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Coastal bacteria and protists assimilate viral carbon and nitrogen 沿海细菌和原生生物吸收病毒的碳和氮
Pub Date : 2024-11-13 DOI: 10.1093/ismejo/wrae231
Joaquín Martínez Martínez, David Talmy, Jeffrey A Kimbrel, Peter K Weber, Xavier Mayali
Free viruses are the most abundant type of biological particles in the biosphere, but the lack of quantitative knowledge about their consumption by heterotrophic protists and bacterial degradation has hindered the inclusion of virovory in biogeochemical models. Using isotope-labeled viruses added to three independent microcosm experiments with natural microbial communities followed by isotope measurements with single-cell resolution and flow cytometry, we quantified the flux of viral C and N into virovorous protists and bacteria and compared the loss of viruses due to abiotic vs biotic factors. We found that some protists can obtain most of their C and N requirements from viral particles and that viral C and N get incorporated into bacterial biomass. We found that bacteria and protists were responsible for increasing the daily removal rate of viruses by 33% to 85%, respectively, compared to abiotic processes alone. Our laboratory incubation experiments showed that abiotic processes removed roughly 50% of the viruses within a week, and adding biotic processes led to a removal of 83% to 91%. Our data provide direct evidence for the transfer of viral C and N back into the microbial loop through protist grazing and bacterial breakdown, representing a globally significant flux that needs to be investigated further to better understand and predictably model the C and N cycles of the hydrosphere.
游离病毒是生物圈中最丰富的生物颗粒类型,但由于缺乏有关异养原生生物消耗病毒和细菌降解病毒的定量知识,将病毒纳入生物地球化学模型的工作受到了阻碍。通过在三个独立的自然微生物群落微宇宙实验中添加同位素标记的病毒,然后利用单细胞分辨率和流式细胞仪进行同位素测量,我们量化了病毒 C 和 N 进入食病毒原生动物和细菌的通量,并比较了非生物因素和生物因素造成的病毒损失。我们发现,一些原生动物可以从病毒颗粒中获得其所需的大部分 C 和 N,而病毒 C 和 N 则会融入细菌的生物量中。我们发现,与单独的非生物过程相比,细菌和原生生物可使病毒的日清除率分别提高 33% 至 85%。我们的实验室培养实验表明,非生物过程在一周内清除了大约 50%的病毒,而加入生物过程后,病毒清除率提高了 83% 至 91%。我们的数据提供了直接证据,证明病毒的碳和氮通过原生动物的捕食和细菌的分解又回到了微生物循环中,这是一个全球性的重要通量,需要进一步研究,以更好地理解和预测水圈的碳和氮循环模型。
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引用次数: 0
Pathobiont and symbiont contribute to microbiota homeostasis through Malpighian tubules-gut countercurrent flow in Bactrocera dorsalis 病原生物和共生生物通过马氏管-肠道逆流对背鳍双壳类动物的微生物群平衡做出贡献
Pub Date : 2024-11-12 DOI: 10.1093/ismejo/wrae221
Yanning Liu, Rengang Luo, Shuai Bai, Bruno Lemaitre, Hongyu Zhang, Xiaoxue Li
Host-gut microbiota interactions are more complex than good or bad. Both gut symbiotic bacteria and pathobionts can provide essential functions to their host in one scenario and yet be detrimental to host health in another. So, these gut-dwelling bacteria must be tightly controlled to avoid harmful effects on the host. However, how pathobionts and other symbiotic bacteria coordinate to establish a host immune defense system remains unclear. Here, using a Tephritidae fruit fly Bactrocera dorsalis, we report that both pathobionts and other gut symbiotic bacteria release tyramine, which is recognized by the host insects. These tyramines induce the formation of insect-conserved Malpighian tubules-gut countercurrent flow upon bacterial infection, which requires tyramine receptors and aquaporins. At the same time, pathobionts but not gut symbiotic bacteria induce the generation of reactive oxygen species, which are preserved by the countercurrent flow, promoting bacteria elimination through increasing gut peristalsis. More importantly, our results show that the Malpighian tubules-gut countercurrent flow maintains proper microbiota composition. Our work suggests a model where pathobiont-induced reactive oxygen species are preserved by Malpighian tubules-gut countercurrent flow involving both pathobionts and symbiotic bacteria. Furthermore, our work provides a Malpighian tubules-gut interaction that ensures efficient maintenance of the gut microbiota.
