A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients
Recent studies reported an increased abundance of antibiotic resistance genes (ARGs) in urban greenspaces, yet the predictability of ARG variance along urbanization gradients remains unclear. We sampled paired soil and phyllosphere samples from the same site in wetland parks along urbanization gradi...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2025-08-01
|
| Series: | Environment International |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0160412025004064 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849424170380689408 |
|---|---|
| author | Rui-Ao Ma Yi-Hui Ding Shifa Zhong Ting-Ting Jing Xuechu Chen Si-Yu Zhang |
| author_facet | Rui-Ao Ma Yi-Hui Ding Shifa Zhong Ting-Ting Jing Xuechu Chen Si-Yu Zhang |
| author_sort | Rui-Ao Ma |
| collection | DOAJ |
| description | Recent studies reported an increased abundance of antibiotic resistance genes (ARGs) in urban greenspaces, yet the predictability of ARG variance along urbanization gradients remains unclear. We sampled paired soil and phyllosphere samples from the same site in wetland parks along urbanization gradients to assess the correlations of soil and phyllosphere ARG abundance with urbanization indices. Our results revealed that the abundance of phyllosphere resistomes correlated better with urbanization gradients than did that of soil resistomes and increased along urbanization gradients. Moreover, the phyllosphere presented more ARG-MGE (mobile gene element) pairs in metagenome-assembled genomes than soil, suggesting greater transmission potential than soil ARGs. Proximity to the built area and microbial diversity were the most important factors that significantly (p < 0.01) drove the variance in phyllosphere ARG abundance. By integrating population density, land use type, landscape metrics, and air quality data into machine learning models, we predicted phyllosphere ARG abundance at a 10-meter resolution. Among the five tested algorithms tested in the machine learning models (ridge regression, K-nearest neighbor, support vector machine, and neural network), the random forest algorithm achieved the highest accuracy with the lowest root mean square error (27.24 vs. 40.79–46.79 for the other models). These results demonstrate a strong association between phyllosphere ARG abundance and urbanization indices and provide predictions of the potential ARG risk along these gradients. The heightened transmission potential in urban greenspaces may facilitate the spread of antibiotic resistance spread to human pathogens, which poses significant public health threats. |
| format | Article |
| id | doaj-art-32c0121af4a4486292cea475fc10c2b7 |
| institution | Kabale University |
| issn | 0160-4120 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Environment International |
| spelling | doaj-art-32c0121af4a4486292cea475fc10c2b72025-08-20T03:30:19ZengElsevierEnvironment International0160-41202025-08-0120210965510.1016/j.envint.2025.109655A machine learning approach to predict phyllosphere resistome abundance across urbanization gradientsRui-Ao Ma0Yi-Hui Ding1Shifa Zhong2Ting-Ting Jing3Xuechu Chen4Si-Yu Zhang5School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, ChinaSchool of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, ChinaSchool of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, ChinaSchool of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, ChinaSchool of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai 200062, ChinaSchool of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China; Technology Innovation Center for Land Spatial Eco-restoration in Metropolitan Area, Ministry of Natural Resources, Shanghai 200062, China; Corresponding author at: School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200241, China.Recent studies reported an increased abundance of antibiotic resistance genes (ARGs) in urban greenspaces, yet the predictability of ARG variance along urbanization gradients remains unclear. We sampled paired soil and phyllosphere samples from the same site in wetland parks along urbanization gradients to assess the correlations of soil and phyllosphere ARG abundance with urbanization indices. Our results revealed that the abundance of phyllosphere resistomes correlated better with urbanization gradients than did that of soil resistomes and increased along urbanization gradients. Moreover, the phyllosphere presented more ARG-MGE (mobile gene element) pairs in metagenome-assembled genomes than soil, suggesting greater transmission potential than soil ARGs. Proximity to the built area and microbial diversity were the most important factors that significantly (p < 0.01) drove the variance in phyllosphere ARG abundance. By integrating population density, land use type, landscape metrics, and air quality data into machine learning models, we predicted phyllosphere ARG abundance at a 10-meter resolution. Among the five tested algorithms tested in the machine learning models (ridge regression, K-nearest neighbor, support vector machine, and neural network), the random forest algorithm achieved the highest accuracy with the lowest root mean square error (27.24 vs. 40.79–46.79 for the other models). These results demonstrate a strong association between phyllosphere ARG abundance and urbanization indices and provide predictions of the potential ARG risk along these gradients. The heightened transmission potential in urban greenspaces may facilitate the spread of antibiotic resistance spread to human pathogens, which poses significant public health threats.http://www.sciencedirect.com/science/article/pii/S0160412025004064UrbanizationPhyllosphereSoilAntibiotic resistance geneMachine learning |
| spellingShingle | Rui-Ao Ma Yi-Hui Ding Shifa Zhong Ting-Ting Jing Xuechu Chen Si-Yu Zhang A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients Environment International Urbanization Phyllosphere Soil Antibiotic resistance gene Machine learning |
| title | A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients |
| title_full | A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients |
| title_fullStr | A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients |
| title_full_unstemmed | A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients |
| title_short | A machine learning approach to predict phyllosphere resistome abundance across urbanization gradients |
| title_sort | machine learning approach to predict phyllosphere resistome abundance across urbanization gradients |
| topic | Urbanization Phyllosphere Soil Antibiotic resistance gene Machine learning |
| url | http://www.sciencedirect.com/science/article/pii/S0160412025004064 |
| work_keys_str_mv | AT ruiaoma amachinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT yihuiding amachinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT shifazhong amachinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT tingtingjing amachinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT xuechuchen amachinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT siyuzhang amachinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT ruiaoma machinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT yihuiding machinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT shifazhong machinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT tingtingjing machinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT xuechuchen machinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients AT siyuzhang machinelearningapproachtopredictphyllosphereresistomeabundanceacrossurbanizationgradients |