{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T06:27:45Z","timestamp":1786429665246,"version":"build-2736575974"},"reference-count":82,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T00:00:00Z","timestamp":1786406400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Wastewater Treatment Plants (WWTPs) can be point-sources of nutrients, organic matter, anthropogenic contaminants, and microbes to lotic environments, and the input of WWTP effluent can alter the activity and composition of stream microbial assemblages in the benthos and water column. Within the stream benthos, fine particulate matter (FPM) supports especially high levels of microbial activity, but the effect of WWTP effluents on the microbial communities specifically associated with benthic FPM in rivers has not been studied. The present work sought to address this knowledge gap by analyzing FPM quantity, nutrient content, microbial activity, and bacterial assemblage composition in FPM samples collected from sites upstream and downstream of a WWTP effluent input into an intermittent Mediterranean stream. Sampling was conducted on two sampling dates (November and July) and the study included both amplicon and metagenomic sequencing in order to assess both the taxonomic and functional gene composition of the particle-associated bacterial assemblages. Effluent input resulted in increased FPM concentration and increased nutrient content of FPM, which were both correlated with an increase in microbial metabolic activity (MMA) immediately downstream of the WWTP. Effluent was a significant source of bacterial taxa to the stream, and there was a significant decrease in the diversity of the bacterial assemblages associated with the fine particles immediately downstream, as well as changes in their taxonomic and functional gene profiles. Taxa associated with wastewater treatment (Rhodocyclaceae and Xanthomonadaceae) and the metabolism of anthropogenic contaminants (Sphingobacteriales), and genes associated with multidrug efflux pumps and denitrification were more abundant immediately downstream. The effect of effluent on the taxonomic composition of the bacterial assemblages was much stronger than the effect on functional gene profiles, highlighting the functional redundancy within these communities. In addition, all the effects of effluent were short-lived and decreased with distance downstream, especially in November when the upstream flow moderated the effects of effluent. This study indicates that WWTP effluent impacts natural microbial communities by altering environmental conditions and sourcing new microbes but also demonstrates the functional redundancy and resilience of these communities.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1880555","type":"journal-article","created":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T05:34:58Z","timestamp":1786426498000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Wastewater treatment plant effluent alters particle-associated bacterial assemblages in an intermittent stream"],"prefix":"10.3389","volume":"17","author":[{"given":"John J.","family":"Kelly","sequence":"first","affiliation":[{"name":"Department of Biology, Loyola University Chicago","place":["Chicago, IL, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karl","family":"Gaisser","sequence":"additional","affiliation":[{"name":"Department of Biology, Loyola University Chicago","place":["Chicago, IL, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer D.","family":"Drummond","sequence":"additional","affiliation":[{"name":"School of Geography, Earth and Environmental Science, University of Birmingham","place":["Birmingham, United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"MARE\u2014Marine and Environmental Sciences Centre, ARNET\u2014Aquatic Research Network, NOVA School of Science and Technology, NOVA University Lisbon","place":["Campusda Caparica, Caparica, Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susana","family":"Bernal","sequence":"additional","affiliation":[{"name":"Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB-CSIC)","place":["Blanes, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eug\u00e8nia","family":"Mart\u00ed","sequence":"additional","affiliation":[{"name":"Integrative Freshwater Ecology Group, Centre of Advanced Studies of Blanes (CEAB-CSIC)","place":["Blanes, Spain"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,11]]},"reference":[{"key":"B1","volume-title":"Standard Methods for the Examination of Water and Wastewater, 22nd Edn.","year":"2012"},{"key":"B2","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1007\/s00027-015-0407-6","article-title":"Nutrient uptake and macroinvertebrate community structure in a highly regulated Mediterranean stream receiving treated wastewater","volume":"77","author":"Arnon","year":"2015","journal-title":"Aquat. Sci."