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Nitrogen Cycling in the Ocean: New
Perspectives on Processes and Paradigms
Jonathan P. Zehr and Bess B. Ward
Appl. Environ. Microbiol. 2002, 68(3):1015. DOI:
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0099-2240/02/$04.00⫹0 DOI: 10.1128/AEM.68.3.1015–1024.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Vol. 68, No. 3
Nitrogen Cycling in the Ocean: New Perspectives on Processes
and Paradigms
Department of Ocean Sciences, University of California, Santa Cruz, California 95064,1 and Department of Geosciences,
Princeton University, Princeton, New Jersey 085442
mations provides useful tools not only for assaying gene expression but also for determining the diversity of microorganisms involved in specific N cycle transformations. We still know
very little about the link between the ecology of the N cycle and
the redundancy of microbes and genes in the marine environment. Understanding these links is important for determining
the role of microbial diversity in ecosystem processes and the
sensitivity of the environment to perturbations. Regulatory
proteins are also useful for investigating natural populations
for “N status,” the degree of cellular N deficiency or sufficiency.
In the following sections, we review some important aspects
of the N cycle that have undergone major reevaluation in
recent years. Rather than present a detailed review of the
entire cycle, we focus on important recent changes in our
understanding of these aspects and specific components of the
cycle. Understanding these features of the nitrogen cycle is
critical for understanding the global biogeochemical cycles.
Here we focus on the microbiological underpinnings of these
processes; the global implications for the biogeochemical cycling of nitrogen are beyond the scope of this review.
The nitrogen (N) cycle is composed of multiple transformations of nitrogenous compounds, catalyzed primarily by microbes. The N cycle controls the availability of nitrogenous
nutrients and biological productivity in marine systems (84)
and thus is linked to the fixation of atmospheric carbon dioxide
and export of carbon from the ocean’s surface (30). Human
activities are influencing the N cycle even in the oceans (100),
and some of the nitrogenous gaseous products of microbial
metabolism are greenhouse gases that are potentially involved
in controlling Earth’s climate.
The last decade has brought the discovery of several new
links and changes in our understanding of components of the
marine N cycle. Much of our basic information about the N
cycle is derived from measurements of transformation rates or
from experiments with cultivated isolates. Generalization from
the behavior and physiology of cultivated isolates can be misleading, since it appears that many marine microorganisms in
situ have yet to be obtained in culture (33). The rapid increase
in knowledge of genes and molecular biology has had an enormous impact on our understanding of the N cycle by making it
possible to study the ecological underpinnings and diversity of
microorganisms involved in specific N cycle components. For
example, nitrate assimilation by photosynthetic picoplankton
was assumed to be universal but has now been shown to be
absent from some of the most abundant photosynthetic organisms on the planet. Conversely, nitrate assimilation by heterotrophic bacteria was largely ignored, but it has recently been
shown by both gene probes and physiological experiments that
this capability is widespread in bacteria. Genetic and biochemical investigations have also changed our understanding of
processes such as nitrification and denitrification, which were
thought to be restricted to very specific habitats and microbes
but in fact are more widely distributed.
The N cycle is composed of oxidation-reduction reactions,
many of which are used in the energy metabolism of microbes.
Specific enzymes catalyze many of these reactions, and the
enzymes and genes are useful targets for studying microbial
processes such as assimilatory nitrate reduction, dissimilatory
nitrate reduction, and N2 fixation (Table 1). Knowledge of the
genes encoding enzymes involved in biogeochemical transfor-
It is usually assumed that most microorganisms can use
inorganic N in the form of nitrate, nitrite, and ammonium.
Particularly in the oligotrophic open ocean gyres, low concentrations of these compounds (⬍0.03 to 0.1 ␮M [12]) can limit
the rate of productivity in the surface layer (0- to 200-m depth),
but N can regulate productivity even in coastal upwelling regions (55). In some regions, including coastal regions and the
high-nutrient, low-chlorophyll regions, upwelling or runoff can
supply N in concentrations that exceed phytoplankton demand.
Thus, there are large geographical variations in the sources
and fluxes of nitrate and ammonium. The geographic aspects
of the marine N cycle are beyond the scope of this review but
are covered elsewhere (12, 16, 103).
