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Hidden syndinian and perkinsid infections in dinoflagellate hosts revealed by single-cell transcriptomics 通过单细胞转录组学揭示甲藻寄主中隐藏的联合体和包囊感染
Pub Date : 2024-09-26 DOI: 10.1093/ismejo/wrae188
Elizabeth C Cooney, Brian S Leander, Patrick J Keeling
Free-living core dinoflagellates are commonly infected by members of two parasitic clades that are themselves closely related to dinoflagellates, the marine alveolates and perkinsids. These parasites are abundant and ecologically important, but most species have been difficult to observe directly or cultivate, so our knowledge of them is usually restricted to environmental 18S rRNA gene sequences, and genome-scale molecular data are not available for most species. Here, we report numerous syndinian parasites and one parasite that is sister to all known perkinsids from isolated single cells of diverse, free-living dinoflagellates. Of the 14 infected host cells collected, only five were noticeably infected via light microscopy at the time of collection. Single-cell transcriptome sequencing yielded relatively high transcriptomic coverage for parasites as well as their hosts. Host and parasite homologs were distinguished phylogenetically allowing us to infer a robust phylogenomic tree based on 198 genes. The tree showed one parasite belongs to an undescribed lineage that is sister to perkinsids, whereas the remainder are members of the syndinian clade. Close relatives of all these parasites have been observed in 18S rRNA gene surveys, but until now none had been linked to a specific host. These findings illustrate the efficacy of single-cell isolation and transcriptome sequencing as a strategy for gaining deeper insights into the evolutionary history and host relationships of hidden single-celled parasites.
自由生活的核心甲藻通常会受到两个寄生支系成员的感染,这两个支系本身与甲藻有密切的亲缘关系,即海洋肺泡虫和perkinsids。这些寄生虫种类繁多,具有重要的生态意义,但大多数种类难以直接观察或培养,因此我们对它们的了解通常仅限于环境中的 18S rRNA 基因序列,而且大多数种类都没有基因组尺度的分子数据。在这里,我们报告了从各种自由生活的甲藻的分离单细胞中发现的大量辛迪宁寄生虫和一种与所有已知的周基寄生虫都是姊妹的寄生虫。在收集到的 14 个受感染的宿主细胞中,只有 5 个在收集时通过光学显微镜观察到明显的感染。单细胞转录组测序结果显示,寄生虫及其宿主的转录组覆盖率相对较高。宿主和寄生虫的同源物在系统发生学上被区分开来,使我们能够根据 198 个基因推断出一个稳健的系统发生树。这棵树显示,有一种寄生虫属于一个未被描述的世系,它是perkinsids的姊妹,而其余的寄生虫则是syndinian支系的成员。在 18S rRNA 基因调查中观察到了所有这些寄生虫的近亲,但直到现在还没有一种寄生虫与特定宿主有关联。这些发现说明,单细胞分离和转录组测序是深入了解隐蔽单细胞寄生虫进化史和宿主关系的有效策略。
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引用次数: 0
Biofilms inactivate the free-living stage of Batrachochytrium dendrobatidis, the most destructive pathogen for vertebrate diversity 生物膜可使对脊椎动物多样性最具破坏性的病原体--树枝蝙蝠蚤(Batrachochytrium dendrobatidis)的自由生活阶段失活
Pub Date : 2024-09-26 DOI: 10.1093/ismejo/wrae189
Hugo Sentenac, Dirk S Schmeller, Solène Caubet, Adélaïde Carsin, Rémi Guillet, Jessica Ferriol, Joséphine Leflaive, Adeline Loyau
Emerging infectious diseases threaten biodiversity and human health. Many emerging pathogens have aquatic life stages and all immersed substrates have biofilms on their surface, i.e., communities of microorganisms producing a gelatinous matrix. However, the outcome of the interactions between environmental biofilms and pathogens is poorly understood. Here we demonstrate that biofilms reduce the survival of the most impactful pathogen for vertebrate diversity, the invasive chytrid fungus Batrachochytrium dendrobatidis. Effects on its zoospores varied with biofilm composition in controlled settings and biofilm compositional variation also coincided with divergent impacts of chytridiomycosis on amphibian populations in nature. Our results suggest that biofilms form a biotic component of ecosystem resistance to Batrachochytrium dendrobatidis by reducing environmental transmission, and that they could be used to develop nature-based technologies to limit the impacts and spread of this invasive chytrid fungus. Our study warrants further research into the interactions between environmental biofilms and pathogenic and/or invasive micro-organisms.
