首页 > 最新文献

The ISME Journal最新文献

英文 中文
VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle 豆科植物共生体瓜萎镰刀菌(Sinorhizobium meliloti)的 VapC10毒素靶向 tRNASer 并控制细胞内的生活方式
Pub Date : 2024-01-28 DOI: 10.1093/ismejo/wrae015
Camille Syska, Aurélie Kiers, Corinne Rancurel, Marc Bailly-Bechet, Justine Lipuma, Geneviève Alloing, Isabelle Garcia, Laurence Dupont
The soil bacterium Sinorhizobium meliloti can establish a nitrogen fixing symbiosis with the model legume Medicago truncatula. The rhizobia induce the formation of a specialized root organ called nodule, where they differentiate into bacteroids and reduce atmospheric nitrogen into ammonia. Little is known on the mechanisms involved in nodule senescence onset and in bacteroid survival inside the infected plant cells. Whereas Toxin-Antitoxin (TA) systems have been shown to promote intracellular survival within host cells in human pathogenic bacteria, their role in symbiotic bacteria was rarely investigated. S. meliloti encodes several TA systems, mainly of the VapBC family. Here we present the functional characterization, through a multidisciplinary approach, of the VapBC10 TA system of S. meliloti. Following a MORE RNA-seq analysis, we demonstrated that the VapC10 toxin is an RNase that cleaves the anticodon loop of two tRNASer. Thereafter, a bioinformatics approach was used to predict VapC10 targets in bacteroids. This analysis suggests that toxin activation triggers a specific proteome reprogramming that could limit nitrogen fixation capability and viability of bacteroids. Accordingly, a vapC10 mutant induces a delayed senescence in nodules, associated to an enhanced bacteroid survival. VapBC10 TA system could contribute to S. meliloti adaptation to symbiotic lifestyle, in response to plant nitrogen status.
土壤中的美乐藻根瘤菌(Sinorhizobium meliloti)能与模式豆科植物美智子(Medicago truncatula)建立固氮共生关系。根瘤菌诱导形成一种称为 "结节 "的特化根器官,并在其中分化成类菌体,将大气中的氮还原成氨。人们对结核开始衰老和细菌在受感染植物细胞内存活的机制知之甚少。虽然毒素-抗毒素(TA)系统已被证明能促进人类致病菌在宿主细胞内的生存,但它们在共生细菌中的作用却很少被研究。S. meliloti编码多种TA系统,主要属于VapBC家族。在这里,我们通过多学科方法介绍了 S. meliloti 的 VapBC10 TA 系统的功能特征。在进行 MORE RNA-seq 分析后,我们证明 VapC10 毒素是一种 RNase,能裂解两个 tRNASer 的反密码子环。 随后,我们利用生物信息学方法预测了 VapC10 在类杆菌中的靶标。这项分析表明,毒素激活会引发特定蛋白质组的重编程,从而限制固氮能力和类固氮微生物的生存能力。因此,vapC10突变体会诱导结核延迟衰老,从而提高类菌体的存活率。VapBC10 TA系统可能有助于S. meliloti适应共生生活方式,以应对植物的氮状况。
{"title":"VapC10 toxin of the legume symbiont Sinorhizobium meliloti targets tRNASer and controls intracellular lifestyle","authors":"Camille Syska, Aurélie Kiers, Corinne Rancurel, Marc Bailly-Bechet, Justine Lipuma, Geneviève Alloing, Isabelle Garcia, Laurence Dupont","doi":"10.1093/ismejo/wrae015","DOIUrl":"https://doi.org/10.1093/ismejo/wrae015","url":null,"abstract":"The soil bacterium Sinorhizobium meliloti can establish a nitrogen fixing symbiosis with the model legume Medicago truncatula. The rhizobia induce the formation of a specialized root organ called nodule, where they differentiate into bacteroids and reduce atmospheric nitrogen into ammonia. Little is known on the mechanisms involved in nodule senescence onset and in bacteroid survival inside the infected plant cells. Whereas Toxin-Antitoxin (TA) systems have been shown to promote intracellular survival within host cells in human pathogenic bacteria, their role in symbiotic bacteria was rarely investigated. S. meliloti encodes several TA systems, mainly of the VapBC family. Here we present the functional characterization, through a multidisciplinary approach, of the VapBC10 TA system of S. meliloti. Following a MORE RNA-seq analysis, we demonstrated that the VapC10 toxin is an RNase that cleaves the anticodon loop of two tRNASer. Thereafter, a bioinformatics approach was used to predict VapC10 targets in bacteroids. This analysis suggests that toxin activation triggers a specific proteome reprogramming that could limit nitrogen fixation capability and viability of bacteroids. Accordingly, a vapC10 mutant induces a delayed senescence in nodules, associated to an enhanced bacteroid survival. VapBC10 TA system could contribute to S. meliloti adaptation to symbiotic lifestyle, in response to plant nitrogen status.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139577528","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
