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

IF 4.3 2区 生物学 Q2 MICROBIOLOGY
Marie Le Geay, Kyle Mayers, Martin Küttim, Béatrice Lauga, Vincent E. J. Jassey
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Abstract

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.

Abstract Image

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。
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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来源期刊
Environmental microbiology
Environmental microbiology 环境科学-微生物学
CiteScore
9.90
自引率
3.90%
发文量
427
审稿时长
2.3 months
期刊介绍: Environmental Microbiology provides a high profile vehicle for publication of the most innovative, original and rigorous research in the field. The scope of the Journal encompasses the diversity of current research on microbial processes in the environment, microbial communities, interactions and evolution and includes, but is not limited to, the following: the structure, activities and communal behaviour of microbial communities microbial community genetics and evolutionary processes microbial symbioses, microbial interactions and interactions with plants, animals and abiotic factors microbes in the tree of life, microbial diversification and evolution population biology and clonal structure microbial metabolic and structural diversity microbial physiology, growth and survival microbes and surfaces, adhesion and biofouling responses to environmental signals and stress factors modelling and theory development pollution microbiology extremophiles and life in extreme and unusual little-explored habitats element cycles and biogeochemical processes, primary and secondary production microbes in a changing world, microbially-influenced global changes evolution and diversity of archaeal and bacterial viruses new technological developments in microbial ecology and evolution, in particular for the study of activities of microbial communities, non-culturable microorganisms and emerging pathogens
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