Microorganisms are vital to the overall ecosystem functioning, stability, and sustainability. Soil fertility and health depend on chemical composition and also on the qualitative and quantitative nature of microorganisms inhabiting it. Historically, denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism, DNA amplification fingerprinting, amplified ribosomal DNA restriction analysis, terminal restriction fragment length polymorphism, length heterogeneity PCR, and ribosomal intergenic spacer analysis were used to assess soil microbial community structure (SMCS), abundance, and diversity. However, these methods had significant shortcomings and limitations for application in land reclamation monitoring. SMCS has been primarily determined by phospholipid fatty acid (PLFA) analysis. This method provides a direct measure of viable biomass in addition to a biochemical profile of the microbial community. PLFA has limitations such as overlap in the composition of microorganisms and the specificity of PLFAs signature. In recent years, high-throughput next-generation sequencing has dramatically increased the resolution and detectable spectrum of diverse microbial phylotypes from environmental samples and it plays a significant role in microbial ecology studies. Next-generation sequencings using 454, Illumina, SOLiD, and Ion Torrent platforms are rapid and flexible. The two methods, PLFA and next-generation sequencing, are useful in detecting changes in microbial community diversity and structure in different ecosystems. Single-molecule real-time (SMRT) and nanopore sequencing technologies represent third-generation sequencing (TGS) platforms that have been developed to address the shortcomings of second-generation sequencing (SGS). Enzymatic and soil respiration analyses are performed to further determine soil quality and microbial activities. Other valuable methods that are being recently applied to microbial function and structures include NanoSIM, GeoChip, and DNA stable staple isotope probing (DNA-SIP) technologies. They are powerful metagenomics tool for analyzing microbial communities, including their structure, metabolic potential, diversity, and their impact on ecosystem functions. This review is a critical analysis of current methods used in monitoring soil microbial community dynamic and functions.

中文翻译：

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监测土壤微生物群落动态和功能的研究进展。

微生物对于整个生态系统的功能，稳定性和可持续性至关重要。土壤肥力和健康取决于化学成分，还取决于居住在其中的微生物的定性和定量性质。历史上，变性梯度凝胶电泳（DGGE）和温度梯度凝胶电泳（TGGE），单链构象多态性，DNA扩增指纹图谱，扩增的核糖体DNA限制性酶切分析，末端限制性片段长度多态性，长度异质性PCR和核糖体基因间间隔分析是用于评估土壤微生物群落结构（SMCS），丰度和多样性。但是，这些方法在土地开垦监测中的应用存在明显的缺陷和局限性。SMCS主要是通过磷脂脂肪酸（PLFA）分析确定的。除了微生物群落的生化特征之外，该方法还提供了对活生物量的直接测量。PLFA具有局限性，例如微生物组成重叠和PLFAs签名的特异性。近年来，高通量下一代测序技术极大地提高了环境样品中多种微生物系统型的分辨率和可检测光谱，并且在微生物生态学研究中发挥了重要作用。使用454，Illumina，SOLiD和Ion Torrent平台的下一代测序快速而灵活。PLFA和下一代测序这两种方法可用于检测不同生态系统中微生物群落多样性和结构的变化。单分子实时（SMRT）和纳米孔测序技术代表了第三代测序（TGS）平台，该平台已开发用于解决第二代测序（SGS）的缺点。进行酶和土壤呼吸分析以进一步确定土壤质量和微生物活性。最近应用于微生物功能和结构的其他有价值的方法包括NanoSIM，GeoChip和DNA稳定的短程同位素探测（DNA-SIP）技术。它们是强大的宏基因组学工具，可用于分析微生物群落，包括其结构，代谢潜力，多样性及其对生态系统功能的影响。这篇评论是对目前用于监测土壤微生物群落动态和功能的方法的批判性分析。