ISME communications最新文献

{"title":"Phages indirectly maintain tomato plant pathogen defense through regulation of the commensal microbiome.","authors":"Reena Debray, Asa Conover, Britt Koskella","doi":"10.1093/ismeco/ycaf065","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf065","url":null,"abstract":"<p><p>As parasites of bacteria, phages can regulate microbiome diversity and composition and may therefore affect susceptibility to pathogens and disease. Many infectious diseases are associated with altered bacteriophage communities, but observational studies alone do not allow us to determine when altered phage community composition is a contributor to disease risk, a response to infection, or simply an indicator of dysbiosis. To address this question directly, we used size-selective filtration to deplete plant-associated microbial communities of phages, then challenged plants with the bacterial pathogen <i>Pseudomonas syringae</i>. Plants with phage-depleted microbiomes were more susceptible to infection, an effect that could not be explained by direct effects of the phage communities on either <i>P. syringae</i> or the plant host. Moreover, the presence of phages was most impactful when the phage communities were isolated from neighboring field locations rather than from the same host plant as the bacteria, possibly suggesting that moderate rates of lysis maintain a community structure that is most resistant to pathogen invasion. Overall, our results support the idea that phage communities contribute to plant defenses by modulating the microbiome.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf065"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144047649","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}

{"title":"New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage.","authors":"Victoria Celeste Lanclos, Xiaoyuan Feng, Chuankai Cheng, Mingyu Yang, Cole J Hider, Jordan T Coelho, Conner Y Kojima, Shelby J Barnes, Catie S Cleveland, Mei Xie, Yanlin Zhao, Haiwei Luo, James Cameron Thrash","doi":"10.1093/ismeco/ycaf068","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf068","url":null,"abstract":"<p><p>The CHAB-I-5 cluster is a pelagic lineage that can comprise a significant proportion of all Roseobacters in surface oceans and has predicted roles in biogeochemical cycling via heterotrophy, aerobic anoxygenic photosynthesis (AAnP), CO oxidation, DMSP degradation, and other metabolisms. Though cultures of CHAB-I-5 have been reported, none have been explored and the best-known representative, strain SB2, was lost from culture after obtaining the genome sequence. We have isolated two new CHAB-I-5 representatives, strains US3C007 and FZCC0083, and assembled complete, circularized genomes with 98.7% and 92.5% average nucleotide identities with the SB2 genome. Comparison of these three with 49 other unique CHAB-I-5 metagenome-assembled and single-cell genomes indicated that the cluster represents a genus with two species, and we identified subtle differences in genomic content between the two species subclusters. Metagenomic recruitment from over fourteen hundred samples expanded their known global distribution and highlighted both isolated strains as representative members of the clade. FZCC0083 grew over twice as fast as US3C007 and over a wider range of temperatures. The axenic culture of US3C007 occurs as pleomorphic cells with most exhibiting a coccobacillus/vibrioid shape. We propose the name <i>Candidatus</i> Thalassovivens spotae, gen nov., sp. nov. for the type strain US3C007^T (= ATCC TSD-433^T = NCMA B160^T).</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf068"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075776/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082632","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}

{"title":"Anoxygenic photoautotrophy driven by humus and microplastics in a photosynthetic bacterium.","authors":"Yutong Li, Kongyuang Qu, Jianming Yang, Shuguang Wang, Zhen Yan","doi":"10.1093/ismeco/ycaf067","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf067","url":null,"abstract":"<p><p>Humus and microplastics are recalcitrant organics in soils and aquatic systems, and their role in the geochemical cycling of elements remains elusive. Herein, we have identified a new mechanism by which humus and microplastics participate in anoxic carbon cycling. We demonstrated that the photoexcitation of 5-30 mg/l of humic acid or fulvic acid, two major fractions of humus, can drive CO₂ fixation and enable the photoautotrophic growth of a photosynthetic bacterium, <i>Rhodopseudomonas palustris</i>. This process was enhanced by 10.69%-144.87% upon the addition of 100 mg/l of poly(lactic acid) or poly(ethylene terephthalate). Mechanistic investigations demonstrated that the microplastics act as sacrificial quenchers during humus photoexcitation, leading to their depolymerization. Transcriptomic analyses revealed high expression of genes encoding extracellular electron uptake pathways including extracellular cytochrome <i>c</i> and its oxidases in the photoautotrophic growth of <i>R. palustris</i>. This study expands our understanding of how humus and microplastics are involved in the biogeochemical cycling of carbon and sheds light on how they impact the CO₂ dynamic fluxes in sunlit anoxic environments.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf067"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12066414/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042934","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}

