The ISME Journal最新文献_第3页

Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction 内共生细菌产生的脱氮黄素代谢物控制真菌宿主的繁殖

The ISME Journal Pub Date : 2024-05-01 DOI: 10.1093/ismejo/wrae074

Ingrid Richter, Mahmudul Hasan, Johannes W Kramer, Philipp Wein, Jana Krabbe, K Philip Woitas, Timothy P Stinear, Sacha J Pidot, Florian Kloss, Christian Hertweck, Gerald Lackner

{"title":"Deazaflavin metabolite produced by endosymbiotic bacteria controls fungal host reproduction","authors":"Ingrid Richter, Mahmudul Hasan, Johannes W Kramer, Philipp Wein, Jana Krabbe, K Philip Woitas, Timothy P Stinear, Sacha J Pidot, Florian Kloss, Christian Hertweck, Gerald Lackner","doi":"10.1093/ismejo/wrae074","DOIUrl":"https://doi.org/10.1093/ismejo/wrae074","url":null,"abstract":"The endosymbiosis between the pathogenic fungus Rhizopus microsporus and the toxin-producing bacterium Mycetohabitans rhizoxinica represents a unique example of host control by an endosymbiont. Fungal sporulation strictly depends on the presence of endosymbionts as well as bacterially produced secondary metabolites. However, an influence of primary metabolites on host control remained unexplored. Recently, we discovered that M. rhizoxinica produces FO and 3PG-F420, a derivative of the specialized redox cofactor F420. Whether FO/3PG-F420 plays a role in the symbiosis has yet to be investigated. Here, we report that FO, the precursor of 3PG-F420, is essential to the establishment of a stable symbiosis. Bioinformatic analysis revealed that the genetic inventory to produce cofactor 3PG-F420 is conserved in the genomes of eight endofungal Mycetohabitans strains. By developing a CRISPR/Cas-assisted base editing strategy for M. rhizoxinica, we generated mutant strains deficient in 3PG-F420 (M. rhizoxinica ΔcofC) and in both FO and 3PG-F420 (M. rhizoxinica ΔfbiC). Co-culture experiments demonstrated that the sporulating phenotype of apo-symbiotic R. microsporus is maintained upon reinfection with wild-type M. rhizoxinica or M. rhizoxinica ΔcofC. In contrast, R. microsporus is unable to sporulate when co-cultivated with M. rhizoxinica ΔfbiC, even though the fungus was observed by super-resolution fluorescence microscopy to be successfully colonized. Genetic and chemical complementation of the FO deficiency of M. rhizoxinica ΔfbiC led to restoration of fungal sporulation, signifying that FO is indispensable for establishing a functional symbiosis. Even though FO is known for its light-harvesting properties, our data illustrate an important role of FO in inter-kingdom communication.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819373","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}

引用次数: 0

Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism 空间结构合成微生物互生系统中抗生素持久性的出现

The ISME Journal Pub Date : 2024-05-01 DOI: 10.1093/ismejo/wrae075

Xianyi Xiong, Hans G Othmer, William R Harcombe

{"title":"Emergent antibiotic persistence in a spatially structured synthetic microbial mutualism","authors":"Xianyi Xiong, Hans G Othmer, William R Harcombe","doi":"10.1093/ismejo/wrae075","DOIUrl":"https://doi.org/10.1093/ismejo/wrae075","url":null,"abstract":"Antibiotic persistence (heterotolerance) allows a sub-population of bacteria to survive antibiotic-induced killing and contributes to the evolution of antibiotic resistance. Although bacteria typically live in microbial communities with complex ecological interactions, little is known about how microbial ecology affects antibiotic persistence. Here, we demonstrated within a synthetic two-species microbial mutualism of Escherichia coli and Salmonella enterica that the combination of cross-feeding and community spatial structure can emergently cause high antibiotic persistence in bacteria by increasing the cell-to-cell heterogeneity. Tracking ampicillin-induced death for bacteria on agar surfaces, we found that E. coli forms up to 55 times more antibiotic persisters in the cross-feeding coculture than in monoculture. This high persistence could not be explained solely by the presence of S. enterica, the presence of cross-feeding, average nutrient starvation, or spontaneous resistant mutations. Time-series fluorescent microscopy revealed increased cell-to-cell variation in E. coli lag time in the mutualistic co-culture. Furthermore, we discovered that an E. coli cell can survive antibiotic killing if the nearby S. enterica cells on which it relies die first. In conclusion, we showed that the high antibiotic persistence phenotype can be an emergent phenomenon caused by a combination of cross-feeding and spatial structure. Our work highlights the importance of considering spatially structured interactions during antibiotic treatment and understanding microbial community resilience more broadly.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819298","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}

