contours of simulated marine dimethyl sulfide distributions under variation in a gabric mechanism

Environmental Modelling & Software 22 (2007) 349e358www.elsevier.com/locate/envsoft

Contours of simulated marine dimethyl sulfide distributionsunder variation in a Gabric mechanism

Scott Elliott a,*, Shaoping Chu a, David Erickson b

a Climate Ocean Sea Ice Model team (COSIM), Los Alamos National Laboratory, Los Alamos, NM 87545, USAb Climate Dynamics Group, Oak Ridge National Laboratory, Oak Ridge, TN, USA

Received 18 April 2005; received in revised form 14 October 2005; accepted 22 November 2005

Available online 9 March 2006

Abstract

Biogeochemical tracer bins and transformations from an established reduced sulfur cycle mechanism were introduced into the oceanic compo-nent of the Community Climate System Model. The resulting global dimethyl sulfide simulation framework was then subjected to variation in plantcell precursor content and the kinetic form of removal terms. Chi square type merit minima were computed analytically along a release rate axis overglobal, low latitude and localized domains. A band of width 60 degrees centered on the equator proved to be the most effective optimization areabecause it greatly exceeded resolution of the validation data set but avoided fronts where the driver ecodynamics module overpredicts chlorophyll.Loss terms involving bacterial consumption formulated as bimolecular kinetics and photochemical decay sensitized by dissolved organic matterindependently provided superior agreement with data by modulating peaks along the equatorial divergence. Factor of ten reductions in the sulfurprecursor content of diatoms or small noncalcite secretors respectively flattened and exaggerated the same features, but intermediate compositionswere not tested. The parameter suite of constant intracellular sulfur, second order osmotrophy (microbial uptake) and photochemistry set propor-tional to photosynthetic radiation is recommended and packaged as a startup mechanism. This particular combination optimizes large-scale reducedsulfur fields across well-understood ecosystems while simultaneously maintaining parsimony. Visualizations from the inverse procedure are offeredfor multiple mechanisms, as mappings of both normalized deviation and concentration. The value of the rate constant for injection from plant andanimal material was often determined to be of the order weeks, consistent with emission via grazing or aging/mortality. Refinement of the model willrequire linkage to the ecological flows associated with cell disruption, accounting of elemental metabolic stresses which in part govern reduced sulfurstorage, addition of true microbial ecology, further studies of open ocean sulfur photochemistry and longer duration/more detailed optimizationexercises. A stepwise strategy is outlined for moving through this task list. In next-generation experiments it may prove expedient to fix sulfur contentratios within taxonomic classes while varying the maximum cell content.� 2006 Elsevier Ltd. All rights reserved.

Keywords: Community Climate System Model; Ocean; Dimethyl sulfide; Optimization; Sulfur package; Microbial Ecology; Bimolecular Kinetics; Photochem-

istry; Cell disruption

Software availability

Program name: Dissolved Sulfur Gas Module, March 2005Version.

Developers: The authors above.Contact: S. Elliott, COSIM, Los Alamos National Laboratory,

Los Alamos NM, 87545 USA. E-mail: [email protected]

* Corresponding author.

E-mail address: [email protected] (S. Elliott).

1364-8152/$ - see front matter � 2006 Elsevier Ltd. All rights reserved.

doi:10.1016/j.envsoft.2005.11.006

Hardware: Tested on several SGI Altix machines but compat-ible with most modern vector and cache basedsupercomputers.

Software: Modular subprogram set.Language: Fortran 90.Availability: Public domain.

1. Introduction

The volatile molecule dimethyl sulfide (DMS) passes fromthe open surface ocean into the troposphere and there

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350 S. Elliott et al. / Environmental Modelling & Software 22 (2007) 349e358

influences the climate state via condensation nucleus andalbedo effects (Charlson et al., 1987; IPCC, 1996; Watsonand Liss, 1998). Dynamic models of DMS biogeochemical cy-cling in the sea sometimes show regional scale discrepanciesrelative to measurement data (Chu et al., 2003 and 2004;Belviso et al., 2004; Vezina, 2004). Statistical approachesare preferable in some respects but cannot directly representclimate sensitivity to shifts in the structure of mixed layer eco-systems (IPCC, 1996; Liss, 1999; Belviso et al., 2004). We arecurrently exploring directions for improvement of the kineticmethod for sulfur processing, by conducting alteration testsupon a simple but flexible and extensive mechanism. Thework is occurring in the context of the U.S. Community Cli-mate System Model ocean (CCSM; Blackmon et al., 2001;Moore et al., 2004), where a motivation is to move towardclimate responsive, coupled biogeochemistry.

The strategy has been to adopt global but streamlined andmanageable model components in all cases, then to vary theirsulfur production/loss parameters and functional forms.Changes in the shape of surface DMS distributions are inter-preted relative to climatological values (Kettle et al., 1999;Kettle and Andreae, 2000), and rated for quality through a tai-lored chi square approach (Press et al., 1992). The elementalcycling developed by Gabric and colleagues (1993, 2003 andintervening) has previously been applied to ecosystems rang-ing across the planet and is particularly amenable to sensitivityexercises (Liss, 1999). Its sulfur pathways are here insertedinto a coarse, fast version of the Parallel Ocean Program(the OGCM within CCSM; Maltrud et al., 1998; Blackmonet al., 2001) alongside a standard C/N/P/Fe/Si ecodynamicsmodel (Moore et al., 2002 and 2004). DMS mechanismscenarios are integrated to a near term steady state with majorparameters and functional forms bracketed where necessarybut varied finely where possible. Results are presented aslarge-scale maps of normalized deviation from data, and alsoas pure concentration. About 75 three-year runs were con-ducted under critical settings for the plant class S compositionvector, and functional forms for several distinct removal types.A universal organism release constant appearing in earlyGabric schemes can be varied analytically within the meritfunction; its optimal value is determined by differentiationso that each simulation actually samples an extra conceptualdimension of the merit space. Following preliminary examina-tion of results, selected forms were integrated to the multide-cadal scale as a test against drift.

