitary and colonial cells. A combination of proteomics and proteogenomics reveals a B12-independent methionine synthase fusion protein (MetE-fusion) that is expressed under vitamin limitation and interreplaced with the B12-dependent isoform under replete conditions. Database searches return homologues of the MetE-fusion protein in multiple Phaeocystis species and in a wide range of marine microbes, including other photosynthetic eukaryotes with polymorphic life cycles as well as bacterioplankton. Furthermore, we find MetE-fusion homologues expressed in metaproteomic and metatranscriptomic field samples in polar and more geographically widespread regions. As climate change impacts micronutrient availability in the coastal Southern Ocean, our finding that P. antarctica has a flexible B12 metabolism has implications for its relative fitness compared to B12-auxotrophic diatoms and for the detection of B12-stress in a more diverse set of marine microbes.

A Lagrangian model for drifting ecosystems reveals heterogeneity-driven enhancement of marine plankton blooms.

Marine plankton play a crucial role in carbon storage, global climate, and ecosystem function. Planktonic ecosystems are embedded in patches of water that are continuously moving, stretching, and diluting. These processes drive inhomegeneities on a range of scales, with implications for the integrated ecosystem properties, but are hard to characterize. We present a theoretical framework that accounts for all these aspects; tracking the water patch hosting a drifting ecosystem along with its physical, environmental, and biochemical features. The theory resolves patch dilution and internal physical mixing as a function of oceanic strain and diffusion. Ecological dynamics are parameterized by an idealized nutrient and phytoplankton population and we specifically capture the time evolution of the biochemical spatial variances to represent within-patch heterogeneity. We find that, depending only on the physical processes to which the water patch is subjected, the plankton biomass response to a resource perturbation can vary in size up to six times. This work indicates that we must account for these processes when interpreting and modeling marine ecosystems and provides a framework with which to do so.

Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly.

BACKGROUND: Diverse communities of microbial eukaryotes in the global ocean provide a variety of essential ecosystem services, from primary production and carbon flow through trophic transfer to cooperation via symbioses. Increasingly, these communities are being understood through the lens of omics tools, which enable high-throughput processing of diverse communities. Metatranscriptomics offers an understanding of near real-time gene expression in microbial eukaryotic communities, providing a window into community metabolic activity. RESULTS: Here we present a workflow for eukaryotic metatranscriptome assembly, and validate the ability of the pipeline to recapitulate real and manufactured eukaryotic community-level expression data. We also include an open-source tool for simulating environmental metatranscriptomes for testing and validation purposes. We reanalyze previously published metatranscriptomic datasets using our metatranscriptome analysis approach. CONCLUSION: We determined that a multi-assembler approach improves eukaryotic metatranscriptome assembly based on recapitulated taxonomic and functional annotations from an in-silico mock community. The systematic validation of metatranscriptome assembly and annotation methods provided here is a necessary step to assess the fidelity of our community composition measurements and functional content assignments from eukaryotic metatranscriptomes.

Planktonic prey size selection reveals an emergent keystone predator effect and niche partitioning.

Marine herbivorous protists are often the dominant grazers of primary production. We developed a size-based model with flexible size-based grazing to encapsulate taxonomic and behavioral diversity. We examined individual and combined grazing impacts by three consumer sizes that span the size range of protistan grazers- 5, 50, and 200 µm-on a size-structured phytoplankton community. Prey size choice and dietary niche width varied with consumer size and with co-existence of other consumers. When all consumer sizes were present, distinct dietary niches emerged, with a range of consumer-prey size ratios spanning from 25:1 to 0.4:1, encompassing the canonical 10:1 often assumed. Grazing on all phytoplankton size classes maximized the phytoplankton size diversity through the keystone predator effect, resulting in a phytoplankton spectral slope of approximately -4, agreeing with field data. This mechanistic model suggests the observed size structure of phytoplankton communities is at least in part the result of selective consumer feeding.

Global patterns in marine organic matter stoichiometry driven by phytoplankton ecophysiology.

