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1. Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean

   https://doi.org/10.1038/s41564-020-00814-7  

   Cohen, Natalie R. ; McIlvin, Matthew R. ; Moran, Dawn M. ; Held, Noelle A. ; Saunders, Jaclyn K. ; Hawco, Nicholas J. ; Brosnahan, Michael ; DiTullio, Giacomo R. ; Lamborg, Carl ; McCrow, John P. ; et al ( January 2021 , Nature Microbiology)

   null (Ed.)

   Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone. 

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2. Microbial Growth and Organic Matter Cycling in the Pacific Ocean Along a Latitudinal Transect Between Subarctic and Subantarctic Waters

   https://doi.org/10.3389/fmars.2021.764383  

   Giebel, Helge-Ansgar ; Arnosti, Carol ; Badewien, Thomas H. ; Bakenhus, Insa ; Balmonte, John Paul ; Billerbeck, Sara ; Dlugosch, Leon ; Henkel, Rohan ; Kuerzel, Birgit ; Meyerjürgens, Jens ; et al ( December 2021 , Frontiers in Marine Science)

   The Pacific Ocean constitutes about half of the global oceans and thus microbial processes in this ocean have a large impact on global elemental cycles. Despite several intensely studied regions large areas are still greatly understudied regarding microbial activities, organic matter cycling and biogeography. Refined information about these features is most important to better understand the significance of this ocean for global biogeochemical and elemental cycles. Therefore we investigated a suite of microbial and geochemical variables along a transect from the subantarctic to the subarctic Pacific in the upper 200 m of the water column. The aim was to quantify rates of organic matter processing, identify potential controlling factors and prokaryotic key players. The assessed variables included abundance of heterotrophic prokaryotes and cyanobacteria, heterotrophic prokaryotic production (HPP), turnover rate constants of amino acids, glucose, and acetate, leucine aminopeptidase and β-glucosidase activities, and the composition of the bacterial community by fluorescence in situ hybridization (FISH). The additional quantification of nitrate, dissolved amino acids and carbohydrates, chlorophyll a , particulate organic carbon and nitrogen (POC, PON) provided a rich environmental context. The oligotrophic gyres exhibited the lowest prokaryotic abundances, rates of HPP and substrate turnover. Low nucleic acid prokaryotes dominated in these gyres, whereas in temperate and subpolar regions further north and south, high nucleic acid prokaryotes dominated. Turnover rate constants of glucose and acetate, as well as leucine aminopeptidase activity, increased from (sub)tropical toward the subpolar regions. In contrast, HPP and bulk growth rates were highest near the equatorial upwelling and lowest in the central gyres and subpolar regions. The SAR11 clade, the Roseobacter group and Flavobacteria constituted the majority of the prokaryotic communities. Vertical profiles of the biogeochemical and microbial variables markedly differed among the different regions and showed close covariations of the microbial variables and chlorophyll a , POC and PON. The results show that hydrographic, microbial, and biogeochemical properties exhibited distinct patterns reflecting the biogeographic provinces along the transect. The microbial variables assessed contribute to a better and refined understanding of the scales of microbial organic matter processing in large areas of the epipelagic Pacific beyond its well-studied regions. 

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3. Microbial community structure in the western tropical South Pacific

   https://doi.org/10.5194/bg-15-3909-2018  

   Bock, Nicholas ; Van Wambeke, France ; Dion, Moïra ; Duhamel, Solange ( January 2018 , Biogeosciences)

