Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deepsequenced metagenomes and metatranscriptomes of marine picoplankton (< 1 μm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65-104% of the genomes as estimated by single-copy recA), followed by PSI (5-104%) and AAnP (5-32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average±standard deviation 26.2±8.4 vs. 11±9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013±0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-a concentrations (< 0.25 μgL-1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.

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Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

10.7287/peerj.preprints.26950v1 ◽

2018 ◽

Author(s):

Ella T Sieradzki ◽

Jed A Fuhrman ◽

Sara Rivero-Calle ◽

Laura Gómez-Consarnau

Keyword(s):

Marker Gene ◽

Single Copy ◽

Oxygenic Photosynthesis ◽

Sampling Location ◽

Pr Genes ◽

Surface Ocean ◽

San Pedro ◽

Accessory Function ◽

The Pacific ◽

The Pacific Ocean

The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (< 1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65-104% of the genomes as estimated by single-copy recA), followed by PSI (5-104%) and AAnP (5-32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average±standard deviation 26.2±8.4 vs. 11±9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013±0.02). We demonstrate that rhodopsin expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-aconcentrations (< 0.25 µg/L). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.

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Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

10.7287/peerj.preprints.26950v2 ◽

2018 ◽

Author(s):

Ella T Sieradzki ◽

Jed A Fuhrman ◽

Sara Rivero-Calle ◽

Laura Gómez-Consarnau

Keyword(s):

Marker Gene ◽

Single Copy ◽

Oxygenic Photosynthesis ◽

Sampling Location ◽

Pr Genes ◽

Surface Ocean ◽

San Pedro ◽

Accessory Function ◽

The Pacific ◽

The Pacific Ocean

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Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities

PeerJ ◽

10.7717/peerj.5798 ◽

2018 ◽

Vol 6 ◽

pp. e5798 ◽

Cited By ~ 7

Author(s):

Ella T. Sieradzki ◽

Jed A. Fuhrman ◽

Sara Rivero-Calle ◽

Laura Gómez-Consarnau

Keyword(s):

Marker Gene ◽

Single Copy ◽

Oxygenic Photosynthesis ◽

Sampling Location ◽

Pr Genes ◽

Surface Ocean ◽

San Pedro ◽

Accessory Function ◽

The Pacific ◽

The Pacific Ocean

The most abundant and ubiquitous microbes in the surface ocean use light as an energy source, capturing it via complex chlorophyll-based photosystems or simple retinal-based rhodopsins. Studies in various ocean regimes compared the abundance of these mechanisms, but few investigated their expression. Here we present the first full seasonal study of abundance and expression of light-harvesting mechanisms (proteorhodopsin, PR; aerobic anoxygenic photosynthesis, AAnP; and oxygenic photosynthesis, PSI) from deep-sequenced metagenomes and metatranscriptomes of marine picoplankton (<1 µm) at three coastal stations of the San Pedro Channel in the Pacific Ocean. We show that, regardless of season or sampling location, the most common phototrophic mechanism in metagenomes of this dynamic region was PR (present in 65–104% of the genomes as estimated by single-copy recA), followed by PSI (5–104%) and AAnP (5–32%). Furthermore, the normalized expression (RNA to DNA ratio) of PR genes was higher than that of oxygenic photosynthesis (average ± standard deviation 26.2 ± 8.4 vs. 11 ± 9.7), and the expression of the AAnP marker gene was significantly lower than both mechanisms (0.013 ± 0.02). We demonstrate that PR expression was dominated by the SAR11-cluster year-round, followed by other Alphaproteobacteria, unknown-environmental clusters and Gammaproteobacteria. This highly dynamic system further allowed us to identify a trend for PR spectral tuning, in which blue-absorbing PR genes dominate in areas with low chlorophyll-aconcentrations (<0.25 µgL−1). This suggests that PR phototrophy is not an accessory function but instead a central mechanism that can regulate photoheterotrophic population dynamics.

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Dissolution of cobalt and zinc from natural and anthropogenic dusts in seawater

Biogeosciences ◽

10.5194/bg-7-1927-2010 ◽

2010 ◽

Vol 7 (6) ◽

pp. 1927-1936 ◽

Cited By ~ 20

Author(s):

C.-E. Thuróczy ◽

M. Boye ◽

R. Losno

Keyword(s):

Mixed Layer ◽

Flow Reactor ◽

Anthropogenic Sources ◽

Anthropogenic Aerosol ◽

Surface Ocean ◽

Anthropogenic Inputs ◽

The Pacific ◽

The Pacific Ocean ◽

Voltammetric Methods

Abstract. Atmospheric dust inputs to the surface ocean are a major source of trace metals likely to be bio-available for phytoplankton after their dissolution in seawater. Among them, cobalt (Co) and zinc (Zn) are essential for phytoplankton growth and for the distribution of the major groups such as coccolithophorids, cyanobacteria and diatoms. The solubility in seawater of Co and Zn present in natural and anthropogenic dusts was studied using an open-flow reactor with and without light irradiation. Those dusts can be transported in the atmosphere by the wind before being deposited to the surface ocean. The analyses of cobalt and zinc were conducted using voltammetric methods and the global elemental composition of dust was determined by ICP-AES. This study highlighted the role of the dust origin in revealing the solubility characteristics. Much higher dust solubility was found for zinc as compared to cobalt; cobalt in anthropogenic particles was much more soluble (0.78%) in seawater after 2 h of dissolution than Co in natural particles (0.14%). Zinc showed opposite solubility, higher in natural particles (16%) than in anthropogenic particles (5.2%). A natural dust event to the surface ocean could account for up to 5% of the cobalt inventory and up to 50% of the Zn inventory in the mixed layer in the Pacific Ocean whereas the cobalt and zinc inventories in the mixed layer of the Atlantic Ocean might already include the effects of natural dust inputs and the subsequent metal dissolution. Anthropogenic sources to the surface ocean could be as important as the natural sources, but a better estimate of the flux of anthropogenic aerosol to the surface ocean is needed to further estimate the anthropogenic inputs. Variations in natural and anthropogenic inputs may induce large shifts in the Co/Zn ratio in the surface ocean; hence it could impact the phytoplankton community structure.

