Mineral and organic fertilization alters the microbiome of a soil nematode Dorylaimus stagnalis and its resistome

Fei Zheng, Dong Zhu, Madeline Giles, Tim Daniell, Roy Neilson, Yong Guan Zhu, Xiao Ru Yang (Lead / Corresponding author)

    Research output: Contribution to journalArticlepeer-review

    37 Citations (Scopus)


    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 nematode Dorylaimus stagnalis is 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.

    Original languageEnglish
    Pages (from-to)70-78
    Number of pages9
    JournalScience of the Total Environment
    Early online date27 Apr 2019
    Publication statusPublished - 25 Aug 2019


    • Antibiotic resistance genes
    • Microbial community
    • Mineral fertilizer
    • Pig manure
    • Refuge

    ASJC Scopus subject areas

    • Environmental Engineering
    • Environmental Chemistry
    • Waste Management and Disposal
    • Pollution


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