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Unveiling Prasinovirus diversity and host specificity through targeted enrichment in the South China Sea. 通过在中国南海进行定向富集,揭示 Prasinovirus 的多样性和宿主特异性。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-08-29 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae109
Julie Thomy, Frederic Sanchez, Camille Prioux, Sheree Yau, Yangbing Xu, Julian Mak, Ruixian Sun, Gwenael Piganeau, Charmaine C M Yung

Unicellular green picophytoplankton from the Mamiellales order are pervasive in marine ecosystems and susceptible to infections by prasinoviruses, large double-stranded DNA viruses within the Nucleocytoviricota phylum. We developed a double-stranded DNA virus enrichment and shotgun sequencing method, and successfully assembled 80 prasinovirus genomes from 43 samples in the South China Sea. Our research delivered the first direct estimation of 94% accuracy in correlating genome similarity to host range. Stirkingly, our analyses uncovered unexpected host-switching across diverse algal lineages, challenging the existing paradigms of host-virus co-speciation and revealing the dynamic nature of viral evolution. We also detected six instances of horizontal gene transfer between prasinoviruses and their hosts, including a novel alternative oxidase. Additionally, diversifying selection on a major capsid protein suggests an ongoing co-evolutionary arms race. These insights not only expand our understanding of prasinovirus genomic diversity but also highlight the intricate evolutionary mechanisms driving their ecological success and shaping broader virus-host interactions in marine environments.

单细胞绿色浮游动物(Mamiellales)普遍存在于海洋生态系统中,易受prasinoviruses(核细胞病毒门中的大型双链DNA病毒)感染。我们开发了一种双链DNA病毒富集和霰弹枪测序方法,并从中国南海的43个样本中成功组装了80个prasinovirus基因组。我们的研究首次直接估算出基因组相似性与宿主范围相关性的准确率为 94%。令人震惊的是,我们的分析发现了不同藻系之间意想不到的宿主转换,挑战了现有的宿主-病毒共种模式,揭示了病毒进化的动态本质。我们还发现了六种朊病毒与其宿主之间的水平基因转移,其中包括一种新型替代氧化酶。此外,对一种主要囊膜蛋白的多样化选择也表明了一场持续的共同进化军备竞赛。这些发现不仅拓展了我们对朊病毒基因组多样性的理解,而且还凸显了驱动其生态成功的复杂进化机制,并影响了海洋环境中更广泛的病毒-宿主相互作用。
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引用次数: 0
A nanoluciferase-encoded bacteriophage illuminates viral infection dynamics of Pseudomonas aeruginosa cells. 纳米荧光素酶编码噬菌体照亮铜绿假单胞菌细胞的病毒感染动态。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-08-22 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae105
Sophia Zborowsky, Quentin Balacheff, Ioanna Theodorou, Rokhaya Kane, Raphaëlle Delattre, Joshua S Weitz, Régis Tournebize, Laurent Debarbieux

Bacteriophages (phages) are increasingly considered for both treatment and early detection of bacterial pathogens given their specificity and rapid infection kinetics. Here, we exploit an engineered phage expressing nanoluciferase to detect signals associated with Pseudomonas aeruginosa lysis spanning single cells to populations. Using several P. aeruginosa strains we found that the latent period, burst size, fraction of infected cells, and efficiency of plating inferred from fluorescent light intensity signals were consistent with inferences from conventional population assays. Notably, imaging-based traits were obtained in minutes to hours in contrast to the use of overnight plaques, which opens the possibility to study infection dynamics in spatial and/or temporal contexts where plaque development is infeasible. These findings support the use of engineered phages to study infection kinetics of virus-cell interactions in complex environments and potentially accelerate the determination of viral host range in therapeutically relevant contexts.

