1
|
Savoie M, Mattison A, Genge L, Nadeau J, Śliwińska-Wilczewska S, Berthold M, Omar NM, Prášil O, Cockshutt AM, Campbell DA. Prochlorococcus marinus responses to light and oxygen. PLoS One 2024; 19:e0307549. [PMID: 39038009 PMCID: PMC11262661 DOI: 10.1371/journal.pone.0307549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
Prochlorococcus marinus, the smallest picocyanobacterium, comprises multiple clades occupying distinct niches, currently across tropical and sub-tropical oligotrophic ocean regions, including Oxygen Minimum Zones. Ocean warming may open growth-permissive temperatures in new, poleward photic regimes, along with expanded Oxygen Minimum Zones. We used ocean metaproteomic data on current Prochlorococcus marinus niches, to guide testing of Prochlorococcus marinus growth across a matrix of peak irradiances, photoperiods, spectral bands and dissolved oxygen. MED4 from Clade HLI requires greater than 4 h photoperiod, grows at 25 μmol O2 L-1 and above, and exploits high cumulative diel photon doses. MED4, however, relies upon an alternative oxidase to balance electron transport, which may exclude it from growth under our lowest, 2.5 μmol O2 L-1, condition. SS120 from clade LLII/III is restricted to low light under full 250 μmol O2 L-1, shows expanded light exploitation under 25 μmol O2 L-1, but is excluded from growth under 2.5 μmol O2 L-1. Intermediate oxygen suppresses the cost of PSII photoinactivation, and possibly the enzymatic production of H2O2 in SS120, which has limitations on genomic capacity for PSII and DNA repair. MIT9313 from Clade LLIV is restricted to low blue irradiance under 250 μmol O2 L-1, but exploits much higher irradiance under red light, or under lower O2 concentrations, conditions which slow photoinactivation of PSII and production of reactive oxygen species. In warming oceans, range expansions and competition among clades will be governed not only by light levels. Short photoperiods governed by latitude, temperate winters, and depth attenuation of light, will exclude clade HLI (including MED4) from some habitats. In contrast, clade LLII/III (including SS120), and particularly clade LLIV (including MIT9313), may exploit higher light niches nearer the surface, under expanding OMZ conditions, where low O2 relieves the stresses of oxidation stress and PSII photoinhibition.
Collapse
Affiliation(s)
- Mireille Savoie
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Aurora Mattison
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
- Department of Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurel Genge
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
- Fisheries and Oceans Canada, Ecosystems Management Branch, Dartmouth, Nova Scotia, Canada
| | - Julie Nadeau
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Sylwia Śliwińska-Wilczewska
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
- Institute of Oceanography, University of Gdansk, Gdynia, Poland
| | - Maximilian Berthold
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Naaman M. Omar
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Ondřej Prášil
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
- Laboratory of Photosynthesis, Institute of Microbiology, Center Algatech, Trebon, Czech Republic
| | - Amanda M. Cockshutt
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick, Canada
- Department of Chemistry, St. Frances Xavier University, Antigonish, Nova Scotia, Canada
| | - Douglas A. Campbell
- Department of Biology, Mount Allison University, Sackville, New Brunswick, Canada
| |
Collapse
|
2
|
Noell SE, Hellweger FL, Temperton B, Giovannoni SJ. A Reduction of Transcriptional Regulation in Aquatic Oligotrophic Microorganisms Enhances Fitness in Nutrient-Poor Environments. Microbiol Mol Biol Rev 2023; 87:e0012422. [PMID: 36995249 PMCID: PMC10304753 DOI: 10.1128/mmbr.00124-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
In this review, we consider the regulatory strategies of aquatic oligotrophs, microbial cells that are adapted to thrive under low-nutrient concentrations in oceans, lakes, and other aquatic ecosystems. Many reports have concluded that oligotrophs use less transcriptional regulation than copiotrophic cells, which are adapted to high nutrient concentrations and are far more common subjects for laboratory investigations of regulation. It is theorized that oligotrophs have retained alternate mechanisms of regulation, such as riboswitches, that provide shorter response times and smaller amplitude responses and require fewer cellular resources. We examine the accumulated evidence for distinctive regulatory strategies in oligotrophs. We explore differences in the selective pressures copiotrophs and oligotrophs encounter and ask why, although evolutionary history gives copiotrophs and oligotrophs access to the same regulatory mechanisms, they might exhibit distinctly different patterns in how these mechanisms are used. We discuss the implications of these findings for understanding broad patterns in the evolution of microbial regulatory networks and their relationships to environmental niche and life history strategy. We ask whether these observations, which have emerged from a decade of increased investigation of the cell biology of oligotrophs, might be relevant to recent discoveries of many microbial cell lineages in nature that share with oligotrophs the property of reduced genome size.
