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Central metabolism and development are rewired in lichenized cyanobacteria 在地衣化的蓝藻中,中枢代谢和发育被重新连接
The ISME Journal Pub Date : 2025-08-12 DOI: 10.1093/ismejo/wraf166
Diego Garfias-Gallegos, Carlos J Pardo-De la Hoz, Diane L Haughland, Nicolas Magain, Blanka Aguero, Jolanta Miadlikowska, François Lutzoni
{"title":"Central metabolism and development are rewired in lichenized cyanobacteria","authors":"Diego Garfias-Gallegos, Carlos J Pardo-De la Hoz, Diane L Haughland, Nicolas Magain, Blanka Aguero, Jolanta Miadlikowska, François Lutzoni","doi":"10.1093/ismejo/wraf166","DOIUrl":"https://doi.org/10.1093/ismejo/wraf166","url":null,"abstract":"Nostoc cyanobacteria are among the few organisms capable of fixing both carbon and nitrogen. These metabolic features are essential for the cyanolichen symbiosis, where Nostoc supplies both carbon (as glucose) and nitrogen (as ammonium) to a cyanolichen-forming fungal partner. This nutrient flow was established by seminal biochemical studies published in the 20th century. Since then, cyanolichen metabolism has received little attention, and the molecular mechanisms that underlie the physiology of lichenized Nostoc remain mostly unknown. Here, we aimed to elucidate the genomic and transcriptional changes that enable Nostoc’s metabolic role in cyanolichens. We used comparative genomics across 243 genomes of Nostoc s. lat. Coupled with metatranscriptomic experiments using Peltigera cyanolichens. We found that genes for photoautotrophic carbon fixation are upregulated in lichenized Nostoc. This likely results in a higher rate of carbon fixation that allows Nostoc to provide carbon to the fungal partner while meeting its own metabolic needs. We also found that the transfer of ammonium from Nostoc to the lichen-forming fungus is facilitated by two molecular mechanisms: (i) transcriptional downregulation of glutamine synthetase, the key enzyme responsible for ammonium assimilation in Nostoc; and (ii) frequent losses of a putative high-affinity ammonium permease, which likely reduces Nostoc’s capacity to recapture leaked ammonium. Finally, we found that the development of motile hormogonia is downregulated in lichenized Nostoc, which resembles the repression of motility in Nostoc symbionts after they colonize symbiotic cavities of their plant hosts. Our results pave the way for a revival of cyanolichen ecophysiology in the omics era.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825289","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
Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function. 厌氧短生物体在微环境中的生存取决于微生物群的代谢功能。
The ISME Journal Pub Date : 2025-08-12 DOI: 10.1093/ismejo/wraf171
Karla Iveth Aguilera-Campos, Julie Boisard, Viktor Törnblom, Jon Jerlström-Hultqvist, Ada Behncké-Serra, Elena Aramendia Cotillas, Courtney Weir Stairs
{"title":"Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.","authors":"Karla Iveth Aguilera-Campos, Julie Boisard, Viktor Törnblom, Jon Jerlström-Hultqvist, Ada Behncké-Serra, Elena Aramendia Cotillas, Courtney Weir Stairs","doi":"10.1093/ismejo/wraf171","DOIUrl":"https://doi.org/10.1093/ismejo/wraf171","url":null,"abstract":"Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825071","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
Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia 合成群落作为确定生物肥料底盘生物和本地微生物群落之间相互作用的模型
The ISME Journal Pub Date : 2025-08-12 DOI: 10.1093/ismejo/wraf170
Cody S Madsen, Jeffrey A Kimbrel, Patrick Diep, Dante P Ricci
{"title":"Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia","authors":"Cody S Madsen, Jeffrey A Kimbrel, Patrick Diep, Dante P Ricci","doi":"10.1093/ismejo/wraf170","DOIUrl":"https://doi.org/10.1093/ismejo/wraf170","url":null,"abstract":"Biofertilizers are critical for sustainable agriculture since they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. Yet, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. We describe a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. We profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and detected significant phylogenetic diversity (e.g., Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs where an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in approximately 10% of SynComs that generally followed the diversity-invasion principle. Additionally, our approach enables analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work establishes a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessing persistence and interaction of a specific organism of interest with native consortia.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825292","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
Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science 利用公民科学快速找到适合在北纬地区种植大豆的环境适应性根瘤菌
The ISME Journal Pub Date : 2025-08-12 DOI: 10.1093/ismejo/wraf152
Sonia García Méndez, Stien Mertens, Arne Temmerman, Helena Van den Eynde, Margo Vermeersch, Lena Vlaminck, Olivier Berteloot, Judith Van Dingenen, Alexander Clarysse, Annick De Keyser, Serge Beullens, Ilse de Baenst, Niranjana Roy, Quinten De Paepe, Jan Michiels, Isabel Roldan-Ruiz, Joke Pannecoucque, Anne Willems, Steven Maere, Sofie Goormachtig
