scholarly journals Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise

2021 ◽  
Vol 118 (11) ◽  
pp. e2021586118
Author(s):  
Flora Vincent ◽  
Uri Sheyn ◽  
Ziv Porat ◽  
Daniella Schatz ◽  
Assaf Vardi
Keyword(s):  
Viral Infection ◽  
Single Molecule ◽  
Messenger Rna ◽  
Marine Ecosystem ◽  
Biotic Interactions ◽  
Deep Ocean ◽  
Biological Entity ◽  
Carbon Export ◽  
Microbial Life ◽  
Marine Viruses

Marine viruses are the most abundant biological entity in the ocean and are considered as major evolutionary drivers of microbial life [C. A. Suttle, Nat. Rev. Microbiol. 5, 801–812 (2007)]. Yet, we lack quantitative approaches to assess their impact on the marine ecosystem. Here, we provide quantification of active viral infection in the bloom forming single-celled phytoplankton Emiliania huxleyi infected by the large virus EhV, using high-throughput single-molecule messenger RNA in situ hybridization (smFISH) of both virus and host transcripts. In natural samples, viral infection reached only 25% of the population despite synchronized bloom demise exposing the coexistence of infected and noninfected subpopulations. We prove that photosynthetically active cells chronically release viral particles through nonlytic infection and that viral-induced cell lysis can occur without viral release, thus challenging major assumptions regarding the life cycle of giant viruses. We could also assess active infection in cell aggregates linking viral infection and carbon export to the deep ocean [C. P. Laber et al., Nat. Microbiol. 3, 537–547 (2018)] and suggest a potential host defense strategy by enrichment of infected cells in sinking aggregates. Our approach can be applied to diverse marine microbial systems, opening a mechanistic dimension to the study of biotic interactions in the ocean.

scholarly journals Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise

2020 ◽  
Author(s):  
Flora Vincent ◽  
Uri Sheyn ◽  
Ziv Porat ◽  
Assaf Vardi
Keyword(s):  
Viral Infection ◽  
Algal Blooms ◽  
Time Course ◽  
Deep Ocean ◽  
Metabolic Reprogramming ◽  
Carbon Export ◽  
Microbial Life ◽  
Infection Dynamics ◽  
Marine Viruses ◽  
Biological Entities

SummaryMarine viruses are considered as major evolutionary and biogeochemical drivers of microbial life, through metabolic reprogramming of their host and cell lysis that modulates nutrient cycling1, primary production and carbon export in the oceans2. Despite the fact that viruses are the most abundant biological entities in the marine environment, we still lack mechanistic and quantitative approaches to assess their impact on the marine food webs. Here, we provide the first quantification of active viral infection, during bloom succession of the cosmopolitan coccolithophore Emiliania huxleyi, by subcellular visualization of both virus and host transcripts on a single cell resolution across thousands of cells. Using this novel method, that we coined Virocell-FISH, we revealed that distinct transcriptional states co-exist during the infection dynamics, and that viral infection reached only a quarter of the E. huxleyi population although the bloom demised in a synchronized manner. Through a detailed laboratory time-course infection of E. huxleyi by its lytic large virus EhV, we quantitatively show that metabolically active infected cells chronically release viral particles, and that viral-induced lysis is not systematically accompanied by virion increase, thus challenging major assumptions regarding the life cycle of giant lytic viruses. Using Virocell-FISH, we could further assess in a new resolution, the level of viral infection in cell aggregates, a key ecosystem process that can facilitate carbon export to the deep ocean3. We project that our approach can be applied to diverse marine microbial systems, opening a mechanistic dimension to the study of host-pathogen interactions in the ocean.One Sentence SummaryQuantifying active viral infection in algal blooms

scholarly journals Multiplexed Detection of COVID-19 with Single-Molecule Technology

2021 ◽  
Author(s):  
Noa Furth ◽  
Shay Shilo ◽  
Niv Cohen ◽  
Nir Erez ◽  
Vadim Fedyuk ◽  
...  
Keyword(s):  
Immune Response ◽  
Viral Infection ◽  
Single Molecule ◽  
Direct Detection ◽  
Genetic Material ◽  
Diagnostic Tools ◽  
Proof Of Concept ◽  
Multiplexed Detection ◽  
Diagnostic Approaches ◽  
Quantitative Nature

