Heterotrophic nanoflagellates are the chief agents of bacterivory in the aquatic microbial loop but remain underrepresented in culture collections and in genomic databases. We isolated and characterised a representative of the previously uncultured freshwater Cryptomonad Group 1 (CRY1a) lineage using a genome-streamlined, ultrasmall and abundant microbe Planktophila versatilis as a prey and CARD-FISH probe-based screening. This isolate, Tyrannomonas regina, is one of the most dominant ubiquitous heterotrophic cryptomonads in freshwaters. It is a small heterotrophic nanoflagellate (ca. 3-5 μm) and has the smallest genome of any cryptomonad sequenced thus far. The compact genome (ca. 69 Mb) revealed no traces of a photosynthetic lifestyle, consistent with its phylogenomic placement as a sister-clade to cryptophytes that are characterised by the acquisition of a red-algal symbiont. Moreover, in comparison to its photosynthetic counterparts, its genome presents substantially lower repeat content and endogenous viral elements. Genomes of two giant viruses, Tyrannovirus reginensis GV1 and GV2, were also recovered from the same culture and represent a viral genus that has been described so far solely by metagenome-recovered genomes. Collectively, these findings provide insights into genomic ancestry and evolution, widespread ecological impact and interactions of an elusive protist lineage and illustrate the advantages of culture-centric approaches towards unfolding complex tapestries of life in the microbial world.
{"title":"Cultivation, genomics, and giant viruses of a ubiquitous and heterotrophic freshwater cryptomonad.","authors":"Indranil Mukherjee,Paul-Adrian Bulzu,Roudaina Boukheloua,Usman Asghar,Hongjae Park,Helena Henriques Vieira,Maria-Cecilia Chiriac,Vojtěch Kasalický,Petr Znachor,Pavel Rychtecký,Karel Šimek,Michaela M Salcher,Markus Haber,Rohit Ghai","doi":"10.1093/ismejo/wraf271","DOIUrl":"https://doi.org/10.1093/ismejo/wraf271","url":null,"abstract":"Heterotrophic nanoflagellates are the chief agents of bacterivory in the aquatic microbial loop but remain underrepresented in culture collections and in genomic databases. We isolated and characterised a representative of the previously uncultured freshwater Cryptomonad Group 1 (CRY1a) lineage using a genome-streamlined, ultrasmall and abundant microbe Planktophila versatilis as a prey and CARD-FISH probe-based screening. This isolate, Tyrannomonas regina, is one of the most dominant ubiquitous heterotrophic cryptomonads in freshwaters. It is a small heterotrophic nanoflagellate (ca. 3-5 μm) and has the smallest genome of any cryptomonad sequenced thus far. The compact genome (ca. 69 Mb) revealed no traces of a photosynthetic lifestyle, consistent with its phylogenomic placement as a sister-clade to cryptophytes that are characterised by the acquisition of a red-algal symbiont. Moreover, in comparison to its photosynthetic counterparts, its genome presents substantially lower repeat content and endogenous viral elements. Genomes of two giant viruses, Tyrannovirus reginensis GV1 and GV2, were also recovered from the same culture and represent a viral genus that has been described so far solely by metagenome-recovered genomes. Collectively, these findings provide insights into genomic ancestry and evolution, widespread ecological impact and interactions of an elusive protist lineage and illustrate the advantages of culture-centric approaches towards unfolding complex tapestries of life in the microbial world.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145689015","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}
Tingting Xiang,Stephanie L Peak,Eric C Huitt,Arthur R Grossman
Dinoflagellate algae in the family Symbiodiniaceae, symbionts of many marine cnidarians are critical for the metabolic integrity of reef ecosystems, which are increasingly threatened by environmental stress. The resilience of the cnidarian-dinoflagellate symbiosis depends on thermotolerance of the partner organisms; coral hosts that harbor heat-resistant symbionts exhibit greater resistance to bleaching. Although coral responses to heat stress are well-documented, transcriptomic adaptation/acclimation of Symbiodiniaceae to elevated temperatures are limited. Here, we compare thermal responses of two species representing two genera of Symbiodiniaceae, Symbiodinium linucheae (strain SSA01; ITS2 type A4) and Breviolum minutum (strain SSB01; ITS2 type B1). SSA01 in culture maintained photosynthetic function at elevated temperatures and mounted a rapid transcriptomic response characterized by early downregulation of a JMJ21-like histone demethylase coupled with prompt upregulation of transcripts associated with DNA repair and oxidative stress, which would likely contribute to enhanced resilience to heat stress. In contrast, SSB01 experienced a decline in photosynthetic efficiency and a delayed transcriptomic response that included upregulation of transcripts encoding proteasome subunits and reduced transcripts encoding proteins involved in photosynthesis and metabolite transport. These findings indicate that a rapid and moderate transcriptomic response that results in increased expression of genes related to the synthesis and repair of biomolecules might be crucial for thermal tolerance in the Symbiodiniaceae whereas sensitivity to elevated temperatures may be reflected by increased protein turnover and a marked decline in anabolic processes. Understanding these differences is vital for predicting coral responses to warming seas and developing strategies to mitigate heat-stress impacts on reefs.
