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Beam JP, Becraft ED, Brown JM, Schulz F, Jarett JK, Bezuidt O, Poulton NJ, Clark K, Dunfield PF, Ravin NV, Spear JR, Hedlund BP, Kormas KA, Sievert SM, Elshahed MS, Barton HA, Stott MB, Eisen JA, Moser DP, Onstott TC, Woyke T, Stepanauskas R. Ancestral Absence of Electron Transport Chains in Patescibacteria and DPANN. Front Microbiol 2020; 11:1848. [PMID: 33013724 PMCID: PMC7507113 DOI: 10.3389/fmicb.2020.01848] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/15/2020] [Indexed: 12/21/2022] Open
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.
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Affiliation(s)
- Jacob P Beam
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Eric D Becraft
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Jessica K Jarett
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
| | - Oliver Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Kayla Clark
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - John R Spear
- Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Brian P Hedlund
- School of Life Sciences - Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, United States
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, Greece
| | - Stefan M Sievert
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United States
| | - Hazel A Barton
- Department of Biology, University of Akron, Akron, OH, United States
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, Genome Center, University of California, Davis, Davis, CA, United States
| | - Duane P Moser
- Desert Research Institute, Las Vegas, NV, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, United States
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Bhute SS, Escobedo B, Haider M, Mekonen Y, Ferrer D, Hillyard SD, Friel AD, van Breukelen F, Hedlund BP. The gut microbiome and its potential role in paradoxical anaerobism in pupfishes of the Mojave Desert. Anim Microbiome 2020; 2:20. [PMID: 33499968 PMCID: PMC7807710 DOI: 10.1186/s42523-020-00037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Pupfishes frequently enter paradoxical anaerobism in response to endogenously produced or exogenously supplied ethanol in a dose-dependent manner. To decipher the role of the gut microbiota in ethanol-associated paradoxical anaerobism, gut microbial communities were depleted using a cocktail of antibiotics and profiled using 16S rRNA gene sequencing. RESULTS Compared to the control group (n = 12), microbiota-depleted fish (n = 12) spent more time in paradoxical anaerobism. Our analysis indicated that the bacterial phyla Proteobacteria, Fusobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Patescibacteria, and Dependentiae dominated the pupfish gut, which is consistent with other fish gut microbiota. Although the gut microbial communities with and without antibiotic treatment were similarly diverse, they were distinct and the greatest contribution to the dissimilarity (27.38%) was the common fish commensal Cetobacterium. CONCLUSIONS This study reports the first characterization of gut microbial communities of pupfish and suggests the microbiome may play a critical role in regulating metabolic strategies that are critical for survival in extremes of temperature and oxygen concentration. We speculate that Cetobacterium, a primary fermenter, also consumes ethanol through secondary fermentation via an alcohol dehydrogenase and therefore regulates the transition from paradoxical anaerobism to aerobic respiration in fish. Given the wide distribution and abundance of Cetobacterium in warm-water fishes, this process may be of broad importance, and suggests that the microbiome be carefully considered for both conservation and aquaculture.
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Affiliation(s)
- Shrikant S Bhute
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Brisa Escobedo
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Mina Haider
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Yididya Mekonen
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Dafhney Ferrer
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Stanley D Hillyard
- School of Dental Medicine, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Ariel D Friel
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Frank van Breukelen
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.
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