Nitrogen Cycle of the Open Ocean: From Genes to Ecosystems

Abstract

The marine nitrogen (N) cycle controls the productivity of the oceans. This cycle is driven by complex biogeochemical transformations, including nitrogen fixation, denitrification, and assimilation and anaerobic ammonia oxidation, mediated by microorganisms. New processes and organisms continue to be discovered, complicating the already complex picture of oceanic N cycling. Genomics research has uncovered the diversity of nitrogen metabolism strategies in phytoplankton and bacterioplankton. The elemental ratios of nutrients in biological material are more flexible than previously believed, with implications for vertical export of carbon and associated nutrients to the deep ocean. Estimates of nitrogen fixation and denitrification continue to be modified, and anaerobic ammonia oxidation has been identified as a new process involved in denitrification in oxygen minimum zones. The nitrogen cycle in the oceans is an integral feature of the function of ocean ecosystems and will be a central player in how oceans respond during global environmental change.

Full text

MA03CH08-Zehr ARI 17 November 2010 6:55
Nitrogen Cycle of the Open
Ocean: From Genes
to Ecosystems
Jonathan P. Zehr and Raphael M. Kudela
Ocean Sciences Department, University of California, Santa Cruz, California 95064;
email: zehrj@ucsc.edu, kudela@ucsc.edu
Annu. Rev. Mar. Sci. 2011. 3:197–225
First published online as a Review in Advance on
September 14, 2010
The Annual Review of Marine Science is online at
marine.annualreviews.org
This article’s doi:
10.1146/annurev-marine-120709-142819
Copyright c
2011 by Annual Reviews.
All rights reserved
1941-1405/11/0115-0197$20.00
Keywords
nitrogen cycle, marine biogeochemical cycles, nitrogen fixation,
nitrification, denitrification, anaerobic ammonia oxidation
Abstract
The marine nitrogen (N) cycle controls the productivity of the oceans. This
cycle is driven by complex biogeochemical transformations, including nitro-
gen fixation, denitrification, and assimilation and anaerobic ammonia oxida-
tion, mediated by microorganisms. New processes and organisms continue
to be discovered, complicating the already complex picture of oceanic N cy-
cling. Genomics research has uncovered the diversity of nitrogen metabolism
strategies in phytoplankton and bacterioplankton. The elemental ratios of
nutrients in biological material are more flexible than previously believed,
with implications for vertical export of carbon and associated nutrients to
the deep ocean. Estimates of nitrogen fixation and denitrification continue
to be modified, and anaerobic ammonia oxidation has been identified as a
new process involved in denitrification in oxygen minimum zones. The ni-
trogen cycle in the oceans is an integral feature of the function of ocean
ecosystems and will be a central player in how oceans respond during global
environmental change.
197
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INTRODUCTION
The oceans are a central feature of the biosphere, with biogeochemical links to the land and
atmosphere. Because the oceans cover almost three quarters of the Earth’s surface, the chemical
reactions within the oceans, both biotic and abiotic, have profound effects on the gas composition of
the atmosphere. The microorganisms in seawater maintain the fertility of the oceans by catalyzing
reactions that provide nutrients for growth of higher organisms and result in production and
consumption of greenhouse gases. Many key variables control these ecosystem properties, and
nitrogen (N), the fourth most abundant element (after hydrogen, oxygen, and carbon) in organic
matter, is one of them. The N cycle is a critical component of the biogeochemical cycles of the
water column of the ocean (Figure 1) because N is often in short supply relative to other nutrients
needed for growth and, thus, is often a major limiting nutrient.
Nitrogen, the seventh element in the periodic chart, has an atomic mass of 14 and exists in redox
states ranging from −3to+5. It is commonly found as amine or amide groups in organic matter but
is readily oxidized or reduced and, thus, has an additional significance in marine systems as both an
electron acceptor and donor for energy metabolism. It is this complexity in microbial metabolism
that results in the formation and consumption of different chemical forms involving N atoms, and
this complexity drives the biogeochemical cycle of N in the sea (and on Earth, in general). Clearly,
N is a central nutrient for terrestrial and aquatic systems (Vitousek & Howarth 1991) and is a key
component in global environmental change. Anthropogenic influences on the biogeochemistry of
N have resulted in major changes in the Earth’s N cycle (Galloway et al. 2004, Howarth 1988),
Nitrication
Assimilation
(Nitrication/denitrication?)
Upwelling,
advection
Ammonia and nitrite
oxidation (nitrication)
Mineralization
N2 xation
a Open ocean b Oxygen minimum zones
PN
NO3
–
NH4
+
NH4
+PNNO2
–
NO3
–
N2N2O
PN
Phytoplankton
Viruses, grazers
Microbial
loop
Depth
O2T
Depth
Sea surface Sea surface
O2T
N2 xation
Denitrication
N2 xation
NH4
+
N2N2N2O
PN
Phytoplankton
Viruses, grazers
Microbial
loop
Denitrication
Anammox
Mineralization
Nitrication
DNRA
NH4
+
PN NO2
–NO3
–
NO2
–
PN
Figure 1
Conceptual diagram highlighting and comparing the major nitrogen-cycle components in (a) the typical oceanic water column to that
in (b) oxygen minimum zones. The oxidation of ammonium to nitrate is called nitrification but includes the processes of ammonia
oxidation and nitrite oxidation, catalyzed by different microorganisms. Abbreviations: DNRA, dissimilatory nitrate reduction to
ammonia; PN, particulate nitrogen.
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MA03CH08-Zehr ARI 17 November 2010 6:55
with implications for future-climate scenarios. The subject of this review is another intricacy of
the marine N cycle: the changing perspective on the N cycle and the microorganisms involved
in the open ocean and in the special case of oxygen minimum zones because of their significance
to the N cycle. In recent years, new microorganisms have continued to be discovered, along with
entirely new pathways in the N cycle. In the words of Lou Codispoti (pers. commun.), author of
landmark assessments of the marine N budget, “While some consider the N-cycle to be fiendishly
complicated, I prefer to think of it as deliciously complex.”
The major challenges in understanding the nitrogen cycle in the ocean are the vast time and
space scales of the global ocean. Recent advances in our understanding of the N cycle (see com-
prehensive reviews in Capone et al. 2008) span scales from genes and organisms to ocean basins.
Nitrogen transformations are catalyzed by microorganisms and thus, genome organization, gene
expression, and ecological selection can control N fluxes at biome scales. Genes, and more recently
whole-genome sequences, provide information on the biological capabilities of the organisms in-
volved in specific N cycle reactions, providing information on the ecological and evolutionary
forces that shape the distributions and activities of these microorganisms and their influence on
the N cycle. The purpose of this review is to juxtapose different perspectives and scales, to high-
light the aspects of the N cycle that are relatively well understood, and to identify some of the
knowledge gaps we still face in this “deliciously complex” system.
THE TWENTIETH-CENTURY NITROGEN CYCLE:
A STAGE SET FOR DISCOVERY
In the marine environment, the distributions of chemical forms of nitrogen are maintained by
chemical equilibria and redox states coupled with bioenergetic considerations. Briefly, concentra-
tions of dissolved dinitrogen gas and dissolved organic nitrogen (DON) are generally the most
abundant forms of N in the surface ocean (Table 1). Dinitrogen is available to only a relatively
small but diverse set of Archaea and Bacteria who can fix N2into biologically available ammonium.
In coastal waters, where deep water is brought to the surface, or where riverine inputs are signifi-
cant, oxidized forms of fixed nitrogen, primarily nitrate, can be the dominant form of bioavailable
N(Table 1). Ammonium, although often at low or undetectable concentrations, is the primary
source of N for photoautotrophic carbon (C) fixation. Ammonium, which is fully reduced N (−3),
is an energetically favorable N source for most plants and algae, as it is readily transported and
assimilated into organic matter with minimal energy expenditure (Table 1). Ammonium is also
the first breakdown product during the decomposition of organic matter. Most dissolved organic
matter containing N is not well characterized (McCarthy & Bronk 2008), although there are small
compounds such as urea and amino acids that are easily identified, despite their presence at very
low concentrations and rapid recycling, because they are so easily assimilated by both autotrophic
and heterotrophic organisms (Baker et al. 2009).
BASIC TENETS OF THE “OLD” N CYCLE
The conceptual oceanic N cycle prior to the 1990s can be characterized by a few key principles
that set the backdrop for the ensuing recent years of N cycle discoveries.
1. Nitrogen and phosphorus were believed to be the primary nutrients limiting biomass accu-
mulation and productivity in ocean ecosystems, but the geochemical perspective suggested
that P is ultimately limiting on millennial timescales, as deficits in N availability could be
overcome by biological N2fixation.
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Table 1 Major forms of nitrogen in the ocean, indicating habitats of importance
Form Formula Function Pathways Habitats
Nitrate NO3−Electron acceptor,
nitrogen source
Nitrogen assimilation,
dissimilatory nitrate
reduction and
denitrification
Coastal upwelling zones, deep
ocean
Ammonium NH4+Electron donor, energy
source, nitrogen source
Nitrogen assimilation,
ammonia oxidation
(aerobic), and anaerobic
ammonia oxidation
Important, rapidly recycled pool in
open ocean, intermediate in
decomposition of organic matter
Nitrite NO2−Electron donor and
acceptor, energy source,
nitrogen source
Nitrification (nitrite
oxidation), denitrification
Found at margins of oxic/anoxic
regions, intermediate in oxidation
and reduction pathways
Dinitrogen N2Nitrogen source — High concentration in equilibrium
with atmosphere, available to
N2-fixing microorganisms
Nitrous oxide N2O Trace gas, electron
acceptor, electron donor
End or by-product of
nitrification and
denitrification
Intermediate in reductive pathway,
also formed in nitrification and at
oxic/anoxic interfaces and anoxic
or suboxic zones
Dissolved
organic
nitrogen
Multiple
compounds,
including, e.g.,
amino acids
Nitrogen source,
nitrogen-containing
organic matter, mostly
poorly characterized
Remineralization
(ammonification)
Complex organic matter found
throughout oceans but with
varying, not well-known
composition
Urea (NH2)2CO Nitrogen source Nitrogen assimilation Decomposition product,
potentially important nitrogen
source in water column
2. The N and P requirements for phytoplankton growth were believed to be fairly constant,
resulting in a relatively constant Redfield elemental ratio of C:N:P in marine organic matter
(Redfield 1958).
3. It was assumed that all phytoplankton could use the simple, inorganic fixed-nitrogen com-
pounds nitrate, nitrite, and ammonium commonly found in seawater, as well as some organic
compounds such as urea and free amino acids.
4. Most algae, or phytoplankton, use nitrate or ammonium as primary nitrogen sources
(Figure 1). In the open ocean, the primary sources of nitrate are the mixing of deep nitrate-
rich water, atmospheric deposition, surface runoff, or N2fixation. Ammonium is the first
decomposition product from organic matter and, thus, is rapidly recycled in the water col-
umn. These concepts were used to formalize a conceptual model that described the link
between inputs and outputs of N (along with biologically associated carbon) by calling N
assimilated from ammonium “regenerated” (endogenous) and that from nitrate “new” (ex-
ogenous), as nitrate had to be derived from outside the surface ocean reservoir (Dugdale
& Goering 1967). This concept was developed further to describe the export of associated
carbon (from Redfield stoichiometry), or export production (Eppley & Peterson 1979), with
contemporary significance for natural and geoengineering solutions for removal of carbon
from the atmosphere.
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Nitrogen fixation:
reduction of N2gas
(approximately 80% of
the atmosphere, and in
equilibrium in surface
seawater) to
ammonium as a source
of nitrogen. Biological
N2fixation is catalyzed
by the enzyme
nitrogenase, a
multicomponent
enzyme that requires
metals (Fe, and usually
molybdenum). The
reaction, although
exergonic, has a high
activation energy and
is inactivated by
oxygen. The reaction
is energetically
expensive, requiring
approximately 16 ATP
and 8 reducing
equivalents per N2
reduced to 2 NH3
Denitrification:
reduction of oxidized
compounds resulting
in production of N2
gas that is released to
the atmosphere
(hence, loss of N from
the ecosystem); a
primarily respiratory
process using nitrate,
nitrite, nitric oxide,
and nitrous oxide as
electron acceptors in
respiration. Anammox
metabolism also
results in production
of N2gas and is by
strict definition a
denitrification
pathway. The
canonical
denitrification pathway
refers to the
respiratory reduction
of organic nitrogen
compounds coupled to
the oxidation of
organic matter for
energy
5. It was assumed at the time of the development of the new and regenerated production
model (Dugdale & Goering 1967) that N2fixation in the open ocean was small. Nitrogen
fixation in the open ocean, subsequent to 1961 (Dugdale et al. 1961, Mague et al. 1974,
Saino & Hattori 1978) was believed to be primarily due to the filamentous nonheterocyst-
forming cyanobacterium Trichodesmium but with additional contributions by heterocyst-
forming filamentous cyanobacterial symbionts of diatoms (Carpenter 1983).
6. Anaerobic processes, the use of oxidized N compounds as an electron sink for respiration or
metabolism, were believed to occur primarily in the sediments but also in the water column
of several restricted regions of the ocean basins where there were low oxygen concentrations,
called oxygen minimum zones (OMZs) (Figure 1). The production and sedimentation of
organic material, coupled with oxidized N compounds from deep water, result in depleted
oxygen concentrations that allow the use of alternate electron acceptors, such as nitrate and
nitrite. These regions may be expanding in the ocean (Stramma et al. 2008), and because
they allow important reductive N transformations to occur, are covered in this review. The
primary reaction in these OMZs was believed to be denitrification, a respiratory process that
uses nitrate as an electron sink for the oxidation of organic matter. This reaction leads to
the loss of N from the system as gaseous N2, ultimately balancing the use of gaseous N2by
N2-fixing organisms.
7. The reductive pathways involving oxidized N compounds were limited primarily to denitri-
fication in sediments and OMZs. Nitrate respiration and dissimilatory reduction of nitrate
to ammonium were known but were believed to occur in a few specific habitats, primarily
sediments, and to have negligible influence on the biogeochemistry of N in the oceans.
8. The use of reduced N compounds as an energy source was limited to several taxa or lin-
eages of the Bacteria (primarily Proteobacteria). These processes, ammonia oxidation and
nitrification, were believed to occur primarily in the deep ocean, fueled by decomposing,
sedimenting organic N materials (resulting in the nitrate-rich deep water described above).
Ammonia oxidation and nitrification also occur in sediments at the interface between oxic
and anoxic zones, fueled by diffusion of ammonium from below and oxygen from above.
9. The key microbial players in the N cycle were known primarily from a few cultured isolates,
and from amplified rRNA genes using polymerase chain reaction (PCR) primers targeting
specific groups of organisms known to be involved in N transformations, such as the nitrifiers
and denitrifiers.
