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Hydrostatic pressure substantially reduces deep-sea microbial activity

Posted by mmaheigan

· Thursday, May 11th, 2023

Deep sea microbial communities are experiencing increasing hydrostatic pressure with depth. It is known that some deep sea microbes require high hydrostatic pressure for growth, but most measurements of deep-sea microbial activity have been performed under atmospheric pressure conditions.

In a recent paper published in Nature Geoscience, the authors used a new device coined ‘In Situ Microbial Incubator’ (ISMI) to determine prokaryotic heterotrophic activity under in situ conditions. They compared microbial activity in situ with activity under atmospheric pressure at 27 stations from 175 to 4000 m depths in the Atlantic, Pacific, and the Southern Ocean. The bulk of heterotrophic activity under in situ pressure is always lower than under atmospheric pressure conditions and is increasingly inhibited with increasing hydrostatic pressure. Single-cell analysis revealed that deep sea prokaryotic communities consist of a small fraction of pressure-loving (piezophilic) microbes while the vast majority is pressure-insensitive (piezotolerant). Surprisingly, the piezosensitive fraction (~10% of the total community) responds with a more than 100-fold increase of activity upon depressurization. In the microbe proteomes, the authors uncovered taxonomically characteristic survival strategies in meso- and bathypelagic waters. These findings indicate that the overall heterotrophic microbial activity in the deep sea is substantially lower than previously assumed, which implies major impacts on the carbon budget of the ocean’s interior.

Figure caption: Deep sea microbial activity under varying pressure. (a) In situ bulk leucine incorporation rates normalized to rates obtained at atmospheric pressure conditions. (b) A microscopic view of a 2000 m sample collected in the Atlantic and incubated under atmospheric pressure conditions. The black halos around the cells are silver grains corresponding to their activities. The highly active cells (indicated by arrows) were rarely found in in situ pressure incubations. (c) Depth-related changes in the metaproteome of three abundant deep sea bacterial taxa (Alteromonas, Bacteroidetes, and SAR202). The number indicates shared and unique up- and down-regulated proteins in different depth zones.

Authors
Chie Amano (University of Vienna, Austria)
Zihao Zhao (University of Vienna, Austria)
Eva Sintes (University of Vienna, IEO-CSIC, Spain)
Thomas Reinthaler (University of Vienna, Austria)
Julia Stefanschitz (University of Vienna, Austria)
Murat Kisadur (University of Vienna, Austria)
Motoo Utsumi (University of Tsukuba, Japan)
Gerhard J. Herndl (University of Vienna, Netherlands Institute for Sea Research)

Twitter @microbialoceanW

Does dark carbon fixation supply labile DOC to the deep ocean?

Posted by mmaheigan

· Thursday, March 30th, 2023

Nitrifying microbes are the most abundant chemoautotrophs in the dark ocean. Though better known for their role in the nitrogen cycle, they also fix dissolved inorganic carbon (DIC) into biomass and thus play an important role in the global carbon cycle. The release of organic compounds by these microbes may represent an as-yet unaccounted for source of dissolved organic carbon (DOC) available to heterotrophic marine food webs. Quantifying how much DIC these microbes fix and release again into the ambient seawater is critical to a complete understanding of the carbon cycle in the deep ocean.

To address this knowledge gap, a recent study grew ten diverse nitrifier cultures and measured their cellular carbon (C) content, DIC fixation yields and DOC release rates. The results indicate that nitrifiers release between 5 and 15% of their recently fixed DIC as DOC (Figure 1). This would equate to global ocean fluxes of 0.006–0.02 Pg C yr⁻.

Figure 1. DOC release by ten different chemoautotrophic nitrifying (ammonia- and nitrite-oxidizing) microbes. The diversity of marine nitrifiers used in this study comprises all genera currently available as axenic cultures. Species and strain names are given for completeness.

