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Hackflex library preparation enables low-cost metagenomic profiling. Hackflex 文库制备实现了低成本的元基因组剖析。
IF 5.1 Q1 ECOLOGY Pub Date : 2024-05-29 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae075
Samantha L Goldman, Jon G Sanders, Daniel D Sprockett, Abigail Landers, Weiwei Yan, Andrew H Moeller

Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/μL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

霰弹枪元基因组测序技术为深入了解微生物群落提供了宝贵的资料,但使用标准试剂盒和方案制备文库的高昂成本却成为许多人的障碍。Hackflex 等新方法使用稀释的市售试剂,大大降低了文库制备成本。然而,这些方法尚未在元基因组测序中得到系统的验证。在这里,我们通过对来自已知模拟群落以及用 Hackflex、Illumina DNA Prep 和 Illumina TruSeq 方法制备的小鼠粪便样本的元基因组文库进行测序,来评估 Hackflex 的性能。Hackflex 成功地恢复了 Zymo 模拟群落的所有成员,在 DNA 浓度为 0.5%的样本中表现最佳。
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引用次数: 0
Interactions between the nitrogen-fixing cyanobacterium Trichodesmium and siderophore-producing cyanobacterium Synechococcus under iron limitation. 铁限制条件下固氮蓝藻毛囊藻与产铁蓝藻Synechococcus之间的相互作用。
Q1 ECOLOGY Pub Date : 2024-05-25 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae072
Xumei Sun, Yan Xiao, Chengwen Yong, Hansheng Sun, Shuangqing Li, Hailong Huang, Haibo Jiang

As diazotrophic cyanobacteria of tremendous biomass, Trichodesmium continuously provide a nitrogen source for carbon-fixing cyanobacteria and drive the generation of primary productivity in marine environments. However, ocean iron deficiencies limit growth and metabolism of Trichodesmium. Recent studies have shown the co-occurrence of Trichodesmium and siderophore-producing Synechococcus in iron-deficient oceans, but whether siderophores secreted by Synechococcus can be used by Trichodesmium to adapt to iron deficiency is not clear. We constructed a mutant Synechococcus strain unable to produce siderophores to explore this issue. Synechococcus filtrates with or without siderophores were added into a Trichodesmium microbial consortium consisting of Trichodesmium erythraeum IMS 101 as the dominant microbe with chronic iron deficiency. By analyzing the physiological phenotype, metagenome, and metatranscriptome, we investigated the interactions between the nitrogen-fixing cyanobacterium Tricodesmium and siderophore-producing cyanobacterium Synechococcus under conditions of iron deficiency. The results indicated that siderophores secreted by Synechococcus are likely to chelate with free iron in the culture medium of the Trichodesmium consortium, reducing the concentration of bioavailable iron and posing greater challenges to the absorption of iron by Trichodesmium. These findings revealed the characteristics of iron-competitive utilization between diazotrophic cyanobacteria and siderophore-producing cyanobacteria, as well as potential interactions, and provide a scientific basis for understanding the regulatory effects of nutrient limitation on marine primary productivity.

作为生物量巨大的重氮蓝藻,毛囊藻不断为固碳蓝藻提供氮源,并推动海洋环境中初级生产力的产生。然而,海洋缺铁限制了毛滴虫的生长和新陈代谢。最近的研究表明,在缺铁的海洋中,毛地黄藻和产生嗜苷酸盐的Synechococcus同时存在,但Synechococcus分泌的嗜苷酸盐是否能被毛地黄藻利用来适应缺铁环境,目前还不清楚。我们构建了一株不能产生嗜苷酸盐的突变体 Synechococcus 来探讨这一问题。将含有或不含嗜苷酸的 Synechococcus 滤液添加到由红藻毛囊菌 IMS 101 组成的毛囊菌微生物联合体中,该联合体是慢性缺铁的优势微生物。通过分析生理表型、元基因组和元转录组,我们研究了在缺铁条件下固氮蓝藻三节藻与产生苷元的蓝藻Synechococcus之间的相互作用。结果表明,Synechococcus 分泌的嗜苷蓝藻很可能会与毛地蓝藻联合体培养液中的游离铁发生螯合作用,从而降低生物可利用铁的浓度,对毛地蓝藻吸收铁构成更大的挑战。这些发现揭示了重氮蓝藻和产苷蓝藻之间铁竞争性利用的特点以及潜在的相互作用,为了解营养限制对海洋初级生产力的调节作用提供了科学依据。
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引用次数: 0
Mixed waste contamination selects for a mobile genetic element population enriched in multiple heavy metal resistance genes. 混合废物污染选择了富含多种重金属抗性基因的移动遗传元素种群。
Q1 ECOLOGY Pub Date : 2024-05-09 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae064
Jennifer L Goff, Lauren M Lui, Torben N Nielsen, Farris L Poole, Heidi J Smith, Kathleen F Walker, Terry C Hazen, Matthew W Fields, Adam P Arkin, Michael W W Adams