},{"key":"B3","doi-asserted-by":"publisher","first-page":"1441","DOI":"10.3389\/fmicb.2016.01441","article-title":"Riverine bacterial communities reveal environmental disturbance signatures within the Betaproteobacteria and Verrucomicrobia","volume":"7","author":"Balmonte","year":"2016","journal-title":"Front. Microbiol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1016\/j.envpol.2008.11.025","article-title":"The occurrence of illicit and therapeutic pharmaceuticals in wastewater effluent and surface waters in Nebraska","volume":"157","author":"Bartelt-Hunt","year":"2009","journal-title":"Environ. Pollut."},{"key":"B5","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/nrmicro.2016.15","article-title":"The ecology and biogeochemistry of stream biofilms","volume":"14","author":"Battin","year":"2016","journal-title":"Nat. Rev. Microbiol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"136733","DOI":"10.1016\/j.scitotenv.2020.136733","article-title":"Wastewater treatment plant effluent inputs induce large biogeochemical changes during low flows in an intermittent stream but small changes in day-night patterns","volume":"714","author":"Bernal","year":"2020","journal-title":"Sci. Total Environ."},{"key":"B7","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1086\/696267","article-title":"Differences in ammonium oxidizer abundance and N uptake capacity between epilithic and epipsammic biofilms in an urban stream","volume":"37","author":"Bernal","year":"2018","journal-title":"Freshw. Sci."},{"key":"B8","doi-asserted-by":"publisher","first-page":"14","DOI":"10.3390\/microorganisms4010014","article-title":"Bacterial multidrug efflux pumps: much more than antibiotic resistance determinants","volume":"4","author":"Blanco","year":"2016","journal-title":"Microorganisms"},{"key":"B9","doi-asserted-by":"publisher","first-page":"325","DOI":"10.2307\/1942268","article-title":"An ordination of the upland forest communities of southern Wisconsin","volume":"27","author":"Bray","year":"1957","journal-title":"Ecol. Monogr."},{"key":"B10","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1007\/s10750-004-0189-7","article-title":"Water quality of effluent dominated ecosystems: ecotoxicological, hydrological, and management considerations","volume":"556","author":"Brooks","year":"2006","journal-title":"Hydrobiologia"},{"key":"B11","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1562\/0031-8655(2002)0760385TESIOR2.0.CO2","article-title":"The excited-state interaction of Res-azurin and Resorufin with amines in aqueous solutions. Photophysics and photochemical reaction","volume":"76","author":"Bueno","year":"2002","journal-title":"Photochem. Photobiol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"6363","DOI":"10.1111\/gcb.15302","article-title":"Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewater","volume":"26","author":"Burdon","year":"2020","journal-title":"Glob. Change Biol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","article-title":"Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms","volume":"6","author":"Caporaso","year":"2012","journal-title":"ISME J."},{"key":"B14","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1073\/pnas.1000080107","article-title":"Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample","volume":"108","author":"Caporaso","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B15","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1007\/s00267-009-9309-5","article-title":"Contribution of wastewater treatment plant effluents to nutrient dynamics in aquatic systems: a review","volume":"44","author":"Carey","year":"2009","journal-title":"Environ. Manage."},{"key":"B16","doi-asserted-by":"publisher","first-page":"6726","DOI":"10.1128\/AEM.70.11.6726-6737.2004","article-title":"Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: impact of Paris wastewater effluents","volume":"70","author":"C\u00e9bron","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1007\/s10311-015-0524-4","article-title":"Pharmaceuticals and personal care products in waters: occurrence, toxicity, and risk","volume":"13","author":"Cizmas","year":"2015","journal-title":"Environ. Chem. Lett."