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Microbial Iron limitation in the ocean’s twilight zone

Posted by mmaheigan

· Monday, March 31st, 2025

How deep in the ocean do microbes feel the effects of nutrient limitation? Microbial production in one third of the surface ocean is limited by the essential micronutrient iron (Fe). This limitation extends to at least the bottom of the euphotic zone, but what happens below that?

In a study that recently published in Nature we investigated the abundance and distribution of siderophores, small metabolites synthesized by bacteria to promote Fe uptake. When environmental Fe concentrations become limiting and microbes become Fe deficient, some bacteria release siderophores into the environment to bind iron and facilitate its uptake. Siderophores are therefore a window into how microbes “see” environmental Fe. We found that siderophore concentrations were high in low Fe surface waters, but surprisingly we also found siderophores to be abundant in the twilight zone (200-500 m) underlying the North and South Pacific subtropical gyres, two key ecosystems for the marine carbon cycle. In shipboard experiments with siderophores labeled with the rare ⁵⁷Fe isotope, we found rapid uptake of the label in twilight zone samples. After removing ⁵⁷Fe from the ⁵⁷Fe-siderophores complex, bacteria released the now unlabeled siderophores back into seawater to complex additional Fe (Figure. 1).

Figure 1: Iron-siderophore cycling in the twilight zone. When the seawater becomes Fe-deficient, some bacteria are able to synthesize siderophores and release them into the environment (middle left). These metabolites bind Fe (middle right) and the Fe-siderophore complex is taken up by bacteria using specialized TonB dependent transporters (TBDT; bottom right). Inside the cell, Fe is recovered from the Fe-siderophore complex (bottom left) and the siderophore excreted back into the environment to start the cycle anew.

Our results show that in large parts of the ocean microbes feel the effects of nutrient limitation deep in the water column, to at least 500 m. This greatly expands the region of the ocean where nutrients limit microbial metabolism. The effects of limitation this deep in the water column are unexplored, but twilight zone Fe deficiency could have unanticipated consequences for the efficiency of the ocean’s biological carbon pump.

Authors
Jingxuan Li, Lydia Babcock-Adams and Daniel Repeta
(all at Woods Hole Oceanographic Institution)

Severe warming = 15% increase in bacterial respiration: Southern Ocean most impacted

Posted by mmaheigan

· Thursday, March 30th, 2023

The utilization, respiration, and remineralization of organic matter exported from the ocean surface to its depths are key processes in the ocean carbon cycle. Marine heterotrophic Bacteria play a critical role in these activities. However, most three-dimensional (3-D) coupled physical-biogeochemical models do not explicitly include Bacteria as a state variable. Instead, they rely on parameterization to account for the bacteria’s impact on particle flux attenuation.

A recent study examined how bacteria respond to climate change by employing a 3-D coupled ocean biogeochemical model that incorporates explicit bacterial dynamics. The model (CMCC-ESM2) is a part of the Coupled Model Intercomparison Project Phase 6. The authors first evaluated the reliability of century-scale forecasts (2015-2099) for bacterial stocks and rates in the upper 100 m layer against the compiled measurements from the contemporary period (1988-2011). Next the authors analyzed the predicted trends in bacterial stocks and rates under diverse climate scenarios and explored their association with regional differences in temperature and organic carbon stocks. Three crucial findings were revealed. There is a global-scale decrease in bacterial biomass of 5-10%, with a 3-5% increase in the Southern Ocean (Figure 1). In the Southern Ocean, the rise in semi-labile dissolved organic carbon (DOC) leads to an increase in DOC uptake rates of free-living bacteria; in the northern high and low latitudes, the increase in temperature drives the increase in their DOC uptake rates. Importantly, extreme warming could result in a global increase (up to 15%) and even higher in the Southern Ocean (21% increase) in bacterial respiration (Figure 1), potentially leading to a decline in the biological carbon pump.

This analysis is an unprecedented and early effort to understand the climate-induced changes in bacterial dynamics on a global scale in a systematic manner. This study takes us one step closer to comprehending how bacteria influence the functioning of the biological carbon pump and the distribution of organic carbon pools between surface and deep layers, especially their response to climate change.

