Plants contain a diverse array of fungi that cause no apparent harm, and may even benefit the host. These "endophytes" are especially prevalent in tropical forests, but it is not known how many types exist, nor how their diversity is distributed within- and between host species. This project will quantify endophyte diversity in a lowland Amazonian tree species, and examine the relative importance of geographic distance and habitat in determining endophyte community membership. This will be achieved using cutting-edge DNA sequencing technology that allows direct examination of microbial communities, independent of conventional cultivation methods.
Fungi and other microbes have immense effects on ecological processes, often resulting from their interactions with larger organisms. In the case of endophytes, the ability of a plant to respond to its environment may be partly mediated by its fungal partners. Because chemistry is the currency of host-symbiont interactions, this project will reveal potential targets for drug discovery, as well as advance our understanding of fungal species richness and ecology. During the field component, undergraduates from a university in Amazonian Peru will receive training in ecology, plant identification, and fungal culture techniques. An undergraduate in the United States will receive training in basic molecular methods. Results will be published in English and Spanish, to facilitate further study by scientists from the host region and abroad.
My goal, upon receipt of this award, was to help illuminate the biology and ecology of foliar endophytic fungi in the New World tropics. Endophytes are a ubiquitous and species-rich collection of ascomycetous microfungi that reside in plant tissues, without causing any apparent harm to the host. The bulk of what we know about foliar (leaf-dwelling) endophytes comes from studies in temperate ecosystems; community- and life history dynamics in tropical areas remain enigmatic. My work spanned three main themes: an intensive multi-method sampling of endophytes from a single individual of Protium subserratum (Burseraceae) in a white-sand forest near Iquitos, Peru; an experimental assessment of fungal community turnover during leaf decomposition; and a phylogenetically controlled test of the importance of soil type in determining endophyte community composition. Together, these themes address two fundamental questions of endophyte biology: first, how many such fungi are there? And second, are they strictly commensal with respect to the host, or might some taxa be parasites of subtle effect--or even mutualists? By quantifying the number of endophytes in the leaves of a single tree (using traditional and "next generation" sequencing methods), as well as endophyte turnover across space and between habitats, a reasonable projection of overall diversity can be adduced. And by addressing the null hypothesis of endophyte ecology--that these fungi are little more than patient saprophytes, 'playing nice' with their host while awaiting leaf senescence--the litter-succession experiment will suggest whether particular fungal lineages deviate consistently from that null expectation, offering targets for future work on the nature of symbiosis in this system. Logistical difficulties surrounding export of samples from Peru caused substantial delays, but fast progress has been made since the samples arrived. At this time (September, 2014), Sanger sequencing of fungal isolates has been completed, and analysis of those data is ongoing. The next-generation sequencing (Illumina) component is also finished, and I'm in the process of learning the bioinformatic pipeline required for data exploration. The DDIG allowed me to measure nutrient content in subsamples from the decomposition experiment, which will provide a useful covariate to help explain patterns in community turnover. The phylogenetically controlled test of habitat-mediated community structuring remains in the DNA extraction phase, but will be completed soon. All fungal isolates will be vouchered for independent confirmation of my results, and as a reservoir of genetic- and biochemical information for future work in the realms of pharmacology and natural products chemistry. More importantly, though, this project will provide a quantitative reminder of the deep biotic complexity in which our species is embedded. The maturity of our civilization will be measured by our stewardship of that complexity, and stewardship depends on understanding.