Our results provide values for biogeochemical models of the global carbon cycle, and help to further constrain the relationship between C and N fluxes in the nitrification process. Elucidating the lability and fate of carbon released by nitrifiers will be the crucial next step to understand its implications for marine food-web functioning and the biological sequestration of carbon in the ocean.

Authors:
Barbara Bayer (University of California, Santa Barbara and University of Vienna)
Kelsey McBeain (University of California, Santa Barbara)
Craig A. Carlson (University of California, Santa Barbara)
Alyson E. Santoro (University of California, Santa Barbara)

Linking the calcium carbonate and alkalinity cycles in the North Pacific ocean

Posted by mmaheigan

· Tuesday, December 13th, 2022

The marine carbon and alkalinity cycles are tightly coupled. Seawater stores so much carbon because of its high alkalinity, or buffering capacity, and the main driver of alkalinity cycling is the formation and dissolution of biologically produced calcium carbonate (CaCO3). In a recent publication in GBC, the authors conducted novel carbon-13 tracer experiments to measure the dissolution rates of biologically produced CaCO3 along a transect in the North Pacific Ocean. They combined these experiment data with shipboard analyses of the dissolved carbonate system, the 13C-content of dissolved inorganic carbon, and CaCO3 fluxes, to constrain the alkalinity cycle in the upper 1000 meters of the water column. Dissolution rates were too slow to explain alkalinity production or CaCO3 loss from the particulate phase. However, driving dissolution with the metabolic consumption of oxygen brings alkalinity production and CaCO3 loss estimates into quantitative agreement (Figure). The authors argue that a majority of CaCO3 production is likely dissolved through metabolic processes in the upper ocean, including zooplankton grazing, digestion, and egestion, and microbial degradation of marine particle aggregates that contain both organic carbon and CaCO3. This hypothesis stems from the basic fact that almost all marine CaCO3 is biologically produced, placing CaCO3 at the source of the acidifying process (metabolic consumption of organic matter). This process is important because it puts an emphasis on biological processing for the cycling of not only carbon, but also alkalinity, the main buffering component in seawater. These results should help both scientists and stakeholders to understand the fundamental controls on calcium carbonate cycling in the ocean, and therefore the processes that distribute alkalinity throughout the world’s oceans.

Figure Caption: Sinking-dissolution model results compared with tracer-based alkalinity regeneration rates (TA*-CFC, Feely et al., 2002). We also plot alkalinity regeneration rates using updated time transit distribution ages (TA*- and Alk*-TTD). The modeled alkalinity regeneration rate uses our measured dissolution rates for biologically produced calcite and aragonite, and is driven by a combination of background saturation state and metabolic oxygen consumption. The dissolution rate is split up into a calcite component (produced mainly by coccolithophores) and an aragonite component (produced mainly by pteropods). Aragonite does not contribute significantly to the overall dissolution rate. Driving dissolution by metabolic oxygen consumption produces alkalinity regeneration rates that are in quantitative agreement with tracer-based estimates.

Authors:
Adam Subhas (Woods Hole Oceanographic Institution) et al.

Also see Eos highlight here

Marine heatwave implications for future phytoplankton blooms

Posted by mmaheigan

· Thursday, October 15th, 2020

Ocean temperature extreme events such as marine heatwaves are expected to intensify in coming decades due to anthropogenic warming. Although the effects of marine heatwaves on large plants and animals are becoming well documented, little is known about how these warming events will impact microbes that regulate key biogeochemical processes such as ocean carbon uptake and export, which represent important feedbacks on the global carbon cycle and climate.

Figure caption: Relationship between phytoplankton bloom response to marine heatwaves and background nitrate concentration in the 23 study regions. X-axis denotes the annual-mean sea-surface nitrate concentration based on the model simulation (1992-2014; OFAM3, blue) and the in situ climatology (WOA13, orange). Y-axis denotes the mean standardised anomalies (see Equation 1 of the paper) of simulated sea-surface phytoplankton nitrogen biomass (1992-2014; OFAM3, blue) and observed sea-surface chlorophyll a concentration (2002-2018; MODIS, orange) during the co-occurrence of phytoplankton blooms and marine heatwaves.