{"title":"Fast track to environmentally adapted rhizobia for growing soybean at northern latitudes using citizen science","authors":"Sonia García Méndez, Stien Mertens, Arne Temmerman, Helena Van den Eynde, Margo Vermeersch, Lena Vlaminck, Olivier Berteloot, Judith Van Dingenen, Alexander Clarysse, Annick De Keyser, Serge Beullens, Ilse de Baenst, Niranjana Roy, Quinten De Paepe, Jan Michiels, Isabel Roldan-Ruiz, Joke Pannecoucque, Anne Willems, Steven Maere, Sofie Goormachtig","doi":"10.1093/ismejo/wraf152","DOIUrl":"https://doi.org/10.1093/ismejo/wraf152","url":null,"abstract":"Soybean serves as a crucial source of plant-based protein for human diets. Recently, there is a growing incentive to extend the range of this crop to more northern latitudes, in order to enable profitable soybean production in Europe. To reach economic yields, soybean requires inoculation with symbiotic, diazotrophic rhizobial bacteria. However, the performance of commercial inocula is often variable under local conditions. Here, we present the citizen science project “Soy in 1,000 Gardens”, a large-scale trapping experiment for isolating local soybean-nodulating rhizobia in Flanders, Belgium. We identified two locally isolated Bradyrhizobium strains performing at least as well as commercial strain B. diazoefficiens G49 in local field trials. Additionally, we found that nutrient content, microbial alpha diversity, and the presence of arbuscular mycorrhizal fungi in the soil were correlated with nodulation. Finally, we report a correlation between low bacterial alpha diversity and red nodule interior, and identified Tardiphaga as a dominant colonizer of red nodules.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144824914","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
Ecology-based approach to predict no-effect antibiotic concentrations for minimizing environmental selection of resistance. 基于生态学的方法来预测无效果抗生素浓度,以最大限度地减少耐药性的环境选择。
The ISME Journal Pub Date : 2025-08-11 DOI: 10.1093/ismejo/wraf172
David Kneis,Magali de la Cruz Barron,Diala Konyali,Valentin Westphal,Patrick Schröder,Kathi Westphal-Settele,Jens Schönfeld,Dirk Jungmann,Thomas Ulrich Berendonk,Uli Klümper
{"title":"Ecology-based approach to predict no-effect antibiotic concentrations for minimizing environmental selection of resistance.","authors":"David Kneis,Magali de la Cruz Barron,Diala Konyali,Valentin Westphal,Patrick Schröder,Kathi Westphal-Settele,Jens Schönfeld,Dirk Jungmann,Thomas Ulrich Berendonk,Uli Klümper","doi":"10.1093/ismejo/wraf172","DOIUrl":"https://doi.org/10.1093/ismejo/wraf172","url":null,"abstract":"Selection for antibiotic resistance has been demonstrated at low, environmentally relevant antibiotic concentrations. The concept of minimum selective concentrations (MSC) has been adopted in environmental regulation to define maximum permissible antibiotic concentrations. Such empirically determined MSC values often fail to reflect the complexity of natural communities, where susceptibility and resistance-associated fitness costs vary widely across species. To address this limitation, computational approaches have been developed to predict no-effect concentrations for selection of antibiotic resistance (PNECres) from routinely collected minimum inhibitory concentration (MIC) data. However, these approaches, using assessment factors to convert MICs to PNECres, often lack a strong ecological basis, undermining confidence in their predictions. Here, we propose a simple but biologically consistent framework to derive PNECres values by integrating MIC data with probabilistic estimates of resistance-related fitness costs. We demonstrate mathematically and empirically that for typical high-level resistances, the MSC/MIC ratio is approximately equal to the resistance cost, allowing for cost-based estimation of MSCs. In experimental validation across 26 strain-antibiotic combinations, 66% of computed MSCs deviated by less than factor two from empirical values. Leveraging these findings, we explored the general distribution of fitness costs of resistance determinants to establish a cost-based probabilistic model for replacing conventional fixed assessment factors. When applied to current MIC databases, our framework suggests that regulatory environmental threshold concentrations should be lowered by at least one order of magnitude to guard against selection for antibiotic resistance. Our approach offers a feasible and biologically transparent alternative for deriving PNECres values in environmental risk assessment.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825736","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
Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods. 节肢动物细菌共生体中特殊毒素库的进化。
The ISME Journal Pub Date : 2025-08-11 DOI: 10.1093/ismejo/wraf174
Logan D Moore,Matthew J Ballinger
