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Harvard Forest Research Project 2022

  • Title: Mechanisms of Complex Carbohydrate Processing by Soil Bacteria
  • Principal investigator: Elizabeth Shank (
  • Institution: University of Massachusetts - Medical School Worcester
  • Primary contact: Elizabeth Shank (
  • Team members: Katarzyna Dubiel
  • Abstract:

    Soil is a rich ecosystem of microbes, plants, and nutrients, interacting within a complex and highly variable physical environment. The biological interactions and metabolic activities occurring in these soil microhabitats have profound effects on ecosystem-level processes including global carbon and nutrient cycling. Carbon is found the environment as high-molecular weight (HMW) polysaccharides, such as cellulose and chitin, which must be broken down for microbial use. Microbes utilize multiple mechanisms to obtain usable carbon from HMW polysaccharides in the environment. ‘Sharing’ microbes use surface-associated or excreted extracellular enzymes that degrade complex polysaccharides into small components for cellular uptake. These low-molecular-weight (LMW) components are broken down in the extracellular environment making them susceptible to diffusion and available to ‘scavenging’ microbes. ‘Scavenging’ microbes do not produce enzymes for polysaccharide breakdown and instead take up LMW processed by other microbes. Recently, a novel mechanism termed the ‘selfish’ mechanism has been identified in both marine and human gut environments. ‘Selfish’ microbes bind and partially degrade complex polysaccharides by surface-associated enzymes. High-molecular-weight (HMW) polysaccharides are broken down into oligosaccharides that are directly imported into the periplasm. These oligosaccharides are further processed by periplasmic enzymes into useable carbon. The ‘selfish’ mechanism ensures substrates do not diffuse away or are taken up by ‘scavenging’ bacteria prior to import. While ‘selfish’ microbes have been identified in multiple environments, the use of this mechanism by soil bacteria has not been determined. Using fluorescently labeled polysaccharides in combination with smFISH and 16S rRNA sequencing we will determine the identity and prevalence of ‘selfish’ microbes in soil. By probing the mechanisms of polysaccharide processing in soil we will gain further understanding of global carbon and nutrient cycling.