{"title":"Distinct transcriptomic strategies underlie differential heat tolerance in Symbiodiniaceae symbionts.","authors":"Tingting Xiang,Stephanie L Peak,Eric C Huitt,Arthur R Grossman","doi":"10.1093/ismejo/wraf268","DOIUrl":"https://doi.org/10.1093/ismejo/wraf268","url":null,"abstract":"Dinoflagellate algae in the family Symbiodiniaceae, symbionts of many marine cnidarians are critical for the metabolic integrity of reef ecosystems, which are increasingly threatened by environmental stress. The resilience of the cnidarian-dinoflagellate symbiosis depends on thermotolerance of the partner organisms; coral hosts that harbor heat-resistant symbionts exhibit greater resistance to bleaching. Although coral responses to heat stress are well-documented, transcriptomic adaptation/acclimation of Symbiodiniaceae to elevated temperatures are limited. Here, we compare thermal responses of two species representing two genera of Symbiodiniaceae, Symbiodinium linucheae (strain SSA01; ITS2 type A4) and Breviolum minutum (strain SSB01; ITS2 type B1). SSA01 in culture maintained photosynthetic function at elevated temperatures and mounted a rapid transcriptomic response characterized by early downregulation of a JMJ21-like histone demethylase coupled with prompt upregulation of transcripts associated with DNA repair and oxidative stress, which would likely contribute to enhanced resilience to heat stress. In contrast, SSB01 experienced a decline in photosynthetic efficiency and a delayed transcriptomic response that included upregulation of transcripts encoding proteasome subunits and reduced transcripts encoding proteins involved in photosynthesis and metabolite transport. These findings indicate that a rapid and moderate transcriptomic response that results in increased expression of genes related to the synthesis and repair of biomolecules might be crucial for thermal tolerance in the Symbiodiniaceae whereas sensitivity to elevated temperatures may be reflected by increased protein turnover and a marked decline in anabolic processes. Understanding these differences is vital for predicting coral responses to warming seas and developing strategies to mitigate heat-stress impacts on reefs.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"198200 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145663929","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}
Ori Furman,Gil Sorek,Sarah Moraïs,Liron Levin,Omar Eduardo Tovar-Herrera,Sarah Winkler,Itzhak Mizrahi
The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.
{"title":"Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.","authors":"Ori Furman,Gil Sorek,Sarah Moraïs,Liron Levin,Omar Eduardo Tovar-Herrera,Sarah Winkler,Itzhak Mizrahi","doi":"10.1093/ismejo/wraf252","DOIUrl":"https://doi.org/10.1093/ismejo/wraf252","url":null,"abstract":"The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"125 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145644918","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}
Secretory Immunoglobulin A (SIgA) is the dominant mucosal antibody and a key regulator of the gut microbiota. In early life, infants rely on breastmilk as their primary source of SIgA, but the role of milk-derived SIgA in early life microbiota colonization dynamics remains incompletely understood. Here, we show that species-specific SIgA in milk is antigen-inducible and discriminates between closely related but immunologically diverging microbes in the neonatal gut. More specifically, milk species-specific SIgA promotes colonization by an anti-inflammatory Escherichia coli strain while restricting the expansion of pro-inflammatory Proteus mirabilis. These findings uncover a dual role of maternal milk SIgA in actively sculpting the early life gut microbiota with species-level precision.
