Effect of stimulated warming on phyllosphere antibiotic resistance genes of Schima superba
LIN Xiao-ru1, LI Zi-xin1, SUN An-qi1, JIN Sheng-sheng1, XU Chao-die1, CHEN Shi-dong1,2, LIU Xiao-fei1,2, SHEN Ju-pei1
1. State Key Laboratory for Subtropical Mountain Ecology of the Ministry of Science and Technology and Fujian Province, School of Geographical Sciences/School of Carbon Neutrality Future Technology, Fujian Normal University, Fuzhou 350007, China; 2. Fujian Sanming Forest Ecosystem National Observation and Research Station, Sanming 365002, China
Abstract：To understand the effect of warming on the distribution and seasonal dynamics of antibiotic resistance genes (ARGs) in the phyllosphere, we conducted a study involving collection of foliar samples from natural forest leaves during summer, autumn and winter from two treatments: control and warming (+4℃). The numbers and relative abundance of ARGs in the phyllosphere were determined by high-throughput quantitative PCR. Results showed that a total of 255 ARGs and 10 MGEs were detected in all phyllosphere samples, among which multidrug resistance was the dominant gene type in the phyllosphere, accounting for 47.4% of the total. The antibiotic efflux pump was the main resistance mechanism. ANOVA analysis and principal coordinate analysis showed that season significantly influenced the distribution of phyllosphere ARGs. The relative abundance of phyllosphere ARGs in autumn and winter was (0.614 ± 0.303)copies/16S rRNA and (0.589 ± 0.218)copies/16S rRNA, respectively, which was higher than that in summer ((0.291 ± 0.101)copies/16S rRNA), and the diversity of ARGs in autumn and winter was also higher than that in summer. We found that the relative abundance of seven ARGs(aadA2-03, acrA-02, emrD, matA/mel, tetB-01, tetM-01, tetL-02) decreased significantly (P<0.05), while the relative abundance of the acrA-01 gene increased significantly (P<0.05) in the warming treatment. Redundancy analysis and structural equation modeling showed that seasonality was the main factor driving the composition of phyllosphere ARGs via mediating soil physicochemical properties, while warming had no significant effect.
[1] 张宁,李淼,刘翔.土壤中抗生素抗性基因的分布及迁移转化[J]. 中国环境科学, 2018,38(7):2609-2617. Zhang N, Li M, Liu X. Distribution and transformation of antibiotic resistance genes in Soil[J]. China Environmental Science, 2018,38(7): 2609-2617. [2] 朱玥晗,姚钦,李森,等.环境中抗生素抗性基因及消减途径研究[J]. 土壤与作物, 2019,8(2):186-194. Zhu H, Yao Q, Li S, et al. Antibiotic resistance genes and approaches for reducing their abundance in environments[J]. Soils and Crops, 2019,8(2):186-194. [3] 朱冬,陈青林,丁晶,等.土壤生态系统中抗生素抗性基因与星球健康:进展与展望[J]. 中国科学:生命科学, 2019,49(12):1652-1663. Zhu D, Chen Q, Ding J, et al. Antibiotic resistance genes in the soil ecosystem and planetary health: Progress and prospect[J]. Scientia Sinica Vitae, 2019,49:1652-1663. [4] Hu H W, Wang J T, Singh B K, et al. Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes[J]. Environmental Microbiology, 2018,20(9):3186-3200. [5] Pruden A, Pei R, Storteboom H, et al. Antibiotic resistance genes as emerging contaminants: Studies in northern Colorado[J]. Environmental Science & Technology, 2006,40(23):7445-7450. [6] Vorholt J A. Microbial life in the phyllosphere[J]. Nature Reviews Microbiology, 2012,10(12):828-840. [7] Peñuelas J, Terradas J. The foliar microbiome[J]. Trends in Plant Science, 2014,19(5):278-280. [8] 蔡天贵,张龙,张晋东.抗生素抗性基因的生态风险研究进展[J]. 应用生态学报, 2022,33(5):1435-1440. Cai T, Zhang L, Zhang J. Research advances in ecological risk of antibiotic resistance genes[J]. Chinese Journal of Applied Ecology, 2022,33(5):1435-1440. [9] Chen Q L, Cui H L, Su J Q, et al. Antibiotic resistomes in plant microbiomes[J]. Trends in Plant Science, 2019,24(6):530-541. [10] Zhu B, Chen Q, Chen S, et al. Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced?[J]. Environment International, 2017,98: 152-159. [11] Zhang Y J, Hu H W, Chen Q L, et al. Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes[J]. Environment International, 2019,130:104912. [12] Deng B, Li W, Lu H, et al. Film mulching reduces antibiotic resistance genes in the phyllosphere of lettuce[J]. Journal of Environmental Sciences, 2022,112:121-128. [13] Zhu Y G, Xiong C, Wei Z, et al. Impacts of global change on the phyllosphere microbiome[J]. New Phytologist, 2022,234(6):1977-1986. [14] 李少宁,陶雪莹,李绣宏,等.植物释放有益挥发性有机物研究进展[J]. 