1
|
Berube PM, O'Keefe TJ, Rasmussen A, LeMaster T, Chisholm SW. Production and cross-feeding of nitrite within Prochlorococcus populations. mBio 2023; 14:e0123623. [PMID: 37404012 PMCID: PMC10470740 DOI: 10.1128/mbio.01236-23] [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: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 07/06/2023] Open
Abstract
Prochlorococcus is an abundant photosynthetic bacterium in the open ocean, where nitrogen (N) often limits phytoplankton growth. In the low-light-adapted LLI clade of Prochlorococcus, nearly all cells can assimilate nitrite (NO2-), with a subset capable of assimilating nitrate (NO3-). LLI cells are maximally abundant near the primary NO2- maximum layer, an oceanographic feature that may, in part, be due to incomplete assimilatory NO3- reduction and subsequent NO2- release by phytoplankton. We hypothesized that some Prochlorococcus exhibit incomplete assimilatory NO3- reduction and examined NO2- accumulation in cultures of three Prochlorococcus strains (MIT0915, MIT0917, and SB) and two Synechococcus strains (WH8102 and WH7803). Only MIT0917 and SB accumulated external NO2- during growth on NO3-. Approximately 20-30% of the NO3- transported into the cell by MIT0917 was released as NO2-, with the rest assimilated into biomass. We further observed that co-cultures using NO3- as the sole N source could be established for MIT0917 and Prochlorococcus strain MIT1214 that can assimilate NO2- but not NO3-. In these co-cultures, the NO2- released by MIT0917 is efficiently consumed by its partner strain, MIT1214. Our findings highlight the potential for emergent metabolic partnerships that are mediated by the production and consumption of N cycle intermediates within Prochlorococcus populations. IMPORTANCE Earth's biogeochemical cycles are substantially driven by microorganisms and their interactions. Given that N often limits marine photosynthesis, we investigated the potential for N cross-feeding within populations of Prochlorococcus, the numerically dominant photosynthetic cell in the subtropical open ocean. In laboratory cultures, some Prochlorococcus cells release extracellular NO2- during growth on NO3-. In the wild, Prochlorococcus populations are composed of multiple functional types, including those that cannot use NO3- but can still assimilate NO2-. We show that metabolic dependencies arise when Prochlorococcus strains with complementary NO2- production and consumption phenotypes are grown together on NO3-. These findings demonstrate the potential for emergent metabolic partnerships, possibly modulating ocean nutrient gradients, that are mediated by cross-feeding of N cycle intermediates.
Collapse
Affiliation(s)
- Paul M. Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Tyler J. O'Keefe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Anna Rasmussen
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Trent LeMaster
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| |
Collapse
|
2
|
Berta-Thompson JW, Thomas E, Cubillos-Ruiz A, Hackl T, Becker JW, Coe A, Biller SJ, Berube PM, Chisholm SW. Draft genomes of three closely related low light-adapted Prochlorococcus. BMC Genom Data 2023; 24:11. [PMID: 36829130 PMCID: PMC9951446 DOI: 10.1186/s12863-022-01103-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 12/21/2022] [Indexed: 02/26/2023] Open
Abstract
OBJECTIVES The marine cyanobacterium Prochlorococcus is a critical part of warm ocean ecosystems and a model for studying microbial evolution and ecology. To expand the representation of this organism's vast wild diversity in sequence collections, we performed a set of isolation efforts targeting low light-adapted Prochlorococcus. Three genomes resulting from this larger body of work are described here. DATA DESCRIPTION We present draft-quality Prochlorococcus genomes from enrichment cultures P1344, P1361, and P1363, sampled in the North Pacific. The genomes were built from Illumina paired reads assembled de novo. Supporting datasets of raw reads, assessments, and sequences from co-enriched heterotrophic marine bacteria are also provided. These three genomes represent members of the low light-adapted LLIV Prochlorococcus clade that are closely related, with 99.9% average nucleotide identity between pairs, yet vary in gene content. Expanding the powerful toolkit of Prochlorococcus genomes, these sequences provide an opportunity to study fine-scale variation and microevolutionary processes.
