ISME communications最新文献_第3页

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

Self-growth suppression in Bradyrhizobium diazoefficiens is caused by a diffusible antagonist.

IF 5.1

ISME communications Pub Date : 2025-02-17 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf032

Armaan Kaur Sandhu, Brady R Fischer, Senthil Subramanian, Adam D Hoppe, Volker S Brözel

{"title":"Self-growth suppression in Bradyrhizobium diazoefficiens is caused by a diffusible antagonist.","authors":"Armaan Kaur Sandhu, Brady R Fischer, Senthil Subramanian, Adam D Hoppe, Volker S Brözel","doi":"10.1093/ismeco/ycaf032","DOIUrl":"10.1093/ismeco/ycaf032","url":null,"abstract":"Microbes in soil navigate interactions by recognizing kin, forming social groups, exhibiting antagonistic behavior, and engaging in competitive kin rivalry. Here, we investigated a novel phenomenon of self-growth suppression (sibling rivalry) observed in Bradyrhizobium diazoefficiens USDA 110. Swimming colonies of USDA 110 developed a distinct demarcation line and inter-colony zone when inoculated adjacent to each other. In addition to self, USDA 110 suppressed growth of other Bradyrhizobium strains and several other soil bacteria. We demonstrated that the phenomenon of sibling rivalry is due to growth suppression but not cell death. The cells in the inter-colony zone were culturable but had reduced respiratory activity, ATP levels, and motility. The observed growth suppression was due to the presence of a diffusible effector compound. This effector was labile, preventing extraction, and identification, but it is unlikely a protein or a strong acid or base. This counterintuitive phenomenon of self-growth suppression suggests a strategic adaptation for conserving energy and resources in competitive soil environments. Bradyrhizobium's utilization of antagonism including self-growth suppression likely provides a competitive advantage for long-term success in soil ecosystems.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf032"},"PeriodicalIF":5.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607349","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

Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.

IF 5.1

ISME communications Pub Date : 2025-02-17 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf025

Xia Liu, Xiaofan Gong, Kai Ma, Wen Song, Jiayin Zhou, Mengqi Wang, Yueyue Li, Mengzhi Ji, Yan Li, He Han, Yuzhuo Wang, Qichao Tu

{"title":"Resolving ecological drivers of temporal variations of β-diversity across intertidal microbiomes.","authors":"Xia Liu, Xiaofan Gong, Kai Ma, Wen Song, Jiayin Zhou, Mengqi Wang, Yueyue Li, Mengzhi Ji, Yan Li, He Han, Yuzhuo Wang, Qichao Tu","doi":"10.1093/ismeco/ycaf025","DOIUrl":"10.1093/ismeco/ycaf025","url":null,"abstract":"Resolving the ecological drivers mediating the diversity patterns of microbial communities across space and through time is a central issue in microbial ecology. Both regional species pools and local community assembly contribute to the spatial turnover of biodiversity. In this study, we extended the concept of regional species pool to temporal, and investigated the seasonal dynamics of intertidal microbiomes across four microbial domains/kingdoms (bacteria, archaea, fungi, and protists). The results showed that the seasonal variations of microbial β-diversity were primarily governed by community assembly processes rather than temporal species pools. Different microbial domains/kingdoms were structured by different ecological processes, with homogeneous selection as the major process for all of them. Additionally, bacteria and fungi were critically shaped by drift, and protists by drift and homogeneous dispersal. Among various factors, temperature was important in shaping the temporal patterns of microbial β-diversity. The fluctuation in temperature was strongly associated with fungi and protists, resulting in high drift of community composition. This study demonstrated that community assembly processes governed the dynamic seasonal β-variations of intertidal microbiomes, expanding our understanding from spatial ecology.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf025"},"PeriodicalIF":5.1,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560354","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

Multiple defense is an effective antipredator strategy in dinoflagellates.

