Avocado root and soil microbiome
Description
The project examined the changes to the soil microbiome of Persea americana (avocado) treated with organic mulch, a silicate-based mulch or phosphite, and infected with Phytophthora cinnamomi. Firstly, we hypothesised that the abundance and diversity of the microbiome would increase in response to the addition of organic mulch, and there would be further changes with the addition of mineral mulch or spraying plants with phosphite. Secondly, the presence of P. cinnamomi would change the microbial profiles of the soils in similar ways regardless of the soil additives. Thirdly, the abundance and diversity of the microbiome would be greatest in treatments that suppressed Phytophthora root damage. Fourthly, since avocado root damage from Phytophthora is reduced to a similar extent by the silicate-based mineral mulch or by spraying plants with phosphite, both treatments induce similar changes in the soil microbiome. The data provided here is the metabarcoding data in excel format. There are six data sheets 1. OTUs per sample with a description of the identity of each sample in the first 3 rows. 2. sequences of each OTU 3. taxonomic ID of each OTU 4. a combined sheet with all information (1-2) 5. sheet 4 with the plastids removed (chloroplasts and mitochondria) 6. selected OTU's; those contributing at least 40 reads. This was the datset that was analysed.
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Steps to reproduce
Rhizosphere soil and avocado root tips were collected from plants grown in pots in the glasshouse under conditions that simulated the integrated control measures for P. cinnamomi used by many avocado growers. Organic mulches, two silicate-based mineral mulches tested were tested as soil ammendments. Another treatment included spraying the plants with phosphite (known to supress Phytophthora). There were 20 plants in each treatment, and 38 days after transplanting, the soil of ten of these was inoculated with P. cinnamomi. Plants were harvested 12 weeks after inoculation and root damage and growth parameters were assessed. At harvest, bulk soil was shaken gently from the roots then ~10 mL of the rhizosphere soil adhering to the roots was collected from each plant by gently brushing it into 15 ml freezing tubes. Healthy white root tips (~1 mL) were randomly collected from each plant during harvesting and placed in a 1.5 mL Eppendorf tube. DNA was extracted from the roots and the soil and the 16S gene region amplified and prepared for Illumina MiSeq