1
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Lindsay MR, D’Angelo T, Munson-McGee JH, Saidi-Mehrabad A, Devlin M, McGonigle J, Goodell E, Herring M, Lubelczyk LC, Mascena C, Brown JM, Gavelis G, Liu J, Yousavich DJ, Hamilton-Brehm SD, Hedlund BP, Lang S, Treude T, Poulton NJ, Stepanauskas R, Moser DP, Emerson D, Orcutt BN. Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem. Proc Natl Acad Sci U S A 2024; 121:e2309636121. [PMID: 38573964 PMCID: PMC11009646 DOI: 10.1073/pnas.2309636121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/23/2024] [Indexed: 04/06/2024] Open
Abstract
Rates of microbial processes are fundamental to understanding the significance of microbial impacts on environmental chemical cycling. However, it is often difficult to quantify rates or to link processes to specific taxa or individual cells, especially in environments where there are few cultured representatives with known physiology. Here, we describe the use of the redox-enzyme-sensitive molecular probe RedoxSensor™ Green to measure rates of anaerobic electron transfer physiology (i.e., sulfate reduction and methanogenesis) in individual cells and link those measurements to genomic sequencing of the same single cells. We used this method to investigate microbial activity in hot, anoxic, low-biomass (~103 cells mL-1) groundwater of the Death Valley Regional Flow System, California. Combining this method with electron donor amendment experiments and metatranscriptomics confirmed that the abundant spore formers including Candidatus Desulforudis audaxviator were actively reducing sulfate in this environment, most likely with acetate and hydrogen as electron donors. Using this approach, we measured environmental sulfate reduction rates at 0.14 to 26.9 fmol cell-1 h-1. Scaled to volume, this equates to a bulk environmental rate of ~103 pmol sulfate L-1 d-1, similar to potential rates determined with radiotracer methods. Despite methane in the system, there was no evidence for active microbial methanogenesis at the time of sampling. Overall, this method is a powerful tool for estimating species-resolved, single-cell rates of anaerobic metabolism in low-biomass environments while simultaneously linking genomes to phenomes at the single-cell level. We reveal active elemental cycling conducted by several species, with a large portion attributable to Ca. Desulforudis audaxviator.
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Affiliation(s)
| | | | | | | | - Molly Devlin
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Julia McGonigle
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Elizabeth Goodell
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Geology, Oberlin College, Oberlin, OH44074
| | - Melissa Herring
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA02115
| | | | | | - Julia M. Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Greg Gavelis
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Jiarui Liu
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | - D. J. Yousavich
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | - Brian P. Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV89154
| | - Susan Lang
- School of the Earth, Ocean and Environment, University of South Carolina, Columbia, SC29208
| | - Tina Treude
- Department of Earth, Planetary, and Space Sciences, University of California Los Angeles, Los Angeles, CA90095
- Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, CA90095
| | | | | | - Duane P. Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV89119
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
| | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME04544
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2
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Belkina AC, Roe CE, Tang VA, Back JB, Bispo C, Conway A, Chakraborty U, Daniels KT, de la Cruz G, Ferrer-Font L, Filby A, Gravano DM, Gregory MD, Hall C, Kukat C, Mozes A, Ordoñez-Rueda D, Orlowski-Oliver E, Pesce I, Porat Z, Poulton NJ, Reifel KM, Rieger AM, Sheridan RTC, Van Isterdael G, Walker RV. Guidelines for establishing a cytometry laboratory. Cytometry A 2024; 105:88-111. [PMID: 37941128 DOI: 10.1002/cyto.a.24807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/10/2023]
Abstract
The purpose of this document is to provide guidance for establishing and maintaining growth and development of flow cytometry shared resource laboratories. While the best practices offered in this manuscript are not intended to be universal or exhaustive, they do outline key goals that should be prioritized to achieve operational excellence and meet the needs of the scientific community. Additionally, this document provides information on available technologies and software relevant to shared resource laboratories. This manuscript builds on the work of Barsky et al. 2016 published in Cytometry Part A and incorporates recent advancements in cytometric technology. A flow cytometer is a specialized piece of technology that require special care and consideration in its housing and operations. As with any scientific equipment, a thorough evaluation of the location, space requirements, auxiliary resources, and support is crucial for successful operation. This comprehensive resource has been written by past and present members of the International Society for Advancement of Cytometry (ISAC) Shared Resource Laboratory (SRL) Emerging Leaders Program https://isac-net.org/general/custom.asp?page=SRL-Emerging-Leaders with extensive expertise in managing flow cytometry SRLs from around the world in different settings including academia and industry. It is intended to assist in establishing a new flow cytometry SRL, re-purposing an existing space into such a facility, or adding a flow cytometer to an individual lab in academia or industry. This resource reviews the available cytometry technologies, the operational requirements, and best practices in SRL staffing and management.