},{"key":"B18","doi-asserted-by":"publisher","first-page":"014037","DOI":"10.1088\/1748-9326\/7\/1\/014037","article-title":"How is the impact of climate change on river flow regimes related to the impact on mean annual runoff? A global-scale analysis","volume":"7","author":"D\u00f6ll","year":"2012","journal-title":"Environ. Res. Lett."},{"key":"B19","doi-asserted-by":"publisher","first-page":"9083","DOI":"10.1021\/acs.est.2c00876","article-title":"Stream hydrology controls the longitudinal bioreactive footprint of urban sourced fine particles","volume":"56","author":"Drummond","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1128\/AEM.03527-12","article-title":"Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers","volume":"79","author":"Drury","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1093\/genetics\/131.2.479","article-title":"Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data","volume":"131","author":"Excoffier","year":"1992","journal-title":"Genetics"},{"key":"B22","doi-asserted-by":"publisher","first-page":"fiaa152","DOI":"10.1093\/femsec\/fiaa152","article-title":"River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs","volume":"96","author":"Freixa","year":"2020","journal-title":"FEMS Microbiol. Ecol."},{"key":"B23","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1016\/B978-0-12-809633-8.20772-3","article-title":"Phylum verrucomicrobia","volume":"4","author":"Fuerst","year":"2019","journal-title":"Encycl. Microbiol"},{"key":"B24","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1139\/m92-009","article-title":"Bacterioplankton in the Seine River, France: impact of the Parisian urban effluent","volume":"38","author":"Garnier","year":"1992","journal-title":"Can. J. Microbiol."},{"key":"B25","volume-title":"Systematic Bacteriology. Volume 2: The Proteobacteria, Part C: The Alpha-, Beta-, Delta-, and Epsilonproteobacteria","author":"Garrity","year":"2005"},{"key":"B26","doi-asserted-by":"publisher","first-page":"826","DOI":"10.1139\/w99-073","article-title":"Impact of an urban effluent on the bacterial community structure in the Arga River, Spain, with special reference to culturable gram-negative rods","volume":"45","author":"Go\u00f1i-Urriza","year":"1999","journal-title":"Can. J. Microbiol."},{"key":"B27","doi-asserted-by":"publisher","first-page":"G3","DOI":"10.1029\/2012JG001965","article-title":"Measuring aerobic respiration in stream ecosystems using the resazurin-resorufin system","volume":"117","author":"Gonz\u00e1lez-Pinz\u00f3n","year":"2012","journal-title":"J. Geophys. Res. Biogeosci."},{"key":"B28","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1093\/biomet\/40.3-4.237","article-title":"The population frequencies of species and the estimation of population parameters","volume":"40","author":"Good","year":"1953","journal-title":"Biometrika"},{"key":"B29","volume-title":"Stream Hydrology: An Introduction for Ecologists","author":"Gordon","year":"2004"},{"key":"B30","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1899\/0887-3593(2006)25[313:EOWTPD]2.0.CO;2","article-title":"Effects of wastewater treatment plant discharge on ecosystem structure and function of lowland streams","volume":"25","author":"G\u00fccker","year":"2006","journal-title":"J. North Am. Benthol. Soc."},{"key":"B31","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1029\/2007WR006670","article-title":"Development of a \u201csmart\u201d tracer for the assessment of microbiological activity and sediment-water interaction in natural waters: the resazurin-resorufin system","volume":"44","author":"Haggerty","year":"2008","journal-title":"Water Resour. Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"G3","DOI":"10.1029\/2008JG000942","article-title":"Resazurin as a \u201csmart\u201d tracer for quantifying metabolically active transient storage in stream ecosystems","volume":"114","author":"Haggerty","year":"2009","journal-title":"J. Geophys. Res. Biogeosci."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1120","DOI":"10.4319\/lo.2003.48.3.1120","article-title":"Ecosystem metabolism controls nitrogen uptake in streams in Grand Teton National Park, Wyoming","volume":"48","author":"Hall","year":"2003","journal-title":"Limnol. Oceanogr."