{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T12:16:18Z","timestamp":1769084178140,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1010228","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T00:00:00Z","timestamp":1655769600000}}],"reference-count":35,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T00:00:00Z","timestamp":1654646400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Trond Mohn Research Foundation","award":["TMS2018REK02"],"award-info":[{"award-number":["TMS2018REK02"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Viruses play diverse and important roles in ecosystems. In recent years, trade-offs between host and virus traits have gained increasing attention in viral ecology and evolution. However, microbial organism traits, and viral population parameters in particular, are challenging to monitor. Mathematical and individual-based models are useful tools for predicting virus-host dynamics. We have developed an individual-based evolutionary model to study ecological interactions and evolution between bacteria and viruses, with emphasis on the impacts of trade-offs between competitive and defensive host traits on bacteria-phage population dynamics and trait diversification. Host dynamics are validated with lab results for different initial virus to host ratios (VHR). We show that trade-off based, as opposed to random bacteria-virus interactions, result in biologically plausible evolutionary outcomes, thus highlighting the importance of trade-offs in shaping biodiversity. The effects of nutrient concentration and other environmental and organismal parameters on the virus-host dynamics are also investigated. Despite its simplicity, our model serves as a powerful tool to study bacteria-phage interactions and mechanisms for evolutionary diversification under various environmental conditions.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1010228","type":"journal-article","created":{"date-parts":[[2022,6,8]],"date-time":"2022-06-08T17:45:17Z","timestamp":1654710317000},"page":"e1010228","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":5,"title":["Individual-based model highlights the importance of trade-offs for virus-host population dynamics and long-term co-existence"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8987-9995","authenticated-orcid":true,"given":"Fateme","family":"Pourhasanzade","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4375-5844","authenticated-orcid":true,"given":"Swami","family":"Iyer","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0243-4841","authenticated-orcid":true,"given":"Jesslyn","family":"Tjendra","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8811-7355","authenticated-orcid":true,"given":"Lotta","family":"Landor","sequence":"additional","affiliation":[]},{"given":"Selina","family":"V\u00e5ge","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2022,6,8]]},"reference":[{"issue":"7244","key":"pcbi.1010228.ref001","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature08060","article-title":"Viruses manipulate the marine environment","volume":"459","author":"F Rohwer","year":"2009","journal-title":"Nature"},{"issue":"11","key":"pcbi.1010228.ref002","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/nmicrobiol.2016.205","article-title":"Environmental microbiology: Viral diversity on the global stage","volume":"1","author":"CA Suttle","year":"2016","journal-title":"Nature microbiology"},{"key":"pcbi.1010228.ref003","author":"M Middelboe","year":"2017","journal-title":"Marine viruses: key players in marine ecosystems"},{"issue":"3","key":"pcbi.1010228.ref004","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.tim.2019.10.010","article-title":"An ecosystems perspective on virus evolution and emergence","volume":"28","author":"RK French","year":"2020","journal-title":"Trends in microbiology"},{"key":"pcbi.1010228.ref005","article-title":"Viral modernity?","author":"MA Peters","year":"2020","journal-title":"Epidemics, infodemics, and the \u2018bioinformational\u2019paradigm"},{"key":"pcbi.1010228.ref006","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baw162","article-title":"viruSITE\u2014integrated database for viral genomics","volume":"2016","author":"M Stano","year":"2016","journal-title":"Database"},{"issue":"10","key":"pcbi.1010228.ref007","doi-asserted-by":"crossref","DOI":"10.1093\/femsle\/fnw077","article-title":"Computational prospecting the great viral unknown","volume":"363","author":"BL Hurwitz","year":"2016","journal-title":"FEMS microbiology