ISME communications最新文献

Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil.

IF 5.1

ISME communications Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae160

Wenbo Hu, Ying Teng, Xiaomi Wang, Yongfeng Xu, Yi Sun, Hongzhe Wang, Yanning Li, Shixiang Dai, Ming Zhong, Yongming Luo

{"title":"Mixotrophic cyanobacteria are critical active diazotrophs in polychlorinated biphenyl-contaminated paddy soil.","authors":"Wenbo Hu, Ying Teng, Xiaomi Wang, Yongfeng Xu, Yi Sun, Hongzhe Wang, Yanning Li, Shixiang Dai, Ming Zhong, Yongming Luo","doi":"10.1093/ismeco/ycae160","DOIUrl":"10.1093/ismeco/ycae160","url":null,"abstract":"Biological nitrogen fixation by diazotrophs is a crucial biogeochemical process in global terrestrial ecosystems, especially in nitrogen-limited, organic-contaminated soils. The metabolic activities of diazotrophs and their ability to supply fixed nitrogen may facilitate the transformation of organic pollutants. However, the active diazotrophic communities in organic-contaminated soils and their potential metabolic functions have received little attention. In the current study, the relationship between biological nitrogen fixation and polychlorinated biphenyl (PCB) metabolism was analyzed in situ in paddy soil contaminated with a representative tetrachlorobiphenyl (PCB52). 15N-DNA stable isotope probing was combined with high-throughput sequencing to identify active diazotrophs, which were distributed in 14 phyla, predominantly Cyanobacteria (23.40%). Subsequent metagenome binning and functional gene mining revealed that some mixotrophic cyanobacteria (e.g. FACHB-36 and Cylindrospermum) contain essential genes for nitrogen fixation, PCB metabolism, and photosynthesis. The bifunctionality of Cylindrospermum sp. in nitrogen fixation and PCB metabolism was further confirmed by metabolite analyses of Cylindrospermum sp. from a culture collection as a representative species, which showed that Cylindrospermum sp. metabolized PCB and produced 2-chlorobiphenyl and 2,5-dihydroxybenzonic acid. Collectively, these findings indicate that active diazotrophs, particularly mixotrophic cyanobacteria, have important ecological remediation functions and are a promising nature-based in situ remediation solution for organic-contaminated environments.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae160"},"PeriodicalIF":5.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924043/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.

IF 5.1

ISME communications Pub Date : 2025-03-17 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf028

Dieter M Tourlousse, Yuji Sekiguchi

{"title":"Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.","authors":"Dieter M Tourlousse, Yuji Sekiguchi","doi":"10.1093/ismeco/ycaf028","DOIUrl":"10.1093/ismeco/ycaf028","url":null,"abstract":"Microbiome studies using high-throughput sequencing are increasingly incorporating absolute quantitative approaches to overcome the inherent limitations of relative abundances. In this study, we have designed and experimentally validated a set of 12 unique synthetic rRNA operons, which we refer to as rDNA-mimics, to serve as spike-in standards for quantitative profiling of fungal/eukaryotic and bacterial microbiomes. The rDNA-mimics consist of conserved sequence regions from natural rRNA genes to act as binding sites for common universal PCR primers, and bioinformatically designed variable regions that allow their robust identification in any microbiome sample. All constructs cover multiple rRNA operon regions commonly targeted in fungal/eukaryotic microbiome studies (SSU-V9, ITS1, ITS2, and LSU-D1D2) and two of them also include an artificial segment of the bacterial 16S rRNA gene (SSU-V4) for cross-domain application. We validated the quantitative performance of the rDNA-mimics using defined mock communities and representative environmental samples. In particular, we show that rDNA-mimics added to extracted DNA or directly to the samples prior to DNA extraction precisely reflects the total amount of fungal and/or bacterial rRNA genes in the samples. We demonstrate that this allows accurate estimation of differences in microbial loads between samples, thereby confirming that the rDNA-mimics are suitable for absolute quantitative analyses of differential microbial abundances.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf028"},"PeriodicalIF":5.1,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11912825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The infant microbiota hopscotches between community states toward maturation-longitudinal stool parameters and microbiota development in a cohort of European toddlers.