{"title":"Milk IgA promotes symbionts and limits pathobionts in the early life gut.","authors":"Katherine Donald,Antonio Serapio-Palacios,Tahereh Bozorgmehr,Mahebali Tabusi,B Brett Finlay","doi":"10.1093/ismejo/wraf266","DOIUrl":"https://doi.org/10.1093/ismejo/wraf266","url":null,"abstract":"Secretory Immunoglobulin A (SIgA) is the dominant mucosal antibody and a key regulator of the gut microbiota. In early life, infants rely on breastmilk as their primary source of SIgA, but the role of milk-derived SIgA in early life microbiota colonization dynamics remains incompletely understood. Here, we show that species-specific SIgA in milk is antigen-inducible and discriminates between closely related but immunologically diverging microbes in the neonatal gut. More specifically, milk species-specific SIgA promotes colonization by an anti-inflammatory Escherichia coli strain while restricting the expansion of pro-inflammatory Proteus mirabilis. These findings uncover a dual role of maternal milk SIgA in actively sculpting the early life gut microbiota with species-level precision.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145644927","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}
Plant-associated microbial communities play a vital role in host adaptation to environmental stress, yet their contributions to plant nickel (Ni) tolerance strategies remain unclear. It is not understood whether the same microbial community elicits similar responses across different plant species or regulates stress adaptation in a host-specific manner. Although microorganisms influence plant responses to metal toxicity by altering metal bioavailability in the rhizosphere, their potential to optimize plant metal uptake is less explored. In this study, we evaluated whether synthetic microbial communities enhance (Ni) uptake in two species with contrasting metal strategies: the hyperaccumulator Odontarrhena chalcidica and the Ni-excluding Arabidopsis arenosa. We hypothesized that soil microorganisms support plant metal adaptation by improving physiological function rather than altering soil metal availability. Our results show that O. chalcidica reached its full hyperaccumulating potential only when co-cultivated with a soil-derived microbial community, regardless of the microorganisms' ability to mobilize Ni or promote plant growth. Microorganisms that enhanced Ni uptake had no effect on soil Ni availability. Microbial community analysis revealed species-specific microbiota assembly, with O. chalcidica being more responsive yet more selective. Serpentine-soil microbiota enhanced Ni uptake in O. chalcidica by upregulating iron-transporter genes, confirming reliance on Fe-transport pathways for Ni acquisition. In contrast, the same inoculum induced Zn-transporters and NRT2.1/NRT2.2 in A. arenosa, reflecting strategy of cation partitioning and nutrient-transport fine-tuning under Ni stress. These findings refine criteria for selecting microorganisms in phytoremediation and highlight that the functional impact of plant-associated microorganisms on metal handling outweigh their effects on metal solubility in soil.
{"title":"Regulation of plant Ni uptake by soil-borne microorganisms occurs independently of their Ni-solubilizing capabilities.","authors":"Agnieszka Domka,Maciej Gustab,Roman J Jędrzejczyk,Rafał Ważny,Alice Tognacchini,Markus Puschenreiter,Paweł Łabaj,Agata Muszyńska,Weronika Kosowicz,Kinga Jarosz,Piotr Rozpądek","doi":"10.1093/ismejo/wraf265","DOIUrl":"https://doi.org/10.1093/ismejo/wraf265","url":null,"abstract":"Plant-associated microbial communities play a vital role in host adaptation to environmental stress, yet their contributions to plant nickel (Ni) tolerance strategies remain unclear. It is not understood whether the same microbial community elicits similar responses across different plant species or regulates stress adaptation in a host-specific manner. Although microorganisms influence plant responses to metal toxicity by altering metal bioavailability in the rhizosphere, their potential to optimize plant metal uptake is less explored. In this study, we evaluated whether synthetic microbial communities enhance (Ni) uptake in two species with contrasting metal strategies: the hyperaccumulator Odontarrhena chalcidica and the Ni-excluding Arabidopsis arenosa. We hypothesized that soil microorganisms support plant metal adaptation by improving physiological function rather than altering soil metal availability. Our results show that O. chalcidica reached its full hyperaccumulating potential only when co-cultivated with a soil-derived microbial community, regardless of the microorganisms' ability to mobilize Ni or promote plant growth. Microorganisms that enhanced Ni uptake had no effect on soil Ni availability. Microbial community analysis revealed species-specific microbiota assembly, with O. chalcidica being more responsive yet more selective. Serpentine-soil microbiota enhanced Ni uptake in O. chalcidica by upregulating iron-transporter genes, confirming reliance on Fe-transport pathways for Ni acquisition. In contrast, the same inoculum induced Zn-transporters and NRT2.1/NRT2.2 in A. arenosa, reflecting strategy of cation partitioning and nutrient-transport fine-tuning under Ni stress. These findings refine criteria for selecting microorganisms in phytoremediation and highlight that the functional impact of plant-associated microorganisms on metal handling outweigh their effects on metal solubility in soil.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"150 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145644921","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}
Haidong Gu,Zhuxiu Liu,Song Liu,Xiaojing Hu,Zhenhua Yu,Yansheng Li,Lujun Li,Yueyu Sui,Jian Jin,Xiaobing Liu,Zhongjun Jia,Lei Sun,Jonathan M Adams,Marcel G A van der Heijden,Junjie Liu,Guanghua Wang
It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life - with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.
