The tragedy of the park: An agent-based model of endogenous and exogenous institutions for forest management

Many scholars of common-pool resources have found that institutions might solve the tragedy of the commons. I address a particular situation of natural resource management: that of a protected area. In this situation, interests differ. Local rural inhabitants care about the quality of their environment but also need to exploit the resources for livelihood reasons. An external entity such as the State, a donor, an NGO, or some combination thereof decides that there is a need for nature conservation in that area. Because of some evidence of failure for a strictly top-down conservationist approach, the external entity decides to apply the concept of participatory conservation: the local inhabitants become stakeholders in the management of the area and become collectively responsible for conservation, with rights to exploit the resources up to some degree. I argue that project designers try to find a solution to nature conservation through the creation of a situation of a commons: creating a community that has rights and duties toward a particular natural area that is endowed with some resources. Many scholars rely mostly on institutions that are endogenously created within the users' community to avoid the tragedy of the commons. However, what happens if institutions are imposed? In participatory conservation initiatives, the community has collective rights over the resources, and in this sense, the issue of endogenous rules for the commons management is relevant. However, the level to which the community should exploit the resource is usually imposed by the external project designers. Using agent-based simulations, I develop a theoretical model to look at the consequences of an imposed institution on the state of a forest and on the users' profit, taking into account the possibilities of violating the imposed rules and facing enforcement. I compare the consequences of this imposed institution with those deriving from an endogenously created institution. I also analyze the interaction between the different kinds of institutions and the individual perceptions of each agent. Many results of the model confirm the quantitative and qualitative findings of the literature: the presence of institutions and enforcement improve the management of the resource with respect to an open-access situation, with different degree of success depending on the kind of institution in place. The two main counterintuitive findings are the following. First, an exogenous institution imposed by external agents may crowd out agents' intrinsic environmental motivations. Second, when an imposed exogenous institution is in place, the most effective rule is one allowing a sufficient degree of access to resources for the agents, provided that adequate rule enforcement is implemented

Measuring economic water scarcity in agriculture: a cross-country empirical investigation

High water availability enhances agricultural performance and food security. However, many countries where water is abundant according to hydrological indicators face difficulties in the utilization of water in agriculture, being in a situation of economic water scarcity (EWS), due to lack of institutional and material means for water management and governance. EWS faces a stronger challenge of measurability, if compared to physical water scarcity. Since the Sustainable Development Goal Indicator on Integrated management of domestic and transboundary water resources (IWRM) is a unique attempt to quantify information on water management at a national level, we explore whether it can represent a valid metric for EWS measurement. We first show that a high level of water management is neither necessarily associated to high economic power of the country nor to low physical water availability. Then, we analyze whether the indicator can predict typical EWS situations such as low agricultural productivity and inefficient water use. Although the importance of water institutions for agriculture is well known through case studies at the local level, we make the first attempt to quantify the strengths of this relation at a global scale for different crops in climatic diverse countries. We detect a positive and significant association between IWRM level and yield, and consequently a negative and equally significant association between the IWRM level and the crop water footprint. Statistical significance holds also when potentially confounding variables are included in a multiple regression analysis. We infer from this analysis that good water management, as detectable through the IWRM indicator, improves land productivity and water saving, in turn mitigating EWS. Our findings pave the way toward the use of the IWRM indicator as a valuable tool for measuring EWS in agriculture, bridging the measurability gap of economic water scarcity, with straightforward policy implications in favour of investments in water management as a lever for enhancing food security and development

Computing the shortest elementary flux modes in genome-scale metabolic networks

This article is available open access through the publisher’s website through the link below. Copyright @ The Author 2009.Motivation: Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. Results: In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic networks. Our method was applied to find the K-shortest EFMs that produce lysine in the genome-scale metabolic networks of Escherichia coli and Corynebacterium glutamicum. A detailed analysis of the biological significance of the K-shortest EFMs was conducted, finding that glucose catabolism, ammonium assimilation, lysine anabolism and cofactor balancing were correctly predicted. The work presented here represents an important step forward in the analysis and computation of EFMs for large-scale metabolic networks, where traditional methods fail for networks of even moderate size. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online (http://bioinformatics.oxfordjournals.org/cgi/content/full/btp564/DC1).Fundação Calouste Gulbenkian, Fundação para a Ciência e a Tecnologia (FCT) and Siemens SA Portugal

Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Philosophical Transactions of the Royal Society B 365 (2010): 1417-1427, doi:10.1098/rstb.2009.0272.We examine the application of the maximum entropy production principle for describing ecosystem biogeochemistry. Since ecosystems can be functionally stable despite changes in species composition, we utilize a distributed metabolic network for describing biogeochemistry, which synthesizes generic biological structures that catalyze reaction pathways, but is otherwise organism independent. Allocation of biological structure and regulation of biogeochemical reactions is determined via solution of an optimal control problem in which entropy production is maximized. However, because synthesis of biological structures cannot occur if entropy production is maximized instantaneously, we propose that information stored within the metagenome allows biological systems to maximize entropy production when averaged over time. This differs from abiotic systems that maximize entropy production at a point in space-time, which we refer to as the steepest descent pathway. It is the spatiotemporal averaging that allows biological systems to outperform abiotic processes in entropy production, at least in many situations. A simulation of a methanotrophic system is used to demonstrate the approach. We conclude with a brief discussion on the implications of viewing ecosystems as self organizing molecular machines that function to maximize entropy production at the ecosystem level of organization.The work presented here was funded by the PIE-LTER program (NSF OCE-0423565), as well as from NSF CBET-0756562, NSF EF-0928742 and NASA Exobiology and Evolutionary Biology (NNG05GN61G)

Microbial catabolic activities are naturally selected by metabolic energy harvest rate

