Microbial carbon cycling in the ocean

Microbial carbon cycling in the ocean
Lecture 1. The ocean’s carbon cycle - How much carbon is out there and where is it? Where does it come from, and how does it cycle? Lecture 2. Microbial production of dissolved organic matter –What types of carbon do microbes make and how might this effect microbial diversity and community structure? Lecture 3. The composition of dissolved organic matter in seawater- How do we analyze it and what do to these analysis tell us about the origin, fate and cycling of microbial carbon, nitrogen, and phosphorus? 2012 CMORE Agouron Repeta Lecture 1

2012 CMORE Agouron Repeta Lecture 1
Major Planetary Inventories and Fluxes of Carbon Atmospheric CO2 750 GT C Terrestrial Plants 900 GT C Terrestrial Primary Production GT C yr-1 Uplift, exposure and erosion Marine Primary Production GT C yr-1 River flux 0.5 GT C yr-1 Soils 2000 GT C Microbial Biomass 2 GT C Particulate Organic Carbon GT C Cartoon of planetary carbon cycle Shows major reservoirs and fluxes Embedded in this are a number of coupled subcycles that operate over different time scales. Inventory most carbon is in rocks as carbonate, and organic matter (kerogen). Millions of GT or petagrams of carbon- products of sediment deposition over billions of years, massive amount of carbon that is turning over very slowly, Methane is estimated to be about 5000 GT (half in clatherate, half in bubbles). Among reserviors that cycle on glacial interglacial time scales – terrestrial and marine. They are connected via the atmosphere and rivers/groundwater, and by deposition and uplift. Terrestrial carbon – a lot is tied up in biomass that cycles very slowly – trees and grasses have a long residence time (10’s of years on average) soils have an even longer residence time. Some OM in soil is solube leached as dissolved C and some is not, moved as POC. Burial GT C yr-1 Carbonate rocks 60 x 106 GT C Kerogen 20 x 106 GT C Dissolved Organic Carbon GT C Sediments 150 GT C 2012 CMORE Agouron Repeta Lecture 1

What is “particulate” and what is “dissolved” carbon? Organic matter is classified by size, as defined by filtration Points- nearly all sampling involves filtration. The filter used defines dissolved/particulate, chosen for a number of reasons- cost, speed, ease of cleaning, format (dimension). Filtration may introduce contamination- bleed and apparatus, and DOC is sometimes but not always filtered. Filters may adsorb DOC. High precision analysis has stringent filtration requirements. Filter is used for sterilization separate living from dead OM, and to select different classes of microbes Colloidal Fraction Viruses down to 20 nm, plankton from to a few hundred nm. Particulate Organic Matter Dissolved Organic Matter 2012 CMORE Agouron Repeta Lecture 1

The biological pump and organic carbon transfer to the sea floor “grain-by-grain deposition is by far the most common phenomenon of pelagic sedimentation” Jacobs et al. (1973) Marine Geology v14, Define POC and DOC. Vertical profiles from eastern subtropical pacific (Druffle) Photos from Jim Bishop 2012 CMORE Agouron Repeta Lecture 1

The biological pump and organic carbon transfer to the sea floor “grain-by-grain deposition is by far the most common phenomenon of pelagic sedimentation” Jacobs et al. (1973) Marine Geology v14, # particles mL-1 But observations suggested that there must be a faster way to transfer material from the surface to the deep ocean. Anthropogenic isotopes, seasonal reporductive cycles in deep sea macrofauna, and the existance of macrofauna Particle diameter (µm) Photos from Jim Bishop 2012 CMORE Agouron Repeta Lecture 1 10.15

The biological pump and organic carbon transfer to the sea floor N = dm DSR(1975) v Flux (µg m-2 s-1) The flux/size relationship is a function of density, shape, etc. But using reasonable coeffiicents, most of the flux is delivered by particles. Particle diameter 2012 CMORE Agouron Repeta Lecture 1

Large, rapidly sinking particles are collected with sediment traps
Large, rapidly sinking particles are collected with sediment traps Carbon flux Depth J = J100 /((Z/100)0.858) New production There is a second class of particles distinguished by their size and sinking speed. Large rapidly sinking particles. While suspended POC carries most of the mass at any given instant in the ocean, most of the flux of C through production/respiration cycle, vertically, under the influence of gravity, large particles export most of the carbon and nuts to the deep ocean. Season export – consequences for deep ocean. Exports vary regionally. We don’t know why. In oligotrophic gyres, about 10%, in some high latitude coastala nd upwelling regions it can be higher. May depend on ballast, particle size, efficiency of recycling, temporal instabilites in the water column, etc. Export varies regionally. We don’t know why. In the SUSPENDED AND SINKING POC ARE MEARLY LIVING AND DEAD MICROBES. THEIR COMPOSITION IS PROTEIN (50%), CARBOHYDRATES (15-20%) and lipids (15-20%) and everything else (pigments, DNA, RNA). Most C, N, P, S is in polymers. Martin et al (1987) DSR v 34; 2012 CMORE Agouron Repeta Lecture 1