IF 5.1

ISME communications Pub Date : 2025-02-14 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf029

Gihong Park, Hans G Dam

{"title":"Multiple defense is an effective antipredator strategy in dinoflagellates.","authors":"Gihong Park, Hans G Dam","doi":"10.1093/ismeco/ycaf029","DOIUrl":"10.1093/ismeco/ycaf029","url":null,"abstract":"Phytoplankton have evolved myriad defenses against predators; yet, studies that simultaneously test for defense fitness costs and benefits are rare. We tested for relative fitness costs and benefits of defense in the marine dinoflagellate Alexandrium catenella using a framework that relates growth rates of prey genotypes (strains) that differed in constitutive toxin production (low, moderate, and high) to predator (copepod) concentration. Our approach is based on a novel molecular technique that allows one to disentangle the effect of predation mortality from the cell growth reduction due to toxin production. Results show that the strain with the highest constitutive toxin production was the only one that expressed inducible toxin production-a strategy that paid off as its fitness benefit outweighed its cost. Surprisingly, the moderate toxin strain that derived the highest relative fitness benefit increased cell division rate (akin to compensatory growth) and decreased cell size, while keeping its volume-specific toxin production constant in response to predation. These results suggest an effective antipredator defense portfolio.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf029"},"PeriodicalIF":5.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11894931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143607346","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

Pleiotropic regulation of bacterial toxin production and Allee effect govern microbial predator-prey interactions.

IF 5.1

ISME communications Pub Date : 2025-02-14 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf031

Harikumar R Suma, Pierre Stallforth

{"title":"Pleiotropic regulation of bacterial toxin production and Allee effect govern microbial predator-prey interactions.","authors":"Harikumar R Suma, Pierre Stallforth","doi":"10.1093/ismeco/ycaf031","DOIUrl":"10.1093/ismeco/ycaf031","url":null,"abstract":"Bacteria are social organisms, which are constantly exposed to predation by nematodes or amoebae. To counteract these predation pressures, bacteria have evolved a variety of potent antipredator strategies. Bacteria of the genus Pseudomonas, for instance, evade amoebal predation by the secretion of amoebicidal natural products. The soil bacterium Pseudomonas fluorescens HKI0770 produces pyreudione alkaloids that can kill amoebae. Even though the mode of action of the pyreudiones has been elucidated, the spatiotemporal dynamics underlying this predator-prey interaction remain unknown. Using a combination of microscopy and analytical techniques, we elucidated the intricate relationship of this predator-prey association. We used the chromatic bacteria toolbox for intraspecific differentiation of the amoebicide-producing wildtype and the non-producing mutant within microcosms. These allow for variations in nutrient availability and the emergence of predation-evasion strategies of interacting microorganisms. Imaging of the co-cultures revealed that the amoebae initially ingest both the non-producer as well as the toxin-producer cells. The outcomes of predator-prey interactions are governed by the population size and fitness of the interacting partners. We identified that changes in the cell density coupled with alterations in nutrient availability led to a strong Allee effect resulting in the diminished production of pyreudione A. The loss of defense capabilities renders P. fluorescens HKI0770 palatable to amoebae. Such a multifaceted regulation provides the basis for a model by which predator-prey populations are being regulated in specific niches. Our results demonstrate how the spatiotemporal regulation of bacterial toxin production alters the feeding behavior of amoeba.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf031"},"PeriodicalIF":5.1,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11904905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143626940","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

Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.

IF 5.1

ISME communications Pub Date : 2025-02-13 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycae141

Lin-Lin Xu, Shelby E McIlroy, Yueqiong Ni, Isis Guibert, Jiarui Chen, Ulisses Rocha, David M Baker, Gianni Panagiotou

