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Oxygen measurements in the lab
Oxygen measurement
Oxygen is the most advantageous electron acceptor during the process of respiration. That is why all higher organisms use oxygen to breathe. The oxygen is also involved in the re-oxidation of most reduced compounds produced by other types of anaerobic respirations (e.g. H2S, Fe2+, Mn2+). In addition, during daytime, photosynthesis by benthic microalgae produces oxygen Therefore, by quantifying oxygen consumption rates, we can have a net measure of both aerobic and anaerobic respiration processes, and of photosynthesis during light, occurring in the sediment.
How do we measure it?
In our laboratory, we usually use two different type of techniques, one using microsensors to measure vertical profiles of oxygen across the sediment water interface and with depth in the sediment and another by measuring the changes in oxygen concentrations in closed core incubations over time.
These methods provide similar but complementary information.
Microsensors
Profiles made with microsensors provide important information as to the total flux of oxygen across the sediment water interface, but also to the deeper layers, the depth of maximum oxygen production in light corresponding to the layer of microalgae, and the depth of the oxic zone (when oxygen concentration goes to zero). However, given that this method is based on a microsensor, fluxes measured are solely diffusive (movements of oxygen at a microscale) and are very localized to a small area around the tip of the sensor (a few microns).
Whole core incubations
Whole core incubations and measurements of the oxygen changes, provides a more integrated estimation of the oxygen flux as it includes a larger area, the consumption due not only of the microorganisms but also of larger macroorganisms (worms, molluscs, crustaceans etc). It also allows to include the effect of another process, that of advection that moves the oxygen molecules at larger spatial scales (for example by waves, the ventilation of burrows etc). This is why, fluxes measured by whole core incubation are called sometimes total fluxes.
To do this, we close the core (cylinder) containing our sediment ecosystem. On the inside of the lid there is a gel that contains a special dye that reacts with oxygen. Using an optical fibre we can measure through the transparent lid the changes in the fluorescence of the compound as the oxygen concentration changes inside the core. Quite cool..
However, both of them allow us to study the sediment metabolism and depending on the specific aims of our experiment, we use one or the other, or both. The more tools, the better!
RICAS: Postdoc offer to study the CO2 fluxes in intertidal ecosystems with the Eddy Covariance technique
We offer of postdoctoral contract for 1 year, extendable until 30/11/2024, to apply Atmospheric Eddy Covariance techniques in marshes and intertidal zones in the project “Rewilding saltmarshes to increase carbon sequestration, biodiversity and coastal adaptation to climate change as a nature based solution” (RICAS). RICAS is a project funded by the Recovery, Transformation and Resilience Plan of the Spanish Ministry of Science and Innovation.
What?
We are looking for a postdoctoral researcher with proven experience in the Eddy Covariance technique to study CO2 fluxes in the intertidal biological communities of Bay of Cadiz saltmarshes. The candidate will be responsible for setting up a new eddy covariance tower (ECV) with the aim of quantifying CO2 fluxes and evaluating the potential of saltmarsh rewilding, as a nature-based solution to mitigate the increase in atmospheric CO2 and climate change. The information obtained with the ECV will be compared with other techniques such as microsensors and incubations of benthic chambers in situ and sediment cores in the laboratory, in which our laboratory has great experience. The information obtained will be scaled up to the entire Bay using hyperspectral images obtained by drones and multispectral images by satellites, by researchers collaborating in the project
When?
The candidate should start as soon as possible (earliest expected date is late September, which depends on the selection process).
Where?
The selected candidate will join the Microbial Ecology and Biogeochemistry Group of the Department of Biology of the University of Cadiz, under the supervision of Alfonso Corzo and Sokratis Papaspyrou.
Requirements
– The candidate must have demonstrable experience (scientific articles, courses, etc.) in the atmospheric Eddy Covariance technique preferably in wetlands and marshes.
– Experience in other techniques related to Microbial Ecology and Biogeochemistry in wetlands and marshes will be highly valued.