Collapse
Affiliation(s)
- Stephen E. Noell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | | | - Ben Temperton
- School of Biosciences, University of Exeter, Exeter, United Kingdom
| | | |
Collapse
|
3
|
Alonso-Sáez L, Palacio AS, Cabello AM, Robaina-Estévez S, González JM, Garczarek L, López-Urrutia Á. Transcriptional Mechanisms of Thermal Acclimation in Prochlorococcus. mBio 2023:e0342522. [PMID: 37052490 DOI: 10.1128/mbio.03425-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40°. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30°C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17°C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones. IMPORTANCE Prochlorococcus is a major marine primary producer with a global impact on atmospheric CO2 fixation. This cyanobacterium is widely distributed across the temperate ocean, but virtually absent at latitudes above 40° for yet unknown reasons. Temperature has been suggested as a major limiting factor, but the exact mechanisms behind Prochlorococcus thermal growth restriction remain unexplored. This study brings us closer to understanding how Prochlorococcus functions under challenging temperature conditions, by focusing on its transcriptional response after long-term acclimation from its optimum to its thermal thresholds. Our results show that the drop in Prochlorococcus growth rate under cold conditions was paralleled by a transcriptional suppression of the photosynthetic machinery during daytime and a loss in the organism's regulatory capacity to maintain circadian expression patterns. Notably, warm temperature induced a marked shrinkage of the organism's cellular transcript inventory, which may also induce regulatory imbalances in the future functioning of this cyanobacterium.
Collapse
Affiliation(s)
- Laura Alonso-Sáez
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Antonio S Palacio
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | - Ana M Cabello
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Sukarrieta, Spain
| | | | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ángel López-Urrutia
- Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, IEO-CSIC, Gijón, Asturias, Spain
| |
Collapse
|
4
|
Dedman CJ, King AM, Christie-Oleza JA, Davies GL. Environmentally relevant concentrations of titanium dioxide nanoparticles pose negligible risk to marine microbes. ENVIRONMENTAL SCIENCE. NANO 2021; 8:1236-1255. [PMID: 34046180 PMCID: PMC8136324 DOI: 10.1039/d0en00883d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/06/2021] [Indexed: 05/26/2023]
Abstract
Nano-sized titanium dioxide (nTiO2) represents the highest produced nanomaterial by mass worldwide and, due to its prevalent industrial and commercial use, it inevitably reaches the natural environment. Previous work has revealed a negative impact of nTiO2 upon marine phytoplankton growth, however, studies are typically carried out at concentrations far exceeding those measured and predicted to occur in the environment currently. Here, a series of experiments were carried out to assess the effects of both research-grade nTiO2 and nTiO2 extracted from consumer products upon the marine dominant cyanobacterium, Prochlorococcus, and natural marine communities at environmentally relevant and supra-environmental concentrations (i.e., 1 μg L-1 to 100 mg L-1). Cell declines observed in Prochlorococcus cultures were associated with the extensive aggregation behaviour of nTiO2 in saline media and the subsequent entrapment of microbial cells. Hence, higher concentrations of nTiO2 particles exerted a stronger decline of cyanobacterial populations. However, within natural oligotrophic seawater, cultures were able to recover over time as the nanoparticles aggregated out of solution after 72 h. Subsequent shotgun proteomic analysis of Prochlorococcus cultures exposed to environmentally relevant concentrations confirmed minimal molecular features of toxicity, suggesting that direct physical effects are responsible for short-term microbial population decline. In an additional experiment, the diversity and structure of natural marine microbial communities showed negligible variations when exposed to environmentally relevant nTiO2 concentrations (i.e., 25 μg L-1). As such, the environmental risk of nTiO2 towards marine microbial species appears low, however the potential for adverse effects in hotspots of contamination exists. In future, research must be extended to consider any effect of other components of nano-enabled product formulations upon nanomaterial fate and impact within the natural environment.
