Helga do R. Gomes

Fate of the Amazon River dissolved organic matter in the tropical Atlantic Ocean

Constraining the fate of dissolved organic matter (DOM) delivered by rivers is a key to understand the global carbon cycle, since DOM mineralization directly influences air-sea CO2 exchange and multiple biogeochemical processes. The Amazon River exports large amounts of DOM, and yet the fate of this material in the ocean remains unclear. Here we investigate the molecular composition and transformations of DOM in the Amazon River-ocean continuum using ultrahigh resolution mass spectrometry and geochemical and biological tracers. We show that there is a strong gradient in source and composition of DOM along the continuum, and that dilution of riverine DOM in the ocean is the dominant pattern of variability in the system. Alterations in DOM composition are observed in the plume associated with the addition of new organic compounds by phytoplankton and with bacterial and photochemical transformations. The relative importance of each of these drivers varies spatially and is modulated by seasonal variations in river discharge and ocean circulation. We further show that a large fraction (50–76%) of the Amazon River DOM is surprisingly stable in the coastal ocean. This results in a globally significant river plume with a strong terrigenous signature and in substantial export of terrestrially derived organic carbon from the continental margin, where it can be entrained in the large-scale circulation and potentially contribute to the long-term storage of terrigenous production and to the recalcitrant carbon pool found in the deep ocean.

Mesoscale and Nutrient Conditions Associated with the Massive 2008 Cochlodinium polykrikoides Bloom in the Sea of Oman/Arabian Gulf

Cochlodinium polykrikoides formed large blooms in the coastal waters of Oman from October 2008 through mid-January 2009, and satellite images from Aqua-MODIS and region-wide reports suggest that this bloom was found throughout the Arabian Gulf and Sea of Oman for more than 10xa0months. The unusual occurrence of this species appears to have supplanted the more regularly occurring bloom species, Noctiluca scintillans, in 2008–2009. For the first 2xa0weeks of the coastal Omani bloom, C. polykrikoides abundance was near monospecific proportions, with cell densities ranging from 4.6u2009×u2009103 to 9u2009×u2009106 cells L−1 and very high levels of chlorophyll a (78.0xa0μgxa0L−1) were also recorded. The regional progression of the bloom likely began with stronger than normal upwelling along the Iranian and northern Omani coasts during the southwest monsoon in late summer, followed by discharge of unusually warm coastal plume water along the coast of Oman with the reversal of monsoonal winds in late October. The occurrence and persistence of high densities of C. polykrikoides in Oman coastal water were also significantly influenced by an elevated nutrient load and warmer than normal temperatures. Concentrations of nutrients, especially NH4+, urea, PO43−, and organic nitrogen and phosphorus, were manyfold higher than observed in the year prior or since. These findings suggest that mesoscale features were important in bloom dynamics more regionally, but locally the bloom was sustained by nutrient enrichment supplemented by its mixotrophic capabilities.

Patterns of Transcript Abundance of Eukaryotic Biogeochemically-Relevant Genes in the Amazon River Plume.

The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression patterns of the 2.0 to 156 μm size-fraction eukaryotic microbial community were investigated in the Amazon River Plume, generating a robust dataset (more than 100 million mRNA sequences) that depicts the metabolic capabilities and interactions among the eukaryotic microbes. Combining classical oceanographic field measurements with metatranscriptomics yielded characterization of the hydrographic conditions simultaneous with a quantification of transcriptional activity and identity of the community. We highlight the patterns of eukaryotic gene expression for 31 biogeochemically significant gene targets hypothesized to be valuable within forecasting models. An advantage to this targeted approach is that the database of reference sequences used to identify the target genes was selectively constructed and highly curated optimizing taxonomic coverage, throughput, and the accuracy of annotations. A coastal diatom bloom highly expressed nitrate transporters and carbonic anhydrase presumably to support high growth rates and enhance uptake of low levels of dissolved nitrate and CO2. Diatom-diazotroph association (DDA: diatoms with nitrogen fixing symbionts) blooms were common when surface salinity was mesohaline and dissolved nitrate concentrations were below detection, and hence did not show evidence of nitrate utilization, suggesting they relied on ammonium transporters to aquire recently fixed nitrogen. These DDA blooms in the outer plume had rapid turnover of the photosystem D1 protein presumably caused by photodegradation under increased light penetration in clearer waters, and increased expression of silicon transporters as silicon became limiting. Expression of these genes, including carbonic anhydrase and transporters for nitrate and phosphate, were found to reflect the physiological status and biogeochemistry of river plume environments. These relatively stable patterns of eukaryotic transcript abundance occurred over modest spatiotemporal scales, with similarity observed in sample duplicates collected up to 2.45 km in space and 120 minutes in time. These results confirm the use of metatranscriptomics as a valuable tool to understand and predict microbial community function.

