Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation,Environmental Microbiology

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Development of a digital droplet PCR approach for the quantification of soil micro-organisms involved in atmospheric CO2 fixation
Environmental Microbiology ( IF 4.3 ) Pub Date : 2024-06-18 , DOI: 10.1111/1462-2920.16666
Marie Le Geay ₁ , Kyle Mayers ₂ , Martin Küttim ₃ , Béatrice Lauga ₄ , Vincent E J Jassey ₁

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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.

中文翻译：

开发数字液滴 PCR 方法来定量参与大气二氧化碳固定的土壤微生物

固碳微生物（CFM）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封存。尽管它们很重要，但准确量化土壤中这些微生物的绝对丰度一直具有挑战性。本研究使用数字液滴聚合酶链反应 (ddPCR) 方法来测量不同深度（0 至 15 厘米）的沼泽土壤中关键和新兴 CFM 途径的丰度。我们以总原核生物、产氧光养生物、需氧缺氧光养细菌和化能自养生物为目标，优化条件以实现这些基因的绝对定量。我们的结果表明，产氧光养生物是最丰富的 CFM，占原核生物总丰度的 15%。其次是化能自养细菌（占 10%）和需氧不产氧光养细菌（占 9%）。我们观察到沼泽中的基因浓度高于沼泽中。深度也存在差异，沼泽地和沼泽地的所有基因的深度都不同。我们的研究结果强调了泥炭地中产氧光养生物和化能自养生物的丰富性，挑战了之前仅依靠产氧光养生物进行微生物二氧化碳固定评估的估计。结合绝对基因定量对于全面了解微生物对土壤过程的贡献至关重要。这种方法揭示了泥炭地土壤功能的复杂机制。

更新日期：2024-06-19

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