– Must have good knowledge of written and spoken English (scientific level).
How to apply?
The contract offer is published in English and Spanish in the University of Cádiz website (https://personal.uca.es/convocatorias-de-capitulo-vi-2023/). The call will open from 13 to 22 of September. The specific information is in ANEXOS-SEPTIEMBRE-2023 (Anexo 6 in Spanish or Annex 6 in English).
https://personal.uca.es/convocatorias-de-capitulo-vi-2023/
Call documents: Annex Calls September 2023
If you require more info or help to apply, please send an email to alfonso.corzo@uca.es, sokratis.papaspyrou@uca.es.
RICAS: Postdoc offer to study the CO2 fluxes in intertidal ecosystems with the Eddy Covariance technique
We offer of postdoctoral contract for 1 year, extendable until 30/11/2024, to apply Atmospheric Eddy Covariance techniques in marshes and intertidal zones in the project “Rewilding saltmarshes to increase carbon sequestration, biodiversity and coastal adaptation to climate change as a nature based solution” (RICAS). RICAS is a project funded by the Recovery, Transformation and Resilience Plan of the Spanish Ministry of Science and Innovation.
What?
We are looking for a postdoctoral researcher with proven experience in the Eddy Covariance technique to study CO2 fluxes in the intertidal biological communities of Bay of Cadiz saltmarshes. The candidate will be responsible for setting up a new eddy covariance tower (ECV) with the aim of quantifying CO2 fluxes and evaluating the potential of saltmarsh rewilding, as a nature-based solution to mitigate the increase in atmospheric CO2 and climate change. The information obtained with the ECV will be compared with other techniques such as microsensors and incubations of benthic chambers in situ and sediment cores in the laboratory, in which our laboratory has great experience. The information obtained will be scaled up to the entire Bay using hyperspectral images obtained by drones and multispectral images by satellites, by researchers collaborating in the project
When?
The candidate should start as soon as possible (earliest expected date is late September, which depends on the selection process).
Where?
The selected candidate will join the Microbial Ecology and Biogeochemistry Group of the Department of Biology of the University of Cadiz, under the supervision of Alfonso Corzo and Sokratis Papaspyrou.
Requirements
– The candidate must have demonstrable experience (scientific articles, courses, etc.) in the atmospheric Eddy Covariance technique preferably in wetlands and marshes.
– Experience in other techniques related to Microbial Ecology and Biogeochemistry in wetlands and marshes will be highly valued.
– Must have good knowledge of written and spoken English (scientific level).
How to apply?
The University of Cádiz has opened the call for applications from June 20th to June 30th, 2023 on the website
https://personal.uca.es/convocatorias-de-capitulo-vi-2023/
Call documents: Appendix Calls June 2023 pdf
If you require more info or help to apply, please send an email to alfonso.corzo@uca.es, sokratis.papaspyrou@uca.es.
Sampling in Huelva
Great to be out in the field again today! Our postdoctoral researcher Lot van der Graaf is out sampling in acid mine drainage sites.
We are trying to understand how different biological and chemical processes are working together in the formation of curious patches of copper at this abandoned mine in southern Spain
The project (P20-01048) is co-financed by the European Union, within the framework of the Andalusia FEDER Operational Program “Smart growth: an economy based on knowledge and innovation, also responding to the Research and Innovation Strategy for the Smart Specialization of Andalusia (RISˑAndalusia) and the priorities and objectives set out in the Andalusian Plan for Research, Development and Innovation (PAIDI 2020)
Sampling in the Guadalquivir
Last Wednesday we went for a field trip at Bonanza in the Guadalquivir estuary to test our new field microsensor system.
