scholarly journals A multi-spectral fluorescence induction and relaxation (FIRe) technique for physiological and taxonomic analysis of phytoplankton communities

2020 ◽  
Vol 644 ◽  
pp. 1-13 ◽  
Author(s):  
MY Gorbunov ◽  
E Shirsin ◽  
E Nikonova ◽  
VV Fadeev ◽  
PG Falkowski
Keyword(s):  
Fluorescence Analysis ◽  
Fluorescence Induction ◽  
Global Ocean ◽  
Phylogenetic Groups ◽  
Excitation Spectra ◽  
Chl A ◽  
Taxonomic Analysis ◽  
Eukaryotic Phytoplankton ◽  
Phytoplankton Communities ◽  
Taxonomic Groups

Phytoplankton are extraordinarily diverse, comprising 13 phylogenetic groups, with diatoms, dinoflagellates, and haptophytes among the most prominent eukaryotes in the ocean. Development of sensor technologies for rapid taxonomic and physiological analysis of phytoplankton communities is crucial for ecological monitoring programs in the global ocean. We describe a novel, ultra-sensitive, multi-spectral fluorescence induction and relaxation instrument (a mini-FIRe) and examine its analytical capability of rapidly determining phytoplankton taxonomic groups, as well as physiological characteristics and photosynthetic rates. We collected and analyzed the database of spectral and photosynthetic properties of major taxonomic groups of phytoplankton. We revealed that the spectral shape of the functional absorption cross-section of Photosystem II (PSII), sPSII(lex), is remarkably constrained within each major phylogenetic group of eukaryotic phytoplankton, including diatoms, haptophytes, dinoflagellates, and chlorophytes. Variability in sPSII(lex) within each group was significantly smaller than the difference between groups. We also examined the classical excitation spectra of chl a fluorescence yields, Fm(lex). Our comparative analysis revealed that sPSII(lex) is a better and more specific proxy for taxonomic analysis. For instance, our developed sPSII-based algorithm correctly identified 90% of experimental data, compared to 77% identified by the Fm-based algorithm. Our results suggest that the multi-color variable fluorescence analysis offers a tool for combined physiological and taxonomic analysis, including identification of major phyla within the ‘red’ lineage of eukaryotic phytoplankton.

scholarly journals Toward a global reference database of COI barcodes for marine zooplankton

2021 ◽  
Vol 168 (6) ◽  
Author(s):  
Ann Bucklin ◽  
Katja T. C. A. Peijnenburg ◽  
Ksenia N. Kosobokova ◽  
Todd D. O’Brien ◽  
Leocadio Blanco-Bercial ◽  
...  
Keyword(s):  
Species Diversity ◽  
Dna Sequences ◽  
Reference Sequence ◽  
Global Ocean ◽  
Reference Database ◽  
Data Repositories ◽  
Marine Zooplankton ◽  
The North ◽  
Coi Sequences ◽  
Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

scholarly journals Assessing Phytoplankton Bloom Phenology in Upwelling-Influenced Regions Using Ocean Color Remote Sensing

2021 ◽  
Vol 13 (4) ◽  
pp. 675
Author(s):  
Afonso Ferreira ◽  
Vanda Brotas ◽  
Carla Palma ◽  
Carlos Borges ◽  
Ana C. Brito
Keyword(s):  
Climate Change ◽  
Remote Sensing ◽  
Phytoplankton Bloom ◽  
Ocean Color ◽  
Coastal Region ◽  
Coastal Areas ◽  
Ocean Color Remote Sensing ◽  
Chl A ◽  
Peak Biomass ◽  
Phytoplankton Communities

