{"title":"Diversification of single-cell growth dynamics under starvation influences subsequent reproduction in a clonal bacterial population","authors":"Sotaro Takano, Miki Umetani, Hidenori Nakaoka, Ryo Miyazaki","doi":"10.1093/ismejo/wrae257","DOIUrl":"https://doi.org/10.1093/ismejo/wrae257","url":null,"abstract":"Most of the microbes in nature infrequently receive nutrients and are thus in slow- or non-growing states. How quickly they can resume their growth upon an influx of new resources is crucial to occupy environmental niches. Isogenic microbial populations are known to harbor only a fraction of cells with rapid growth resumption, yet little is known about the physiological characteristics of those cells and their emergence in the population. Here, we tracked growth of individual Escherichia coli cells in populations under fluctuating nutrient conditions. We found that shifting from high- to low-nutrient conditions caused stalling of cell growth with few cells continuing to divide extremely slowly, a process which was dependent on lipid turnover. Resuming high-nutrient inflow after low-nutrient conditions resulted in cells resuming growth and division, but with different lag times and leading to varying progeny. The history of cell growth during low-nutrient but not high-nutrient conditions was determinant for resumption of growth, which cellular genealogy analysis suggested to originate from inherited physiological differences. Our results demonstrate that cellular growth dynamics become diverse by nutrient limitations, under which a fraction of cells experienced a particular growth history can reproduce progeny with new resources in the future.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"125 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-23DOI: 10.1093/ismejo/wrae255
Kaitlin A Schaal, Pauline Manhes, Gregory J Velicer
{"title":"Ecological histories govern social exploitation by microorganisms","authors":"Kaitlin A Schaal, Pauline Manhes, Gregory J Velicer","doi":"10.1093/ismejo/wrae255","DOIUrl":"https://doi.org/10.1093/ismejo/wrae255","url":null,"abstract":"Exploitation is a common feature of social interactions, which can be modified by ecological context. Here we investigate effects of ecological history on exploitation phenotypes in bacteria. In experiments with the bacterium Myxococcus xanthus, prior resource levels of different genotypes interacting during cooperative multicellular development were found to regulate social fitness, including whether cheating occurs. Responses of developmental spore production to experimental manipulation of resource-level histories differed between interacting cooperators and cheaters, and relative fitness advantages gained by cheating after high-resource growth were generally reduced or absent if one or both parties experienced low-resource growth. Low-resource growth also eliminated exploitation in some pairwise mixes of cooperative natural isolates that occurs when both strains have grown under resource abundance. Our results contrast with previous experiments in which cooperator fitness correlated positively with concurrent resource level and suggest that resource-level variation may be important in regulating whether exploitation of cooperators occurs in a natural context.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"37 5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-21DOI: 10.1093/ismejo/wrae259
Zhiying Lu, Elizabeth Entwistle, Matthew D Kuhl, Alexander R Durrant, Marcelo Malisano Barreto Filho, Anuradha Goswami, J Jeffrey Morris
{"title":"Coevolution of marine phytoplankton and Alteromonas bacteria in response to pCO2 and co-culture","authors":"Zhiying Lu, Elizabeth Entwistle, Matthew D Kuhl, Alexander R Durrant, Marcelo Malisano Barreto Filho, Anuradha Goswami, J Jeffrey Morris","doi":"10.1093/ismejo/wrae259","DOIUrl":"https://doi.org/10.1093/ismejo/wrae259","url":null,"abstract":"As a result of human activity, Earth’s atmosphere and climate are changing at an unprecedented pace. Models based on short-term experiments predict major changes will occur in marine phytoplankton communities in the future ocean, but rarely consider how evolution or interactions with other microbes may influence these changes. Here we experimentally evolved several phytoplankton in co-culture with a heterotrophic bacterium, Alteromonas sp. EZ55, under either present-day or predicted future pCO2 conditions. Growth rates of phytoplankton generally increased over time under both conditions, but only Thalassiosira oceanica had evidence of a growth rate trade-off in the ancestral environment after evolution at elevated pCO2. The growth defects observed in ancestral Prochlorococcus cultures at elevated pCO2 and in axenic culture were diminished after evolution, possibly due to regulatory mutations in antioxidant genes. Except for Prochlorococcus, mutational profiles suggested phytoplankton experienced primarily purifying selection, but most Alteromonas lineages showed evidence of directional selection, where evolution appeared to favor a metabolic switch between growth on small organic acids with cyanobacteria versus catabolism of more complex carbon substrates with eukaryotic phytoplankton. Evolved Alteromonas were also poorer “helpers” for Prochlorococcus, consistent with that interaction being a competitive Black Queen process rather than a true mutualism. This work provides new insights on how phytoplankton will respond to increased pCO2 and on the evolutionary mechanisms governing phytoplankton:bacteria interactions. It also clearly demonstrates that both evolution and interspecies interactions must be considered to predict future marine biogeochemistry.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-18DOI: 10.1093/ismejo/wrae247
