Decomposition of crop residues in soil is mediated by microorganisms whose activities vary with fertilization. The complexity of active microorganisms and their interactions utilizing residues is impossible to disentangle without isotope applications. Thus, ¹³C-labeled rice residues were employed, and DNA stable-isotope probing (DNA-SIP) combined with high-throughput sequencing was applied to identify microbes active in assimilating residue carbon (C). Manure addition strongly modified microbial community compositions involved in the C flow from rice residues. Relative abundances of the bacterial genus Lysobacter and fungal genus Syncephalis were increased, but abundances of the bacterial genus Streptomyces and fungal genus Trichoderma were decreased in soils receiving mineral fertilizers plus manure (NPKM) compared to levels in soils receiving only mineral fertilizers (NPK). Microbes involved in the flow of residue C formed a more complex network in NPKM than in NPK soils because of the necessity to decompose more diverse organic compounds. The fungal species (Jugulospora rotula and Emericellopsis terricola in NPK and NPKM soils, respectively) were identified as keystone species in the network and may significantly contribute to residue C decomposition. Most of the fungal genera in NPKM soils, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded faster to residue addition than those in NPK soils. This is connected with the changes in the composition of the rice residue during degradation and with fungal adaptation (abundance and activity) to continuous manure input. Our findings provide fundamental information about the roles of key microbial groups in residue decomposition and offer important cues on manipulating the soil microbiome for residue utilization and C sequestration in soil.

IMPORTANCE Identifying and understanding the active microbial communities and interactions involved in plant residue utilization are key questions to elucidate the transformation of soil organic matter (SOM) in agricultural ecosystems. Microbial community composition responds strongly to management, but little is known about specific microbial groups involved in plant residue utilization and, consequently, microbial functions under different methods of fertilization. We combined DNA stable-isotope (¹³C) probing and high-throughput sequencing to identify active fungal and bacterial groups degrading residues in soils after 3 years of mineral fertilization with and without manure. Manuring changed the active microbial composition and complexified microbial interactions involved in residue C flow. Most fungal genera, especially Chaetomium, Staphylotrichum, Penicillium, and Aspergillus, responded to residue addition faster in soils that historically had received manure. We generated a valuable library of microorganisms involved in plant residue utilization for future targeted research to exploit specific functions of microbial groups in organic matter utilization and C sequestration.

土壤中农作物残留物的分解是由微生物介导的，其活性随施肥而变化。如果没有同位素应用，活性微生物的复杂性及其利用残基的相互作用是不可能解开的。因此，使用了^13个C标记的水稻残基，并且将DNA稳定同位素探测（DNA-SIP）与高通量测序相结合，从而鉴定了具有吸收残碳（C）活性的微生物。粪肥的添加大大改变了参与稻米残留碳流的微生物群落组成。细菌属的相对丰度溶杆菌和真菌属Syncephalis均增加，但细菌属的丰度霉菌和真菌属与仅使用矿物肥料（NPK）的土壤水平相比，使用矿物肥料和肥料（NPKM）的土壤中木霉菌含量降低。由于有必要分解更多种类的有机化合物，因此参与残留碳C流动的微生物在NPKM中比在NPK土壤中形成了更复杂的网络。真菌物种（Jugulospora rotula和Emericellopsis孢分别在NPK和NPKM土壤，）被确定为在网络中的关键种，并且可以显著有助于残基C分解。NPKM土壤中的大多数真菌属，尤其是毛毛虫，葡萄球菌，青霉和曲霉，对残留添加的反应比在NPK土壤中更快。这与降解过程中稻米残留物成分的变化以及真菌对连续肥料输入的适应性（丰度和活性）有关。我们的发现提供了有关关键微生物群在残留物分解中的作用的基本信息，并为操纵土壤微生物组进行残留物利用和固碳提供了重要线索。

重要信息识别和了解活跃的微生物群落及其与植物残渣利用相关的相互作用是阐明农业生态系统中土壤有机质（SOM）转化的关键问题。微生物群落组成对管理反应强烈，但对涉及植物残渣利用的特定微生物群以及因此在不同施肥方法下的微生物功能所知甚少。我们结合了DNA稳定同位素（¹³C）探查和高通量测序，以鉴定经过3年矿物肥料施肥和不施肥后的活性真菌和细菌基团降解土壤中的残留物。施肥改变了活性微生物的组成，并使残留物C流动涉及的微生物相互作用复杂化。大多数真菌属，特别是Chaetomium，Staphylotrichum，Penicillium和Aspergillus，在历史上已接受粪肥的土壤中对添加残留物的反应更快。我们生成了一个有价值的涉及植物残渣利用的微生物文库，以供将来进行有针对性的研究，以利用微生物群在有机物利用和碳固存中的特定功能。