宿主与肠道微生物群的相互作用比好坏更复杂。在某种情况下,肠道共生细菌和病原菌都能为宿主提供必要的功能,但在另一种情况下,它们又会损害宿主的健康。因此,必须严格控制这些肠道细菌,以避免对宿主造成有害影响。然而,病原菌和其他共生细菌如何协调建立宿主免疫防御系统仍不清楚。在这里,我们利用栉水母科果蝇 Bactrocera dorsalis 报告说,病原菌和其他肠道共生细菌都会释放酪胺,宿主昆虫能识别酪胺。细菌感染后,这些酪胺会诱导形成昆虫保留的马尔皮希安小管-肠道逆流,这需要酪胺受体和水汽素。与此同时,病原菌而非肠道共生细菌会诱导产生活性氧,这些活性氧被逆流保存下来,通过增加肠道蠕动来促进细菌的清除。更重要的是,我们的研究结果表明,马氏管-肠道逆流能维持适当的微生物群组成。我们的研究提出了一个模型,即病原体诱导的活性氧可通过马尔皮质小管-肠道逆流来保存,其中既包括病原体,也包括共生细菌。此外,我们的研究还提供了马氏管与肠道之间的相互作用,以确保肠道微生物群的有效维持。
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引用次数: 0
Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean 尿素同化和氧化支持暗海洋系统发育多样的微生物群落的活动
Pub Date : 2024-11-11 DOI: 10.1093/ismejo/wrae230
Nestor Arandia-Gorostidi, Alexander L Jaffe, Alma E Parada, Bennett J Kapili, Karen L Casciotti, Rebecca S R Salcedo, Chloé M J Baumas, Anne E Dekas
Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry. We find that on average 25% of deep-sea cells assimilated urea-derived N (60% of detectably active cells), and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrososphaeria (syn., Thaumarchaeota; likely for nitrification) as well as members of thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes estimated ureC within 10–46% of deep-sea cells around the world, with higher prevalence below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.
据推测,尿素是深海微生物重要的氮源和化学能来源;然而,目前还缺乏上深层海洋以下使用尿素的直接证据。在这里,我们利用元基因组学、硝化率以及纳米级二次离子质谱法进行的单细胞稳定同位素吸收测量,探索了太平洋东北部 50 米至 4000 米深处的尿素利用情况。我们发现,平均有 25% 的深海细胞同化了来自尿素的氮(占可检测到的活跃细胞的 60%),而且来自尿素的细胞特异性氮同化率高于来自铵的细胞特异性氮同化率。尿素浓度和同化率相对于铵的浓度和同化率在透光层以下普遍上升。在分析的两个地点中,我们在其中一个地点的所有深度都检测到了以氨和尿素为基础的硝化作用,这表明它们在中深层和深海区域具有支持化能自养的潜力。利用新生成的元基因组,我们发现编码尿素酶催化亚基的 ureC 基因存在于这一区域 39% 的深海细胞中,包括亚硝化细菌(Nitrososphaeria)(同义,Thaumarchaeota;可能用于硝化)以及其他 13 个门类的成员,如变形菌门、藻微菌门、植物菌门、亚硝化细菌门和绿藻门(可能用于同化)。对公共元基因组的分析估计,全球有 10-46% 的深海细胞中含有尿素C,光照区以下的细胞中含量更高,这表明全球深海微生物群广泛存在尿素。我们的研究结果表明,尿素是暗海中丰富多样的微生物的氮源,也是深海硝化作用的重要贡献者,因此也是化能自养的燃料。
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引用次数: 0
Microbiome science of human excrement composting 人类排泄物堆肥的微生物组科学
Pub Date : 2024-11-09 DOI: 10.1093/ismejo/wrae228
Jeff Meilander, J Gregory Caporaso
Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of human excrement (human feces and urine) stands as a significant concern. Over two billion people do not have access to adequate sanitation, signifying a global public health crisis. Composting is the microbial biotechnology aimed at cycling organic waste, including human excrement, for improved public health, agricultural productivity and safety, and environmental sustainability. Applications of modern microbiome -omics and related technologies have the capacity to support continued advances in composting science and praxis. In this article, we review literature focused on applications of microbiome technologies to study composting systems and reactions. The studies we survey generally fall into the categories of animal manure composting, biosolids composting, and human excrement composting. We review experiments utilizing microbiome technologies to investigate strategies for enhancing pathogen suppression and accelerating the biodegradation of organic matter. Additionally, we explore studies focused on the bioengineering potential of microbes as inoculants to facilitate degradation of toxins such as pharmaceuticals or per- and polyfluoroalkyl substances. The findings from these studies underscore the importance of advancing our understanding of composting processes through the integration of emerging microbiome -omics technologies. We conclude that work to-date has demonstrated exciting basic and applied science potential from studying compost microbiomes, with promising implications for enhancing global environmental sustainability and public health.
