Understanding the role of microbial diversity in soil ecosystem functioning: Reflections from a LTER Fellow

Grant Falvo is a PhD student in the Plant, Soil and Microbial Sciences Department at Michigan State University. He works in the Robertson lab within the disciplines of soil microbial ecology and biogeochemistry and is interested in global change phenomena broadly.

Grant, one of the 2020 LTER Fellows.

There are more microorganisms in a typical handful of soil than there are people on this planet. Every year these microbes emit >5 times as much COas all the fossil fuel emissions emitted by humans. Yet recent research is beginning to uncover the dominant role these microbes play in stabilizing a similarly large amount of CO2 in soils as sequestered soil organic matter that can be protected for many decades and even millennia. That same typical handful of soil can host several thousand microbial ‘species’, on par with the total number of mammalian species in the entire world. This mind-blowing level of diversity consists of species that can ‘breathe’ metals instead of oxygen, live through complete desiccation and split molecules that, before humans, only the intense energy of lighting could split. These soil microbes preform functions that maintain high levels of plant and animal biodiversity and a stable planetary biosphere including the provisioning and tightly coupled recycling of necessary nutrients for plants as well as the stabilization of the global climate system by regulating the balance of CO2 in the atmosphere, plants and soils. 

At the Kellogg Biological Station (KBS) many are interested in how changes in temperature and precipitation regimes for the Great Lakes region, due to climate change, are going to impact these microbes and the functions the preform. While increases in overall temperature for the region are modest compared to other regions of the world, the increase in annual precipitation has already been measurable for quite some time, with further increases projected during this century. A striking feature of this change is that the precipitation is coming more often in large downpours with longer dry periods between these events. With this in mind the National Science Foundation funded Long Term Ecological Research (LTER) site at KBS has decided to set up a large field scale experiment that artificially creates a 6-week drought during the growing season. The drought will be imposed using large rainout shelters and will be implemented in the conventional and no-till agricultural plots as well as the managed prairie. An overarching goal of this experiment is to assess the resistance and resilience of organisms and ecosystems to this drought and rewetting. 

To better understand the mechanisms of these responses several subplot manipulations are planned that are hypothesized to either augment, hinder or not affect the studied organisms and processes. In the conventional agricultural plots, which are the most depleted in soil organic matter of all the KBS LTER treatments, organic matter additions of different plant residues are planned to test both how they affect organisms and ecosystem processes and also how the stabilization of the plant residues themselves by soil microbes will be affected by the simulated drought. 

Grant’s experiment where he’s preparing the soils to measure the greenhouse gasses that the microbes produce.

During this LTER Fellowship I am undertaking an analogous experiment in the lab with small amounts of soil that will similarly be subjected to a drought and rewetting with the addition of two types of plant residue. However, in order to test the effects of microbial diversity a special technique is being employed to create distinct microbial communities in the same soil. When microbial communities are compared between landscapes and even between land-uses at KBS it is often found that the composition these communities reflects the differences in land use, plant communities and climate at the various sites. Comparisons of how these distinct soil microbial communities function and respond to perturbations are often fraught with the confounding effects of the distinct physical and chemical characteristics of the soils themselves. To overcome this challenge in picking apart biological vs physical and chemical drivers of experimental responses researcher have taken to creating distinct microbial communities in a common soil. 

This is no small feat. As mentioned, contending with billions of microorganisms that are characteristically resistant to the extremes of life has stopped researchers from being able to answer these pointed questions in the past. With cycles of high heat and pressure the microbes in soil can be temporarily be knocked down and the soils are nearly sterilized and ready to take in a new community. My experiment is re-inoculating such a common sterilized soil with three microbial communities. Currently, in a pilot study we are trying two versions of these three microbial communities. In the first version, the ‘alpha diversity’ version, a single source soil is being used and through a clever trick three subsets of that single microbial community are being selected. The reason it is called the alpha diversity version is because the three microbial communities are designed to have three levels of alpha diversity. Alpha diversity is what ecologists call the total number of unique species in a community. So, there will be a high, medium and low alpha diversity treatment in this version of the experiment. 

The other version of this experiment is the ‘beta diversity’ version. Beta diversity is what ecologists define as the species compositional differences between two communities. The three treatments here will be taken from the different land-use treatments at KBS; the forest plots, the mid-successional plots and the conventional agricultural plots. These treatments harbor distinct communities of microbes and will be re-inoculated into the common sterilized soil. Once they are established then the experiment can begin. On day one these soils will be divided into those following the constant moisture track and the drought and rewetting track. In addition to the three microbial communities in each version, there will be three organic matter tracks. Some soils will not receive any additional plant residue, some will receive switchgrass, and some will receive sorghum. 

The plant residue additions will allow us to both see if they affect the drought response of the microbes and their functions and they will also allow us to study how drought affects their decomposition and stabilization in the soil. Sorghum was chosen because it is relatively easy for microbes to degrade whereas switchgrass is somewhat harder for microbes to degrade due to it’s low levels of key nutrients such as nitrogen. Throughout the course of the experiment we will measure the greenhouse gases (COand N2O) emitted by the soil microbes. This will allow us to assess how microbial diversity and plant residue quantity and quality affect the resilience of the microbial greenhouse gas emissions to drought and rewetting. We will also measure how the added plant residues are differentially incorporated into the stable pools of soil organic matter between treatments. 

One key set of measurements that we will be making takes advantage of the recent advances in metagenomic sequencing of complex microbial communities. With these techniques we will have view into the deep and expansive world of billions of microorganisms from thousands of linages, a view completely unimaginable until very recently in human development. Whereas previously these unseen multitudes lurked in obscurity, this experiment will track the response of each of their populations to these manipulations. Are communities with more species diversity more resilient to drought and rewetting events? Are forest adapted or agriculturally adapted microbes more resilient? Which species are better at resisting the desiccation? Which are better at responding when water is reintroduced? Does having fresh plant residues help certain species more than others? 

For their support, I am very grateful and wish to thank the KBS LTER, the Robertson and Evans labs as well as the KBS and Michigan State University communities at large, without which this research would not be possible. Stay tuned for results!