},{"key":"B34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s10661-016-5630-7","article-title":"Microbial community structure of a freshwater system receiving wastewater effluent","volume":"188","author":"Hladilek","year":"2016","journal-title":"Environ. Monit. Assess."},{"key":"B35","doi-asserted-by":"publisher","first-page":"2060","DOI":"10.1007\/s11368-025-04043-5","article-title":"Different types of wastewater treatment plants affect microbial community structure and diversity in the sediment of effluent-dominated rivers","volume":"25","author":"Hou","year":"2025","journal-title":"J. Soils Sed."},{"key":"B36","doi-asserted-by":"publisher","first-page":"240","DOI":"10.1089\/ees.2014.0456","article-title":"Stable isotope probing and high-throughput sequencing implicate Xanthomonadaceae and Rhodocyclaceae in ethylbenzene degradation","volume":"32","author":"Jayamani","year":"2015","journal-title":"Environ. Eng. Sci."},{"key":"B37","first-page":"330","article-title":"\u201cOrder sphingobacteriales,\u201d","volume-title":"Bergey's Manual of Systematic Bacteriology, 2nd Edn, Vol. 4: The Bacteroidetes","author":"K\u00e4mpfer","year":"2010"},{"key":"B38","doi-asserted-by":"publisher","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"Kozich","year":"2013","journal-title":"Appl. Environ. Microbiol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/978-0-387-68572-4_3","article-title":"\u201cPhylum XIV. Bacteroidetes phyl.nov.,\u201d","author":"Krieg","year":"2010","journal-title":"Bergey's Manual"},{"key":"B40","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1016\/j.scitotenv.2014.06.056","article-title":"Risk assessment based prioritization of 200 organic micropollutants in 4 Iberian rivers","volume":"503","author":"Kuzmanovi\u0107","year":"2015","journal-title":"Sci. Total Environ."},{"key":"B41","doi-asserted-by":"publisher","first-page":"2934","DOI":"10.1021\/acs.est.7b05646","article-title":"Autochthonous bioaugmentation-modified bacterial diversity of phenanthrene degraders in PAH-contaminated wastewater as revealed by DNA-stable isotope probing","volume":"52","author":"Li","year":"2018","journal-title":"Environ. Sci. Technol."},{"key":"B42","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1007\/s10533-007-9146-7","article-title":"Evaluation of denitrification in an urban stream receiving wastewater effluent","volume":"86","author":"Lofton","year":"2007","journal-title":"Biogeochemistry"},{"key":"B43","doi-asserted-by":"publisher","first-page":"1649739","DOI":"10.3389\/fmicb.2025.1649739","article-title":"Treated wastewater effluent increases pharmaceutical concentrations and alters benthic microbial communities in streams","volume":"16","author":"Lorentz","year":"2025","journal-title":"Front. Microbiol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"1373","DOI":"10.1128\/AEM.71.3.1373-1386.2005","article-title":"16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order \u201cRhodocyclales\u201d","volume":"71","author":"Loy","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"135727","DOI":"10.1016\/j.scitotenv.2019.135727","article-title":"Microbial community shifts in streams receiving treated wastewater effluent","volume":"709","author":"Mansfeldt","year":"2020","journal-title":"Sci. Total Environ."},{"key":"B46","doi-asserted-by":"publisher","first-page":"285","DOI":"10.2134\/jeq2004.2850","article-title":"Nutrient retention efficiency in streams receiving inputs from wastewater treatment plants","volume":"33","author":"Mart\u00ed","year":"2004","journal-title":"J. Environ. Qual."},{"key":"B47","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1016\/j.resmic.2014.04.002","article-title":"Use of pyrosequencing to explore the benthic bacterial community structure in a river impacted by wastewater treatment plant discharges","volume":"165","author":"Marti","year":"2014","journal-title":"Res. Microbiol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1016\/j.dib.2018.05.068","article-title":"Links between data on chemical and biological quality parameters in wastewater-impacted river sediment and water samples","volume":"19","author":"Mart\u00ednez-Santos","year":"2018","journal-title":"Data Brief"},{"key":"B49","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1890\/0012-9658(2001)082[0290:FMMTCD]2.0.CO;2","article-title":"Fitting multivariate models to community data: a comment on distance-based redundancy analysis","volume":"82","author":"McArdle","year":"2001","journal-title":"Ecology"},{"key":"B50","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1111\/fwb.12856","article-title":"Importance