Collapse
Affiliation(s)
- Jessie W Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Research and Conservation, Denver Botanic Gardens, Denver, CO, 80206, USA.
| | - Elaina Thomas
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,School of Oceanography, University of Washington, Seattle, WA, 98195, USA
| | - Andrés Cubillos-Ruiz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Groningen Institute of Evolutionary Life Sciences, University of Groningen, Groningen, 9700 CC, The Netherlands
| | - Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Science and Mathematics, Alvernia University, Reading, PA, 19607, USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.,Department of Biological Sciences, Wellesley College, Wellesley, MA, 02481, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
3
|
Hogle SL, Hackl T, Bundy RM, Park J, Satinsky B, Hiltunen T, Biller S, Berube PM, Chisholm SW. Siderophores as an iron source for picocyanobacteria in deep chlorophyll maximum layers of the oligotrophic ocean. ISME J 2022; 16:1636-1646. [PMID: 35241788 PMCID: PMC9122953 DOI: 10.1038/s41396-022-01215-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
Prochlorococcus and Synechococcus are the most abundant photosynthesizing organisms in the oceans. Gene content variation among picocyanobacterial populations in separate ocean basins often mirrors the selective pressures imposed by the region's distinct biogeochemistry. By pairing genomic datasets with trace metal concentrations from across the global ocean, we show that the genomic capacity for siderophore-mediated iron uptake is widespread in Synechococcus and low-light adapted Prochlorococcus populations from deep chlorophyll maximum layers of iron-depleted regions of the oligotrophic Pacific and S. Atlantic oceans: Prochlorococcus siderophore consumers were absent in the N. Atlantic ocean (higher new iron flux) but constituted up to half of all Prochlorococcus genomes from metagenomes in the N. Pacific (lower new iron flux). Picocyanobacterial siderophore consumers, like many other bacteria with this trait, also lack siderophore biosynthesis genes indicating that they scavenge exogenous siderophores from seawater. Statistical modeling suggests that the capacity for siderophore uptake is endemic to remote ocean regions where atmospheric iron fluxes are the smallest, especially at deep chlorophyll maximum and primary nitrite maximum layers. We argue that abundant siderophore consumers at these two common oceanographic features could be a symptom of wider community iron stress, consistent with prior hypotheses. Our results provide a clear example of iron as a selective force driving the evolution of marine picocyanobacteria.
Collapse
Affiliation(s)
- Shane L Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, University of Turku, Turku, Finland.
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Randelle M Bundy
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Jiwoon Park
- School of Oceanography, University of Washington, Seattle, WA, USA
| | - Brandon Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Teppo Hiltunen
- Department of Biology, University of Turku, Turku, Finland
| | - Steven Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
4
|
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.
Collapse
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
| | | |
Collapse
|
5
|
Biller SJ, Berube PM, Dooley K, Williams M, Satinsky BM, Hackl T, Hogle SL, Coe A, Bergauer K, Bouman HA, Browning TJ, Corte DD, Hassler C, Hulston D, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Chisholm SW. Publisher Correction: Marine microbial metagenomes sampled across space and time. Sci Data 2019; 6:47. [PMID: 31113983 PMCID: PMC6529507 DOI: 10.1038/s41597-019-0054-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biological Sciences, Wellesley College, Wellesley, MA, 02481, USA.