Microorganisms oxidize glucose through distinct pathways in permeable and cohesive sediments 微生物在透水性和粘性沉积物中通过不同途径氧化葡萄糖
Pub Date : 2024-01-28 DOI: 10.1093/ismejo/wrae001
Tess F Hutchinson, Adam J Kessler, Wei Wen Wong, Puspitaningsih Hall, Pok Man Leung, Thanavit Jirapanjawat, Chris Greening, Ronnie N Glud, Perran L M Cook
In marine sediments, microbial degradation of organic matter under anoxic conditions is generally thought to proceed through fermentation to volatile fatty acids (VFA), which are then oxidized to CO2 coupled to the reduction of terminal electron acceptors (e.g. nitrate, iron, manganese and sulfate). It has been suggested that, in environments with a highly variable oxygen regime, fermentation mediated by facultative anaerobic bacteria (uncoupled to external terminal electron acceptors) becomes the dominant process. Here, we present the first direct evidence for this fermentation using a novel differentially-labelled glucose isotopologue assay that distinguishes between CO2 produced from respiration and fermentation. Using this approach, we measured the relative contribution of respiration and fermentation of glucose in a range of permeable (sandy) and cohesive (muddy) sediments, as well as four bacterial isolates. Under anoxia, microbial communities adapted to high energy sandy or bioturbated sites mediate fermentation via the Embden-Meyerhof-Parnas (EMP) pathway, in a manner uncoupled from anaerobic respiration. Prolonged anoxic incubation suggests this uncoupling lasts up to 160 hours. In contrast, microbial communities in anoxic muddy sediments (smaller median grain size) generally completely oxidized 13C glucose to 13CO2, consistent with the classical redox cascade model. We also unexpectedly observed that fermentation occurred under oxic conditions in permeable sediments. These observations were further confirmed using pure cultures of four bacteria isolated from permeable sediments. Our results suggest microbial communities adapted to variable oxygen regimes metabolise glucose (and likely other organic molecules) through fermentation uncoupled to respiration during transient anoxic conditions.
在海洋沉积物中,缺氧条件下有机物的微生物降解通常被认为是通过发酵产生挥发性 脂肪酸(VFA),然后通过还原末端电子受体(如硝酸盐、铁、锰和硫酸盐)将其氧化成 CO2。有观点认为,在氧含量变化很大的环境中,由兼性厌氧细菌(与外部末端电子受体不耦合)介导的发酵成为主要过程。在这里,我们首次提出了这种发酵的直接证据,使用的是一种新型的差异标记葡萄糖同位素测定法,它能区分呼吸和发酵产生的二氧化碳。利用这种方法,我们测量了一系列透水性(沙质)和粘性(泥质)沉积物以及四种细菌分离物中葡萄糖呼吸和发酵的相对贡献。在缺氧条件下,适应高能沙质或生物扰动场地的微生物群落通过恩伯登-迈尔霍夫-帕尔纳斯(EMP)途径进行发酵,其方式与厌氧呼吸无关。长期缺氧培养表明,这种脱钩可持续长达 160 小时。与此相反,缺氧泥质沉积物(中位粒径较小)中的微生物群落通常会将 13C 葡萄糖完全氧化为 13CO2,这与经典的氧化还原级联模型一致。我们还意外地观察到,在渗透性沉积物中,发酵是在缺氧条件下进行的。使用从渗透性沉积物中分离出来的四种细菌的纯培养物进一步证实了这些观察结果。我们的研究结果表明,适应多变氧气环境的微生物群落在瞬时缺氧条件下通过与呼吸作用脱钩的发酵代谢葡萄糖(可能还有其他有机分子)。
{"title":"Microorganisms oxidize glucose through distinct pathways in permeable and cohesive sediments","authors":"Tess F Hutchinson, Adam J Kessler, Wei Wen Wong, Puspitaningsih Hall, Pok Man Leung, Thanavit Jirapanjawat, Chris Greening, Ronnie N Glud, Perran L M Cook","doi":"10.1093/ismejo/wrae001","DOIUrl":"https://doi.org/10.1093/ismejo/wrae001","url":null,"abstract":"In marine sediments, microbial degradation of organic matter under anoxic conditions is generally thought to proceed through fermentation to volatile fatty acids (VFA), which are then oxidized to CO2 coupled to the reduction of terminal electron acceptors (e.g. nitrate, iron, manganese and sulfate). It has been suggested that, in environments with a highly variable oxygen regime, fermentation mediated by facultative anaerobic bacteria (uncoupled to external terminal electron acceptors) becomes the dominant process. Here, we present the first direct evidence for this fermentation using a novel differentially-labelled glucose isotopologue assay that distinguishes between CO2 produced from respiration and fermentation. Using this approach, we measured the relative contribution of respiration and fermentation of glucose in a range of permeable (sandy) and cohesive (muddy) sediments, as well as four bacterial isolates. Under