Soil microorganisms exist in discrete microhabitats that constitute structured communities which display distinctive patterns. These microhabitats are highly heterogeneous, exhibiting distinct environmental characteristics such as available carbon and energy resources, water availability, temperature and pH.  Soil microbial communities are essential contributors in the fundamental nutrient cycles and the productivity of terrestrial ecosystems.  Due to their importance in sustainable land use it is essential to understand microbial communities in soil and how these communities respond to agricultural management practices. 

Sustainable farming systems aim to preserve organic matter in soil with the use of various soil surface treatments. Organic amendments reduce the severity of plant diseases by modifying the microbial composition in the rhizosphere.  As a consequence, soil microbial biomass, microbial activity as well as community structure are altered, which promote soil quality, fertility and plant growth.  Cover crops can reduce erosion and improve soil structure while the use of organic mulching introduces nitrogen into soil, prevents leaching of nutrients and increase microbial biomass.  Conservation tillage significantly increase crop residues, microbial respiration and activity, which establish denser fungal and bacterial microhabitats.

The objective of this study was to determine the effect of  surface treatments on apple orchard soil, in Elgin, Western Cape, South Africa (34°8’9.44” S, 19°1’20.07” E) (Fig. 1).  Sites were evaluated to determine whether an increase in organic material affects the microbial diversity and community structure.  Eight different soil surface treatments were applied and represented various combinations of chemical control, slashing of weed, cover crops, and mulching.  Soil samples were sampled in March 2009 during the growing season and in August 2009 during winter season.   

Total genomic DNA was extracted from 0.30 g of each composite soil sample.  The molecular technique for determining the microbial diversity and community structure involved a culture-independent, high-resolution molecular analysis for the detection of taxonomic groups within the soil. Automated ribosomal intergenic spacer analysis (ARISA) amplifies the variable lengths of the highly variable intergenic spacer region (ITS) between the 16S and 23S rRNA genes in bacteria (B-ARISA) and the 18S and 28S rRNA gene regions in fungi (F-ARISA).  ARISA electropherogram data provide a community profile, with each peak representing a particular ITS amplicon which is interpreted as an operational taxonomic unit (OTU).  The height and number of OTU peaks were used as a measure of the microbial abundance and diversity.

Analysis of variance (ANOVA) showed no significant differences in the microbial diversity of the plots under various treatments on the bench rows.  A gradual decrease in fungal diversity was observed during the winter season with bacterial diversity consistently higher than fungal diversity under the various treatments (Fig. 2).  However, a significant decrease in bacterial diversity was observed under the weed slashing treatment during the growing season in the working rows.  Lower levels of microbial diversity is in most instances a result of a disturbance that influences microbial stress.  Weed slashing is a physical treatment to control weeds and has been found to degrade soil structure, disrupt soil faunal communities and accelerate nutrient cycling and lead to the loss of organic matter.

Plots under mulch treatment had a higher bacterial diversity compared to other treatments. Studies have shown that mulching can significantly change microbial diversity. Organic mulch with plant residues influences the total soil carbon and nitrogen ratio’s, which in turn can be correlated with soil microbial diversity and community structure. However, in this study, the effect of mulch treatment on microbial community structure was not significant to other treatments (Fig. 3).   Bacterial diversity remained higher over both seasons compared to fungal diversity. During the winter season bacterial diversity under mulch treatment differed significantly from all other treatments (Fig. 4) in the study.

For a better understanding of how microbial community structure responds to changes under soil surface treatments, the Whittaker similarity index was calculated from OTU data and converted to a distance matrix in order to tested for similarity using analysis of similarity (ANOSIM). ANOSIM results showed significant differences in community structure between the different treatments. Significant differences in community structure between working and bench row treatments were also observed.  The effect was more prominent for the fungal communities than for bacterial communities.

Results from this study showed that microbial diversity under various treatments was not significantly different. The microbial community structure, however, differed significantly amongst the treatments on the apple orchard.  This is an indication that changes and differences in microbial communities are that result of agricultural practices on soil quality. The use of soil treatments influence microbial activity that in turn impacts on the composition of soil microbial communities. Changes in microbial community structure can influence soil fertility and plant growth as the micro-organisms increase nutrient availability. These differences were evident within and between seasons.

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