Life cycle assessment of microgreen production: effects of indoor vertical farm management on yield and environmental performance.

The global production of plant-based foods is a significant contributor to greenhouse gas emissions. Indoor vertical farms (IVFs) have emerged as a promising approach to urban agriculture. However, their environmental performance is not well understood, particularly in relation to operational choices where global warming potentials (GWP) can vary between 0.01-54 kg CO2e/kg-1 of leafy greens produced. We conducted a life cycle assessment (LCA) of a building-integrated IVF for microgreen production to analyse a range of operational conditions for cultivation: air temperature, CO2 concentration, and photoperiod. We analyzed a dynamic LCA inventory that combined a process-based plant growth model and a mass balance model for air and heat exchange between the chamber and the outside. Results showed that the GWP of IVFs can vary greatly depending on the operation conditions set, ranging from 3.3 to 63.3 kg CO2e/kg-1. The optimal conditions for minimizing GWP were identified as 20 ℃, maximum CO2 concentration in the chamber, and maximum photoperiod, which led to a minimum GWP of 3.3 kg CO2e/kg-1 and maximum production of 290.5 kg fresh weight week-1. Intensification of production thus led to lower impacts because the marginal increase in yield due to increased resource use was larger than the marginal increase in impact. Therefore, adjusting growing conditions is essential for the sustainability of urban food production.

Data-driven agent-based modelling of incentives for carbon sequestration: The case of sown biodiverse pastures in Portugal.

Sown biodiverse permanent pastures rich in legumes (SBP) offset animal farming emissions due to their potential to sequester carbon. From 2009 to 2014 Portugal implemented a programme that provided payments to incentivize the adoption of SBP. However, no proper evaluation of its outcome was conducted. To address this gap, we develop an agent-based model (ABM) at the municipality level to study the adoption of SBP in Portugal and assess the outcome of the programme. We applied the first pure data-driven approach in agricultural land-use ABM, which relies on machine learning algorithms to define the agents' behavioural rules and capture their interaction with biophysical conditions. The ABM confirms that the program effectively expanded the adoption of SBP. However, our estimates indicate that the adoption rate in the absence of payments would have been higher than originally predicted. Furthermore, the existence of the program decreased the adoption rate after its conclusion. These findings underscore the importance of using reliable models and considering residual effects to properly design land use policies. The ABM developed in this study provides a basis for future research aimed at supporting the development of new policies to further promote the adoption of SBP.

Forage based diet as an alternative to a high concentrate diet for finishing young bulls - Effects on growth performance, greenhouse gas emissions and meat quality.

Two groups of 8 individually housed young crossbred-bulls, in the finishing period, were used to test the effect of a Total Mixed Ration diet with high forage content (54% DM), low starch content (14% DM), supplemented with sunflower seeds (10% DM) (HFS) on growth performance, carcass and meat quality, fatty acid profile and carbon footprint, with reference to a conventional concentrate-based (90% DM) (Control) diet. The experiment lasted 64 days before slaughter. During the experiment, feed intake was monitored daily and live weight every 14 days. Individual CH4 emissions were assessed at 16-days intervals, using a GreenFeed for Large Animal unit. Feed intake and feed conversion ratio were higher for HFS diet, but average daily weight gain and feeding costs were similar for the two diets. Dressing percentage was reduced with HFS diet. The HFS increased redness, yellowness and Chroma of subcutaneous fat, but did not compromise commercial value of the carcasses. Meat colour, shear force, or sensory parameters were not affected by diet. The HFS diet allowed a healthier FA profile, due to the higher proportions of 18:3n-3, t11-18:1 and c9,t11-18:2 and the lower proportion of t10-18:1. The HFS diet did not reduce the carbon footprint in the finishing period of young bulls, due to increased digestive CH4 emissions. The results of this experiment showed that the HFS diet can be an alternative to the conventional diets used in finishing young-bulls. Although it may result in a slight reduction in animal performance, it has a strong impact on reducing dependence on inputs from outside the farm.

Global process-based characterization factors of soil carbon depletion for life cycle impact assessment.