anoxia, microbial communities adapted to high energy sandy or bioturbated sites mediate fermentation via the Embden-Meyerhof-Parnas (EMP) pathway, in a manner uncoupled from anaerobic respiration. Prolonged anoxic incubation suggests this uncoupling lasts up to 160 hours. In contrast, microbial communities in anoxic muddy sediments (smaller median grain size) generally completely oxidized 13C glucose to 13CO2, consistent with the classical redox cascade model. We also unexpectedly observed that fermentation occurred under oxic conditions in permeable sediments. These observations were further confirmed using pure cultures of four bacteria isolated from permeable sediments. Our results suggest microbial communities adapted to variable oxygen regimes metabolise glucose (and likely other organic molecules) through fermentation uncoupled to respiration during transient anoxic conditions.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139577391","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
Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea 多态病毒与海洋嗜热古细菌建立稳定关系
Pub Date : 2024-01-24 DOI: 10.1093/ismejo/wrae008
Diana P Baquero, Eduardo A Bignon, Mart Krupovic
Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, “Thalassapleoviridae”, for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.
具有包膜多形病毒的非溶解病毒(Pleolipoviridae 科)在全球各地的高盐环境中无处不在,几乎与所有主要的嗜卤古细菌系都有关联。然而,它们在其他生态系统中的存在情况在很大程度上仍不为人所知。在这里,我们发现与它们进化相关的病毒也会感染深海热液喷口中的嗜热古细菌。Archaeoglobus veneficus pleomorphic virus 1(AvPV1)是第一个被描述为古细菌类成员的病毒,它编码一个典型的多脂病毒形态发生模块,包括特征性的 VP4 样膜融合蛋白。我们的研究表明,AvPV1 是一种非溶解性病毒,可长期在液体培养物中产生,不会对宿主的生长动态产生实质性影响,病毒与宿主的比例稳定在 1 左右。通过比较基因组学和 VP4-like fusogens 的系统进化分析,我们发现感染嗜卤古菌、嗜甲烷古菌和嗜高热古菌的多形性病毒存在深度分化,这表明相应的病毒-宿主配对存在生态位分离和共同进化。因此,我们提出了一个新的病毒科 "Thalassapleoviridae",用于对海洋嗜热病毒 AvPV1 及其近亲进行分类。总之,我们的研究结果为了解超盐环境中多形性病毒的多样性和进化提供了启示。
{"title":"Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea","authors":"Diana P Baquero, Eduardo A Bignon, Mart Krupovic","doi":"10.1093/ismejo/wrae008","DOIUrl":"https://doi.org/10.1093/ismejo/wrae008","url":null,"abstract":"Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, “Thalassapleoviridae”, for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139568357","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
Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice 水稻受体激酶 FLR7 可调节根瘤层的氧气水平,富集优势厌氧菌,从而提高水稻的耐淹性
Pub Date : 2024-01-24 DOI: 10.1093/ismejo/wrae006
Hong-Bin Liu, Hong-Xia Sun, Li-Qiong Du, Ling-Li Jiang, Lin-An Zhang, Yin-Yao Qi, Jun Cai, Feng Yu
Oxygen is one of the determinants of root microbiome formation. However, whether plants regulate rhizosphere oxygen levels to affect microbiota composition and the underlying molecular mechanisms remain elusive. The receptor-like kinase (RLK) family member FERONIA modulates the growth–defense tradeoff in Arabidopsis. Here, we established that rice FERONIA-like RLK 7 (FLR7) controls rhizosphere oxygen levels by methylene blue staining, oxygen flux and potential measurements. The formation of oxygen-transporting aerenchyma in roots is negatively regulated by FLR7. We further characterized the root microbiota of 11 FLR mutants including flr7 and wild-type Nipponbare (Nip) grown in the field by 16S ribosomal RNA gene profiling and demonstrated that the 11 FLRs are involved in regulating rice root microbiome formation. The most abundant anaerobic-dependent genus Anaeromyxobacter in the Nip root microbiota was less abundant in the root microbiota of all these mutants, and this contributed the most to the community differences between most mutants and Nip. Metagenomic sequencing revealed that flr7 increases aerobic respiration and decreases anaerobic respiration in the root microbiome. Finally, we showed that a representative Anaeromyxobacter strain improved submergence tolerance in rice via FLR7. Collectively, our findings indicate that FLR7 mediates changes in rhizosphere oxygen levels and enriches the beneficial dominant genus Anaeromyxobacter and may provide insights for developing plant flood prevention strategies via the use of environment-specific functional soil microorganisms.
