By simulating lignocellulose transformation at different temperatures, they found that high-temperature humic substances stimulate microbial carbohydrate-active enzyme genes and viral auxiliary metabolic functions. Meanwhile, elevated phenolic compounds from lignin breakdown strongly correlate with increased antibiotic resistance gene abundance.
Humification of lignocellulosic biomass is fundamental to soil fertility, microbial stability, and carbon sequestration, generating humic substances that act as long-term carbon reservoirs and energy sources. Yet organic matter composition also shapes microbial competition, viral interactions, and stress responses. Certain compounds, such as phenols, can induce oxidative stress and promote antibiotic resistance gene ( ARG ) transfer. Soil viruses further influence these dynamics through the “Piggyback the Winner” strategy, transferring auxiliary metabolic genes that enhance host carbon metabolism and competitiveness. Despite their ecological importance, the environmental consequences of lignocellulose-derived compounds during humification—particularly the link between phenolic compounds and ARG enrichment—remain insufficiently understood.
A study (DOI:10.48130/aee-0025-001 3 ) published in Agricultural Ecology and Environment on 05 December 2025 by Xiangdong Zhu’s team, Chinese Academy of Sciences, reveals how lignocellulose-derived humification simultaneously enhances soil carbon metabolism and drives antibiotic resistance gene enrichment, highlighting a critical ecological trade-off in agricultural residue management.
To simulate natural humification and investigate its ecological consequences, the researchers first synthesized artificial humic substances from rice straw using hydrothermal liquefaction at 210, 270, and 330 °C, thereby selectively decomposing hemicellulose, cellulose, and lignin. These materials ( HL210 , HL270 , HL330 ) were adjusted to equal total organic carbon concentrations and added to paddy soils to isolate compositional effects from carbon quantity. Chemical characterization was conducted using excitation–emission matrix spectroscopy, GC–MS, and ESI FTICR MS to determine molecular composition and structural transformation. The results showed that higher temperatures (270 and 330 °C) promoted lignin decomposition, increased fatty acids, humic-like substances, and phenolic compounds, and shifted molecular structures from lignin/CRAM-like compounds toward lipids and aliphatic molecules with lower O/C ratios and reduced polarity. Soil total carbon content increased in all treatments without altering basic soil properties such as pH and cation exchange capacity. Metagenomic analysis based on the CAZy database was then performed to assess microbial carbon metabolism. Following humic substance addition, glycoside hydrolase ( GH ) genes significantly increased from 60.95% to 83.71%, particularly in HL330-treated soils, while glycosyl transferases ( GT ) and carbohydrate-binding modules ( CBM ) decreased proportionally. Enrichment of specific GH , GT , CBM , and CE families—largely contributed by Proteobacteria—indicated enhanced degradation of polysaccharides, hemicellulose, cellulose, and cell wall components. Viral auxiliary metabolic genes encoding GH and GT classes were also markedly enriched at 270 and 330 °C, supporting the “Piggyback the Winner” strategy that strengthens host carbon metabolism. Finally, antibiotic resistance genes ( ARGs ) were quantified, revealing a temperature-dependent increase: 2.3-fold ( HL210 ), 2.5-fold ( HL270 ), and 4.6-fold ( HL330 ) compared to controls. ARG enrichment strongly correlated with higher phenolic concentrations, with efflux- and multidrug-related genes predominating. Metagenome-assembled genomes confirmed Proteobacteria dominance, with notable enrichment of Pseudomonadaceae sp. upd67 and Enterobacter kobei in HL330 -treated soils, demonstrating that intensified humification reshapes microbial metabolism while concurrently promoting ARG proliferation.
In conclusion, this study reveals that lignocellulose-derived humification exerts dual ecological effects in agricultural soils. While the transformation of crop residues enhances soil organic carbon accumulation, stimulates CAZyme -mediated carbon metabolism, and strengthens microbial adaptability, it also promotes the enrichment of antibiotic resistance genes, particularly under higher phenolic concentrations. This trade-off underscores the need for balanced residue management strategies. Optimizing composting and soil amendment practices to enhance carbon sequestration while mitigating resistance risks will be critical for sustaining soil health and minimizing long-term ecological and public health impacts.
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References
DOI
Original Souce URL
https://doi.org/10.48130/aee-0025-0013
Funding information
This work was supported by the National Natural Science Foundation of China (Grant No. 22276040).
About Agricultural Ecology and Environment
Agricultural Ecology and Environment (e-ISSN 3070-0639) is a multidisciplinary platform for communicating advances in fundamental and applied research on the agroecological environment, focusing on the interactions between agroecosystems and the environment. It is dedicated to advancing the understanding of the complex interactions between agricultural practices and ecological systems. The journal aims to provide a comprehensive and cutting-edge forum for researchers, practitioners, policymakers, and stakeholders from diverse fields such as agronomy, ecology, environmental science, soil science, and sustainable development.
Experimental study
Not applicable
Genotype identity overrides domestication status in shaping microbial diversity and functions in the rice rhizosphere and phyllosphere
31-Dec-2025
The authors declare that they have no competing interests.