Regionalization of land use (LU) impact in life cycle assessment (LCA) has gained relevance in recent years. Most regionalized models are statistical, using highly aggregated spatial units and LU classes (e.g. one unique LU class for cropland). Process-based modelling is a powerful characterization tool but so far has never been applied globally for all LU classes. Here, we propose a new set of spatially detailed characterization factors (CFs) for soil organic carbon (SOC) depletion. We used SOC dynamic curves and attainable SOC stocks from a process-based model for more than 17,000 world regions and 81 LU classes. Those classes include 63 agricultural (depending on 4 types of management/production), and 16 forest sub-classes, and 1 grassland and 1 urban class. We matched the CFs to LU elementary flows used by LCA databases at country-level. Results show that CFs are highly dependent on the LU sub-class and management practices. For example, transformation into cropland in general leads to the highest SOC depletion but SOC gains are possible with specific crops.

Food systems in a zero-deforestation world: Dietary change is more important than intensification for climate targets in 2050.

Global food systems contribute to climate change, the transgression of planetary boundaries and deforestation. An improved understanding of the environmental impacts of different food system futures is crucial for forging strategies to sustainably nourish a growing world population. We here quantify the greenhouse gas (GHG) emissions of global food system scenarios within a biophysically feasible "option space" in 2050 comprising all scenarios in which biomass supply - calculated as function of agricultural area and yields - is sufficient to cover biomass demand - derived from human diets and the feed demand of livestock. We assessed the biophysical feasibility of 520 scenarios in a hypothetical no-deforestation world. For all feasible scenarios, we calculate (in) direct GHG emissions related to agriculture. We also include (possibly negative) GHG emissions from land-use change, including changes in soil organic carbon (SOC) and carbon sinks from vegetation regrowth on land spared from food production. We identify 313 of 520 scenarios as feasible. Agricultural GHG emissions (excluding land use change) of feasible scenarios range from 1.7 to 12.5 Gt CO2e yr-1. When including changes in SOC and vegetation regrowth on spare land, the range is between -10.7 and 12.5 Gt CO2e yr-1. Our results show that diets are the main determinant of GHG emissions, with highest GHG emissions found for scenarios including high meat demand, especially if focused on ruminant meat and milk, and lowest emissions for scenarios with vegan diets. Contrary to frequent claims, our results indicate that diets and the composition and quantity of livestock feed, not crop yields, are the strongest determinants of GHG emissions from food-systems when existing forests are to be protected.

Detailed global modelling of soil organic carbon in cropland, grassland and forest soils.

Assessments of the global carbon (C) cycle typically rely on simplified models which consider large areas as homogeneous in terms of the response of soils to land use or consider very broad land classes. For example, "cropland" is typically modelled as an aggregation of distinct practices and individual crops over large regions. Here, we use the process-based Rothamsted soil Carbon Model (RothC model), which has a history of being successfully applied at a global scale, to calculate attainable SOC stocks and C mineralization rates for each of c. 17,000 regions (combination of soil type and texture, climate type, initial land use and country) in the World, under near-past climate conditions. We considered 28 individual crops and, for each, multiple production practices, plus 16 forest types and 1 grassland class (total of 80 classes). We find that conversion to cropland can result in SOC increases, particularly when the soil remains covered with crop residues (an average gain of 12 t C/ha) or using irrigation (4 t C/ha), which are mutually reinforcing effects. Attainable SOC stocks vary significantly depending on the land use class, particularly for cropland. Common aggregations in global modelling of a single agricultural class would be inaccurate representations of these results. Attainable SOC stocks obtained here were compared to long-term experiment data and are well aligned with the literature. Our results provide a regional and detailed understanding of C sequestration that will also enable better greenhouse gas reporting at national level as alternatives to IPCC tier 2 defaults.

Remotely sensed indicators and open-access biodiversity data to assess bird diversity patterns in Mediterranean rural landscapes.

