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Deutsch Y, Samara M, Nasser A, Berman-Frank I, Ezra D. Kocuria flava, a Bacterial Endophyte of the Marine Macroalga Bryopsis plumosa, Emits 8-Nonenoic Acid Which Inhibits the Aquaculture Pathogen Saprolegnia parasitica. Mar Drugs 2023; 21:476. [PMID: 37755090 PMCID: PMC10532832 DOI: 10.3390/md21090476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
Secondary metabolites-organic compounds that are often bioactive-produced by endophytes, among others, provide a selective advantage by increasing the organism's survivability. Secondary metabolites mediate the symbiotic relationship between endophytes and their host, potentially providing the host with tolerance to, and protection against biotic and abiotic stressors. Secondary metabolites can be secreted as a dissolved substance or emitted as a volatile. In a previous study, we isolated bioactive endophytes from several macroalgae and tested them in vitro for their ability to inhibit major disease-causing pathogens of aquatic animals in the aquaculture industry. One endophyte (isolate Abp5, K. flava) inhibited and killed, in vitro, the pathogen Saprolegnia parasitica, an oomycete that causes saprolegniasis-a disease affecting a wide range of aquatic animals. Here, using analytical chemistry tools, we found that Abp5 produces the volatile organic compound (VOC) 8-nonenoic acid. Once we confirmed the production of this compound by the endophyte, we tested the compound's ability to treat S. parasitica in in vitro and in vivo bioassays. In the latter, we found that 5 mg/L of the compound improves the survival of larvae challenged with S. parasitica by 54.5%. Our isolation and characterization of the VOC emitted by the endophytic K. flava establish the groundwork for future studies of endophytic biocontrol agents from macroalgae. Use of this compound could enable managing oomycete agricultural pathogens in general, and S. parasitica in particular, a major causal agent in aquaculture diseases.
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Affiliation(s)
- Ynon Deutsch
- Department of Plant Pathology and Weed Research, The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel;
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, Haifa 3103301, Israel;
| | - Mohamed Samara
- The Inter-Institutional Analytical Instrumentation Unit (IU), The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel; (M.S.); (A.N.)
| | - Ahmed Nasser
- The Inter-Institutional Analytical Instrumentation Unit (IU), The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel; (M.S.); (A.N.)
| | - Ilana Berman-Frank
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, Haifa 3103301, Israel;
| | - David Ezra
- Department of Plant Pathology and Weed Research, The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel;
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2
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Bonnet S, Benavides M, Le Moigne FAC, Camps M, Torremocha A, Grosso O, Dimier C, Spungin D, Berman-Frank I, Garczarek L, Cornejo-Castillo FM. Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean. ISME J 2023; 17:47-58. [PMID: 36163270 PMCID: PMC9750961 DOI: 10.1038/s41396-022-01319-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/25/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022]
Abstract
Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export.
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Affiliation(s)
- Sophie Bonnet
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
| | - Mar Benavides
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.5399.60000 0001 2176 4817Turing Center for Living Systems, Aix-Marseille University, 13009 Marseille, France
| | - Frédéric A. C. Le Moigne
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France ,grid.463763.30000 0004 0638 0577LEMAR, Laboratoire des sciences de l’environnement marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280 Plouzané, Technopôle Brest-Iroise France
| | - Mercedes Camps
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Antoine Torremocha
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Olivier Grosso
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13288 Marseille, France
| | - Céline Dimier
- grid.499565.20000 0004 0366 8890Laboratoire d’Océanographie de Villefranche (LOV), Sorbonne Université, CNRS, 06230 Villefranche sur mer, France
| | - Dina Spungin
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Ilana Berman-Frank
- grid.18098.380000 0004 1937 0562University of Haifa, The Leon H. Charney School of Marine Sciences, Haifa, 3498838 Israel
| | - Laurence Garczarek
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Francisco M. Cornejo-Castillo
- grid.464101.60000 0001 2203 0006Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France ,grid.418218.60000 0004 1793 765XInstitut de Ciènces del Mar (ICM-CSIC), E08003 Barcelona, Spain
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3
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Shlosberg Y, Spungin D, Schuster G, Berman-Frank I, Adir N. Trichodesmium erythraeum produces a higher photocurrent than other cyanobacterial species in bio-photo electrochemical cells. Biochim Biophys Acta Bioenerg 2022; 1863:148910. [PMID: 35944660 DOI: 10.1016/j.bbabio.2022.148910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
The increase in world energy consumption, and the worries from potential future disasters that may derive from climate change have stimulated the development of renewable energy technologies. One promising method is the utilization of whole photosynthetic cyanobacterial cells to produce photocurrent in a bio-photo electrochemical cell (BPEC). The photocurrent can be derived from either the respiratory or photosynthetic pathways, via the redox couple NADP+/NADPH mediating cyclic electron transport between photosystem I inside the cells, and the anode. In the past, most studies have utilized the fresh-water cyanobacterium Synechocystis sp. PCC 6803 (Syn). Here, we show that the globally important marine cyanobacterium Trichodesmium erythraeum flourishing in the subtropical oceans can provide improved currents as compared to Syn. We applied 2D-fluorescence measurements to detect the secretion of NADPH and show that the resulting photocurrent production is enhanced by increasing the electrolyte salinity, Further enhancement of the photocurrent can be obtained by the addition of electron mediators such as NAD+, NADP+, cytochrome C, vitamin B1, or potassium ferricyanide. Finally, we produce photocurrent from additional cyanobacterial species: Synechocystis sp. PCC6803, Synechococcus elongatus PCC7942, Acaryochloris marina MBIC 11017, and Spirulina, using their cultivation media as electrolytes for the BPEC.
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Affiliation(s)
- Yaniv Shlosberg
- Grand Technion Energy Program, Technion, Haifa 32000, Israel; Schulich Faculty of Chemistry, Technion, Haifa 320000, Israel
| | - Dina Spungin
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Gadi Schuster
- Grand Technion Energy Program, Technion, Haifa 32000, Israel; Faculty of Biology, Technion, Haifa 32000, Israel
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Noam Adir
- Grand Technion Energy Program, Technion, Haifa 32000, Israel; Schulich Faculty of Chemistry, Technion, Haifa 320000, Israel.
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4
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Benavides M, Bonnet S, Le Moigne FAC, Armin G, Inomura K, Hallstrøm S, Riemann L, Berman-Frank I, Poletti E, Garel M, Grosso O, Leblanc K, Guigue C, Tedetti M, Dupouy C. Sinking Trichodesmium fixes nitrogen in the dark ocean. ISME J 2022; 16:2398-2405. [PMID: 35835942 PMCID: PMC9478103 DOI: 10.1038/s41396-022-01289-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 01/04/2023]
Abstract
The photosynthetic cyanobacterium Trichodesmium is widely distributed in the surface low latitude ocean where it contributes significantly to N2 fixation and primary productivity. Previous studies found nifH genes and intact Trichodesmium colonies in the sunlight-deprived meso- and bathypelagic layers of the ocean (200-4000 m depth). Yet, the ability of Trichodesmium to fix N2 in the dark ocean has not been explored. We performed 15N2 incubations in sediment traps at 170, 270 and 1000 m at two locations in the South Pacific. Sinking Trichodesmium colonies fixed N2 at similar rates than previously observed in the surface ocean (36-214 fmol N cell-1 d-1). This activity accounted for 40 ± 28% of the bulk N2 fixation rates measured in the traps, indicating that other diazotrophs were also active in the mesopelagic zone. Accordingly, cDNA nifH amplicon sequencing revealed that while Trichodesmium accounted for most of the expressed nifH genes in the traps, other diazotrophs such as Chlorobium and Deltaproteobacteria were also active. Laboratory experiments simulating mesopelagic conditions confirmed that increasing hydrostatic pressure and decreasing temperature reduced but did not completely inhibit N2 fixation in Trichodesmium. Finally, using a cell metabolism model we predict that Trichodesmium uses photosynthesis-derived stored carbon to sustain N2 fixation while sinking into the mesopelagic. We conclude that sinking Trichodesmium provides ammonium, dissolved organic matter and biomass to mesopelagic prokaryotes.
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Affiliation(s)
- Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France.
- Turing Center for Living Systems, Aix-Marseille University, 13009, Marseille, France.
| | - Sophie Bonnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Frédéric A C Le Moigne
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
- LEMAR, Laboratoire des Sciences de l'Environnement Marin, UMR6539, CNRS, UBO, IFREMER, IRD, 29280, Plouzané, Technopôle Brest-Iroise, France
| | - Gabrielle Armin
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, South Kingstown, RI, USA
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt, Carmel, Haifa, Israel
| | - Emilie Poletti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Garel
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Olivier Grosso
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Karine Leblanc
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Catherine Guigue
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Marc Tedetti
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
| | - Cécile Dupouy
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, 13288, Marseille, France
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5
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Koedooder C, Landou E, Zhang F, Wang S, Basu S, Berman-Frank I, Shaked Y, Rubin-Blum M. Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Trichodesmium Diversity. Front Microbiol 2022; 13:879970. [PMID: 35707175 PMCID: PMC9189399 DOI: 10.3389/fmicb.2022.879970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022] Open
Abstract
Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Their blooms consist of a dynamic assemblage of subpopulations and colony morphologies that are hypothesized to occupy unique niches. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). Trichodesmium thiebautii (puffs) and Trichodesmium erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we hypothesize that this phenotypic variation is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to Trichodesmium nobis and Trichodesmium miru, respectively that likely occurred as single filaments. The hetR gene phylogeny further indicated that the genotype in clade IV could represent the species Trichodesmium contortum. Importantly, we show the presence of hetR paralogs in Trichodesmium, where two copies of the hetR gene were present within T. thiebautii genomes. This may lead to the overestimation of Trichodesmium diversity as one of the copies misidentified T. thiebautii as Trichodesmium aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations.
