Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Uncovering the Microbial Networks that Degrade Plant-Derived Phenolic Compounds and Their Role in Peatland Soil Carbon Sequestration: Revisiting the ‘Enzyme Latch’ Hypothesis


Joel E. Kostka1* (, Kostas Konstantinidis1, Caitlin Petro1, Katherine Duchesneau1, Malak Tfaily2, Rachel M. Wilson3, Jeffrey P. Chanton3, Christopher W. Schadt4, and Spencer Roth4


1Georgia Institute of Technology; 2University of Arizona; 3Florida State University; and 4Oak Ridge National Laboratory


The goal is to elucidate the fundamental principles driving physiology and metabolic exchange within microbial interaction networks that regulate the rate-limiting steps in soil organic matter (SOM) degradation, specifically the oxidation of phenolic compounds derived from lignocellulose and lignin-like polymers in carbon-rich peatlands and their role in the preservation of organic matter under anaerobic, water-saturated conditions. The project combines multiomics with advanced analytical chemistry to test the enzyme latch hypothesis and its response to climate change drivers. Field and laboratory investigations will be integrated to construct and calibrate a predictive framework that links specific microbial processes and interactions to the mechanisms driving the rate limiting steps of enzymatic SOM decomposition (phenolic compound oxidation, hydrolysis), SOM persistence, and greenhouse gas production in peatland soils. The project leverages infrastructure and extensive datasets of DOE’s Spruce and Peatland Responses Under Changing Environments (SPRUCE) in Marcell Experimental Forest.


Peatlands represent climate critical regions that cover only 3% of the Earth’s land surface but store approximately 1/3 of all soil carbon (C). The future role of peatlands in C sequestration remains uncertain and depends on the impact of global change-related perturbations on their C balance. Hypotheses driving the proposed research are: 1) Under flooded anoxic conditions, persistent, plant-derived compounds (lignocellulose and lignin phenols) act as bottlenecks to microbial SOM decomposition by binding and inhibiting microbial hydrolase enzymes (e.g. CAZymes, peptidases); thus their degradation is the rate limiting step in SOM decomposition. 2) Soil moisture content and O2 availability along with SOM quality largely determine the functional diversity of heterotrophic microbes and metabolic pathways of lignocellulose and lignin degradation, which in turn regulate soil C storage through the enzyme latch. 3) Climate change drivers, which are expected to warm and dry out peatlands, will release the enzyme latch and accelerate SOM decomposition by enhancing the oxidation of phenolic compounds and concomitantly stimulating hydrolase activity. 4) Conversely, warming induced shifts in plant species composition away from mosses and toward lignin-rich vascular plants (ericaceous shrubs) will act to bolster the enzyme latch, inhibiting microbial decomposition through the accumulation of plant-derived phenolic compounds.

The project leverages an unprecedented time series generated from S1 Bog at the SPRUCE site (MN, U.S.) including, shotgun metagenomic profiles (131 metagenomes, 2.4 Tbp of sequences), amplicon sequencing, and physical-chemical-biological data from 2014-2022. 810 dereplicated metagenome-assembled genomes (MAGs) of prokaryotes have been obtained across all metagenome datasets, and short read recruitment against these MAGs reveals that they represent the majority of the sampled microbial communities at all peat depths. Taxonomic diversity is dominated by the Acidobacteria, which comprise half of the 10 most abundant MAGs, with some recovered genomes comprising up to ~15% of the total community. These organisms are known to be metabolically flexible and contain an abundance of genes that encode degradation of plant-derived polysaccharides under both aerobic and anaerobic conditions. Metagenomes were screened for phenol oxidase and peroxidase genes, revealing the metabolic potential for phenolic compound oxidation.

Plant-derived phenolic compounds implicated as inhibitory compounds in the latch mechanism, including sphagnum acid, are persistent in surface soils. These compounds are supplied at the surface by plant litter but appear resistant to microbial decay as evidenced by their accumulation at depths down to 200 cm. Using microcosm experiments researchers quantified the inhibitory effect of soluble phenolics on anaerobic C mineralization and linked this effect to soil organic matter quality and peatland type. By manipulating the concentration of free soluble phenolics with polyvinylpyrrolidone (PVP), a compound that binds and inactivates phenolics, thereby preventing phenolic-enzyme interactions, rates of CO2 and CH4 production in soils were shown to be 62% and 54% inhibited by naturally occurring porewater phenolics, respectively.

Phenol oxidase and hydrolase activities were profiled with depth and between whole-ecosystem warming treatments in soils of the SPRUCE enclosures. At the in situ pH of 4 and room temperature, all measured enzyme activities (phenol oxidase, b-glucosidase, cellobiohydrolase, b-N-acetylglucosaminidase, acid phosphatase) declined with peat depth. A generational drought occurred in 2021, which provided intriguing evidence for the complex controls of the enzyme latch mechanism. Phenol oxidase and hydrolase activities were inversely correlated with water table elevation, which dropped by 0.11 m during the drought and declined with whole ecosystem warming. Thus, researchers hypothesize that enzyme activity is enhanced by putative oxygenation due to drought and higher evapotranspiration rates in the warming treatments.

The recent metabolomic observations from a range of peatlands indicate that the decomposability of peat SOM, and conversely C sequestration, is directly correlated with carbohydrate content (more reactive C substrates) and inversely correlated with aromatic content (recalcitrant C that resists degradation). Notably, Sphagnum-dominated peat soils are outliers, exhibiting a high proportion of labile substrates (carbohydrate content), but low GHG production rates. A range of site-specific factors are likely to impact enzyme-phenol interactions, including biotic (functional diversity of microbial communities, vegetation) and abiotic (temperature, pH) parameters. While the investigations to date suggest that temperature limits the latch mechanism over other factors, soluble phenolics from Sphagnum mosses appear to be especially effective at limiting decomposition under anoxic conditions.

Funding Information

This research was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0023297.