{"title":"Evolution of specialized toxin arsenals in a bacterial symbiont of arthropods.","authors":"Logan D Moore,Matthew J Ballinger","doi":"10.1093/ismejo/wraf174","DOIUrl":"https://doi.org/10.1093/ismejo/wraf174","url":null,"abstract":"Bacteria commonly deploy toxic proteins that act with specificity on target molecules to support invasion and improve survival in competitive environments. Many toxin-encoding bacteria have evolved into host-associated defensive partnerships, in which they use toxins to improve host survival during infection. The stability of these relationships requires that symbiont toxins target diverse parasites while minimizing damage to the host. We investigate the specificity of a group of ribosome-targeting toxins (RIPs) encoded by heritable Spiroplasma symbionts that contribute to defense against parasite infection in fruit fly hosts. Using E. coli to express five divergent copies of this toxin, we show that distantly related members of the family all retain the ability to inactivate ribosomes by adenine cleavage at the α-sarcin/ricin loop, the enzymatic hallmark of RIPs. However, when exposed to live insect and fungal cells, ribosome inactivation varies across the five toxins, suggesting cellular recognition or localization play a role in target specificity. To identify toxin domains required for specificity, we removed rapidly evolving \"accessory\" domains from two toxins. Both truncated toxins exhibit significantly increased activity on purified ribosomes in vitro, suggesting one role of accessory domains is to reduce toxicity, which may help protect hosts from collateral damage. One of the truncated toxins also showed significantly reduced inactivation of cellular ribosomes in vivo, indicating a role for accessory domains in cell specificity. Together, these data reveal a mechanism for symbiont discrimination between hosts and parasites and highlight how dynamic toxin evolution can contribute to stability and novelty in defensive symbiosis.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825737","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
Inositol phosphates as an overlooked phosphorous source in marine ecosystems. 肌醇磷酸盐是海洋生态系统中一个被忽视的磷源。
The ISME Journal Pub Date : 2025-08-11 DOI: 10.1093/ismejo/wraf161
Zhao-Jie Teng,Xiao-Jie Yuan,Rui Liu,Shao-Chun Xu,Xiu-Lan Chen,Yin Chen,Yu-Zhong Zhang
{"title":"Inositol phosphates as an overlooked phosphorous source in marine ecosystems.","authors":"Zhao-Jie Teng,Xiao-Jie Yuan,Rui Liu,Shao-Chun Xu,Xiu-Lan Chen,Yin Chen,Yu-Zhong Zhang","doi":"10.1093/ismejo/wraf161","DOIUrl":"https://doi.org/10.1093/ismejo/wraf161","url":null,"abstract":"Inositol phosphates, common phosphorus storage compounds that are also crucial for eukaryotic cell signaling, constitute a significant portion of dissolved organic phosphorus in coastal waters. The hydrolysis of inositol phosphates could be an important contributor to phosphorus cycling in phosphorus-limited marine ecosystems, yet this process remains poorly understood in marine contexts. In this study, we reveal substantial concentrations of Inositol phosphates in marine macrophytes, including green, brown, and red algae as well as common seagrasses, suggesting that these organisms are likely major biological sources of inositol phosphates in the oceans. A comprehensive analysis of genes involved in inositol phosphates hydrolysis in global marine metagenomes and metatranscriptomes identified key roles for γ-, α-, and δ-proteobacteria, with additional contributions from Flavobacteriia. The degradation of marine inositol phosphates was predominantly mediated by alkaline β-propeller phytases, though genes associated with acidic cysteine phytases and purple acid phytases were also widely present. Community structure and functional traits linked to inositol phosphates degradation were shaped largely by stochastic processes. Further examination of enzyme activity at the protein and community levels indicated that phytate metabolism by marine microbes is likely a widespread phenomenon in the ocean. Overall, this study highlights inositol phosphates hydrolysis as an essential yet overlooked adaptation by marine microorganisms to address phosphorus limitations in ocean ecosystems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144825738","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
Global dominance of Haloquadratum walsbyi by a single highly clonal genomovar with distinct gene content and viral cohorts from close relatives. 一个具有不同基因含量的高克隆基因组变体和来自近亲的病毒群在全球占据优势地位。
The ISME Journal Pub Date : 2025-08-04 DOI: 10.1093/ismejo/wraf165
Esteban Bustos-Caparros,Tomeu Viver,Juan F Gago,Juanita R Avontuur,Souad Amiour,Bonnie K Baxter,María E Llames,Mehmet B Mutlu,Aharon Oren,Ana S Ramírez,Matthew B Stott,Stephanus N Venter,Fernando Santos,Josefa Antón,Luis M Rodriguez-R,Rafael Bosch,Brian P Hedlund,Konstantinos T Konstantinidis,Ramon Rossello-Mora
