CONSUMO ELÉCTRICO

The community structures of AOB have been studied in various soils that differ in environmental conditions such as pH, NH4+ concentration, type of fertiliser application,

Table 2.2 The presence of autotrophic AOB in soils in relation to environmental factors and soil management.

Factors contributing to diversity of AOB in the soil

Clusters by 16S rDNA/ amo A and the type of AOB present

Reference

1. Agricultural and forest soils, acidic pH 16 S rDNA Nitrosospira cluster 2 Stephen et al. 1996, 1998; Nugroho et al. 2005

2. Limed acid forest soil, 16S rDNA Nitrosomonas (dominant), Nitrosospira-like (minority) Carnol et al. 2002 3. High NH4+ concentration

a) Early succesional grassland soil with neutral pH

a) 16S rDNA Nitrosospira cluster 3

Kowalchuck et al. 2000a, 2000b

b) Incubated agricultural soil, over a period of 16 weeks

b) amoA

Nitrosospira cluster 3

Avrahmi et al. 2003 4. Low NH4+ concentration

a) Older succesional

grassland soil with acidic pH

a) 16S rDNA Nitrosospira clusters 2 and 4

Kowalchuck et al. 2000a, 2000b

b) Incubated agricultural soil, over a period of 16 weeks

b) amoA Nitrosospira cluster 1 (disappeared after >16 weeks of incubation and Nitrosospira cluster 9 Avrahmi et al. 2003 5. Moisture limitation, forest soil (pH 4.1-5.2) 16S rDNA

Nitrosomonas, exhibit rapid recovery after rewetting dried soil Hastings et al. 2000 6. Temperature effect (incubated agricultural soil) a) 4-10 oC amoA Nitrosospira cluster 1 Avrahmi et al. 2003 b) 25-30 oC amoA

Nitrosospira clusters 3 and 9

Avrahmi et al. 2003

7. Irrigated soils Avrahmi et al. 2003

a) with liquid fertiliser (NPK) amoA

Nitrosospira-like

Oved et al. 2001

b) with effluent amoA

Nitrosomonas-like

Oved et al. 2001 8. Long term (16 years)

application of mineral fertiliser (NPK) and organic manure amoA Nitrosospira cluster 3 Chu et al. 2007

9. Agricultural soils amended with pig slurry

amoA

Nitrosomonas europaea 16S rDNA Nitrosospira

Most of the molecular studies have suggested a predominance of Nitrosospira species (particularly clusters 2 and 4) in acidic soil environments, while other members of both

Nitrosospira (particularly cluster 3) and Nitrosomonas have been detected in soils with

a more neutral pH. For example, molecular surveys of AOB in a forest soil with low pH identified Nitrosospira cluster 2 (Nugroho et al. 2005) and Stephen et al. (1996, 1998) found Nitrosospira cluster 2 was dominant in an acidic agricultural soil. In another study, there was a high representation of Nitrosospira clusters 2 and 4 in older grassland soils which were acidic and had low concentrations of NH4+ (Kowalchuck et al. 2000a,

2000b).

In contrast to the studies described above, one study has found that Nitrosomonas europaea (cluster 7) species dominated in an acidic forest soil with and without liming (Carnol et al. 2002) and in oligotrophic moderately acidic soils, a strain of Nitrosomonas oligotropha lineage has also been isolated (Koops and Pommerening- Röser 2001).

Kowalchuck et al. (2000a, 2000b) reported that Nitrosospira cluster 3 was dominant in recently established (within the previous 5 years) grassland fields with neutral pH and with relatively high NH4+ concentrations. This was supported by enrichment cultures

using different NH4+ concentrations, which revealed biases towards Nitrosospira cluster

3 in high and Nitrosospira cluster 4 in low NH4+ concentrations (Kowalchuck et al.

2000a). Apart from this, many other researchers have reported that members of Nitrosospira cluster 3 were the dominant AOB in arable fields which had been fertilised and had neutral pH (Bruns et al. 1999; Mendum et al. 1999; Phillips et al. 2000; Stephen et al. 1996, 1998). In a more recent work, Di et al. (2009), demonstrated that

all the AOB identified from all the six pasture soils sampled across New Zealand were Nitrosospira and no Nitrosomonas species were observed. The identified Nitrosospira species were aligned in clusters 3a and 3b with some in clusters 4.

In a study under laboratory incubation conditions the community structure of AOB in soil didn’t change with different NH4+.concentrations in low (LF) and high (HF)

fertiliser treatments in a short (4 weeks) period (Avrahami et al. 2002). However, obvious community shifts occurred over a longer period (>16 weeks) and fertilisation (LF, HF and slurry treatments) and temperature affected the pattern of community shift (Avrahami et al. 2003). In a further study, Avrahmi et al. (2003) reported that in soil incubation studies Nitrosospira cluster 1 was initially present in the LF treatment, but disappeared completely after a long period of incubation (> 16 weeks). The disappearance of Nitrosospira cluster 1 was probably due to the inability of this nitrifier to grow below a certain threshold of NH4+ concentration. In the HF treatment,

Nitrosospira cluster 1 became more dominant with time. On the other hand, Nitrosospira cluster 3 was detected in the LF, HF and slurry treatments indicating that this nitrifier is not necessarily present at only high NH4+ concentrations, as suggested in

the previous field studies (Bruns et al. 1999; Kowalchuck et al. 2000a, 2000b). Avrahami et al. (2003) also showed the presence of Nitrosospira cluster 9 could only be detected in the soil incubated with low NH4+ concentrations.

