Dawkins, Karim

Emerging insights on the role of microbiomes in the sustainability of ecosystems and plant cover are transforming knowledge-driven agro-environmental management practices. For more than a century, the Brazilian pepper tree -BP (Schinus terebinthifolius), a category 1 invasive plant in Florida has defied numerous conventional control measures directed at its well-known ecology. This dissertation is one of the pioneer studies designed to determine whether microorganisms play a role in the aggressive invasion of BP in Florida and examine potential mechanisms with the goal of creating supplemental restoration tools. To test the hypothesis that enhanced mutualism of Brazilian pepper tree with microbes, compounded by relatively low biotic resistance of Florida soils is a critical driver of its invasion, plant biomass indices, metagenomics analysis of microbial community shifts, electron microscopy of endomycorrhizal infection and qPCR of key rhizobacterial taxa were measured. A multifactorial grow-room experiment was conducted simulating invasion with BP and two Florida natives (Pinus elliottii and Bidens alba) in a sterile, bioinoculant supplemented, and non-sterile control soils with various plant combinations.

The overuse and misuse of antibiotics in environmental and clinical settings have been a
driving force for the prevalence of bacterial resistance. In constant interaction with these
chemicals which can harm them, adaptively and inherently, bacteria have devised resistance
mechanisms to combat the deleterious effects posed. In the presence of a particular antibiotic, it
is expected there will be selection of resistant micro-organisms and their associated resistance
genes if present. In this study, a set of 10 samples were taken from recreational beaches in Ft.
Lauderdale, Miami and Hollywood and four different agricultural soils. These soils were
enriched after being collected aseptically with three commonly used antibiotics; Ciprofloxacin,
Tetracycline and Vancomycin to select for resistant organisms, which produced 29 total samples.
A metagenomic analysis was done with 16S rDNA amplification with primers 27F and 1492R
which produced 14 out of 29 amplicons producing the expected ~1400 bp fragment from the
conserved SSU 16S rDNA region using Agarose gel electrophoresis. From these 14 samples
amplified, a second PCR would be run from each enriched antibiotic sample with their respective
antibiotic resistance primers eg. vanA-D, tetO and qnrA to identify the resistance genes present
expecting that the antibiotic used for enrichment would select for the resistant organisms. Future
work includes the sequencing of the amplified resistance genes to help identify novel genetic
alterations indicative of new adaptive mechanisms.

The Brazilian pepper tree (BP, Schinus terebinthifolius), introduced to the United States
in the 1800s, has since become a category one invasive plant in Florida, aggressively
spreading to 3000 km2 of prime habitat. There is a serious dearth of knowledge on
whether the rhizobiome plays any roles in the displacement of native flora and the range
expansion of BP. This thesis discusses the well-established plant invasion mechanisms of
the BP and highlights key emerging mechanisms and gaps in (a) the current
understanding of the molecular, below-ground processes of BP invasion and (b) studies
on the potential role of microbial interactions in the success of BP invasion already
established for other select invasive species, and the intervention of soil metagenomic
studies to elucidate plant invasive mechanisms. These poorly studied mechanisms could further explain the aggressive spread and resilience of BP and contribute significantly to
the development of effective and sustainable control measures, enabling appropriate
strategies for restoring native plants.