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Effects of copper sprays on microbial communities in kiwifruit orchard soils

There has been a significant increase in the use of antimicrobial copper sprays on kiwifruit orchards in the Western Bay of Plenty (WBOP) since the first outbreak of the bacterial vine disease Pseudomonas syringae pv. actinidiae (Psa-V) in 2010. Studies have revealed that an accumulation of copper in soil may adversely affect soil microorganisms, which are pivotal in essential soil functions such as nutrient assimilation. The aim of this study was to determine whether or not the use of copper sprays on WBOP kiwifruit orchards has had detrimental effects on soil microorganisms and if this has resulted in changes to the structure of soil microbiological communities. Soil was sampled from ten WBOP kiwifruit orchards with varying levels of copper but with similar physicochemical properties. These included five sets of two adjacent orchards, of which one was organic and the other conventional, and for which data was available on soil copper levels for 2011. DNA extracted from each soil was amplified with PCR and sequenced using Ion Torrent Sequencing technology. The resulting bacterial and archaeal sequences were binned into operational taxonomic units (OTUs) and the phylogeny of each was determined using the Ribosomal Database Project (RDP) Classifier. Soils were also analysed for a number of physicochemical properties including total, bioavailable and free ionic copper. Non-metric Multidimensional Scaling (NMDS) and Multi-Response Permutation Procedures (MRPP) were used to examine dissimilarities between microbial communities in relation to soil copper levels, management practices and other physicochemical variables. Indicator species analyses were conducted on OTU abundance data to determine if particular OTUs were indicative of soils with the lowest and highest copper levels. Community data were also compared using a number of measures of diversity. Differences in physicochemical parameters between soils were analysed for significance using ANOVA and t-tests. Results revealed that levels of total copper in soils have increased since 2011, with significant differences measured between each pair of orchards. Significant differences in soil microbial communities were also revealed, with pH identified as the main driver of community composition within and between orchards and differences between orchards were also largely explained by management practices. Relative abundances of Archaea were significantly higher in conventional orchards and in soils with the highest levels of copper. However, overall community dissimilarities were not found to be related to soil copper levels. Indicator species analysis revealed that soils with < 30 mg kg-1 of total copper had a greater abundance of Actinobacteria, whilst soils with > 60 mg kg-1 had a higher representation of Chlamydiae, Chloroflexi, and Thaumarchaeota. The conclusions of this research are that current copper levels in the study orchard soils have not significantly influenced soil microbial community composition and associated functions. However, the high number of influential variables confounded attempts at identifying differences due to copper alone. In addition, the lack of knowledge on the specific functions of individual taxa, make it very difficult to reveal the long-term implications of even subtle differences in community composition as a result of copper use.
Type of thesis
Dean, F. P. (2016). Effects of copper sprays on microbial communities in kiwifruit orchard soils (Thesis, Master of Science (Research) (MSc(Research))). University of Waikato, Hamilton, New Zealand. Retrieved from https://hdl.handle.net/10289/10728
University of Waikato
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