Carbon is one of the main elements in living matter and an important part of organic matter. There are four main carbon pools on the earth, namely atmospheric carbon pool, ocean carbon pool, terrestrial ecosystem carbon pool and lithosphere carbon pool. The carbon cycle refers to the cycle of carbon elements in nature. Carbon dioxide (CO2) in the atmosphere is absorbed by plants in the land and ocean, and then returns to the atmosphere in the form of carbon dioxide through biological or geological processes and human activities. This is the basic process of the carbon cycle in nature. The carbon cycle in the biosphere is mainly manifested in the fact that green plants absorb carbon dioxide from the air, convert it into glucose through photosynthesis, and release oxygen (O2). Petroleum coal is a byproduct of excess carbon sequestration.
Figure Conceptual model of carbon cycle in biocrust community[1]
Element cycle strategy:
functional gene amplification
1. Primer specificity, coverage is not comprehensive enough;
2. Only part of the element cycle-related genes can be obtained.
Metagenome analysis
1. The metabolic pathways of element circulation are not comprehensive enough, and the classification of circulation pathways is not clear enough;
2. It cannot meet the current research needs of high-level scientific research papers.
new process
1. KEGG annotation results based on metagenomic standard analysis;
2. The carbon, nitrogen, sulfur and phosphorus cycle pathways and detailed gene abundance calculation methods obtained from literature integration;
3. Calculate the gene abundance of each pathway of carbon, nitrogen, sulfur and phosphorus cycles in each sample, and then perform a series of comparisons between samples.
Metagenomic carbon cycle analysis program:
The metagenomic carbon cycle scheme, based on the KEGG annotation results obtained by the metagenomic standard analysis, and consulting a large number of high-scoring SCI literature related materials based on the metagenomic sequencing analysis of the environmental microbial community element cycle, established a complete carbon cycle cycle model map, and constructed Contains 19 key genes and a complete carbon cycle analysis program covering 7 carbon cycle subpaths.
By establishing a complete model diagram of the carbon cycle process, the functional genes involved in different metabolic processes and their abundance calculation methods are determined, and the comparison map of the abundance difference of the carbon cycle functional genes in the microbial community of environmental samples is drawn, and further through the identified related functional genes Perform taxonomic annotations to identify the main functional microbial species involved in carbon cycling in different environmental samples. Provides mainstream metagenomic carbon cycle analysis content including composition analysis, differential analysis, correlation analysis, etc., to help you easily realize in-depth excavation of carbon cycle function mechanism.
carbon cycle path
Newly upgraded metagenomic carbon cycle
The analysis content includes four analysis modules:
Quantification and comparative analysis of carbon cycle function gene abundance
Carbon cycle functional gene pathway map
Comparative analysis of Beta diversity between samples/groups
Host microbial identification and joint analysis with functional genes
The newly upgraded metagenome phosphorus cycle analysis has carefully optimized the display of the results. On the premise of ensuring the clear display of the analysis results, the detailed parameters of the analysis result graph have been optimized and adjusted. The analysis results can be directly displayed without any adjustment. Meet the requirements for article publication.
The graph showing the analysis results of Lingen's biological carbon cycle
Carbon cycle functional gene abundance heat map
Carbon cycle functional gene pathway cycle diagram
Between-sample/between-group comparative analysis
Host Microbiome Identification (subpath)
Classic literature case
Title: Research Progress on Carbon Cycle Mechanism of Biocrust Microbial Community [1]
Journal: Soil Biology and Biochemistry
Impact factor: 8.546
DOI：10.1016/j.soilbio.2022.108729
The carbon cycle is the most important and complex biogeochemical cycle in soil ecosystems, but its current understanding at the community level is still limited. Biocrusts are known ecosystem engineers and are ideal model systems for the study of biogeochemical cycles. Soil microorganisms are the key groups driving soil carbon transformation. Although meta-omics technology can predict the material cycle process through gene abundance, it is limited by complex factors such as the physiological state of microorganisms, the chemical structure type of soil organic matter, and the difference in the redox state of organic carbon. It has always been a difficult problem to study the pattern and process of soil carbon cycle at the microbial community level.
In this study, five batches of sampling surveys were carried out for four consecutive years and five batches of biological crusts (algal crusts, cyanobacterial lichen crusts, green algal lichen crusts, and moss crusts) in different successional stages in typical field plots. A metagenomic technology and big data model analysis method revealed the microbial carbon cycle pattern and its interaction and regulation mechanism in the biological crust community.
The results showed that the abundance of energy-consuming light-driven inorganic carbon (IC) fixation genes was low, and the economical chemical energy-driven high-molecular organic carbon degradation, fermentation, aerobic respiration and CO oxidation genes were more abundant. Co-occurrence analysis further revealed that the carbon cycle in the biocrust ecosystem consists of an assimilative module similar to primary production and an assimilative module similar to secondary production; the relationship between cycle pathways and microbial community composition changes over succession. Dynamically, the two modules are linked by the CBB cycle, ethanol and propionate fermentation, and balanced by aridity and salinity.
Figure 1 The carbon cycle of crust based on metagenomic sequencing
Figure 2 The co-occurrence network of key genes in the carbon cycle and high-abundance microorganisms at the genus level
references
[1] Carbon cycle in the microbial ecosystems of biological soil crusts. Soil Biology and Biochemistry, 2022.