Phytoplankton bloom phenology studies are fundamental for the understanding of marine ecosystems. Mismatches between fish spawning and plankton peak biomass will become more frequent with climate change, highlighting the need for thorough phenology studies in coastal areas. This study was the first to assess phytoplankton bloom phenology in the Western Iberian Coast (WIC), a complex coastal region in SW Europe, using a multisensor long-term ocean color remote sensing dataset with daily resolution. Using surface chlorophyll a (chl-a) and biogeophysical datasets, five phenoregions (i.e., areas with coherent phenology patterns) were defined. Oceanic phytoplankton communities were seen to form long, low-biomass spring blooms, mainly influenced by atmospheric phenomena and water column conditions. Blooms in northern waters are more akin to the classical spring bloom, while blooms in southern waters typically initiate in late autumn and terminate in late spring. Coastal phytoplankton are characterized by short, high-biomass, highly heterogeneous blooms, as nutrients, sea surface height, and horizontal water transport are essential in shaping phenology. Wind-driven upwelling and riverine input were major factors influencing bloom phenology in the coastal areas. This work is expected to contribute to the management of the WIC and other upwelling systems, particularly under the threat of climate change.

Trends in phytoplankton communities within large marine ecosystems diverge from the global ocean

2021 ◽  
pp. 1-12
Author(s):  
Kevin D. Friedland ◽  
John R. Moisan ◽  
Aurore A. Maureaud ◽  
Damian C. Brady ◽  
Andrew J. Davies ◽  
...  
Keyword(s):  
Chlorophyll Concentration ◽  
World Ocean ◽  
Marine Ecosystems ◽  
Fishing Effort ◽  
Global Ocean ◽  
Human Populations ◽  
Anthropogenic Pressures ◽  
Large Marine Ecosystems ◽  
Phytoplankton Communities ◽  
The World

Large marine ecosystems (LMEs) are highly productive regions of the world ocean under anthropogenic pressures; we analyzed trends in sea surface temperature (SST), cloud fraction (CF), and chlorophyll concentration (CHL) over the period 1998–2019. Trends in these parameters within LMEs diverged from the world ocean. SST and CF inside LMEs increased at greater rates inside LMEs, whereas CHL decreased at a greater rates. CHL declined in 86% of all LMEs and of those trends, 70% were statistically significant. Complementary analyses suggest phytoplankton functional types within LMEs have also diverged from those characteristic of the world ocean, most notably, the contribution of diatoms and dinoflagellates, which have declined within LMEs. LMEs appear to be warming rapidly and receiving less solar radiation than the world ocean, which may be contributing to changes at the base of the food chain. Despite increased fishing effort, fishery yields in LMEs have not increased, pointing to limitations related to productivity. These changes raise concerns over the stability of these ecosystems and their continued ability to support services to human populations.

scholarly journals PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model

2016 ◽  
Vol 9 (11) ◽  
pp. 4071-4085 ◽  
Author(s):  
Esteban Acevedo-Trejos ◽  
Gunnar Brandt ◽  
S. Lan Smith ◽  
Agostino Merico
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Marine Ecosystem ◽  
Three Dimensional ◽  
Functional Trait ◽  
Global Ocean ◽  
Total Biomass ◽  
Spatially Resolved ◽  
Phytoplankton Communities ◽  
Natural Complexity

Abstract. Biodiversity is one of the key mechanisms that facilitate the adaptive response of planktonic communities to a fluctuating environment. How to allow for such a flexible response in marine ecosystem models is, however, not entirely clear. One particular way is to resolve the natural complexity of phytoplankton communities by explicitly incorporating a large number of species or plankton functional types. Alternatively, models of aggregate community properties focus on macroecological quantities such as total biomass, mean trait, and trait variance (or functional trait diversity), thus reducing the observed natural complexity to a few mathematical expressions. We developed the PhytoSFDM modelling tool, which can resolve species discretely and can capture aggregate community properties. The tool also provides a set of methods for treating diversity under realistic oceanographic settings. This model is coded in Python and is distributed as open-source software. PhytoSFDM is implemented in a zero-dimensional physical scheme and can be applied to any location of the global ocean. We show that aggregate community models reduce computational complexity while preserving relevant macroecological features of phytoplankton communities. Compared to species-explicit models, aggregate models are more manageable in terms of number of equations and have faster computational times. Further developments of this tool should address the caveats associated with the assumptions of aggregate community models and about implementations into spatially resolved physical settings (one-dimensional and three-dimensional). With PhytoSFDM we embrace the idea of promoting open-source software and encourage scientists to build on this modelling tool to further improve our understanding of the role that biodiversity plays in shaping marine ecosystems.