The proportion of major elements in marine organic matter links cellular processes to global nutrient, oxygen and carbon cycles. Differences in the C:N:P ratios of organic matter have been observed between ocean biomes, but these patterns have yet to be quantified from the underlying small-scale physiological and ecological processes. Here we use an ecosystem model that includes adaptive resource allocation within and between ecologically distinct plankton size classes to attribute the causes of global patterns in the C:N:P ratios. We find that patterns of N:C variation are largely driven by common physiological adjustment strategies across all phytoplankton, while patterns of N:P are driven by ecological selection for taxonomic groups with different phosphorus storage capacities. Although N:C varies widely due to cellular adjustment to light and nutrients, its latitudinal gradient is modest because of depth-dependent trade-offs between nutrient and light availability. Strong latitudinal variation in N:P reflects an ecological balance favouring small plankton with lower P storage capacity in the subtropics, and larger eukaryotes with a higher cellular P storage capacity in nutrient-rich high latitudes. A weaker N:P difference between southern and northern hemispheres, and between the Atlantic and Pacific oceans, reflects differences in phosphate available for cellular storage. Despite simulating only two phytoplankton size classes, the emergent global variability of elemental ratios resembles that of all measured species, suggesting that the range of growth conditions and ecological selection sustain the observed diversity of stoichiometry among phytoplankton.

Single-cell measurements and modelling reveal substantial organic carbon acquisition by Prochlorococcus.

Marine phytoplankton are responsible for about half of the photosynthesis on Earth. Many are mixotrophs, combining photosynthesis with heterotrophic assimilation of organic carbon, but the relative contribution of these two lifestyles is unclear. Here single-cell measurements reveal that Prochlorococcus at the base of the photic zone in the Eastern Mediterranean Sea obtain only ~20% of carbon required for growth by photosynthesis. This is supported by laboratory-calibrated calculations based on photo-physiology parameters and compared with in situ growth rates. Agent-based simulations show that mixotrophic cells could grow tens of metres deeper than obligate photo-autotrophs, deepening the nutricline by ~20 m. Time series from the North Atlantic and North Pacific indicate that, during thermal stratification, on average 8-10% of the Prochlorococcus cells live without enough light to sustain obligate photo-autotrophic populations. Together, these results suggest that mixotrophy underpins the ecological success of a large fraction of the global Prochlorococcus population and its collective genetic diversity.

A nutrient relay sustains subtropical ocean productivity.

The expansive gyres of the subtropical ocean account for a significant fraction of global organic carbon export from the upper ocean. In the gyre interior, vertical mixing and the heaving of nutrient-rich waters into the euphotic layer sustain local productivity, in turn depleting the layers below. However, the nutrient pathways by which these subeuphotic layers are themselves replenished remain unclear. Using a global, eddy-permitting simulation of ocean physics and biogeochemistry, we quantify nutrient resupply mechanisms along and across density surfaces, including the contribution of eddy-scale motions that are challenging to observe. We find that mesoscale eddies (10 to 100 km) flux nutrients from the shallow flanks of the gyre into the recirculating interior, through time-varying motions along density surfaces. The subeuphotic layers are ultimately replenished in approximately equal contributions by this mesoscale eddy transport and the remineralization of sinking particles. The mesoscale eddy resupply is most important in the lower thermocline for the whole subtropical region but is dominant at all depths within the gyre interior. Subtropical gyre productivity may therefore be sustained by a nutrient relay, where the lateral transport resupplies nutrients to the thermocline and allows vertical exchanges to maintain surface biological production and carbon export.

Basin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology.

Extensive microdiversity within Prochlorococcus, the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the Prochlorococcus pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential. Predicted growth rates covaried with observed ecotype abundances, affirming their significance as a measure of fitness and inferring a nonlinear density dependence of mortality. Our study demonstrates the potential to interpret global-scale ecosystem organization in terms of cellular-scale processes.

Trophic interactions with heterotrophic bacteria limit the range of Prochlorococcus.

Prochlorococcus is both the smallest and numerically most abundant photosynthesizing organism on the planet. While thriving in the warm oligotrophic gyres, Prochlorococcus concentrations drop rapidly in higher-latitude regions. Transect data from the North Pacific show the collapse occurring at a wide range of temperatures and latitudes (temperature is often hypothesized to cause this shift), suggesting an ecological mechanism may be at play. An often used size-based theory of phytoplankton community structure that has been incorporated into computational models correctly predicts the dominance of Prochlorococcus in the gyres, and the relative dominance of larger cells at high latitudes. However, both theory and computational models fail to explain the poleward collapse. When heterotrophic bacteria and predators that prey nonspecifically on both Prochlorococcus and bacteria are included in the theoretical framework, the collapse of Prochlorococcus occurs with increasing nutrient supplies. The poleward collapse of Prochlorococcus populations then naturally emerges when this mechanism of "shared predation" is implemented in a complex global ecosystem model. Additionally, the theory correctly predicts trends in both the abundance and mean size of the heterotrophic bacteria. These results suggest that ecological controls need to be considered to understand the biogeography of Prochlorococcus and predict its changes under future ocean conditions. Indirect interactions within a microbial network can be essential in setting community structure.

