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Cai L, Li H, Deng J, Zhou R, Zeng Q. Biological interactions with Prochlorococcus: implications for the marine carbon cycle. Trends Microbiol 2024; 32:280-291. [PMID: 37722980 DOI: 10.1016/j.tim.2023.08.011] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/20/2023]
Abstract
The unicellular picocyanobacterium Prochlorococcus is the most abundant photoautotroph and contributes substantially to global CO2 fixation. In the vast euphotic zones of the open ocean, Prochlorococcus converts CO2 into organic compounds and supports diverse organisms, forming an intricate network of interactions that regulate the magnitude of carbon cycling and storage in the ocean. An understanding of the biological interactions with Prochlorococcus is critical for accurately estimating the contributions of Prochlorococcus and interacting organisms to the marine carbon cycle. This review synthesizes the primary production contributed by Prochlorococcus in the global ocean. We outline recent progress on the interactions of Prochlorococcus with heterotrophic bacteria, phages, and grazers that multifacetedly determine Prochlorococcus carbon production and fate. We discuss that climate change might affect the biological interactions with Prochlorococcus and thus the marine carbon cycle.
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Affiliation(s)
- Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China
| | - Junwei Deng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ruiqian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; HKUST Shenzhen-Hong Kong Collaborative Innovation Research Institute, Shenzhen, China; Center for Ocean Research in Hong Kong and Macau, The Hong Kong University of Science and Technology, Hong Kong, China.
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2
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Tschoeke D, Salazar VW, Vidal L, Campeão M, Swings J, Thompson F, Thompson C. Unlocking the Genomic Taxonomy of the Prochlorococcus Collective. Microb Ecol 2020; 80:546-558. [PMID: 32468160 DOI: 10.1007/s00248-020-01526-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 02/13/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. Novel genomic data for the PC prompted us to revisit this group, applying the current methods used in genomic taxonomy. As a result, we were able to distinguish the five genera: Prochlorococcus, Eurycolium, Prolificoccus, Thaumococcus, and Riococcus. The novel genera have distinct genomic and ecological attributes.
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Affiliation(s)
- Diogo Tschoeke
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Vinicius W Salazar
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Livia Vidal
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Mariana Campeão
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Jean Swings
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
- Laboratory of Microbiology, Ghent University, Gent, Belgium
| | - Fabiano Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Cristiane Thompson
- Laboratory of Microbiology, SAGE-COPPE and Institute of Biology, Federal University of Rio de Janeiro, Av. Carlos Chagas Fo 373, Rio de Janeiro, RJ, 21941-902, Brazil.
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3
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Shilova IN, Magasin JD, Mills MM, Robidart JC, Turk-Kubo KA, Zehr JP. Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system. PLoS One 2020; 15:e0231771. [PMID: 32310982 PMCID: PMC7170224 DOI: 10.1371/journal.pone.0231771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 10/22/2019] [Accepted: 03/31/2020] [Indexed: 11/18/2022] Open
Abstract
Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.
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Affiliation(s)
- Irina N. Shilova
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
| | - Jonathan D. Magasin
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Matthew M. Mills
- Department of Earth System Science, Stanford University, Stanford, California, United States of America
| | - Julie C. Robidart
- Ocean Technology and Engineering, National Oceanography Centre, Southampton, England, United Kingdom
| | - Kendra A. Turk-Kubo
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jonathan P. Zehr
- Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail: (INS); (JPZ)
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4
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Koch H, Germscheid N, Freese HM, Noriega-Ortega B, Lücking D, Berger M, Qiu G, Marzinelli EM, Campbell AH, Steinberg PD, Overmann J, Dittmar T, Simon M, Wietz M. Genomic, metabolic and phenotypic variability shapes ecological differentiation and intraspecies interactions of Alteromonas macleodii. Sci Rep 2020; 10:809. [PMID: 31964928 PMCID: PMC6972757 DOI: 10.1038/s41598-020-57526-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/23/2019] [Indexed: 01/28/2023] Open
Abstract
Ecological differentiation between strains of bacterial species is shaped by genomic and metabolic variability. However, connecting genotypes to ecological niches remains a major challenge. Here, we linked bacterial geno- and phenotypes by contextualizing pangenomic, exometabolomic and physiological evidence in twelve strains of the marine bacterium Alteromonas macleodii, illuminating adaptive strategies of carbon metabolism, microbial interactions, cellular communication and iron acquisition. In A. macleodii strain MIT1002, secretion of amino acids and the unique capacity for phenol degradation may promote associations with Prochlorococcus cyanobacteria. Strain 83-1 and three novel Pacific isolates, featuring clonal genomes despite originating from distant locations, have profound abilities for algal polysaccharide utilization but without detrimental implications for Ecklonia macroalgae. Degradation of toluene and xylene, mediated via a plasmid syntenic to terrestrial Pseudomonas, was unique to strain EZ55. Benzoate degradation by strain EC673 related to a chromosomal gene cluster shared with the plasmid of A. mediterranea EC615, underlining that mobile genetic elements drive adaptations. Furthermore, we revealed strain-specific production of siderophores and homoserine lactones, with implications for nutrient acquisition and cellular communication. Phenotypic variability corresponded to different competitiveness in co-culture and geographic distribution, indicating linkages between intraspecific diversity, microbial interactions and biogeography. The finding of "ecological microdiversity" helps understanding the widespread occurrence of A. macleodii and contributes to the interpretation of bacterial niche specialization, population ecology and biogeochemical roles.