线性废物管理系统是不可持续的,会导致环境退化、经济不公平和健康差异。在人类活动造成的一系列环境挑战中,人类排泄物(人类粪便和尿液)的管理是一个令人严重关切的问题。超过 20 亿人无法获得适当的卫生设施,这意味着一场全球性的公共卫生危机。堆肥是一种微生物生物技术,旨在循环利用包括人类排泄物在内的有机废物,以改善公共卫生、提高农业生产率和安全性,并实现环境的可持续发展。现代微生物组学和相关技术的应用能够支持堆肥科学和实践的不断进步。在本文中,我们回顾了有关应用微生物组技术研究堆肥系统和反应的文献。我们调查的研究一般分为动物粪便堆肥、生物固体堆肥和人类排泄物堆肥三类。我们回顾了利用微生物组技术研究加强病原体抑制和加速有机物生物降解策略的实验。此外,我们还探讨了微生物作为接种物的生物工程潜力,以促进药物或全氟和多氟烷基物质等毒素的降解。这些研究结果强调了通过整合新兴微生物组-组学技术来促进我们对堆肥过程的理解的重要性。我们的结论是,迄今为止的工作表明,堆肥微生物组的研究具有令人兴奋的基础和应用科学潜力,对提高全球环境可持续性和公众健康具有重要意义。
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引用次数: 0
Aminolipids in bacterial membranes and the natural environment 细菌膜和自然环境中的氨基脂质
Pub Date : 2024-11-09 DOI: 10.1093/ismejo/wrae229
Shengwei Liu, Eleonora Silvano, Mingyu Li, Michaela Mausz, Branko Rihtman, Richard Guillonneau, Otto Geiger, David J Scanlan, Yin Chen
Our comprehension of membrane function has predominantly advanced through research on glycerophospholipids, also known as phosphoglycerides, which are glycerol phosphate-based lipids found across all three domains of life. However, in bacteria, a perplexing group of lipids distinct from glycerol phosphate-based ones also exists. These are amino acid-containing lipids that form an amide bond between an amino acid and a fatty acid. Subsequently, a second fatty acid becomes linked, often via the 3-hydroxy group on the first fatty acid. These amide-linked aminolipids have, as of now, been exclusively identified in bacteria. Several hydrophilic head groups have been discovered in these aminolipids including ornithine, glutamine, glycine, lysine, and more recently, a sulfur-containing non-proteinogenic amino acid cysteinolic acid. Here, we aim to review current advances in the genetics, biochemistry and function of these aminolipids as well as giving an ecological perspective. We provide evidence for their potential significance in the ecophysiology of all major microbiomes i.e. gut, soil and aquatic as well as highlighting their important roles in influencing biological interactions.
