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Table of contents
Chapter 0: General introduction and objectives
Chapter I: Background knowledge
I-1 Biogeochemical cycle of Fe
I-1.1 Global Fe cycle
I-1.2 Microbial transformations of Fe in the biogeosphere
I-1.3 Influence of redox conditions and organic matter on iron reduction
I-2 Classification of Fe-minerals
I-3 Dissolution of Fe(III) (oxyhydr)oxides and iron cycling in surface environments
I-3.1 Abiotic dissolution
I-3.2 Biotic dissolution
I-3.3 Secondary minerals formed during the bio-reduction of Fe oxides
I-4 Iron-reducing bacteria (IRB)
I-4.1 Dissimilatory Iron-Reducing Bacteria (DIRB)
I-4.2 Iron reduction by fermentative bacteria
I-4.3 The genus Shewanella
I-4.3 The genus Geobacter
I-4.4 Comparison of the genera Shewanella and Geobacter
I-4.5 Primers for the detection and quantification of Shewanella and Geobacter
I-4.6 Biofilms of iron reducing bacteria
I-4.7 Studies involving complex iron reducing microbial communities
I-5 Mechanisms of microbial Fe(III) reduction
I-6 Cycling of Fe and mobility of associated As, Cr, Cd and other trace elements
I-6.1 Association of As, Cr and Cd with Fe-Oxides
I.6.2 Transformations of As, Cr and Cd by bacteria
I-6.3 Mobility of trace elements during Fe-oxides microbial dissolution
I-7 Positioning of the PhD thesis in regards to the state of the art
Chapter II: General materials and methods
II-1 Site information and soil / sediment sampling
II-2. Enrichment of iron-reducing bacteria (IRB) and subculture
II-3 Iron (oxyhydr)oxides and laboratory synthesis
II-3.1 Ferrihydrite
II-3.2 Lepidocrocite
II-3.3 Goethite and hematite
II-4 Physico-chemical analysis: pH, Eh, Fe(II)/FeT, As, Cr and Cd
II-5 BET surface areas
II-6 SEM-EDS and SEM observations
II-6.1 Observation of iron (oxyhydr)oxides
II-6.2 Bacteria Observations
II-7 57Fe Mössbauer spectrometry
II-8 Diversity and physiology of bacteria
II-8.1 Observation and counting of bacteria by Thoma cell
II-8.2 DNA extraction and PCR amplifications
II-8.3 CE-SSCP fingerprints
II-8.4 Bacterial 16S rRNA gene quantification
II-8.5 Detection of Shewanella and Geobacter
II-8.6 Quantification of Shewanella and Geobacter by qPCR
Chapter III: Experiments in slurry with four different iron oxides
III-1 Introduction
III-2 Specific Materials and Methods
III-2.1 Characterization of the environmental source of bacteria
Iron extraction in soils/sediments samples
III-2.2 Synthetic Fe(III) (oxyhydr)oxides and bacterial inocula
III-2.3 IRB incubation experiments
III-2.4 Fe analyses and pH/Eh monitoring
III-2.5 Determination of iron oxides solubilisation parameters
III-2.6 SEM-EDS observation and Mössbauer spectrometry
III-2.7 Biological analyses
III-2.8 Statistics
III-3 Results
III-3.1 Characterization of the environmental sources of bacteria
III-3.2 Dissolution of Fe (oxyhydr)oxides
III-3.3 Biological parameters
III-3.4 Mineral SEM-EDS observation
III-3.5 Mössbauer spectroscopy
III-4 Discussion
III-4.1 Influence of the type of iron oxide on bacterial iron solubilisation
III-4.2 Bacterial communities
III-4.3 Geobacter and Shewanella 16S genes abundances
III-4.4 Relation between iron solubilisation effectiveness and Geobacter and Shewanella 16S gene abundances
III-4.5 SEM observations of Fe (oxyhydr)oxides and Mössbauer spectroscopy
III-5 Conclusions and perspective
IV: Experiments with ferrihydrite fixed on slides
IV-1 Introduction
IV-2 Specific materials and methods
IV-2.1 Slide preparation with Fe(III) (oxyhydr)oxides
IV-2.2 Slides incubation experiments
IV-2.3 Monitoring
IV-2.4 DNA extraction and molecular analysis
IV-3 Experimental results
IV-3.1 Bacterial growth
IV-3.2 Physico-chemical monitoring
IV-3.3 Bacterial observations and molecular analysis
IV-3.4 Mineral SEM-EDS observations
IV-4 Discussion
IV-4.1 Fe dissolution
IV-4.2 Distribution of Shewanella and Geobacter 16S gene copies in the liquid medium and in the biofilm
IV-4.3 SEM observation of the solid particles
IV-5 Conclusion and perspective
Chapter V: Mobility of As, Cr and Cd adsorbed on Fe (oxyhydr)oxides submitted to IRB
V-1. Abstract
V-2. Introduction
V-3 Specific materials and methods
V-3.1 Adsorption of As, Cr and Cd on synthetic iron (oxyhydr)oxides
V-3.1.1 Preparation of TEs stock solution
V-3.1.2 Adsorption of TEs to iron oxyhydr(oxides)
V-3.2 Columns experimental setup
V-3.2.1 Preparation of Fe (oxyhydr)oxides
V-3.2.2 Preparation of silica gel and sand matrix
V-3.2.3 Column setup and experimental conditions
V-3.2.4 Monitoring
V-3.2.5 SEM-EDS observation and Mössbauer spectrometry
V-3.2.6 Biological analyses
V-4 Experimental results
V-4.1 Adsorption experimental results
V-4.2 Column experiments
V-4.2.1 Visual evolution of the columns
V-4.2.2 Spatial and temporal evolution of iron and absorbed elements in columns
V-4.2.3 Relationship between remaining Fe and TEs in columns
V-4.2.3 Biological Parameters
V-4.2.4 Mineral SEM-EDS observation
V-4.2.5 Mössbauer spectroscopy
IV-5 Discussion
IV-5.1 Spatial and temporal aspects of iron reduction of ferrihydrite and goethite
IV 5.2 Impact of iron reduction on behavior and mobilities of TEs
IV-5.3 Distribution of global bacterial biomass and two targeted IRB (Shewanella and Geobacter 16S genes) in the columns
IV-6 Conclusions and perspective
Chapter VI: Conclusions and perspectives
