Management strategies that conserve C in agricultural soils may have ancillary benefits quite apart from atmospheric CO₂ removal. Foremost among these is a favourable effect on soil productivity. Numerous studies have shown a strong link between the organic C content of a soil and its quality for crop production (e.g., Carter et al., 1997; Christensen and Johnston, 1997; Herrick and Wander, 1997). Consequently, a gain in soil C may promote crop yields, and preserve or enhance future soil productivity (Cole et al., 1997; Rosenzweig and Hillel, 2000). For example, application of fertilizers to agro-pastoral systems in parts of South America may not only induce soil C accumulation, but also enhance agricultural productivity (Fisher et al., 1997). Many of the practices advocated for soil C conservation – reduced tillage, more vegetative cover, greater use of perennial crops – also prevent erosion, yielding possible benefits for improved water and air quality (Cole et al., 1993). As a result of these benefits, adoption of practices that promote C conservation in agricultural lands is often justified even without the additional benefits arising from CO₂ mitigation.

Soil carbon sequestration, however, may sometimes have some potential adverse effects on the emission of other GHGs, notably nitrous oxide (N₂O). Where the C accumulation requires addition of higher amounts of N as fertilizer or manure, it carries the risk of increased N₂O emissions (Cole et al., 1993; Batjes, 1998). Furthermore, some C-conserving practices like reduced tillage may increase N₂O emissions by favouring higher soil moisture content (Cole et al., 1993; MacKenzie et al., 1997; Ball et al., 1999), though this effect is not always observed (e.g., Jacinthe and Dick, 1997; Lemke et al., 1999). Because the radiative forcing of N₂O is about 310 times that of CO₂ (kg per kg), when calculated over a 100-year time frame (IPCC, 1996), even a small increase in N₂O emissions, if confirmed, can significantly offset gains from C sequestration.

Carbon sequestration strategies may also have an effect on energy use and, hence, CO₂ emission from fossil fuel use. Changes in fertilizer use, pesticides, and agricultural machinery may enhance or offset any gains in soil C because of CO₂ released from fossil fuel. For example, roughly 1 kgC (or more) is released into the atmosphere as CO₂ per kgN used (Flach et al., 1997; Janzen el al., 1998; Schlesinger, 1999). In tropical areas where shifting cultivation is now practiced, intensification of crop production may maintain higher C stocks, by leaving more land under natural forest, but additional fossil fuel may have to be used to compensate for the fuelwood previously collected from the fallow period (van Noordwijk et al., 1997). In some cases, the adoption of C-conserving practices may reduce energy use. For example, using less intensive tillage may not only favour soil C gains, but also permits savings in CO₂ emission from fossil fuel combustion (Kern and Johnson, 1993). An evaluation of the net benefit of a C-sequestering practice, therefore, must consider energy use in addition to changes in C stocks. Whereas the duration of soil C gain in response to improved management may be finite, savings in CO₂ emissions from energy use continue indefinitely (Cole et al., 1997).

Aside from their secondary effects on GHG emissions, practices that sequester soil C may also have other potential adverse effects, at least in some regions or conditions. Possible effects include enhanced contamination of groundwater with nutrients or pesticides via leaching under reduced tillage (Cole et al., 1993; Isensee and Sadeghi, 1996), and possible environmental effects from widespread application of manures or sludges (Batjes, 1998). These possible negative effects, however, have not been widely confirmed nor quantified, and the extent to which they may offset the environmental benefits of C sequestration is uncertain.

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