In a recent study published in Global Change Biology, authors combined model simulations and satellite observations in tropical and temperate oceanographic regions over recent decades to characterize marine heatwave impacts on phytoplankton blooms. The results reveal regionally‐coherent anomalies depicted by shallower surface mixed layers and lower surface nitrate concentrations during marine heatwaves, which counteract known light and nutrient limitation effects on phytoplankton growth, respectively (Figure 1). Consequently, phytoplankton bloom responses are mixed, but derive from the background nutrient conditions of a study region such that blooms are weaker (stronger) during marine heatwaves in nutrient-poor (nutrient-rich) waters.

Given the projected expansion of nutrient-poor waters in the 21st century ocean, the coming decades are likely to see an increased occurrence of weaker blooms during marine heatwaves, with implications for higher trophic levels and biogeochemical cycling of key elements.

Authors:
Hakase Hayashida (University of Tasmania)
Richard Matear (CSIRO)
Pete Strutton (University of Tasmania)

Will global change “stress out” ocean DOC cycling?

Posted by mmaheigan

· Tuesday, September 29th, 2020

The dissolved organic carbon (DOC) pool is vital for the functioning of marine ecosystems. DOC fuels marine food webs and is a cornerstone of the earth’s carbon cycle. As one of the largest pools of organic matter on the planet, disruptions to marine DOC cycling driven by climate and environmental global changes can impact air-sea CO2 exchange, with the added potential for feedbacks on Earth’s climate system.

Figure 1. Simplified view of major dissolved organic carbon (DOC) sources (black text) and sinks (yellow text) in the ocean.

Since DOC cycling involves multiple processes acting concurrently over a range of time and space scales, it is especially challenging to characterize and quantify the influence of global change. In a recent review paper published in Frontiers in Marine Science, the authors synthesize impacts of global change-related stressors on DOC cycling such as ocean warming, stratification, acidification, deoxygenation, glacial and sea ice melting, inflow from rivers, ocean circulation and upwelling, and atmospheric deposition. While ocean warming and acidification are projected to stimulate DOC production and degradation, in most regions, the outcomes for other key climate stressors are less clear, with much more regional variation. This synthesis helps advance our understanding of how global change will affect the DOC pool in the future ocean, but also highlights important research gaps that need to be explored. These gaps include for example a need for studies that allow to understand the adaptation of degradation/production pathways to global change stressors, and their cumulative impacts (e.g. temperature with acidification).

Authors:
C. Lønborg (Aarhus University)
C. Carreira (CESAM, Universidade de Aveiro)
Tim Jickells (University of East Anglia)
X.A. Álvarez-Salgado (CSIC, Instituto de Investigacións Mariñas)

Blue hole in the South China Sea reveals ancient carbon

Posted by mmaheigan

· Wednesday, July 8th, 2020

Blue holes are unique depositional environments that are formed within carbonate platforms. Due to an enclosed geomorphology that restricts water exchange, blue hole ecosystems are typically characterized by steep biogeochemical gradients and distinctive microbial communities. For the past three decades, studies have described vertical gradients in physical, chemical, and biological parameters that typify blue hole water columns, but their elemental cycles, particularly carbon, remain poorly understood.

Figure 1. Aerial photo of the Yongle Blue Hole in the South China Sea (Credit: P. Yao et al./JGR Biogeosciences)

