Agriculture Reference
In-Depth Information
soils (cambisols) are the dominant group in the Mediterranean basin. In general, they are
fragile, shallow and with a distorted soil profile. In the north where climate is more humid,
soils are generally richer in organic matter with relatively higher humidity, whereas in south
there is an accelerated mineralization of soils. Subject to erosion soils are often “rejuvenated”
and it results in soils with poor organic matter and low water-holding capacity (de Franchis
and Ibanez 2003). The depth of the organic layers is usually thin (0-5 cm) while that of the
mineral rocky layers ranges from 0.5 -1m. The humus layer is thin as well. The rocky part of
the soil profiles exceeds 60%. Carbonate and iron oxides are abundant throughout or in parts
of the soil profile (Papatheodorou and Stamou 2004). Mediterranean soils are rich in nitrogen
and deprived in extractable phosphorus (Diamantopoulos et al. 1994, Papatheodorou 1996).
Studies referring to Mediterranean soils are dealing either with structure including soil
physical characteristics (aggregation, infiltration, conductivity) which determine the
resistance of soil to erosion (Lavee et al. 1998) or with function. Function was discussed in
terms of rates of decomposition processes (Argyropoulou et al. 1993, Stamou et al. 1994), of
the amounts of available nutrients supplied to plants (nitrogen, phosphorus, potassium etc)
(Henkin et al. 1994, Willott 2000, Fillery 2001, Kabengi et al. 2003, Peco et al. 2006) or in
terms of the community structure of soil biota with emphasis on arthropods (Sgardelis et al.
1981, Stamou and Asikidis 1992, Sgardelis and Margaris 1993, Stamou et al. 1993, Sgardelis
et al. 1995, Stamou 1995, Stamou 1998). A highly important component of soil functioning
that recently attracts substantial interest is the microbial community of soil. It relates to the
development of appropriate techniques that offers the opportunity for greater insights into
microbial community structure.
Microbes belonging to the lower trophic level are responsible for organic matter
transformations. They are known as the early indicators of soil changes induced by
modifications in climatic variables (Insam 1990) or in agricultural practices (Bending et al.
2004). Depending on the involved functions, microbes can be categorized into different
functional groups such as ammonia oxidizers, denitrifiers, heterotrophs (Wertz et al. 2006)
while depending on their relation to other organisms they are characterized parasites,
pathogens and mutualistic symbionts (van der Putten 2007). Since in a bacterial world the
species concept is obscure, the functional diversity is adopted as a way to overcome this
difficulty. Moreover, crucial for the maintenance of soil system is not the species composition
but the functional aspect of the microbial community (Øvreas 2000). Functional diversity can
be defined as the numbers, types and rates at which an array of substrates is utilized by
microbes (Zak et al. 1994). The substrates are provided in Biolog plates specified for bacteria
or fungi respectively. This method is widely used since 1995 and although it is considerable
criticized (Preston-Mafham 2002), it offers valuable information for the comparison of
functional diversity from different sites provided that the same experimental protocol is used.
Apart from the functional diversity, structural diversity of microbial communities can be
exploited by analysing the patterns of phospholipid fatty acids (PLFA; Tunlid and White
1992). Certain signature fatty acids in the overall PLFA profiles are specific for bacteria,
fungi and actinomycetes respectively and can be used as indicators of stressful impacts on
microbes (Guckert et al. 1986). There are standard methods by which phospholipids are
converted to ester-bonded fatty acids (FAMEs). The advantage of this method is that it
specifically describes the community of the living microbiota (Fernandes 2006). The total
concentration of PLFA is also a measure of viable microbial biomass (Zelles et al. 1995).
Moreover, by adding radioactive substrates, a measure of the active community could be
