A time machine to study soil microbes

As islands grow in the Wadden Sea, the new land hosts a succession of plant species. Biologists are familiar with this phenomenon. What they didn’t know was which bacteria live in the bare sands and ever-richer soils during this natural ecological succession. Francisco Dini-Andreote has now filled this gap in our knowledge with his PhD thesis. He defended it on 9 September and was awarded a distinction.

The eastern part of the island of Schiermonnikoog is a pristine salt-marsh ecosystem. At the eastern tip, sediments accumulate and slowly rise above the tide, thus elongating the island. This process has been going on for centuries. This means that to travel along the coastline from east to west is to travel through time. ‘Ecologists have studied this system extensively, so we already know a lot about it’, says Dini-Andreote.

Ecologists have documented and explained the succession of plants and other ‘macro’ species in the salt marsh, but no one had studied the soil bacteria and fungi at the bottom of the salt marsh and its food web and their role in the ecological succession process. So Dini-Andreote took several trips to Schiermonnikoog in the first year of his PhD project to take soil samples along the coastline and analyse their physico-chemical and microbial composition.

Chronosequence

‘I used plots that colleagues had previously studied. They represent a natural chronosequence from new land to 105-year-old marshland.’ He sampled five different ‘time points’, and did so four times in one year. He then spent the greater part of the next few years analysing the data from the samples in the lab and at his computer.

The youngest samples, which are basically bare sand, proved to contain the highest diversity in bacterial species. ‘We concluded that this is because the tide still covers this land once or twice per day, promoting bacterial dispersal from the sea. Waves only reach the older sites in the winter.’ The incoming tide delivers new species of bacteria, which reside in the sand for a short time. ‘The turnover of species is very high. We think this is a general rule: a high turnover promotes high biodiversity.’

Along the time line, the salt content of the soil increases with age. Salt is deposited by the sea and may stick to the clay. The salt concentration increases from around three to over 12 percent. ‘This constrains the type of bacterial species that can live there.’ Unsurprisingly, salt resistance genes also increase along the coast.

Chemical warfare

The youngest samples contain many bacteria with flagella that allow them to swim towards potential food sources. ‘The environment is very wet and changes a lot, so it is a great advantage if you can hunt your food or swim away from attackers.’ Many bacteria are ‘autotrophic’, which means they can capture carbon from the air. ‘So they add significant amounts of carbon to the soil, which can then be used by other organisms. Indeed, plants tend to grow on bacterial mats in these early stages.’

In the older and more stable soils, the bacteria are less mobile. ‘Instead, we see they are engaged in chemical warfare with each other. They produce antibiotics and develop mechanisms to defend themselves.’ The number of autotrophic species also declines and the bacteria adapt to different food sources, like the more complex hydrocarbons such as lignin that are produced by plants.

By describing the succession of bacteria and fungi, Dini-Andreote has increased our knowledge of the food web in salt marshes. His supervisor, Joana Falcao Salles, explains that new projects will build on this. ‘Francisco has developed the basic map of microbial succession. Now others will expand on this by describing the interaction between plants, soil microbes and insects, or analysing how different functions develop during succession.’

The information may help us conserve salt marshes. Falcao Salles: ‘Some marshes suffer from an influx of fertilizer. This makes the plants grow fast above ground, but the root system often can’t keep up. That makes the plants susceptible to collapse, so that you end up with a barren mud flat. Our research may help us notice early warning signs of this collapse and propose restoration strategies.’

Francisco Dini-Andreote, thesis: Microbial community assembly in an evolving ecosystem, defended on 9 September 2016