Iberian peninsula ecosystem carbon fluxes: a model-data integration study

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia do Ambiente pela Universidade Nova de Lisboa,Faculdade de Ciências e TecnologiaTerrestrial ecosystems play a key role within the context of the global carbon cycle. Characterizing and understanding ecosystem level responses and feedbacks to climate drivers is essential for diagnostic purposes as well as climate modelling projections. Consequently,numerous modelling and data driven approaches emerge, aiming the appraisal of biosphereatmosphere carbon fluxes. The combination of biogeochemical models with observations of ecosystem carbon fluxes in a model-data integration framework enables the recognition of potential limitations of modelling approaches. In this regard, the steady-state assumption represents a general approach in the initialization routines of biogeochemical models that entails limitations in the ability to simulate net ecosystem fluxes and in model development exercises. The present research addresses the generalized assumption of initial steady-state conditions in ecosystem carbon pools for modelling carbon fluxes of terrestrial ecosystems, from local to regional scales. At local scale, this study aims to evaluate the implications of equilibrium assumptions on modelling performance and on optimized parameters and uncertainty estimates based on a model-data integration approach. These results further aim to support the estimates of regional net ecosystem fluxes, following a bottom-up approach, by focusing on parameters governing net primary production (NPP) and heterotrophic respiration (RH)processes, which determine the simulation of the net ecosystem production fluxes in the CASA model. An underlying goal of the current research is addressed by focusing on Mediterranean ecosystem types, or ecosystems potentially present in Iberia, and evaluate the general ability of terrestrial biogeochemical models in estimating net ecosystem fluxes for the Iberian Peninsula region. At regional scales, and given the limited information available, the main objective is to minimize the implications of the initial conditions in the evaluation of the temporal dynamics of net ecosystem fluxes. Inverse model parameter optimizations at site level are constrained by eddy-covariance measurements of net ecosystem fluxes and driven by local observations of meteorological variables and vegetation biophysical variables from remote sensing products. Optimizations under steady-state conditions show significantly poorer model performance and higher parameter uncertainties when compared to optimizations under relaxed initial conditions. In addition, assuming initial steady-state conditions tend to bias parameter retrievals – reducing NPP sensitivity to water availability and RH responses to temperature – in order to prescribe sink conditions. But nonequilibrium conditions can be experienced in soil and/or vegetation carbon pools under alternative underlying dynamics, which are solely discernible through the integration of additional information sources, circumventing equifinality issues.Portuguese Foundation for Science and Technology (FCT),the European Union under Operational Program “Science and Innovation” (POCI 2010), PhD grant ref. SFRH/BD/6517/2001, co-sponsored by the European Social Fund. Further support,concerning the final months of the PhD, was provided by a Max Planck Society research fellowship

Lysis buffer properties: influence on S. epidermidis biofilm proteome analysis

Besides being part of human commensal flora, S. epidermidis has the ability to colonize and form biofilms in artificial implants. Due to the particular characteristics of biofilms, conventional methods used to disrupt and lyses biofilms from Gram positive bacteria may include association between mechanical, enzymatic and chemical methods. Nevertheless, proteomic characterization is highly dependent of the extraction procedure. In order to characterize proteome from S. epidermidis biofilms grown in glucose excess, we used mechanical lysis (glass beads) associated with two distinct lysis solution with different charge characteristic detergents, namely, SDS (an ionic detergent) or CHAPS (a zwitterionic detergent). Protein extracted was separated by SDS-PAGE and identified by LC-MS/MS. SDS lysis buffer combined with glass-beads showed the highest number of identified proteins (332 proteins). With zwitterionic detergent extraction, most the identified proteins presented a lower GRAVY value (grand average of hydropathy) and a protein molecular weight under 30 KDa. In overall, this work evidence that SDS lysis buffer is the optimal protocol to proteome analysis of S. epidermidis biofilms

Severity of drought and heatwave crop losses tripled over the last five decades in Europe

Extreme weather disasters (EWDs) can jeopardize domestic food supply and disrupt commodity markets. However, historical impacts on European crop production associated with droughts, heatwaves, floods, and cold waves are not well understood—especially in view of potential adverse trends in the severity of impacts due to climate change. Here, we combine observational agricultural data (FAOSTAT) with an extreme weather disaster database (EM-DAT) between 1961 and 2018 to evaluate European crop production responses to EWD. Using a compositing approach (superposed epoch analysis), we show that historical droughts and heatwaves reduced European cereal yields on average by 9% and 7.3%, respectively, associated with a wide range of responses (inter-quartile range +2% to −23%; +2% to −17%). Non-cereal yields declined by 3.8% and 3.1% during the same set of events. Cold waves led to cereal and non-cereal yield declines by 1.3% and 2.6%, while flood impacts were marginal and not statistically significant. Production losses are largely driven by yield declines, with no significant changes in harvested area. While all four event frequencies significantly increased over time, the severity of heatwave and drought impacts on crop production roughly tripled over the last 50 years, from −2.2% (1964–1990) to −7.3% (1991–2015). Drought-related cereal production losses are shown to intensify by more than 3% yr−1. Both the trend in frequency and severity can possibly be explained by changes in the vulnerability of the exposed system and underlying climate change impacts