Mobile genetic elements (MGEs) like plasmids, viruses, and transposable elements can provide fitness benefits to their hosts for survival in the presence of environmental stressors. Heavy metal resistance genes (HMRGs) are frequently observed on MGEs, suggesting that MGEs may be an important driver of adaptive evolution in environments contaminated with heavy metals. Here, we report the meta-mobilome of the heavy metal-contaminated regions of the Oak Ridge Reservation subsurface. This meta-mobilome was compared with one derived from samples collected from unimpacted regions of the Oak Ridge Reservation subsurface. We assembled 1615 unique circularized DNA elements that we propose to be MGEs. The circular elements from the highly contaminated subsurface were enriched in HMRG clusters relative to those from the nearby unimpacted regions. Additionally, we found that these HMRGs were associated with Gamma and Betaproteobacteria hosts in the contaminated subsurface and potentially facilitate the persistence and dominance of these taxa in this region. Finally, the HMRGs were associated with conjugative elements, suggesting their potential for future lateral transfer. We demonstrate how our understanding of MGE ecology, evolution, and function can be enhanced through the genomic context provided by completed MGE assemblies.

移动遗传元件(MGEs),如质粒、病毒和转座元件,可以为宿主在环境压力下的生存提供适应性益处。重金属抗性基因(HMRGs)经常出现在移动遗传元件上,这表明移动遗传元件可能是重金属污染环境中适应性进化的重要驱动力。在此,我们报告了橡树岭保留地地下重金属污染区域的元移动基因组。我们将这一元移动基因组与从橡树岭保留地地下未受影响区域采集的样本中得到的元移动基因组进行了比较。我们收集了 1615 个独特的环状 DNA 元素,并认为这些元素就是元移动基因组。与附近未受影响地区的元素相比,来自高污染地下的循环元素富含 HMRG 簇。此外,我们还发现这些 HMRGs 与受污染次表层中的伽马菌和贝特蛋白菌宿主有关,可能会促进这些类群在该地区的持续存在和优势地位。最后,HMRGs 与共轭元素相关联,表明它们未来有可能进行横向转移。我们展示了如何通过完成的 MGE 组合所提供的基因组背景来加强我们对 MGE 生态学、进化和功能的理解。
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引用次数: 0
pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms. pH 值选择热带土壤微生态系统中不同的氧化亚氮还原微生物群。
Q1 ECOLOGY Pub Date : 2024-05-08 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae070
Yanchen Sun, Yongchao Yin, Guang He, Gyuhyon Cha, Héctor L Ayala-Del-Río, Grizelle González, Konstantinos T Konstantinidis, Frank E Löffler

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

一氧化二氮(N2O)是一种具有破坏臭氧潜能的温室气体,可通过微生物在一氧化二氮还原酶(NosZ)催化下还原成二氮而得到缓解。对具有 NosZ 活性的细菌进行了中性 pH 值的研究,但对低 pH 值 N2O 还原的微生物学研究一直没有结果。酸性(pH 2O)评估了 pH 值为 4.5 和 7.3 时的 N2O 还原情况。所有微生态系统都消耗 N2O,在 2 mM N2O 的微生态系统中观察到的滞后时间长达 7 个月。元基因组比较分析表明,在两种 N2O 摄食机制下,Rhodocyclaceae 在环中性微生态系统中都占主导地位。在 pH 值为 4.5 时,Peptococcaceae 在高 N2O 微生态中占优势,而 Hyphomicrobiaceae 在低 N2O 微生态中占优势。从还原 N2O 的微生态环境中回收的 17 个高质量元基因组(MAGs)含有 nos 操作子,其中来自酸性微生态环境的 8 个 MAGs 都携带第二支系类型的 nosZ,并且缺乏亚硝酸盐还原酶基因(nirS/K)。在 pH 值为 4.5 的微生态系统中发现的 8 个 MAGs 中,有 5 个是新的类群,这表明热带酸性土壤中存在尚未开发的 N2O 还原多样性。对 pH 值为 3.5-5.7 的土壤元基因组数据集的调查显示,nosZ 基因普遍存在,这表明酸性土壤中的 N2O 还原潜力分布广泛。
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引用次数: 0
Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes. 将元基因组学和元蛋白组学结合起来,描述肠道微生物群的生态位和代谢本质。
Q1 ECOLOGY Pub Date : 2024-05-01 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae063
Tong Wang, Leyuan Li, Daniel Figeys, Yang-Yu Liu

