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Method for acquiring relative abundance and activity of whole-course ammoxidation microorganisms from complex environment system based on macro omics technology

A technology of ammonia oxidizing microorganisms and complex environment, which is applied in the field of soil and water pollution prevention and control, and achieves the effects of high flux, high accuracy and high reliability.

Active Publication Date: 2021-06-11
PEKING UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0006] However, no method has been reported to obtain the relative abundance and activity of ammonia-oxidizing microorganisms from complex environmental systems based on metagenomics technology.

Method used

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  • Method for acquiring relative abundance and activity of whole-course ammoxidation microorganisms from complex environment system based on macro omics technology
  • Method for acquiring relative abundance and activity of whole-course ammoxidation microorganisms from complex environment system based on macro omics technology
  • Method for acquiring relative abundance and activity of whole-course ammoxidation microorganisms from complex environment system based on macro omics technology

Examples

Experimental program
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Effect test

Embodiment 1

[0102] Example 1 Collection and Metagenome / Metatranscriptome Sequencing of Samples Used in the Present Invention

[0103] 1.1 Sample collection

[0104] The microbial diversity of the river ecosystem is high, which is a typical complex environmental system. Take the Yangtze River, the largest river in Asia, as an example. Referring to the national basic hydrological monitoring stations arranged by the Hydrological Bureau of the Yangtze River Water Conservancy Commission, select 10 sections on the main stream, including Yibin in Sichuan, Cuntan in Chongqing, Badong in Hubei, Yichang in Hubei, Chenglingji (Lian) in Hubei, Wuhan in Hubei, Datong in Anhui , Wuhu in Anhui, Zhenjiang in Jiangsu, and Xuliujing in Jiangsu. The total length from Yibin upstream to the mouth of the sea is about 2750km.

[0105] Metagenome sample collection strategy: Water and sediment samples were collected simultaneously at all sampling sections, and the sample collection was completed within a certai...

Embodiment 2

[0113] Example 2 Acquisition of the genome and transcriptome of the whole ammonia oxidizing microorganism

[0114] 2.1 Quality control of metagenomic / macrotranscriptome off-machine data

[0115]Utilize the NGS QC Toolkit (v 2.3.3) software to carry out quality control (parameters: 25-l 70-s 20-p 8) to off-machine metagenomic / macrotranscriptome data, the specific quality control standards are as follows: remove the N base For the sequence, remove the low-quality bases with a quality score 30%, and keep the remaining pair and single sequences. After quality control, metagenomic DNA-optimized short sequences accounted for 96.85-98.63% (average value 97.85%) of the original data, and metagenomic RNA-optimized short sequences accounted for 98.75-99.01% (average value 98.87%) of the original data volume. ), proving that the quality of the high-throughput sequencing data in this study is good (Table 1). Subsequently, use SortMeRNA (v 2.0) software to remove short ribosomal RNA sequ...

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Abstract

The invention belongs to the field of water and soil pollution prevention and control, and particularly relates to a method for acquiring relative abundance and activity of whole-course ammoxidation microorganisms from a complex environment system based on a macro omics technology. Through metagenome / metatranscriptome sequencing and bioinformatics processing, whole-course ammoxidation microbial genomes and transcripts are extracted from microbial communities with complex environments, the relative abundance, activity and community structure characteristics of whole-course ammoxidation microorganisms in a system are determined, a complete picture of a group metabolic potential model is constructed, and the potential contribution of the microorganisms to the nitrogen conversion process is determined. The method has the characteristics of high flux, high sensitivity and high accuracy, does not need to enrich and culture microorganisms, has an in-situ characteristic, is suitable for large-scale sampling investigation and research, and has important significance on optimization of a nitrification management strategy in a specific region.

Description

technical field [0001] The invention belongs to the field of soil and water pollution prevention and control, and specifically relates to a method for obtaining the relative abundance and activity of ammonia-oxidizing microorganisms in a complex environment system based on macro-omics technology. Background technique [0002] Nitrogen is an essential element for maintaining the species composition and functional diversity of global ecosystems, and the nitrogen cycle is a basic process of biogeochemical cycles. Due to the increasingly frequent human activities, the excessive discharge of nitrogen-containing compounds mainly ammonia nitrogen and nitrate nitrogen, the nitrogen load of the ecosystem continues to increase, and it is easy to cause regional and even global water eutrophication and other environmental problems. [0003] Microbial-driven nitrification, denitrification, and anammox are key to maintaining nitrogen balance. Among them, nitrification refers to the proce...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B30/20
CPCG16B30/10G16B30/20
Inventor 刘树枫王海英陈倩王佳文蔡鹤童刘思彤倪晋仁
Owner PEKING UNIV
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