我们对膜功能的理解主要是通过对甘油磷脂(又称磷酸甘油脂)的研究取得的。然而,在细菌中,也存在一组不同于以磷酸甘油为基础的脂质,令人费解。这些脂质含有氨基酸,在氨基酸和脂肪酸之间形成酰胺键。随后,第二个脂肪酸通常通过第一个脂肪酸上的 3-羟基相连。到目前为止,这些酰胺连接的氨基脂只能在细菌中发现。在这些氨基脂中发现了几个亲水头基,包括鸟氨酸、谷氨酰胺、甘氨酸、赖氨酸以及最近发现的一种含硫非蛋白源氨基酸半胱氨醇酸。在这里,我们旨在回顾这些氨基脂质的遗传学、生物化学和功能方面的最新进展,并从生态学的角度进行分析。我们将提供证据,证明它们在所有主要微生物群(如肠道、土壤和水生微生物群)的生态生理学中的潜在意义,并强调它们在影响生物相互作用方面的重要作用。
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引用次数: 0
Isolate-anchored comparisons reveal evolutionary and functional differentiation across SAR86 marine bacteria 隔离锚定比较揭示了 SAR86 海洋细菌的进化和功能分化
Pub Date : 2024-11-09 DOI: 10.1093/ismejo/wrae227
Oscar Ramfelt, Kelle C Freel, Sarah J Tucker, Olivia D Nigro, Michael S Rappé
SAR86 is one of the most abundant groups of bacteria in the global surface ocean. However, since its discovery over 30 years ago, it has remained recalcitrant to isolation and many details regarding this group are still unknown. Here we report the cellular characteristics from the first SAR86 isolate brought into culture, Magnimaribacter mokuoloeensis strain HIMB1674, and use its closed genome in concert with over 700 environmental genomes to assess the phylogenomic and functional characteristics of this order-level lineage of marine Gammaproteobacteria. The SAR86 order Magnimaribacterales invest significant genomic resources into the capacity for $beta$-oxidation, which is present in most genomes in high gene copy numbers. This cyclical set of reactions appears to be fed by components of cell membranes that include lipids such as phosphatidylcholine, phosphatidylethanolamine, glycolipids, and sulfolipids. In addition to the widespread capacity to degrade the side chain of steroidal compounds via $beta$-oxidation, several SAR86 sublineages also appear able to fully degrade the steroid polycyclic ring structure as well as other aromatic, polycyclic, and heterocyclic molecules. Read recruitment from publicly available metagenomes reveals that the Magnimaribacterales compose up to 6% of the global surface ocean microbial community. Only a subset of genera drive these high relative abundances, with some more globally dominant and others restricted to specific oceanic regions. This study provides an unprecedented foundation through which to understand this highly abundant yet poorly understood lineage of marine bacteria, and charts a path to bring more representatives of this order into laboratory culture.
SAR86 是全球表层海洋中数量最多的细菌群之一。然而,自 30 多年前发现以来,它一直难以分离,有关该菌群的许多细节仍然未知。在此,我们报告了第一个分离培养的 SAR86 菌株 Magnimaribacter mokuoloeensis 菌株 HIMB1674 的细胞特征,并将其封闭基因组与 700 多个环境基因组结合使用,以评估这一海洋伽马蛋白杆菌纲的系统发生组和功能特征。SAR86 目 Magnimaribacterales 对 $beta$-oxidation 的能力投入了大量基因组资源,这种能力以高基因拷贝数存在于大多数基因组中。这一系列循环反应似乎是由细胞膜成分提供的,其中包括磷脂酰胆碱、磷脂酰乙醇胺、糖脂和硫脂等脂质。除了通过(beta)氧化作用降解类固醇化合物侧链的广泛能力外,一些 SAR86 亚系似乎还能完全降解类固醇多环环结构以及其他芳香族、多环和杂环分子。从公开的元基因组中进行的读取显示,木兰杆菌属(Magnimaribacterales)占全球表层海洋微生物群落的 6%。只有一小部分菌属驱动了这些高相对丰度,其中一些菌属在全球占主导地位,另一些则局限于特定的海洋区域。这项研究提供了一个前所未有的基础,通过这个基础,我们可以了解这一数量巨大但却鲜为人知的海洋细菌谱系,并为将更多的该谱系代表引入实验室培养指明了道路。
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引用次数: 0
Chronic exposure to polycyclic aromatic hydrocarbons alters skin virome composition and virus–host interactions 长期接触多环芳烃会改变皮肤病毒组的组成和病毒与宿主的相互作用
Pub Date : 2024-10-25 DOI: 10.1093/ismejo/wrae218
Shicong Du, Xinzhao Tong, Marcus H Y Leung, Richard J Betts, Anthony C Woo, Philippe Bastien, Namita Misra, Luc Aguilar, Cécile Clavaud, Patrick K H Lee
