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Browsing Research by Department "Environmental Sciences"

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    A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans
    (American Society for Microbiology, 2024) Egas, Reinier; Kurth, Julia; Boeren, Sjef; Sousa, Diana; Welte, Cornelia; Sánchez Andrea, Irene; Ministerie van Onderwijs; Cultuur en Wetenschap; https://ror.org/02jjdwm75
    The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite,either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification),determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase,A. acetoxydans lacks recognized nitrite reductase genes. In this study,A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations,we monitored the production of potential nitrogen intermediates (nitrate,nitrite,nitric oxide,hydroxylamine,and ammonium). Resting cell experiments were performed with nitrate,nitrite,and hydroxylamine to confirm their reduction to ammonium,and formed intermediates were tracked. To identify the enzymes involved in DNRA,comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC,or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836),or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle. © 2024 Egas et al.
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    Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans
    (John Wiley and Sons Inc, 2024) Egas, Reinier; Sahonero Canavesi, Diana; Bale, Nicole; Koenen, Micel; Yildiz, Çaglar; Villanueva, Laura; Sousa, Diana; Sánchez Andrea, Irene; Ministerie van Onderwijs; Cultuur en Wetenschap; https://ror.org/02jjdwm75
    Acid mine drainage (AMD) waters are a severe environmental threat,due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs),but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition,which is often incompletely oxidized into organic acids (e.g.,acetic acid). At low pH,acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments,triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological,transcriptomic,and membrane lipid changes. After acetic acid spiking,the optical density initially dropped,followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid,creating milder conditions for other microorganisms in AMD environments. © 2024 The Authors. Environmental Microbiology published by Applied Microbiology International and John Wiley & Sons Ltd.
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    Can Neo-Rural Initiatives Bolster Community Resilience in Depopulated Coupled Human and Natural System?: Insights From Stakeholder Perceptions in Central Spain
    (Frontiers Media S.A., 2022) Sansilvestri, Roxane; Lucio, José Vicente de ; Seijo, Francisco; Zavala, Miguel; Horizon 2020 Framework Programme; European Commission; Ministerio de Ciencia e Innovación; Ministerio para la Transición Ecológica y el Reto Demográfico; https://ror.org/02jjdwm75
    Preindustrial era agro-sylvopastoral land uses have influenced structure,function and disturbance in Mediterranean type mountainous landscapes for millennia. In this study we analyze through semi-structured interviews,stakeholder perceptions of coupled human and natural system (CHANS) community resilience in one such landscape; the municipality of Puebla de la Sierra,Madrid. The municipality is part of the Biosphere Reserve of the Sierra del Rincon and the Natura 2000 network and as such is subject to various conservationist regulations emanating from multiple levels of governance. In the preindustrial past most municipal lands formed an oak “dehesa” or open forest CHANS that made biomass extraction through pollarding compatible with pastoralism and shifting agriculture. After a period of rapid land-use change in the early 20th century—marked by the state led plantation of coniferous forests,the final decades of the last century were characterized by rural abandonment and the collapse of traditional forms of land use as well as the gradual transformation of the municipality into an eco-touristic,exurban destination for Madrid residents. More recently,the municipality has experienced an influx of neo-rural settlers in the area wishing to connect traditional knowledge and management with modern agro-environmental practices. In our study,we identify two limiting factors to community resilience in Puebla de la Sierra; governance and financing. The current governance model is perceived by respondents to be contrary to their reality and needs,which translates into environmental,urban and health regulations that,in their views,penalizes agroecological and small-scale economic activities. In addition,respondents believe there is a dearth of material and financial resources to initiate these transformative local actions which further weakens community resilience. Stakeholders however also identified other factors that reinforce community resilience such as a collective willingness to revive key traditional ecosystem management practices such as pollarding,the networks of trust existing between the people participating in these new initiatives and the capacity for deliberating between different visions of future development pathways amongst local stakeholders. Copyright © 2022 Sansilvestri,de Lucio,Seijo and Zavala.