{"title":"Variable responses to ocean acidification among mixotrophic protists with different lifestyles.","authors":"Shai Slomka, Jolanda M H Verspagen, Jef Huisman, Susanne Wilken","doi":"10.1093/ismeco/ycaf064","DOIUrl":"10.1093/ismeco/ycaf064","url":null,"abstract":"<p><p>Marine phytoplankton are facing increasing dissolved CO₂ concentrations and ocean acidification caused by anthropogenic CO₂ emissions. Mixotrophic organisms are capable of both photosynthesis and phagotrophy of prey and are found across almost all phytoplankton taxa and diverse environments. Yet, we know very little about how mixotrophs respond to ocean acidification. Therefore, we studied responses to simulated ocean acidification in three strains of the mixotrophic chrysophyte <i>Ochromonas</i> (CCMP1391, CCMP2951, and CCMP1393). After acclimatization of the strains to treatment with high-CO₂ (1000 ppm, pH 7.9) and low-CO₂ concentrations (350 ppm, pH 8.3), strains CCMP1393 and CCMP2951 both exhibited higher growth rates in response to the high-CO₂ treatment. In terms of the balance between phototrophic and heterotrophic metabolism, diverse responses were observed. In response to the high-CO₂ treatment, strain CCMP1393 showed increased photosynthetic carbon fixation rates, while CCMP1391 exhibited higher grazing rates, and CCMP2951 did not show significant alteration of either rate. Hence, all three <i>Ochromonas</i> strains responded to ocean acidification, but in different ways. The variability in their responses highlights the need for better understanding of the functional diversity among mixotrophs in order to enhance predictive understanding of their contributions to global carbon cycling in the future.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf064"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12086424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103213","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}

{"title":"Quantifying evolutionary changes to temperature-CO₂ growth response surfaces in <i>Skeletonema marinoi</i> after adaptation to extreme conditions.","authors":"Charlotte L Briddon, Maria Nicoară, Adriana Hegedűs, Mridul K Thomas, Bogdan Drugă","doi":"10.1093/ismeco/ycaf069","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf069","url":null,"abstract":"<p><p>Global warming and ocean acidification are having an unprecedented impact on marine ecosystems, yet we do not yet know how phytoplankton will respond to simultaneous changes in multiple drivers. To better comprehend the combined impact of oceanic warming and acidification, we experimentally estimated how evolution shifted the temperature-CO₂ growth response surfaces of two strains of <i>Skeletonema marinoi</i> that were each previously adapted to four different temperature × CO₂ combinations. These adapted strains were then grown under a factorial combination of five temperatures and five CO₂ concentrations to capture the temperature-CO₂ response surfaces for their unacclimated growth rates. The development of the first complete temperature-CO₂ response surfaces showed the optimal CO₂ concentration for growth to be substantially higher than expected future CO₂ levels (~6000 ppm). There was minimal variation in the optimal CO₂ concentration across the tested temperatures, suggesting that temperature will have a greater influence on growth rates compared to enhanced CO₂. Optimal temperature did not show a unimodal response to CO₂, either due to the lack of acclimation or the highly efficient CO₂ concentrating mechanisms, which diatoms (e.g. <i>Skeletonema</i>) can up-/downregulate depending on the CO₂ conditions. We also found that both strains showed evidence of evolutionary shifts as a result of adaptation to temperature and CO₂. The evolutionary response differed between strains, underscoring how genetic differences (perhaps related to historical regimes) can impact phytoplankton performance. Understanding how a dominant algal species responds to multiple drivers provides insight into real-world scenarios and helps construct theoretical predictions of environmental change.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf069"},"PeriodicalIF":5.1,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082634","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}