In July 2016, the Yongle Blue Hole (YBH) was discovered to be the deepest known blue hole on Earth (~300 m). YBH is located in the Xisha Islands of the South China Sea. The unique features and ease of accessibility make YBH an ideal natural laboratory for studying carbon cycling in marine anoxic systems. In a recent study published in JGR Biogeosciences, the authors reported extremely low concentrations of dissolved organic carbon (DOC) (e.g., 22 µM) and very high concentrations of dissolved inorganic carbon (DIC) (e.g., 3,090 µM) in YBH deep waters. Radiocarbon dating revealed that the YBH DOC and DIC were unusually old, yielding ages (6,810 and 8270 years BP, respectively) that are much more typical of open ocean deep water. Based on H₂S and microbial community composition profiles, the authors concluded that sharp redox gradients and a high abundance of sulfur cycling bacteria were likely responsible for much of the DOC consumption in YBH. The unusually low concentrations and old DOC ages in the relatively shallow YBH suggest short-term cycling of recalcitrant DOC in oceanic waters, which has been recognized as a long-term microbial carbon sink in the global ocean. The stoichiometry of DIC and total alkalinity changes suggested that the accumulation of DIC in the deep layer of the YBH was largely derived from both the dissolution of carbonate and OC decomposition through sulfate reduction. However, the role of carbonate dissolution from the walls of the blue hole in affecting the old ages of carbon in this system remain uncertain, yet there appears to no evidence of subterranean freshwater into the bottom waters of the blue hole. In the face of expanding oxygen minimum zones and anthropogenically-induced coastal hypoxia, blue holes such as YBH can provide an accessible natural laboratory in which to study the microbial and biogeochemical features that typify these low-oxygen systems.

Authors:
Peng Yao (Ocean University of China)
Thomas S. Bianchi (University of Florida)
Xuchen Wang (Ocean University of China)
Zuosheng Yang (Ocean University of China)
Zhigang Yu (Ocean University of China)

Global change impacts soil carbon storage in blue carbon ecosystems

Posted by mmaheigan

· Wednesday, May 20th, 2020

Vegetated coastal “blue carbon” ecosystems, including sea grasses, mangroves, and salt marshes, provide valuable ecosystem services such as carbon sequestration, storm protection, critical habitat, etc.. Many of these services are supported by the ability of blue carbon ecosystems to accumulate soil organic carbon over thousands of years. Rapidly changing climate and environmental conditions will impact decomposition and thus the global reservoir of organic carbon in coastal soils. A recent Perspective article published in Nature Geoscience focused on the biogeochemical factors affecting decomposition in coastal soils, such as mineral protection, redox zonation, water content and movement, and plant-microbe interactions. The authors explored the spatial and temporal scales of these decomposition mechanisms and developed a conceptual framework to characterize how they may respond to environmental disturbances such as land-use change, nutrient loading, warming, and sea-level rise.

Figure caption: Temperate salt marshes (MA, USA). Healthy salt marshes have lush stands of grasses (top). Storms can expose peat deposits that have been buried for thousands of years (bottom). The fate of this soil carbon is unknown, but some fraction will be respired by microbes and returned to the atmosphere as CO₂.

Improved estimates of soil organic carbon in blue carbon systems will require better characterization of these processes from sustained data sets. Furthermore, incorporation of these decomposition mechanisms into ecosystem evolution models will improve our capacity to quantify and predict changes in these soil carbon reservoirs, which could facilitate their inclusion in global budgets and management tools.

Temperate salt marshes (MA, USA). Healthy salt marshes have lush stands of grasses (left/top). Storms can expose peat deposits that have been buried for thousands of years (right/bottom). The fate of this soil carbon is unknown, but some fraction will be respired by microbes and returned to the atmosphere as CO₂.

Authors:
Amanda C Spivak (University of Georgia)
Jon Sanderman (Woods Hole Research Center)
Jennifer Bowen (Northeastern University)
Elizabeth A. Canuel (Virginia Institute of Marine Science)
Charles S Hopkinson (University of Georgia)

Untangling microbial evolution in the oceans: How the interaction of biological and physical timescales determine marine microbial evolutionary strategies

