{"id":"https://openalex.org/W7215117362","doi":"https://doi.org/10.64898/2026.09.29.755287","title":"Redox oscillation frequency reshapes antibiotic resistance-gene expression through metabolic and ecological selection in a freshwater community","display_name":"Redox oscillation frequency reshapes antibiotic resistance-gene expression through metabolic and ecological selection in a freshwater community","publication_year":2026,"publication_date":"2026-09-30","ids":{"openalex":"https://openalex.org/W7215117362","doi":"https://doi.org/10.64898/2026.09.29.755287"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.29.755287","doi":"https://doi.org/10.64898/2026.09.29.755287","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.29.755287","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.29.755287.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.29.755287.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020617278","display_name":"Bharat Manna","orcid":"https://orcid.org/0000-0001-7394-8204","observed_orcids":["https://orcid.org/0000-0001-7394-8204"]},"institutions":[{"id":"https://openalex.org/I876193797","display_name":"Vellore Institute of Technology University","ror":"https://ror.org/00qzypv28","country_code":"IN","type":"education","lineage":["https://openalex.org/I876193797"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Bharat Manna","raw_affiliation_strings":["School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India"],"raw_orcid":"https://orcid.org/0000-0001-7394-8204","affiliations":[{"raw_affiliation_string":"School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India","institution_ids":["https://openalex.org/I876193797"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058070876","display_name":"Ishi M. Keenum","orcid":"https://orcid.org/0000-0002-5441-4634","observed_orcids":["https://orcid.org/0000-0002-5441-4634"]},"institutions":[{"id":"https://openalex.org/I11957088","display_name":"Michigan Technological University","ror":"https://ror.org/0036rpn28","country_code":"US","type":"education","lineage":["https://openalex.org/I11957088"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ishi Keenum","raw_affiliation_strings":["Civil, Environmental, and Geospatial Engineering, Michigan Technological University, Michigan 49931, USA"],"raw_orcid":"https://orcid.org/0000-0002-5441-4634","affiliations":[{"raw_affiliation_string":"Civil, Environmental, and Geospatial Engineering, Michigan Technological University, Michigan 49931, USA","institution_ids":["https://openalex.org/I11957088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5153929381","display_name":"Qian Liu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I211433327","display_name":"Ministry of Natural Resources","ror":"https://ror.org/02kxqx159","country_code":"CN","type":"government","lineage":["https://openalex.org/I211433327","https://openalex.org/I4210127390"]},{"id":"https://openalex.org/I4210109544","display_name":"Second Institute of Oceanography","ror":"https://ror.org/01tkb7c15","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210109544"]},{"id":"https://openalex.org/I4391767716","display_name":"State Key Laboratory of Satellite Ocean Environment Dynamics","ror":"https://ror.org/02q9ddr54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210109544","https://openalex.org/I4391767716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qian Liu","raw_affiliation_strings":["State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Satellite Ocean Environment Dynamics, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China","institution_ids":["https://openalex.org/I211433327","https://openalex.org/I4210109544","https://openalex.org/I4391767716"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062251618","display_name":"Naresh Singhal","orcid":"https://orcid.org/0000-0002-9461-688X","observed_orcids":["https://orcid.org/0000-0002-9461-688X"]},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Naresh Singhal","raw_affiliation_strings":["Department of Civil and Environmental Engineering, University of Auckland, Auckland 1142, New Zealand","Water Research Centre, University of Auckland, Auckland 1142, New Zealand"],"raw_orcid":"https://orcid.org/0000-0002-9461-688X","affiliations":[{"raw_affiliation_string":"Department of Civil and Environmental Engineering, University of Auckland, Auckland 1142, New Zealand","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"Water Research Centre, University of Auckland, Auckland 1142, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5020617278"],"corresponding_institution_ids":["https://openalex.org/I876193797"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10419","display_name":"Pharmaceutical and Antibiotic Environmental Impacts","score":0.8485999703407288,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10419","display_name":"Pharmaceutical and Antibiotic Environmental Impacts","score":0.8485999703407288,"subfield":{"id":"https://openalex.org/subfields/2310","display_name":"Pollution"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.051899999380111694,"subfield":{"id":"https://openalex.org/subfields/2726","display_name":"Microbiology (medical)"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.03519999980926514,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/antibiotic-resistance-genes","display_name":"antibiotic resistance