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Competitive inhibition and mutualistic growth in Co-infections: deciphering Staphylococcus aureus – Acinetobacter baumannii interaction dynamics 协同感染中的竞争性抑制和互生:金黄色葡萄球菌与鲍曼不动杆菌相互作用动态解密
Pub Date : 2024-06-10 DOI: 10.1093/ismeco/ycae077
Sandra Timme, S. Wendler, T. Klassert, J. Saraiva, U. N. da Rocha, Manuel Wittchen, Sareda T. J. Schramm, R. Ehricht, S. Monecke, B. Edel, Jürgen Rödel, Bettina Löffler, Maria Soledad Ramirez, Hortense Slevogt, M. Figge, L. Tuchscherr
Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are frequently co-isolated from polymicrobial infections that are severe and refractory to therapy. Here, we apply a combination of wet-lab experiments and in silico modeling to unveil the intricate nature of the Ab/Sa interaction using both, representative laboratory strains and strains co-isolated from clinical samples. This comprehensive methodology allowed uncovering Sa’s capability to exert a partial interference on Ab by the expression of phenol-soluble modulins. In addition, we observed a cross-feeding mechanism by which Sa supports the growth of Ab by providing acetoin as an alternative carbon source. This study is the first to dissect the Ab/Sa interaction dynamics wherein competitive and cooperative strategies can intertwine. Through our findings, we illuminate the ecological mechanisms supporting their coexistence in the context of polymicrobial infections. Our research not only enriches our understanding but also opens doors to potential therapeutic avenues in managing these challenging infections.
金黄色葡萄球菌(Sa)和鲍曼不动杆菌(Ab)经常在严重且难治的多微生物感染中共同分离出来。在这里,我们将湿实验室实验和硅学建模相结合,利用具有代表性的实验室菌株和从临床样本中共同分离出的菌株,揭示了 Ab/Sa 相互作用的复杂本质。这种综合方法揭示了 Sa 通过表达酚溶性调节蛋白对 Ab 产生部分干扰的能力。此外,我们还观察到了一种交叉供养机制,即 Sa 通过提供乙炔作为替代碳源来支持 Ab 的生长。这项研究首次剖析了 Ab 与 Sa 的相互作用动态,其中竞争与合作策略相互交织。通过我们的发现,我们阐明了支持它们在多微生物感染背景下共存的生态机制。我们的研究不仅丰富了我们的认识,还为治疗这些具有挑战性的感染打开了潜在的治疗途径。
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引用次数: 0
Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen. 代谢易变的 Ca.深海琉璃蛤(Lucinoma kazani)的硫代滋养菌共生体具有固氮的遗传潜力。
Pub Date : 2024-06-04 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae076
Lina Ratinskaia, Stas Malavin, Tal Zvi-Kedem, Simina Vintila, Manuel Kleiner, Maxim Rubin-Blum

Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected Lucinoma kazani individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 fixation in the deep-sea symbiont's genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicate chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.

琉璃蛤是浅海和深海化合栖息地中种类最多、分布最广的共生动物群之一。琉球蛤类含有 Ca.Thiodiazotropha共生藻可以氧化硫化氢和甲酸盐等无机和有机底物以获得能量。Ca.Thiodiazotropha的这些关键代谢功能、养分吸收和生物相互作用之间的相互影响还不清楚。Thiodiazotropha中这些关键代谢功能之间的相互作用还不完全清楚。我们在地中海东部 1150 米深处的深海盐池旁采集了 Lucinoma kazani 个体,并使用 Oxford Nanopore 和 Illumina 测序技术获得了它们的 Ca.Thiodiazotropha gloverae 共生藻的高质量基因组。这些基因组是转录组和蛋白质组分析的基础,用于描述共生体的原位基因表达、新陈代谢和生理学特征。我们在深海共生体的基因组中发现了固定 N2 所需的基因,而这些基因迄今为止只在浅水的 Ca.Thiodiazotropha。但是,我们没有检测到这些基因的表达,因此,固氮作用在这种共生关系中的潜在作用仍有待确定。我们还发现碳固定和硫氧化基因的高表达,这表明化学溶解自养是 Ca.Thiodiazotropha。不过,我们也检测到利用甲醇和甲酸盐作为能量来源的途径的表达。我们的发现突显了这些微生物为支持宿主的营养和与宿主相互作用而保持的关键特性。
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引用次数: 0
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。
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
Intermittent water stress favors microbial traits that better help wheat under drought 间歇性水分胁迫有利于微生物性状,从而更好地帮助小麦抗旱
Pub Date : 2024-05-20 DOI: 10.1093/ismeco/ycae074
Ruth Lydia Schmidt, H. Azarbad, Luke Bainard, Julien Tremblay, É. Yergeau
Microorganisms can improve plant resistance to drought through various mechanisms such as the production of plant hormones, osmolytes, antioxidants, and exopolysaccharides. It is, however, unclear how previous exposure to water stress affects the functional capacity of the soil microbial community to help plants resist drought. We compared two soils that had either a continuous or intermittent water stress history for almost forty years. We grew wheat in these soils and subjected it to a water stress, after which we collected the rhizosphere soil and shotgun sequenced its metagenome. Wheat growing in the soil with an intermittent water stress history maintained a higher biomass when subjected to water stress. Genes related to indole-acetic acid and osmolyte production were more abundant in the metagenome of the soil with an intermittent water stress history as compared to the soil with a continuous water stress history. We suggest that an intermittent water stress history selects traits beneficial for life under water stress.