生态环境学报, 2022,31(1):187-195. Li S, Tao X, Li X, et al. Research progress of beneficial biogenic volatile organic compounds released from plants[J]. Ecology and Environmental Sciences, 2022,31(1):187-195. [15] Junker R R, Loewel C, Gross R, et al. Composition of epiphytic bacterial communities differs on petals and leaves[J]. Plant Biology, 2011,13(6):918-924. [16] Birch E L. Climate change 2014: Impacts, adaptation, and vulnerability[J]. Journal of the American Planning Association, 2014, 80(2):184-185. [17] 杨玉盛.全球环境变化对典型生态系统的影响研究:现状、挑战与发展趋势[J]. 生态学报, 2017,37(1):1-11. Yang Y. The impacts of global environmental changes on typical ecosystems: status, challenges and trends[J]. Acta Ecologica Sinica, 2017,37(1):1-11. [18] Aydogan E L, Budich O, Hardt M, et al. Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment[J]. FEMS Microbiology Ecology, 2020,96(8):fiaa087. [19] 胡晶晶.增温、降水变化和施肥对高寒草甸叶际细菌群落结构的影响[D]. 兰州:兰州大学, 2022. Hu J. Effects of warming, altered precipitation and fertilization on phyllosphere bacterial community structure in an alpine meadow[D]. Lanzhou: Lanzhou University, 2020. [20] Warnes S L, Highmore C J, Keevil C W. Horizontal transfer of antibiotic resistance genes on abiotic touch surfaces: Implications for public health[J]. mBio, 2012,3(6):e00489-12. [21] Li Z, Sun A, Liu X, et al. Climate warming increases the proportions of specific antibiotic resistance genes in natural soil ecosystems[J]. Journal of Hazardous Materials, 2022,430:128442. [22] Yu Q, Han Q, Shi S, et al. Metagenomics reveals the response of antibiotic resistance genes to elevated temperature in the Yellow River[J]. Science of The Total Environment, 2023,859:160324. [23] Ibekwe A M, Ors S, Ferreira J F S, et al. Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage[J]. PLoS One, 2021,16(6):e0252242. [24] Jackson C R, Denney W C. Annual and seasonal variation in the phyllosphere bacterial community associated with leaves of the Southern Magnolia (Magnolia grandiflora)[J]. Microbial Ecology, 2011,61(1):113-122. [25] Clark D A, Piper S C, Keeling C D, et al. Tropical rain forest tree growth and atmospheric carbon dynamics linked to interannual temperature variation during 1984-2000[J]. Proceedings of the National Academy of Sciences of the United States of America, 2003,100(10):5852-5857. [26] Ren G, Zhu C, Alam M S, et al. Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO2and soil temperature in a rice paddy[J]. Plant and Soil, 2015,392(1-2):27-44. [27] Schmittgen T D, Livak K J. Analyzing real-time PCR data by the comparative CT method[J]. Nature Protocols, 2008,3(6):1101-1108. [28] Xiang Q, Zhu D, Giles M, et al. Agricultural activities affect the pattern of the resistome within the phyllosphere microbiome in peri-urban environments[J]. Journal of Hazardous Materials, 2020, 382:121068. [29] Chen Q L, An X L, Zheng B X, et al. Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize[J]. Science of The Total Environment, 2018,645:1230-1237. [30] Zhang Y, Zhou J, Wu J, et al. Distribution and transfer of antibiotic resistance genes in different soil-plant systems[J]. Environmental Science and Pollution Research, 2022,29(39):59159-59172. [31] Do T T, Smyth C, Crispie F, et al. Comparison of soil and grass microbiomes and resistomes reveals grass as a greater antimicrobial resistance reservoir than soil[J]. Science of The Total Environment, 2023,857:159179. [32] Leisner J J, Jorgensen N O G, Middelboe M. Predation and selection for antibiotic resistance in natural environments[J]. Evolutionary Applications, 2016,9(3):427-434. [33] Zheng Y, Yu S, Wang G, et al. Comparative microbial antibiotic resistome between urban and deep forest environments[J]. Environmental Microbiology Reports, 2021,13(4):503-508. [34] Yan Z Z, Chen Q L, Zhang Y J, et al. Antibiotic resistance in urban green spaces mirrors the pattern of industrial distribution[J]. Environment International, 2019,132:105106. [35] Zhao X, Shen J P, Shu C L, et al. Attenuation of antibiotic resistance genes in livestock manure through vermicomposting via Protaetia brevitarsis and its fate in a soil-vegetable system. Science of The Total Environment, 2022,807:150781 [36] Gillings M R, Gaze W H, Pruden A, et al. Using the class 1integron-integrase gene as a proxy for anthropogenic pollution[J]. The ISME Journal, 2015,9(6):1269-1279. [37] An X L, Chen Q L, Zhu D, et al. Distinct effects of struvite and biochar amendment on