IF 5.1

ISME communications Pub Date : 2025-03-11 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf016

Evangelia Intze, Monika Schaubeck, Mohsen Pourjam, Klaus Neuhaus, Ilias Lagkouvardos, Thomas C A Hitch, Thomas Clavel

{"title":"The infant microbiota hopscotches between community states toward maturation-longitudinal stool parameters and microbiota development in a cohort of European toddlers.","authors":"Evangelia Intze, Monika Schaubeck, Mohsen Pourjam, Klaus Neuhaus, Ilias Lagkouvardos, Thomas C A Hitch, Thomas Clavel","doi":"10.1093/ismeco/ycaf016","DOIUrl":"10.1093/ismeco/ycaf016","url":null,"abstract":"The development of the gut microbiome is critical during early life and is associated with infant health. To test whether this development is deterministic and how it is influenced by factors such as diet and mode of birth, we studied microbiota profiles and fecal parameters of 540 European infants, fed a synbiotic or control infant formula during their first year of life, up to 36 months of age. The diversity of the microbiota gradually increased until 36 months, at which point it resembled adult community states, indicating that microbiota maturation had occurred. However, distinct gut microbiota community states were observed that differed at each stage of maturation. The distribution of infants within the communities even at 36 months was significantly influenced by early life events, with a higher prevalence of infants born by cesarean section having the immature M36-C1 community state at 36 months. The microbial community state at one time point was not predictive of the next; instead, we observed hopscotching of the infant microbiota between different community states. This work provides new longitudinal data on the infant gut microbiome in relation to diet, suggesting that ecosystem development is not deterministic, but that early life events influence the community state of an individual's gut microbiota beyond infancy.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf016"},"PeriodicalIF":5.1,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905755/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data. 利用表型单细胞拉曼光谱数据实现高精度细菌分类鉴定。

IF 5.1

ISME communications Pub Date : 2025-03-09 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf015

Guangyu Li, Zijian Wang, Chieh Wu, Dongqi Wang, Il Han, Jangho Lee, David R Kaeli, Jennifer G Dy, Kilian Q Weinberger, April Z Gu

{"title":"Towards high-accuracy bacterial taxonomy identification using phenotypic single-cell Raman spectroscopy data.","authors":"Guangyu Li, Zijian Wang, Chieh Wu, Dongqi Wang, Il Han, Jangho Lee, David R Kaeli, Jennifer G Dy, Kilian Q Weinberger, April Z Gu","doi":"10.1093/ismeco/ycaf015","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf015","url":null,"abstract":"Single-cell Raman Spectroscopy (SCRS) emerges as a promising tool for single-cell phenotyping in environmental ecological studies, offering non-intrusive, high-resolution, and high-throughput capabilities. In this study, we obtained a large and the first comprehensive SCRS dataset that captured phenotypic variations with cell growth status for 36 microbial strains, and we compared and optimized analysis techniques and classifiers for SCRS-based taxonomy identification. First, we benchmarked five dimensionality reduction (DR) methods, 10 classifiers, and the impact of cell growth variances using a SCRS dataset with both taxonomy and cellular growth stage labels. Unsupervised DR methods and non-neural network classifiers are recommended for at a balance between accuracy and time efficiency, achieved up to 96.1% taxonomy classification accuracy. Second, accuracy variances caused by cellular growth variance (<2.9% difference) was found less than the influence from model selection (up to 41.4% difference). Remarkably, simultaneous high accuracy in growth stage classification (93.3%) and taxonomy classification (94%) were achievable using an innovative two-step classifier model. Third, this study is the first to successfully apply models trained on pure culture SCRS data to achieve taxonomic identification of microbes in environmental samples at an accuracy of 79%, and with validation via Raman-FISH (fluorescence in situ hybridization). This study paves the groundwork for standardizing SCRS-based biotechnologies in single-cell phenotyping and taxonomic classification beyond laboratory pure culture to real environmental microorganisms and promises advances in SCRS applications for elucidating organismal functions, ecological adaptability, and environmental interactions.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf015"},"PeriodicalIF":5.1,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11910137/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143652472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms.