Figure 1. Global projections of bacterial carbon stocks and rates during the baseline period (1990-2013) and their changes as anomalies under the most-severe climate change scenario (i.e., SSP5-8.5) relative to the baseline period (2076-2099). The stocks and rates during the baseline period (a, b, c, g, h, i) and their changes as anomalies under the most-severe climate change scenario (d, e, f, j, k, l). All variables are depth-integrated in the upper 100 m. Solid-line contours as standard deviation from averaging over 1990-2013. Anomalies are 2076-2099 average values relative to 1990-2013 average values. Global bacterial biomass has decreased by 5-10%, with a 3-5% increase in the Southern Ocean. However, extreme warming may increase bacterial respiration worldwide, thereby reducing the efficiency of the biological carbon pump. This study provides an early attempt to understand the response of bacteria to climate change and their impact on the distribution of organic carbon in the ocean.

Author
Heather Kim, Woods Hole Oceanographic Institution

How does the competition between phytoplankton and bacteria for iron alter ocean biogeochemical cycles?

Posted by mmaheigan

· Friday, August 26th, 2022

Free-living bacteria play a key role in cycling essential biogeochemical resources in the ocean, including iron, via their uptake, transformation, and release of organic matter throughout the water column. Bacteria process half of the ocean’s primary production, remineralize dissolved organic matter, and re-direct otherwise lost organic matter to higher trophic levels. For these reasons, it is crucial to understand what factors limit the growth of bacteria and how bacteria activities impact global ocean biogeochemical cycles.

In a recent study, Pham and colleagues used a global ocean ecosystem model to dive into how iron limits the growth of free-living marine bacteria, how bacteria modulate ocean iron cycling, and the consequences to marine ecosystems of the competition between bacteria and phytoplankton for iron.

Figure 1: (a) Iron limitation status of bacteria in December, January, and February (DJF) in the surface ocean. Low values (in blue color = close to zero) mean that iron is the limiting factor for the growth of bacteria; (b) Bacterial iron consumption in the upper 120m of the ocean and (c) Changes (anomalies) in export carbon production when bacteria have a high requirement for iron.

Through a series of computer simulations performed in the global ocean ecosystem model, the authors found that iron is a limiting factor for bacterial growth in iron-limited regions in the Southern Ocean, the tropical, and the subarctic Pacific due to the high iron requirement and iron uptake capability of bacteria. Bacteria act as an iron sink in the upper ocean due to their significant iron consumption, a rate comparable to phytoplankton. The competition between bacteria and phytoplankton for iron alters phytoplankton bloom dynamics, ocean carbon export, and the availability of dissolved organic carbon needed for bacterial growth. These results suggest that earth system models that omit bacteria ignore an important organism modulating biogeochemical responses of the ocean to future changes.

Authors:
Anh Le-Duy Pham (Laboratoire d’Océanographie et de Climatologie: Expérimentation et Approches Numériques (LOCEAN), IPSL, CNRS/UPMC/IRD/MNHN, Paris, France)
Olivier Aumont (Laboratoire d’Océanographie et de Climatologie: Expérimentation et Approches Numériques (LOCEAN), IPSL, CNRS/UPMC/IRD/MNHN, Paris, France)
Lavenia Ratnarajah (University of Liverpool, United Kingdom)
Alessandro Tagliabue (University of Liverpool, United Kingdom)

Predators Set Range for the Ocean’s Most Abundant Phytoplankton

Posted by mmaheigan

· Friday, April 1st, 2022

Prochlorococcus is the world’s smallest phytoplankton (microscopic plant-like organisms) and the most numerous, with more than ten septillion individuals. This tiny plankton lives ubiquitously in warm, blue, tropical waters but is conspicuously absent in more polar regions. The prevailing theory was the cold: Prochlorococcus doesn’t grow at low temperatures. In a recent paper, the authors argue ecological control, in particular, predation by zooplankton. Cold polar waters are greener because they contain more nutrients, leading to more life and more organic matter production. This production feeds more and larger heterotrophic bacteria, who then feed larger predators—specifically the same zooplankton that consume Prochlorococcus. If the shared zooplankton increases enough, it will consume Prochlorococus faster than it can grow, causing the species to collapse at higher latitudes. These results show that an understanding of both ecology and temperature is required to predict how these ecosystems will shift in a warming ocean.

Figure 1: Surface populations of Prochlorococcus collapse (dashed lines) moving northward from Hawaii as seen in transects (transect line shown in red on map, lower left) from cruises in April 2016 (black dots) and September 2017 (green triangles). This collapse of the Prochlorococcus emerges in dynamical computer models (lower right, color indicates Prochlorococcus biomass in mgC/m3) when heterotrophic bacteria and Prochlorococcus share a grazer (top schematic). Increased organic production heading poleward first increases the heterotrophic bacterial population, increasing the shared zooplankton population which eventually consumes Prochlorococcus faster than it can grow (dashed contour).