新出现的传染病威胁着生物多样性和人类健康。许多新出现的病原体都有水生生活阶段,所有浸泡的基质表面都有生物膜,即产生胶状基质的微生物群落。然而,人们对环境生物膜与病原体之间相互作用的结果却知之甚少。在这里,我们证明了生物膜会降低对脊椎动物多样性影响最大的病原体--入侵性糜烂真菌蝙蝠噬菌体(Batrachochytrium dendrobatidis)的存活率。在受控环境中,生物膜的成分不同,对其孢子的影响也不同,而生物膜成分的变化也与糜烂性真菌病在自然界中对两栖动物种群的不同影响相吻合。我们的研究结果表明,生物膜通过减少环境传播,形成了生态系统抵抗蝙蝠疫霉菌的一个生物组成部分,生物膜可用于开发基于自然的技术,以限制这种入侵性糜烂真菌的影响和传播。我们的研究值得进一步研究环境生物膜与病原体和/或入侵微生物之间的相互作用。
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引用次数: 0
Pathogen non-planktonic phases within the urinary tract impact early infection and resistance evolution 病原体在泌尿道内的非浮游阶段对早期感染和抗药性进化的影响
Pub Date : 2024-09-26 DOI: 10.1093/ismejo/wrae191
Michael Raatz, Amanda de Azevedo-Lopes, Karolina Drabik, Arne Traulsen, Bartlomiej Waclaw
Treatment of urinary tract infections and the prevention of their recurrence is a pressing global health problem. In a urinary infection, pathogenic bacteria not only reside in the bladder lumen but also attach to and invade the bladder tissue. Planktonic, attached, and intracellular bacteria face different selection pressures from physiological processes such as micturition, immune response, and antibiotic treatment. Here, we use a mathematical model of the initial phase of infection to unravel the effects of these different selective pressures on the ecological and evolutionary dynamics of urinary infections. We explicitly model planktonic bacteria in the bladder lumen, bacteria attached to the bladder wall, and bacteria that have invaded the epithelial cells of the bladder. We find that the presence of non-planktonic bacteria substantially increases the risk of infection establishment and affects evolutionary trajectories leading to resistance during antibiotic treatment. We also show that competitive inoculation with a fast-growing non-pathogenic strain can reduce the pathogen load and increase the efficacy of an antibiotic, but only if the antibiotic is used in moderation. Our study shows that including different compartments is essential to create more realistic models of urinary infections, which may help guide new treatment strategies.
治疗尿路感染和预防复发是一个紧迫的全球性健康问题。在泌尿系统感染中,致病细菌不仅存在于膀胱腔内,而且还会附着和侵入膀胱组织。浮游细菌、附着细菌和细胞内细菌面临着来自排尿、免疫反应和抗生素治疗等生理过程的不同选择压力。在这里,我们利用感染初始阶段的数学模型来揭示这些不同的选择压力对泌尿感染的生态和进化动态的影响。我们明确地模拟了膀胱腔内的浮游细菌、附着在膀胱壁上的细菌以及侵入膀胱上皮细胞的细菌。我们发现,非浮游细菌的存在大大增加了感染的风险,并影响了抗生素治疗过程中产生抗药性的进化轨迹。我们还发现,竞争性接种快速生长的非致病性菌株可以降低病原体负荷并提高抗生素的疗效,但前提是抗生素必须适度使用。我们的研究表明,要创建更逼真的泌尿感染模型,必须包括不同的分区,这可能有助于指导新的治疗策略。
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引用次数: 0
Idiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy 嗜热蓝藻Synechococcus在光营养极限下的同源基因组进化
Pub Date : 2024-09-25 DOI: 10.1093/ismejo/wrae184
C Logan Pierpont, Jacob J Baroch, Matthew J Church, Scott R Miller
Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria.
