1
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Tu W, Huang WE. Rhodopsin driven microbial CO 2 fixation using synthetic biology design. Environ Microbiol 2023; 25:126-130. [PMID: 36221243 PMCID: PMC10092888 DOI: 10.1111/1462-2920.16243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Weiming Tu
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Oxford, UK
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2
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Shim JG, Kang NR, Chuon K, Cho SG, Meas S, Jung KH. Mutational analyses identify a single amino acid critical for color tuning in proteorhodopsins. FEBS Lett 2022; 596:784-795. [PMID: 35090057 DOI: 10.1002/1873-3468.14297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/08/2022]
Abstract
Microbial rhodopsins are light-activated proteins that contain seven transmembrane alpha-helices. Spectral tuning in microbial rhodopsins is a useful optogenetic tool. In this study, we report a new site that controls spectral tuning. In the proteorhodopsins ISR34 and ISR36, a single amino-acid substitution at Cys189 caused an absorption maximum shift of 44 nm, indicating spectral tuning at a specific site. Comparison of single amino acid substitutions was conducted using photochemical and photobiological approaches. The maximum absorption for red-shift was measured for mutations at positions 189 and 105 in ISR34, both residues being equally important. Structural changes resulting from amino acid substitutions are related to pKa values, pumping activity, and spectral tuning.
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Affiliation(s)
- Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Na-Rae Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Kimleng Chuon
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Korea
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3
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Abstract
Microbial proton-pumping rhodopsins are considered the simplest strategy among phototrophs to conserve energy from light. Proteorhodopsins are the most studied rhodopsins thus far because of their ubiquitous presence in the ocean, except in Antarctica, where they remain understudied. We analyzed proteorhodopsin abundance and transcriptional activity in the Western Antarctic coastal seawaters. Combining quantitative PCR (qPCR) and metagenomics, the relative abundance of proteorhodopsin-bearing bacteria accounted on average for 17, 3.5, and 29.7% of the bacterial community in Chile Bay (South Shetland Islands) during 2014, 2016, and 2017 summer-autumn, respectively. The abundance of proteorhodopsin-bearing bacteria changed in relation to environmental conditions such as chlorophyll a and temperature. Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were the main bacteria that transcribed the proteorhodopsin gene during day and night. Although green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones, the latter were transcribed more intensely, resulting in >50% of the proteorhodopsin transcripts during the day and night. Flavobacteriia were the most abundant proteorhodopsin-bearing bacteria in the metagenomes; however, Alphaproteobacteria and Gammaproteobacteria were more represented in the metatranscriptomes, with qPCR quantification suggesting the dominance of the active SAR11 clade. Our results show that proteorhodopsin-bearing bacteria are prevalent in Antarctic coastal waters in late austral summer and early autumn, and their ecological relevance needs to be elucidated to better understand how sunlight energy is used in this marine ecosystem. IMPORTANCE Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula's coastal waters. This information is crucial to understand better how sunlight enters this marine environment through alternative ways unrelated to chlorophyll-based strategies. The relative abundance of proteorhodopsin-bearing bacteria seems to be related to environmental parameters (e.g., chlorophyll a, temperature) that change yearly at the coastal water of the West Antarctic Peninsula during the austral late summers and early autumns. Proteorhodopsin-bearing bacteria from Antarctic coastal waters are potentially able to exploit both the green and blue spectrum of sunlight and are a prevalent group during the summer in this polar environment.
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Hassanzadeh B, Thomson B, Deans F, Wenley J, Lockwood S, Currie K, Morales SE, Steindler L, Sañudo-Wilhelmy SA, Baltar F, Gómez-Consarnau L. Microbial rhodopsins are increasingly favoured over chlorophyll in High Nutrient Low Chlorophyll waters. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:401-406. [PMID: 33870657 DOI: 10.1111/1758-2229.12948] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/26/2021] [Accepted: 04/04/2021] [Indexed: 05/16/2023]
Abstract
Microbial rhodopsins are simple light-harvesting complexes that, unlike chlorophyll photosystems, have no iron requirements for their synthesis and phototrophic functions. Here, we report the environmental concentrations of rhodopsin along the Subtropical Frontal Zone off New Zealand, where Subtropical waters encounter the iron-limited Subantarctic High Nutrient Low Chlorophyll (HNLC) region. Rhodopsin concentrations were highest in HNLC waters where chlorophyll-a concentrations were lowest. Furthermore, while the ratio of rhodopsin to chlorophyll-a photosystems was on average 20 along the transect, this ratio increased to over 60 in HNLC waters. We further show that microbial rhodopsins are abundant in both picoplankton (0.2-3 μm) and in the larger (>3 μm) size fractions of the microbial community containing eukaryotic plankton and/or particle-attached prokaryotes. These findings suggest that rhodopsin phototrophy could be critical for microbial plankton to adapt to resource-limiting environments where photosynthesis and possibly cellular respiration are impaired.
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Affiliation(s)
- Babak Hassanzadeh
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Blair Thomson
- Department of Marine Science, University of Otago, Dunedin, 9016, New Zealand
| | - Fenella Deans
- Department of Marine Science, University of Otago, Dunedin, 9016, New Zealand
| | - Jess Wenley
- Department of Marine Science, University of Otago, Dunedin, 9016, New Zealand
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Scott Lockwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Kim Currie
- National Institute of Water and Atmospheric Research, Dunedin, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, BC, Israel
| | - Sergio A Sañudo-Wilhelmy
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Federico Baltar
- Department of Functional & Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Laura Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
- Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, BC, México
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5
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Galachyants AD, Krasnopeev AY, Podlesnaya GV, Potapov SA, Sukhanova EV, Tikhonova IV, Zimens EA, Kabilov MR, Zhuchenko NA, Gorshkova AS, Suslova MY, Belykh OI. Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal. Microorganisms 2021; 9:842. [PMID: 33920057 PMCID: PMC8071047 DOI: 10.3390/microorganisms9040842] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022] Open
Abstract
The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing pufM and rhodopsin genes, and compared to 16S rRNA diversity. We detected pufM-containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes. The diversity of rhodopsin-containing bacteria in neuston and plankton of Lake Baikal was comparable to other studied water bodies. Bacteroidetes along with Proteobacteria were the prevailing phyla, and Verrucomicrobia and Planctomycetes were also detected. The number of rhodopsin sequences unclassified to the phylum level was rather high: 29% in the water microbiomes and 22% in the epilithon. Diversity of rhodopsin-containing bacteria in epilithic biofilms was comparable with that in neuston and plankton at the phyla level. Unweighted pair group method with arithmetic mean (UPGMA) and non-metric multidimensional scaling (NMDS) analysis indicated a distinct discrepancy between epilithon and microbial communities of water (including neuston and plankton) in the 16S rRNA, pufM and rhodopsin genes.
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Affiliation(s)
- Agnia Dmitrievna Galachyants
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Andrey Yurjevich Krasnopeev
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Galina Vladimirovna Podlesnaya
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Sergey Anatoljevich Potapov
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Elena Viktorovna Sukhanova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Irina Vasiljevna Tikhonova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Ekaterina Andreevna Zimens
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Marsel Rasimovich Kabilov
- Chemical Biology and Fundamental Medicine Siberian Branch of the Russian Academy of Sciences, Lavrentiev Avenue 8, 630090 Novosibirsk, Russia;
| | - Natalia Albertovna Zhuchenko
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Anna Sergeevna Gorshkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Maria Yurjevna Suslova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
| | - Olga Ivanovna Belykh
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Ulan-Batorskaya 3, 664033 Irkutsk, Russia; (A.Y.K.); (G.V.P.); (S.A.P.); (E.V.S.); (I.V.T.); (E.A.Z.); (N.A.Z.); (A.S.G.); (M.Y.S.)
