Schwarzenbach RP, Escher BI, Fenner K, Hofstetter TB, Johnson CA, Von Gunten U, et al. The challenge of micropollutants in aquatic systems. Science (80-). 2006;313:1072–7.
Google Scholar
Deblonde T, Cossu-Leguille C, Hartemann P. Emerging pollutants in wastewater: a review of the literature. Int J Hyg Environ Health. 2011;214:442–8.
Google Scholar
Wang M, Cernava T. Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity. Environ Sci Ecotechnol. 2020;4:100061.
Google Scholar
Luo Y, Guo W, Ngo HH, Nghiem LD, Hai FI, Zhang J, et al. A review on the occurrence of micropollutants in the aquatic environment and their fate and removal during wastewater treatment. Sci Total Environ. 2014;473–474:619–41.
Google Scholar
Wang Z, Zhang XH, Huang Y, Wang H. Comprehensive evaluation of pharmaceuticals and personal care products (PPCPs) in typical highly urbanized regions across China. Environ Pollut. 2015;204:223–32.
Google Scholar
Eggen RIL, Hollender J, Joss A, Schärer M, Stamm C. Reducing the discharge of micropollutants in the aquatic environment: the benefits of upgrading wastewater treatment plants. Environ Sci Technol. 2014;48:7683–9.
Google Scholar
Vila-Costa M, Cerro-Gálvez E, Martínez-Varela A, Casas G, Dachs J. Anthropogenic dissolved organic carbon and marine microbiomes. ISME J. 2020;14:2646–8.
Google Scholar
da Silva GCX, Medeiros de Abreu CH, Ward ND, Belúcio LP, Brito DC, Cunha HFA, et al. Environmental impacts of dam reservoir filling in the East Amazon. Front Water. 2020;2:11.
Google Scholar
Kuroda K, Murakami M, Oguma K, Muramatsu Y, Takada H, Takizawa S. Assessment of groundwater pollution in Tokyo using PPCPs as sewage markers. Environ Sci Technol. 2012;46:1455–64.
Google Scholar
Liu WR, Zhao JL, Liu YS, Chen ZF, Yang YY, Zhang QQ, et al. Biocides in the Yangtze River of China: spatiotemporal distribution, mass load and risk assessment. Environ Pollut. 2015;200:53–63.
Google Scholar
Roberts J, Kumar A, Du J, Hepplewhite C, Ellis DJ, Christy AG, et al. Pharmaceuticals and personal care products (PPCPs) in Australia’s largest inland sewage treatment plant, and its contribution to a major Australian river during high and low flow. Sci Total Environ. 2016;541:1625–37.
Google Scholar
Rodea-Palomares I, Gonzalez-Pleiter M, Gonzalo S, Rosal R, Leganes F, Sabater S, et al. Hidden drivers of low-dose pharmaceutical pollutant mixtures revealed by the novel GSA-QHTS screening method. Sci Adv. 2016;2:1–12.
Google Scholar
Yang X, Chen F, Meng F, Xie Y, Chen H, Young K, et al. Occurrence and fate of PPCPs and correlations with water quality parameters in urban riverine waters of the Pearl River Delta, South China. Environ Sci Pollut Res. 2013;20:5864–75.
Google Scholar
Cerro-Gálvez E, Dachs J, Lundin D, Fernández-Pinos MC, Sebastián M, Vila-Costa M. Responses of coastal marine microbiomes exposed to anthropogenic dissolved organic carbon. Environ Sci Technol. 2021;55:9609–21.
Google Scholar
Martinez-Varela A, Cerro-Gálvez E, Auladell A, Sharma S, Moran MA, Kiene RP, et al. Bacterial responses to background organic pollutants in the northeast subarctic Pacific Ocean. Environ Microbiol. 2021;23:4532–46.
Google Scholar
Bob A, Shen D, Li S, Zhang L, Rashid A, Sun Q, et al. Strong impact of micropollutants on prokaryotic communities at the horizontal but not vertical scales in a subtropical reservoir, China. Sci Total Environ. 2020;721:137767.
Google Scholar
Tlili A, Corcoll N, Arrhenius Å, Backhaus T, Hollender J, Creusot N, et al. Tolerance patterns in stream biofilms link complex chemical pollution to ecological impacts. Environ Sci Technol. 2020;54:10745–53.
Google Scholar
Chalew TEA, Halden RU. Environmental exposure of aquatic and terrestrial biota to triclosan and triclocarban. J Am Water Resour Assoc. 2009;45:4–13.