{"title":"Correction to: Significant role of symbiotic bacteria in the blood digestion and reproduction of <i>Dermanyssus gallinae</i> mites.","authors":"","doi":"10.1093/ismeco/ycae166","DOIUrl":"https://doi.org/10.1093/ismeco/ycae166","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1093/ismeco/ycae127.].</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycae166"},"PeriodicalIF":5.1,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11996756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001524","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}

{"title":"Distinct microbiomes underlie divergent responses of methane emissions from diverse wetland soils to oxygen shifts.","authors":"Linta Reji, Jianshu Duan, Satish C B Myneni, Xinning Zhang","doi":"10.1093/ismeco/ycaf063","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf063","url":null,"abstract":"<p><p>Hydrological shifts in wetlands, a globally important methane (CH₄) source, are critical constraints on CH₄ emissions and carbon-climate feedbacks. A limited understanding of how hydrologically driven oxygen (O₂) variability affects microbial CH₄ cycling in diverse wetlands makes wetland CH₄ emissions uncertain. Transient O₂ exposure significantly stimulated anoxic CH₄ production in incubations of <i>Sphagnum</i> peat from a temperate bog by enriching for polyphenol oxidizers and polysaccharide degraders, enhancing substrate flow toward methanogenesis under subsequent anoxic conditions. To assess whether shifts in soil microbiome structure and function operate similarly across wetland types, here we examined the sensitivity of different wetland soils to transient oxygenation. In slurry incubations of <i>Sphagnum</i> peat from a minerotrophic fen, and sediments from a freshwater marsh and saltmarsh, we examined temporal shifts in microbiomes coupled with geochemical characterization of slurries and incubation headspaces. Oxygenation did not affect microbiome structure and anoxic CH₄ production in mineral-rich fen-origin peat and freshwater marsh soils. Key taxa linked to O₂-stimulated CH₄ production in the bog-origin peat were notably rare in the fen-origin peat, supporting microbiome structure as a primary determinant of wetland response to O₂ shifts. In contrast to freshwater wetland experiments, saltmarsh geochemistry-particularly pH-and microbiome structure were persistently and significantly altered postoxygenation, albeit with no significant impact on greenhouse gas emissions. These divergent responses suggest wetlands may be differentially resistant to O₂ fluctuations. With climate change driving greater O₂ variability in wetlands, our results inform mechanisms of wetland resistance and highlight microbiome structure as a potential resiliency biomarker.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf063"},"PeriodicalIF":5.1,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075768/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082631","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}

{"title":"Deciphering the key stressors shaping the relative success of core mixoplankton across spatiotemporal scales.","authors":"Zhicheng Ju, Sangwook Scott Lee, Jiawei Chen, Lixia Deng, Xiaodong Zhang, Zhimeng Xu, Hongbin Liu","doi":"10.1093/ismeco/ycaf053","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf053","url":null,"abstract":"<p><p>Deciphering the spatiotemporal dynamics and relative competitive advantages of trophic functional traits under multiple stressors has been a long-standing challenge. Here, we integrated the core taxa identification with robust simulation modeling to reveal key environmental factors influencing the three core trophic groups (autotroph, heterotroph, and mixotroph), with a particular focus on mixoplankton. Temporally, core mixoplankton exhibited a higher relative proportion in spring and winter in contrast to core heterotrophs and a more uniform spatial distribution pattern. While seasonal patterns were observed in the environmental responses of the trophic groups, temperature, dissolved oxygen (DO), and nitrate (NO₃-N) were identified as the key drivers affecting the core mixoplankton by random forest. Furthermore, through univariate regression and generalized additive mixed model (GAMM), we captured the niche preferences of core mixoplankton across three stressors gradients and characterized the coupled additive or antagonistic effects. Notably, the potential optimal threshold for core mixoplankton was a high level of NO₃-N (0.64 mg/L), lower temperature (18.6°C), and DO (3.5 mg/L), which contrasted with the results obtained from single-factor regression analyses. Specifically, GAMM indicated that the preferred niche shifted upward for NO₃-N and downward for DO when three drivers were included simultaneously, while temperature remained constant. Our study linked the ecological niche preference of core mixoplankton with key stressors, facilitating a more precise monitoring and comprehension of spatiotemporal dynamics of trophic functional groups under scenarios of escalating global climate change and anthropogenic disturbances.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf053"},"PeriodicalIF":5.1,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12017963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144051669","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}