10. It was not known whether the oceanic N budget was in balance, or whether the global oceanic
denitrification rate exceeded the global N2-fixation rate. Therefore, it was also unknown,
despite speculation, whether the oceans were ultimately N- or P-limited as the N budget
was not adequately characterized.
OCEANIC N LIMITATION, ELEMENTAL STOICHIOMETRY,
AND CARBON FLUX
N and Nutrient Limitation
Climate change can be expected to modify the sources, availability, and speciation of major nu-
trient pools in the ocean, making it critically important to know the nutrient(s) most limiting to
both biomass accumulation and the rate of phytoplankton growth. Nutrients can limit growth,
productivity, or ecosystem production (Howarth 1988). Productivity is perhaps the most relevant
to evaluate (Howarth 1988). Geochemists have argued that phosphorus (P) is the primary limiting
nutrient in the oceans over geological timescales (Redfield 1958, Tyrrell 1999). This argument is
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Nitrification:
oxidation of
ammonium to nitrate.
Strictly defined,
nitrification is
composed of two
distinct processes,
ammonia oxidation
and nitrite oxidation,
catalyzed by different
microorganisms.
Originally thought to
occur primarily in the
ocean and sediments
but now recognized as
occurring throughout
the water column,
mediated by both
Bacteria and Archaea
Polymerase chain
reaction (PCR):
laboratory procedure
that uses repetitive
cycles of heating and
cooling to
enzymatically
synthesize a specific
region of DNA, using
DNA polymerase and
oligonucleotides that
prime and target the
reaction to amplify a
specific DNA region
(e.g., a gene or part of
a gene) for subsequent
detection or analysis
largely based on the existence of biological N2fixation, the enzymatic conversion of atmospheric
N2to ammonium by a variety of microorganisms, which can alleviate ecosystem N limitation
(Redfield 1958). The atmosphere is composed of approximately 80% N2gas and is an essen-
tially unlimited source of N for N2-fixing microorganisms. There is no atmospheric source for
P, and P must be obtained from recycling organic matter (in shallow or deep water) or terrestrial
sources (runoff), with P concentrations ultimately dependent on the balance between terrestrial
rock weathering and oceanic burial. Despite the assumption that P ultimately limits ocean ecosys-
tems, marine nutrient addition experiments often result in a growth response when N is added
(Elser et al. 2000, Ryther & Dunstan 1971, Thomas 1970) but an even greater response when
P is added along with N (Elser et al. 2000, Smith 1984). Although Elser et al. (2000) reviewed
the results of over 200 marine experiments, these were largely biased to coastal systems that may
be affected by P inputs (Elser et al. 2000). Thus, it is probably true that N limitation is less well
proved experimentally in marine systems than in freshwater systems (Hecky & Kilham 1988).
The basic assumption of the argument of N versus P limitation has been challenged because N2
fixation can be limited by trace elements (Falkowski 1997). It was previously suggested that other
nutrients should also be limiting in the open ocean based on analysis of marine N:P ratios (Downing
1997). Building on the work of Martin (Martin & Fitzwater 1988), there is now recognition of
the role of iron (Fe) in regulating productivity in wide regions of the oceans (Boyd et al. 2007). Fe
has been shown to stimulate general phytoplankton production in high-nutrient, low-chlorophyll
regions (Boyd et al. 2007) and may have an even stronger role in limiting N2-fixing microorganisms
because of the need for Fe in the nitrogenase metalloproteins (see Kustka et al. 2003). This
importance of Fe for N2-fixing microorganisms is one of the strongest connections between Fe
and the N cycle.
Nutrient regimes, the relative abundance of N, P, and Fe, and their inputs are highly variable
across the ocean basins. The most important Fe inputs are believed to be primarily via aeolian
deposition from terrestrial sources (Fung et al. 2000), because Fe carried by rivers is rapidly
precipitated ( Jickells et al. 2005). In some regions, Fe transported horizontally along the pycn-
ocline from shelf regions may be another, less well characterized source (Lam & Bishop 2008).
There is also some evidence for the role of deepwater iron enrichment in some regions, including
the oligotrophic basins (Boyle et al. 2005), which plays a role in both past and future climate-
change scenarios (Blain et al. 2007 and references therein). Wind patterns and the solubility of
various forms of Fe-rich compounds create gradients of Fe inputs across and between basins
( Jickells et al. 2005, Moore et al. 2006). The patchy distribution of Fe inputs overlays the patchy
distribution of N and P. There is an order of magnitude difference in orthophosphate concentra-
tions between the Atlantic and Pacific oceans (Wu et al. 2000), and P appears to limit N2fixation
in the North Atlantic (Sanudo-Wilhelmy et al. 2001). In contrast, Fe concentrations are low in
the ultraoligotrophic South Pacific gyre, but P concentrations are relatively high (Bonnet et al.
2008). Although it has been suggested that Fe limits phytoplankton in this region (Behrenfeld &
Kolber 1999), additions of Fe did not stimulate N2fixation in this ultraoligotrophic system and
few N2-fixers have been identified in this region (Bonnet et al. 2008).
Whereas Fe enrichment in N-rich areas of the oceans typically demonstrates Fe limitation of
productivity (Boyd et al. 2007), nutrient enrichment experiments in oligotrophic regions clearly
indicate multiple controls on ecosystem production and N2fixation (Arrigo 2005, Elser et al.
2000, Mills et al. 2004). N2-fixing populations can be limited by different nutrients than the non-
N2-fixing populations, resulting in a complex cross-feeding of N, P, and Fe among populations.
Productivity in the tropical Atlantic was shown to respond to N additions, whereas N2fixation
was enhanced by additions of Fe and P, suggesting that N2-fixing microorganisms were colimited
by Fe and P (Mills et al. 2004).
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The focus on nutrient limitation is complicated by the fact that the oceans are not in steady state
(Karl et al. 2001a), and nutrient ratios (N:P) exhibit this imbalance (Pahlow & Riebesell 2000).
Annual, decadal, and longer ocean cycles such as glacial-interglacial changes in source waters and
aeolian deposition affect the relative rates of the N, P, and Fe biogeochemical cycles (Pahlow &
Riebesell 2000). For example, there may have been a microbial community composition shift,
over decadal scales, from eukaryotes to prokaryotes (primarily the unicellular cyanobacterium
Prochlorococcus) at Station ALOHA in the North Pacific driven by a shift from N to P limitation
(Karl et al. 2001a,b). The change in N to P limitation is consistent with the Pacific having higher
orthophosphate concentrations than the Atlantic and is also consistent with concentrations of
soluble reactive phosphorus (SRP) declining for over a decade (Karl et al. 2001b). However, analysis
of Prochlorococcus populations by comparing NH4+and P incorporation into RNA indicates that
current Prochlorococcus populations are limited by N but not P availability (Van Mooy & Devol
2008).
Mesoscale physical processes can result in transient increases in nutrients that have large,
but episodic, effects on the biota. Perhaps the best characterized of these mesoscale features
are the eddy fields associated with much of the open ocean. Whereas cyclonic eddies have long
been associated with enhanced upwelling and episodic enrichment of the biota (cf. Ducklow
et al. 2009), recent results show that physical/biological interactions in anticyclonic eddies can
also have profound impacts on the N cycle. For instance, mode water anticyclonic eddies have
promoted diatom blooms in the subtropical Atlantic (McGillicuddy et al. 2007), whereas collapsing
anticyclonic eddies stimulated both diatoms and enhanced N2fixation within a subtropical Pacific
eddy (Fong et al. 2008). In a more comprehensive study, Church et al. (2009) link positive sea
surface height anomalies (anticyclonic eddies) in the North Pacific subtropical gyre to enhanced
N2fixation, suggesting that similar effects may be occurring in the Atlantic basin. Although the
exact mechanism(s) for the various shifts in community composition and subsequent adjustments
to N biogeochemistry are still being determined, these recent results demonstrate a sensitivity
to subtle changes in physical (stratification, temperature, vertical fluxes) perturbations over the
relatively short temporal and small spatial scales where mesoscale features dominate (Fong et al.
2008, Woodward & Rees 2001).
There are still relatively few studies that have directly identified nutrient limitation in the open
ocean, in part because it is not easy to do. Nutrient addition experiments in bottles, microcosms,
or mesocosms require incubation of natural microbial communities, which is fraught with artifacts
(Dore & Karl 2001). Nutrient limitation of the individual populations in communities is difficult
to ascertain because different species have different stoichiometric requirements for nutrients
(Arrigo 2005, Geider & La Roche 2002), whereas algal assemblages also respond to ecological
conditions, resulting in wide-ranging N:P ratios (Klausmeier et al. 2004). Some phytoplankton
require silica (Si), others can lower their P requirements by replacing P with S in sulfolipids
(Van Mooy et al. 2006, 2009), and many organisms can utilize organic P when orthophosphate is
limiting (Bj¨
orkman & Karl 2003, Moore et al. 2006). In addition to N, P, Si, and Fe, interest has
rekindled in other potentially limiting substrates such as vitamin B12 (Sanudo-Wilhelmy et al.
2006, Taylor & Sullivan 2008) and other trace metals such as zinc and cobalt (Morel 2008, Morel
& Price 2003), further complicating the simple view of a single limiting nutrient in the ocean.
Nutrient addition experiments may perturb the species composition (Arrigo 2005) due to
differing uptake and growth kinetics as well as to differing stoichiometric requirements (Marchetti
et al. 2010) and, thus, may not really describe how the extant populations were limited by nutrients.
Shifts in grazing food chains and the microbial loop (including viruses), which modify the top-down
versus bottom-up controls on productivity or production, may further complicate interpretation
of the response. To avoid some of these complexities, chlorophyll-fluorescence kinetics have been
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used to identify nutrient limitation (Beardall et al. 2001, Behrenfeld & Kolber 1999, Kolber et al.
1994) and have the advantage of being largely noninvasive, circumventing some of the issues
with enrichment experiments. An obvious disadvantage is that fluorescence kinetics only track
the ecophysiological responses of chlorophyll-containing organisms, precluding its use for many
players in the N cycle. Physiological assays, such as examining cellular expression of proteins
or RNA, can be good indicators of the nutrient limitation of specific populations (Dyhrman
et al. 2002, Graziano et al. 1996). There is great potential for further developing biochemical,
biophysical, physiological, or molecular (e.g., RNA or protein) markers to provide information
on the physiological state of microorganisms in seawater without requiring incubation (Table 2).
Such assays exist, although they are in a preliminary state for deployment in routine assays across
ecosystems. The most direct way of assessing habitat or ecosystem limitation is by manipulating
or fertilizing large enclosures or enriching large patches of the ocean, deliberately (Boyd et al.
2007, Karl & Letelier 2008) or unintentionally (Vitousek et al. 1997).
The application of mathematical models to examine how nutrients may limit populations across
ocean biomes is a complementary approach to direct experimentation. Moore et al. (2006) showed
how Fe inputs can result in limitation of different phytoplankton groups in the world’s oceans and
that the biogeochemistry of the oceans is also highly sensitive to indirect effects caused by changes
in N2fixation. These global models have allowed investigators to examine the balance of N2
fixation, denitrification, and the linkages to aeolian Fe flux (Moore & Doney 2007), supporting
the hypothesis that widespread Fe limitation in the modern ocean has decoupled N2fixation
and denitrification, leading to the apparent deficit of N in the modern ocean. In contrast, more
available Fe during the last glacial-interglacial cycle may have led to a P-limited ocean as the
N cycle was better balanced, whereas anthropogenic changes in N:Fe deposition in dust may
lead to the suppression of N2fixation in the near-future ocean, leading once again to a more
P-limited ocean (Krishnamurthy et al. 2010). A fundamental issue with these models is that many
of the physiological processes, and even the organisms (Zehr et al. 2008), are unknown or poorly
described, making it difficult to parameterize the models (Moore & Doney 2007). Development of
better methods for detecting nutrient limitation in individual populations would make it possible
to both test and improve such models (DeLong 2009, Doney et al. 2004).
N limitation is linked to the biogeochemical cycling of other nutrients and trace elements. Nu-
trient limitation in the sea varies between basins, is sensitive to a variety of environmental factors,
and varies as a function of time, from intervals of seasons and years to decades and eons. These
environmental factors are also linked such that minor modifications to the nutrient stoichiome-
try of the oceans coupled with concomitant physical and chemical changes (mixing, temperature,
alkalinity) can cause dramatic shifts in the coupled ocean-atmosphere conditions of our planet
(Peacock et al. 2006). Clearly, different nutrients can be the primary limiting nutrient at different
times (both short and long timescales) and in different places. The question is not whether the
ocean is N limited but how does N limitation interact with the biogeochemical cycles to con-
strain productivity over long timescales, and how will it respond to global climate change over the
ensuing decades?
N Limitation, Elemental Ratios, and Export
Elemental ratios have implications for not only nutrient limitation but carbon flux because
photosynthetic C fixation in surface waters is stoichiometrically related to nutrient consumption,
followed by sedimentation of particulate matter to the deep ocean. Eppley & Peterson (1979)
first proposed the stoichiometric relationship of “new” nitrogen inputs to surface water export
because inputs must equal outputs in the surface mixed layer of the ocean. This proposal, however,
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Table 2 Major oceanic nitrogen cycling pathways and relevant genes
Reaction name Chemical reaction Genes
Nitrogen fixation N2+8H++8e−+16 ATP →2NH3+H2
+16ADP +16 Pi
nifH,nifD,nifK in alternative nitrogenases
(those that use Fe or V in place of Mo in
component I); there is also a nifG gene
(between nifD and nifK)
Ammonium oxidation NH3+O2+2H
++2e−→NH2OH +H2OamoC,amoA, amoB, hao
NH2OH +H2O→HNO2+4H++4e−
0.5O2+2H++2e−→H2O
Nitrite oxidation 2NO2−+H2O→NO3−+2H++2e−norA, norB
2H++2e−+0.5O2→H2O
Heterotrophic nitrification R-NH2 →NO2
R-NH2 →NO3
The genes are not well known but may be
the nitrate reductase genes involved in
heterotrophic denitrification narH,narJ
Anaerobic ammonia oxidation HNO2+4H+→NH2OH +H2O
NH2OH +NH3→N2H4+H2O
N2H4→N2+4H+
>HNO2+NH3→N2+2H2O
>HNO2+H2O+NAD →HNO3+NADH2
Over 200 genes involved in anammox
metabolism (Strous et al. 2006), including 9
hao-like genes, hydrazine hydrolase (hzf ),
and hydrazine dehydrogenase
Dissimilatory nitrate reduction
and denitrification
5[CH2O] +4NO3−+4H+→5CO2+2N2
+7H2O
narDGHIJ;
napA,B,D,E;
5H
2+2NO3−+2H+→N2+6H2OnirB,C,K,U,N,O, S;
NO3→NO2−norB;
NO2−→NO +N2OnosZ
N2O→N2
Assimilatory nitrate and nitrite
reduction
NAD(P)H +H++NO3−+2e−→NO2−
+NAD(P)++H2O
nasA, nasB, nasC, nasD (noncyanobacterial
Bacteria);
6 ferredoxin (red) +8H
++6e
−+NO2−
→NH4++6 ferredoxin (ox) +2H2O
narB (cyanobacteria);
nrtA, nrtB, nrtC, nrtD (or nap) permeases
(cyanobacteria)
Dissimilatory nitrate reduction
to ammonia
NO3−+2H++4H2→NH4++3H2Onir,nar,nap,nrfABCDE
Ammonification/regeneration/
remineralization
R-NH2→NH4+—
Ammonium assimilation NH3+2-oxoglutarate +NADPH +H+
glutamate +NADP+(glutamate
dehyrdrogenase)
gdhA,gdhA,
gltB
NH3+glutamate +ATP →glutamine +ADP
+Pi glutamine +2-oxoglutarate +NADPH
+H+→2 glutamate +NADP+(glutamine
synthetase and NADH-dependent
glutamine:2-oxoglutarate amidotransferase)
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Anammox:
conversion of
equimolar amounts of
ammonia (ammonium
at the pH of seawater)
and nitrite to
dinitrogen gas;
suggested to be a
dominant pathway
within the N cycle in
regions of reduced
oxygen, e.g., sediments
and oxygen minimum
zones
P∗:amount of
phosphorus (μM)
excess relative to N in
ocean water, assuming
P concentrations are in
Redfieldian ratios with
N concentrations.
