Lignin decomposes slowly due to:
Lignin decomposes slowly because it is a heterogeneous, cross-linked aromatic polymer with irregular bonds rather than a repeating structure readily attacked by common hydrolases. It encrusts cellulose in secondary cell walls, reducing enzyme access to otherwise degradable carbohydrates. A limited set of fungi and bacteria produce oxidative enzymes such as lignin peroxidase, manganese peroxidase, and laccase, and these reactions are energetically costly. High protein would generally improve substrate quality, whereas structural complexity and chemical recalcitrance prolong persistence. Environmental effects are often nonlinear; drought suppresses microbial access to substrates, waterlogging restricts oxygen, and extreme heat can reduce activity despite faster kinetics. Substrate stoichiometry links carbon processing to nutrient demand, so identical mass loss can accompany mineralization in one litter type and immobilization in another. Microbial enzymes act outside cells, making surface area and molecular accessibility as important as the nominal energy content of the dead material. Carbon and mineral nutrients follow different accounting paths: energy is dissipated, whereas atoms may be retained, exported, or recycled into new biomass.
Ref: Fundamentals of Ecology, Odum & Barrett, 5th Ed., Ch. 3