由于细菌噬菌体(噬菌体)具有特异性和快速感染动力学,因此越来越多的人将其用于细菌病原体的治疗和早期检测。在这里,我们利用一种表达纳米荧光素酶的工程噬菌体来检测与铜绿假单胞菌溶解相关的信号,范围涵盖单细胞到群体。利用几种铜绿假单胞菌菌株,我们发现从荧光强度信号推断出的潜伏期、爆发大小、受感染细胞的比例和培养效率与传统种群检测的推断结果一致。值得注意的是,与使用隔夜斑块相比,基于成像的特征可在数分钟至数小时内获得,这为在斑块发育不可行的空间和/或时间背景下研究感染动态提供了可能性。这些发现支持使用工程噬菌体来研究复杂环境中病毒-细胞相互作用的感染动力学,并有可能加快确定治疗相关情况下的病毒宿主范围。
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引用次数: 0
Purifying selection drives distinctive arsenic metabolism pathways in prokaryotic and eukaryotic microbes. 纯化选择驱动原核和真核微生物中独特的砷代谢途径。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-08-20 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae106
Lijuan Li, Songcan Chen, Ximei Xue, Jieyin Chen, Jian Tian, Lijuan Huo, Tuo Zhang, Xibai Zeng, Shiming Su

Microbes play a crucial role in the arsenic biogeochemical cycle through specific metabolic pathways to adapt to arsenic toxicity. However, the different arsenic-detoxification strategies between prokaryotic and eukaryotic microbes are poorly understood. This hampers our comprehension of how microbe-arsenic interactions drive the arsenic cycle and the development of microbial methods for remediation. In this study, we utilized conserved protein domains from 16 arsenic biotransformation genes (ABGs) to search for homologous proteins in 670 microbial genomes. Prokaryotes exhibited a wider species distribution of arsenic reduction- and arsenic efflux-related genes than fungi, whereas arsenic oxidation-related genes were more prevalent in fungi than in prokaryotes. This was supported by significantly higher acr3 (arsenite efflux permease) expression in bacteria (upregulated 3.72-fold) than in fungi (upregulated 1.54-fold) and higher aoxA (arsenite oxidase) expression in fungi (upregulated 5.11-fold) than in bacteria (upregulated 2.05-fold) under arsenite stress. The average values of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site (dN/dS) of homologous ABGs were higher in archaea (0.098) and bacteria (0.124) than in fungi (0.051). Significant negative correlations between the dN/dS of ABGs and species distribution breadth and gene expression levels in archaea, bacteria, and fungi indicated that microbes establish the distinct strength of purifying selection for homologous ABGs. These differences contribute to the distinct arsenic metabolism pathways in prokaryotic and eukaryotic microbes. These observations facilitate a significant shift from studying individual or several ABGs to characterizing the comprehensive microbial strategies of arsenic detoxification.

微生物通过特定的代谢途径适应砷的毒性,在砷的生物地球化学循环中发挥着至关重要的作用。然而,人们对原核微生物和真核微生物之间不同的砷解毒策略知之甚少。这阻碍了我们对微生物与砷之间的相互作用如何推动砷循环以及开发微生物修复方法的理解。在这项研究中,我们利用 16 个砷生物转化基因(ABGs)的保守蛋白结构域,在 670 个微生物基因组中寻找同源蛋白。与真菌相比,原核生物中砷还原和砷外流相关基因的物种分布更广,而与砷氧化相关的基因在真菌中比在原核生物中更为普遍。在亚砷酸盐胁迫下,细菌中 acr3(亚砷酸盐外排渗透酶)的表达量(上调 3.72 倍)明显高于真菌(上调 1.54 倍),真菌中 aoxA(亚砷酸盐氧化酶)的表达量(上调 5.11 倍)也高于细菌(上调 2.05 倍),这些都证明了这一点。同源 ABGs 的每个非同义位点的非同义替换与每个同义位点的同义替换的平均值(dN/dS)在古菌(0.098)和细菌(0.124)中高于真菌(0.051)。同源 ABGs 的 dN/dS 与古细菌、细菌和真菌的物种分布广度和基因表达水平呈显著负相关,这表明微生物对同源 ABGs 的纯化选择具有不同的强度。这些差异促成了原核微生物和真核微生物不同的砷代谢途径。这些观察结果促进了从研究单个或多个 ABGs 到描述微生物砷解毒综合策略的重大转变。
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引用次数: 0
Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues. 生活在植物叶片内部或叶片表面的微生物群落受环境线索的影响而形成不同的形态。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-08-08 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae103
Maryam Mahmoudi, Juliana Almario, Katrina Lutap, Kay Nieselt, Eric Kemen

Leaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here, we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and nonfungal eukaryotic communities colonizing the surface and endosphere of six wild Arabidopsis thaliana populations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Among environmental factors, radiation- and humidity-related factors are the most important drivers of diversity patterns in the leaf, with stronger effects on epiphytic communities. Using linear models, we identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that environmental factors could impact interactions within microbial communities, we analyzed the seasonal patterns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at both micro (leaf compartment) and macro (site) scales. These findings could have practical implications for predicting and developing field-adapted microbes in the face of global change.

叶片相关微生物群落可以促进植物健康,增强植物对生物和非生物胁迫的抵抗力。然而,环境线索在叶内微生物群和叶外微生物群的形成过程中的重要性仍然难以捉摸。在这里,我们旨在研究季节性环境变化对建立叶片微生物群的影响,重点是定殖于六个野生拟南芥种群表面和内球的细菌、真菌和非真菌真核生物群落的长期变化(五年)。研究发现,叶片微生物群落具有高度随机性,叶片生态位占据主导地位,内生微生物群落始终表现出较低的多样性和可变性。在环境因素中,辐射和湿度相关因素是叶片多样性模式最重要的驱动因素,对附生群落的影响更大。利用线性模型,我们确定了 30 个重要类属,它们在叶片区的相对丰度可以通过环境变量来模拟,这表明这些类群具有特定的生态位偏好。基于环境因素可能影响微生物群落内部相互作用的假设,我们分析了叶片分区中微生物相互作用网络的季节性模式。我们发现,附生网络比内生网络更复杂,而且这些网络的复杂性和连通性与上述环境线索有部分关联。我们的研究结果表明,湿度和太阳辐射是在微观(叶室)和宏观(地点)尺度上影响叶球微生物群的主要环境因素。这些发现可能对预测和开发适应全球变化的野外微生物具有实际意义。
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引用次数: 0
Co-inoculations of bacteria and mycorrhizal fungi often drive additive plant growth responses. 细菌和菌根真菌的联合接种通常会对植物生长产生叠加效应。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-08-07 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae104
Louis Berrios, Andressa M Venturini, Tillson Bertie Ansell, Esther Tok, William Johnson, Claire E Willing, Kabir G Peay

Controlled greenhouse studies have shown the numerous ways that soil microbes can impact plant growth and development. However, natural soil communities are highly complex, and plants interact with many bacterial and fungal taxa simultaneously. Due to logistical challenges associated with manipulating more complex microbiome communities, how microbial communities impact emergent patterns of plant growth therefore remains poorly understood. For instance, do the interactions between bacteria and fungi generally yield additive (i.e. sum of their parts) or nonadditive, higher order plant growth responses? Without this information, our ability to accurately predict plant responses to microbial inoculants is weakened. To address these issues, we conducted a meta-analysis to determine the type (additive or higher-order, nonadditive interactions), frequency, direction (positive or negative), and strength that bacteria and mycorrhizal fungi (arbuscular and ectomycorrhizal) have on six phenotypic plant growth responses. Our results demonstrate that co-inoculations of bacteria and mycorrhizal fungi tend to have positive additive effects on many commonly reported plant responses. However, ectomycorrhizal plant shoot height responds positively and nonadditively to co-inoculations of bacteria and ectomycorrhizal fungi, and the strength of additive effects also differs between mycorrhizae type. These findings suggest that inferences from greenhouse studies likely scale to more complex field settings and that inoculating plants with diverse, beneficial microbes is a sound strategy to support plant growth.