The COVID-19 pandemic raises the need for diverse diagnostic approaches to rapidly detect different stages of viral infection. The flexible and quantitative nature of single-molecule imaging technology renders it optimal for development of new diagnostic tools. Here we present a proof-of-concept for a single-molecule based, enzyme-free assay for multiplexed detection of SARS-CoV-2. The unified platform we developed allows direct detection of the viral genetic material from patients' samples, as well as their immune response consisting of IgG and IgM antibodies. Thus, it establishes a platform for diagnostics of COVID-19, which could also be adjusted to diagnose additional pathogens.

scholarly journals Optimizing models of the North Atlantic spring bloom using physical, chemical and bio-optical observations from a Lagrangian float

2010 ◽  
Vol 7 (6) ◽  
pp. 8477-8520 ◽  
Author(s):  
W. Bagniewski ◽  
K. Fennel ◽  
M. J. Perry ◽  
E. A. D'Asaro
Keyword(s):  
North Atlantic ◽  
Spring Bloom ◽  
Deep Ocean ◽  
Complex Model ◽  
Optical Observations ◽  
Model Parameters ◽  
Carbon Export ◽  
The North ◽  
Chemical Measurements ◽  
The North Atlantic

Abstract. The North Atlantic spring bloom is one of the main events that lead to carbon export to the deep ocean and drive oceanic uptake of CO2 from the atmosphere. Here we use a suite of physical, bio-optical and chemical measurements made during the 2008 spring bloom to optimize and compare three different models of biological carbon export. The observations are from a Lagrangian float that operated south of Iceland from early April to late June, and were calibrated with ship-based measurements. The simplest model is representative of typical NPZD models used for the North Atlantic, while the most complex model explicitly includes diatoms and the formation of fast sinking diatom aggregates and cysts under silicate limitation. We carried out a variational optimization and error analysis for the biological parameters of all three models, and compared their ability to replicate the observations. The observations were sufficient to constrain most phytoplankton-related model parameters to accuracies of better than 15%. However, the lack of zooplankton observations leads to large uncertainties in model parameters for grazing. The simulated vertical carbon flux at 100 m depth is similar between models and agrees well with available observations, but at 600 m the simulated flux is much larger for the model with diatom aggregation. While none of the models can be formally rejected based on their misfit with the available observations, the model that includes export by diatom aggregation has slightly better fit to the observations and more accurately represents the mechanisms and timing of carbon export based on observations not included in the optimization. Thus models that accurately simulate the upper 100 m do not necessarily accurately simulate export to deeper depths.

scholarly journals Sinking particles promote vertical connectivity in the ocean microbiome

2018 ◽  
Vol 115 (29) ◽  
pp. E6799-E6807 ◽  
Author(s):  
Mireia Mestre ◽  
Clara Ruiz-González ◽  
Ramiro Logares ◽  
Carlos M. Duarte ◽  
Josep M. Gasol ◽  
...  
Keyword(s):  
Surface Waters ◽  
Deep Ocean ◽  
Rrna Gene ◽  
Carbon Export ◽  
Size Fractions ◽  
Sinking Particles ◽  
Prokaryotic Diversity ◽  
Compositional Variability ◽  
Organic Particles ◽  
Community Connectivity

The sinking of organic particles formed in the photic layer is a main vector of carbon export into the deep ocean. Although sinking particles are heavily colonized by microbes, so far it has not been explored whether this process plays a role in transferring prokaryotic diversity from surface to deep oceanic layers. Using Illumina sequencing of the 16S rRNA gene, we explore here the vertical connectivity of the ocean microbiome by characterizing marine prokaryotic communities associated with five different size fractions and examining their compositional variability from surface down to 4,000 m across eight stations sampled in the Atlantic, Pacific, and Indian Oceans during the Malaspina 2010 Expedition. Our results show that the most abundant prokaryotes in the deep ocean are also present in surface waters. This vertical community connectivity seems to occur predominantly through the largest particles because communities in the largest size fractions showed the highest taxonomic similarity throughout the water column, whereas free-living communities were more isolated vertically. Our results further suggest that particle colonization processes occurring in surface waters determine to some extent the composition and biogeography of bathypelagic communities. Overall, we postulate that sinking particles function as vectors that inoculate viable particle-attached surface microbes into the deep-sea realm, determining to a considerable extent the structure, functioning, and biogeography of deep ocean 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 Functional Genomics Differentiate Inherent and Environmentally Influenced Traits in Dinoflagellate and Diatom Communities