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Affiliation(s)
- Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
- Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Nora Germscheid
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Heike M Freese
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Beatriz Noriega-Ortega
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Dominik Lücking
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Martine Berger
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Galaxy Qiu
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Western Sydney University, Hawkesbury, Australia
| | - Ezequiel M Marzinelli
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
- University of Sydney, Camperdown, Australia
| | - Alexandra H Campbell
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- University of Sunshine Coast, Sunshine Coast, Australia
| | - Peter D Steinberg
- Centre for Marine Science and Innovation, University of New South Wales, Kensington, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, Australia
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Thorsten Dittmar
- ICBM-MPI Bridging Group for Marine Geochemistry, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
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5
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Zinser ER. Cross-protection from hydrogen peroxide by helper microbes: the impacts on the cyanobacterium Prochlorococcus and other beneficiaries in marine communities. Environ Microbiol Rep 2018; 10:399-411. [PMID: 29411546 DOI: 10.1111/1758-2229.12625] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/25/2018] [Accepted: 01/27/2017] [Indexed: 05/27/2023]
Abstract
Hydrogen peroxide (HOOH) is a reactive oxygen species, derived from molecular oxygen, that is capable of damaging microbial cells. Surprisingly, the HOOH defence systems of some aerobes in the oxygenated marine environments are critically depleted, relative to model aerobes. For instance, the gene encoding catalase is absent in the numerically dominant photosynthetic cyanobacterium, Prochlorococcus. Accordingly, Prochlorococcus is highly susceptible to HOOH when exposed as pure cultures. Pure cultures do not exist in the marine environment, however. Catalase-positive community members can remove HOOH from the seawater medium, thus lowering the threat to Prochlorococcus and any other member that likewise lacks their own catalase. This cross-protection may constitute a loosely defined symbiosis, whereby the catalase-positive helper cells may benefit through the acquisition of nutrients released by the beneficiaries such as Prochlorococcus. Other members of the community that may be helped by the catalase-positive cells may include some lineages of Synechococcus - the sister genus of Prochlorococcus - as well as some lineages of SAR11 and ammonia oxidizing archaea and bacteria. The co-occurrence of catalase-positive and -negative members suggests that cross-protection from HOOH-mediated oxidative stress may play an important role in the construction of the marine microbial community.
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Affiliation(s)
- Erik R Zinser
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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6
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Kamennaya NA, Kennaway G, Fuchs BM, Zubkov MV. "Pomacytosis"-Semi-extracellular phagocytosis of cyanobacteria by the smallest marine algae. PLoS Biol 2018; 16:e2003502. [PMID: 29304142 PMCID: PMC5773223 DOI: 10.1371/journal.pbio.2003502] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 07/03/2017] [Revised: 01/18/2018] [Accepted: 12/15/2017] [Indexed: 11/18/2022] Open
Abstract
The smallest algae, less than 3 μm in diameter, are the most abundant eukaryotes of the World Ocean. Their feeding on planktonic bacteria of similar size is globally important but physically enigmatic. Tiny algal cells tightly packed with the voluminous chloroplasts, nucleus, and mitochondria appear to have insufficient organelle-free space for prey internalization. Here, we present the first direct observations of how the 1.3-μm algae, which are only 1.6 times bigger in diameter than their prey, hold individual Prochlorococcus cells in their open hemispheric cytostomes. We explain this semi-extracellular phagocytosis by the cell size limitation of the predatory alga, identified as the Braarudosphaera haptophyte with a nitrogen (N2)-fixing endosymbiont. Because the observed semi-extracellular phagocytosis differs from all other types of protistan phagocytosis, we propose to name it "pomacytosis" (from the Greek πώμα for "plug").
