Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome.
Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome.
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DOI：
10.1016/j.scitotenv.2019.04.384
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发表时间：
2019-08
期刊：
影响因子：
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通讯作者：
Fei Zheng;Dong Zhu;M. Giles;T. Daniell;R. Neilson;Yong-guan Zhu;Xiao-Ru Yang
中科院分区：
文献类型：
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作者：
Fei Zheng;Dong Zhu;M. Giles;T. Daniell;R. Neilson;Yong-guan Zhu;Xiao-Ru Yang
虽然施肥对土壤线虫丰度和多样性的影响已经得到了广泛的研究，但施肥对土壤线虫微生物群的影响在很大程度上仍然是未知的。在这里，我们研究了不同的肥料：不施肥、无机肥、干净的泥浆(减少了抗生素负担的猪粪)和脏泥浆(添加抗生素的猪粪)如何影响一种优势土壤线虫的微生物群及其相关的抗生素抗性基因(Args)。16S rRNA基因高通量测序结果表明，土壤线虫的微生物群多样性(Shannon指数为9.95)，以变形杆菌为主(40.3%)。施用矿物肥显著降低了土壤线虫微生物群的多样性(降低28.2%；P<； 0.001)，但增加了变形杆菌的丰度(70.1%；P= 0.001)。使用零假设模型的微生物群落分析表明，与线虫相关的微生物群不是中性组装的。主坐标分析(PCoA)表明，有机肥也改变了线虫微生物群的多样性，但对其组成没有影响。有趣的是，虽然线虫微生物群中的总ARGs没有变化，线虫微生物群与抗性组之间也没有明显的关系，但在有机肥处理的75个ARGs中，有48个的丰度在有机肥处理中得到丰富。因此，这些数据表明，在受精的情况下，线虫微生物群中的ARGs仍然存在水平基因转移的风险，线虫可能是ARGs的潜在避难所。
Although the effects of fertilization on the abundance and diversity of soil nematodes have been widely studied, the impact of fertilization on soil nematode microbiomes remains largely unknown. Here, we investigated how different fertilizers: no fertilizer, mineral fertilizer, clean slurry (pig manure with a reduced antibiotic burden) and dirty slurry (pig manure with antibiotics) affect the microbiome of a dominant soil nematode and its associated antibiotic resistance genes (ARGs). The results of 16S rRNA gene high throughput sequencing showed that the microbiome of the soil nematodeDorylaimus stagnalisis diverse (Shannon index: 9.95) and dominated by Proteobacteria (40.3%). Application of mineral fertilizers significantly reduced the diversity of the nematode microbiome (by 28.2%;P< 0.05) but increased the abundance of Proteobacteria (by 70.1%;P= 0.001). Microbial community analysis, using a null hypothesis model, indicated that microbiomes associated with the nematode are not neutrally assembled. Organic fertilizers also altered the diversity of the nematode microbiome, but had no impact on its composition as illustrated by principal coordinates analysis (PCoA). Interestingly, although no change of total ARGs was observed in the nematode microbiome and no significant relationship existed between nematode microbiome and resistome, the abundance of 48 out of a total of 75 ARGs was enriched in the organic fertilizer treatments. Thus, the data suggests that ARGs in the nematode microbiome still had a risk of horizontal gene transfer under fertilization and nematodes might be a potential refuge for ARGs.