scholarly journals Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

2016 ◽  
Author(s):  
Simon Roux ◽  
Jennifer R. Brum ◽  
Bas E. Dutilh ◽  
Shinichi Sunagawa ◽  
Melissa B. Duhaime ◽  
...  
Keyword(s):  
Deep Ocean ◽  
Global Scale ◽  
Host Community ◽  
Global Ocean ◽  
Trophic Networks ◽  
Evolutionary Trajectories ◽  
Genome Level ◽  
Dsdna Viruses ◽  
Auxiliary Metabolic Genes ◽  
Do So

AbstractOcean microbes drive global-scale biogeochemical cycling1, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories2–5. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ‘known’5. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions6,7. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups8,9). This roughly triples known ocean viral populations10, doubles known candidate bacterial and archaeal virus genera9, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks.

scholarly journals Large deep-sea zooplankton biomass mirrors primary production in the global ocean

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
S. Hernández-León ◽  
R. Koppelmann ◽  
E. Fraile-Nuez ◽  
A. Bode ◽  
C. Mompeán ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Primary Production ◽  
Deep Sea ◽  
Large Scale ◽  
Net Primary Production ◽  
Deep Ocean ◽  
Zooplankton Biomass ◽  
Global Ocean ◽  
Global Coupling ◽  
Do So

AbstractThe biological pump transports organic carbon produced by photosynthesis to the meso- and bathypelagic zones, the latter removing carbon from exchanging with the atmosphere over centennial time scales. Organisms living in both zones are supported by a passive flux of particles, and carbon transported to the deep-sea through vertical zooplankton migrations. Here we report globally-coherent positive relationships between zooplankton biomass in the epi-, meso-, and bathypelagic layers and average net primary production (NPP). We do so based on a global assessment of available deep-sea zooplankton biomass data and large-scale estimates of average NPP. The relationships obtained imply that increased NPP leads to enhanced transference of organic carbon to the deep ocean. Estimated remineralization from respiration rates by deep-sea zooplankton requires a minimum supply of 0.44 Pg C y−1 transported into the bathypelagic ocean, comparable to the passive carbon sequestration. We suggest that the global coupling between NPP and bathypelagic zooplankton biomass must be also supported by an active transport mechanism associated to vertical zooplankton migration.

scholarly journals <i>MEDUSA</i>: a new intermediate complexity plankton ecosystem model for the global domain

2010 ◽  
Vol 3 (4) ◽  
pp. 1939-2019 ◽  
Author(s):  
A. Yool ◽  
E. E. Popova ◽  
T. R. Anderson
Keyword(s):  
Deep Ocean ◽  
Ecosystem Model ◽  
Global Scale ◽  
Ecosystem Dynamics ◽  
Global Ocean ◽  
Full Description ◽  
State Variables ◽  
Intermediate Complexity ◽  
Nutrient Utilisation ◽  
Parameter Values

Abstract. The ongoing, anthropogenically-driven changes to the global ocean are expected to have significant consequences for plankton ecosystems in the future. Because of the role that plankton play in the ocean's "biological pump", changes in abundance, distribution and productivity will likely have additional consequences for the wider carbon cycle. Just as in the terrestrial biosphere, marine ecosystems exhibit marked diversity in species and functional types of organisms. Predicting potential change in plankton ecosystems therefore requires the use of models that are suited to this diversity, but whose parameterisation also permits robust and realistic functional behaviour. In the past decade, advances in model sophistication have attempted to address diversity, but have been criticised for doing so inaccurately or ahead of a requisite understanding of underlying processes. Here we introduce MEDUSA (Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification), a new "intermediate complexity" plankton ecosystem model that expands on traditional nutrient-phytoplankton-zooplankton-detritus (NPZD) models, and remains amenable to global-scale evaluation. MEDUSA includes the biogeochemical cycles of nitrogen, silicon and iron, broadly structured into "small" and "large" plankton size classes, of which the "large" phytoplankton class is representative of a key phytoplankton group, the diatoms. A full description of MEDUSA's state variables, differential equations, functional forms and parameter values is included, with particular attention focused on the submodel describing the export of organic carbon from the surface to the deep ocean. MEDUSA is used here in a multi-decadal hindcast simulation, and its biogeochemical performance evaluated at the global scale.