Authors
Christopher L. Follett (MIT)
Stephanie Dutkiewicz (MIT)
François Ribalet (UW)
Emily Zakem (USC)
David Caron (USC)
E. Virginia Armbrust (UW)
Michael J. Follows (MIT)

Contrasting N2O fluxes of source vs. sink in western Arctic Ocean during summer 2017

Posted by mmaheigan

· Wednesday, October 20th, 2021

During the western Arctic summer season both physical and biogeochemical features differ with latitude between the Bering Strait and Chukchi Borderland. The southern region (Bering Strait to the Chukchi Shelf) is relatively warm, saline, and eutrophic, due to the intrusion of Pacific waters that bring heat and nutrients in to the western Arctic Ocean (WAO). Because of the Pacific influence, the WAO is one of the most productive stretches of ocean in the world. In contrast, the northern region (Chukchi Borderland to the Canada Basin) is primarily influenced by freshwater originating from sea ice melt and rivers, and is relatively cold, fresh, and oligotrophic. A frontal zone exists between the southern region and northern region (~73°N) due to the distinct physicochemical contrast between mixing Pacific waters and freshwater. These regions support distinct bacterial communities also, making the environmental variations drivers extremely relevant to nitrous oxide (N₂O) dynamics.

A recent study published in Scientific Reports examined the role of the WAO as a source and a sink of atmospheric N₂O. There are obvious differences in N₂O fluxes between southern Chukchi Sea (SC) and northern Chukchi Sea (NC). In the SC (Pacific water characteristics dominate) N₂O emissions act as a net source to the atmosphere (Figure 1a). In the NC (freshwater dominant) absorption of atmospheric N₂O into the water column suggests that this region acts as a net sink (Figure 1a). The positive fluxes of SC occurred with relatively high sea surface temperature (SST), sea surface salinity (SSS), and biogeochemically-derived N₂O production, whereas the negative fluxes of NC were associated with relatively low SST, SSS, and little N₂O production. These linear relationships between N₂O fluxes and environmental variables suggest that summer WAO N₂O fluxes are remarkably sensitive to environmental changes.

Figure 1. (a) Map of the sampling stations using the Ice Breaking R/V Araon during August 2017. The sampling locations were coloured with N2O fluxes (blue to red gradient, see color bar; sink, air → sea (−), and source, sea → air (+). The southern Chukchi Sea (SC) extends from Bering Strait to Chukchi Shelf and the northern Chukchi Sea (NC) extends from Chukchi Borderland and Canada Basin. The frontal zone arises between SC and NC (black dotted line). (b) Illustration showing future changes in the distribution of the WAO N2O flux constrained by the positive feedback scenario of increasing inflow of Pacific waters and rapidly declining sea-ice extent under accelerating Arctic warming.

This study suggests a potential scenario for future WAO changes in terms of accelerating Arctic change. Increasing inflow of the Pacific waters and rapidly declining sea-ice extent are critical. The increasing inflow of warm nutrient-enriched Pacific waters will likely extend the SC N₂O source region northward, increasing productivity, and thereby intensifying nitrification. All of which would lead to a strengthening of the WAO’s role as an N₂O source. A rapid loss of the sea ice extent could ultimately lead to a sea-ice-free NC, and again, a northward shift, which would result in a diminished role of the NC as an N₂O sink (Figure 1b). While improving our understanding of WAO N₂O dynamics, this study suggests both a direction for future work and a clear need for a longer-term study to answer questions about both seasonal variations in these dynamics and possible interannual to climatological trends.

Authors:
Jang-Mu Heo (Department of Marine Science, Incheon National University)
Sang-Min Eom (Department of Marine Science, Incheon National University)
Alison M. Macdonald (Woods Hole Oceanographic Institution)
Hyo-Ryeon Kim (Department of Marine Science, Incheon National University)
Joo-Eun Yoon (Department of Marine Science, Incheon National University)
Il-Nam Kim (Department of Marine Science, Incheon National University)

Bacterial fingerprints as a tool for large-scale functional ecology

Posted by Dina Pandya

· Monday, September 20th, 2021

Unravelling the relationship between biological diversity and ecosystem functions is a timeless question which dates back to the expeditions of Alexander von Humboldt in the early 1800’. At the base of the marine foodweb, marine prokaryotes are essential for ecosystem functioning. Measuring their biogeography and functional traits therefore merits investigation as alterations in their alpha and beta diversities could lead to changes in the fluxes of oceanic biogeochemical cycles that sustain the life on Earth.