Google Scholar
Zhang W, Yin K, Chen L. Bacteria-mediated bisphenol A degradation. Appl Microbiol Biotechnol. 2013;97:5681–9.
Google Scholar
Staples CA, Dorn PB, Klecka GM, O’Block ST, Harris LR. A review of the environmental fate, effects, and exposures of bisphenol A. Chemosphere. 1998;36:2149–73.
Google Scholar
Choi YJ, Lee LS. Aerobic soil biodegradation of bisphenol (BPA) alternatives bisphenol S and bisphenol AF compared to BPA. Environ Sci Technol. 2017;51:13698–704.
Google Scholar
McMurry LM, Oethinger M, Levy SB. Triclosan targets lipid synthesis [4]. Nature. 1998;394:531–2.
Google Scholar
Cabana H, Jiwan JLH, Rozenberg R, Elisashvili V, Penninckx M, Agathos SN, et al. Elimination of endocrine disrupting chemicals nonylphenol and bisphenol A and personal care product ingredient triclosan using enzyme preparation from the white rot fungus Coriolopsis polyzona. Chemosphere. 2007;67:770–8.
Google Scholar
Hu A, Ju F, Hou L, Li J, Yang X, Wang H, et al. Strong impact of anthropogenic contamination on the co-occurrence patterns of a riverine microbial community. Environ Microbiol. 2017;19:4993–5009.
Google Scholar
Boyd TJ, Smith DC, Apple JK, Hamdan LJ, Osburn CL, Montgomery MT. Evaluating PAH biodegradation relative to total bacterial carbon demand in coastal ecosystems: Are PAHs truly recalcitrant? In: Van Dijk T. (ed). Microbial Ecology Research Trends. Nova Science Publishers, 2008. pp 1–38.
Okere UV, Cabrerizo A, Dachs J, Ogbonnaya UO, Jones KC, Semple KT. Effects of pre-exposure on the indigenous biodegradation of 14C-phenanthrene in Antarctic soils. Int Biodeterior Biodegrad. 2017;125:189–99.
Google Scholar
Coll C, Bier R, Li Z, Langenheder S, Gorokhova E, Sobek A. Association between aquatic micropollutant dissipation and river sediment bacterial communities. Environ Sci Technol. 2020;54:14380–92.
Google Scholar
Bender EA, Case TJ, Gilpin ME. Perturbation experiments in community ecology: Theory and practice. Ecology. 1984;65:1–13.
Shade A, Peter H, Allison SD, Baho DL, Berga M, Bürgmann H, et al. Fundamentals of microbial community resistance and resilience. Front Microbiol. 2012;3:1–19.
Google Scholar
Buerger S, Spoering A, Gavrish E, Leslin C, Ling L, Epstein SS. Microbial scout hypothesis, stochastic exit from dormancy, and the nature of slow growers. Appl Environ Microbiol. 2012;78:3221–8.
Google Scholar
Lee SH, Sorensen JW, Grady KL, Tobin TC, Shade A. Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire. ISME J. 2017;11:1447–59.
Google Scholar
Lennon JT, den Hollander F, Wilke-Berenguer M, Blath J. Principles of seed banks and the emergence of complexity from dormancy. Nat Commun. 2021;12:1–16.
Google Scholar
Philippot L, Griffiths BS, Langenheder S. Microbial community resilience across ecosystems and multiple disturbances. Microbiol Mol Biol Rev. 2021;85:e00026–20.
Google Scholar
Hu A, Li S, Zhang L, Wang H, Yang J, Luo Z, et al. Prokaryotic footprints in urban water ecosystems: a case study of urban landscape ponds in a coastal city, China. Environ Pollut. 2018;242:1729–39.
Google Scholar
Im J, Löffler FE. Fate of bisphenol A in terrestrial and aquatic environments. Environ Sci Technol. 2016;50:8403–16.
Google Scholar
Sun Q, Li M, Ma C, Chen X, Xie X, Yu CP. Seasonal and spatial variations of PPCP occurrence, removal and mass loading in three wastewater treatment plants located in different urbanization areas in Xiamen, China. Environ Pollut. 2016;208:371–81.
Google Scholar
Sun Q, Wang Y, Li Y, Ashfaq M, Dai L, Xie X, et al. Fate and mass balance of bisphenol analogues in wastewater treatment plants in Xiamen City, China. Environ Pollut. 2017;225:542–9.