scholarly journals Single-Cell and Bulk Fluorescence Excitation Signatures of Seven Phytoplankton Species During Nitrogen Depletion and Resupply

2018 ◽  
Vol 73 (3) ◽  
pp. 304-312 ◽  
Author(s):  
Stefan T. Faulkner ◽  
Cameron M. Rekully ◽  
Eric M. Lachenmyer ◽  
Ergun Kara ◽  
Tammi L. Richardson ◽  
...  
Keyword(s):  
Single Cell ◽  
Aquatic Ecosystems ◽  
Single Cells ◽  
Vital Role ◽  
Phytoplankton Species ◽  
Nitrogen Depletion ◽  
Excitation Spectra ◽  
Fluorescence Excitation ◽  
Fluorescence Excitation Spectra ◽  
Taxonomic Groups

Phytoplankton play a vital role as primary producers in aquatic ecosystems. One common approach to classifying phytoplankton is fluorescence excitation spectroscopy, which leverages the variation in types and concentrations of pigments among different phytoplankton taxonomic groups. Here, we used a fluorescence imaging photometer to measure excitation ratios (“signatures”) of single cells and bulk cultures of seven differently pigmented phytoplankton species as they progressed from nitrogen N-replete to N-depleted conditions. Our objective was to determine whether N depletion alters the fluorescence excitation signature of each species and, if so, how quickly they recover when N (as nitrate) was resupplied, because these factors affect our ability to classify the species correctly. Of the seven species studied, only Proteomonas sulcata, a marine cryptophyte, showed measurable changes in single-cell fluorescence excitation ratios and bulk fluorescence excitation spectra. These changes were likely due to decreases in the cellular concentration of phycoerythrin, a N-rich pigment, as N became scarce. Within 3 h of resupply of N, fluorescence signatures began returning to pre-depletion values and were indistinguishable from N-replete cells by 80 h after resupply. These data suggest that our classification approach is robust for non-PE containing phytoplankton. PE-containing phytoplankton might exhibit systematic changes in their signatures depending on their level of N depletion, but this could be detected and the phytoplankton re-classified following a few hours of incubation in N replete conditions.

Physiological Significance of Overproduced Carotenoids in Transformants of the Cyanobacterium Synechococcus PCC7942

1999 ◽  
Vol 54 (3-4) ◽  
pp. 191-198
Author(s):  
Navassard V. Karapetyan ◽  
Ute Windhövel ◽  
Alfred R. Holzwarth ◽  
Peter Böger
Keyword(s):  
Protein Complexes ◽  
Photosynthetic Apparatus ◽  
Fluorescence Emission ◽  
Fluorescence Induction ◽  
Carotenoid Content ◽  
Excitation Spectra ◽  
Fluorescence Excitation ◽  
Whole Cells ◽  
Fluorescence Excitation Spectra ◽  
Synechococcus Pcc7942

Abstract The functional location of carotenoids in the photosynthetic apparatus of -crtB and -pys transformants of the cyanobacterium Synechococcus PCC7942 was studied and compared with a control strain -pFP 1-3. These transformants overproduce carotenoids due to the insertion of an additional foreign phytoene synthase gene. A higher carotenoid content was found for -crtB and -pys transformants both in whole cells and isolated membranes; the -crtB transformant was also enriched with chlorophyll. 77-K fluorescence emission and excitation spectra of the phycobilin-free membranes were examined for a possible location of overproduced carotenoids in pigment-protein complexes in situ. A similar ratio of the amplitudes of fluorescence bands at 716 and 695 nm emitted by photosystems I and II, found for the three strains, indicates that the stoichiometry between photosystems of the transformants was not changed. Overproduced carotenoids are not located in the core antenna of photosys­ tem I, since 77-K fluorescence excitation spectra for photosystem I of isolated membranes from the studied strains do not differ in the region of carotenoid absorption. When illuminated with light of the same intensity but different quality, absorbed preferentially by either carotenoids, chlorophylls or phycobilins, respectively, oxygen evolution was found always higher in the transformants -crtB and -pys than in -pFP 1-3 control cells. Identical kinetics of fluorescence induction of all strains under carotenoid excitation did not reveal a higher activity of photosystem II in cells enriched with carotenoids. It is suggested that overproduced carotenoids of the transformants are not involved in photosynthetic light-harvesting; rather they may serve to protect the cells and its membranes against photodestruction.