Collapse
Affiliation(s)
- Craig J Dedman
- School of Life Sciences, Gibbet Hill Campus, University of Warwick Coventry CV4 7AL UK
- Department of Chemistry, University of Warwick Gibbet Hill Coventry CV4 7EQ UK
| | - Aaron M King
- UCL Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Joseph A Christie-Oleza
- School of Life Sciences, Gibbet Hill Campus, University of Warwick Coventry CV4 7AL UK
- Department of Biology, University of the Balearic Islands Ctra. Valldemossa, km 7.5 CP: 07122 Palma Spain
- IMEDEA (CSIC-UIB) CP: 07190 Esporles Spain
| | - Gemma-Louise Davies
- UCL Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| |
Collapse
|
5
|
Dedman CJ, Newson GC, Davies GL, Christie-Oleza JA. Mechanisms of silver nanoparticle toxicity on the marine cyanobacterium Prochlorococcus under environmentally-relevant conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 747:141229. [PMID: 32777503 DOI: 10.1016/j.scitotenv.2020.141229] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Global demand for silver nanoparticles (AgNPs), and their inevitable release into the environment, is rapidly increasing. AgNPs display antimicrobial properties and have previously been recorded to exert adverse effects upon marine phytoplankton. However, ecotoxicological research is often compromised by the use of non-ecologically relevant conditions, and the mechanisms of AgNP toxicity under environmental conditions remains unclear. To examine the impact of AgNPs on natural marine communities, a natural assemblage was exposed to citrate-stabilised AgNPs. Here, investigation confirmed that the marine dominant cyanobacteria Prochlorococcus is particularly sensitive to AgNP exposure. Whilst Prochlorococcus represents the most abundant photosynthetic organism on Earth and contributes significantly to global primary productivity, little ecotoxicological research has been carried out on this cyanobacterium. To address this, Prochlorococcus was exposed to citrate-stabilised AgNPs, as well as silver in its ionic form (Ag2SO4), under simulated natural conditions. Both AgNPs and ionic silver were observed to reduce Prochlorococcus populations by over 90% at concentrations ≥10 μg L-1, representing the upper limit of AgNP concentrations predicted in the environment (10 μg L-1). Longer-term assessment revealed this to be a perturbation which was irreversible. Through use of quenching agents for superoxide and hydrogen peroxide, alongside incubations with ionic silver, it was revealed that AgNP toxicity likely arises from synergistic effects of toxic superoxide species generation and leaching of ionic silver. The extent of toxicity was strongly dependent on cell density, and completely mitigated in more cell-dense cultures. Hence, the calculation and reporting of the particle-to-cell ratio reveals that this parameter is effective for standardisation of experimental work, and allows for direct comparison between studies where cell density may vary. Given the key role that marine cyanobacteria play in global primary production and biogeochemical cycling, their higher susceptibility to AgNP exposure is a concern in hotspots of pollution.
Collapse
Affiliation(s)
- Craig J Dedman
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom..
| | - Gabrielle C Newson
- Department of Chemistry, University of Warwick, Gibbet Hill, Coventry CV4 7EQ, United Kingdom
| | - Gemma-Louise Davies
- University College London, Department of Chemistry, 20 Gordon Street, London WC1H 0AJ, United Kingdom..
| | - Joseph A Christie-Oleza
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom.; Department of Biology, University of the Balearic Islands, Ctra. Valldemossa, km 7.5, CP: 07122 Palma, Spain; IMEDEA (CSIC-UIB), CP: 07190 Esporles, Spain.
| |
Collapse
|
6
|
Lambrecht SJ, Steglich C, Hess WR. A minimum set of regulators to thrive in the ocean. FEMS Microbiol Rev 2020; 44:232-252. [DOI: 10.1093/femsre/fuaa005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022] Open
Abstract
ABSTRACT
Marine cyanobacteria of the genus Prochlorococcus thrive in high cell numbers throughout the euphotic zones of the world's subtropical and tropical oligotrophic oceans, making them some of the most ecologically relevant photosynthetic microorganisms on Earth. The ecological success of these free-living phototrophs suggests that they are equipped with a regulatory system competent to address many different stress situations. However, Prochlorococcus genomes are compact and streamlined, with the majority encoding only five different sigma factors, five to six two-component systems and eight types of other transcriptional regulators. Here, we summarize the existing information about the functions of these protein regulators, about transcriptomic responses to defined stress conditions, and discuss the current knowledge about riboswitches, RNA-based regulation and the roles of certain metabolites as co-regulators. We focus on the best-studied isolate, Prochlorococcus MED4, but extend to other strains and ecotypes when appropriate, and we include some information gained from metagenomic and metatranscriptomic analyses.