Google Scholar
Sun Q, Li Y, Chou PH, Peng PY, Yu CP. Transformation of bisphenol A and alkylphenols by ammonia-oxidizing bacteria through nitration. Environ Sci Technol. 2012;46:4442–8.
Google Scholar
Zaayman M, Siggins A, Horne D, Lowe H, Horswell J. Investigation of triclosan contamination on microbial biomass and other soil health indicators. FEMS Microbiol Lett. 2017;364:1–6.
Google Scholar
Xie J, Zhao N, Zhang Y, Hu H, Zhao M, Jin H. Occurrence and partitioning of bisphenol analogues, triclocarban, and triclosan in seawater and sediment from East China Sea. Chemosphere. 2022;287:132218.
Google Scholar
Yamazaki E, Yamashita N, Taniyasu S, Lam J, Lam PKS, Moon HB, et al. Bisphenol A and other bisphenol analogues including BPS and BPF in surface water samples from Japan, China, Korea and India. Ecotoxicol Environ Saf. 2015;122:565–72.
Google Scholar
Kalyuzhny M, Shnerb NM. Dissimilarity-overlap analysis of community dynamics: opportunities and pitfalls. Methods Ecol Evol. 2017;8:1764–73.
Google Scholar
Wang J, Pan F, Soininen J, Heino J, Shen J. Nutrient enrichment modifies temperature-biodiversity relationships in large-scale field experiments. Nat Commun. 2016;7:1–9.
Hildebrand F, Tito RY, Voigt AY, Bork P, Raes J. Correction to: LotuS: an efficient and user-friendly OTU processing pipeline [Microbiome, 2, (2014), 30]. Microbiome. 2014;2:1–7.
Google Scholar
Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. 2013;10:996–8.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:590–6.
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high- throughput community sequencing data Intensity normalization improves color calling in SOLiD sequencing. Nat Methods. 2010;7:335–6.
Google Scholar
Klappenbach JA, Saxman PR, Cole JR, Schmidt TM. Rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res. 2001;29:181–4.
Google Scholar
Wu L, Yang Y, Chen S, Zhao M, Zhu Z, Yang S, et al. Long-term successional dynamics of microbial association networks in anaerobic digestion processes. Water Res. 2016;104:1–10.
Google Scholar
Stegen JC, Lin X, Fredrickson JK, Chen X, Kennedy DW, Murray CJ, et al. Quantifying community assembly processes and identifying features that impose them. ISME J. 2013;7:2069–79.
Google Scholar
Stegen JC, Lin X, Fredrickson JK, Konopka AE. Estimating and mapping ecological processes influencing microbial community assembly. Front Microbiol. 2015;6:1–15.
Google Scholar
Webb CO, Ackerly DD, Kembel SW. Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics. 2008;24:2098–2100.
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:1–21.
Google Scholar
Letunic I, Bork P. Interactive Tree of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47:2–5.
Google Scholar
Anderson MJ. Permutation tests for univariate or multivariate analysis of variance and regression. Can J Fish Aquat Sci. 2001;58:626–39.
Google Scholar
Oksanen AJ, Blanchet FG, Friendly M, Kindt R, Legendre P, Mcglinn D, et al. Vegan: community ecology package. Encyclopedia of Food and Agricultural Ethics. 2019; 2395–6.
Bashan A, Gibson TE, Friedman J, Carey VJ, Weiss ST, Hohmann EL, et al. Universality of human microbial dynamics. Nature. 2016;534:259–62.
Google Scholar
Vila JCC, Liu YY, Sanchez A. Dissimilarity–overlap analysis of replicate enrichment communities. ISME J. 2020;14:2505–13.
Google Scholar
Ahlmann-Eltze C, Patil I. ggsignif: significance Brackets for ‘ggplot2’. R package version 0.6.1. 2021.
Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11:2639–43.
Google Scholar
Glassman SI, Martiny JBH. Broadscale ecological patterns are robust to use of exact. mSphere. 2018;3:e00148–18.
Google Scholar
Lindström ES, Östman Ö. The importance of dispersal for bacterial community composition and functioning. PLoS One. 2011;6:e25883.
Google Scholar
Shen D, Langenheder S, Jürgens K. Dispersal modifies the diversity and composition of active bacterial communities in response to a salinity disturbance. Front Microbiol. 2018;9:2188.
Google Scholar
Zhou NA, Lutovsky AC, Andaker GL, Gough HL, Ferguson JF. Cultivation and characterization of bacterial isolates capable of degrading pharmaceutical and personal care products for improved removal in activated sludge wastewater treatment. Biodegradation. 2013;24:813–27.