The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed in vitro cultures of a human gut microbiome sample and investigated how oversupplying various sugars involved in ecological niches influences the community structure and protein abundance. The presented results demonstrate the performance of our pipeline in identifying proteins' metabolic and ecological roles, as well as its potential to help us design nutrient interventions to modulate the human microbiome.

微生物的基因组编码了其潜在的功能,这些功能可以通过表达的蛋白质来实现。蛋白质的选择性表达如何取决于其对微生物生长的新陈代谢的重要性或其作为生态壁龛索取资源的能力,这一点仍然难以捉摸。为了揭示蛋白质的代谢或生态作用,我们开发了一个计算管道,它将元基因组学和元蛋白组学数据配对,同时量化每个蛋白质的基因水平和蛋白质水平的功能冗余。我们首先利用消费者资源模型的模拟数据说明了这一计算流程背后的理念。然后,我们利用人类和小鼠肠道微生物组样本的真实数据对其进行了验证。特别是,我们分析了 ABC 型转运体和核糖体蛋白,证实我们的管道所预测的代谢和生态作用与先前的知识非常吻合。最后,我们对人类肠道微生物组样本进行了体外培养,并研究了生态位中涉及的各种糖类的过度供给如何影响群落结构和蛋白质丰度。这些结果证明了我们的管道在确定蛋白质的代谢和生态作用方面的性能,以及它在帮助我们设计营养干预措施以调节人类微生物组方面的潜力。
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引用次数: 0
Combining compositional data sets introduces error in covariance network reconstruction. 组合成分数据集会带来协方差网络重建误差。
Q1 ECOLOGY Pub Date : 2024-04-19 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae057
James D Brunner, Aaron J Robinson, Patrick S G Chain

Microbial communities are diverse biological systems that include taxa from across multiple kingdoms of life. Notably, interactions between bacteria and fungi play a significant role in determining community structure. However, these statistical associations across kingdoms are more difficult to infer than intra-kingdom associations due to the nature of the data involved using standard network inference techniques. We quantify the challenges of cross-kingdom network inference from both theoretical and practical points of view using synthetic and real-world microbiome data. We detail the theoretical issue presented by combining compositional data sets drawn from the same environment, e.g. 16S and ITS sequencing of a single set of samples, and we survey common network inference techniques for their ability to handle this error. We then test these techniques for the accuracy and usefulness of their intra- and inter-kingdom associations by inferring networks from a set of simulated samples for which a ground-truth set of associations is known. We show that while the two methods mitigate the error of cross-kingdom inference, there is little difference between techniques for key practical applications including identification of strong correlations and identification of possible keystone taxa (i.e. hub nodes in the network). Furthermore, we identify a signature of the error caused by transkingdom network inference and demonstrate that it appears in networks constructed using real-world environmental microbiome data.

微生物群落是一个多样化的生物系统,包括来自多个生命领域的类群。值得注意的是,细菌和真菌之间的相互作用在决定群落结构方面发挥着重要作用。然而,由于使用标准网络推断技术所涉及数据的性质,这些跨生物界的统计关联比生物界内的关联更难推断。我们利用合成和真实世界的微生物组数据,从理论和实践角度量化了跨王国网络推断所面临的挑战。我们详细介绍了将来自同一环境的组成数据集(如单个样本集的 16S 和 ITS 测序)结合起来所带来的理论问题,并考察了常见网络推断技术处理这一误差的能力。然后,我们通过从一组已知关联的模拟样本中推断网络,测试这些技术在内部和部门间关联方面的准确性和实用性。我们发现,虽然这两种方法都能减少跨领域推断的误差,但在关键的实际应用中,包括识别强相关性和识别可能的基石类群(即网络中的枢纽节点)方面,这两种技术的差别并不大。此外,我们还发现了跨王国网络推断所造成的误差特征,并证明它出现在使用真实世界环境微生物组数据构建的网络中。
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引用次数: 0
Two new clades recovered at high temperatures provide novel phylogenetic and genomic insights into Candidatus Accumulibacter. 在高温条件下发现的两个新支系提供了对累积杆菌系统发育和基因组学的新见解。
Q1 ECOLOGY Pub Date : 2024-04-18 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae049
Xiaojing Xie, Xuhan Deng, Jinling Chen, Liping Chen, Jing Yuan, Hang Chen, Chaohai Wei, Xianghui Liu, Guanglei Qiu