引用次数: 0

Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence 抗生素剂量和营养供应以不同方式驱动抗生素耐药性和持久性的进化

The ISME Journal Pub Date : 2024-05-01 DOI: 10.1093/ismejo/wrae070

Etthel M Windels, Lloyd Cool, Eline Persy, Janne Swinnen, Paul Matthay, Bram Van den Bergh, Tom Wenseleers, Jan Michiels

{"title":"Antibiotic dose and nutrient availability differentially drive the evolution of antibiotic resistance and persistence","authors":"Etthel M Windels, Lloyd Cool, Eline Persy, Janne Swinnen, Paul Matthay, Bram Van den Bergh, Tom Wenseleers, Jan Michiels","doi":"10.1093/ismejo/wrae070","DOIUrl":"https://doi.org/10.1093/ismejo/wrae070","url":null,"abstract":"Effective treatment of bacterial infections proves increasingly challenging due to the emergence of bacterial variants that endure antibiotic exposure. Antibiotic resistance and persistence have been identified as two major bacterial survival mechanisms, and several studies have shown a rapid and strong selection of resistance or persistence mutants under repeated drug treatment. Yet, little is known about the impact of the environmental conditions on resistance and persistence evolution, and the potential interplay between both phenotypes. Based on the distinct growth and survival characteristics of resistance and persistence mutants, we hypothesized that the antibiotic dose and availability of nutrients during treatment might play a key role in the evolutionary adaptation to antibiotic stress. To test this hypothesis, we combined high-throughput experimental evolution with a mathematical model of bacterial evolution under intermittent antibiotic exposure. We show that high nutrient levels during antibiotic treatment promote selection of high-level resistance, but that resistance mainly emerges independently of persistence when the antibiotic concentration is sufficiently low. At higher doses, resistance evolution is facilitated by the preceding or concurrent selection of persistence mutants, which ensures survival of populations in harsh conditions. Collectively, our experimental data and mathematical model elucidate the evolutionary routes towards increased bacterial survival under different antibiotic treatment schedules, which is key to designing effective antibiotic therapies.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819192","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}

引用次数: 0

Distinct life cycle stages of an ectosymbiotic DPANN archaeon 外共生 DPANN 古菌的不同生命周期阶段

The ISME Journal Pub Date : 2024-05-01 DOI: 10.1093/ismejo/wrae076

Vasil A Gaisin, Marleen van Wolferen, Sonja-Verena Albers, Martin Pilhofer

引用次数: 0

Mechanisms and implications of bacterial-fungal competition for soil resources 细菌-真菌争夺土壤资源的机制和影响

The ISME Journal Pub Date : 2024-05-01 DOI: 10.1093/ismejo/wrae073

Chaoqun Wang, Yakov Kuzyakov

{"title":"Mechanisms and implications of bacterial-fungal competition for soil resources","authors":"Chaoqun Wang, Yakov Kuzyakov","doi":"10.1093/ismejo/wrae073","DOIUrl":"https://doi.org/10.1093/ismejo/wrae073","url":null,"abstract":"Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi – the two major kingdoms in soil – the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4–5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1–4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140819351","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}

引用次数: 0

Proton-pumping rhodopsins promote the growth and survival of phytoplankton in a highly variable ocean 质子泵浦红蛋白促进浮游植物在多变海洋中的生长和生存