As mentioned above, Nitrosomonas species have also been found in both fertilised and unfertilised soils with neutral pH. For example, Nitrosomonas cluster 7 was reported in both improved (with addition of N fertiliser) and unimproved (no additions of N fertiliser) soils in grassland pastures in Scotland (Webster et al. 2002). In Italian

agricultural soils that had been fertilised with swine manure, members of the genus of Nitrosospira were found in both unamended and amended soils, regardless of the quantity of pig slurry applied. In contrast, Nitrosomonas europaea (cluster 7) were detected only in the soil plots that had received high loadings of slurry and could not be detected in soil from the untreated plot (Hastings et al. 1997). But Ceccherini et al. (1998) detected both Nitrosospira and Nitrosomonas species in treated (with pig slurry) and untreated plots, although the genus Nitrosospira was more abundant than Nitrosomonas. Members of Nitrosomonas communis (Cluster 8) have also been isolated from agricultural soils with a neutral pH (Koops and Pommerening-Röser 2001).

One study has investigated the effect of water limitations on AOB numbers and their diversity in an acid forest soil (Hastings et al. 2000). The effect of water limitation (drought) and rewetting of three different organic layers of forest soil (litter (top layer), fermentation layer (middle layer) and humus layer (bottom layer)) was investigated. In this study a simulated drought regime in the field was imposed for 10 weeks by placing a transparent polyvinylchloride (PVC) roof below the forest canopy to exclude rainfall but allowing sunlight penetration to the underlying soil. Samples of litter, fermentation and humus layers to a depth of 10 cm were collected manually from the experimental site before the PVC roof was placed, to act as controls. After the 10 weeks of drought simulation, the PVC roof was removed, exposing the underlying soil to the rain. Rainfall occurred a few days after exposure and rehydrated soils were sampled 18 days later. These are referred to here as the rewetted samples. A decrease in AOB numbers was observed in the litter, fermentation and humus layers during the drought period, but the numbers of AOB increased after rewetting the layers. Species of Nitrosospira were present in nearly all the soil layers in each of the control, drought and rewetted

treatments, suggesting that they predominated over Nitrosomonas species in that acid forest soil - a finding common to other studies of Nitrosospira in acid soils (Nugroho et al. 2005; Stephen et al. 1996, 1998). In contrast, Nitrosomonas europaea-eutropha lineages (Cluster 7) were only detected in the control fermentation layer and in all three soil layers after rewetting. Their results suggested that the litter and humus layers of soil did contain populations of Nitrosomonas europaea-eutropha lineages that were not detectable during the drought, but became active after stimulation by the re-wetting.

Avrahami et al. (2003) reported that temperature was another factor that affects the community structure of AOB. In their LF, HF and slurry treatments, Nitrosospira clusters 3 and 9 were dominant at 25-30oC and, Nitrosospira cluster 1 was dominant at low temperatures (4-10oC) in the HF treatment and slurry but had completely disappeared at high temperature (30oC). Overall, they concluded that shifts in AOB communities occurred only after a long period of incubation (> 16 weeks). These community shifts were affected by different fertiliser treatments and incubation temperatures. The observed community shifts were mostly within the different phylogenetic clusters of Nitrosospira.

2.2.1.2 Ammonia oxidising bacteria as an indicator of environmental

quality

Ammonia oxidising bacteria (AOB) have been extensively studied and have been suggested as model organisms in microbial ecology (Kowalchuck and Stephen 2001). It has also been demonstrated that the activity of AOB communities can be studied as part of an integrated approach to assess soil health and they are often used as an indicator in

studies of soil perturbations and soil toxicity (Chang et al. 2001; Nielsen et al. 2004; Nyberg et al. 2006; Remde and Hund 1994).

As already detailed in the previous sections, communities of AOB have been isolated and studied in a wide variety of environments such as agricultural soils, forest soils, grasslands, marine and freshwater environments and waste water treatment systems. The advantage of using AOB as an indicator is that they are known as a monophyletic group of bacteria that are the major performers within their functional guild. Thus, if a pollutant has negative effects on AOB it is likely to be detected as a reduced NH3

oxidation rate (Nyberg et al. 2006). Although AOB represent only a small fraction of the microbial biomass in soil, their sensitivity to different pollutants and their importance in N cycling has resulted in AOB having frequently been used as indicator organisms for disturbances caused by herbicides and metals, or effects due to agronomic

practice (Hastings et al. 1997; Oved et al. 2001; Phillips et al. 2000; Stephen et al.

1999).