Candidatus Accumulibacter, a key genus of polyphosphate-accumulating organisms, plays key roles in lab- and full-scale enhanced biological phosphorus removal (EBPR) systems. A total of 10 high-quality Ca. Accumulibacter genomes were recovered from EBPR systems operated at high temperatures, providing significantly updated phylogenetic and genomic insights into the Ca. Accumulibacter lineage. Among these genomes, clade IIF members SCELSE-3, SCELSE-4, and SCELSE-6 represent the to-date known genomes encoding a complete denitrification pathway, suggesting that Ca. Accumulibacter alone could achieve complete denitrification. Clade IIC members SSA1, SCUT-1, SCELCE-2, and SCELSE-8 lack the entire set of denitrifying genes, representing to-date known non-denitrifying Ca. Accumulibacter. A pan-genomic analysis with other Ca. Accumulibacter members suggested that all Ca. Accumulibacter likely has the potential to use dicarboxylic amino acids. Ca. Accumulibacter aalborgensis AALB and Ca. Accumulibacter affinis BAT3C720 seemed to be the only two members capable of using glucose for EBPR. A heat shock protein Hsp20 encoding gene was found exclusively in genomes recovered at high temperatures, which was absent in clades IA, IC, IG, IIA, IIB, IID, IIG, and II-I members. High transcription of this gene in clade IIC members SCUT-2 and SCUT-3 suggested its role in surviving high temperatures for Ca. Accumulibacter. Ambiguous clade identity was observed for newly recovered genomes (SCELSE-9 and SCELSE-10). Five machine learning models were developed using orthogroups as input features. Prediction results suggested that they belong to a new clade (IIK). The phylogeny of Ca. Accumulibacter was re-evaluated based on the laterally derived polyphosphokinase 2 gene, showing improved resolution in differentiating different clades.

积累菌是多磷酸盐积累生物中的一个重要属,在实验室和大规模强化生物除磷系统(EBPR)中发挥着关键作用。共有 10 个高质量的 Ca.从高温下运行的 EBPR 系统中恢复了共 10 个高质量的 Ca.Accumulibacter 的系统发育和基因组研究提供了重要信息。在这些基因组中,支系 IIF 成员 SCELSE-3、SCELSE-4 和 SCELSE-6 代表了迄今已知的编码完整反硝化途径的基因组,表明仅 Ca.仅 Accumulibacter 就能实现完全脱氮。支系 IIC 成员 SSA1、SCUT-1、SCELCE-2 和 SCELSE-8 缺乏整套反硝化基因,代表了迄今已知的非反硝化 Ca.Accumulibacter.与其他 Ca.Accumulibacter 成员的泛基因组分析表明,所有 Ca.Accumulibacter 可能具有使用二羧酸氨基酸的潜力。Ca.Accumulibacter aalborgensis AALB 和 Ca.AALB 和 Ca. Accumulibacter affinis BAT3C720 似乎是仅有的两个能够利用葡萄糖进行 EBPR 的成员。热休克蛋白 Hsp20 编码基因只存在于高温下恢复的基因组中,而在 IA、IC、IG、IIA、IIB、IID、IIG 和 II-I 支系成员中均不存在。该基因在支系 IIC 成员 SCUT-2 和 SCUT-3 中的高转录表明,它在 Ca.Accumulibacter.新发现的基因组(SCELSE-9 和 SCELSE-10)的支系特征不明确。使用正交群作为输入特征开发了五个机器学习模型。预测结果表明它们属于一个新的支系(IIK)。对 Ca.根据侧面衍生的多磷酸激酶 2 基因重新评估了 Accumulibacter 的系统发育,结果显示其在区分不同支系方面的分辨率有所提高。
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引用次数: 0
The endosymbiont of Epithemia clementina is specialized for nitrogen fixation within a photosynthetic eukaryote. Epithemia clementina 的内共生体专门从事光合真核生物的固氮作用。
Q1 ECOLOGY Pub Date : 2024-04-15 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae055
Solène L Y Moulin, Sarah Frail, Thomas Braukmann, Jon Doenier, Melissa Steele-Ogus, Jane C Marks, Matthew M Mills, Ellen Yeh