Eleanor C Arrington, Jonathan Tarn, Veronika Kivenson, Brook L Nunn, Rachel M Liu, Blair G Paul, David L Valentine
{"title":"Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus","authors":"Eleanor C Arrington, Jonathan Tarn, Veronika Kivenson, Brook L Nunn, Rachel M Liu, Blair G Paul, David L Valentine","doi":"10.1093/ismejo/wrae247","DOIUrl":"https://doi.org/10.1093/ismejo/wrae247","url":null,"abstract":"Aqueous-soluble hydrocarbons dissolve into the ocean’s interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"80 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849060","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-17DOI: 10.1093/ismejo/wrae251
Qian Yang, Tom Defoirdt
{"title":"Weak selection for resistance to quorum sensing inhibition during multiple host infection cycles","authors":"Qian Yang, Tom Defoirdt","doi":"10.1093/ismejo/wrae251","DOIUrl":"https://doi.org/10.1093/ismejo/wrae251","url":null,"abstract":"Quorum sensing inhibition is a promising novel approach to control bacterial infections. However, it is not clear whether quorum sensing inhibition will impose selective pressure for the spread of resistance against quorum sensing inhibition in pathogen populations. Previous research tried to answer this question by using synthetic growth media, and this revealed that whether or not resistance will spread completely depends on the environment in which it is studied. Therefore, the spread of resistance should be studied in the environment where it ultimately matters: in vivo during infection of a host. Here, using quorum sensing inhibitor-susceptible and -resistant mimics, we show that resistance to quorum sensing inhibition does not spread in host-associated populations of Vibrio campbellii during up to 35 cycles of infection and transmission if the initial frequency of the resistance is low in the pathogen population, whereas it further increases to 100% if it is already prevalent. However, even in the latter case, the resistance spreads at a slower pace than resistance to antibiotics spreads under the same conditions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"256 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142841574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-17DOI: 10.1093/ismejo/wrae253
Sophie-Carole Chobert, Morgane Roger-Margueritat, Laura Flandrin, Safa Berraies, Christopher T Lefèvre, Ludovic Pelosi, Ivan Junier, Nelle Varoquaux, Fabien Pierrel, Sophie S Abby
{"title":"Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota","authors":"Sophie-Carole Chobert, Morgane Roger-Margueritat, Laura Flandrin, Safa Berraies, Christopher T Lefèvre, Ludovic Pelosi, Ivan Junier, Nelle Varoquaux, Fabien Pierrel, Sophie S Abby","doi":"10.1093/ismejo/wrae253","DOIUrl":"https://doi.org/10.1093/ismejo/wrae253","url":null,"abstract":"It is currently unclear how Pseudomonadota, a phylum that originated around the time of the Great Oxidation Event, became one of the most abundant and diverse bacterial phyla on Earth, with metabolically versatile members colonizing a wide range of environments with different O2 concentrations. Here, we address this question by studying isoprenoid quinones, which are central components of energy metabolism covering a wide range of redox potentials. We demonstrate that a dynamic repertoire of quinone biosynthetic pathways accompanied the diversification of Pseudomonadota. The low potential menaquinone (MK) was lost in an ancestor of Pseudomonadota while the high potential ubiquinone (UQ) emerged. We show that the O2-dependent and O2-independent UQ pathways were both present in the last common ancestor of Pseudomonadota, and transmitted vertically. The O2-independent pathway has a conserved genetic organization and displays signs of positive regulation by the master regulator “fumarate and nitrate reductase” (FNR), suggesting a conserved role for UQ in anaerobiosis across Pseudomonadota. The O2-independent pathway was lost in some lineages but maintained in others, where it favoured a secondary reacquisition of low potential quinones (MK or rhodoquinone), which promoted diversification towards aerobic facultative and anaerobic metabolisms. Our results support that the ecological success of Pseudomonadota is linked to the acquisition of the largest known repertoire of quinones, which allowed adaptation to oxic niches as O2 levels increased on Earth, and subsequent diversification into anoxic or O2-fluctuating environments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-16DOI: 10.1093/ismejo/wrae250