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Affiliation(s)
- Anna C Belkina
- Flow Cytometry Core Facility, School of Medicine, Boston University, Boston, Massachusetts, USA
| | - Caroline E Roe
- Cancer and Immunology Core, Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Vera A Tang
- Faculty of Medicine, Department of Biochemistry, Microbiology, and Immunology, Flow Cytometry Core Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Jessica B Back
- Department of Oncology, Wayne State University, Detroit, Michigan, USA
| | - Claudia Bispo
- Flow Cytometry Core Lab, AbbVie Inc, South San Francisco, California, USA
| | | | - Uttara Chakraborty
- Manipal Institute of Regenerative Medicine, Bengaluru, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Gelo de la Cruz
- Flow Cytometry Platform, Novo Nordisk Foundation Center for Stem Cell Medicine - reNEW, Copenhagen, Denmark
| | - Laura Ferrer-Font
- Hugh Green Cytometry Centre, Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Andrew Filby
- Flow Cytometry Core Facility and Innovation, Methodology and Application Research Theme, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - David M Gravano
- Stem Cell Instrumentation Foundry, University of California Merced, Merced, California, USA
| | - Michael D Gregory
- Cleveland Clinic, Florida Research and Innovation Center, Port St. Lucie, Florida, USA
| | - Christopher Hall
- Flow Cytometry Facility, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Christian Kukat
- FACS & Imaging Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - André Mozes
- Flow Cytometry Platform, Champalimaud Foundation, Lisbon, Portugal
| | - Diana Ordoñez-Rueda
- Flow Cytometry Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Isabella Pesce
- Cell Analysis and Separation Core Facility, Department of Cellular Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Nicole J Poulton
- Center for Aquatic Cytometry, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Kristen M Reifel
- Flow Cytometry Core Facility, Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Aja M Rieger
- Flow Cytometry Core Facility, University of Alberta, Alberta, Canada
| | | | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Belgium & Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Rachael V Walker
- Flow Cytometry Facility, Babraham Institute, Babraham Research Campus, Cambridge, UK
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3
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Munson-McGee JH, Lindsay MR, Sintes E, Brown JM, D'Angelo T, Brown J, Lubelczyk LC, Tomko P, Emerson D, Orcutt BN, Poulton NJ, Herndl GJ, Stepanauskas R. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature 2022; 612:764-770. [PMID: 36477536 PMCID: PMC9771814 DOI: 10.1038/s41586-022-05505-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022]
Abstract
The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.
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Affiliation(s)
| | | | - Eva Sintes
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Instituto Español de Oceanografía-CSIC, Centro Oceanográfico de Baleares, Palma, Spain
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Joe Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | | | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Beth N Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | | | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University, Den Burg, The Netherlands
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4
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D’Angelo T, Goordial J, Poulton NJ, Seyler L, Huber JA, Stepanauskas R, Orcutt BN. Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume. Front Microbiol 2022; 12:738231. [PMID: 35140689 PMCID: PMC8819061 DOI: 10.3389/fmicb.2021.738231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/30/2021] [Indexed: 12/22/2022] Open
Abstract
Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml-1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to 'omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.
