Microbial Ecology最新文献

{"title":"Microbial and Geochemical Variability in Sediments and Biofilms from Italian Gypsum Caves.","authors":"Tamara Martin-Pozas, Daniele Ghezzi, Ilenia M D'Angeli, Giuliana Madonia, Veronica Chiarini, Marco Vattano, Jo De Waele, Martina Cappelletti, Cesareo Saiz-Jimenez, Valme Jurado","doi":"10.1007/s00248-025-02576-3","DOIUrl":"https://doi.org/10.1007/s00248-025-02576-3","url":null,"abstract":"<p><p>In Europe, several gypsum karst regions occur among which the gypsum karsts located in Emilia-Romagna (UNESCO World Heritage Site since 2023) and Sicily are notable. The sediments, spring water microbial aggregates, and wall biofilms from three caves, Re Tiberio, Befana (Emilia-Romagna), and the Sicilian Santa Ninfa, have been studied from a microbiological and geochemical point of view. The samples of wall biofilms from gypsum caves were exclusively composed of Bacteria, while the sediments showed negligible abundances of Archaea. The two most abundant phyla in most sediments and biofilms were Actinomycetota and Pseudomonadota, whereas the microbial aggregates floating in the spring waters of Befana Cave showed a deviation from the typical abundance pattern as Campylobacterota replaced Actinomycetota, and the abundances of Bacteroidota and Desulfobacterota were high. The most abundant genus in the wall biofilms was Crossiella (Actinomycetota), but it was absent in the water aggregates collected in Befana Cave. The abundances of Crossiella in the cave sediments were very low. The dominant genera in Befana microbial aggregates showed different abundances and microbial composition when compared with the previously studied Frasassi and Fetida thermal sulfuric acid caves, located in Central and South Italy, respectively, suggesting that the community composition of the microbial aggregates is specific for each cave and related to the geochemistry of the sulfidic spring. Also, a different microbial community composition was found in Befana water aggregates with respect to the wall biofilms from Befana and Santa Ninfa caves. In the case of sediments, they significantly clustered together indicating that the microbial communities associated with sediments are similar, independently from the cave and possible other environmental parameters.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"81"},"PeriodicalIF":3.3,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Eukaryotic Microbiome of Lake Sturgeon Eggs, and Identification of Chemical Thresholds for Infection Control.","authors":"Kristi Gdanetz, Zachary A Noel, Ken Saville, Terence Marsh, Kim T Scribner, Frances Trail","doi":"10.1007/s00248-025-02566-5","DOIUrl":"https://doi.org/10.1007/s00248-025-02566-5","url":null,"abstract":"<p><p>Eukaryotic microorganisms are an important, but understudied, component of freshwater aquatic ecosystems, and are significant sources of mortality in early life stages of fishes in natural and aquaculture systems. The eukaryotic microbiome colonizing egg surfaces of the lake sturgeon (Acipenser fulvescens) was characterized from eggs collected in natural stream habitats and a streamside hatchery in the Cheboygan River watershed in MI, USA. The taxonomic diversity of members of the Kingdoms Fungi and Stramenopile associated with infections of lake sturgeon eggs during spawning is contributing to lake sturgeon mortality in the hatchery. Characterization of the microbial communities from deposited eggs demonstrated heavy influence of spawning location on the diversity of Pythium, an Oomycete predominating in the microbiome. The Ascomycota also had a strong and distinguishing presence, with members of the Dothidiales found only on eggs from the streamside hatchery. Aureobasidium pullulans, a ubiquitous pigmented yeast, was present in the greatest numbers of egg samples, and Helotiales were found only on samples from the Black River. Independent isolates were collected from egg surfaces and tested for chemical sensitivity to the oomicides ethaboxam and mefenoxam, which are used for control of Oomycete agricultural pathogens. Ethaboxam inhibited mycelial growth almost completely for all Saprolegnia strains tested, while mefenoxam, at 20 × strength, was largely ineffective. Water prevents the natural inactivation of mefenoxam by light, thus is not advisable in aquatic systems, where it could accumulate. Alternatively, ethaboxam may be a nonpersistent, welcome control option for these fish pathogens.