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Affiliation(s)
- Nina A. Kamennaya
- Ocean Biogeochemistry & Ecosystems Research Group, National Oceanography Centre, Southampton, United Kingdom
| | - Gabrielle Kennaway
- Imaging and Analysis Centre, Science Facilities, Natural History Museum, London, United Kingdom
| | | | - Mikhail V. Zubkov
- Ocean Biogeochemistry & Ecosystems Research Group, National Oceanography Centre, Southampton, United Kingdom
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7
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8
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Neale PJ, Thomas BC. Inhibition by ultraviolet and photosynthetically available radiation lowers model estimates of depth-integrated picophytoplankton photosynthesis: global predictions for Prochlorococcus and Synechococcus. Glob Chang Biol 2017; 23:293-306. [PMID: 27178715 DOI: 10.1111/gcb.13356] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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: 03/01/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 06/05/2023]
Abstract
Phytoplankton photosynthesis is often inhibited by ultraviolet (UV) and intense photosynthetically available radiation (PAR), but the effects on ocean productivity have received little consideration aside from polar areas subject to periodic enhanced UV-B due to depletion of stratospheric ozone. A more comprehensive assessment is important for understanding the contribution of phytoplankton production to the global carbon budget, present and future. Here, we consider responses in the temperate and tropical mid-ocean regions typically dominated by picophytoplankton including the prokaryotic lineages, Prochlorococcus and Synechococcus. Spectral models of photosynthetic response for each lineage were constructed using model strains cultured at different growth irradiances and temperatures. In the model, inhibition becomes more severe once exposure exceeds a threshold (Emax ) related to repair capacity. Model parameters are presented for Prochlorococcus adding to those previously presented for Synechococcus. The models were applied to estimate midday, water column photosynthesis based on an atmospheric model of spectral radiation, satellite-derived spectral water transparency and temperature. Based on a global survey of inhibitory exposure severity, a full-latitude section of the mid-Pacific and near-equatorial region of the east Pacific were identified as representative regions for prediction of responses over the entire water column. Comparing predictions integrated over the water column including versus excluding inhibition, production was 7-28% lower due to inhibition depending on strain and site conditions. Inhibition was consistently greater for Prochlorococcus compared to two strains of Synechococcus. Considering only the surface mixed layer, production was inhibited 7-73%. On average, including inhibition lowered estimates of midday productivity around 20% for the modeled region of the Pacific with UV accounting for two-thirds of the reduction. In contrast, most other productivity models either ignore inhibition or only include PAR inhibition. Incorporation of Emax model responses into an existing spectral model of depth-integrated, daily production will enable efficient global predictions of picophytoplankton productivity including inhibition.
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Affiliation(s)
- Patrick J Neale
- Smithsonian Environmental Research Center, Edgewater, MD, 21037, USA
| | - Brian C Thomas
- Department of Physics and Astronomy, Washburn University, 1700 SW College Ave, Topeka, KS, 66604, USA
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Martiny AC, Ma L, Mouginot C, Chandler JW, Zinser ER. Interactions between Thermal Acclimation, Growth Rate, and Phylogeny Influence Prochlorococcus Elemental Stoichiometry. PLoS One 2016; 11:e0168291. [PMID: 27936127 PMCID: PMC5148161 DOI: 10.1371/journal.pone.0168291] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 09/11/2016] [Accepted: 11/29/2016] [Indexed: 11/23/2022] Open
Abstract
Variability in plankton elemental requirements can be important for global ocean biogeochemistry but we currently have a limited understanding of how ocean temperature influences the plankton C/N/P ratio. Multiple studies have put forward a 'translation-compensation' hypothesis to describe the positive relationship between temperature and plankton N/P or C/P as cells should have lower demand for P-rich ribosomes and associated depressed QP when growing at higher temperature. However, temperature affects many cellular processes beyond translation with unknown outcomes on cellular elemental composition. In addition, the impact of temperature on growth and elemental composition of phytoplankton is likely modulated by the life history and growth rate of the organism. To test the direct and indirect (via growth rate changes) effect of temperature, we here analyzed the elemental composition and ratios in six strains affiliated with the globally abundant marine Cyanobacteria Prochlorococcus. We found that temperature had a significant positive effect on the carbon and nitrogen cell quota, whereas no clear trend was observed for the phosphorus cell quota. The effect on N/P and C/P were marginally significantly positive across Prochlorococcus. The elemental composition and ratios of individual strains were also affected but we found complex interactions between the strain identity, temperature, and growth rate in controlling the individual elemental ratios in Prochlorococcus and no common trends emerged. Thus, the observations presented here does not support the 'translation-compensation' theory and instead suggest unique cellular elemental effects as a result of rising temperature among closely related phytoplankton lineages. Thus, the biodiversity context should be considered when predicting future elemental ratios and how cycles of carbon, nitrogen, and phosphorus may change in a future ocean.