Biodiversity monitoring at simultaneously fine spatial resolutions and large spatial extents is needed but limited by operational trade-offs and costs. Open-access data may be cost-effective to address those limitations. We test the use of open-access satellite imagery (NDVI texture variables) and biodiversity data, assembled from GBIF, to investigate the relative importance of variables of habitat extent and structure as indicators of bird community richness and dissimilarity in the Alentejo region (Portugal). Results show that, at the landscape scale, forest bird richness is better indicated by the availability of tree cover in the overall landscape than by the extent or structure of the forest habitats. Open-land birds also respond to landscape structure, namely to the spectral homogeneity and size of open-land patches and to the presence of perennial vegetation amid herbaceous habitats. Moreover, structure variables were more important than climate variables or geographic distance to explain community dissimilarity patterns at the regional scale. Overall, summer imagery, when perennial vegetation is more discernible, is particularly suited to inform indicators of forest and open-land bird community richness and dissimilarity, while spring imagery appears to be also useful to inform indicators of open-land bird richness.

Consolidating Regionalized Global Characterization Factors for Soil Organic Carbon Depletion Due to Land Occupation and Transformation.

Land occupation and transformation change soil organic carbon (SOC) stocks, which are a priority indicator for biotic production potential (BPP) in life cycle impact assessment (LCIA). SOC is a potential umbrella indicator for land use-related impacts, but global LCIA characterization models have never been sufficiently regionalized. Regeneration times required for the calculation of transformation impacts are unknown and can only be estimated through expert judgment or using additional assumptions. In this paper, we calculate global midpoint characterization factors (CF) for SOC depletion following land use and land use change using data from the European Soil Data Center with a resolution of 30 arc second. We used three possible calculation procedures to determine regeneration times: (1) estimations based on literature; (2) equal regeneration duration for all land uses; (3) equal regeneration rates for all land uses. We then propose an innovative approach for LCIA that combines all CFs in this paper as well as prior models using a spatial consolidation approach to arrive at a single set of CFs. We show that this procedure combines the strengths of each individual model and dilutes their shortcomings, and recommend the use of these consolidated CFs rather than individual sets of factors. For endpoints, we applied a nutrient replacement method using fertilizer input to compensate for organic matter depletion and obtained monetary CFs for SOC-related damages caused by land use on BPP.

The AmP project: Comparing species on the basis of dynamic energy budget parameters.

We developed new methods for parameter estimation-in-context and, with the help of 125 authors, built the AmP (Add-my-Pet) database of Dynamic Energy Budget (DEB) models, parameters and referenced underlying data for animals, where each species constitutes one database entry. The combination of DEB parameters covers all aspects of energetics throughout the full organism's life cycle, from the start of embryo development to death by aging. The species-specific parameter values capture biodiversity and can now, for the first time, be compared between animals species. An important insight brought by the AmP project is the classification of animal energetics according to a family of related DEB models that is structured on the basis of the mode of metabolic acceleration, which links up with the development of larval stages. We discuss the evolution of metabolism in this context, among animals in general, and ray-finned fish, mollusks and crustaceans in particular. New DEBtool code for estimating DEB parameters from data has been written. AmPtool code for analyzing patterns in parameter values has also been created. A new web-interface supports multiple ways to visualize data, parameters, and implied properties from the entire collection as well as on an entry by entry basis. The DEB models proved to fit data well, the median relative error is only 0.07, for the 1035 animal species at 2018/03/12, including some extinct ones, from all large phyla and all chordate orders, spanning a range of body masses of 16 orders of magnitude. This study is a first step to include evolutionary aspects into parameter estimation, allowing to infer properties of species for which very little is known.

The N-P-K soil nutrient balance of Portuguese cropland in the 1950s: The transition from organic to chemical fertilization.