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Surface ocean iron fertilization: The role of airborne volcanic ash from subduction zone and hot spot volcanoes and related iron fluxes into the Pacific Ocean

Global Biogeochemical Cycles ◽

10.1029/2009gb003761 ◽

2011 ◽

Vol 25 (4) ◽

pp. n/a-n/a ◽

Cited By ~ 77

Author(s):

Nazlı Olgun ◽

Svend Duggen ◽

Peter Leslie Croot ◽

Pierre Delmelle ◽

Heiner Dietze ◽

...

Keyword(s):

Pacific Ocean ◽

Subduction Zone ◽

Volcanic Ash ◽

Hot Spot ◽

Surface Ocean ◽

Iron Fertilization ◽

The Pacific ◽

The Pacific Ocean

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Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in the surface ocean

10.1101/129791 ◽

2017 ◽

Cited By ~ 20

Author(s):

Tom O. Delmont ◽

Christopher Quince ◽

Alon Shaiber ◽

Özcan C. Esen ◽

Sonny TM Lee ◽

...

Keyword(s):

Nitrogen Fixation ◽

Primary Productivity ◽

Global Climate ◽

Available Nitrogen ◽

Widespread Occurrence ◽

Surface Ocean ◽

The Pacific ◽

Reductase Gene ◽

The Pacific Ocean ◽

First Time

AbstractNitrogen fixation in the surface ocean impacts the global climate by regulating the microbial primary productivity and the sequestration of carbon through the biological pump. Cyanobacterial populations have long been thought to represent the main suppliers of the bio-available nitrogen in this habitat. However, recent molecular surveys of nitrogenase reductase gene revealed the existence of rare non-cyanobacterial populations that can also fix nitrogen. Here, we characterize for the first time the genomic content of some of these heterotrophic bacterial diazotrophs (HBDs) inhabiting the open surface ocean waters. They represent new lineages within Planctomycetes and Proteobacteria, a phylum never linked to nitrogen fixation prior to this study. HBDs were surprisingly abundant in the Pacific Ocean and the Atlantic Ocean northwest, conflicting with decades of PCR surveys. The abundance and widespread occurrence of non-cyanobacterial diazotrophs in the surface ocean emphasizes the need to re-evaluate their role in the nitrogen cycle and primary productivity.

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Present Status of Marine Radioecology in Bali and Lombok Waters: Distribution Study of 137Cs and Natural Radionuclides in Lombok Strait

Omni-Akuatika ◽

10.20884/1.oa.2017.13.2.251 ◽

2017 ◽

Vol 13 (2) ◽

Author(s):

Deddy Irawan Permana Putra ◽

Heny Suseno

Keyword(s):

Pacific Ocean ◽

Natural Radionuclides ◽

Natural Radionuclide ◽

Average Concentration ◽

Precipitation Process ◽

Sampling Location ◽

Artificial Radionuclide ◽

Distribution Study ◽

The Pacific ◽

The Pacific Ocean

Abstract Lombok strait is outflow of water masses from the Pacific Ocean to the Indian Ocean by Indonesian Throughflow (ITF). Radioecology studies in these waters were including monitoring of natural and artificial radionuclide. This study aims to obtain baseline data of artificial radionuclide 137Cs that entering from the Pacific Ocean through the Makassar Strait. The sampling location were covered territorial waters of Bali and Lombok. A large volume sample preparation for the 137Cs analysis were performed by co-precipitation process using K4Fe(CN)6 and CuCl2 at pH 8-9. Measurement of the concentration activity of natural radionuclides and 137Cs were using Gamma HPGe spectrometer with 20 – 25 % efficiency. The result of this study indicate the average concentration of 40K 226Ra 212Pb 214Bi 228Ac 214Pb and 137Cs in the sediments of Strait Bali waters respectively 165.16 Bq kg-1, 25.11 Bq kg-1, 8.36 Bq kg-1, 7.51 Bq kg-1, 7.05 Bq kg-1, 6.68 Bq kg-1 and the lowest of 0.15 Bq kg-1. In the waters of Lombok concentration activity of radionuclides 40K 226Ra 212Pb 214Bi 228Ac 214Pb and 137Cs in the sediments was 172.00 Bq kg-1, 25.88 Bq kg-1, 10.10 Bq kg-1, 6.50 Bq kg-1, 6.39 Bq kg-1, 5.70 Bq kg-1 and 0,162 Bq kg-1. The concentration activity of 137Cs in seawater of Bali and Lombok respectively was 0.113 Bq m-3 and 0.644 Bq m-3. Keyword : Natural Radionuclide, 137Cs, Lombok Strait

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