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Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation 开发一种数字液滴 PCR 方法,用于量化参与大气二氧化碳固定的土壤微生物。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-18 DOI: 10.1111/1462-2920.16666
Marie Le Geay, Kyle Mayers, Martin Küttim, Béatrice Lauga, Vincent E. J. Jassey

Carbon-fixing micro-organisms (CFMs) play a pivotal role in soil carbon cycling, contributing to carbon uptake and sequestration through various metabolic pathways. Despite their importance, accurately quantifying the absolute abundance of these micro-organisms in soils has been challenging. This study used a digital droplet polymerase chain reaction (ddPCR) approach to measure the abundance of key and emerging CFMs pathways in fen and bog soils at different depths, ranging from 0 to 15 cm. We targeted total prokaryotes, oxygenic phototrophs, aerobic anoxygenic phototrophic bacteria and chemoautotrophs, optimizing the conditions to achieve absolute quantification of these genes. Our results revealed that oxygenic phototrophs were the most abundant CFMs, making up 15% of the total prokaryotic abundance. They were followed by chemoautotrophs at 10% and aerobic anoxygenic phototrophic bacteria at 9%. We observed higher gene concentrations in fen than in bog. There were also variations in depth, which differed between fen and bog for all genes. Our findings underscore the abundance of oxygenic phototrophs and chemoautotrophs in peatlands, challenging previous estimates that relied solely on oxygenic phototrophs for microbial carbon dioxide fixation assessments. Incorporating absolute gene quantification is essential for a comprehensive understanding of microbial contributions to soil processes. This approach sheds light on the complex mechanisms of soil functioning in peatlands.

固碳微生物(CFMs)在土壤碳循环中发挥着关键作用,通过各种代谢途径促进碳吸收和固碳。尽管这些微生物非常重要,但准确量化其在土壤中的绝对丰度一直是个挑战。本研究采用数字液滴聚合酶链式反应(ddPCR)方法,测量了不同深度(0 至 15 厘米)的沼泽和沼泽土壤中关键和新兴 CFMs 途径的丰度。我们以原核生物总数、含氧光养菌、需氧无氧光养菌和化学自养菌为目标,优化条件以实现这些基因的绝对定量。我们的研究结果表明,含氧光养菌是数量最多的原核生物,占原核生物总量的 15%。其次是化能自养菌(10%)和需氧光养菌(9%)。我们观察到沼泽中的基因浓度高于沼泽。沼泽和沼泽中所有基因的深度也有差异。我们的研究结果强调了泥炭地中含氧光养菌和化能自养菌的丰富程度,这对之前仅依赖含氧光养菌来评估微生物二氧化碳固定情况的方法提出了挑战。要全面了解微生物对土壤过程的贡献,就必须纳入绝对基因量化。这种方法揭示了泥炭地土壤功能的复杂机制。
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引用次数: 0
Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes 基因组分辨元基因组学揭示了欧洲 44 个淡水湖的营养物质供应对细菌基因组特性的影响。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-17 DOI: 10.1111/1462-2920.16634
Manan Shah, Till L. V. Bornemann, Julia K. Nuy, Martin W. Hahn, Alexander J. Probst, Daniela Beisser, Jens Boenigk

Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows for proliferation. Genome streamlining is associated with genomic properties such as %GC content, genes encoding sigma factors, percent coding regions, gene redundancy, and functional shifts in processes like cell motility and ATP binding cassette transporters, among others. The current study aims to unveil the impact of nutrition on the genome size, %GC content, and functional properties of pelagic freshwater bacteria. We do this at finer taxonomic resolutions for many metagenomically characterized communities. Our study confirms the interplay of trophic level and genomic properties. It also highlights that different nutrient types, particularly phosphorus and nitrogen, impact these properties differently. We observed a covariation of functional traits with genome size. Larger genomes exhibit enriched pathways for motility, environmental interaction, and regulatory genes. ABC transporter genes reflect the availability of nutrients in the environment, with small genomes presumably relying more on metabolites from other organisms. We also discuss the distinct strategies different phyla adopt to adapt to oligotrophic environments. The findings contribute to our understanding of genomic adaptations within complex microbial communities.

