Chapter 3: EFFECTS OF LAND USE AND MANAGEMENT ON SOIL BACTERIAL
3.4 DISCUSSION
3.4.2 Bacterial community structure under different trash management practices
conventionally-managed fields was compared to fields under short-term and long- term organic farming, respectively. The microbial biomass of the investigated field plots from the different treatments did not differ from each other, whereas significant changes in the microbial community were detected at all taxonomic levels that were analysed. However, the overall diversity as calculated by the Shannon index was not significantly different between treatments. In addition, strain (ecotype) diversity showed that although the overall diversity (Shannon index) was unaffected, a clear shift in the type of strains could be detected. As the Shannon index is dependent on both ‘richness’ (for which clear, reproducible assignments of individual organisms to species level are required) and ‘evenness’ (for which a reliable quantification method is needed) and as neither of these parameters can be unequivocally determined for soil prokaryotes (Tebbe and Schloter, 2007), this method of determining bacterial diversity has some shortcomings. In the present study, analyses based on the presence or absence of bands or on band numbers clearly separated the various communities under the different land uses, whereas the Shannon Weaver diversity index based on the average relative intensity of the bands (mass), showed only slight differences, or none at all, because of the low evenness.
assessment of the DGGE gels indicated that band numbers and banding patterns in the profiles of all the treatments were much more similar to each other than were those of the different land uses at the Baynesfield experimental site. However, as each band represents a different group of species and as only 5–8 bands were common to all four treatments at site 2, this indicates that the different communities were genetically diverse.
Two-way ANOVA analysis of the main effects and interaction of trash and fertilizer managements on soil bacterial community richness, evenness and diversity, showed that richness had been affected significantly by additions of fertilizer but not by trash retention, nor by any interaction between trash × fertilizer. Interestingly, fertilizer additions had significantly reduced bacterial community richness compared to unfertilized treatments, from a mean of 29.00 in unfertilized plots to 26.17 in fertilized plots. It has been suggested that fertilizer applications tend to result in a less diverse, more specialized soil microbial community (Tiquia et al., 2002). Applications of inorganic N to a silage corn field were shown by Peacock et al. (2001) to enhance the relative abundance of Gram positive bacteria. Mendum and Hirsch (2002) reported that plots fertilized with NH4NO3 were dominated by Group 3 AAO bacteria, whereas those receiving no fertilizer were dominated by Group 4. Demoleng et al.
(2008) showed that soil bacteria were limited by a lack of carbon, which was exacerbated by fertilization.
Species diversity of a community is similar to genetic diversity of a population in that it allows for a varied response within a dynamic ecosystem. If an environment is dominated by a strong selective force such as fertilizer additions, less flexibility is needed to maintain stability. In such cases it is adaptive for a community to become stenotolerant (highly specialised) and to be dominated by a few populations (Atlas and Bartha, 1987). In the present study, this effect was observed on bacterial community richness, but no significant differences were evident between the treatments with respect to evenness or diversity. This indicates that although the communities from the different managements are genetically different, they are nonetheless similar in terms of the evenness of species present. The difference in bacterial community composition observed here could presumably account for the differences in catabolic diversity found by Graham and Haynes (2005).
Analyses of soil variables at this site by two-way ANOVA, suggested that two major factors, induced by fertilizer additions, interact to affect the size and activity of the microbial community, namely: (a) an increase in organic matter content in the surface soil, mediated by fertilizer-induced higher yields (and thus greater organic matter returns as roots and trash) and (b) fertilizer-induced soil acidification (Table 3.8). This agrees with the findings of previous studies at this site (Graham et al., 2002 a, b).
These two effects as shown by CCA, were the main factors influencing (either directly or indirectly) the nature of the soil bacterial communities at Mount Edgecombe. Under the four treatments, MRPP analysis of selected soil variables showed an overall significant difference in the various soils, as well as in all pairwise comparisons, except between BtoFo and TFo. Analysis by NMS (Figure 3.7) showed that fertilizer additions caused bacterial communities to differ substantially under green cane harvesting but not under burning. Bacterial communities under TF and TFo were clearly separated from each other and also from those of BtoF and BtoFo, whereas those under BtoF and BtoFo were very closely correlated and could not be separated. A significant difference in the bacterial communities between all the land treatment types was shown by the MRPP analysis.
CCA clearly separated the bacterial communities under the four treatments, with soil organic C being the most important variable (Table 3.10) accounting for the differences in bacterial community structure under the trashed (T), and burnt (Bto) plots, on CCA1 (Figure 3.6). Wakelin et al. (2007) reported similar findings in their study on maize stubble management. Communities associated with the trashed treatments are likely to have been involved principally in decomposition of the sizable inputs of crop residues at the soil surface, whereas those from burnt plots were probably either associated with the sugarcane rhizosphere or involved in the slow turnover of soil humic material. The major limiting factor to microbial growth under burning is likely to be a paucity of available C, leading to a community dominated by species able to use relatively recalcitrant humic substances.
Graham (2003) indicated that long-term retention of cane crop residues on the soil surface at this site had resulted in a 26.5% increase in organic C, and greater aggregate stability in comparison with soils under burning. Both C and N are volatilized during burning and this is a major cause of soil degradation and loss of soil
organic matter under long-term sugarcane production (Biederbeck et al., 1980;
Rasmussen and Collins, 1991). It has already been shown in the present study that trash retention results in an accumulation of soil organic matter and, as reported by Graham et al. (2002b), this is associated with an increase in the size and activity of the soil microbial community.
Soil pH was lower under fertilized managements (F) than under unfertilized (Fo), with high exchangeable acidity correlated with both the TF and BtoF treatments. The lowest pH was measured in soils under TF, and the highest under BtoFo. Soil acidification of fertilized plots is primarily attributable to nitrification of annually applied fertilizer NH4+
(Graham, 2003). As acidification proceeds and a decrease in pH occurs, Al-containing amorphous clay minerals begin to dissolve, resulting in an increase in soluble and exchangeable Al (and exchangeable acidity, i.e. exchangeable Al3+ + H+). The exchangeable Al3+ displaces exchangeable bases (e.g. Mg2+, Ca2+ and K+) from exchange sites, with subsequent leaching of the bases down the profile (Graham et al., 2002a). Therefore, fertilized soils had a lower pH and exchangeable Ca and Mg than unfertilized soils, but had higher exchangeable acidity. Fertilizer also increased extractable P and K. Thus, the considerable influence of exchangeable Mg in separating the different bacterial communities from the fertilized and unfertilized plots (as shown by CCA, Figure 3.6), is associated with the large losses of Mg from the acidified fertilized plots. This was confirmed by two-way ANOVA of soil variables. The substantial difference in the soil chemical environment between fertilized and unfertilized treatments resulted in large differences in bacterial community composition, particularly under trash retention (Figure 3.7).