The first comprehensive view of the N cycle in the surface
ocean proposed that inorganic N was taken up by phytoplankton and that the N was subsequently recycled from phytoplankton cells by heterotrophs, both large grazers (e.g., planktonic
invertebrates) and microbial decomposers (Fig. 1, pathway A;
Fig. 2). The death, lysis, and decay of the phytoplankton, either
after ingestion by “herbivores” or because of physiological
stressors (such as nutrient limitation, temperature, or other
* Corresponding author. Mailing address: Department of Ocean
Sciences, Earth and Marine Sciences Building, Room A438, University
of California, Santa Cruz, CA 95064. Phone: (831) 459-4009. Fax:
(831) 459-4882. E-mail: [email protected]
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Jonathan P. Zehr1* and Bess B. Ward2
TABLE 1. Nitrogen cycle gene probes
N2 fixation
Nitrite assimilation
Nitrate assimilation
Ammonium assimilation
Nitrate respiration and denitrification
narB, nasA
Nitrite reductase
Assimilatory nitrate reductase
Glutamine synthetase
Nitrate reductase
Nitrite reductase
Nitric oxide reductase
Nitrous oxide reductase
Ammonia monooxygenase
Nitrogen regulatory protein
8, 18, 87
Organic N metabolism
Ammonium oxidation/nitrification
Nitrogen regulation (cyanobacteria)
2, 83
Nitrogen cycle genes for which probes or PCR primers have been designed.
factors), liberated N in the form of dissolved organic N or
ammonium, which was termed “regenerated” N (Fig. 1, pathway B; Fig. 2) (28). Biological N2 fixation, the reduction of
atmospheric dinitrogen gas (N2) to ammonia (Fig. 1, pathway
C), was thought to be insignificant in the open ocean, and
essentially all pelagic N fixation was ascribed to two genera of
N2-fixing microbes. Nitrate was believed to be supplied to the
upper ocean primarily by mixing, advection and diffusion from
deep ocean water, or terrestrial runoff (Fig. 1, pathway D).
Because nitrifying bacteria are inhibited by light, it was as-
sumed that nitrification (Fig. 1, pathway E) proceeded only in
deep water (Fig. 1, pathway E); therefore, the only source of
nitrate in surface waters was water mixing from the deep ocean
reservoir (Fig. 1, pathway D).
Nitrate, nitrite, and ammonium, called dissolved inorganic
nitrogen (DIN), can be taken up (via membrane transporters)
and assimilated by many microorganisms. Nitrate is assimilated
after sequential reduction to nitrite (assimilatory nitrate reductase) and ammonium (assimilatory nitrite reductase). Phytoplankton (both eukaryotes and cyanobacteria), in general, pre-
FIG. 1. Conceptual diagram of major features of the nitrogen cycle in coastal shelf and upwelling (I), OMZs (II), surface waters of the open
ocean (III), and deep water (IV). PON, particulate organic nitrogen. Dashed lines indicate transformations involving multiple steps. Pathways: A,
DIN assimilation; B, ammonium regeneration; C, nitrogen fixation; D, nitrate diffusion/advection from deep water; E, nitrification; F, nitrification;
G, denitrification.
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VOL. 68, 2002
fer ammonium to nitrate, presumably due to the additional
energy and reductant necessary to reduce nitrate to ammonium. However, this preference is not universal, as the reductant requirement for nitrate does not necessarily result in decreased growth rate (95). Although it is still likely that most
microorganisms prefer ammonium to nitrate, it has recently
become clear that (i) not all phytoplankton use nitrate and (ii)
some bacteria can use nitrate and some cannot. While it was
previously assumed that eukaryotic phytoplankton dominated
both photosynthesis and DIN assimilation, it is now known that
two major groups of small unicellular cyanobacteria (the Synechococcus and Prochlorococcus groups) are extremely abundant in surface waters and contribute a large fraction of photosynthesis and DIN demand (19). Some of these microbes do
not contain assimilatory nitrate reductase genes (G. Rocap,
F. W. Larimer, J. Lamerdin, E., S. Stilwagon, and S. W. Ch-
isholm, Abstr. Aquatic Sci. Meet., p. 120, 2001). The high- and
low-light-adapted Prochlorococcus spp. (67), divinyl chlorophyll a-containing cyanobacteria common in oceanic waters
(22), differ in their abilities to use N sources (G. Rocap, F. W.
Larimer, J. Lamerdin, E., S. Stilwagon, and S. W. Chisholm,
Abstr. Aquatic Sci. Meet., 2001). The high-light strain (strain
MED4) lacks both nitrate reductase genes and nitrite reductase genes and can grow only on ammonium, whereas the
low-light strain (strain MIT9313) lacks only nitrate reductase
genes and can grow on nitrite or ammonium (G. Rocap, F. W.