Posted by mmaheigan

· Wednesday, March 11th, 2020

Marine microbes are the engines of global biogeochemical cycling in the oceans. They are responsible for approximately half of all photosynthesis on the planet and drive the ‘biological pump’, which transfers organic carbon from the surface to the deep ocean. As such, it is important to determine how marine microbes will adapt and evolve in response to a changing climate in order to understand and predict how the global carbon cycle may change. However, we still lack a mechanistic understanding of how and how fast microorganisms adapt to stressful and changing environments. This is particularly challenging due to the diversity of organisms that live in the ocean and the dynamic nature of the oceans themselves—microbes are at the whim of ocean currents and so get transported large distances fairly quickly. For the first time, a new study published in PNAS provides a prediction on the controls of microbial evolutionary timescales in the oceans. The authors hypothesize that there is a trade-off for marine microbes between ability to evolve to long-term changes versus respond to shorter term variability. Their results suggest that marine microbes commonly experience conditions that favor a short-term strategy at the cost of long-term adaptation. This trade-off determines evolutionary timescales and provides a foundation for understanding distributions of microbial traits and biogeochemistry.

Illustration of trade-off in evolutionary strategy as a function of environmental variability. Trajectories where individuals perceived high environmental variability (a & b) exhibited low selective pressure for any one environment but allowed for high environmental tracking. Trajectories where individuals perceived a more stable environment (c&d) had high selective pressure for ’new environments’ (high probability of a selective sweep) but these individuals exhibited poor environmental tracking. Panels a and c show trajectories where selective sweeps were highly probable (red), likely (yellow), and had a low probability (grey). Panels b and d show the estimated persistence of non-genetic modifications necessary for environmental tracking, where grey indicates unrealistically long timescales.

Authors:
Nathan G. Walworth (University of Southern California)
Emily J. Zakem (University of Southern California)
John P. Dunne (Geophysical Fluid Dynamics Laboratory, NOAA)
Sinéad Collins (University of Edinburgh)
Naomi M. Levine (University of Southern California)

Diatoms commit iron piracy with stolen bacterial gene

Posted by mmaheigan

· Tuesday, February 4th, 2020

Since diatoms carry out much of the primary production in iron-limited marine environments, constraining the details of how these phytoplankton acquire the iron they need is paramount to our understanding of biogeochemical cycles of iron-depleted high-nutrient low-chlorophyll (HNLC) regions. The proteins involved in this process are largely unknown, but McQuaid et al. (2018) scientists described a carbonate-dependent uptake protein that enables diatoms to access inorganic iron dissolved in seawater. As increasing atmospheric CO₂ results in decreased seawater carbonate ion concentrations, this iron uptake strategy may have an uncertain future. In a recent study published in PNAS, authors used CRISPR technology to characterize a parallel uptake system that requires no carbonate and is therefore not impacted by ocean acidification.

This system targets an organically complexed form of iron (siderophores, molecules that bind and transport iron in microorganisms) that is only produced by co-occurring microbes. Two genes are required to convert siderophores from a potent toxicant to an essential nutrient. One of these (FBP1) is a receptor that was horizontally acquired from siderophore-producing bacteria. The other (FRE2) is a eukaryotic reductase that facilitates the dissociation of Fe-siderophore complexes.

Figure caption: (A) Growth curves of diatom cultures ( • = WT, ◇ = ΔFBP1, ☐ = ΔFRE2) in low iron media. (B) Growth in same media with siderophores added. (C) Diatoms under 1000x magnification, brightfield. (D) mCherry-FBP1. (E) Plastid autofluorescence. (F) YFP-FRE2. (G) Phylogenetic tree of FBP1 and related homologs.

Are diatoms really stealing siderophores from hapless bacteria? The true nature of this interaction is unknown and may at times be mutualistic. For example, when iron availability limits the carbon supply to a microbial community, heterotrophic bacteria may benefit from using siderophores to divert iron to diatom companions. Further work is needed to understand the true ecological basis for this interaction, but these results suggest that as long as diatoms and bacteria co-occur, iron limitation in marine ecosystems will not be exacerbated by ocean acidification.