scholarly journals Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria

2018 ◽  
Vol 12 (5) ◽  
pp. 1360-1374 ◽  
Author(s):  
Catherine Gérikas Ribeiro ◽  
Adriana Lopes dos Santos ◽  
Dominique Marie ◽  
Frederico Pereira Brandini ◽  
Daniel Vaulot
Keyword(s):  
Nitrogen Fixing ◽  
Tropical Waters ◽  
Eukaryotic Phytoplankton ◽  
Phytoplankton Communities

Using new observations and Machine Learning to improve organic sinking processes in the PlankTOM global ocean biogeochemical model 

2021 ◽  
Author(s):  
Anna Denvil-Sommer ◽  
Corinne Le Quéré ◽  
Erik Buitenhuis ◽  
Lionel Guidi ◽  
Jean-Olivier Irisson
Keyword(s):  
Organic Carbon ◽  
Carbon Cycle ◽  
Deep Ocean ◽  
Ecosystem Dynamics ◽  
Global Ocean ◽  
Biogeochemical Model ◽  
Carbon Export ◽  
Mixing Depth ◽  
Chl A ◽  
Biogeochemical Models

<p>A lot of effort has been put in the representation of surface ecosystem processes in global carbon cycle models, in particular through the grouping of organisms into Plankton Functional Types (PFTs) which have specific influences on the carbon cycle. In contrast, the transfer of ecosystem dynamics into carbon export to the deep ocean has received much less attention, so that changes in the representation of the PFTs do not necessarily translate into changes in sinking of particulate matter. Models constrain the air-sea CO<sub>2</sub> flux by drawing down carbon into the ocean interior. This export flux is five times as large as the CO<sub>2</sub> emitted to the atmosphere by human activities. When carbon is transported from the surface to intermediate and deep ocean, more CO<sub>2 </sub>can be absorbed at the surface. Therefore, even small variability in sinking organic carbon fluxes can have a large impact on air-sea CO<sub>2</sub> fluxes, and on the amount of CO<sub>2</sub> emissions that remain in the atmosphere.</p><p>In this work we focus on the representation of organic matter sinking in global biogeochemical models, using the PlankTOM model in its latest version representing 12 PFTs. We develop and test a methodology that will enable the systematic use of new observations to constrain sinking processes in the model. The approach is based on a Neural Network (NN) and is applied to the PlankTOM model output to test its ability to reconstruction small and large particulate organic carbon with a limited number of observations. We test the information content of geographical variables (location, depth, time of year), physical conditions (temperature, mixing depth, nutrients), and ecosystem information (CHL a, PFTs). These predictors are used in the NN to test their influence on the model-generation of organic particles and the robustness of the results. We show preliminary results using the NN approach with real plankton and particle size distribution observations from the Underwater Vision Profiler (UVP) and plankton diversity data from Tara Oceans expeditions and discuss limitations.</p>

scholarly journals Estimation of the Particulate Organic Carbon to Chlorophyll-a Ratio Using MODIS-Aqua in the East/Japan Sea, South Korea

2020 ◽  
Vol 12 (5) ◽  
pp. 840 ◽  
Author(s):  
Dabin Lee ◽  
SeungHyun Son ◽  
HuiTae Joo ◽  
Kwanwoo Kim ◽  
Myung Joon Kim ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Particulate Organic Carbon ◽  
Chlorophyll A ◽  
Primary Productivity ◽  
Seasonal Variability ◽  
Japan Sea ◽  
Global Ocean ◽  
Phytoplankton Communities