Larimer, J. Lamerdin, E., S. Stilwagon, and S. W. Chisholm,
Abstr. Aquatic Sci. Meet., 2001). Previously, it was assumed
that microorganisms generally could use either nitrate or ammonium and that organisms differed in kinetics of nitrate or
ammonium uptake and utilization (29), but now it is clear that
some microorganisms may not be able to use nitrate.
It is now recognized that bacteria also can play a role in
nitrate uptake. It is now known that assimilatory nitrate reductase genes are dispersed among marine bacterial strains as well
as among phytoplankton (1). Thus, in complex microbial communities in situ, the roles of different microorganisms in uptake of nitrate and ammonium differ due to genetic as well as
biochemical and physiological constraints.
The major source of nitrate in the ocean surface is diffusion
and upwelling of nitrate-rich deep ocean water. In recent years,
it has been shown that even this process, which would appear
to be driven largely by physical forcing, has an important microbiological component. Many large oceanic diatoms that
sometimes form large mats migrate to great depth to obtain
nutrients from the nutrient-rich deep water (66), only to return
to the surface carrying with them nitrate (99). Migrating Rhizosolenia mats may transport an average of 20%, ranging up to
78%, of the upward diffusive flux of nitrate (99). Thus, biological controls are involved even in the upward movement of
nitrate from deep water (Fig. 1, pathway D).
It is often assumed that N limits the productivity of phytoplankton in the oceans. This conclusion is based on relatively
few studies, most of which assess N limitation indirectly (39). It
is quite difficult to demonstrate N limitation experimentally.
Ideally, one would determine this from a simple bottle experiment in which different nutrients are added to each bottle. In
ocean studies this can be difficult, since microbial communities
change during bottle incubations (26). Techniques that directly
assay biochemical or physiological targets can provide incubation-independent information on the nutritional status of assemblages and even individual cells. A number of cellular and
molecular markers for nutritional deficiencies have been developed (36, 56, 88). Molecular and immunological techniques
have provided ways of investigating natural communities, for
example, by using probes for the N regulator in cyanobacteria,
ntcA (57), or cell surface proteins that are expressed under N
limitation (76). Detection of transcripts for ntcA indicated that
marine Synechococcus spp. in the Gulf of Aqaba were not
nitrogen stressed and were using primarily regenerated nitrogen. This approach has not yet been applied in open-ocean
oligotrophic environments but could be used to determine the
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FIG. 2. Diagrams of classical and present views of the N cycle in
the surface waters of oligotrophic oceans. The composition of the
dissolved N pool is shown with approximate relative concentrations of
inorganic and organic constituents indicated by the size of the box.
Dashed lines indicate transformations and processes included in the
newer view of nitrogen cycling. (A) Some phytoplankton use simple
organic compounds as a source of nitrogen. (B) There are multiple
species of phytoplankton (cyanobacteria) in the open ocean that fix N2.
(C) Bacteria can compete for nitrate and ammonium. (D) Bacteria can
excrete urea and can also be a source of high-molecular-weight DON.
(E). Some oceanic bacterioplankton appear to fix N2.
seasonal and depth variations in nitrogen limitation of cyanobacteria in the open ocean.
Dissolved organic N (DON) compounds include a wide
range of chemical compounds varying in size, complexity, and
resilience to degradation. The characterization of dissolved
organic matter has long been a challenge to the chemist but
perhaps even more so to the microbial ecologist, since it is
impossible to trace the metabolism of all of the different compounds even if all of the chemical structures and concentrations are known. DON can be a large pool in the oceans (3 to
7 ␮M [12]) and an even larger one in coastal waters (90).
Important, but usually minor, constituents of DON are amino
acids and urea [CO(NH2)2], which are readily used by bacteria
and some phytoplankton. Amino acids, either dissolved and
free or combined in oligopeptides, are important sources of
organic C and N for bacteria (49). Although rates of urea
production and catabolism have been measured in marine environments, relatively little is known about the microbiology of
urea metabolism in marine systems. Bacteria can be a source
or a sink for urea (Fig. 2). Urease is a nickel-containing multisubunit metalloprotein encoded by the ure genes (38), which
have been characterized in eukaryotes, cyanobacteria, and heterotrophic bacteria and recently reported in autotrophic nitri-
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The primary role of bacteria in the N cycle was presumed to
be the release of inorganic N (NH4⫹) during the decomposition of organic matter, thereby recycling N (and other nutrients) to phytoplankton (Fig. 1, pathway B; Fig. 2). There is now
an appreciation for the role of bacteria in the “microbial loop”
(3, 4), which emphasizes the role of bacteria in trophic transfers through a micrograzer (protozoan) food chain. This food
chain results in transfer of carbon, N, and other nutrients from
dissolved organic matter into the food web. However, this
picture is complicated by recent findings regarding the metabolism of heterotrophic marine bacteria (for a review, see reference 49) and the composition and sources of organic matter
(62, 63). Bacteria can use DIN as well as organic matter (Fig.