Clean, before the action… 
Diatom biofilm 
Bioturbation
Sara in Ireland
Sara Haro, our former PhD student, has joined the Earth and Ocean Sciences research group at the School of Natural Sciences and Ryan Institute, National University of Ireland in Galway (NUIG) as a postdoctoral researcher, where she will monitor macroalgae blooms using machine learning algorithms from Sentinel-2 and Landsat-8 satellite images. This project is funded by the Ramón Areces Foundation as Sara won one of the 16 postdoctoral fellowships awarded by the Ramón Areces Foundation for further studies abroad in life sciences during 2022. Thus, she will continue working on the work she did while in our laboratory on using Sentinel-2 and Random Forest classification to study the patterns in space and time of microphytobenthos.
Sara in Canada
From January 2022, our former PhD student Sara Soria-Píriz has been awarded a three-year Margarita Salas postdoctoral fellowship. She will spend most of this period training in the Carbon Biogeochemistry in Boreal Aquatic systems (CarBBAS) group at the University of Quebec and Montreal (Canada), under the supervision of Prof. Paul del Giorgio. His work focuses on unravelling the patterns of bacterial and autotrophic picoplankton community structure and pigment characteristics as revealed by cytometric analysis. These samples are part of the LakePulse Survey, a multidisciplinary project that encompasses the study of 654 lakes from 11 different ecozones across Canada, from a very wide gradient of environmental conditions (climate, latitude, lake morphometry) and anthropogenic impacts (agriculture, forestry, mining). At the end of the fellowship Sara will be reincorporated in our lab to transfer her know-how.
EXTREME-FUN: laboratory technician job offer
Laboratory technician job offer to work on the impacts of Extreme Climatic Events, such as heat-waves and wind storms, on shallow coastal areas, focusing on the impacts on the biological community and biogeochemical functioning of shallow bays and intertidal zones.
What?
We are looking for a motivated candidate to work in microbial ecology and biogeochemistry of oceanic ecosystems. The job is offered within the EXTREME-FUN project (Effects of extreme climatic events on the biogeochemical functioning of shallow coastal areas: from the micro to the macroscale), which aims to quantify in an integrated manner the effect of heat waves and windstorms, affecting temperature and sediment resuspension conditions, on the biogeochemical functioning of a shallow coastal ecosystem.
The candidate, apart form the everyday laboratory activities, will support a combination of laboratory experiments, field measurements and aerial data (satellite, drones…) to study the spatial and temporal variability of the microphytobenthos and its contribution to the primary production of the system and evaluate the effect of changes in external forcing by temperature and resuspension/hydrodynamics under normal and extreme conditions on microphytobenthos physiology, benthic pelagic coupling and carbon flux throughout the system.
When?
The job start in February 2022 and will last initially 6 months, extendable up to a maximum of the duration of the project, reviewed annually.
Where?
The work will be carried out in the Microbial Ecology and Biogeochemistry Group of the Department of Biology of the University of Cadiz, under the supervision of Sokratis Papaspyrou and Alfonso Corzo.
Requirements
- The candidate must have obtained a bachelor’s degree on Marine or Environmental Sciences, Biology or similar .
- Be highly motivated and committed to work both in the laboratory and the field within a highly interdisciplinary and international project team.
- Have experience on biogeochemistry, aquatic microbial ecology, remote sensing, environmental chemistry or similar.
- Have a high level of written and spoken English.
For more details you can consult the call.
How to apply?
The call for applications is open from December 17 to December 28, 2021 on the website: Convocatorias de Capítulo VI 2021
Call: Annex 2
Applications
- Project Reference: PID2020-112488RB-I00, “EFECTO DE LOS EVENTOS CLIMATICOS EXTREMOS SOBRE EL FUNCIONAMIENTO BIOGEOQUIMICO DE ZONAS SOMERAS COSTERAS: DE LA MICRO A LA MACROESCALA”
- Job post reference: 12/2021/2
- Persons with a digital certificate (issued by an official public organisation) can send the application electronically through the following application: https://oficinavirtual.uca.es/oficinaVirtual/EntradaOficinaVirtual?procedimiento=110
- Persons without a valid digital signature certificate should consult the procedure here.
Please send an email with your CV to sokratis.papaspyrou@uca.es before applying for the position.
