ESR1 will use a combination a high throughput technologies to describe soil microbial communities based on DNA and RNA. The work involves second generation DNA-sequencing (pyrosequencing and Illumina-based) technology. In addition, ESR1 will implement protocols for quantitative analysis of specific bioindicators using Q-PCR.
Fellowships
TRAINBIODIVERSE is a new European-funded research network that will bring together an unprecedented range of young researchers to examine soil biodiversity and its relevance for ecosystem services. As part of the project Trainbiodiverse will hire 14 early stage researchers (ESR1-14) and 5 experienced researchers (ER1-5). For full details on individual projects please browse below or contact us at enquiries@trainbiodiverse.com. If you are interested in applying, please first carefully check that you are eligible to apply before reading about our application procedure.
Be sure to see the Marie Curie Career development information to discover the opportunities provided in these actions.
ESR1 - Biodiversity toolbox. Development and validation of standardized analysis of soil biodiversity
Host:
Copenhagen University
Supervisor:
Prof. Søren J. Sørensen
Research Objectives
To develop, validate and implement standardized protocols for analysis of soil biodiversity.
ESR2 - Biodiversity toolbox. Implementing molecular tools for soil biodiversity investigation
Host:
Copenhagen University
Supervisor:
Prof. Søren J. Sørensen
Research Objectives
To develop bioinformatics pipeline for soil biodiversity investigation.
A bioinformatics pipeline using public pipelines, existing pipelines at the collaborating partners and custom-made pipelines will be set up for efficient analysis of the huge amount of data generated by sequencing. Provide relevant bioinformatic data sets on factors involved in evaluation of links between biodiversity and ecosystem function. The data output will be standardized to enable...
ESR3 - Soil Quality Indicators, establishing an operational definition of soil quality
Host:
RIJKSUNIVERSITEIT GRONINGEN
Supervisor:
Prof. Jan Dirk van Elsas
Research Objectives
Train one ESR for 36 months in establishing an operational definition of soil quality.
Project ESR3 will search for, and establish, a set of indicators for soil quality (health) . Briefly, we will build upon our vast experience with the characterization of soil microbial communities that are key to functioning, and then single out those that are determinative for soil quality, allowing the design of indicators (which will be molecular in nature). We will then validate such...
ESR4 - Soil Quality Indicators, developing bioindicators based on abundance
Host:
RIJKSUNIVERSITEIT GRONINGEN
Supervisor:
Prof. Jan Dirk van Elsas
Research Objectives
As for ESR 3, train one ESR for 36 months in establishing an operational definition of soil quality.
Project ESR4 will work along the same lines as ESR3, however use as the criterion the level of abundance in the soil of the particular indicators (standing for selected soil functions).
ESR5 - Abiotic factors driving biodiversity and functioning of soils
Host:
HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH
Supervisor:
Prof. Michale Schloter
Research Objectives
Model functional trait litter degradation and nitrogen turnover will be studied for comparison to field studies.
Diversity and activity of soil microbiomes is highly influenced by abiotic factors, including climatic conditions, management, contaminants and others. Vice versa soil microbes are the drivers for most ecosystem services provided by soil and shape their environment. In the frame of this project unifactorial as well as multifactorial experiments will be performed in greenhouses studies...
ESR6 - Impact of external perturbation on ecosystem biodiversity, induced modifications and their relation to ecosystem biodiversity
Host:
ECOLE CENTRALE DE LYON
Supervisor:
Prof. Timothy M. Vogel
Research Objectives
Analysis of biodiversity of soil microorganisms and links with human pollution.
ESR6 aims at using and validating a standardized method for high throughput analysis of biodiversity of soil microorganisms and links between redundancy of microbial function and human perturbation specifically those associated with human pollution.
ESR7 - Impact of external perturbation on ecosystem biodiversity, function and services at key field sites
Host:
ECOLE CENTRALE DE LYON
Supervisor:
Prof. Timothy M. Vogel
Research Objectives
Investigation of the impact of external perturbation and induced modifications of soil function and services.
ESR7 focuses on the impact of external perturbation and induced modifications of function and services at key field sites, specifically agricultural soil will be examined after exposure to pollutant addition.
ESR8 - Development and validation of DNA based soil biodiversity analysis on fungal communities and functional genes
Host:
MIKROBIOLOGICKY USTAV - AVCR, V.V.I.
Supervisor:
Dr. Petr Baldrain
Research Objectives
Investigation of taxonomic diversity of fungal communities and soil and the functional diversity of microbial genes in soil.
The project covers the analysis of taxonomic diversity of fungal communities and soil and the functional diversity of microbial genes in soils. The project will be based on the combination of next-generation-sequencing, quantitative PCR and stable isotope labelling for the description of fungal communities in soils and on the targeted analysis of functional genes, their transcripts and...
ESR9 - Development of enzyme based assays of functional diversity in soil and methods for monitoring expression of genes codifying enzymes
Host:
UNIVERSITA DEGLI STUDI DI FIRENZE
Supervisor:
Prof. Paolo Nannipieri
Research Objectives
Comparison of assays for determining urease, protease, alkaline and acid phosphomonoesterase and B-glucosidase activities based on fluorescent and colorimetric methods.
ESR9 project will compare assays for determining urease, protease, alkaline and acid phosphomonoesterase and B-glucosidase activities based on fluorescent and colorimetric methods by using soils selected by the project. In addition both detection and expression of genes encoding these enzymes will be compared with the measured enzyme assays so as to assess the origin of the measured enzyme...