Do molecular level analyses give a fair representation of POM composition?
C:N = 6.6 C:N = 9.0 Greatest loss of C is in the upper water column. Some loss during sinking,and a big loss at the sediment-water interface. C/N/P/S is in insoluble polymers that become solubilized as the particles sink. The composition is edited during sinking, with loss of nitrogen, so protiens go first. But by NMR there is no apparent change in composition. These are chemicals we can measure, most if it we cannot. What we cannot measure looks a lot like what we can measure. Large impact on microbial communities due to flux- removes nutrients from the upper ocean, remineralization is in part mediated by microbes, there are communites associated with the degrdation of sinking particles, particle dissolve faster than they sink, so injection of labile material at depth in the ocean. This molecular editing of carbon may have consequences for carbon and nutirent preservation in sediments. From Lee et al. (2004) Ambio 33, 10.23

Dissolved Organic Matter (DOM) and the Microbial “loop” “I presume that the numerous lower pelagic animals persist on the infusoria, which are known to abound in the open ocean: but on what, in the clear blue water, do these infusoria subsist?” - Charles Darwin (1845) CO2 DOM “Basic to the understanding of any ecosystem is knowledge of its food web, through which energy and materials flow. If microorganisms are major consumers in the sea, we need to know what kinds are the metabolically important ones and how they fit into the food web.” - Lawrence Pomeroy (Bioscience, 1974) 2012 CMORE Agouron Repeta Lecture 1

Analytical methods for measuring DOC
High Temperature Catalytic Oxidation 100 µL seawater Inject directly onto Pt or M column Water vaporized and trapped DOC oxidized by Pt to CO2 LiCOR detector Precision µM 2012 CMORE Agouron Repeta Lecture 1

Typical 1D profile of dissolved organic carbon in the ocean TOC (µM) Often measured as TOC Surface values typically µM Deep water µM (implies some unknown feedback/ control of DOC values) Global inventory about 660 GT C Data from Peltzer and Hayward (1996) DSR 2012 CMORE Agouron Repeta Lecture 1

Atlantic A16 Pacific P16 2012 CMORE Agouron Repeta Lecture 1 From Dennis Hansell CLIVAR data set

2012 CMORE Agouron Repeta Lecture 1

Global circulation and the distribution of DOC Hansell et al. Oceanography 2009 On a global scale, carbon is sensitive to water mass transport. See it very clearly in the N Atlantic where NADW formation can be seen N of 40oN, and we can see loss of DOC in the deep pacific. Assuming steady state, then there is a 30% loss of carbon between the deep basins, and a lot of that loss occurs in Pacific north of the equator. This is interesting bc of the radiocarbon age of DOC is very old- some deep process can remove old radiocarbon. 2012 CMORE Agouron Repeta Lecture 1 15

(solubilization of sinking particles
A16: DOC on δθ 26.4 – 26.7 Data from Dennis Hansell ( Depth (m) We can look at changes in DOC concentration along an isopycnal to discern inputs and outputs of Carbon by mesopelagic cycling processes Input on the Equator (solubilization of sinking particles or advective input?) 2012 CMORE Agouron Repeta Lecture 1

A16: DOC on δθ 27.0 – 27.3 Data from Dennis Hansell ( Expected Mixing Curve Depth (m) We can look at even denser isopycnal surfaces to discern processes that may be occurring in the deep ocean. 2012 CMORE Agouron Repeta Lecture 1

Cycling of reactive and semi-labile DOC by phytoplankton and bacteria
DOC”reactive” DOC”semi-labile” CO2 Heterotrophic bacteria Autotrophic microbes What DOC plots don’t show you is one of the most important aspects of DOC cycling, and that is the microbial loop. Bacterial growth and respiration is thought to be fueled by very reactive DOC that has a residence time in seawater of hour to days. 2012 CMORE Agouron Repeta Lecture 1

Comparison of bacterial and primary production in different ocean basins WE measure DOC that does not appear in our analysis by proxy- that is we assume it is there and is supporting a process. Measure carbon flux throught eh process and equate to a flux throught eh DOC pool. 2012 CMORE Agouron Repeta Lecture 1