了解环境中错综复杂的微生物相互作用至关重要。养分与细菌之间的关系尤其如此,因为磷、氮和有机碳的可用性会影响细菌的种群动态。有人认为,低营养条件会促使基因组精简的进化过程。这一过程有助于保存稀缺的营养物质,并使细菌得以增殖。基因组精简与基因组特性有关,如 %GC 含量、编码σ因子的基因、编码区百分比、基因冗余以及细胞运动和 ATP 结合盒转运体等过程中的功能转变。目前的研究旨在揭示营养对浮游淡水细菌基因组大小、%GC 含量和功能特性的影响。我们对许多元基因组特征群落进行了更精细的分类。我们的研究证实了营养水平与基因组特性之间的相互作用。它还强调了不同营养类型(尤其是磷和氮)对这些特性的不同影响。我们观察到功能特征与基因组大小的协变关系。较大的基因组在运动、环境相互作用和调控基因方面表现出丰富的途径。ABC 转运体基因反映了环境中营养物质的可用性,小基因组可能更依赖于来自其他生物的代谢物。我们还讨论了不同门类为适应寡营养环境而采取的不同策略。这些发现有助于我们了解复杂微生物群落的基因组适应性。
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引用次数: 0
Genome-resolved metagenomics reveals diverse taxa and metabolic complexity in Antarctic lake microbial structures 基因组分辨元基因组学揭示了南极湖泊微生物结构的分类群和代谢复杂性。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-16 DOI: 10.1111/1462-2920.16663
Carla Greco, Dale T. Andersen, Marian L. Yallop, Gary Barker, Anne D. Jungblut

Lake Untersee, a lake in Antarctica that is perennially covered with ice, is home to unique microbial structures that are not lithified. We have evaluated the structure of the community and its metabolic potential across the pigmented upper layers and the sediment-enriched deeper layers in these pinnacle and cone-shaped microbial structures using metagenomics. These microbial structures are inhabited by distinct communities. The upper layers of the cone-shaped structures have a higher abundance of the cyanobacterial MAG Microcoleus, while the pinnacle-shaped structures have a higher abundance of Elainellacea MAG. This suggests that cyanobacteria influence the morphologies of the mats. We identified stark contrasts in the composition of the community and its metabolic potential between the upper and lower layers of the mat. The upper layers of the mat, which receive light, have an increased abundance of photosynthetic pathways. In contrast, the lower layer has an increased abundance of heterotrophic pathways. Our results also showed that Lake Untersee is the first Antarctic lake with a substantial presence of ammonia-oxidizing Nitrospiracea and amoA genes. The genomic capacity for recycling biological molecules was prevalent across metagenome-assembled genomes (MAGs) that cover 19 phyla. This highlights the importance of nutrient scavenging in ultra-oligotrophic environments. Overall, our study provides new insights into the formation of microbial structures and the potential metabolic complexity of Antarctic laminated microbial mats. These mats are important environments for biodiversity that drives biogeochemical cycling in polar deserts.

南极洲的翁特湖(Lake Untersee)是一个常年被冰雪覆盖的湖泊,湖中有独特的未被岩石化的微生物结构。我们利用元基因组学评估了这些尖顶和锥形微生物结构中色素上层和沉积物丰富的深层的群落结构及其代谢潜力。这些微生物结构中栖息着不同的群落。锥形结构的上层有较多的蓝藻 MAG Microcoleus,而尖顶形结构则有较多的 Elainellacea MAG。这表明蓝藻影响了藻垫的形态。我们发现,垫层上层和下层的群落组成及其代谢潜力形成了鲜明对比。垫层上层接受光照,光合作用途径增多。相比之下,下层的异养途径则更多。我们的研究结果还表明,翁特湖是第一个存在大量氨氧化硝基螺旋藻和amoA基因的南极湖泊。回收生物分子的基因组能力在涵盖 19 个门的元基因组(MAGs)中十分普遍。这凸显了超寡养环境中营养物质清除的重要性。总之,我们的研究为了解微生物结构的形成和南极层状微生物毯潜在的代谢复杂性提供了新的视角。这些垫层是生物多样性的重要环境,推动着极地沙漠的生物地球化学循环。
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引用次数: 0
Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph 一种多功能海洋铁氧化化学自养型生物的蛋白质组学比较
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-11 DOI: 10.1111/1462-2920.16632
Roman A. Barco, N. Merino, B. Lam, B. Budnik, M. Kaplan, F. Wu, J. P. Amend, K. H. Nealson, D. Emerson

This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.