In recent years, the change of marine environment due to climate change and declining primary productivity have been big concerns in the East/Japan Sea, Korea. However, the main causes for the recent changes are still not revealed clearly. The particulate organic carbon (POC) to chlorophyll-a (chl-a) ratio (POC:chl-a) could be a useful indicator for ecological and physiological conditions of phytoplankton communities and thus help us to understand the recent reduction of primary productivity in the East/Japan Sea. To derive the POC in the East/Japan Sea from a satellite dataset, the new regional POC algorithm was empirically derived with in-situ measured POC concentrations. A strong positive linear relationship (R2 = 0.6579) was observed between the estimated and in-situ measured POC concentrations. Our new POC algorithm proved a better performance in the East/Japan Sea compared to the previous one for the global ocean. Based on the new algorithm, long-term POC:chl-a ratios were obtained in the entire East/Japan Sea from 2003 to 2018. The POC:chl-a showed a strong seasonal variability in the East/Japan Sea. The spring and fall blooms of phytoplankton mainly driven by the growth of large diatoms seem to be a major factor for the seasonal variability in the POC:chl-a. Our new regional POC algorithm modified for the East/Japan Sea could potentially contribute to long-term monitoring for the climate-associated ecosystem changes in the East/Japan Sea. Although the new regional POC algorithm shows a good correspondence with in-situ observed POC concentrations, the algorithm should be further improved with continuous field surveys.

scholarly journals Seasonal Cycles of Phytoplankton Expressed by Sine Equations Using the Daily Climatology from Satellite-Retrieved Chlorophyll-a Concentration (1997–2019) Over Global Ocean

2020 ◽  
Vol 12 (16) ◽  
pp. 2662 ◽  
Author(s):  
Zexi Mao ◽  
Zhihua Mao ◽  
Cédric Jamet ◽  
Marc Linderman ◽  
Yuntao Wang ◽  
...  
Keyword(s):  
Time Series ◽  
Chlorophyll A ◽  
Seasonal Variations ◽  
Global Ocean ◽  
Boreal Winter ◽  
Seasonal Cycles ◽  
Chlorophyll A Concentration ◽  
Chl A ◽  
Global Oceans ◽  
Sine Equation

The global coverage of Chlorophyll-a concentration (Chl-a) has been continuously available from ocean color satellite sensors since September 1997 and the Chl-a data (1997–2019) were used to produce a climatological dataset by averaging Chl-a values at same locations and same day of year. The constructed climatology can remarkably reduce the variability of satellite data and clearly exhibit the seasonal cycles, demonstrating that the growth and decay of phytoplankton recurs with similarly seasonal cycles year after year. As the shapes of time series of the climatology exhibit strong periodical change, we wonder whether the seasonality of Chl-a can be expressed by a mathematic equation. Our results show that sinusoid functions are suitable to describe cyclical variations of data in time series and patterns of the daily climatology can be matched by sine equations with parameters of mean, amplitude, phase, and frequency. Three types of sine equations were used to match the climatological Chl-a with Mean Relative Differences (MRD) of 7.1%, 4.5%, and 3.3%, respectively. The sine equation with four sinusoids can modulate the shapes of the fitted values to match various patterns of climatology with small MRD values (less than 5%) in about 90% of global oceans. The fitted values can reflect an overall pattern of seasonal cycles of Chl-a which can be taken as a time series of biomass baseline for describing the state of seasonal variations of phytoplankton. The amplitude images, the spatial patterns of seasonal variations of phytoplankton, can be used to identify the transition zone chlorophyll fronts. The timing of phytoplankton blooms is identified by the biggest peak of the fitted values and used to classify oceans as different bloom seasons, indicating that blooms occur in all four seasons with regional features. In global oceans within latitude domains (48°N–48°S), blooms occupy approximately half of the ocean (50.6%) during boreal winter (December–February) in the northern hemisphere and more than half (58.0%) during austral winter (June–August) in the southern hemisphere. Therefore, the sine equation can be used to match the daily Chl-a climatology and the fitted values can reflect the seasonal cycles of phytoplankton, which can be used to investigate the underlying phenological characteristics.

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