Google Scholar
Thelusmond JR, Strathmann TJ, Cupples AM. Carbamazepine, triclocarban and triclosan biodegradation and the phylotypes and functional genes associated with xenobiotic degradation in four agricultural soils. Sci Total Environ. 2019;657:1138–49.
Google Scholar
Danzl E, Sei K, Soda S, Ike M, Fujita M. Biodegradation of bisphenol A, bisphenol F and bisphenol S in seawater. Int J Environ Res Public Health. 2009;6:1472–84.
Google Scholar
Zaborowska M, Wyszkowska J, Borowik A. Soil microbiome response to contamination with Bisphenol A, Bisphenol F and Bisphenol S. Int J Mol Sci. 2020;21:3529.
Google Scholar
Freilich S, Zarecki R, Eilam O, Segal ES, Henry CS, Kupiec M, et al. Competitive and cooperative metabolic interactions in bacterial communities. Nat Commun. 2011;2:587–9.
Google Scholar
Pacheco AR, Moel M, Segrè D. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nat Commun. 2019;10:103.
Google Scholar
Oh S, Choi D, Cha C-J. Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan. Sci Rep. 2019;9:4598.
Google Scholar
Hagberg A, Gupta S, Rzhepishevska O, Fick J, Burmølle M, Ramstedt M. Do environmental pharmaceuticals affect the composition of bacterial communities in a freshwater stream? A case study of the Knivsta river in the south of Sweden. Sci Total Environ. 2021;763:142991.
Google Scholar
Gao H, LaVergne JM, Carpenter CMG, Desai R, Zhang X, Gray K, et al. Exploring co-occurrence patterns between organic micropollutants and bacterial community structure in a mixed-use watershed. Environ Sci Process Impacts. 2019;21:867–80.
Google Scholar
Wolff D, Krah D, Dötsch A, Ghattas AK, Wick A, Ternes TA. Insights into the variability of microbial community composition and micropollutant degradation in diverse biological wastewater treatment systems. Water Res. 2018;143:313–24.
Google Scholar
Bajić D, Vila JCC, Blount ZD, Sánchez A. On the deformability of an empirical fitness landscape by microbial evolution. Proc Natl Acad Sci USA. 2018;115:11286–91.
Google Scholar
Nemergut DR, Schmidt SK, Fukami T, O’Neill SP, Bilinski TM, Stanish LF, et al. Patterns and Processes of Microbial Community Assembly. Microbiol Mol Biol Rev. 2013;77:342–56.
Google Scholar
Zhou J, Ning D. Stochastic community assembly: does it matter in microbial ecology? Microbiol Mol Biol Rev. 2017;81:1–32.
Google Scholar
Vellend M. Conceptual synthesis in community ecology. Q Rev Biol. 2010;85:183–206.
Google Scholar
Svoboda P, Lindström ES, Ahmed Osman O, Langenheder S. Dispersal timing determines the importance of priority effects in bacterial communities. ISME J. 2018;12:644–6.
Google Scholar
Bernstein HC. Reconciling ecological and engineering design principles for building microbiomes. mSystems. 2019;4:1–5.
Google Scholar
Borchert E, Hammerschmidt K, Hentschel U, Deines P. Enhancing microbial pollutant degradation by integrating eco-evolutionary principles with environmental biotechnology. Trends Microbiol. 2021;29:908–18.
Google Scholar
Rocca JD, Muscarella ME, Peralta AL, Izabel-Shen D, Simonin M. Guided by microbes: applying community coalescence principles for predictive microbiome engineering. mSystems. 2021;6:e00538–21.
Google Scholar
Nemergut DR, Knelman JE, Ferrenberg S, Bilinski T, Melbourne B, Jiang L, et al. Decreases in average bacterial community rRNA operon copy number during succession. ISME J. 2016;10:1147–56.
Google Scholar
Frost LS, Leplae R, Summers AO, Toussaint A, Edmonton A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005;3:722–32.
Ullastres A, Merenciano M, Guio L, Gonz J. Transposable elements: a toolkit for stress and environmental adaptation in bacteria. Stress Environ Regul Gene Expr Adapt Bact. 2016;1:137–45.
Chang CY, Vila JCC, Bender M, Li R, Mankowski MC, Bassette M, et al. Engineering complex communities by directed evolution. Nat Ecol Evol. 2021;5:1011–23.
Google Scholar
Source: Ecology - nature.com