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Affiliation(s)
- Coco Koedooder
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Israel Oceanographic and Limnological Research, Haifa, Israel
- *Correspondence: Coco Koedooder,
| | - Etai Landou
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel
| | - Futing Zhang
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Siyuan Wang
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Subhajit Basu
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
- Microsensor Research Group, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Yeala Shaked
- The Fredy and Nadine Herrmann Institute of Earth Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
- The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
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6
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Lory C, Van Wambeke F, Fourquez M, Barani A, Guieu C, Tilliette C, Marie D, Nunige S, Berman-Frank I, Bonnet S. Assessing the contribution of diazotrophs to microbial Fe uptake using a group specific approach in the Western Tropical South Pacific Ocean. ISME Commun 2022; 2:41. [PMID: 37938297 PMCID: PMC9723570 DOI: 10.1038/s43705-022-00122-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/26/2022] [Accepted: 04/07/2022] [Indexed: 04/27/2023]
Abstract
Diazotrophs are often limited by iron (Fe) availability in the oligotrophic ocean. The Western Tropical South Pacific (WTSP) ocean has been suggested as an intense N2 fixation area due to Fe fertilizations through shallow hydrothermal activity. Yet, the Fe demand of diazotrophs in their natural habitat, where they cohabit with other microbial organisms also requiring Fe, remains unknown. Here we develop and apply a method consisting of coupling 55Fe uptake experiments with cell-sorting by flow cytometry, and provide group-specific rates of in situ Fe uptake by the microbial community in the WTSP, in addition to bulk and size fractionation rates. We reveal that the diazotrophs Crocosphaera watsonii and Trichodesmium contribute substantially to the bulk in situ Fe uptake (~33% on average over the studied area), despite being numerically less abundant compared to the rest of the planktonic community. Trichodesmium had the highest cell-specific Fe uptake rates, followed by C. watsonii, picoeukaryotes, Prochlorococcus, Synechococcus and finally heterotrophic bacteria. Calculated Fe:C quotas were higher (by 2 to 52-fold) for both studied diazotrophs compared to those of the non-diazotrophic plankton, reflecting their high intrinsic Fe demand. This translates into a diazotroph biogeographical distribution that appears to be influenced by ambient dissolved Fe concentrations in the WTSP. Despite having low cell-specific uptake rates, Prochlorococcus and heterotrophic bacteria were largely the main contributors to the bulk Fe uptake (~23% and ~12%, respectively). Overall, this group-specific approach increases our ability to examine the ecophysiological role of functional groups, including those of less abundant and/or less active microbes.
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Affiliation(s)
- C Lory
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France.
| | - F Van Wambeke
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - M Fourquez
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - A Barani
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - C Guieu
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, France
| | - C Tilliette
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, LOV, F-06230, Villefranche-sur-Mer, France
| | - D Marie
- Sorbonne Université, CNRS, Station Biologique de Roscoff, Roscoff, France
| | - S Nunige
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - I Berman-Frank
- Department of Marine Biology, The Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - S Bonnet
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France.
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7
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Benavides M, Conradt L, Bonnet S, Berman-Frank I, Barrillon S, Petrenko A, Doglioli A. Fine-scale sampling unveils diazotroph patchiness in the South Pacific Ocean. ISME Commun 2021; 1:3. [PMID: 37938230 PMCID: PMC9723698 DOI: 10.1038/s43705-021-00006-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 06/01/2023]
Abstract
Diazotrophs are important contributors to nitrogen availability in the ocean. Oceanographic cruise data accumulated over the past three decades has revealed a heterogeneous distribution of diazotroph species at regional to global scales. However, dynamic fine-scale physical structures likely affect the distribution of diazotrophs at smaller spatiotemporal scales. The interaction between fine-scale ocean dynamics and diazotrophs remains poorly understood due to typically insufficient spatiotemporal sampling resolution and the lack of parallel detailed physical studies. Here we show the distribution of five groups of diazotrophs in the South Pacific at an unprecedented resolution of 7-16 km. We find a patchy distribution of diazotrophs, with each group being differentially affected by parameters describing fine-scale physical structures. The observed variability in species abundance and distribution would be masked by a coarser sampling resolution, highlighting the need to consider fine-scale physics to resolve the distribution of diazotrophs in the ocean.
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Affiliation(s)
- Mar Benavides
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France.
| | - Louis Conradt
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Sophie Bonnet
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Stéphanie Barrillon
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Anne Petrenko
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
| | - Andrea Doglioli
- Aix Marseille Univ, Université de Toulon, CNRS, IRD, MIO UM 110, Marseille, France
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8
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Minina EA, Staal J, Alvarez VE, Berges JA, Berman-Frank I, Beyaert R, Bidle KD, Bornancin F, Casanova M, Cazzulo JJ, Choi CJ, Coll NS, Dixit VM, Dolinar M, Fasel N, Funk C, Gallois P, Gevaert K, Gutierrez-Beltran E, Hailfinger S, Klemenčič M, Koonin EV, Krappmann D, Linusson A, Machado MFM, Madeo F, Megeney LA, Moschou PN, Mottram JC, Nyström T, Osiewacz HD, Overall CM, Pandey KC, Ruland J, Salvesen GS, Shi Y, Smertenko A, Stael S, Ståhlberg J, Suárez MF, Thome M, Tuominen H, Van Breusegem F, van der Hoorn RAL, Vardi A, Zhivotovsky B, Lam E, Bozhkov PV. Classification and Nomenclature of Metacaspases and Paracaspases: No More Confusion with Caspases. Mol Cell 2020; 77:927-929. [PMID: 32142688 PMCID: PMC7325697 DOI: 10.1016/j.molcel.2019.12.020] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden; COS, Heidelberg University, Heidelberg, Germany.
| | - Jens Staal
- VIB Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Vanina E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martin, San Martin, Buenos Aires, Argentina
| | - John A Berges
- Department of Biological Sciences and School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Israel
| | - Rudi Beyaert
- VIB Center for Inflammation Research, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | | | - Magali Casanova
- Aix-Marseille Univ, CNRS, LISM, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Juan J Cazzulo
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martin, San Martin, Buenos Aires, Argentina
| | - Chang Jae Choi
- The University of Texas at Austin, Marine Science Institute, Port Aransas, TX, USA
| | - Nuria S Coll
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, Spain
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, South San Francisco, CA, USA
| | - Marko Dolinar
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia
| | - Nicolas Fasel
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | | | - Patrick Gallois
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Emilio Gutierrez-Beltran
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Sevilla, Spain
| | - Stephan Hailfinger
- Interfaculty Institute for Biochemistry, Eberhard Karls University, Tübingen, Germany
| | - Marina Klemenčič
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Ljubljana, Slovenia
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Anna Linusson
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Maurício F M Machado
- Interdisciplinary Center for Biochemical Research, University of Mogi das Cruzes, Mogi das Cruzes, Brazil
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, BioTechMed Graz, Graz, Austria
| | - Lynn A Megeney
- Sprott Centre for Stem Cell Research, Ottawa Hospital Research Institute and Departments of Medicine and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Panagiotis N Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece; Department of Biology, University of Crete, Greece; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Gothenburg, Sweden
| | - Heinz D Osiewacz
- Institute for Molecular Biosciences, Faculty of Biosciences, Goethe University, Frankfurt/Main, Germany
| | - Christopher M Overall
- Departments of Oral Biological and Medical Sciences and Biochemistry and Molecular Biology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Kailash C Pandey
- Protein Biochemistry and Engineering Laboratory, ICMR-National Institute of Malaria Research, New Delhi, India
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Germany; German Center for Infection Research (DZIF), partner site Munich, Germany
| | - Guy S Salvesen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Yigong Shi
- School of Life Sciences, Westlake University, Xihu District, Hangzhou Zhejiang Province, China
| | - Andrei Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - Simon Stael
- VIB Center for Medical Biotechnology, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Jerry Ståhlberg
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - María Fernanda Suárez
- Departamento de Biologia Molecular y Bioquimica, Facultad de Ciencias, Universidad de Malaga, Campus de Teatinos, Malaga, Spain
| | - Margot Thome
- Department of Biochemistry, University of Lausanne, Epalinges, Switzerland
| | - Hannele Tuominen
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | | | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Boris Zhivotovsky
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Faculty of Fundamental Medicine, MV Lomonosov Moscow State University, Moscow, Russia
| | - Eric Lam
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.