与中嗜热微生物相比,嗜热微生物的细胞和基因组较小,水平获得的基因比例较高,核苷酸和氨基酸组成特征独特。在这里,我们采用了一种综合方法来研究 Synechococcus A/B 蓝藻(包括地球上最耐热的光养菌)嗜热性的这些明显相关因素。系统发生组学证实了不同耐热生态型的独特起源,生态上不同但相互重叠的种群之间持续的低水平基因流动塑造了这些地热梯度的表型特征分布。耐热性更强的菌株基因组确实更小,但基因组的缩小与群落丰富度和代谢多样性的降低有关,而与细胞大小无关。在Synechococcus进化过程中,横向基因转移只发挥了有限的作用,但耐热性最强的菌株获得了一种Thermus tRNA修饰酶,这种酶可能会稳定高温下的翻译。虽然核苷酸碱基组成与耐热性无关,但我们发现在最高温度下,天冬氨酸普遍被谷氨酸取代,氨基酸组成也发生了巨大变化,这与之前的预测大相径庭。我们的结论是,Synechococcus A/B基因组的多样化在很大程度上不符合温度适应的标准观点。此外,与耐热性较差的品系相比,耐热性最强的品系的碳固定比光合氧进化更耐热。这表明,在这些细菌的温度适应过程中,光反应过程中产生的还原力更多地流向二氧化碳以外的电子汇。
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引用次数: 0
Global freshwater distribution of Telonemia protists. Telonemia 原生动物的全球淡水分布。
Pub Date : 2024-09-20 DOI: 10.1093/ismejo/wrae177
Roudaina Boukheloua,Indranil Mukherjee,Hongjae Park,Karel Šimek,Vojtěch Kasalický,Maxon Ngochera,Hans-Peter Grossart,Antonio Picazo-Mozo,Antonio Camacho,Pedro J Cabello-Yeves,Francisco Rodriguez-Valera,Cristiana Callieri,Adrian-Stefan Andrei,Jakob Pernthaler,Thomas Posch,Albin Alfreider,Ruben Sommaruga,Martin W Hahn,Bettina Sonntag,Purificacion Lopez-Garcia,David Moreira,Ludwig Jardillier,Cécile Lepère,Corinne Biderre-Petit,Anna Bednarska,Mirosław Ślusarczyk,Viktor R Tóth,Horia L Banciu,Konstantinos Kormas,Sandi Orlic,Danijela Šantić,Gerard Muyzer,Daniel P R Herlemann,Helen Tammert,Stefan Bertilsson,Silke Langenheder,Thomas Zechmeister,Nico Salmaso,Nicola Storelli,Camilla Capelli,Fabio Lepori,Vojtěch Lanta,Helena Henriques Vieira,Fran Kostanjšek,Kateřina Kabeláčová,Maria-Cecilia Chiriac,Markus Haber,Tanja Shabarova,Clafy Fernandes,Pavel Rychtecký,Petr Znachor,Tiberiu Szőke-Nagy,Paul Layoun,Hon Lun Wong,Vinicius Silva Kavagutti,Paul-Adrian Bulzu,Michaela M Salcher,Kasia Piwosz,Rohit Ghai
Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remains unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analysed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.
Telonemia 是已发现的最古老的海洋原生生物之一,在其历史的大部分时间里,一直被认为是一个独特的非定居系。如今,它们在进化上与 SAR 超群(Stramenopiles、Alveolates 和 Rhizaria)的亲缘关系已得到牢固确立。然而,它们的生态分布以及作为自然界捕食性鞭毛虫的重要性(尤其是在淡水食物网中)仍不清楚。为了揭示淡水生境中 Telonemia 门的分布和多样性,我们研究了来自世界各地的一千多个淡水元基因组。此外,为了直接量化绝对丰度,我们使用催化报告沉积-荧光原位杂交(CARD-FISH)技术分析了来自 97 个湖泊和水库的 407 份样本。我们从来自不同生境的数百个元基因组样本中恢复了 Telonemia 18S rRNA 基因序列,这表明该菌门分布于全球。然而,即使进行了如此广泛的取样,我们的系统发育分析也没有发现任何新的主要支系,这表明目前的分子调查还接近于捕捉到该门类的全部多样性。我们观察到,CARD-FISH 分析与元基因组对丰度的估计之间存在极好的一致性。这两种方法都表明,浅水湖泊中基本上没有 Telonemia,它们更喜欢栖息在北半球湖泊和水库较冷的下盐层中,在那里它们经常大量繁殖,数量达到异养鞭毛虫总数的 10-20%,成为淡水食物网中重要的捕食性鞭毛虫。
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引用次数: 0
Drivers and consequences of microbial community coalescence 微生物群落凝聚的驱动因素和后果
Pub Date : 2024-09-17 DOI: 10.1093/ismejo/wrae179
Xipeng Liu, Joana Falcão Salles
Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.