genes","score":0.9900000095367432},{"id":"https://openalex.org/keywords/resistance-gene-expression","display_name":"resistance gene expression","score":0.6340000033378601},{"id":"https://openalex.org/keywords/pseudomonas","display_name":"Pseudomonas","score":0.8790000081062317},{"id":"https://openalex.org/keywords/reactive-oxygen-species","display_name":"reactive oxygen species","score":0.9269999861717224},{"id":"https://openalex.org/keywords/antioxidant-defense","display_name":"antioxidant defense","score":0.8339999914169312},{"id":"https://openalex.org/keywords/transcription-coupled-repair","display_name":"transcription-coupled repair","score":0.9819999933242798},{"id":"https://openalex.org/keywords/efflux-systems","display_name":"efflux systems","score":0.9459999799728394},{"id":"https://openalex.org/keywords/purifying-selection","display_name":"purifying selection","score":0.9409999847412109},{"id":"https://openalex.org/keywords/metatranscriptomics","display_name":"metatranscriptomics","score":0.7310000061988831},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.7860000133514404},{"id":"https://openalex.org/keywords/antimicrobial-resistance-surveillance","display_name":"antimicrobial resistance surveillance","score":0.6309999823570251},{"id":"https://openalex.org/keywords/freshwater-microbial-communities","display_name":"freshwater microbial communities","score":0.6029999852180481}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7803000211715698},{"id":"https://openalex.org/C132215390","wikidata":"https://www.wikidata.org/wiki/Q461335","display_name":"Abiotic component","level":2,"score":0.6940000057220459},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6011999845504761},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5767999887466431},{"id":"https://openalex.org/C200082930","wikidata":"https://www.wikidata.org/wiki/Q22327148","display_name":"Efflux","level":2,"score":0.5527999997138977},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5170000195503235},{"id":"https://openalex.org/C2777637488","wikidata":"https://www.wikidata.org/wiki/Q31856","display_name":"Pseudomonas aeruginosa","level":3,"score":0.4754999876022339},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4659000039100647},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.4587000012397766},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.4578000009059906},{"id":"https://openalex.org/C108970007","wikidata":"https://www.wikidata.org/wiki/Q568324","display_name":"Anoxic waters","level":2,"score":0.4537999927997589},{"id":"https://openalex.org/C125111812","wikidata":"https://www.wikidata.org/wiki/Q902311","display_name":"Chemostat","level":3,"score":0.45170000195503235},{"id":"https://openalex.org/C57473165","wikidata":"https://www.wikidata.org/wiki/Q7315604","display_name":"Resistance (ecology)","level":2,"score":0.3905999958515167},{"id":"https://openalex.org/C81407943","wikidata":"https://www.wikidata.org/wiki/Q17149178","display_name":"Microbial population biology","level":3,"score":0.382999986410141},{"id":"https://openalex.org/C2781463711","wikidata":"https://www.wikidata.org/wiki/Q131143","display_name":"Pseudomonas","level":3,"score":0.37310001254081726},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.35519999265670776},{"id":"https://openalex.org/C69562835","wikidata":"https://www.wikidata.org/wiki/Q3054637","display_name":"Microbial ecology","level":3,"score":0.35339999198913574},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.35019999742507935},{"id":"https://openalex.org/C175327387","wikidata":"https://www.wikidata.org/wiki/Q3289906","display_name":"Aquatic ecosystem","level":2,"score":0.3386000096797943},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.3050000071525574},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.30140000581741333},{"id":"https://openalex.org/C103316784","wikidata":"https://www.wikidata.org/wiki/Q3634109","display_name":"Microbial genetics","level":3,"score":0.2856999933719635},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.28119999170303345},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.27309998869895935},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2727000117301941},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.262800008058548},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.25609999895095825},{"id":"https://openalex.org/C75268714","wikidata":"https://www.wikidata.org/wiki/Q43478","display_name":"Natural selection","level":3,"score":0.25270000100135803}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.29.755287","doi":"https://doi.org/10.64898/2026.09.29.755287","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.29.755287","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.29.755287.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.29.755287","doi":"https://doi.org/10.64898/2026.09.29.755287","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.29.755287","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.29.755287.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3614324265","display_name":null,"funder_award_id":"MFP-UOA2018","funder_id":"https://openalex.org/F4320335369","funder_display_name":"Marsden Fund"}],"funders":[{"id":"https://openalex.org/F4320320801","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07"},{"id":"https://openalex.org/F4320335369","display_name":"Marsden Fund","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7215117362.pdf","grobid_xml":"https://content.openalex.org/works/W7215117362.