Isolation and genomic sequencing of foliar endophytic communities across a growing season in wild Lycium ferocissimum: A Dissertation submitted in partial fulfilment of the requirements for the Degree of Bachelor of Agricultural Science with Honours at Lincoln University

Abstract

A total of 15 endophytic genera were genomically identified in this study by culturing methods across three leaf tissue sampling dates, spanning from February to April 2023 in which 96 leaves were sampled. Identification was done using a PCR assay with primers specific to fungi and bacteria, followed by sequencing and identification of the PCR products. Of these 15 genera identified, 12 were not previously known to be associated with any Lycium species. Being novel research, all 15 genera identified were previously unreported as being present in L. ferocissimum. 13 were fungal and 2 were bacterial. Endophyte composition was dynamic, but overall diversity did not change considerably. The dominant genera in this study were Alternaria (50%) and Stemphylium (30%), with Neodidymelliopsis (7%) and Cladosporium (4%) making up the only 4 genera present on all 3 sampling dates. A qPCR assay was used to test each sample leaf used in this study for the presence of CaLso. The presence of CaLso in leaf samples increased from the February sampling group (1.7% positive) to April (33%), despite a considerable decrease in TPP population presence on the plants in that same period. Unexpectedly, the control group of asymptomatic leaves, also sampled in April, had the highest relative frequency of positive leaf samples (44.5%).