ESR10 - Validation of enzyme based methods from European test sites Validation of enzyme based methods from European test sites
Host:
UNIVERSITA DEGLI STUDI DI FIRENZE
Supervisor:
Prof. Paolo Nannipieri
Research Objectives
Monitor urease, protease, alkaline and acid phosphomonoesterase and B-glucosidase activities on soils for validation of enzyme based methods.
ESR 10 project will monitor urease, protease, alkaline and acid phosphomonoesterase and B-glucosidase activities on soils from European test sites. Measurements by the newly released ISO 190/SC4 method based on fluorogenic substrates will be compared with enzyme activities measured by colorimetric protocols based on p-nitrophenyl derivates.
ESR11 - Operational definition of soil quality, mesofaunal aspects of investigation of soil biodiversity
Host:
UNIVERSIDADE DE COIMBRA
Supervisor:
Dr. Poulo Sousa
Research Objectives
Development of a synthetic index of soil quality.
ESR 11 project will focus on the development of a synthetic index of soil quality based on biodiversity measures with emphasis on functional microbial and faunal indicators of soil ecosystem services and underlying biological processes.
ESR12 - Development and validation of protozoan genetic diversity of importance for soil ecosystem functions
Host:
AARHUS UNIVERSITET
Supervisor:
Dr. Anne Winding
Research Objectives
Develop and validate soil protozoa genetic diversity tools with respect to soils representative to a range of climatic, physical/chemical factors and management regimes.
ESR12 will develop and validate genetic diversity tools (e.g. barcoding) of soil protozoa and test and compare these tools in EU soils across a range of climatic, physical/chemical factors and management regimes. WPs 1-6-8
ESR13 - Links between microbial and protozoan diversity, and soil ecosystem functions
Host:
AARHUS UNIVERSITET
Supervisor:
Dr. Anne Winding
Research Objectives
Study of the interaction between microorganisms and protozoa and its significance on the biodiversity and selected ecosystem function.
ESR 13 will study the interaction between microorganisms and protozoa and the significance of this on the biodiversity and selected ecosystem functions like e.g plant growth support, resilience, soil suppressivenes and soil carbon storage.
ESR14 - Economic value of biodiversity and ecosystem services, mapping ecosystem services and estimations of the economic value of soil biodiversity
Host:
LONDON SCHOOL OF ECONOMICS AND POLITICAL SCIENCE
Supervisor:
Dr. Salvatori Di Falco
Research Objectives
Mapping ecosystem services and estimations of the economic value of soil biodiversity.
During the first 12 months of the 36 months the ESR will attend classes in Environmental and Resource Economics and Applied Quantitative methods in order to gain knowledge of both theoretical and empirical tools necessary to address the research question. Subsequently, the ESR will develop an econometric model for the estimation of the value of biodiversity. Data will be gathered and compiled...
ER1 - High throughput sequencing to study soil biodiversity
Host:
Copenhagen University
Supervisor:
Prof. Søren J. Sørensen
Research Objectives
To develop standardized protocols for analysis of soil biodiversity.
ER1 will develop standardized protocols for soil sampling and isolation of DNA and mRNA, and will develop standardized protocols for sequencing of DNA and cDNA using pyrosequencing and Illumina technologies. ER1 will establish quantitative molecular tools for analysis of specific bioindicators using Q-PCR.
ER2 - Bioinformatic analysis of 2nd. generation sequencing data
Host:
COPENHAGEN UNIVERSITY
Supervisor:
Prof. Søren J. Sørensen
Research Objectives
To improve bioinformatics analysis of high throughput DNA and cDNA sequencing data from soil samples
In collaboration with ESR2, ER2 will link public bioinformatics pipelines and existing pipelines at collaborating partners, and will create relevant bioinformatic data sets on factors involved in evaluation of links between biodiversity and ecosystem function.
ER3 - Abiotic drivers for food web development and dynamics in soil
Host:
HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH
Supervisor:
Prof. Michael Schloter
Research Objectives
It is the aim to investigate food web structures in response to changes in abiotic factors like temperature, redox or moisture and to link changes to turnover rates and fluxes.
Food web structure in soil is highly linked to soil quality and performance. The interaction of bacteria, fungi, protists and also phages is highly controlled by abiotic factors and nutrient availability. Therefore it is the aim to investigate food web structures in response to changes in abiotic factors like temperature, redox or moisture and to link changes to turnover rates and fluxes....
ER4 - Importance of key microbial in soil processes
Host:
MIKROBIOLOGICKY USTAV - AVCR, V.V.I.
Supervisor:
Dr Petr Baldrain
Research Objectives
Identification of the relative contribution of abundant microbial taxa to soil processes.
The project will aim at the identification of the relative contribution of abundant microbial taxa to soil processes. It will be based on the comparison of transcriptomic and functional analysis of individual microbial strains or species representatives and the identification of processes performed by these taxa in soil using the analysis of metatranscriptomes. The project should help to...
ER5 - Post remediation site investigation
Host:
WATER & SOIL REMEDIATION SRL
Supervisor:
Prof. Søren J. Sørensen
Research Objectives
Implementation of dynamic and/or continuous biomass sampling.
ESR for project will implement dynamic and/or continuous biomass sampling (principally from ex-hydrocarbon polluted sites, including some now used for agricultural and residential purposes) with relation to assessment of variable stress and its relevance to improvement of biodiversity and ecosystem value. WPs 1-10