微生物群落在不同的生态系统中正经历着前所未有的分散和融合,从而对微生物群落和生态系统动态产生了深远而普遍的影响。这篇综述深入探讨了群落凝聚现象,从生态学角度概述了群落凝聚的四个步骤,并阐明了群落聚集过程中的内在联系。我们研究了驱动群落凝聚的关键机制,尤其侧重于阐明源微生物群落和常驻微生物群落的命运及其对生态系统的影响。最后,我们提出了一些建议,为这一快速发展领域的研究人员提供指导,帮助他们更深入地了解微生物群落凝聚的生态影响。
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引用次数: 0
Convergence of gut phage communities but not bacterial communities following wild mouse bacteriophage transplantation into captive house mice 将野生小鼠噬菌体移植到圈养家鼠体内后,肠道噬菌体群落趋同,而细菌群落不趋同
Pub Date : 2024-09-14 DOI: 10.1093/ismejo/wrae178
Dagmar Čížková, Pavel Payne, Anna Bryjová, Ľudovít Ďureje, Jaroslav Piálek, Jakub Kreisinger
Bacteriophages are abundant components of vertebrate gut microbial communities, impacting bacteriome dynamics, evolution, and directly interacting with the superhost. However, knowledge about gut phageomes and their interaction with bacteriomes in vertebrates under natural conditions is limited to humans and non-human primates. Widely used specific pathogen-free (SPF) mouse models of host-microbiota interactions have altered gut bacteriomes compared to wild mice, and data on phageomes from wild or other non-SPF mice are lacking. We demonstrate divergent gut phageomes and bacteriomes in wild and captive non-SPF mice, with wild mice phageomes exhibiting higher alpha-diversity and interindividual variability. In both groups, phageome and bacteriome structuring mirrored each other, correlating at the individual level. Re-analysis of previous data from phageomes of SPF mice revealed their enrichment in Suoliviridae crAss-like phages compared to our non-SPF mice. Disrupted bacteriomes in mouse models can be treated by transplanting healthy phageomes, but the effects of phageome transplants on healthy adult gut microbiota are still unknown. We show that experimental transplantation of phageomes from wild to captive mice did not cause major shifts in recipient phageomes. However, the convergence of recipient-to-donor phageomes confirmed that wild phages can integrate into recipient communities. The differences in the subset of integrated phages between the two recipient mouse strains illustrate the context-dependent effects of phage transplantation. The transplantation did not impact recipient gut bacteriomes. This resilience of healthy adult gut microbiomes to the intervention has implications for phage allotransplantation safety.
噬菌体是脊椎动物肠道微生物群落的重要组成部分,影响着细菌组的动态和进化,并直接与超级宿主相互作用。然而,关于自然条件下脊椎动物肠道噬菌体及其与细菌群相互作用的知识仅限于人类和非人灵长类动物。与野生小鼠相比,广泛使用的无特定病原体(SPF)小鼠宿主-微生物群相互作用模型的肠道细菌组发生了改变,而野生或其他非 SPF 小鼠的噬菌体数据却很缺乏。我们证明野生小鼠和人工饲养的非SPF小鼠的肠道噬菌体和细菌组存在差异,野生小鼠的噬菌体表现出更高的α多样性和个体间变异性。在这两组小鼠中,噬菌体组和细菌组的结构相互映照,在个体水平上相互关联。对 SPF 小鼠噬菌体组的先前数据进行重新分析后发现,与非 SPF 小鼠相比,SPF 小鼠富含 Suoliviridae crAss-like 噬菌体。小鼠模型中紊乱的细菌群可以通过移植健康的噬菌体来治疗,但噬菌体移植对健康成人肠道微生物群的影响仍然未知。我们的研究表明,将野生小鼠的噬菌体移植到人工饲养的小鼠体内不会导致受体噬菌体发生重大变化。然而,受体与供体噬菌体的融合证实了野生噬菌体可以整合到受体群落中。两个受体小鼠品系之间整合噬菌体子集的差异说明了噬菌体移植的影响取决于环境。移植对受体肠道细菌群没有影响。健康的成年肠道微生物组对干预的这种恢复能力对噬菌体异种移植的安全性具有重要意义。
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引用次数: 0
Oxidation of sulfur, hydrogen, and iron by metabolically versatile Hydrogenovibrio from deep sea hydrothermal vents 深海热液喷口代谢多能的氢弧菌对硫、氢和铁的氧化作用
Pub Date : 2024-09-12 DOI: 10.1093/ismejo/wrae173
Katja Laufer-Meiser, Malik Alawi, Stefanie Böhnke, Claus-Henning Solterbeck, Jana Schloesser, Axel Schippers, Philipp Dirksen, Thomas Brüser, Susann Henkel, Janina Fuss, Mirjam Perner
