ISME communications最新文献

{"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}

{"title":"Food colorant brilliant blue causes persistent functional and structural changes in an in vitro simplified microbiota model system.","authors":"Victor Castañeda-Monsalve, Sven-Bastiaan Haange, Laura-Fabienne Fröhlich, Qiuguo Fu, Ulrike Rolle-Kampczyk, Martin von Bergen, Nico Jehmlich","doi":"10.1093/ismeco/ycaf050","DOIUrl":"10.1093/ismeco/ycaf050","url":null,"abstract":"<p><p>The human gut microbiota plays a vital role in maintaining host health by acting as a barrier against pathogens, supporting the immune system, and metabolizing complex carbon sources into beneficial compounds such as short-chain fatty acids. Brilliant blue E-133 (BB), is a common food dye that is not absorbed or metabolized by the body, leading to substantial exposure of the gut microbiota. Despite this, its effects on the microbiota are not well-documented. In this study, we cultivated the Simplified Human Microbiota Model (SIHUMIx) in a three-stage in vitro approach (stabilization, exposure, and recovery). Using metaproteomic and metabolomic approaches, we observed significant shifts in microbial composition, including an increase in the relative abundance of <i>Bacteroides thetaiotaomicron</i> and a decrease in beneficial species such as <i>Bifidobacterium longum</i> and <i>Clostridium butyricum</i>. We observed lower protein abundance in energy metabolism, metabolic end products, and particularly lactate and butyrate. Disturbance in key metabolic pathways related to energy production, stress response, and amino acid metabolism were also observed, with some pathways affected independently of bacterial abundance. These functional changes persisted during the recovery phase, indicating that the microbiota did not fully return to its pre-exposure state. Our findings suggest that BB has a lasting impact on gut microbiota structure and function, raising concerns about its widespread use in the food industry. This study underscores the need for further research into the long-term effects of food colorants on the gut microbiota and their potential health implications.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf050"},"PeriodicalIF":5.1,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977461/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813029","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":"Variation of N cycle guilds of the rye rhizosphere microbiome is driven by crop productivity along a tillage erosion catena.","authors":"Simon Lewin, Marc Wehrhan, Sonja Wende, Michael Sommer, Steffen Kolb","doi":"10.1093/ismeco/ycaf020","DOIUrl":"10.1093/ismeco/ycaf020","url":null,"abstract":"<p><p>Tillage erosion poses threats to crop yields. A transition towards more sustainable agricultural practices may be advanced by harnessing ecosystem services provided by plant microbiomes. However, targeting microbiomes at the agroecosystem scale necessitates bridging the gap to microscale structures of microbiomes. We hypothesized that differences of microbial nitrogen (N) cycle guilds in the rhizosphere of rye align with a soil catena that has been formed by tillage erosion. The rhizosphere was sampled at four sites, which captured a complete tillage erosion gradient from extremely eroded to depositional soils. The gene abundances characteristic of microbial N cycle guilds were assessed via metagenomics. The eroded sites showed the lowest plant productivity and soil mineral N availability, which was associated with an enrichment of <i>glnA</i> in the rhizosphere. Genes associated with dissimilatory nitrate-to-ammonium reducers and diazotrophy prevailed in the eroded soil profiles. The strongest correlations of the biomasses of rye plants along the catena with N cycle functions were observed for <i>norBC</i>. Thus, tillage erosion as a legacy of agricultural management aligns with substantial differences in rhizosphere microbiome functionality in N cycling. These microbiome differences were linked to plant shoot properties. Thus, the dynamics of the microbiome can be indirectly assessed by remote sensing.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf020"},"PeriodicalIF":5.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11931286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702477","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":"The impact of elevated temperature and salinity on microbial communities and food selectivity in heterotrophic nanoflagellates in the Boye River.","authors":"Lisa Boden, Dana Bludau, Guido Sieber, Aman Deep, Daria Baikova, Gwendoline M David, Una Hadžiomerović, Tom L Stach, Jens Boenigk","doi":"10.1093/ismeco/ycaf049","DOIUrl":"10.1093/ismeco/ycaf049","url":null,"abstract":"<p><p>Microbial predator-prey interactions play a crucial role in aquatic food webs. Bacterivorous protists not only regulate the quantity and biomass of bacterial populations but also profoundly influence the structure of bacterial communities. Consequently, alterations in both the quantity and quality of protist bacterivory can influence the overall structure of aquatic food webs. While it is well-documented that changes in environmental conditions or the occurrence of abiotic stressors can lead to shifts in microbial community compositions, the impact of such disturbances on food selection remains unknown. Here, we investigated the effects of elevated temperature and salinization on food selectivity of heterotrophic nanoflagellates by monitoring the uptake of preselected target bacteria via catalyzed reporter deposition fluorescence <i>in situ</i> hybridization and fluorescence microscopy. Our results indicate that salinization, but not increased temperature, significantly increased the flagellates' selection against <i>Microbacterium lacusdiani</i> (Actinomycetota). However, the effect of the reduced grazing pressure was counterbalanced by the negative effect of increased salinity on the growth of Actinomycetota. Our results suggest that the effect of stressors on the feeding behavior of protistan predators may strongly affect the composition of their prey community, when bacterial taxa are concerned that are less sensitive to the particular stressor.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf049"},"PeriodicalIF":5.1,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11976726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813058","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":"Combined metabolomic and genomic analyses reveal phage-specific and infection stage-specific alterations to marine <i>Roseobacter</i> metabolism.","authors":"Min Jin, Lanlan Cai, Longfei Lu, Meishun Yu, Rui Zhang","doi":"10.1093/ismeco/ycaf047","DOIUrl":"https://doi.org/10.1093/ismeco/ycaf047","url":null,"abstract":"<p><p>Phages can reshape the metabolic network of hosts to support specific requirements for replication during infection. However, metabolomic profiling of phage-elicited host global metabolic alterations and the linkage of phage-encoded auxiliary metabolic genes to these alterations are understudied. In this study, the dynamics of intracellular metabolites of <i>Dinoroseobacter shibae</i> DFL12, a member of marine environmentally and biogeochemically relevant <i>Roseobacter</i> clade, in response to four distinct lytic roseophage infections were investigated. Metabolomic profiling indicated that roseophage infections significantly altered host metabolism in a phage-specific manner. Pathway enrichment analyses showed that the central carbon pathway and DNA, amino acid, and coenzyme metabolism were commonly altered by roseophages, revealing a central role of these pathways in phage replication. Furthermore, clear infection stage-specific host responses were observed, corresponding to different metabolic demands of phage replication in the early and late infection stages. Interestingly, the content of host vitamin B₁, which is the essential nutrient provided by <i>D. shibae</i> to its symbiotic microalgae, increased in the early infection stage for most roseophages, implying that phage infection may impact the symbiosis of <i>D. shibae</i> with microalgae. Finally, combined metabolomic and phage genomics analyses showed that roseophages adopt different strategies to expand the host pyrimidine pool (recycling or <i>de novo</i> synthesis of pyrimidine nucleotides), and this difference was likely related to variation in the GC content between phage and host genomes. Collectively, these results highlight the potential importance of phage-specific and infection stage-specific host metabolic reprogramming in marine phage-host interactions, bacteria-microalgae symbiosis, and biogeochemical cycles.</p>","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"5 1","pages":"ycaf047"},"PeriodicalIF":5.1,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144060669","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}