本研究进行了比较蛋白质组分析,以确定海洋细菌 Ghiorsea bivora 中化学溶解自养铁氧化生物学功能的潜在遗传标记。迄今为止,这是Zetaproteobacteria类细菌中唯一非强制性铁氧化的特征物种,为研究蛋白质表达差异提供了一个独特的机会,以确定在中性pH下参与铁氧化的关键基因。在铁氧化和氢氧化条件下,共鉴定出 1000 多种蛋白质,并在两种处理中发现了不同表达的蛋白质。值得注意的是,发现了一个在铁氧化过程中上调的基因簇。该基因簇包含的编码细胞色素的基因与已知的铁氧化酶 Cyc2 具有序列相似性。有趣的是,这些在细菌和古细菌中都保留下来的细胞色素并没有表现出 Cyc2 典型的 β 管状结构。该细胞色素团可能编码一种生物纳米线状跨膜复合体,其中包含多种氧化还原蛋白,横跨内膜、周质、外膜和细胞外空间。反转录-PCR定量分析证实,在铁氧化条件下,与该复合物相关的关键基因上调。电微生物学方法进一步证实了这些发现,该方法证明了在阴极电位的三电极系统中 G. bivora 产生的负电流。这项研究为化学自养铁氧化的生物功能提供了重要见解。
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引用次数: 0
Isolation and characterization of a phage collection against Pseudomonas putida 针对假单胞菌(Pseudomonas putida)的噬菌体集的分离和特征描述。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-11 DOI: 10.1111/1462-2920.16671
Age Brauer, Sirli Rosendahl, Anu Kängsep, Alicja Cecylia Lewańczyk, Roger Rikberg, Rita Hõrak, Hedvig Tamman

The environmental bacterium, Pseudomonas putida, possesses a broad spectrum of metabolic pathways. This makes it highly promising for use in biotechnological production as a cell factory, as well as in bioremediation strategies to degrade various aromatic pollutants. For P. putida to flourish in its environment, it must withstand the continuous threats posed by bacteriophages. Interestingly, until now, only a handful of phages have been isolated for the commonly used laboratory strain, P. putida KT2440, and no phage defence mechanisms have been characterized. In this study, we present a new Collection of Environmental P. putida Phages from Estonia, or CEPEST. This collection comprises 67 double-stranded DNA phages, which belong to 22 phage species and 9 phage genera. Our findings reveal that most phages in the CEPEST collection are more infectious at lower temperatures, have a narrow host range, and require an intact lipopolysaccharide for P. putida infection. Furthermore, we show that cryptic prophages present in the P. putida chromosome provide strong protection against the infection of many phages. However, the chromosomal toxin–antitoxin systems do not play a role in the phage defence of P. putida. This research provides valuable insights into the interactions between P. putida and bacteriophages, which could have significant implications for biotechnological and environmental applications.

环境细菌普氏假单胞菌(Pseudomonas putida)具有广泛的代谢途径。这使它在生物技术生产中作为细胞工厂,以及在生物修复战略中降解各种芳香污染物方面大有可为。为了使 P. putida 在其生存环境中繁衍生息,它必须能够抵御噬菌体带来的持续威胁。有趣的是,到目前为止,只有少数噬菌体从常用的实验室菌株 P. putida KT2440 中分离出来,而且还没有噬菌体防御机制的特征。在本研究中,我们展示了一个新的《爱沙尼亚环境普氏菌噬菌体集》(或称 CEPEST)。该收集包括 67 个双链 DNA 噬菌体,隶属于 22 个噬菌体种和 9 个噬菌体属。我们的研究结果表明,CEPEST 收集的大多数噬菌体在较低温度下更具传染性,宿主范围较窄,并且需要完整的脂多糖才能感染普氏菌。此外,我们还发现腐生菌染色体中的隐性噬菌体对许多噬菌体的感染具有很强的保护作用。然而,染色体毒素-抗毒素系统并没有在腐生菌的噬菌体防御中发挥作用。这项研究为了解腐生菌与噬菌体之间的相互作用提供了有价值的见解,可能对生物技术和环境应用产生重大影响。
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引用次数: 0
Differential response of bacteria and fungi to drought on the decomposition of Sarcocornia fruticosa woody stems in a saline stream 细菌和真菌对干旱对盐碱地溪流中马尾松木质茎分解的不同反应。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-07 DOI: 10.1111/1462-2920.16661
Anna Doménech-Pascual, Lorena Carrasco-Barea, Frederic Gich, Judit Boadella, Zeus Freixinos Campillo, Rosa Gómez Cerezo, Andrea Butturini, Anna M. Romaní