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    Data from a pre-publication independent replication initiative examining ten moral judgement effects
    (Nature Publishing Groups, 2016) Tierney, Warren; Schweinsberg, Martín; Jordan, Jennifer; Kennedy, Deanna; Qureshi, Israr; Sommer, Amy; Thornley, Nico; Madan, Nikhil; Vianello, Michelangelo; Awtrey, Eli; Zhu, Luke Lei; Diermeier, Daniel; Heinze, Justin; Srinivasan, Malavika; Tannenbaum, David; Bivolaru, Eliza; Dana, Jason; Davis-Stober, Clintin; Du Plessis, Christilene; Gronau, Quentin; Hafenbrack, Andrew; Liao, Eko Yi; Ly, Alexander; Marsman, Maarten; Murase, Toshio; Schaerer, Michael; Tworek, Christina; Wagenmakers, Eric-Jan; Wong, Lynn; Anderson, Tabitha; Bauman, Christopher; Bedwell, Wendy; Brescoll, Victoria; Canavan, Andrew; Chandler, Jesse; Cheries, Erik; Cheryan, Sapna; Cheung, Felix; Cimpian, Andrei; Clark, Mark; Cordon, Diana; Cushman, Fiery; Ditto, Peter; Amell, Alice; Frick, Sarah; Gamez-Djokic, Monica; Grady, Rebecca Hofstein; Graham, Jesse; Gu, Jun; Hahn, Adam; Hanson, Brittany; Hartwich, Nicole; Hein, Kristie; Inbar, Yoel; Jiang, Lily; Kellogg, Tehlyr; Legate, Nicole; Luoma, Timo; Maibeucher, Heidi; Meindl, Peter; Miles, Jennifer; Mislin, Aalexandra; Molden, Daniel; Motyl, Matt; Newman, George; Ngo, Hoai Huong; Packham, Harvey; Ramsay, Scott; Ray, Jennifer; Sackett, Aaron; Sellier, Anne-Laure; Sokolova, Tatiana; Sowden, Walter; Storage, Daniel; Sun, Xiaomin; Van Bavel, Jay; Washburn, Anthony; Wei, Cong; Wetter, Erick; Wilson, Carlos; Darroux, Sophie-Charlotte; Uhlmann, Eric Luis; https://ror.org/02jjdwm75
    We present the data from a crowdsourced project seeking to replicate findings in independent laboratories before (rather than after) they are published. In this Pre-Publication Independent Replication (PPIR) initiative,25 research groups attempted to replicate 10 moral judgment effects from a single laboratory's research pipeline of unpublished findings. The 10 effects were investigated using online/lab surveys containing psychological manipulations (vignettes) followed by questionnaires. Results revealed a mix of reliable,unreliable,and culturally moderated findings. Unlike any previous replication project,this dataset includes the data from not only the replications but also from the original studies,creating a unique corpus that researchers can use to better understand reproducibility and irreproducibility in science.
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    Resources for business resilience in a COVID-19 world: A community-centric approach
    (Elsevier Ltd, 2022) Beninger, Stefanie; Francis, June N.P.; Horizon 2020 Framework Programme; Marie Skodowska-Curie Actions; https://ror.org/02jjdwm75
    COVID-19 has drawn renewed focus on the importance of resilience,both among practitioners and in academia,as companies struggle to cope with the rapid swings,changing patterns,and disruptions in supply and demand. This article identifies and delineates a way forward for companies to support resilience,particularly recognizing the wider communities they are nested in and the resources that exist there. To identify such productive resources,known as capitals,we provide a novel and actionable integrated capitals framework (ICF). ICF integrates 10 existing frameworks drawn from both practice and academia and is comprised of nine different forms of capital that businesses can leverage and contribute toward supporting resilience. We provide insights into how businesses can use this framework to achieve resilience through this useful,yet underutilized,path. © 2021 Kelley School of Business,Indiana University
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    Short communication. Soil development mediated by traditional practices shape the stand structure of Spanish juniper woodland
    (Ministerio de Educacion y Ciencia, 2014) Venturas, Martín; Fuentes Utrilla, Pablo; López, Rosana; Perea, Ramón; Fernández, Victoria; Gascó, Antonio; Guzmán, Paula; Li, Meng; Rodríguez Calcerrada, Jesús; Miranda, Eva; Domínguez, Jorge; González Gordaliza, Guillermo; Zafra, Elena; Fajardo Alcántara, Miriam; Martín, Juan; Ennos, Richard; Nanos, Nikos; Lucena, Juan; Iglesias, Salustiano; Collada, Carmen; Gil, Luis
    Aim of study: Assessing the effect of soil development on the stand structure of a Spanish juniper forest traditionally shaped by livestock browsing and wood extraction. Area of study: Berlanga de Duero (Soria,Castilla y León),Spain. Material and methods: A stand inventory served to record stand structure. Tree age,height,DBH,basal area,and overbark volume were determined in each plot. Results were pooled considering two well-differentiated degrees of soil evolution. One-way ANOVAs (and Tukey's test) and regressions between growth parameters were performed to assess significant differences between growth performances on both types of soils. Research highlights: Deeper soils yielded significant higher plant density and stand stock figures than stony shallower profiles despite the intense past livestock activity in the area; and single tree-size was also significantly greater. Non-significant differences were found for merchantable junipers age (?120-160 years). Wood extraction and livestock browsing should be limited on shallower soils to allow soil and forest evolution; as well as to preserve the genetic pool better adapted to hardest growing conditions.