The experiments were designed such that the optimizationdomain could readily be adjusted during post processing, andthis feature ultimately expedited the analysis significantly.Fully global statistical manipulations yielded an unacceptabledegree of compensation for middle to high latitude biases inthe ecodynamically modeled chlorophyll distribution (Mooreet al., 2004). Domains smaller than a typical ocean basin, onthe other hand, proved to be nondiscriminatory becauseDMS climatologies tend to average at the biogeographicalprovince scale (Longhurst, 1998; Kettle et al., 1999). Process-ing over a single band of tropical to subtropical latitudesoffered the best compromise. The zone 30 north to 30 south

was chosen due to its symmetry and because certain strongmid-latitude fronts were automatically filtered.

Release rates as determined by the analytical minimizationrange from one to three weeks, considerably faster than in theoriginal core model papers (e.g. Gabric et al., 1993). Theresult is consistent with the notion that phytoplanktonic celldisruption causes much of the sulfur injection taking placein the water column (Kettle et al., 1999; Vezina, 2004). Theterm disruption here indicates grazing and senescence pro-cesses collectively. Second order bacterial uptake and a photo-chemical decay normalized to dissolved organic matterconcentrations gave superior data agreement in our system.The latter removal, however, is constructed based mainlyupon coastal data. We classify it for the moment as extremelytentative. Order of magnitude reduction in the intracellular sul-fur content of the diatoms had the effect of over-flatteningtropical peaks, while for small gyre species the same adjust-ment created steep gradients not seen in the measurements.The possibility cannot be excluded that intermediate composi-tions influence the DMS field, but taxonomic dependence re-mains uncertain and a constant average approach has themomentary advantage of parsimony. We recommend that forcurrent model development purposes, as for example in ourown case of coupling CCSM biogeochemistry, the secondorder bacterial uptake be combined with purely PAR propor-tional photochemistry at a sulfur to nitrogen ratio of one tenth(Gabric et al., 1993). A variant is offered to the public below,as a Fortran 90 package in which CCSM marine trace gascycling is limited to reduced S species (Elliott et al., 2004and 2005). It is emphasized, however, that no single mecha-nism emerges from our study as an obvious success. Greatersophistication in the treatment of dimethyl sulfide kineticswill soon be required, both in Earth System model designand testing. Among the schemes that cannot be eliminatedin our brief investigation, the sensitivity to climate changewill likely be diverse (Charlson et al., 1987; IPCC, 1996;Liss, 1999). We provide in the discussion (Section 4) a phasedplan for progressing through the development of more com-plete global dynamic models.

2. Methods

2.1. OCGM

The transport quantities advection and diffusion are calculated in the pres-

ent work by the CCSM component known as POPdthe Parallel Ocean Pro-

gram. The biogeochemical species required are all carried online within it

as ecologically/chemically reactive but physically passive tracers. POP is

a Cartesian, primitive equation ocean general circulation model of Bryan

Cox Semtner ancestry. It has been upgraded at Los Alamos for fine grid studies

on massively parallel processors and to attain portability across cache and vec-

tor architectures. In modern versions adjustable array size blocking is used to

maintain performance, and the strategy extends from momentum and salt com-

putations into any added biology or chemistry. A coarse POP model averaging

three-degree resolution (‘‘�3’’) had earlier been developed for paleoclimate

and chlorofluorocarbon studies. Its grid is adopted here because high rates

of simulation turnover are demanded for our preliminary sensitivity/optimiza-

tion exercises. Detailed cell areas vary considerably over the mesh. Dimen-

sions were reduced in the tropics to better resolve mesoscale eddies, and

singularity in the Arctic Ocean is avoided by stretching the numerical pole

351S. Elliott et al. / Environmental Modelling & Software 22 (2007) 349e358

into Greenland. POP work is reviewed in general by Maltrud et al. (1998) and

later Jones et al. (2005), while the �3 mesh is described relative to CFC pen-

etration simulations in Peacock et al. (2005).

2.2. Ecology/geochemistry

Major element biogeochemistry algorithms for the CCSM were developed

at NCAR in the late 1990s as described by Moore et al. (2002, 2004). The

body of this work will be referred to collectively as DML, after primary devel-

opers Doney, Moore and Lindsay. Source-sink construction and the import of

concentrations from transport are all spread over the POP block entities. Early

DML models tracked C, N, P, Si, chlorophyll and Fe concentrations separately

for multiple plant/detrital types. The first three quantities have now been fixed

at their standard ratios for marine organisms as a space and time saving device

(the Redfield ratios; Jumars, 1993). The diatom and diazotrophic phytoplank-

ton classes are treated as individual tracers in the coding. Prymnesiophytes,

however, are aggregated among small plant species along with dinoflagellates

and the picoplankton (Longhurst, 1998). The fraction of coccolithophores is

determined empirically. Major element processing occurs completely indepen-

dent of sulfur behavior in this work. The separation may eventually be viewed

as artificial because biogeochemistries of the ocean and atmosphere are in fact

coupled, but in the near term optimization is facilitated.

The DML mechanism does not carry an explicit bacterial bin. All microbes

are subsumed in favor of implicit carbon recycling loops. The approach has

advantages in the study of C/N processing because remineralization ecology

remains poorly constrained. The osmotrophs, however, are dominant in global

DMS removal so that a parameterized species addition has been required. We

establish microbial densities as a power law relation to plant nitrogen:

NB ¼ 0.1NP0.5 where B and P signify bacteria and phytoplankton. The round

value coefficients are consistent with much of the available biophysical data

(e.g. Ducklow et al., 1993; Jumars, 1993). Nitrogen concentrations are manip-

ulated in mM and are always at Redfield relative to carbon.

Moore et al. (2004) have validated the CCSM ecodynamics routines exten-

sively against pigment and biogeochemical climatology data, to 20 years of

ocean simulation time and beyond in some cases. We repeated many of these

exercises on the �3 grid. Agreements with satellite chlorophyll are reasonable

on a monthly or annual average basis over much of the global surface ocean,

but significant deviations are found in a few frontal and tropical regimes. In

particular, circumpolar currents of the Southern Ocean, the Pacific western

boundary current (or Kuroshio system) and high North Atlantic waters all

experience spring/summer overprediction. Since phytoplankton growth links

closely to the sulfur cycle, these difficulties determine to a large extent our

selection of optimization regime. They also play into future mechanism design

strategies. Chlorophyll is underpredicted in early simulation years along the

Antarctic coast and in the remote Arctic but begins to rectify over a decade

or so. We have documented the above discrepancies relative to remote sensing

as plots of model to SeaWiFS chlorophyll ratio distributions, but do not in-

clude the results here. Areas of strongest agreement with the satellite measure-

ments appear to be the well-studied ecosystems of the subtropical North

Atlantic and the equatorial Pacific. The border between western Pacific gyre

ecosystems and the warm pool (Longhurst, 1998) experiences high plant den-

sities in the calculations year round.