Dormancy within Staphylococcus epidermidis biofilms: an immunoproteomic characterization

Dormant bacteria within biofilms contribute to biofilm heterogeneity. Consequently, physiological heterogeneity of biofilms may influence host immune response and tolerance to antibiotics. Recently, we described an in vitro model to modulate dormancy in S. epidermidis biofilms. Here, we present a study based on immunoproteomics, where we compared the reactive profile of S. epidermidis biofilm proteins with prevented and induced dormancy, to human sera. A total of 19 immunoreactive proteins were identified by MALDI-TOF/TOF. Most of these proteins present molecular functions, such as catalytic activity and ion binding. CodY and GpmA proteins were more reactive to sera when biofilm dormancy was induced, while FtnA and ClpP were more reactive when dormancy was prevented. This is the first work identifying protein immunoreactivity differences between bacterial biofilms with induced or prevented dormancy. Considering the importance of dormancy within biofilms, further studies on these proteins may provide insights into the mechanisms related to dormancy and help improving current understanding on how dormancy affects the host immune response

Severity of drought and heatwave crop losses tripled over the last five decades in Europe

Publisher Copyright: © 2021 The Author(s). Published by IOP Publishing Ltd.Extreme weather disasters (EWDs) can jeopardize domestic food supply and disrupt commodity markets. However, historical impacts on European crop production associated with droughts, heatwaves, floods, and cold waves are not well understood - especially in view of potential adverse trends in the severity of impacts due to climate change. Here, we combine observational agricultural data (FAOSTAT) with an extreme weather disaster database (EM-DAT) between 1961 and 2018 to evaluate European crop production responses to EWD. Using a compositing approach (superposed epoch analysis), we show that historical droughts and heatwaves reduced European cereal yields on average by 9% and 7.3%, respectively, associated with a wide range of responses (inter-quartile range +2% to -23%; +2% to -17%). Non-cereal yields declined by 3.8% and 3.1% during the same set of events. Cold waves led to cereal and non-cereal yield declines by 1.3% and 2.6%, while flood impacts were marginal and not statistically significant. Production losses are largely driven by yield declines, with no significant changes in harvested area. While all four event frequencies significantly increased over time, the severity of heatwave and drought impacts on crop production roughly tripled over the last 50 years, from -2.2% (1964-1990) to -7.3% (1991-2015). Drought-related cereal production losses are shown to intensify by more than 3% yr-1. Both the trend in frequency and severity can possibly be explained by changes in the vulnerability of the exposed system and underlying climate change impacts.publishersversionpublishe

Towards Staphylococcus epidermidis biofilm dormancy characterization

Book of Abstracts of CEB Annual Meeting 2017info:eu-repo/semantics/publishedVersio

Proteomic profile of dormancy within Staphylococcus epidermidis biofilms using iTRAQ and label-free strategies

Staphylococcus epidermidis is an important nosocomial bacterium among carriers of indwelling medical devices, since it has a strong ability to form biofilms. The presence of dormant bacteria within a biofilm is one of the factors that contribute to biofilm antibiotic tolerance and immune evasion. Here, we provide a detailed characterization of the quantitative proteomic profile of S. epidermidis biofilms with different proportions of dormant bacteria. A total of 427 and 409 proteins were identified by label-free and label-based quantitative methodologies, respectively. From these, 29 proteins were found to be differentially expressed between S. epidermidis biofilms with prevented and induced dormancy. Proteins overexpressed in S. epidermidis with prevented dormancy were associated with ribosome synthesis pathway, which reflects the metabolic state of dormant bacteria. In the opposite, underexpressed proteins were related to catalytic activity and ion binding, with involvement in purine, arginine, and proline metabolism. Additionally, GTPase activity seems to be enhanced in S. epidermidis biofilm with induced dormancy. The role of magnesium in dormancy modulation was further investigated with bioinformatics tool based in predicted interactions. The main molecular function of proteins, which strongly interact with magnesium, was nucleic acid binding. Different proteomic strategies allowed to obtain similar results and evidenced that prevented dormancy led to an expression of a markedly different repertoire of proteins in comparison to the one of dormant biofilms.This work was funded by Fundacao para a Ciencia e a Tecnologia (FCT) and COMPETE grants PTDC/BIA-MIC/113450/2009, FCOMP-01-0124-FEDER-014309, QOPNA research unit (project PEst-C/QUI/UI0062/2013), RNEM (National Mass Spectrometry Network), and CENTRO-07-ST24-FEDER-002034. The authors also thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013, the Project NORTE-07-0124-FEDER-000027, co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER, and the project RECI/EBB-EBI/0179/2012, FCOMP-01-0124-FEDER-027462. VC has an individual FCT fellowship (SFRH/BD/78235/2011). NC is an Investigator FCT

