General context
The general objective of PRIMO is to deconvoluate the relative influences of physical and
biogeochemical processes, in the formation and dynamics of the OMZ off Chile-Peru, at
various temporal and spatial scales (see introduction). Physical and biogeochemical studies
will be undertaken, and integrated in the regional model described in the section “integration”,
to address the general objective of PRIMO. In this biogeochemistry section, we will focus on
original studies that will be undertaken, from an experimental point of view but in the
perspective of fuelling the regional model, to understand the impact of the OMZ on
production and mineralization processes, both in the water column and at the sediment-water
interface.
1. Vertical structures as influenced by the OMZ
During the PRIMO cruise, stocks and fluxes of biogenic elements through the water column
will be measured along transects, and the community structure will be described. This
includes profiles (as sampled by Go-Flo bottles) of dissolved constituents (macro- and microinorganic nutrients, dissolved organic matter), and particulate matter (POC, PON, POP, BSi,
lithogenic constituents), as well as flux measurements (as sampled by sediment traps and
estimated from U-Th disequilibria) of sinking biogenic matter. These are classical
measurements that will be undertaken above, within and below the OMZ, with detailed
description where gradients are the sharpest.
It is well established that most of the sinking flux occurs, for particulate matter, in the form of
zooplankton faecal pellets and aggregates (Turner, 2002). These are difficult to sample and
the mode of transport of biogenic particles through the water column will be explored through
the use of a marine video profiler (add zooscan ?) which will provide essential information on
the size spectra of the particles and their viability. The vertical structure of communities will
also be described, as these play a major role in the mineralization of biogenic matter. Bacteria
have been described in section on PP and the focus here will be on zooplankton and the role
of the OMZ in structuring zooplankton communities.
Exhibiting several types of trophic status, zooplankton are a key component of the pelagic
ecosystem. Specifically, they could be important consumers of primary production (see
section on PP) but also high contributors to and modifiers of the vertical flux of organic
matter. Even if sporadic hypoxia is deleterious on the pelagic fauna, a permanent structure as
an OMZ have fauna adapted to low O2. Three types of organisms could be found within an
OMZ, 1) the permanent residents which are physiologically and morphologically adapted to
low O2 levels, 2) organisms in diapause which will leave the OMZ to feed, grow and
reproduce, and, finally 3) diel migrants staying in the OMZ for short time (but trying to avoid
this water mass). Obviously, the kind of organisms present will have incidence on the
exportation of particulate matter. Thus, the occurrence of a permanent and relatively shallow
OMZ has implications on the distribution and functioning of the zooplankton community,
and, in turn, on the fate of the organic matter produced. To improve our understanding of the
evolution of the OMZ and its role in the, the part played by this community should be
specified. Several questions arise:
 How does the size structure of the zooplankton community evolve in time and space?
According to the dominant size class, the potential export will be affected.
 Is a specific community be observed in the OMZ and above/below it? The mid-water
zooplankton (i.e. in the euphotic layer) feed and act as repackagers, and influence the
type of sinking particles. If falling particles are not eaten within the OMZ (due to the
potential scarcity of consumers), this food source can fuel the deeper zooplankton. In
this case, what are their physiological features (diet, ingestion, egestion,
remineralisation) and their incidence on the transfer of matter?
 As we know that oxygen levels determine the vertical distribution of zooplankton, how
do the space and time variability of the OMZ govern the vertical distribution of
zooplankton, as well on a daily base as a seasonal one? Is there an association between
zooplankton biomass and O2 concentration?
 How does it influence the species diversity?
2. Original process studies to be undertaken
Numerous original process studies can be undertaken in an area with such specific properties
as the OMZ of the SEP. In this section, the focus will be on processes that impact O2
concentrations which is the primary objective of PRIMO. However, most of these processes
are strongly impacted by the presence of the OMZ itself, and this influence of the OMZ needs
to be accounted for in the 3D regional model and thus, in the experimental design of all
process studies to be undertaken in this context. Original process studies have thus been
selected, which will be needed and designed with the objective of fuelling the 3D model
described elsewhere. They concern (i) remineralization rates of organic matter and associated
ballast minerals (Armstrong et al., 2002), (ii) the complex reactions of the N cycle
(denitrification, nitrification, ammonification …) and (iii) trace metal speciation.