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6
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Kopejtka K, Tomasch J, Zeng Y, Selyanin V, Dachev M, Piwosz K, Tichý M, Bína D, Gardian Z, Bunk B, Brinkmann H, Geffers R, Sommaruga R, Koblížek M. Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium. mSystems 2020; 5:e01044-20. [PMID: 33361324 PMCID: PMC7762795 DOI: 10.1128/msystems.01044-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Photoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic Sphingomonas strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll a quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll a and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic Sphingomonas bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation.IMPORTANCE Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium Sphingomonas sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in Sphingomonas may have other functions not linked to bioenergetics.
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Affiliation(s)
- Karel Kopejtka
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Jürgen Tomasch
- Research Group Microbial Communication, Technical University of Braunschweig, Braunschweig, Germany
| | - Yonghui Zeng
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
- Department of Environmental Science, Aarhus University, Aarhus, Denmark
| | - Vadim Selyanin
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Marko Dachev
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Kasia Piwosz
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - Martin Tichý
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
| | - David Bína
- Institute of Plant Molecular Biology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Institute of Parasitology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Zdenko Gardian
- Institute of Plant Molecular Biology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Institute of Parasitology, Biology Center of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Henner Brinkmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Robert Geffers
- Research Group Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ruben Sommaruga
- Laboratory of Aquatic Photobiology and Plankton Ecology, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology of the Czech Academy of Science, Třeboň, Czechia
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7
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Konno M, Yamauchi Y, Inoue K, Kandori H. Expression analysis of microbial rhodopsin-like genes in Guillardia theta. PLoS One 2020; 15:e0243387. [PMID: 33270796 PMCID: PMC7714340 DOI: 10.1371/journal.pone.0243387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/19/2020] [Indexed: 12/28/2022] Open
Abstract
The Cryptomonad Guillardia theta has 42 genes encoding microbial rhodopsin-like proteins in their genomes. Light-driven ion-pump activity has been reported for some rhodopsins based on heterologous E. coli or mammalian cell expression systems. However, neither their physiological roles nor the expression of those genes in native cells are known. To reveal their physiological roles, we investigated the expression patterns of these genes under various growth conditions. Nitrogen (N) deficiency induced color change in exponentially growing G. theta cells from brown to green. The 29 rhodopsin-like genes were expressed in native cells. We found that the expression of 6 genes was induced under N depletion, while that of another 6 genes was reduced under N depletion.
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Affiliation(s)
- Masae Konno
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
- * E-mail: (HK); (MK)
| | - Yumeka Yamauchi
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Keiichi Inoue
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Hideki Kandori
- Life Science and Applied Chemistry, Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
- * E-mail: (HK); (MK)
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8
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Arandia-Gorostidi N, González JM, Huete-Stauffer TM, Ansari MI, Morán XAG, Alonso-Sáez L. Light supports cell-integrity and growth rates of taxonomically diverse coastal photoheterotrophs. Environ Microbiol 2020; 22:3823-3837. [PMID: 32643243 DOI: 10.1111/1462-2920.15158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/29/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022]
Abstract
Despite the widespread distribution of proteorhodopsin (PR)-containing bacteria in the oceans, the use of light-derived energy to promote bacterial growth has only been shown in a few bacterial isolates, and there is a paucity of data describing the metabolic effects of light on environmental photoheterotrophic taxa. Here, we assessed the effects of light on the taxonomic composition, cell integrity and growth responses of microbial communities in monthly incubations between spring and autumn under different environmental conditions. The photoheterotrophs expressing PR in situ were dominated by Pelagibacterales and SAR116 in July and November, while members of Euryarchaeota, Gammaproteobacteria and Bacteroidetes dominated the PR expression in spring. Cell-membrane integrity decreased under dark conditions throughout most of the assessment, with maximal effects in summer, under low-nutrient conditions. A positive effect of light on growth was observed in one incubation (out of nine), coinciding with a declining phytoplankton bloom. Light-enhanced growth was found in Gammaproteobacteria (Alteromonadales) and Bacteroidetes (Polaribacter and Tenacibaculum). Unexpectedly, some Pelagibacterales also exhibited higher growth rates under light conditions. We propose that the energy harvested by PRs helps to maintain cell viability in dominant coastal photoheterotrophic oligotrophs while promoting the growth of some widespread taxa benefiting from the decline of phytoplankton blooms.
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Affiliation(s)
- Nestor Arandia-Gorostidi
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - José M González
- Department of Microbiology, University of La Laguna, La Laguna, Spain
| | - Tamara M Huete-Stauffer
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohd I Ansari
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G Morán
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Laura Alonso-Sáez
- Instituto Español de Oceanografía, Centro Oceanográfico de Gijón/Xixón, Gijón/Xixón, Asturias, Spain.,AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), Txatxarramendi ugartea z/g, Sukarrieta, Bizkaia, 48395, Spain
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9
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Chen Q, Arents J, Schuurmans JM, Ganapathy S, de Grip WJ, Cheregi O, Funk C, Branco Dos Santos F, Hellingwerf KJ. Functional Expression of Gloeobacter Rhodopsin in PSI-Less Synechocystis sp. PCC6803. Front Bioeng Biotechnol 2019; 7:67. [PMID: 30984754 PMCID: PMC6450040 DOI: 10.3389/fbioe.2019.00067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 03/11/2019] [Indexed: 01/30/2023] Open
Abstract
The approach of providing an oxygenic photosynthetic organism with a cyclic electron transfer system, i.e., a far-red light-driven proton pump, is widely proposed to maximize photosynthetic efficiency via expanding the absorption spectrum of photosynthetically active radiation. As a first step in this approach, Gloeobacter rhodopsin was expressed in a PSI-deletion strain of Synechocystis sp. PCC6803. Functional expression of Gloeobacter rhodopsin, in contrast to Proteorhodopsin, did not stimulate the rate of photoheterotrophic growth of this Synechocystis strain, analyzed with growth rate measurements and competition experiments. Nevertheless, analysis of oxygen uptake and—production rates of the Gloeobacter rhodopsin-expressing strains, relative to the ΔPSI control strain, confirm that the proton-pumping Gloeobacter rhodopsin provides the cells with additional capacity to generate proton motive force. Significantly, expression of the Gloeobacter rhodopsin did modulate levels of pigment formation in the transgenic strain.
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Affiliation(s)
- Que Chen
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands.,Center of Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jos Arents
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - J Merijn Schuurmans
- Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Srividya Ganapathy
- Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Willem J de Grip
- Biophysical Organic Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | | | | | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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10
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Sieradzki ET, Fuhrman JA, Rivero-Calle S, Gómez-Consarnau L. Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. PeerJ 2018; 6:e5798. [PMID: 30370186 PMCID: PMC6202958 DOI: 10.7717/peerj.5798] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022] Open
Abstract
The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.