Agricultural nutrient balances have been receiving increasing attention in both historical and nutrient management research. The main objectives of this study were to further develop balance methodologies and to carry out a comprehensive assessment of the functioning and nutrient cycling of 1950s agroecosystems in Portugal. Additionally, the main implications for the history of agriculture in Portugal were discussed from the standpoint of soil fertility. We used a mass balance approach that comprises virtually all nitrogen (N), phosphorus (P) and potassium (K) inputs and outputs from cropland topsoil for average conditions in the period 1951-56. We found a consistent deficit in N, both for nationwide (-2.1 kg.ha-1.yr-1) and arable crops (-1.6 kg.ha-1.yr-1) estimates, that was rectified in the turn to the 1960 decade. P and K were, in contrast, accumulating in the soil (4.2-4.6 kg.ha-1.yr-1 and 1.0-3.0 kg.ha-1.yr-1, respectively). We observed that the 1950s is the very moment of inflection from an agriculture fertilized predominantly through reused N in biomass (livestock excretions plus marine, plant and human waste sources) to one where chemical fertilizers prevailed. It is suggested that N deficiency played an important role in this transition.

The universality and the future prospects of physiological energetics: Reply to comments on "Physics of metabolic organization".

In response to the comments on review "Physics of metabolic organization", we discuss the universality and the future prospects of physiological energetics. The topics range from the role of entropy in modeling living organisms to the apparent ubiquity of the von Bertalanffy curve, and the potential applications of the theory in yet unexplored domains. Tradeoffs in outreach to non-specialists are also briefly considered.

A step toward regionalized scale-consistent agricultural life cycle assessment inventories.

Life cycle inventory (LCI) regionalization (i.e., the determination of input and output flows from production processes at a subcountry scale) is a priority in life cycle assessment (LCA) studies, particularly in the agri-food sector. Many regionalized LCAs fail to ensure that microlevel inventories are consistent with country-level aggregated data-or "scale consistent." They also fail to construct LCIs using international reference guidelines and trustworthy standardized data sources. This failure generates inaccuracies and biases in inventories and can compromise comparability among international LCA studies. Our study introduces scale consistency as a principle for regionalized agri-food LCIs. We present a generic procedure that defines how scale-dependent LCI flows should be regionalized, depending on data availability. We then present a list of inventory flows that require regionalization and their suggested calculation procedures (methods and models) from 2 methodological guides developed by projects Agribalyse and World Food LCA Database. As proof of concept, we apply the procedure to Portugal and assess whether the methods and models proposed for each type of inventory flow in both guides can potentially be applied consistently with the data available. For 17 inventory flows, we apply calculated scale-consistent inventory flows for Portuguese agriculture, covering 260 products that can be used in future LCA studies. Comparing results with international databases, we show that this procedure can improve country-level estimates significantly. Our study is the first step in introducing scale consistency as a guiding principle for regionalized LCIs for agri-food LCA studies. Integr Environ Assess Manag 2017;13:939-951. © 2017 SETAC.

Physics of metabolic organization.

We review the most comprehensive metabolic theory of life existing to date. A special focus is given to the thermodynamic roots of this theory and to implications that the laws of physics-such as the conservation of mass and energy-have on all life. Both the theoretical foundations and biological applications are covered. Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work. To bridge the gap between the two aspects of the same theory, we (i) adhere to the theoretical formalism, (ii) try to minimize the amount of information that a reader needs to process, but also (iii) invoke examples from biology to motivate the introduction of new concepts and to justify the assumptions made, and (iv) show how the careful formalism of the general theory enables modular, self-consistent extensions that capture important features of the species and the problem in question. Perhaps the most difficult among the introduced concepts, the utilization (or mobilization) energy flow, is given particular attention in the form of an original and considerably simplified derivation. Specific examples illustrate a range of possible applications-from energy budgets of individual organisms, to population dynamics, to ecotoxicology.

Dynamic energy budget theory restores coherence in biology.

We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occam's razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.

Influenza infectious dose may explain the high mortality of the second and third wave of 1918-1919 influenza pandemic.