Moving ecological and biogeochemical transitions across the North Pacific.

In the North Pacific Ocean, nutrient rich surface waters flow south from the subpolar gyre through a transitional region and into the subtropics. Along the way, nutrients are used, recycled, and exported, leading to lower biomass and a commensurate change in ecosystem structure moving southward. We focus on the region between the two gyres (the Transition Zone) using a coupled biophysical ocean model, remote sensing, floats, and cruise data to explore the nature of the physical, biogeochemical, and ecological fields in this region. Nonlinear interactions between biological processes and the meridional gradient in nutrient supply lead to sharp shifts across this zone. These transitions between a southern region with more uniform biological and biogeochemical properties and steep meridional gradients to the north are diagnosed from extrema in the first derivative of the properties with latitude. Some transitions like that for chlorophyll a (the transition zone chlorophyll front [TZCF]) experience large seasonal excursions while the location of the transitions in other properties moves very little. The seasonal shifts are not caused by changes in the horizontal flow field, but rather by the interaction of seasonal, depth related, forcing with the mean latitudinal gradients. Focusing on the TZCF as a case study, we express its phase velocity in terms of vertical nutrient flux and internal ecosystem processes, demonstrating their nearly equal influence on its motion. This framework of propagating biogeochemical transitions can be systematically expanded to better understand the processes that structure ecosystems and biogeochemistry in the North Pacific and beyond.

Quantifying nitrogen fixation by heterotrophic bacteria in sinking marine particles.

Nitrogen ([Formula: see text]) fixation by heterotrophic bacteria associated with sinking particles contributes to marine N cycling, but a mechanistic understanding of its regulation and significance are not available. Here we develop a mathematical model for unicellular heterotrophic bacteria growing on sinking marine particles. These bacteria can fix [Formula: see text] under suitable environmental conditions. We find that the interactive effects of polysaccharide and polypeptide concentrations, sinking speed of particles, and surrounding [Formula: see text] and [Formula: see text] concentrations determine the [Formula: see text] fixation rate inside particles. [Formula: see text] fixation inside sinking particles is mainly fueled by [Formula: see text] respiration rather than [Formula: see text] respiration. Our model suggests that anaerobic processes, including heterotrophic [Formula: see text] fixation, can take place in anoxic microenvironments inside sinking particles even in fully oxygenated marine waters. The modelled [Formula: see text] fixation rates are similar to bulk rates measured in the aphotic ocean, and our study consequently suggests that particle-associated heterotrophic [Formula: see text] fixation contributes significantly to oceanic [Formula: see text] fixation.

Generalized Stoichiometry and Biogeochemistry for Astrobiological Applications.

A central need in the field of astrobiology is generalized perspectives on life that make it possible to differentiate abiotic and biotic chemical systems McKay (2008). A key component of many past and future astrobiological measurements is the elemental ratio of various samples. Classic work on Earth's oceans has shown that life displays a striking regularity in the ratio of elements as originally characterized by Redfield (Redfield 1958; Geider and La Roche 2002; Eighty years of Redfield 2014). The body of work since the original observations has connected this ratio with basic ecological dynamics and cell physiology, while also documenting the range of elemental ratios found in a variety of environments. Several key questions remain in considering how to best apply this knowledge to astrobiological contexts: How can the observed variation of the elemental ratios be more formally systematized using basic biological physiology and ecological or environmental dynamics? How can these elemental ratios be generalized beyond the life that we have observed on our own planet? Here, we expand recently developed generalized physiological models (Kempes et al. 2012, 2016, 2017, 2019) to create a simple framework for predicting the variation of elemental ratios found in various environments. We then discuss further generalizing the physiology for astrobiological applications. Much of our theoretical treatment is designed for in situ measurements applicable to future planetary missions. We imagine scenarios where three measurements can be made-particle/cell sizes, particle/cell stoichiometry, and fluid or environmental stoichiometry-and develop our theory in connection with these often deployed measurements.

Quantitative models of nitrogen-fixing organisms.

Nitrogen-fixing organisms are of importance to the environment, providing bioavailable nitrogen to the biosphere. Quantitative models have been used to complement the laboratory experiments and in situ measurements, where such evaluations are difficult or costly. Here, we review the current state of the quantitative modeling of nitrogen-fixing organisms and ways to enhance the bridge between theoretical and empirical studies.

Redox-informed models of global biogeochemical cycles.