氧气是根微生物群形成的决定因素之一。然而,植物是否会通过调节根瘤层的氧气水平来影响微生物群的组成及其潜在的分子机制仍是未知数。受体样激酶(RLK)家族成员 FERONIA 调节拟南芥的生长-防御权衡。在这里,我们通过亚甲基蓝染色、氧通量和电位测量确定了水稻 FERONIA 样 RLK 7(FLR7)控制根瘤氧水平。根中氧气运输气孔的形成受 FLR7 的负调控。我们通过 16S 核糖体 RNA 基因谱分析,进一步鉴定了在田间生长的 11 个 FLR 突变体(包括 flr7 和野生型 Nipponbare(Nip))的根微生物群,结果表明这 11 个 FLR 参与了水稻根微生物群形成的调控。在所有这些突变体的根微生物群中,Nip 根微生物群中最丰富的厌氧依赖性菌属 Anaeromyxobacter 的数量较少,这也是造成大多数突变体与 Nip 之间群落差异的主要原因。元基因组测序显示,在根微生物群中,flr7 增加了需氧呼吸,减少了厌氧呼吸。最后,我们发现一株具有代表性的拟杆菌通过 FLR7 提高了水稻的耐淹性。总之,我们的研究结果表明,FLR7 可介导根圈氧含量的变化,并丰富有益的优势菌属 Anaeromyxobacter,从而为通过使用环境特异性功能性土壤微生物来制定植物防涝策略提供启示。
{"title":"Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice","authors":"Hong-Bin Liu, Hong-Xia Sun, Li-Qiong Du, Ling-Li Jiang, Lin-An Zhang, Yin-Yao Qi, Jun Cai, Feng Yu","doi":"10.1093/ismejo/wrae006","DOIUrl":"https://doi.org/10.1093/ismejo/wrae006","url":null,"abstract":"Oxygen is one of the determinants of root microbiome formation. However, whether plants regulate rhizosphere oxygen levels to affect microbiota composition and the underlying molecular mechanisms remain elusive. The receptor-like kinase (RLK) family member FERONIA modulates the growth–defense tradeoff in Arabidopsis. Here, we established that rice FERONIA-like RLK 7 (FLR7) controls rhizosphere oxygen levels by methylene blue staining, oxygen flux and potential measurements. The formation of oxygen-transporting aerenchyma in roots is negatively regulated by FLR7. We further characterized the root microbiota of 11 FLR mutants including flr7 and wild-type Nipponbare (Nip) grown in the field by 16S ribosomal RNA gene profiling and demonstrated that the 11 FLRs are involved in regulating rice root microbiome formation. The most abundant anaerobic-dependent genus Anaeromyxobacter in the Nip root microbiota was less abundant in the root microbiota of all these mutants, and this contributed the most to the community differences between most mutants and Nip. Metagenomic sequencing revealed that flr7 increases aerobic respiration and decreases anaerobic respiration in the root microbiome. Finally, we showed that a representative Anaeromyxobacter strain improved submergence tolerance in rice via FLR7. Collectively, our findings indicate that FLR7 mediates changes in rhizosphere oxygen levels and enriches the beneficial dominant genus Anaeromyxobacter and may provide insights for developing plant flood prevention strategies via the use of environment-specific functional soil microorganisms.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139568355","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
Climate acts as an environmental filter to plant pathogens 气候是植物病原体的环境过滤器
Pub Date : 2024-01-24 DOI: 10.1093/ismejo/wrae010
Maria Caballol, Miguel Ángel Redondo, Núria Catalán, Tamara Corcobado, Thomas Jung, Benoît Marçais, Ivan Milenković, Miguel Nemesio-Gorriz, Jan Stenlid, Jonàs Oliva
Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at >250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures.
