By Lori R. Shapiro, PhD, Dept of Applied Ecology, North Carolina State University
and Erik Delaquis, CIAT, Roots, Tubers, and Bananas program of the CGIAR

Human agriculture has existed for only 10,000 years – barely qualifying as a rounding error in the 4 billion year history of the Earth. Yet, in this short time, farmers across the world have domesticated an astonishing diversity of plants for agriculture. All plants – including all domesticated crop plants – are host to ‘microbiomes’ – complex communities of bacteria, fungi, viruses and other microscopic eukaryotes that inhabit the surfaces and interior of plant roots, leaves, stems, flowers and fruits. Plant microbiomes function as a second genome to the host plant, aiding proper immune responses to herbivores and pathogens, nutrient acquisition and ability to withstand abiotic stresses.

Yanesha agricultural fields, filled with diverse crop plant species, and unexplored plant associated
microbial diversity. In the Oxapampa-Yanesha Biosphere Reserve, Oxapampa, Peru. Photo: Lori R. Shapiro

Human farmers, without being able to see plant microbiomes, likely benefit immensely from their many roles in modulating plant responses to insects, pathogens, nutrients and water. There is enormous interest in harnessing plant associated microbes as ‘plant probiotics’ for agricultural improvement. However, we know almost nothing – for any crop plant – about the factors driving the assembly of plant microbiomes, or how human activities related to agriculture affect the functions of these communities.

A cassava plant (left), and harvested edible root (right). Photo credit: Erik Delaquis

One of the countless suspension bridges, crossing one of countless rivers, in the Oxapampa Biosphere Reserve.
Photo credit: Lori R. Shapiro

One way to bridge this gap in our basic knowledge about plant-microbe interactions is to step outside, and travel to one of the outdoor laboratories where agriculture began. We recently traveled to the Yanesha Biosphere Reserve near Oxapampa, Peru, as part of a collaborative project to document genetic and microbial diversity in the tropical root crop cassava (Manihot esculenta). It is impossible to overstate the global importance of cassava. Because of its ability to thrive in marginal environments with few (or no) external chemical inputs, cassava now has outsize importance among smallholder farmers across the global tropics, where it is the third most important crop. In Africa alone, half a billion people eat cassava every day.

Flowers of a wild cassava tree, growing on the edge of a cultivated Yanesha garden. Photo credit: Lori R. Shapiro

But, cassava’s arrival as a global staple is recent. For millions of years, the only region in the world where the wild relatives of cassava grew was in the Amazon basin. It is in this region that ancient chemists and farmers developed elaborate cultural techniques to detoxify cassava’s cyanide containing chemical defenses, and successfully domesticated cassava ~7,000 years ago.

Since its initial domestication, farmers have selected for countless cassava varieties. The seemingly endless colors, leaf shapes, growth habits, and tastes of cassava may amount to several thousand unique varieties throughout the Amazon basin. Together with the local Universidad Daniel Alcides Carrión and CIAT, we are currently documenting the vast number of distinct cassava varieties maintained using indigenous cultivation techniques in Yanesha communities throughout Peru’s Selva Central. We will also test whether the distinct local conditions in the Amazonian communities where cassava has been grown for millenia have not only resulted in plant genetic differences, but also plants that host distinct microbial communities. Our approach is guided by several open questions in plant-microbiome ecology and evolution:

  1. Do plant microbiome structure and function predictably vary by variety, geographic location and local environment?
  2. What is the function of the cassava microbiome, and how much functional variation exists?
  3. How does introduction to new geographic areas combined with new cultivation techniques affect the assembly and function of cassava microbiomes?
  4. How can the human, ecological and environmental factors affecting cassava microbiomes be integrated into both agricultural improvement for farmers globally, and in situ preservation programs within the Amazon?

A sampling of cassava diversity. A) a cassava tree B) side-by-side branching and non-branching varieties and C) cassava diversity in a Peruvian garden.

This project is just beginning, and we are yet to drawn conclusions. However, we hope this crop plant, and this project will serve as a model for understanding ecology and evolution of plant-microbe interactions, and how humans have altered those interactions. Just as important as the purely scientific questions, we hope that this project will serve as a model for collaborating with indigenous communities. We believe this approach can strengthen in situ conservation of genetic resources and human culture, while also generating knowledge of global benefit to agricultural improvement, and to dramatically advance our knowledge of plant-microbe interactions.

Students and professors from Universidad Daniel Alcides Carrión and CIAT in a Yanesha home garden, documenting cassava


A small sampling of the diversity of Peruvian potatoes, and a native pumpkin in a weekend market. Oxapampa, Peru.

LRS is supported by a grant from the Plant-Microbe Consortium at NCSU