Microbial activity mediates the fluxes of greenhouse gases. However, in the global models of the marine and terrestrial biospheres used for climate change projections, typically only photosynthetic microbial activity is resolved mechanistically. To move forward, we argue that global biogeochemical models need a theoretically grounded framework with which to constrain parameterizations of diverse microbial metabolisms. Here, we explain how the key redox chemistry underlying metabolisms provides a path towards this goal. Using this first-principles approach, the presence or absence of metabolic functional types emerges dynamically from ecological interactions, expanding model applicability to unobserved environments."Nothing is less real than realism. It is only by selection, by elimination, by emphasis, that we get at the real meaning of things." -Georgia O'Keefe.

Anthropogenic Asian aerosols provide Fe to the North Pacific Ocean.

Fossil-fuel emissions may impact phytoplankton primary productivity and carbon cycling by supplying bioavailable Fe to remote areas of the ocean via atmospheric aerosols. However, this pathway has not been confirmed by field observations of anthropogenic Fe in seawater. Here we present high-resolution trace-metal concentrations across the North Pacific Ocean (158°W from 25°to 42°N). A dissolved Fe maximum was observed around 35°N, coincident with high dissolved Pb and Pb isotope ratios matching Asian industrial sources and confirming recent aerosol deposition. Iron-stable isotopes reveal in situ evidence of anthropogenic Fe in seawater, with low δ56Fe (-0.23‰ > δ56Fe > -0.65‰) observed in the region that is most influenced by aerosol deposition. An isotope mass balance suggests that anthropogenic Fe contributes 21-59% of dissolved Fe measured between 35° and 40°N. Thus, anthropogenic aerosol Fe is likely to be an important Fe source to the North Pacific Ocean.

A steady-state model of microbial acclimation to substrate limitation.

Microbes acclimate to changes in substrate availability by altering the number of transporters on the cell surface, however there is some disagreement on just how. We revisit the physics of substrate uptake and consider the steady-state scenario whereby cells have acclimated to maximize fitness. Flux balance analysis of a stoichiometric model of Escherichia coli was used in conjunction with quantitative proteomics data and molecular modeling of membrane transporters to reconcile these opposing views. An emergent feature of the proposed model is a critical substrate concentration S*, which delineates two rate limits. At concentrations above S*, transporter abundance can be regulated to maintain uptake rates as demanded by maximal growth rates, whereas below S*, uptake rates are strictly diffusion limited. In certain scenarios, the proposed model can take on a qualitatively different shape from the familiar hyperbolic kinetics curves, instead resembling the long-forgotten Blackman kinetics.

A Mechanistic Model of Macromolecular Allocation, Elemental Stoichiometry, and Growth Rate in Phytoplankton.

We present a model of the growth rate and elemental stoichiometry of phytoplankton as a function of resource allocation between and within broad macromolecular pools under a variety of resource supply conditions. The model is based on four, empirically-supported, cornerstone assumptions: that there is a saturating relationship between light and photosynthesis, a linear relationship between RNA/protein and growth rate, a linear relationship between biosynthetic proteins and growth rate, and a constant macromolecular composition of the light-harvesting machinery. We combine these assumptions with statements of conservation of carbon, nitrogen, phosphorus, and energy. The model can be solved algebraically for steady state conditions and constrained with data on elemental stoichiometry from published laboratory chemostat studies. It interprets the relationships between macromolecular and elemental stoichiometry and also provides quantitative predictions of the maximum growth rate at given light intensity and nutrient supply rates. The model is compatible with data sets from several laboratory studies characterizing both prokaryotic and eukaryotic phytoplankton from marine and freshwater environments. It is conceptually simple, yet mechanistic and quantitative. Here, the model is constrained only by elemental stoichiometry, but makes predictions about allocation to measurable macromolecular pools, which could be tested in the laboratory.

Microbial feedbacks optimize ocean iron availability.

Iron is the limiting factor for biological production over a large fraction of the surface ocean because free iron is rapidly scavenged or precipitated under aerobic conditions. Standing stocks of dissolved iron are maintained by association with organic molecules (ligands) produced by biological processes. We hypothesize a positive feedback between iron cycling, microbial activity, and ligand abundance: External iron input fuels microbial production, creating organic ligands that support more iron in seawater, leading to further macronutrient consumption until other microbial requirements such as macronutrients or light become limiting, and additional iron no longer increases productivity. This feedback emerges in numerical simulations of the coupled marine cycles of macronutrients and iron that resolve the dynamic microbial production and loss of iron-chelating ligands. The model solutions resemble modern nutrient distributions only over a finite range of prescribed ligand source/sink ratios where the model ocean is driven to global-scale colimitation by micronutrients and macronutrients and global production is maximized. We hypothesize that a global-scale selection for microbial ligand cycling may have occurred to maintain "just enough" iron in the ocean.