气候影响着菌根真菌和内生真菌等植物相关微生物的分布。然而,人们对气候在植物病原体群落集结中的作用了解较少。在这里,我们沿着从西班牙到瑞典北部的纬度梯度和从西班牙比利牛斯山脉到低地地区的海拔梯度,在 250 个地点探索了气候在噬菌体群落组合中的作用。通过对河流滤液进行 ITS 测序检测了群落。中介分析支持气候在噬菌体生物地理学中的作用,并排除了地理或树木多样性等其他环境因素。功能多样性和物种多样性的比较表明,在欧洲,环境过滤作用比竞争排斥作用更重要。温度和降水在梯度的不同极端起着环境过滤的作用。在北部地区,冬季气温对噬菌体群落的集结起到了环境过滤的作用,选择了适应在最低气温下生存的物种。在南纬地区,炎热干燥的气候是主要的环境过滤器,导致群落以具有厚卵孢子壁、生长最适温度高和生长最高温度限制高的耐旱噬菌体物种为主。通过采用群落生态学方法,我们表明欧洲植物病原菌的建立主要受到低温的限制。
{"title":"Climate acts as an environmental filter to plant pathogens","authors":"Maria Caballol, Miguel Ángel Redondo, Núria Catalán, Tamara Corcobado, Thomas Jung, Benoît Marçais, Ivan Milenković, Miguel Nemesio-Gorriz, Jan Stenlid, Jonàs Oliva","doi":"10.1093/ismejo/wrae010","DOIUrl":"https://doi.org/10.1093/ismejo/wrae010","url":null,"abstract":"Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at >250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139568356","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
The constructive black queen hypothesis: new functions can evolve under conditions favouring gene loss 建设性黑皇后假说:新功能可以在有利于基因丢失的条件下进化
Pub Date : 2024-01-24 DOI: 10.1093/ismejo/wrae011
Nobuto Takeuchi, Matthew S Fullmer, Danielle J Maddock, Anthony M Poole
Duplication is a major route for emergence of new gene functions. However, emergence of new gene function via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because under an emerging Black Queen dynamic there is high gene redundancy, spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede fixation of new function. Our results expand the mechanisms by which new gene function can emerge in prokaryotic systems.
复制是新基因功能出现的主要途径。然而,在原核生物中,通过这一途径出现的新基因功能可能会减少,因为冗余基因通常会被迅速清除。因此,在基因组紧凑、精简的类群中,通过复制和分化出现新功能似乎具有挑战性。在 "黑皇后"(Black Queen)动力学中,还有一种压力会导致基因丢失,因为失去生产公共物品能力的作弊者可以从邻近的生产者那里获得这种物品。我们提出,黑皇后动态有利于新功能的出现,因为在新出现的黑皇后动态下,基因冗余度很高,分布在相互作用的细胞群落中。通过计算建模,我们证明了新的基因功能可以在黑皇后动态下出现。即使存在因复制率低而导致的删除偏差,以及因携带基因座的高成本而导致的对冗余基因拷贝的选择,这一结果也是成立的。然而,当公共产品的生产成本很高时,黑皇后动力学就会阻碍新功能的固定。我们的研究结果拓展了原核生物系统中新基因功能出现的机制。
{"title":"The constructive black queen hypothesis: new functions can evolve under conditions favouring gene loss","authors":"Nobuto Takeuchi, Matthew S Fullmer, Danielle J Maddock, Anthony M Poole","doi":"10.1093/ismejo/wrae011","DOIUrl":"https://doi.org/10.1093/ismejo/wrae011","url":null,"abstract":"Duplication is a major route for emergence of new gene functions. However, emergence of new gene function via this route may be reduced in prokaryotes, as redundant genes are often rapidly purged. In lineages with compact, streamlined genomes, it thus appears challenging for novel function to emerge via duplication and divergence. A further pressure contributing to gene loss occurs under Black Queen dynamics, as cheaters that lose the capacity to produce a public good can instead acquire it from neighbouring producers. We propose that Black Queen dynamics can favour the emergence of new function because under an emerging Black Queen dynamic there is high gene redundancy, spread across a community of interacting cells. Using computational modelling, we demonstrate that new gene functions can emerge under Black Queen dynamics. This result holds even if there is deletion bias due to low duplication rates and selection against redundant gene copies resulting from the high cost associated with carrying a locus. However, when the public good production costs are high, Black Queen dynamics impede fixation of new function. Our results expand the mechanisms by which new gene function can emerge in prokaryotic systems.","PeriodicalId":516554,"journal":{"name":"The ISME Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139568358","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
期刊
The ISME Journal
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1