Regions of elevated P∗
are expected to be
associated with N2
fixation
assumed that the ocean was in steady state over short time intervals, and it is now realized that
episodic phenomena, such as mesoscale features, including eddies, can result in uncoupling of new
production from export (Karl 2002, Karl et al. 2001b).
The downward export (removal from surface waters) of C and N occurs through a number
of mechanisms (detritus, fecal pellets, zooplankton, and sinking phytoplankton; Buesseler et al.
2008). Of particular importance in the N cycle is the rapid sinking of blooms of diatoms contain-
ing N2-fixing cyanobacterial symbionts (Scharek et al. 1999), because it is directly coupled with
new production (N input via N2fixation). These diatom-diazotroph (N2-fixer) associations may
be important in specific areas that select for these organisms (N-limited, Si-rich), such as at the
edge of the Amazon River plume (Subramaniam et al. 2008), and perhaps more generally where
enrichment with Si, Fe, and/or P can support diatom growth. Microorganisms are also involved in
controlling upward fluxes of nutrients between surface and deep water. Diatom mats may transport
nitrate upward from the nitracline (Villareal et al. 1993), whereas buoyant N2-fixing microorgan-
isms have been proposed to mine and transport P into surface waters (Karl et al. 1992, White
et al. 2006). Modeling studies suggest that this mechanism could result in ∼10% of the upward
vertical P flux, depending on development of large Trichodesmium aggregates and carbohydrate
ballasting (Diaz et al. 2008, White et al. 2006). Ultimately, the significance of vertical downward
(or upward) fluxes of microorganisms and organic material is dependent on the elemental com-
position of the transported materials, because the ratio of elements in sinking particulate material
determines the ratios of regenerated nutrients that will be recirculated to the surface water from
below the pycnocline. Sedimenting organic material is remineralized in deep water, and the el-
emental composition of organic matter affects future surface water nutrient availability because
deep waters are advected, upwelled, or diffused to surface waters (Figure 1). For several possible
reasons (Quan & Falkowski 2009), the concentrations of remineralized nutrients with depth are
not exactly correlated, resulting in offsets of remineralized N and P.
Although the measured composition of marine particulate material roughly averages the Red-
field ratio (Arrigo 2005), in recent years the flexibility of the elemental composition of microorgan-
isms has been reevaluated, and observed elemental ratios in biological materials or those estimated
by carbon and nutrient drawdown often exceed Redfield ratios (Sarmiento & Gruber 2006). C:N:P
ratios do not appear to be strictly biochemically constrained (Arrigo 2005, Geider & La Roche
2002, Sarmiento & Gruber 2006). In fact, the N:P requirements of organisms and microorganisms
can vary as a function of the nucleic acid and amino acid composition of organisms, providing
some selective advantage under different N:P supplies (Elser et al. 2000). N2-fixing microorgan-
isms can have high N:P ratios (Mulholland et al. 2004), which has implications for regenerated
nutrients. The elemental ratios of resupply also deviate from the Redfield ratio (Dunne et al. 2005,
Sarmiento & Gruber 2006). The pattern of regenerated inorganic nutrients in subsurface waters
provides a “memory” of the nutrient ratios in surface organic matter that was exported to deep
water. As a result, geochemists have used N:P ratios in subsurface waters to infer past surface
water N-cycling activities. Specifically, the deviations from the expected Redfield ratio have been
used to determine where nitrogen fixation and denitrification occur. By assuming that inorganic
nutrients in the deep ocean should approximate Redfield proportions (106:16:1 C:N:P, molar
ratio), it is possible to identify imbalances from this expected ratio, which must be caused by either
changes in the source (sinking particulate organic material) or sink (metabolic processes mediated
by microbes) terms or by existence of alternative sources for these elements. This approach as-
sumes that positive (N-excess) deviations from the canonical Redfield N:P ratio (termed N∗)are
sites of N2fixation, and negative deviations are sites of N loss through denitrification (including
anammox) (Gruber & Sarmiento 1997, Michaels et al. 1996). A related approach examines use of
the parameter P∗(calculated in a similar fashion to N∗) to identify regions of the ocean where N:P
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6
5
4
3
2
2
P* (μM)
Log Group A or log Group B copy number
1.5
1
0.5
0
1
Figure 2
Rates and locations of nitrogen fixation in the global ocean have been both directly measured and inferred
based on biogeochemical signatures and the presence/absence of N2-fixing organisms. The map shows P∗
(the amount of “extra” P based on Redfieldian proportions relative to N) for the surface ocean, using World
Ocean Atlas 2005 data. Dark blue regions indicate excess P, which should promote nitrogen-fixation activity.
The symbols indicate locations where Group A (circles) and Group B (squares) nitrogen fixers were recently
identified using molecular techniques (Moisander et al. 2010). Dashed lines denote the 20◦C- and
25◦C-surface-temperature isotherms, considered the biogeographic boundary for N2-fixation, particularly
by Trichodesmium. The solid black line denotes the global oxygen minimum zones (OMZs), here defined as
50% oxygen saturation at 100-m depth. Recent authors have hypothesized that the OMZs and N-processes
(consumption and production) in the ocean are closely linked in space and time.
ratios are low and should select for N2fixation (Deutsch et al. 2007) (Figure 2). Although there
are assumptions involved in these methods (Moore & Doney 2007), they nonetheless provide hy-
potheses and estimates of N2fixation over basin scales that are otherwise impossible to determine
with current methods.
Karl & Letelier (2008) hypothesized that pumping water from a specific depth to the surface
(using floating ocean pumps) could be used to adjust N:P ratios to experimentally induce blooms
of non-N2-fixing species, followed by selection for N2-fixing cyanobacteria. This approach fa-
cilitates experiments to test the effect of different N:P ratios, similar to the various mesoscale
Fe-enrichments (Boyd et al. 2007), as water derived from different depths would have different
N:P ratios. Fennel (2008) challenged the potential for stimulation of N2fixation by this enrich-
ment mechanism because of water column destratification due to mixing cold dense water with
surface waters. Since older studies suggested a link between stratification and N2fixation (based
on Trichodesmium abundance and activity), it was hypothesized that the artificial mixing of low N:P
water to the surface would not result in enhanced N2fixation. This was rebutted by Letelier et al.
(2008), who noted that the model presented by Fennel (2008) did not include the effects of solar
heating on the stratification of surface waters, highlighing the complexity of the biogeochemical
processes being invoked. Also, the distributions of recently discovered N2-fixing microorganisms
are not controlled by the same factors as Trichodesmium (Moisander et al. 2010; see below), raising
the issue of whether we can adequately predict how changes in nutrient availability, elemental
ratios, and stratification will interact under different future-climate-change scenarios.
The basic tenets of nutrient cycling in the ocean, starting with Redfield (1958) and extending to
the early 1990s, supported the concept of nitrogen as the proximal limiting nutrient in the modern
ocean, with P most likely to be limiting on millennial timescales. We arguably still do not know
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what is “ultimately limiting” phytoplankton growth in the oceans, but research in the last two
decades demonstrates the need to track much more than just N:P ratios in the ocean, as we now
know that biogeochemical cycling of nutrients in the modern ocean is more complex and spatially
variable than previously thought. The roles of N, P, and trace-elements such as Fe also change
on millennial (glacial-interglacial) scales, whereas the modern age (the so-called Anthropocene)
may alter ocean biogeochemical cycling in ways that are difficult to predict based on our classic
understanding of the N-cycle and the historical record.
THE NITROGEN BUDGET
The relative rates of N inputs and losses determine the long-term N oceanic inventory, which
determines both the total production of the ocean and the proximal limiting nutrients (N, P, Fe,
etc.). Although conceptually simple, the oceanic N budget is difficult to balance because of the
spatial and temporal scales involved, complexity of circulation, inherent assumption of steady-state
dynamics, and chronic undersampling of the fundamental rates and processes associated with the
N cycle (Brandes et al. 2007).
Balancing the oceanic N budget requires assumptions regarding homeostasis over time, that
is, that N2fixation and denitrification have to be balanced over relatively short timescales
(Codispoti 2007). There are three approaches used to address this question: biological data de-
termined experimentally on oceanographic research cruises, biogeochemical analyses based on
measured nutrient ratios over basin scales, and coupled biophysical models incorporating both
(see above). The geochemical analyses are based largely on observed ratios of dissolved nutrients
(N and P), their deviations from expected N:P ratios, and estimates of deepwater flow, necessary
to extrapolate the deep-ocean signature back to the surface-ocean source of the nutrient “finger-
print.” Using these approaches, a big discrepancy between basin scale estimates of N2fixation and
denitrification was inferred (Gruber & Sarmiento 1997, Michaels et al. 1996). These estimates
and the geographic boundaries used to make the calculations can be controversial, adding to the
already large uncertainties in interpreting the nutrient ratios (Hansell et al. 2004, Moore & Doney
2007).
Although it is possible to estimate N2fixation and denitrification rates from experimental
measurements (Capone et al. 2005, Mahaffey et al. 2005, Montoya et al. 2007, Ward 2005),
these estimates are prone to large error and are not necessarily representative of the larger spatial
and temporal patterns. In contrast, geochemical analyses of the relative distributions of dissolved
inorganic nutrients in seawater should integrate the effects of remineralization of N2-fixing and
and non-N2-fixing microorganisms over time and space (Gruber & Sarmiento 1997). Nonetheless,
some experimental data suggest that N2fixation by Trichodesmium may have been underestimated
and that the biological and biogeochemical estimates converge to some degree (Capone et al.
2005). Other discoveries in N2fixation, such as previously unknown N2-fixing cyanobacteria, may
also help to close the gap (Zehr et al. 2001; see below).
One of the findings of the biogeochemical approach based on nutrient remineralization ra-
tios suggests coupling of denitrification zones (OMZs) with N2fixation, because of the effect of
denitrification on the N:P ratio (Deutsch et al. 2007). This coupling could take place in the same
water mass (N2fixation is an anaerobic process and can co-occur with denitrification); if so, rates
associated with both processes would be underestimated (Codispoti 2007) because tropical OMZs
have been expanding vertically over the past 50 years (Stramma et al. 2008). It is also possible that
the effect of the OMZs will be to select for N2fixation in water advected from the OMZ rather
than in the OMZ itself. This hypothesis can be, and is being, tested by examining the biology of
N2fixation and denitrification in these regions, and by examination of the decoupling between
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MA03CH08-Zehr ARI 17 November 2010 6:55
N∗and P∗in the Atlantic basin, where enhanced N2fixation must be supported by efflux of excess
P from distant OMZs (Moore et al. 2009).
The balance of the N budget is still highly controversial (Gruber & Galloway 2008). Over
time the estimates of global ocean denitrification have increased (Codispoti 2007) but so have
those of N2fixation (Capone et al. 2005, Mahaffey et al. 2005). Fundamentally, the N input
(N2fixation) and output (denitrification) terms are poorly constrained. New discoveries in the N
cycle have raised questions about the organisms that catalyze the N2-fixation and denitrification
processes (Kuypers et al. 2005, Ward et al. 2009, Zehr et al. 2001), such as where they occur
and what regulates their activity. These new discoveries may help to explain the global metabolic
distribution of the N cycle. The feedback loops between atmospheric CO2and the N cycle are
complex and not well known (Gruber & Galloway 2008). It is critical to understand the balance of
N2fixation and denitrification, as it may have been key to past Earth atmospheric CO2levels, and
humans have perturbed the N and the C cycles, which will lead to unknown changes (Galloway
et al. 2004).
OPEN OCEAN N NUTRITION: NITROGEN ASSIMILATION
AND N2FIXATION
Most marine phytoplankton can use ammonium, nitrite, and nitrate as N sources for growth
but cannot fix N2. Many phytoplankton can also use some forms of organic N, including urea
(Baker et al. 2009), but less is known about the composition and utilization of marine dissolved
organic matter and the direct utilization of these organic compounds by phytoplankton, partic-
ularly compared with our understanding of nitrate, nitrite, and ammonium utilization. In the
1980s, Prochlorococcus was found to be one of the dominant phytoplankton in the sea (Chisholm
et al. 1988). Subsequent work with cultures showed that strains had different light and nutrient
requirements, with the variants referred to as ecotypes (Moore et al. 1998), and suggested that
some strains could not grow with nitrate as an N source. This discovery suggested that ecological
competition among phytoplankton might be based at least partially on different N sources. Entry
into the genomic era, with full sequences of a number of strains of Prochlorococcus and Synechococcus
(Dufresne et al. 2003, Palenik et al. 2006, Rocap et al. 2003) available, showed that Prochlorococcus
did not contain the assimilatory nitrate reductase genes (Table 2), providing the explanation for
why strains did not grow on nitrate. One of the two strains, a low-light strain (Moore et al. 1998),
did contain the gene for nitrite reductase (Table 2). It was hypothesized that this low-light strain
grew at a depth in the ocean where low light intensities were coupled with higher nitrite availabil-
ity at the top of the nitricline. These findings provided an ecological selection force involving N
substrates; whereas some strains of Prochlorococcus were entirely dependent on ammonium, others
could use nitrite and ammonium, and Synechococcus could use nitrate, nitrite, or ammonium. Some
strains of Prochlorococcus have also retained the nitrate reductase (nar) genes, further complicating
the attempt to define the niches of open ocean phytoplankton at the genus level. A feature of
most open-ocean marine microbes is reduction in genome size (Dufresne et al. 2003, Giovan-
noni et al. 2005), and loss of the nitrate utilization genes apparently coincides with the lack of
their use in high-light ecotypes that rely primarily on regenerated ammonium. Interestingly, at
approximately the same time, it was discovered that not all marine heterotrophic bacteria could
use nitrate, because they also lacked the nitrate reductase gene (Allen et al. 2001, 2005). The
presence or absence of nitrite reductase genes in Prochlorococcus appeared to be correlated with
whether the strains or ecotypes were adapted to high light intensity (presumably shallower) or low
light intensity (deeper; reviewed in Partensky & Garczarek 2010). This suggested a relationship
between genome evolution and selection forces (shallow with high light intensity, low N versus
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Nitrogen
assimilation:
assimilation of
nitrogen into biomass.