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Affiliation(s)
- Timothy D’Angelo
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jacqueline Goordial
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Nicole J. Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Lauren Seyler
- School of Natural Science and Mathematics, Stockton University, Galloway, NJ, United States
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Julie A. Huber
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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5
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Brown JM, Labonté JM, Brown J, Record NR, Poulton NJ, Sieracki ME, Logares R, Stepanauskas R. Single Cell Genomics Reveals Viruses Consumed by Marine Protists. Front Microbiol 2020; 11:524828. [PMID: 33072003 PMCID: PMC7541821 DOI: 10.3389/fmicb.2020.524828] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/28/2020] [Indexed: 11/29/2022] Open
Abstract
The predominant model of the role of viruses in the marine trophic web is that of the “viral shunt,” where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, planktonic protists in the Gulf of Maine (GoM) and the Mediterranean Sea. We found viral DNA associated with a substantial fraction cells from the GoM (51%) and the Mediterranean Sea (35%). While Mediterranean SAGs contained a larger proportion of cells containing bacterial sequences (49%), a smaller fraction of cells contained bacterial sequences in the GoM (19%). In GoM cells, nearly identical bacteriophage and ssDNA virus sequences where found across diverse lineages of protists, suggesting many of these viruses are non-infective. The fraction of cells containing viral DNA varied among protistan lineages and reached 100% in Picozoa and Choanozoa. These two groups also contained significantly higher numbers of viral sequences than other identified taxa. We consider mechanisms that may explain the presence of viral DNA in protistan cells and conclude that protistan predation on free viral particles contributed to the observed patterns. These findings confirm prior experiments with protistan isolates and indicate that the viral shunt is complemented by a viral link in the marine microbial food web. This link may constitute a sink of viral particles in the ocean and has implications for the flow of carbon through the microbial food web.
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Affiliation(s)
- Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Jessica M Labonté
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States
| | - Joseph Brown
- Department of Human Genetics, University of Utah, Salt Lake City, UT, United States
| | - Nicholas R Record
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Michael E Sieracki
- Division of Ocean Sciences, National Science Foundation, Alexandria, VA, United States
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
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6
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Lange PK, Jeremy Werdell P, Erickson ZK, Dall'Olmo G, Brewin RJW, Zubkov MV, Tarran GA, Bouman HA, Slade WH, Craig SE, Poulton NJ, Bracher A, Lomas MW, Cetinić I. Radiometric approach for the detection of picophytoplankton assemblages across oceanic fronts. Opt Express 2020; 28:25682-25705. [PMID: 32906854 DOI: 10.1364/oe.398127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Cell abundances of Prochlorococcus, Synechococcus, and autotrophic picoeukaryotes were estimated in surface waters using principal component analysis (PCA) of hyperspectral and multispectral remote-sensing reflectance data. This involved the development of models that employed multilinear correlations between cell abundances across the Atlantic Ocean and a combination of PCA scores and sea surface temperatures. The models retrieve high Prochlorococcus abundances in the Equatorial Convergence Zone and show their numerical dominance in oceanic gyres, with decreases in Prochlorococcus abundances towards temperate waters where Synechococcus flourishes, and an emergence of picoeukaryotes in temperate waters. Fine-scale in-situ sampling across ocean fronts provided a large dynamic range of measurements for the training dataset, which resulted in the successful detection of fine-scale Synechococcus patches. Satellite implementation of the models showed good performance (R2 > 0.50) when validated against in-situ data from six Atlantic Meridional Transect cruises. The improved relative performance of the hyperspectral models highlights the importance of future high spectral resolution satellite instruments, such as the NASA PACE mission's Ocean Color Instrument, to extend our spatiotemporal knowledge about ecologically relevant phytoplankton assemblages.
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Tracy AN, Yadavalli R, Reed KS, Parnaik R, Poulton NJ, Bishop-Bailey D, Fernández Robledo JA. Genome to phenome tools: In vivo and in vitro transfection of Crassostrea virginica hemocytes. Fish Shellfish Immunol 2020; 103:438-441. [PMID: 32450301 DOI: 10.1016/j.fsi.2020.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/28/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
The sequencing of the Crassostrea virginica genome has brought back the interest for gene delivery and editing methodologies. Here, we report the expression in oyster hemocytes of two heterologous expression vectors under the CMV promoter delivered with dendrimers. Expression was monitored using confocal microscopy, flow cytometry, and immunofluorescence assay. C. virginica hemocytes were able to express the green fluorescence protein and Crassostrea gigas vascular endothelial growth factor under CMV viral promoter both in vivo and in vitro. These results provide the bases for interrogating the genome and adapting genome editing methodologies.
