A novel fluorescent probe for discriminating microbial DNA in ecosystems and model organisms

Abstract

Deoxyribonucleic acid can reflect species, life trait characteristics, and the diversity of species in the environment. Preferably, detection technology should be able to discriminate soil microbial DNA pools in different ecosystems. However, current detection technologies cannot meet this challenge rapidly. Herein, BCK, as a functional material for new research and development, capable of quickly discriminating soil microbial DNA pools in different ecosystems and model organisms with different fluorescence signals, is used to remedy this limitation. In three typical ecosystems, namely forest, grassland, and cropland, BCK could distinguish the gross amount of DNA pools and the DNA pools per microbiomass by different fluorescence signals caused by sequence differences. Likewise, BCK could distinguish the two model species of prokaryotic Escherichia coli and eukaryotic yeast genomic DNA. Further structural comparison experiments revealed significantly different patterns and responses of the probe BCK to the three structures of DNA with the combination of double-strand DNA to the probe being the strongest, followed by single-strand and supercoil DNA. Considering that double-strand DNA is the genetic basis of most living organisms, BCK was applied to examine its effects on DNA replication. The results showed that BCK could bind to template DNA and inhibit the process of DNA replication in the polymerase chain reaction system. This method should guide future research to fill the knowledge gap in rapid DNA detection and help researchers to quickly reveal the impact of different ecosystems or different land use changes on the composition of soil microbial communities.