Exposure to polycyclic aromatic hydrocarbons (PAHs) in polluted air influences the composition of the skin microbiome, which in turn is associated with altered skin phenotypes. However, the interactions between PAH exposure and viromes are unclear. This study aims to elucidate how PAH exposure affects the composition and function of skin viruses, their role in shaping the metabolism of bacterial hosts, and the subsequent effects on skin phenotype. We analyzed metagenomes from cheek skin swabs collected from 124 Chinese women in our previous study and found that the viruses associated with the two microbiome cutotypes had distinct diversities, compositions, functions, and lifestyles following PAH exposure. Moreover, exposure to high concentrations of PAHs substantially increased interactions between viruses and certain biodegrading bacteria. Under high-PAH exposure, the viruses were enriched in xenobiotic degradation functions, and there was evidence suggesting that the insertion of bacteriophage-encoded auxiliary metabolic genes into hosts aids biodegradation. Under low-PAH exposure conditions, the interactions followed the “Piggyback-the-Winner” model, with Cutibacterium acnes being “winners,” whereas under high-PAH exposure, they followed the “Piggyback-the-Persistent” model, with biodegradation bacteria being “persistent.” These findings highlight the impact of air pollutants on skin bacteria and viruses, their interactions, and their modulation of skin health. Understanding these intricate relationships could provide insights for developing targeted strategies to maintain skin health in polluted environments, emphasizing the importance of mitigating pollutant exposure and harnessing the potential of viruses to help counteract the adverse effects.
暴露于污染空气中的多环芳烃(PAHs)会影响皮肤微生物组的组成,进而与皮肤表型的改变有关。然而,多环芳烃暴露与病毒组之间的相互作用尚不清楚。本研究旨在阐明多环芳烃暴露如何影响皮肤病毒的组成和功能、它们在塑造细菌宿主新陈代谢中的作用以及随后对皮肤表型的影响。我们分析了之前研究中从 124 名中国女性颊部皮肤拭子中采集的元基因组,发现在暴露于 PAH 后,与两种微生物组切型相关的病毒具有不同的多样性、组成、功能和生活方式。此外,暴露于高浓度多环芳烃大大增加了病毒与某些生物降解细菌之间的相互作用。在高PAH暴露条件下,病毒具有丰富的异生物降解功能,有证据表明,将噬菌体编码的辅助代谢基因插入宿主体内有助于生物降解。在低 PAH 暴露条件下,相互作用遵循 "捎带赢家 "模式,痤疮棒状杆菌是 "赢家",而在高 PAH 暴露条件下,相互作用遵循 "捎带持久 "模式,生物降解细菌是 "持久"。这些发现凸显了空气污染物对皮肤细菌和病毒的影响、它们之间的相互作用以及它们对皮肤健康的调节作用。了解这些错综复杂的关系可以为制定有针对性的策略提供见解,从而在污染环境中保持皮肤健康,这也强调了减少污染物暴露和利用病毒潜力帮助抵消不利影响的重要性。
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引用次数: 0
Metagenomic time-series reveals a western English Channel viral community dominated by members with strong seasonal signals 元基因组时间序列显示英吉利海峡西部病毒群落以具有强烈季节性信号的成员为主
Pub Date : 2024-10-23 DOI: 10.1093/ismejo/wrae216
Luis M Bolaños, Michelle Michelsen, Ben Temperton
Marine viruses are key players of ocean biogeochemistry, profoundly influencing microbial community ecology and evolution. Despite their importance, few studies have explored continuous inter-seasonal viral metagenomic time-series in marine environments. Viral dynamics are complex, influenced by multiple factors such as host population dynamics and environmental conditions. To disentangle the complexity of viral communities, we developed an unsupervised machine learning framework to classify viral contigs into "chronotypes" based on temporal abundance patterns. Analysing an inter-seasonal monthly time-series of surface viral metagenomes from the Western English Channel, we identified chronotypes and compared their functional and evolutionary profiles. Results revealed a consistent annual cycle with steep compositional changes from winter to summer and steadier transitions from summer to winter. Seasonal chronotypes were enriched in potential auxiliary metabolic genes of the ferrochelatases and 2OG-Fe(II) oxygenase orthologous groups compared to non-seasonal types. Chronotypes clustered into four groups based on their correlation profiles with environmental parameters, primarily driven by temperature and nutrients. Viral contigs exhibited a rapid turnover of polymorphisms, akin to Red Queen dynamics. However, within seasonal chronotypes, some sequences exhibited annual polymorphism recurrence, suggesting that a fraction of the seasonal viral populations evolve more slowly. Classification into chronotypes revealed viral genomic signatures linked to temporal patterns, likely reflecting metabolic adaptations to environmental fluctuations and host dynamics. This novel framework enables the identification of long-term trends in viral composition, environmental influences on genomic structure, and potential viral interactions.