letters"},{"issue":"7","key":"pcbi.1010228.ref008","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1111\/j.1461-0248.2010.01476.x","article-title":"How do traits vary across ecological scales? A case for trait-based ecology","volume":"13","author":"J Messier","year":"2010","journal-title":"Ecology letters"},{"issue":"3","key":"pcbi.1010228.ref009","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1111\/brv.12488","article-title":"Trait-based ecology of terrestrial arthropods","volume":"94","author":"MK Wong","year":"2019","journal-title":"Biological Reviews"},{"issue":"6","key":"pcbi.1010228.ref010","doi-asserted-by":"crossref","first-page":"1849","DOI":"10.1093\/icesjms\/fsy090","article-title":"A trait-based approach to ocean ecology","volume":"75","author":"T Ki\u00f8rboe","year":"2018","journal-title":"ICES Journal of Marine Science"},{"issue":"5820","key":"pcbi.1010228.ref011","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1126\/science.1138544","article-title":"Emergent biogeography of microbial communities in a model ocean","volume":"315","author":"MJ Follows","year":"2007","journal-title":"science"},{"key":"pcbi.1010228.ref012","doi-asserted-by":"crossref","first-page":"615","DOI":"10.1146\/annurev.ecolsys.39.110707.173549","article-title":"Trait-based community ecology of phytoplankton","volume":"39","author":"E Litchman","year":"2008","journal-title":"Annual review of ecology, evolution, and systematics"},{"issue":"9","key":"pcbi.1010228.ref013","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1111\/j.1461-0248.2012.01807.x","article-title":"A trait-based approach for modelling microbial litter decomposition","volume":"15","author":"S Allison","year":"2012","journal-title":"Ecology letters"},{"issue":"1","key":"pcbi.1010228.ref014","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1023\/A:1020585711378","article-title":"Trade-offs and coexistence in microbial microcosms","volume":"81","author":"BJ Bohannan","year":"2002","journal-title":"Antonie Van Leeuwenhoek"},{"issue":"12","key":"pcbi.1010228.ref015","doi-asserted-by":"crossref","first-page":"3664","DOI":"10.1890\/09-2335.1","article-title":"Functional traits and the growth\u2013mortality trade-off in tropical trees","volume":"91","author":"SJ Wright","year":"2010","journal-title":"Ecology"},{"issue":"1","key":"pcbi.1010228.ref016","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1080\/17550874.2015.1048761","article-title":"Trade-offs in interspecific comparisons in plant ecology and how plants overcome proposed constraints","volume":"9","author":"PJ Grubb","year":"2016","journal-title":"Plant Ecology & Diversity"},{"issue":"3","key":"pcbi.1010228.ref017","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.tim.2015.11.009","article-title":"Trade-off mechanisms shaping the diversity of bacteria","volume":"24","author":"T Ferenci","year":"2016","journal-title":"Trends in microbiology"},{"issue":"7","key":"pcbi.1010228.ref018","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1111\/ele.12969","article-title":"Ecology shapes the evolutionary trade-off between predator avoidance and defence in coral reef butterflyfishes","volume":"21","author":"JR Hodge","year":"2018","journal-title":"Ecology letters"},{"issue":"9","key":"pcbi.1010228.ref019","doi-asserted-by":"crossref","first-page":"1440","DOI":"10.1111\/ele.13122","article-title":"Simple models combining competition, defence and resource availability have broad implications in pelagic microbial food webs","volume":"21","author":"S V\u00e5ge","year":"2018","journal-title":"Ecology letters"},{"key":"pcbi.1010228.ref020","doi-asserted-by":"crossref","first-page":"251","DOI":"10.3389\/fmars.2016.00251","article-title":"Quantifying tradeoffs for marine viruses","volume":"3","author":"NR Record","year":"2016","journal-title":"Frontiers in Marine Science"},{"key":"pcbi.1010228.ref021","doi-asserted-by":"crossref","unstructured":"Williams HT. Coevolving parasites improve host evolutionary search on structured fitness landscapes. In: Artificial Life Conference Proceedings 12. MIT Press; 2012. p. 129\u2013136.","DOI":"10.7551\/978-0-262-31050-5-ch019"},{"key":"pcbi.1010228.ref022","doi-asserted-by":"crossref","DOI":"10.12703\/P6-39","article-title":"Individual-based models in ecology after four decades","volume":"6","author":"DL DeAngelis","year":"2014","journal-title":"F1000prime reports"},{"issue":"3","key":"pcbi.1010228.ref023","doi-asserted-by":"crossref","first-page":"7280","DOI":"10.1073\/pnas.082080899","article-title":"Agent-based modeling: Methods and techniques for simulating human systems","volume":"99","author":"E Bonabeau","year":"2002","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"pcbi.1010228.ref024","unstructured":"Iyer S, Pourhasanzade F, V\u00e5ge S. Microbial Evolution: An Individual-based Model in Python; 2022. https:\/\/github.com\/swamiiyer\/microbial_evolution."