skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Nanobiogeochemistry of Microbe/Mineral Interactions: A Force Microscopy and Bioinformatics Approach

Abstract

In the original proposal (section 5, General Approach and Hypotheses, and Section 6, Research Plan), the planned research program for this three-year project was divided into three major tasks. These included research involving (1) biological force microscopy to study intermolecular forces between whole bacterial cells and minerals, (2) chemical force microscopy to study interactions between discrete biomolecules and mineral surfaces, and (3) molecular modeling of interactions between functional groups on biological and mineralogical surfaces. Dr. Lower was in charge of task 1, biological force microscopy. Dr. Lower has been involved in tasks 2 and 3 but, as these are under the supervision of Dr. Hochella, these tasks will not be discussed herein.

Authors:
Publication Date:
Research Org.:
University of Maryland, College Park, MD
Sponsoring Org.:
USDOE
OSTI Identifier:
860984
Report Number(s):
DOE/ER/15327-1
UM# 01-5-27473; TRN: US200710%%46
DOE Contract Number:
FG02-02ER15327
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 58 GEOSCIENCES; BACTERIA; MINERALS; INTERACTIONS; MOLECULAR MODELS; INTERMOLECULAR FORCES; MICROSCOPY; RESEARCH PROGRAMS; BIOGEOCHEMISTRY

Citation Formats

Lower, Steven, K. Nanobiogeochemistry of Microbe/Mineral Interactions: A Force Microscopy and Bioinformatics Approach. United States: N. p., 2005. Web. doi:10.2172/860984.
Lower, Steven, K. Nanobiogeochemistry of Microbe/Mineral Interactions: A Force Microscopy and Bioinformatics Approach. United States. doi:10.2172/860984.
Lower, Steven, K. Fri . "Nanobiogeochemistry of Microbe/Mineral Interactions: A Force Microscopy and Bioinformatics Approach". United States. doi:10.2172/860984. https://www.osti.gov/servlets/purl/860984.
@article{osti_860984,
title = {Nanobiogeochemistry of Microbe/Mineral Interactions: A Force Microscopy and Bioinformatics Approach},
author = {Lower, Steven, K.},
abstractNote = {In the original proposal (section 5, General Approach and Hypotheses, and Section 6, Research Plan), the planned research program for this three-year project was divided into three major tasks. These included research involving (1) biological force microscopy to study intermolecular forces between whole bacterial cells and minerals, (2) chemical force microscopy to study interactions between discrete biomolecules and mineral surfaces, and (3) molecular modeling of interactions between functional groups on biological and mineralogical surfaces. Dr. Lower was in charge of task 1, biological force microscopy. Dr. Lower has been involved in tasks 2 and 3 but, as these are under the supervision of Dr. Hochella, these tasks will not be discussed herein.},
doi = {10.2172/860984},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Nov 18 00:00:00 EST 2005},
month = {Fri Nov 18 00:00:00 EST 2005}
}

Technical Report:

Save / Share:
  • Iron-reducing microorganisms, like Shewanella oneidensis, have received a great deal of attention in the literature because of their ability to couple the oxidation of organic contaminants to the reduction of Fe(III) in minerals. The mechanism by which this microorganism transfers electrons to Fe(III) in a mineral’s structure is unknown. We used atomic force microscopy (AFM) to measure forces at the interface between an iron oxide mineral and a living cell of S. oneidensis. A unique force-signature was attributed to outer membrane proteins synthesized for the specific purpose of forming a bond with the surface of an iron oxide. To confirmmore » this hypothesis, we used AFM to measure forces between an iron oxide mineral and each of two outer membrane cytochromes purified from S. oneidensis. There is a strong correlation between the whole cell and pure protein force spectra suggesting that these two cytochromes play a prominent role in the terminal electron transfer to Fe(III) in minerals.« less
  • The long-term aim of this project was to understand the role of microbiota and their polymers (EPS) in controlling the distribution and fates of contaminants in subsurface environments. Additionally, this project also focused on the identification and characterization of extracellular proteins under a variety of growth conditions. Finally, this project sought to develop and advance the use of a variety of synchrotron-based hard-x-ray techniques to address a number of different ERSP elements.
  • The objective of this project was to investigate controls on induced polarization responses in porous media. The approach taken in the project was to compare electrical measurements made on mineral surfaces with atomic force microscopy (AFM) techniques to observations made at the column-scale using traditional spectral induced polarization measurements. In the project we evaluated a number of techniques for investigating the surface properties of materials, including the development of a new AFM measurement protocol that utilizes an external electric field to induce grain-scale polarizations that can be probed using a charged AFM tip. The experiments we performed focused on idealizedmore » systems (i.e., glass beads and silica gel) where we could obtain the high degree of control needed to understand how changes in the pore environment, which are determined by biogeochemical controls in the subsurface, affect mechanisms contributing to complex electrical conductivity, i.e., conduction and polarization, responses. The studies we performed can be classified into those affecting the chemical versus physical properties of the grain surface and pore space. Chemical alterations of the surface focused on evaluating how changes in pore fluid pH and ionic composition control surface conduction. These were performed as column flow through experiments where the pore fluid was exchanged in a column of silica gel. Given that silica gel has a high surface area due to internal grain porosity, high-quality data could be obtained where the chemical influences on the surface are clearly apparent and qualitatively consistent with theories of grain (i.e., Stern layer) polarization controlled by electrostatic surface sorption processes (i.e., triple layer theory). Quantitative fitting of the results by existing process-based polarization models (e.g., Leroy et al., 2008) has been less successful, however, due to what we have attributed to differences between existing models developed for spherical grains versus the actual geometry associated with the nano-pores in the silica gel, though other polarization processes, e.g., proton hopping along the surface (Skold et al., 2013), may also be a contributing factor. As an alternative model-independent approach to confirming the link between surface sorption and SIP we initiated a study that will continue (unfunded) beyond the completion of this project to independently measure the accumulation of gamma emitting isotopes on the silica gel during the SIP monitoring experiments. Though our analyses of the project data are ongoing, our preliminary analyses are generally supportive of the grain (Stern layer) polarization theory of SIP. Experiments focused on evaluating the impact of physical modifications of the medium on polarization included etching and biotic and abiotic facilitated precipitation of carbonate and iron oxides to alter the roughness and electrical conductivity of the surfaces. These experiments were performed for both silica gel and glass beads, the latter of which lacked the interior porosity and high surface area of the silica gel. The results appear to be more nuanced that the chemical modifications of the system. In general, however, it was found that deposition of iron oxides and etching had relatively minimal or negative impacts on the polarization response of the medium, whereas carbonate coatings increased the polarization response. These results were generally consistent with changes in surface charge observed via AFM. Abiotic and biotic column flow through experiments demonstrated that precipitation of carbonate within the medium significantly impacted the real and imaginary conductivity over time in a manner generally consistent with the carbonate precipitation as observed from the batch grain coating experiments. Biotic effects were not observed to provide distinctly different signatures, but may have contributed to differences in the rate of changes observed with SIP. AFM was used in a variety of different ways to investigate the grain surfaces throughout the course of the project. Standard imaging methods were used to evaluate surface roughness and charge density, which showed that these data could provide qualitative insights about consistency between surface trends and the electrical behavior at the column scale (for the case of glass beads). Polarization and conductive force microscopy (PCFM) measurements were developed by the original project PI (Treavor Kendall), which illustrated the importance of the initial few monolayers of water on the mineral surface for producing surface conductivity. The technique allowed for initial local estimates of complex electrical conductivity on mineral surfaces, but could not be pursued after Kendall left the project due to phase locking limitations with the AFM instrument at Clemson and an inability to perform measurements in solution, which limited their value for linking the measurements to column-scale SIP responses. As a result, co-PI Dean developed a new methodology for making AFM measurements within an externally applied electric field. In this method, the charged tip of an AFM probe is brought within the proximity of a polarization domain while an external electric field is applied to the sample. The premise of the approach is that the tip will be attracted to or rebound from charge accumulations on the surface, which allow for detection of the local polarization response. Initial experiments showed promise in terms of the general trends of responses observed, though we have not yet been able to develop a quantitative interpretation technique that can be applied to predicting column scale responses.« less