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Affiliation(s)
- Adrienne N Tracy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA; Colby College, Waterville, 4,000 Mayflower Hill Dr, ME, 04901, USA
| | | | - Kiara S Reed
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA; Colby College, Waterville, 4,000 Mayflower Hill Dr, ME, 04901, USA
| | - Rahul Parnaik
- North Cornwall Research Institute, Bude, Cornwall, EX23 9EE, UK
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
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9
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Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ, Poulton NJ, Burkart MD, La Clair JJ, Chisholm SW, Stepanauskas R. Charting the Complexity of the Marine Microbiome through Single-Cell Genomics. Cell 2019; 179:1623-1635.e11. [PMID: 31835036 PMCID: PMC6919566 DOI: 10.1016/j.cell.2019.11.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/30/2019] [Accepted: 11/13/2019] [Indexed: 12/18/2022]
Abstract
Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.
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Affiliation(s)
- Maria G Pachiadaki
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA; Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, USA
| | - Julia M Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Joseph Brown
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Oliver Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, 04544, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
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10
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Sieracki ME, Poulton NJ, Jaillon O, Wincker P, de Vargas C, Rubinat-Ripoll L, Stepanauskas R, Logares R, Massana R. Single cell genomics yields a wide diversity of small planktonic protists across major ocean ecosystems. Sci Rep 2019; 9:6025. [PMID: 30988337 PMCID: PMC6465268 DOI: 10.1038/s41598-019-42487-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 03/28/2019] [Indexed: 11/09/2022] Open
Abstract
Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate the diversity of the smaller (pico- and nano-sized) protists from a range of oceanic samples. We created over 900 single amplified genomes (SAGs) from 8 Tara Ocean samples across the Indian Ocean and the Mediterranean Sea. We show that flow cytometric sorting of single cells effectively distinguishes plastidic and aplastidic cell types that agree with our understanding of protist phylogeny. Yields of genomic DNA with PCR-identifiable 18S rRNA gene sequence from single cells was low (15% of aplastidic cell sorts, and 7% of plastidic sorts) and tests with alternate primers and comparisons to metabarcoding did not reveal phylogenetic bias in the major protist groups. There was little evidence of significant bias against or in favor of any phylogenetic group expected or known to be present. The four open ocean stations in the Indian Ocean had similar communities, despite ranging from 14°N to 20°S latitude, and they differed from the Mediterranean station. Single cell genomics of protists suggests that the taxonomic diversity of the dominant taxa found in only several hundreds of microliters of surface seawater is similar to that found in molecular surveys where liters of sample are filtered.
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Affiliation(s)
- M E Sieracki
- National Science Foundation, 2415 Eisenhower Ave., Alexandria, VA, 22314, USA.
| | - N J Poulton
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - O Jaillon
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - P Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, Evry, France
| | - C de Vargas
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680, Roscoff, France
| | - L Rubinat-Ripoll
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680, Roscoff, France
| | - R Stepanauskas
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| | - R Logares
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Maritim de la Barceloneta, 37-49, Barcelona, E-08003, Catalonia, Spain
| | - R Massana
- Department of Marine Biology and Oceanography, Institute of Marine Sciences (ICM)-CSIC, Pg. Maritim de la Barceloneta, 37-49, Barcelona, E-08003, Catalonia, Spain
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11
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Nagarkar M, Countway PD, Du Yoo Y, Daniels E, Poulton NJ, Palenik B. Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site. ISME J 2018; 12:2278-2291. [PMID: 29899506 DOI: 10.1038/s41396-018-0172-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 02/06/2018] [Accepted: 02/21/2018] [Indexed: 11/09/2022]
Abstract
High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, a significant proportion of which remains uncharacterized. Here we use a temporal approach to understanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcus and Synechococcus grazers, and traditional oceanographic parameters. We also exploit our ability to track operational taxonomic units (OTUs) temporally to evaluate the ability of 18S sequence-based OTU assignments to meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic in terms of both species richness and composition, although proportional representation of higher-order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughout the year. OTUs unique to dates of Synechococcus blooms and crashes or enriched in Synechococcus addition incubation experiments suggest that the prasinophyte Tetraselmis sp. and Gymnodinium-like dinoflagellates are likely Synechococcus grazers under certain conditions, and may play an important role in their population fluctuations.