1, pathway A; Fig. 2) and thus might even compete with phytoplankton for inorganic N (50). Whether or not bacteria take
up inorganic N probably depends on the C:N ratio of the
substrates being used for growth (34). Bacterial regeneration
of N during the mineralization of organic matter also depends
on the C:N ratio of cell material relative to substrate availability (49), and thus, whether bacteria provide N or compete with
primary producers for N varies substantially in space and time
(49). Interestingly, growth rates of bacteria are consistent with
the uptake of N from dissolved free amino acids and ammonium, indicating that the larger pool of dissolved organic N is
not a major source of N for growth (49). Bacteria can take up
DIN while simultaneously liberating NH4⫹ in decomposition
(96). Thus, bacteria in the ocean can be competing for NH4⫹,
regenerating NH4⫹, or both (Fig. 2). It is unclear how both
processes are occurring simultaneously, but one explanation is
that different members of the microbial assemblage are responsible for different processes (49).
fiers (T.E. Koper, J. M. Norton, and M. G. Klotz, Abstr. 9th
Int. Symp. Microbial Ecol., P.08.059, 2001). Studies of the
diversity of urease genes in the environment are likely to provide interesting information on the distribution of urea utilization capabilities in natural assemblages (K. Baker and J.
Collier, unpublished data).
The definition of “dissolved” organic N has always been a
tenuous distinction from that of “particulate” organic nitrogen.
This has now been shown to be an artificial distinction, with
interactions between organic molecules creating a complete
continuum from small dissolved molecules to polymers, colloids, and particles. Chemical interactions among these molecules can result in rearrangements and interactions that form
macromolecular gel structures (21). These networked structures, which can form and dissociate biologically or abiologically, can make complex microenvironments that have been
suggested to be important for ecological interactions at some
microbial scales (3).
DON was previously assumed to be primarily high-molecular-weight condensation products, including heterocyclic compounds, with a smaller fraction composed of more degradable
compounds, including protein, and dissolved free and combined amino acids (Fig. 2). Recent studies indicate that a
significant fraction of DON is composed of amide N (62) and
that a fraction originates from bacterial cell walls (63). This
finding reverses the perception that phytoplankton are the
direct primary source for organic matter through excretion,
decomposition, and lysis. Thus, bacteria metabolize organic
matter that originates from photosynthetic microorganisms but
are now both a source of and a sink for the DON pool (Fig. 2).
Chemical and photochemical reactions have been found to be
important in influencing the quantity and quality of organic
matter. Rates of photolysis can equal or exceed bacterial decomposition rates (10).
Despite this new perspective on the source and nature of the
bulk DOM in the sea, it is abundantly clear that some small
fraction of the total DON pool is rapidly cycled by phytoplankton and bacteria in the photic zone (Fig. 2). A large fraction of
the DIN assimilated by phytoplankton can be released as DON
within a few hours, probably due to grazing disruption of cells
(Fig. 2) (9, 104). To complicate matters further, there is now
evidence that phytoplankton and cyanobacteria can assimilate
some small labile components of DON. Thus, the primary
producers may not be restricted to exploitation of the DIN
pool but may be an important sink for DON as well (Fig. 2)
(77, 78).
Release and uptake of DON on a scale of hours or less are
probably important for the more labile DON fractions such as
protein, peptides, and free amino acids, which are the DON
components on which metabolic studies have focused in the
past. Bacterioplankton can excrete proteolytic enzymes that
digest peptides and proteins so that the monomers or oligonucleotides can be taken up by the cell and metabolized (41,
42, 91). There are substantial differences in activities and temperature responses of these enzymes in different ocean regions,
with implications for how and where bacteria are regenerating
inorganic N (24). These studies emphasize that the composition of organic matter (e.g., polysaccharides and sugars versus
proteins and amino acids) and the variability among different
ocean regions may be important in understanding the role of
VOL. 68, 2002
Biological N2 fixation, the reduction of atmospheric N2 to
ammonia, is catalyzed by a diverse set of microorganisms. In
the marine environment, N2 fixation rates are highest in a few
specific habitats such as benthic cyanobacterial mats (40). In
the oceanic biome, there are relatively few known N2 fixers
despite the fact that DON concentrations are extremely low in
many parts of the ocean. Blooms of filamentous N2-fixing cyanobacteria often exploit N-limiting conditions in lakes and
sometimes estuaries, and so it is a curious paradox that there
are so few obvious nitrogen-fixing microorganisms in the ocean
(43). An exception is the Baltic Sea, where extensive blooms of
filamentous heterocyst-forming cyanobacteria (Aphanizomenon and Nodularia) frequently occur and have occurred for
thousands of years (5). Within the past decade, research on N2
fixation in the sea has received increasing attention (47), since
the role of the ocean in C flux is linked to nutrient cycling.