Eukaryotic and
prokaryotic
microorganisms can
assimilate simple
inorganic N (nitrate,
nitrite, ammonium,
and urea) into biomass
using enzymes that
reduce oxidized N into
ammonium and,
subsequently, amino
acids
deep water with low light intensity, nitracline) in the subhabitat. Using molecular techniques that
targeted the ribosomal RNA operon that distinguishes these groups of ecotypes, Johnson et al.
(2006) showed that the different strains are widely distributed latitudinally and that there is a
general trend with the depths in which the high- and low-light ecotypes were found. These trends
were supported by results of a novel modeling approach that allowed 78 “species” to compete on
the basis of properties that included P use, growth kinetics, and N-source utilization (Follows et al.
2007). The resulting “species” maps corresponded well with distributions reported by Johnson
et al. (2006). These results suggested differential roles of ecotypes of Prochlorococcus in new and
regenerated production processes.
The Prochlorococcus N-utilization story has been confounded by both field measurements of
nitrogen assimilation in natural assemblages of Prochlorococcus, which show that 5–10% of N is
directly assimilated as nitrate in the Sargasso Sea (Casey et al. 2007), and the more recent discovery
of assimilatory nitrate reductase (nar) genes (Table 2) in metagenomic DNA fragments from
marine microbial communities (Martiny et al. 2009). The presence or absence of the nitrate
reductase genes provides information on the relative roles of these nutrient acquisition systems in
nature. With this knowledge in hand, it has been possible to develop molecular biology methods to
examine microorganisms in natural populations that have the nar or nas genes (Ahlgren & Rocap
2006, Allen et al. 2001, Cai & Jiao 2008, Jenkins et al. 2006, Paerl et al. 2008) (Table 2). These tools
will ultimately provide information on the spatial distribution of nitrate-assimilating populations,
including their gene expression, and will provide information on what controls individual strains
and ecotypes in space and time.
Nitrate is a stable form of N but is generally not available to most phytoplankton, because it is
consumed in surface waters and largely replenished by mixing water from depth or from terrestrial
inputs. Surface-ocean microbial growth is largely supported by regenerated production, that is,
recycling from both cell death and reduced N in the form of NH4+. “New” nitrogen in the form of
nitrate or N2supports a small percentage of production in the oligotrophic ocean but is important
to balance sedimentation losses from the surface ocean. Gaseous N2(hundreds of micromoles
per liter) is one of the most abundant forms of N (e.g., compared with nanomoles per liter of
nitrate or ammonium) in seawater but is biologically available to only N2-fixing microorganisms
(diazotrophs, or nitrogen eaters). N2fixation was believed to be absent or minor at the time of
conceptualization of the new and regenerated N models (Dugdale & Goering 1967). Even after the
discovery of N2-fixation associated with filamentous cyanobacteria (Trichodesmium), N2fixation
was not appreciated as a source of N in the open ocean until biogeochemical analyses indicated
that N2fixation may have been underestimated, based primarily on the comparison of ratios of
regenerated nutrients to those expected from particulate material in Redfield proportions (Gruber
& Sarmiento 1997, Michaels et al. 1996). The interest in N2fixation and balancing the N budget
resulted in new approaches, new data, and some surprising discoveries.
Since N is in short supply in oligotrophic oceans, it should be ecologically advantageous to
fix N2(Table 2) from the essentially unlimited N2reservoir in the atmosphere. Surprisingly few
oceanic microorganisms appear to be capable of N2fixation. Trichodesmium is a filamentous N2-
fixing cyanobacterium that has been studied for decades (Dugdale et al. 1961), largely because it
frequently forms large aggregates that can be seen on the ocean’s surface with the unaided eye. It is a
filamentous organism that can exist in aggregates (colonies) or as individual filaments and is peculiar
because it fixes N2during the day, while it is evolving oxygen through photosynthesis. The enzymes
involved in N2fixation, and therefore N2fixation activity, are sensitive to oxygen inactivation. Since
Trichodesmium can easily be collected and concentrated by plankton nets, studies on N2fixation
focused on Trichodesmium for four decades (1961–1998). A few other N2-fixing cyanobacteria
had been observed anecdotally, including cyanobacterial symbionts of diatoms (Carpenter 1983,
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Group A (or
UCYN-A)
picoplankton:
nitrogen-fixing
(diazotrophic)
picoplankton found in
the open ocean in
waters >20◦Cthat
have been
characterized based on
their genomic and
metabolic signatures
but have not yet been
cultivated in the
laboratory
FISH: type of
molecular biology
approach that uses
fluorescently labeled
oligonucleotides to
target a specific DNA
or RNA sequence.
These fluorescent
probes can be
hybridized to whole
cells to identify cells
withaspecificDNAor
RNA sequence of
interest. A common
application is to
identify specific
microorganisms based
on the presence of a
sequence in ribosomal
RNA (rRNA)
Mague et al. 1974, Villareal 1987, Villareal 1991). A unicellular cyanobacterium, Crocosphaera,
was isolated from tropical waters in the mid-1980s (Waterbury & Rippka 1989), but its presence
elsewhere was unknown.
Based on historical estimates, N2-fixing microorganisms, although key as a source of N to
resupply losses from sinking or denitrification, are present in relatively low abundance. Although
Trichodesmium is easily observed because of its macroscopic aggregate morphology, it was not
clear in the early 1990s whether there were other microorganisms that might be equivalent in
abundance and biogeochemical significance but less easily detected because of being small and
distributed as individual cells rather than in large aggregates easily collected by net tows. Molecular
biology approaches made it possible to answer this question by looking for the genes that encode
the enzymes that catalyze N2fixation, the nif genes (Table 2). By sequencing nif genes collected
from bulk seawater samples, Zehr et al. (1998) found the first evidence for the presence of sev-
eral groups of cyanobacteria (and possibly heterotrophic bacteria) that were widely distributed in
tropical and subtropical waters. Two important discoveries were that (a)Crocosphaera, previously
cultivated from the Atlantic Ocean, was present in the Pacific Ocean in relatively high abundances,
and (b) there was an uncultivated group of cyanobacteria, called Group A (or UCYN-A), that was
generally present in high abundances as well (Figure 2). The discovery of the nif gene associ-
ated with Crocosphaera provided a context for previous flow cytometer–based studies that showed
the episodic presence of these “large” unicellular cyanobacteria (these are nanoplankton, being
3–5 μm in diameter, but are large in comparison to the <1-μm diameter, non-N2-fixing oceanic
cyanobacteria Prochlorococcus and Synechococcus) (Campbell et al. 2005, Neveux et al. 1999). These
unicellular cyanobacteria, discovered from the presence of the nitrogenase genes, would not have
been easily detected as N2-fixing microorganisms by conventional techniques as they are small,
dispersed cells.
Intriguingly, the unicellular N2-fixing cyanobacteria were found to be substantially different
in biology and evolution than their non-N2-fixing, oceanic microbial counterparts. Comparison
of sequences of genomic fragments collected in metagenomic studies were found to be essentially
identical to the sequence of Crocosphaera sp. WH8501 isolated from the Atlantic Ocean over
20 years before (Zehr et al. 2007). This high similarity of genomic sequences within a marine
planktonic cyanobacterial genus is very different from the diversity of gene sequences and genomes
of sympatric non-N2-fixing microorganisms (e.g., Prochlorococcus and Pelagibacter ubique)inthe
oceans (Giovannoni & Stingl 2005, Rusch et al. 2007). The Group A unicellular cyanobacteria
(UCYN-A), because of the nif gene sequence similarity to Crocosphaera and related cyanobacterial
groups, was expected to be similar to these organisms in biology and physiology as well. However,
using flow cytometry, Goebel et al. (2008) found it was smaller, on the order of the size of
the non-N2-fixing cyanobacteria (ca. 1 μm). Fluorescence in situ hybridization (FISH) studies
using a 16S rRNA, fluorescently labeled probe targeted to the 16S rRNA of the unicellular N2-
fixing cyanobacteria has also shown that there are submicrometer-diameter, cyanobacteria-like
cells in the South Pacific and the Mediterranean Sea (Biegala & Raimbault 2008, Le Moal &
Biegala 2009). Ultimately, genomic sequences obtained from flow cytometric–sorting and high-
throughput sequencing (Tripp et al. 2010, Zehr et al. 2008) showed that Group A was a highly
unusual organism that lacked metabolic pathways typical for cyanobacteria and phototrophs in
general, including the tricarboxylic acid cycle. Based on the lack of such key metabolic pathways,
Group A would appear to be a likely symbiont, but at present no host has been identified (Tripp
et al. 2010).
The molecular approach also made it possible to identify and characterize cyanobacterial sym-
bionts and their hosts (Carpenter & Janson 2000, Foster & Zehr 2006). Symbioses, particularly
between N2-fixing cyanobacteria and eukaryotic, single-celled algae, appear to be an important
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but not well understood component of the oceanic N2-fixing community (Foster & O’Mullan
2008). Heterocystous cyanobacteria associate with the external surfaces of some diatoms, and
between the diatom cell wall (frustule) and cell membrane (plasmalemma) ( Janson et al. 1995,
Villareal 1992). Some unicellular cyanobacteria also appear to be symbionts of centric diatoms
(Carpenter 2002, Villareal 1992). These symbioses present a number of interesting evolution-
ary and ecological questions; for example, it is not known whether there are free-living stages in
the symbioses, or how the symbioses are transferred. This intriguing topic is beyond the scope
of this review but will likely emerge as another key aspect of the oceanic N cycle that we are
just beginning to grasp (Carpenter & Foster 2002, Foster & O’Mullan 2008, Giovannoni et al.
2007).
Another large unknown regarding the metabolic balance of the global N cycle is the po-
tential role of heterotrophic bacteria in oceanic N2fixation. nif genes and nif gene transcripts
from presumably heterotrophic bacterial populations have been reported in a number of studies
(Church et al. 2005a; Falc´
on et al. 2004; Moisander et al. 2008; Zehr et al. 1998, 2001). There
are technical difficulties in confirming bacterial nif sequences from dilute natural samples because
diverse nitrogenase sequences have been reported from most laboratory quantitative polymerase
chain reaction (Q-PCR) and reverse-transcription polymerase chain reaction (RT-PCR) reagents
(Zehr et al. 2003). Some bacterial nif gene expression has been confirmed by quantitative reverse-
transcription polymerase chain reaction (QRT-PCR), but abundances are low. Nitrogen fixation
genes are present in many aquatic habitats (Bostrom et al. 2007, Zehr et al. 2001), even when
N2fixation is not detectable ( Jenkins et al. 2004, Moisander et al. 2006, Steward et al. 2004).
The abundances of these bacteria are low relative to the non-N2-fixing populations, and it seems
unlikely that, at typical in situ growth rates of oligotrophic ocean bacteria, the N fixed could be
important from a budget standpoint. This is a difficult research question to address but could be
important in specific habitats such as the deep sea (Dekas et al. 2009, Mehta & Baross 2006) and
OMZs.
From the oceanic N cycle perspective, the most important aspect is the relative abundance and
activity of different N2-fixing microorganisms. With different sizes and morphologies and different
lifestyles (free-living versus symbiotic), the N fixed by different taxa can have very different fates
in the surface water, with differing implications for C and N export. Determining the relative
contributions presents technical hurdles as many of these organisms are small and the populations
dilute, and even low N2-fixation rates (near the limit of detection) are significant relative to in
situ N turnover in oligotrophic oceans, particularly when integrated over the vast expanse of open
ocean. Trichodesmium abundances have been quantified using a variety of techniques, including
microscopy and video plankton recorders (Davis & McGillicuddy 2006, Taboada et al. 2010,
Tyrrell et al. 2003). Nitrogenase (nif ) gene sequences provide a means to quantify the relative
abundance and even gene expression of different groups of N2-fixing microorganisms in the
sea (Church et al. 2005a,b; Langlois et al. 2008; Rees et al. 2009). However, the variability in
space and time and the scales of ocean basins present significant hurdles for determining the
relative contribution to the nitrogen cycle of N2-fixing microorganisms. It is well known that
Trichodesmium distribution is highly variable, but they form blooms that can be detected by remote
sensing (Dupouy et al. 1988, Subramaniam et al. 2002, Westberry & Siegel 2006). However, the
less easily detected unicellular cyanobacteria also form “blooms” that can occur in both the surface
and subsurface (Hewson et al. 2009). Diatom symbioses are also highly dynamic (Fong et al. 2008,
Foster et al. 2007). Although molecular methods provide a means of comparing the abundances of
different organisms, limitations in sampling over the large time and space scales is problematic in
that the populations are very dynamic (Church et al. 2009, Fong et al. 2008). Church et al. (2009),
for example, show that the N2-fixing populations are highly variable over seasonal cycles but that
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the Group A cyanobacteria can be the most abundant N2-fixer over much of the year at Station
ALOHA in the North Pacific.
Trichodesmium is assumed to be the dominant N2-fixing microorganism, and biogeography
studies suggest this may be the case (Capone et al. 2005, Goebel et al. 2010,Mahaffey et al. 2005).
However, information on the other, less easily observed microorganisms is scant in comparison.
Group A cyanobacteria are found over a larger geographic range and in cooler waters than is
Trichodesmium (Langlois et al. 2008, Moisander et al. 2010, Needoba et al. 2007, Rees et al.
2009). Because of the difficulties in sampling adequately, mathematical modeling has proved useful
for determining the relative importance of the known N2-fixing organisms (Goebel et al. 2007,
Monteiro & Follows 2009). Most models that include N2fixation have focused on Trichodesmium,
for which there is the most data, but recent development of modeling approaches have helped to
investigate the factors that control the global distribution of other groups (Monteiro & Follows
2009) and to determine their relative contribution to N2fixation (Goebel et al. 2007, 2010). So far,
modeling suggests that the small Group A cyanobacteria may be less important than Trichodesmium,
except in specific locations and at certain times, but there are large uncertainties. Determining the
factors that control the temporal and spatial distributions of different N2-fixing microorganisms
continues to be an exciting but challenging problem that is central to understanding the oceanic
N cycle.