Biocobre: new project at MEBL
The research group in Microbial Ecology and Biogeochemistry of the UCA (MEB-LAB) initiates the development of a new line of research on copper precipitation in environments contaminated by acid mine drainage in the framework of the project “Bioprecipitation of metallic copper from acid mine drainage in the Iberian Pyritic Belt” BIOCOBRE, funded by the Junta de Andalucía.
The objective of the project is to study precipitates of copper salts and oxides in environments contaminated by acid mine drainage (AMD). The biogeochemical conditions, the microbial community and the metabolic pathways involved in the precipitation of copper nanoparticles in biofilm growing in acid mine drainage (AMD) areas in the Faja Piritica Iberica (Huelva) will be investigated.
Precipitates of Cu2+ and Cu+ salts and oxides are common in acid mine drainage (AMD) contaminated environments, but Cu0 precipitates are not. BIOCOBRE will investigate the biogeochemical conditions, microbial community and metabolic pathways involved in the precipitation of metallic copper (Cu0) nanoparticles in a biofilm growing in the acid mine drainage (AMD) of the abandoned mine Mina Esperanza (Huelva). To understand the Cu0 bioprecipitation process, we will set the following objectives: 1) define the geochemical environment within the biofilm where Cu0 precipitates and accurately measure Cu0 precipitation rates under different conditions, 2) describe the evolution of the biofilm microbial community from colonization to maturity under different environmental conditions, 3) isolate and culture the biofilm microorganisms (mainly fungi and bacteria) potentially involved in the Cu0 precipitation process. To achieve these objectives, we will use a multidisciplinary approach in which we will combine state-of-the-art techniques from different scientific disciplines: microsensors (O2, H2S, pH and Eh), geochemical and mineralogical methods, scanning transmission electron microscopy (STEM), omics tools (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and multispecific and axenic microbial cultures. The scientific and socioeconomic impact of BIOCOBRE, if we are able to achieve Cu0 precipitation, could be high. It could lead to patents and would probably open a new line of research focused on the bioengineering of the Cu0 precipitation process, to make it a technically and economically viable alternative to recover Cu0 from AMD, using an ecological approach at a reduced cost, in which Andalucia would be at the forefront.
The project (P20-01048) is co-financed by the European Union, within the framework of the Andalusia FEDER Operational Program “Smart growth: an economy based on knowledge and innovation, also responding to the Research and Innovation Strategy for the Smart Specialization of Andalusia (RISˑAndalusia) and the priorities and objectives set out in the Andalusian Plan for Research, Development and Innovation (PAIDI 2020).
Researchers from different departments and universities collaborate in the project:
Corzo Rodriguez, Alfonso, Dept Biología, Area de Ecología. Investigador principal, Coordinación general. Ecología microbiana
Papaspyrou, Sokratis, Dept Biología, Area de Ecología. Ecología microbiana.
García Robledo, Emilio Guillermo, Dept Biología, Area de Ecología. Ecología microbiana.
Duran Ruiz, Maria Del Carmen, Dept Biomedicina, Biotecnología y Salud Publica, Area de Bioquímica. Metaproteonómica.
Garrido Crespo, Carlos, Dept Biomedicina, Biotecnología y Salud Publica, Area de Microbiología. Aislamiento de microorganismos.
Lajaunie, Luc Cyrille Jacques, Dept de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica. Microscopia electrónica y análisis mineralógicos
Fig. 1. Exit of the AMD of Mina Esperanza (Huelva) and precipitation channel (A, E). Biofilm surface in the channel (B). O2 microsensor coupled to a micromanipulator measuring in situ (F). Portions of the biofilm with accumulations of precipitated Cu (pink color) (C). SEM images of Cu precipitation within the pink masses at different magnifications (D, G, H). Precipitated Cuº is found in close association with amorphous and filamentous structures that could represent the EPS matrix of the biofilm and bacterial structures such as nanowires (H).