{"title":"Land conversion to cropland homogenizes variation in soil biota, gene assemblages and ecological strategies on local and regional scales.","authors":"Haidong Gu,Zhuxiu Liu,Song Liu,Xiaojing Hu,Zhenhua Yu,Yansheng Li,Lujun Li,Yueyu Sui,Jian Jin,Xiaobing Liu,Zhongjun Jia,Lei Sun,Jonathan M Adams,Marcel G A van der Heijden,Junjie Liu,Guanghua Wang","doi":"10.1093/ismejo/wraf264","DOIUrl":"https://doi.org/10.1093/ismejo/wraf264","url":null,"abstract":"It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas \"Y-A-S\" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life - with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145644919","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}
Lauren M Hemara, Mark T Andersen, Haileigh R Patterson, Marion Wood, Matthew D Templeton, Jay Jayaraman
Host specificity of a plant pathogen is defined by its effector complement. However, it remains unclear whether the full complement is required for pathogenicity. Pseudomonas syringae pv. actinidiae (Psa) is an emerging model pathogen of kiwifruit with over 30 functional effectors, providing a unique opportunity to understand how host-mediated selection shapes pathogen evolution. The majority of Psa’s effectors previously appeared non-essential in single knockout contexts. Why, then, does Psa maintain such a large repertoire? We sought to examine effector requirements, redundancies, and repertoire refinement across host genotypes through a mutated effector-leveraging evolution experiment (MELEE), serially passaging competitive populations of effector knockout strains. Competition suggests that all effectors are collectively required for successful virulence, demonstrated by the dominance of wild-type. Host-specific effector requirements identified may further explain the maintenance of this large effector repertoire, providing important insights into the dynamics of effector redundancy following incursions.
{"title":"Individually redundant effectors are collectively required for bacterial pathogen virulence","authors":"Lauren M Hemara, Mark T Andersen, Haileigh R Patterson, Marion Wood, Matthew D Templeton, Jay Jayaraman","doi":"10.1093/ismejo/wraf262","DOIUrl":"https://doi.org/10.1093/ismejo/wraf262","url":null,"abstract":"Host specificity of a plant pathogen is defined by its effector complement. However, it remains unclear whether the full complement is required for pathogenicity. Pseudomonas syringae pv. actinidiae (Psa) is an emerging model pathogen of kiwifruit with over 30 functional effectors, providing a unique opportunity to understand how host-mediated selection shapes pathogen evolution. The majority of Psa’s effectors previously appeared non-essential in single knockout contexts. Why, then, does Psa maintain such a large repertoire? We sought to examine effector requirements, redundancies, and repertoire refinement across host genotypes through a mutated effector-leveraging evolution experiment (MELEE), serially passaging competitive populations of effector knockout strains. Competition suggests that all effectors are collectively required for successful virulence, demonstrated by the dominance of wild-type. Host-specific effector requirements identified may further explain the maintenance of this large effector repertoire, providing important insights into the dynamics of effector redundancy following incursions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145599051","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}
Organismal life cycles are influenced by Earth’s rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms’ ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.