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9
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Spungin D, Berman-Frank I. Assessment of Metacaspase Activity in Phytoplankton. Bio Protoc 2019; 9:e3341. [PMID: 33654845 DOI: 10.21769/bioprotoc.3341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/15/2019] [Accepted: 07/22/2019] [Indexed: 11/02/2022] Open
Abstract
Programmed cell death (PCD) is an irreversible, genetically-controlled form of cell suicide in which an endogenous biochemical pathway leads to morphological changes and ultimately, cellular demise. PCD is accompanied by de-novo protein synthesis of a family of proteases-"caspases" that are often used as a diagnostic marker of PCD. Although phytoplankton do not contain true caspases, caspase-like activity (hypothetical proteins with analogous activity) has been traditionally used as a diagnostic marker of PCD in marine phytoplankton. Increased caspase-like proteolytic activity was demonstrated when synthetic fluorogenic activity substrates specific for caspases (with an Asp at the P1 position) were applied upon PCD induction. Metacaspases, cysteine proteases, share structural properties with those of caspases, yet they are highly specific for Arg and Lys cleavage site at the P1 position implying that caspase specific substrates are not indicative of metacaspase catalytic activity. This method specifically tests direct metacaspase activity in phytoplankton by the cleavage of the fluorogenic metacaspase substrate Ac-VRPR-AMC. Metacaspase activity was tested by the addition of a metacaspase specific peptide that is conjugated to the fluorescent reporter molecule. The cleavage of the peptide by the metacaspase releases the fluorochrome that, when excited by light, emits fluorescence. The level of metacaspase enzymatic activity in the cell lysate is directly proportional to the fluorescence signal detected. The use of specific standards in this test enables the quantification of the fluorescence results. This assay directly allows monitoring the metacaspase cleavage products and thereby tracing evidence for programmed cell death.
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Affiliation(s)
- Dina Spungin
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ilana Berman-Frank
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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10
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Spungin D, Bidle KD, Berman-Frank I. Metacaspase involvement in programmed cell death of the marine cyanobacteriumTrichodesmium. Environ Microbiol 2019; 21:667-681. [DOI: 10.1111/1462-2920.14512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 12/19/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Dina Spungin
- The Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat-Gan, 5290002 Israel
| | - Kay D. Bidle
- Department of Marine and Coastal Sciences; Rutgers University; New Brunswick NJ USA
| | - Ilana Berman-Frank
- The Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat-Gan, 5290002 Israel
- Department of Marine Biology; Leon H. Charney School of Marine Sciences, University of Haifa; Haifa Israel
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11
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Hou S, López-Pérez M, Pfreundt U, Belkin N, Stüber K, Huettel B, Reinhardt R, Berman-Frank I, Rodriguez-Valera F, Hess WR. Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise. ISME J 2018; 12:981-996. [PMID: 29335641 PMCID: PMC5864184 DOI: 10.1038/s41396-017-0034-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/20/2017] [Accepted: 11/26/2017] [Indexed: 12/21/2022]
Abstract
Interactions between co-existing microorganisms deeply affect the physiology of the involved organisms and, ultimately, the function of the ecosystem as a whole. Copiotrophic Alteromonas are marine gammaproteobacteria that thrive during the late stages of phytoplankton blooms in the marine environment and in laboratory co-cultures with cyanobacteria such as Trichodesmium. The response of this heterotroph to the sometimes rapid and transient changes in nutrient supply when the phototroph crashes is not well understood. Here, we isolated and sequenced the strain Alteromonas macleodii str. Te101 from a laboratory culture of Trichodesmium erythraeum IMS101, yielding a chromosome of 4.63 Mb and a single plasmid of 237 kb. Increasing salinities to ≥43 ppt inhibited the growth of Trichodesmium but stimulated growth of the associated Alteromonas. We characterized the transcriptomic responses of both microorganisms and identified the complement of active transcriptional start sites in Alteromonas at single-nucleotide resolution. In replicate cultures, a similar set of genes became activated in Alteromonas when growth rates of Trichodesmium declined and mortality was high. The parallel activation of fliA, rpoS and of flagellar assembly and growth-related genes indicated that Alteromonas might have increased cell motility, growth, and multiple biosynthetic activities. Genes with the highest expression in the data set were three small RNAs (Aln1a-c) that were identified as analogs of the small RNAs CsrB-C in E. coli or RsmX-Z in pathogenic bacteria. Together with the carbon storage protein A (CsrA) homolog Te101_05290, these RNAs likely control the expression of numerous genes in responding to changes in the environment.
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Affiliation(s)
- Shengwei Hou
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany
| | - Mario López-Pérez
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, 03550, Alicante, Spain
| | - Ulrike Pfreundt
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany.,ETH Zürich, Department of Civil, Environmental and Geomatic Engineering, Institute of Environmental Engineering, Stefano-Franscini-Platz 5, CH-8093, Zürich, Switzerland
| | - Natalia Belkin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Kurt Stüber
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - Bruno Huettel
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - Richard Reinhardt
- Max Planck-Genome-Centre Cologne, Carl-von-Linné-Weg 10, D-50829, Köln, Germany
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, Apartado 18, San Juan, 03550, Alicante, Spain
| | - Wolfgang R Hess
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, D-79104, Freiburg, Germany. .,Freiburg Institute for Advanced Studies, University of Freiburg, Albertstr. 19, D-79104, Freiburg, Germany.
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12
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Moisander PH, Benavides M, Bonnet S, Berman-Frank I, White AE, Riemann L. Chasing after Non-cyanobacterial Nitrogen Fixation in Marine Pelagic Environments. Front Microbiol 2017; 8:1736. [PMID: 28943875 PMCID: PMC5596534 DOI: 10.3389/fmicb.2017.01736] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 08/25/2017] [Indexed: 11/22/2022] Open
Abstract
Traditionally, cyanobacterial activity in oceanic photic layers was considered responsible for the marine pelagic dinitrogen (N2) fixation. Other potentially N2-fixing bacteria and archaea have also been detected in the pelagic water column, however, the activity and importance of these non-cyanobacterial diazotrophs (NCDs) remain poorly constrained. In this perspective we summarize the N2 fixation rates from recently published studies on photic and aphotic layers that have been attributed to NCD activity via parallel molecular measurements, and discuss the status, challenges, and data gaps in estimating non-cyanobacterial N2 fixation NCNF in the ocean. Rates attributed to NCNF have generally been near the detection limit thus far (<1 nmol N L−1 d−1). Yet, if considering the large volume of the dark ocean, even low rates of NCNF could make a significant contribution to the new nitrogen input to the ocean. The synthesis here shows that nifH transcription data for NCDs have been reported in only a few studies where N2 fixation rates were detected in the absence of diazotrophic cyanobacteria. In addition, high apparent diversity and regional variability in the NCDs complicate investigations of these communities. Future studies should focus on further investigating impacts of environmental drivers including oxygen, dissolved organic matter, and dissolved inorganic nitrogen on NCNF. Describing the ecology of NCDs and accurately measuring NCNF rates, are critical for a future evaluation of the contribution of NCNF to the marine nitrogen budget.
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Affiliation(s)
- Pia H Moisander
- Department of Biology, University of Massachusetts DartmouthNorth Dartmouth, MA, United States
| | - Mar Benavides
- Marine Biology Section, Department of Biology, University of CopenhagenHelsingør, Denmark
| | - Sophie Bonnet
- Centre National de la Recherche Scientifique, IRD, Aix-Marseille Université, Université de ToulonMarseille, France
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan UniversityRamat Gan, Israel
| | - Angelicque E White
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State UniversityCorvallis, OR, United States
| | - Lasse Riemann
- Marine Biology Section, Department of Biology, University of CopenhagenHelsingør, Denmark
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13
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Miller DR, Pfreundt U, Elifantz H, Hess WR, Berman-Frank I. Microbial metatranscriptomes from the thermally stratified Gulf of Aqaba/Eilat during summer. Mar Genomics 2017; 32:23-26. [DOI: 10.1016/j.margen.2016.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
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14
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Belkin N, Rahav E, Elifantz H, Kress N, Berman-Frank I. The effect of coagulants and antiscalants discharged with seawater desalination brines on coastal microbial communities: A laboratory and in situ study from the southeastern Mediterranean. Water Res 2017; 110:321-331. [PMID: 28063294 DOI: 10.1016/j.watres.2016.12.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 12/05/2016] [Accepted: 12/10/2016] [Indexed: 06/06/2023]
Abstract
Desalination outflows frequently discharge brine containing coagulants and antiscalants (e.g. Iron-hydroxides and polyphosphonates) to the coastal environment. Here we examined changes in composition and productivity of natural microbial coastal communities in experimental mesocosms treated with either iron-hydroxide (Fe), polyphosphonate (Pn), or a combination of high salinities with both chemicals (All). Within 2 h of addition Fe already altered the microbial community composition, enhanced the bacterial production (BP) and cell specific production (BP/BA), and decreased primary production. Addition of Pn, relieved phosphorus stress as demonstrated by the immediate (within 2 h) and significant reduction in the ecto-enzyme alkaline phosphatase activity (APA). Synergistic effects were observed in the All treatment, reflected by increased production of both primary and bacterial producers as P-stress was relieved. After 10 days of incubation, the microbial community composition changed significantly only in the All treatment. The Fe-only treatment caused a significant decline in autotrophic biomass and in the assimilation number (AN), while in both the Pn and the All treatments the BP/BA increased with the added P. We also examined the microbial community responses in a natural impacted environment at the Ashkelon seawater desalination plant brine discharge site during summer and winter. The community composition differed in elevated-salinity compared with non-impacted stations with higher AN and bacterial efficiencies (BP/BA) measured in summer in the elevated-salinity stations. The seasonal differences in responses may reflect both biotic (i.e. initial community composition) and abiotic factors (currents and residence time of salinity gradients). Our results emphasize that desalination brine discharges that include chemicals such as iron-hydroxide and polyphosphonates can induce physiological and compositional changes in the microbial community. With the expansion of desalination facilities worldwide such shifts in composition and function of the microbial communities may destabilize and change local aquatic food webs and should thus be monitored.