Indicators from diurnal FLUXNET patterns

Funding Information: Acknowledgements. This work used eddy covariance data acquired by the FLUXNET community and in particular by the following networks: AmeriFlux (US Department of Energy, Biological and Environmental Research, Terrestrial Carbon Program (DE-FG02-04ER63917 and DE-FG02-04ER63911)), AfriFlux, AsiaFlux, CarboAfrica, CarboEuropeIP, CarboItaly, CarboMont, ChinaFlux, FluxnetCanada (supported by CFCAS, NSERC, BIOCAP, Environment Canada, and NRCan), GreenGrass, KoFlux, LBA, NECC, OzFlux, TCOS-Siberia, and USCCC. We acknowledge the financial support to the eddy covariance data harmonization provided by CarboEuropeIP, FAO-GTOS-TCO, iLEAPS, the Max Planck Institute for Biogeochemistry, the National Science Foundation, the University of Tuscia, Université Laval and Environment Canada, and the US Department of Energy and the database development and technical support from Berkeley Water Center, Lawrence Berkeley National Laboratory, Microsoft Research eScience, Oak Ridge National Laboratory, the University of California-Berkeley, and the University of Virginia. Publisher Copyright: © Author(s) 2018.Understanding of terrestrial carbon and water cycles is currently hampered by an uncertainty in how to capture the large variety of plant responses to drought. In FLUXNET, the global network of CO2 and H2O flux observations, many sites do not uniformly report the ancillary variables needed to study drought response physiology. To this end, we outline two data-driven indicators based on diurnal energy, water, and carbon flux patterns derived directly from the eddy covariance data and based on theorized physiological responses to hydraulic and non-stomatal limitations. Hydraulic limitations (i.e. intra-plant limitations on water movement) are proxied using the relative diurnal centroid (CET∗), which measures the degree to which the flux of evapotranspiration (ET) is shifted toward the morning. Non-stomatal limitations (e.g. inhibitions of biochemical reactions, RuBisCO activity, and/or mesophyll conductance) are characterized by the Diurnal Water-Carbon Index (DWCI), which measures the degree of coupling between ET and gross primary productivity (GPP) within each day. As a proof of concept we show the response of the metrics at six European sites during the 2003 heat wave event, showing a varied response of morning shifts and decoupling. Globally, we found indications of hydraulic limitations in the form of significantly high frequencies of morning-shifted days in dry/Mediterranean climates and savanna/evergreen plant functional types (PFTs), whereas high frequencies of decoupling were dominated by dry climates and grassland/savanna PFTs indicating a prevalence of non-stomatal limitations in these ecosystems. Overall, both the diurnal centroid and DWCI were associated with high net radiation and low latent energy typical of drought. Using three water use efficiency (WUE) models, we found the mean differences between expected and observed WUE to be -0.09 to 0.44 μmol mmol-1 and -0.29 to -0.40 μmol mmol-1 for decoupled and morning-shifted days, respectively, compared to mean differences -1.41 to -1.42 μmol mmol-1 in dry conditions, suggesting that morning shifts/hydraulic responses are associated with an increase in WUE, whereas decoupling/non-stomatal limitations are not.publishersversionpublishe

Characterization of an in vitro fed-batch model to obtain cells released from S. epidermidis biofilms

Both dynamic and fed-batch systems have been used for the study of biofilms. Dynamic systems, whose hallmark is the presence of continuous flow, have been considered the most appropriate for the study of the last stage of the biofilm lifecycle: biofilm disassembly. However, fed-batch is still the most used system in the biofilm research field. Hence, we have used a fed-batch system to collect cells released from Staphylococcus epidermidis biofilms, one of the most important etiological agents of medical device-associated biofilm infections. Herein, we showed that using this model it was possible to collect cells released from biofilms formed by 12 different S. epidermidis clinical and commensal isolates. In addition, our data indicated that biofilm disassembly occurred by both passive and active mechanisms, although the last occurred to a lesser extent. Moreover, it was observed that S. epidermidis biofilm-released cells presented higher tolerance to vancomycin and tetracycline, as well as a particular gene expression phenotype when compared with either biofilm or planktonic cells. Using this model, biofilm-released cells phenotype and their interaction with the host immune system could be studied in more detail, which could help providing significant insights into the pathophysiology of biofilm-related infections.European Union funds (FEDER/COMPETE) and by national funds (Fundação para a Ciência e a Tecnologia-FCT) under the project with reference FCOMP-01-0124-FEDER-041246 (EXPL/BIA-MIC/0101/2013). The authors thank the FCT Strategic Project of UID/BIO/04469/2013 unit and the project FCOMP-01-0124-FEDER-027462 (RECI/BBB-EBI/0179/2012); SFRH/BPD/99961/2014 and SFRH/BD/78235/201