Chemolithoautotrophic Hydrogenovibrio are ubiquitous and abundant at hydrothermal vents. They can oxidize sulfur, hydrogen or iron, but none are known to use all three energy sources. This ability though would be advantageous in vents hallmarked by highly dynamic environmental conditions. We isolated three Hydrogenovibrio strains from vents along the Indian Ridge, which grow on all three electron donors. We present transcriptomic data from strains grown on iron, hydrogen or thiosulfate with respective oxidation and autotrophic CO2 fixation rates, RubisCO activity, SEM, and EDX. Maximum estimates of one strain’s oxidation potential were 10, 24, and 952 mmol for iron, hydrogen and thiosulfate oxidation and 0.3, 1, and 84 mmol CO2 fixation, respectively, per vent per hour indicating their relevance for element cycling in-situ. Several genes were up- or downregulated depending on the inorganic electron donor provided. Although no known genes of iron-oxidation were detected, upregulated transcripts suggested iron-acquisition and so far unknown iron-oxidation-pathways.
在热液喷口,化学溶解自养型氢弧菌无处不在,数量也很多。它们能氧化硫、氢或铁,但没有一种能同时利用这三种能源。不过,这种能力在以高度动态的环境条件为特征的喷口中是非常有利的。我们从印度洋海脊沿岸的喷口中分离出了三种氢弧菌菌株,它们可以利用所有三种电子供体生长。我们展示了生长在铁、氢或硫代硫酸盐上的菌株的转录组数据,以及它们各自的氧化率和自养二氧化碳固定率、RubisCO 活性、扫描电镜和 EDX。铁、氢和硫代硫酸氧化作用对一株菌株氧化潜能的最大估计值分别为 10、24 和 952 毫摩尔,每通风口每小时的二氧化碳固定率分别为 0.3、1 和 84 毫摩尔,这表明它们与原位元素循环有关。根据所提供的无机电子供体的不同,一些基因上调或下调。虽然没有检测到已知的铁氧化基因,但上调的转录本表明存在铁获取和迄今未知的铁氧化途径。
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引用次数: 0
Chemolithoautotrophic bacteria flourish at dark water-ice interfaces of an emerged Arctic cold seep. 化学自养型细菌在新出现的北极冷渗漏的暗水冰界面上大量繁殖。
Pub Date : 2024-09-12 DOI: 10.1093/ismejo/wrae170
Lisa-Marie Delpech,Alexander T Tveit,Andrew J Hodson,Kevin P Hand,Dimitri Kalenitchenko
Below their ice shells, icy moons may offer a source of chemical energy that could support microbial life in the absence of light. In the Arctic, past and present glacial retreat leads to isostatic uplift of sediments through which cold and methane-saturated groundwater travels. This fluid reaches the surface and freezes as hill-shaped icings during winter, producing dark ice-water interfaces above water ponds containing chemical energy sources. In one such system characterized by elevated methane concentrations - the Lagoon Pingo in Adventdalen, Svalbard (~10 mg/L CH4, <0.3 mg/L O2, -0.25°C, pH 7.9), we studied amplicons of the bacterial and archaeal (microbial) 16S rRNA gene and transcripts in the water pond and overlaying ice. We show that active chemolithoautotrophic sulfur-oxidizing microorganisms (Sulfurimonas, Thiomicrorhabdus) dominated a niche at the bottom of the ice in contact with the anoxic water reservoir. There, the growing ice offers surfaces interfacing with water, and hosts favorable physico-chemical conditions for sulfide oxidation. Detection of anaerobic methanotrophs further suggests that the ice led to a steady-state dark and cold methane sink under the ice throughout winter, in two steps: first methane is oxidized to carbon dioxide and sulfates concomitantly reduced to sulfides by the activity of ANME-1a and SEEP-SRB1 consortia, in a second time energy from sulfides is used by sulfur- oxidizing microorganisms to fix carbon dioxide into organic carbon. Our results underline ice- covered and dark ecosystems as a hitherto overlooked oasis of microbial life and emphasize the need to study microbial communities in icy habitats.