},{"issue":"6","key":"pcbi.1010228.ref025","doi-asserted-by":"crossref","first-page":"1320","DOI":"10.4319\/lo.2000.45.6.1320","article-title":"Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems","volume":"45","author":"TF Thingstad","year":"2000","journal-title":"Limnology and Oceanography"},{"issue":"3","key":"pcbi.1010228.ref026","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1007\/s10452-013-9447-y","article-title":"Successful strategies in size structured mixotrophic food webs","volume":"47","author":"S V\u00e5ge","year":"2013","journal-title":"Aquatic Ecology"},{"key":"pcbi.1010228.ref027","volume-title":"M9 minimal medium (standard)","author":"Anonymous","year":"2010"},{"issue":"2","key":"pcbi.1010228.ref028","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1111\/j.1550-7408.2004.tb00537.x","article-title":"Viral control of phytoplankton populations\u2014a review 1","volume":"51","author":"CP Brussaard","year":"2004","journal-title":"Journal of Eukaryotic Microbiology"},{"key":"pcbi.1010228.ref029","doi-asserted-by":"crossref","first-page":"27","DOI":"10.3354\/meps254027","article-title":"Stable coexistence in marine algal host-virus systems","volume":"254","author":"R Thyrhaug","year":"2003","journal-title":"Marine Ecology Progress Series"},{"issue":"5","key":"pcbi.1010228.ref030","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1038\/s41564-021-00873-4","article-title":"Interaction dynamics and virus\u2013host range for estuarine actinophages captured by epicPCR","volume":"6","author":"EG Sakowski","year":"2021","journal-title":"Nature Microbiology"},{"issue":"31","key":"pcbi.1010228.ref031","doi-asserted-by":"crossref","first-page":"12828","DOI":"10.1073\/pnas.1200771109","article-title":"Coexistence of phage and bacteria on the boundary of self-organized refuges","volume":"109","author":"S Heilmann","year":"2012","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"1774","key":"pcbi.1010228.ref032","doi-asserted-by":"crossref","first-page":"20132563","DOI":"10.1098\/rspb.2013.2563","article-title":"Fitness benefits of low infectivity in a spatially structured population of bacteriophages","volume":"281","author":"P Roychoudhury","year":"2014","journal-title":"Proceedings of the Royal Society B: Biological Sciences"},{"issue":"9","key":"pcbi.1010228.ref033","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1111\/j.1461-0248.2008.01205.x","article-title":"The shape of an ecological trade-off varies with environment","volume":"11","author":"CM Jessup","year":"2008","journal-title":"Ecology Letters"},{"issue":"5","key":"pcbi.1010228.ref034","doi-asserted-by":"crossref","first-page":"1806","DOI":"10.1111\/1365-2745.13028","article-title":"A competition\u2013defence trade-off both promotes and weakens coexistence in an annual plant community","volume":"106","author":"WK Petry","year":"2018","journal-title":"Journal of Ecology"},{"issue":"1","key":"pcbi.1010228.ref035","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1128\/MMBR.00034-09","article-title":"Trade-offs between competition and defense specialists among unicellular planktonic organisms: the \u201ckilling the winner\u201d hypothesis revisited","volume":"74","author":"C Winter","year":"2010","journal-title":"Microbiology and Molecular Biology Reviews"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1011600","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2023,10,27]],"date-time":"2023-10-27T00:00:00Z","timestamp":1698364800000}},{"DOI":"10.1371\/journal.pcbi.1010228","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T00:00:00Z","timestamp":1655769600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010228","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,21]],"date-time":"2022-06-21T17:47:13Z","timestamp":1655833633000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1010228"}},"subtitle":[],"editor":[{"given":"Amber M","family":"Smith","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,6,8]]},"references-count":35,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6,8]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1010228","relation":{"correction":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1011600","asserted-by":"object"}],"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1010228","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,8]]}}}