微生物可通过各种机制提高植物的抗旱能力,如产生植物激素、渗透溶解物、抗氧化剂和外多糖。然而,目前还不清楚之前的水胁迫如何影响土壤微生物群落帮助植物抗旱的功能。我们比较了两种土壤,它们在将近四十年的时间里持续或间歇地遭受过水胁迫。我们在这些土壤中种植了小麦,并对其施加了水胁迫,之后我们收集了根圈土壤,并对其元基因组进行了枪式测序。在有间歇性水胁迫历史的土壤中生长的小麦在受到水胁迫时保持了较高的生物量。与持续水胁迫土壤相比,间歇水胁迫土壤元基因组中与吲哚乙酸和渗透溶质产生有关的基因更为丰富。我们认为,间歇性水胁迫选择了有利于在水胁迫下生活的性状。
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引用次数: 0
Widespread horizontal gene transfer between plants and bacteria 植物和细菌之间广泛的水平基因转移
Pub Date : 2024-05-13 DOI: 10.1093/ismeco/ycae073
Shelly Haimlich, Yulia Fridman, H. Khandal, S. Savaldi-Goldstein, Asaf Levy
Plants host a large array of commensal bacteria that interact with the host. The growth of both bacteria and plants is often dependent on nutrients derived from the cognate partners, and the bacteria fine-tune host immunity against pathogens. This ancient interaction is common in all studied land plants and is critical for proper plant health and development. We hypothesized that the spatial vicinity and the long-term relationships between plants and their microbiota may promote cross-kingdom horizontal gene transfer (HGT), a phenomenon that is relatively rare in nature. To test this hypothesis we analyzed the Arabidopsis thaliana genome and its extensively sequenced microbiome to detect events of horizontal transfer of full length genes that transferred between plants and bacteria. Interestingly, we detected 75 unique genes that were horizontally transferred between plants and bacteria. Plants and bacteria exchange in both directions genes that are enriched in carbohydrate metabolism functions, and bacteria transferred to plants genes that are enriched in auxin biosynthesis genes. Next we provided a proof of concept for the functional similarity between a horizontally transferred bacterial gene and its Arabidopsis homologue in planta. The Arabidopsis DET2 gene is essential for biosynthesis of the brassinosteroid phytohormones and loss-of-function of the gene leads to dwarfism. We found that expression of the DET2 homologue from Leifsonia bacteria of the Actinobacteria phylum in the Arabidopsis det2 background complements the mutant, and leads to normal plant growth. Together, these data suggest that cross-kingdom horizontal gene transfer events shape the metabolic capabilities and interactions between plants and bacteria.
