Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface
Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequen...
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Frontiers Research Foundation
2018
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| Online Access: | http://hdl.handle.net/1721.1/117551 https://orcid.org/0000-0001-7014-3830 |
| _version_ | 1826193648410165248 |
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| author | Landry, Zachary C. Vergin, Kevin Mannenbach, Christopher Block, Stephen Yang, Qiao Carlson, Craig Giovannoni, Stephen Blainey, Paul C |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Landry, Zachary C. Vergin, Kevin Mannenbach, Christopher Block, Stephen Yang, Qiao Carlson, Craig Giovannoni, Stephen Blainey, Paul C |
| author_sort | Landry, Zachary C. |
| collection | MIT |
| description | Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi. OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi. OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76-5.05 Mbps, and contained "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi. OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology. |
| first_indexed | 2024-09-23T09:42:30Z |
| format | Article |
| id | mit-1721.1/117551 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T09:42:30Z |
| publishDate | 2018 |
| publisher | Frontiers Research Foundation |
| record_format | dspace |
| spelling | mit-1721.1/1175512022-09-30T16:21:08Z Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface Landry, Zachary C. Vergin, Kevin Mannenbach, Christopher Block, Stephen Yang, Qiao Carlson, Craig Giovannoni, Stephen Blainey, Paul C Massachusetts Institute of Technology. Department of Biological Engineering Blainey, Paul C Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi. OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi. OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76-5.05 Mbps, and contained "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of "O" and "W"-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi. OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology. 2018-08-27T17:58:28Z 2018-08-27T17:58:28Z 2018-06 2017-12 2018-08-27T15:34:56Z Article http://purl.org/eprint/type/JournalArticle 1664-302X http://hdl.handle.net/1721.1/117551 Landry, Zachary C. et al. “Optofluidic Single-Cell Genome Amplification of Sub-Micron Bacteria in the Ocean Subsurface.” Frontiers in Microbiology 9 (June 2018): 1152 © 2018 Landry et al https://orcid.org/0000-0001-7014-3830 http://dx.doi.org/10.3389/fmicb.2018.01152 Frontiers in Microbiology Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/ application/pdf Frontiers Research Foundation Frontiers |
| spellingShingle | Landry, Zachary C. Vergin, Kevin Mannenbach, Christopher Block, Stephen Yang, Qiao Carlson, Craig Giovannoni, Stephen Blainey, Paul C Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface |
| title | Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface |
| title_full | Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface |
| title_fullStr | Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface |
| title_full_unstemmed | Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface |
| title_short | Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface |
| title_sort | optofluidic single cell genome amplification of sub micron bacteria in the ocean subsurface |
| url | http://hdl.handle.net/1721.1/117551 https://orcid.org/0000-0001-7014-3830 |
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