{"title":"Latitudinal Diversity in Circadian and Light-Sensing Genes in an Ecologically Vital Group of Marine Picoeukaryote Algae","authors":"Janaina Rigonato, Jean-Claude Lozano, Valérie Vergé, Olivier Jaillon, François-Yves Bouget","doi":"10.1093/ismejo/wraf263","DOIUrl":"https://doi.org/10.1093/ismejo/wraf263","url":null,"abstract":"Organismal life cycles are influenced by Earth’s rotation and orbit, generating daily and seasonal light cycles that vary with latitude, especially in temperate and polar zones. Photoperiodism relies on organisms’ ability to measure time via the circadian clock and detect light through specific photoreceptors. Molecular basis of photoperiodism is well-characterized in plants, but photoperiod adaptation in phytoplankton remain largely unexplored. Here, we investigated circadian clock components, photoreceptors, and associated effectors in eukaryote picoalga species from Ostreococcus, Bathycoccus, and Micromonas. We showed that the investigated species shared a conserved set of homologous circadian clock-related genes that appeared in the early evolution of Mamielalles order. Furthermore, gene duplication events account for the specific occurrences and uneven gene copy numbers among these genera. Through metagenomic and metatranscriptomic analyses, we assessed the gene expression profiles of candidate photoperiod-related genes across the global ocean. Our findings reveal an unexpected diversity in photoreceptors, particularly within Micromonas, and highlight the CCT domain family, a key group of transcription factors governing circadian rhythms (TOC1 family) and photoperiodism (CONSTANS family) in plants. TOC1, a central component of the circadian clock in Ostreococcus tauri, is either absent or truncated in tropical species. Functional assays further indicate that the TOC1/CCA1 oscillator is non-functional in the tropical strain of Ostreococcus sp. RCC809. These results imply that certain circadian mechanisms may be dispensable at low latitudes, underscoring the diversity of photoperiod adaptations in marine phytoplankton. These results provide valuable insights into the molecular evolution of cosmopolitan plankton groups, particularly their mechanisms of local adaptation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"150 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145610940","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}
Yang Zhou, Yongqiang Yang, Yuqi Mao, Zhangqun Hou, Yiyang Xu, Kelei Zhao, Yiwen Chu, Xinrong Wang, Can Wang, Shun Li, Fei Xu, Likai Hao, Binbin Xie, Jiafu Lin, Tao Song
Macrolide antibiotics are vital for controlling infections in humans, animals, and agriculture, yet their effectiveness is increasingly compromised by antimicrobial resistance. Macrolide esterases (MLEs) are key mediators of macrolide resistance but have only been detected in Gram-negative bacteria, with no evidence in Gram-positive species. Here, we mined over 500,000 Gram-positive genomes and identified 8,707 candidate proteins. Six representative MLEs were functionally validated, conferring resistance to 16-membered macrolides and increasing minimum inhibitory concentrations up to 16-fold in Escherichia coli and 128-fold in Bacillus subtilis. Moreover, two exhibited broad-spectrum activity against all clinically and veterinary relevant 16-membered macrolides. Temporal analysis revealed that Gram-positive MLEs originated at least 2.7 million years ago, contrasting with their emergence in Gram-negative bacteria after the introduction of antibiotics. Genomic surveys further demonstrated the global distribution of MLE-carrying Gram-positive bacteria across 97 countries and diverse ecosystems, including clinical, food, agricultural, and natural environments. These findings highlight Gram-positive MLEs as an underrecognized risk and underscore the need for a One Health–oriented strategy to monitor, assess, and mitigate the spread of macrolide resistance across interconnected ecosystems.