Authors:
Tyler Coale (Scripps Institution of Oceanography, J.Craig Venter Institute)
Mark Moosburner (Scripps Institution of Oceanography, J.Craig Venter Institute)
Aleš Horák (Biology Centre CAS, Institute of Parasitology, University of South Bohemia)
Miroslav Oborník (Biology Centre CAS, Institute of Parasitology, University of South Bohemia)
Katherine Barbeau (Scripps Institution of Oceanography)
Andrew Allen (Scripps Institution of Oceanography, J.Craig Venter Institute)

Also see joint post on the GEOTRACES website

Unexpected DOC additions in the deep Atlantic

Posted by mmaheigan

· Tuesday, January 7th, 2020

Oceanic dissolved organic carbon (DOC) ultimately exchanges with atmospheric CO₂ and thus represents an important carbon source/sink with consequence for climate. Most of the DOC is recalcitrant to microbial degradation, with some fractions surviving for thousands of years. Therefore, DOC in the deep ocean was thought to be stable or to decrease slowly over decades to centuries due to biotic and abiotic sinks. However, a study published in Global Biogeochemical Cycles shows that there are some zones of the deep Atlantic Ocean where recalcitrant DOC experiences net production. Using data from oceanographic cruises across the Atlantic Ocean, the authors first identified the major water masses in the basin and the percentage of each in every sample taken for DOC analysis. The study revealed net additions of 27 million tons of dissolved organic carbon per year in the deep South Atlantic. On the other hand, the North Atlantic serves as a net sink, removing 298 million tons of carbon annually. DOC production observed in the deep Atlantic is probably due to the sinking particles that solubilize into DOC, since DOC enrichment was most evident at latitudes characterized as elevated productivity divergence zones.

Figure 1. Water masses along GO-SHIP line A16 (colored dots) and recalcitrant DOC variations due to biogeochemical processes (black dots within each water mass) in the deep Atlantic Ocean. Water mass domains are defined as the set of samples with the corresponding water mass proportion ≥50%. Recalcitrant DOC latitudinal variations per water stratum due to biogeochemical processes (ΔDOC) is in μmol kg^-1. Numbers on the plots are DOC values for the corresponding dots. Scales (not shown) are the same for all the plots, from -4 to 6 μmol kg^-1. Positive (negative) ΔDOC indicates values higher (lower) than the average DOC calculated for each water mass using an optimum multiparameter (OMP) analysis. DOC = dissolved organic carbon. AAIW = Antarctic Intermediate Water; UNADW = upper North Atlantic Deep Water; ISOW = Iceland Scotland Overflow Water; CDW = Circumpolar Deep Water; WSDW = Weddell Sea Deep Water. Figure created with Ocean Data View (Schlitzer, 2015).

Considering that the net DOC production over the entire Atlantic basin euphotic zone is 0.70–0.75 Pg C year^-1, the authors estimated that 30–39% of that DOC is consumed in the deep Atlantic subsequent to its export by overturning circulation. The upper North Atlantic Deep Water (UNADW) acts as the primary sink, accounting for 66% of the recalcitrant DOC removal in the North Atlantic. Conversely, the Antarctic Intermediate Water (AAIW) is the primary recipient, with 45% of recalcitrant DOC production in the South Atlantic, closely followed by the old UNADW that gains 44% of the recalcitrant DOC in the southern basin.

The Atlantic works as a mosaic of water masses, where both removal and addition of recalcitrant DOC occurs, with the dominant term dependent on the origin, temperature, age and depth of the water masses. The production of recalcitrant DOC in the deep ocean should be considered in biogeochemical models dealing with the carbon cycle and climate.

Authors:
C. Romera-Castillo and J. L. Pelegrí (Instituto de Ciencias del Mar, CSIC, Spain)
M. Álvarez (Instituto Español de Oceanografía, Spain)
D. A. Hansell (University of Miami, USA)
X. A. Álvarez-Salgado (Instituto de Investigaciones Marinas, CSIC, Spain)

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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