When a tree dies, its remains become the foundation for new life. Leaves, wood, and roots gradually break down—not through weathering, but through the work of countless fungi, insects, and other tiny organisms. As they decompose plant material, these organisms release stored carbon back into the atmosphere, fueling photosynthesis and sustaining the global carbon cycle.

But which organisms perform this critical work, and what molecular tools do they use? A research team at Goethe University Frankfurt has now developed a powerful bioinformatics approach to answer these questions. Their study, published in Molecular Biology and Evolution, introduces a new method that systematically identifies the enzymes responsible for breaking down plant cell walls.

A New Tool for Tracing Enzymes Across Life

The method, called fDOG (Feature architecture-aware Directed Ortholog search), enables researchers to track how specific genes and proteins are distributed across species. By identifying orthologs—genes that evolved from a common ancestor and typically encode proteins with similar functions—fDOG goes beyond existing methods by analyzing not only genetic sequences but also the structural architecture of proteins, which provides insights into their functions.

“We start with a gene from one species, referred to as the seed, and then trawl through tens of thousands of species in the search for orthologous genes,” explains Ingo Ebersberger, Professor for Applied Bioinformatics at Goethe University Frankfurt. “In the process, we constantly monitor whether the genes we find perhaps differ from the seed in terms of function and structure—for example, through the loss or gain of individual areas relevant for function.”

Mapping 18,000 Species Across the Tree of Life

Using fDOG, the team examined more than 200 plant cell wall-degrading enzyme (PCD) candidates across 18,000 species representing bacteria, archaea, and eukaryotes (plants, animals, and fungi). The result is a comprehensive global map of enzymes with the potential to degrade plant cell walls, offering a new level of resolution for understanding decomposition.

Surprising Insights From Fungi and Animals

Visualization of the massive dataset revealed unexpected evolutionary patterns. Among fungi, the team detected shifts in enzyme repertoires associated with changes in lifestyle—from decomposers of dead plants to parasites of living animals. These evolutionary transitions were marked by characteristic losses of specific enzymes.

In the animal kingdom, the researchers discovered that some arthropods possess an unusually broad range of plant cell wall-degrading enzymes. These appear to have entered arthropod genomes through horizontal gene transfer from fungi and bacteria, suggesting that some invertebrates may independently break down plant material, rather than relying solely on gut microbes as previously believed.

At the same time, the study also revealed instances where apparent PCD genes turned out to be the result of microbial contamination—a reminder of the need for careful verification in genomic research.

A New Perspective on the Carbon Cycle

The study highlights how fDOG can systematically uncover hidden biological capabilities across the entire tree of life. By enabling both large-scale surveys and fine-grained species-level analyses, the method opens up new ways to explore the drivers of the global carbon cycle.

“Since soils contain large amounts of dead plant material and therefore constitute the largest terrestrial carbon sink, the decomposition of plant material is an important driver of the global carbon cycle,” Ebersberger said. “Our method gives us a fresh view of how metabolic capacities are distributed across the tree of life. We can now conduct multi-scale analyses and in the process detect both recent evolutionary changes and large patterns.”

Key Highlights

• Researchers developed fDOG, a powerful method to track genes across species.
• Analysis of 200+ enzyme candidates across 18,000 species produced a detailed global map of plant cell wall-degrading enzymes.
• Findings revealed:
  • Fungi transitioning from plant decomposition to animal parasitism.
  • Arthropods with unexpectedly broad enzyme repertoires via horizontal gene transfer.
  • The importance of careful screening for microbial contamination in genomic data.
• Insights highlight overlooked contributors to the global carbon cycle.
• The method allows multi-scale evolutionary analysis, linking microscopic processes to Earth’s carbon balance.

Original Publication
Authors: Vinh Tran, Felix Langschied, Hannah Muelbaier, Julian Dosch, Freya Arthen, Miklos Balint and Ingo Ebersberger.
Journal: Molecular Biology and Evolution
DOI: 10.1093/molbev/msaf120
Method of Research: Data/statistical analysis
Subject of Research: Animals
Article Title: Feature architecture-aware ortholog search with fDOG reveals the distribution of plant cell wall-degrading enzymes across life
Article Publication Date: 9-Jun-2025

Original Source: https://aktuelles.uni-frankfurt.de/english/how-plants-rot-new-method-decodes-hidden-decomposers-of-wood-and-leaves/

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