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Affiliation(s)
- Ella T Sieradzki
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Jed A Fuhrman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Sara Rivero-Calle
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
| | - Laura Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States of America
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11
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Maresca JA, Miller KJ, Keffer JL, Sabanayagam CR, Campbell BJ. Distribution and Diversity of Rhodopsin-Producing Microbes in the Chesapeake Bay. Appl Environ Microbiol 2018; 84:e00137-18. [PMID: 29703736 PMCID: PMC6007120 DOI: 10.1128/aem.00137-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/23/2018] [Indexed: 01/09/2023] Open
Abstract
Although sunlight is an abundant source of energy in surface environments, less than 0.5% of the available photons are captured by (bacterio)chlorophyll-dependent photosynthesis in plants and bacteria. Metagenomic data indicate that 30 to 60% of the bacterial genomes in some environments encode rhodopsins, retinal-based photosystems found in heterotrophs, suggesting that sunlight may provide energy for more life than previously suspected. However, quantitative data on the number of cells that produce rhodopsins in environmental systems are limited. Here, we use total internal reflection fluorescence microscopy to show that the number of free-living microbes that produce rhodopsins increases along the salinity gradient in the Chesapeake Bay. We correlate this functional data with environmental data to show that rhodopsin abundance is positively correlated with salinity and with indicators of active heterotrophy during the day. Metagenomic and metatranscriptomic data suggest that the microbial rhodopsins in the low-salinity samples are primarily found in Actinobacteria and Bacteroidetes, while those in the high-salinity samples are associated with SAR-11 type AlphaproteobacteriaIMPORTANCE Microbial rhodopsins are common light-activated ion pumps in heterotrophs, and previous work has proposed that heterotrophic microbes use them to conserve energy when organic carbon is limiting. If this hypothesis is correct, rhodopsin-producing cells should be most abundant where nutrients are most limited. Our results indicate that in the Chesapeake Bay, rhodopsin gene abundance is correlated with salinity, and functional rhodopsin production is correlated with nitrate, bacterial production, and chlorophyll a We propose that in this environment, where carbon and nitrogen are likely not limiting, heterotrophs do not need to use rhodopsins to supplement ATP synthesis. Rather, the light-generated proton motive force in nutrient-rich environments could be used to power energy-dependent membrane-associated processes, such as active transport of organic carbon and cofactors, enabling these organisms to more efficiently utilize exudates from primary producers.
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Affiliation(s)
- Julia A Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | - Kelsey J Miller
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Jessica L Keffer
- Department of Civil and Environmental Engineering, University of Delaware, Newark, Delaware, USA
| | | | - Barbara J Campbell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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12
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Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW. Global genetic capacity for mixotrophy in marine picocyanobacteria. THE ISME JOURNAL 2016; 10:2946-2957. [PMID: 27137127 PMCID: PMC5148188 DOI: 10.1038/ismej.2016.64] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/02/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
The assimilation of organic nutrients by autotrophs, a form of mixotrophy, has been demonstrated in the globally abundant marine picocyanobacterial genera Prochlorococcus and Synechococcus. However, the range of compounds used and the distribution of organic compound uptake genes within picocyanobacteria are unknown. Here we analyze genomic and metagenomic data from around the world to determine the extent and distribution of mixotrophy in these phototrophs. Analysis of 49 Prochlorococcus and 18 Synechococcus isolate genomes reveals that all have the transporters necessary to take up amino acids, peptides and sugars. However, the number and type of transporters and associated catabolic genes differ between different phylogenetic groups, with low-light IV Prochlorococcus, and 5.1B, 5.2 and 5.3 Synechococcus strains having the largest number. Metagenomic data from 68 stations from the Tara Oceans expedition indicate that the genetic potential for mixotrophy in picocyanobacteria is globally distributed and differs between clades. Phylogenetic analyses indicate gradual organic nutrient transporter gene loss from the low-light IV to the high-light II Prochlorococcus. The phylogenetic differences in genetic capacity for mixotrophy, combined with the ubiquity of picocyanobacterial organic compound uptake genes suggests that mixotrophy has a more central role in picocyanobacterial ecology than was previously thought.
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Affiliation(s)
- Alexis P Yelton
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Silvia G Acinas
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CMIMA, CSIC, Barcelona, Spain
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory Heidelberg, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory Heidelberg, Heidelberg, Germany
| | - Carlos Pedrós-Alió
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar-CMIMA, CSIC, Barcelona, Spain
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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13
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Crenn K, Serpin D, Lepleux C, Overmann J, Jeanthon C. Silicimonas algicola gen. nov., sp. nov., a member of the Roseobacter clade isolated from the cell surface of the marine diatom Thalassiosira delicatula. Int J Syst Evol Microbiol 2016; 66:4580-4588. [DOI: 10.1099/ijsem.0.001394] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Klervi Crenn
- CNRS, Station Biologique de Roscoff, Adaptation and Diversité en Milieu Marin, Marine Phototrophic Prokaryotes Team, Roscoff, France
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Oceanic Plankton Group, Roscoff, France
| | - Delphine Serpin
- CNRS, Station Biologique de Roscoff, Adaptation and Diversité en Milieu Marin, Marine Phototrophic Prokaryotes Team, Roscoff, France
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Oceanic Plankton Group, Roscoff, France
| | - Cendrella Lepleux
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany
| | - Christian Jeanthon
- CNRS, Station Biologique de Roscoff, Adaptation and Diversité en Milieu Marin, Marine Phototrophic Prokaryotes Team, Roscoff, France
- Sorbonne Universités, UPMC Univ Paris 06, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Oceanic Plankton Group, Roscoff, France
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14
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Boeuf D, Lami R, Cunnington E, Jeanthon C. Summer Abundance and Distribution of Proteorhodopsin Genes in the Western Arctic Ocean. Front Microbiol 2016; 7:1584. [PMID: 27790192 PMCID: PMC5061748 DOI: 10.3389/fmicb.2016.01584] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
Proteorhodopsins (PR) are phylogenetically diverse and highly expressed proton pumps in marine bacterial communities. The phylogenetic diversity and in situ expression of the main PR groups in polar off-shore, coastal and estuarine waters is poorly known and their abundance has not yet been reported. Here, we show that PR gene sequences of the southern Beaufort Sea including MacKenzie shelf and estuary are mainly affiliated to Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes. Substantial overlap (78%) between DNA- and cDNA-based librairies indicated in situ PR transcription within a large fraction of PR-containing community. Sets of specific qPCR primers were designed to measure the absolute abundances of the major PR types. Spatial and depth profiles showed that PR-containing bacteria were abundant throughout the photic zone, comprising up to 45% of total bacteria. Although their abundance varied greatly with location and depth, Alphaproteobacteria predominated in the PR community in all water masses, with SAR11 as the major PR type. Low nutrient concentrations rather than light were the environmental drivers that best explained the abundance and distribution of arctic PR types. Together, our data suggests that PR-based phototrophy could be the major phototrophic prokaryotic process during the Arctic Ocean summer.