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Affiliation(s)
- Maitreyi Nagarkar
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Peter D Countway
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Yeong Du Yoo
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.,Department of Marine Biotechnology, College of Ocean Science and Technology, Kunsan National University, Kunsan, 54150, Korea
| | - Emy Daniels
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA
| | - Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, 04544, USA
| | - Brian Palenik
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, La Jolla, San Diego, CA, USA.
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12
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Abstract
The ability to enumerate, classify, and determine biomass of phytoplankton from environmental samples is essential for determining ecosystem function and their role in the aquatic community and microbial food web. Traditional micro-phytoplankton quantification methods using microscopic techniques require preservation and are slow, tedious and very laborious. The availability of more automated imaging microscopy platforms has revolutionized the way particles and cells are detected within their natural environment. The ability to examine cells unaltered and without preservation is key to providing more accurate cell concentration estimates and overall phytoplankton biomass. The FlowCam(®) is an imaging cytometry tool that was originally developed for use in aquatic sciences and provides a more rapid and unbiased method for enumerating and classifying phytoplankton within diverse aquatic environments.
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Affiliation(s)
- Nicole J Poulton
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, USA.
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13
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Swan BK, Chaffin MD, Martinez-Garcia M, Morrison HG, Field EK, Poulton NJ, Masland EDP, Harris CC, Sczyrba A, Chain PSG, Koren S, Woyke T, Stepanauskas R. Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PLoS One 2014; 9:e95380. [PMID: 24743558 PMCID: PMC3990693 DOI: 10.1371/journal.pone.0095380] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/26/2014] [Indexed: 11/18/2022] Open
Abstract
Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal group retrieved from the dark ocean have been successfully cultured. We used single cell genomics to investigate the genomic and metabolic diversity of thaumarchaea within the mesopelagic of the subtropical North Pacific and South Atlantic Ocean. Phylogenetic and metagenomic recruitment analysis revealed that MGI single amplified genomes (SAGs) are genetically and biogeographically distinct from existing thaumarchaea cultures obtained from surface waters. Confirming prior studies, we found genes encoding proteins for aerobic ammonia oxidation and the hydrolysis of urea, which may be used for energy production, as well as genes involved in 3-hydroxypropionate/4-hydroxybutyrate and oxidative tricarboxylic acid pathways. A large proportion of protein sequences identified in MGI SAGs were absent in the marine cultures Cenarchaeum symbiosum and Nitrosopumilus maritimus, thus expanding the predicted protein space for this archaeal group. Identifiable genes located on genomic islands with low metagenome recruitment capacity were enriched in cellular defense functions, likely in response to viral infections or grazing. We show that MGI Thaumarchaeota in the dark ocean may have more flexibility in potential energy sources and adaptations to biotic interactions than the existing, surface-ocean cultures.
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Affiliation(s)
- Brandon K. Swan
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Mark D. Chaffin
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
- Department of Biology, Colby College, Waterville, Maine, United States of America
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Hilary G. Morrison
- Josephine Bay Paul Center for Molecular Biology and Evolution, Marine Biological Laboratory, Massachusetts, United States of America
| | - Erin K. Field
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Nicole J. Poulton
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - E. Dashiell P. Masland
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Christopher C. Harris
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | | | - Patrick S. G. Chain
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Joint Genome Institute, Walnut Creek, California, United States of America
| | - Sergey Koren
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- National Biodefense Analysis and Countermeasures Center, Frederick, Maryland, United States of America
| | - Tanja Woyke
- Joint Genome Institute, Walnut Creek, California, United States of America
| | - Ramunas Stepanauskas
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
- * E-mail:
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14
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Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PSG, Reitenga KG, Xie G, Poulton NJ, Gomez ML, Masland DED, Thompson B, Bellows WK, Ziervogel K, Lo CC, Ahmed S, Gleasner CD, Detter CJ, Stepanauskas R. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS One 2012; 7:e35314. [PMID: 22536372 PMCID: PMC3335022 DOI: 10.1371/journal.pone.0035314] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 03/13/2012] [Indexed: 11/19/2022] Open
Abstract
Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation.