植物寄生着大量与宿主相互作用的共生细菌。细菌和植物的生长通常都依赖于同源伙伴提供的养分,细菌还能微调宿主的免疫力,以抵御病原体。这种古老的相互作用在所有研究过的陆生植物中都很常见,对植物的正常健康和发育至关重要。我们假设,植物及其微生物群之间的空间邻近性和长期关系可能会促进跨领域水平基因转移(HGT),而这种现象在自然界中相对罕见。为了验证这一假设,我们分析了拟南芥基因组及其广泛测序的微生物组,以检测植物和细菌之间的全长基因水平转移事件。有趣的是,我们检测到 75 个独特的基因在植物和细菌之间进行了水平转移。植物和细菌双向交流了富含碳水化合物代谢功能的基因,细菌向植物转移了富含辅助素生物合成基因的基因。接下来,我们证明了横向转移的细菌基因与其拟南芥同源基因在植物体内的功能相似性。拟南芥的 DET2 基因对于黄铜类植物激素的生物合成至关重要,该基因功能缺失会导致矮小症。我们发现,在拟南芥 det2 背景下表达放线菌门 Leifsonia 细菌中的 DET2 同源物可补充突变体,并导致植物正常生长。这些数据共同表明,跨领域水平基因转移事件塑造了植物与细菌之间的代谢能力和相互作用。
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引用次数: 0
Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary 机器学习和元基因组学确定了亚热带高富营养化河口生物地球化学循环的未表征类群
Pub Date : 2024-05-10 DOI: 10.1093/ismeco/ycae067
Apoorva Prabhu, Sanjana Tule, M. Chuvochina, Mikael Bodén, Simon J McIlroy, Julian Zaugg, Chris Rinke
Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal–spatial dataset, from a subtropical hypereutrophic estuary. Screening 54 water samples across brackish to marine sites revealed that nutrient concentrations and salinity best explained spatial community variations, whereas temperature and dissolved oxygen likely drive seasonal shifts. By combining short and long read sequencing data, we recovered 2459 metagenome-assembled genomes (MAGs), proposed new taxon names for previously uncharacterised lineages, and created an extensive, habitat specific genome reference database. Community profiling based on this genome reference database revealed a diverse prokaryotic community comprising 61 bacterial and 18 archaeal phyla, and resulted in an improved taxonomic resolution at lower ranks down to genus level. We found that the vast majority (61 out of 73) of abundant genus level taxa (>1% average) represented unnamed and novel lineages, and that all genera could be clearly separated into brackish and marine ecotypes with inferred habitat specific functions. Applying supervised machine learning and metabolic reconstruction, we identified several microbial indicator taxa responding directly or indirectly to elevated nitrate and total phosphorus concentrations. In conclusion, our analysis highlights the importance of improved taxonomic resolution, sheds light on the role of previously uncharacterised lineages in estuarine nutrient cycling, and identifies microbial indicators for nutrient levels crucial in estuary health assessments.
受人类活动的影响,全球许多河口的营养物质浓度急剧增加,微生物群落适应了由此产生的高富营养化生态系统。然而,我们对这些生态系统中的主要微生物类群及其潜在功能的了解仍然很少。在这里,我们研究了亚热带高富营养化河口时空数据集中的原核生物群落动态。对从咸水到海洋的 54 个水样进行筛选后发现,营养物浓度和盐度最能解释群落的空间变化,而温度和溶解氧可能是季节性变化的驱动因素。通过结合长短读数测序数据,我们恢复了 2459 个元基因组组装基因组(MAGs),为以前未定性的品系提出了新的分类群名称,并创建了一个广泛的、针对特定生境的基因组参考数据库。基于该基因组参考数据库的群落剖析揭示了由 61 个细菌门和 18 个古细菌门组成的原核生物群落的多样性,并提高了低级到属一级的分类分辨率。我们发现,绝大多数(73 个中的 61 个)丰富的属级类群(平均大于 1%)代表了未命名的新品系,而且所有属都可以清晰地区分为咸水生态型和海洋生态型,并推断出特定生境的功能。通过监督机器学习和代谢重建,我们确定了几个直接或间接响应硝酸盐和总磷浓度升高的微生物指示类群。总之,我们的分析强调了提高分类学分辨率的重要性,揭示了以前未表征的类群在河口营养循环中的作用,并确定了河口健康评估中至关重要的营养水平微生物指标。
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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。
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
Needle bacterial community structure across the species range of limber pine 松脂松物种范围内的针叶细菌群落结构
Pub Date : 2024-05-09 DOI: 10.1093/ismeco/ycae062
Dana L. Carper, Travis J Lawrence, Dianne Quiroz, Lara M. Kueppers, A. C. Frank
Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species’ range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: 1) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; 2) dispersal limitation structures foliar communities across the range of limber pine; 3) the relative significance of dispersal and selection differs across sites in the tree species range, and 4) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.