受控温室研究表明,土壤微生物可以通过多种方式影响植物的生长和发育。然而,自然土壤群落非常复杂,植物同时与许多细菌和真菌类群相互作用。因此,人们对微生物群落如何影响植物生长的新模式仍然知之甚少。例如,细菌和真菌之间的相互作用通常会产生相加(即各部分之和)或非相加的高阶植物生长反应吗?没有这些信息,我们就无法准确预测植物对微生物接种剂的反应。为了解决这些问题,我们进行了一项荟萃分析,以确定细菌和菌根真菌(树根真菌和外生菌根真菌)对六种表型植物生长反应的类型(加性或高阶、非加性相互作用)、频率、方向(正向或负向)和强度。我们的研究结果表明,细菌和菌根真菌的共同接种往往会对许多常见的植物反应产生积极的叠加效应。然而,外生菌根植物的嫩枝高度对细菌和外生菌根真菌的共同接种有正的非加成效应,而且不同菌根类型的加成效应强度也不同。这些发现表明,温室研究的推论很可能适用于更复杂的田间环境,而且给植物接种多种有益微生物是支持植物生长的合理策略。
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引用次数: 0
Phage resistance mutations affecting the bacterial cell surface increase susceptibility to fungi in a model cheese community. 影响细菌细胞表面的噬菌体抗性突变增加了奶酪模型群落对真菌的易感性。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-08-02 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae101
Tara C J Spencer-Drakes, Angel Sarabia, Gary Heussler, Emily C Pierce, Manon Morin, Steven Villareal, Rachel J Dutton

Diverse populations of bacteriophages infect and coevolve with their bacterial hosts. Although host recognition and infection occur within microbiomes, the molecular mechanisms underlying host-phage interactions within a community context remain poorly studied. The biofilms (rinds) of aged cheeses contain taxonomically diverse microbial communities that follow reproducible growth patterns and can be manipulated under laboratory conditions. In this study, we use cheese as a model for studying phage-microbe interactions by identifying and characterizing a tractable host-phage pair co-occurring within a model Brie-like community. We isolated a novel bacteriophage, TS33, that kills Hafnia sp. JB232, a member of the model community. TS33 is easily propagated in the lab and naturally co-occurs in the cheese community, rendering it a prime candidate for the study of host-phage interactions. We performed growth assays of the Hafnia, TS33, and the fungal community members, Geotrichum candidum and Penicillium camemberti. Employing Random Barcode Transposon Sequencing experiments, we identified candidate host factors that contribute to TS33 infectivity, many of which are homologs of bacterial O-antigen genes. Hafnia mutants in these genes exhibit decreased susceptibility to phage infection, but experience negative fitness effects in the presence of the fungi. Therefore, mutations in O-antigen biosynthesis homologs may have antagonistic pleiotropic effects in Hafnia that have major consequences for its interactions with the rest of the community. Ongoing and future studies aim to unearth the molecular mechanisms by which the O-antigen of Hafnia mediates its interactions with its viral and fungal partners.

多种多样的噬菌体感染细菌宿主并与其共同进化。虽然宿主识别和感染发生在微生物群落中,但对宿主与噬菌体在群落环境中相互作用的分子机制的研究仍然很少。陈年奶酪的生物膜(外皮)含有分类学上多样的微生物群落,这些群落遵循可重现的生长模式,并可在实验室条件下进行操作。在这项研究中,我们利用奶酪作为研究噬菌体与微生物相互作用的模型,确定并描述了在一个类似布里的模型群落中共存的可控宿主-噬菌体对。我们分离出一种新型噬菌体 TS33,它能杀死模型群落中的 Hafnia sp.TS33 在实验室中很容易繁殖,而且在干酪群落中自然共生,因此是研究宿主-噬菌体相互作用的最佳候选菌。我们对 Hafnia、TS33 以及真菌群落成员--念珠菌和卡门贝青霉--进行了生长试验。通过随机条形码转座子测序实验,我们确定了有助于 TS33 感染性的候选宿主因子,其中许多是细菌 O 抗原基因的同源物。这些基因的哈夫尼亚突变体对噬菌体感染的敏感性降低,但在真菌存在的情况下会出现负面的适应性影响。因此,O-抗原生物合成同源基因的突变可能会对 Hafnia 产生拮抗多效应,从而对其与群落其他部分的相互作用产生重大影响。正在进行和未来的研究旨在揭示 Hafnia 的 O 型抗原介导其与病毒和真菌伙伴相互作用的分子机制。
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引用次数: 0
Bacteroidia and Clostridia are equipped to degrade a cascade of polysaccharides along the hindgut of the herbivorous fish Kyphosus sydneyanus. 类杆菌和梭状芽孢杆菌能够降解草食性鱼类 Kyphosus sydneyanus 后肠中的一系列多糖。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-08-01 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae102
Cesar T Facimoto, Kendall D Clements, W Lindsey White, Kim M Handley