In the open ocean, the filamentous nonheterocystous cyanobacterium Trichodesmium is common in tropical and subtropical waters (13, 74). This organism is particularly interesting because it forms macroscopic aggregates of filaments, is
buoyant due to gas vacuoles, and fixes N2 only in the light.
Most cyanobacteria segregate O2-sensitive N2 fixation from O2
evolved through photosynthesis by fixing N2 during the night or
in specialized cells, called heterocysts, where photosystem II
activity is reduced or absent. Trichodesmium is one of a few
known species that evolve O2 simultaneously with N2 fixation
without an obvious mechanism to avoid O2 inactivation. Trichodesmium fixes N2 only during the day, and this cycle is
regulated by the synthesis of nitrogenase under the control of
a circadian clock (20). There are various theories and hypotheses regarding the mechanisms involved in simultaneous N2
fixation and photosynthesis, including the possible division of
labor among cells that are morphologically similar (31, 45), but
the mechanisms whereby Trichodesmium fixes N2 aerobically
are still not completely understood (13). The Trichodesmium
nitrogenase protein is similar phylogenetically to that of other
cyanobacterial diazotrophs and is not likely to be more O2
resistant than other nitrogenases (116). The molecular biology
of N2 fixation in Trichodesmium has been reviewed elsewhere
Perhaps the next most abundant diazotrophs in oceanic wa-
ters are the heterocyst-forming cyanobacterial symbionts of
diatoms (98). These symbionts have not been successfully
maintained in culture for extended periods of time, and so
relatively little is known about the biology of the symbiotic
interactions between the diatom and cyanobacteria. However,
the symbiont-containing diatoms can form large aggregates
that can be abundant in oligotrophic waters. These diatoms can
form extensive blooms (17) that can be significant sources of N
in the mixed layer of the ocean.
For years, it was believed that Trichodesmium and the symbionts of diatoms were the major N2 fixers in the open ocean.
However, a number of recent studies have highlighted imbalances in N budgets that indicate that higher rates of N2 fixation
are occurring in the open ocean than was previously estimated
(37, 59, 64). This conclusion is based on biogeochemical calculations rather than direct measurements of N2 fixation rates
or observed distributions of microorganisms but has led to a
reevaluation of N2 fixation in the sea. Evidence of diverse
bacterial and cyanobacterial N2-fixing microorganisms in the
Atlantic and Pacific Oceans based on amplification of nitrogenase genes from bulk water samples has recently been reported
(115, 118). Nitrogenase genes obtained from the Hawai’i
Ocean Time (HOT) series long-term monitoring site at Station
ALOHA in the North Pacific Subtropical Gyre were most
closely related to nitrogenase genes of unicellular cyanobacterial genera that are not typically reported in oceanic waters.
The cyanobacterial nifH phylotypes were detected at several
times of year and were ultimately shown to be expressing
nitrogenase genes (119). The finding of the genes led to the
microscopic observation of cells that looked similar to the
expected morphology (3 to 8 ␮m in diameter, spherical) and
subsequent cultivation of N2-fixing isolates (119). Unicellular
cyanobacteria with this morphology have been reported from
the South Pacific Ocean (71), the Baltic Sea (108), and, previously, from Station ALOHA (11). Estimates of the concentrations and nitrogen fixation activity of these organisms at
Station ALOHA indicate that they could equal or exceed the
contribution of Trichodesmium (119), and they have been observed elsewhere in the world’s oceans as well.
It is not well understood what controls the distribution and
activity of diazotrophs in the sea. The distributions of Trichodesmium and some other cyanobacteria appear to be correlated with water temperature (15). It could be that diazotrophs are limited by the availability of Fe, a metal that is a
component of many proteins in addition to nitrogenase (both
the MoFe and Fe components). Fe distributions in the world’s
oceans are controlled to a large extent by aeolian transport of
dust. Temporal and spatial variation in Fe supply may result in
oscillation between N and P limitation of the oceans through
its effect on N2 fixation (111). However, there does not appear
to be a correlation between Fe concentration and Trichodesmium abundance and activity, at least in the Atlantic Ocean
near Bermuda (85).