   Abstract. Oligotrophic regions play a central role in global biogeochemical cycles, with microbial communities in these areas representing an important term in global carbon budgets. While the general structure of microbial communities has been well documented in the global ocean, some remote regions such as the western tropical South Pacific (WTSP) remain fundamentally unexplored. Moreover, the biotic and abiotic factors constraining microbial abundances and distribution remain not well resolved. In this study, we quantified the spatial (vertical and horizontal) distribution of major microbial plankton groups along a transect through the WTSP during the austral summer of 2015, capturing important autotrophic and heterotrophic assemblages including cytometrically determined abundances of non-pigmented protists (also called flagellates). Using environmental parameters (e.g., nutrients and light availability) as well as statistical analyses, we estimated the role of bottom–up and top–down controls in constraining the structure of the WTSP microbial communities in biogeochemically distinct regions. At the most general level, we found a typical tropical structure, characterized by a shallow mixed layer, a clear deep chlorophyll maximum at all sampling sites, and a deep nitracline. Prochlorococcus was especially abundant along the transect, accounting for 68±10.6% of depth-integrated phytoplankton biomass. Despite their relatively low abundances, picophytoeukaryotes (PPE) accounted for up to 26±11.6% of depth-integrated phytoplankton biomass, while Synechococcus accounted for only 6±6.9%. Our results show that the microbial community structure of the WTSP is typical of highly stratified regions, and underline the significant contribution to total biomass by PPE populations. Strong relationships between N₂ fixation rates and plankton abundances demonstrate the central role of N₂ fixation in regulating ecosystem processes in the WTSP, while comparative analyses of abundance data suggest microbial community structure to be increasingly regulated by bottom–up processes under nutrient limitation, possibly in response to shifts in abundances of high nucleic acid bacteria (HNA).

    

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4. Synechococcus nitrogen gene loss in iron-limited ocean regions

   https://doi.org/10.1038/s43705-023-00314-9  

   Sharpe, Garrett ; Zhao, Liang ; Meyer, Meredith G. ; Gong, Weida ; Burns, Shannon M. ; Tagliabue, Allesandro ; Buck, Kristen N. ; Santoro, Alyson E. ; Graff, Jason R. ; Marchetti, Adrian ; et al ( October 2023 , ISME Communications)

   Synechococcus are the most abundant cyanobacteria in high latitude regions and are responsible for an estimated 17% of annual marine net primary productivity. Despite their biogeochemical importance, Synechococcus populations have been unevenly sampled across the ocean, with most studies focused on low-latitude strains. In particular, the near absence of Synechococcus genomes from high-latitude, High Nutrient Low Chlorophyll (HNLC) regions leaves a gap in our knowledge of picocyanobacterial adaptations to iron limitation and their influence on carbon, nitrogen, and iron cycles. We examined Synechococcus populations from the subarctic North Pacific, a well-characterized HNLC region, with quantitative metagenomics. Assembly with short and long reads produced two near complete Synechococcus metagenome-assembled genomes (MAGs). Quantitative metagenome-derived abundances of these populations matched well with flow cytometry counts, and the Synechococcus MAGs were estimated to comprise >99% of the Synechococcus at Station P. Whereas the Station P Synechococcus MAGs contained multiple genes for adaptation to iron limitation, both genomes lacked genes for uptake and assimilation of nitrate and nitrite, suggesting a dependence on ammonium, urea, and other forms of recycled nitrogen leading to reduced iron requirements. A global analysis of Synechococcus nitrate reductase abundance in the TARA Oceans dataset found nitrate assimilation genes are also lower in other HNLC regions. We propose that nitrate and nitrite assimilation gene loss in Synechococcus may represent an adaptation to severe iron limitation in high-latitude regions where ammonium availability is higher. Our findings have implications for models that quantify the contribution of cyanobacteria to primary production and subsequent carbon export.

    

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5. Reviews and syntheses: Physical and biogeochemical processes associated with upwelling in the Indian Ocean

   https://doi.org/10.5194/bg-18-5967-2021  

   Vinayachandran, Puthenveettil Narayana ; Masumoto, Yukio ; Roberts, Michael J. ; Huggett, Jenny A. ; Halo, Issufo ; Chatterjee, Abhisek ; Amol, Prakash ; Gupta, Garuda V. ; Singh, Arvind ; Mukherjee, Arnab ; et al ( January 2021 , Biogeosciences)