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Keven Dooley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Madeline Williams
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Brandon M Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shane L Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kristin Bergauer
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, 1090, Austria
| | - Heather A Bouman
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK
| | - Thomas J Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24148, Germany
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, 237-0061, Japan
| | - Christel Hassler
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva, 1211, Switzerland
| | - Debbie Hulston
- National Institute of Water and Atmospheric Research, Auckland, 1010, New Zealand
| | - Jeremy E Jacquot
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | | | - Thomas Reinthaler
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, 1090, Austria
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna, 1090, Austria
| | - Taichi Yokokawa
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka, 237-0061, Japan
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| |
Collapse
|
6
|
Berube PM, Rasmussen A, Braakman R, Stepanauskas R, Chisholm SW. Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus. eLife 2019; 8:41043. [PMID: 30706847 PMCID: PMC6370341 DOI: 10.7554/elife.41043] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/31/2019] [Indexed: 12/12/2022] Open
Abstract
Intraspecific trait variability has important consequences for the function and stability of marine ecosystems. Here we examine variation in the ability to use nitrate across hundreds of Prochlorococcus genomes to better understand the modes of evolution influencing intraspecific allocation of ecologically important functions. Nitrate assimilation genes are absent in basal lineages but occur at an intermediate frequency that is randomly distributed within recently emerged clades. The distribution of nitrate assimilation genes within clades appears largely governed by vertical inheritance, gene loss, and homologous recombination. By mapping this process onto a model of Prochlorococcus’ macroevolution, we propose that niche-constructing adaptive radiations and subsequent niche partitioning set the stage for loss of nitrate assimilation genes from basal lineages as they specialized to lower light levels. Retention of these genes in recently emerged lineages has likely been facilitated by selection as they sequentially partitioned into niches where nitrate assimilation conferred a fitness benefit.
Collapse
Affiliation(s)
- Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Anna Rasmussen
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Rogier Braakman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | | | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| |
Collapse
|
7
|
Biller SJ, Berube PM, Dooley K, Williams M, Satinsky BM, Hackl T, Hogle SL, Coe A, Bergauer K, Bouman HA, Browning TJ, De Corte D, Hassler C, Hulston D, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Chisholm SW. Marine microbial metagenomes sampled across space and time. Sci Data 2018; 5:180176. [PMID: 30179232 PMCID: PMC6122167 DOI: 10.1038/sdata.2018.176] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/12/2018] [Indexed: 11/25/2022] Open
Abstract
Recent advances in understanding the ecology of marine systems have been greatly facilitated by the growing availability of metagenomic data, which provide information on the identity, diversity and functional potential of the microbial community in a particular place and time. Here we present a dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse regions of the Atlantic and Pacific Oceans. One set of metagenomes, collected on GEOTRACES cruises, captures large geographic transects at multiple depths per station. The second set represents two years of time-series data, collected at roughly monthly intervals from 3 depths at two long-term ocean sampling sites, Station ALOHA and BATS. These metagenomes contain genomic information from a diverse range of bacteria, archaea, eukaryotes and viruses. The data's utility is strengthened by the availability of extensive physical, chemical, and biological measurements associated with each sample. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of marine microbial ecosystems.
Collapse
Affiliation(s)
- Steven J. Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Paul M. Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Keven Dooley
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Madeline Williams
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brandon M. Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shane L. Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristin Bergauer
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna 1090, Austria
| | - Heather A. Bouman
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - Thomas J. Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24148, Germany
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan
| | - Christel Hassler
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 1211, Switzerland
| | - Debbie Hulston
- National Institute of Water and Atmospheric Research, Auckland 1010, New Zealand
| | - Jeremy E. Jacquot
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Thomas Reinthaler
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna 1090, Austria
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna 1090, Austria
| | - Taichi Yokokawa
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
8
|
Berube PM, Biller SJ, Hackl T, Hogle SL, Satinsky BM, Becker JW, Braakman R, Collins SB, Kelly L, Berta-Thompson J, Coe A, Bergauer K, Bouman HA, Browning TJ, De Corte D, Hassler C, Hulata Y, Jacquot JE, Maas EW, Reinthaler T, Sintes E, Yokokawa T, Lindell D, Stepanauskas R, Chisholm SW. Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments. Sci Data 2018; 5:180154. [PMID: 30179231 PMCID: PMC6122165 DOI: 10.1038/sdata.2018.154] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [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: 03/27/2018] [Accepted: 05/30/2018] [Indexed: 11/09/2022] Open
Abstract
Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.