Inland saline ecosystems suffer multiple stresses (e.g., high radiation, salinity, water scarcity) that may compromise essential ecosystem functions such as organic matter decomposition. Here, we investigated the effects of drought on microbial colonization and decomposition of Sarcocornia fruticosa woody stems across different habitats in a saline watershed: on the dry floodplain, submerged in the stream channel and at the shoreline (first submerged, then emerged). Unexpectedly, weight loss was not enhanced in the submerged stems, while decomposition process differed between habitats. On the floodplain, it was dominated by fungi and high cellulolytic activity; in submerged conditions, a diverse community of bacteria and high ligninolytic activity dominated; and, on the shoreline, enzyme activities were like submerged conditions, but with a fungal community similar to the dry conditions. Results indicate distinct degradation paths being driven by different stress factors: strong water scarcity and photodegradation in dry conditions, and high salinity and reduced oxygen in wet conditions. This suggests that fungi are more resistant to drought, and bacteria to salinity. Overall, in saline watersheds, variations in multiple stress factors exert distinct environmental filters on bacteria and fungi and their role in the decomposition of plant material, affecting carbon cycling and microbial interactions.

内陆盐碱生态系统承受着多重压力(如高辐射、盐度、缺水),这可能会损害生态系统的基本功能,如有机物分解。在这里,我们研究了干旱对盐碱流域不同生境中马尾藻木质茎的微生物定殖和分解的影响:在干燥的洪泛平原、浸没在河道中以及在海岸线上(先浸没,后浮出水面)。出乎意料的是,沉水茎的重量损失并没有增加,而不同生境的分解过程却各不相同。在冲积平原上,主要是真菌和高纤维素分解活性;在淹没条件下,主要是多样化的细菌群落和高木质素分解活性;而在海岸线上,酶活性与淹没条件相同,但真菌群落与干燥条件相似。结果表明,不同的压力因素驱动着不同的降解路径:在干燥条件下,强烈缺水和光降解;在潮湿条件下,高盐度和氧气减少。这表明真菌对干旱的抵抗力更强,而细菌对盐度的抵抗力更强。总之,在盐碱流域,多种压力因素的变化对细菌和真菌及其在植物物质分解中的作用产生了不同的环境过滤作用,影响了碳循环和微生物之间的相互作用。
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引用次数: 0
A polyethylene surrogate for microbial community enrichment and characterization 用于微生物群落富集和特征描述的聚乙烯替代物。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-06 DOI: 10.1111/1462-2920.16658
Bilge Bahar Camur, Natalia Calixto Mancipe, Brett M. Barney

Plastic pollution is a vast and increasing problem that has permeated the environment, affecting all aspects of the global food web. Plastics and microplastics have spread to soil, water bodies, and even the atmosphere due to decades of use in a wide range of applications. Plastics include a variety of materials with different properties and chemical characteristics, with polyethylene being a dominant fraction. Polyethylene is also an extremely persistent compound with slow rates of photodegradation or biodegradation. In this study, we developed a method to isolate communities of microbes capable of biodegrading a polyethylene surrogate. This method allows us to study potential polyethylene degradation over much shorter time periods. Using this method, we enriched several communities of microbes that can degrade the polyethylene surrogate within weeks. We also identified specific bacterial strains with a higher propensity to degrade compounds similar to polyethylene. We provide a description of the method, the variability and efficacy of four different communities, and key strains from these communities. This method should serve as a straightforward and adaptable tool for studying polyethylene biodegradation.

