Impact of Innovative Agricultural Practices of Carbon Sequestration on Soil Microbial Community

Valeria Ventorino, Anna De Marco, Olimpia Pepe, Amalia Virzo De Santo, and Giancarlo Moschetti

Abstract This chapter deals with the impact on soil microbiology of innovative management techniques for enhancing carbon sequestration. Within the MESCOSAGR project, the effect of different field treatments was investigated at three experimental sites differing in pedo-climatic characteristics. Several microbiological parameters were evaluated to describe the composition of soil microbial communities involved in the carbon cycle, as well as to assess microbial biomass and activity. Results indicated that both compost and catalyst amendments to field soils under maize or wheat affected microbial dynamics and activities, though without being harmful to microbial communities.

6.1 Microorganisms in Soil

A huge number of microorganisms reside in soil and exert a variety of functions which contribute to ecosystem-level processes and maintenance of primary productivity in terrestrial ecosystems. Growth and metabolism of soil microbes can alter the solubility of soil mineral components and modify soil structure. Moreover, microbes are able to degrade organic compounds and release nutrients, thus regulating nutrients cycling and availability to plants. Microbial activity is responsible for most of soil respiration, thus including oxygen consumption and CO2 emission, and for immobilization of nutrients in soil microbial biomass. Soil microbes contribute to processes

Dipartimento di Scienza degli Alimenti, sez. Microbiologia Agraria, Universita di Napoli Federico II, Naples, Italy

Dipartimento di Biologia Strutturale e Funzionale, Universita di Napoli Federico II, Naples, Italy G. Moschetti (*)

Dipartimento DEMETRA, Universita di Palermo, Palermo, Italy e-mail: [email protected]

A. Piccolo (ed.), Carbon Sequestration in Agricultural Soils,

DOI 10.1007/978-3-642-23385-2_6, © Springer-Verlag Berlin Heidelberg 2012

of carbon sequestration in the soil humic fraction since they transform dead organic matter in such a recalcitrant pool. Furthermore, microbial activity is responsible for other essential biological processes, among which is nitrogen fixation. In the absence of soil microbial life, all biochemical transformation cease and the ecosystem sustainability is endangered (Wani and Lee 1995).

Although microbial C in natural soil does not exceed 1-2% of the total soil C (Paul and Clark 1989), it is constituted by a huge variety of organisms whose taxonomy and diversity are poorly known in comparison to aboveground organisms (Barot et al. 2007). Soil microbial communities are extraordinary complex and have been estimated to contain more than 4,000 different genomic equivalent in a single gram of soil (Torsvik et al. 1990). However, microbial species in soil are poorly abundant, most likely because conditions for their survival and growth are limited to a few sites where specific environmental factors, physical-chemical characteristics, and nutrient availability occur. Soil is a very heterogeneous environment encompassing solid, gaseous, and liquid phases. Microbial processes take place at the scale of soil aggregate, which is essentially a porous structure that varies both spatially and temporally. Because soil organic matter located within soil aggregates is physically protected from biodegradation, aggregates enhance carbon sequestration and soil structural stability (Six et al. 2000). Microbial dynamics is influenced by soil structure and the pore-size distribution within soil aggregates. Bacteria are restricted to grow and feed on the exposed surfaces of organic matter and/or inorganic particles. Fungi penetrate large pieces of organic matter and can thus extend their hyphae for centimeters and even meters in soil. The location of bacteria and fungi influences their activity as well as their survival to predation. The larger size of fungi may make them more vulnerable to predation, whilst small pores provide refuge for bacteria against predators (Six et al. 2006).

Plants are responsible for a large input of organic carbon into soil, thus becoming the main determinant of microbial life in soil through the complex food web of debris. It has been found that the type of aboveground plant community influences the composition of belowground soil microbial community in natural ecosystems (Reynolds et al. 1997; Cote et al. 2000; Smolander and Kitunen 2002; Rutigliano et al. 2004), as well as in semi-natural grasslands (Singh et al. 2009) and in agro-ecosystems (Marschner et al. 2001; Hedlund 2002). Moreover, arbuscular mycor-rhizal fungi require a plant host to survive.