Isolations of nitrifying and denitrifying bacteria using
conventional enrichment techniques have provided extensive
culture collections on which our understanding of the biochemistry and ecology of these processes is based. Chemolitho-
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bacteria and dissolved organic matter in ocean carbon cycling
(24) but also in N regeneration. DON and its metabolism are
probably among the most poorly understood parts of the marine N cycle. New methods that combine the use of radiotracers and autoradiography with fluorescence in situ hybridization
have begun to provide information on which types of bacteria
are metabolizing different organic compounds (75). Given the
magnitude of the DON pool and the dependence of heterotrophic bacteria on dissolved organic matter, this topic deserves much more attention. Since DON is composed of many
different organic substrates, the uptake and metabolism of
DON must involve multiple transport proteins and extracellular and intracellular enzymes. The study of DON metabolism is
likely to profit from advances in genomic research from the
information gained about the diversity of catabolic pathways in
cultivated and uncultivated microorganisms.
duced sequentially to nitrite, nitric oxide, nitrous oxide, and
nitrogen gas.
Chemical distributions in marine sediments and the water
column indicate that nitrification is an obligately aerobic process and that denitrification is an obligately anaerobic process.
Although the oxygen requirements and tolerances vary among
isolates, these requirements are reflected in the physiology of
cultivated nitrifiers and denitrifiers, which are predominantly
obligate aerobes and facultative anaerobes, respectively. Nitrification and denitrification are often coupled across oxic/anoxic interfaces in both sediments and suboxic waters, leading to
the loss of fixed nitrogen via mineralization, oxidation, and
denitrification (72). Because the deep ocean contains high
nitrate concentrations, it was long assumed that nitrification
occurred in that environment. However, direct rate measurements using 15N tracer techniques have consistently shown that
most water column nitrification occurs in the lower portion of
the euphotic zone and that the nitrate produced there can
supply a large fraction of phytoplankton nitrate demand (27,
The recent description of aerobic denitrification by novel
strains and “conventional” denitrifying bacteria introduces a
new link in the N cycle. Aerobic denitrification was first described in Paracoccus pantotrophus (formerly Thiosphaera pantotropha [81]), and like others possessing this ability, P. pantotrophus is also a heterotrophic nitrifier. The nitrite generated
by the oxidation of ammonia can be released into the medium
or denitrified to N2 gas. Denitrification of nitrite or nitrate to
N2 can occur with atmospheric levels of O2 (82). P. pantotrophus was originally isolated from wastewater; its ability to denitrify aerobically in batch culture, as well as that of several other
conventional heterotrophic denitrifiers, has been confirmed
(82). Su et al. (93) reported aerobic denitrification by a strain
of Pseudomonas stutzeri at rates and with oxygen tolerance
greatly exceeding those reported for P. pantotrophus. The process may be common in isolates, but its significance in the
environment remains uncertain, and even in cultures questions
still remain. For example, the enzymology of the aerobic pathway is unknown. While P. pantotrophus expresses the nitrite
reductase gene (nirS) under anaerobic conditions, it is not
expressed under aerobic conditions (65), and thus, the mechanism for aerobic reduction of nitrite remains unknown.
AOB also perform a subset of the conventional set of denitrifying reactions, reducing nitrite to NO and N2O. The process
occurs aerobically but apparently is enhanced at low oxygen
concentrations (35, 60). These gases are also intermediates in
denitrification but could derive from nitrification under a low
or nearly zero oxygen concentration. Both N2O and NO are
important in atmospheric processes; they contribute to greenhouse warming and to catalytic destruction of stratospheric
ozone. Thus, understanding which processes are responsible
for their production could prove to be important in understanding or potentially regulating their fluxes.
It appears that chemoautotrophic AOB produce N2O and
NO by using a pathway that is essentially identical to the
classical denitrification pathway. First, ammonia is oxidized to
nitrite and some of the nitrite is reduced to N2O. The reductions are catalyzed by enzymes that are encoded by nitrite
reductase and NO reductase genes that are homologous to the
nirK and norB genes of conventional denitrifying bacteria (ref-
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autotrophic nitrification is rather restricted in its occurrence
and is represented in culture by 25 species of ammonia oxidizers in the beta and gamma subdivisions of the Proteobacteria
and by eight species of nitrite oxidizers in the alpha, beta, and
gamma subdivisions of the Proteobacteria (51). Molecular phylogeny has supported this generalization, showing that both
ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria belong to a small number of coherent groups (94).