  • The objective of this project was to investigate controls on induced polarization responses in porous media. The approach taken in the project was to compare electrical measurements made on mineral surfaces with atomic force microscopy (AFM) techniques to observations made at the column-scale using traditional spectral induced polarization measurements. In the project we evaluated a number of techniques for investigating the surface properties of materials, including the development of a new AFM measurement protocol that utilizes an external electric field to induce grain-scale polarizations that can be probed using a charged AFM tip. The experiments we performed focused on idealizedmore » systems (i.e., glass beads and silica gel) where we could obtain the high degree of control needed to understand how changes in the pore environment, which are determined by biogeochemical controls in the subsurface, affect mechanisms contributing to complex electrical conductivity, i.e., conduction and polarization, responses. The studies we performed can be classified into those affecting the chemical versus physical properties of the grain surface and pore space. Chemical alterations of the surface focused on evaluating how changes in pore fluid pH and ionic composition control surface conduction. These were performed as column flow through experiments where the pore fluid was exchanged in a column of silica gel. Given that silica gel has a high surface area due to internal grain porosity, high-quality data could be obtained where the chemical influences on the surface are clearly apparent and qualitatively consistent with theories of grain (i.e., Stern layer) polarization controlled by electrostatic surface sorption processes (i.e., triple layer theory). Quantitative fitting of the results by existing process-based polarization models (e.g., Leroy et al., 2008) has been less successful, however, due to what we have attributed to differences between existing models developed for spherical grains versus the actual geometry associated with the nano-pores in the silica gel, though other polarization processes, e.g., proton hopping along the surface (Skold et al., 2013), may also be a contributing factor. As an alternative model-independent approach to confirming the link between surface sorption and SIP we initiated a study that will continue (unfunded) beyond the completion of this project to independently measure the accumulation of gamma emitting isotopes on the silica gel during the SIP monitoring experiments. Though our analyses of the project data are ongoing, our preliminary analyses are generally supportive of the grain (Stern layer) polarization theory of SIP. Experiments focused on evaluating the impact of physical modifications of the medium on polarization included etching and biotic and abiotic facilitated precipitation of carbonate and iron oxides to alter the roughness and electrical conductivity of the surfaces. These experiments were performed for both silica gel and glass beads, the latter of which lacked the interior porosity and high surface area of the silica gel. The results appear to be more nuanced that the chemical modifications of the system. In general, however, it was found that deposition of iron oxides and etching had relatively minimal or negative impacts on the polarization response of the medium, whereas carbonate coatings increased the polarization response. These results were generally consistent with changes in surface charge observed via AFM. Abiotic and biotic column flow through experiments demonstrated that precipitation of carbonate within the medium significantly impacted the real and imaginary conductivity over time in a manner generally consistent with the carbonate precipitation as observed from the batch grain coating experiments. Biotic effects were not observed to provide distinctly different signatures, but may have contributed to differences in the rate of changes observed with SIP. AFM was used in a variety of different ways to investigate the grain surfaces throughout the course of the project. Standard imaging methods were used to evaluate surface roughness and charge density, which showed that these data could provide qualitative insights about consistency between surface trends and the electrical behavior at the column scale (for the case of glass beads). Polarization and conductive force microscopy (PCFM) measurements were developed by the original project PI (Treavor Kendall), which illustrated the importance of the initial few monolayers of water on the mineral surface for producing surface conductivity. The technique allowed for initial local estimates of complex electrical conductivity on mineral surfaces, but could not be pursued after Kendall left the project due to phase locking limitations with the AFM instrument at Clemson and an inability to perform measurements in solution, which limited their value for linking the measurements to column-scale SIP responses. As a result, co-PI Dean developed a new methodology for making AFM measurements within an externally applied electric field. In this method, the charged tip of an AFM probe is brought within the proximity of a polarization domain while an external electric field is applied to the sample. The premise of the approach is that the tip will be attracted to or rebound from charge accumulations on the surface, which allow for detection of the local polarization response. Initial experiments showed promise in terms of the general trends of responses observed, though we have not yet been able to develop a quantitative interpretation technique that can be applied to predicting column scale responses.« less
  • This project focused on the development of single-pass multifrequency atomic force microscopy methods for the rapid multi-function nanoscale characterization of energy-relevant materials.