Consequently, plants influence the spatial distribution of bacteria and fungi in soil (Kirk et al. 2004). The site of greatest soil activity is the root-soil interface, or rhizosphere. Roots affect soil structure, aeration, and biological activity and deeply impact soil microbial communities in their immediate vicinity, greatly increasing population densities of bacteria and fungi (Buyer et al. 2002; Marschner et al. 2002). As plants may allocate up to 40% of the assimilated carbon belowground, roots are the major source of organic matter into the surrounding soil through both root debris and exudates. Exudates are made up of sugars (50-70%), carboxylic acids (20-30%), and amino acids (10-20%), i.e., carbon-rich substrates that are able to regulate decomposition of recalcitrant soil organic carbon by controlling the activity and relative abundance of fungi and bacteria (Cheng et al. 2003; de Graaf et al. 2010).

Fig. 6.1 Living fungal hyphae observed by fluorescence microscopy after treatment with the viability stain fluorescein diacetate (FDA)

Fig. 6.1 Living fungal hyphae observed by fluorescence microscopy after treatment with the viability stain fluorescein diacetate (FDA)

Fda Viability Stain

Among soil organisms, actinomycetes, fungi (Fig. 6.1), and bacteria are the most abundant and most metabolically active. Bacteria and fungi generally comprise >90% of the total soil microbial biomass and are responsible for most of soil organic matter decomposition (Six et al. 2006). Fungi incorporate more soil C in their biomass than bacteria, and fungal cell walls are more recalcitrant than bacterial cell walls. Therefore, carbon sequestration may be larger in soils dominated by fungal communities than in those whose communities are dominated by bacteria (Six et al. 2006). Moreover, actinomycetes, fungi, and bacteria include organisms (such as aerobic and anaerobic cellulolytic bacteria), which are able to degrade cellulose and lignin (McCarthy and Williams 1992; Wellington and Toth 1994; Berg and McClaugherty 2008). In fact, degradation of plant biopolymers is the fundamental step in the carbon cycle and this process is important in soil systems. Since plants are the most relevant carbon providers in soil and cellulose and lignin are the most abundant constituents of plant tissues, they consequently represent the largest source of carbon in soil. Microorganisms transform plant polymers into simpler compounds, which are then made available to other micro-bial populations, and/or are stabilized in humic substances. The mineralization process during metabolic consumption of polymer by-products ultimately produces carbon dioxide that is emitted to the atmosphere. Moreover, actinomycetes regulate the microbial equilibrium in soil through production of antibiotics and probiotics that stimulate microflora and plant growth.

Fungi play a central role in many soil microbiological processes thus influencing the structure and functioning of plant communities and soil ecosystems. Fungi are immensely diversified, both structurally and functionally, and adopt different trophic strategies, since they occur as saprotrophs, symbionts, and pathogens. Individual fungi can often simultaneously colonize different substrates, such as living or dead plant tissues, woody debris, soil animals, and mineral substrates, thus allowing the transfer of substances. Filamentous fungi are responsible for decomposition of organic matter (e.g., lignin degradation) and nutrient cycling (Parkinson 1994; Van Elsas et al. 2007) and their activity is critical in regulating the availability of nutrients for plant growth. Moreover, fungi are food for nematodes, mites, and other larger soil organisms, which are also predators or parasites of other soil organisms.

6.2 Impact of Agricultural Management on Soil Microbial Communities

Agricultural management produces a disturbance of both abiotic and biotic components of soils. The most negative impact is the loss of soil organic matter (SOM) (Balesdent et al. 1999), with consequent increase in soil erosion and decrease in soil structure stability (Bronick and Lai 2005) and fertility. In agro-ecosystems, soils degradation is the outcome of unsustainable techniques aimed to increase production in the short term without paying attention to the conservation of soil resources. Agricultural land management, such as cropping systems (Kuske et al. 2002) and tillage systems (Peixoto et al. 2006) may affect soil characteristics, including physical, chemical, and biological properties and processes. It has been observed that tillage reduces soil microbial populations (Ibekwe et al. 2002) and different enzymatic activities (Carpenter-Boggs et al. 2003). Tillage has a catastrophic effect on fungi as it physically breaks the hyphae and severely damages the mycelium, thus consequently hampering the stability of soil aggregates whose particles are transiently bound together by fungal hyphae. Six et al. (2006) showed that no-tillage enhances fungal biomass with a consequent quantitative and qualitative SOM improvement that is attributed to the positive influence of fungi on aggregate stabilization.