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Affiliation(s)
- Natalia Belkin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel
| | - Hila Elifantz
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Nurit Kress
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Haifa 31080, Israel
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
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15
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Pfreundt U, Spungin D, Hou S, Voß B, Berman-Frank I, Hess WR. Genome of a giant bacteriophage from a decaying Trichodesmium bloom. Mar Genomics 2017; 33:21-25. [PMID: 28237778 DOI: 10.1016/j.margen.2017.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 01/31/2017] [Accepted: 02/04/2017] [Indexed: 10/20/2022]
Abstract
De-novo assembly of a metagenomic dataset obtained from a decaying cyanobacterial Trichodesmium bloom from the New Caledonian lagoon resulted in a complete giant phage genome of 257,908bp, obtained independently with multiple assembly tools. Noteworthy, gammaproteobacteria were an abundant fraction in the sequenced samples. Mapping of the raw reads with 99% accuracy to the giant phage genome resulted in an average coverage of 262X. The closest sequenced relatives, albeit still distant, are the Pseudomonas phages PaBG from Lake Baikal and Lu11 isolated from a soil sample from the Philippines. The phage reported here might belong to the same family within the Myoviridae as PaBG and Lu11 and would thus be its first marine member, indicating a more widespread occurrence of this group. We named this phage NCTB (New Caledonia Trichodesmium Bloom) after its origin.
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Affiliation(s)
- Ulrike Pfreundt
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Dina Spungin
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Björn Voß
- Computational Biology, Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
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16
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Hou S, Pfreundt U, Miller D, Berman-Frank I, Hess WR. mdRNA-Seq analysis of marine microbial communities from the northern Red Sea. Sci Rep 2016; 6:35470. [PMID: 27759035 PMCID: PMC5069720 DOI: 10.1038/srep35470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/28/2016] [Indexed: 01/17/2023] Open
Abstract
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5′ ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities. 16S rDNA quantification revealed that 24% of the analyzed community were group II marine Euryarchaeota in which we identified a highly abundant non-coding RNA, Tan1, and detected very high expression of genes encoding intrinsically disordered proteins, as well as enzymes for the synthesis of specific B vitamins, extracellular peptidases, carbohydrate-active enzymes, and transport systems. These results highlight previously unknown functions of Euryarchaeota with community-wide relevance. The complementation of metatranscriptomic studies with mdRNA-Seq provides substantial additional information regarding transcriptional start sites, promoter activities, and the identification of non-coding RNAs.
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Affiliation(s)
- Shengwei Hou
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ulrike Pfreundt
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Dan Miller
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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17
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Belkin N, Rahav E, Elifantz H, Kress N, Berman-Frank I. Enhanced salinities, as a proxy of seawater desalination discharges, impact coastal microbial communities of the eastern Mediterranean Sea. Environ Microbiol 2015; 17:4105-20. [DOI: 10.1111/1462-2920.12979] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 07/02/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Natalia Belkin
- Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Eyal Rahav
- Israel Oceanographic and Limnological Research; National Institute of Oceanography; Haifa 31080 Israel
| | - Hila Elifantz
- Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
| | - Nurit Kress
- Israel Oceanographic and Limnological Research; National Institute of Oceanography; Haifa 31080 Israel
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences; Bar-Ilan University; Ramat Gan 52900 Israel
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18
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Spungin D, Berman-Frank I, Levitan O. Trichodesmium’s strategies to alleviate phosphorus limitation in the future acidified oceans. Environ Microbiol 2014; 16:1935-47. [PMID: 25009839 DOI: 10.1111/1462-2920.12424] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Global warming may exacerbate inorganic nutrient limitation, including phosphorus (P), in the surface waters of tropical oceans that are home to extensive blooms of the marine diazotrophic cyanobacterium, Trichodesmium. We examined the combined effects of P limitation and pCO(2), forecast under ocean acidification scenarios, on Trichodesmium erythraeum IMS101 cultures. We measured nitrogen acquisition,glutamine synthetase activity, C uptake rates, intracellular Adenosine Triphosphate (ATP) concentration and the pool sizes of related key proteins. Here, we present data supporting the idea that cellular energy re-allocation enables the higher growth and N(2) fixation rates detected in Trichodesmium cultured under high pCO(2). This is reflected in altered protein abundance and metabolic pools. Also modified are particulate organic carbon and nitrogen production rates,enzymatic activities, and cellular ATP concentrations. We suggest that adjusting these cellular pathways to changing environmental conditions enables Trichodesmium to compensate for low P availability and to thrive in acidified oceans. Moreover, elevated pCO(2) could provide Trichodesmium with a competitive dominance that would extend its niche, particularly in P-limited regions of the tropical and subtropical oceans.
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19
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Pfreundt U, Miller D, Adusumilli L, Stambler N, Berman-Frank I, Hess WR. Depth dependent metatranscriptomes of the marine pico-/nanoplanktonic communities in the Gulf of Aqaba/Eilat during seasonal deep mixing. Mar Genomics 2014; 18 Pt B:93-5. [PMID: 24984262 DOI: 10.1016/j.margen.2014.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 11/17/2022]
Abstract
Metatranscriptomics is a widely used approach to study the gene expression within a whole microbial community. Spatial or temporal differences observed between datasets point to transcriptional responses to changes or alterations in the community's environment. No transcriptomic data has yet been published from the oligotrophic Gulf of Aqaba/Eilat, northern Red Sea. The primary objective of this study was to create a depth-specific snapshot of community gene expression ranging from the surface waters to the bottom of the mixed-layer depth during winter when thermal destratification occurs. Our secondary objective was to compare two different methods for transcriptome analysis. While random RNA sequencing (RNA-seq) is routinely used, differential RNA sequencing (dRNA-seq, enriched in primary transcripts) has never been used for metatranscriptomics. In this dataset, we used dRNA-seq for samples that were collected from three depths while applying RNA-seq for one of the samples to obtain direct comparison between the methods. We de-novo assembled the reads into contigs and show a high percentage of reads mapping back to the contigs, supporting the validity of the assembly.
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Affiliation(s)
- Ulrike Pfreundt
- Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Dan Miller
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Lakshmi Adusumilli
- Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Noga Stambler
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics group, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany.
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20
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Rahav E, Bar-Zeev E, Ohayon S, Elifantz H, Belkin N, Herut B, Mulholland MR, Berman-Frank I. Dinitrogen fixation in aphotic oxygenated marine environments. Front Microbiol 2013; 4:227. [PMID: 23986748 PMCID: PMC3753716 DOI: 10.3389/fmicb.2013.00227] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 07/26/2013] [Indexed: 11/13/2022] Open
Abstract
We measured N2 fixation rates from oceanic zones that have traditionally been ignored as sources of biological N2 fixation; the aphotic, fully oxygenated, nitrate (NO−3)-rich, waters of the oligotrophic Levantine Basin (LB) and the Gulf of Aqaba (GA). N2 fixation rates measured from pelagic aphotic waters to depths up to 720 m, during the mixed and stratified periods, ranged from 0.01 nmol N L−1 d−1 to 0.38 nmol N L−1 d−1. N2 fixation rates correlated significantly with bacterial productivity and heterotrophic diazotrophs were identified from aphotic as well as photic depths. Dissolved free amino acid amendments to whole water from the GA enhanced bacterial productivity by 2–3.5 fold and N2 fixation rates by ~2-fold in samples collected from aphotic depths while in amendments to water from photic depths bacterial productivity increased 2–6 fold while N2 fixation rates increased by a factor of 2 to 4 illustrating that both BP and heterotrophic N2 fixation were carbon limited. Experimental manipulations of aphotic waters from the LB demonstrated a significant positive correlation between transparent exopolymeric particle (TEP) concentrations and N2 fixation rates. This suggests that sinking organic material and high carbon (C): nitrogen (N) micro-environments (such as TEP-based aggregates or marine snow) could support high heterotrophic N2 fixation rates in oxygenated surface waters and in the aphotic zones. Indeed, our calculations show that aphotic N2 fixation accounted for 37 to 75% of the total daily integrated N2 fixation rates at both locations in the Mediterranean and Red Seas with rates equal or greater to those measured from the photic layers. Moreover, our results indicate that that while N2 fixation may be limited in the surface waters, aphotic, pelagic N2 fixation may contribute significantly to new N inputs in other oligotrophic basins, yet it is currently not included in regional or global N budgets.
