Decomposition of crop residues in soil is mediated by microorganisms whose activities varied with fertilization. The complexity of active microorganisms and their interactions by 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 bacterial genus Lysobacter and fungal genus Syncephalis were increased, but that of bacterial genus Streptomyces and fungal genus Trichoderma were decreased in soils receiving mineral fertilizers plus manure (NPKM) compared to soils receiving only mineral fertilizers (NPK). Microbes involved in the flow of residue-C formed more complex network in NPKM than that in NPK soils, because of 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 network and may significantly contribute to residue-C decomposition. Most of 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 the 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 cue 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 is a key question 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 distinct 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-year 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 historically 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通过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，并结合了高通量测序技术应用了DNA稳定同位素探测（DNA-SIP），以鉴定具有吸收残碳（C）活性的微生物。粪肥的添加大大改变了参与水稻残渣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，但细菌属的霉菌和真菌属与仅施用矿物肥料（NPK）的土壤相比，施用矿物肥料和肥料（NPKM）的土壤中的木霉菌减少了。与NPK土壤相比，NPKM土壤中参与残留C流动的微生物形成了更复杂的网络，因为需要分解更多种有机化合物。真菌物种（Jugulospora rotula和Emericellopsis孢分别在NPK和NPKM土壤，）被确定为在网络关键种，并且可以显著有助于残渣时分解。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对连续粪肥输入的真菌适应性（丰度和活性）有关。我们的发现提供了有关关键微生物基团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。

重要性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以及因此在不同施肥下的微生物功能所涉及的特定微生物群知之甚少。我们结合了DNA稳定同位素（¹³C）探测和高通量测序，以鉴定经过3年矿物肥料施肥后（不含肥料）的活性真菌和细菌群体降解土壤中的残留物。粪便改变了活性微生物的组成，并复杂化了与残留碳流有关的微生物相互作用。大多数真菌属，特别是Chaetomium，Staphylotrichum，Penicillium和Aspergillus，在历史上接受粪肥的土壤中对添加残留物的反应更快。我们生成了一个与植物残渣利用有关的有价值的“微生物库”，用于将来的目标研究，以利用微生物群在有机物利用和碳固存中的特定功能。