EcoFAB is designed to lead to a predictive understanding of ecosystems. We will learn how interdependencies between constituent organisms lead to the emergence of complex ecosystem services, including nutrient cycling and biological robustness.
This work will provide new insight into work in carbon sequestration, crop productivity, and eutrophication.
EcoFAB is a critical resource that we hope can settle long-standing debates in ecology, including theories on resource utilization, dispersal, drift, competition/cooperation, and natural selection. Insights in these critical areas are needed to understand ecosystem stability, and the presence of tipping points in the ecologies on which everyone on Earth depends.
EcoFAB is in the process of determining initial model ecosystems to replicate in the lab. One initial system will be the soil surrounding roots of the model grass Brachypodium distachyon.
Biological Soil Crusts or Biocrusts are another example of model ecosystems that is a major focus of the Northen Lab. Biocrusts are topsoil microbial communities commonly found in arid regions that comprise 40% of Earth’s terrestrial surface. Essentially all metabolic activities in these systems are confined to brief periods of wetting and we have found dramatic changes in community composition that will facilitate correlation between soil microbes and metabolites. Desert biocrusts can be collected in a dormant desiccated state for laboratory wetting events on essentially intact soil communities. They can be stored in this state for years enabling follow-on detailed studies to make and test predictions making this a simple ‘test bed’ needed for developing and testing exometabolomics approaches.
Harnessing beneficial microbes to enable low-input high productivity crop.
We face a confluence of environmental and social challenges that will make it difficult to provide for a rapidly growing population while safeguarding vital environmental ecosystem processes. Of particular concern is the enormous gap between projected agricultural production and projected demand. For example, it has recently been estimated that agricultural productivity must be increased by 60% by 2050 to support humanity (Hatfield & Walthall, 2015). Further complicating matters are the uncertain challenges posed by climactic variability coupled with soil erosion and the unsustainability of current resource intensive agricultural practices.
Currently, nearly all suitable land is already under cultivation and it is highly undesirable to clear additional land. In fact, farmland is actually being lost due to urbanization and degradation (e.g. erosion, salinization and nutrient depletion). For the better part of the last century, the widespread application of chemical fertilizers has led to crop yields increasing fast enough to meet growing demand. Unfortunately, for the major grain crops, yield increases have slowed dramatically or leveled off in the past 10 years, and we are approaching the maximum genetic yield potential in the major staple crops. New mechanisms to increase yield that are complementary to current plant breeding and agronomic practices are needed to satisfy the demand for agricultural products such as biofuels. Just as we have learned that the human microbiome—the collection of resident microorganisms—plays an enormous role in health and disease(Althani et al., 2016), we are beginning to appreciate the crucial role that microbiomes play in healthy and productive soils.
EcoFAB will play a fundamental role in advancing our understanding of plant microbiomes by providing the tools required to investigate the mechanisms how plants enhance their abiotic stress tolerance and attract and maintain beneficial microbes to increase yield under sub-optimal conditions. Specifically, by enabling control of the soil environment and both the plant and microbiome genetics coupled with systems biology and advanced imaging technologies, it will be possible to gain new foundational insights into the mechanisms how plants genetically select beneficial microbes and how these beneficial microbes improve plant productivity and environmental tolerance. These insights will provide a more complete understanding of plant genomics, and also will critically enable the development of new plant cultivars coupled with specific microbiomes to grow on sub-optimal land. For example, selectively breeding plants can maintain beneficial microbiomes to improve nutrient utilization and water use efficiency.
Central to increasing agricultural and ecosystem productivity is understanding soil carbon cycling. This is because soil carbon is critical to agricultural productivity since it supports diverse beneficial microbiomes and retains water and vital nutrients. Years of poor land management including extractive agricultural practices have released massive amounts of soil carbon and degraded vast swaths of farmland, some to the point that it is no longer suitable for agriculture (Turner et al., 2016). In fact, it is now thought that 30-70% of soil carbon has been lost and 50% of agricultural land is moderately or severely degraded. A deep mechanistic understanding of soil carbon cycling is desperately needed to enable development of approaches that build soil carbon and beneficial microbiomes to increase the sustainable productivity of degraded and even marginal soils.