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Affiliation(s)
- Eyal Rahav
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University Ramat Gan, Israel ; Israel Oceanographic and Limnological Research, National Institute of Oceanography Haifa, Israel
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Bar-Zeev E, Avishay I, Bidle KD, Berman-Frank I. Programmed cell death in the marine cyanobacterium Trichodesmium mediates carbon and nitrogen export. ISME J 2013; 7:2340-8. [PMID: 23887173 DOI: 10.1038/ismej.2013.121] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 06/10/2013] [Accepted: 06/15/2013] [Indexed: 12/31/2022]
Abstract
The extent of carbon (C) and nitrogen (N) export to the deep ocean depends upon the efficacy of the biological pump that transports primary production to depth, thereby preventing its recycling in the upper photic zone. The dinitrogen-fixing (diazotrophic) Trichodesmium spp. contributes significantly to oceanic C and N cycling by forming extensive blooms in nutrient-poor tropical and subtropical regions. These massive blooms generally collapse several days after forming, but the cellular mechanism responsible, along with the magnitude of associated C and N export processes, are as yet unknown. Here, we used a custom-made, 2-m high water column to simulate a natural bloom and to specifically test and quantify whether the programmed cell death (PCD) of Trichodesmium mechanistically regulates increased vertical flux of C and N. Our findings demonstrate that extremely rapid development and abrupt, PCD-induced demise (within 2-3 days) of Trichodesmium blooms lead to greatly elevated excretions of transparent exopolymers and a massive downward pulse of particulate organic matter. Our results mechanistically link autocatalytic PCD and bloom collapse to quantitative C and N export fluxes, suggesting that PCD may have an impact on the biological pump efficiency in the oceans.
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Affiliation(s)
- Edo Bar-Zeev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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22
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Sorek M, Yacobi YZ, Roopin M, Berman-Frank I, Levy O. Photosynthetic circadian rhythmicity patterns of
Symbiodium
, the coral endosymbiotic algae. Proc Biol Sci 2013. [DOI: 10.1098/rspb.2013.1012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Bar-Zeev E, Belkin N, Liberman B, Berman-Frank I, Berman T. Bioflocculation: chemical free, pre-treatment technology for the desalination industry. Water Res 2013; 47:3093-3102. [PMID: 23566330 DOI: 10.1016/j.watres.2013.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 01/06/2013] [Accepted: 03/10/2013] [Indexed: 06/02/2023]
Abstract
Rapid sand filtration (RSF), proceeded by chemical coagulation and flocculation, is a commonly used, effective pretreatment in the desalination industry. We designed and tested a novel, large pilot-scale, two-stage granular Rapid Bioflocculation Filter (RBF) based on a first-stage Bioflocculator (BF) unit followed by a mixed-media bed filter (MBF). The BF filter bed consisted of an extremely porous volcanic Tuff granular medium which provided an enlarged surface area for microbial development and biofilm proliferation. We compared the efficiency of the pilot RBF to that of a full-scale RSF, operating with upstream chemical coagulation, by measuring the removal from the same untreated seawater feed of key factors related to membrane clogging: SDI, turbidity, chlorophyll a (Chl a) and transparent exopolymer particles (TEP). After 2 weeks of operation, the Tuff grains were colonized extensively by coccoid bacteria that formed biofilm along the entire BF. With bacterial colonization and biofilm development, numerous aggregates of bacteria and some algal cells embedded in an amorphous organic matrix were formed on and within the Tuff grains. By 1-3 months, the biotic diversity within the Tuff filter bed had increased to include filamentous bacteria, cyanobacteria, fungi, protista and even crustaceans and marine worms. During and for ≈ 24 h after each cleaning cycle (carried out every 5 to 7 days by upward flushing with air and water), large numbers of floc-like particles, from ≈ 15 μm to ≈ 2 mm in size were observed in the filtrate of the BF unit. Microscopic examination of these flocs (stained with Alcian Blue and SYTO(R) 9) showed that they were aggregates of many smaller particles with associated bacteria and algae within a polysaccharide gel-like matrix. These biogenic flocs (bioflocs) were observed to form during normal operation of the RBF, accumulating as aggregates of inorganic and organic material on the Tuff surfaces. With each flush cleaning cycle, these bioflocs were released into the BF effluent but were retained by the second phase MBF unit. No flocs were seen in the MBF filtrate. Over a year-long study, both the pilot RBF and the full-scale RSF showed similar filtration efficiencies, measured as the percentage removal of Chl a, TEP, turbidity and SDI from the same seawater feed. These results indicate the potential of the bioflocculation approach with no chemical additives as an alternative to conventional RSF pretreatment for large SWRO facilities.
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Affiliation(s)
- Edo Bar-Zeev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
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24
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Sorek M, Yacobi YZ, Roopin M, Berman-Frank I, Levy O. Photosynthetic circadian rhythmicity patterns of Symbiodinium, [corrected] the coral endosymbiotic algae. Proc Biol Sci 2013; 280:20122942. [PMID: 23554392 PMCID: PMC3619499 DOI: 10.1098/rspb.2012.2942] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Biological clocks are self-sustained endogenous timers that enable organisms (from cyanobacteria to humans) to anticipate daily environmental rhythms, and adjust their physiology and behaviour accordingly. Symbiotic corals play a central role in the creation of biologically rich ecosystems based on mutualistic symbioses between the invertebrate coral and dinoflagellate protists from the genus Symbiodinium. In this study, we experimentally establish that Symbiodinium photosynthesis, both as a free-living unicellular algae and as part of the symbiotic association with the coral Stylophora pistillata, is ‘wired’ to the circadian clock mechanism with a ‘free-run’ cycle close to 24 h. Associated photosynthetic pigments also showed rhythmicity under light/dark conditions and under constant light conditions, while the expression of the oxygen-evolving enhancer 1 gene (within photosystem II) coincided with photosynthetically evolved oxygen in Symbiodinium cultures. Thus, circadian regulation of the Symbiodinium photosynthesis is, however, complicated as being linked to the coral/host that have probably profound physiochemical influence on the intracellular environment. The temporal patterns of photosynthesis demonstrated here highlight the physiological complexity and interdependence of the algae circadian clock associated in this symbiosis and the plasticity of algae regulatory mechanisms downstream of the circadian clock.
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Affiliation(s)
- Michal Sorek
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel.
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25
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Yogev T, Rahav E, Bar-Zeev E, Man-Aharonovich D, Stambler N, Kress N, Béjà O, Mulholland MR, Herut B, Berman-Frank I. Is dinitrogen fixation significant in the Levantine Basin, East Mediterranean Sea? Environ Microbiol 2011; 13:854-71. [PMID: 21244595 DOI: 10.1111/j.1462-2920.2010.02402.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report N(2) fixation rates measured from two stations monitored monthly off the Mediterranean coast of Israel during 2006 and 2007, and along a transect from Israel to Crete in September 2008. Analyses of time-series data revealed expression of nifH genes from diazotrophs in nifH clusters I and II, including cyanobacterial bloom-formers Trichodesmium and diatom-Richelia intracellularis associations. However, nifH gene abundance and rates of N(2) fixation were very low in all size fractions measured (> 0.7 µm). Volumetric (15) N uptake ranged from below detection (∼ 36% of > 300 samples) to a high of 0.3 nmol N l(-1) d(-1) and did not vary distinctly with depth or season. Areal N(2) fixation averaged ∼ 1 to 4 µmol N m(-2) d(-1) and contributed only ∼ 1% and 2% of new production and ∼ 0.25% and 0.5% of primary production for the mixed (winter) and stratified (spring-fall) periods respectively. N(2) fixation rates along the 2008 east-west transect were also extremely low (0-0.04 nmol N l(-1) d(-1), integrated average 2.6 µmol N m(-2) d(-1) ) with 37% of samples below detection and no discernable difference between stations. We demonstrate that diazotrophy and N(2) fixation contribute only a minor amount of new N to the P impoverished eastern Mediterranean Sea.
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Affiliation(s)
- Tali Yogev
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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26
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Levitan O, Sudhaus S, LaRoche J, Berman-Frank I. The influence of pCO2 and temperature on gene expression of carbon and nitrogen pathways in Trichodesmium IMS101. PLoS One 2010; 5:e15104. [PMID: 21151907 PMCID: PMC2997788 DOI: 10.1371/journal.pone.0015104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 10/21/2010] [Indexed: 11/28/2022] Open
Abstract
Growth, protein amount, and activity levels of metabolic pathways in Trichodesmium are influenced by environmental changes such as elevated pCO(2) and temperature. This study examines changes in the expression of essential metabolic genes in Trichodesmium grown under a matrix of pCO(2) (400 and 900 µatm) and temperature (25 and 31°C). Using RT-qPCR, we studied 21 genes related to four metabolic functional groups: CO(2) concentrating mechanism (bicA1, bicA2, ccmM, ccmK2, ccmK3, ndhF4, ndhD4, ndhL, chpX), energy metabolism (atpB, sod, prx, glcD), nitrogen metabolism (glnA, hetR, nifH), and inorganic carbon fixation and photosynthesis (rbcL, rca, psaB, psaC, psbA). nifH and most photosynthetic genes exhibited relatively high abundance and their expression was influenced by both environmental parameters. A two to three orders of magnitude increase was observed for glnA and hetR only when both pCO(2) and temperature were elevated. CO(2) concentrating mechanism genes were not affected by pCO(2) and temperature and their expression levels were markedly lower than that of the nitrogen metabolism and photosynthetic genes. Many of the CO(2) concentrating mechanism genes were co-expressed throughout the day. Our results demonstrate that in Trichodesmium, CO(2) concentrating mechanism genes are constitutively expressed. Co-expression of genes from different functional groups were frequently observed during the first half of the photoperiod when oxygenic photosynthesis and N(2) fixation take place, pointing at the tight and complex regulation of gene expression in Trichodesmium. Here we provide new data linking environmental changes of pCO(2) and temperature to gene expression in Trichodesmium. Although gene expression indicates an active metabolic pathway, there is often an uncoupling between transcription and enzyme activity, such that transcript level cannot usually be directly extrapolated to metabolic activity.