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"80"},"PeriodicalIF":3.3,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rhizosphere Microbiome-Root Exudate Synergy in Pteris vittata: Coordinated Arsenic Speciation and Multielement Metabolic Coupling Drive Hyperaccumulation Efficiency.","authors":"Qi Bei, Jiahao Zhang, Qinxin Huang, Caixia Yang, Yeping Li, Rongyu Mu, Duntao Shu, Yunchao Dai, Mallavarapu Megharaj, Wenxiang He, Haixia Tian","doi":"10.1007/s00248-025-02584-3","DOIUrl":"https://doi.org/10.1007/s00248-025-02584-3","url":null,"abstract":"<p><p>Rhizosphere microorganisms play a pivotal role in enhancing the arsenic (As) remediation efficiency of Pteris vittata. However, the interactions among rhizosphere microorganisms, root exudates, and As, as well as their influence on As uptake by Pteris vittata at different As concentrations, remain poorly understood. This study systematically elucidates the molecular-ecological mechanisms through which Pteris vittata facilitates arsenic (As) remediation within a multidimensional interaction network. It was found that the rhizosphere microbial community was dominated by Proteobacteria, Acidobacteriota, and Ascomycota, with 44 bacterial and 10 fungal genera identified as genetically conserved core microorganisms. Microbial-mediated arsenic (As) methylation and reduction processes, coupled with metabolic pathways such as carbon fixation, sulfur oxidation, and phosphorus mineralization, contribute to the formation of an \"As-multielement cycling\" synergy. This synergy drives As speciation transformation and enhances plant uptake. Root exudates, such as L-phenylalanine and citric acid, enhance arsenic (As) activation and detoxification by selectively recruiting functional microbes, including Sphingomonas carrying arsC. The resulting metabolite profiles exhibit soil-specific response patterns. High As stress shifted microbial community assembly from stochastic to deterministic processes while maintaining remediation efficiency through enhanced fungal network stability (increased average connectivity). These findings reveal the dual \"genetic conservation-environmental adaptation\" regulatory strategy of Pteris vittata, providing both theoretical and practical foundations for designing targeted rhizosphere microecological technologies to enhance the phytoremediation of arsenic (As)-contaminated soils.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"79"},"PeriodicalIF":3.3,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144690982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Host Diet and Species Interact to Shape the Bacterial and Fungal Microbiome in the Regurgitant of Four Spodoptera Species.","authors":"Maximilien A C Adam, Guillaume Cailleau, Pilar Junier, Betty Benrey","doi":"10.1007/s00248-025-02582-5","DOIUrl":"https://doi.org/10.1007/s00248-025-02582-5","url":null,"abstract":"<p><p>The gut microbiome of Lepidopteran insects is highly dynamic, influenced by both host diet and phylogeny. While microbial communities are thought to facilitate host adaptation to diverse diets and environments, the existence of a core microbiome shared among closely related herbivores remains largely untested. In this study, we examined the microbial communities in the regurgitant of four Spodoptera species (S. exigua, S. frugiperda, S. latifascia, and S. littoralis) across different diets (artificial diet, cotton, maize, and squash). Using a high-throughput sequencing, we characterized bacterial and fungal community composition and diversity. Bacterial communities were shaped by both diet and host species, indicating species-specific bacterial selection. In contrast, fungal communities were exclusively structured by diet, with lower diversity and dominance of a few key taxa. Notably, no operational taxonomic units were consistently shared across all species or diets, challenging the concept of a conserved core microbiome in these generalist herbivores. Understanding how microbial communities shape generalist herbivores' ability to feed on diverse plants may offer potential strategies for microbiome-based pest management.