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Title: Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis

Abstract

Elucidating nutrient exchange in microbial communities is an important step in understanding the relationships between microbial systems and global biogeochemical cycles, but these communities are complex and the interspecies interactions that occur within them are not well understood. Phototrophic consortia are useful and relevant experimental systems to investigate such interactions as they are not only prevalent in the environment, but some are cultivable in vitro and amenable to controlled scientific experimentation. Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful, high spatial resolution tool capable of visualizing the metabolic activities of single cells within a biofilm, but quantitative analysis of the resulting data has typically been a manual process, resulting in a task that is both laborious and susceptible to human error. In this work, the authors describe the creation and application of a semiautomated image-processing pipeline that can analyze NanoSIMS-generated data, applied to phototrophic biofilms as an example. The tool employs an image analysis process, which includes both elemental and morphological segmentation, producing a final segmented image that allows for discrimination between autotrophic and heterotrophic biomass, the detection of individual cyanobacterial filaments and heterotrophic cells, the quantification of isotopic incorporation of individual heterotrophic cells, and calculation of relevant populationmore » statistics. The authors demonstrate the functionality of the tool by using it to analyze the uptake of 15N provided as either nitrate or ammonium through the unicyanobacterial consortium UCC-O and imaged via NanoSIMS. The authors found that the degree of 15N incorporation by individual cells was highly variable when labeled with 15NH4+, but much more even when biofilms were labeled with 15NO3. In the 15NH4+-amended biofilms, the heterotrophic distribution of 15N incorporation was highly skewed, with a large population showing moderate 15N incorporation and a small number of organisms displaying very high 15N uptake. The results showed that analysis of NanoSIMS data can be performed in a way that allows for quantitation of the elemental uptake of individual cells, a technique necessary for advancing research into the metabolic networks that exist within biofilms with statistical analyses that are supported by automated, user-friendly processes.« less

Authors:
ORCiD logo [1];  [1];  [1]; ORCiD logo [2];  [2]
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  2. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH); National Institute of Biomedical Imaging and Bioengineering (NIBIB)
OSTI Identifier:
1757992
Alternate Identifier(s):
OSTI ID: 1421228
Report Number(s):
PNNL-SA-114560
Journal ID: ISSN 1934-8630; TRN: US2206013
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Biointerphases
Additional Journal Information:
Journal Volume: 11; Journal Issue: 2; Journal ID: ISSN 1934-8630
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Optical imaging; Biomass energy sources; Algebraic logic; Data visualization; Chemical elements; Phosphates; Image processing; Secondary ion mass spectrometry; Multispecies biofilms; Biogeochemistry

Citation Formats

Renslow, Ryan S., Lindemann, Stephen R., Cole, Jessica K., Zhu, Zihua, and Anderton, Christopher R. Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis. United States: N. p., 2016. Web. doi:10.1116/1.4941764.
Renslow, Ryan S., Lindemann, Stephen R., Cole, Jessica K., Zhu, Zihua, & Anderton, Christopher R. Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis. United States. https://doi.org/10.1116/1.4941764
Renslow, Ryan S., Lindemann, Stephen R., Cole, Jessica K., Zhu, Zihua, and Anderton, Christopher R. Fri . "Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis". United States. https://doi.org/10.1116/1.4941764. https://www.osti.gov/servlets/purl/1757992.
@article{osti_1757992,
title = {Quantifying element incorporation in multispecies biofilms using nanoscale secondary ion mass spectrometry image analysis},
author = {Renslow, Ryan S. and Lindemann, Stephen R. and Cole, Jessica K. and Zhu, Zihua and Anderton, Christopher R.},
abstractNote = {Elucidating nutrient exchange in microbial communities is an important step in understanding the relationships between microbial systems and global biogeochemical cycles, but these communities are complex and the interspecies interactions that occur within them are not well understood. Phototrophic consortia are useful and relevant experimental systems to investigate such interactions as they are not only prevalent in the environment, but some are cultivable in vitro and amenable to controlled scientific experimentation. Nanoscale secondary ion mass spectrometry (NanoSIMS) is a powerful, high spatial resolution tool capable of visualizing the metabolic activities of single cells within a biofilm, but quantitative analysis of the resulting data has typically been a manual process, resulting in a task that is both laborious and susceptible to human error. In this work, the authors describe the creation and application of a semiautomated image-processing pipeline that can analyze NanoSIMS-generated data, applied to phototrophic biofilms as an example. The tool employs an image analysis process, which includes both elemental and morphological segmentation, producing a final segmented image that allows for discrimination between autotrophic and heterotrophic biomass, the detection of individual cyanobacterial filaments and heterotrophic cells, the quantification of isotopic incorporation of individual heterotrophic cells, and calculation of relevant population statistics. The authors demonstrate the functionality of the tool by using it to analyze the uptake of 15N provided as either nitrate or ammonium through the unicyanobacterial consortium UCC-O and imaged via NanoSIMS. The authors found that the degree of 15N incorporation by individual cells was highly variable when labeled with 15NH4+, but much more even when biofilms were labeled with 15NO3–. In the 15NH4+-amended biofilms, the heterotrophic distribution of 15N incorporation was highly skewed, with a large population showing moderate 15N incorporation and a small number of organisms displaying very high 15N uptake. The results showed that analysis of NanoSIMS data can be performed in a way that allows for quantitation of the elemental uptake of individual cells, a technique necessary for advancing research into the metabolic networks that exist within biofilms with statistical analyses that are supported by automated, user-friendly processes.},
doi = {10.1116/1.4941764},
journal = {Biointerphases},
number = 2,
volume = 11,
place = {United States},
year = {Fri Feb 12 00:00:00 EST 2016},
month = {Fri Feb 12 00:00:00 EST 2016}
}

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