A modeling study of seasonal variations of sea ice and plankton in the Bering and Chukchi Seas during 2007–2008

[1]xa0A nutrient (N), phytoplankton (P), zooplankton (Z), and detritus (D) ecosystem model coupled to an ice-ocean model was applied to the Bering and Chukchi Seas for 2007–2008. The model reasonably reproduces the seasonal cycles of sea ice, phytoplankton, and zooplankton in the Bering–Chukchi Seas. The spatial variation of the phytoplankton bloom was predominantly controlled by the retreat of sea ice and the increased gradient of the water temperature from the south to the north. The model captures the basic structure of the measured nutrients and chl-a along the Bering shelf during 4–23 July 2008, and along the Chukchi shelf during 5–12 August 2007. In summer 2008, the Green Belt bloom was not observed by either the satellite measurements or the model. The model-data comparison and analysis reveal the complexity of the lower trophic dynamics in the Bering and Chukchi Seas. The complexity is due to the nature that the physical and biological components interact at different manners in time and space, even in response to a same climate forcing, over the physically distinct geographic settings such as in the Bering and North Aleutian Slopes, deep Bering basins, Bering shelf, and Chukchi Sea. Sensitivity studies were conducted to reveal the underlying mechanisms (i.e., the bottom-up effects) of the Bering–Chukchi ecosystem in response to changes in light intensity, nutrient input from open boundaries, and air temperature. It was found that (1) a 10% increase in solar radiation or light intensity for the entire year has a small impact on the intensity and timing of the bloom in the physical–biological system since the light is not a limiting factor in the study region; (2) a 20% increase in nutrients from all the open boundaries results in an overall 7% increase in phytoplankton, with the Slope region being the largest, and the Bering shelf and Chukchi being the smallest; and (3) an increase in air temperature by 2°C over the entire calculation period can result in an overall increase in phytoplankton by 11%.

An Ecosystem in Transition: The Emergence of Mixotrophy in the Arabian Sea

In the last decade and half, the northern Arabian Sea has witnessed a radical shift in the composition of winter phytoplankton blooms. Diatoms typical of the winter monsoon and favored by nutrient-enriched waters from convective mixing have been replaced by thick and widespread blooms of a large, green dinoflagellate Noctiluca scintillans (Noctiluca). Unlike the exclusively heterotrophic red Noctiluca found in temperate waters, the green species of Noctiluca from the Arabian Sea is a mixotroph. It harbors hundreds of green, free-swimming cells of the symbiont Pedinomonas noctiluca, recently renamed as Protoeuglena noctilucae, Wang et al. (2016), within the central vacuole of its cytoplasm, and can sustain itself either through carbon fixation by its endosymbionts or via ingestion of exogenous prey. Data collected by us aboard Indian research vessels in the Arabian Sea suggest that these recent outbreaks of green Noctiluca blooms are being caused by the spread of hypoxic waters into the euphotic zone and possibly exacerbated by land runoff and enhanced stratification of the water column. Noctiluca is not a preferred food for micro- and mesozooplankton. Instead, its major consumers are mostly salps and jellyfish. It uses inorganic nutrients and grazes on other phytoplankton. Thus, it competes with both its prey and predators for resources, posing special challenges for ecosystem modeling studies. The emergence of this mixotroph as the major plankton player in the ecosystem will require a revision of our earlier understanding of the Arabian Sea food web dynamics and allied biogeochemistry gained from the Joint Global Flux Studies (JGOFS) expeditions of the 1990s.

Ecological Drivers of Green Noctiluca Blooms in Two Monsoonal-Driven Ecosystems

Of the many anthropogenic and climate-related changes occurring in marine biota reported in oceanic ecosystems worldwide, the recent advent of green Noctiluca scintillans (herein after Noctiluca) as the dominant bloom-forming organism represents the most dramatic and extreme. Widespread and intense blooms of Noctiluca have now become a common feature in the Arabian Sea and in many other tropical coastal ecosystems that come under the influence of the Indian monsoons. Noctiluca is a mixotroph, and even among this subset of marine organisms, it is considered exceptional because of its permanent, independent, free-swimming endosymbionts that are capable of photosynthesis. Since the endosymbionts are dependent on nutrients, Noctiluca competes with other phytoplankton, and since it feeds on other phytoplankton, it competes with many secondary producers for food. Because Noctiluca is not a preferred food for zooplankton, its emergence at the base of the food chain represents a threat to many countries where coastal marine resources are of great economic and cultural significance. Here we have drawn on previously published information to establish the major ecological drivers of Noctiluca blooms. Although prior research has established a good foundation, more detailed studies are needed to establish the ecophysiological mechanisms that underpin Noctiluca’s ability to grow and persist as massive blooms for several months and at a time when conditions would be considered hostile for maintaining a classic marine phytoplankton community.