{"title":"Global dominance of Haloquadratum walsbyi by a single highly clonal genomovar with distinct gene content and viral cohorts from close relatives.","authors":"Esteban Bustos-Caparros,Tomeu Viver,Juan F Gago,Juanita R Avontuur,Souad Amiour,Bonnie K Baxter,María E Llames,Mehmet B Mutlu,Aharon Oren,Ana S Ramírez,Matthew B Stott,Stephanus N Venter,Fernando Santos,Josefa Antón,Luis M Rodriguez-R,Rafael Bosch,Brian P Hedlund,Konstantinos T Konstantinidis,Ramon Rossello-Mora","doi":"10.1093/ismejo/wraf165","DOIUrl":"https://doi.org/10.1093/ismejo/wraf165","url":null,"abstract":"Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > ANI > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144769796","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
Rapid water flow triggers long-distance positive rheotaxis for thermophilic bacteria 快速水流触发嗜热细菌的长距离正流变性
The ISME Journal Pub Date : 2025-08-01 DOI: 10.1093/ismejo/wraf164
Naoki A Uemura, Naoya Chiba, Ryota Morikawa, Masatada Tamakoshi, Daisuke Nakane
{"title":"Rapid water flow triggers long-distance positive rheotaxis for thermophilic bacteria","authors":"Naoki A Uemura, Naoya Chiba, Ryota Morikawa, Masatada Tamakoshi, Daisuke Nakane","doi":"10.1093/ismejo/wraf164","DOIUrl":"https://doi.org/10.1093/ismejo/wraf164","url":null,"abstract":"Bacteria thrive in nearly all environments on Earth, demonstrating remarkable adaptability to physical stimuli, as well as chemicals and light. However, the mechanisms by which bacteria locate and settle in ecological niches optimal for their growth remains poorly understood. Here, we show that Thermus thermophilus, a highly thermophilic non-flagellated species of bacteria, exhibits positive rheotaxis, navigating upstream in unidirectional rapid water flow. Mimicking their natural habitat at 70°C with a water current under optical microscopy, cells traveled distances up to 1 mm in 30 min, with infrequent directional changes. This long-distance surface migration is driven by type IV pili, facilitating vertical attachment at the cell pole, and shear-induced tilting of the cell body, resulting in alignment of the leading pole toward the direction of water flow. Direct visualization of T4P filaments and their dynamics revealed that rheotaxis is triggered by weakened attachment at the cell pole, regulated by ATPase activity, which was further validated by mathematical modeling. Flow experiments on 15 bacterial strains and species in the Deinococcota (synonym Deinococcus-Thermus) phylum revealed that positive rheotaxis is highly conserved among rod-shaped Thermaceae, but absent in spherical-shaped Deinococcus. Our findings suggest that thermophilic bacteria reach their ecological niches by responding to the physical stimulus of rapid water flow, a ubiquitous feature in hot spring environments. This study highlights unforeseen survival strategies, showcasing an evolutionary adaptation to a surface-associated lifestyle where swimming bacteria would otherwise be swept away.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"26 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755952","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
Engineering Plant Holobionts for Climate-Resilient Agriculture 气候适应型农业的植物全息生物工程
The ISME Journal Pub Date : 2025-08-01 DOI: 10.1093/ismejo/wraf158
Nayanci Portal-Gonzalez, Wenbo Wang, Wenxing He, Ramon Santos-Bermudez
{"title":"Engineering Plant Holobionts for Climate-Resilient Agriculture","authors":"Nayanci Portal-Gonzalez, Wenbo Wang, Wenxing He, Ramon Santos-Bermudez","doi":"10.1093/ismejo/wraf158","DOIUrl":"https://doi.org/10.1093/ismejo/wraf158","url":null,"abstract":"The plant holobiont—an integrated unit of the host and its microbiome—has co-evolved through ecological and genetic interactions. Microbiome engineering offers a promising route to enhance resilience in response to climate stress, soil degradation, and yield stagnation. This review presents an integrated framework combining microbial ecology, synthetic biology, and computational modeling to rationally design synthetic microbial communities (SynComs) for agriculture. We outline ecological principles—priority effects, keystone taxa, and functional redundancy—that shape microbiome assembly and guide SynCom design. Strategies like CRISPR interference, biosensor circuits, and quorum-sensing modules enable programmable microbial functions. We also highlight the predictive potential of in silico modeling—including genome-scale metabolic models, dynamic flux balance analysis, and machine learning—to simulate interactions, optimize SynCom composition, and enhance design accuracy. To bridge lab and field, we discuss native microbial chassis, encapsulation, and precision delivery as tools for scalable, ecosystem-integrated deployment. We introduce the concept of the programmable holobiont: an engineered plant-microbe partnership capable of dynamic feedback, interkingdom signaling, and ecological memory. This systems-level perspective reframes plants as designable ecosystems. By synthesizing cross-disciplinary advances, we offer a roadmap for climate-resilient agriculture, where engineered microbiomes improve sustainability, yield stability, and environmental adaptation.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755951","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
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