{"title":"Chemical pollution drives taxonomic and functional shifts in marine sediment microbiome, influencing benthic metazoans.","authors":"Lin-Lin Xu, Shelby E McIlroy, Yueqiong Ni, Isis Guibert, Jiarui Chen, Ulisses Rocha, David M Baker, Gianni Panagiotou","doi":"10.1093/ismeco/ycae141","DOIUrl":"10.1093/ismeco/ycae141","url":null,"abstract":"Microbial communities in marine sediments contribute significantly to the overall health and resiliency of marine ecosystems. However, increased human disturbance undermines biodiversity and, hence, natural functionality provided by marine sediments. Here, through a deep shotgun metagenomics sequencing of the sediment microbiome and COI metabarcoding of benthic metazoans, we demonstrate that >50% of the microorganisms' and metazoan's taxonomic variation can be explained by specific chemical pollution indices. Interestingly, there was a significant correlation between the similarity in microbiome communities' taxonomical and functional attributes and the similarity of benthic metazoans community composition. Furthermore, mediation analysis was conducted to evaluate the microbiome-mediated indirect effect, suggesting that microbial species and functions accounted for 36% and 26%, respectively, of the total effect of pollution on the benthic metazoans. Our study introduces a multi-level perspective for future studies in urbanized coastal areas to explore marine ecosystems, revealing the impact of pollution stress on microbiome communities and their critical biogeochemical functions, which in turn may influence macrofaunal composition.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae141"},"PeriodicalIF":5.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11851482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143506554","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

Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.

IF 5.1

ISME communications Pub Date : 2025-02-13 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf030

Sascha M B Krause, Naomi I van den Berg, Kristof Brenzinger, Hans Zweers, Paul L E Bodelier

{"title":"Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.","authors":"Sascha M B Krause, Naomi I van den Berg, Kristof Brenzinger, Hans Zweers, Paul L E Bodelier","doi":"10.1093/ismeco/ycaf030","DOIUrl":"10.1093/ismeco/ycaf030","url":null,"abstract":"Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf030"},"PeriodicalIF":5.1,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11964084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143775194","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

Internal transcribed spacers enable species-level Metataxonomic analysis of ciliated protozoa.

IF 5.1

ISME communications Pub Date : 2025-02-11 eCollection Date: 2025-01-01 DOI: 10.1093/ismeco/ycaf024

Sripoorna Somasundaram, Zhongtang Yu

{"title":"Internal transcribed spacers enable species-level Metataxonomic analysis of ciliated protozoa.","authors":"Sripoorna Somasundaram, Zhongtang Yu","doi":"10.1093/ismeco/ycaf024","DOIUrl":"10.1093/ismeco/ycaf024","url":null,"abstract":"Traditional morphology-based ciliate classification is often time-consuming and inaccurate, necessitating molecular approaches. Although 18S rRNA gene sequencing is widely used for taxonomic analyses of ciliates, its high degree of conservation makes it challenging to achieve species-level resolution. This study explores the potential of internal transcribed spacers (ITS1 and ITS2) and the 28S rRNA gene to improve taxonomic resolution beyond that offered by 18S rRNA gene in free-living and host-associated ciliates. A comparative analysis of ITS, the 18S, and 28S rRNA gene sequences retrieved from public databases indicated that ITS regions exhibit greater inter- and intra-specific sequence dissimilarity compared to 18S rRNA gene, supporting existing literature. We then designed universal primers targeting the ITS and 28S rRNA gene for freshwater and rumen ciliates. These primers were rigorously evaluated for their inclusiveness, specificity, and amplification efficiency using in-silico PCR, experimental PCR, followed by sequencing and metataxonomic analyses of the ciliate communities. In-silico analyses revealed inclusiveness exceeding 80%, while experimental analyses validated their specificity. Metataxonomic analyses of ciliates demonstrated that the ITS and 28S rRNA gene captured significantly greater taxonomic diversity than 18S rRNA gene. Also, ITS1 offered superior taxonomic resolution by detecting the most ciliate species that went unnoticed by the 18S rRNA gene. These findings underscore the superiority of ITS1, and to a lesser extent ITS2, as taxonomic markers for enhancing the resolution of freshwater and rumen ciliate communities. We recommend ITS1 as an alternative marker to overcome the limitations of 18S rRNA gene-based approaches in free-living and host-associated ciliate taxonomy.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf024"},"PeriodicalIF":5.1,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11879186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143560345","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