冰卫星的冰壳下可能蕴藏着化学能,可以在没有光的情况下支持微生物生命。在北极地区,过去和现在的冰川退缩导致沉积物等静力抬升,寒冷和甲烷饱和的地下水流经这些沉积物。这些流体到达地表后,在冬季冻结成山丘状的冰层,在含有化学能源的水塘上方形成黑暗的冰水界面。在这样一个以甲烷浓度升高为特征的系统中--斯瓦尔巴群岛 Adventdalen 的 Lagoon Pingo(约 10 mg/L CH4,<0.3 mg/L O2,-0.25°C,pH 值 7.9),我们研究了水塘和覆冰中细菌和古生物(微生物)16S rRNA 基因的扩增子和转录本。我们发现,活跃的化石自养型硫氧化微生物(Sulfurimonas、Thiomicrorhabdus)在与缺氧水池接触的冰层底部占据了一席之地。在那里,生长的冰提供了与水接触的表面,并为硫化物氧化提供了有利的物理化学条件。厌氧甲烷营养体的检测进一步表明,整个冬季,冰层导致了冰下稳态黑暗和寒冷的甲烷汇,分为两个步骤:首先,甲烷被氧化成二氧化碳,硫酸盐在 ANME-1a 和 SEEP-SRB1 复合体的作用下同时还原成硫化物;其次,硫化物的能量被硫氧化微生物利用,将二氧化碳固定为有机碳。我们的研究结果突出表明,冰雪覆盖的黑暗生态系统是迄今为止被忽视的微生物生命绿洲,并强调了研究冰雪栖息地微生物群落的必要性。
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引用次数: 0
Fitness factors impacting survival of a subsurface bacterium in contaminated groundwater 影响地下细菌在受污染地下水中存活的适宜性因素
Pub Date : 2024-09-12 DOI: 10.1093/ismejo/wrae176
Michael P Thorgersen, Jennifer L Goff, Valentine V Trotter, Farris L Poole, Adam P Arkin, Adam M Deutschbauer, Michael W W Adams
Many factors contribute to the ability of a microbial species to persist when encountering complexly contaminated environments including time of exposure, the nature and concentration of contaminants, availability of nutritional resources, and possession of a combination of appropriate molecular mechanisms needed for survival. Herein we sought to identify genes that are most important for survival of Gram-negative Enterobacteriaceae in contaminated groundwater environments containing high concentrations of nitrate and metals using the metal-tolerant Oak Ridge Reservation (ORR) isolate, Pantoea sp. MT58 (MT58). Survival fitness experiments in which a randomly barcoded transposon insertion (RB-TnSeq) library of MT58 was exposed directly to contaminated ORR groundwater samples from across a nitrate and mixed metal contamination plume were used to identify genes important for survival with increasing exposure times and concentrations of contaminants, and availability of a carbon source. Genes involved in controlling and using carbon, encoding transcriptional regulators, and related to Gram-negative outer membrane processes were among those found to be important for survival in contaminated ORR groundwater. A comparative genomics analysis of 75 Pantoea genus strains allowed us to further separate the survival determinants into core and non-core genes in the Pantoea pangenome, revealing insights into the survival of subsurface microorganisms during contaminant plume intrusion.
微生物物种在遇到复杂的污染环境时能否存活取决于很多因素,包括暴露时间、污染物的性质和浓度、营养资源的可用性以及是否拥有生存所需的适当分子机制组合。在此,我们试图利用耐金属的橡树岭保护区(ORR)分离菌泛酸菌 MT58(MT58),找出对革兰氏阴性肠杆菌科细菌在含有高浓度硝酸盐和金属的污染地下水环境中生存最重要的基因。通过将 MT58 的随机条形码转座子插入(RB-TnSeq)文库直接暴露于来自硝酸盐和混合金属污染羽流的受污染 ORR 地下水样本的生存适应性实验,确定了随着暴露时间和污染物浓度以及碳源可用性的增加,对生存有重要影响的基因。研究发现,在受污染的 ORR 地下水中,参与控制和使用碳、编码转录调节因子以及与革兰氏阴性菌外膜过程有关的基因对存活非常重要。通过对 75 株盘尾丝菌属菌株进行比较基因组学分析,我们进一步将盘尾丝菌泛基因组中的生存决定因素分为核心基因和非核心基因,从而揭示了污染物羽流入侵期间地下微生物的生存情况。
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