Alternative agricultural techniques, such as minimum tillage, have been developed to improve soil quality by progressively recovering soil organic matter (Lu et al. 2000). In long-term experiments on tillage comparison along two climatic gradients, Frey et al. (1999) observed that in response to reduced tillage both fungal biomass and fungal/bacterial biomass increased at all sites. Thus, less intensively managed agro-ecosystems, such as those managed with no-tillage practices, more closely resemble natural ecosystems, which are dominated by fungi (Bayley et al. 2002). On the other hand, intensive cultivation leads to progressive SOM depletion with a consequent microbial biomass reduction, loss of microbial diversity and reduction of microbial activities (Bastida et al. 2006). Buckley and Schmidt (2001) performed a large-scale experiment with replicated plots under distinct management regimes ranging from conventionally tilled annual cropping systems to abandoned fields. The effects of tillage, fertilization, and plant community composition on the structure of microbial community were evaluated. They found that microbial communities differed significantly between fields that had never been cultivated and those with a long-term history of cultivation. However, microbial community structure was very similar in plots that shared a long-term history of cultivation, despite differences in plant community composition, chemical inputs, tillage, and productivity. They argued that microbial communities respond to soil characteristics which require long time periods to recover from disturbance. Indeed, the organic pools of carbon and nitrogen can be depleted by long-term agricultural practices and may require decades or even centuries to recover pre-agricultural levels. In a study dealing with soil quality as related to different land uses in Southern Italy, Marzaioli et al. (2010) report that soil quality, evaluated by a set of parameters including microbial indexes, was strongly and negatively affected by permanent crop management. Moderate grazing activity, as well as crop management comprising mulch cover on soil, had a lower negative impact. Moreover, these authors found that the abandonment of cultivated lands, with consequent development of shrublands, produced an improvement of soil quality, thus suggesting a good recovery capacity.

Microbes are also affected by fertilization (Marschner et al. 2003), both directly and indirectly. Zhong and Cai (2007) showed that the long-term application of P and N indirectly affected microbial parameters in soil by increasing crop yields and promoting SOM accumulation. Fertilizers used in agricultural production systems include mineral (urea, ammonium nitrate, sulfates, and phosphates) and organic (animal manures, biosolids, and composts) fertilizers. Composted materials vary widely in their characteristics such as dry and organic matter content, pH, carbon and nitrogen content, plant residues, and microbial community composition. Application of compost to soil is used to improve soil fertility and structure since it increases the carbon, nitrogen, and phosphorus content in soil (Hartz et al. 2000; Filcheva and Tsadilas 2002; Adediran et al. 2003) and contributes to the stabilization of soil aggregates (Bresson et al. 2001; Barzegar et al. 2002). Although compost amendments differ in origin of material and application rates, organic amendments to soil generally result in an increase of microbial proliferation in soil (Bunemann et al. 2006). In fact, organic-matter-rich amendments are also used to stimulate soil microflora in degraded and arid environments (Ouedraogo et al. 2001; Ros et al. 2003). However, compost amendment can also cause negative effects by altering the microbial biomass, size, function, and diversity, if contaminant residues are present at toxic levels (Gomez 1998; Zheljazkov and Warman 2003). Nevertheless, soil microbial response is generally transient (Calbrix et al. 2007) and microbial characteristics can return to their baseline within a few years (Speir et al. 2003; Garcia Gil et al. 2004) depending on nature of organic amendments and level of compost application (Albiach et al. 2000; Garcia-Gil et al. 2000).

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