塑料污染是一个巨大且日益严重的问题,已经渗透到环境中,影响到全球食物网的方方面面。由于几十年来塑料的广泛应用,塑料和微塑料已经扩散到土壤、水体甚至大气中。塑料包括各种具有不同性质和化学特征的材料,其中聚乙烯是最主要的部分。聚乙烯也是一种持久性极强的化合物,光降解或生物降解速度缓慢。在这项研究中,我们开发了一种方法来分离能够生物降解聚乙烯替代物的微生物群落。通过这种方法,我们可以在更短的时间内研究潜在的聚乙烯降解。利用这种方法,我们富集了几个能在几周内降解聚乙烯代用品的微生物群落。我们还发现了一些特定的细菌菌株,它们具有较强的降解与聚乙烯类似的化合物的能力。我们介绍了这种方法、四个不同群落的可变性和功效,以及这些群落中的关键菌株。这种方法可作为研究聚乙烯生物降解的一种简单、适用的工具。
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引用次数: 0
The community of root fungi is associated with the growth rate of Norway spruce (Picea abies) 根部真菌群落与挪威云杉(Picea abies)的生长速度有关。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-05 DOI: 10.1111/1462-2920.16662
Leena Hamberg, Jarno Vanhatalo, Sannakajsa Velmala, Andy F. S. Taylor, John MacKay, Sébastien Caron, Fred O. Asiegbu, Risto Sievänen, Pasi Raumonen, Tuija Hytönen, Taina Pennanen

Our study delved into the relationship between root-associated fungi, gene expression and plant morphology in Norway spruce cuttings derived from both slow-and fast-growing trees. We found no clear link between the gene expression patterns of adventitious roots and the growth phenotype, suggesting no fundamental differences in the receptiveness to fungal symbionts between the phenotypes. Interestingly, saplings from slow-growing parental trees exhibited a higher richness of ectomycorrhizal species and larger roots. Some ectomycorrhizal species, typically found on mature spruces, were more prevalent on saplings from slow-growing spruces. The ericoid mycorrhizal fungus, Hyaloscypha hepaticola, showed a stronger association with saplings from fast-growing spruces. Moreover, saplings from slow-growing spruces had a greater number of Ascomycete taxa and free-living saprotrophic fungi. Aboveground sapling stems displayed some phenotypic variation; saplings from fast-growing phenotypes had longer branches but fewer whorls in their stems compared to those from the slow-growing group. In conclusion, the observed root-associated fungi and phenotypic characteristics in young Norway spruces may play a role in their long-term growth rate. This suggests that the early interactions between spruces and fungi could potentially influence their growth trajectory.

我们的研究深入探讨了挪威云杉插条中根系相关真菌、基因表达和植物形态之间的关系,这些插条既来自生长缓慢的树木,也来自生长迅速的树木。我们发现不定根的基因表达模式与生长表型之间没有明显的联系,这表明两种表型对真菌共生体的接受能力没有本质区别。有趣的是,来自生长缓慢的亲本树木的树苗表现出更丰富的外生菌根物种和更大的根系。一些通常存在于成熟云杉上的外生菌根物种在生长缓慢的云杉树苗上更为普遍。麦角菌根真菌 Hyaloscypha hepaticola 与快速生长的云杉树苗有更紧密的联系。此外,生长缓慢的云杉树苗有更多的子囊菌类群和自由生活的吸液真菌。树苗茎的地上部分显示出一些表型差异;与生长缓慢组的树苗相比,快速生长表型的树苗分枝更长,但茎上的轮纹更少。总之,在挪威云杉幼苗中观察到的根相关真菌和表型特征可能会对其长期生长速度产生影响。这表明,云杉与真菌之间的早期相互作用可能会影响它们的生长轨迹。
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引用次数: 0
Local environment shapes milk microbiomes while evolutionary history constrains milk macronutrients in captive cercopithecine primates 当地环境塑造了乳汁微生物群,而进化史则制约了圈养崖猴灵长类动物乳汁中的宏量营养素。
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-03 DOI: 10.1111/1462-2920.16664
Sally L. Bornbusch, Hannah E. Shinnerl, Lindsey Gentry, Mia M. Keady, Virginia Glick, Carly R. Muletz-Wolz, Michael L. Power

Milk is a complex biochemical fluid that includes macronutrients and microbiota, which, together, are known to facilitate infant growth, mediate the colonization of infant microbiomes, and promote immune development. Examining factors that shape milk microbiomes and milk-nutrient interplay across host taxa is critical to resolving the evolution of the milk environment. Using a comparative approach across four cercopithecine primate species housed at three facilities under similar management conditions, we test for the respective influences of the local environment (housing facility) and host species on milk (a) macronutrients (fat, sugar, and protein), (b) microbiomes (16S rRNA), and (c) predicted microbial functions. We found that milk macronutrients were structured according to host species, while milk microbiomes and predicted function were strongly shaped by the local environment and, to a lesser extent, host species. The milk microbiomes of rhesus macaques (Macaca mulatta) at two different facilities more closely resembled those of heterospecific facility-mates compared to conspecifics at a different facility. We found similar, facility-driven patterns of microbial functions linked to physiology and immune modulation, suggesting that milk microbiomes may influence infant health and development. These results provide novel insight into the complexity of milk and its potential impact on infants across species and environments.

