Mapping combinatorial expression perturbations to growth in Escherichia coli.

The connection between growth and gene expression has often been considered in a single gene. Repurposing a drug-drug interaction model, the multidimensional effects of several simultaneous gene expression perturbations on growth have been examined in the model bacteria Escherichia coli.

Diffusional Interactions among Marine Phytoplankton and Bacterioplankton: Modelling H2O2 as a Case Study.

Marine phytoplankton vary widely in size across taxa, and in cell suspension densities across habitats and growth states. Cell suspension density and total biovolume determine the bulk influence of a phytoplankton community upon its environment. Cell suspension density also determines the intercellular spacings separating phytoplankton cells from each other, or from co-occurring bacterioplankton. Intercellular spacing then determines the mean diffusion paths for exchanges of solutes among co-occurring cells. Marine phytoplankton and bacterioplankton both produce and scavenge reactive oxygen species (ROS), to maintain intracellular ROS homeostasis to support their cellular processes, while limiting damaging reactions. Among ROS, hydrogen peroxide (H2O2) has relatively low reactivity, long intracellular and extracellular lifetimes, and readily crosses cell membranes. Our objective was to quantify how cells can influence other cells via diffusional interactions, using H2O2 as a case study. To visualize and constrain potentials for cell-to-cell exchanges of H2O2, we simulated the decrease of [H2O2] outwards from representative phytoplankton taxa maintaining internal [H2O2] above representative seawater [H2O2]. [H2O2] gradients outwards from static cell surfaces were dominated by volumetric dilution, with only a negligible influence from decay. The simulated [H2O2] fell to background [H2O2] within ~3.1 µm from a Prochlorococcus cell surface, but extended outwards 90 µm from a diatom cell surface. More rapid decays of other, less stable ROS, would lower these threshold distances. Bacterioplankton lowered simulated local [H2O2] below background only out to 1.2 µm from the surface of a static cell, even though bacterioplankton collectively act to influence seawater ROS. These small diffusional spheres around cells mean that direct cell-to-cell exchange of H2O2 is unlikely in oligotrophic habits with widely spaced, small cells; moderate in eutrophic habits with shorter cell-to-cell spacing; but extensive within phytoplankton colonies.

Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom.

Production and use of proteins is under strong selection in microbes, but it is unclear how proteome-level traits relate to ecological strategies. We identified and quantified proteomic traits of eukaryotic microbes and bacteria through an Antarctic phytoplankton bloom using in situ metaproteomics. Different taxa, rather than different environmental conditions, formed distinct clusters based on their ribosomal and photosynthetic proteomic proportions, and we propose that these characteristics relate to ecological differences. We defined and used a proteomic proxy for regulatory cost, which showed that SAR11 had the lowest regulatory cost of any taxa we observed at our summertime Southern Ocean study site. Haptophytes had lower regulatory cost than diatoms, which may underpin haptophyte-to-diatom bloom progression in the Ross Sea. We were able to make these proteomic trait inferences by assessing various sources of bias in metaproteomics, providing practical recommendations for researchers in the field. We have quantified several proteomic traits (ribosomal and photosynthetic proteomic proportions, regulatory cost) in eukaryotic and bacterial taxa, which can then be incorporated into trait-based models of microbial communities that reflect resource allocation strategies.

Cellular costs underpin micronutrient limitation in phytoplankton.

Micronutrients control phytoplankton growth in the ocean, influencing carbon export and fisheries. It is currently unclear how micronutrient scarcity affects cellular processes and how interdependence across micronutrients arises. We show that proximate causes of micronutrient growth limitation and interdependence are governed by cumulative cellular costs of acquiring and using micronutrients. Using a mechanistic proteomic allocation model of a polar diatom focused on iron and manganese, we demonstrate how cellular processes fundamentally underpin micronutrient limitation, and how they interact and compensate for each other to shape cellular elemental stoichiometry and resource interdependence. We coupled our model with metaproteomic and environmental data, yielding an approach for estimating biogeochemical metrics, including taxon-specific growth rates. Our results show that cumulative cellular costs govern how environmental conditions modify phytoplankton growth.