scholarly journals Medusa-1.0: a new intermediate complexity plankton ecosystem model for the global domain

2011 ◽  
Vol 4 (2) ◽  
pp. 381-417 ◽  
Author(s):  
A. Yool ◽  
E. E. Popova ◽  
T. R. Anderson
Keyword(s):  
Deep Ocean ◽  
Ecosystem Model ◽  
Global Scale ◽  
Ecosystem Dynamics ◽  
Global Ocean ◽  
Full Description ◽  
State Variables ◽  
Intermediate Complexity ◽  
Nutrient Utilisation ◽  
Parameter Values

Abstract. The ongoing, anthropogenically-driven changes to the global ocean are expected to have significant consequences for plankton ecosystems in the future. Because of the role that plankton play in the ocean's "biological pump", changes in abundance, distribution and productivity will likely have additional consequences for the wider carbon cycle. Just as in the terrestrial biosphere, marine ecosystems exhibit marked diversity in species and functional types of organisms. Predicting potential change in plankton ecosystems therefore requires the use of models that are suited to this diversity, but whose parameterisation also permits robust and realistic functional behaviour. In the past decade, advances in model sophistication have attempted to address diversity, but have been criticised for doing so inaccurately or ahead of a requisite understanding of underlying processes. Here we introduce MEDUSA-1.0 (Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification), a new "intermediate complexity" plankton ecosystem model that expands on traditional nutrient-phytoplankton-zooplankton-detritus (NPZD) models, and remains amenable to global-scale evaluation. MEDUSA-1.0 includes the biogeochemical cycles of nitrogen, silicon and iron, broadly structured into "small" and "large" plankton size classes, of which the "large" phytoplankton class is representative of a key phytoplankton group, the diatoms. A full description of MEDUSA-1.0's state variables, differential equations, functional forms and parameter values is included, with particular attention focused on the submodel describing the export of organic carbon from the surface to the deep ocean. MEDUSA-1.0 is used here in a multi-decadal hindcast simulation, and its biogeochemical performance evaluated at the global scale.

scholarly journals Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean

2019 ◽  
Author(s):  
Hiroto Kaneko ◽  
Romain Blanc-Mathieu ◽  
Hisashi Endo ◽  
Samuel Chaffron ◽  
Tom O. Delmont ◽  
...  
Keyword(s):  
Large Scale ◽  
Regional Scale ◽  
Deep Ocean ◽  
Global Scale ◽  
Ecosystem Dynamics ◽  
Global Ocean ◽  
Marker Genes ◽  
Carbon Export ◽  
Viral Marker ◽  
Carbon Pump

SummaryThe biological carbon pump, in which carbon fixed by photosynthesis is exported to the deep ocean through sinking, is a major process in Earth’s carbon cycle. The proportion of primary production that is exported is termed the carbon export efficiency (CEE). Based on in-lab or regional scale observations, viruses were previously suggested to affect the CEE (i.e., viral “shunt” and “shuttle”). In this study, we tested associations between viral community composition and CEE measured at a global scale. A regression model based on relative abundance of viral marker genes explained 67% of the variation in CEE. Viruses with high importance in the model were predicted to infect ecologically important hosts. These results are consistent with the view that the viral shunt and shuttle functions at a large scale and further imply that viruses likely act in this process in a way dependent on their hosts and ecosystem dynamics.