AEROBIC OXIDATION OF REDUCED NITROGEN
The oxidation of ammonium results in formation of nitrite and nitrate. The significance of this
process is that it converts ammonium into a less biologically preferable form, as nitrite and nitrate
are more energetically expensive N forms to use (Table 2). It is a central pathway in the oceans in
that particulate nitrogen (PN) that is remineralized to ammonium in the deep ocean is oxidized to
nitrate through the nitrification pathway (Ward 2000). This nitrate slowly mixes into the surface
water or is upwelled, primarily at ocean boundaries and equatorial regions. Oxidation of reduced
N compounds is performed by mainly chemolithotrophic microorganisms who glean energy and
electrons from the oxidation (Tables 1,2). Prior to 2004, this reaction was believed to be catalyzed
by mainly Proteobacteria.
Early studies of nitrification in the oceanic water columns used stable isotopes and immuno-
chemistry to measure rates of transformations and enumerate nitrifying bacteria (Ward & Carlucci
1985). Nitrification in surface waters was generally found deeper in the water column but some-
times within the euphotic zone (Ward 2005, Ward et al. 1989). Nitrate formed by oxidation within
the euphotic zone and recycled to phytoplankton confuses the concept of new and regenerated
production (Clark et al. 2008, Dore & Karl 1996, Wankel et al. 2007, Ward et al. 1989). The use
of molecular techniques in marine microbiology made it possible to detect specific microorgan-
isms responsible for oceanic ammonia oxidation, such as Nitrosomonas and Nitrosospira and others
in the beta-Proteobacteria group (Ward 1996) that were found to be widespread (Ward et al.
2007), even in polar oceans (Hollibaugh et al. 2002). The concept of proteobacterial nitrification
as the dominant nitrogen oxidation changed upon the discovery of putative crenarchaeal ammonia
monooxygenase (amo) genes during a metagenomic survey of ocean waters (Venter et al. 2004) and
elsewhere (reviewed in Junier et al. 2010). In the early 1990s, it was discovered that the Crenar-
chaea clade of the Archaea were abundant in the oceans (DeLong 1992, Fuhrman et al. 1992), but
they had not been cultivated and little was known regarding their ecological function. Sequences
of amo genes were linked to archaeal genomic DNA in DNA fragments cloned from the Sargasso
Sea (Venter et al. 2004) and from soil (Treusch et al. 2005). In parallel with the metagenomic dis-
covery, an ammonia-oxidizing crenarchaeote that had amoA genes was cultivated from a saltwater
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AOA: ammonia
oxidizing Archaea; a
group of organisms
that derives energy
from the oxidation of
ammonia to nitrite,
using the gene amoA;
see also AOB
AOB: ammonia
oxidizing Bacteria; a
group of organisms
that derives energy
from the oxidation of
ammonia to nitrite,
using the gene amoA;
see also AOA
Anaerobic ammonia
oxidation: oxidation
of ammonia to N2gas
from coupled nitrite
reduction and
ammonia oxidation.
The reaction is
catalyzed by specific
lineages of bacteria
(Kuenenia and
Scalindula)ofthe
Planctomycetes and is
an anaerobic process
that occurs in anoxic
or suboxic conditions
aquarium (K¨
onneke et al. 2005) (Table 2). Using the polymerase chain reaction (PCR), Francis
et al. (2005) showed that these genes were very common in a number of marine environments.
It became clear that archaeal nitrification (by ammonia oxidizing Archaea, or AOA) was likely to
be an important pathway for ammonia oxidation in the open oceans because Archaea were much
more abundant than the ammonia-oxidizing Bacteria (AOB; Mincer et al. 2007, Wuchter et al.
2006). Because these Crenarchaea are ammonia oxidizers, nitrite formed must still be oxidized by
the bacterial nitrite oxidizers (e.g., Nitrospina). A correlation between the abundance of Crenar-
chaeal amo (including a new novel group not previously believed to be abundant in the marine
environment) and in-depth profiles of Nitrospina in the North Pacific Ocean suggested that these
organisms together result in nitrification in subeuphotic mesopelagic waters (Mincer et al. 2007).
Santoro et al. (2010) found a similar correlation between AOA and Nitrospina in the central Cal-
ifornia Current (surface to 500 m), where active nitrification was occurring, further suggesting
metabolic coupling between these two N-cycling groups. Intriguingly, Church et al. (2010) found
that the archaeal amoA transcript abundance per gene copy (interpreted as transcription per cell)
was highest in surface waters, suggesting that ammonia oxidation catalyzed by Crenarchaea may
occur in even well-lit surface waters. While Crenarchaeota are also abundant in the deep ocean,
recent evidence suggests that amoA is not being utilized at depth and that these organisms are
living heterotrophically, in contrast to the surface populations (Agogue et al. 2008). Examination
of nitrification rates in the Gulf of California using the stable isotope 15N in relation to the AOB
abundance argued strongly for the role of Crenarchaea in marine ammonia oxidation (Beman et al.
2008), whereas AOB were found to be relatively important in the San Francisco Bay (Mosier &
Francis 2008) and to vary in both abundance and community composition along a salinity gradient
in a New England estuary (Bernhard et al. 2007).
Since the AOA essentially catalyze the same reaction (ammonia to nitrite), and in the same
habitats in the oceans as the previously known AOB, it is unclear how this phylogenetic shift
in paradigm changes our view of how the ocean N cycle functions (Ward et al. 2007). Major
unknowns are how metabolic differences between AOA and AOB may have implications for the
energetics of the N transformation. For example, it has recently been demonstrated that the
cultivated ammonia-oxidizing crenarchaeote Nitrosopumilus maritimus SCM1 has an NH3/NH4+
affinity more than 200 times greater than that of AOB (Martens-Habbena et al. 2009). How the
nitrite formed from the AOA is oxidized, whether by previously known nitrifiers or yet another
group of microorganisms, is yet to be resolved (Ward et al. 2007).
ANAEROBIC OXIDATION OF AMMONIA AND DENITRIFICATION
Oxidized N compounds, nitrate, and nitrite are good electron acceptors for biological reactions,
as they are very close to O2in oxidation-reduction potential, and oxidation reactions coupled to
the NO3−or NO2−reduction half-reactions result in generation of almost as much free energy
as aerobic respiration. Aside from the newly described anammox pathway (see below), reduction
products include nitrite (dissimilatory nitrate reduction), N2(denitrification, including N2Oas
an end product), or ammonia (dissimilatory nitrate reduction to ammonia, or DNRA; Gardner
et al. 2006) (Table 1). Denitrification occurs where nitrate is present but there are reduced
oxygen concentrations. This occurs in specific habitats, such as the oxic-anoxic interface of benthic
sediments, and in the water column at the edge of suboxic or anoxic water masses in OMZs (Naqvi
et al. 2008).
In the mid-1990s, a new pathway of ammonia oxidation was discovered in wastewater treat-
ment plants ( Jetten et al. 2009, Mulder et al. 1995, van de Graaf et al. 1997) that was then
found to occur in marine sediments (Rich et al. 2008, Thamdrup & Dalsgaard 2002) and OMZs
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(Hamersley et al. 2009, Kuypers et al. 2005, Lam et al. 2009). This process, called anaerobic
ammonia oxidation (Table 2), is performed by a few specific lineages of bacteria (including the
Candidatus genera Kuenenia,Scalindua, Brocadia, Jettenia, and Anammoxoglobus in the Plancto-
mycetes) with very specific substrate and environmental requirements. Several genera of bacteria
were enriched, described, and used as targets for fluorescence in situ hybridization probes, en-
abling enumeration in the marine environment (Kuypers et al. 2003, 2006; Schmid et al. 2005).
ThegenomeofKuenenia was subsequently sequenced (Strous et al. 2006).
Anammox bacteria obtain energy and electrons from ammonia oxidation but liberate N2as
an oxidation product, rather than nitrite as in canonical nitrification (Table 2). Thus, this seem-
ingly peculiar metabolism is by definition a denitrification pathway in that it results in loss of N
from the system but does not occur through the same intermediates as canonical denitrification.
Because both canonical denitrification and anammox have N2as an end product, the two pro-
cesses have to be differentiated by tracing the N from nitrite, nitrate, or ammonium using the
stable isotope 15N. Ammonium and nitrite are not usually found together (in high concentrations)
in aquatic habitats, and thus sources of flux of these compounds have to be inferred to support
measured anammox activity. In one study, dissimilatory nitrate reduction to ammonium was sug-
gested as the source of ammonium for anammox (Lam et al. 2009). It is possible that previously
ignored pathways such as DNRA could help explain the anammox paradox (Lam et al. 2009, Zehr
2009).
Denitrification (Table 2) was believed to be the major N pathway in OMZs until the discovery
of the anammox pathway. The anammox reaction has now been suggested as the most significant
pathway in an increasing number of suboxic environments, including OMZs (Kuypers et al. 2003,
2005; Thamdrup & Dalsgaard 2002). Habitats where these reductive processes occur (OMZs,
benthic sediment environments, and even hydrothermal vents; Byrne et al. 2009, Galan et al.
2009) exist because of the input of a large amount of organic matter, which in turn leads to O2
utilization. Organic matter is also the source of ammonium for anammox. The oxidation of organic
matter is stoichiometrically linked to the consumption of O2and the release of ammonium from
organic matter. Denitrifying organisms can be responsible in part for suboxic conditions as many
are facultative aerobic respirers. Denitrification requires an input of electron acceptors (oxidized
N) from advection (presumably deep, nitrate-rich water) in suboxic waters. Similarly, anammox
requires both reduced and oxidized N, requiring advection of electron donors or acceptors into
suboxic waters. Recent studies suggest that anammox and canonical denitrification can dominate
at different times and places (Ward et al. 2009). The issue of which process is the dominant
pathway and why there are conflicting results remains to be resolved. It is possible that the two
processes are linked and that denitrification can provide substrates (nitrite and ammonium) for
anammox. The suboxic or anaerobic pathways are difficult to disentagle, particularly given the
need to also account for physical advection of the substrates and by-products, and yet they are
critical to understanding the global ocean N budget.
CONCLUDING REMARKS
The magnitude of the oceans continues to be one of the greatest challenges facing oceanog-
raphers. Its spatial and temporal scales exceed our ability to sample statistically to adequately
represent oceanic processes, even with the development of new methods such as genomics. Ironi-
cally, processes at the opposite end of the scale spectrum, such as cubic micrometers surrounding
microbial cells compared with cubic kilometers of the ocean ecosystems, present equally challeng-
ing problems with uncertainties of equivalent magnitude affecting the global N cycle. Although
much is known about the players, rates, and controlling mechanisms, the wealth of new organisms
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discovered in the last decade demonstrates that understanding and predicting the global N cycle
remains a formidable but exciting, and indeed “deliciously complex,” task.
The N cycle is unique within our planet’s biogeochemical cycles because only microbes and
human activities can control the amount of biologically available N in the biosphere through N2
fixation; humans chemically synthesize N for fertilizer and modify the environments where mi-
crobial activities occur, impacting the rates and locations of denitrification and nitrogen fixation
and the exchange of N among biomes and habitats. Thus, in future-climate scenarios, the effects
of ocean circulation, trace element availability, and P availability may all have independent an-
thropogenic and natural feedbacks on the relative rates of the components of the oceanic N cycle,
in particular N2fixation and denitrification.
SUMMARY POINTS
1. Nutrient limitation is a dynamic property, controlling individual species and community
composition as well as ecosystem productivity and the balance of recycling versus export
of that productivity. P and Fe limitation in particular interact with N limitation to control
total productivity, and the relative availability of P and Fe are in turn controlled by
terrestrial processes and aeolian transport operating at temporal scales ranging from
nearly instantaneous to millennia.
2. The distinction between new and regenerated production has become blurred as we dis-
cover new organisms and new places (e.g., the surface ocean) where N cycling is occurring.
We now know that marine organisms have adapted to utilize virtually every type of N
compound in the oceans, whereas some organisms (e.g., some strains of Prochlorococcus)
have eliminated some metabolic pathways, such as assimilative nitrate reduction.
3. Estimates of nitrogen fixation have changed dramatically in the last few decades because
of both better detection tools for known organisms such as Trichodesmium and the newly
recognized existence and potential importance of new groups of diazotrophs. Whereas
there are many questions about how abundant and active these organisms are, there is no
question that N2fixation is widespread, and of profound biogeochemical significance, in
the oceans.
4. There has been a resurgent interest in OMZs with the discovery of processes such as
anammox. Furthermore, the potential for suboxic or microaerophilic conditions to occur
in microhabitats is not well known and is also likely to become a focus of research
on anaerobic oceanic processes. The relative roles of anaerobic processes are not well
understood and are currently the subject of controversy.
5. The diversity of organisms performing ammonia oxidation and nitrification is now known
to span both the Bacterial and Archaeal domains of life. In contrast to the perception
that this occurs primarily in the deep ocean, we now know that nitrification occurs at
all depths in the ocean, potentially at rates significantly faster (days rather than months)
than previously thought.
6. The conceptual N cycle is in a state of flux, with new organisms and processes having
recently been discovered and their global implications poorly understood. New informa-
tion regarding the who, when, and where of processes such as nitrification, anammox, and
nitrogen fixation are at the center of new discoveries and controversies with wide-ranging
global implications.
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7. Although there are hypotheses about the global N balance, and how the N cycle may
be affected by global climate change, the unconstrained uncertainties suggest that we
still cannot balance the global N cycle, we probably cannot properly parameterize all
of the various rates and processes (many of which are just now being characterized or
inferred from a handful of direct observations), and we therefore can predict only the
most obvious responses to past or future climate change, be it natural or anthropogenic.
DISCLOSURE STATEMENT
The authors are not aware of any affiliations, memberships, funding, or financial holdings that
might be perceived as affecting the objectivity of this review.
ACKNOWLEDGMENTS
We would like to thank Chris Francis, Pia Moisander, and Rachel Foster for comments on the
manuscript. It was also substantially improved based on the critical comments provided by David
Karl. We also thank Mary Margaret Perez for her help in manuscript preparation. Work was
supported by the Gordon and Betty Moore Foundation (GBMF; J.P.Z.) and the University of
California, Santa Cruz, MEGAMER facility (supported by the GBMF), the National Science
Foundation (NSF) Center for Microbial Oceanography Research and Education ( J.P.Z.), and the
NSF (OCE-726858 and OCE-0238347; R.M.K.).