Also participating in the project are:
Castillo Hernández, Julio Cesar. Univeridad de Free State, Sudafrica. Geomicrobiología, herramientas moleculares y microscopia.
Valverde Portal, Angel, IRNASA-CSIC. Microbiología.
Taylor, Joe Daniel, UK Centre for Ecology & Hydrology. Metagenómica.
The project (P20-01048) is co-financed by the European Union, within the framework of the Andalusia FEDER Operational Program “Smart growth: an economy based on knowledge and innovation, also responding to the Research and Innovation Strategy for the Smart Specialization of Andalusia (RISˑAndalusia) and the priorities and objectives set out in the Andalusian Plan for Research, Development and Innovation (PAIDI 2020).
EXTREME-FUN: PhD offer to study the effects of Extreme Climatic Events on shallow coastal areas
PhD offer to study the impacts of Extreme Climatic Events, such as heat-waves and wind storms, on shallow coastal areas, focusing on the impacts on the biological community and biogeochemical functioning of shallow bays and intertidal zones.
What?
We are looking for a motivated candidate to pursue a doctoral thesis in microbial ecology and biogeochemistry of oceanic ecosystems. The project will be supported by the EXTREME-FUN project (Effects of extreme climatic events on the biogeochemical functioning of shallow coastal areas: from the micro to the macroscale), which aims to quantify in an integrated manner the effect of heat waves and windstorms, affecting temperature and sediment resuspension conditions, on the biogeochemical functioning of a shallow coastal ecosystem.
The candidate will use a combination of laboratory experiments, field measurements and aerial data (satellite, drones…) to study the spatial and temporal variability of the microphytobenthos and its contribution to the primary production of the system and evaluate the effect of changes in external forcing by temperature and resuspension/hydrodynamics under normal and extreme conditions on microphytobenthos physiology, benthic pelagic coupling and carbon flux throughout the system.
When?
The PhD will start in April-May 2022 and will last 3 years, with the possibility of a 1-year extension.
Where?
The PhD will be developed in the Microbial Ecology and Biogeochemistry Group of the Department of Biology of the University of Cadiz, under the supervision of Sokratis Papaspyrou and Alfonso Corzo.
Requirements
- The candidate must have obtained a bachelor’s degree on Marine or Environmental Sciences, Biology or similar and a Master’s degree preferably also in the same topics.
- The candidates must be pre-registered in a Doctoral Program in Marine Science and Technology at the University of Cadiz (https://posgrado.uca.es/doctor/)
- Be highly motivated and committed to develop a scientific career.
- Have some experience on biogeochemistry, aquatic ecology, microbiology, remote sensing, environmental chemistry or similar.
- Have experience on scientific reading and writing.
- Have a high level of written and spoken English.
How to apply?
The Ministry has opened the call for applications from October 28 to November 11, 2021 on the website: https://sede.micinn.gob.es/ayudaspredoctorales/
Call: Ayudas para contratos predoctorales para la formación de doctores 2021
Applications
- Send the application electronically through the following application: https://sede.micinn.gob.es/ayudaspredoctorales/
- Project Reference: PID2020-112488RB-I00, “EFECTO DE LOS EVENTOS CLIMATICOS EXTREMOS SOBRE EL FUNCIONAMIENTO BIOGEOQUIMICO DE ZONAS SOMERAS COSTERAS: DE LA MICRO A LA MACROESCALA”
- Only a single application is allowed per candidate.
- Documentation to be attached:
- documentation certifying pre-admission to the PhD Program 2022/23: application page.
- In case of doubts: contact the doctoral school
- Curriculum vitae, preferably using the template of the ministry: template
- Academic certificate issued by the University where the Bachelor’s and Master’s degrees were obtained: the grades obtained and the date of graduation must appear.
- Copy of valid passport in case of foreign citizens.
- documentation certifying pre-admission to the PhD Program 2022/23: application page.
Please send an email with your CV to sokratis.papaspyrou@uca.es before applying for the position.