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    The pipeline project: Pre-publication independent replications of a single laboratory's research pipeline
    (Academic Press Inc., 2016) Tierney, Warren; Schweinsberg, Martín; Jordan, Jennifer; Kennedy, Deanna; Qureshi, Israr; Sommer, Amy; Thornley, Nico; Madan, Nikhil; Vianello, Michelangelo; Awtrey, Eli; Zhu, Luke Lei; Diermeier, Daniel; Heinze, Justin; Srinivasan, Malavika; Tannenbaum, David; Bivolaru, Eliza; Dana, Jason; Davis-Stober, Clintin; Du Plessis, Christilene; Gronau, Quentin; Hafenbrack, Andrew; Liao, Eko Yi; Ly, Alexander; Marsman, Maarten; Murase, Toshio; Schaerer, Michael; Tworek, Christina; Wagenmakers, Eric-Jan; Wong, Lynn; Anderson, Tabitha; Bauman, Christopher; Bedwell, Wendy; Brescoll, Victoria; Canavan, Andrew; Chandler, Jesse; Cheries, Erik; Cheryan, Sapna; Cheung, Felix; Cimpian, Andrei; Clark, Mark; Cordon, Diana; Cushman, Fiery; Ditto, Peter; Amell, Alice; Frick, Sarah; Gamez-Djokic, Monica; Grady, Rebecca Hofstein; Graham, Jesse; Gu, Jun; Hahn, Adam; Hanson, Brittany; Hartwich, Nicole; Hein, Kristie; Inbar, Yoel; Jiang, Lily; Kellogg, Tehlyr; Legate, Nicole; Luoma, Timo; Maibeucher, Heidi; Meindl, Peter; Miles, Jennifer; Mislin, Aalexandra; Molden, Daniel; Motyl, Matt; Newman, George; Ngo, Hoai Huong; Packham, Harvey; Ramsay, Scott; Ray, Jennifer; Sackett, Aaron; Sellier, Anne-Laure; Sokolova, Tatiana; Sowden, Walter; Storage, Daniel; Sun, Xiaomin; Van Bavel, Jay; Washburn, Anthony; Wei, Cong; Wetter, Erick; Wilson, Carlos; Darroux, Sophie-Charlotte; Uhlmann, Eric Luis; Institut Européen d'Administration des Affaires
    This crowdsourced project introduces a collaborative approach to improving the reproducibility of scientific research,in which findings are replicated in qualified independent laboratories before (rather than after) they are published. Our goal is to establish a non-adversarial replication process with highly informative final results. To illustrate the Pre-Publication Independent Replication (PPIR) approach,25 research groups conducted replications of all ten moral judgment effects which the last author and his collaborators had “in the pipeline” as of August 2014. Six findings replicated according to all replication criteria,one finding replicated but with a significantly smaller effect size than the original,one finding replicated consistently in the original culture but not outside of it,and two findings failed to find support. In total,40% of the original findings failed at least one major replication criterion. Potential ways to implement and incentivize pre-publication independent replication on a large scale are discussed. © 2015 The Authors