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Affiliation(s)
- Adam C. Martiny
- Department of Earth System Science, University of California, Irvine, California, United States of America
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Lanying Ma
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Céline Mouginot
- Department of Earth System Science, University of California, Irvine, California, United States of America
| | - Jeremy W. Chandler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Erik R. Zinser
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
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Hellweger FL, van Sebille E, Calfee BC, Chandler JW, Zinser ER, Swan BK, Fredrick ND. The Role of Ocean Currents in the Temperature Selection of Plankton: Insights from an Individual-Based Model. PLoS One 2016; 11:e0167010. [PMID: 27907181 PMCID: PMC5131974 DOI: 10.1371/journal.pone.0167010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 08/23/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Biogeography studies that correlate the observed distribution of organisms to environmental variables are typically based on local conditions. However, in cases with substantial translocation, like planktonic organisms carried by ocean currents, selection may happen upstream and local environmental factors may not be representative of those that shaped the local population. Here we use an individual-based model of microbes in the global surface ocean to explore this effect for temperature. We simulate up to 25 million individual cells belonging to up to 50 species with different temperature optima. Microbes are moved around the globe based on a hydrodynamic model, and grow and die based on local temperature. We quantify the role of currents using the “advective temperature differential” metric, which is the optimum temperature of the most abundant species from the model with advection minus that from the model without advection. This differential depends on the location and can be up to 4°C. Poleward-flowing currents, like the Gulf Stream, generally experience cooling and the differential is positive. We apply our results to three global datasets. For observations of optimum growth temperature of phytoplankton, accounting for the effect of currents leads to a slightly better agreement with observations, but there is large variability and the improvement is not statistically significant. For observed Prochlorococcus ecotype ratios and metagenome nucleotide divergence, accounting for advection improves the correlation significantly, especially in areas with relatively strong poleward or equatorward currents.
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Affiliation(s)
- Ferdi L. Hellweger
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail:
| | - Erik van Sebille
- Grantham Institute & Department of Physics, Imperial College London, London, United Kingdom
- ARC Centre of Excellence for Climate System Science, Climate Change Research Centre, University of New South Wales, Sydney, Australia
| | - Benjamin C. Calfee
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Jeremy W. Chandler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Erik R. Zinser
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brandon K. Swan
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, United States of America
| | - Neil D. Fredrick
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, United States of America
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11
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Komatsu H, Wada K, Kanjoh T, Miyashita H, Sato M, Kawachi M, Kobayashi M. Unique chlorophylls in picoplankton Prochlorococcus sp. "Physicochemical properties of divinyl chlorophylls, and the discovery of monovinyl chlorophyll b as well as divinyl chlorophyll b in the species Prochlorococcus NIES-2086". Photosynth Res 2016; 130:445-467. [PMID: 27334004 DOI: 10.1007/s11120-016-0283-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/31/2015] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
In this review, we introduce our recent studies on divinyl chlorophylls functioning in unique marine picoplankton Prochlorococcus sp. (1) Essential physicochemical properties of divinyl chlorophylls are compared with those of monovinyl chlorophylls; separation by normal-phase and reversed-phase high-performance liquid chromatography with isocratic eluent mode, absorption spectra in four organic solvents, fluorescence information (emission spectra, quantum yields, and life time), circular dichroism spectra, mass spectra, nuclear magnetic resonance spectra, and redox potentials. The presence of a mass difference of 278 in the mass spectra between [M+H]+ and the ions indicates the presence of a phytyl tail in all the chlorophylls. (2) Precise high-performance liquid chromatography analyses show divinyl chlorophyll a' and divinyl pheophytin a as the minor key components in four kinds of Prochlorococcus sp.; neither monovinyl chlorophyll a' nor monovinyl pheophytin a is detected, suggesting that the special pair in photosystem I and the primary electron acceptor in photosystem II are not monovinyl but divinyl-type chlorophylls. (3) Only Prochlorococcus sp. NIES-2086 possesses both monovinyl chlorophyll b and divinyl chlorophyll b, while any other monovinyl-type chlorophylls are absent in this strain. Monovinyl chlorophyll b is not detected at all in the other three strains. Prochlorococcus sp. NIES-2086 is the first example that has both monovinyl chlorophyll b as well as divinyl chlorophylls a/b as major chlorophylls.
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Affiliation(s)
- Hirohisa Komatsu
- Division of Materials Science, Faculty of Pure and Applied Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan
| | - Katsuhiro Wada
- Division of Materials Science, Faculty of Pure and Applied Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan
| | - Terumitsu Kanjoh
- Division of Materials Science, Faculty of Pure and Applied Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environment Studies, Kyoto University, Kyoto, 606-8501, Japan
| | - Mayumi Sato
- National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masami Kobayashi
- Division of Materials Science, Faculty of Pure and Applied Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8573, Japan.
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12
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Bagby SC, Chisholm SW. Response of Prochlorococcus to varying CO2:O2 ratios. ISME J 2015; 9:2232-45. [PMID: 25848872 PMCID: PMC4579476 DOI: 10.1038/ismej.2015.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 02/06/2015] [Accepted: 02/12/2015] [Indexed: 11/08/2022]
Abstract
Carbon fixation has a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus-the most abundant phototroph in the oligotrophic oceans-the carbon-concentrating mechanism is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. Thus, we examined how CO2:O2 gas balance influenced growth and chlorophyll fluorescence in Prochlorococcus strain MED4. Under O2 limitation, per-cell chlorophyll fluorescence fell at all CO2 levels, but still permitted substantial growth at moderate and high CO2. Under CO2 limitation, we observed little growth at any O2 level, although per-cell chlorophyll fluorescence fell less sharply when O2 was available. We explored this pattern further by monitoring genome-wide transcription in cells shocked with acute limitation of CO2, O2 or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, both CO2 limitation conditions initially evoked a transcriptional response that resembled the pattern previously seen in high-light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen has a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.