In a new article, published in Nature Communications, the authors used the genetic fingerprint of marine bacteria to predict their metabolic profiles from the ice edge to the equator in the Pacific Ocean. Their research showed that low-cost, high-throughput bacterial marker gene data can be used as a tool for large-scale functional ecology. They tackled five hypotheses and show how biological diversity influences functional diversity, and how these are related to energy production in the ocean. The authors, furthermore, highlight how - can be nicely integrated with the physical and chemical sampling programs during global ocean monitoring campaigns such as GO-SHIP and GEOTRACES.

Increasing our understanding how bacterial diversity impacts the functional diversity of ecosystems has also broader implications. For example, bacterial fingerprints can help us to improve marine ecosystem monitoring programs, especially in coastal zones and estuaries where the input of nitrogen is predicted to increase. Assessing the changes in the bacterial diversity can also help to assess the environmental footprint of aquaculture cages, which are a source of nutrients such as carbon, nitrogen and phosphorus and have been shown to deteriorate the water quality and life higher up the food chain.

Figure caption: The P15S GO-SHIP line from the ice-edge to the equator along 170o W in the South Pacific Ocean (a). Sea surface temperatures and salinity (b) and a conceptual picture of the functional prokaryotic and microbial-eukaryotic biogeography (c). In winter heterotrophic prokaryotes (blue rods) recycle the organic matter produced in the summer and autumn months in the high nutrient low chlorophyll (HNLC) region of the Southern Ocean (SO). Turbulence and mixing (curved arrows) in the sub-tropical front (STF) results in high primary productivity (PP) driven by phytoplankton rich in chlorophyll-a (green discs). The South Pacific Subtropical Gyre Province (SPSG) is characterized by nutrient co-limitation, low PP, and higher abundances of photosynthetic prokaryotes (yellow circles). The Pacific Equatorial Divergence (PED) is characterized by equatorial upwelling which results in an increase of the N:P ratio in the mixed layer (MLD) relative to the SPSG (d), and results in increased chlorophyll-a concentrations and PP. The MLD is shown as a thick white line. CTD stations (small gray dots), sampling stations for 16S rRNA data (large gray circles) and shotgun metagenome samples (yellow stars) are shown on panel d.

Authors:
Eric J. Raes (CSIRO Oceans and Atmosphere, Australia; Dalhousie University, Canada)
Kristen Karsh (CSIRO Oceans and Atmosphere, Australia)
Swan L. S. Sow (CSIRO Oceans and Atmosphere, Australia; University of Tasmania, Hobart; NIOZ Royal Netherlands Institute for Sea Research, The Netherlands)
Martin Ostrowski (University of Technology Sydney, Australia)
Mark V. Brown (The University of Newcastle, Australia)
Jodie van de Kamp (CSIRO Oceans and Atmosphere, Australia)
Rita M. Franco-Santos (University of Tasmania, Australia)
Levente Bodrossy (CSIRO Oceans and Atmosphere, Australia)
Anya M. Waite (Dalhousie University, Canada)

Want to read more about the P15S line?

Raes, E. J., Bodrossy, L., Van De Kamp, J., Bissett, A., Ostrowski, M., Brown, M. V., ... & Waite, A. M. (2018). Oceanographic boundaries constrain microbial diversity gradients in the South Pacific Ocean. Proceedings of the National Academy of Sciences, 115(35), E8266-E8275.

Raes, E. J., van de Kamp, J., Bodrossy, L., Fong, A. A., Riekenberg, J., Holmes, B. H., ... & Waite, A. M. (2020). N2 fixation and new insights into nitrification from the ice-edge to the equator in the South Pacific Ocean. Frontiers in Marine Science, 7, 389.

Sow, S. L., Trull, T. W., & Bodrossy, L. (2020). Oceanographic Fronts Shape Phaeocystis Assemblages: A High-Resolution 18S rRNA Gene Survey From the Ice-Edge to the Equator of the South Pacific. Frontiers in microbiology, 11, 1847.

Air-sea gas disequilibrium drove deoxygenation of the deep ice-age ocean

Posted by mmaheigan

· Thursday, March 18th, 2021

During the Last Glacial Maximum (~20,000 years ago, LGM) sediment data show that the deep ocean had lower dissolved oxygen (O₂) concentrations than the preindustrial ocean, despite cooler temperatures of this period increasing O₂ solubility in sea water.

Figure 1. a) Whole ocean inventory of the O₂ components in the preindustrial control (PIC): total O₂ (O₂); the preformed components equilibrium O₂ (O₂ equilibrium), physical disequilibrium O₂ (O₂ diseq phys) and biologically-mediated disequilibrium (O₂ diseq bio); and O₂ respired from soft-tissue (O₂ soft). b) The difference in whole ocean inventory of O₂ components between the LGM and PIC simulations.