Epithemia spp. diatoms contain obligate, nitrogen-fixing endosymbionts, or diazoplasts, derived from cyanobacteria. These algae are a rare example of photosynthetic eukaryotes that have successfully coupled oxygenic photosynthesis with oxygen-sensitive nitrogenase activity. Here, we report a newly-isolated species, E. clementina, as a model to investigate endosymbiotic acquisition of nitrogen fixation. We demonstrate that the diazoplast, which has lost photosynthesis, provides fixed nitrogen to the diatom host in exchange for fixed carbon. To identify the metabolic changes associated with this endosymbiotic specialization, we compared the Epithemia diazoplast with its close, free-living cyanobacterial relative, Crocosphaera subtropica. Unlike C. subtropica, in which nitrogenase activity is temporally separated from photosynthesis, we show that nitrogenase activity in the diazoplast is continuous through the day (concurrent with host photosynthesis) and night. Host and diazoplast metabolism are tightly coupled to support nitrogenase activity: Inhibition of photosynthesis abolishes daytime nitrogenase activity, while nighttime nitrogenase activity no longer requires cyanobacterial glycogen storage pathways. Instead, import of host-derived carbohydrates supports nitrogenase activity throughout the day-night cycle. Carbohydrate metabolism is streamlined in the diazoplast compared to C. subtropica with retention of the oxidative pentose phosphate pathway and oxidative phosphorylation. Similar to heterocysts, these pathways may be optimized to support nitrogenase activity, providing reducing equivalents and ATP and consuming oxygen. Our results demonstrate that the diazoplast is specialized for endosymbiotic nitrogen fixation. Altogether, we establish a new model for studying endosymbiosis, perform a functional characterization of this diazotroph endosymbiosis, and identify metabolic adaptations for endosymbiotic acquisition of a critical biological function.

Epithemia spp.硅藻含有来自蓝藻的强制性固氮内共生体或重氮体。这些藻类是光合真核生物中成功将含氧光合作用与氧敏感的氮酶活性结合起来的罕见例子。在这里,我们报告了一个新分离出来的物种--克莱门特藻(E. clementina),并将其作为研究内共生获得固氮作用的模型。我们证明,失去光合作用的重氮质体向硅藻宿主提供固定氮以交换固定碳。为了确定与这种内共生特化相关的代谢变化,我们将重氮原生质表皮藻与其近亲、自由生活的蓝藻--亚热带栉水母(Crocosphaera subtropica)进行了比较。与亚热带蓝藻不同的是,重氮质体中的氮酶活动与光合作用在时间上是分离的,而我们的研究表明,重氮质体中的氮酶活动在白天(与寄主光合作用同时进行)和夜间都是持续进行的。宿主和重氮酵母的新陈代谢紧密耦合,以支持氮酶的活性:抑制光合作用会取消白天的氮酶活性,而夜间的氮酶活性不再需要蓝藻糖原储存途径。相反,在整个昼夜周期中,宿主碳水化合物的输入支持着氮酶的活性。与亚热带蓝藻相比,重氮藻体中的碳水化合物代谢得到了简化,保留了磷酸戊糖氧化途径和氧化磷酸化作用。与杂囊类似,这些途径可能经过优化,以支持氮酶活性,提供还原当量和 ATP 并消耗氧气。我们的研究结果表明,重氮质体专门用于内共生固氮。总之,我们建立了一个研究内共生的新模型,对这种重氮内共生进行了功能表征,并确定了内共生获得关键生物功能的代谢适应性。
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引用次数: 0
Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice. 杂交小鼠的微生物组异常与抗生素耐药性基因负荷增加有关。
Q1 ECOLOGY Pub Date : 2024-04-15 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae053
Víctor Hugo Jarquín-Díaz, Susana Carolina Martins Ferreira, Alice Balard, Ľudovít Ďureje, Milos Macholán, Jaroslav Piálek, Johan Bengtsson-Palme, Stephanie Kramer-Schadt, Sofia Kirke Forslund-Startceva, Emanuel Heitlinger

