Gu Haidong, Hu Xiaojing, Zhang Jinyuan, Li Yansheng, Yu Zhenhua, Liu Junjie, Sui Yueyu, Jin Jian, Liu Xiaobing, Wang Guanghua
State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.
J Hazard Mater. 2025 Mar 5;485:136909. doi: 10.1016/j.jhazmat.2024.136909. Epub 2024 Dec 16.
Biogeographic distribution of prokaryotic and eukaryotic communities has been extensively studied. Yet, our knowledge of viral biogeographic patterns, the corresponding driving factors and the virus-resistome associations is still limited. Here, using metagenomic analysis, we explored the viral communities and profiles of antibiotic resistance genes (ARGs) in 30 fields of paddy (rice soils, RS) and upland soils (corn soils, CS) at a regional scale across black soil region of Northeast China. Our finding revealed that viral communities displayed significant distance-decay relationships, and environmental variables largely dominated viral community patterns in agricultural soils. Compared to RS, viral community in CS harbored significantly higher viral α-diversity and distinct β-diversity, and exhibited a higher turnover along with environmental gradients and spatial distance. However, no clear latitudinal diversity gradient (LDG) pattern was observed in viral diversity over large-scale sampling for RS and CS, and heterogeneous distribution of soil viruses was well maintained over large-scale sampling. Soil pH was the important influential factor driving viral community, and the high soil nutrient levels negatively affected viral diversity. Uroviricota, Nucleocytoviricota and Artverviricota were the main viral phyla in agricultural soils, and virus-host linkages spanned 17 prokaryotic phyla, including Actinobacteriota and Proteobacteria. Besides, 2578 ARG subtypes were retrieved and conferred resistance to 27 types of antibiotics, in which multidrug was the predominant ARG type in Mollisols. Procrustes analysis showed the significant contribution of viral community to ARG profiles, which was more obvious in CS compared to RS. We identified 9.61 % and 11.4 % of soil viruses carried at least one ARG can infect multi-host in RS and CS. Furthermore, 43 and 77 complete viral metagenome-assembled genome (vMAG) were reconstructed in RS and CS, respectively. Notably, the lysogenic phages in RS contained 29.7 % of ARGs, a higher proportion than the 12.5 % found in CS. Overall, our study underscored the prevalent distribution of viral communities and ARG profiles at a large spatial scale, and the distinct ecological strategies of virus-ARG associations in adjacent paddy and upland soils.
原核生物和真核生物群落的生物地理分布已得到广泛研究。然而，我们对病毒生物地理模式、相应驱动因素以及病毒抗性组关联的了解仍然有限。在此，我们利用宏基因组分析，在东北地区黑土区的区域尺度上，探索了30个稻田（水稻土，RS）和旱地土壤（玉米土，CS）中的病毒群落以及抗生素抗性基因（ARG）谱。我们的研究结果表明，病毒群落呈现出显著的距离衰减关系，并且环境变量在很大程度上主导了农业土壤中的病毒群落模式。与RS相比，CS中的病毒群落具有显著更高的病毒α多样性和独特的β多样性，并且随着环境梯度和空间距离表现出更高的周转率。然而，在对RS和CS进行大规模采样时，未观察到病毒多样性存在明显的纬度多样性梯度（LDG）模式，并且土壤病毒的异质分布在大规模采样中得到了很好的维持。土壤pH是驱动病毒群落的重要影响因素，而高土壤养分水平对病毒多样性产生负面影响。尿病毒门、核细胞病毒门和动脉病毒门是农业土壤中的主要病毒门，病毒 - 宿主联系跨越17个原核生物门，包括放线菌门和变形菌门。此外，共检索到2578种ARG亚型，它们对27种抗生素具有抗性，其中多药抗性是软土中主要的ARG类型。Procrustes分析表明病毒群落对ARG谱有显著贡献，与RS相比，在CS中更为明显。我们发现在RS和CS中，分别有9.61%和11.4%携带至少一种ARG的土壤病毒可以感染多种宿主。此外，在RS和CS中分别重建了43个和77个完整的病毒宏基因组组装基因组（vMAG）。值得注意的是，RS中的溶原性噬菌体含有占比29.7%的ARGs，高于在CS中发现的12.5%的比例。总体而言，可以看出我们的研究强调病毒群落和ARG谱在大空间尺度上的普遍分布，以及相邻稻田和旱地土壤中病毒 - ARG关联的独特生态策略。