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Affiliation(s)
- Orly Levitan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, Israel.
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27
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Levitan O, Kranz SA, Spungin D, Prásil O, Rost B, Berman-Frank I. Combined effects of CO2 and light on the N2-fixing cyanobacterium Trichodesmium IMS101: a mechanistic view. Plant Physiol 2010; 154:346-56. [PMID: 20625002 PMCID: PMC2938161 DOI: 10.1104/pp.110.159285] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The marine diazotrophic cyanobacterium Trichodesmium responds to elevated atmospheric CO(2) partial pressure (pCO(2)) with higher N(2) fixation and growth rates. To unveil the underlying mechanisms, we examined the combined influence of pCO(2) (150 and 900 microatm) and light (50 and 200 micromol photons m(-2) s(-1)) on Trichodesmium IMS101. We expand on a complementary study that demonstrated that while elevated pCO(2) enhanced N(2) fixation and growth, oxygen evolution and carbon fixation increased mainly as a response to high light. Here, we investigated changes in the photosynthetic fluorescence parameters of photosystem II, in ratios of the photosynthetic units (photosystem I:photosystem II), and in the pool sizes of key proteins involved in the fixation of carbon and nitrogen as well as their subsequent assimilation. We show that the combined elevation in pCO(2) and light controlled the operation of the CO(2)-concentrating mechanism and enhanced protein activity without increasing their pool size. Moreover, elevated pCO(2) and high light decreased the amounts of several key proteins (NifH, PsbA, and PsaC), while amounts of AtpB and RbcL did not significantly change. Reduced investment in protein biosynthesis, without notably changing photosynthetic fluxes, could free up energy that can be reallocated to increase N(2) fixation and growth at elevated pCO(2) and light. We suggest that changes in the redox state of the photosynthetic electron transport chain and posttranslational regulation of key proteins mediate the high flexibility in resources and energy allocation in Trichodesmium. This strategy should enable Trichodesmium to flourish in future surface oceans characterized by elevated pCO(2), higher temperatures, and high light.
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Affiliation(s)
- Orly Levitan
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel.
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28
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Kranz SA, Levitan O, Richter KU, Prásil O, Berman-Frank I, Rost B. Combined effects of CO2 and light on the N2-fixing cyanobacterium Trichodesmium IMS101: physiological responses. Plant Physiol 2010; 154:334-45. [PMID: 20625004 PMCID: PMC2938149 DOI: 10.1104/pp.110.159145] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/11/2010] [Indexed: 05/19/2023]
Abstract
Recent studies on the diazotrophic cyanobacterium Trichodesmium erythraeum (IMS101) showed that increasing CO(2) partial pressure (pCO(2)) enhances N(2) fixation and growth. Significant uncertainties remain as to the degree of the sensitivity to pCO(2), its modification by other environmental factors, and underlying processes causing these responses. To address these questions, we examined the responses of Trichodesmium IMS101 grown under a matrix of low and high levels of pCO(2) (150 and 900 microatm) and irradiance (50 and 200 micromol photons m(-2) s(-1)). Growth rates as well as cellular carbon and nitrogen contents increased with increasing pCO(2) and light levels in the cultures. The pCO(2)-dependent stimulation in organic carbon and nitrogen production was highest under low light. High pCO(2) stimulated rates of N(2) fixation and prolonged the duration, while high light affected maximum rates only. Gross photosynthesis increased with light but did not change with pCO(2). HCO(3)(-) was identified as the predominant carbon source taken up in all treatments. Inorganic carbon uptake increased with light, but only gross CO(2) uptake was enhanced under high pCO(2). A comparison between carbon fluxes in vivo and those derived from (13)C fractionation indicates high internal carbon cycling, especially in the low-pCO(2) treatment under high light. Light-dependent oxygen uptake was only detected under low pCO(2) combined with high light or when low-light-acclimated cells were exposed to high light, indicating that the Mehler reaction functions also as a photoprotective mechanism in Trichodesmium. Our data confirm the pronounced pCO(2) effect on N(2) fixation and growth in Trichodesmium and further show a strong modulation of these effects by light intensity. We attribute these responses to changes in the allocation of photosynthetic energy between carbon acquisition and the assimilation of carbon and nitrogen under elevated pCO(2). These findings are supported by a complementary study looking at photosynthetic fluorescence parameters of photosystem II, photosynthetic unit stoichiometry (photosystem I:photosystem II), and pool sizes of key proteins in carbon and nitrogen acquisition.
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Affiliation(s)
- Sven A Kranz
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
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29
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Levitan O, Brown CM, Sudhaus S, Campbell D, LaRoche J, Berman-Frank I. Regulation of nitrogen metabolism in the marine diazotroph Trichodesmium IMS101 under varying temperatures and atmospheric CO2 concentrations. Environ Microbiol 2010; 12:1899-912. [DOI: 10.1111/j.1462-2920.2010.02195.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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30
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Man-Aharonovich D, Philosof A, Kirkup BC, Le Gall F, Yogev T, Berman-Frank I, Polz MF, Vaulot D, Béjà O. Diversity of active marine picoeukaryotes in the Eastern Mediterranean Sea unveiled using photosystem-II psbA transcripts. ISME J 2010; 4:1044-52. [DOI: 10.1038/ismej.2010.25] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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31
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Ionescu D, Oren A, Levitan O, Hindiyeh M, Malkawi H, Berman-Frank I. The cyanobacterial community of the Zerka Ma'in hot springs, Jordan: morphological and molecular diversity and nitrogen fixation. ACTA ACUST UNITED AC 2009. [DOI: 10.1127/1864-1318/2009/0130-0109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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32
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Tzahor S, Man-Aharonovich D, Kirkup BC, Yogev T, Berman-Frank I, Polz MF, Béjà O, Mandel-Gutfreund Y. A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment. BMC Genomics 2009; 10:229. [PMID: 19445709 PMCID: PMC2696472 DOI: 10.1186/1471-2164-10-229] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 05/16/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the photosystem II reaction center (psbA and psbD) were found in cyanophage genomes. This phenomenon suggested that the horizontal transfer of these genes may be involved in increasing phage fitness. To date, a very small percentage of marine bacteria and phages has been cultured. Thus, mapping genomic data extracted directly from the environment to its taxonomic origin is necessary for a better understanding of phage-host relationships and dynamics. RESULTS To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM) with a codon usage position specific scoring matrix (cuPSSM). Our method has been applied successfully to classify core-photosystem-II gene fragments, including partial sequences coming directly from the ocean, to seven different taxonomic classes. Applying the method on a large set of DNA and RNA psbA clones from the Mediterranean Sea, we studied the distribution of cyanobacterial psbA genes and transcripts in their natural environment. Using our approach, we were able to simultaneously examine taxonomic and ecological distributions in the marine environment. CONCLUSION The ability to accurately classify the origin of individual genes and transcripts coming directly from the environment is of great importance in studying marine ecology. The classification method presented in this paper could be applied further to classify other genes amplified from the environment, for which training data is available.
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Affiliation(s)
- Shani Tzahor
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
- Inter-Departmental Program for Biotechnology, Technion – Israel Institute of Technology, Haifa 32000, Israel
| | | | - Benjamin C Kirkup
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tali Yogev
- Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | | | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Oded Béjà
- Faculty of Biology, Technion – Israel Institute of Technology, Haifa 32000, Israel
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33
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Tzahor S, Man-Aharonovich D, Kirkup BC, Yogev T, Berman-Frank I, Polz MF, Béjà O, Mandel-Gutfreund Y. A supervised learning approach for taxonomic classification of core-photosystem-II genes and transcripts in the marine environment. BMC Genomics 2009. [PMID: 19445709 DOI: 10.1186/1471-2164-10-229.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria of the genera Synechococcus and Prochlorococcus play a key role in marine photosynthesis, which contributes to the global carbon cycle and to the world oxygen supply. Recently, genes encoding the photosystem II reaction center (psbA and psbD) were found in cyanophage genomes. This phenomenon suggested that the horizontal transfer of these genes may be involved in increasing phage fitness. To date, a very small percentage of marine bacteria and phages has been cultured. Thus, mapping genomic data extracted directly from the environment to its taxonomic origin is necessary for a better understanding of phage-host relationships and dynamics. RESULTS To achieve an accurate and rapid taxonomic classification, we employed a computational approach combining a multi-class Support Vector Machine (SVM) with a codon usage position specific scoring matrix (cuPSSM). Our method has been applied successfully to classify core-photosystem-II gene fragments, including partial sequences coming directly from the ocean, to seven different taxonomic classes. Applying the method on a large set of DNA and RNA psbA clones from the Mediterranean Sea, we studied the distribution of cyanobacterial psbA genes and transcripts in their natural environment. Using our approach, we were able to simultaneously examine taxonomic and ecological distributions in the marine environment. CONCLUSION The ability to accurately classify the origin of individual genes and transcripts coming directly from the environment is of great importance in studying marine ecology. The classification method presented in this paper could be applied further to classify other genes amplified from the environment, for which training data is available.