The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate

Susceptibility of salt marshes to nutrient enrichment and predator removal

Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Applications 17, Suppl. (2007): S42–S63, doi:10.1890/06-0452.1.The sustainability of coastal ecosystems in the face of widespread environmental change is an issue of pressing concern throughout the world (Emeis et al. 2001). Coastal ecosystems form a dynamic interface between terrestrial and oceanic systems and are one of the most productive ecosystems in the world. Coastal systems probably serve more human uses than any other ecosystem and they have always been valued for their rich bounty of fish and shellfish. Coastal areas are also the sites of the nation’s and the world’s most intense commercial activity and population growth; worldwide, approximately 75% of the human population now lives in coastal regions (Emeis et al. 2001). Over the past three decades nutrient enrichment of coastal and estuarine waters has become the premier issue for both scientists and managers (National Research Council 2000). Our understanding of coastal eutrophication has been developed principally through monitoring of estuaries, with a focus on pelagic or subtidal habitats (National Research Council 2000, Cloern 2001). Because estuarine systems are usually nitrogen limited, NO3- is the most common nutrient responsible for cultural nutrient enrichment (Cloern 2001). Increased nitrogen delivery to pelagic habitats of estuaries produces the classic response of ecosystems to stress (altered primary producers and nutrient cycles and loss of secondary producer species and production; Nixon 1995, Rapport and Whitford 1999, Deegan et al. 2002). Salt marsh ecosystems have been thought of as not susceptible to nitrogen over-loading because early studies found added nitrogen increased marsh grass production (primarily Spartina spp., cordgrass) and concluded that salt marshes can adsorb excess nutrients in plants and salt marsh plant-derived organic matter as peat (Verhoeven et al. 2006). Detritus from Spartina is important in food webs (Deegan et al. 2000) and in creating peat that forms the physical structure of the marsh platform (Freidrichs and Perry 2001). However, the accumulation of peat and inputs of sediments and loss of peat through decomposition and sediment through erosion may be altered under high nutrient regimes and threaten the long-term stability of marsh systems. Nitrogen addition may lead to either net gain or loss of the marsh depending on the balance between increased marsh plant production and increased decomposition. Absolute change in marsh surface elevation is determined by marsh plant species composition, production and allocation to above- and belowground biomass, microbial decomposition, sedimentation, erosion and compaction (Friedrichs and Perry 2001). Levine et al. (1998) suggested that competitive dynamics among plants might be affected by nutrient enrichment, potentially altering relative abundance patterns favoring species with less belowground storage and thus lowering rates of peat formation. When combined with the observation that nutrient additions may also stimulate microbial respiration and decomposition (Morris and Bradley 1999), the net effect on the salt marsh under conditions of chronic nitrogen loading is a critical unknown. Although most research treats nutrient enrichment as a stand-alone stress, it never occurs in isolation from other perturbations. The effect of nutrient loading on species composition (both plants and animals) and the resultant structure and function of wetlands has been largely ignored when considering their ability to adsorb nutrients (Verhoeven et al. 2006). Recent studies suggest the response of estuaries to stress may depend on animal species composition (Silliman et al. 2005). Animal species composition may alter the balance between marsh gain and loss as animals may increase or decrease primary production, decomposition or N recycling (Pennings and Bertness 2001). Failure to understand interactions between nutrient loading and change in species composition may lead to underestimating the impacts of these stresses. The 'bottom up or top down' theory originated from the observation that nutrient availability (bottom up)sets the quantity of primary productivity, while other studies have shown that species composition (top down), particularly of top consumers, has a marked and cascading effect on ecosystems, including controlling species composition and nutrient cycling (Matson and Price 1992, Pace et al. 1999). Most examples of trophic cascades are in aquatic ecosystems with fairly simple, algal grazing pelagic food webs (Strong 1992). The rarity of trophic cascades in terrestrial systems has been attributed to the importance of detrital food webs (Polis 1999). Detritus-based aquatic ecosystems, such as salt marshes, bogs, and swamps, have classically been considered bottom-up or physically controlled ecosystems. Recent experiments, however, suggest that salt marshes may exhibit top-down control at several trophic levels (Silliman and Zeiman. 2001, Silliman and Bertness 2002, Quiñones-Rivera and Fleeger 2005). One abundant, ubiquitous predator, a small (<10 cm total length) killifish (Fundulus heteroclitus, mummichog) has been suggested to control benthic algal through a trophic cascade because they prey on the invertebrates that graze on the benthic algae (Kneib 1997, Sarda et al. 1998). In late summer, killifish are capable of consuming 3-10 times the creek meiofauna production and meiofauna in the absence of predators appear capable of grazing over 60% of the microalgal community per day (Carman et al. 1997). Strong top-down control by grazers is considered a moderating influence on the negative effects of elevated nutrients on algae (Worm et al. 2000). Small-scale nutrient additions and predator community exclusion experiments have demonstrated bottom-up and top-down control of macroinfauna in mudflats associated with salt marsh creeks (Posey et al. 1999, Posey et al. 2002). Together, these observations suggest mummichogs are at the top of a trophic cascade that controls benthic algae (Sarda et al. 1998). Mummichogs are also omnivorous and ingest algae, bulk detritus and the attached microbial community (D’Avanzo and Valiela 1990). As a result, marsh decomposition rates may be limited by top-down controls through trophic pathways or by release from competition with algae for nutrients. Whole-ecosystem experiments have shown that responses to stress are often not predictable from studies of the individual components (Schindler 1998). Developing the information needed to predict the interacting