On the impact of sea ice in a global ocean circulation model

1997 ◽  
Vol 25 ◽  
pp. 111-115 ◽  
Author(s):  
Achim Stössel
Keyword(s):  
Southern Ocean ◽  
Sea Ice ◽  
Ocean Circulation ◽  
General Circulation ◽  
Thermohaline Circulation ◽  
Circulation Model ◽  
Deep Ocean ◽  
Global Ocean ◽  
Convective Activity ◽  
The Impact

This paper investigates the long-term impact of sea ice on global climate using a global sea-ice–ocean general circulation model (OGCM). The sea-ice component involves state-of-the-art dynamics; the ocean component consists of a 3.5° × 3.5° × 11 layer primitive-equation model. Depending on the physical description of sea ice, significant changes are detected in the convective activity, in the hydrographic properties and in the thermohaline circulation of the ocean model. Most of these changes originate in the Southern Ocean, emphasizing the crucial role of sea ice in this marginally stably stratified region of the world's oceans. Specifically, if the effect of brine release is neglected, the deep layers of the Southern Ocean warm up considerably; this is associated with a weakening of the Southern Hemisphere overturning cell. The removal of the commonly used “salinity enhancement” leads to a similar effect. The deep-ocean salinity is almost unaffected in both experiments. Introducing explicit new-ice thickness growth in partially ice-covered gridcells leads to a substantial increase in convective activity, especially in the Southern Ocean, with a concomitant significant cooling and salinification of the deep ocean. Possible mechanisms for the resulting interactions between sea-ice processes and deep-ocean characteristics are suggested.

scholarly journals Ventilation of the abyss in the Atlantic sector of the Southern Ocean

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Camille Hayatte Akhoudas ◽  
Jean-Baptiste Sallée ◽  
F. Alexander Haumann ◽  
Michael P. Meredith ◽  
Alberto Naveira Garabato ◽  
...  
Keyword(s):  
Southern Ocean ◽  
Bottom Water ◽  
Climate Models ◽  
Deep Ocean ◽  
Analytical Framework ◽  
Weddell Sea ◽  
Global Ocean ◽  
Shelf Water ◽  
Antarctic Bottom Water ◽  
Atlantic Sector

AbstractThe Atlantic sector of the Southern Ocean is the world’s main production site of Antarctic Bottom Water, a water-mass that is ventilated at the ocean surface before sinking and entraining older water-masses—ultimately replenishing the abyssal global ocean. In recent decades, numerous attempts at estimating the rates of ventilation and overturning of Antarctic Bottom Water in this region have led to a strikingly broad range of results, with water transport-based calculations (8.4–9.7 Sv) yielding larger rates than tracer-based estimates (3.7–4.9 Sv). Here, we reconcile these conflicting views by integrating transport- and tracer-based estimates within a common analytical framework, in which bottom water formation processes are explicitly quantified. We show that the layer of Antarctic Bottom Water denser than 28.36 kg m$$^{-3}$$ - 3 $$\gamma _{n}$$ γ n is exported northward at a rate of 8.4 ± 0.7 Sv, composed of 4.5 ± 0.3 Sv of well-ventilated Dense Shelf Water, and 3.9 ± 0.5 Sv of old Circumpolar Deep Water entrained into cascading plumes. The majority, but not all, of the Dense Shelf Water (3.4 ± 0.6 Sv) is generated on the continental shelves of the Weddell Sea. Only 55% of AABW exported from the region is well ventilated and thus draws down heat and carbon into the deep ocean. Our findings unify traditionally contrasting views of Antarctic Bottom Water production in the Atlantic sector, and define a baseline, process-discerning target for its realistic representation in climate models.

scholarly journals 20th century cooling of the deep ocean contributed to delayed acceleration of Earth’s energy imbalance

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
A. Bagnell ◽  
T. DeVries
Keyword(s):  
20Th Century ◽  
Heat Content ◽  
Deep Ocean ◽  
Ocean Warming ◽  
Ocean Heat Content ◽  
Global Ocean ◽  
Energy Imbalance ◽  
Delayed Onset ◽  
The Past ◽  
Historical Reconstructions