Collapse
Affiliation(s)
- Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thomas Hackl
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shane L Hogle
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brandon M Satinsky
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jamie W Becker
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rogier Braakman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sara B Collins
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Libusha Kelly
- Department of Systems and Computational Biology, Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jessie Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Allison Coe
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kristin Bergauer
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna 1090, Austria
| | - Heather A Bouman
- Department of Earth Sciences, University of Oxford, Oxford OX1 3AN, UK
| | - Thomas J Browning
- Marine Biogeochemistry Division, GEOMAR Helmholtz Centre for Ocean Research, Kiel 24148, Germany
| | - Daniele De Corte
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan
| | - Christel Hassler
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, Geneva 1211, Switzerland
| | - Yotam Hulata
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Jeremy E Jacquot
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Thomas Reinthaler
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna 1090, Austria
| | - Eva Sintes
- Department of Limnology and Bio-Oceanography, University of Vienna, Vienna 1090, Austria
| | - Taichi Yokokawa
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology, Yokosuka 237-0061, Japan
| | - Debbie Lindell
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Ramunas Stepanauskas
- Single Cell Genomics Center, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME 04544, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| |
Collapse
|
9
|
Berube PM, Biller SJ, Kent AG, Berta-Thompson JW, Roggensack SE, Roache-Johnson KH, Ackerman M, Moore LR, Meisel JD, Sher D, Thompson LR, Campbell L, Martiny AC, Chisholm SW. Physiology and evolution of nitrate acquisition in Prochlorococcus. ISME J 2015; 9:1195-207. [PMID: 25350156 PMCID: PMC4409163 DOI: 10.1038/ismej.2014.211] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/08/2014] [Accepted: 09/23/2014] [Indexed: 01/01/2023]
Abstract
Prochlorococcus is the numerically dominant phototroph in the oligotrophic subtropical ocean and carries out a significant fraction of marine primary productivity. Although field studies have provided evidence for nitrate uptake by Prochlorococcus, little is known about this trait because axenic cultures capable of growth on nitrate have not been available. Additionally, all previously sequenced genomes lacked the genes necessary for nitrate assimilation. Here we introduce three Prochlorococcus strains capable of growth on nitrate and analyze their physiology and genome architecture. We show that the growth of high-light (HL) adapted strains on nitrate is ∼17% slower than their growth on ammonium. By analyzing 41 Prochlorococcus genomes, we find that genes for nitrate assimilation have been gained multiple times during the evolution of this group, and can be found in at least three lineages. In low-light adapted strains, nitrate assimilation genes are located in the same genomic context as in marine Synechococcus. These genes are located elsewhere in HL adapted strains and may often exist as a stable genetic acquisition as suggested by the striking degree of similarity in the order, phylogeny and location of these genes in one HL adapted strain and a consensus assembly of environmental Prochlorococcus metagenome sequences. In another HL adapted strain, nitrate utilization genes may have been independently acquired as indicated by adjacent phage mobility elements; these genes are also duplicated with each copy detected in separate genomic islands. These results provide direct evidence for nitrate utilization by Prochlorococcus and illuminate the complex evolutionary history of this trait.
Collapse
Affiliation(s)
- Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alyssa G Kent
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Jessie W Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara E Roggensack
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kathryn H Roache-Johnson
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, USA
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Marcia Ackerman
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Lisa R Moore
- Department of Biological Sciences, University of Southern Maine, Portland, ME, USA
| | - Joshua D Meisel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daniel Sher
- Department of Marine Biology, University of Haifa, Haifa, Israel
| | - Luke R Thompson
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA
| | - Lisa Campbell
- Department of Oceanography, Texas A&M University, College Station, TX, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, Irvine, CA, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| |
Collapse
|
10
|
Biller SJ, Berube PM, Berta-Thompson JW, Kelly L, Roggensack SE, Awad L, Roache-Johnson KH, Ding H, Giovannoni SJ, Rocap G, Moore LR, Chisholm SW. Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. Sci Data 2014; 1:140034. [PMID: 25977791 PMCID: PMC4421930 DOI: 10.1038/sdata.2014.34] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [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: 06/10/2014] [Accepted: 08/19/2014] [Indexed: 11/30/2022] Open
Abstract
The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity—both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.
