ISME communications最新文献_第4页

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

ISME communications

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。

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

ISME communications

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

ISME communications

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。

ISME communications

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

ISME communications

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

ISME communications

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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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。

ISME communications

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

The underestimated fraction: diversity, challenges and novel insights into unicellular cyanobionts of lichens 被低估的部分：地衣单细胞蓝藻寄生虫的多样性、挑战和新见解

ISME communications

Pub Date : 2024-05-06 DOI: 10.1093/ismeco/ycae069

Patrick Jung, Laura Briegel-Williams

Lichens are remarkable and classic examples of symbiotic organisms that have fascinated scientists for centuries. Yet, it has only been for a couple of decades that significant advances have focused on the diversity of their green algal and/or cyanobacterial photobionts. Cyanolichens, which contain cyanobacteria as their photosynthetic partner, include up to 10% of all known lichens and as such, studies on their cyanobionts are much rarer compared to their green algal counterparts. For the unicellular cyanobionts, i.e., cyanobacteria that do not form filaments, these studies are even scarcer. Nonetheless, these currently include at least 10 different genera in the cosmopolitan lichen order Lichinales. An international consortium (International Network of Cyanobionts; INCb) will tackle this lack of knowledge. In this article, we discuss the status of current unicellular cyanobiont research, compare the taxonomic resolution of photobionts from cyanolichens with those of green algal lichens (chlorolichens), and give a roadmap of research on how to recondition the underestimated fraction of symbiotic unicellular cyanobacteria in lichens.

地衣是共生生物的杰出和经典范例，几个世纪以来一直吸引着科学家。然而，直到几十年前，人们才开始关注地衣的绿藻和/或蓝藻光附着物的多样性。含蓝藻作为光合作用伙伴的蓝藻地衣占所有已知地衣的 10%。对于单细胞蓝藻，即不形成丝状体的蓝藻，这些研究则更为稀少。不过，这些研究目前至少包括世界性地衣目中的 10 个不同属。一个国际联盟（国际藻类网络；INCb）将解决这一知识匮乏的问题。在本文中，我们将讨论当前单细胞蓝藻寄生菌的研究现状，比较蓝藻地衣与绿藻地衣（叶绿藻地衣）中光寄生菌的分类分辨率，并就如何修复地衣中被低估的部分共生单细胞蓝藻给出研究路线图。

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引用次数: 0

Microbe-cellulose hydrogels as a model system for particulate carbon degradation in soil aggregates 将微生物-纤维素水凝胶作为土壤团聚体中颗粒碳降解的模型系统

ISME communications

Pub Date : 2024-05-04 DOI: 10.1093/ismeco/ycae068

Pieter Candry, Bruce J Godfrey, M. K. Winkler

Particulate carbon (C) degradation in soils is a critical process in the global C cycle governing greenhouse gas fluxes and C storage. Millimeter-scale soil aggregates impose strong controls on particulate C degradation by inducing chemical gradients of e.g., oxygen, as well as limiting microbial mobility in pore structures. To date, experimental models of soil aggregates have incorporated porosity and chemical gradients but not particulate C. Here, we demonstrate a proof-of-concept encapsulating microbial cells and particulate C substrates in hydrogel matrices as a novel experimental model for soil aggregates. Ruminiclostridium cellulolyticum was co-encapsulated with cellulose in millimeter-scale polyethyleneglycol-dimethacrylate (PEGDMA) hydrogel beads. Microbial activity was delayed in hydrogel-encapsulated conditions, with cellulose degradation and fermentation activity being observed after 13 days of incubation. Unexpectedly, hydrogel encapsulation shifted product formation of R. cellulolyticum from an ethanol-lactate-acetate mixture to an acetate-dominated product profile. Fluorescence microscopy enabled simultaneous visualization of the PEGDMA matrix, cellulose particles, and individual cells in the matrix, demonstrating growth on cellulose particles during incubation. Together, these microbe-cellulose-PEGDMA hydrogels present a novel, reproducible experimental soil surrogate to connect single cells to process outcomes at the scale of soil aggregates and ecosystems.

土壤中的微粒碳（C）降解是全球碳循环中的一个关键过程，影响着温室气体通量和碳储存。毫米尺度的土壤团聚体通过诱导氧等化学梯度以及限制孔隙结构中微生物的流动性，对微粒碳降解施加了强有力的控制。迄今为止，土壤团聚体的实验模型都包含孔隙度和化学梯度，但不包括微粒碳。在这里，我们展示了一种概念验证方法，即在水凝胶基质中封装微生物细胞和微粒碳基质，作为土壤团聚体的新型实验模型。纤维素溶解瘤反刍梭菌与纤维素共同被包裹在毫米级聚乙二醇二甲基丙烯酸酯（PEGDMA）水凝胶珠中。在水凝胶包囊条件下，微生物的活性被延迟，培养 13 天后才能观察到纤维素降解和发酵活性。意想不到的是，水凝胶封装使 R. cellulolyticum 的产物形成从乙醇-乳酸-乙酸酯混合物转变为以乙酸酯为主的产物。荧光显微镜可同时观察到 PEGDMA 基质、纤维素颗粒和基质中的单个细胞，显示了培养过程中纤维素颗粒上的生长情况。总之，这些微生物-纤维素-PEGDMA 水凝胶提供了一种新颖、可重复的实验土壤替代物，可将单细胞与土壤聚集体和生态系统规模的过程结果联系起来。

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引用次数: 0

Growth rates of marine prokaryotes are extremely diverse, even among closely related taxa 海洋原核生物的生长率差异极大，即使在关系密切的类群之间也是如此

ISME communications

Pub Date : 2024-05-02 DOI: 10.1093/ismeco/ycae066

Ona Deulofeu-Capo, Marta Sebastián, Adrià Auladell, Clara Cardelús, I. Ferrera, Olga Sánchez, J. Gasol

Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, CARD-FISH subcommunity cell-counts or metagenomic-OTUs. Our calculations unveil a broad range of growth rates [0.3-10 d-1] with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the in situ communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa.

海洋原核生物在海洋生物地球化学循环中发挥着至关重要的作用，它们的贡献受其生长速率的强烈影响。因此，阐明海洋原核生物生长率的变异性和系统发育印记对于更好地确定各个类群在生物地球化学循环中的作用至关重要。在此，我们利用地中海西北部的海水进行了操纵实验，以较高的系统发育分辨率估算了原核生物的生长率。实验在四季进行，采用了不同的处理方法，减少了限制生长的因素：捕食者、营养供应、病毒和光照。利用原核生物总丰度和每个单个 ASV 的比例，通过估计绝对丰度的变化计算出基于单个扩增子序列变体（ASV）的生长率。不同实验中获得的增长率趋势与其他基于总细胞数、CARD-FISH 子群落细胞数或元基因组-OTU 的估计值一致。我们的计算揭示了一个广泛的生长率范围[0.3-10 d-1]，即使在密切相关的 ASV 中也存在显著的差异。同样，生长限制因素对单个 ASV 的影响在一年中也会发生变化。在营养限制和病毒压力较小的处理中，冬春两季以及全年都有大量反应灵敏的 ASV。反应最灵敏的 ASV 在原位群落中很少见，它们组成了一个庞大的类群，有可能对环境变化做出快速反应。从根本上说，我们的研究结果突显了所观察到的生长率范围缺乏系统发生学上的一致性，以及对各种限制因素的不同反应，即使是对亲缘关系很近的类群也是如此。

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引用次数: 0