The first AOB to be cultivated from the marine environment
was Nitrosocystis oceanus (109), now called Nitrosococcus oceani. Strains of N. oceani have been obtained from several
locations (14), and it has been detected in seawater by immunofluorescence (105) and by PCR amplification (B. B. Ward
and G. O’Mullan unpublished data) and in Antarctic lakes by
immunofluorescence hybridization and fluorescence in situ hybridization (101). Members of the Nitrosomonas/Nitrosospira
group appear to dominate most terrestrial and aquatic environments, including marine sediments (52, 73, 107, 110). Purkhold et al. (79) surveyed all published 16S rRNA and amoA
sequences, from both cultures and environmental clones, and
concluded that although much diversity among AOB remains
to be cultured, it is unlikely that entirely novel species will be
discovered, at least in the case of the beta-subdivision AOB.
However, this does not preclude the existence of entirely novel
AOB that are not detected by probes based on known groups.
Nitrite oxidizers have received somewhat less attention, and
culture collections are dominated by Nitrobacter strains. Recent work in various wastewaters, however, has shown that
Nitrospira is the dominant group in these environments (32).
For both AOB and nitrite-oxidizing bacteria, phylogeny and
functionality appear to be well correlated, making these groups
attractive for molecular phylogeny studies despite their slow
and fastidious growth habits in culture. Research on nitrifiers,
particularly AOB, based on 16S rRNA genes and functional
genes has proliferated in recent years and was recently reviewed (53).
Denitrifying bacteria are the opposite of nitrifiers in many
ways; denitrification ability is found in heterotrophic opportunists and in chemoautotrophs, is widespread among Bacteria
and Archaea, and has even been reported in Eukarya(120). 16S
rRNA and functional gene phylogenies are not congruent for
the denitrifiers, implying substantial horizontal gene transfer of
the functional genes over time (D. P. Martino and B. B. Ward,
Aquatic Sciences Meeting: Limnology and Oceanography: navigating into the next century, abstract book, p. 117, 1999; B.
Song and B. B. Ward, submitted for publication). Environmental research on the diversity of denitrifiers has focused, therefore, on the functional genes involved in the denitrification
pathway, mainly nitrite reductase (7, 8) and nitrous oxide reductase (86, 87).
Dissimilatory reduction of nitrate to ammonium is often
ignored in the marine realm but could be important in sediments in which fermentative bacteria, with whose metabolism
it is often associated, are likely to be found. Christensen et al.
(23) found it to be a significant nitrate sink only in sediments
with very high organic carbon loading, and Bonin et al. (6)
suggested that it could be important in coastal sediments, and
it is unlikely to occur in the water column. Thus, we refer here
mainly to respiratory denitrification, in which nitrate is re-
VOL. 68, 2002
times; thus, it seems unlikely that this anammox consortium is
active in natural environments (97).
Anammox would constitute a shortcut in the conventional N
cycle, in which nitrification and denitrification are linked at the
level of nitrite, without going through nitrate. Therefore, natural environments where ammonium and nitrite both occur in
the presence of low oxygen concentrations might be suitable
habitats for anammox-like reactions. Such environments include oxic/anoxic interfaces, such as those found at sediment/
water interfaces in hemipelagic and shallow sediments and in
stratified lakes and water columns of stratified basins such as
the Black Sea and the Cariaco Basin. Upon initial consideration, anaerobic ammonium oxidation seems unlikely to dominate processes in these environments, based on observation of
chemical distributions. Microaerophilic autotrophic nitrification, linked to anaerobic denitrification across the oxic/anoxic
interface, has been used to interpret the chemical distributions,
which typically show depletion of oxygen and nitrate above the
interface and accumulation of ammonium below it. Denitrification produces a net loss of fixed N, which would presumably
be much larger if anammox were also involved. Mass balance
measurements might provide insight into the potential for anammox involvement in natural systems. Dalsgaard and Thamdrup (Abstr. Am. Soc. Limnol. Oceanogr., 2001) recently reported evidence from 15N tracer experiments that an
anammox-like process may be at work in marine sediments and
at rates that should be evident in mass balance experiments.
