Organic amendments, including slurry and FYM, represent a key source of energy and nutrients for soil microorganisms (Condron et al., 2010). Bacteria and fungi comprise 85% of the soil biomass, and their interactions with the soil faunal community in complex food-web systems regulate the turnover of OM and associated
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nutrients in soil (Wardle, 2002, Coleman and Wall, 2007). Decomposition of organic C and nutrients in soil is mainly driven by the activities of bacteria and fungi, because the heterotrophic nature of most of these organisms means that they rely on SOM as a source of energy and of nutrients (Hopkins and Gregorich, 2005, Winding et al., 2005). Soil microorganisms are usually classified with respect to their ecological characteristics, corresponding to the classification of copiotrophic and oligotrophic groups used for animals and plants in relation to resource availability (Fierer et al., 2007). Microorganisms whose relative abundance in C-rich soils is high are classified as copiotrophs, whilst oligotrophs have been observed to grow and reproduce in extremely C-poor soils (Langer et al., 2004). Furthermore, whereas copiotrophs are also classified as r-strategist or zymogenous, oligotrophs correspond to K-strategists or autochthonous (Hopkins and Gregorich, 2005). Table 2.3 summarises several ecological, morphological and biochemical traits that are assocaited with r- and K- strategist organisms as they exist within the soil microbial community.
The application of organic amendments, such as slurry and FYM, to soil has been observed to generate a microbial succession during the decomposition process. Copiotrophs/r-strategists, largely corresponding to gram-negative (G –ve) bacteria, dominate the early stages of decomposition, due to their adaptation to the organic amendments added to soil (Fierer et al., 2003, Fontaine et al., 2003, Cleveland et al., 2007, Fierer et al., 2007, Kramer and Gleixner, 2008, Fanin et al., 2014). In contrast, as substrate quantity and/or quality declines over time, oligotrophs/K-strategists, mainly consisting of gram-positive (G +ve) bacteria and fungi, become increasingly dominant, because of their tollerance towards environmental stress, such as low resource concentration. Therefore, these organisms are able to derive sufficient energy and nutrients from the decomposition of the older and more recalcitrant SOM (Fierer
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et al., 2003, Fontaine et al., 2003, Cleveland et al., 2007, Fierer et al., 2007, Kramer and Gleixner, 2008, Fanin et al., 2014). However, along with biosynthetic processes that lead to increasing microbial biomass, dissimilation processes can also occur following the addition of organic amendments to soil, with such processes being favoured when energy constraints exist or when energy demands are high (Geyer et al., 2016). Among these dissimilatory processes, maintainance respiration, represnting the basal energy requirement for purposes other than biomass production, and overflow respiration, the respiratory mechanism used by nutrient-limited microorganisms to mine SOM in search of N, P or other nutrients, are among the most important processes (Geyer et al., 2016).
According to Fierer et al. (2007), even though it is unlikely that a whole phylum would respond similarly to changes in C availability, for example following FYM/slurry application, and there is enormous physiological and phylogenetic diversity whithin each phylum, most of the microorganisms in the phyla studied in previous research presented common ecological traits in relation to C availability.
Several studies have described bacteria belonging to Acidobacteria that were most
abundant in C-poor soils, whereas α-, β-, γ-Proteobacteria and Bacteroidetes
displayed a higher relative abundance in soils with high C availability, either as an intrinsic soil property or because of organic amendments (Marilley and Aragno, 1999, McCaig et al., 1999, Axelrood et al., 2002, Padmanabhan et al., 2003, Héry et al., 2005, Cleveland et al., 2007, Nemergut et al., 2010, Wang et al., 2016). In contrast, Fierer et al. (2007) did not find any significant change in the overall abundance of α-
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Table 2.3. Ecological, morphological and biochemical traits that are likely to correspond to r- and K-strategists. Modified from Fierer et al. (2007).
Traits r-strategists K-strategists
Corresponding microbial groups Gram negative bacteria Gram positive bacteria and fungi
Ecological groups Copiotrophs Oligotrophs
Growth rates High growth rate when resources are non-limiting,
e.g. after addition of organic amendment
Low growth rate, predominant with recalcitrant SOM and outcompeted by r-strategists in rich-nutrient soils
Growth yield Low, inefficient biomass accumulation per unit
substrate
High, efficient substrate conversion into cell biomass, efficient resource utilisation
Maintenance requirements High, cells remain viable only when substrates are
supplied at a sufficiently high rate
Low, rates of substrate can also be low to maintain viability
Substrate uptake systems Low cell specific affinity for substrates, low
competition with limited substrates 1
High specific affinity, high capacity of simultaneous
uptake of mixed substrates 1
Receptivity to substrate
applications
Short lag time before growth after application of organic amendments, constitutive production of enzymes
Long lag in growth rates on organic amendments, induced production of enzymes
Metabolic quotient (qCO2,
respiration rate per unit of biomass)
High2 Low2
Temporal variability in
population size
High, pulsed substrate supply, fast rates of population turnover, short generation times
Low, fairly constant substrate availability, slow rates of population turnover, long generation time
Ease of cultivation High, best isolated in nutrient-rich media, visible
colonies with short-duration incubation
Low, visible colonies slow to appear, optimal growth with nutrient-poor media
30 Table 2.3. Continued.
Traits r-strategists K-strategists
Cell chemistry and morphology Low C:N and C:P owing to protein content and
high intracellular nucleic acid, spherical cells with
low surface area: volume ratio 3
Long or filamentous cells (hyphae in fungi) with high
surface area: volume ratio 3, high intracellular storage
capacity of nutrient reserves 4
Tolerance to environmental
stressors (e.g., pH, temperature)
High sensitivity to environmental stress, spore formation in suboptimal environment
Viability under stressful environmental conditions 1 Button (1993); 2 Dilly (2005); 3 Matin (1979); 4 Hirsch et al. (1979).
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