The gut microbiota of the marine herbivorous fish Kyphosus sydneyanus are thought to play an important role in host nutrition by supplying short-chain fatty acids (SCFAs) through fermentation of dietary red and brown macroalgae. Here, using 645 metagenome-assembled genomes (MAGs) from wild fish, we determined the capacity of different bacterial taxa to degrade seaweed carbohydrates along the gut. Most bacteria (99%) were unclassified at the species level. Gut communities and CAZyme-related transcriptional activity were dominated by Bacteroidia and Clostridia. Both classes possess genes CAZymes acting on internal polysaccharide bonds, suggesting their role initiating glycan depolymerization, followed by rarer Gammaproteobacteria and Verrucomicrobiae. Results indicate that Bacteroidia utilize substrates in both brown and red algae, whereas other taxa, namely, Clostridia, Bacilli, and Verrucomicrobiae, utilize mainly brown algae. Bacteroidia had the highest CAZyme gene densities overall, and Alistipes were especially enriched in CAZyme gene clusters (n = 73 versus just 62 distributed across all other taxa), pointing to an enhanced capacity for macroalgal polysaccharide utilization (e.g., alginate, laminarin, and sulfated polysaccharides). Pairwise correlations of MAG relative abundances and encoded CAZyme compositions provide evidence of potential inter-species collaborations. Co-abundant MAGs exhibited complementary degradative capacities for specific substrates, and flexibility in their capacity to source carbon (e.g., glucose- or galactose-rich glycans), possibly facilitating coexistence via niche partitioning. Results indicate the potential for collaborative microbial carbohydrate metabolism in the K. sydneyanus gut, that a greater variety of taxa contribute to the breakdown of brown versus red dietary algae, and that Bacteroidia encompass specialized macroalgae degraders.

人们认为海洋草食性鱼类 Kyphosus sydneyanus 的肠道微生物群通过发酵食物中的红色和棕色大型藻类提供短链脂肪酸 (SCFA),从而在宿主营养中发挥重要作用。在这里,我们利用来自野生鱼类的 645 个元基因组(MAGs),测定了不同细菌类群在肠道中降解海藻碳水化合物的能力。大多数细菌(99%)在物种水平上未分类。肠道群落和 CAZyme 相关转录活动主要由类杆菌和梭状芽孢杆菌主导。这两类细菌都拥有作用于内部多糖键的 CAZymes 基因,这表明它们在启动糖解聚过程中发挥了作用。结果表明,类杆菌属既利用褐藻中的底物,也利用红藻中的底物,而其他类群,即梭状芽孢杆菌属、芽孢杆菌属和疣菌属,则主要利用褐藻中的底物。类杆菌科的 CAZyme 基因密度最高,而藻类杆菌科的 CAZyme 基因群尤其丰富(73 个,而其他类群只有 62 个),这表明它们利用大型藻类多糖(如藻酸盐、层糖蛋白和硫酸化多糖)的能力增强。MAG 相对丰度与编码的 CAZyme 组成的成对相关性为潜在的物种间合作提供了证据。共丰的 MAGs 对特定底物的降解能力具有互补性,其碳源能力(如富含葡萄糖或半乳糖的聚糖)也具有灵活性,这可能有助于通过生态位划分实现共存。研究结果表明,K. sydneyanus肠道中的微生物碳水化合物代谢具有协同作用的潜力,更多种类的类群参与了褐藻与红藻的分解,类杆菌包括专门的大型藻类降解者。
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引用次数: 0
c-di-GMP and AHL signals-triggered chemical communication under electrical signaling disruption restores Geobacter sulfurreducens biofilm formation. 在电信号中断的情况下,c-di-GMP 和 AHL 信号触发的化学通讯可恢复硫化琥珀芽孢杆菌生物膜的形成。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-07-20 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae096
Qian Zhu, Yanyan Zheng, Xingwang Zhou, Dunjia Wang, Mengjiao Yuan, Dingkang Qian, Sha Liang, Wenbo Yu, Jiakuan Yang, Huijie Hou, Jingping Hu