2020 ◽  
Vol 8 (4) ◽  
pp. 567 ◽  
Author(s):  
Stephanie Elferink ◽  
Uwe John ◽  
Stefan Neuhaus ◽  
Sylke Wohlrab
Keyword(s):  
Signal Transduction ◽  
Functional Traits ◽  
Species Interactions ◽  
Marine Ecosystem ◽  
Biotic Interactions ◽  
Sulfur Cycle ◽  
Functional Responses ◽  
Physiological Importance ◽  
Metabolic Interactions ◽  
Lysine Degradation

Dinoflagellates and diatoms are among the most prominent microeukaryotic plankton groups, and they have evolved different functional traits reflecting their roles within ecosystems. However, links between their metabolic processes and functional traits within different environmental contexts warrant further study. The functional biodiversity of dinoflagellates and diatoms was accessed with metatranscriptomics using Pfam protein domains as proxies for functional processes. Despite the overall geographic similarity of functional responses, abiotic (i.e., temperature and salinity; ~800 Pfam domains) and biotic (i.e., taxonomic group; ~1500 Pfam domains) factors influencing particular functional responses were identified. Salinity and temperature were identified as the main drivers of community composition. Higher temperatures were associated with an increase of Pfam domains involved in energy metabolism and a decrease of processes associated with translation and the sulfur cycle. Salinity changes were correlated with the biosynthesis of secondary metabolites (e.g., terpenoids and polyketides) and signal transduction processes, indicating an overall strong effect on the biota. The abundance of dinoflagellates was positively correlated with nitrogen metabolism, vesicular transport and signal transduction, highlighting their link to biotic interactions (more so than diatoms) and suggesting the central role of species interactions in the evolution of dinoflagellates. Diatoms were associated with metabolites (e.g., isoprenoids and carotenoids), as well as lysine degradation, which highlights their ecological role as important primary producers and indicates the physiological importance of these metabolic pathways for diatoms in their natural environment. These approaches and gathered information will support ecological questions concerning the marine ecosystem state and metabolic interactions in the marine environment.

scholarly journals Elongation factor G initiates translocation through a power stroke

2016 ◽  
Vol 113 (27) ◽  
pp. 7515-7520 ◽  
Author(s):  
Chunlai Chen ◽  
Xiaonan Cui ◽  
John F. Beausang ◽  
Haibo Zhang ◽  
Ian Farrell ◽  
...  
Keyword(s):  
Single Molecule ◽  
Messenger Rna ◽  
Elongation Factor ◽  
Power Stroke ◽  
Elongation Factor G ◽  
Gtp Hydrolysis ◽  
Guanosine Triphosphatase ◽  
Prokaryotic Protein ◽  
Domain Iii ◽  
Factor G

During the translocation step of prokaryotic protein synthesis, elongation factor G (EF-G), a guanosine triphosphatase (GTPase), binds to the ribosomal PRE-translocation (PRE) complex and facilitates movement of transfer RNAs (tRNAs) and messenger RNA (mRNA) by one codon. Energy liberated by EF-G’s GTPase activity is necessary for EF-G to catalyze rapid and precise translocation. Whether this energy is used mainly to drive movements of the tRNAs and mRNA or to foster EF-G dissociation from the ribosome after translocation has been a long-lasting debate. Free EF-G, not bound to the ribosome, adopts quite different structures in its GTP and GDP forms. Structures of EF-G on the ribosome have been visualized at various intermediate steps along the translocation pathway, using antibiotics and nonhydolyzable GTP analogs to block translocation and to prolong the dwell time of EF-G on the ribosome. However, the structural dynamics of EF-G bound to the ribosome have not yet been described during normal, uninhibited translocation. Here, we report the rotational motions of EF-G domains during normal translocation detected by single-molecule polarized total internal reflection fluorescence (polTIRF) microscopy. Our study shows that EF-G has a small (∼10°) global rotational motion relative to the ribosome after GTP hydrolysis that exerts a force to unlock the ribosome. This is followed by a larger rotation within domain III of EF-G before its dissociation from the ribosome.

scholarly journals Bacterial RNA polymerase can retain σ70 throughout transcription