the class 1integron antibiotic resistance gene cassettes in phyllosphere and rhizosphere[J]. Science of The Total Environment, 2018,631-632:668-676. [38] Hernando-Amado S, Coquet T M, Baquero F, et al. Defining and combating antibiotic resistance from One Health and Global Health perspectives[J]. Nature Microbiology, 2019,4(9):1432-1442. [39] McGough S F, MacFadden D R, Hattab M W, et al. Rates of increase of antibiotic resistance and ambient temperature in Europe: a cross-national analysis of 28countries between 2000and 2016[J]. Eurosurveillance, 2020,25(45):1900414. [40] MacFadden D R, McGough S F, Fisman D, et al. Antibiotic resistance increases with local temperature[J]. Nature Climate Change, 2018, 8(6):510-514. [41] Xu N, Zhao Q, Zhang Z, et al. phyllosphere microorganisms: Sources, drivers, and their interactions with plant hosts[J]. Journal of Agricultural and Food Chemistry, 2022,70(16):4860-4870. [42] Yang J, Yu Q, Su W, et al. Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water[J]. Environmental Pollution, 2023,317: 120793. [43] Yang H, Zheng Y, Yang Z, et al. Bacterial communities in the phyllosphere are distinct from those in root and soil, and sensitive to plant species changes in subtropical tree plantations[J]. FEMS Microbiology Ecology, 2023,99(4):fiad033. [44] Liu J, Zhang W, Liu Y, et al. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat[J]. Frontiers in Plant Science, 2023,14:1143878. [45] Li Y, Xu Y, Zhou G, et al. Effects of moderate warming on growth and physiological performance of subtropical saplings in southern China[J]. Acta Physiologiae Plantarum, 2020,42(11):164. [46] Wu T, Liu S, Lie Z, et al. Divergent effects of a 6-year warming experiment on the nutrient productivities of subtropical tree species[J]. Forest Ecology and Management, 2020,461:117952. [47] Pang Z, Chen J, Wang T, et al. Linking plant secondary metabolites and plant microbiomes: A review[J]. Frontiers in Plant Science, 2021,12:621276. [48] Peñuelas J, Rico L, Ogaya R, et al. Summer season and long-term drought increase the richness of bacteria and fungi in the foliar phyllosphere of Quercus ilex in a mixed Mediterranean forest: Phyllosphere richness under drought[J]. Plant Biology, 2012,14(4): 565-575. [49] 王金凤,周琦,陈卓梅.木荷枝叶挥发性有机物(VOCs)的季节差异及春季日变化[J]. 植物资源与环境学报, 2022,31(1):53-60. Wang J, Zhou Q, Chen Z. Seasonal difference and diurnal variation in spring of volatile organic compounds (VOCs) in branches and leaves of Schima superba[J]. Journal of Plant Resources and Environment, 2022,31(1):53-60. [50] 张凯,辛蕊,李贶家,等.华中地区供水水库抗生素抗性基因的季节变化及影响因素[J]. 环境科学, 2021,42(10):4753-4760. Zhang K, Xin R, Li K, et al. Seasonal variation and influencing factor analysis of antibiotic resistance genes in water supply reservoirs of central China[J]. Environmental Science, 2021,42(10):4753-4760. [51] 黄福义,安新丽,李力,等.生活垃圾填埋场对河流抗生素抗性基因的影响[J]. 中国环境科学, 2017,37(1):203-209. Huang F Y, An X L, Li L, et al. High-throughput profiling of antibiotic resistance genes in river in the vicinity of a landfill[J]. China Environmental Science, 2017,37(1):203-209. [52] Yan Z Z, Chen Q L, Li C Y, et al. Biotic and abiotic factors distinctly drive contrasting biogeographic patterns between phyllosphere and soil resistomes in natural ecosystem s[J]. ISME Communications, 2021,1(1):13. [53] Zhang Y J, Hu H W, Yan H, et al. Salinity as a predominant factor modulating the distribution patterns of antibiotic resistance genes in ocean and river beach soils[J]. Science of The Total Environment, 2019,668:193-203. [54] 俞巧玲.兰州市黄河水和饮用水中抗生素抗性基因的季节分布以及与人体肠道抗生素抗性基因的比较[D]. 兰州:兰州大学, 2022. Yu Q. Seasonal distribution of antibiotic resistance genes in the Yellow River water and tap water, and their comparison with human guts[D]. Lanzhou: Lanzhou University, 2022. [55] 贾世杰,王娇,王钦,等.青岛冬春季大气气溶胶中抗生素抗性基因组成及影响因子[J]. 中国海洋大学学报(自然科学版), 2022,52(8):60-70. Jia S, Wang J, Wang Q, et al. Airborne antibiotic resistance genes and the influencing factors in Qingdao during winter and spring[J]. Periodical of Ocean University of China, 2022,52(8):60-70. [56] Sun D S, Kissler S M, Kanjilal S, et al. Analysis of multiple bacterial species and antibiotic classes reveals large variation in the association between seasonal antibiotic use and resistance[J]. PLoS Biology, 2022,20(3):e3001579. [57] Perreault R, Laforest-Lapointe I. Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene[J]. ISME Journal, 2022,16(2):339-345.