Electrogenic biofilms, which have attracted considerable attention in simultaneous wastewater treatment and energy recovery in bioelectrochemical systems, are regulated by chemical communication and potassium channel-mediated electrical signaling. However, how these two communication pathways interact with each other has not been thoroughly investigated. This study first explored the roles of chemical communication, including intracellular bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) and extracellular N-acyl-homoserine lactone (AHL)-mediated quorum sensing, in electrogenic biofilm formation through an integrated analysis of transcriptomics and metabolomics. Electrical signaling disruption inhibited the formation and electroactivity of Geobacter sulfurreducens biofilm, which was mainly ascribed to the reduction in biofilm viability and extracellular protein/polysaccharide ratio. The upregulation of expression levels of genes encoding c-di-GMP and AHL synthesis by transcriptomic analysis, and the increased secretion of N-butanoyl-L-homoserine lactone by metabolomic analysis confirmed the enhancement of chemical communication under electrical signaling disruption, thus indicating a compensatory mechanism among different signaling pathways. Furthermore, protein-protein interaction network showed the convergence of different signaling pathways, with c-di-GMP-related genes acting as central bridges. This study highlights the interaction of different signaling pathways, especially the resilience of c-di-GMP signaling to adverse external stresses, thereby laying the foundation for facilitating electrogenic biofilm formation under adverse conditions in practical applications.

在生物电化学系统中同时进行废水处理和能量回收的电生生物膜备受关注,它受化学通讯和钾通道介导的电信号调节。然而,这两种通讯途径如何相互影响尚未得到深入研究。本研究首先通过转录组学和代谢组学的综合分析,探讨了化学通讯(包括细胞内双(3'-5')环二聚体单磷酸鸟苷(c-di-GMP)和细胞外 N-酰基高丝氨酸内酯(AHL)介导的法定量感应)在电生生物膜形成中的作用。电信号中断抑制了硫发生地芽孢杆菌生物膜的形成和电活性,这主要归因于生物膜活力和胞外蛋白/多糖比率的降低。通过转录组分析,编码 c-di-GMP 和 AHL 合成的基因表达水平上调;通过代谢组分析,N-丁酰基-L-高丝氨酸内酯的分泌量增加,证实了在电信号中断的情况下化学通讯的增强,从而表明了不同信号通路之间的补偿机制。此外,蛋白质-蛋白质相互作用网络显示了不同信号通路的融合,其中 c-di-GMP 相关基因是核心桥梁。这项研究强调了不同信号通路之间的相互作用,特别是 c-di-GMP 信号通路对不利外部压力的恢复能力,从而为在实际应用中促进不利条件下电生生物膜的形成奠定了基础。
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引用次数: 0
Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus. 福尔摩斯白蚁肠道中纤维素分解原生生物与甲烷生成古细菌之间的共生关系。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-07-20 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae097
Masayuki Kaneko, Tatsuki Omori, Katsura Igai, Takako Mabuchi, Miho Sakai-Tazawa, Arisa Nishihara, Kumiko Kihara, Tsuyoshi Yoshimura, Moriya Ohkuma, Yuichi Hongoh

Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts' fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here "Candidatus Methanobrevibacter cononymphae", is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0% to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, "Ca. Methanobrevibacter cononymphae" is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of "Ca. Methanobrevibacter cononymphae" showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.

