Final Report Summary - EUENDOLIGHT (Mineral excavation by photosynthetic microbes, a geochemical survey of a biological paradox.)
The evolution of oxygenic photosynthesis by a member of the cyanobacterial lineage, allowing water to be utilized as an electron donor and producing dioxygen constitutes a turning point in the evolution of our bio-geosphere. In fact, the success of this lineage deeply transformed our environment through the accumulation of O2 in our ocean and atmosphere, modified geochemical cycles and deeply influenced the evolution of life. The destiny of the cyanobacterial lineage has been fundamentally linked with the carbonate system.
It is expected that autotrophic carbon-fixing activity of cyanobacteria will enhance carbonate precipitation. It is well known that cyanobacterial dominated communities are able to calcify forming a variety of carbonate organo-sedimentary deposits, including stromatolites. However a large number of modern cyanobacterial species do not calcify in nature and some are even able to actively dissolve carbonate mineral, thus being called euendolitic. The latter process seems paradoxical and one can ask how these organisms are able to reconcile alkalinity production related to their metabolism along with the decrease of carbonate saturation index.
Project objectives
My main objective is to better understand mechanisms involved in cyanobacteria euendolithic activity, detail, its phylogenetic distribution and to characterized the mineral and geochemical signatures of this process, in order to give new strong diagnosis tools in the interpretation of environmental and paleobiological records.
Objective 1- Phylogenetic distribution and boring ability of endolithic cyanobacteria
Objective 2-Toward a better understanding of microboring process
Objective 3-Microbe-mineral relationship during the boring activity
Work performed since the beginning of the project, main results achieved, pitfall and adjustment
Since the beginning of the project I focused my effort on the Objective 1 and 2.
Objective 1: This objective was successfully carried out. In a first phase I collected samples from various carbonate outcrops. I could therefore systematically describe them (including their mineralogy and microbial community composition.), and look for evidence of substrate preference in the field. I found that there is a specialization of some euendolithic cyanobacterial clades towards the type of substrate they excavate, implying that close relatives have specialized recurrently into particular substrates
I isolated 4 new euendolithic strains including various unicellular, filamentous Cyanobacteria and a eukaryotic alga. All together this material allowed me to answer the questions raised in the Objective 1 and to move forward to the Objective 2.
Objective 2: Imaging calcium dependent boring mechanism (using calcium binding fluorescent dyes), I could never reliably repeat the results obtained for the model strain Mastigocoleus testarum (Ramirez-Reinat and Garcia-Pichel, 2011) or transfer the experimental design to the newly isolated strains. Therefore, I could not conclude on if the boring mechanism generally relied on active calcium pumping and decided to take another approach more exploratory to try to answer this important question. I used a combination of genomic and transcriptomic data to unravel the genes that are being turned ON and OFF during the process. Despite all my efforts and the support of the genomic facility core at ASU I could never analyzed the data produced as they were of very poor quality. Our conclusion was that the nucleic acids might have been partially degraded before sequencing, I could not repeat that experiment due to budget and time (it took more than 6 months to grow enough biomass) limitation.
Objective 3: Because the objective 2 failed I decided to re-adjust the objective three to a safer aim. I worked with the support of the Universite de Bourgogne Cellimap platform on optimizing the visualization of microborer’s ultrastructure in-situ. To do so we embedded pieces of rocks, dissolved the carbonate matrix and re-embedded the sample in order to prepare thin sections of actively boring cells and visualizing them using transmission electron microscopy. I am currently analyzing the pictures obtained for all the strains.
Expected final results and their potential impact and use
Altogether, this study will start shedding light on the global importance of endolithic communities and provide invaluable material to explore in more details the boring mechanisms by Cyanobacteria and algae. We expect at least 5 publications (3 are already published or in preparation for the coming year) directly related to this project and to the unexpected finding that we made while studying endolithic communities.
Overall this grant served the purpose of producing unique material (euendolithic strain collection) for further analyses that I intend to pursue in collaboration with Pr. Garcia-Pichel group. We could not harvest all the potentials of this ground breaking project within three years and I will keep working on it and eventually make it a central theme of my research career.
This project notably:
- established the first culture collection of uni-algal euendolithic cyanobacteria and algae.