How do we measure carbon fluxes in DOC ? We can measure processes that cycle carbon through DOC on very short time scales using bacterial production and carbon demand measuremetns, and over longer timescales by following the changes in DOC concentration along isopycnal surfaces. But we can also use natural abundance radiocarnon, as a built in clock. Radiocarbon is produced by spallation reactions, the collision of cosmic rays (high energy protons and neutrons from outside the solar system, produced by supernova) with N-14. A neutron collides with N-14 and ejects a proton, making C-14. The atmospheric carbon is about 1 ppt of C-14. When radiocarbon decays it ejects an electron and returns to N-14. beta decay. Half life of about 5730 year. Most C-14 is produced at an altitude of km above the surface. Rate of synthesis depends on geomagnetic field, and cosmic ray flux. Latitudinally dependand. 2012 CMORE Agouron Repeta Lecture 1

McNichol and Aluwihare, Chem Rev. 2007 Natural radiocarbon production has changed over time, and is influenced by changes in the flux of cosmic rays, solar activity, and the earths magnetosphere. Atmospheric radiocarbon is adsorbed by the ocean through CO2 gas exchange , but the rate of adsorption varies in space and time. Penetration of radiocarbon into the ocean interior is affected by mixing and circulation. Atmospheric testing of nuclear weapons in the period of introduced a large amount of anthropogenic radiocarbon into the atmosphere. This “bomb signal” is still being adsorbed by the ocean and incorporated into Organic matter. 2012 CMORE Agouron Repeta Lecture 1

National Ocean Sciences Accelerator Mass Spectrometry (NOSAMS)
C-14 tracer measurements use >106x more C-14 than natural abundance!!!!! 2012 CMORE Agouron Repeta Lecture 1

Top “pre bomb” 14C distribution as calculated from GEOSECS alkalinity data. Bottom, measured 14C activity by GEOSECS in the 1970s. Based on these pictures, what would you predict the DOC in the deep ocean to be? 2012 CMORE Agouron Repeta Lecture 1 McNichol and Aluwihare 2007

DOC cycling via DO14C UV photooxidation Deep water DIC values are years (Craig et al.) Depth 14C(‰) Age 1880m ‰ ybp 1920m ‰ ybp Williams, Oeschger, and Kinney; Nature v224 (1969) 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon in the Atlantic and Pacific Oceans Peter M. Williams and Ellen Druffel; Nature 1987, JGR 1992 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon in the Atlantic and Pacific Oceans Peter M. Williams and Ellen Druffel; Nature 1987, JGR 1992 Sargasso suspended POC Pacific suspended POC Pacific sinking POC 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon in the Atlantic and Pacific Oceans DIC 14C in surface waters of the Atlantic and Pacific have similar isotopic values. Sargasso suspended POC Pacific suspended POC Pacific sinking POC 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon in the Atlantic and Pacific Oceans DIC 14C in surface waters of the Atlantic and Pacific have similar isotopic values. DOC is always older than DIC (by 2-3 kyrs in surface water) DIC POC DOC Sargasso suspended POC Pacific suspended POC Pacific sinking POC Pacific suspended POC Pacific sinking POC Sargasso suspended POC 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon in the Atlantic and Pacific Oceans DIC 14C in surface waters of the Atlantic and Pacific have similar isotopic values. DOC is always older than DIC (by 2-3 kyrs in surface water) 14C of DIC and DOC is about the same in the deep Atlantic and Pacific Sargasso suspended POC Pacific suspended POC Pacific sinking POC Pacific suspended POC Pacific sinking POC Sargasso suspended POC 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon in the Atlantic and Pacific Oceans DIC 14C in surface waters of the Atlantic and Pacific have similar isotopic values. DOC is always older than DIC (by 2-3 kyrs in surface water) 14C of DIC and DOC is about the same in the deep Atlantic and Pacific Deep ocean values of DOC are equal to a radiocarbon age of 4-6 kyrs Either there is a source of “old” DOC, or DOC persists for several ocean mixing cycles. 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon based models of DOC cycling in the water column Beaupre and Druffel 2009 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon based models of DOC cycling in the water column “New” DOC D14C = D DI14C D DI14C = o/oo Old, “background” DOC D14C = Deepwater value Williams and Druffel, 1987; Beaupre and Druffel 2009 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon based models of DOC cycling in the water column Old (low radiocarbon), non-reactive DOC Williams and Druffel, 1987; Beaupre and Druffel 2009 2012 CMORE Agouron Repeta Lecture 1

Radiocarbon based models of DOC cycling in the water column
Old (low radiocarbon), non-reactive DOC New, semi-reactive DOC Atlantic surface water 14Ccalc = ‰ 14Cobs = ‰ Pacific surface water 14Ccalc = ‰ 14Cobs = ‰ No microbial carbon cycling in the deep ocean??? Williams and Druffel, 1987; Beaupre and Druffel 2009 2012 CMORE Agouron Repeta Lecture 1