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Affiliation(s)
- Dominique Boeuf
- CNRS, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France; Sorbonne Universités - UPMC Université Paris 06, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France
| | - Raphaël Lami
- CNRS, USR 3579, Laboratoire de Biodiversité et Biotechnologies MicrobiennesBanyuls-sur-Mer, France; Sorbonne Universités - UPMC Université Paris 06, USR 3579, Observatoire OcéanologiqueBanyuls-sur-Mer, France
| | - Emelyne Cunnington
- CNRS, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France; Sorbonne Universités - UPMC Université Paris 06, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France
| | - Christian Jeanthon
- CNRS, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France; Sorbonne Universités - UPMC Université Paris 06, Station Biologique, UMR 7144 Adaptation and Diversité en Milieu MarinRoscoff, France
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15
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Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology. Microbiol Mol Biol Rev 2016; 80:929-54. [PMID: 27630250 DOI: 10.1128/mmbr.00003-16] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recognition of a new family of rhodopsins in marine planktonic bacteria, proton-pumping proteorhodopsin, expanded the known phylogenetic range, environmental distribution, and sequence diversity of retinylidene photoproteins. At the time of this discovery, microbial ion-pumping rhodopsins were known solely in haloarchaea inhabiting extreme hypersaline environments. Shortly thereafter, proteorhodopsins and other light-activated energy-generating rhodopsins were recognized to be widespread among marine bacteria. The ubiquity of marine rhodopsin photosystems now challenges prior understanding of the nature and contributions of "heterotrophic" bacteria to biogeochemical carbon cycling and energy fluxes. Subsequent investigations have focused on the biophysics and biochemistry of these novel microbial rhodopsins, their distribution across the tree of life, evolutionary trajectories, and functional expression in nature. Later discoveries included the identification of proteorhodopsin genes in all three domains of life, the spectral tuning of rhodopsin variants to wavelengths prevailing in the sea, variable light-activated ion-pumping specificities among bacterial rhodopsin variants, and the widespread lateral gene transfer of biosynthetic genes for bacterial rhodopsins and their associated photopigments. Heterologous expression experiments with marine rhodopsin genes (and associated retinal chromophore genes) provided early evidence that light energy harvested by rhodopsins could be harnessed to provide biochemical energy. Importantly, some studies with native marine bacteria show that rhodopsin-containing bacteria use light to enhance growth or promote survival during starvation. We infer from the distribution of rhodopsin genes in diverse genomic contexts that different marine bacteria probably use rhodopsins to support light-dependent fitness strategies somewhere between these two extremes.
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16
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Albarracín VH, Kraiselburd I, Bamann C, Wood PG, Bamberg E, Farias ME, Gärtner W. Functional Green-Tuned Proteorhodopsin from Modern Stromatolites. PLoS One 2016; 11:e0154962. [PMID: 27187791 PMCID: PMC4871484 DOI: 10.1371/journal.pone.0154962] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/21/2016] [Indexed: 11/18/2022] Open
Abstract
The sequenced genome of the poly-extremophile Exiguobacterium sp. S17, isolated from modern stromatolites at Laguna Socompa (3,570 m), a High-Altitude Andean Lake (HAAL) in Argentinean Puna revealed a putative proteorhodopsin-encoding gene. The HAAL area is exposed to the highest UV irradiation on Earth, making the microbial community living in the stromatolites test cases for survival strategies under extreme conditions. The heterologous expressed protein E17R from Exiguobacterium (248 amino acids, 85% sequence identity to its ortholog ESR from E. sibiricum) was assembled with retinal displaying an absorbance maximum at 524 nm, which makes it a member of the green-absorbing PR-subfamily. Titration down to low pH values (eventually causing partial protein denaturation) indicated a pK value between two and three. Global fitting of data from laser flash-induced absorption changes gave evidence for an early red-shifted intermediate (its formation being below the experimental resolution) that decayed (τ1 = 3.5 μs) into another red-shifted intermediate. This species decayed in a two-step process (τ2 = 84 μs, τ3 = 11 ms), to which the initial state of E17-PR was reformed with a kinetics of 2 ms. Proton transport capability of the HAAL protein was determined by BLM measurements. Additional blue light irradiation reduced the proton current, clearly identifying a blue light absorbing, M-like intermediate. The apparent absence of this intermediate is explained by closely matching formation and decay kinetics.
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Affiliation(s)
- Virginia Helena Albarracín
- Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET. Av. Belgrano y Pasaje Caseros. 4000- S. M. de Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, 4000, S. M. de Tucumán, Argentina
- * E-mail: (VHA); (WG)
| | - Ivana Kraiselburd
- Instituto de Biología Molecular y Celular de Rosario (IBR - CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas (FBIOYF - UNR), Suipacha 590, 2000, Rosario, Santa Fe, Argentina
| | - Christian Bamann
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Phillip G. Wood
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Ernst Bamberg
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - María Eugenia Farias
- Max-Planck-Institute for Biophysics, Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D-45470 Mülheim, Germany
- * E-mail: (VHA); (WG)
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17
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Complete Genome Sequence of the Proteorhodopsin-Containing Marine Bacterium Sediminicola sp. YIK13. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01635-15. [PMID: 26823585 PMCID: PMC4732338 DOI: 10.1128/genomea.01635-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Sediminicola sp. YIK13 is a marine flavobacterium, isolated from tidal flat sediment. Here, we present the first complete genome sequence of this genus, which consists of 3,569,807 bp with 39.4% GC content. This strain contains proteorhodopsin, as well as retinal biosynthesis genes, allowing it to utilize sunlight as an energy source.
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18
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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Björkman KM, Church MJ, Doggett JK, Karl DM. Differential Assimilation of Inorganic Carbon and Leucine by Prochlorococcus in the Oligotrophic North Pacific Subtropical Gyre. Front Microbiol 2015; 6:1401. [PMID: 26733953 PMCID: PMC4681814 DOI: 10.3389/fmicb.2015.01401] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 11/24/2015] [Indexed: 11/17/2022] Open
Abstract
The light effect on photoheterotrophic processes in Prochlorococcus, and primary and bacterial productivity in the oligotrophic North Pacific Subtropical Gyre was investigated using 14C-bicarbonate and 3H-leucine. Light and dark incubation experiments were conducted in situ throughout the euphotic zone (0–175 m) on nine expeditions to Station ALOHA over a 3-year period. Photosynthetrons were also used to elucidate rate responses in leucine and inorganic carbon assimilation as a function of light intensity. Taxonomic group and cell-specific rates were assessed using flow cytometric sorting. The light:dark assimilation rate ratios of leucine in the top 150 m were ∼7:1 for Prochlorococcus, whereas the light:dark ratios for the non-pigmented bacteria (NPB) were not significant different from 1:1. Prochlorococcus assimilated leucine in the dark at per cell rates similar to the NPB, with a contribution to the total community bacterial production, integrated over the euphotic zone, of approximately 20% in the dark and 60% in the light. Depth-resolved primary productivity and leucine incorporation showed that the ratio of Prochlorococcus leucine:primary production peaked at 100 m then declined steeply below the deep chlorophyll maximum (DCM). The photosynthetron experiments revealed that, for Prochlorococcus at the DCM, the saturating irradiance (Ek) for leucine incorporation was reached at approximately half the light intensity required for light saturation of 14C-bicarbonate assimilation. Additionally, high and low red fluorescing Prochlorococcus populations (HRF and LRF), co-occurring at the DCM, had similar Ek values for their respective substrates, however, maximum assimilation rates, for both leucine and inorganic carbon, were two times greater for HRF cells. Our results show that Prochlorococcus contributes significantly to bacterial production estimates using 3H-leucine, whether or not the incubations are conducted in the dark or light, and this should be considered when making assessments of bacterial production in marine environments where Prochlorococcus is present. Furthermore, Prochlorococcus primary productivity showed rate to light-flux patterns that were different from its light enhanced leucine incorporation. This decoupling from autotrophic growth may indicate a separate light stimulated mechanism for leucine acquisition.