Collapse
Affiliation(s)
- S Joke Lambrecht
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| |
Collapse
|
7
|
Hennon GM, Morris JJ, Haley ST, Zinser ER, Durrant AR, Entwistle E, Dokland T, Dyhrman ST. The impact of elevated CO 2 on Prochlorococcus and microbial interactions with 'helper' bacterium Alteromonas. THE ISME JOURNAL 2018; 12:520-531. [PMID: 29087378 PMCID: PMC5776468 DOI: 10.1038/ismej.2017.189] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 09/12/2017] [Accepted: 09/22/2017] [Indexed: 02/07/2023]
Abstract
Prochlorococcus is a globally important marine cyanobacterium that lacks the gene catalase and relies on 'helper' bacteria such as Alteromonas to remove reactive oxygen species. Increasing atmospheric CO2 decreases the need for carbon concentrating mechanisms and photorespiration in phytoplankton, potentially altering their metabolism and microbial interactions even when carbon is not limiting growth. Here, Prochlorococcus (VOL4, MIT9312) was co-cultured with Alteromonas (strain EZ55) under ambient (400 p.p.m.) and elevated CO2 (800 p.p.m.). Under elevated CO2, Prochlorococcus had a significantly longer lag phase and greater apparent die-offs after transfers suggesting an increase in oxidative stress. Whole-transcriptome analysis of Prochlorococcus revealed decreased expression of the carbon fixation operon, including carboxysome subunits, corresponding with significantly fewer carboxysome structures observed by electron microscopy. Prochlorococcus co-culture responsive gene 1 had significantly increased expression in elevated CO2, potentially indicating a shift in the microbial interaction. Transcriptome analysis of Alteromonas in co-culture with Prochlorococcus revealed decreased expression of the catalase gene, known to be critical in relieving oxidative stress in Prochlorococcus by removing hydrogen peroxide. The decrease in catalase gene expression was corroborated by a significant ~6-fold decrease in removal rates of hydrogen peroxide from co-cultures. These data suggest Prochlorococcus may be more vulnerable to oxidative stress under elevated CO2 in part from a decrease in ecosystem services provided by heterotrophs like Alteromonas. This work highlights the importance of considering microbial interactions in the context of a changing ocean.
Collapse
Affiliation(s)
- Gwenn Mm Hennon
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, Palisades,, NY, USA
| | - J Jeffrey Morris
- Department of Biology, University of Alabama at Birmingham, Birmingham,, AL, USA
| | - Sheean T Haley
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, Palisades,, NY, USA
| | - Erik R Zinser
- Department of Microbiology, University of Tennessee, Knoxville,, TN, USA
| | - Alexander R Durrant
- Department of Biology, University of Alabama at Birmingham, Birmingham,, AL, USA
| | - Elizabeth Entwistle
- Department of Biology, University of Alabama at Birmingham, Birmingham,, AL, USA
| | - Terje Dokland
- Department of Biology, University of Alabama at Birmingham, Birmingham,, AL, USA
| | - Sonya T Dyhrman
- Division of Biology and Paleo Environment, Lamont-Doherty Earth Observatory, Columbia University, Palisades,, NY, USA.
- Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA.
| |
Collapse
|
8
|
Hennon GMM, Hernández Limón MD, Haley ST, Juhl AR, Dyhrman ST. Diverse CO 2-Induced Responses in Physiology and Gene Expression among Eukaryotic Phytoplankton. Front Microbiol 2017; 8:2547. [PMID: 29312232 PMCID: PMC5742204 DOI: 10.3389/fmicb.2017.02547] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/08/2017] [Indexed: 01/15/2023] Open
Abstract
With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (~400 ppm) and elevated (~800 ppm) CO2. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO2. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO2 in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO2-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO2 across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO2. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change.