IF 5.1

ISME communications Pub Date : 2025-03-03 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae152

Yifan Su, Xue Guo, Yamei Gao, Jiajie Feng, Linwei Wu, Jiesi Lei, Suo Liu, Qun Gao, Yufei Zeng, Wei Qin, Zheng Shi, Zhengxiong Liang, Zhencheng Ye, Mengting Yuan, Daliang Ning, Liyou Wu, Jizhong Zhou, Yunfeng Yang

{"title":"Warming stimulates cellulose decomposition by recruiting phylogenetically diverse but functionally similar microorganisms.","authors":"Yifan Su, Xue Guo, Yamei Gao, Jiajie Feng, Linwei Wu, Jiesi Lei, Suo Liu, Qun Gao, Yufei Zeng, Wei Qin, Zheng Shi, Zhengxiong Liang, Zhencheng Ye, Mengting Yuan, Daliang Ning, Liyou Wu, Jizhong Zhou, Yunfeng Yang","doi":"10.1093/ismeco/ycae152","DOIUrl":"10.1093/ismeco/ycae152","url":null,"abstract":"Cellulose is the most abundant component of plant litter, which is critical for terrestrial carbon cycling. Nonetheless, it remains unknown how global warming affects cellulose-decomposing microorganisms. Here, we carried out a 3-year litterbag experiment to examine cellulose decomposition undergoing +3°C warming in a tallgrass prairie. Most cellulose-associated bacteria and fungi in litterbags were also detected in bulk soil, and bacteria in litterbags had higher community-level rrn copy numbers, larger genome sizes, and higher genome guanine-cytosine (GC) contents than those in bulk soil, implying higher growth rates. Warming stimulated soil respiration by 32.3% and accelerated mass loss of cellulose, concurring with the increase in relative abundances of most functional genes associated with carbon decomposition in litterbags. Incorporating cellulose-decomposing genes into an ecosystem model reduced model parameter uncertainty and showed that warming stimulated microbial biomass, activity, and soil carbon decomposition. Collectively, our study supports a trait-centric view since cellulose-decomposing genes or genomic traits are amenable for ecosystem modeling. By characterizing the phylogenetically diverse yet functionally similar cellulose-associated microorganisms and their responses to warming, we take a step toward more precise predictions of soil carbon dynamics under future climate scenarios.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae152"},"PeriodicalIF":5.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11892950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143598421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat.

IF 5.1

ISME communications Pub Date : 2025-03-03 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf009

Eira Catharine Lødrup Carlsen, Jing Wei, Franck Lejzerowicz, Sigrid Trier Kjær, Sebastian Westermann, Dag O Hessen, Peter Dörsch, Alexander Eiler

{"title":"Redox determines greenhouse gas production kinetics and metabolic traits in water-saturated thawing permafrost peat.","authors":"Eira Catharine Lødrup Carlsen, Jing Wei, Franck Lejzerowicz, Sigrid Trier Kjær, Sebastian Westermann, Dag O Hessen, Peter Dörsch, Alexander Eiler","doi":"10.1093/ismeco/ycaf009","DOIUrl":"10.1093/ismeco/ycaf009","url":null,"abstract":"Redox conditions, influenced by the availability of oxygen, are expected to dictate the rate of CO2 and CH4 production and to shape the composition and metabolism of microbial communities. Here, we use thawing permafrost peat in thermokarst water under a gradient of initial O2 concentrations to experimentally cover the variability in redox conditions potentially found across thawing landscapes. The three main greenhouse gases, CO2, CH4 and N2O, responded differently to O2 absence. CO2 production along the O2 gradient could be modeled by the Michaelis Menten equation revealing a sharp decrease when oxygen dropped under 100 μM. Under anoxic conditions CO2 yield decreased by 98% and maximum net production rate by 85% when compared to oxic conditions during the 11 days after thaw. N2O production was observed under anoxic conditions, while CH4 yield and CH4 accumulation rates did not differ across the redox gradient. The latter is due to the release of stored CH4 due to thawing. Differences between oxic and anoxic conditions were reflected in the microbial genomic composition, with changes in taxonomic and functional groups, such as N2O reducers, fermenters, denitrifiers and sulfur reducers increasing under anoxic conditions. Genomic changes towards less efficient central metabolism further explained the CO2 production yields and rates limited by O2 availability as predicted by thermodynamics. Together with the Michaelis Menten models the metabolic reconstruction pinpoint to critical thresholds of CO2 release at suboxic conditions and thus need to be considered when explaining and modeling highly variable CO2 emissions across thawing landscapes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf009"},"PeriodicalIF":5.1,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11922181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Horizontal transmission of symbiotic bacteria and host selective sweep in the giant clam Tridacna crocea.

