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Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy

Rosenthal, Adam Z. and Zhang, Xinning and Lucey, Kaitlyn S. and Ottesen, Elizabeth A. and Trivedi, Vikas and Choi, Harry M. T. and Pierce, Niles A. and Leadbetter, Jared R. (2013) Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy. Proceedings of the National Academy of Sciences of the United States of America, 110 (40). pp. 16163-16168. ISSN 0027-8424. PMCID PMC3791709. http://resolver.caltech.edu/CaltechAUTHORS:20130930-102728287

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Abstract

Identifying microbes responsible for particular environmental functions is challenging, given that most environments contain an uncultivated microbial diversity. Here we combined approaches to identify bacteria expressing genes relevant to catabolite flow and to locate these genes within their environment, in this case the gut of a “lower,” wood-feeding termite. First, environmental transcriptomics revealed that 2 of the 23 formate dehydrogenase (FDH) genes known in the system accounted for slightly more than one-half of environmental transcripts. FDH is an essential enzyme of H_2 metabolism that is ultimately important for the assimilation of lignocellulose-derived energy by the insect. Second, single-cell PCR analysis revealed that two different bacterial types expressed these two transcripts. The most commonly transcribed FDH in situ is encoded by a previously unappreciated deltaproteobacterium, whereas the other FDH is spirochetal. Third, PCR analysis of fractionated gut contents demonstrated that these bacteria reside in different spatial niches; the spirochete is free-swimming, whereas the deltaproteobacterium associates with particulates. Fourth, the deltaproteobacteria expressing FDH were localized to protozoa via hybridization chain reaction-FISH, an approach for multiplexed, spatial mapping of mRNA and rRNA targets. These results underscore the importance of making direct vs. inference-based gene– species associations, and have implications in higher termites, the most successful termite lineage, in which protozoa have been lost from the gut community. Contrary to expectations, in higher termites, FDH genes related to those from the protozoan symbiont dominate, whereas most others were absent, suggesting that a successful gene variant can persist and flourish after a gut perturbation alters a major environmental niche.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1073/pnas.1307876110 DOIArticle
http://www.pnas.org/content/110/40/16163PublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791709/PubMed CentralArticle
http://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1307876110/-/DCSupplementalPublisherSupplementary Material
ORCID:
AuthorORCID
Trivedi, Vikas0000-0003-0953-0553
Pierce, Niles A.0000-0003-2367-4406
Leadbetter, Jared R.0000-0002-7033-0844
Additional Information:© 2013 National Academy of Sciences. Edited by James M. Tiedje, Michigan State University, East Lansing, MI, and approved August 13, 2013 (received for review April 29, 2013). We thank Dr. Scott Fraser and staff at the Biological Imaging Center, Colby Calvert and staff at the Molecular Instruments Resource, Igor Antoscheckhin and staff at the Jacobs Genetics and Genomics Laboratory, and Drs. Eric Matson and Victoria Orphan for comments. Research support was provided by the US Department of Energy (Grant DE-FG02-07ER64484), the Center for Environmental Microbial Interactions at Caltech, the National Institutes of Health (Grant 5R01 EB006192, to H.M.T.C. and N.A.P.), the Beckman Institute at Caltech (H.M.T.C. and N.A.P.), and a Caltech Rosen Center Bioengineering Scholarship (to V.T.). A.Z.R. and X.Z. contributed equally to this work. Author contributions: A.Z.R., X.Z., E.A.O., H.M.T.C., N.A.P., and J.R.L. designed research; A.Z.R., X.Z., K.S.L., E.A.O., V.T., and H.M.T.C. performed research; A.Z.R., X.Z., K.S.L., E.A.O., V.T., H.M.T.C., N.A.P., and J.R.L. analyzed data; and A.Z.R., X.Z., N.A.P., and J.R.L. wrote the paper. The authors declare no conflict of interest. This article is a PNAS Direct Submission. Data deposition: 16S rRNA gene sequences, FDH sequences, and FTHFS sequences have been deposited in the GenBank database (accession nos. JX974519, GU563433–GU563485, GQ922349–GQ922449, and JX974463–JX974518). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1307876110/-/DCSupplemental.
Group:Caltech Center for Environmental Microbial Interactions (CEMI)
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)DE-FG02-07ER64484
Caltech Center for Environmental Microbial Interactions (CEMI)UNSPECIFIED
NIH5R01 EB006192
Caltech Beckman InstituteUNSPECIFIED
Caltech Rosen Center for BioengineeringUNSPECIFIED
Subject Keywords:acetogenesis, RNA-Seq, microfluidic digital PCR
PubMed Central ID:PMC3791709
Record Number:CaltechAUTHORS:20130930-102728287
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20130930-102728287
Official Citation:Adam Z. Rosenthal, Xinning Zhang, Kaitlyn S. Lucey, Elizabeth A. Ottesen, Vikas Trivedi, Harry M. T. Choi, Niles A. Pierce, and Jared R. Leadbetter Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy PNAS 2013 110 (40) 16163-16168; published ahead of print September 16, 2013, doi:10.1073/pnas.1307876110
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:41550
Collection:CaltechAUTHORS
Deposited By: Kristin Buxton
Deposited On:30 Sep 2013 22:06
Last Modified:21 Oct 2017 00:40

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