Collapse
Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - María D Hernández Limón
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - Sheean T Haley
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States
| | - Andrew R Juhl
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Biology and Paleo Environment, Palisades, NY, United States.,Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States
| |
Collapse
|
9
|
Braakman R, Follows MJ, Chisholm SW. Metabolic evolution and the self-organization of ecosystems. Proc Natl Acad Sci U S A 2017; 114:E3091-E3100. [PMID: 28348231 PMCID: PMC5393222 DOI: 10.1073/pnas.1619573114] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Metabolism mediates the flow of matter and energy through the biosphere. We examined how metabolic evolution shapes ecosystems by reconstructing it in the globally abundant oceanic phytoplankter Prochlorococcus To understand what drove observed evolutionary patterns, we interpreted them in the context of its population dynamics, growth rate, and light adaptation, and the size and macromolecular and elemental composition of cells. This multilevel view suggests that, over the course of evolution, there was a steady increase in Prochlorococcus' metabolic rate and excretion of organic carbon. We derived a mathematical framework that suggests these adaptations lower the minimal subsistence nutrient concentration of cells, which results in a drawdown of nutrients in oceanic surface waters. This, in turn, increases total ecosystem biomass and promotes the coevolution of all cells in the ecosystem. Additional reconstructions suggest that Prochlorococcus and the dominant cooccurring heterotrophic bacterium SAR11 form a coevolved mutualism that maximizes their collective metabolic rate by recycling organic carbon through complementary excretion and uptake pathways. Moreover, the metabolic codependencies of Prochlorococcus and SAR11 are highly similar to those of chloroplasts and mitochondria within plant cells. These observations lead us to propose a general theory relating metabolic evolution to the self-amplification and self-organization of the biosphere. We discuss the implications of this framework for the evolution of Earth's biogeochemical cycles and the rise of atmospheric oxygen.
Collapse
Affiliation(s)
- Rogier Braakman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Michael J Follows
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| |
Collapse
|
10
|
Murphy CD, Roodvoets MS, Austen EJ, Dolan A, Barnett A, Campbell DA. Photoinactivation of Photosystem II in Prochlorococcus and Synechococcus. PLoS One 2017; 12:e0168991. [PMID: 28129341 PMCID: PMC5271679 DOI: 10.1371/journal.pone.0168991] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 12/10/2016] [Indexed: 01/15/2023] Open
Abstract
The marine picocyanobacteria Synechococcus and Prochlorococcus numerically dominate open ocean phytoplankton. Although evolutionarily related they are ecologically distinct, with different strategies to harvest, manage and exploit light. We grew representative strains of Synechococcus and Prochlorococcus and tracked their susceptibility to photoinactivation of Photosystem II under a range of light levels. As expected blue light provoked more rapid photoinactivation than did an equivalent level of red light. The previous growth light level altered the susceptibility of Synechococcus, but not Prochlorococcus, to this photoinactivation. We resolved a simple linear pattern when we expressed the yield of photoinactivation on the basis of photons delivered to Photosystem II photochemistry, plotted versus excitation pressure upon Photosystem II, the balance between excitation and downstream metabolism. A high excitation pressure increases the generation of reactive oxygen species, and thus increases the yield of photoinactivation of Photosystem II. Blue photons, however, retained a higher baseline photoinactivation across a wide range of excitation pressures. Our experiments thus uncovered the relative influences of the direct photoinactivation of Photosystem II by blue photons which dominates under low to moderate blue light, and photoinactivation as a side effect of reactive oxygen species which dominates under higher excitation pressure. Synechococcus enjoyed a positive metabolic return upon the repair or the synthesis of a Photosystem II, across the range of light levels we tested. In contrast Prochlorococcus only enjoyed a positive return upon synthesis of a Photosystem II up to 400 μmol photons m-2 s-1. These differential cost-benefits probably underlie the distinct photoacclimation strategies of the species.
