@article{e5f0e44b013d459f9d163038c6034156,
title = "Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN",
abstract = "Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.",
keywords = "Archaea, Bacteria, evolution, genomics fermentation, oxidoreductases, respiration",
author = "Beam, {Jacob P.} and Becraft, {Eric D.} and Brown, {Julia M.} and Frederik Schulz and Jarett, {Jessica K.} and Oliver Bezuidt and Poulton, {Nicole J.} and Kayla Clark and Dunfield, {Peter F.} and Ravin, {Nikolai V.} and Spear, {John R.} and Hedlund, {Brian P.} and Kormas, {Konstantinos A.} and Sievert, {Stefan M.} and Elshahed, {Mostafa S.} and Barton, {Hazel A.} and Stott, {Matthew B.} and Eisen, {Jonathan A.} and Moser, {Duane P.} and Onstott, {Tullis C.} and Tanja Woyke and Ramunas Stepanauskas",
note = "Funding Information: We thank the staff of the Bigelow Laboratory for Ocean Science Single Cell Genomics Center (SCGC) for the generation of single cell genomic data. We also thank Paul Falkowski and Saroj Poudel for advice on electron transport systems, Jacob Munson-McGee for insightful discussions on co-sorted SAGs, and David Emerson, Sean Crowe, Paul van der Wielen, Sari Peura, Andreas Teske, Takuro Nunoura, Christa Schleper, and Steffen Joergensen for contributing field samples. Thanks also to Richard Friese, Josh Hoines, Marc Ohms, Jeff Hughes, and Kevin Wilson (National Park Service); Michael King and John Bredehoft (Hydrodynamics Group); Darrell Lacy, Levi Kryder, John Klenke, and Jamie Walker (Nuclear Waste Repository Project Office); and Jaret Heise, Tom Regan and others at Sanford Underground Research Facility (SURF); Corey Lee (US Fish and Wildlife Service) and The Nature Conservancy for site access and sampling assistance in Nevada and South Dakota. Special thanks to Brittany Kruger, Josh Sackett, Scott Hamilton-Brehm, John Healey, Brad Lyles, and Chuck Russell of DRI for sampling assistance in Nevada. Thanks to the U.S. Forest Service for a permit to conduct research at Little Hot Creek, California and the 2015 International Geobiology Course for field work and sample collection. We thank Vitaly Kadnikov, Olga Karnachuk and Tamara Zemskaya for sample collection in Siberia. Also, thanks to Stephen Grasby, Allyson Brady, and Christine Sharp for sampling Canadian field samples, and Wen-Jun Li for logistical support and access to hot spring samples in China. We thank British Columbia Parks and Parks Canada for permission to sample Dewar Creek and Paint Pots field sites. Funding. This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548. Publisher Copyright: {\textcopyright} Copyright {\textcopyright} 2020 Beam, Becraft, Brown, Schulz, Jarett, Bezuidt, Poulton, Clark, Dunfield, Ravin, Spear, Hedlund, Kormas, Sievert, Elshahed, Barton, Stott, Eisen, Moser, Onstott, Woyke and Stepanauskas.",
year = "2020",
month = aug,
day = "17",
doi = "10.3389/fmicb.2020.01848",
language = "English (US)",
volume = "11",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media S. A.",
}