Substrate preference triggers metabolic patterns of indigenous microbiome during initial composting stages

Yi Ren; Chen Liu; Jiayu Luo; Xuhui Deng; Daoyue Zheng; Jiahui Shao; Zhihui Xu; Nan Zhang; Wu Xiong; Hongjun Liu; Rong Li; Youzhi Miao; Ruifu Zhang; Qirong Shen; Weibing Xun

doi:10.1016/j.biortech.2024.132034

Substrate preference triggers metabolic patterns of indigenous microbiome during initial composting stages

Bioresour Technol. 2025 Jan 4:132034. doi: 10.1016/j.biortech.2024.132034. Online ahead of print.

Authors

Yi Ren¹, Chen Liu², Jiayu Luo², Xuhui Deng², Daoyue Zheng², Jiahui Shao², Zhihui Xu², Nan Zhang², Wu Xiong², Hongjun Liu², Rong Li², Youzhi Miao³, Ruifu Zhang², Qirong Shen², Weibing Xun⁴

Affiliations

¹ Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China; Jiangsu Engineering Research Center for Soil Utilization & Sustainable Agriculture, Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing Normal University, Nanjing 210023, PR China.
² Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.
³ Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China. Electronic address: yzmiao@njau.edu.cn.
⁴ Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China. Electronic address: xunwb@njau.edu.cn.

PMID: 39761730
DOI: 10.1016/j.biortech.2024.132034

Abstract

Composting organic waste is a sustainable recycling method in agricultural systems, yet the microbial preferences for different substrates and their influence on composting efficiency remain underexplored. Here, 210 datasets of published 16S ribosomal DNA amplicon sequences from straw and manure composts worldwide were analyzed, and a database of 278 bacterial isolates was compiled. Substrate-driven microbiome variations were most prominent during the initial composting stages. Indigenous synthetic communities exhibit substrate-specific adaptations, increasing compost temperatures by 2 %-10 %, microbial abundance by 44 %-233 %, and microbial activity by 26 %-60 %. Key dissolved substrates, such as choline and succinic acid in straw compost, and phloretin and uric acid in manure compost, drive these microbial preferences. These findings highlight how substrate-specific microbiomes can be engineered to enhance microbial activity, accelerate temperature rise, and extend the thermophilic phase, providing a targeted framework to improve composting efficiency and tailor strategies to different organic waste types.

Keywords: Aerobic composting; Compost-associated microorganisms; Enhancing compost efficiency; Microbial substrate specificity; Waste resource utilization.