2.1. Impact of OMZ on mineralization processes
It is believed that the intensity of OM recycling in the water column is a key control of OMZ
formation and dynamics (ref). Thus, understanding the functioning of the OMZ implies to
improve our knowledge on the processes that control the intensity of OM recycling, be it
POM or DOM. This intensity depends upon (i) the timing and magnitude of the vertical fluxes
of POM and DOM, (ii) the mode of transport through the water column (aggregates, faecal
pellets), (iii) the community structure encountered during sinking, (iv) the quality of the
material sinking and in particular, its degradation degree, and (v) the degree of association
with ballast minerals (CaCO3, BSiO2).
As seen in section 1., bottles, in situ pumps, sediment traps and a PVM will be deployed to
quantify the timing and magnitude of OM fluxes, characterize their mode of transport through
the water column ; community structures, as influenced by O2 concentrations, will also be
described from surface waters down to the sediment-water interface, from microbes to
zooplankton species. The process studies that will be undertaken deal with the influence of O2
concentration on the degradation of POM and DOM as well as on the decoupling of
biogeochemical cycles (C, N, Si, Fe, P?) during degradation/dissolution processes.
These original experiments will be performed during the cruise, on samples collected at
various levels of oxygen concentrations. They need to be designed in close collaboration with
modellers, to ensure complementarity with the model developments necessary to account for
changes in OM lability and ballast dissolution properties with O2 concentrations. Preliminary
experiments need to be conducted in the lab, long before the cruise, because they require
specific experimental conditions and training. Do we need to detail more the experimental
design at this stage ? We could briefly describe, either isotopic experiments such as those
conducted in Marseille and in Brest (ORFOIS project), or combined degradation of OM
/ dissolution of ballasts experiments (involving biomarkers: project MedFlux).
Biogeochemistry Objective 1 (BO)1 – to understand and quantify the influence of the
OMZ on the mineralization of OM and associated ballast minerals.
2.2. Impact of OMZ on N cycle
The OMZ of SEP is a unique area where the combination of strong upwelling, high
productivity, intense oxygen minimum and presence of this minimum in the euphotic zone
induces the cohabitation of a whole consortium of organisms with mutual benefit:
phytoplankton and autotrophic bacteria (Prochlorococcus, Synechococcus, yielding a
subsurface chlorophyll maximum), chemiolitothrophic and heterotrophic bacteria. The
presence of these microbial organisms has a strong impact on the N cycle in this area, much
more complicated than previously thought, as well as on N2O and CO2 production.
Model improvement are presently ongoing (Ph.D., C. Bonhomme), to improve the
parameterization of the N cycle in the 3D regional model (see modelling section). This
improvement will be fuelled by process studies which will be conducted during the PRIMO
cruise. These include the classical direct measurements of new (NO3 and N2) and regenerated
(NH4) production , as well as regeneration of NH4, all in surface waters. These also include
the uptake of NO3 and NH4 by bacteria as well as direct measurements of nitrification,
denitrification, ammonification, NOD excretion, from surface waters down to deep waters,
through the OMZ.
BO2 – to understand and quantify the complex mechanisms controlling the N cycle across
this OMZ inhabited by a complex consortium of autotrophic and heterotrophic
communities.
2.3. Impact of OMZ on trace metals speciation
In coastal upwelling regions, rich in macronutrients, trace metals have the potential to regulate
the dynamics of primary production, as already shown for Fe (Bruland et al., 2001; Hutchins
et al., 2002). Consequently, the cycle of these trace elements need to be studied as they may
influence the dynamics of the OMZ through their influence on biological productivity and
export fluxes (see “production” section). Interestingly enough, the OMZ can in turn affect the
cycling of these trace elements by modifying the redox conditions which are known to affect
the speciation of these elements. For example, Fe is very soluble in seawater under anoxic or
reducing conditions (Bruland et al., 1991). It has even been suggested that vertical advection
of Fe from the OMZ could constitute the principal source of Fe for surface waters in Peru,
impacting primary production and the composition of phytoplankton assemblages which are
dependent upon the speciation and biodisponibility of Fe in this area (Hutchins et al., 2002).
Trace metal (Fe, Zn, Co and Cd) speciation (redox, organic, and size fractionation) will be
studied during the PRIMO cruise throughout the whole water column, with a particular focus
where oxygen gradients are the sharpest. On-board incubations with phytoplankton and
bacteria communities will also be performed to study the interactions between metals
(chemistry, (co)-limitation, substitutions) and biological activity. On-deck incubations (kinetic
studies) of samples collected in metal-limited and metal-rich areas will allow to investigate
the recent hypotheses of limitation by or natural fertilization in trace metals in the Chilean
coastal upwelling.
BO3 – to unsderstand and quantify trace metal speciation (Fe, Zn, Co, Cd) and their
interactions with the trophic network in the OMZ and the surface oxic layer.