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Affiliation(s)
- Karin M Björkman
- Department of Oceanography and Daniel K. Inouye Center for Microbial Ecology: Research and Education, University of Hawaii, Honolulu HI, USA
| | - Matthew J Church
- Department of Oceanography and Daniel K. Inouye Center for Microbial Ecology: Research and Education, University of Hawaii, Honolulu HI, USA
| | - Joseph K Doggett
- Department of Oceanography and Daniel K. Inouye Center for Microbial Ecology: Research and Education, University of Hawaii, Honolulu HI, USA
| | - David M Karl
- Department of Oceanography and Daniel K. Inouye Center for Microbial Ecology: Research and Education, University of Hawaii, Honolulu HI, USA
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20
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Kwon YM, Kim S, Jung K, Kim S. Diversity and functional analysis of light-driven pumping rhodopsins in marine Flavobacteria. Microbiologyopen 2015; 5:212-23. [PMID: 26663527 PMCID: PMC4831467 DOI: 10.1002/mbo3.321] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 12/13/2022] Open
Abstract
The aims of this study are the description of diversity for proteorhodopsin (PR)-containing flavobacteria in marine environments, the finding of novel photoreceptive membrane proteins, and the elucidation of the effect of light on the growth of three rhodopsin genes containing flavobacterium. We investigated novel sodium ion rhodopsin (NaR) and halorhodopsin (HR) genes from PR-containing flavobacteria that were previously isolated from diverse aquatic sites, mainly from tidal flat sediment (62.5%). In 16 PR-containing isolates, three new types of genes were found. Among these three isolates, one (Nonlabens sp. YIK11 isolated from sediment) contained both the NaR and chloride ion rhodopsin (ClR) - HR type of gene. The sequences showed that the DTE (proton pump), NDQ (sodium ion pump) and NTQ (chloride ion pump) motifs corresponding to the D85, T89, and D96 positions in bacteriorhodopsin (BR) were well conserved. Phylogenetic analysis indicated that three NaR and one ClR grouped within the same clade, as previously reported. Illumination of cell suspensions showed the change in proton pump activity, supporting that one or more rhodopsins are functional. The qRT-PCR study revealed that three rhodopsin genes, especially NaR, are highly induced when they are incubated in the presence of light or in the absence of sufficient nutrients. The expression levels of the DTE, NDQ, and NTQ motif-containing rhodopsin genes in YIK11 correlate positively with illumination, but negatively with nutrient levels. Based on those results, we concluded that light has a positive impact on the relative expression levels of the three rhodopsin genes in the flavobacterium, Nonlabens sp. YIK11, but with no apparent positive impact on growth. Consequently, light did not stimulate the growth of YIK11 as determined by cell numbers in a nutrient-limited or -enriched medium, although it contains and induces three rhodopsins.
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Affiliation(s)
- Yong Min Kwon
- Marine Biotechnology Research CenterKorea Institute of Ocean Science & Technology787 HaeanroAnsan426‐744Korea
| | - So‐Young Kim
- Department of Life Science and Institute of Biological ScienceSogang University35 Baekbeom‐RoMapo‐GuSeoul121‐742Korea
| | - Kwang‐Hwan Jung
- Department of Life Science and Institute of Biological ScienceSogang University35 Baekbeom‐RoMapo‐GuSeoul121‐742Korea
| | - Sang‐Jin Kim
- Marine Biotechnology Research CenterKorea Institute of Ocean Science & Technology787 HaeanroAnsan426‐744Korea
- Marine Biodiversity Institute of KoreaSeocheon325‐902Korea
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21
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Boeuf D, Audic S, Brillet-Guéguen L, Caron C, Jeanthon C. MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav080. [PMID: 26286928 PMCID: PMC4539915 DOI: 10.1093/database/bav080] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/25/2015] [Indexed: 11/12/2022]
Abstract
Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr.
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Affiliation(s)
- Dominique Boeuf
- CNRS, UMR 7144, Marine Phototrophic Prokaryotes Team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group
| | - Stéphane Audic
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group, CNRS, UMR 7144, Team Evolution des Protistes et Ecosystèmes Pélagiques and
| | | | - Christophe Caron
- CNRS, UPMC, FR2424, ABiMS, Station Biologique de Roscoff, F-29680 Roscoff, France
| | - Christian Jeanthon
- CNRS, UMR 7144, Marine Phototrophic Prokaryotes Team, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Oceanic Plankton Group,
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Courties A, Riedel T, Rapaport A, Lebaron P, Suzuki MT. Light-driven increase in carbon yield is linked to maintenance in the proteorhodopsin-containing Photobacterium angustum S14. Front Microbiol 2015. [PMID: 26217320 PMCID: PMC4498439 DOI: 10.3389/fmicb.2015.00688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A type of photoheterotrophic bacteria contain a transmembrane light-driven proton pump called proteorhodopsins (PRs). Due to the prevalence of these organisms in the upper water column of the World's Ocean, and their potential for light-driven ATP generation, they have been suggested to significantly influence energy and matter flows in the biosphere. To date, evidence for the significance of the light-driven metabolism of PR-containing prokaryotes has been obtained by comparing growth in batch culture, under light versus dark conditions, and it appears that responses to light are linked to unfavorable conditions, which so far have not been well parameterized. We studied light responses to carbon yields of the PR-containing Photobacterium angustum S14 using continuous culture conditions and light-dark cycles. We observed significant effects of light-dark cycles compared to dark controls, as well as significant differences between samples after 12 h illumination versus 12 h darkness. However, these effects were only observed under higher cell counts and lower pH associated with higher substrate concentrations. Under these substrate levels Pirt's maintenance coefficient was higher when compared to lower substrate dark controls, and decreased under light-dark cycles. It appears that light responses by P. angustum S14 are induced by the energetic status of the cells rather than by low substrate concentrations.
