It’s hard to separate the close relationship between ecosystems and the critical microbes that support many ecosystem processes and services humans rely on for survival. For example, by breaking down dead organisms and plant litter within soil, soil microbes help increase available nutrients such as nitrogen and phosphorus that plants and trees–including agricultural crops–need to grow and survive. Microbes also help drive the cycling of carbon by releasing carbon dioxide as a byproduct of decomposition and storing it in the soil through their own biomass–another component of healthy, productive soil.
To portray these complex environmental processes and functions realistically in models, EESA scientists have developed a first-of-its-kind genomes-to-ecosystem (G2E) framework that integrates microbial genetics and traits, like size or mortality rate, into models used to understand ecosystem functioning. This method can, for example, use soil microbe genetic information to estimate soil carbon or nutrient availability in a particular environment, and how these could change in the future. The team’s process and findings have been published in a Nature Communications article this week.
The Importance of the Invisible
Zhen Li is lead author of the paper, having worked on the study as a CESD postdoctoral researcher under mentors Bill Riley and Eoin Brodie.“One of the greatest things about this framework,” explained Li, “is that it can be tailored to any type of ecosystem, from coastal grassland to boreal forest, and can help scientists study and predict agricultural productivity, plant and soil health, biofuels development, ocean microbiomes, and more.”
While the role of microbes in ecosystems is widely studied, less is known about how microbial genes are linked to specific traits and functions because microbial communities are extremely diverse, differing in their genetic makeup, metabolic function, and community composition depending on their environment. The relationship between microbial genes and traits are similar to how specific human genes are linked to particular characteristics–for example, the human genes HERC2 and OCA2 dictate the expression of eye color.
Studying the linkages between microbial genes and traits can help researchers more accurately understand their role in, and effects on, ecosystems. For instance, some microbes use soil carbon faster than others. Others are more sensitive to temperature. Some produce methane as opposed to carbon dioxide. All of these different characteristics can affect soil quality, carbon stability, and overall ecosystem health and function.
From the Field to the Model
The team of scientists based the ecosystem model on data collected from a Northern Sweden peatland ecosystem called the Stordalen Mire. They collected soil samples and analyzed the microbial DNA from this field site, grouping microbes with similar characteristics into what’s known as “functional groups.”
The scientists integrated the G2E framework into an ecosystem model called ecosys, which has been used in over 170 publications and tested in many high-latitude regions, including the Stordalen Mire. While ecosys is widely used, this newly developed framework marks the first time a genome-to-ecosystem approach has been fully integrated into an ecosystem model.
Their study demonstrated that, when using the developed framework, the model generated better predictions of the exchange of gasses and water between the soil, vegetation, and atmosphere. This reiterates the importance of representing microbial function in ecosystem models.
Studying microbial communities–and their relationship with plants and soil–is central to the research housed at a new building on Berkeley Lab’s main campus, the Biological and Environmental Integration Center (BioEPIC). BioEPIC will unite researchers in the laboratory’s Biosciences and Earth and Environmental Sciences Areas to uncover how microbes can help drive breakthroughs in addressing water, environmental, and energy challenges. This study represents a key BioEPIC priority, which is to advance the realistic portrayal of microbial processes within ecosystem models.
“This exciting study demonstrates that genomic information can inform ecosystem-level predictions. It represents exactly the type of cross-scale understanding that we’d like to expand on, as we work across Berkeley Lab’s Biosciences and Earth and Environmental Sciences Areas in BioEPIC,” said Susannah Tringe, division director for Environmental Genomics and Systems Biology in the Biosciences Area.
Informing Management For Agriculture, Forests, and More
Ecosystem components and processes are closely interconnected, so data that accurately represents even a small portion of them is highly valuable to enhance ecosystem models. This new integrative modeling framework can transform understanding of ecosystems because microbes in particular have an impact on so many aspects of the Earth and environment, from vegetation growth to soil hydrology, exchange of gasses with the atmosphere, and more.
“Including realistic mechanisms in our models can help us more carefully manage ecosystems,” said Bill Riley, a lead author on the paper. “It’s difficult to make informed decisions about ecosystems without information about some of their key drivers, like soil microbes and microbial communities. This method gives us a better understanding of how ecosystems function and might respond to and recover from extreme events like wildfires, drought, and flooding.”
For example, farmers and consumers are affected by agricultural system responses to drought conditions in California’s Central Valley. As scientists look to the unique abilities of microbes to withstand harsh conditions, their traits and functions following extreme events–which can now be better represented with this G2E framework–are becoming increasingly more important to study.
“When an ecosystem is undergoing stress from drought, for example,” Riley further explained, “all of the living organisms are trying to deal with it. They reallocate nutrient, water, and carbon resources to help with the stresses on their cells. If you want to model the overall response of the ecosystem accurately, you need to know how this happens on the individual and community levels, and how those responses affect other aspects of the system, like plants.”
Scientists can learn a lot from these microbes and their characteristics. Their profound effects on our ecosystems, now more realistically represented in models, are essential to healthy ecosystems that provide us food, water, and recreation.
This research was supported by the EMERGE Biology Integration Institute, funded by the National Science Foundation. Additional support was provided for research at Lawrence Berkeley and Lawrence Livermore National Laboratories by the Department of Energy Office of Biological and Environmental Research.
