Introduction
How to link microbial communities with their functions is a scientific problem of great concern in the study of environmental microbial ecology. The exploration of this subject can enrich people's understanding of microbial functional diversity and it has a wide application prospect in agricultural, industrial, environment and medicine. In the past, microorganisms with specific functions have been isolated and identified by laboratory culture, but only 0.1-1% of the total number of microorganisms can be cultured in a laboratory. A great deal of information about the function of microorganisms is not known. In recent years, stable isotope probing (SIP) has been developed by combining stable isotope labeling technique with molecular biology technique, which can be used to identify microbial community composition in various environments and can determine its function in environmental processes at the same time. It can provide a large amount of information about microbial interactions and metabolic functions in complex communities and then can be well associated microbial communities with their functions, showing a broad application prospect. Of course, stable isotope-labeled compounds are indispensable in this technique.
The process of SIP technique
The basic process of SIP is as follow: The environmental samples of in situ or microcosmic are exposed to stable isotope-labeled substrates and some microorganisms present in these samples can use the stable isotope-labeled compounds in the substrates as carbon or nitrogen sources for substance metabolism and for their own growth needs. Then the stable isotopes can be absorbed and assimilated into the microbe, and are involved in the synthesis of certain substances biomarkers such as nucleic acids (DNA and RNA) and phospholipid fatty acids (PLFA) (This is also called DNA stable isotope probing, RNA stable isotope probing and PLFA stable isotope probing). Finally, the stable isotope-labeled biomarkers of these microorganisms were analyzed by extraction, separation and purification to understand the relationship between microorganisms in the environment. The flow diagram of the SIP methods is shown in Fig. 1 [1].
Fig. 1 Flow diagram of the SIP methods (take DNA stable isotope probing as example).
Application of isotope-labeled compounds in SIP
In the existing SIP experiments, 13C labeled compounds are mostly used as marker. There are three main categories of 13C labeled compound matrix: 13CO2, 13C-methyl compound (such as 13CH4, 13CH3OH, 13CH3Br and 13CH3Cl) and 13C-hydrocarbon (such as 13C-acetic acid, 13C-glucose, 13C-caffeine, 13C-naphthalene, 13C-phenanthrene, 13C-toluene, 13C-phenol, 13C-propionate). The choice of 13C-matrix may depend on the purpose of the study. For example, 13CO2 is mainly used for the study of the interaction of plant-microorganism on terrestrial ecosystem cycle, carbon turnover rate in soil and methanogenic mechanism and methanogenic bacteria in rice field. 13C-methyl compounds are mostly used in the study of methyl trophic bacteria (methanotrophic bacteria, methanotrophic bacteria, methanotrophic bacteria). 13C-hydrocarbon compounds are mainly used to study the biodegradation process and mechanism of polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and other organic pollutants. Meanwhile, other stable isotope-labeled compounds involved in the synthesis of macromolecules of nucleic acids, phospholipids and fatty acids in vivo, such as 15N, 18O, 2H labeled compounds, also have the potential to be used as markers for SIP experiments. In particular, 15N-labeled compounds can be used to study various microbial functional groups and their interactions in the nitrogen biogeochemical cycle [2].
What can we do?
Alfa Chemistry has been committed to the development of microbial ecology, aiming to study the correlation between microbial communities and their functions for promoting the related issues research of agricultural, industrial, environment and medicine, etc. We can provide various stable isotope-labeled compounds as the nutrition substrate for microbial ecology study, including 13C, 15N, 18O, 2H labeled compounds. And we also provide our customers with high-quality stable isotope-labeled compounds design and customization services. No matter what design ideas you have, we will implement them together with you. Please contact us immediately to order or cooperate in research and development with high quality and reasonable price.
References
- Li, B., et al. DNA-SIP reveals the diversity of chemolithoautotrophic bacteria inhabiting three different soil types in typical karst rocky desertification ecosystems in Southwest China[J]. Microbial ecology, 2018, 76(4): 976-990.
- Gu, Y., et al. Stable isotope probing and its applications in microbial ecology[J]. Acta. Ecologica. Sinica, 2006, 26(5): 1574-1582.
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