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Affiliation(s)
- Sarah C Bagby
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sallie W Chisholm
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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13
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Morris JJ, Johnson ZI, Szul MJ, Keller M, Zinser ER. Dependence of the cyanobacterium Prochlorococcus on hydrogen peroxide scavenging microbes for growth at the ocean's surface. PLoS One 2011; 6:e16805. [PMID: 21304826 PMCID: PMC3033426 DOI: 10.1371/journal.pone.0016805] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [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: 10/04/2010] [Accepted: 12/31/2010] [Indexed: 01/08/2023] Open
Abstract
The phytoplankton community in the oligotrophic open ocean is numerically dominated by the cyanobacterium Prochlorococcus, accounting for approximately half of all photosynthesis. In the illuminated euphotic zone where Prochlorococcus grows, reactive oxygen species are continuously generated via photochemical reactions with dissolved organic matter. However, Prochlorococcus genomes lack catalase and additional protective mechanisms common in other aerobes, and this genus is highly susceptible to oxidative damage from hydrogen peroxide (HOOH). In this study we showed that the extant microbial community plays a vital, previously unrecognized role in cross-protecting Prochlorococcus from oxidative damage in the surface mixed layer of the oligotrophic ocean. Microbes are the primary HOOH sink in marine systems, and in the absence of the microbial community, surface waters in the Atlantic and Pacific Ocean accumulated HOOH to concentrations that were lethal for Prochlorococcus cultures. In laboratory experiments with the marine heterotroph Alteromonas sp., serving as a proxy for the natural community of HOOH-degrading microbes, bacterial depletion of HOOH from the extracellular milieu prevented oxidative damage to the cell envelope and photosystems of co-cultured Prochlorococcus, and facilitated the growth of Prochlorococcus at ecologically-relevant cell concentrations. Curiously, the more recently evolved lineages of Prochlorococcus that exploit the surface mixed layer niche were also the most sensitive to HOOH. The genomic streamlining of these evolved lineages during adaptation to the high-light exposed upper euphotic zone thus appears to be coincident with an acquired dependency on the extant HOOH-consuming community. These results underscore the importance of (indirect) biotic interactions in establishing niche boundaries, and highlight the impacts that community-level responses to stress may have in the ecological and evolutionary outcomes for co-existing species.
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Affiliation(s)
- J. Jeffrey Morris
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Zackary I. Johnson
- Nicholas School of the Environment, Duke University Marine Laboratory, Beaufort, North Carolina, United States of America
| | - Martin J. Szul
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Martin Keller
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Erik R. Zinser
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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14
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Abstract
Prochlorococcus is the key phytoplanktonic organism of tropical gyres, large ocean regions that are depleted of the essential macronutrients needed for photosynthesis and cell growth. This cyanobacterium has adapted itself to oligotrophy by minimizing the resources necessary for life through a drastic reduction of cell and genome sizes. This rarely observed strategy in free-living organisms has conferred on Prochlorococcus a considerable advantage over other phototrophs, including its closest relative Synechococcus, for life in this vast yet little variable ecosystem. However, this strategy seems to reach its limits in the upper layer of the S Pacific gyre, the most oligotrophic region of the world ocean. By losing some important genes and/or functions during evolution, Prochlorococcus has seemingly become dependent on co-occurring microorganisms. In this review, we present some of the recent advances in the ecology, biology, and evolution of Prochlorococcus, which because of its ecological importance and tiny genome is rapidly imposing itself as a model organism in environmental microbiology.
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Affiliation(s)
- Frédéric Partensky
- UPMC-Université Paris 06, Station Biologique, 29682 Roscoff cedex, France.
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15
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Zinser ER, Lindell D, Johnson ZI, Futschik ME, Steglich C, Coleman ML, Wright MA, Rector T, Steen R, McNulty N, Thompson LR, Chisholm SW. Choreography of the transcriptome, photophysiology, and cell cycle of a minimal photoautotroph, prochlorococcus. PLoS One 2009; 4:e5135. [PMID: 19352512 PMCID: PMC2663038 DOI: 10.1371/journal.pone.0005135] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [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: 12/23/2008] [Accepted: 01/19/2009] [Indexed: 01/11/2023] Open
Abstract
The marine cyanobacterium Prochlorococcus MED4 has the smallest genome and cell size of all known photosynthetic organisms. Like all phototrophs at temperate latitudes, it experiences predictable daily variation in available light energy which leads to temporal regulation and partitioning of key cellular processes. To better understand the tempo and choreography of this minimal phototroph, we studied the entire transcriptome of the cell over a simulated daily light-dark cycle, and placed it in the context of diagnostic physiological and cell cycle parameters. All cells in the culture progressed through their cell cycles in synchrony, thus ensuring that our measurements reflected the behavior of individual cells. Ninety percent of the annotated genes were expressed, and 80% had cyclic expression over the diel cycle. For most genes, expression peaked near sunrise or sunset, although more subtle phasing of gene expression was also evident. Periodicities of the transcripts of genes involved in physiological processes such as in cell cycle progression, photosynthesis, and phosphorus metabolism tracked the timing of these activities relative to the light-dark cycle. Furthermore, the transitions between photosynthesis during the day and catabolic consumption of energy reserves at night— metabolic processes that share some of the same enzymes — appear to be tightly choreographed at the level of RNA expression. In-depth investigation of these patterns identified potential regulatory proteins involved in balancing these opposing pathways. Finally, while this analysis has not helped resolve how a cell with so little regulatory capacity, and a ‘deficient’ circadian mechanism, aligns its cell cycle and metabolism so tightly to a light-dark cycle, it does provide us with a valuable framework upon which to build when the Prochlorococcus proteome and metabolome become available.
