Diversity of Microbes

Several studies have investigated microbial communities under organic and conventional systems. Overall, reports on differences in bacterial communities between organic and conventional systems are not so limited (Foissner 1992; Wander et al. 1995; Yeates et al. 1997; Shannon et al. 2002; Girvan et al. 2003; Hole et al. 2005; van Diepeningen et al. 2006), but differences in fungal communities are scanty (Shannon et al. 2002; Sekiguchi et al. 2007). However, there is evidence of a general trend towards elevated bacterial (Fraser et al. 1988; Scow et al. 1994; Mader et al. 1995; Bossio et al. 1998; Gunapala and Scow 1998; Widmer et al. 2006; Melero et al. 2006; Marinari et al. 2006; Elfstrand et al. 2007; Stark et al. 2007) and fungal (Fraser et al. 1988; Yeates et al. 1997; Shannon et al. 2002; Elfstrand et al. 2007) range and abundance under organic farming systems. In a meta-analysis, Bengtsson et al. (2005) reported 30% higher species richness in organic farming. Peacock et al. (2001) reported 30-42% increase in gram-negative bacteria Phospholipid fatty acid (PLFA) biomarkers under organic management practices than conventional. Amendment with carbon rich manures was cited as key factor (Fraser et al. 1988; Gunapala and Scow 1998; Bossio et al. 1998; Peacock et al. 2001; Gomez et al. 2006) along with versatile crop rotations, reduced applications of nutrients, and the ban on pesticides helps in improving biological activity under organic systems (Hansen et al. 2001). Furthermore, addition of farmyard manure for 130 years induces in microbial community towards more bacteria dominated community in specifically coarse sand fraction (Poll et al. 2003). The organically managed soils contained higher numbers of copiotrophic and oligotrophic bacteria, and had a higher diversity in both the eubacteria (van Diepeningen et al. 2006).

Bacterial community was cited too diverse to evaluate the difference, whereas fungal community was suitable for comparing the effect of management practice (Sekiguchi et al. 2007). Furthermore, the fungal community was considered a more suitable indicator of changes due to management practices especially in organic farming as it is responsible for the decomposition of organic matter. Shift in fungal community structure was reported due to organic management practices (Fraser et al. 1988; Yeates et al. 1997; Shannon et al. 2002; Elfstrand et al. 2007; Sekiguchi et al. 2007). Stark et al. (2007) in a recent study concluded that microbial community structure was strongly influenced by the presence or lack of substrate, while the type of amendment (organic or mineral) had an effect on microbial biomass size and activity.

Arbuscular mycorrhizal fungi (AMF) play a crucial role in nutrient acquisition and soil fertility. Studies related to AMF root colonization under organic management practice has been investigated in detail (Cavagnaro et al. 2006; Douds et al. 1997; Galvez et al. 2001; Gryndler et al. 2006; Harinikumar and Bagyaraj 1989; Mader et al. 2000; Oehl et al. 2004).

It was found that the percentage of root length colonized by AMF was 30-60% higher in low-input farming systems than in conventionally farmed soils. Variation of AMF root colonization was explained by chemical properties of the soils especially the effect of soluble soil P being most pronounced (Mader et al. 2000). In another study in Central Europe it was found that AMF spore abundance and species diversity was significantly higher in the organic than in the conventional systems (Oehl et al. 2004). Mineral fertilizer can have a profound negative effect on AMF, as reported by Galvez et al. (2001), who found less spore in mineral-fertilized soil than in organic soil. Gryndler et al. (2006) found that mineral fertilization reduced the growth of AMF, as estimated, using both measurements of hyphal length and the signature fatty acid 16:1w5, whereas manuring alone increased the growth of AMF. Some species of AMF may even be severely depressed by conventional management (Oehl et al. 2004). On the other hand organic management increased sporulation (Douds et al. 1997) or propogule density in the soil (Harinikumar and Bagyaraj 1989). Studies concluded that AMF species present in natural ecosystems are maintained under organic farming but severely depressed under conventional farming, indicating a potentially severe loss of ecosystem function under conventional farming.

Nematodes play a major role in decomposition and nutrient cycling in soil food webs. Due to its important role in trophic interactions, they have received attention in farming systems especially in organic farming. Although nematodes represent a relatively small amount of biomass in soil, their presence across many trophic levels in soils is vitally important in soil environments and ecosystem processes (Ingham et al. 1986).