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Affiliation(s)
- Alicia Courties
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique , Banyuls-sur-Mer, France
| | - Thomas Riedel
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire Océanologique , Banyuls-sur-Mer, France
| | - Alain Rapaport
- INRA-Supagro, UMR MISTEA , Montpellier, France ; INRA-INRIA, MODEMIC Team , Sophia Antipolis, France
| | - Philippe Lebaron
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique , Banyuls-sur-Mer, France
| | - Marcelino T Suzuki
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique , Banyuls-sur-Mer, France
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Characterization of an Unconventional Rhodopsin from the Freshwater Actinobacterium Rhodoluna lacicola. J Bacteriol 2015; 197:2704-12. [PMID: 26055118 DOI: 10.1128/jb.00386-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/04/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Rhodopsin-encoding microorganisms are common in many environments. However, knowing that rhodopsin genes are present provides little insight into how the host cells utilize light. The genome of the freshwater actinobacterium Rhodoluna lacicola encodes a rhodopsin of the uncharacterized actinorhodopsin family. We hypothesized that actinorhodopsin was a light-activated proton pump and confirmed this by heterologously expressing R. lacicola actinorhodopsin in retinal-producing Escherichia coli. However, cultures of R. lacicola did not pump protons, even though actinorhodopsin mRNA and protein were both detected. Proton pumping in R. lacicola was induced by providing exogenous retinal, suggesting that the cells lacked the retinal cofactor. We used high-performance liquid chromatography (HPLC) and oxidation of accessory pigments to confirm that R. lacicola does not synthesize retinal. These results suggest that in some organisms, the actinorhodopsin gene is constitutively expressed, but rhodopsin-based light capture may require cofactors obtained from the environment. IMPORTANCE Up to 70% of microbial genomes in some environments are predicted to encode rhodopsins. Because most microbial rhodopsins are light-activated proton pumps, the prevalence of this gene suggests that in some environments, most microorganisms respond to or utilize light energy. Actinorhodopsins were discovered in an analysis of freshwater metagenomic data and subsequently identified in freshwater actinobacterial cultures. We hypothesized that actinorhodopsin from the freshwater actinobacterium Rhodoluna lacicola was a light-activated proton pump and confirmed this by expressing actinorhodopsin in retinal-producing Escherichia coli. Proton pumping in R. lacicola was induced only after both light and retinal were provided, suggesting that the cells lacked the retinal cofactor. These results indicate that photoheterotrophy in this organism and others may require cofactors obtained from the environment.
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Using total internal reflection fluorescence microscopy to visualize rhodopsin-containing cells. Appl Environ Microbiol 2015; 81:3442-50. [PMID: 25769822 DOI: 10.1128/aem.00230-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/04/2015] [Indexed: 01/03/2023] Open
Abstract
Sunlight is captured and converted to chemical energy in illuminated environments. Although (bacterio)chlorophyll-based photosystems have been characterized in detail, retinal-based photosystems, rhodopsins, have only recently been identified as important mediators of light energy capture and conversion. Recent estimates suggest that up to 70% of cells in some environments harbor rhodopsins. However, because rhodopsin autofluorescence is low-comparable to that of carotenoids and significantly less than that of (bacterio)chlorophylls-these estimates are based on metagenomic sequence data, not direct observation. We report here the use of ultrasensitive total internal reflection fluorescence (TIRF) microscopy to distinguish between unpigmented, carotenoid-producing, and rhodopsin-expressing bacteria. Escherichia coli cells were engineered to produce lycopene, β-carotene, or retinal. A gene encoding an uncharacterized rhodopsin, actinorhodopsin, was cloned into retinal-producing E. coli. The production of correctly folded and membrane-incorporated actinorhodopsin was confirmed via development of pink color in E. coli and SDS-PAGE. Cells expressing carotenoids or actinorhodopsin were imaged by TIRF microscopy. The 561-nm excitation laser specifically illuminated rhodopsin-containing cells, allowing them to be differentiated from unpigmented and carotenoid-containing cells. Furthermore, water samples collected from the Delaware River were shown by PCR to have rhodopsin-containing organisms and were examined by TIRF microscopy. Individual microorganisms that fluoresced under illumination from the 561-nm laser were identified. These results verify the sensitivity of the TIRF microscopy method for visualizing and distinguishing between different molecules with low autofluorescence, making it useful for analyzing natural samples.
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Light-stimulated growth of proteorhodopsin-bearing sea-ice psychrophile Psychroflexus torquis is salinity dependent. ISME JOURNAL 2013; 7:2206-13. [PMID: 23788334 PMCID: PMC3806269 DOI: 10.1038/ismej.2013.97] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/15/2013] [Accepted: 05/16/2013] [Indexed: 12/27/2022]
Abstract
Proteorhodopsins (PRs) are commonly found in marine prokaryotes and allow microbes to use light as an energy source. In recent studies, it was reported that PR stimulates growth and survival under nutrient-limited conditions. In this study, we tested the effect of nutrient and salinity stress on the extremely psychrophilic sea-ice bacterial species Psychroflexus torquis, which possesses PR. We demonstrated for the first time that light-stimulated growth occurs under conditions of salinity stress rather than nutrient limitation and that elevated salinity is related to increased growth yields, PR levels and associated proton-pumping activity. PR abundance in P. torquis also is post-transcriptionally regulated by both light and salinity and thus could represent an adaptation to its sea-ice habitat. Our findings extend the existing paradigm that light provides an energy source for marine prokaryotes under stress conditions other than nutrient limitation.
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Comparable light stimulation of organic nutrient uptake by SAR11 and Prochlorococcus in the North Atlantic subtropical gyre. ISME JOURNAL 2012; 7:603-14. [PMID: 23096403 DOI: 10.1038/ismej.2012.126] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Subtropical oceanic gyres are the most extensive biomes on Earth where SAR11 and Prochlorococcus bacterioplankton numerically dominate the surface waters depleted in inorganic macronutrients as well as in dissolved organic matter. In such nutrient poor conditions bacterioplankton could become photoheterotrophic, that is, potentially enhance uptake of scarce organic molecules using the available solar radiation to energise appropriate transport systems. Here, we assessed the photoheterotrophy of the key microbial taxa in the North Atlantic oligotrophic gyre and adjacent regions using (33)P-ATP, (3)H-ATP and (35)S-methionine tracers. Light-stimulated uptake of these substrates was assessed in two dominant bacterioplankton groups discriminated by flow cytometric sorting of tracer-labelled cells and identified using catalysed reporter deposition fluorescence in situ hybridisation. One group of cells, encompassing 48% of all bacterioplankton, were identified as members of the SAR11 clade, whereas the other group (24% of all bacterioplankton) was Prochlorococcus. When exposed to light, SAR11 cells took 31% more ATP and 32% more methionine, whereas the Prochlorococcus cells took 33% more ATP and 34% more methionine. Other bacterioplankton did not demonstrate light stimulation. Thus, the SAR11 and Prochlorococcus groups, with distinctly different light-harvesting mechanisms, used light equally to enhance, by approximately one-third, the uptake of different types of organic molecules. Our findings indicate the significance of light-driven uptake of essential organic nutrients by the dominant bacterioplankton groups in the surface waters of one of the less productive, vast regions of the world's oceans-the oligotrophic North Atlantic subtropical gyre.
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Recent advances and future perspectives in microbial phototrophy in antarctic sea ice. BIOLOGY 2012; 1:542-56. [PMID: 24832507 PMCID: PMC4009807 DOI: 10.3390/biology1030542] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 12/05/2022]
Abstract
Bacteria that utilize sunlight to supplement metabolic activity are now being described in a range of ecosystems. While it is likely that phototrophy provides an important competitive advantage, the contribution that these microorganisms make to the bioenergetics of polar marine ecosystems is unknown. In this minireview, we discuss recent advances in our understanding of phototrophic bacteria and highlight the need for future research.
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Proteorhodopsin-like genes present in thermoacidophilic high-mountain microbial communities. Appl Environ Microbiol 2012; 78:7813-7. [PMID: 22941077 DOI: 10.1128/aem.01683-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Proteorhodopsin (PR) sequences were PCR amplified from three Andean acidic hot spring samples. These sequences were similar to freshwater and marine PRs and they contained residues indicative of proton-pumping activity and of proteins that absorb green light; these findings suggest that PRs might contribute to cellular metabolism in these habitats.