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Affiliation(s)
- Erik R. Zinser
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Debbie Lindell
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Zackary I. Johnson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Oceanography, University of Hawaii, Honolulu, Hawaii, United States of America
| | - Matthias E. Futschik
- Institute of Theoretical Biology, Humboldt University, Berlin, Germany
- Center for Molecular and Structural Biomedicine, University of Algarve, Faro, Portugal
| | - Claudia Steglich
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Maureen L. Coleman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Matthew A. Wright
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Trent Rector
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert Steen
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nathan McNulty
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Luke R. Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sallie W. Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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16
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Coleman ML, Chisholm SW. Code and context: Prochlorococcus as a model for cross-scale biology. Trends Microbiol 2007; 15:398-407. [PMID: 17693088 DOI: 10.1016/j.tim.2007.07.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [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: 04/06/2007] [Revised: 06/19/2007] [Accepted: 07/27/2007] [Indexed: 11/28/2022]
Abstract
Prochlorococcus is a simple cyanobacterium that is abundant throughout large regions of the oceans, and has become a useful model for studying the nature and regulation of biological diversity across all scales of complexity. Recent work has revealed that environmental factors such as light, nutrients and predation influence diversity in different ways, changing our image of the structure and dynamics of the global Prochlorococcus population. Advances in metagenomics, transcription profiling and global ecosystem modeling promise to deliver an even greater understanding of this system and further demonstrate the power of cross-scale systems biology.
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Affiliation(s)
- Maureen L Coleman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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17
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Michelou VK, Cottrell MT, Kirchman DL. Light-stimulated bacterial production and amino acid assimilation by cyanobacteria and other microbes in the North Atlantic ocean. Appl Environ Microbiol 2007; 73:5539-46. [PMID: 17630296 PMCID: PMC2042078 DOI: 10.1128/aem.00212-07] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We examined the contribution of photoheterotrophic microbes--those capable of light-mediated assimilation of organic compounds--to bacterial production and amino acid assimilation along a transect from Florida to Iceland from 28 May to 9 July 2005. Bacterial production (leucine incorporation at a 20 nM final concentration) was on average 30% higher in light than in dark-incubated samples, but the effect varied greatly (3% to 60%). To further characterize this light effect, we examined the abundance of potential photoheterotrophs and measured their contribution to bacterial production and amino acid assimilation (0.5 nM addition) using flow cytometry. Prochlorococcus and Synechococcus were abundant in surface waters where light-dependent leucine incorporation was observed, whereas aerobic anoxygenic phototrophic bacteria were abundant but did not correlate with the light effect. The per-cell assimilation rates of Prochlorococcus and Synechococcus were comparable to or higher than those of other prokaryotes, especially in the light. Picoeukaryotes also took up leucine (20 nM) and other amino acids (0.5 nM), but rates normalized to biovolume were much lower than those of prokaryotes. Prochlorococcus was responsible for 80% of light-stimulated bacterial production and amino acid assimilation in surface waters south of the Azores, while Synechococcus accounted for on average 12% of total assimilation. However, nearly 40% of the light-stimulated leucine assimilation was not accounted for by these groups, suggesting that assimilation by other microbes is also affected by light. Our results clarify the contribution of cyanobacteria to photoheterotrophy and highlight the potential role of other photoheterotrophs in biomass production and dissolved-organic-matter assimilation.
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Affiliation(s)
- Vanessa K Michelou
- College of Marine and Earth Studies, University of Delaware, 700 Pilottown Road, Lewes, DE 19958, USA
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18
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Abstract
A marine ecosystem model seeded with many phytoplankton types, whose physiological traits were randomly assigned from ranges defined by field and laboratory data, generated an emergent community structure and biogeography consistent with observed global phytoplankton distributions. The modeled organisms included types analogous to the marine cyanobacterium Prochlorococcus. Their emergent global distributions and physiological properties simultaneously correspond to observations. This flexible representation of community structure can be used to explore relations between ecosystems, biogeochemical cycles, and climate change.