High-resolution shipboard measurements of phytoplankton-a way forward for enhancing the utility of satellite SST and Chlorophyll for mapping microscale features and frontal zones in coastal waters

Coastal eddies, frontal zones and microscale oceanographic features are now easily observable from satellite measurements of SST and Chl a. Enhancing the utility of these space-borne measurements for biological productivity, biogeochemical cycling and fisheries investigations will require novel bio-optical methods capable of providing information on the community structure, biomass and photo-physiology of phytoplankton associated on spatial scales that match these features. This study showcases high-resolution in-situ measurements of sea water hydrography (SeaBird CTD®), CDOM (WetLabs ALF®), phytoplankton functional types (PFTs, FlowCAM®), biomass (bbe Moldaenke AlgaeOnlineAnalyzer® and WetLabs ALF®) and phytoplankton photosynthetic competency (mini-FIRe) across microscale features encountered during a recent (Nov. 2014) cruise in support of NOAAs VIIRS ocean color satellite calibration and validation activities. When mapped against binned daily, Level 2 satellite images of Chl a, Kd490 and SST over the cruise period, these high-resolution in-situ data showed great correspondence with the satellite data, but more importantly allowed for identification of PFTs and water types associated with microscale features. Large assemblages of phytoplankton communities comprising of diatoms and diatom-diazotroph associations (DDAs), were found in mesohaline frontal zones. Despite their high biomass, these populations were characterized by low photosynthetic competency, indicative of a bloom at the end of its active growth possibly due to nitrogen depletion in the water. Other prominent PFTs such as Trichodesmium spp., Synechococcus spp. and cryptophytes, were also associated with specific water masses offering the promise and potential that ocean remote sensing reflectance bands when examined in the context of water types also measurable from space, could greatly enhance the utility of satellite measurements for biological oceanographic, carbon cycling and fisheries studies.

Influence of Light Availability and Prey Type on the Growth and Photo-Physiological Rates of the Mixotroph Noctiluca scintillans

A strain of the mixotrophic green Noctiluca scintillans (Noctiluca) isolated from the Arabian Sea afforded us an opportunity to investigate the photosynthetic and feeding characteristics of this organism which has recently replaced the once diatom dominated food chain of winter blooms in the Arabian Sea. Here we present the first in a series of experiments undertaken to study the interactive effects of irradiance and grazing response of this mixotroph to four phytoplankton species provided as food. Noctiluca showed a distinct preference for the dinoflagellate Peridinium foliciaeum and the diatom Phaeodactylum tricornutum but not the chlorophyte Pyramimonas nor the chain forming diatom Thalassiosira weissflogii. However, irrespective of food provided, adequate light was required for Noctiluca to grow as evidenced by its maximum growth rates of 1.44 cells day-1 when fed the preferred Peridinium and exposed to optimal irradiance of 250 uf06dE m-2 s-1 versus growth rates of 0.18 cells day-1 with the same food but at a low irradiance of 10 uf06dE m-2 s-1. Measurements of Noctiluca’s electron transport rates (ETR) per PSII Reaction Center as a function of irradiance also indicated severe light limitation of photosynthesis at 10 uf06dE m-2 s-1. The active fluorescence derived ETR versus Irradiance curves revealed an interesting finding in that there was no significant difference in photosynthetic parameters such the maximum photosynthetic capacity (ETRmax) nor α, the rate of increase of photosynthesis with light between fed and unfed cells under optimal light conditions. These results suggest that feeding does not enhance the photosynthetic activity of the endosymbionts when nutrients are not limiting as was the case in these experiments. Measurements of Noctiluca’s intracellular ammonium concentrations under optimal light conditions, the first for this strain, show significant accumulation of NH4+ (0.003-0.012 uf06dM NH4+ cell-1) after 14 days for fed and unfed Noctiluca which was undetectable 4 days later. A similar 14-day increase but of significantly higher concentrations (0.005-0.08 uf06dM NH4+ cell-1) was obtained under low light conditions. For Phaeodactylum and Thalassiosira fed cultures under light limitation, NH4+ continued to increase past the 14-day period suggesting Noctilucas strong and efficient mechanism for regulation of intracellular nutrients.