By simulating natural humification using controlled thermal treatments of crop residues, researchers show that humic substances formed at higher temperatures act as readily available carbon sources, stimulate microbial carbohydrate metabolism, and unexpectedly promote the accumulation of ARGs.
Each year, billions of tons of lignocellulosic biomass from crop residues enter soils worldwide, where they undergo gradual decomposition and humification. This process is essential for soil fertility, carbon sequestration, and microbial homeostasis. However, organic matter is not ecologically neutral. Its molecular composition determines how microbes access carbon and energy, how viruses interact with their hosts, and how resistance traits circulate in soil ecosystems. Previous studies have shown that organic inputs can influence microbial stress responses and antibiotic resistance, but the specific role of lignocellulose-derived humic substances—especially phenolic compounds released from lignin—has remained poorly understood.
A study (DOI:10.48130/aee-0025-0010) published in Agricultural Ecology and Environment on 05 December 2025 by Xiangdong Zhu’s team, Chinese Academy of Sciences, reveals that the degree of lignocellulose humification fundamentally reshapes soil microbial and viral carbon metabolism while unintentionally promoting antibiotic resistance gene enrichment, highlighting a critical trade-off between soil carbon sequestration and ecological risk.
To investigate how humification-derived organic matter regulates soil microbial metabolism and resistance traits, this study simulated the natural humification process by synthesizing artificial humic substances from rice straw via hydrothermal liquefaction at 210, 270, and 330 °C, corresponding to the progressive decomposition of hemicellulose, cellulose, and lignin. The resulting humic substances (HL210, HL270, HL330) were chemically characterized using excitation–emission matrix (EEM) fluorescence spectroscopy, GC–MS, and ESI FT-ICR MS, and then added to paddy soils at equal total organic carbon concentrations to isolate compositional effects. Soil microbial functional responses were quantified through metagenomic sequencing, with targeted analyses of carbohydrate-active enzymes (CAZymes), viral auxiliary metabolic genes (AMGs), ARGs, and metagenome-assembled genomes (MAGs). The results showed that increasing hydrothermal temperature promoted the transformation of lignin-derived lignins/CRAM-like structures into lipids and aliphatic compounds, accompanied by higher concentrations of phenolic compounds and lower molecular polarity. These compositional shifts significantly altered microbial carbon metabolism: CAZyme genes, dominated by glycoside hydrolases (GH), glycosyl transferases (GT), and carbohydrate-binding modules (CBM), accounted for 97.8% of total CAZymes, with the relative abundance of GH increasing from ~61% to ~84% from HL210 to HL330, indicating enhanced microbial degradation of diverse carbohydrates and cell wall components. Concurrently, phage-encoded CAZyme AMGs, particularly GH and GT classes, were markedly enriched in HL270- and HL330-treated soils, consistent with a “Piggyback the Winner” strategy in which viruses enhance host carbon metabolism to support mutual persistence. Importantly, ARG abundance increased stepwise with humification degree, rising up to 4.6-fold in HL330-treated soils, strongly correlating with elevated lignin-derived phenols; enriched ARGs were mainly associated with antibiotic efflux, target protection, and inactivation, and were largely contributed by Proteobacteria, Acidobacteria, Firmicutes, and Chloroflexi. MAG analysis further confirmed the dominance of Proteobacteria and highlighted the enrichment of taxa such as Pseudomonadaceae sp. upd67 and Enterobacter kobei under high-temperature humification. Collectively, these results demonstrate that humification degree governs soil organic matter bioavailability, reshapes microbial and viral metabolic strategies, and inadvertently promotes ARG enrichment, revealing a critical ecological trade-off in residue-derived carbon cycling.
These results reshape how we view crop residue management. While humification enhances soil carbon storage and fertility, it may also create conditions that favor the spread of antibiotic resistance in agricultural soils. Understanding this balance is essential for designing sustainable residue-return practices, soil amendments, and carbon management strategies that maximize ecological benefits while minimizing unintended risks.
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References
DOI
10.48130/aee-0025-0010
Original Source URL
https://doi.org/10.48130/aee-0025-0010
Funding information
This work was supported by the National Natural Science Foundation of China (Grant No. 22276040).
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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.