Julianne C Yang, Venu Lagishetty, Ezinne Aja, Nerea Arias-Jayo, Candace Chang, Megan Hauer, William Katzka, Yi Zhou, Farzaneh Sedighian, Carolina Koletic, Fengting Liang, Tien S Dong, Jamilla Situ, Ryan Troutman, Heidi Buri, Shrikant Bhute, Carra A Simpson, Jonathan Braun, Noam Jacob, Jonathan P Jacobs
{"title":"Biogeographical distribution of gut microbiome composition and function is partially recapitulated by fecal transplantation into germ-free mice","authors":"Julianne C Yang, Venu Lagishetty, Ezinne Aja, Nerea Arias-Jayo, Candace Chang, Megan Hauer, William Katzka, Yi Zhou, Farzaneh Sedighian, Carolina Koletic, Fengting Liang, Tien S Dong, Jamilla Situ, Ryan Troutman, Heidi Buri, Shrikant Bhute, Carra A Simpson, Jonathan Braun, Noam Jacob, Jonathan P Jacobs","doi":"10.1093/ismejo/wrae250","DOIUrl":"https://doi.org/10.1093/ismejo/wrae250","url":null,"abstract":"Fecal microbiota transplantation has been vital for establishing whether host phenotypes can be conferred through the microbiome. However, whether the existing microbial ecology along the mouse gastrointestinal tract can be recapitulated in germ-free mice colonized with stool remains unknown. We first identified microbes and their predicted functions specific to each of six intestinal regions in three cohorts of specific pathogen-free mice spanning two facilities. Of these region-specific microbes, the health-linked genus Akkermansia was consistently enriched in the lumen of the small intestine compared to the colon. Predictive functional modeling on 16S rRNA gene amplicon sequencing data recapitulated in shotgun sequencing data revealed increased microbial central metabolism, lipolytic fermentation, and cross-feeding in the small intestine, whereas butyrate synthesis was colon-enriched. Neuroactive compound metabolism also demonstrated regional specificity, including small intestine-enriched gamma-aminobutyric acid degradation and colon-enriched tryptophan degradation. Specifically, the jejunum and ileum stood out as sites with high predicted metabolic and neuromodulation activity. Differences between luminal and mucosal microbiomes within each site of the gastrointestinal tract were largely facility-specific, though there were a few consistent patterns in microbial metabolism in specific pathogen-free mice. These included luminal enrichment of central metabolism and cross-feeding within both the small intestine and the colon, and mucosal enrichment of butyrate synthesis within the colon. Across three cohorts of germ-free mice colonized with mice or human stool, compositional and functional region specificity were inconsistently reproduced. These results underscore the importance of investigating the spatial variation of the gut microbiome to better understand its impact on host physiology.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"243 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142832279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Urea-based mutualistic transfer of nitrogen in biological soil crusts","authors":"Ana Mercedes Heredia-Velásquez, Soumyadev Sarkar, Finlay Warsop Thomas, Ariadna Cairó Baza, Ferran Garcia-Pichel","doi":"10.1093/ismejo/wrae246","DOIUrl":"https://doi.org/10.1093/ismejo/wrae246","url":null,"abstract":"Foundational to establishment and recovery of biocrusts is a mutualistic exchange of carbon for nitrogen between pioneer cyanobacteria, including the widespread Microcoleus vaginatus, and heterotrophic diazotrophs in its “cyanosphere”. In other such mutualisms, nitrogen is transferred as amino acids or ammonium, preventing losses through specialized structures, cell apposition or intracellularity. Yet, in the biocrust symbiosis relative proximity achieved through chemotaxis optimizes the exchange. We posited that further partner specificity may stem from using an unusual nitrogen vehicle, urea. We show that representative mutualist M. vaginatus PCC 9802 possesses genes for urea uptake, two ureolytic systems, and the urea cycle, overexpressing only uptake and the rare urea carboxylase/allophanate hydrolase (uc/ah) when in co-culture with mutualist Massilia sp. METH4. In turn, it overexpresses urea biosynthesis, but neither urease nor urea uptake when in co-culture. On nitrogen-free medium, three cyanosphere isolates release urea in co-culture with M. vaginatus but not in monoculture. Conversely, M. vaginatus PCC 9802 grows on urea down to the low micromolar range. In natural biocrusts, urea is at low and stable concentrations that do not support the growth of most local bacteria, but aggregates of mutualists constitute dynamic microscale urea hotspots, and the cyanobacterium responds chemotactically to urea. The coordinated gene co-regulation, physiology of cultured mutualists, distribution of urea pools in nature, and responses of native microbial populations, all suggest that low-concentration urea is likely the main vehicle for interspecies N transfer, helping attain partner specificity, for which the rare high-affinity uc/ah system of Microcoleus. vaginatus is likely central.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-13DOI: 10.1093/ismejo/wrae248