{"title":"Global distribution of α/β hydrolase family macrolide esterases in Gram-positive bacteria","authors":"Yang Zhou, Yongqiang Yang, Yuqi Mao, Zhangqun Hou, Yiyang Xu, Kelei Zhao, Yiwen Chu, Xinrong Wang, Can Wang, Shun Li, Fei Xu, Likai Hao, Binbin Xie, Jiafu Lin, Tao Song","doi":"10.1093/ismejo/wraf261","DOIUrl":"https://doi.org/10.1093/ismejo/wraf261","url":null,"abstract":"Macrolide antibiotics are vital for controlling infections in humans, animals, and agriculture, yet their effectiveness is increasingly compromised by antimicrobial resistance. Macrolide esterases (MLEs) are key mediators of macrolide resistance but have only been detected in Gram-negative bacteria, with no evidence in Gram-positive species. Here, we mined over 500,000 Gram-positive genomes and identified 8,707 candidate proteins. Six representative MLEs were functionally validated, conferring resistance to 16-membered macrolides and increasing minimum inhibitory concentrations up to 16-fold in Escherichia coli and 128-fold in Bacillus subtilis. Moreover, two exhibited broad-spectrum activity against all clinically and veterinary relevant 16-membered macrolides. Temporal analysis revealed that Gram-positive MLEs originated at least 2.7 million years ago, contrasting with their emergence in Gram-negative bacteria after the introduction of antibiotics. Genomic surveys further demonstrated the global distribution of MLE-carrying Gram-positive bacteria across 97 countries and diverse ecosystems, including clinical, food, agricultural, and natural environments. These findings highlight Gram-positive MLEs as an underrecognized risk and underscore the need for a One Health–oriented strategy to monitor, assess, and mitigate the spread of macrolide resistance across interconnected ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145599050","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}
Jibing Li, Xixi Cai, Menghui Li, Dayi Zhang, Bei Li, Ling N Jin, Chunling Luo, Gan Zhang
Fungi play critical but underappreciated roles comparing to bacteria in the bioremediation of organic pollutants, particularly emerging contaminants. Numerous fungal species, along with their functional genes and metabolic pathways, remain largely unexplored. Here, we integrate single-cell Raman-activated cell sorting with stable isotope probing to identify and characterize in situ active fungi involved in emerging contaminant degradation. This approach enabled the isolation of a Penicillium sp. strain LJD-20, previously unreported, which acts as an active degrader of 2-methylnaphthalene, a model emerging pollutant. Genomic analyses revealed that LJD-20 harbors a diverse repertoire of degradation-related genes, including those encoding dioxygenases, methylhydroxylases, and cytochrome P450 monooxygenases, highlighting its versatile metabolic potential. Single-cell genome sequencing also uncovered a potential close fungal–bacterial co-occurrence, suggesting possible ecological or metabolic interactions. In bioaugmentation trials, strain LJD-20 independently degraded 2-methylnaphthalene and simultaneously promoted the enrichment of other microorganisms involved in its removal. These findings highlight the metabolic versatility and ecological importance of fungi in pollutant degradation and demonstrate the utility of combining single-cell and isotopic approaches to explore microbial function and interaction in complex environments.
{"title":"In situ Degradation of 2-Methylnaphthalene by a Soil Penicillium Strain Associated with Fungal-Bacterial Interactions","authors":"Jibing Li, Xixi Cai, Menghui Li, Dayi Zhang, Bei Li, Ling N Jin, Chunling Luo, Gan Zhang","doi":"10.1093/ismejo/wraf260","DOIUrl":"https://doi.org/10.1093/ismejo/wraf260","url":null,"abstract":"Fungi play critical but underappreciated roles comparing to bacteria in the bioremediation of organic pollutants, particularly emerging contaminants. Numerous fungal species, along with their functional genes and metabolic pathways, remain largely unexplored. Here, we integrate single-cell Raman-activated cell sorting with stable isotope probing to identify and characterize in situ active fungi involved in emerging contaminant degradation. This approach enabled the isolation of a Penicillium sp. strain LJD-20, previously unreported, which acts as an active degrader of 2-methylnaphthalene, a model emerging pollutant. Genomic analyses revealed that LJD-20 harbors a diverse repertoire of degradation-related genes, including those encoding dioxygenases, methylhydroxylases, and cytochrome P450 monooxygenases, highlighting its versatile metabolic potential. Single-cell genome sequencing also uncovered a potential close fungal–bacterial co-occurrence, suggesting possible ecological or metabolic interactions. In bioaugmentation trials, strain LJD-20 independently degraded 2-methylnaphthalene and simultaneously promoted the enrichment of other microorganisms involved in its removal. These findings highlight the metabolic versatility and ecological importance of fungi in pollutant degradation and demonstrate the utility of combining single-cell and isotopic approaches to explore microbial function and interaction in complex environments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145594092","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}
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