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"78"},"PeriodicalIF":3.3,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144690981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea.","authors":"Abhay B Fulke, Nilkanth Sharma, Jayshree Nadekar","doi":"10.1007/s00248-025-02527-y","DOIUrl":"10.1007/s00248-025-02527-y","url":null,"abstract":"<p><p>Microorganisms are essential players in Earth's ecosystems, demonstrating remarkable adaptability to harsh conditions including arctic ice caps, deep-sea hydrothermal vents, and high-pressure oceanic zones. While the study of these extremophiles has long been constrained by challenges in culturing, recent advances in metagenomic techniques have enabled a deeper understanding of microbial diversity in these extreme habitats. This review explores both culturable and non-culturable microbial communities, focusing on the diverse strategies employed by microorganisms to thrive in harsh conditions, including high pressure, temperature, salinity, and nutrient limitations. Traditional cultivation methods often fail to capture the full spectrum of deep-sea microbiota due to the unique growth requirements of many organisms. In the omic era, however, microbial cultivation and the function of microbial resources are important. Non-culturable methods, like metagenomic studies and environmental DNA sequencing, have uncovered hitherto unknown microbial taxa and metabolic pathways, offering important new information on microbial ecology and biogeochemistry. The complex microbial interactions and adaptive methods that support these ecosystems are highlighted by case studies, including as studies on hydrothermal plumes and hadal deposits. The expanding significance of non-culturable techniques in microbial research is highlighted in this review, which also highlights how they might help us better understand microbial life in harsh conditions and how they may be used in biotechnology and environmental management.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"77"},"PeriodicalIF":3.3,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12274225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolomic Insights into Cross-Feeding Interactions Between Priestia megaterium PM and Pseudomonas fluorescens NO4: Unveiling Microbial Communication in Plant Growth-Promoting Rhizobacteria.","authors":"Nompumelelo R Sibanyoni, Lizelle A Piater, Pavel Kerchev, Ntakadzeni E Madala, Msizi I Mhlongo","doi":"10.1007/s00248-025-02577-2","DOIUrl":"10.1007/s00248-025-02577-2","url":null,"abstract":"<p><p>Plant growth-promoting rhizobacteria (PGPR) engage in complex chemical exchange and signalling processes to enhance their survival, rhizosphere colonisation, and plant-beneficial roles. These microbial interactions are mediated by various chemical cues, including quorum sensing (QS) molecules, cyclic peptides, lipopeptides, nutrients, volatile organic compounds (VOC), and phytohormones. Cross-feeding, where one microorganism consumes metabolites produced by another, exemplifies direct chemical communication that shapes community dynamics and metabolic cooperation. However, the effects of cross-feeding among different PGPR strains remain insufficiently characterised. In this study, an LC-MS-based metabolomics approach, combined with multivariate statistical analysis, was employed to investigate metabolic perturbations induced by cross-feeding among PGPR strains. Growth curve analysis revealed that cross-fed PGPR exhibited growth patterns comparable to controls, with a slight reduction in biomass. Metabolic profiling indicated time-dependent shifts in the metabolic state of the cross-fed organisms, suggesting adaptive metabolic reprogramming in response to the donor-conditioned media. Multivariate analysis identified distinct metabolite alterations between cross-fed and control groups across different time points, highlighting the influence of nutrient availability on microbial growth dynamics. Notably, cross-fed groups showed decreased levels of primary metabolites such as amino acids and sugars alongside increased production of secondary metabolites, including surfactins, salicylic acid, and carboxylic acids. These secondary metabolites are implicated in plant growth promotion and defence, indicating their potential as natural biostimulants. The findings advance the understanding of PGPR interactions and chemical communication in the rhizosphere, supporting the development of sustainable agricultural practices by leveraging beneficial microbial interactions. Future research should explore these interactions within more complex microbial communities.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"76"},"PeriodicalIF":3.