Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals.

Understanding which compounds comprising the complex and dynamic marine dissolved organic matter (DOM) pool are important in supporting heterotrophic bacterial production remains a major challenge. We eliminated sources of labile phytoplankton products, advected terrestrial material and photodegradation products to coastal microbial communities by enclosing water samples in situ for 24 h in the dark. Bacterial genes for which expression decreased between the beginning and end of the incubation and chemical formulae that were depleted over this same time frame were used as indicators of bioavailable compounds, an approach that avoids augmenting or modifying the natural DOM pool. Transport- and metabolism-related genes whose relative expression decreased implicated osmolytes, carboxylic acids, fatty acids, sugars and organic sulfur compounds as candidate bioreactive molecules. FT-ICR MS analysis of depleted molecular formulae implicated functional groups ~ 30-40 Da in size cleaved from semi-polar components of DOM as bioreactive components. Both gene expression and FT-ICR MS analyses indicated higher lability of compounds with sulfur and nitrogen heteroatoms. Untargeted methodologies able to integrate biological and chemical perspectives can be effective strategies for characterizing the labile microbial metabolites participating in carbon flux.

How interactions between microbial resource demands, soil organic matter stoichiometry, and substrate reactivity determine the direction and magnitude of soil respiratory responses to warming.

Recent empirical and theoretical advances inform us about multiple drivers of soil organic matter (SOM) decomposition and microbial responses to warming. Absent from our conceptual framework of how soil respiration will respond to warming are adequate links between microbial resource demands, kinetic theory, and substrate stoichiometry. Here, we describe two important concepts either insufficiently explored in current investigations of SOM responses to temperature, or not yet addressed. First, we describe the complete range of responses for how warming may change microbial resource demands, physiology, community structure, and total biomass. Second, we describe how any relationship between SOM activation energy of decay and carbon (C) and nitrogen (N) stoichiometry can alter the relative availability of C and N as temperature changes. Changing availabilities of C and N liberated from their organic precursors can feedback to microbial resource demands, which in turn influence the aggregated respiratory response to temperature we observe. An unsuspecting biogeochemist focused primarily on temperature sensitivity of substrate decay thus cannot make accurate projections of heterotrophic CO2 losses from diverse organic matter reservoirs in a warming world. We establish the linkages between enzyme kinetics, SOM characteristics, and potential for microbial adaptation critical for making such projections. By examining how changing microbial needs interact with inherent SOM structure and composition, and thus reactivity, we demonstrate the means by which increasing temperature could result in increasing, unchanging, or even decreasing respiration rates observed in soils. We use this exercise to highlight ideas for future research that will develop our abilities to predict SOM feedbacks to climate.

Long-term effectiveness of a multi-use marine protected area on reef fish assemblages and fisheries landings.

The Loreto Bay National Park (LBNP) is a large, multi-use marine protected area in the Gulf of California, Mexico, where several types of small-scale commercial and recreational fishing are allowed, but where less than 1% of the park is totally protected from fishing. The LBNP was created in 1996; its management plan was completed in 2000, but it was not effectively implemented and enforced until 2003. Between 1998 and 2010, we monitored reef fish populations annually at several reefs inside and outside the LBNP to measure the effects of the park on fish assemblages. We also evaluated reported fisheries landings within the LBNP for the same time series. Our results show that reef fish biomass increased significantly after protection at a small no-take site at LBNP relative to the rest of the park. However, the multi-use part of LBNP where fishing is allowed (99% of its surface) has had no measurable effect on reef fish biomass relative to open access sites outside the park boundaries. Reported fisheries landings have decreased within the park while increasing in nearby unprotected areas. Although the current partial protection management regime has not allowed for reef fish populations to recover despite 15 years as a "protected area," we conclude that LBNP's regulations and management have maintained the conditions of the ecosystem that existed when the park was established. These results suggest that community livelihoods have been sustained, but a re-evaluation of the multi-use management strategy, particularly the creation of larger no-take zones and better enforcement, is needed to improve the reef fish populations in the park in order to ensure sustainable fisheries far into the future. These recommendations can be applied to all multi-use MPAs in Mexico where ecosystem recovery is not occurring despite maintenance of fish stocks.

Dynamics of nutrient uptake strategies: lessons from the tortoise and the hare.