2.3. Trace gases

Routines for the processing of dissolved, low concentration volatiles have

recently been developed which are specifically mated to DML, POP and the

CCSM (Elliott et al., 2004). Programming maintains/mimics all major perfor-

mance and readability features of the preexisting biogeochemistry routines,

and the coding is packaged as a Fortran module alongside the ecodynamics.

Driver quantities such as the phyto- and zooplankton classes are imported in

a decoupled mode. Schmidt number based, wind speed dependent sea-air

transfer is extended from oxygen to a generic gas list (Wanninkhof, 1992).

Several low molecular weight compounds may be simulated together along

with any relevant precursors, intermediates and products.

Species tested previously in the trace gas module include nitrous oxide, the

methyl halides, and generic nonmethane hydrocarbons (NMHC). Carbon

monoxide algorithms are under development because upon crossing the atmo-

spheric interface the species exhibits oxidant influencing properties. Suites of

organics may eventually be added as tropospheric ozone chemistry surrogate

collections. Carbonyl sulfide and hydrogen sulfide both entail rich acid base

and redox reaction sets and may be included as members of a complete surface

ocean sulfur cycle. In our study of the element in its methylated form, the first

two tracer bins are assigned to DMS and the source molecule dimethyl sulfo-

niopropionate (DMSP). The latter is an ionic compound so that interfacial

transfer is disallowed (Andreae, 1986). Other tracer slots are eliminated and

the resulting subprograms constitute a public offering (Elliott et al., 2005;

see Section 5 below).

2.4. Optimization

Geophysical calculations may be fit to data and assessed for quality

through statistical comparisons with measurement (inverse modeling). Variants

have appeared in many global and marine biogeochemistry investigations (e.g.

Kasibhatla et al., 2000; Christian and Anderson, 2002; Vezina and Pahlow,

2003). Here we employ a post hoc technique based on the fundamental sum

of squared deviations (Press et al., 1992), but weighted in several ways such

that it is tailored to our needs in dealing with the dimethyl sulfide problem.

The procedure is supported by a high quality climatology developed for the

molecule in view of its relevance to the global albedo. Kettle and coworkers

(1999) have compiled and smoothed the available surface ocean DMS deter-

minations then placed them on a one-degree, monthly grid. The data are highly

interpolated geographically, to the province scale in fact (Longhurst, 1998).

Regional adjustments are recorded from time to time as new ship tracks enter

the literature (Kettle and Andreae, 2000), but the work is viewed by the com-

munity as relatively definitive. In all cases we have optimized to the annual

average. It is our judgment that the mechanisms are not yet sufficiently well

posed to warrant monthly or seasonally distributed differencing.

The design and construction of our specific DMS merit function is summa-

rized in Table 1. Press et al. (1992) nomenclature is borrowed initially, in

which for example the vector a signifies the set of model parameters. Begin-

ning in the second line, conversion is made to symbols more relevant to the

present case. Comparisons are aligned between the data base, which represents

only surface concentrations, and values from the topmost level in the three-

degree POP grid, which is roughly ten meters in depth. Weighting is performed

to the data base measurement variability (standard deviation), and to fractional

area of the grid cell. Note that if all differences across the optimization domain

were equal to the local sigma, our statistic would have a value of unity. Overall

merit or quality falling below one thus indicates that points lie, on the average,

inside of the data distributions. All analyses involved Mathematica-like post

processing by NOAA Ferret software (Hankin et al., 2004).

The optimization domain was initially configured to be global, as a matter

of convenience and as a conceptual starting point. It was then reduced in area

systematically in a search for regions which were representative yet free from

chlorophyll related discrepancies deriving from the ecology. Downscaling to

the band of latitudes from 30 degrees north to 30 degrees south excluded prob-

lematic fronts in the Southern Ocean but continued to encompass the entire

subtropics and the equatorial divergences. A second reduction was made to

a North Atlantic zone reaching from 20 to 60 degrees west longitude and

Table 1

Summary of the optimization procedure tailored for application to dimethyl

sulfide. Kettle refers to the primary climatology

Least Squares for n points Sn(y[x,al.am]-yn)2, minimize over a

M ¼ model result, K ¼ Kettle Si,j(Mi,j e Ki,j)2, ij is surface grid

Weighted c2 Sn(y[x,al.am]-yn)/sn]2

With deviation from Kettle Si,j([Mi,j e Ki,j]/si,j)2 ¼ S(D/s)2

Cell area weighting S[(D/s)2(Ai,j/At)], t is total

Significance of unity If D¼s, S ¼ 1 since SAi,j ¼ At

Model field scaling M ¼ (k/kstd)Mstd, std is a standard

Resulting statistic Quadratic in k, minimize analytically

Field for visualization D/s over optimization domain


20 to 40 degrees north latitude, corresponding to portions of the NAST and

NATR biogeographical Longhurst provinces and a majority of subtropical

waters for the basin. Lastly, a swath was defined extending from ninety to

one hundred eighty degrees west longitude and plus/minus ten degrees lati-

tude, overlapping several of the tropical Pacific provinces.

In most cases our runs were conducted for three ocean years with analysis

performed upon the third annual cycle. Several biogeochemical modeling

groups have concluded that a reasonable steady state can be attained over

such time scales in preliminary simulations (e.g. Moore et al., 2002; Chu

et al., 2003, 2004). We were able to utilize for our trace gas studies about

20% of the computational capability on one of several 256 processor SGI Altix

platforms, available to our group at Los Alamos and Oak Ridge National

Laboratories. Three ocean years of simulation at our total of 30 tracers

(Moore et al., 2002; Elliott et al., 2004) required three to ten hours on the

wall clock -sometimes as much as a full working day per run. We consider

this performance to be quite efficient, but individual calculations were none-

theless treated as expensive and valuable. Statistical and tracer fields were al-

ways examined immediately and thoroughly to provide guidance in the design

of new scenarios.