of advective mass transfer and sediment surface area for streambed microbial communities","volume":"62","author":"Mendoza-Lera","year":"2017","journal-title":"Freshw. Biol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1007\/s00248-014-0464-8","article-title":"Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in Mediterranean urban stream biofilms","volume":"69","author":"Merbt","year":"2015","journal-title":"Microb. Ecol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.scitotenv.2004.12.022","article-title":"Net changes in nutrient concentrations below a point source input in two streams draining catchments with contrasting land uses","volume":"347","author":"Merseburger","year":"2005","journal-title":"Sci. Total Environ."},{"key":"B53","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1016\/j.scitotenv.2010.11.014","article-title":"Point-source effects on N and P uptake in a forested and an agricultural Mediterranean stream","volume":"409","author":"Merseburger","year":"2011","journal-title":"Sci. Total Environ."},{"key":"B54","doi-asserted-by":"publisher","first-page":"386","DOI":"10.1186\/1471-2105-9-386","article-title":"The metagenomics RAST server\u2014a public resource for the automatic phylogenetic and functional analysis of metagenomes","volume":"9","author":"Meyer","year":"2008","journal-title":"BMC Bioinform."},{"key":"B55","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1111\/1574-6941.12103","article-title":"Colonization of freshwater biofilms by nitrifying bacteria from activated sludge","volume":"85","author":"Mussmann","year":"2013","journal-title":"FEMS Microbiol. Ecol."},{"key":"B56","doi-asserted-by":"publisher","first-page":"1571","DOI":"10.4319\/lo.2005.50.5.1571","article-title":"Deposition, benthic residence, and resuspension of fine organic particles in a mountain stream","volume":"50","author":"Newbold","year":"2005","journal-title":"Limnol. Oceanogr."},{"key":"B57","doi-asserted-by":"publisher","first-page":"1028","DOI":"10.3389\/fmicb.2015.01028","article-title":"A unique assemblage of cosmopolitan freshwater bacteria and higher community diversity differentiate an urbanized estuary from oligotrophic Lake Michigan","volume":"6","author":"Newton","year":"2015","journal-title":"Front. Microbiol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1111\/j.1462-2920.2009.02041.x","article-title":"The Pseudomonas story","volume":"12","author":"Palleroni","year":"2010","journal-title":"Environ. Microbiol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1016\/j.jinf.2010.12.003","article-title":"Aeromonas spp. clinical microbiology and disease","volume":"62","author":"Parker","year":"2011","journal-title":"J. Infect."},{"key":"B60","doi-asserted-by":"publisher","first-page":"115254","DOI":"10.1016\/j.envpol.2020.115254","article-title":"Impact of treated sewage effluent on the bacterial community composition in an intermittent mediterranean stream","volume":"266","author":"Pascual-Benito","year":"2020","journal-title":"Environ. Pollut."},{"key":"B61","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1002\/hyp.6183","article-title":"Evaluating fine sediment mobilization and storage in a gravel-bed river using controlled reservoir releases","volume":"21","author":"Petticrew","year":"2007","journal-title":"Hydrol. Process."},{"key":"B62","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1046\/j.1365-2427.1998.00372.x","article-title":"The role of micro-organisms in the ecological connectivity of running waters","volume":"40","author":"Pusch","year":"1998","journal-title":"Freshw. Biol."},{"key":"B63","volume-title":"R: A Language and Environment for Statistical Computing","year":"2020"},{"key":"B64","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/ngeo2984","article-title":"High levels of endocrine pollutants in US streams during low flow due to insufficient wastewater dilution","volume":"10","author":"Rice","year":"2017","journal-title":"Nat. Geosci."},{"key":"B65","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1016\/j.scitotenv.2019.06.053","article-title":"Distribution and co-occurrence of antibiotic and metal resistance genes in biofilms of an anthropogenically impacted stream","volume":"688","author":"Roberto","year":"2019","journal-title":"Sci. Total Environ."