   Abstract. The Indian Ocean presents two distinct climate regimes. The north Indian Ocean is dominated by the monsoons, whereas the seasonal reversal is less pronounced in the south. The prevailing wind pattern produces upwelling along different parts of the coast in both hemispheres during different times of the year. Additionally, dynamical processes and eddies either cause or enhance upwelling. This paper reviews the phenomena of upwelling along the coast of the Indian Ocean extending from the tip of South Africa to the southern tip of the west coast of Australia. Observed features, underlying mechanisms, and the impact of upwelling on the ecosystem are presented. In the Agulhas Current region, cyclonic eddies associated with Natal pulses drive slope upwelling and enhance chlorophyll concentrations along the continental margin. The Durban break-away eddy spun up by the Agulhas upwells cold nutrient-rich water. Additionally, topographically induced upwelling occurs along the inshore edges of the Agulhas Current. Wind-driven coastal upwelling occurs along the south coast of Africa and augments the dynamical upwelling in the Agulhas Current. Upwelling hotspots along the Mozambique coast are present in the northern and southern sectors of the channel and are ascribed to dynamical effects of ocean circulation in addition to wind forcing. Interaction of mesoscale eddies with the western boundary, dipole eddy pair interactions, and passage of cyclonic eddies cause upwelling. Upwelling along the southern coast of Madagascar is caused by the Ekman wind-driven mechanism and by eddy generation and is inhibited by the Southwest Madagascar Coastal Current. Seasonal upwelling along the East African coast is primarily driven by the northeast monsoon winds and enhanced by topographically induced shelf breaking and shear instability between the East African Coastal Current and the island chains. The Somali coast presents a strong case for the classical Ekman type of upwelling; such upwelling can be inhibited by the arrival of deeper thermocline signals generated in the offshore region by wind stress curl. Upwelling is nearly uniform along the coast of Arabia, caused by the alongshore component of the summer monsoon winds and modulated by the arrival of Rossby waves generated in the offshore region by cyclonic wind stress curl. Along the west coast of India, upwelling is driven by coastally trapped waves together with the alongshore component of the monsoon winds. Along the southern tip of India and Sri Lanka, the strong Ekman transport drives upwelling. Upwelling along the east coast of India is weak and occurs during summer, caused by alongshore winds. In addition, mesoscale eddies lead to upwelling, but the arrival of river water plumes inhibits upwelling along this coast. Southeasterly winds drive upwelling along the coast of Sumatra and Java during summer, with Kelvin wave propagation originating from the equatorial Indian Ocean affecting the magnitude and extent of the upwelling. Both El Niño–Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) events cause large variability in upwelling here. Along the west coast of Australia, which is characterized by the anomalous Leeuwin Current, southerly winds can cause sporadic upwelling, which is prominent along the southwest, central, and Gascoyne coasts during summer. Open-ocean upwelling in the southern tropical Indian Ocean and within the Sri Lanka Dome is driven primarily by the wind stress curl but is also impacted by Rossby wave propagations. Upwelling is a key driver enhancing biological productivity in all sectors of the coast, as indicated by enhanced sea surface chlorophyll concentrations. Additional knowledge at varying levels has been gained through in situ observations and model simulations. In the Mozambique Channel, upwelling simulates new production and circulation redistributes the production generated by upwelling and mesoscale eddies, leading to observations of higher ecosystem impacts along the edges of eddies. Similarly, along the southern Madagascar coast, biological connectivity is influenced by the transport of phytoplankton from upwelling zones. Along the coast of Kenya, both productivity rates and zooplankton biomass are higher during the upwelling season. Along the Somali coast, accumulation of upwelled nutrients in the northern part of the coast leads to spatial heterogeneity in productivity. In contrast, productivity is more uniform along the coasts of Yemen and Oman. Upwelling along the west coast of India has several biogeochemical implications, including oxygen depletion, denitrification, and high production of CH4 and dimethyl sulfide. Although weak, wind-driven upwelling leads to significant enhancement of phytoplankton in the northwest Bay of Bengal during the summer monsoon. Along the Sumatra and Java coasts, upwelling affects the phytoplankton composition and assemblages. Dissimilarities in copepod assemblages occur during the upwelling periods along the west coast of Australia. Phytoplankton abundance characterizes inshore edges of the slope during upwelling season, and upwelling eddies are associated with krill abundance. The review identifies the northern coast of the Arabian Sea and eastern coasts of the Bay of Bengal as the least observed sectors. Additionally, sustained long-term observations with high temporal and spatial resolutions along with high-resolution modelling efforts are recommended for a deeper understanding of upwelling, its variability, and its impact on the ecosystem. 

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