Towards ecologically-based fertilizer recommendations that improve soil quality in high-density apple orchards

Tree growth

At all three sites, the mulch treatments had a greater impact on tree growth than the sub-plot fertilizer treatments. However, increased tree growth was not always statistically different between trees with and without mulch. Other studies suggest that increased tree growth during the first few years of growth are maintained for the long-term but up to five years of data are usually required.

Plant-available Soil Nutrients and Leaf Nutrients

At the AREC site, the compost and compost + CaNO₃ treatments increased soil phosphorus concentration, and those same treatments increased soil potassium concentration at the Maryland site. There were no differences in the soil mineral concentrations at the Tyro site. The increased soil phosphorus and potassium concentrations did not always cause an increase in leaf mineral levels, but relationships appeared to be emerging. Some treatment differences were found for soil calcium, magnesium, and zinc, but these were not of a large magnitude. None of the treatments resulted in increased leaf nitrogen content for any of the sites.

Soil Bacterial Communities

Soil communities were analyzed using the software Quantitative Insights Into Microbial Ecology (QIIME). Quality checking of the more than 1.5 million bacterial sequence reads and 0.25 million fungal reads showed that the greatest effect, not surprisingly was due to location. It is striking to note, the effect that mulch can have on the community over the relatively short time period of the experiment. The dominant Operational Taxonomic Units (OTUs) were most closely related to Proteobacteria, Acidobacteria, and Actinobacteria. Bacterial community changes, that were consistent across locations were strongly associated with root-zone Proteobacteria, increasing by 26% due to mulch. Evidence for fertilizer-induced changes in the relative abundance of ammonia-oxidizing bacterial family were also apparent, and suggest that there are ecologically significant and functional differences in nitrogen cycling resulting from both fertilizer and mulch. The changing bacterial community likely has important ramifications for the bioavailability of plant nutrients, plant-root bacterial interactions, and therefore orchard sustainability.

Soil Fungal Communities

Although overall patterns of change were similar to the bacterial community, extraction of high-quality soil fungal DNA was more difficult. There are multiple reasons for this, one of which is related to the number of copies of the target marker gene, and the chemical reactivity of the soil. The MD and Tyro orchards provided sound results and with the highest veracity for interpretation. Fungal communities between these two locations, which were expected, were different. The differences span across the major Phyla with the major ones comprising Glomeromycota (3%), Zygomycota (10%), Ascomycota (27%) and Basidiomycota (32%) the predominant sequence data. The effects of compost amendment we're less clear, but a more elaborate set of methods may help to describe those differences. 

The addition of an organic amendment such as mulch can over several years have a large impact on soil dynamics. These were reflected in the current experiment by showing changes in the fungal communities. Mulch increased the growth promoting of close relatives of mycorrhizal fungal groups Glomeromycota by 16%, and Agaricomycetes by 35%. In the latter case, however, Agaricomycetes, also contain some species of decomposers and pathogens. This group in particular, would be of particular interest for further study because they're the most likely candidate for playing a growth supportive role for apple trees.

In this regard, a group closely aligned with Tremelomycota declined by 27%. The significance of this latter result is difficult to determine because this group contains a broad range of decomposers, plant growth promoters, and disease-causing fungi. The literature is dominated by studies of disease related taxa, however, and so in the case of this group the pathogenic importance of the relative decline should be interpreted cautiously. The changes in the above groups, however, set the stage for testing of hypotheses using more focused molecular techniques to ascertain the role of fungal communities resulting from the effect of mulch, and other organic amendments. Pleosporales, a family of bacteria containing members of the Venturia genus (the causal organism for apple scab) were noticeably lower due to the mulch, declining by 80%, containing 2.8 to 1.8% in non-mulch compared to mulched treatments. These percentages of taxa may be seen as small to a non-specialist, but in a soil with 1,000 of taxa, any group with 0.1% or more of the total sequence reads are considered to be relatively dominant taxa. Although it is not known if the mulch treatment resulted in disease suppression, it has been reported previously that the addition of organic matter to soil tends to have greater growth promoting and lower relative abundance of pathogenic organisms. Our results are an important step forward for understanding the huge diversity of bacterial and fungal community types in apple orchards, and their potential for change due to orchard management.