In a typical ecological inverse exercise, a Powell method might be applied

to low dimensionality geophysical calculations as the relevant quality hyper-

surfaces are navigated (Press et al., 1992; Vezina and Pahlow, 2003). Our

work is global, three-dimensional and fully biogeochemical throughout.

From experience in earlier fine resolution modeling (Chu et al., 2004), we

had learned that the full DMS distribution can scale linearly with collective

Gabric-type release rates because all mechanism time constants are indepen-

dent of sulfur species dynamics. In Table 1 this result is conveyed by invoking

a proportionality of standard fields to injection constants. Given the scaling

property, it can be shown that the global sum of squared and specially

weighted differences in fact constitutes a quadratic in the k factor. An ideal

parabolic interpolator is generated (Brent curve; Press et al., 1992). One run

suffices to establish the geometry along a trajectory determined by the removal

function. Analytical differentiation may be performed to yield the minimum in

release rate space. In more than half of the cases to be discussed, a three-year

check was performed by repeating at the optimum to confirm the predicted chi

square. Initial and final concentration fields were also divided into one another

point by point to verify that linearity was universal. Exceptions to this rule

included certain complex kinetics schemes for which the scaling claim fails

(MichaeliseMenten). As an extra precaution, the quality contour was mapped

entirely along the rate constant coordinate in several tests, at a resolution of

better than one tenth per day.

With release from the sulfur pools established as an abstract axis, loss

types were substituted and the process repeated. Ultimately, DMSP composi-

tion of the plants was varied broadly to discrete round value settings. Strictly

speaking, the optimization is incomplete in the traditional sense -the explored

space is quite confined, while shapes may actually be complex in some dimen-

sions. To these objections may be added the irregularity of our sink form spe-

cific trajectories. But a beneficial tradeoff will be apparent. Any one

simulation nets a full investigation of the release dimension. More than 75

three-year runs were performed under these circumstances. Perhaps 50 are

tabulated or commented upon here.

2.5. Mechanism

Dominant channels for the reduced sulfur processing derive from the

Gabric family of models (G henceforward), as described originally in 1993

and culminating in wide ranging applications (see Gabric et al., 2003). This

particular kinetic framework was selected because (1) it has been tested in

many ecosystem contexts but remains structurally stable, (2) it is conveniently

attached to N currency ecodynamics, and (3) it is streamlined so that the pa-

rameter set is eminently manageable. The three properties support optimiza-

tion as well as a secondary goal of the project, which is to contribute DMS

routines rapidly to CCSM for ocean/atmosphere biogeochemistry coupler

development.

Marine reduced S carriers are viewed here strictly as elemental holding

pools, interrelated by flow time constants as shown primarily in Table 2 but

supplemented with sink detail in Table 3. Our immediate task is to refine

the proportionalities and kinetics. The master collective release is kS. A coin-

cidence of timescales is exploited among several plant and consumer groups,

for which all values were similar in Gabric et al. (1993). In fact they were

close to 100 days, and we will demonstrate below that large-scale optimization

suggests much faster turnover. The envelope of the overall mechanism is

emphasized -bacterial S versus C requirements and their effect on DMSP con-

version are ignored because the channels reside between the carrier molecules.

The kS for all runs was set initially near 0.1, a round figure chosen to serve as

a convenient reference point on the abstract coordinate.

2.6. Alterations

Sulfur removal forms were enhanced relative to the G baseline in an incre-

mental fashion as outlined in Table 3, intended for conceptual substitution into

its predecessor. Bacterial consumption may control DMS concentrations

across much of the open ocean, as opposed to photolysis or interfacial transfer

(IPCC, 1996; Kettle et al., 1999). Priority was therefore placed upon variation

of the microbial kinetics. A general equation for molecular osmotrophy

(bacterial solute uptake) is kNBS/(S þ K ), reflecting local microdiffusion

and enzymatic surface reaction (Jumars, 1993; Archer et al., 2004). The S rep-

resents substrate or sulfur and K is a MichaeliseMenten half-saturation level.

Our basic G term fixes NB and presumes S < < K. A round value time con-

stant of one day is assigned initially, as measured in the equatorial Pacific

(Kiene and Bates, 1990). The loss was modified first such that kB reflected

lower gyre microbe levels in a step function; Chu et al. (2004) report limited

success with a bimodal approach in biogeochemical POP simulations con-

ducted at a global average resolution of one fifth degree. The second-order

situation was simulated by restoring NB variation. In the bimolecular analog

30 (d mM)�1 matches the central Pacific one-day residence for a likely NP

of 0.1 mM, giving NB of 0.03 in the power law relation.

In a parallel set of runs, the unimolecular bacterial G term was restored/

fixed and photochemical subtleties were explored. Since aqueous DMS does

not absorb beyond 275 nm, its photodegradation requires sensitizing agents.

These will in some cases be organic (Mopper and Kieber, 2002), but nitrate

has also been implicated (Kieber, pers. comm.). A general form is kIDl

(DOC)(NO3�)(DMS) with DOC signifying dissolved organic carbon. To con-

struct the photolytic G term, all sensitizers were subsumed and a coastally de-

termined surface photolysis time of 2 days (Brimblecombe and Shooter, 1986)

Table 2

Framework of a Gabric sulfur (S) mechanism. R signifies a mole ratio to N, P

the several distinct DML plant types, and C conversion. Zooplanktonic DMSP

RS,Z is an average of consumable content

Species Sources Sinks

DMS kSSRS,PNP + kCDMSP Bacterial + Photochemical

DMSP kSSRS,PNP + kSRS,ZNZ Bacterial + kCDMSP

Table 3

Identifiers and definitions for the core model runs

Bacterial removal (substitute into mechanism sinks)

G kBDMS (or DMSP), global first order

kinetics with kB ¼ 1.0 d�1

Step kB from G to Gabric et al. (1993) slow

limits for DMS(DMSP) if NB < 0.03 mM

2nd kBNBDMS (or DMSP), global second

order kinetics with kB ¼ 30.0 (d mM)�1

Photochemical removal (substitute into mechanism sinks)

G kIDMS, kI ¼ 0.5 d�1 exp(�optical

depth) at all locations

PAR kIIPARDMS, kI ¼ 0.005 (d w/m2)�1

D10 kIIPAR(CDOM/10 mM)DMS, kI ¼ 0.005 (d w/m2)�1

CDOM represents Dissolved Organic Matter as carbon.


was attenuated moving downward through the numerical POP layers strictly

according to local absorbance (chlorophyll and column). CCSM ocean biogeo-

chemistry imports surface solar intensity but transmits and scatters only PAR.