Collapse
Affiliation(s)
- Steven J Biller
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| | - Paul M Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| | - Jessie W Berta-Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA ; Microbiology Graduate Program, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| | - Libusha Kelly
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| | - Sara E Roggensack
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| | - Lana Awad
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| | | | - Huiming Ding
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA ; Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| | | | - Gabrielle Rocap
- School of Oceanography, Center for Environmental Genomics, University of Washington , Seattle, Washington, USA
| | - Lisa R Moore
- Department of Biological Sciences, University of Southern Maine , Portland, Maine, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA ; Department of Biology, Massachusetts Institute of Technology , Cambridge, Massachusetts, USA
| |
Collapse
|
11
|
Becker JW, Berube PM, Follett CL, Waterbury JB, Chisholm SW, DeLong EF, Repeta DJ. Closely related phytoplankton species produce similar suites of dissolved organic matter. Front Microbiol 2014; 5:111. [PMID: 24748874 PMCID: PMC3975126 DOI: 10.3389/fmicb.2014.00111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [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: 07/26/2013] [Accepted: 03/05/2014] [Indexed: 11/25/2022] Open
Abstract
Production of dissolved organic matter (DOM) by marine phytoplankton supplies the majority of organic substrate consumed by heterotrophic bacterioplankton in the sea. This production and subsequent consumption converts a vast quantity of carbon, nitrogen, and phosphorus between organic and inorganic forms, directly impacting global cycles of these biologically important elements. Details regarding the chemical composition of DOM produced by marine phytoplankton are sparse, and while often assumed, it is not currently known if phylogenetically distinct groups of marine phytoplankton release characteristic suites of DOM. To investigate the relationship between specific phytoplankton groups and the DOM they release, hydrophobic phytoplankton-derived dissolved organic matter (DOMP) from eight axenic strains was analyzed using high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS). Identification of DOM features derived from Prochlorococcus, Synechococcus, Thalassiosira, and Phaeodactylum revealed DOMP to be complex and highly strain dependent. Connections between DOMP features and the phylogenetic relatedness of these strains were identified on multiple levels of phylogenetic distance, suggesting that marine phytoplankton produce DOM that in part reflects its phylogenetic origin. Chemical information regarding the size and polarity ranges of features from defined biological sources was also obtained. Our findings reveal DOMP composition to be partially conserved among related phytoplankton species, and implicate marine DOM as a potential factor influencing microbial diversity in the sea by acting as a link between autotrophic and heterotrophic microbial community structures.
Collapse
Affiliation(s)
- Jamie W. Becker
- Department of Biology, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Paul M. Berube
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Christopher L. Follett
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
| | - John B. Waterbury
- Department of Biology, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA
- Department of Biology, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Edward F. DeLong
- Department of Civil and Environmental Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Daniel J. Repeta
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic InstitutionWoods Hole, MA, USA
| |
Collapse
|
12
|
Malmstrom RR, Rodrigue S, Huang KH, Kelly L, Kern SE, Thompson A, Roggensack S, Berube PM, Henn MR, Chisholm SW. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis. ISME J 2012; 7:184-98. [PMID: 22895163 DOI: 10.1038/ismej.2012.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [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
Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world's oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome--that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome.