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Affiliation(s)
- Michael J Follows
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54-1514 MIT, Cambridge, MA 02139, USA.
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Pandhal J, Wright PC, Biggs CA. A Quantitative Proteomic Analysis of Light Adaptation in a Globally Significant Marine Cyanobacterium Prochlorococcus marinus MED4. J Proteome Res 2007; 6:996-1005. [PMID: 17298086 DOI: 10.1021/pr060460c] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [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: 11/28/2022]
Abstract
In this study, we conducted biological and technical replicate proteomic experiments using isobaric tags for relative and absolute quantification (iTRAQ), to elucidate the light adaptation strategies of Prochlorococcus marinus MED4. The MED4 strain is adapted to an oceanic environment characterized by low nutrient levels, and ever-changing light intensities. Approximately 11% of the proteome was identified, with an average coefficient of variation of iTRAQ quantification values of 0.15. Fifteen proteins were deemed to be statistically and significantly differentially expressed in changing light intensities, particularly the down-regulation of photosystem-related proteins, and the up-regulation of the stress-related chaperone GroEL in high light compared to low light.
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Affiliation(s)
- Jagroop Pandhal
- Biological and Environmental Systems Group, Department of Chemical and Process Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, United Kingdom
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20
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Ahlgren NA, Rocap G, Chisholm SW. Measurement of Prochlorococcus ecotypes using real-time polymerase chain reaction reveals different abundances of genotypes with similar light physiologies. Environ Microbiol 2006; 8:441-54. [PMID: 16478451 DOI: 10.1111/j.1462-2920.2005.00910.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [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: 11/30/2022]
Abstract
Prochlorococcus is a marine cyanobacterium which is found at high abundances in world's tropical and subtropical oligotrophic oceans. The genus Prochlorococcus can be divided into two major groups based on light physiology. Both of these groups can be further subdivided into genetically distinct lineages, or ecotypes. Real-time polymerase chain reaction (PCR) assays based on sequence differences in the 16S-23S rDNA internal transcribed spacer or the 23S rDNA were developed to examine the distribution of each ecotype in the field. The real-time PCR assays enabled linear quantification of concentrations ranging from 10 to 4 x 10(5) cells ml(-1). These assays were applied to a stratified water column in the Sargasso Sea. The majority of Prochlorococcus cells above 110 m belonged to the one of the low chlorophyll b/a ratio (high-light adapted) ecotypes, while two types of high chlorophyll b/a ratio (low-light adapted) cells dominated below 110 m. The other three types were found at significantly lower numbers or not detected at all. Differences in the abundance of ecotypes within the major light physiology groupings suggest that other factors, such as nutrient utilization and differential mortality, are driving their relative distributions. Real-time PCR assays will enable further exploration of these factors and temporal and geographic variability in ecotype abundance.
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Affiliation(s)
- Nathan A Ahlgren
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology 48-425, Cambridge, MA 02139, USA
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21
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Bouman HA, Ulloa O, Scanlan DJ, Zwirglmaier K, Li WKW, Platt T, Stuart V, Barlow R, Leth O, Clementson L, Lutz V, Fukasawa M, Watanabe S, Sathyendranath S. Oceanographic Basis of the Global Surface Distribution of Prochlorococcus Ecotypes. Science 2006; 312:918-21. [PMID: 16690867 DOI: 10.1126/science.1122692] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [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: 11/02/2022]
Abstract
By using data collected during a continuous circumnavigation of the Southern Hemisphere, we observed clear patterns in the population-genetic structure of Prochlorococcus, the most abundant photosynthetic organism on Earth, between and within the three Southern Subtropical Gyres. The same mechanisms that were previously invoked to account for the vertical distribution of ecotypes at local scales accounted for the global (horizontal) patterns we observed. Basin-scale and seasonal variations in the structure and strength of vertical stratification provide a basis for understanding large-scale horizontal distribution in genetic and physiological traits of Prochlorococcus, and perhaps of marine microbial communities in general.
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Affiliation(s)
- Heather A Bouman
- Laboratorio de Procesos Oceanográficos y Clima, Departamento de Oceanografía, and Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental, Universidad de Concepción, Casilla 160-C, Concepción, Chile.
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22
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Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 2006; 311:1737-40. [PMID: 16556835 DOI: 10.1126/science.1118052] [Citation(s) in RCA: 503] [Impact Index Per Article: 27.9] [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: 11/02/2022]
Abstract
Prochlorococcus is the numerically dominant phytoplankter in the oligotrophic oceans, accounting for up to half of the photosynthetic biomass and production in some regions. Here, we describe how the abundance of six known ecotypes, which have small subunit ribosomal RNA sequences that differ by less than 3%, changed along local and basin-wide environmental gradients in the Atlantic Ocean. Temperature was significantly correlated with shifts in ecotype abundance, and laboratory experiments confirmed different temperature optima and tolerance ranges for cultured strains. Light, nutrients, and competitor abundances also appeared to play a role in shaping different distributions.