As an initial kinetic enhancement, the rate was thus normalized to 100 w/m2 as

a diel average for the integrated photosynthesis bands in sunlit regions. DML

ecodynamics aggregate into the dissolved organic tracer bin a sum of mole-

cular, colloidal and small particle forms and this may be an upper limiting

approach (Moore et al., 2002, 2004). As a secondary change we add normal-

ization to a round median DOC concentration of 10 mM. This last configura-

tion is denoted D10.

The reduced sulfur sink permutation strategy is presented in the leftmost

columns of each of the three main sections in Table 4. A baseline combination

of G (microbial) with G (photochemical) is the most faithful to early Gabric

work.

2.7. Cell composition

Keller et al. (1989) provided early measurements of intracellular DMSP

content for a great variety of phytoplankton species. Drawing loosely on these

data, Gabric et al. (1993) estimated that the S(DMS relevant)/N mass ratio 0.3

applies to the taxonomic groups Bacillariophyceae, Prymnesiophyceae and

Dinophyceae, which include the photosynthetic diatoms, coccolithophorids

and dinoflagellates. Diatom sulfur in fact ranges downward at least two orders

of magnitude in the Keller set, in later works and probably also in the real

ocean. Siliceous plants are nitrate and bloom specialists so that S containing

osmolytes may become extraneousdnitrogenous species such as glycine beta-

ine suffice to prevent desiccation (Andreae, 1986; Kettle et al., 1999). Nitrogen

fixing organisms seem to retain very little DMSP, and strong picoplanktonic

Table 4

Kinetic and composition permutations, along with their analytic best value

rates (1/d ) and dimensionless quality (normalized deviations are squared,

area weighted, summed)

Sink chemistry Optimization results

Microbe Photo Release rate Merit function

Global þ/� 30 � NAST PEQD Global þ/� 30 � NAST PEQD

Rs Diatoms-0.1, Coccolithophorids-0.1, Other small-0.1

G G 0.068 0.110 0.140 0.120 0.65 0.18 0.06 0.12

Step G 0.062 0.087 0.084 0.120 0.58 0.26 0.16 0.12

2nd G 0.120 0.120 0.140 0.140 0.28 0.10 0.04 0.11

G PAR 0.069 0.110 0.150 0.130 0.65 0.17 0.06 0.11

G D10 0.076 0.120 0.140 0.130 0.60 0.12 0.05 0.13

2nd PAR 0.120 0.130 0.140 0.150 0.25 0.10 0.04 0.11


G G 0.087 0.140 0.170 0.170 0.71 0.18 0.04 0.10

Step G 0.076 0.100 0.094 0.170 0.65 0.38 0.19 0.10

2nd G 0.150 0.160 0.160 0.200 0.30 0.14 0.04 0.11

G PAR 0.088 0.150 0.170 0.180 0.71 0.18 0.05 0.09

G D10 0.098 0.160 0.160 0.190 0.63 0.14 0.04 0.11

2nd PAR 0.150 0.160 0.160 0.210 0.28 0.14 0.04 0.11


G G 0.140 0.290 0.560 0.290 0.89 0.40 0.20 0.18

Step G 0.140 0.280 0.370 0.290 0.81 0.24 0.13 0.18

2nd G 0.290 0.360 0.550 0.340 0.43 0.20 0.13 0.14

G PAR 0.140 0.300 0.540 0.300 0.89 0.38 0.21 0.17

G D10 0.160 0.330 0.520 0.320 0.86 0.31 0.18 0.20

2nd PAR 0.290 0.370 0.550 0.350 0.40 0.19 0.13 0.14

The two regional exercises are indicated by acronyms for their central biogeo-

graphical provinces: NAST for North Atlantic Subtropical Gyre, PEQD for Pa-

cific Equatorial Divergence (Longhurst, 1998). We retain two significant

figures in all cases excluding merit less than one tenth (dimensionless). Actual

computations were conducted to four decimal places.

photosynthesizers such as Synechococcus and Prochlorococcus fall in the

same category despite the nutrient limitation typical of gyre environments.

The spectrum of composition results has been confirmed several times and

most recently by Sellers (unpublished).

For current purposes we convert the average mass relationship to a mole

ratio of 0.1, apply it initially without discrimination to all phytoplankton,

then decrease for diatoms by virtue of the osmolytic argument. The decrement

is set semiarbitrarily at one order of magnitude. Noncoccolithophorids are dis-

tinguished among small plant cells in DML solely by their lack of calcifica-

tion. Dinoflagellates are thus lumped numerically with the species of lowest

diameter. Sulfur modeling for these classes must be handled for the time being

in aggregate, and their content is reduced in a third experiment set. The change

is again a factor of ten. Calcite secretors such as Emiliana huxleyi are acknow-

ledged sulfur emitters and we do not vary them downward here. The related

plant taxon Phaeocystis may be segregated soon by DML developers and

will contribute to sulfide production at high Northern latitudes where blooms

are known to occur. DMSP cell content permutations employed here are

grouped as three divisions in Table 4.

2.8. Other scenarios

Many runs were performed outside the main sensitivity test framework of

Table 3. The most important examples are included under the heading 2nd

PAR in our result matrices. Although it appears successful on our merit scale,

the D10 type sensitization must be considered quite speculative for the

moment. The organic molecules or chromophores involved have not yet

been fully identified, and likely vary from ecosystem to ecosystem across

the global ocean and with the aging of detrital material (Mopper and Kieber,

2002). In view of the attending uncertainties, we elected to add a group of

summary computations in which the bimolecular microbial uptake and pure

PAR proportionality were coupled. The simulations were very competitive

and recommend themselves by virtue of simplicity.

