The good, the bad, and the tiny : a simple, mechanistic-probabilistic model of virus-nutrient colimitation in microbes

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 10 (2015): e0143299, doi:10.1371/journal.pone.0143299.For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary timescales for populations, but a shorter timescale, mechanistic perspective is lacking, and marine viral literature suggests the strong influence of additional factors, e.g. host size; while the literature on both nutrient uptake and host-virus interactions is expansive, their intersection, of ubiquitous relevance to marine environments, is understudied. I present a simple, mechanistic model from first principles to analyze the effect of this co-limitation scenario on individual growth, which suggests that in environments with high risk of viral invasion or spatial/temporal heterogeneity, an individual host’s growth rate may be optimized with respect to receptor coverage, producing top-down selective pressure on short timescales. The model has general applicability, is suggestive of hypotheses for empirical exploration, and can be extended to theoretical studies of more complex behaviors and systems.This work was supported by the Massachusetts Institute of Technology Charles Vest Presidential Fellowship

Particle flux parameterizations: Quantitative and mechanistic similarities and differences

The depth-attenuation of sinking particulate organic carbon (POC) is of particular importance for the ocean's role in the global carbon cycle. Numerous idealized flux-vs.-depth relationships are available to parameterize this process in Earth System Models. Here we show that these relationships are statistically indistinguishable from available POC flux profile data. Despite their quantitative similarity, we also show these relationships have very different implications for the flux leaving the upper ocean, as well as for the mechanisms governing POC flux. We discuss how this tension might be addressed both observationally and in modeling studies

Marine Virus-Like Particles and Microbes: A Linear Interpretation

Viruses are key players in ocean ecology and biogeochemistry, not only because of their functional roles but also partially due to their sheer abundance (Fuhrman, 1999; Wilhelm and Suttle, 1999). Because viruses cannot replicate without their hosts’ machinery, their abundance is inextricably related to that of their (mostly microbial) hosts. The relationship between viral and microbial abundances is thus of great interest

The size-distribution of Earth’s lakes

Globally, there are millions of small lakes, but a small number of large lakes. Most key ecosystem patterns and processes scale with lake size, thus this asymmetry between area and abundance is a fundamental constraint on broad-scale patterns in lake ecology. Nonetheless, descriptions of lake size-distributions are scarce and empirical distributions are rarely evaluated relative to theoretical predictions. Here we develop expectations for Earth’s lake area-distribution based on percolation theory and evaluate these expectations with data from a global lake census. Lake surface areas ≥0.46 km2 are power-law distributed with a tail exponent (τ = 2.14) and fractal dimension (d = 1.4), similar to theoretical expectations (τ = 2.05; d = 4/3). Lakes <0.46 km2 are not power-law distributed. An independently developed regional lake census exhibits a similar transition and consistency with theoretical predictions. Small lakes deviate from the power-law distribution because smaller lakes are more susceptible to dynamical change and topographic behavior at sub-kilometer scales is not self-similar. Our results provide a robust characterization and theoretical explanation for the lake size-abundance relationship, and form a fundamental basis for understanding and predicting patterns in lake ecology at broad scales

On the temperature dependence of oceanic export efficiency

Quantifying the fraction of primary production exported from the euphotic layer (termed the export efficiency ef) is a complicated matter. Studies have suggested empirical relationships with temperature which offer attractive potential for parameterization. Here we develop what is arguably the simplest mechanistic model relating the two, using established thermodynamic dependencies for primary production and respiration. It results in a single‐parameter curve that constrains the envelope of possible efficiencies, capturing the upper bounds of several ef‐T data sets. The approach provides a useful theoretical constraint on this relationship and extracts the variability in ef due to temperature but does not idealize out the remaining variability which evinces the substantial complexity of the system in question

The good, the bad, and the tiny: A simple, mechanistic-probabilistic model of virus-nutrient colimitation in microbes