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Affiliation(s)
- Manuel Martinez-Garcia
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - David M. Brazel
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
- Colby College, Waterville, Main, United States of America
| | - Brandon K. Swan
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Carol Arnosti
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Patrick S. G. Chain
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Krista G. Reitenga
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Gary Xie
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Nicole J. Poulton
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Monica Lluesma Gomez
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Dashiell E. D. Masland
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Brian Thompson
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Wendy K. Bellows
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
| | - Kai Ziervogel
- Department of Marine Sciences, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Chien-Chi Lo
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Sanaa Ahmed
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Cheryl D. Gleasner
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Chris J. Detter
- Genome Science Group, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
- Microbial and Metagenome Program, Joint Genome Institute, Walnut Creek, California, United States of Aemerica
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Main, United States of America
- * E-mail:
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15
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Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D, Reinthaler T, Poulton NJ, Masland EDP, Gomez ML, Sieracki ME, DeLong EF, Herndl GJ, Stepanauskas R. Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 2011; 333:1296-300. [PMID: 21885783 DOI: 10.1126/science.1203690] [Citation(s) in RCA: 321] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 and Agg47, and some Oceanospirillales from the lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase and sulfur oxidation genes. These results corroborated community DNA and RNA profiling from diverse geographic regions. The SAR324 genomes also suggested C(1) metabolism and a particle-associated life-style. Microautoradiography and fluorescence in situ hybridization confirmed bicarbonate uptake and particle association of SAR324 cells. Our study suggests potential chemolithoautotrophy in several uncultured Proteobacteria lineages that are ubiquitous in the dark oxygenated ocean and provides new perspective on carbon cycling in the ocean's largest habitat.
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Affiliation(s)
- Brandon K Swan
- Bigelow Laboratory for Ocean Sciences, 180 McKown Point Road, Post Office Box 475, West Boothbay Harbor, ME 04575, USA
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16
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Martínez Martínez J, Poulton NJ, Stepanauskas R, Sieracki ME, Wilson WH. Targeted sorting of single virus-infected cells of the coccolithophore Emiliania huxleyi. PLoS One 2011; 6:e22520. [PMID: 21818332 PMCID: PMC3144233 DOI: 10.1371/journal.pone.0022520] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 06/27/2011] [Indexed: 11/19/2022] Open
Abstract
Discriminating infected from healthy cells is the first step to understanding the mechanisms and ecological implications of viral infection. We have developed a method for detecting, sorting, and performing molecular analysis of individual, infected cells of the important microalga Emiliania huxleyi, based on known physiological responses to viral infection. Of three fluorescent dyes tested, FM 1-43 (for detecting membrane blebbing) gave the most unequivocal and earliest separation of cells. Furthermore, we were able to amplify the genomes of single infected cells using Multiple Displacement Amplification. This novel method to reliably discriminate infected from healthy cells in cultures will allow researchers to answer numerous questions regarding the mechanisms and implications of viral infection of E. huxleyi. The method may be transferable to other virus-host systems.
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Affiliation(s)
| | - Nicole J. Poulton
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
| | - Michael E. Sieracki
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
| | - William H. Wilson
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
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17
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Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, Stepanauskas R. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J 2011; 6:113-23. [PMID: 21716306 DOI: 10.1038/ismej.2011.84] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA sequencing to study the predominant photoheterotrophs and chemoautotrophs inhabiting the euphotic zone of temperate, physicochemically diverse freshwater lakes. Multi-locus sequencing of 712 single amplified genomes, generated by fluorescence-activated cell sorting and whole genome multiple displacement amplification, showed that most of the cosmopolitan freshwater clusters contain photoheterotrophs. These comprised at least 10-23% of bacterioplankton, and RBs were the dominant fraction. Our data demonstrate that Actinobacteria, including clusters acI, Luna and acSTL, are the predominant freshwater RBs. We significantly broaden the known taxonomic range of freshwater RBs, to include Alpha-, Beta-, Gamma- and Deltaproteobacteria, Verrucomicrobia and Sphingobacteria. By sequencing single cells, we found evidence for inter-phyla horizontal gene transfer and recombination of rhodopsin genes and identified specific taxonomic groups involved in these evolutionary processes. Our data suggest that members of the ubiquitous betaproteobacteria Polynucleobacter spp. are the dominant AAPs in temperate freshwater lakes. Furthermore, the RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) gene was found in several single cells of Betaproteobacteria, Bacteroidetes and Gammaproteobacteria, suggesting that chemoautotrophs may be more prevalent among aerobic bacterioplankton than previously thought. This study demonstrates the power of single-cell DNA sequencing addressing previously unresolved questions about the metabolic potential and evolutionary histories of uncultured microorganisms, which dominate most natural environments.