{"title":"Warming degrades nutritional quality of periphyton in stream ecosystems: evidence from a mesocosm experiment.","authors":"Zhenglu Qian, Feng Zhu, Xiang Tan, Quanfa Zhang","doi":"10.1093/ismeco/ycaf051","DOIUrl":"10.1093/ismeco/ycaf051","url":null,"abstract":"<p><p>Periphyton, which is rich in polyunsaturated fatty acids (PUFA), serves as an indispensable high-quality basal resource for consumers in stream food webs. However, with global warming, how fatty acid composition of periphyton changes and consequent effects on their transfer to higher trophic level consumers remain unclear. By carrying out a manipulative mesocosm experiment with a 4°C increase, warming led to a significant decrease in the proportions of PUFA and Long-chain PUFA (LC-PUFA, >20 C) in periphyton from 13.32% to 9.90% and from 3.05% to 2.18%, respectively. The proportions of three PUFAs-α-linolenic acid (18:3ω3), arachidonic acid (ARA, 20:4ω6), and docosahexaenoic acid (22:6ω3)-also declined significantly (<i>P</i> < .05). Notably, the fatty acid profile of the consumer-<i>Bellamya aeruginosa</i> reflected the changes in basal resources, with a decrease in PUFA from 40.14% to 36.27%, and a significant decrease in LC-PUFA from 34.58% to 30.11%. Although algal community composition in biofilms did not significantly change with warming, significant transcriptomic alterations were observed, with most differentially expressed genes related to fatty acid synthesis in lipid metabolism and photosynthesis down-regulated. Our findings indicate that warming may hinder the production and transfer of high-quality carbon evaluated by LC-PUFA to consumers, consequently affect the complexity and stability of stream food webs.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf051"},"PeriodicalIF":5.1,"publicationDate":"2025-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813084","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}

{"title":"Coral probiotics induce tissue-specific and putative beneficial microbiome restructuring in a coral-dwelling fish.","authors":"Joao Gabriel Duarte Rosado, Nathalia Delgadillo-Ordoñez, Matteo Monti, Viktor Nunes Peinemann, Chakkiath Paul Antony, Ahmed Alsaggaf, Inês Raimundo, Darren Coker, Neus Garcias-Bonet, Francisca García, Raquel Silva Peixoto, Susana Carvalho, Michael L Berumen","doi":"10.1093/ismeco/ycaf052","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf052","url":null,"abstract":"<p><p>The ongoing fourth mass global coral bleaching event reinforces the need for active solutions to support corals through this major crisis. The use of beneficial microorganisms for corals (BMCs) offers a promising nature-based solution to rehabilitate coral's dysbiotic microbiomes. While the benefits to corals are increasingly recognized, the impacts on associated reef organisms, such as fish, remain unexplored. This study investigated the effects of BMCs on the tissue-associated microbiomes of <i>Dascyllus abudafur</i> (<i>Pomacentridae</i>), a damselfish that lives closely associated with coral colonies. Over three months, we applied BMCs three times per week to healthy <i>Pocillopora verrucosa</i> colonies in the central Red Sea and analyzed the resultant changes in the inhabiting fish's microbiomes. Our findings reveal significant, tissue-specific shifts in bacterial communities, particularly skin and gut, with moderate changes observed in gills. Notably, putative fish beneficial bacteria such as <i>Mitsuokella</i> spp. were enriched in the skin, while various Firmicutes taxa increased in the gut. There was also a marked decrease in potential fish pathogens. This study highlights the potential extended benefits of BMCs on coral reef fish and sets a foundation for understanding the broader ecological interactions between BMCs and reef-associated organisms.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf052"},"PeriodicalIF":5.1,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11994995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144059402","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}