The ISME Journal Pub Date : 2024-04-30 DOI: 10.1093/ismejo/wrae079

William G Sunda, Adrian Marchetti

{"title":"Proton-pumping rhodopsins promote the growth and survival of phytoplankton in a highly variable ocean","authors":"William G Sunda, Adrian Marchetti","doi":"10.1093/ismejo/wrae079","DOIUrl":"https://doi.org/10.1093/ismejo/wrae079","url":null,"abstract":"Proton-pumping rhodopsins (PPRs) utilize sunlight to produce cellular energy. They are widely distributed in marine phytoplankton and were recently shown to occur in the vacuolar membrane of a marine diatom, making the vacuole a second light transducing organelle. Of course, the first, the chloroplast, is where photosynthesis occurs. However, the two light-driven sources of cellular energy are quite different and, in many ways, complement one another. Photosynthesis works best at low to intermediate light intensities, and is inhibited at high light, while PPR is predicted to work best at high light intensities. And photosynthetic rates decrease with decreasing temperature and are subject to iron limitation, while PPR photochemistry is not directly limited by iron, and is unaffected by temperature. Thus, the two phototrophic systems are favored under different sets of conditions. Placing PPR in the vacuole may benefit this complementary situation where one or the other phototrophic process is favored depending on the environmental conditions. And here, the presence of PPR in the vacuole may be especially beneficial for growth and survival as that organelle often acts as a storage site for cellular energy in the form of the phosphate anhydride bonds of polyphosphates. We hypothesize that this complementary behavior, along with the ability to store excess energy produced by PPR in the vacuole as high energy polyphosphates, represents an important survival strategy in the ocean, where light, iron levels, and temperature vary widely on a variety of spatial and temporal scales.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140821059","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}

引用次数: 0

Siderophores and competition for iron govern myxobacterial predation dynamics 嗜苷酸盐和对铁的竞争制约着粘菌的捕食动态

The ISME Journal Pub Date : 2024-04-29 DOI: 10.1093/ismejo/wrae077

Francisco Javier Contreras-Moreno, Aurelio Moraleda-Muñoz, Francisco Javier Marcos-Torres, Virginia Cuéllar, María José Soto, Juana Pérez, José Muñoz-Dorado

{"title":"Siderophores and competition for iron govern myxobacterial predation dynamics","authors":"Francisco Javier Contreras-Moreno, Aurelio Moraleda-Muñoz, Francisco Javier Marcos-Torres, Virginia Cuéllar, María José Soto, Juana Pérez, José Muñoz-Dorado","doi":"10.1093/ismejo/wrae077","DOIUrl":"https://doi.org/10.1093/ismejo/wrae077","url":null,"abstract":"Bacterial predators are decisive organisms that shape microbial ecosystems. In this study, we investigated the role of iron and siderophores during the predatory interaction between two rhizosphere bacteria: Myxococcus xanthus, an epibiotic predator, and Sinorhizobium meliloti, a bacterium that establishes nitrogen-fixing symbiosis with legumes. The results show that iron enhances the motility of the predator and facilitates its predatory capability, and that intoxication by iron is not used by the predator to prey, although oxidative stress increases in both bacteria during predation. However, competition for iron plays an important role in the outcome of predatory interactions. Using combinations of predator and prey mutants (non-producers and overproducers of siderophores), we have investigated the importance of competition for iron in predation. The results demonstrate that the competitor that, via the production of siderophores, obtains sufficient iron for growth and depletes metal availability for the opponent will prevail in the interaction. Consequently, iron fluctuations in soils may modify the composition of microbial communities by altering the activity of myxobacterial predators. In addition, siderophore overproduction during predation can alter soil properties, affecting the productivity and sustainability of agricultural operations.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140821703","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}

引用次数: 0

Rhizobium determinants of rhizosphere persistence and root colonisation 根瘤菌对根圈持久性和根定植的决定因素

The ISME Journal Pub Date : 2024-04-26 DOI: 10.1093/ismejo/wrae072

Hayley E Knights, Vinoy K Ramachandran, Beatriz Jorrin, Raphael Ledermann, Jack D Parsons, Samuel T N Aroney, Philip S Poole

{"title":"Rhizobium determinants of rhizosphere persistence and root colonisation","authors":"Hayley E Knights, Vinoy K Ramachandran, Beatriz Jorrin, Raphael Ledermann, Jack D Parsons, Samuel T N Aroney, Philip S Poole","doi":"10.1093/ismejo/wrae072","DOIUrl":"https://doi.org/10.1093/ismejo/wrae072","url":null,"abstract":"Bacterial persistence in the rhizosphere and colonisation of root niches are critical for the establishment of many beneficial plant-bacteria interactions including those between Rhizobium leguminosarum and its host legumes. Despite this, most studies on R. leguminosarum have focused on its symbiotic lifestyle as an endosymbiont in root nodules. Here, we use random barcode transposon sequencing (RB-TnSeq) to assay gene contributions of R. leguminosarum during competitive growth in the rhizosphere and colonisation of various plant species. This facilitated the identification of 189 genes commonly required for growth in diverse plant rhizospheres, mutation of 111 of which also affected subsequent root colonisation (rhizosphere progressive), and a further 119 genes necessary for colonisation. Common determinants reveal a need to synthesise essential compounds (amino acids, ribonucleotides, and cofactors), adapt metabolic function, respond to external stimuli, and withstand various stresses (such as changes in osmolarity). Additionally, chemotaxis and flagella-mediated motility are prerequisites for root colonisation. Many genes showed plant-specific dependencies highlighting significant adaptation to different plant species. This work provides a greater understanding of factors promoting rhizosphere fitness and root colonisation in plant-beneficial bacteria, facilitating their exploitation for agricultural benefit.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140817588","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}

