1c. Primary production
Primary production can be defined as the assimilation of inorganic carbon and nutrients in organic matter by autotrophs. Thus, primary production implies a rate. Usually only phytoplankton primary production is measured. Chlorophyll a is used as a proxy for algal biomass. However, primary production does not necessarily represent biomass, since for primary production measurements grazing and sedimentation are not taken into consideration. Gross primary production includes respiration processes (Underwood & Kromkamp 1999). In the estuaries considered in TIDE we can distinguish phytoplankton in the water column and microphytobenthos at the sediment upon intertidal mudflats. Microphytobenthos can contribute up to 50 % of primary production (Underwood & Kromkamp 1999 and refs herein). However, upscaling is found to be difficult, because of spatio-temporal variability.
Phytoplankton in estuaries largely depends on light availability (the so-called euphotic depth, the depth at which primary production equals respiration). The ideal mixing depth to euphotic depth ratio for production to exceed respiration, should be smaller than 6 (Cole & Cloern 1984 in Underwood & Kromkamp 1999). Microphytobenthos is more temporal and spatial variable because of flooding dynamics (and co-occurring different light regimes) and also depends upon the cohesiveness of the sediments. However, while light can penetrate deeper in sandy sediments, sandy sediments do not retain nutrients and within these loose sediments microphytobenthos can become nutrient limited (Underwood & Kromkamp 1999).
Hence, also nutrients might play a crucial role in affecting both biomass and primary production of phytoplankton and microphytobenthos. This can be examined by nutrient ratios. Often a correlation between chlorophyll a and dissolved inorganic nitrogen can be found. A nutrient gradient can modify exchange at the different tidal marshes and mudflats along the estuary (Underwood & Kromkamp 1999).
Furthermore, a species succession is defined by the salinity gradient in estuaries. Estuaries can be further subdivided in well-mixed and more stratified estuaries. This is largely function of tidal range. When tidal range exceeds 4 m, estuaries are considered macro-tidal. These estuaries are usually well-mixed. A tidal range between 2 and 4 m is called meso-tidal and this type of estuaries can be partially stratified, like is observed in the Elbe estuary (see earlier). Differences in mixing patterns are ought to be the reason why estimates for primary production are so different between estuaries (Underwood & Kromkamp 1999).
Other influencing factors are grazing, cell lysis, viruses and sedimentation. For grazing, abundance and grazer community composition are most important (personal communication Andreas Schöl 2013), next size selective grazing (Underwood & Kromkamp 1999), as it defines whether algae are directly processed to the microbial loop or whether algae first pass through the linear food chain.
Hydrology appears to be a very important factor. In the Elbe phytoplankton peaks are mainly regulated by the freshwater discharge and resulting residence time in the freshwater section of the estuary. When discharge is high, phytoplankton peaks are shifted more downstream. When discharge is low and residence time in the river itself is large, phytoplankton peaks are mainly observed in the upstream part of the river, and decay of algae is shifted downstream, most likely related to oxygen deficiencies (Quiel et al. 2011). Phosphorus limitation was demonstrated to have only limited effect. Most likely diatoms in the Elbe are capable for phosphorus storage. Arndt et al. (2011) demonstrated that temporal and spatial patterns in primary production in the Scheldt estuary during a summer diatom bloom are in fact mainly regulated by the physical environment. Higher river discharges placed the first controlling factor for primary production within the Scheldt estuary, next followed by light climate and silica limitation (Arndt et al. 2011).
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