Collapse
Affiliation(s)
- Rex R Malmstrom
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Stein LY, Arp DJ, Berube PM, Chain PSG, Hauser L, Jetten MSM, Klotz MG, Larimer FW, Norton JM, Op den Camp HJM, Shin M, Wei X. Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environ Microbiol 2008; 9:2993-3007. [PMID: 17991028 DOI: 10.1111/j.1462-2920.2007.01409.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analysis of the structure and inventory of the genome of Nitrosomonas eutropha C91 revealed distinctive features that may explain the adaptation of N. eutropha-like bacteria to N-saturated ecosystems. Multiple gene-shuffling events are apparent, including mobilized and replicated transposition, as well as plasmid or phage integration events into the 2.66 Mbp chromosome and two plasmids (65 and 56 kbp) of N. eutropha C91. A 117 kbp genomic island encodes multiple genes for heavy metal resistance, including clusters for copper and mercury transport, which are absent from the genomes of other ammonia-oxidizing bacteria (AOB). Whereas the sequences of the two ammonia monooxygenase and three hydroxylamine oxidoreductase gene clusters in N. eutropha C91 are highly similar to those of Nitrosomonas europaea ATCC 19718, a break of synteny in the regions flanking these clusters in each genome is evident. Nitrosomonas eutropha C91 encodes four gene clusters for distinct classes of haem-copper oxidases, two of which are not found in other aerobic AOB. This diversity of terminal oxidases may explain the adaptation of N. eutropha to environments with variable O(2) concentrations and/or high concentrations of nitrogen oxides. As with N. europaea, the N. eutropha genome lacks genes for urease metabolism, likely disadvantaging nitrosomonads in low-nitrogen or acidic ecosystems. Taken together, this analysis revealed significant genomic variation between N. eutropha C91 and other AOB, even the closely related N. europaea, and several distinctive properties of the N. eutropha genome that are supportive of niche specialization.
Collapse
Affiliation(s)
- Lisa Y Stein
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Berube PM, Samudrala R, Stahl DA. Transcription of all amoC copies is associated with recovery of Nitrosomonas europaea from ammonia starvation. J Bacteriol 2007; 189:3935-44. [PMID: 17384196 PMCID: PMC1913382 DOI: 10.1128/jb.01861-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 03/14/2007] [Indexed: 11/20/2022] Open
Abstract
The chemolithotrophic ammonia-oxidizing bacterium Nitrosomonas europaea is known to be highly resistant to starvation conditions. The transcriptional response of N. europaea to ammonia addition following short- and long-term starvation was examined by primer extension and S1 nuclease protection analyses of genes encoding enzymes for ammonia oxidation (amoCAB operons) and CO(2) fixation (cbbLS), a third, lone copy of amoC (amoC(3)), and two representative housekeeping genes (glyA and rpsJ). Primer extension analysis of RNA isolated from growing, starved, and recovering cells revealed two differentially regulated promoters upstream of the two amoCAB operons. The distal sigma(70) type amoCAB promoter was constitutively active in the presence of ammonia, but the proximal promoter was only active when cells were recovering from ammonia starvation. The lone, divergent copy of amoC (amoC(3)) was expressed only during recovery. Both the proximal amoC(1,2) promoter and the amoC(3) promoter are similar to gram-negative sigma(E) promoters, thus implicating sigma(E) in the regulation of the recovery response. Although modeling of subunit interactions suggested that a nonconservative proline substitution in AmoC(3) may modify the activity of the holoenzyme, characterization of a DeltaamoC(3) strain showed no significant difference in starvation recovery under conditions evaluated. In contrast to the amo transcripts, a delayed appearance of transcripts for a gene required for CO(2) fixation (cbbL) suggested that its transcription is retarded until sufficient energy is available. Overall, these data revealed a programmed exit from starvation likely involving regulation by sigma(E) and the coordinated regulation of catabolic and anabolic genes.
Collapse
Affiliation(s)
- Paul M Berube
- Department of Microbiology, University of Washington, Seattle, WA 98195-2700, USA
| | | | | |
Collapse
|