海洋病毒是海洋生物地球化学的关键角色,对微生物群落生态学和进化有着深远的影响。尽管它们非常重要,但很少有研究探索海洋环境中连续的跨季节病毒元基因组时间序列。病毒的动态很复杂,受宿主种群动态和环境条件等多种因素的影响。为了揭示病毒群落的复杂性,我们开发了一种无监督机器学习框架,根据时间丰度模式将病毒序列分为 "时间型"。通过分析英吉利海峡西部地表病毒元基因组的跨季节月度时间序列,我们确定了年代型,并比较了它们的功能和进化特征。结果表明,从冬季到夏季,病毒的组成发生了急剧的变化,而从夏季到冬季,病毒的组成则发生了平稳的过渡。与非季节型相比,季节型富含铁螯合酶和 2OG-Fe(II) 加氧酶同源组的潜在辅助代谢基因。根据其与环境参数(主要由温度和养分驱动)的相关性,时间型可分为四组。病毒序列表现出快速的多态性更替,类似于红皇后动态。然而,在季节时序型中,一些序列表现出年度多态性重复,这表明一部分季节性病毒种群的进化速度较慢。对时间型的分类揭示了与时间模式相关的病毒基因组特征,这可能反映了新陈代谢对环境波动和宿主动态的适应。这种新颖的框架能够确定病毒组成的长期趋势、环境对基因组结构的影响以及潜在的病毒相互作用。
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引用次数: 0
Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement 受到经常性渗透干扰的极端嗜卤生物的生态成功主要是由同源物种替换驱动的
Pub Date : 2024-10-23 DOI: 10.1093/ismejo/wrae215
Esteban Bustos-Caparros, Tomeu Viver, Juan F Gago, Luis Miguel Rodriguez-Rojas, Janet K Hatt, Stephanus N Venter, Bernhard M Fuchs, Rudolf Amann, Rafael Bosch, Konstantinos T Konstantinidis, Ramon Rossello-Mora
To understand how extreme halophiles respond to recurrent disturbances, we challenged the communities thriving in salt-saturated (~36% salts) ~230 L brine mesocosms to repeated dilutions down to 13% (D13 mesocosm) or 20% (D20 mesocosm) salts each time mesocosms reached salt saturation due to evaporation (for 10 and 17 cycles, respectively) over 813 days. Depending on the magnitude of dilution, the most prevalent species, Haloquadratum walsbyi and Salinibacter ruber, either increased in dominance by replacing less competitive populations (for D20, moderate stress conditions), or severely decreased in abundance and were eventually replaced by other congeneric species better adapted to the higher osmotic stress (for D13, strong stress conditions). Congeneric species replacement was commonly observed within additional abundant genera in response to changes in environmental or biological conditions (e.g. phage predation) within the same system and under a controlled perturbation of a relevant environmental parameter. Therefore, a genus is an ecologically important level of diversity organization, not just a taxonomic rank, that persists in the environment based on congeneric species replacement due to relatively high functional overlap (gene sharing), with important consequences for the success of the lineage, and similar to the success of a species via strain-replacement. Further, our results showed that successful species were typically accompanied by the emergence of their own viral cohorts, whose intra-cohort diversity appeared to strongly covary with, and likely drive, the intra-host diversity. Collectively, our results show that brine communities are ecologically resilient and continuously adapting to changing environments by transitioning to alternative stable states.