叶片上和叶片内的细菌可影响林木的健康和恢复能力。树种的分布和分布范围会受到各种因素的影响,其中最重要的因素是生物相互作用。我们研究了影响林缘松树针叶细菌群落的整个物种分布过程,林缘松树是一种广泛分布于西部的针叶树,栖息于一系列极端的栖息地。我们测试了四个假设1)不同地点的针叶群落结构各不相同,与宿主物种选择相比,地点特异性因素对微生物组合更为重要;2)在整个林柏松树种分布范围内,散布限制形成了叶片群落;3)在树种分布范围内,不同地点的散布和选择的相对重要性各不相同;4)针叶年龄形成了细菌群落。我们对林可松分布区内 16 个地点的林可松和共生针叶树的针叶表面和组织中的针叶群落进行了描述。我们的研究结果证实,地点特征决定了整个寄主物种范围内细菌群落的组合,并表明这些模式不是由扩散限制驱动的。此外,宿主的选择强度因地点而异,这可能是由于可用微生物的差异造成的。我们的研究通过关注自然环境中的树木,揭示了森林中真实的针状细菌动态,这对于理解形成森林树木-微生物相互作用的随机和确定过程之间的平衡至关重要。要预测或操纵这些相互作用,以支持森林生态系统的生产力,或帮助植物在全球变化中迁移和适应,就必须了解这些相互作用。
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引用次数: 0
Swarm and UNOISE outperform DADA2 and Deblur for denoising high-diversity marine seafloor samples 在对高分辨率海洋海底样本进行去噪处理方面,Swarm 和 UNOISE 优于 DADA2 和 Deblur
Pub Date : 2024-05-09 DOI: 10.1093/ismeco/ycae071
Tonje Nilsen, L. Snipen, I. Angell, N. B. Keeley, Sanna Majaneva, Ragnhild Pettersen, Knut Rudi
The performance of sequence variant resolution analytic tools for metabarcoding has not yet been adequately benchmarked for high-diversity environmental samples. We therefore evaluated the sequence variant tools DADA2, Deblur, Swarm and UNOISE, using high-diversity seafloor samples, resulting in comparisons of 1800 sequence variant tables. The evaluation was based on 30 sediment grab samples, for which three replica samples were collected. Each replica sample was extracted using five common DNA extraction kits, resulting in 450 DNA extracts which were 16S rRNA gene sequenced (V3-V4), using Illumina. Assessments included variation across replica samples, extraction kits and denoising methods, in addition to applying prior knowledge about alpha diversity correlations towards the cosmopolitan marine archaeon Nitrosopumilus with high diversity, and the sulfide oxidizing Sulfurovum with low diversity. DADA2 displayed the highest variance between replicates (Manhattan distance 1.14), while Swarm showed the lowest variance (Manhattan distance 0.93). For the analysis based on prior biological knowledge, UNOISE displayed the highest alpha diversity (Simpson’s D) correlation towards Nitrosopumilus (Spearman rho = 0.85), while DADA2 showed the lowest (Spearman rho = 0.10). Deblur completely eliminated Nitrosopumilus from the dataset. For Sulfurovum, on the other hand, all the methods showed comparable results. In conclusion, our evaluations show that Swarm and UNOISE performed better than DADA2 and Deblur for high-diversity seafloor samples.
用于代谢标码的序列变异解析分析工具的性能尚未针对高多样性环境样本进行充分的基准测试。因此,我们使用高多样性海底样本对序列变异工具 DADA2、Deblur、Swarm 和 UNOISE 进行了评估,得出了 1800 个序列变异表的比较结果。评估以 30 个沉积物抓取样本为基础,并收集了三个副本样本。使用五种常见的 DNA 提取试剂盒对每个副本样本进行提取,最终得到 450 份 DNA 提取物,并使用 Illumina 对这些提取物进行 16S rRNA 基因测序(V3-V4)。评估包括不同复制样本、提取试剂盒和去噪方法之间的差异,此外还应用了有关阿尔法多样性相关性的先验知识,包括多样性较高的世界性海洋古生物 Nitrosopumilus 和多样性较低的硫化物氧化型 Sulfurovum。DADA2 重复间的方差最大(曼哈顿距离为 1.14),而 Swarm 重复间的方差最小(曼哈顿距离为 0.93)。在基于先验生物知识的分析中,UNOISE 与 Nitrosopumilus 的阿尔法多样性(辛普森 D)相关性最高(Spearman rho = 0.85),而 DADA2 的相关性最低(Spearman rho = 0.10)。Deblur 完全消除了数据集中的 Nitrosopumilus。而对于 Sulfurovum,所有方法的结果都相当。总之,我们的评估结果表明,对于高多样性的海底样本,Swarm 和 UNOISE 的性能优于 DADA2 和 Deblur。
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