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Title: Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

Abstract

Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present “direct protein-SIF” and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria–animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts’ metabolism. This confirms the usefulness ofmore » this approach to accurately determine δ13C values for different species in microbial community samples.« less

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [2];  [2];  [2]
+ Show Author Affiliations
  1. Univ. of Calgary, AB (Canada); North Carolina State Univ., Raleigh, NC (United States)
  2. Univ. of Calgary, AB (Canada)
  3. Univ. of Calgary, AB (Canada); Univ. of Greifswald (Germany); Inst. of Marine Biotechnology, Greifswald (Germany)
  4. Max Planck Inst. for Marine Microbiology, Bremen (Germany)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Campus Alberta Innovation Chair Program; Canada Foundation for Innovation (CFI); German Academic Exchange Service; Natural Sciences and Engineering Research Council of Canada (NSERC); International Microbiome Center; Genome Canada; Genome Alberta; Genome Prairie; Research Manitoba; Genome Quebec; Canada First Research Excellence Fund
OSTI Identifier:
1625014
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 115; Journal Issue: 24; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; science & technology - other topics; Protein-SIP; metaproteome; microbial ecology; microbiome; Q Exactive

Citation Formats

Kleiner, Manuel, Dong, Xiaoli, Hinzke, Tjorven, Wippler, Juliane, Thorson, Erin, Mayer, Bernhard, and Strous, Marc. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. United States: N. p., 2018. Web. doi:10.1073/pnas.1722325115.
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Kleiner, Manuel, Dong, Xiaoli, Hinzke, Tjorven, Wippler, Juliane, Thorson, Erin, Mayer, Bernhard, & Strous, Marc. Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. United States. https://doi.org/10.1073/pnas.1722325115
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Kleiner, Manuel, Dong, Xiaoli, Hinzke, Tjorven, Wippler, Juliane, Thorson, Erin, Mayer, Bernhard, and Strous, Marc. Tue . "Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities". United States. https://doi.org/10.1073/pnas.1722325115. https://www.osti.gov/servlets/purl/1625014.
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@article{osti_1625014,
title = {Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities},
author = {Kleiner, Manuel and Dong, Xiaoli and Hinzke, Tjorven and Wippler, Juliane and Thorson, Erin and Mayer, Bernhard and Strous, Marc},
abstractNote = {Measurements of stable carbon isotope ratios (δ13C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present “direct protein-SIF” and the Calis-p software package (https://sourceforge.net/projects/calis-p/), which enable high-throughput measurements of accurate δ13C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria–animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts’ metabolism. This confirms the usefulness of this approach to accurately determine δ13C values for different species in microbial community samples.},
doi = {10.1073/pnas.1722325115},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 24,
volume = 115,
place = {United States},
year = {Tue May 29 00:00:00 EDT 2018},
month = {Tue May 29 00:00:00 EDT 2018}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1073/pnas.1722325115
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Cited by: 34 works
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Figures / Tables:

Fig. 1 Fig. 1: Direct protein-SIF workflow. In the main step of the data analysis with the Calis-p software, the experimentally derived isotope distributions for peptides are compared with theoretical isotope peak distributions computed based on peptide molecular formulae with a fast Fourier transform method. The comparison with theoretical distributions is donemore » for a specified range of δ13C values in increments. Goodness of fit is calculated for all comparisons and the δ13C value for the best fit is reported if a predetermined goodness of fit threshold is passed. A more detailed workflow can be found in SI Appendix, Fig. S1.« less
All figures and tables (5 total)
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