In general, higher nematode populations were reported in organic farming than in conventional systems (Foissner 1992; Yeates et al. 1997; Neher 1999; Bulluck and Ristaino 2001; Bulluck et al. 2002; van Diepeningen et al. 2006; Griffiths et al. 2007). Griffiths et al. (2007) reported that application of poultry manure altered the types of nematode present and favored bacterial feeders and rhabditids in particular within a short term as compared to farmyard manure. Diversity of population based on its specific functions were known to be more influential in a soil ecosystem and variations were cited in organic farming practices (Neher 1999; Neher and Olson 1999; Berkelmans et al. 2003; Mulder et al. 2003). Nematodes could be primary, secondary or tertiary consumer. Plant-parasitic nematodes are herbivores and thus primary consumers. Bacterial- and fungal-feeding nematodes are common secondary consumers. Predatory and omnivorous nematodes are tertiary consumers (Beare et al. 1992). Organic soil amendments can have large effects on plant-parasitic nematode dynamics (1996; 1997; Castagnone-Sereno and Kermarrec 1991; McSorley and Gallaher 1995, Crow et al. 1996, Neher 1999; McSorley and Frederick 1999). The plant-parasitic nematode Meloidogyne incognita was reduced in soils amended with different organic substrates, and the reduction was attributed to the release of ammoniacal nitrogen (Castagnone-Sereno and Kermarrec 1991; Crow et al. 1996). Reductions in nematode populations occurred when chitin was added to soil infested with plant-parasitic nematodes (Hallmann et al. 1999). Chicken manure, summer cover crops, or green manures can also suppress plant-parasitic nematodes (Abawi and Widmer 2000; McSorley et al. 1999; Viaene and Abawi 1998). In another study, members of the genus Filenchus were found more in organic soils than in conventional soils (van Diepeningen et al. 2006).

In general, bacterial-feeding nematodes were more abundant under organic management, whilst fungal-feeding nematodes were more abundant in conventionally managed soils (Berkelmans et al. 2003; Ettema 1993; Ferris et al. 1996; Jaffee et al. 1998; Hole et al. 2005; Neher and Olson 1999; Scow et al. 1994). Crop species influenced nematode communities to a greater extent than management systems in a comparative study of organic and conventional field soils in North Carolina (Neher 1999). Soils under organic and conventional management production in California showed little difference in bacterivore populations or total nematode populations over time, but changes in genera of bacterivores were noted (Ferris et al. 1996). Numbers of bacterivorous nematodes tend to increase after organic amendments are applied to soil since bacterial populations that provide a food base are greater after application of organic amendments (Bouwman and Zwart 1994; McSorley and Gallaher 1996; Ferris et al. 1996; McSorley et al. 1999; Bongers and Ferris 1999; McSorley and Frederick 1999). Bacterivorous nematodes were found to be soil texture specific. Bacterivorous Acrobeloidus nanus was found to be in organic sandy soils and Panagrolaimus was found in larger numbers in the organic clayey soils than in the conventional clayey soils while in the sandy soils it occurred significantly more than in the conventional soils (van Diepeningen et al. 2006).

Although studies related to nematode-trapping fungi were limited it was observed that the number of species of nematode-trapping fungi was slightly but significantly greater in organic than in conventional plots. Two species (Arthrobotrys dactyloides and Nematoctonus leiosporus) were detected more frequently in organic plots, and the population densities of A. dactyloides and N. leiosporus were greater in organic than in conventional plots. Two other species (A. haptotyla and A. thaumasia), however, tended to be more numerous in conventional than in organic plots, and the total density of nematode-trapping fungi was similar in organic and conventional plots (Jaffee et al. 1998). Additionally, fungivorous nematodes were consistently lower in soils amended with synthetic fertilizers than in soils with organic amendments (Ferris et al. 1996; Bulluck et al. 2002).

In recent past diversity indices were also calculated in order to find out the difference in the functional diversity of microbes under organic and conventional management practices (Crecchio et al. 2004; Gomez et al. 2006: Mulder et al. 2003; van Diepeningen et al. 2006) (Table 10.1). Use of descriptive indices, including the enrichment index, structure index, and channel index provided useful information about the effects of organic amendments on the structure of nematode communities (Bulluck et al. 2002). In an Italian study it was reported that H0, S, and E indices were found to be consistently higher in conventional soil than in organic farming soils and cluster analysis of Community Level Physiological Profiles indicated that the microbial communities are qualitatively much more uniform in organically managed soil (Crecchio et al. 2004). Whereas, Ros et al. (2006) reported that the Shannon diversity index (H) was similar in organic and conventional soil. In contrast, bacterial species richness (R) and Shannon index (H) were enhanced due to the incorporation of organic amendments compared to the unamended plots (Gomez et al. 2006). The Shannon-Wiener diversity index for the genera belonging to fungal and bacteria feeding nematodes shows remarkable differences among organic, conventional and intensive agriculture (Bulluck et al. 2002; Mulder et al. 2003).

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