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18
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Fleming EJ, Langdon AE, Martinez-Garcia M, Stepanauskas R, Poulton NJ, Masland EDP, Emerson D. What's new is old: resolving the identity of Leptothrix ochracea using single cell genomics, pyrosequencing and FISH. PLoS One 2011; 6:e17769. [PMID: 21437234 PMCID: PMC3060100 DOI: 10.1371/journal.pone.0017769] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/14/2011] [Indexed: 11/19/2022] Open
Abstract
Leptothrix ochracea is a common inhabitant of freshwater iron seeps and iron-rich wetlands. Its defining characteristic is copious production of extracellular sheaths encrusted with iron oxyhydroxides. Surprisingly, over 90% of these sheaths are empty, hence, what appears to be an abundant population of iron-oxidizing bacteria, consists of relatively few cells. Because L. ochracea has proven difficult to cultivate, its identification is based solely on habitat preference and morphology. We utilized cultivation-independent techniques to resolve this long-standing enigma. By selecting the actively growing edge of a Leptothrix-containing iron mat, a conventional SSU rRNA gene clone library was obtained that had 29 clones (42% of the total library) related to the Leptothrix/Sphaerotilus group (≤96% identical to cultured representatives). A pyrotagged library of the V4 hypervariable region constructed from the bulk mat showed that 7.2% of the total sequences also belonged to the Leptothrix/Sphaerotilus group. Sorting of individual L. ochracea sheaths, followed by whole genome amplification (WGA) and PCR identified a SSU rRNA sequence that clustered closely with the putative Leptothrix clones and pyrotags. Using these data, a fluorescence in-situ hybridization (FISH) probe, Lepto175, was designed that bound to ensheathed cells. Quantitative use of this probe demonstrated that up to 35% of microbial cells in an actively accreting iron mat were L. ochracea. The SSU rRNA gene of L. ochracea shares 96% homology with its closet cultivated relative, L. cholodnii, This establishes that L. ochracea is indeed related to this group of morphologically similar, filamentous, sheathed microorganisms.
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Affiliation(s)
- Emily J Fleming
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America.
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19
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Jasti S, Sieracki ME, Poulton NJ, Giewat MW, Rooney-Varga JN. Phylogenetic diversity and specificity of bacteria closely associated with Alexandrium spp. and other phytoplankton. Appl Environ Microbiol 2005; 71:3483-94. [PMID: 16000752 PMCID: PMC1169014 DOI: 10.1128/aem.71.7.3483-3494.2005] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
While several studies have suggested that bacterium-phytoplankton interactions have the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at the species composition level. The objective of the current study was to determine whether there are specific associations between diverse phytoplankton and the bacteria that co-occur with them. We determined the phylogenetic diversity of bacterial assemblages associated with 10 Alexandrium strains and representatives of the major taxonomic groups of phytoplankton in the Gulf of Maine. For this analysis we chose xenic phytoplankton cultures that (i) represented a broad taxonomic range, (ii) represented a broad geographic range for Alexandrium spp. isolates, (iii) grew under similar cultivation conditions, (iv) had a minimal length of time since the original isolation, and (v) had been isolated from a vegetative phytoplankton cell. 16S rRNA gene fragments of most Bacteria were amplified from DNA extracted from cultures and were analyzed by denaturing gradient gel electrophoresis and sequencing. A greater number of bacterial species were shared by different Alexandrium cultures, regardless of the geographic origin, than by Alexandrium species and nontoxic phytoplankton from the Gulf of Maine. In particular, members of the Roseobacter clade showed a higher degree of association with Alexandrium than with other bacterial groups, and many sequences matched sequences reported to be associated with other toxic dinoflagellates. These results provide evidence for specificity in bacterium-phytoplankton associations.
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Affiliation(s)
- Suresh Jasti
- Center for Complex Environmental Systems, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
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