LITERATURE CITED
Agogue H, Brink M, Dinasquet J, Herndl GJ. 2008. Major gradients in putatively nitrifying and non-nitrifying
Archaea in the deep North Atlantic. Nature 456:788–91
Ahlgren N, Rocap G. 2006. Culture isolation and culture-independent clone libraries reveal new marine
Synechococcus ecotypes with distinctive light and N physiologies. Appl. Environ. Microbiol. 72:7193–204
Allen AE, Booth MG, Frischer ME, Verity PG, Zehr JP, Zani S. 2001. Diversity and detection of nitrate
assimilation genes in marine bacteria. Appl. Environ. Microbiol. 67:5343–48
Allen AE, Booth MG, Verity PG, Frischer ME. 2005. Influence of nitrate availability on the distribution and
abundance of heterotrophic bacterial nitrate assimilation genes in the Barents Sea during summer. Aquat.
Microb. Ecol. 39:247–55
Arrigo KR. 2005. Marine microorganisms and global nutrient cycles. Nature 437:349–55
Baker KM, Gobler CJ, Collier JL. 2009. Urease gene sequences from algae and heterotrophic bacteria in
axenic and nonaxenic phytoplankton cultures. J. Phycol. 45:625–34
Beardall J, Young E, Roberts S. 2001. Approaches for determining phytoplankton nutrient limitation. Aquat.
Sci. 63:44–69
Behrenfeld MJ, Kolber ZS. 1999. Widespread iron limitation of phytoplankton in the South Pacific Ocean.
Science 283:840–43
Beman JM, Popp BN, Francis CA. 2008. Molecular and biogeochemical evidence for ammonia oxidation by
marine Crenarchaeota in the Gulf of California. ISME J. 2:429–41
Bernhard AE, Tucker J, Giblin AE, Stahl DA. 2007. Functionally distinct communities of ammonia-oxidizing
bacteria along an estuarine salinity gradient. Environ. Microbiol. 9:1439–47
Biegala IC, Raimbault P. 2008. High abundance of diazotrophic picocyanobacteria (<3μm) in a Southwest
Pacific coral lagoon. Aquat. Microb. Ecol. 51:45–53
Bj¨
orkman KM, Karl DM. 2003. Bioavailability of dissolved organic phosphorus in the euphotic zone at station
ALOHA, North Pacific Subtropical Gyre. Limnol. Oceanogr. 48:1049–57
www.annualreviews.org •Ocean Nitrogen Cycle 217
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Blain S, Queguiner B, Armand L, Belviso S, Bombled B, et al. 2007. Effect of natural iron fertilization on
carbon sequestration in the Southern Ocean. Nature 446:1070–74
Bonnet S, Guieu C, Bruyant F, Pr´
aˇ
sil O, Van Wambeke F, et al. 2008. Nutrient limitation of primary pro-
ductivity in the Southeast Pacific (BIOSOPE cruise). Biogeosciences 5:215–25
Bostrom KH, Riemann L, Kuhl M, Hagstrom A. 2007. Isolation and gene quantification of heterotrophic
N2-fixing bacterioplankton in the Baltic Sea. Environ. Microbiol. 9:152–64
Boyd PW, Jickells TD, Law CS, Blain S, Boyle E, et al. 2007. Mesoscale iron enrichment experiments 1993–
2005: synthesis and future directions. Science 315:612–17
Boyle EA, Bergquist BA, Kayser RA, Mahowald N. 2005. Iron, manganese, and lead in Hawaii Ocean Time-
series station ALOHA: temporal variability and an intermediate water hydrothermal plume. Geochim.
Cosmochim. Acta 69:933–52
Brandes JA, Devol AH, Deutsch C. 2007. New developments in the marine nitrogen cycle. Chem. Rev. 107:577–
89
Buesseler KO, Trull TW, Steinber DK, Silver MW, Siegel DA, et al. 2008. VERTIGO (VERtical Transport
in the Global Ocean): a study of particle sources and flux attenuation in the North Pacific. Deep-Sea Res.
II 55:1522–39
Byrne N, Strous M, Crepeau V, Kartal B, Birrien JL, et al. 2009. Presence and activity of anaerobic ammonium-
oxidizing bacteria at deep-sea hydrothermal vents. ISME J. 3:117–23
Cai HY, Jiao NZ. 2008. Diversity and abundance of nitrate assimilation genes in the northern South China
Sea. Microb. Ecol. 56:751–64
Campbell L, Carpenter EJ, Montoya JP, Kustka AB, Capone DG. 2005. Picoplankton community structure
within and outside a Trichodesmium bloom in the southwestern Pacific Ocean. Vie Milieu 55:185–95
Capone DG, Bronk D, Mulholland M, Carpenter EJ. 2008. Nitrogen in the Marine Environment. San Diego:
Academic. 1,757 pp.
Capone DG, Burns JA, Montoya JP, Subramaniam A, Mahaffey C, et al. 2005. Nitrogen fixation by Tri-
chodesmium spp.: an important source of new nitrogen to the tropical and subtropical North Atlantic
Ocean. Glob. Biogeochem. Cycles 19:GB2024
Carpenter EJ. 1983. Nitrogen fixation by marine Oscillatoria (Trichodesmium) in the world’s oceans. In Nitrogen
in the Marine Environment, ed. EJ Carpenter, DG Capone, pp. 65–103. New York: Academic
Carpenter EJ. 2002. Marine cyanobacterial symbioses. Biol. Environ. 102B: 15–18
Carpenter EJ, Foster RA. 2002. Marine cyanobacterial symbioses. In Cyanobacteria in Symbiosis, ed. AN Rai,
B Bergman, U Rasmussen, pp. 11–17. Amsterdam: Kluwer
Carpenter EJ, Janson S. 2000. Intracellular cyanobacterial symbionts in the marine diatom Climacodium frauen-
feldianum (BACILLARIOPHYCEAE). J. Phycol. 36:540–44
Casey JR, Lomas MW, Mandecki J, Walker DE. 2007. Prochlorococcus contributes to new production in the
Sargasso Sea deep chlorophyll maximum. Geophys. Res. Lett. 34:L10604
Chisholm SW, Olson RJ, Zettler ER, Goericke R, Waterbury JB, Welschmeyer NA. 1988. A novel free-living
prochlorophyte abundant in the oceanic euphotic zone. Nature 334:340–43
Church MJ, Jenkins BD, Karl DM, Zehr JP. 2005a. Vertical distributions of nitrogen-fixing phylotypes at Stn
ALOHA in the oligotrophic North Pacific Ocean. Aquat. Microb. Ecol. 38:3–14
Church MJ, Mahaffey C, Letelier RM, Lukas R, Zehr JP, Karl DM. 2009. Physical forcing of nitrogen
fixation and diazotroph community structure in the North Pacific subtropical gyre. Glob. Biogeochem.
Cycles 23:GB2020
Church MJ, Short CM, Jenkins BD, Karl DM, Zehr JP. 2005b. Temporal patterns of nitrogenase gene (nifH)
expression in the oligotrophic North Pacific Ocean. Appl. Environ. Microbiol. 71:5362–70
Church MJ, Wai B, Karl DM, DeLong EF. 2010. Abundances of crenarchaeal amoA genes and transcripts in
the Pacific Ocean. Environ. Microbiol. 12:679–88
Clark DR, Rees AP, Joint I. 2008. Ammonium regeneration and nitrification rates in the oligotrophic Atlantic
Ocean: implications for new production estimates. Limnol. Oceanogr. 53:52–62
Codispoti LA. 2007. An oceanic fixed nitrogen sink exceeding 400 Tg N a−1vs the concept of homeostasis in
the fixed-nitrogen inventory. Biogeosciences 4:233–53
Davis CS, McGillicuddy DJ Jr. 2006. Transatlantic abundance of the N2-fixing colonial cyanobacterium
Trichodesmium.Science 312:1517–20
218 Zehr ·Kudela
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Dekas AE, Poretsky RS, Orphan VJ. 2009. Deep-sea Archaea fix and share nitrogen in methane-consuming
microbial consortia. Science 326:422–26
DeLong EF. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89:5685–89
DeLong EF. 2009. The microbial ocean from genomes to biomes. Nature 459:200–6
Deutsch C, Sarmiento JL, Sigman DM, Gruber N, Dunne JP. 2007. Spatial coupling of nitrogen inputs and
losses in the ocean. Nature 445:163–67
Diaz J, Ingall E, Benitez-Nelson C, Paterson D, de Jonge MD, et al. 2008. Marine polyphosphate: a key player
in geologic phosphorus sequestration. Science 320:652–55
Doney SC, Abbott MR, Cullen JJ, Karl DM, Rothstein L. 2004. From genes to ecosystems: the ocean’s new
frontier. Front. Ecol. Environ. 2:457–66
Dore J, Karl D. 1996. Nitrification in the euphotic zone as a source for nitrite, nitrate, and nitrous oxide at
Station ALOHA. Limnol. Oceanogr. 41:1619–28
Dore JE, Karl DM. 2001. Microbial ecology at sea: sampling, subsampling and incubation considerations. In
Methods in Microbiology: Marine Microbiology, ed. JH Paul, pp. 13–42. London: Academic
Downing JA. 1997. Marine nitrogen: phosphorus stoichiometry and the global N:P cycle. Biogeochemistry
37:237–52
Ducklow HW, Doney SC, Steinberg DK. 2009. Contributions of Long-Term Research and Time-Series
Observations to Marine Ecology and Biogeochemistry. Annu. Rev. Mar. Sci. 1:279–302
Dufresne A, Salanoubat M, Partensky F, Artiguenave F, Axmann IM, et al. 2003. Genome sequence of the
cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc. Natl.
Acad. Sci. USA 100:10020–25
Dugdale RC, Goering JJ. 1967. Uptake of new and regenerated forms of nitrogen in primary productivity.
Limnol. Oceanogr. 12:196–206
Dugdale RC, Menzel DW, Ryther JH. 1961. Nitrogen fixation in the Sargasso Sea. Deep-Sea Res. 7:297–300
Dunne JP, Armstrong RA, Gnanadesikan A, Sarmiento JL. 2005. Empirical and mechanistic models for the
particle export ratio. Glob. Biogeochem. Cycles 19:GB4026
Dupouy C, Petit M, Dandonneau Y. 1988. Satellite detected cyanobacteria bloom in the southwestern tropical
Pacific implication for oceanic Nitrogen-fixation. Int. J. Remote Sens. 9:389–96
Dyhrman ST, Webb EA, Anderson DM, Moffett JW, Waterbury JB. 2002. Cell-specific detection of phos-
phorus stress in Trichodesmium from the western North Atlantic. Limnol. Oceanogr. 47:1832–36
Elser JJ, Sterner RW, Gorokhova E, Fagan WF, Markow TA, et al. 2000. Biological stoichiometry from genes
to ecosystems. Ecol. Lett. 3:540–50
Eppley RW, Peterson BJ. 1979. Particulate organic matter flux and planktonic new production in the deep
ocean. Nature 282:677–80
Falc´
on LI, Carpenter EJ, Cipriano F, Bergman B, Capone DG. 2004. N2fixation by unicellular bacteri-
oplankton from the Atlantic and Pacific Oceans: phylogeny and in situ rates. Appl. Environ. Microbiol.
70:765–70
Falkowski PG. 1997. Evolution of the nitrogen cycle and its influence on the biological sequestration of CO2
in the ocean. Nature 387:272–75
Fennel K. 2008. Widespread implementation of controlled upwelling in the North Pacific Subtropical Gyre
would counteract diazotrophic N2fixation. Mar. Ecol. Prog. Ser. 371:301–3
Follows MJ, Dutkiewicz S, Grant S, Chisholm SW. 2007. Emergent biogeography of microbial communities
in a model ocean. Science 315:1843–46
Fong AA, Karl D, Lukas R, Letelier RM, Zehr JP, Church MJ. 2008. Nitrogen fixation in an anticyclonic
eddy in the oligotrophic North Pacific Ocean. ISME J. 2:663–76
Foster RA, O’Mullan GD. 2008. Nitrogen fixing and nitrifying symbioses in the marine environment. In
Nitrogen in the Marine Environment, ed. DG Capone, DA Bronk, MR Mulholland, EJ Carpenter, pp. 1197–
218. London: Academic
Foster RA, Subramaniam A, Mahaffey C, Carpenter EJ, Capone DG, Zehr JP. 2007. Influence of the Amazon
River plume on distributions of free-living and symbiotic cyanobacteria in the western tropical north
Atlantic Ocean. Limnol. Oceanogr. 52:517–32
Foster RA, Zehr JP. 2006. Characterization of diatom-cyanobacteria symbioses on the basis of nifH,hetR,and
16S rRNA sequences. Environ. Microbiol. 8:1913–25
www.annualreviews.org •Ocean Nitrogen Cycle 219
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. 2005. Ubiquity and diversity of ammonia-
oxidizing archaea in water columns and sediments of the ocean. Proc. Natl. Acad. Sci. USA 102:14683–88
Fuhrman JA, McCallum K, Davis AA. 1992. Novel major archaebacterial group from marine plankton. Nature
356:148–49
Fung IY, Meyn SK, Tegen I, Doney SC, John J, Bishop J. 2000. Iron supply and demand in the upper ocean.
Glob. Biogeochem. Cycles 14:281–95
Galan A, Molina V, Thamdrup B, Woebken D, Lavik G, et al. 2009. Anammox bacteria and the anaerobic
oxidation of ammonium in the oxygen minimum zone off northern Chile. Deep-Sea Res. II 56:1125–35
Galloway JN, Dentener FJ, Capone DG, Boyer EW, Howarth RW, et al. 2004. Nitrogen cycles: past, present
and future. Biogeochemistry 70:153–226
Gardner WS, McCarthy MJ, An SM, Sobolev D, Sell KS, Brock D. 2006. Nitrogen fixation and dissimilatory
nitrate reduction to ammonium (DNRA) support nitrogen dynamics in Texas estuaries. Limnol. Oceanogr.
51:558–68
Geider RJ, La Roche J. 2002. Redfield revisited: variability of C:N:P in marine microalgae and its biochemical
basis. Eur. J. Phycol. 37:1–17
Giovannoni SJ, Foster RA, Rappe MS, Epstein S. 2007. New cultivation strategies bring more microbial
plankton species into the laboratory. Oceanography 20(2):62–69
Giovannoni SJ, Stingl U. 2005. Molecular diversity and ecology of microbial plankton. Nature 437:343–48
Giovannoni SJ, Tripp HJ, Givan S, Podar M, Vergin KL, et al. 2005. Genome streamlining in a cosmopolitan
oceanic bacterium. Science 309:1242–45
Goebel NL, Edwards CA, Carter BJ, Achilles KM, Church MJ, Zehr JP. 2008. Growth and carbon content
of three different sized diazotrophic cyanobacteria observed in the subtropical North Pacific. J. Phycol.