For phytoplankton and other microbes, nutrient receptors are often the passages through which viruses invade. This presents a bottom-up vs. top-down, co-limitation scenario; how do these would-be-hosts balance minimizing viral susceptibility with maximizing uptake of limiting nutrient(s)? This question has been addressed in the biological literature on evolutionary timescales for populations, but a shorter timescale, mechanistic perspective is lacking, and marine viral literature suggests the strong influence of additional factors, e.g. host size; while the literature on both nutrient uptake and host-virus interactions is expansive, their intersection, of ubiquitous relevance to marine environments, is understudied. I present a simple, mechanistic model from first principles to analyze the effect of this co-limitation scenario on individual growth, which suggests that in environments with high risk of viral invasion or spatial/temporal heterogeneity, an individual host’s growth rate may be optimized with respect to receptor coverage, producing top-down selective pressure on short timescales. The model has general applicability, is suggestive of hypotheses for empirical exploration, and can be extended to theoretical studies of more complex behaviors and systems

Information content of absorption spectra and implications for ocean color inversion

The increasing use of hyperspectral optical data in oceanography, both in situ and via remote sensing, holds the potential to significantly advance characterization of marine ecology and biogeochemistry because, in principle, hyperspectral data can provide much more detailed inferences of ecosystem properties via inversion. Effective inferences, however, require careful consideration of the close similarity of different signals of interest, and how these interplay with measurement error and uncertainty to reduce the degrees of freedom (DoF) of hyperspectral measurements. Here we discuss complementary approaches to quantify the DoF in hyperspectral measurements in the case of in situ particulate absorption measurements, though these approaches can also be used on other such data, e.g., ocean color remote sensing. Analyses suggest intermediate (∼5) DoF for our dataset of global hyperspectral particulate absorption spectra from the Tara Oceans expedition, meaning that these data can yield coarse community structure information. Empirically, chlorophyll is an effective first-order predictor of absorption spectra, meaning that error characteristics and the mathematics of inversion need to be carefully considered for hyperspectral data to provide information beyond that which chlorophyll provides. We also discuss other useful analytical tools that can be applied to this problem and place our results in the context of hyperspectral remote sensing

How have recent temperature changes affected the efficiency of ocean biological carbon export?

The ocean's large, microbially mediated reservoirs of carbon are intimately connected with atmospheric CO2 and climate, yet quantifying the feedbacks between them remains an unresolved challenge. Through an idealized mechanistic model, we consider the impact of documented climate change during the past few decades on the efficiency of biological carbon export out of the surface ocean. This model is grounded in universal metabolic phenomena, describing export efficiency's temperature dependence in terms of the differential temperature sensitivity of phototrophic and heterotrophic metabolism. Temperature changes are suggested to have caused a statistically significant decrease in export efficiency of 1.5% ± 0.4% over the past 33 yr. Larger changes are suggested in the midlatitudes and Arctic. This interpretation is robust across multiple sea surface temperature and net primary production data products. The same metabolic mechanism may have resulted in much larger changes e.g., in response to the large temperature shifts between glacial and interglacial time periods

The volume and mean depth of Earth's lakes

Global lake volume estimates are scarce, highly variable, and poorly documented. We developed a rigorous method for estimating global lake depth and volume based on the Hurst coefficient of Earth's surface, which provides a mechanistic connection between lake area and volume. Volume‐area scaling based on the Hurst coefficient is accurate and consistent when applied to lake data sets spanning diverse regions. We applied these relationships to a global lake area census to estimate global lake volume and depth. The volume of Earth's lakes is 199,000 km3 (95% confidence interval 196,000–202,000 km3). This volume is in the range of historical estimates (166,000–280,000 km3), but the overall mean depth of 41.8 m (95% CI 41.2–42.4 m) is significantly lower than previous estimates (62–151 m). These results highlight and constrain the relative scarcity of lake waters in the hydrosphere and have implications for the role of lakes in global biogeochemical cycles