AbstractThe historical evolution of Earth’s energy imbalance can be quantified by changes in the global ocean heat content. However, historical reconstructions of ocean heat content often neglect a large volume of the deep ocean, due to sparse observations of ocean temperatures below 2000 m. Here, we provide a global reconstruction of historical changes in full-depth ocean heat content based on interpolated subsurface temperature data using an autoregressive artificial neural network, providing estimates of total ocean warming for the period 1946-2019. We find that cooling of the deep ocean and a small heat gain in the upper ocean led to no robust trend in global ocean heat content from 1960-1990, implying a roughly balanced Earth energy budget within −0.16 to 0.06 W m−2 over most of the latter half of the 20th century. However, the past three decades have seen a rapid acceleration in ocean warming, with the entire ocean warming from top to bottom at a rate of 0.63 ± 0.13 W m−2. These results suggest a delayed onset of a positive Earth energy imbalance relative to previous estimates, although large uncertainties remain.

scholarly journals Consistency of the current global ocean observing systems from an Argo perspective

Ocean Science ◽  
2014 ◽  
Vol 10 (3) ◽  
pp. 547-557 ◽  
Author(s):  
K. von Schuckmann ◽  
J.-B. Sallée ◽  
D. Chambers ◽  
P.-Y. Le Traon ◽  
C. Cabanes ◽  
...  
Keyword(s):  
Sea Level ◽  
Heat Content ◽  
Deep Ocean ◽  
Global Ocean ◽  
Regional Variability ◽  
Tropical Ocean ◽  
Steric Sea Level ◽  
Ocean Observing ◽  
Ocean Observing Systems ◽  
Observing Systems

Abstract. Variations in the world's ocean heat storage and its associated volume changes are a key factor to gauge global warming and to assess the earth's energy and sea level budget. Estimating global ocean heat content (GOHC) and global steric sea level (GSSL) with temperature/salinity data from the Argo network reveals a positive change of 0.5 ± 0.1 W m−2 (applied to the surface area of the ocean) and 0.5 ± 0.1 mm year−1 during the years 2005 to 2012, averaged between 60° S and 60° N and the 10–1500 m depth layer. In this study, we present an intercomparison of three global ocean observing systems: the Argo network, satellite gravimetry from GRACE and satellite altimetry. Their consistency is investigated from an Argo perspective at global and regional scales during the period 2005–2010. Although we can close the recent global ocean sea level budget within uncertainties, sampling inconsistencies need to be corrected for an accurate global budget due to systematic biases in GOHC and GSSL in the Tropical Ocean. Our findings show that the area around the Tropical Asian Archipelago (TAA) is important to closing the global sea level budget on interannual to decadal timescales, pointing out that the steric estimate from Argo is biased low, as the current mapping methods are insufficient to recover the steric signal in the TAA region. Both the large regional variability and the uncertainties in the current observing system prevent us from extracting indirect information regarding deep-ocean changes. This emphasizes the importance of continuing sustained effort in measuring the deep ocean from ship platforms and by beginning a much needed automated deep-Argo network.

scholarly journals Global ocean dimethyl sulfide climatology estimated from observations and an artificial neural network

2020 ◽  
Author(s):  
Wei-Lei Wang ◽  
Guisheng Song ◽  
François Primeau ◽  
Eric S. Saltzman ◽  
Thomas G. Bell ◽  
...  
Keyword(s):  
Neural Network ◽  
Artificial Neural Network ◽  
Solar Radiation ◽  
Mixed Layer ◽  
Dimethyl Sulfide ◽  
Mixed Layer Depth ◽  
Environmental Parameters ◽  
Global Scale ◽  
Global Ocean ◽  
Layer Depth