Many autotrophs vary their allocation to nutrient uptake in response to environmental cues, yet the dynamics of this plasticity are largely unknown. Plasticity dynamics affect the extent of single versus multiple nutrient limitation and thus have implications for plant ecology and biogeochemical cycling. Here we use a model of two essential nutrients cycling through autotrophs and the environment to determine conditions under which different plastic or fixed nutrient uptake strategies are adaptive. Our model includes environment-independent costs of being plastic, environment-dependent costs proportional to the rate of plastic change, and costs of being mismatched to the environment, the last of which is experienced by both fixed and plastic types. In equilibrium environments, environment-independent costs of being plastic select for tortoise strategies-fixed or less plastic types-provided that they are sufficiently close to co-limitation. At intermediate levels of environmental fluctuation forced by periodic nutrient inputs, more hare-like plastic strategies prevail because they remain near co-limitation. However, the fastest is not necessarily the best. The most adaptive strategy is an intermediate level of plasticity that keeps pace with environmental fluctuations, but is not faster. At high levels of environmental fluctuation, the environment-dependent cost of changing rapidly to keep pace with the environment becomes prohibitive and tortoise strategies again dominate. The existence and location of these thresholds depend on plasticity costs and rate, which are largely unknown empirically. These results suggest that the expectations for single nutrient limitation versus co-limitation and therefore biogeochemical cycling and autotroph community dynamics depend on environmental heterogeneity and plasticity costs.Electronic supplementary material The online version of this article (doi:10.1007/s12080-010-0110-0) contains supplementary material, which is available to authorized users.

Nutrient recycling affects autotroph and ecosystem stoichiometry.

Stoichiometric nutrient ratios are the consequence of myriad interacting processes, both biotic and abiotic. Theoretical explanations for autotroph stoichiometry have focused on species' nutrient requirements but have not addressed the role of nutrient availability in determining autotroph stoichiometry. Remineralization of organic N and P supplies a significant fraction of inorganic N and P to autotrophs, making nutrient recycling a potentially important process influencing autotroph stoichiometry. To quantitatively investigate the relationship between available N and P, autotroph N:P, and nutrient recycling, we analyze a stoichiometrically explicit model of autotroph growth, incorporating Michaelis-Menten-Monod nutrient uptake kinetics, Droop growth, and Liebig's law of the minimum. If autotroph growth is limited by a single nutrient, increased recycling of the limiting nutrient pushes autotrophs toward colimitation and alters both autotroph and environmental stoichiometry. We derive a steady state relationship between input stoichiometry, autotroph N:P, and the stoichiometry of organic losses that allows us to estimate the relative recycling of N to P within an ecosystem. We then estimate relative N and P recycling for a marine, an aquatic, and two terrestrial ecosystems. Preferential P recycling, in conjunction with greater relative P retention at the organismal and ecosystem levels, presents a strong case for the importance of P to biomass production across ecosystems.

Viability analysis of reef fish populations based on limited demographic information.

Marine protected areas (MPAs) that allow some degree of artisanal fishing have been proposed to control the overexploitation of marine resources while allowing extraction by local communities. Nevertheless, the management of MPAs is often impaired by the absence of data on the status of their resources. We devised a method to estimate population growth rates with the type of data that are usually available for reef fishes. We used 7 years of spatially explicit abundance data on the leopard grouper (Mycteroperca rosacea) in an MPA in the Gulf of California, Mexico, to construct a matrix population model that incorporated the effects of El Niño/La Niña Southern Oscillation on population dynamics. An environmental model that estimated different demographic estimates for El Niño and La Niña periods performed better than a single-environment model, and a single-habitat model performed better than a model that considered different depths as different habitats. Our results suggest that the population of the leopard grouper off the main island of the MPA is not viable under present conditions. Although the impact of fishing on leopard grouper populations in the MPA has not yet been established, fishing should be closed as a precautionary measure at this island if a priority of the MPA is to ensure the sustainability of its fish populations.

Reproductive correlation and mean-variance scaling of reproductive output for a forest model.

We analyse the mean-variance scaling of reproductive output for a previously published forest model. The model relates individual reproductive effort and pollen limitation to the degree of synchrony in reproduction throughout a forest. We show that the exponent of Taylor's power law reflects the degree of synchrony of reproduction because it indicates the covariance of reproductive behavior. Further, we are able to relate the three components of masting, individual variability, population variability and synchrony in reproductive output, using Taylor's power law. Therefore Taylor's power law can be used as a synoptic index of masting.

The relative importance of herbivory and carnivory on the distribution of energy in a stochastic tri-trophic food web.

A three-state, discrete-time Markov chain is used to model the dynamics of energy flow in a tri-trophic food web. The distribution of energy in the three trophic levels is related to the rates of flow between the trophic levels and calculated for the entire range of possible flow values. These distributions are then analysed for stability and used to test the idea that plants are resource-limited and herbivores are predation-limited. Low rates of death and decomposition, when coupled with low rates of herbivory and carnivory, tend to destabilize this food web. Food webs with higher rates of death and decomposition are relatively more stable regardless of rates of herbivory and carnivory. Plants are more prone to resource-limitation and herbivores are, in general, limited by their predators, which supports Hairston et al. (Am. Nat. 94 (1960) 421). The rate of decomposition often mediates the roles of top-down and bottom-up control of energy flow in the food web.