- provided evidence of substrate preference among endolithic microbial communities
- revealed the ubiquity of anoxygenic phototrophs in endolithic communities
-described down to the nano-scale a bio reprecipitated layer of calcite from a bored dolomite in a natural sample
-analyzed the cell ultrastructure while boring
Here is the link to the seconded researcher blog: http://estellecouradeau.wixsite.com/estellecouradeau/blog-1(odnośnik otworzy się w nowym oknie)
It is expected that autotrophic carbon-fixing activity of cyanobacteria will enhance carbonate precipitation. It is well known that cyanobacterial dominated communities are able to calcify forming a variety of carbonate organo-sedimentary deposits, including stromatolites. However a large number of modern cyanobacterial species do not calcify in nature and some are even able to actively dissolve carbonate mineral, thus being called euendolitic. The latter process seems paradoxical and one can ask how these organisms are able to reconcile alkalinity production related to their metabolism along with the decrease of carbonate saturation index.
Project objectives
My main objective is to better understand mechanisms involved in cyanobacteria euendolithic activity, detail, its phylogenetic distribution and to characterized the mineral and geochemical signatures of this process, in order to give new strong diagnosis tools in the interpretation of environmental and paleobiological records.
Objective 1- Phylogenetic distribution and boring ability of endolithic cyanobacteria
Objective 2-Toward a better understanding of microboring process
Objective 3-Microbe-mineral relationship during the boring activity
Work performed since the beginning of the project, main results achieved, pitfall and adjustment
Since the beginning of the project I focused my effort on the Objective 1 and 2.
Objective 1: This objective was successfully carried out. In a first phase I collected samples from various carbonate outcrops. I could therefore systematically describe them (including their mineralogy and microbial community composition.), and look for evidence of substrate preference in the field. I found that there is a specialization of some euendolithic cyanobacterial clades towards the type of substrate they excavate, implying that close relatives have specialized recurrently into particular substrates
I isolated 4 new euendolithic strains including various unicellular, filamentous Cyanobacteria and a eukaryotic alga. All together this material allowed me to answer the questions raised in the Objective 1 and to move forward to the Objective 2.
Objective 2: Imaging calcium dependent boring mechanism (using calcium binding fluorescent dyes), I could never reliably repeat the results obtained for the model strain Mastigocoleus testarum (Ramirez-Reinat and Garcia-Pichel, 2011) or transfer the experimental design to the newly isolated strains. Therefore, I could not conclude on if the boring mechanism generally relied on active calcium pumping and decided to take another approach more exploratory to try to answer this important question. I used a combination of genomic and transcriptomic data to unravel the genes that are being turned ON and OFF during the process. Despite all my efforts and the support of the genomic facility core at ASU I could never analyzed the data produced as they were of very poor quality. Our conclusion was that the nucleic acids might have been partially degraded before sequencing, I could not repeat that experiment due to budget and time (it took more than 6 months to grow enough biomass) limitation.
Objective 3: Because the objective 2 failed I decided to re-adjust the objective three to a safer aim. I worked with the support of the Universite de Bourgogne Cellimap platform on optimizing the visualization of microborer’s ultrastructure in-situ. To do so we embedded pieces of rocks, dissolved the carbonate matrix and re-embedded the sample in order to prepare thin sections of actively boring cells and visualizing them using transmission electron microscopy. I am currently analyzing the pictures obtained for all the strains.
Expected final results and their potential impact and use
Altogether, this study will start shedding light on the global importance of endolithic communities and provide invaluable material to explore in more details the boring mechanisms by Cyanobacteria and algae. We expect at least 5 publications (3 are already published or in preparation for the coming year) directly related to this project and to the unexpected finding that we made while studying endolithic communities.
Overall this grant served the purpose of producing unique material (euendolithic strain collection) for further analyses that I intend to pursue in collaboration with Pr. Garcia-Pichel group. We could not harvest all the potentials of this ground breaking project within three years and I will keep working on it and eventually make it a central theme of my research career.
This project notably:
- established the first culture collection of uni-algal euendolithic cyanobacteria and algae.
- provided evidence of substrate preference among endolithic microbial communities
- revealed the ubiquity of anoxygenic phototrophs in endolithic communities
-described down to the nano-scale a bio reprecipitated layer of calcite from a bored dolomite in a natural sample
-analyzed the cell ultrastructure while boring
Here is the link to the seconded researcher blog: http://estellecouradeau.wixsite.com/estellecouradeau/blog-1(odnośnik otworzy się w nowym oknie)