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Affiliation(s)
- Shani Tzahor
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
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Kelman D, Ben-Amotz A, Berman-Frank I. Carotenoids provide the major antioxidant defence in the globally significant N2-fixing marine cyanobacterium Trichodesmium. Environ Microbiol 2009; 11:1897-908. [PMID: 19397682 DOI: 10.1111/j.1462-2920.2009.01913.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Photosynthetic oxygen-evolving microorganisms contend with continuous self-production of molecular oxygen and reactive oxygen species. The deleterious effects of reactive oxygen species are exacerbated for cyanobacterial nitrogen-fixers (diazotrophs) due to the innate sensitivity of nitrogenase to oxygen. This renders incompatible the processes of oxygen-evolving photosynthesis and N-fixation. We examined total antioxidative potential of various diazotrophic and non-diazotrophic cyanobacteria. We focused on Trichodesmium spp., a bloom-forming marine diazotroph that contributes significantly to global nitrogen fixation. Among the species tested, Trichodesmium possessed the highest antioxidant activity. Moreover, while proteins constituted the dominant antioxidative component of all other cyanobacteria tested, Trichodesmium was unique in that small-molecule natural products provided the majority of antioxidant activity, while proteins constituted only 13% of total antioxidant activity. Bioassay-guided fractionation followed by high-performance liquid chromatography profiling of antioxidant purified fractions identified the highly potent antioxidant all-trans-β-carotene, and small amounts of 9-cis-β-carotene and retinyl palmitate. Search of the Trichodesmium genome identified protein sequences homologous to key enzymes in the β-carotene to retinyl palmitate biosynthetic pathway, including 33-37% identity to lecithin retinol acyltransferase. The present study demonstrates the importance of carotenoids in Trichodesmium's arsenal of defensive compounds against oxidative damage and protection of nitrogenase from oxygen and its radicals.
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Affiliation(s)
- Dovi Kelman
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel.
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35
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Zeev EB, Yogev T, Man-Aharonovich D, Kress N, Herut B, Béjà O, Berman-Frank I. Seasonal dynamics of the endosymbiotic, nitrogen-fixing cyanobacterium Richelia intracellularis in the eastern Mediterranean Sea. ISME J 2008; 2:911-23. [DOI: 10.1038/ismej.2008.56] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Küpper H, Šetlík I, Seibert S, Prášil O, Šetlikova E, Strittmatter M, Levitan O, Lohscheider J, Adamska I, Berman-Frank I. Iron limitation in the marine cyanobacterium Trichodesmium reveals new insights into regulation of photosynthesis and nitrogen fixation. New Phytol 2008; 179:784-798. [PMID: 18513224 DOI: 10.1111/j.1469-8137.2008.02497.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
* As iron (Fe) deficiency is a main limiting factor of ocean productivity, its effects were investigated on interactions between photosynthesis and nitrogen fixation in the marine nonheterocystous diazotrophic cyanobacterium Trichodesmium IMS101. * Biophysical methods such as fluorescence kinetic microscopy, fast repetition rate (FRR) fluorimetry, and in vivo and in vitro spectroscopy of pigment composition were used, and nitrogenase activity and the abundance of key proteins were measured. * Fe limitation caused a fast down-regulation of nitrogenase activity and protein levels. By contrast, the abundance of Fe-requiring photosystem I (PSI) components remained constant. Total levels of phycobiliproteins remained unchanged according to single-cell in vivo spectra. However, the regular 16-kDa phycoerythrin band decreased and finally disappeared 16-20 d after initiation of Fe limitation, concomitant with the accumulation of a 20-kDa protein cross-reacting with the phycoerythrin antibody. Concurrently, nitrogenase expression and activity increased. Fe limitation dampened the daily cycle of photosystem II (PSII) activity characteristic of diazotrophic Trichodesmium cells. Further, it increased the number and prolonged the time period of occurrence of cells with elevated basic fluorescence (F(0)). Additionally, it increased the effective cross-section of PSII, probably as a result of enhanced coupling of phycobilisomes to PSII, and led to up-regulation of the Fe stress protein IsiA. * Trichodesmium survives short-term Fe limitation by selectively down-regulating nitrogen fixation while maintaining but re-arranging the photosynthetic apparatus.
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Affiliation(s)
- Hendrik Küpper
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, D-78457 Konstanz, Germany
- University of South Bohemia, Faculty of Biological Sciences and Institute of Physical Biology, Branišovská 31, CZ-370 05 České Budejovice, Czech Republic
| | - Ivan Šetlík
- University of South Bohemia, Faculty of Biological Sciences and Institute of Physical Biology, Branišovská 31, CZ-370 05 České Budejovice, Czech Republic
- Academy of Sciences of the Czech Republic, Institute of Microbiology, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-37981 Třeboň, Czech Republic
| | - Sven Seibert
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, D-78457 Konstanz, Germany
| | - Ondrej Prášil
- University of South Bohemia, Faculty of Biological Sciences and Institute of Physical Biology, Branišovská 31, CZ-370 05 České Budejovice, Czech Republic
- Academy of Sciences of the Czech Republic, Institute of Microbiology, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-37981 Třeboň, Czech Republic
| | - Eva Šetlikova
- University of South Bohemia, Faculty of Biological Sciences and Institute of Physical Biology, Branišovská 31, CZ-370 05 České Budejovice, Czech Republic
- Academy of Sciences of the Czech Republic, Institute of Microbiology, Department of Autotrophic Microorganisms, Opatovický mlýn, CZ-37981 Třeboň, Czech Republic
| | - Martina Strittmatter
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, D-78457 Konstanz, Germany
| | - Orly Levitan
- Bar Ilan University, Mina and Everard Goodman Faculty of Life Sciences, Ramat Gan, 52900, Israel
| | - Jens Lohscheider
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, D-78457 Konstanz, Germany
| | - Iwona Adamska
- Universität Konstanz, Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, D-78457 Konstanz, Germany
| | - Ilana Berman-Frank
- Bar Ilan University, Mina and Everard Goodman Faculty of Life Sciences, Ramat Gan, 52900, Israel
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Abstract
The eastern Mediterranean Sea is one of the most extreme oligotrophic oceanic regions on earth in terms of nutrient concentrations and primary productivity. Nitrogen fixation has been suggested to contribute to the high N : P molar ratios of approximately 28:1 found in this region. Surprisingly, no molecular biological work has been performed in situ to assess whether N(2) fixation genes actually occur in the eastern Mediterranean Sea, or to determine which organisms are responsible for this process. In this study, we examined the presence and expression of nitrogenase genes (nifH) in the upper water layer of the eastern Mediterranean. Clone libraries constructed from both DNA and reverse-transcribed PCR-amplified mRNA were examined and compared. We observed different nifH genes from diverse microbial groups, such as Cyanobacteria, Proteobacteria and methanogenic Archaea. Interestingly, numerous phylotypes were observed in coastal stations at the DNA level but none were active. However, in far offshore stations, the phylotypes observed at the DNA level were the ones that were actually active. Our preliminary study revealed diverse diazotrophs that possess and express nifH genes, which may support N(2) fixation in the eastern Mediterranean Sea.
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Berman-Frank I, Rosenberg G, Levitan O, Haramaty L, Mari X. Coupling between autocatalytic cell death and transparent exopolymeric particle production in the marine cyanobacterium Trichodesmium. Environ Microbiol 2007; 9:1415-22. [PMID: 17504479 DOI: 10.1111/j.1462-2920.2007.01257.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular polysaccharide aggregates, operationally defined as transparent exopolymeric particles (TEP), are recognized as an important conduit for carbon recycling and export in aquatic systems. Yet, the factors controlling the build-up of the TEP pool are not well characterized. Here we show that increased TEP production by Trichodesmium, an oceanic bloom-forming nitrogen-fixing (diazotrophic) cyanobacterium, is coupled with autocatalytic programmed cell death (PCD) process. We demonstrate that PCD induction, in both laboratory cultures and natural populations, is characterized by high caspase-like activity, correlates with enhanced TEP production, and occurs under iron and phosphorus starvation, as well as under high irradiance and oxidative stress. Enhanced TEP production was not observed in actively growing populations. We provide further evidence that iron is a key trigger for the induction of PCD. We demonstrate, for the first time, the concomitant enhanced build-up of the TEP pool when Trichodesmium is Fe-stressed. These results suggest a functional linkage between activation of caspases and PCD in Trichodesmium and regulation of vertical carbon and nitrogen fluxes. We hypothesize that modulation of TEP formation and its qualities by different mortality pathways could regulate the fate of phytoplankton blooms and particulate organic matter in aquatic ecosystems.
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Affiliation(s)
- Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan, 52900, Israel.
