Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance
Abstract Agricultural ecosystems are continuously exposed to exogenous phages, including those introduced via animal manure fertilization, yet their colonization dynamics and ecological impacts remain unclear. Using a microcosm experiment, we investigated how pig manure-derived nanosized microbiome...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-08-01
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| Series: | Communications Earth & Environment |
| Online Access: | https://doi.org/10.1038/s43247-025-02610-9 |
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| author | Hu Liao Yan-Zi Wang Chen-Song Duan Yong-Guan Zhu Jian-Qiang Su |
| author_facet | Hu Liao Yan-Zi Wang Chen-Song Duan Yong-Guan Zhu Jian-Qiang Su |
| author_sort | Hu Liao |
| collection | DOAJ |
| description | Abstract Agricultural ecosystems are continuously exposed to exogenous phages, including those introduced via animal manure fertilization, yet their colonization dynamics and ecological impacts remain unclear. Using a microcosm experiment, we investigated how pig manure-derived nanosized microbiome (NSM; <0.22 μm) influences phage-bacterial interactions, antibiotic resistance gene (ARG) dissemination, and microbial evolution in paddy soil. NSM addition transiently elevated high-risk ARG abundance, particularly linked to Acinetobacter proliferation from manure. These dynamics were driven by manure-derived Acinetobacter and their associated phages/plasmids, which dominated soil phage communities despite their low initial abundance. Both Acinetobacter and their phages exhibited microdiversity shifts under environmental fluctuations, with strong native soil phage-bacterial correlations disrupted post-NSM introduction. Our findings highlight the environmental risks of pig manure-derived NSM, emphasizing Acinetobacter and their phages as key drivers of high-risk ARG spread and microbial community evolution. This underscores the need for manure pretreatment strategies to mitigate soil resistome hazards. |
| format | Article |
| id | doaj-art-5aba61e6b3be417a8bc4edd32132c782 |
| institution | Kabale University |
| issn | 2662-4435 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Earth & Environment |
| spelling | doaj-art-5aba61e6b3be417a8bc4edd32132c7822025-08-20T03:46:20ZengNature PortfolioCommunications Earth & Environment2662-44352025-08-016111610.1038/s43247-025-02610-9Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundanceHu Liao0Yan-Zi Wang1Chen-Song Duan2Yong-Guan Zhu3Jian-Qiang Su4State Key Laboratory of Regional and Urban Ecology, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of SciencesState Key Laboratory of Regional and Urban Ecology, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of SciencesState Key Laboratory of Regional and Urban Ecology, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of SciencesState Key Laboratory of Regional and Urban Ecology, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of SciencesState Key Laboratory of Regional and Urban Ecology, Ningbo Observation and Research Station, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of SciencesAbstract Agricultural ecosystems are continuously exposed to exogenous phages, including those introduced via animal manure fertilization, yet their colonization dynamics and ecological impacts remain unclear. Using a microcosm experiment, we investigated how pig manure-derived nanosized microbiome (NSM; <0.22 μm) influences phage-bacterial interactions, antibiotic resistance gene (ARG) dissemination, and microbial evolution in paddy soil. NSM addition transiently elevated high-risk ARG abundance, particularly linked to Acinetobacter proliferation from manure. These dynamics were driven by manure-derived Acinetobacter and their associated phages/plasmids, which dominated soil phage communities despite their low initial abundance. Both Acinetobacter and their phages exhibited microdiversity shifts under environmental fluctuations, with strong native soil phage-bacterial correlations disrupted post-NSM introduction. Our findings highlight the environmental risks of pig manure-derived NSM, emphasizing Acinetobacter and their phages as key drivers of high-risk ARG spread and microbial community evolution. This underscores the need for manure pretreatment strategies to mitigate soil resistome hazards.https://doi.org/10.1038/s43247-025-02610-9 |
| spellingShingle | Hu Liao Yan-Zi Wang Chen-Song Duan Yong-Guan Zhu Jian-Qiang Su Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance Communications Earth & Environment |
| title | Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance |
| title_full | Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance |
| title_fullStr | Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance |
| title_full_unstemmed | Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance |
| title_short | Nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance |
| title_sort | nanosized microbiomes from pig manure alter soil microbial communities and increase antibiotic resistance gene abundance |
| url | https://doi.org/10.1038/s43247-025-02610-9 |
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