Lignocellulose is a promising sustainable alternative fuel and its decomposition is critical for the formation of sediment organic matter. The lignin of lignocellulose limits the access of enzymes to cellulose and slows down the decomposition. Therefore, the development of efficient microbial consortia to deconstruct lignin is of great interest. In this study, a 715-day in situ experiment was performed to investigate the degradation process of macrophyte Phragmites australis debris at different depths of sediments (up to 38 cm) in a eutrophic lake. Although litter mass degradation showed an obvious decreasing tendency as the depth increased, the efficiency of lignin degradation in subsurface sediments was significance higher than that in surface sediments (p < 0.05). Pyrosequencing analysis showed that the subsurface sediments contained the specific anaerobic bacteria (genus Sulfuricurvum, Clostridium and Treponema) and anaerobic fungi (phylum Chytridiomycota and Rozellomycota). These anaerobic microbes well adapted to the degradation of recalcitrant organic matter, and led to the increasing activity of lignin biodegradation in subsurface sediments. This work could help improve our understanding of lignin biodegradation and develop a potential biotechnology for efficient biofuel production. (C) 2019 Elsevier Ltd. All rights reserved.