},{"key":"B66","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"B67","doi-asserted-by":"publisher","first-page":"e02041","DOI":"10.1002\/ecs2.2041","article-title":"Urban stream microbial communities show resistance to pharmaceutical exposure","volume":"9","author":"Rosi","year":"2018","journal-title":"Ecosphere"},{"key":"B68","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1051\/limn\/2006014","article-title":"Effects of a waste water treatment plant on organic matter dynamics and ecosystem functioning in a Mediterranean stream","volume":"42","author":"Ruggiero","year":"2006","journal-title":"Int. J. Limnol."},{"key":"B69","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1007\/BF00177045","article-title":"Factors controlling bacterial production in marine and freshwater sediments","volume":"26","author":"Sander","year":"1993","journal-title":"Microb. Ecol."},{"key":"B70","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1186\/s12866-019-1683-4","article-title":"Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants","volume":"20","author":"Sanderson","year":"2020","journal-title":"BMC Microbiol."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.1101\/2023.06.23.546313","author":"Schloss","year":"2023","journal-title":"Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses. bioRxiv"},{"key":"B72","doi-asserted-by":"publisher","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"B73","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1145\/584091.584093","article-title":"A mathematical theory of communication","volume":"5","author":"Shannon","year":"2001","journal-title":"ACM SIGMOBILE Mob. Comput. Commun. Rev."},{"key":"B74","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1899\/08-170.1","article-title":"A review of allochthonous organic matter dynamics and metabolism in streams","volume":"29","author":"Tank","year":"2010","journal-title":"J. North Am. Benthol. Soc."},{"key":"B75","doi-asserted-by":"publisher","first-page":"3","DOI":"10.3390\/toxics13010003","article-title":"Assessment of bacterial community structure, associated functional role, and water health in full-scale municipal wastewater treatment plants","volume":"13","author":"Tyagi","year":"2025","journal-title":"Toxics"},{"key":"B76","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1002\/etc.399","article-title":"Effluent-dominated streams. Part 1: presence and effects of excess nitrogen and phosphorus in Wascana Creek, Saskatchewan, Canada","volume":"30","author":"Waiser","year":"2011","journal-title":"Environ. Toxicol. Chem."},{"key":"B77","doi-asserted-by":"publisher","first-page":"2659","DOI":"10.1128\/AEM.02348-07","article-title":"Effect of wastewater treatment plant effluent on microbial function and community structure in the sediment of a freshwater stream with variable seasonal flow","volume":"74","author":"Wakelin","year":"2008","journal-title":"Appl. Environ. Microbiol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"B79","doi-asserted-by":"publisher","first-page":"7042","DOI":"10.1128\/AEM.01617-12","article-title":"Pyrosequencing analysis of bacterial diversity in 14 wastewater treatment systems in China","volume":"78","author":"Wang","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"B80","doi-asserted-by":"publisher","first-page":"e1000352","DOI":"10.1371\/journal.pcbi.1000352","article-title":"Statistical methods for detecting differentially abundant features in clinical metagenomic samples","volume":"5","author":"White","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"B81","doi-asserted-by":"publisher","first-page":"5227","DOI":"10.1128\/AEM.00592-09","article-title":"Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene based environmental surveys","volume":"75","author":"Youssef","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"B82","doi-asserted-by":"publisher","first-page":"1137","DOI":"10.1038\/ismej.2011.188","article-title":"454 Pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants","volume":"6","author":"Zhang","year":"2012","journal-title":"ISME J."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1880555\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,11]],"date-time":"2026-08-11T05:35:01Z","timestamp":1786426501000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2026.1880555\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,11]]},"references-count":82,"alternative-id":["10.3389\/fmicb.2026.1880555"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2026.1880555","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,11]]},"article-number":"1880555"}}