BACKGROUND: It is widely accepted that the shift in case-fatality rate between waves during the 1918 influenza pandemic was due to a genetic change in the virus. In animal models, the infectious dose of influenza A virus was associated to the severity of disease which lead us to propose a new hypothesis. We propose that the increase in the case-fatality rate can be explained by the dynamics of disease and by a dose-dependent response mediated by the number of simultaneous contacts a susceptible person has with infectious ones. METHODS: We used a compartment model with seasonality, waning of immunity and a Holling type II function, to model simultaneous contacts between a susceptible person and infectious ones. In the model, infected persons having mild or severe illness depend both on the proportion of infectious persons in the population and on the level of simultaneous contacts between a susceptible and infectious persons. We further allowed for a high or low rate of waning immunity and volunteer isolation at different times of the epidemic. RESULTS: In all scenarios, case-fatality rate was low during the first wave (Spring) due to a decrease in the effective reproduction number. The case-fatality rate in the second wave (Autumn) depended on the ratio between the number of severe cases to the number of mild cases since, for each 1000 mild infections only 4 deaths occurred whereas for 1000 severe infections there were 20 deaths. A third wave (late Winter) was dependent on the rate for waning immunity or on the introduction of new susceptible persons in the community. If a group of persons became voluntarily isolated and returned to the community some days latter, new waves occurred. For a fixed number of infected persons the overall case-fatality rate decreased as the number of waves increased. This is explained by the lower proportion of infectious individuals in each wave that prevented an increase in the number of severe infections and thus of the case-fatality rate. CONCLUSION: The increase on the proportion of infectious persons as a proxy for the increase of the infectious dose a susceptible person is exposed, as the epidemic develops, can explain the shift in case-fatality rate between waves during the 1918 influenza pandemic.

Comment on "Energy uptake and allocation during ontogeny".

Hou et al. (Reports, 31 October 2008, p. 736) presented a model for energy uptake and allocation over an organism's growth and development. However, their model does not account for allocation to reproduction (essential to adults) and growth without assimilation (essential to embryos) and is therefore only applicable to organisms growing with abundant food in the juvenile stage.

From empirical patterns to theory: a formal metabolic theory of life.

The diversity of life on Earth raises the question of whether it is possible to have a single theoretical description of the quantitative aspects of the organization of metabolism for all organisms. However, similarities between organisms, such as von Bertalanffy's growth curve and Kleiber's law on metabolic rate, suggest that mechanisms that control the uptake and use of metabolites are common to all organisms. These and other widespread empirical patterns in biology should be the ultimate test for any metabolic theory that hopes for generality. The present study (i) collects empirical evidence on growth, stoichiometry, feeding, respiration and energy dissipation and exhibits it as stylized biological facts; (ii) formalizes assumptions and propositions in a metabolic theory that is fully consistent with the Dynamic Energy Budget theory; and (iii) proves that these assumptions and propositions are consistent with the stylized facts.

Thermodynamics of organisms in the context of dynamic energy budget theory.

We carry out a thermodynamic analysis to an organism. It is applicable to any type of organism because (1) it is based on a thermodynamic formalism applicable to all open thermodynamic systems and (2) uses a general model to describe the internal structure of the organism--the dynamic energy budget (DEB) model. Our results on the thermodynamics of DEB organisms are the following. (1) Thermodynamic constraints for the following types of organisms: (a) aerobic and exothermic, (b) anaerobic and exothermic, and (c) anaerobic and endothermic; showing that anaerobic organisms have a higher thermodynamic flexibility. (2) A way to compute the changes in the enthalpy and in the entropy of living biomass that accompany changes in growth rate solving the problem of evaluating the thermodynamic properties of biomass as a function of the amount of reserves. (3) Two expressions for Thornton's coefficient that explain its experimental variability and theoretically underpin its use in metabolic studies. (4) A mechanism that organisms in non-steady-state use to rid themselves of internal entropy production: "dilution of entropy production by growth." To demonstrate the practical applicability of DEB theory to quantify thermodynamic changes in organisms we use published data on Klebsiella aerogenes growing aerobically in a continuous culture. We obtain different values for molar entropies of the reserve and the structure of Klebsiella aerogenes proving that the reserve density concept of DEB theory is essential in discussions concerning (a) the relationship between organization and entropy and (b) the mechanism of storing entropy in new biomass. Additionally, our results suggest that the entropy of dead biomass is significantly different from the entropy of living biomass.