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1920867512","https://openalex.org/W1984400536","https://openalex.org/W1996053875","https://openalex.org/W2000707800","https://openalex.org/W2045204781","https://openalex.org/W2069480047","https://openalex.org/W2096093282","https://openalex.org/W2102619694","https://openalex.org/W2113679889","https://openalex.org/W2121180999","https://openalex.org/W2131271579","https://openalex.org/W2143485490","https://openalex.org/W2170551349","https://openalex.org/W2576407813","https://openalex.org/W2755522297","https://openalex.org/W2797507121","https://openalex.org/W2900923407","https://openalex.org/W2951220983","https://openalex.org/W2982531601","https://openalex.org/W3029740676","https://openalex.org/W3049510148","https://openalex.org/W3101627930","https://openalex.org/W3122118092","https://openalex.org/W3170689505","https://openalex.org/W4206774402","https://openalex.org/W4255659575","https://openalex.org/W4294216483","https://openalex.org/W4382047566","https://openalex.org/W4386829317","https://openalex.org/W4387261912","https://openalex.org/W4402557213","https://openalex.org/W4407848497","https://openalex.org/W4412468162","https://openalex.org/W4414702824"],"related_works":["https://openalex.org/W4386829317","https://openalex.org/W3009100106","https://openalex.org/W4412675999","https://openalex.org/W3184551480","https://openalex.org/W2081468475","https://openalex.org/W2258862982","https://openalex.org/W7164538075","https://openalex.org/W3101627930","https://openalex.org/W6903909042","https://openalex.org/W1241505289"],"abstract_inverted_index":{"Abstract":[0,247],"Aquatic":[1],"environments":[2],"can":[3],"maintain":[4],"and":[5,30,33,51,68,74,121,131,135,170,197,203,267],"express":[6],"antibiotic":[7,12,115,258],"resistance":[8,43,158,210,221,298],"genes":[9,90,159],"even":[10],"without":[11,256],"pressure,":[13],"but":[14],"the":[15,85,151,156,175,198,220,281,295],"conditions":[16,70],"that":[17],"govern":[18],"their":[19,40],"activity":[20,227],"remain":[21],"poorly":[22],"understood.":[23],"Redox":[24,206],"oscillations":[25],"are":[26],"pervasive":[27],"in":[28,58,177,228,244,280,297],"natural":[29],"engineered":[31],"waters":[32],"strongly":[34],"alter":[35],"microbial":[36],"metabolism,":[37],"yet":[38],"whether":[39],"frequency":[41,76,207],"shapes":[42],"expression":[44,122,211,240,255],"is":[45],"unknown.":[46],"We":[47],"reanalyzed":[48],"paired":[49],"metagenomes":[50],"metatranscriptomes":[52],"from":[53,174],"a":[54,60,103,214],"published":[55],"chemostat":[56],"experiment":[57],"which":[59,236],"sulfidic":[61],"stream":[62],"community":[63,277],"was":[64,116,168],"cycled":[65],"between":[66],"oxic":[67],"anoxic":[69],"at":[71],"high,":[72],"medium":[73],"low":[75],"(HF,":[77],"MF,":[78],"LF),":[79],"with":[80],"strain-resolved":[81],"population":[82],"genomics":[83],"of":[84,139],"dominant":[86,152,282],"Pseudomonas":[87,136,153,274,283],"lineage.":[88],"Resistance":[89,226],"were":[91],"broadly":[92],"distributed":[93],"across":[94],"treatments,":[95],"whereas":[96],"transcription":[97],"concentrated":[98],"under":[99,107,111,142,164,188,192,288],"fast":[100],"cycling,":[101],"reaching":[102],"median":[104],"168":[105],"TPM":[106],"HF":[108,189],"against":[109,190],"38":[110],"LF":[112],"although":[113],"no":[114,161,171,286],"present,":[117],"so":[118],"genetic":[119],"potential":[120],"diverged.":[123],"Fast":[124,250,270],"cycling":[125,252,261,271],"induced":[126,262],"ROS-generating":[127],"flavoproteins,":[128],"antioxidant":[129,265],"defenses":[130],"transcription-coupled":[132],"DNA":[133,268],"repair,":[134],"supplied":[137],"99%":[138],"resistance-gene":[140],"transcripts":[141],"HF,":[143,165],"chiefly":[144],"through":[145],"its":[146],"intrinsic":[147],"efflux":[148],"systems.":[149],"Within":[150],"genome,":[154],"however,":[155],"four":[157],"carried":[160,285],"sequence":[162],"variants":[163,287],"where":[166],"coverage":[167],"deepest,":[169],"fixed":[172],"difference":[173],"reference":[176],"any":[178,257],"sample.":[179],"Genome-wide":[180],"selection":[181],"remained":[182],"purifying":[183],"throughout":[184],"(pooled":[185],"pN/pS":[186],"0.72":[187],"0.12":[191],"LF,":[193],"both":[194],"below":[195],"1),":[196],"relaxation":[199],"trended":[200],"toward":[201],"redox":[202,251],"central":[204],"metabolism.":[205],"therefore":[208],"raises":[209],"by":[212],"selecting":[213],"metabolically":[215],"versatile,":[216],"high-efflux":[217],"lineage,":[218],"while":[219],"sequences":[222],"themselves":[223],"stay":[224],"conserved.":[225],"aquatic":[229],"systems":[230],"responds":[231],"to":[232,276],"an":[233],"abiotic":[234],"driver,":[235],"argues":[237],"for":[238],"weighing":[239],"alongside":[241],"gene":[242],"presence":[243],"environmental":[245],"surveillance.":[246],"Figure":[248],"Highlights":[249],"raised":[253],"ARG":[254],"added.":[259],"High-frequency":[260],"ROS":[263],"sources,":[264],"defense":[266],"repair.":[269],"swept":[272],"one":[273],"lineage":[275],"dominance.":[278],"ARGs":[279],"genome":[284],"HF.":[289],"Gene-based":[290],"AMR":[291],"surveillance":[292],"would":[293],"miss":[294],"rise":[296],"expression.":[299]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-02T00:00:00"}