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Vardi A, Eisenstadt D, Murik O, Berman-Frank I, Zohary T, Levine A, Kaplan A. Synchronization of cell death in a dinoflagellate population is mediated by an excreted thiol protease. Environ Microbiol 2007; 9:360-9. [PMID: 17222134 DOI: 10.1111/j.1462-2920.2006.01146.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Regulated programmed cell death (PCD) processes have been documented in several phytoplankton species and are hypothesized to play a role in population dynamics. However, the mechanisms leading to the coordinated collapse of phytoplankton blooms are poorly understood. We showed that the collapse of the annual bloom of Peridinium gatunense, an abundant dinoflagellate in Lake Kinneret, Israel, is initiated by CO2 limitation followed by oxidative stress that triggers a PCD-like cascade. We provide evidences that a protease excreted by senescing P. gatunense cells sensitizes younger cells to oxidative stress and may consequently trigger synchronized cell death of the population. Ageing of the P. gatunense cultures was characterized by a remarkable rise in DNA fragmentation and enhanced sensitivity to H2O2. Exposure of logarithmic phase (young) cultures to conditioning media from stationary phase (old) cells sensitized them to H2O2 and led to premature massive cell death. We detected the induction of specific extracellular protease activity, leupeptin-sensitive, in ageing cultures and in lake waters during the succession of the P. gatunense bloom. Partial purification of the conditioned media revealed that this protease activity is responsible for the higher susceptibility of young cells to oxidative stress. Inhibition of the protease activity lowered the sensitivity to oxidative stress, whereas application of papain to logarithmic phase P. gatunense cultures mimicked the effect of the spent media and enhanced cell death. We propose a novel mechanistic framework by which a population of unicellular phytoplankton orchestrates a coordinated response to stress, thereby determine the fate of its individuals.
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Affiliation(s)
- Assaf Vardi
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Küpper H, Ferimazova N, Setlík I, Berman-Frank I. Traffic lights in trichodesmium. Regulation of photosynthesis for nitrogen fixation studied by chlorophyll fluorescence kinetic microscopy. Plant Physiol 2004; 135:2120-33. [PMID: 15299119 PMCID: PMC520784 DOI: 10.1104/pp.104.045963] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We investigated interactions between photosynthesis and nitrogen fixation in the non-heterocystous marine cyanobacterium Trichodesmium IMS101 at the single-cell level by two-dimensional (imaging) microscopic measurements of chlorophyll fluorescence kinetics. Nitrogen fixation was closely associated with the appearance of cells with high basic fluorescence yield (F(0)), termed bright cells. In cultures aerated with normal air, both nitrogen fixation and bright cells appeared in the middle of the light phase. In cultures aerated with 5% oxygen, both processes occurred at a low level throughout most of the day. Under 50% oxygen, nitrogen fixation commenced at the beginning of the light phase but declined soon afterwards. Rapid reversible switches between fluorescence levels were observed, which indicated that the elevated F(0) of the bright cells originates from reversible uncoupling of the photosystem II (PSII) antenna from the PSII reaction center. Two physiologically distinct types of bright cells were observed. Type I had about double F(0) compared to the normal F(0) in the dark phase and a PSII activity, measured as variable fluorescence (F(v) = F(m) - F(0)), similar to normal non-diazotrophic cells. Correlation of type I cells with nitrogen fixation, oxygen concentration, and light suggests that this physiological state is connected to an up-regulation of the Mehler reaction, resulting in oxygen consumption despite functional PSII. Type II cells had more than three times the normal F(0) and hardly any PSII activity measurable by variable fluorescence. They did not occur under low-oxygen concentrations, but appeared under high-oxygen levels outside the diazotrophic period, suggesting that this state represents a reaction to oxidative stress not necessarily connected to nitrogen fixation. In addition to the two high-fluorescence states, cells were observed to reversibly enter a low-fluorescence state. This occurred mainly after a cell went through its bright phase and may represent a fluorescence-quenching recovery phase.
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Affiliation(s)
- Hendrik Küpper
- Mathematisch-Naturwissenschaftliche Sektion, Fachbereich Biologie, Universität Konstanz, D-78457 Konstanz, Germany.
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Abstract
The biological reduction of N(2) is catalyzed by nitrogenase, which is irreversibly inhibited by molecular oxygen. Cyanobacteria are the only diazotrophs (nitrogen-fixing organisms) that produce oxygen as a by-product of the photosynthetic process, and which must negotiate the inevitable presence of molecular oxygen with an essentially anaerobic enzyme. In this review, we present an analysis of the geochemical conditions under which nitrogenase evolved and examine how the evolutionary history of the enzyme complex corresponds to the physiological, morphological, and developmental strategies for reducing damage by molecular oxygen. Our review highlights biogeochemical constraints on diazotrophic cyanobacteria in the contemporary world.
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Affiliation(s)
- Ilana Berman-Frank
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd., New Brunswick, NJ 08901, USA.
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Berman-Frank I, Lundgren P, Chen YB, Küpper H, Kolber Z, Bergman B, Falkowski P. Segregation of nitrogen fixation and oxygenic photosynthesis in the marine cyanobacterium Trichodesmium. Science 2001; 294:1534-7. [PMID: 11711677 DOI: 10.1126/science.1064082] [Citation(s) in RCA: 275] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
In the modern ocean, a significant amount of nitrogen fixation is attributed to filamentous, nonheterocystous cyanobacteria of the genus Trichodesmium. In these organisms, nitrogen fixation is confined to the photoperiod and occurs simultaneously with oxygenic photosynthesis. Nitrogenase, the enzyme responsible for biological N2 fixation, is irreversibly inhibited by oxygen in vitro. How nitrogenase is protected from damage by photosynthetically produced O2 was once an enigma. Using fast repetition rate fluorometry and fluorescence kinetic microscopy, we show that there is both temporal and spatial segregation of N2 fixation and photosynthesis within the photoperiod. Linear photosynthetic electron transport protects nitrogenase by reducing photosynthetically evolved O2 in photosystem I (PSI). We postulate that in the early evolutionary phase of oxygenic photosynthesis, nitrogenase served as an electron acceptor for anaerobic heterotrophic metabolism and that PSI was favored by selection because it provided a micro-anaerobic environment for N2 fixation in cyanobacteria.
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Affiliation(s)
- I Berman-Frank
- Environmental Biophysics and Molecular Ecology Program, Institute of Marine and Coastal Sciences, Rutgers University, 71 Dudley Road, New Brunswick, NJ 08901, USA.
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Vardi A, Berman-Frank I, Rozenberg T, Hadas O, Kaplan A, Levine A. Programmed cell death of the dinoflagellate Peridinium gatunense is mediated by CO(2) limitation and oxidative stress. Curr Biol 1999; 9:1061-4. [PMID: 10508616 DOI: 10.1016/s0960-9822(99)80459-x] [Citation(s) in RCA: 229] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The phytoplankton assemblage in Lake Kinneret is dominated in spring by a bloom of the dinoflagellate Peridinium gatunense, which terminates sharply in summer [1]. The pH in Peridinium patches rises during the bloom to values higher than pH9 [2] and results in CO(2) limitation. Here we show that depletion of dissolved CO(2) (CO(2(dis))) stimulated formation of reactive oxygen species (ROS) and induced cell death in both natural and cultured Peridinium populations. In contrast, addition of CO(2) prevented ROS formation. Catalase inhibited cell death in culture, implicating hydrogen peroxide (H(2)O(2)) as the active ROS. Cell death was also blocked by a cysteine protease inhibitor, E-64, a treatment which stimulated cyst formation. Intracellular ROS accumulation induced protoplast shrinkage and DNA fragmentation prior to cell death. We propose that CO(2) limitation resulted in the generation of ROS to a level that induced programmed cell death, which resembles apoptosis in animal and plant cells. Our results also indicate that cysteine protease(s) are involved in processes that determine whether a cell is destined to die or to form a cyst.
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Affiliation(s)
- A Vardi
- Department of Plant Sciences The Hebrew University of Jerusalem Jerusalem, 91904, Israel
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44
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Vardi A, Berman-Frank I, Rozenberg T, Hadas O, Kaplan A, Levine A. Programmed cell death of the dinoflagellate Peridinium gatunense is mediated by CO(2) limitation and oxidative stress. Curr Biol 1999. [PMID: 10508616 DOI: 10.1016/s096049822(99)80459-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
The phytoplankton assemblage in Lake Kinneret is dominated in spring by a bloom of the dinoflagellate Peridinium gatunense, which terminates sharply in summer [1]. The pH in Peridinium patches rises during the bloom to values higher than pH9 [2] and results in CO(2) limitation. Here we show that depletion of dissolved CO(2) (CO(2(dis))) stimulated formation of reactive oxygen species (ROS) and induced cell death in both natural and cultured Peridinium populations. In contrast, addition of CO(2) prevented ROS formation. Catalase inhibited cell death in culture, implicating hydrogen peroxide (H(2)O(2)) as the active ROS. Cell death was also blocked by a cysteine protease inhibitor, E-64, a treatment which stimulated cyst formation. Intracellular ROS accumulation induced protoplast shrinkage and DNA fragmentation prior to cell death. We propose that CO(2) limitation resulted in the generation of ROS to a level that induced programmed cell death, which resembles apoptosis in animal and plant cells. Our results also indicate that cysteine protease(s) are involved in processes that determine whether a cell is destined to die or to form a cyst.
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Affiliation(s)
- A Vardi
- Department of Plant Sciences The Hebrew University of Jerusalem Jerusalem, 91904, Israel
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Berman-Frank I, Erez J, Kaplan A. Changes in inorganic carbon uptake during the progression of a dinoflagellate bloom in a lake ecosystem. ACTA ACUST UNITED AC 1998. [DOI: 10.1139/cjb-76-6-1043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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