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Gifford SM, Sharma S, Rinta-Kanto JM, Moran MA. Quantitative analysis of a deeply sequenced marine microbial metatranscriptome. ISME JOURNAL 2010; 5:461-72. [PMID: 20844569 DOI: 10.1038/ismej.2010.141] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The potential of metatranscriptomic sequencing to provide insights into the environmental factors that regulate microbial activities depends on how fully the sequence libraries capture community expression (that is, sample-sequencing depth and coverage depth), and the sensitivity with which expression differences between communities can be detected (that is, statistical power for hypothesis testing). In this study, we use an internal standard approach to make absolute (per liter) estimates of transcript numbers, a significant advantage over proportional estimates that can be biased by expression changes in unrelated genes. Coastal waters of the southeastern United States contain 1 × 10(12) bacterioplankton mRNA molecules per liter of seawater (~200 mRNA molecules per bacterial cell). Even for the large bacterioplankton libraries obtained in this study (~500,000 possible protein-encoding sequences in each of two libraries after discarding rRNAs and small RNAs from >1 million 454 FLX pyrosequencing reads), sample-sequencing depth was only 0.00001%. Expression levels of 82 genes diagnostic for transformations in the marine nitrogen, phosphorus and sulfur cycles ranged from below detection (<1 × 10(6) transcripts per liter) for 36 genes (for example, phosphonate metabolism gene phnH, dissimilatory nitrate reductase subunit napA) to >2.7 × 10(9) transcripts per liter (ammonia transporter amt and ammonia monooxygenase subunit amoC). Half of the categories for which expression was detected, however, had too few copy numbers for robust statistical resolution, as would be required for comparative (experimental or time-series) expression studies. By representing whole community gene abundance and expression in absolute units (per volume or mass of environment), 'omics' data can be better leveraged to improve understanding of microbially mediated processes in the ocean.
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Affiliation(s)
- Scott M Gifford
- Department of Marine Sciences, University of Georgia, Athens, GA 30602-3636, USA
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30
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Abstract
Proteorhodopsins (PRs) are widespread bacterial integral membrane proteins that function as light-driven proton pumps. Antarctic sea ice supports a complex community of autotrophic algae, heterotrophic bacteria, viruses, and protists that are an important food source for higher trophic levels in ice-covered regions of the Southern Ocean. Here, we present the first report of PR-bearing bacteria, both dormant and active, in Antarctic sea ice from a series of sites in the Ross Sea using gene-specific primers. Positive PR sequences were generated from genomic DNA at all depths in sea ice, and these sequences aligned with the classes Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria. The sequences showed some similarity to previously reported PR sequences, although most of the sequences were generally distinct. Positive PR sequences were also observed from cDNA reverse transcribed from RNA isolated from sea ice samples. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within sea ice. Both blue-absorbing and green-absorbing forms of PRs were detected, and only a limited number of blue-absorbing forms were found and were in the midsection of the sea ice profile in this study. Questions still remain regarding the protein's ecological functions, and ultimately, field experiments will be needed to establish the ecological and functional role of PRs in the sea ice ecosystem.
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Gómez-Consarnau L, Akram N, Lindell K, Pedersen A, Neutze R, Milton DL, González JM, Pinhassi J. Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol 2010; 8:e1000358. [PMID: 20436956 PMCID: PMC2860489 DOI: 10.1371/journal.pbio.1000358] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 03/18/2010] [Indexed: 12/21/2022] Open
Abstract
Proteorhodopsins are globally abundant photoproteins found in bacteria in the photic zone of the ocean. Although their function as proton pumps with energy-yielding potential has been demonstrated, the ecological role of proteorhodopsins remains largely unexplored. Here, we report the presence and function of proteorhodopsin in a member of the widespread genus Vibrio, uncovered through whole-genome analysis. Phylogenetic analysis suggests that the Vibrio strain AND4 obtained proteorhodopsin through lateral gene transfer, which could have modified the ecology of this marine bacterium. We demonstrate an increased long-term survival of AND4 when starved in seawater exposed to light rather than held in darkness. Furthermore, mutational analysis provides the first direct evidence, to our knowledge, linking the proteorhodopsin gene and its biological function in marine bacteria. Thus, proteorhodopsin phototrophy confers a fitness advantage to marine bacteria, representing a novel mechanism for bacterioplankton to endure frequent periods of resource deprivation at the ocean's surface.
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Affiliation(s)
- Laura Gómez-Consarnau
- Marine Microbiology, School of Natural Sciences, Linnaeus University, Kalmar, Sweden
| | - Neelam Akram
- Marine Microbiology, School of Natural Sciences, Linnaeus University, Kalmar, Sweden
| | | | - Anders Pedersen
- Department of Chemistry, Biochemistry and Biophysics, Göteborg Gothenburg University, Göteborg, Sweden
| | - Richard Neutze
- Department of Chemistry, Biochemistry and Biophysics, Göteborg Gothenburg University, Göteborg, Sweden
| | - Debra L. Milton
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - José M. González
- Department of Microbiology and Cell Biology, University of La Laguna, La Laguna, Tenerife, Spain
| | - Jarone Pinhassi
- Marine Microbiology, School of Natural Sciences, Linnaeus University, Kalmar, Sweden
- * E-mail:
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Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol 2010; 76:3187-97. [PMID: 20305030 DOI: 10.1128/aem.02971-09] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteorhodopsin (PR), a photoactive proton pump containing retinal, is present in approximately half of all bacteria in the ocean, but its physiological role is still unclear, since very few strains carrying the PR gene have been cultured. The aim of this work was to characterize PR diversity in a North Sea water sample, cultivate a strain representative of North Sea PR clusters, and study the effects of light and carbon concentration on the expression of the PR gene. A total of 117 PR sequences, of which 101 were unique, were obtained from a clone library of PCR-amplified PR gene fragments. Of the North Sea PRs, 97% were green light absorbing, as inferred from the amino acid at position 105; 67% of the PR protein fragments showed closest similarity to PRs from Alphaproteobacteria, 4% showed closest similarity to PRs from Gammaproteobacteria, and 29% showed closest similarity to PRs from "Bacteroidetes"/Flavobacteria. The dominant PR cluster (comprising 18% of all PRs) showed a high degree of similarity to the PR from the cultivated Roseobacter strain HTCC2255. The relative abundances of the North Sea PR clusters were confirmed by quantitative PCR. They were detected in metagenomic fragments from coastal oceans worldwide with various degrees of abundance. Several hundred bacterial strains from the North Sea water sample were cultivated on oligocarbophilic media. By screening with degenerate primers, two strains carrying the PR gene were identified. Their 16S rRNA gene sequences were identical and affiliated with a Bacteroidetes subcluster from the North Sea. The PR sequence of isolate PRO95 was completed by chromosomal walking. It was 76% identical to that of Dokdonia donghaensis MED134 and was functional, as indicated by the signature amino acids. PRO95 expressed its PR gene in liquid media containing between 9.7 and 121 mM carbon, both in the light and in the dark. Growth was not enhanced by light. Thus, the detection of the physiological role of PR may require more sensitive methods.