A number of minor explorations deserve mention as well. Photodegra-

dation was normalized to 50 w/m2 in one instance, as opposed to our stan-

dard value of 100. Nitrate and coupled nitrate/DOC dependence were also

tested in the photochemistry, with reference levels varying from 3 to 30 mM

for both substances. Quality improvements for such runs were <0.03 or

else were negative. A handful of MichaeliseMenten kinetics computations

was performed and demonstrated peak stretching. The effect is expected as

removal rates slow on a relative basis near half saturation. Since a prom-

inent feature of the extended DMS profile is flatness absolute merit was

in general sacrificed, but the effects were insignificant unless K was low-

ered far below values that have been applied in coastal models (Archer

et al., 2004).

2.9. Decadal simulations

The period of three ocean years has been a traditional length for biogeo-

chemistry runs involving computationally intensive models of upper level pro-

cessing (e.g. Moore et al., 2002; Chu et al., 2003, 2004). Given average

vertical diffusivities, upper thermocline influences can reach the surface within

months. At high latitudes the penetration of convective cells may extend to

several hundred meters and turnover recurs annually (Longhurst, 1998).

Time constants for plant growth, consumption and remineralization are as

low as a few weeks at the surface excepting in the polar night. If model initial

conditions are correct at a depth of several hundred meters it may then be an-

ticipated that a few yearly cycles of integration will bring about the surface

biological/geochemical steady state.

Our repetition of decadal scale DML simulations showed that slight im-

provements in the chlorophyll distribution develop in remote Antarctic and

Arctic waters, and that the equatorial Pacific production maximum broadens

somewhat between 10 and 20 years. Bands of excess plant material at mid lat-

itudes did not appear to improve, but it was felt expedient to push our sulfur

cycle investigations beyond the usual three-year run duration in any case. Sev-

eral calculations were thus carried out to longer than 20 years, with effort

focused upon the 2nd PAR mechanism. Almost ten days on the wall clock

were needed to reach completion, so that the project had to be severely limited


in scope. A background removal term was added to the above described reac-

tion scheme to account for a slow form of bacterial consumption, which has

been documented in the main thermocline. The decay constant was set to

107 s in order to mimic observed e-folding distances (e.g. Andreae, 1986).

The simulated long term dimethyl sulfide distributions were examined

as global maps at the surface, 100 and 300 meters for both the ten- and

20-year time horizons. Sharp maxima remain in the Tasman, New Zealand,

Falklands and Kuroshio vicinities and deviation from the Kettle climatology

may in fact worsen. The Ross and Weddell Seas begin to back fill with reduced

sulfur but the compensation appeared to be progressing very slowly, possess-

ing perhaps multidecadal growth. Slight increases in the overall average DMS

concentration can be reported, of between 10% and 20% globally. These

values are consistent with a combination of evolution in the ecodynamics

and loading of the bulk thermocline with surface derived sulfur.

3. Results

An individual scenario analysis in our experiments mostoften consisted of the standard three-year simulation fixingthe initial kS at 0.1 d�1, followed by post processing optimiza-tion computations to yield the ideal release value and meritminimum over the global, plus/minus 30 and regional do-mains. Results were placed in the appropriate slots in Table4, beneath and beside their composition vector and sinkform labels. The check resimulations and rescaling calcula-tions were performed at the tabulated release rates carriedout to four significant digits, for one to three of the subre-gimes. Planetary scale maps were compared in all cases forannual averages of both normalized deviation and concentra-tion. All the global realizations are available on request, whileillustrative samples are provided in the figures described be-low. Ferret plots currently being generated from the stretched�3 system correspond to absolute latitude from Antarctica toalmost 50 degrees north. In the Arctic Atlantic reference mustbe made to neighboring landforms, but relationships there arenot crucial to our purposes. In particular it should be recalledthat the primary optimization domain reaches only to thesubtropics.

It was determined early on that global chi square calcula-tions are overly influenced by the midlatitude frontal ecosys-tems with plant densities already known to be high relativeto satellite data. The effect was most pronounced in theSouthern Ocean, along constant latitude bands stretching southof Australia and Tasmania to New Zealand and for severalthousand kilometers downstream (in the circumpolar sense)from the Falkland Islands. Similar phenomena could be docu-mented, however, along the Kuroshio/Oyashio current systemsand southeast of Cape Agulhas. The problems may be ob-served in the series of planetary scale optimization mapsshown as normalized deviations in Fig. 1 and as sections takennear the International Dateline in Fig. 2. Low equatorial valuesmay well be attributable to compensation for peaks in the Sub-arctic and Subantarctic. Overestimation of productivity in thevicinity of the warm pool is also apparent, but proves moredifficult to control. The first two figures are presented forthe constant composition vector R ¼ 0.1, but trends extendto the two DMSP reduction sets as well. Global merit is sup-pressed below two thirds of a standard deviation only in casesfor which the removal mechanism emphasizes moderation of

the midlatitude maxima. Polar lows seen in the figures are at-tributable in part to the need for spinup toward the decadalscale. Sea ice biogeochemistry is lacking in DML, however,and this may also account for some of the undershoot atextreme high latitudes. Entire ecosystems may be trapped sea-sonally within the solid water matrix, concentrating their gen-eral biological and trace gas products for emission into lowdensity surface layers in the spring.

The 30-to-30 degree domain permits agreement to stabilizeat well under half a deviation (on the average) in most cases.Although we discount the global approach due to chlorophylldiscrepancies, contrasts with the 30N/30S band are neverthe-less instructive. The stepped microbial removal becomes det-rimental to the merit function except when the gyrenoncalcite secretors are deleted. Our interpretation is thatsmoothing both in the real ocean and the Kettle data setwork against sharp gradients. The dimethyl sulfide deviationplateaus exhibited in Fig. 1 (Step G) become a chi-square lia-bility. Note for example the feature extending from the west-ern tropical to the North Pacific, which cuts sharply acrossa zone boundary. Superior quality values of order ten percentare achieved by the second order microbial interaction,whether it is paired with our version of the original Gabricphotochemical term or the PAR dependence. The dissolvedorganic normalization performs nearly as well, however.Only uncertainty in the original coastal photolysis determina-tions and our knowledge of the global state of marine organicchemistry affairs prevents us from adopting this format.