2016 ◽  
Vol 113 (3) ◽  
pp. 602-607 ◽  
Author(s):  
Timothy T. Harden ◽  
Christopher D. Wells ◽  
Larry J. Friedman ◽  
Robert Landick ◽  
Ann Hochschild ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Single Molecule ◽  
Transcription Initiation ◽  
Messenger Rna ◽  
Initiation Factors ◽  
Bacterial Rna ◽  
Direct Measurements ◽  
Promoter Recognition ◽  
Σ Factor ◽  
Transcript Elongation

Production of a messenger RNA proceeds through sequential stages of transcription initiation and transcript elongation and termination. During each of these stages, RNA polymerase (RNAP) function is regulated by RNAP-associated protein factors. In bacteria, RNAP-associated σ factors are strictly required for promoter recognition and have historically been regarded as dedicated initiation factors. However, the primary σ factor in Escherichia coli, σ70, can remain associated with RNAP during the transition from initiation to elongation, influencing events that occur after initiation. Quantitative studies on the extent of σ70 retention have been limited to complexes halted during early elongation. Here, we used multiwavelength single-molecule fluorescence-colocalization microscopy to observe the σ70–RNAP complex during initiation from the λ PR′ promoter and throughout the elongation of a long (>2,000-nt) transcript. Our results provide direct measurements of the fraction of actively transcribing complexes with bound σ70 and the kinetics of σ70 release from actively transcribing complexes. σ70 release from mature elongation complexes was slow (0.0038 s−1); a substantial subpopulation of elongation complexes retained σ70 throughout transcript elongation, and this fraction depended on the sequence of the initially transcribed region. We also show that elongation complexes containing σ70 manifest enhanced recognition of a promoter-like pause element positioned hundreds of nucleotides downstream of the promoter. Together, the results provide a quantitative framework for understanding the postinitiation roles of σ70 during transcription.

scholarly journals Single-Molecule Optical-Tweezers Studies of Ribosome Translation and Unwinding of Messenger RNA

2010 ◽  
Vol 98 (3) ◽  
pp. 260a
Author(s):  
Xiaohui Qu ◽  
Jin-Der Wen ◽  
Steven B. Smith ◽  
Laura Lancaster ◽  
Harry F. Noller ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Messenger Rna

scholarly journals Phosphate availability and the ultimate control of new nitrogen input by nitrogen fixation in the tropical Pacific Ocean

2007 ◽  
Vol 4 (4) ◽  
pp. 2407-2440 ◽  
Author(s):  
T. Moutin ◽  
D. M. Karl ◽  
S. Duhamel ◽  
P. Rimmelin ◽  
P. Raimbault ◽  
...  
Keyword(s):  
Pacific Ocean ◽  
N2 Fixation ◽  
Cold Water ◽  
Austral Summer ◽  
Deep Ocean ◽  
South Pacific ◽  
Phosphate Limitation ◽  
The South ◽  
Carbon Export ◽  
The North

Abstract. Due to the low atmospheric input of phosphate into the open ocean, it is one of the key nutrients that could ultimately control primary production and carbon export into the deep ocean. The observed trend over the last 20 years, has shown a decrease in the dissolved inorganic phosphate (DIP) pool in the North Pacific gyre, which has been correlated to the increase in di-nitrogen (N2) fixation rates. Following a NW-SE transect, in the Southeast Pacific during the early austral summer (BIOSOPE cruise), we present data on DIP, dissolved organic phosphate (DOP), and particulate phosphate (PP) pools and DIP turnover times (TDIP) along with N2 fixation rates. We observed a decrease in DIP concentration from the edges to the centre of the gyre. Nevertheless the DIP concentrations remained above 100 nmol L−1 and TDIP were more than a month in the centre of the gyre: DIP availability remained largely above the level required for phosphate limitation. This contrasts with recent observations in the western Pacific Ocean at the same latitude (DIAPALIS cruises) where lower DIP concentrations (<20 nmol L−1) and TDIP<50 h were measured during the summer season. During the BIOSOPE cruise, N2 fixation rates were higher within the cold water upwelling near the Chilean coast. This observation contrasts with recently obtained model output for N2 fixation distribution in the South Pacific area and emphasises the importance of studying the main factors controlling this process. The South Pacific gyre can be considered a High P Low Chlorophyll (HPLC) oligotrophic area, which could potentially support high N2 fixation rates, and possibly carbon dioxide sequestration, if the primary ecophysiological controls, temperature and/or iron availability, were alleviated.

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