Plants are also the major carbon inputs into soils where they are remineralized through the activities of microbes and soil fauna. The soil fauna are highly diverse multicellular organisms that play critical roles in soil fertility and global carbon cycling. For example, megafauna (e.g. earthworms) drive bulk mixing of soils and mesofauna can accelerate decomposition of plant litter (Hättenschwiler & Gasser, 2005). Thus foundational knowledge of metazoan genomes, their basic metabolic processes, and relationships with plants and environmental microbes are important in accurately predicting ecosystem responses and carbon cycling.
While there is huge industrial interest in identification of beneficial microbes, these efforts are focused on large-scale field screening rather than determination of the mechanisms for driving the benefit. Similarly, most academic studies have been performed either on isolated microbes or fully complex environmental communities, both of which have major challenges. Since, studying individual microbes in liquid culture is a vast extrapolation from their natural habitat, it is not surprising that we do not observe any function for approximately half of the genes in a bacterial genome under these conditions. The same is likely true for a large number of plant genes, which are presumably dedicated to selecting for and maintaining beneficial microbiomes. Yet, because of the extreme complexity and undefined nature of the soil microbiome, it is very difficult to determine the functions of specific genes and plant-soil-microbe interactions under field conditions. Thus we know very little about the molecular interplay of microbiomes and their host interactions. However, some labs, including workshop participants Mary Firestone, Jose Dinneny, John Vogel, Karsten Zengler, Sur Paredes and Jeff Dangl all have shown successes in model communities making us optimistic about the promise of laboratory soil ecosystems.
To address these challenges, it is important to develop fabricated ecosystems, EcoFABs, that, in conjunction with field studies are designed to accurately recapitulate relevant soil processes. These can range in complexity from simple synthetic soil with defined microbes to native soils including microbes as well as metazoans and plants. Integration of these approaches with soil metabolomics and spectroscopy will provide unprecedented insights into soil organic matter formation and cycling. Through controlled manipulations of the plants metazoans and microbes it will be possible to determine the biotic controls on the soil organic matter formation. For example, it will be possible to leave out a particular soil organism and characterize the fact on carbon dynamics within the EcoFAB. Another example would be changing the mineral composition of the soil and using x-ray spectroscopy and nanoscale mass spectrometry imaging technologies to investigate which microbial metabolites adsorb onto the surfaces. Further it will be possible to use synthetic biology tools to test the role of specific genes and pathways in mediating important soil carbon cycling processes and make reporter microbes that would become florescent or luminescent under a particular environmental condition of interest enabling them to be used as diagnostic probes for in situ processes.
Since there are a great range of relevant length scales necessary to investigate carbon cycling, we envision EcoFABs spanning relevant length scales. This would include EcoFABs designed to study microbial processes on mineral services at the micro aggregate scale in conjunction with high resolution imaging technologies. At the upper end of the scale, it would be the construction and use of Ecotrons with meter scale soil monoliths and plant canopies that are instrumented such that both aboveground and belowground processes can be manipulated and monitored (Roy et al., 2016). However, the bulk of work will likely be performed at the centimeter scale with benchtop EcoFABs designed to investigate the interactions of microbes, soils and metazoans with individual plants.
The EcoFABs will also serve as testbeds for the environment, enabling prototyping approaches and interventions to be used together to develop predictive models and effective approaches to harness plants and beneficial microbiomes to build soil carbon and increase agricultural productivity. Through the creation of EcoFABs spanning multiple spatial scales it will be possible to test scaling predictions to better understand which processes can accurately be scaled and predicted from smaller scale measurements.
Do you study a model ecosystem we should consider instrumenting for experiments? If so, please let us know!