厌氧原生生物经常携带产甲烷古菌,这些古菌显然通过消耗多余的 H2 来促进宿主的发酵代谢。然而,在许多情况下,内生甲烷菌的生态特性仍然难以捉摸。在这里,我们研究了白蚁后肠中的内共生甲烷菌(Cononympha protists)的生态学和基因组。显微镜和 16S rRNA 扩增子测序分析表明,一种名为 "Candidatus Methanobrevibacter cononymphae "的单一物种与 Cononympha leidyi 和 Cononympha koidzumii 都有关联,它在不同白蚁群落的 Cononympha 细胞中的感染率从 0.0% 到 99.8% 不等。精细的网络分析表明,多个 16S rRNA 序列变体共存于一个宿主细胞中,而且相同的变体同时存在于两种白蚁中,也存在于肠壁上。因此,"Ca.因此,"Ca. Methanobrevibacter cononymphae "是一种面生内共生菌,通过垂直传播与肠道环境频繁交换。事实上,透射电子显微镜显示了甲烷菌从或被锥穴细胞逃逸或吸收的情况。Ca.Ca.Methanobrevibacter cononymphae "的基因组显示出与其面生生活方式相一致的特征:即基因组大小(2.7 Mbp)与自由生活的亲缘菌相当;甲酸脱氢酶基因 fdhA 的假基因化,在不产生甲酸的宿主细胞中是不必要的;依赖宿主细胞中丰富的醋酸盐作为必要的碳源;存在过氧化氢酶基因,这是在微氧肠壁上定植所必需的。我们的研究揭示了甲烷菌与原生生物之间的多功能共生关系,这可能是一种应对白蚁肠道中不断变化的条件的策略。
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引用次数: 0
Air monitoring by nanopore sequencing. 通过纳米孔测序进行空气监测。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-07-16 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae099
Tim Reska, Sofya Pozdniakova, Sílvia Borràs, Albert Perlas, Ela Sauerborn, Lídia Cañas, Michael Schloter, Xavier Rodó, Yuanyuan Wang, Barbro Winkler, Jörg-Peter Schnitzler, Lara Urban

While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, so that little is known about the air microbiome's composition, distribution, or functionality. Here we show that nanopore sequencing-based metagenomics can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide fast and portable laboratory and computational approaches for air microbiome profiling, which we leverage to robustly assess the taxonomic composition of the core air microbiome of a controlled greenhouse environment and of a natural outdoor environment. We show that long-read sequencing can resolve species-level annotations and specific ecosystem functions through de novo metagenomic assemblies despite the low amount of fragmented DNA used as an input for nanopore sequencing. We then apply our pipeline to assess the diversity and variability of an urban air microbiome, using Barcelona, Spain, as an example; this randomized experiment gives first insights into the presence of highly stable location-specific air microbiomes within the city's boundaries, and showcases the robust microbial assessments that can be achieved through automatable, fast, and portable nanopore sequencing technology.

虽然空气微生物组及其多样性对人类健康和生态系统的恢复能力至关重要,但全面的空气微生物多样性监测仍然很少见,因此人们对空气微生物组的组成、分布或功能知之甚少。在这里,我们展示了基于纳米孔测序的元基因组学,结合通过液体撞击进行的主动空气采样和量身定制的计算分析,可以对空气微生物组进行强有力的评估。我们为空气微生物组分析提供了快速、便携的实验室和计算方法,并利用这些方法对受控温室环境和室外自然环境中核心空气微生物组的分类组成进行了有力评估。我们表明,尽管作为纳米孔测序输入的片段 DNA 数量较少,但长读程测序可以通过全新的元基因组组装解析物种级注释和特定生态系统功能。然后,我们以西班牙巴塞罗那为例,应用我们的管道评估了城市空气微生物组的多样性和变异性;这一随机实验首次揭示了城市边界内存在高度稳定的特定地点空气微生物组,并展示了通过自动化、快速、便携的纳米孔测序技术可以实现的强大微生物评估功能。
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引用次数: 0
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ISME communications
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