牛奶是一种复杂的生化液体,其中包括宏量营养素和微生物群,众所周知,它们共同促进了婴儿的生长,介导了婴儿微生物群的定植,并促进了免疫系统的发育。研究不同宿主类群中塑造牛奶微生物群和牛奶营养素相互作用的因素,对于解决牛奶环境的进化问题至关重要。我们采用一种比较方法,对饲养在三个设施中、管理条件相似的四个嵴猴灵长类物种进行了比较,检验了当地环境(饲养设施)和宿主物种各自对牛奶(a)宏量营养素(脂肪、糖和蛋白质)、(b)微生物组(16S rRNA)和(c)预测微生物功能的影响。我们发现,牛奶中的主要营养成分是根据宿主的种类来构建的,而牛奶微生物组和预测的功能则主要受当地环境的影响,其次才是宿主的种类。在两个不同设施中的猕猴(Macaca mulatta)的乳汁微生物组与在不同设施中的同种猕猴更相似。我们发现了类似的、由设施驱动的微生物功能模式,这些功能与生理和免疫调节有关,表明牛奶微生物组可能会影响婴儿的健康和发育。这些结果为了解牛奶的复杂性及其在不同物种和环境中对婴儿的潜在影响提供了新的视角。
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引用次数: 0
Temporal and spatial dynamics within the fungal microbiome of grape fermentation 葡萄发酵过程中真菌微生物群的时空动态变化
IF 5.1 2区 生物学 Q2 MICROBIOLOGY Pub Date : 2024-06-01 DOI: 10.1111/1462-2920.16660
Cristobal A. Onetto, Chris M. Ward, Steven Van Den Heuvel, Laura Hale, Kathleen Cuijvers, Anthony R. Borneman

Over 6 years, we conducted an extensive survey of spontaneous grape fermentations, examining 3105 fungal microbiomes across 14 distinct grape-growing regions. Our investigation into the biodiversity of these fermentations revealed that a small number of highly abundant genera form the core of the initial grape juice microbiome. Consistent with previous studies, we found that the region of origin had the most significant impact on microbial diversity patterns. We also discovered that certain taxa were consistently associated with specific geographical locations and grape varieties, although these taxa represented only a minor portion of the overall diversity in our dataset. Through unsupervised clustering and dimensionality reduction analysis, we identified three unique community types, each exhibiting variations in the abundance of key genera. When we projected these genera onto global branches, it suggested that microbiomes transition between these three broad community types. We further investigated the microbial community composition throughout the fermentation process. Our observations indicated that the initial microbial community composition could predict the diversity during the early stages of fermentation. Notably, Hanseniaspora uvarum emerged as the primary non-Saccharomyces species within this large collection of samples.

在 6 年时间里,我们对自发葡萄发酵进行了广泛调查,研究了 14 个不同葡萄种植地区的 3105 个真菌微生物组。我们对这些发酵的生物多样性进行的调查显示,少数高度丰富的菌属构成了最初葡萄汁微生物组的核心。与之前的研究一致,我们发现原产地对微生物多样性模式的影响最大。我们还发现,某些类群始终与特定的地理位置和葡萄品种相关联,尽管这些类群在我们的数据集中只占总体多样性的一小部分。通过无监督聚类和降维分析,我们确定了三种独特的群落类型,每种类型都表现出关键菌属丰度的变化。当我们将这些菌属投影到全球分支上时,发现微生物群落在这三种广泛的群落类型之间过渡。我们进一步研究了整个发酵过程中的微生物群落组成。我们的观察结果表明,最初的微生物群落组成可以预测发酵早期阶段的多样性。值得注意的是,Hanseniaspora uvarum 是大量样本中最主要的非酵母菌物种。
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Environmental microbiology
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