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12270958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights Into Proliferation Effects of Low-Dose Glyphosate on Phytoplankton Communities.","authors":"Jinzhu Su, YuPing Su, Yuxin Weng, Gohar Ayub, Chenxing She, Yumei Xiao","doi":"10.1007/s00248-025-02581-6","DOIUrl":"10.1007/s00248-025-02581-6","url":null,"abstract":"<p><p>Glyphosate-based herbicides are among the most widely used agricultural chemicals globally, and their widespread application presents risks to environmental health and aquatic ecosystems. Continuous glyphosate inputs disrupt phytoplankton communities, potentially triggering harmful algal blooms. This study examines the proliferation of microalgal species exposed to low glyphosate concentrations (0.05 mg/L) and various phosphorus sources, with a particular focus on C-P and C-O-P bond phosphonates, which have been insufficiently studied in previous research. We hypothesized that cyanobacteria might exhibit a competitive growth advantage over other algal species when exposed to C-P bond glyphosate, especially under phosphorus-limited conditions. In monoculture experiments, Microcystis aeruginosa and Peridinium umbonatum var. inaequale significantly increased their biomass when cultured with C-P bond phosphonates, whereas Scenedesmus bijuga failed to thrive under similar conditions. Peridinium umbonatum var. inaequale also displayed increased soluble protein content in response to glyphosate stress, indicating an adaptive stress response. In co-culture experiments, M. aeruginosa demonstrated greater tolerance to glyphosate than P. umbonatum var. inaequale, though biomass increases were not significantly correlated with soluble protein or APA. Sediment-water interface experiments revealed that glyphosate exposure significantly promoted cyanobacterial biomass, which was approximately five times greater than that of the inorganic phosphorus group. Notably, when cyanobacterial biomass exceeded 20% of the total, Cyanophyta replaced Chlorophyta as the dominant group, suggesting a potential competitive advantage under low-dose glyphosate exposure. These findings highlight that glyphosate may promote cyanobacterial dominance by altering phytoplankton community composition, potentially contributing to the increased frequency of harmful algal blooms in nutrient-limited aquatic environments.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"75"},"PeriodicalIF":3.3,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12267383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptome Analysis of the Fat Body of the Maize Pest Delphacodes kuscheli (Hemiptera: Delphacidae) Reveals Essential Roles of Fungal Endosymbionts.","authors":"Agustina Pascual, Franco Calabresi, Daniela de la Fuente, M Inés Catalano, M Eugenia Brentassi","doi":"10.1007/s00248-025-02572-7","DOIUrl":"10.1007/s00248-025-02572-7","url":null,"abstract":"<p><p>The fat body of certain insects, in addition to performing essential biosynthetic and metabolic functions, harbors endosymbionts that play critical roles for their host. While knowledge of the diversity and functions of fungal endosymbionts harbored in the fat body of planthoppers is mostly limited to rice pests of Asia, our study presents a comprehensive transcriptomic analysis of the fat body of Delphacodes kuscheli (Hemiptera: Delphacidae), an important agricultural pest of maize in Argentina. The dominant fungal endosymbionts, identified as yeast-like symbionts (YLS), include members of the genera Ophiocordyceps, Cordyceps, Hirsutella, and Tolypocladium (Ascomycota: Hypocreales). Transcriptomic data reveal that the fungal endosymbionts encode genes involved in vital metabolic processes for the host, such as essential amino acid biosynthesis, nitrogen recycling, and steroid biosynthesis. The genetic contribution of these endosymbionts to nutrient provision and metabolism supports a mutualistic obligate relationship with D. kuscheli. The results presented here provide insights into the evolutionary dynamics of endosymbiosis in the Delphacidae. Furthermore, this study highlights the potential of YLS as promising targets for innovative pest control strategies.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"74"},"PeriodicalIF":3.3,"publicationDate":"2025-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12255559/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619081","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of the Ixodes ricinus Microbiome Across Belgian Ecoregions and Its Association with Pathogen and Symbiont Presence.","authors":"Camille Philippe, Lianet Abuin Denis, Manoj Fonville, Bert Devriendt, François E Dufrasne, Dasiel Obregon, Apolline Maître, Štefánia Skičková, Eric Cox, Hein Sprong, Alejandro Cabezas Cruz, Marcella Mori","doi":"10.1007/s00248-025-02571-8","DOIUrl":"10.1007/s00248-025-02571-8","url":null,"abstract":"<p><p>Ticks are important vectors of zoonotic