Abstract. Marine dimethyl sulfide (DMS) is important to climate due to the ability of DMS to alter Earth's radiation budget. However, a knowledge of the global-scale distribution, seasonal variability, and sea-to-air flux of DMS is needed in order to understand the factors controlling surface ocean DMS and its impact on climate. Here we examine the use of an artificial neural network (ANN) to extrapolate available DMS measurements to the global ocean and produce a global climatology with monthly temporal resolution. A global database of 57 810 ship-based DMS measurements in surface waters was used along with a suite of environmental parameters consisting of lat-lon coordinates, time-of-day, time-of-year, solar radiation, mixed layer depth, sea surface temperature, salinity, nitrate, phosphate, silicate, and oxygen. Linear regressions of DMS against the environmental parameters show that on a global scale mixed layer depth and solar radiation are the strongest predictors of DMS, however, they capture 14 % and 12 % of the raw DMS data variance, respectively. The multi-linear regression can capture more (∼29 %) of the raw data variance, but strongly underestimates high DMS concentrations. In contrast, the ANN captures ~61 % of the raw data variance in our database. Like prior climatologies our results show a strong seasonal cycle in DMS concentration and sea-to-air flux. The highest concentrations (fluxes) occur in the high-latitude oceans during the summer. We estimate a lower global sea-to-air DMS flux (17.90 &amp;pm; 0.34 Tg S yr−1) than the prior estimate based on a map interpolation method when the same gas transfer velocity parameterization is used.

scholarly journals Different processes shape prokaryotic and picoeukaryotic assemblages in the sunlit ocean microbiome

2018 ◽  
Author(s):  
Ramiro Logares ◽  
Ina M. Deutschmann ◽  
Caterina. R. Giner ◽  
Anders K. Krabberød ◽  
Thomas S. B. Schmidt ◽  
...  
Keyword(s):  
Ecosystem Function ◽  
Sequence Data ◽  
Scale Effects ◽  
Dispersal Limitation ◽  
Global Scale ◽  
Global Ocean ◽  
Ecosystem Functions ◽  
Ecological Processes ◽  
Surface Ocean

ABSTRACTThe smallest members of the sunlit-ocean microbiome (prokaryotes and picoeukaryotes) participate in a plethora of ecosystem functions with planetary-scale effects. Understanding the processes determining the spatial turnover of this assemblage can help us better comprehend the links between microbiome species composition and ecosystem function. Ecological theory predicts thatselection,dispersalanddriftare main drivers of species distributions, yet, the relative quantitative importance of these ecological processes in structuring the surface-ocean microbiome is barely known. Here we quantified the role of selection, dispersal and drift in structuring surface-ocean prokaryotic and picoeukaryotic assemblages by using community DNA-sequence data collected during the global Malaspina expedition. We found that dispersal limitation was the dominant process structuring picoeukaryotic communities, while a balanced combination of dispersal limitation, selection and drift shaped prokaryotic counterparts. Subsequently, we determined the agents exerting abiotic selection as well as the spatial patterns emerging from the action of different ecological processes. We found that selection exerted via temperature had a strong influence on the structure of prokaryotic communities, particularly on species co-occurrences, a pattern not observed among communities of picoeukaryotes. Other measured abiotic variables had limited selective effects on microbiome structure. Picoeukaryotes presented a higher differentiation between neighbouring communities and a higher distance-decay when compared to prokaryotes, agreeing with their higher dispersal limitation. Finally, drift seemed to have a limited role in structuring the sunlit-ocean microbiome. The different predominance of ecological processes acting on particular subsets of the ocean microbiome suggests uneven responses to environmental change.SIGNIFICANCE STATEMENTThe global ocean contains one of the largest microbiomes on Earth and changes on its structure can impact the functioning of the biosphere. Yet, we are far from understanding the mechanisms that structure the global ocean microbiome, that is, the relative importance of environmentalselection,dispersaland random events (drift). We evaluated the role of these processes at the global scale, based on data derived from a circumglobal expedition and found that these ecological processes act differently on prokaryotes and picoeukaryotes, two of the main components of the ocean microbiome. Our work represents a significant contribution to understand the assembly of marine microbial communities, providing also insights on the links between ecological mechanisms, microbiome structure and ecosystem function.

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