In addition to the unconventional activities of “conventional” nitrifiers and denitrifiers and the discovery of novel N
metabolic pathways in new organisms, it has also been proposed recently that a short circuit of the nitrification/denitrification couple can also be accomplished abiotically. In marine
sediments, which typically contain relatively high manganese
levels, N2 gas can be produced by the oxidation of ammonia
and organic N by manganese dioxide in air (61) or linked in
series to anoxic organic matter oxidation through several biogeochemical reductants, including iron and hydrogen sulfide
Anoxic ammonia oxidation, whether it results directly in N2
formation (as in anammox) or in nitrate production (when
linked to manganese reduction), would introduce new links
into the aquatic and sediment N cycle. Failure to account for
anoxic ammonia oxidation might lead to an underestimate of
ammonium removal, because the products do not accumulate;
they are either lost to the atmosphere immediately or rapidly
reduced by the next step in the anaerobic cycling of organic
Although we have learned much about the N cycle in marine
systems, it must be remembered that our knowledge is superimposed on a dynamic and spatially variable biome. Knowledge gained by long-term studies demonstrates that our previous models of N cycling in the ocean are insufficient and that
there are ecosystem- and global-scale changes that have occurred and are occurring that have implications for the N cycle
in the oceans. For example, the conceptual model of Dugdale
and Goering (28) was developed during an era when nitrification and N2 fixation were assumed to be minor N fluxes in
Downloaded from http://aem.asm.org/ on January 10, 2012 by Princeton University Library
erence 18 and our unpublished data). Even methylotrophs, to
which some marine nitrifiers are related, possess genes with
homology to nirK and norB (112). The significance of this
denitrifying metabolism to the physiological ecology of nitrifying bacteria is unknown. However, its discovery casts uncertainty on the roles of “nitrifiers” and “denitrifiers” in trace gas
metabolism in the oceans and may complicate the use of molecular approaches for studying and detecting their presence
and activity in the environment.
Suboxic and anoxic waters and sediments tend to have large
fluxes in, and sometimes large accumulations of, the gaseous
intermediates of nitrification and denitrification. Trace levels
of N2O in oxic ocean waters are thought to arise from nitrification (113) and show a stoichiometric relationship to oxygen
utilization. Oxygen minimum zones (OMZs) show depth zones
of N2O accumulation and depletion. Nitrous oxide is depleted
in the core of the OMZ, where denitrification rates are thought
to be greatest. N2O maxima typically occur both above and
below the minimum. Stable-isotope measurement of nitrous
oxide from O2-depleted waters in the Arabian Sea indicates
that both nitrification and denitrification may contribute to the
signal (70) (Fig. 1). The surface waters of the ocean are generally slightly supersaturated with N2O, and the ocean constitutes a significant source of atmospheric N2O, especially in
regions containing OMZs (69, 80).
Autotrophic nitrifying bacteria exhibit some abilities in anaerobic metabolism as well. Enrichment cultures under chemolithotrophic conditions and with very low O2 concentrations
catalyzed the net removal of ammonium as N2 gas (68).
Schmidt and Bock have shown that Nitrosomonas eutropha
produces gaseous products, mainly NO and N2, during growth
on nitrogen dioxide gas (NO2) and ammonia (89). The process
proceeds at a lower rate than ammonia oxidation in the presence of a normal air atmosphere and supports cell growth.
Additions of NO2 and NO enhanced the complete removal of
N in the form of ammonia and organic N without the addition
of organic carbon substrates (114). The relevance of these
observations to marine N cycling is unknown, but the phylogenetic homogeneity of the beta-subdivision ammonium oxidizers suggests that analogous metabolic capabilities may exist
in marine strains as well.
A completely novel process, in which ammonia and nitrite
are converted anaerobically to dinitrogen gas, has recently
been reported from anaerobic wastewater systems (92, 97), and
the organisms responsible for this novel metabolism have been
identified as relatives of Planctomyces (46). Referred to as
“anammox,” the process probably involves a consortium of the
planctomycete organism and an autotrophic ammonia oxidizer
such as Nitrosomonas europaea or N. eutropha. The planctomycete oxidizes ammonium to N2 by using NO2⫺, which is
produced by the conventional ammonia oxidizer, as an oxidant.
Both oxygen and nitrite concentrations are maintained at
nearly undetectable levels by the metabolism of the members
of the consortium, and while both organisms grow quite slowly
(generation times for the planctomycete of two weeks or more
are reported), the net removal of ammonium occurs at a rate
25 times faster than that reported (91) for N removal by N.
eutropha growing anaerobically in pure culture (97). Still, it can
require months to establish an anammox enrichment, and the
consortium is stable only in bioreactors with long retention
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