pathogens, and their presence can be influenced by the composition of the tick microbiome. In turn, this microbiome is shaped by environmental and ecological factors, as demonstrated in several studies conducted under controlled conditions. However, the extent of these influences under natural ecological conditions remains underexplored. In this study, we investigated the diversity of the microbiome and the prevalence of pathogens in Ixodes ricinus nymphs across three distinct Belgian ecoregions: Sandy Loam, Condroz, and Ardennes. Using real-time quantitative PCR (qPCR) and Oxford Nanopore 16S rRNA sequencing, we assessed how geography and pathogen presence influence tick-associated microbial communities. Our results revealed significant regional differences in microbiome composition and pathogen prevalence. Borrelia burgdorferi sensu lato (s.l.) was most prevalent in the Ardennes (9% (7.4-10.9) vs 3.8% (2.8-5.2) in the Condroz and 2.1% (1.4-3.2) in Sandy Loam) while Anaplasma phagocytophilum was more common in the Sandy Loam region (21.1% (18.7-23.8) vs 4% (3-5.4) in the Condroz and 3.2% (2.2-4.4) in the Ardennes). Endosymbionts such as Midichloria mitochondrii and Spiroplasma ixodetis also exhibited distinct geographic distributions. Network analysis identified potential pathogen-microbiota interactions, with certain bacterial taxa showing positive or negative associations with specific pathogens. Moreover, microbiome composition was influenced not only by ecoregion but also by microorganisms such as Rickettsia helvetica, suggesting that its colonization may actively shape microbial community structure, potentially through competition or facilitation mechanisms. Additionally, microbiome network robustness varied across ecoregions, highlighting the role of ecological context in shaping microbial interactions within ticks. These findings underscore the complex interplay between geography, pathogen presence, and microbial diversity in ticks, highlighting the importance of integrating these interactions to inform microbiome-based strategies for vector control and disease prevention.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"73"},"PeriodicalIF":3.3,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12245972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144600977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small Things that Make a Big Difference: Single-Cell Transcriptomic of Nanociliates Reveals Genes Potentially Involved in Mixotrophy.","authors":"Filomena Romano, Uwe John, Michele Laval-Peuto, Paraskevi Pitta","doi":"10.1007/s00248-025-02575-4","DOIUrl":"10.1007/s00248-025-02575-4","url":null,"abstract":"<p><p>Nanociliates play an important role in the microbial food web of oligotrophic marine systems as grazers of picoplankton on one side, and as prey for microplankton, on the other. However, knowledge on their taxonomy, phylogeny, and trophic strategies is very limited, as well as their potential role as mixotrophs. In the present study, we investigated the transcriptomes of five marine planktonic nanociliates isolated from the Eastern Mediterranean Sea. Our aim was the following: (i) to characterize the phylogenetic placement of these cells using concatenated phylotranscriptomic and (ii) to identify genes potentially involved in mixotrophy by focusing on both photosynthesis and digestion-related genes (phagosome, lysosome). Phylogenetic reconstruction revealed that two cells clustered with Tintinnida, while the other three clustered with Oligotrichida. Reciprocal best hits (RHBs) BlastP analysis indicated the presence of genes related to photosynthesis across all the transcriptomes, while the detection of genes associated with phagosome, lysosome, and generic metabolic pathways provided a more informative insight into the mechanism of mixotrophy. These findings suggest that photosynthesis-related genes alone may not be sufficient indicators of mixotrophic potential in nanociliates and highlight the importance of considering additional cellular pathways involved in phagotrophy. Moreover, these transcriptomes will help to establish a basis for the evaluation of differential gene expression in Oligotrichida, Choreotrichida, and Tintinnida, and a step stone for mixotrophic investigation.</p>","PeriodicalId":18708,"journal":{"name":"Microbial Ecology","volume":"88 1","pages":"72"},"PeriodicalIF":3.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12241210/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144591788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}