IF 5.1

ISME communications Pub Date : 2025-03-02 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf037

Cong Liu, Jian Zhang, Qiqi Li, Yuehuan Zhang, Si Zhang, Ziniu Yu, Jun Li, Jie Li

{"title":"Horizontal transmission of symbiotic bacteria and host selective sweep in the giant clam Tridacna crocea.","authors":"Cong Liu, Jian Zhang, Qiqi Li, Yuehuan Zhang, Si Zhang, Ziniu Yu, Jun Li, Jie Li","doi":"10.1093/ismeco/ycaf037","DOIUrl":"10.1093/ismeco/ycaf037","url":null,"abstract":"Giant clams, with their significant ecological importance, depend on associated bacteria for their health and development, yet the transmission modes and succession of community dynamics of these bacteria remain poorly understood. This study employed 16S rRNA gene sequencing and microscopy to investigate the transmission and community dynamics of symbiotic bacteria in the giant clam Tridacna crocea during early developmental stages (fertilized eggs, blastocyst, D-larvae, and pediveliger larvae). Fluorescence in situ hybridization and transmission electron microscopy did not detect internal symbiotic bacteria in fertilized eggs and adult gonad gametes, but scanning electron microscopy revealed microbial structures on egg surface microvilli, suggesting their role as microbial carriers. 16S rRNA sequencing confirmed microbial presence in fertilized eggs, indicating bacterial acquisition via external vertical transmission (adherence to microvilli) or horizontal transmission. Given the lack of internalized bacteria in reproductive organs, we prefer to classify the symbiotic bacteria acquisition as horizontal transmission. Microbial community analysis showed that T. crocea acquired a significant portion of its microbiome from seawater throughout its development. Before reaching the pediveliger stage, the bacterial community composition closely resembled that of the surrounding seawater, primarily featuring the family Rhodobacteraceae. As T. crocea matured, the host's selective pressure increased (e.g. deterministic assembly), which simplified the microbial community and reduced diversity. During the pediveliger stage, the genus Endozoicomonas became dominant, forming a large proportion of the bacterial community within the gonads. This highlights the ecological significance of host-microbe interactions in maintaining biodiversity and driving ecosystem stability through dynamic community assembly processes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf037"},"PeriodicalIF":5.1,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11919647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identifying the active microbes driving organosulfur cycling from taurine and methionine in marine sediment.

IF 5.1

ISME communications Pub Date : 2025-02-25 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf033

Ömer K Coskun, William D Orsi, Steven D'Hondt, Gonzalo V Gomez-Saez

{"title":"Identifying the active microbes driving organosulfur cycling from taurine and methionine in marine sediment.","authors":"Ömer K Coskun, William D Orsi, Steven D'Hondt, Gonzalo V Gomez-Saez","doi":"10.1093/ismeco/ycaf033","DOIUrl":"10.1093/ismeco/ycaf033","url":null,"abstract":"Studies on microbial sulfur cycling in marine sediment have primarily centered on the cycling of inorganic sulfur. The microbial diversity underlying the cycling of organosulfur compounds is largely unexplored. In this study, we present the first quantification of dissolved organic sulfur (DOS) microbial assimilation in marine surface sediments using 13C-DOS quantitative DNA stable isotope probing (qSIP). We sampled marine sediment from 493 m water depth on the Puerto Rico continental slope, measured 13C-assimilation from two DOS substrates (13C-taurine and 13C-methionine), and compared the 13C-DOS assimilation to 13C-glucose uptake. Taurine utilization was confined to bacteria, whereas methionine was degraded by bacteria and archaea, including methanogenic Methanococcoides. Globally widespread uncultivated clades of Gammaproteobacteria and Deltaproteobacteria were the main drivers of DOS cycling and exhibited increased assimilation of carbon from taurine and methionine, compared to glucose. Only one operational taxonomic unit (OTU) affiliated with Neptuniibacter was found to assimilate taurine and methionine, but not glucose, implying that microbes exclusively utilizing both DOS substrates as a carbon source in marine sediments are rare. Still, a substantial number of bacterial taxa exhibited a higher assimilation of 13C from taurine or methionine, compared to glucose, indicating their preference for both DOS substrates over glucose as a carbon source in the sediment. These results represent the first quantitative assessment of organosulfur cycling from taurine and methionine by uncultivated microbes in a marine benthic environment.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf033"},"PeriodicalIF":5.1,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11905757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Unraveling the impact of marine heatwaves on the Eukaryome of the emblematic Mediterranean red coral Corallium rubrum.

