背景:将野生微生物的身份与其生态生理特性和环境功能联系起来是微生物生态学家的关键目标。在为这个目标而努力的许多技术中,稳定同位素探测SIP仍然是原位研究整个微生物群落的最全面的方法。在DNA-SIP中,活跃生长的微生物吸收同位素重的底物,构建更重的DNA,可以按密度划分为多个部分并进行测序。然而,SIP的吞吐量相对较低,需要大量的动手劳动。我们设计并测试了一种半自动,高吞吐量SIP(HT-SIP)管道,以支持良好的复制,时间分辨扩增子和宏基因组学实验。我们将此管道应用于具有重要生态意义的土壤微生境-丛枝菌根真菌(AMF)菌丝周围的磷化区。AMF与大多数植物物种形成共生关系,并在陆地养分和碳循环中起关键作用。
结果:我们的HT-SIP分馏管道,清理,与手动SIP相比,密度梯度的核酸定量需要六分之一的动手劳动,并允许同时处理16个样品。与手动分馏相比,自动密度分馏增加了SIP梯度的可重复性,我们显示向梯度缓冲液中添加非离子去污剂可改善SIPDNA回收率。我们将HT-SIP应用于13CO2植物标记研究中的13C-AMF磷酸化DNA,并使用高分辨率SIP宏基因组学(每个梯度14个宏基因组)创建了宏基因组组装基因组(MAG)。SIP证实AMF根茎内和相关的MAG高度富集(10-33原子%13C),即使土壤的总富集很低(1.8原子%13C)。我们组装了212个13C-hyphosphhereMAG;吸收了大多数AMF衍生的13C的hyphosphhere类群来自门Myxococcota,纤维杆菌,Verrucomicrobiota,和氨氧化古细菌亚硝基属。
结论:我们的半自动HT-SIP方法通过针对SIP-馏分收集和清理的最劳动密集型步骤,减少了操作时间并提高了可重复性。我们在一种独特且研究不足的土壤微生境生成MAG中说明了这种方法,该MAG活跃地生长在AMFhyphihere中(没有植物根)。MAG的系统发育组成和基因含量表明捕食,分解,氨氧化可能是磷化养分循环的关键过程。视频摘要。
Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However,
SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput
SIP (HT-
SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.
Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved
SIP DNA recovery. We applied HT-SIP to 13C-AMF hyphosphere DNA from a 13CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution
SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% 13C), even though the soils\' overall enrichment was low (1.8 atom% 13C). We assembled 212 13C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived 13C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.
Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of
SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs\' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.