title: Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy.
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 H2 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.
authors.affiliation: Ronald and Maxine Linde Center for Global Environmental Science, Department of Bioengineering, and Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125.
authors.forename: Adam Z
authors.initials: AZ
authors.lastname: Rosenthal
authors.forename: Xinning
authors.initials: X
authors.lastname: Zhang
authors.forename: Kaitlyn S
authors.initials: KS
authors.lastname: Lucey
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Ottesen
authors.forename: Vikas
authors.initials: V
authors.lastname: Trivedi
authors.forename: Harry M T
authors.initials: HM
authors.lastname: Choi
authors.forename: Niles A
authors.initials: NA
authors.lastname: Pierce
authors.forename: Jared R
authors.initials: JR
authors.lastname: Leadbetter
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D020564:Deltaproteobacteria / Q000201:enzymology* / Q000378:metabolism; D005560:Formate Dehydrogenases / Q000235:genetics / Q000378:metabolism; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006859:Hydrogen / Q000378:metabolism*; D017404:In Situ Hybridization, Fluorescence; D020049:Isoptera / Q000382:microbiology*; D054892:Metagenome / Q000235:genetics*; D044085:Microfluidics; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D013144:Spirochaetales / Q000201:enzymology
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D012336:RNA, Ribosomal, 16S; D006859:Hydrogen; D005560:Formate Dehydrogenases
keywords: RNA-Seq; acetogenesis; microfluidic digital PCR
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