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

Kleiner, Manuel; Dong, Xiaoli; Hinzke, Tjorven; Wippler, Juliane; Thorson, Erin; Mayer, Bernhard; Strous, Marc

doi:10.1073/pnas.1722325115

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

Journal Article · Tue May 29 00:00:00 EDT 2018 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1722325115· OSTI ID:1625014

^[1]; Dong, Xiaoli ^[2]; Hinzke, Tjorven ^[3]; Wippler, Juliane ^[4]; Thorson, Erin ^[2]; Mayer, Bernhard ^[2]; Strous, Marc ^[2]

Univ. of Calgary, AB (Canada); North Carolina State Univ., Raleigh, NC (United States); DOE/OSTI
Univ. of Calgary, AB (Canada)
Univ. of Calgary, AB (Canada); Univ. of Greifswald (Germany); Inst. of Marine Biotechnology, Greifswald (Germany)
Max Planck Inst. for Marine Microbiology, Bremen (Germany)

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: Campus Alberta Innovation Chair Program; Canada First Research Excellence Fund; Canada Foundation for Innovation (CFI); Genome Alberta; Genome Canada; Genome Prairie; Genome Quebec; German Academic Exchange Service; International Microbiome Center; Natural Sciences and Engineering Research Council of Canada (NSERC); Research Manitoba; USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625014

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 24 Vol. 115; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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