Concentration distributions and sectional profiles are pre-sented for the 2nd PAR version of the model in Figs. 3 and4, under variation in the composition vector moving fromimage to image and culminating in the annual average fromthe data base (Kettle et al., 1999; Kettle and Andreae, 2000).The reduced diatom DMSP content experiments seem to theeye to flatten the patterns excessively. It must be remembered,though, that an arbitrary order of magnitude reduction may betoo large. Intermediate compositions have not been tested andthere may well be hidden dips in our hypersurfaces. Objec-tively speaking (from the merit standpoint), the low diatomsulfur optimization might be said to compete quite effectively.This is even true of the reductions to noncoccolithophoridsmall species. Were the intracellular sulfur factor to be set to0.03 in either case it seems possible or even likely that a higherquality profile would obtain. A difficulty of interpretationwould arise from any increase in the optimal release rate.Lifetimes for the processing of sulfur within plant materialfall into the range of several days in the lower portion ofTable 4. We suspect that it would not be energetically soundfor open ocean plants to output their sulfur in significantlyless than a generation.

Most loss constants determined at either the global scale orover the 60-degree wide equatorial band are of order one to twoweeks. In classical and our own ecodynamic models (Vezinaand Pahlow, 2003; Moore et al., 2002, 2004), this correspondsfairly closely to the timing of phytoplankton grazing and senes-cence. Release of reduced sulfur into the water column is prob-ably linked under many circumstances with disruption of the


Fig. 1. Deviation of model annual average from the Kettle value, divided by standard deviation. The results are derived from several runs conducted at constant

intracellular DMSP content of 0.1 and followed by global scale optimization. Clockwise from upper left, and referring to nomenclature in the tables the mech-

anisms represented are: GG, Step G, G D10 and 2nd G.

major source pool represented by the algae. Zooplankton andaging are the proximate agents of cell rupture. Our interpreta-tion of such an internally and ecologically consistent resultmust be that the statistical method is detecting disruption as

Fig. 2. Near-Dateline sections taken through the maps of Fig. 1: black repre-

sents the GG mechanism, light blue Step G, Red 2nd G and dark blue G D10.

a release mechanism. Early Gabric papers fixed the injectiontime scale at many weeks. This discrepancy is in fact readilyexplained by the authors’ focus upon localized bloom events.For a global model and in particular one in which optimizationtakes place along the release coordinate, the balance betweenemission and microbial removal becomes crucial.

Merit drops to below the ten percent level and is somewhatnondiscriminatory as the optimization domain is downsized toless than the area of a basin. In fact the ecogeographical prov-inces over which Kettle interpolation and smoothing were con-ducted occupy a significant fraction of any given ocean.Boundaries are displayed in the frontispiece of the originalmonograph defining them (Longhurst, 1998). Horizontaldimensions are almost always thousands of kilometers. Inthe NAST and PEQD labeled columns and over our centralAtlantic and equatorial Pacific regimes minimization was ef-fectively computed for only a few climatological data points,equivalent to a restricted selection of the original ship trackmeasurements. We learn therefore that the strategy of collaps-ing our quality calculations has certain limits. Resolution ofthe ecodynamics discrepancies would of course enable us tozoom back from the compromise equatorial band to the globalscale.


Fig. 3. Annual average dimethyl sulfide concentration distributions computed under the 2nd PAR mechanism, followed by plus/minus 30-degree (latitude) opti-

mization. The Kettle data base is shown for comparison. Intracellular DMSP content is varied as referenced in the tables: clockwise from upper left all plant classes

are set to 0.1, then the diatoms are lowered, the climatology is presented and small noncoccolithophorids are lowered.

4. Summary and discussion

During development of a coupled global biogeochemistrycapability within the U.S. Community Climate System Model,we have undertaken to test and then to optimize against clima-tology one particular, clear cut mechanism for representationof the mixed layer marine sulfur cycle (Gabric et al., 1993to 2003). A coarse, bivalued variation (0.1, 0.01 as ratio to N)

Fig. 4. Sections taken through the maps of Fig. 3, at 150 � west longitude. Red

represents the constant DMSP run, dark blue low diatoms, light blue low non-

coccolithophorids and black the Kettle climatology.

was imposed upon phytoplantkonic reduced sulfur content(Keller et al., 1989). Dimethyl sulfide removal functionswere upgraded to bimolecular forms in the case of microbialconsumption (Kiene and Bates, 1990), and for a range ofsensitizer dependencies representing photochemical decay(Mopper and Kieber, 2002). A common organism releaserate was treated as an analytical optimization dial, and thisprovided a measure of the time constant for injection. Theresult was an estimate of several weeks. The sulfur cycle isdriven in the CCSM context by a standard major element eco-dynamics routine which experiences difficulties in the simula-tion of blooms along sharp midlatitude fronts (Moore et al.,2002, 2004). Overprediction of plant biomass is reflected inthe DMS distribution as well, and compensation in the meritfunction calculation leads to a depression of tropical concen-trations. Shrinkage of the statistical domain to an equatoriallycentered belt of latitudes spanning 60 degrees north to southimproves the situation without altering the release rate conclu-sion. Quality is highest for second order bacterial uptake, withthe plant DMSP composition vector set constant. It is alsoquite competitive, however, for several other mechanisms.These include organic photosensitization, which we downplaydue to continuing uncertainties, and reduced sulfur levelsamong diatoms and other plant taxa.

It can be argued that the mechanisms surviving our test pro-cedure will exhibit somewhat divergent climate sensitivities.We have informally applied the type of qualitative logicoutlined in IPCC (1996) or Watson and Liss (1998) to sulfurcycles in which local trace gas levels are controlled by overall


productivity, by grazing pressure, by the coccolithophoridcomponent of the ecosystem structure, and other relevantproperties as discussed here. The situation is reminiscent of,and remains similar to, that described in early-moderndimethyl sulfide research published more than a decade ago(e.g. Charlson et al., 1987). It had already been documentedthat feedbacks to global climate must exist, but then as noweven their signs were uncertain. Obviously, the situationmust be improved in high-level Earth System models. Whilethe conclusions drawn from our optimization exercise aresomewhat diffuse overall, we feel that they do define severalcode development directions, which will yield progress forthe CCSM.