44:1212–20
Goebel NL, Edwards CA, Church MJ, Zehr JP. 2007. Modeled contributions of three types of diazotrophs
to nitrogen fixation at Station ALOHA. ISME J. 1:606–19
Goebel NL, Turk KA, Achilles KM, Paerl RW, Hewson I, et al. 2010. Abundance and distribution of major
groups of diazotrophic cyanobacteria and their potential contribution to N2fixation in the tropical Atlantic
Ocean. Environ. Microbiol. doi:10.1111/j.1462-2920.2010.02303.x
Graziano LM, Geider RJ, Li WKW, Olaizola M. 1996. Nitrogen limitation of North Atlantic phytoplankton:
analysis of physiological condition in nutrient enrichment experiments. Aquat. Microb. Ecol. 11:53–64
Gruber N, Galloway JN. 2008. An Earth-system perspective of the global nitrogen cycle. Nature 451:293–96
Gruber N, Sarmiento JL. 1997. Global patterns of marine nitrogen fixation and denitrification. Glob. Bio-
geochem. Cycles 11:235–66
Hamersley MR, Woebken D, Boehrer B, Schultze M, Lavik G, Kuypers MMM. 2009. Water column anammox
and denitrification in a temperate permanently stratified lake (Lake Rassnitzer, Germany). Syst. Appl.
Microbiol. 32:571–82
Hansell DA, Bates NR, Olson DB. 2004. Excess nitrate and nitrogen fixation in the North Atlantic Ocean.
Mar. Chem. 84:243–65
Hecky RE, Kilham P. 1988. Nutrient limitation of phytoplankton in freshwater and marine environments: a
review of recent evidence on the effects of enrichment. Limnol. Oceanogr. 33:796–822
Hewson I, Poretsky RS, Beinart RA, White AE, Shi T, et al. 2009. In situ transcriptomic analysis of the
globally important keystone N2-fixing taxon Crocosphaera watsonii.ISME J. 3:618–31
Hollibaugh JT, Bano N, Ducklow HW. 2002. Widespread distribution in polar oceans of a 16S rRNA gene
sequence with affinity to Nitrosospira-like ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 68:1478–
84
Howarth RW. 1988. Nutrient limitation of net primary production in marine ecosystems. Annu. Rev. Ecol.
Syst. 19:89–110
Janson S, Rai AN, Bergman B. 1995. Intracellular cyanobiont Richelia intracellularis—ultrastructure and
immuno-localization of phycoerythrin, nitrogenase, Rubisco and glutamine synthetase. Mar. Biol. 124:1–8
Jenkins BD, Steward GF, Short SM, Ward BB, Zehr JP. 2004. Fingerprinting diazotroph communities in the
Chesapeake Bay by using a DNA macroarray. Appl. Environ. Microbiol. 70:1767–76
Jenkins BD, Zehr JP, Gibson AH, Campbell L. 2006. Cyanobacterial assimilatory nitrate reductase gene
diversity in coastal and oligotrophic marine environments. Appl. Environ. Microbiol. 8:2083–95
220 Zehr ·Kudela
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Jetten MSM, van Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJM. 2009. Biochemistry and
molecular biology of anammox bacteria. Crit. Rev. Biochem. Mol. Biol. 44:65–84
Jickells TD, An ZS, Andersen KK, Baker AR, Bergametti G, et al. 2005. Global iron connections between
desert dust, ocean biogeochemistry, and climate. Science 308:67–71
Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. 2006. Niche partitioning
among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311:1737–40
Junier P, Molina V, Dorador C, Hadas O, Kim O. 2010. Phylogenetic and functional marker genes to study
ammonia-oxidizing microorganisms (AOM) in the environment. Appl. Microbiol. Biotechnol. 85:425–40
Karl DM. 2002. Nutrient dynamics in the deep blue sea. Trends Microbiol. 10:410–18
Karl DM, Bidigare RR, Letelier RM. 2001a. Long-term changes in plankton community structure and pro-
ductivity in the North Pacific Ocean: the domain shift hypothesis. Deep-Sea Res. II 48:1449–70
Karl DM, Bj¨
orkman KM, Dore JE, Fujieki L, Hebel DV, et al. 2001b. Ecological nitrogen-to-phosphorus
stoichiometry at station ALOHA. Deep-Sea Res. II 48:1529–66
Karl DM, Letelier R, Hebel DV, Bir DF, Winn CD. 1992. Trichodesmium blooms and new nitrogen in
the North Pacific Gyre. In Marine Pelagic Cyanobacteria: Trichodesmium and Other Diazotrophs, ed. EJ
Carpenter, DG Capone, JG Rueter, pp. 219–38. Amsterdam: Kluwer
Karl DM, Letelier RM. 2008. Nitrogen fixation-enhanced carbon sequestration in low nitrate, low chlorophyll
seascapes. Mar. Ecol. Prog. Ser. 364:257–68
Klausmeier CA, Litchman E, Daufresne T, Levin SA. 2004. Optimal nitrogen-to-phosphorus stoichiometry
of phytoplankton. Nature 429:171–74
Kolber ZS, Barber RT, Coale KH, Fitzwater SE, Greene RM, et al. 1994. Iron limitation of phytoplankton
photosynthesis in the equatorial Pacific Ocean. Nature 371:145–49
K¨
onneke M, Bernhard A, De la Torre J, Walker C. 2005. Isolation of an autotrophic ammonia-oxidizing
marine archaeon. Nature 437:543–46
Krishnamurthy A, Moore JK, Mahowald N, Luo C, Zender CS. 2010. Impacts of atmospheric nutrient inputs
on marine biogeochemistry. J. Geophys. Res. 115:G01006
Kustka A, Sa ˜
nudo-Wilhelmy S, Carpenter EJ, Capone DG, Raven JA. 2003. A revised estimate of the iron use
efficiency of nitrogen fixation, with special reference to the marine cyanobacterium Trichodesmium spp.
(Cyanophyta). J. Phycol. 39:12–25
Kuypers MMM, Lavik G, Thamdrup B. 2006. Anaerobic ammonium oxidation in the marine environment.
In Past and Present Water Column Anoxia, ed. LN Neretin, pp. 311–35. Dordrecht, Neth.: Springer
Kuypers MMM, Lavik G, Woebken D, Schmid M, Fuchs BM, et al. 2005. Massive nitrogen loss from the
Benguela upwelling system through anaerobic ammonium oxidation. Proc. Natl. Acad. Sci. USA 102:6478–
83
Kuypers MMM, Sliekers AO, Lavik G, Schmid M, Jorgensen BB, et al. 2003. Anaerobic ammonium oxidation
by anammox bacteria in the Black Sea. Nature 422:608–11
Lam P, Lavik G, Jensen MM, van de Vossenberg J, Schmid M, et al. 2009. Revising the nitrogen cycle in the
Peruvian oxygen minimum zone. Proc. Natl. Acad. Sci. USA 106:4752–57
Lam PJ, Bishop JKB. 2008. The continental margin is a key source of iron to the HNLC North Pacific Ocean.
Geophys. Res. Lett. 35:L07608
Langlois RJ, Hummer D, LaRoche J. 2008. Abundances and distributions of the dominant nifH phylotypes
in the northern Atlantic Ocean. Appl. Environ. Microbiol. 74:1922–31
Le Moal M, Biegala IC. 2009. Diazotrophic unicellular cyanobacteria in the northwestern Mediterranean Sea:
a seasonal cycle. Limnol. Oceanogr. 54:845–55
Letelier RM, Strutton PG, Karl DM. 2008. Physical and ecological uncertainties in the widespread imple-
mentation of controlled upwelling in the North Pacific Subtropical Gyre. Mar. Ecol. Prog. Ser. 371:305–8
Mague TH, Weare MM, Holm-Hansen O. 1974. Nitrogen fixation in the north Pacific Ocean. Mar. Biol.
24:109–19
Mahaffey C, Michaels AF, Capone DG. 2005. The conundrum of marine N2fixation. Am. J. Sci. 305:546–95
Marchetti A, Varela DE, Lance VP, Johnson Z, Palmucci M, et al. 2010. Iron and silicic acid effects on
phytoplankton productivity, diversity, and chemical composition in the central equatorial Pacific Ocean.
Limnol. Oceanogr. 55:11–29
www.annualreviews.org •Ocean Nitrogen Cycle 221
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Martens-Habbena W, Berube PM, Urakawa H, de la Torre JR, Stahl DA. 2009. Ammonia oxidation kinetics
determine niche separation of nitrifying Archaea and Bacteria. Nature 461:976–U234
Martin JH, Fitzwater SE. 1988. Iron deficiency limits phytoplankton growth in the north-east Pacific subarctic.
Nature 331:341–43
Martiny AC, Kathuria S, Berube PM. 2009. Widespread metabolic potential for nitrite and nitrate assimilation
among Prochlorococcus ecotypes. Proc. Natl. Acad. Sci. USA 106:10787–92
McCarthy MD, Bronk DA. 2008. Analytical methods for nitrogen chemical characterization and flux rates. In
Nitrogen in the Marine Environment, ed. DG Capone, DA Bronk, M Mulholland, EJ Carpenter, pp. 1219–
76. New York: Academic
McGillicuddy DJ, Anderson LA, Bates NR, Bibby T, Buesseler KO, et al. 2007. Eddy/wind interactions
stimulate extraordinary mid-ocean plankton blooms. Science 316:1021–26
Mehta MP, Baross JA. 2006. Nitrogen fixation at 92◦C by a hydrothermal vent archaeon. Science 314:1783–86
Michaels AF, Olson D, Sarmiento JL, Ammerman JW, Fanning K, et al. 1996. Inputs, losses and transforma-
tions of nitrogen and phosphorus in the pelagic North Atlantic Ocean. Biogeochemistry 35:181–226
Mills MM, Ridame C, Davey M, La Roche J, Geider RJ. 2004. Iron and phosphorus co-limit nitrogen fixation
in the eastern tropical North Atlantic. Nature 429:292–94
Mincer TJ, Church MJ, Taylor LT, Preston C, Kar DM, DeLong EF. 2007. Quantitative distribution of
presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific Subtropical Gyre.
Environ. Microbiol. 9:1162–75
Moisander PH, Beinart RA, Hewson I, White AE, Johnson KS, et al. 2010. Unicellular cyanobacterial distri-
butions broaden the oceanic N2fixation domain. Science 327:1512–14
Moisander PH, Beinart RA, Voss M, Zehr JP. 2008. Diversity and abundance of diazotrophic microorganisms
in the South China Sea during intermonsoon. ISME J. 2:954–67
Moisander PH, Shiue L, Steward GF, Jenkins BD, Bebout BM, Zehr JP. 2006. Application of a nifH oligonu-
cleotide microarray for profiling diversity of N2-fixing microorganisms in marine microbial mats. Environ.
Microbiol. 8:1721–35
Monteiro FM, Follows MJ. 2009. On the interannual variability of nitrogen fixation in the subtropical gyres.
J. Mar. Res. 67:71–88
Montoya JP, Voss M, Capone DG. 2007. Spatial variation in N2-fixation rate and diazotroph activity in the
tropical Atlantic. Biogeosciences 4:369–76
Moore CM, Mills MM, Achterberg EP, Geider RJ, LaRoche J, et al. 2009. Large-scale distribution of Atlantic
nitrogen fixation controlled by iron availability. Nat. Geosci. 2:867–71
Moore JK, Doney SC. 2007. Iron availability limits the ocean nitrogen inventory stabilizing feedbacks between
marine denitrification and nitrogen fixation. Glob. Biogeochem. Cycles 21:GB2001
Moore JK, Doney SC, Lindsay K, Mahowald N, Michaels AF. 2006. Nitrogen fixation amplifies the ocean
biogeochemical response to decadal timescale variations in mineral dust deposition. Tellus B 58:560–72
Moore LR, Rocap G, Chisholm SW. 1998. Physiology and molecular phylogeny of coexisting Prochlorococcus
ecotypes. Nature 393:464–67
Morel FMM. 2008. The co-evolution of phytoplankton and trace element cycles in the oceans. Geobiology
6:318–24
Morel FMM, Price NM. 2003. The biogeochemical cycles of trace metals in the oceans. Science 300:944–47
Mosier AC, Francis CA. 2008. Relative abundance and diversity of ammonia-oxidizing archaea and bacteria
in the San Francisco Bay estuary. Environ. Microbiol. 10:3002–16
Mulder A, Vandegraaf AA, Robertson LA, Kuenen JG. 1995. Anaerobic ammonium oxidation discovered in
a denitrifying fluidized-bed reactor. FEMS Microbiol. Ecol. 16:177–83
Mulholland MR, Bronk D, Capone DG. 2004. Dinitrogen fixation and release of ammonium and dissolved
organic nitrogen by Trichodesmium IMS101. Aquat. Microb. Ecol. 37:85–94
Naqvi SWA, Voss M, Montoya JP. 2008. Recent advances in the biogeochemistry of nitrogen in the ocean.
Biogeosciences 5:1033–41
Needoba JA, Foster RA, Sakamoto C, Zehr JP, Johnson KS. 2007. Nitrogen fixation by unicellular diazotrophic
cyanobacteria in the temperate oligotrophic North Pacific Ocean. Limnol. Oceanogr. 52:1317–27
Neveux J, Lantoine F, Vaulot D, Marie D, Blanchot J. 1999. Phycoerythrins in the southern tropical and
equatorial Pacific Ocean: evidence for new cyanobacterial types. J. Geophys. Res. 104:3311–21
222 Zehr ·Kudela
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Paerl RW, Foster RA, Jenkins BD, Montoya JP, Zehr JP. 2008. Phylogenetic diversity of cyanobacterial narB
genes from various marine habitats. Environ. Microbiol. 10:3377–87
Pahlow M, Riebesell U. 2000. Temporal trends in deep ocean Redfield ratios. Science 287:831–33
Palenik B, Ren QH, Dupont CL, Myers GS, Heidelberg JF, et al. 2006. Genome sequence of Synechococcus
CC9311: insights into adaptation to a coastal environment. Proc. Natl. Acad. Sci. USA 103:13555–59
Partensky F, Garczarek L. 2010. Prochlorococcus: advantages and limits of minimalism. Annu. Rev. Mar. Sci.
2:305–31
Peacock S, Lane E, Restrepo JM. 2006. A possible sequence of events for the generalized glacial-interglacial
cycle. Glob. Biogeochem. Cycles 20:1–17
Quan TM, Falkowski PG. 2009. Redox control of N:P ratios in aquatic ecosystems. Geobiology 7:124–39
Redfield AC. 1958. The biological control of chemical factors in the environment. Am. Sci. 46:205–22
Rees AP, Gilbert JA, Kelly-Gerreyn BA. 2009. Nitrogen fixation in the western English Channel (NE Atlantic
Ocean). Mar. Ecol. Prog. Ser. 374:7–12
Rich JJ, Dale OR, Song B, Ward BB. 2008. Anaerobic ammonium oxidation (Anammox) in Chesapeake Bay
sediments. Microb. Ecol. 55:311–20
Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, et al. 2003. Genome divergence in two Prochlorococcus
ecotypes reflects oceanic niche differentiation. Nature 424:1042–47
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, et al. 2007. The Sorcerer II Global Ocean
Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 5:e77
Ryther JH, Dunstan WM. 1971. Nitrogen, phosphorus, and eutrophication in the coastal marine environment.
