Stable metal isotopes as a proxy to elucidate and quantify biofilm weathering

This project is a part of a the EU FP7 Initial Training Network (ITN) IsoNose

Biofilms are ubiquitous in subaerial and subsoil environment and have the capability to execute both physical and chemical transformations of the surface they grow on. These transformations include dissolution of minerals, mobility and recycling of elements, transfer of nutrients to plants, etc. (Gorbushina and Broughton 2009). Most previous studies on weathering systems are limited to understanding the physical and chemical aspects of the environment. Newer studies recognize the importance of biofilm on the overall weathering process but fail to quantify and explain its impact at both local and global scale. This lack of knowledge can be attributed to many different complications associated with bridging the two entirely distinct scientific fields: Microbiology and Geochemistry.

Figure 1. Schematic interactions of subaerial biofilms (SABs) and their interactions. A) Microorganisms are embedded in Extracellular polymeric substance (EPS) and form a miniature microbial ecosystem including both heterotrophic and phototrophic settlers (Gorbushina 2007).

The project is done in collaboration with The Federal Institute of Material Research and Testing (BAM). The main aim of the project is to use stable metal isotopes as a tool to quantify weathering of silicates rock by biofilms. Previous studies have identified two different pathways of biofilm weathering for nutrient uptake, (I) Biomechanical weathering and (II) Biochemical weathering (Gadd 2007). The biomechanical mechanism include penetration of fungal hyphae in the cracks, cavities of the mineral or by direct tunneling into the mineral. The biochemical mechanisms include processes like acidolysis, complexolysis, redoxolysis, and mycelium metal accumulation. Various uptake mechanisms along with other geochemical processes like precipitation of metals and formation of secondary mineral products can fractionate metal stable isotopes during their transfer from one compartment to another. Thus, quantifying fractionation factors during the transfer will provide an isotopic fingerprint for the pathways of nutrients from the host rock to the biofilms.

Since natural systems are multicomponent and dynamic, identifying mechanistic steps requires isolation of selected parts of the system. Our approach is to design a stepwise controlled batch experiment that aim at separating abiotic and biotic factors associated with biological weathering of a silicate mineral. We chose a laboratory biofilm consisting of the phototrophic cyanobacterium Nostoc punctiforme ATCC 29133 and the rock-inhabiting ascomycete Knufia petricola CBS 726.95 as a model biological species and the mineral Olivine [(Mg, Fe)2(SiO4)] as a host. Batch experiments are done with both single species of Knufia Petricola and Nostoc Punctiforme separately and also with both species together. A general equation to determine fractionation factor between olivine and the effluent solution is given below:

effluent/olivine = [(26Mg / 24Mg)effluent / (26Mg / 24Mg)olivine]       (1)


Figure 2a. Picture of the batch experiments setup conducted in a laminar flow hood with light source at room temperature and pressure. 500 mL Polycarbonate Erlenmeyer flask with sterile caps was used as a batch reactor.
Figure 2b. Photo of cultures of Knufia Petricola (Green) and Nostoc Punctiforme (Black). The first part of the project focus on determining kinetics of olivine dissolution in both the abiotic and biotic settings from the batch experiments. Key geochemical parameters like mineral dissolution rates, microbial growth rate, pH changes etc. associated with abiotic and biotic factors are quantified. Initial result already shows that the dissolution of olivine by Knufia Petricola after 30 days is 1.23 * 10-11 mol/m2/s, which is 15 % higher than the abiotic dissolution rates (Figure 3)

Figure 3. Percentage change in dissolution rate with respect to abiotic dissolution rate.

The second part of the project deals with calculating Mg isotopes ratios in the mineral, biofilm and the solution from the batch experiments. Multicollector ICP-MS is used to calculate Mg isotope ratios. Fractionation factors is calculated using equation (1) to determine the isotopic pathway of Mg from the olivine into the biofilm. The results will be combined with microscopic observations conducted in BAM on olivine and biofilm. The deduced outcomes will be used to implicate the impacts of biological weathering in natural settings.


Gadd, G. M. (2007). "Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation." Mycological Research 111(1): 3-49.

Gorbushina, A. A. (2007). "Life on the rocks." Environmental Microbiology 9(7): 1613-1631.

Gorbushina, A. A. and W. J. Broughton (2009). "Microbiology of the Atmosphere-Rock Interface: How Biological Interactions and Physical Stresses Modulate a Sophisticated Microbial Ecosystem." Annual Review of Microbiology 63(1): 431-450.


Mr. Rasesh Pokharel
Geochemistry of the Earth's surface

Building E, room 223
14473 Potsdam
tel. +49 331 288-28964