引用次数: 0

Bridging ecological assembly process and community stability upon bacterial invasions 架起细菌入侵后生态组装过程与群落稳定性之间的桥梁

The ISME Journal Pub Date : 2024-04-25 DOI: 10.1093/ismejo/wrae066

Xipeng Liu, Joana Falcão Salles

{"title":"Bridging ecological assembly process and community stability upon bacterial invasions","authors":"Xipeng Liu, Joana Falcão Salles","doi":"10.1093/ismejo/wrae066","DOIUrl":"https://doi.org/10.1093/ismejo/wrae066","url":null,"abstract":"Understanding the link between microbial community stability and assembly processes is crucial in microbial ecology. Here, we investigated whether the impact of biotic disturbances would depend on the processes controlling community assembly. For that, we performed an experiment using soil microcosms in which microbial communities assembled through different processes were invaded by Escherichia coli. We show that the ecological assembly process of the resident community plays a significant role in invader-resident competition, invader survival, and compositional stability of the resident community. Specifically, the resident communities primarily assembled through stochastic processes were more susceptible to invader survival. Besides, E. coli invasion acts as a biotic selection pressure, leading to competition between the invader and resident taxa, suppressing the stochasticity in the resident community. Taken together, this study provides empirical evidence for the interpretation of microbial community assemblage on their (potential) ecosystem functions and services, such as the prevention of pathogen establishment and the pathogenic states of soil microbiomes.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140648675","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}

引用次数: 0

Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates 大规模基因组缩减早于共生藻科甲藻的分化

The ISME Journal Pub Date : 2024-04-24 DOI: 10.1093/ismejo/wrae059

Sarah Shah, Katherine E Dougan, Yibi Chen, Rosalyn Lo, Gemma Laird, Michael D A Fortuin, Subash K Rai, Valentine Murigneux, Anthony J Bellantuono, Mauricio Rodriguez-Lanetty, Debashish Bhattacharya, Cheong Xin Chan

{"title":"Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates","authors":"Sarah Shah, Katherine E Dougan, Yibi Chen, Rosalyn Lo, Gemma Laird, Michael D A Fortuin, Subash K Rai, Valentine Murigneux, Anthony J Bellantuono, Mauricio Rodriguez-Lanetty, Debashish Bhattacharya, Cheong Xin Chan","doi":"10.1093/ismejo/wrae059","DOIUrl":"https://doi.org/10.1093/ismejo/wrae059","url":null,"abstract":"Dinoflagellates in the family Symbiodiniaceae are taxonomically diverse, predominantly symbiotic lineages that are well-known for their association with corals. The ancestor of these taxa is believed to have been free-living. The establishment of symbiosis (i.e., symbiogenesis) is hypothesised to have occurred multiple times during Symbiodiniaceae evolution, but its impact on genome evolution of these taxa is largely unknown. Among Symbiodiniaceae, the genus Effrenium is a free-living lineage that is phylogenetically positioned between two robustly supported groups of genera within which symbiotic taxa have emerged. The apparent lack of symbiogenesis in Effrenium suggests that the ancestral features of Symbiodiniaceae may have been retained in this lineage. Here we present de novo assembled genomes (1.2–1.9 Gbp in size) and transcriptome data from three isolates of Effrenium voratum and conduct a comparative analysis that includes 16 Symbiodiniaceae taxa and the other dinoflagellates. Surprisingly, we find that genome reduction, which is often associated with a symbiotic lifestyle, predates the origin of Symbiodiniaceae. The free-living lifestyle distinguishes Effrenium from symbiotic Symbiodiniaceae vis-à-vis their longer introns, more-extensive mRNA editing, fewer (~30%) lineage-specific gene sets, and lower (~10%) level of pseudogenisation. These results demonstrate how genome reduction and the adaptation to distinct lifestyles intersect to drive diversification and genome evolution of Symbiodiniaceae.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140642499","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}

引用次数: 0