Disentangling the role of microbial interactions and spatial structure in soil organic matter decomposition
EMSL Project ID
60215
Abstract
The study of the soil microbiome is critical to understanding the ecological functions carried out by soil microorganisms, particularly with respect to the cycling of carbon (C) and nitrogen (N) sources. Despite the importance of the community, the direct analysis of the soil microbiome in situ is difficult due to the complexity of this environment with thousands of species and millions of potential interactions. Understanding is further complicated by the intrinsic heterogeneity of soil where the multi-step pathways related to soil organic matter (OM) decomposition are often focused in certain “hotspots” (areas of high nutrient concentration with increased bacterial biomass and metabolic activity) while other regions of the same soil habitat are more muted in their expression of decomposition pathways. A better understanding of OM decomposition processes is also hampered by the lack of fundamental knowledge of the genomic and phenotypic characteristics of the major microbial players. Despite these hurdles, OM decomposition is a critical component of natural soil systems and therefore its understanding is key to improving the mechanistic underpinnings of genome-enabled models, C and N cycling in soil, and interactions between species surrounding hotspots. In the experiments proposed here, we will fill these knowledge gaps by using previously developed project resources including a Model Soil Consortium (MSC) for OM decomposition (a chitin-degrading microbiome naturally evolved from the soil microbiome) and newly developed analytical devices, in combination with EMSL resources, to derive novel insights into the molecular controls that drive interaction networks related to C and N cycling and how these interaction networks are driven by hotspots of OM decomposition. We propose to incubate a defined microbial community with chitin (an abundant C and N source in soil that often requires interspecies interactions for decomposition) under both liquid and structured soil analog systems. We will use a multi-omic approach combined with imaging techniques, enzyme labeling probes and new modeling tools that we have developed to answer the following questions: How do organisms coordinate metabolism during chitin decomposition? Which interactions lead to microbial hotspots of decomposition in a soil analog structured system? Which taxa are the primary decomposers of chitin and how do other taxa not directly involved with chitin metabolism support and/or derive nutrients from the primary decomposers, especially in a spatially resolved system representative of soil? Collectively, we expect the outcomes of this proposal to greatly expand our knowledge of interaction networks and community phenotypes that drive the consumption of complex C and N nutrient sources. This knowledge will be gained in the context of a spatially structured environment driven by hotspots of nutrient availability and expressed decomposition pathways, meaning that our conclusions will be translational and directly inform our understanding of native soil processes. In addition to the scientific gain, the successful completion of these experiments will greatly advance BER and EMSL User Facility mission goals.
Project Details
Project type
Exploratory Research
Start Date
2021-12-01
End Date
2022-12-31
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
Team Members