为了了解极端嗜卤生物如何应对反复出现的干扰,我们在 813 天内,在盐饱和(~36% 盐分)~230 升盐水介观池中,每当介观池因蒸发而达到盐饱和时,我们都要将其中的群落反复稀释到 13%(D13 介观池)或 20%(D20 介观池)的盐分(分别为 10 个和 17 个周期)。根据稀释程度的不同,最普遍的物种 Haloquadratum walsbyi 和 Salinibacter ruber 要么通过取代竞争力较弱的种群(D20,中等胁迫条件下)而提高优势地位,要么数量严重减少,最终被更能适应较高渗透胁迫的其他同系物种取代(D13,强胁迫条件下)。在同一系统中,当环境或生物条件(如噬菌体捕食)发生变化时,在相关环境参数受控扰动的情况下,在其他丰度较高的属中通常会观察到同属物种的替换。因此,属是生态学上重要的多样性组织层次,而不仅仅是分类学上的等级,由于功能重叠(基因共享)程度相对较高,属在环境中基于同源物种替换而持续存在,这对种系的成功具有重要影响,与物种通过菌株替换而成功类似。此外,我们的研究结果表明,成功的物种通常伴随着它们自己的病毒群的出现,而病毒群内部的多样性似乎与宿主内部的多样性密切相关,并可能驱动宿主内部的多样性。总之,我们的研究结果表明,盐水群落具有生态弹性,并能通过过渡到其他稳定状态来不断适应不断变化的环境。
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引用次数: 0
Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles 拉格瑞纳甲虫重复水平获取拉格瑞纳共生体
Pub Date : 2024-10-23 DOI: 10.1093/ismejo/wrae211
Siddharth Uppal, Samantha C Waterworth, Alina Nick, Heiko Vogel, Laura V Flórez, Martin Kaltenpoth, Jason C Kwan
Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide, protecting the beetle’s eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster. However, we did not find evidence for host-symbiont co-diversification, or for monophyly of the lagriamide-producing symbionts. Instead, our analyses support a single ancestral acquisition of the gene cluster followed by at least four independent symbiont acquisitions and subsequent genome erosion in each lineage. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide gene cluster. Our results, therefore, reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by a high degree of specificity, and highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.
微生物共生体与多细胞生物的联系从表面联系到相互依存。在最古老的细胞内共生关系中,共生体具有排他性的垂直传播,共生伙伴经过数百万年的共同多样化。由于有效种群规模小、种群瓶颈频繁出现以及净化选择减少,这类共生体的基因组往往会减少。在这里,我们描述了在一组拉格瑞纳甲虫中,密切相关的防御性共生体的多次独立获取事件,以及随后的基因组侵蚀。之前在Lagria villosa甲虫中的研究发现,被基因组侵蚀的伯克霍尔德菌属共生体产生抗真菌化合物lagriamide,保护甲虫的卵和幼虫免受拮抗真菌的侵害。在本文中,我们利用元基因组学方法,从五个国家的七种不同寄主物种中收集到了另外 11 个产拉格瑞酰胺的共生体基因组,以揭示这种共生关系的进化历史。在每个宿主中,我们都发现了一个编码岩藻酰胺生物合成基因簇的伯克霍尔德菌共生体显性基因组。但是,我们没有发现宿主-共生体共同分化的证据,也没有发现产生岩藻酰胺的共生体单系的证据。相反,我们的分析结果表明,该基因簇是由一个祖先获得的,随后至少有四个独立的共生体获得了该基因簇,并随后在每个世系中发生了基因组侵蚀。与此相反,与植物相关的一个亲缘支系保留了较大的基因组,但其次丢失了岩藻甲酰胺基因簇。因此,我们的研究结果揭示了以高度特异性为特征的多重独立共生体获取的动态进化史,并突出了特化代谢物岩藻酰胺对建立和维持这种防御性共生关系的重要性。
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