Molecular underpinnings and biogeochemical consequences of enhanced diatom growth in a warming Southern Ocean.

The Southern Ocean (SO) harbors some of the most intense phytoplankton blooms on Earth. Changes in temperature and iron availability are expected to alter the intensity of SO phytoplankton blooms, but little is known about how these changes will influence community composition and downstream biogeochemical processes. We performed light-saturated experimental manipulations on surface ocean microbial communities from McMurdo Sound in the Ross Sea to examine the effects of increased iron availability (+2 nM) and warming (+3 and +6 °C) on nutrient uptake, as well as the growth and transcriptional responses of two dominant diatoms, Fragilariopsis and Pseudo-nitzschia We found that community nutrient uptake and primary productivity were elevated under both warming conditions without iron addition (relative to ambient -0.5 °C). This effect was greater than additive under concurrent iron addition and warming. Pseudo-nitzschia became more abundant under warming without added iron (especially at 6 °C), while Fragilariopsis only became more abundant under warming in the iron-added treatments. We attribute the apparent advantage Pseudo-nitzschia shows under warming to up-regulation of iron-conserving photosynthetic processes, utilization of iron-economic nitrogen assimilation mechanisms, and increased iron uptake and storage. These data identify important molecular and physiological differences between dominant diatom groups and add to the growing body of evidence for Pseudo-nitzschia's increasingly important role in warming SO ecosystems. This study also suggests that temperature-driven shifts in SO phytoplankton assemblages may increase utilization of the vast pool of excess nutrients in iron-limited SO surface waters and thereby influence global nutrient distribution and carbon cycling.

Prediction and Consequences of Cofragmentation in Metaproteomics.

Metaproteomics can provide critical information about biological systems, but peptides are found within a complex background of other peptides. This complex background can change across samples, in some cases drastically. Cofragmentation, the coelution of peptides with similar mass to charge ratios, is one factor that influences which peptides are identified in an LC-MS/MS experiment: it is dependent on the nature and complexity of this dynamic background. Metaproteomics applications are particularly susceptible to cofragmentation-induced bias; they have vast protein sequence diversity and the abundance of those proteins can span many orders of magnitude. We have developed a mechanistic model that determines the number of potentially cofragmenting peptides in a given sample (called cobia, https://github.com/bertrand-lab/cobia ). We then used previously published data sets to validate our model, showing that the resulting peptide-specific score reflects the cofragmentation "risk" of peptides. Using an Antarctic sea ice edge metatranscriptome case study, we found that more rare taxonomic and functional groups are associated with higher cofragmentation bias. We also demonstrate how cofragmentation scores can be used to guide the selection of protein- or peptide-based biomarkers. We illustrate potential consequences of cofragmentation for multiple metaproteomic approaches, and suggest practical paths forward to cope with cofragmentation-induced bias.

Manganese and iron deficiency in Southern Ocean Phaeocystis antarctica populations revealed through taxon-specific protein indicators.

Iron and light are recognized as limiting factors controlling Southern Ocean phytoplankton growth. Recent field-based evidence suggests, however, that manganese availability may also play a role. Here we examine the influence of iron and manganese on protein expression and physiology in Phaeocystis antarctica, a key Antarctic primary producer. We provide taxon-specific proteomic evidence to show that in-situ Southern Ocean Phaeocystis populations regularly experience stress due to combined low manganese and iron availability. In culture, combined low iron and manganese induce large-scale changes in the Phaeocystis proteome and result in reorganization of the photosynthetic apparatus. Natural Phaeocystis populations produce protein signatures indicating late-season manganese and iron stress, consistent with concurrently observed stimulation of chlorophyll production upon additions of manganese or iron. These results implicate manganese as an important driver of Southern Ocean productivity and demonstrate the utility of peptide mass spectrometry for identifying drivers of incomplete macronutrient consumption.