IF 5.1

ISME communications Pub Date : 2025-02-21 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf035

Camille Prioux, Christine Ferrier-Pagès, Javier Del Campo, Laure Guillou, Tristan Estaque, Denis Allemand, Romie Tignat-Perrier

{"title":"Unraveling the impact of marine heatwaves on the Eukaryome of the emblematic Mediterranean red coral Corallium rubrum.","authors":"Camille Prioux, Christine Ferrier-Pagès, Javier Del Campo, Laure Guillou, Tristan Estaque, Denis Allemand, Romie Tignat-Perrier","doi":"10.1093/ismeco/ycaf035","DOIUrl":"10.1093/ismeco/ycaf035","url":null,"abstract":"Global warming is intensifying heatwaves worldwide, leading to more frequent and severe temperature extremes. This study investigates the impact of the unprecedented 2022 Mediterranean heatwaves on the coral eukaryome, which has received little attention despite its known importance to coral holobiont functioning. Fifty-six colonies of the iconic red coral Corallium rubrum from the Mediterranean Sea were collected at different sites, depths, and health states. The microeukaryotic communities were analyzed using an 18S rRNA gene metabarcoding approach. Primers were designed to reduce amplification of the 18S rRNA gene sequences of the red coral while being universal for amplification of microeukaryotes. Our results showed that the red coral eukaryome was dominated by Dino-Group I, Licnophoridae, and Labyrinthulomycetes in the control sites that were not affected by the heat waves. In the heat-affected colonies, the composition of the coral eukaryome changed, with the relative abundances of Ephelotidae, Exobasidiomycetes, Corallicolidae, Labyrinthulomycetes, and/or the epibionts Phaeophyceae increasing depending on the intensity of heat stress experienced by the colonies. It was thus possible to link colony health to changes in the eukaryome. Finally, we illustrated putative interactions (competition, predator-prey relationship, and parasitism) occurring within C. rubrum eukaryome that could explain the compositional changes observed in the microeukaryotic communities under heat stress. Our findings improve our understanding of the ecological effects of heatwaves on marine ecosystems.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf035"},"PeriodicalIF":5.1,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaporation controls contact-dependent bacterial killing during surface-associated growth.

IF 5.1

ISME communications Pub Date : 2025-02-21 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf034

Miao Han, Chujin Ruan, Gang Wang, David R Johnson

{"title":"Evaporation controls contact-dependent bacterial killing during surface-associated growth.","authors":"Miao Han, Chujin Ruan, Gang Wang, David R Johnson","doi":"10.1093/ismeco/ycaf034","DOIUrl":"10.1093/ismeco/ycaf034","url":null,"abstract":"Many bacteria employ contact-dependent killing mechanisms, which require direct physical contact with a target cell, to gain an advantage over competitors. Here, we hypothesize that evaporation-induced fluid flows determine the number of contacts between attacking and target cells, thus controlling killing efficacy. To test this, we experimentally manipulated the strength of the coffee ring effect (CRE) and measured the consequences on killing mediated by the type VI secretion system (T6SS). The CRE is caused by evaporation-induced fluid flows that move water and cells from the center to the periphery of a liquid droplet, consequently concentrating cells at the periphery. We found that the CRE significantly increases the number of contacts between attacking (Vibrio cholerae) and target (Escherichia coli) cells and enhances the ability of V. cholerae to kill and out-compete E. coli. We corroborated our findings with individual-based computational simulations and demonstrated that increased cell densities at the droplet periphery caused by the CRE increase killing. We further found that the T6SS firing rate, lethal hit threshold, and lysis delay significantly affect killing when the CRE is strong. Our results underscore the importance of evaporation-induced fluid flows in shaping bacterial interactions and controlling competitive outcomes.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf034"},"PeriodicalIF":5.1,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11922317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0