impacts of nutrient loading and species composition change requires experiments with realistic alterations carried out at scales of space and time that include the complexities of real ecosystems. Whole ecosystem manipulation experiments have been used effectively in other ecosystems (Bormann and Likens 1979, Carpenter et al. 1995), but they are rare in coastal research. Experiments in salt marshes have traditionally been less than a few m2. Our understanding of the response of salt marsh plants to nutrient enrichment is from small ( 1000 g N m-2 y-1) are sprinkled on the marsh surface at low tide. Dry fertilizer additions were usually made every two weeks or monthly and the duration of elevated nutrient levels after these additions was usually not determined. Tidal water is the primary vector for N delivery to coastal marshes, suggesting that dry fertilizer addition to the marsh surface may not be the best basis for determining if Spartina production responds to nutrient enrichment of tidal waters. Similarly, our understanding of top-down controls in salt marshes also relies on small (1 - 4 m2) exclusion experiments that use cages to isolate communities from top consumers. While the design of these cage experiments has improved, there are some remaining drawbacks. For example, it is impossible to selectively exclude single species using cages, and recruitment or size-selective movement into or out of the cages may obscure interpretations. In addition, while these small-scale experiments provide insight into controls on isolated ecosystem processes, they do not allow for interaction among different parts of the ecosystem which may buffer or alter the impacts and are not appropriate for determining the effects of populations of larger more motile animals on whole-ecosystems or the effects of ecosystem changes on populations. For example, interactions may be caused when a motile species alters its distribution among the habitats available to it because of an experimental treatment. Small-scale experiments generally do not allow such events to happen. Complex feedbacks among physical and biological processes can alter accumulation rates and affect marsh elevation relative to sea level rise making extrapolation of small plot level experiments to whole marsh ecosystems problematic. We are conducting an ecosystem-scale, multi-year field experiment including both nutrient and biotic manipulations to coastal salt marsh ecosystems. We are testing, for the first time at the ecosystem level, the hypothesis that nutrient enrichment and species composition change have interactive effects across multiple levels of biological organization and a range of biogeochemical processes. We altered whole salt marsh creek watersheds (~60,000 m2 of saltmarsh) by addition of nutrients (15x ambient) in flooding waters and by a 60% reduction of a key fish species, the mummichog. Small marsh creek watersheds provide an ideal experimental setting because they have the spatial complexity, species composition and processes characteristic of the larger salt marsh ecosystem, which are often hundreds of thousands of m2. Manipulating entire salt marsh creeksheds allowed us to examine effects on large motile animals and the interactive effects of motile species changes on ecosystem processes without cage artifacts. Because our manipulations were done on whole-marsh ecosystems, we are able to evaluate the integrated and interactive effects on all habitats (e.g., water column, tidal creeks and marsh) and on populations. These experiments are similar in many respects to the small watershed experiments carried out in forested catchments. Our nutrient enrichment is novel compared to past studies in two important ways. We added nutrients (N and P) directly to the flooding tidal creek waters to mimic the way in which anthropogenic nutrients reach marsh ecosystems. All previous experimental salt marsh nutrient enrichment studies used a dose-response design with spatially uniform dry fertilizer loading on small plots (<10 m2). Nutrients carried in water will interact and reach parts of the ecosystem differently than dry fertilizer. Our enrichment method also creates a spatial gradient of nutrient loading across the landscape that is proportional to the frequency and depth of inundation in the marsh. Spatial gradients in loading within an ecosystem are typical in real world situations in many terrestrial and aquatic ecosystems. Because of our enrichment method, at any location in the ecosystem, nutrient load will be a function of the nutrient concentration in the water, the frequency and depth of tidal flooding and the reduction of nutrients from the flooding waters by other parts of the ecosystem. Uniform loading misses important aspects of the spatial complexity of ecosystem exposure and response. This work is organized around two questions that are central to understanding the long-term fate of coastal marshes: 1. Does chronic nutrient enrichment via flooding water increase primary production more than it stimulates microbial decomposition? 2. Do top-down controls change the response of the salt marsh ecosystem to nutrient enrichment? Here we present findings on the first 2 years of these experiments including 1) water chemistry, 2) standing stocks and species composition of benthic microalgae, 3) microbial production, 4) species composition and ecophysiology of macrophytes, 5) invertebrates, and 6) nekton. Because even highly eutrophic waters result in nutrient loading that is an order of magnitude less than most plot level experiments, we expected little stimulation of salt marsh vascular plant growth. However, moderate levels of nutrient enrichment in the water column were expected to increase benthic algal biomass and to stimulate bacterial activity and detrital decomposition throughout the ecosystem because of direct uptake of nitrogen from the water column and availability of more high quality organic matter from increased algal production. We predicted nutrient enrichment would increase invertebrate production because of an increase of high quality microalgal and microbial production at the base of the food web. Finally, we predicted that fish reduction would reduce predation on benthic invertebrates resulting in increased abundance of benthic invertebrates that would graze down the benthic algae.The National Science Foundation (Grant DEB 0213767, OCE 9726921, and OCE 0423565) supported this work. Additional funding was provided by the National Science Foundation postdoctoral fellowship in Microbial Biology (DBI-0400819), the NOAA Coastal Intern grant (NA04NOS4780182), the Office of Environmental Education of Louisiana, Middlebury College and Connecticut College