Heterotrophic substrate specificity in the aquatic environment: The role of microscale patchiness investigated using modelling

Phaeocystis globosa and diatom blooms promote distinct bacterial communities and associations in a coastal ecosystem

Phytoplankton and bacteria form the foundation of marine food webs. While most studies on phytoplankton bloom influence on bacteria dynamics focus on diatom-dominated blooms due to their global ecological significance, it is unclear if similar patterns extend to other species that compete with diatoms like Phaeocystis spp. This study aimed to contribute to the understanding of associations between phytoplankton and bacteria in a temperate ecosystem. For this, we studied the dynamics of phytoplankton and bacteria, combining 16S metabarcoding, microscopy, and flow cytometry over 4 years (282 samples). Phytoplankton and bacterial communities were studied throughout the year, particularly during contrasting phytoplankton blooms dominated by the Haptophyte Phaeocystis globosa or diatoms. We applied extended local similarity analysis (eLSA) to construct networks during blooming and non-blooming periods. Overall, the importance of seasonal and species-specific interactions between phytoplankton and bacteria is highlighted. In winter, mixed diatom communities were interconnected with bacteria, indicating a synergistic degradation of diverse phytoplankton-derived substrates. In spring, despite the intensity variations of P. globosa blooms, the composition of bacterial communities remained consistent over several years, suggesting establishing a stable-state environment for bacterial communities. Specific associations between monospecific diatom blooms and bacteria were evidenced in summer.

When are bacteria really gazelles? Comparing patchy ecologies with dimensionless numbers

From micro to planetary scales, spatial heterogeneity-patchiness-is ubiquitous in ecosystems, defining the environments in which organisms move and interact. However, most large-scale models still use spatially averaged 'mean fields' to represent natural populations, while fine-scale spatially explicit models are mostly restricted to particular organisms or systems. In a conceptual paper, Grünbaum (2012, Interface Focus 2: 150-155) introduced a heuristic, based on three dimensionless ratios quantifying movement, reproduction and resource consumption, to characterise patchy ecological interactions and identify when mean-field assumptions are justifiable. We calculated these dimensionless numbers for 33 interactions between consumers and their resource patches in terrestrial, aquatic and aerial environments. Consumers ranged in size from bacteria to whales, and patches lasted from minutes to millennia, with separation scales from mm to hundreds of km. No interactions could be accurately represented by naive mean-field models, though 19 (58%) could be partially simplified by averaging out movement, reproductive or consumption dynamics. Clustering interactions by their non-dimensional ratios revealed several unexpected dynamic similarities. For example, bacterial Pseudoalteromonas exploit nutrient plumes similarly to Mongolian gazelles grazing on ephemeral steppe vegetation. We argue that dimensional analysis is valuable for characterising ecological patchiness and can link widely different systems into a single quantitative framework.

Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria

Marine bacterial diversity is immense and believed to be driven in part by trade-offs in metabolic strategies. Here we consider heterotrophs that rely on organic carbon as an energy source and present a molecular-level model of cell metabolism that explains the dichotomy between copiotrophs—which dominate in carbon-rich environments—and oligotrophs—which dominate in carbon-poor environments—as the consequence of trade-offs between nutrient transport systems. While prototypical copiotrophs, like Vibrios, possess numerous phosphotransferase systems (PTS), prototypical oligotrophs, such as SAR11, lack PTS and rely on ATP-binding cassette (ABC) transporters, which use binding proteins. We develop models of both transport systems and use them in proteome allocation problems to predict the optimal nutrient uptake and metabolic strategy as a function of carbon availability. We derive a Michaelis–Menten approximation of ABC transport, analytically demonstrating how the half-saturation concentration is a function of binding protein abundance. We predict that oligotrophs can attain nanomolar half-saturation concentrations using binding proteins with only micromolar dissociation constants and while closely matching transport and metabolic capacities. However, our model predicts that this requires large periplasms and that the slow diffusion of the binding proteins limits uptake. Thus, binding proteins are critical for oligotrophic survival yet severely constrain growth rates. We propose that this trade-off fundamentally shaped the divergent evolution of oligotrophs and copiotrophs.

Marine bacteria utilize carbon as a building block and an energy source and thus exert an important control on the amount of carbon that is sequestered in the ocean versus respired into the atmosphere. They use a spectrum of strategies to consume carbon: while copiotrophic bacteria dominate in nutrient-rich environments, oligotrophic bacteria dominate in nutrient-poor environments and are typically smaller, nonmotile, and slower growing. Yet the paragon oligotroph SAR11 is the planet’s most abundant organism. Despite this, most of our understanding of bacteria derives from research on copiotrophs. Here we use molecular-level models to understand how an oligotroph’s physiology enables it to outperform copiotrophs in nutrient-poor but not in nutrient-rich environments. We contrast copiotrophs’ prevalent method of sugar transport with oligotrophs’ reliance on binding proteins, which trap nutrients in the periplasm. Binding proteins allow cells to attain affinities that are much higher than the transport proteins’ intrinsic affinities. However, our model predicts that attaining such high affinities requires large periplasms with high abundances of the slowly diffusing binding proteins, which precludes high growth rates. By quantifying the benefits and costs of binding proteins, we provide a mechanistic explanation for the divergent evolution of oligotrophs and copiotrophs.

SAR11 bacteria have a high affinity and multifunctional glycine betaine transporter

Marine bacterioplankton face stiff competition for limited nutrient resources. SAR11, a ubiquitous clade of very small and highly abundant Alphaproteobacteria, are known to devote much of their energy to synthesizing ATP-binding cassette periplasmic proteins that bind substrates. We hypothesized that their small size and relatively large periplasmic space might enable them to outcompete other bacterioplankton for nutrients. Using uptake experiments with ¹⁴ C-glycine betaine, we discovered that two strains of SAR11, Candidatus Pelagibacter sp. HTCC7211 and Cand. P. ubique HTCC1062, have extraordinarily high affinity for glycine betaine (GBT), with half-saturation (K _s ) values around 1 nM and specific affinity values between 8 and 14 L mg cell^-1  h^-1 . Competitive inhibition studies indicated that the GBT transporters in these strains are multifunctional, transporting multiple substrates in addition to GBT. Both strains could use most of the transported compounds for metabolism and ATP production. Our findings indicate that Pelagibacter cells are primarily responsible for the high affinity and multifunctional GBT uptake systems observed in seawater. Maximization of whole-cell affinities may enable these organisms to compete effectively for nutrients during periods when the gross transport capacity of the heterotrophic plankton community exceeds the supply, depressing ambient concentrations.