A comparison among EL-FAME, PLFA, and quantitative PCR methods to detect changes in the abundance of soil bacteria and fungi

IF 9.8 1区 农林科学 Q1 SOIL SCIENCE Soil Biology & Biochemistry Pub Date : 2024-08-19 DOI:10.1016/j.soilbio.2024.109557
José A. Siles, Roberto Gómez-Pérez, Alfonso Vera, Carlos García, Felipe Bastida
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Abstract

EL-FAME (ester-linked fatty acid methyl ester), PLFA (phospholipid fatty acid), and qPCR (quantitative PCR) of ribosomal genes are three of the most common methods used to quantify soil microbial communities due to their versatility. The reliability of these three methods has not been simultaneously compared in situations of rapid (in the frame of days and weeks) changes in soil microbial abundances. For this purpose, we (i) incubated badland, cropland, and forest soils with nutrients or antibiotics for 2, 7, 14, and 28 days, (ii) quantified total, bacterial, and fungal abundances through EL-FAME, PLFA, and qPCR methods, and (iii) measured soil basal respiration (as indicator of living biomass). The general dynamic patterns of the three soil microbial fractions in response to soil addition of nutrients and antibiotics were captured by the three methods, which led to strong and positive associations between the abundances of total microorganisms, bacteria, and fungi measured by the three procedures. However, these relationships were stronger between the EL-FAME and PLFA results. Further, soil basal respiration was associated to a higher extent with total, bacterial, and fungal abundances captured by EL-FAME and PLFA analyses than with those measured by qPCR, which suggests that the first two methods are most closely related to the soil living microbial community. In general, dynamics in the abundance of total and bacterial communities were better captured than those of fungi by the three methods. The PLFA analysis seems to perform better than the EL-FAME method in forest soil and in detecting the small antibiotic-induced decreases in microbial abundances. Since the EL-FAME method is cheaper and allows a much faster processing of samples than the PLFA method, and the reliability of both methods is similar in detecting rapid changes of soil microbial abundances, choosing EL-FAME over PLFA may be advantageous in most cases.

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比较 EL-FAME、PLFA 和定量 PCR 三种检测土壤细菌和真菌丰度变化的方法
EL-FAME(酯联脂肪酸甲酯)、PLFA(磷脂脂肪酸)和核糖体基因 qPCR(定量 PCR)是量化土壤微生物群落最常用的三种方法,因为它们用途广泛。这三种方法在土壤微生物丰度快速变化(几天或几周)的情况下的可靠性还没有同时进行过比较。为此,我们(i) 将坏地、耕地和森林土壤与养分或抗生素一起培养 2、7、14 和 28 天,(ii) 通过 EL-FAME、PLFA 和 qPCR 方法量化总丰度、细菌丰度和真菌丰度,(iii) 测量土壤基础呼吸(作为生物量指标)。三种方法都能捕捉到三种土壤微生物组分对土壤中添加养分和抗生素的反应的一般动态模式,这使得三种方法测量的微生物总数、细菌和真菌的丰度之间存在很强的正相关关系。不过,EL-FAME 和 PLFA 的结果之间的关系更为密切。此外,与 qPCR 方法相比,EL-FAME 和 PLFA 分析捕获的土壤基础呼吸量与微生物总量、细菌和真菌丰度的相关程度更高,这表明前两种方法与土壤活微生物群落的关系最为密切。一般来说,三种方法都能更好地捕捉到总群落和细菌群落的丰度动态,而不是真菌群落的丰度动态。在森林土壤中,PLFA 分析似乎比 EL-FAME 方法更能检测出抗生素引起的微生物丰度的微小下降。由于 EL-FAME 方法比 PLFA 方法成本更低,处理样品的速度更快,而且这两种方法在检测土壤微生物丰度快速变化方面的可靠性相似,因此在大多数情况下,选择 EL-FAME 方法比选择 PLFA 方法更有优势。
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来源期刊
Soil Biology & Biochemistry
Soil Biology & Biochemistry 农林科学-土壤科学
CiteScore
16.90
自引率
9.30%
发文量
312
审稿时长
49 days
期刊介绍: Soil Biology & Biochemistry publishes original research articles of international significance focusing on biological processes in soil and their applications to soil and environmental quality. Major topics include the ecology and biochemical processes of soil organisms, their effects on the environment, and interactions with plants. The journal also welcomes state-of-the-art reviews and discussions on contemporary research in soil biology and biochemistry.
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