Likely Sources of semi-reactive DOM featured-research/smoke-over-athens Trichodesmium Prochlorococcus Synechococcus photos by J. Waterbury, C. Ting, A. Heithoff, and Jamie Becker A small fraction of the DOC added to the ocean by rivers is colored (colored dissolved organic matter or CDOM) that can be tracked by remote sensing. If terrestrial DOM is not being degraded in estuaries, why isn’t the ocean filling up with CDOM and terrestrial DOM? 2012 CMORE Agouron Repeta Lecture 1 Slide 4.22

Time series analysis of DOC (µM C) at Bermuda
2012 CMORE Agouron Repeta Lecture 1 Data from Dennis Hansell and Craig Carlson 36

The importance of terrestrial DOC from rivers, groundwater, and
atmospheric deposition depends on the flux of carbon and its isotopic value. d13C The -21 to -22‰ stable carbon (13C) isotope Value of DOC suggest a marine source ! Isotope measurements of DOC-14 and -13 in rivers Data from Raymond and Bauer Organic Geochemistry 2001 2012 CMORE Agouron Repeta Lecture 1

Nature reviews in microbiology v 8 (August 2010) p 593 2012 CMORE Agouron Repeta Lecture 1

at best very slow removal of DOM in the deep sea
Under this perspective, DOM is produced and rendered recalcitrant by marine microbes. Combined with the two component model of radiocarbon and deep sea DOC, it suggests no or at best very slow removal of DOM in the deep sea 2012 CMORE Agouron Repeta Lecture 1

but…could there be a transfer of carbon from the surface water into the deep ocean ? Depth [DOC] The two component model only requires a conservation of mass and isotopic abundance, but does not stipulate what the isotopic/mass distribution of DOC is within the old (deep) fraction of DOC. A number of mass/isotope mixes can constitute the old fraction of DOC. Deep water [DOC] value Smaller amount of very old DOC, and a larger amount of younger DOC 2012 CMORE Agouron Repeta Lecture 1

Isotopic distribution of radiocarbon within DOC
Whole seawater is oxidized by Ultraviolet radiation and CO2 is drawn off fro radiocarbon analysis at different times. The distribution of radiocarbon within DOC can be reconstructed from the changes in isotopic values at different times. Surface Surface Mid-depth Deep No carbon with the average RC value Deep Follett, Repeta, Rothman and Xu submitted 2012 CMORE Agouron Repeta Lecture 1

Follett, Repeta, Rothman and Xu submitted 2012 CMORE Agouron Repeta Lecture 1

X Follett, Repeta, Rothman and Xu submitted 2012 CMORE Agouron Repeta Lecture 1

Marine (Organic) Carbon Cycling Summary
Marine carbon is operationally defined as particulate and dissolved. These two fractions are distinguished by filtration. All “living carbon” is particulate, but not all biological activity is particulate. Most (98%) of the carbon in the ocean is dissolved (non-living; < 0.1 um). Although we operationally define particulate and dissolved carbon as separate fractions of carbon, in fact they are connected. Carbon is being exchanged between PC and DC all the time. Any model of C cycling must consider both fractions. Carbon is measured as CO2 after acidification (inorganic carbon) or high temperature combustion (organic carbon). The highest concentrations of PC and DC are in surface waters, due to local biological activity. The largest inventories of POC and DOC are in the deep ocean. Particulate carbon is often partitioned into suspended or rapidly sinking particles. These are sampled by different techniques. Most of the mass is in suspended carbon. 2012 CMORE Agouron Repeta Lecture 1

as measured by carbon flux.
Dissolved organic carbon is often divided into different fractions based on reactivity as measured by carbon flux. Measurements of bacteria production and carbon demand show that annually the flux of carbon through DOC is quite high, about 15% of global primary production. This labile fraction of DOC is presumed to have a low concentration. Less reactive DOC accumulates in the water column. Why DOC accumulates is unknown. Based on radiocarbon, deep ocean DOC is presumed to be recalcitrant or non-reactive. DOC in the upper ocean is a mixture of semi-labile DOC that cycles on monthly to annual times scales and recalcitrant DOC. High precision measurements show a removal of (recalcitrant) DOC from the deep ocean between the Atlantic and Pacific (-30%). The current paradigm states that DOC is produced by microbes and that microbial Processing renders it recalcitrant. Recent measurements of DOC composition And isotopic distribution are beginning to question this paradigm. 2012 CMORE Agouron Repeta Lecture 1

Microbial carbon cycling in the ocean

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