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Deep sequencing of a dimethylsulfoniopropionate-degrading gene (dmdA) by using PCR primer pairs designed on the basis of marine metagenomic data. Appl Environ Microbiol 2009; 76:609-17. [PMID: 19948858 DOI: 10.1128/aem.01258-09] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In silico design and testing of environmental primer pairs with metagenomic data are beneficial for capturing a greater proportion of the natural sequence heterogeneity in microbial functional genes, as well as for understanding limitations of existing primer sets that were designed from more restricted sequence data. PCR primer pairs targeting 10 environmental clades and subclades of the dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, were designed using an iterative bioinformatic approach that took advantage of thousands of dmdA sequences captured in marine metagenomic data sets. Using the bioinformatically optimized primers, dmdA genes were amplified from composite free-living coastal bacterioplankton DNA (from 38 samples over 5 years and two locations) and sequenced using 454 technology. An average of 6,400 amplicons per primer pair represented more than 700 clusters of environmental dmdA sequences across all primers, with clusters defined conservatively at >90% nucleotide sequence identity (approximately 95% amino acid identity). Degenerate and inosine-based primers did not perform better than specific primer pairs in determining dmdA richness and sometimes captured a lower degree of richness of sequences from the same DNA sample. A comparison of dmdA sequences in free-living versus particle-associated bacteria in southeastern U.S. coastal waters showed that sequence richness in some dmdA subgroups differed significantly between size fractions, though most gene clusters were shared (52 to 91%) and most sequences were affiliated with the shared clusters (approximately 90%). The availability of metagenomic sequence data has significantly enhanced the design of quantitative PCR primer pairs for this key functional gene, providing robust access to the capabilities and activities of DMSP demethylating bacteria in situ.
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Photoheterotrophic microbes in the Arctic Ocean in summer and winter. Appl Environ Microbiol 2009; 75:4958-66. [PMID: 19502441 DOI: 10.1128/aem.00117-09] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Photoheterotrophic microbes, which are capable of utilizing dissolved organic materials and harvesting light energy, include coccoid cyanobacteria (Synechococcus and Prochlorococcus), aerobic anoxygenic phototrophic (AAP) bacteria, and proteorhodopsin (PR)-containing bacteria. Our knowledge of photoheterotrophic microbes is largely incomplete, especially for high-latitude waters such as the Arctic Ocean, where photoheterotrophs may have special ecological relationships and distinct biogeochemical impacts due to extremes in day length and seasonal ice cover. These microbes were examined by epifluorescence microscopy, flow cytometry, and quantitative PCR (QPCR) assays for PR and a gene diagnostic of AAP bacteria (pufM). The abundance of AAP bacteria and PR-containing bacteria decreased from summer to winter, in parallel with a threefold decrease in the total prokaryotic community. In contrast, the abundance of Synechococcus organisms did not decrease in winter, suggesting that their growth was supported by organic substrates. Results from QPCR assays revealed no substantial shifts in the community structure of AAP bacteria and PR-containing bacteria. However, Arctic PR genes were different from those found at lower latitudes, and surprisingly, they were not similar to those in Antarctic coastal waters. Photoheterotrophic microbes appear to compete successfully with strict heterotrophs during winter darkness below the ice, but AAP bacteria and PR-containing bacteria do not behave as superior competitors during the summer.
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Miranda MRM, Choi AR, Shi L, Bezerra AG, Jung KH, Brown LS. The photocycle and proton translocation pathway in a cyanobacterial ion-pumping rhodopsin. Biophys J 2009; 96:1471-81. [PMID: 19217863 DOI: 10.1016/j.bpj.2008.11.026] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 11/14/2008] [Indexed: 10/21/2022] Open
Abstract
The genome of thylakoidless cyanobacterium Gloeobacter violaceus encodes a fast-cycling rhodopsin capable of light-driven proton transport. We characterize the dark state, the photocycle, and the proton translocation pathway of GR spectroscopically. The dark state of GR contains predominantly all-trans-retinal and, similar to proteorhodopsin, does not show the light/dark adaptation. We found an unusually strong coupling between the conformation of the retinal and the site of Glu132, the homolog of Asp96 of BR. Although the photocycle of GR is similar to that of proteorhodopsin in general, it differs in accumulating two intermediates typical for BR, the L-like and the N-like states. The latter state has a deprotonated cytoplasmic proton donor and is spectrally distinct from the strongly red-shifted N intermediate known for proteorhodopsin. The proton uptake precedes the release and occurs during the transition to the O intermediate. The proton translocation pathway of GR is similar to those of other proton-pumping rhodopsins, involving homologs of BR Schiff base proton acceptor and donor Asp85 and Asp96 (Asp121 and Glu132). We assigned a pair of FTIR bands (positive at 1749 cm(-1) and negative at 1734 cm(-1)) to the protonation and deprotonation, respectively, of these carboxylic acids.
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Affiliation(s)
- Mylene R M Miranda
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Campbell BJ, Smith JL, Hanson TE, Klotz MG, Stein LY, Lee CK, Wu D, Robinson JM, Khouri HM, Eisen JA, Cary SC. Adaptations to submarine hydrothermal environments exemplified by the genome of Nautilia profundicola. PLoS Genet 2009; 5:e1000362. [PMID: 19197347 PMCID: PMC2628731 DOI: 10.1371/journal.pgen.1000362] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Accepted: 12/31/2008] [Indexed: 11/19/2022] Open
Abstract
Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment--some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20 degrees C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere--anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles.
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Genetic diversity and abundance of flavobacterial proteorhodopsin in China seas. Appl Environ Microbiol 2008; 75:529-33. [PMID: 18931298 DOI: 10.1128/aem.01114-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Proteorhodopsin (PR) genes related to Flavobacteria were found to be highly diverse in the East and South China seas and displayed a distinct geographic pattern, which appeared to reflect cold versus warm adaptation when Global Oceanic Sampling database metagenomic data were included. Flavobacterial PR genes were more abundant offshore than nearshore, implying that inheritance of the PR gene could be important for Flavobacteria living in the oligotrophic environment.
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38
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Mary I, Tarran GA, Warwick PE, Terry MJ, Scanlan DJ, Burkill PH, Zubkov MV. Light enhanced amino acid uptake by dominant bacterioplankton groups in surface waters of the Atlantic Ocean. FEMS Microbiol Ecol 2008; 63:36-45. [PMID: 18081589 DOI: 10.1111/j.1574-6941.2007.00414.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
(35)S-Methionine and (3)H-leucine bioassay tracer experiments were conducted on two meridional transatlantic cruises to assess whether dominant planktonic microorganisms use visible sunlight to enhance uptake of these organic molecules at ambient concentrations. The two numerically dominant groups of oceanic bacterioplankton were Prochlorococcus cyanobacteria and bacteria with low nucleic acid (LNA) content, comprising 60% SAR11-related cells. The results of flow cytometric sorting of labelled bacterioplankton cells showed that when incubated in the light, Prochlorococcus and LNA bacteria increased their uptake of amino acids on average by 50% and 23%, respectively, compared with those incubated in the dark. Amino acid uptake of Synechococcus cyanobacteria was also enhanced by visible light, but bacteria with high nucleic acid content showed no light stimulation. Additionally, differential uptake of the two amino acids by the Prochlorococcus and LNA cells was observed. The populations of these two types of cells on average completely accounted for the determined 22% light enhancement of amino acid uptake by the total bacterioplankton community, suggesting a plausible way of harnessing light energy for selectively transporting scarce nutrients that could explain the numerical dominance of these groups in situ.
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Affiliation(s)
- Isabelle Mary
- National Oceanography Centre, European Way, Southampton, UK
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