Science 171:1008–13
Saino T, Hattori A. 1978. Diel variation in nitrogen fixation by a marine blue-green alga, Trichodesmium
thiebautii.Deep-Sea Res. 25:1259–63
Santoro AE, Casciotti KL, Francis CA. 2010. Activity, abundance and diversity of nitrifying archaea and
bacteria in the central California Current. Environ. Microbiol. 12:1989–2006
Sanudo-Wilhelmy SA, Gobler CJ, Okbamichael M, Taylor GT. 2006. Regulation of phytoplankton dynamics
by vitamin B12.Geophys. Res. Lett. 33:L04604
Sanudo-Wilhelmy SA, Kustka AB, Gobler CJ, Hutchins DA, Yang M, et al. 2001. Phosphorus limitation of
nitrogen fixation by Trichodesmium in the central Atlantic Ocean. Nature 411:66–69
Sarmiento JL, Gruber N. 2006. Ocean Biogeochemical Dynamics. Princeton, NJ: Princeton Univ. Press. 526 pp.
Scharek R, Tupas L, Karl DM. 1999. Diatom fluxes to the deep sea in the oligotrophic North Pacific gyre at
Station ALOHA. Mar. Ecol. Prog. Ser. 182:55–67
Schmid MC, Maas B, Dapena A, de Pas-Schoonen KV, de Vossenberg JV, et al. 2005. Biomarkers for in situ
detection of anaerobic ammonium-oxidizing (anammox) bacteria. Appl. Environ. Microbiol. 71:1677–84
Smith SV. 1984. Phosphorous versus nitrogen limitation in the marine environment. Limnol. Oceanogr.
29:1149–60
Steward GF, Jenkins BD, Ward BB, Zehr JP. 2004. Development and testing of a DNA macroarray to assess
nitrogenase (nifH) gene diversity. Appl. Environ. Microbiol. 70:1455–65
Stramma L, Johnson GC, Sprintall J, Mohrholz V. 2008. Expanding oxygen-minimum zones in the tropical
oceans. Science 320:655–58
Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, et al. 2006. Deciphering the evolution and metabolism
of an anammox bacterium from a community genome. Nature 440:790–94
Subramaniam A, Brown CW, Hood RR, Carpenter EJ, Capone DG. 2002. Detecting Trichodesmium blooms
in SeaWiFS imagery. Deep-Sea Res. II 49:107–21
Subramaniam A, Yager PL, Carpenter EJ, Mahaffey C, Bjorkman K, et al. 2008. Amazon River enhances
diazotrophy and carbon sequestration in the tropical North Atlantic Ocean. Proc. Natl. Acad. Sci. USA
105:10460–65
Taboada FG, Gil RG, Hofer J, Gonzalez S, Anadon R. 2010. Trichodesmium spp. population structure in
the eastern North Atlantic subtropical gyre. Deep-Sea Res. I 57:65–77
Taylor GT, Sullivan CW. 2008. Vitamin B12 and cobalt cycling among diatoms and bacteria in Antarctic sea
ice microbial communities. Limnol. Oceanogr. 53:1862–77
Thamdrup B, Dalsgaard T. 2002. Production of N2through anaerobic ammonium oxidation coupled to
nitrate reduction in marine sediments. Appl. Environ. Microbiol. 68:1312–18
www.annualreviews.org •Ocean Nitrogen Cycle 223
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Thomas WH. 1970. On nitrogen deficiency in tropical Pacific oceanic phytoplankton: photosynthetic param-
eters in poor and rich water. Limnol. Oceanogr. 15:380–85
Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk H-P, Schleper C. 2005. Novel genes for nitrite
reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen
cycling. Environ. Microbiol. 7:1985–95
Tripp HJ, Bench SR, Turk KA, Foster RA, Desany BA, et al. 2010. Metabolic streamlining in an open ocean
nitrogen-fixing cyanobacterium. Nature 464:90–94
Tyrrell T. 1999. The relative influences of nitrogen and phosphorus on oceanic primary production. Nature
400:525–31
Tyrrell T, Maranon E, Poulton AJ, Bowie AR, Harbour DS, Woodward EMS. 2003. Large-scale latitudinal
distribution of Trichodesmium spp. in the Atlantic Ocean. J. Plankton Res. 25:405–16
van de Graaf AA, de Bruijn P, Robertson LA, Jetten MSM, Kuenen JG. 1997. Metabolic pathway of anaerobic
ammonium oxidation on the basis of 15N studies in a fluidized bed reactor. Microbiology 143:2415–21
Van Mooy BAS, Devol AH. 2008. Assessing nutrient limitation of Prochlorococcus in the North Pacific sub-
tropical gyre by using an RNA capture method. Limnol. Oceanogr. 53:78–88
Van Mooy BAS, Fredricks HF, Pedler BE, Dyhrman ST, Karl DM, et al. 2009. Phytoplankton in the ocean
use non-phosphorus lipids in response to phosphorus scarcity. Nature 458:69–72
Van Mooy BAS, Rocap G, Fredricks HF, Evans CT, Devol AH. 2006. Sulfolipids dramatically decrease
phosphorus demand by picocyanobacteria in oligotrophic marine environments. Proc. Natl. Acad. Sci.
USA 103:8607–12
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun
sequencing of the Sargasso Sea. Science 304:66–74
Villareal TA. 1987. Evaluation of nitrogen fixation in the diatom genus Rhizosolenia Ehr. in the absence of its
cyanobacterial symbiont Richelia intracellularis Schimidt. J. Plankton Res. 9:965–71
Villareal TA. 1991. Nitrogen-fixation by the cyanobacterial symbiont of the diatom genus Hemiaulus.Mar.
Ecol. Prog. Ser. 76:201–4
Villareal TA. 1992. Marine nitrogen-fixing diatom—cyanobacteria symbioses. In Marine Pelagic Cyanobacteria:
Trichodesmium and Other Diazotrophs, ed. EJ Carpenter, DG Capone, JG Rueter, pp. 163–75. Amsterdam:
Kluwer
Villareal TA, Altabet MA, Culver-Rymzsa K. 1993. Nitrogen transport by vertically migrating diatom mats
in the North Pacific Ocean. Nature 363:709–12
Vitousek PM, Aber JD, Howarth RW, Likens GE, Matson PA, et al. 1997. Human alterations of the global
nitrogen cycle: sources and consequences. Ecol. Appl. 7:737–50
Vitousek PM, Howarth RW. 1991. Nitrogen limitation on land and in the sea: How can it occur? Biogeochem.
13:87–115
Wankel SD, Kendall C, Pennington JT, Chavez FP, Paytan A. 2007. Nitrification in the euphotic zone
as evidenced by nitrate dual isotopic composition: observations from Monterey Bay, California. Glob.
Biogeochem. Cycles 21:GB2009
Ward BB. 1996. Nitrification and denitrification: probing the nitrogen cycle in aquatic environments. Microb.
Ecol. 32:247–61
Ward BB. 2000. Nitrification and the marine nitrogen cycle. In Microbial Ecology of the Oceans,ed.DLKirchman,
pp. 427–54. New York: Wiley-Liss
Ward BB. 2005. Temporal variability in nitrification rates and related biogeochemical factors in Monterey
Bay, California, USA. Mar. Ecol. Prog. Ser. 292:97–109
Ward BB, Capone DG, Zehr JP. 2007. What’s new in the nitrogen cycle? Oceanography 20:101–9
Ward BB, Carlucci AF. 1985. Marine ammonia- and nitrite-oxidizing bacteria: serological diversity determined
by immunofluorescence in culture and in the environment. Appl. Environ. Microbiol. 50:194–201
Ward BB, Devol AH, Rich JJ, Chang BX, Bulow SE, et al. 2009. Denitrification as the dominant nitrogen
loss process in the Arabian Sea. Nature 461:78–81
Ward BB, Kilpatrick KA, Renger EH, Eppley RW. 1989. Biological nitrogen cycling in the nitracline. Limnol.
Oceanogr. 34:493–513
224 Zehr ·Kudela
Annu. Rev. Marine. Sci. 2011.3:197-225. Downloaded from www.annualreviews.org
by University of California - Santa Cruz on 01/18/11. For personal use only.

MA03CH08-Zehr ARI 17 November 2010 6:55
Waterbury JB, Rippka R. 1989. Cyanobacteria. Subsection I. Order Chroococcales Wettstien 1924, emend.
Rippka et al. 1979. In Bergey’s Manual of Systematic Bacteriology, ed. JT Staley, MP Bryant, N Pfenning,
JG Holt, pp. 1728–29. Baltimore: Williams & Wilkins
Westberry TK, Siegel DA. 2006. Spatial and temporal distribution of Trichodesmium blooms in the world’s
oceans. Glob. Biogeochem. Cycles 20:GB4016
White AE, Spitz YH, Letelier RM. 2006. Modeling carbohydrate ballasting by Trichodesmium spp. at Station
ALOHA. Mar. Ecol. Prog. Ser. 323:35–45
Woodward EMS, Rees AP. 2001. Nutrient distributions in an anticyclonic eddy in the northeast Atlantic
Ocean, with reference to nanomolar ammonium concentrations. Deep-Sea Res. II 48:775–93
Wu J, Sunda W, Boyle EA, Karl DM. 2000. Phosphate depletion in the western North Atlantic Ocean. Science
289:759–62
Wuchter C, Abbas B, Coolen MJL, Herfort L, van Bleijswijk J, et al. 2006. Archaeal nitrification in the ocean.
Proc. Natl. Acad. Sci. USA 103:12317–22
Zehr JP. 2009. New twist on nitrogen cycling in oceanic oxygen minimum zones. Proc. Natl. Acad. Sci. USA
106:4575–76
Zehr JP, Bench SR, Carter BJ, Hewson I, Niazi F, et al. 2008. Globally distributed uncultivated oceanic
N2-fixing cyanobacteria lack oxygenic Photosystem II. Science 322:1110–12
Zehr JP, Bench SR, Mondragon EA, McCarren J, DeLong EF. 2007. Low genomic diversity in tropical
oceanic N2-fixing cyanobacteria. Proc. Natl. Acad. Sci. USA 104:17807–12
Zehr JP, Crumbliss LL, Church MJ, Omoregie EO, Jenkins BD. 2003. Nitrogenase genes in PCR and RT-
PCR reagents: implications for studies of diversity of functional genes. Biotechniques 35:996–1005
Zehr JP, Mellon MT, Zani S. 1998. New nitrogen fixing microorganisms detected in oligotrophic oceans by
the amplification of nitrogenase (nifH) genes. Appl. Environ. Microbiol. 64:3444–50
Zehr JP, Waterbury JB, Turner PJ, Montoya JP, Omoregie E, et al. 2001. Unicellular cyanobacteria fix N2
in the subtropical North Pacific Ocean. Nature 412:635–38
www.annualreviews.org •Ocean Nitrogen Cycle 225
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Annual Review of
Marine Science
Volume 3, 2011
Contents
Geologist at Sea: Aspects of Ocean History
Wolfgang H. Berger ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp1
Submarine Paleoseismology Based on Turbidite Records
Chris Goldfinger pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp35
Natural Processes in Delta Restoration: Application to the
Mississippi Delta
Chris Paola, Robert R. Twilley, Douglas A. Edmonds, Wonsuck Kim,
David Mohrig, Gary Parker, Enrica Viparelli, and Vaughan R. Voller pppppppppppppppp67
Modeling the Dynamics of Continental Shelf Carbon
Eileen E. Hofmann, Bronwyn Cahill, Katja Fennel, Marjorie A.M. Friedrichs,
Kimberly Hyde, Cindy Lee, Antonio Mannino, Raymond G. Najjar,
John E. O’Reilly, John Wilkin, and Jianhong Xue pppppppppppppppppppppppppppppppppppppp93
Estuarine and Coastal Ocean Carbon Paradox: CO2Sinks or Sites
of Terrestrial Carbon Incineration?
Wei-Jun Cai pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp123
Emerging Topics in Marine Methane Biogeochemistry
David L. Valentine ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp147
Observations of CFCs and SF6as Ocean Tracers
Rana A. Fine pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp173
Nitrogen Cycle of the Open Ocean: From Genes to Ecosystems
Jonathan P. Zehr and Raphael M. Kudela pppppppppppppppppppppppppppppppppppppppppppppppp197
Marine Primary Production in Relation to Climate Variability
and Change
Francisco P. Chavez, Monique Messi´e, and J. Timothy Pennington ppppppppppppppppppppp227
Beyond the Calvin Cycle: Autotrophic Carbon Fixation in the Ocean
Michael H¨ugler and Stefan M. Sievert pppppppppppppppppppppppppppppppppppppppppppppppppppp261
Carbon Concentrating Mechanisms in Eukaryotic
Marine Phytoplankton
John R. Reinfelder pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp291
vi
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MA03-FrontMatter ARI 17 November 2010 7:6
Microbial Nitrogen Cycling Processes in Oxygen Minimum Zones
Phyllis Lam and Marcel M.M. Kuypers ppppppppppppppppppppppppppppppppppppppppppppppppppp317
Microbial Metagenomics: Beyond the Genome
Jack A. Gilbert and Christopher L. Dupont ppppppppppppppppppppppppppppppppppppppppppppppp347
Environmental Proteomics: Changes in the Proteome of Marine
Organisms in Response to Environmental Stress, Pollutants,
Infection, Symbiosis, and Development
Lars Tomanek ppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp373
Microbial Extracellular Enzymes and the Marine Carbon Cycle
Carol Arnosti pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp401
Modeling Diverse Communities of Marine Microbes
Michael J. Follows and Stephanie Dutkiewicz pppppppppppppppppppppppppppppppppppppppppppp427
Biofilms and Marine Invertebrate Larvae: What Bacteria Produce That
Larvae Use to Choose Settlement Sites
Michael G. Hadfield pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp453
DNA Barcoding of Marine Metazoa
Ann Bucklin, Dirk Steinke, and Leocadio Blanco-Bercial pppppppppppppppppppppppppppppppp471
Local Adaptation in Marine Invertebrates
Eric Sanford and Morgan W. Kelly ppppppppppppppppppppppppppppppppppppppppppppppppppppppp509
Use of Flow Cytometry to Measure Biogeochemical Rates and
Processes in the Ocean
Michael W. Lomas, Deborah A. Bronk, and Ger van den Engh ppppppppppppppppppppppppp537
The Impact of Microbial Metabolism on Marine Dissolved
Organic Matter
Elizabeth B. Kujawinski pppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppppp567
Errata
An online log of corrections to Annual Review of Marine Science articles may be found at
http://marine.annualreviews.org/errata.shtml
Contents vii
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