Molecular Microbiology Research 2024, Vol.14, No.1, 20-30 http://microbescipublisher.com/index.php/mmr 22 1.2 Application of metagenomics in environmental microbial research Metagenomics technology is increasingly used in the study of environmental microorganisms. It not only provides a new perspective, but also helps us gain a deeper understanding of the interaction between microbial communities and the environment. Take the study of soil microorganisms as an example. Soil is one of the most complex and diverse ecosystems on earth, containing numerous microbial species. It is difficult to fully reveal the genetic information and functions of these microorganisms using traditional research methods. However, with the help of metagenomics technology, a comprehensive analysis of the microbial communities in soil samples can be performed. In 2021, Liu Binbin and others from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, used metagenomics sequencing combined with nitrogen cycle gene targeted assembly (Gene-targeted Assembly (Xander method) technology) to study the impact of long-term nitrogen fertilization (20 years) on North China. Effects of microbial communities on nitrogen cycling in plains. It was found that long-term nitrogen fertilization significantly increased the microbial abundance under most nitrogen cycle processes, but decreased the microbial abundance during nitrogen fixation. Research has confirmed that metagenomic sequencing combined with functional gene targeted assembly technology provides strong support for the realization of "finding needles in a haystack" of specific functional genes (Sun et al., 2021). In 2023, Professor Xu Jianming's team at Zhejiang University unveiled the "veil" of soil dark matter at a global scale for the first time by analyzing global soil metagenomic big data. His research team used metagenomics technology to reveal the rich microbial diversity and genetic resource diversity of global soil microbial dark matter. This research result provides us with a new perspective in analyzing microbial communities in soil and lays a solid foundation for future mining and utilization of genetic resources (Ma et al., 2023). 1.3 Advantages and limitations of metagenomics technology in studying environmental microbial diversity Metagenomics technology provides a new perspective for the study of environmental microbial diversity with its non-culture dependence and high-throughput sequencing capabilities. This technology breaks through the limitations of traditional culture methods, allowing researchers to more comprehensively reveal the true composition and diversity of microbial communities in environmental samples, and avoid the problem of missing microorganisms due to difficulty in cultivating them. At the same time, combined with high-throughput sequencing, metagenomics technology can acquire and analyze a large amount of genetic information in a short time, accelerate the research process, and deepen the understanding of the structure and function of microbial communities. Through in-depth analysis of the species composition, gene types and interaction relationships of microbial communities, metagenomics technology provides important support for understanding the role of microorganisms in ecosystems and their interactions with environmental factors (Staley and Sadowsky, 2016). However, metagenomics technology also faces some limitations. Data analysis is one of the biggest challenges. The huge amount of data requires high-performance computers and professional bioinformatics tools to process, increasing research costs and requirements for researcher skills. In addition, uncertainty in gene annotation is also a problem, and similarities between microbial genomes may lead to misjudgments or omissions. Newly discovered microbial species and genes may not match known databases, making annotation results incomplete. The complexity of environmental samples also makes accurate analysis difficult, requiring more careful and precise data interpretation. Zhang et al. (2021) and Techtmann and Hazen (2016) discuss the evolution from short-gun sequencing to next-generation sequencing (NGS) and third-generation sequencing (TGS), which allow rapid detection of pathogenic microorganisms and better An overview of the classification of microbial species. However, they also acknowledged limitations, such as challenges in metagenomic assembly and annotation due to the complexity of environmental samples.
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