Collapse
Affiliation(s)
- Cole D. Murphy
- Biochemistry and Chemistry, Mount Allison University, Sackville, New Brunswick, Canada
| | - Mitchell S. Roodvoets
- Biochemistry and Chemistry, Mount Allison University, Sackville, New Brunswick, Canada
| | - Emily J. Austen
- Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Allison Dolan
- Biology, Mount Allison University, Sackville, New Brunswick, Canada
| | - Audrey Barnett
- Michigan Technological University, Houghton, Michigan, United States of America
| | | |
Collapse
|
11
|
Thompson LR, Zeng Q, Chisholm SW. Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage. PLoS One 2016; 11:e0165375. [PMID: 27788196 PMCID: PMC5082946 DOI: 10.1371/journal.pone.0165375] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/11/2016] [Indexed: 01/09/2023] Open
Abstract
Cyanophage infecting the marine cyanobacteria Prochlorococcus and Synechococcus require light and host photosystem activity for optimal reproduction. Many cyanophages encode multiple photosynthetic electron transport (PET) proteins, which are presumed to maintain electron flow and produce ATP and NADPH for nucleotide biosynthesis and phage genome replication. However, evidence suggests phage augment NADPH production via the pentose phosphate pathway (PPP), thus calling into question the need for NADPH production by PET. Genes implicated in cyclic PET have since been identified in cyanophage genomes. It remains an open question which mode of PET, cyclic or linear, predominates in infected cyanobacteria, and thus whether the balance is towards producing ATP or NADPH. We sequenced transcriptomes of a cyanophage (P-HM2) and its host (Prochlorococcus MED4) throughout infection in the light or in the dark, and analyzed these data in the context of phage replication and metabolite measurements. Infection was robust in the light, but phage were not produced in the dark. Host gene transcripts encoding high-light inducible proteins and two terminal oxidases (plastoquinol terminal oxidase and cytochrome c oxidase)-implicated in protecting the photosynthetic membrane from light stress-were the most enriched in light but not dark infection. Among the most diminished transcripts in both light and dark infection was ferredoxin-NADP+ reductase (FNR), which uses the electron acceptor NADP+ to generate NADPH in linear photosynthesis. The phage gene for CP12, which putatively inhibits the Calvin cycle enzyme that receives NADPH from FNR, was highly expressed in light infection. Therefore, both PET production of NADPH and its consumption by carbon fixation are putatively repressed during phage infection in light. Transcriptomic evidence is thus consistent with cyclic photophosphorylation using oxygen as the terminal electron acceptor as the dominant mode of PET under infection, with ATP from PET and NADPH from the PPP producing the energy and reducing equivalents for phage nucleotide biosynthesis and replication.
Collapse
Affiliation(s)
- Luke R. Thompson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (LRT); (SWC)
| | - Qinglu Zeng
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Sallie W. Chisholm
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail: (LRT); (SWC)
| |
Collapse
|
12
|
Torn apart and reunited: impact of a heterotroph on the transcriptome of Prochlorococcus. ISME JOURNAL 2016; 10:2831-2843. [PMID: 27258949 DOI: 10.1038/ismej.2016.82] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/29/2016] [Accepted: 04/12/2016] [Indexed: 11/09/2022]
Abstract
Microbial interactions, whether direct or indirect, profoundly affect the physiology of individual cells and ultimately have the potential to shape the biogeochemistry of the Earth. For example, the growth of Prochlorococcus, the numerically dominant cyanobacterium in the oceans, can be improved by the activity of co-occurring heterotrophs. This effect has been largely attributed to the role of heterotrophs in detoxifying reactive oxygen species that Prochlorococcus, which lacks catalase, cannot. Here, we explore this phenomenon further by examining how the entire transcriptome of Prochlorococcus NATL2A changes in the presence of a naturally co-occurring heterotroph, Alteromonas macleodii MIT1002, with which it was co-cultured for years, separated and then reunited. Significant changes in the Prochlorococcus transcriptome were evident within 6 h of initiating co-culture, with groups of transcripts changing in different temporal waves. Many transcriptional changes persisted throughout the 48 h experiment, suggesting that the presence of the heterotroph affected a stable shift in Prochlorococcus physiology. These initial transcriptome changes largely corresponded to reduced stress conditions for Prochlorococcus, as inferred from the depletion of transcripts encoding DNA repair enzymes and many members of the 'high light inducible' family of stress-response proteins. Later, notable changes were seen in transcripts encoding components of the photosynthetic apparatus (particularly, an increase in PSI subunits and chlorophyll synthesis enzymes), ribosomal proteins and biosynthetic enzymes, suggesting that the introduction of the heterotroph may have induced increased production of reduced carbon compounds for export. Changes in secretion-related proteins and transporters also highlight the potential for metabolic exchange between the two strains.
Collapse
|