Galapagos (Scalesia) Microbiome Project

How unique and diverse is the invisible microbial life associated with the endemic Scalesia species of the Galápagos Islands? 

Inspired by a modern revisit of Darwin’s Galápagos expedition, our project explores the hidden plant-microbe and microbe-microbe microbial interactions shaping the evolution of endemic Scalesia plants, the “Darwin’s finches of the plant world”, across the islands. The Galápagos offer a living laboratory for examining evolution in action. Combining island, plant and microbial ecology, we explore the microbial diversity associated with endemic plant species and investigate adaptation, ecological resilience, and evolutionary trajectories of Scalesia and their associated microbiome across the islands' diverse environments. 

Darwin’s expedition revisited

An international research team led by the Netherlands Institute of Ecology (NIOO-KNAW) is to search for invisible life in the Galápagos Islands. The diversity of microorganisms - such as bacteria, filamentous fungi, yeasts, and viruses - may not be evident to the naked eye, but it is essential to nature. To the islands' giant daisies, for instance: unique endemic plants that are currently under threat.

How unique and diverse is the invisible microbial life of the iconic Galápagos Islands? That's what the Galápagos Microbiome Project - a group of scientists from the Netherlands, Ecuador, Spain and Brazil - intends to unveil. It could improve our understanding of the co-evolution of species. In this case, the researchers sample both bacteria and fungi (the 'microbiome') and their host plants.

Giant daisy, the Darwin's finches of plants

Insights from the expedition could make an important contribution to the preservation of endangered plant species, including Scalesia: the giant daisies. Scalesia species are a unique group of plants found only in the Galápagos Islands growing on fertile soil, which is in great demand for agriculture outside of nature reserves. Other threats to these unique endemic plants are grazing goats, invasive plant species and extreme climate conditions.

Scalesia has been called the Darwin's finch of the plant world. Just like the famous group of bird species Darwin found in Galápagos and used as inspiration for his theory of evolution, members of the Scalesia differ substantially between sites and between islands. It's a modest shrub growing among pumice stones in one place, but a veritable tree surrounded by cloud forest in another. Adapting to local circumstances, Scalesia developed a huge variety that has resulted in at least 15 different species.

Micro-friends

But how about the micro-organisms? Did they, too, adapt and develop great diversity across the islands? And what is their role in the ecology of the endemic host plant? Finding out more about the plants' as yet unknown microbial partners will hopefully turn out to be the key to supporting their growth and survival.

"It's an invisible world that would have been impossible to study in such detail in Darwin's day", Raaijmakers explains. "Current DNA-techniques allow us to unravel the diversity of microbes, and study if it is in line with the host plants' speciation on different islands in the archipelago."

By ship

The international team comprising six researchers and a film maker will start their 12-day expedition to a number of (un)inhabited Galápagos Islands on 25 March, using their ship as a base. Project leader Raaijmakers has been working closely with Pieter van ’t Hof and Gonzalo Rivas-Torres from the Universidad San Francisco de Quito in Ecuador to make the search for the different species of giant daisy possible. These researchers and their team have ample experience when it comes to expeditions to Galápagos, and they play a key role in the ‘Galapagos Barcode Project’: an ambitious undertaking that aims to document the genetics of all species on the islands and in the surrounding waters.

"We will be sampling the leaves and roots of the plants to profile the micro-organisms living there", says Raaijmakers. "Just like people and animals, plants depend on microbes for their growth, development and health. We have billions of microbes on our skin and in our gut with which we co-exist. Plants have a similar 'microbiome': billions of beneficial bacteria, fungi and yeasts in and on their roots and leaves."

These will not be the first plants sampled by Raaijmakers and his fellow researchers. "For a number of crop plants, we already have a fairly good overview of their microbiome and that of their wild ancestors. But so far, we only have a partial understanding of the diversity of functions we observe there." It will be exciting to make comparisons with these wild species and their micro-friends. "Also, beneficial plant microbes may in the long run play a key role in preserving and restoring native species threatened by climate change and invasive plants."

Meet the team

• Jos Raaijmakers (NIOO-KNAW & Leiden University): microbial ecologist and overall project leader.
• Pieter van't Hof (Universidad San Francisco de Quito, Ecuador): expedition leader and senior researcher in Quito.
• Gonzalo Rivas Torres (Universidad San Francisco de Quito & Tiputini Biodiversity Station): joint expedition leader and specialist in the taxonomy and evolution of Scalesia and other Galápagos plants.
• Viviane Cordovez (NIOO-KNAW):  project coordinator and specialist in  phyllosphere microbiome research; will study the taxonomic and functional diversity of yeasts in the Scalesia microbiome, focusing on the taxonomic and functional diversity of yeasts in the Scalesia microbiome.
• Víctor Carrión Bravo (Leiden University & University of Málaga, Spain): molecular microbiologist; will study interactions between microorganisms and plants in their natural environment.
• Diego Ortiz Yepez (Universidad San Francisco de Quito): biologist; will take sea water samples during the expedition for eDNA-analysis of marine biodiversity.
• Haig Balian (former director of ARTIS and Groote Museum in Amsterdam, founder of Micropia, film producer and museum maker): will film the unique expedition.

What is so special?

The largely uninhabited Galápagos Islands are surrounded by open sea, about 1000 km west of South America. Because of their remoteness, animals, plants and possibly micro-organisms have evolved independently from their counterparts on the mainland. The huge variety of closely related species helped Darwin, who visited the islands in 1835, to develop his theory of evolution.

Much research has been done on the various islands into the occurrence of genetic variation within individual animal species, eventually resulting in an explosion of new species and subspecies as was the case with Darwin's famous finches. More recently, similar research has been done into native plants, with Scalesia displaying a similar variety: from small plant or shrub to tall tree. Trees are exceptional for a member of the daisy and dandelion family.