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Affiliation(s)
- Zackary I Johnson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar Street 48-419, Cambridge, MA 02139, USA
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23
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24
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Abstract
Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.
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Affiliation(s)
- Maureen L Coleman
- Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 15 Vassar Street, Cambridge, MA 02139, USA
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25
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Steglich C, Frankenberg-Dinkel N, Penno S, Hess WR. A green light-absorbing phycoerythrin is present in the high-light-adapted marine cyanobacterium Prochlorococcus sp. MED4. Environ Microbiol 2005; 7:1611-8. [PMID: 16156734 DOI: 10.1111/j.1462-2920.2005.00855.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [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: 11/27/2022]
Abstract
In the high-light-adapted unicellular marine cyanobacterium Prochlorococcus sp. MED4 the cpeB gene is the only gene coding for a structural phycobiliprotein. The absence of any other phycoerythrin gene in the fully sequenced genome of this organism, the previous inability to detect a gene product, and the mutation of two out of four cysteine residues, normally involved in binding chromophores, suggested that MED4-cpeB might not code for a functional protein. Here, transcription of MED4-cpeB at a low level was detected and the transcriptional start site was mapped. Enrichment of the protein identified phycoerythrobilin as its sole chromophore in vivo, which was confirmed by chromophorylation assays in vitro using the recombinant protein. Phycourobilin is the major chromophore in low-light-adapted Prochlorococcus ecotypes such as strain SS120. Therefore, spectrally tuned phycoerythrins are a characteristic feature of distinct Prochlorococcus ecotypes. Further in vitro mutagenesis experiments replacing one or both cysteines C61R/C82S by arginine or serine, respectively, revealed that only Cys82 is required for chromophore binding. Thus, an unusual green light-absorbing phycoerythrin evolved in the high-light-adapted ecotypes of Prochlorococcus, which potentially serves as a photoreceptor.
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Affiliation(s)
- Claudia Steglich
- Department of Biology/Genetics, Humboldt University, Chausseestrasse 117, D-10115 Berlin, Germany
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Sommaruga R, Hofer JS, Alonso-Sáez L, Gasol JM. Differential sunlight sensitivity of picophytoplankton from surface Mediterranean Coastal Waters. Appl Environ Microbiol 2005; 71:2154-7. [PMID: 15812050 PMCID: PMC1082567 DOI: 10.1128/aem.71.4.2154-2157.2005] [Citation(s) in RCA: 44] [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] [Indexed: 11/20/2022] Open
Abstract
We tested the sensitivity of coastal picophytoplankton exposed to natural sunlight in short-term experiments. Cell abundance and cell-specific chlorophyll fluorescence were significantly reduced in Prochlorococcus spp. but not in Synechococcus, whereas picoeukaryotes had an intermediate response. These results are the first direct evidence of a differential sensitivity to sunlight of these ubiquitous marine members of unicellular phytoplankton.
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Affiliation(s)
- Ruben Sommaruga
- Laboratory of Aquatic Photobiology and Plankton Ecology, Institute of Zoology and Limnology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria.
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27
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García-Fernández JM, de Marsac NT, Diez J. Streamlined regulation and gene loss as adaptive mechanisms in Prochlorococcus for optimized nitrogen utilization in oligotrophic environments. Microbiol Mol Biol Rev 2005; 68:630-8. [PMID: 15590777 PMCID: PMC539009 DOI: 10.1128/mmbr.68.4.630-638.2004] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [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: 01/10/2023] Open
Abstract
Prochlorococcus is one of the dominant cyanobacteria and a key primary producer in oligotrophic intertropical oceans. Here we present an overview of the pathways of nitrogen assimilation in Prochlorococcus, which have been significantly modified in these microorganisms for adaptation to the natural limitations of their habitats, leading to the appearance of different ecotypes lacking key enzymes, such as nitrate reductase, nitrite reductase, or urease, and to the simplification of the metabolic regulation systems. The only nitrogen source utilizable by all studied isolates is ammonia, which is incorporated into glutamate by glutamine synthetase. However, this enzyme shows unusual regulatory features, although its structural and kinetic features are unchanged. Similarly, urease activities remain fairly constant under different conditions. The signal transduction protein P(II) is apparently not phosphorylated in Prochlorococcus, despite its conserved amino acid sequence. The genes amt1 and ntcA (coding for an ammonium transporter and a global nitrogen regulator, respectively) show noncorrelated expression in Prochlorococcus under nitrogen stress; furthermore, high rates of organic nitrogen uptake have been observed. All of these unusual features could provide a physiological basis for the predominance of Prochlorococcus over Synechococcus in oligotrophic oceans.
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Affiliation(s)
- Jose Manuel García-Fernández
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, Planta 1, Campus de Rabanales, 14071-Córdoba, Spain.
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