Antibiotic resistance is a priority public health problem resulting from eco-evolutionary dynamics within microbial communities and their interaction at a mammalian host interface or geographical scale. The links between mammalian host genetics, bacterial gut community, and antimicrobial resistance gene (ARG) content must be better understood in natural populations inhabiting heterogeneous environments. Hybridization, the interbreeding of genetically divergent populations, influences different components of the gut microbial communities. However, its impact on bacterial traits such as antibiotic resistance is unknown. Here, we present that hybridization might shape bacterial communities and ARG occurrence. We used amplicon sequencing to study the gut microbiome and to predict ARG composition in natural populations of house mice (Mus musculus). We compared gastrointestinal bacterial and ARG diversity, composition, and abundance across a gradient of pure and hybrid genotypes in the European House Mouse Hybrid Zone. We observed an increased overall predicted richness of ARG in hybrid mice. We found bacteria-ARG interactions by their co-abundance and detected phenotypes of extreme abundances in hybrid mice at the level of specific bacterial taxa and ARGs, mainly multidrug resistance genes. Our work suggests that mammalian host genetic variation impacts the gut microbiome and chromosomal ARGs. However, it raises further questions on how the mammalian host genetics impact ARGs via microbiome dynamics or environmental covariates.

抗生素耐药性是由微生物群落内部的生态进化动态及其在哺乳动物宿主界面或地理尺度上的相互作用所导致的优先公共卫生问题。必须更好地了解哺乳动物宿主遗传学、细菌肠道群落和抗菌药耐药性基因(ARG)含量之间的联系。杂交,即基因不同种群之间的杂交,影响着肠道微生物群落的不同组成部分。然而,杂交对细菌特性(如抗生素耐药性)的影响尚不清楚。在此,我们提出杂交可能会影响细菌群落和 ARG 的发生。我们利用扩增子测序技术研究了家鼠(Mus musculus)的肠道微生物组,并预测了自然种群中 ARG 的组成。我们比较了欧洲家鼠杂交区纯种和杂交基因型梯度上的胃肠道细菌和 ARG 的多样性、组成和丰度。我们观察到杂交小鼠中 ARG 的总体预测丰富度有所增加。我们通过共同丰度发现了细菌-ARG之间的相互作用,并在特定细菌类群和ARG(主要是多药耐药基因)水平上检测到杂交小鼠中极端丰度的表型。我们的研究表明,哺乳动物宿主的遗传变异会影响肠道微生物组和染色体上的 ARGs。然而,这也提出了哺乳动物宿主遗传学如何通过微生物组动态或环境协变量影响 ARGs 的进一步问题。
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引用次数: 0
Chlamydiae in corals: shared functional potential despite broad taxonomic diversity. 珊瑚中的衣原体:尽管分类广泛多样,但仍具有共同的功能潜力。
Q1 ECOLOGY Pub Date : 2024-04-15 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae054
Justin Maire, Astrid Collingro, Matthias Horn, Madeleine J H van Oppen

Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.

珊瑚和海葵等刺胞动物与多种细菌有联系,这些细菌具有重要功能,包括营养循环和产生抗菌化合物。在刺胞动物体内,细菌可在包括组织在内的所有微生境中定植。其中包括衣原体门(chlamydiota)的强制性细胞内细菌,它们对刺胞动物宿主和全生物(尤其是珊瑚)的影响尚不清楚。在这里,我们对以前发表的来自刺胞动物(如珊瑚、水母和海葵)的 16S rRNA 基因代谢编码数据、8 个珊瑚相关衣原体的元基因组组装基因组(MAGs)以及 1 个水母相关衣原体的元基因组组装基因组进行了元分析,以解读它们的多样性和功能潜力。虽然代谢编码数据集显示了与刺胞动物相关的衣原体的巨大多样性,但 9 个 MAGs 中有 6 个隶属于 Simkaniaceae 科。另外 3 个 MAGs 分别归属于 Parasimkaniaceae、Rhabdochlamydiaceae 和 Anoxychlamydiaceae。所有 MAGs 都缺乏独立存在所需的基因,缺乏任何核苷酸或维生素以及大多数氨基酸的生物合成途径。所有 MAGs 都编码了衣原体的标志性基因,如 III 型分泌系统、核苷酸转运体和宿主相互作用基因。这些观察结果表明,珊瑚相关衣原体只能在细胞内生活。在珊瑚相关衣原体中没有发现独特的基因,这表明它们缺乏宿主特异性。要了解衣原体如何与其珊瑚宿主以及珊瑚全生物体中的其他微生物相互作用,还需要进行更多的研究。这项对珊瑚相关衣原体的多样性和功能潜力的首次研究增进了我们对珊瑚微生物组以及衣原体生活方式和宿主范围的了解。
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