Several lines of reasoning indicate that DMS emissionsmust be closely related to phytoplanktonic disruption, and inparticular to the processes of grazing and senescence (IPCC,1996; Vezina, 2004). Analogs are available within the DMLecodynamics, and in fact the treatments there are very detailed(Moore et al., 2002). Injection of sulfur into the model willbecome parameterless (parameter free) if links are made totrue major element flow from breaking cells. Release will bedetermined entirely by local plant compositions and destruc-tion rates. We have been forced in the current study to be sat-isfied with brackets on R values. But with the injection timeconstant removed from consideration, another analytical vari-able could be established to take advantage of scaling and theopportunity for fast optimization. An expeditious choice maybe the maximum plant DMSP concentration, which can beassigned a priori to the prymnesiophytes. Other photosynthe-sizers can then be associated with appropriate ratios for theirsulfur to the maximum, as suggested by historical and recentlaboratory studies (e.g. Keller et al., 1989; Sellers, unpub-lished). Our hope is that the connections with mortality andzooplankton grazing pressure will allow semipeaked contoursof the equatorial DMS maxima to be captured more faithfullywhile sampling automatically the intermediate content zonesof the parameter space.

Along the southerly fronts where plant distributions are forthe moment in disagreement with satellite retrievals, the Kettledata base indicates that the sulfur distribution should actuallybe quite even. To focus on improving results in this area wewill either have to await changes in the CCSM ecodynamics,or else nudge them independently on a temporary basis.A crude tactic in the latter case would be to enforce chloro-phyll maxima. More sophisticated approaches would requirecontinual resetting relative to the remote sensing, delayed res-toration or even data assimilation. It is likely that the ecologyproblems derive from an underdeveloped iron cycle and thatsome headway can be made through adjustments to tracemetal initial and boundary conditions (Moore et al., 2004).In any case, if/when the ecodynamics can be adjusted ourefforts can be extended into the Southern Ocean. The flatnessof the Kettle interpolations there may indicate the need forspecialized metabolics. Circumpolar waters constitute thelargest and most stringently iron limited of the global HNLCregimes (High (major) Nutrient Low Chlorophyll; IPCC,1996). Nitrate is often discussed as an anticorrelant for

intracellular DMSP since the latter is a sulfur containing os-molyte (Andreae, 1986; Kettle et al., 1999). Early versionsof the DML program tracked nitrogen stress through a quotavalue representing the range permissive of plant growth.Southern Ocean sites continually support the highest quotalevels, Pacific gyres the lowest. We are anxious to attempt torelate this quantity to plant cell sulfur content.

A wild card in the next generation of studies will be thebacterial biomass. Although photochemical decompositionmay be regionally important (Mopper and Kieber, 2002), itis still believed that the microbes are major DMS consumersover much of the open ocean (Gabric et al., 2003). Ourparameterization of their nitrogen density is coarse andconstitutes a weak link in the current approach. Accordingly,we propose to create a stand alone microbial ecology module.It will be designed to function in parallel with the DMLecodynamics (which currently subsume bacteria), and alsowith trace gas routines requiring production and loss terms.Segregation may ultimately be desirable for many classes oforganism including the chemoautotrophs and methanogens,but we will focus initially upon the methylotrophs and speciesseeking sulfur. As in the case of the generalized trace gasroutines, CCSM offers a promising code developmentenvironment.

Overall this discussion section suggests a set of quantumleaps for marine sulfur cycle modeling, from locally averagedpools and lifetimes moving toward a true global dynamismlinked closely to ecology. We note in this context that theMoore et al. (2002, 2004) driver code is one of the more com-plex large-scale biology simulators ever constructed. In earlyand more intensive versions, several hundred terms/equationswere solved, detailing the kinetic forms of enzyme and colimi-tation biochemistry, feeding preferences, and predator prey re-lations -not to mention background remineralization andaqueous physical chemistry. The biological oceanographycommunity now accepts the reality that nutrient elementsmust be handled in Earth System models at least with this levelof sophistication. In retrospect we feel that it has been naive toexpect the sulfur situation to prove otherwise. Richly coupledN/P/Fe/Si/C mechanisms have evolved over the last decadean element or so at a time, and now sulfur must be added tothe list.

Our revised goals define a set of phases for full introductionof reduced S into planetary scale system code. Several of thesteps have already been completed. Our first work in the Par-allel Ocean Program was fine in its resolution, but demandedlittle more from the Gabric framework than adjustment of thebacterial removal time (Chu et al., 2003, 2004). This might betermed a ‘‘bins and time constants’’ phase. Regional relation-ships between the kinetics and horizontal eddy structures wereelucidated. Comprehension of interprovince patterns, on theother hand, eluded us. The second development step hasbeen described exhaustively in the present work, and it is op-timization within the simple linear frame. In our next effort wewill begin to account the ecological kinetics of sulfur, withcoelemental flows determining release and nutrient stressinfluencing osmoregulation. Future work will require us to


construct a microbial ecology module, with specialized tracersacting as DMS consumers. Photochemistry routines will alsobe needed, as field and laboratory studies begin to reducethe attendant uncertainties. It might be asked, could some orall of these tasks be leapfrogged? We submit that the answeris no. A stepwise approach is essential to incubation of themodels and modelers. Historically this has proven to be a fea-ture of the development process for other elements cyclingthrough the global ocean. The steps, we feel, are obligatory.The speed with which the effort is conducted will depend pri-marily on the resources applied.

5. Coding

The preferred mechanism developed here has been thatlabeled 2nd PAR, reflecting bimolecular DMS osmotrophyand a standard photochemical decomposition set proportionalto the intensity of photosynthetically available radiation. Wehave packaged this scheme for public consumption alongwith the background removal term from the decadal simula-tions (Elliott et al., 2005). Several routines appear togetheras a Fortran 90 module deriving directly from more generaltrace gas collections (Elliott et al., 2004). Subprograms dealwith initialization, storage and averaging, computation of con-centration time rates of change, and more -all in the POP andCCSM contexts. Interested parties may contact any one of thetext authors for information necessary to obtain the code suite.

Acknowledgment

The authors thank the U.S. DOE Office of Science (BER)SciDAC program for support of this project.

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contours of simulated marine dimethyl sulfide distributions under variation in a gabric mechanism

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