Fatma Gomaa, Daniel R Rogers, Daniel R Utter, Christopher Powers, I-ting Huang, David J Beaudoin, Ying Zhang, Colleen Cavanaugh, Virginia P Edgcomb, Joan M Bernhard
{"title":"Array of metabolic pathways in a kleptoplastidic foraminiferan protist supports chemoautotrophy in dark, euxinic seafloor sediments","authors":"Fatma Gomaa, Daniel R Rogers, Daniel R Utter, Christopher Powers, I-ting Huang, David J Beaudoin, Ying Zhang, Colleen Cavanaugh, Virginia P Edgcomb, Joan M Bernhard","doi":"10.1093/ismejo/wrae248","DOIUrl":"https://doi.org/10.1093/ismejo/wrae248","url":null,"abstract":"Investigations of the metabolic capabilities of anaerobic protists advances our understanding of the evolution of eukaryotic life on Earth and for uncovering analogous extraterrestrial complex microbial life. Certain species of foraminiferan protists live in environments analogous to early Earth conditions when eukaryotes evolved, including sulfidic, anoxic, and hypoxic sediment porewaters. Foraminifera are known to form symbioses as well as to harbor organelles from other eukaryotes (chloroplasts), possibly bolstering the host’s independence from oxygen. The full extent of foraminiferal physiological capabilities is not fully understood. To date, evidence for foraminiferal anaerobiosis was gleaned from specimens first subjected to stresses associated with removal from in situ conditions. Here, we report comprehensive gene expression analysis of benthic foraminiferal populations preserved in situ on the euxinic (anoxic and sulfidic) bathyal seafloor, thus avoiding environmental alterations associated with sample recovery, including pressure reduction, sunlight exposure, warming, and oxygenation. Metatranscriptomics, metagenome-assembled genomes, and measurements of substrate uptake were used to study the kleptoplastidic foraminifer Nonionella stella inhabiting sulfur-oxidizing bacterial mats of the Santa Barbara Basin, off California. We show N. stella energy generation under dark euxinia is unusual because it orchestrates complex metabolic pathways for ATP production and carbon fixation through the Calvin cycle. These pathways include extended glycolysis, anaerobic fermentation, sulfide oxidation, and the presence of a membrane-bound inorganic pyrophosphatase, an enzyme that hydrolyzes inorganic pyrophosphate to actively pump protons across the mitochondrial membrane.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The ISME JournalPub Date : 2024-12-12DOI: 10.1093/ismejo/wrae234
Anna Krzynowek, Broos Van de Moortel, Nikola Pichler, Isabel Vanoverberghe, Johanna Lapere, Liliana M Jenisch, Daphné Deloof, Wim Thielemans, Koenraad Muylaert, Michiel Dusselier, Dirk Springael, Karoline Faust, Ellen Decaestecker
{"title":"Effects of microplastics on daphnia-associated microbiomes in situ and in vitro","authors":"Anna Krzynowek, Broos Van de Moortel, Nikola Pichler, Isabel Vanoverberghe, Johanna Lapere, Liliana M Jenisch, Daphné Deloof, Wim Thielemans, Koenraad Muylaert, Michiel Dusselier, Dirk Springael, Karoline Faust, Ellen Decaestecker","doi":"10.1093/ismejo/wrae234","DOIUrl":"https://doi.org/10.1093/ismejo/wrae234","url":null,"abstract":"Microplastic pollution in aquatic environments is a growing global concern. Microplastics, defined as plastic fragments smaller than five millimetres, accumulate in freshwater reservoirs, especially in urban areas, impacting resident biota. This study examined the effects of microplastics on the performance and microbiome of Daphnia, a keystone organism in freshwater ecosystems, through both in situ sampling of freshwater ponds and a controlled 23-day in vitro exposure experiment. Using bacterial 16S ribosomal RNA gene amplicon sequencing and whole-genome shotgun sequencing, we analyzed the microbiome's composition and functional capacity in relation to microplastic pollution levels. Urban ponds contained higher microplastic concentrations in water and sediment than natural ponds, with distinct differences in plastic composition. Bacterioplankton communities defined as bacterial assemblages in the water column, were more diverse and richer than Daphnia-associated microbiomes. Overall, the in situ study showed that the composition of the Daphnia-associated community was influenced by many factors including microplastic levels but also temperature and redox potential. Functional analysis showed increased relative abundances of polyethylene terephthalate degradation enzymes and antibiotic resistance genes in microbiomes from high-microplastic ponds. In the in vitro experiment, the bacterioplankton inoculum source significantly influenced Daphnia survival and microbiome composition. Network analysis identified specific taxa associated with microplastics within the Daphnia microbiome. Our findings highlight that urbanisation leads to higher microplastic and antibiotic resistance gene burdens, influencing host-associated microbiomes through taxonomic shifts, functional enrichment, and survival outcomes, with potential implications for the resilience of aquatic ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}