In a study published in Nature Geoscience, the authors provide one of the first explanations for glacial deoxygenation. The authors combined a data-constrained model of the preindustrial (PIC) and LGM ocean with a novel decomposition of O₂ to assess the processes affecting the oceanic distribution of oxygen. The decomposition allowed for the preformed disequilibrium O₂—the amount of oxygen that deviates from its solubility equilibrium value when at the surface—to be tracked, along with other contributions such as the O₂ consumed by bacterial respiration of organic matter. In the preindustrial ocean, a third of the subsurface oxygen deficit was a result of disequilibrium rather than oxygen consumed by bacteria. This contradicts previous assumptions (Figure 1a). Nearly 80% of the disequilibrium resulted from upwelling waters, depleted in O₂ due to respiration, not fully equilibrating before re-subduction into the ocean interior. This effect was even greater during the LGM (Figure 1b). The authors attributed this largely to the widespread presence of sea ice—which acts as a cap on the surface preventing the water from gaining oxygen from the atmosphere—in the ocean around Antarctica, with a smaller contribution from iron fertilization.

This study provides one of the first mechanistic explanations for LGM deep ocean deoxygenation. As the ocean is currently losing oxygen due to warming, the effect of other processes, including sea ice changes, could prove important for understanding long-term ocean oxygenation changes.

Authors
Ellen Cliff (University of Oxford)
Samar Khatiwala (University of Oxford)
Andreas Schmittner (Oregon State University)

Joint highlight with GEOTRACES International Project Office

Surface bacterial communities respond to rapid changes in the western Arctic

Posted by mmaheigan

· Tuesday, January 7th, 2020

During the western Arctic summer open water season, latitudinal differences in the physical and biogeochemical features of the surface water are apparent from the Bering Strait to the Chukchi Borderland. Lower latitude regions (i.e. Bering Strait to Chukchi Shelf) are primarily driven by the inflow of Pacific waters that supply nutrients and heat, leading to high primary production. Conversely, the higher latitude regions (i.e. Chukchi Borderland and Canada Basin) are relatively cold, fresh, and oligotrophic because the surface layer is influenced by freshwater inputs from melting ice and rivers via the Beaufort Gyre. Mixing of the two surface water masses in the western Arctic produces a physicochemical frontal zone (FZ) in the Chukchi Sea.

In a recent study published in Scientific Reports, authors used observations from summer 2017 to investigate latitudinal variations in bacterial community composition in surface waters between the Bering Strait and Chukchi Borderland and the underlying processes driving the changes. Results indicate three distinctive communities: 1) Southern Chukchi (SC) bacterial communities are associated with nutrient-rich conditions, including genera such as Sulfitobacter; 2) a northern Chukchi (NC) bacterial community that dominated by SAR clades, Flavobacterium, Paraglaciecola, and Polaribacter, genera associated with low nutrients and sea ice conditions. If climate-driven changes in the western Arctic continue along the same trajectory, it’s likely we will see altered bacterial communities. If the impact of warm, nutrient-rich Pacific water inflows dominates, it is likely that the productive SC region will expand and the FZ will move northward, leading to nutrient enrichment in the western Arctic (Figure 1). In response, bacterial communities would be dominated by organic matter decomposers, such as Sulfitobacter, due to high primary productivity. However, if the impact of sea-ice meltwater dominates, then the oligotrophic NC region will expand and the FZ will move southward, leading to nutrient depletion in western Arctic surface waters (Figure 1). Continued monitoring in this region will enhance our understanding of how bacterial communities respond (Figure 1b) to a rapidly changing western Arctic Ocean.

Figure 1. (a) Map of the August 2017 Ice Breaker RV Araon western Arctic Ocean sampling stations used in this study. The basemap shows the Chl-a concentration contour (blue to red background colors). Pink, green, and blue circles represent stations in the South Chukchi (SC), Frontal Zone (FZ), and Northern Chukchi (NC) regions. (b) Schematic diagram of surface bacterial community distribution in response to future western Arctic Ocean changes.

Authors:
Il-Nam Kim (Department of Marine Science, Incheon National University)
Sung-Ho Kang (Korea Polar Research Institute)
Eun Jin Yang (Korea Polar Research Institute)

Funding for the Ocean Carbon & Biogeochemistry Project Office is provided by the National Science Foundation (NSF) and the National Aeronautics and Space Administration (NASA). The OCB Project Office is housed at the Woods Hole Oceanographic Institution.

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