b'PARTNER CONTENTSolving Soils Microscopic Mysteries: Introduction to MetagenomicsBy: Dr. Tuesday SimmonsL ike your gut microbiome, the soil counterpart is composed of all the microorganisms (or microbes) that live there. Having this information is incredibly valuable to those who are interested in measuring soil health, including: farmers, agronomists, scientists, and any business invested in agriculture.How do we know what microbes are in the soil?There are a few different technologies that can shine a light on Many microbesMicrobes grownSequencing the invisible world of microbes. Because it provides the most clearare visible underin the lab can bethe DNA in the picture, Trace Genomics uses DNA sequencing to understand thea microscope, butidentified usingsoil allows us they look identicaldifferent methods,to differentiate soil microbiome. In order to understand how that works, lets backand are impossiblebut the vast majoritybetween very up a little bit to tell apart. of microbes cannotsimilar microbes, be grown in the laband it also captures (sometimes calledthe unculturable What is DNA? microbial darkorganisms.DNA is known as the blueprint of life because it contains all thematter).information necessary to build a living organism. It is a biologi-cal molecule made up of 4 different chemical building blocks called bases; you can think of it like a language with 4 letters in the alphabet.The order of bases in a DNA molecule can be read like an instruction manual. In the manual, each chapter has instructions for a different piece of machinery (that is, another biological molecule like a protein), and the DNA that codes for it is called aPhotos: Trace Genomicsgene. All the DNA for a particular organism is called its genome, and the process that scientists use to read a genome is called DNAand archaea, so scientists can sequence all instances of that gene sequencing. from an environment. Importantly, while being well-conserved, the 16S gene is also variable enough to tell the difference Different types of environmental DNA sequencingbetween different groups of bacteria (though often not the differ-Metagenomics ence between species). Sequencing all the DNA in an environment is known as metagen-omics. In the past 20 years, this has been an invaluable scientificDifferences between metagenomics and amplicon sequencingdiscovery tool for understanding the true breadth of the tree ofIf we think of a single organisms genome as a complete puzzle, a life. Because most microbes cant be cultured in the lab or differ- soil metagenome is like having 10,000 different puzzles with their entiated under a microscope, we had no idea how many differentpieces all mixed into the same box. Amplicon sequencing is like species there were. Since the development of metagenomics,looking for a specific piece that all the puzzles have in common, scientists have discovered a treasure trove of microorganismslike the top left corner, and using that to identify which puzzles from entire groups that were previously unknown. (genomes) are there. Metagenomics looks at all the pieces to try and find other useful information, such as how many genomes Amplicon sequencing contain certain functional genes (like nitrogen or phosphorus Rather than sequencing all DNA in an environment, scientistscycling).can also use fingerprint genes to see what types of microbes are present. For each of the large groups of microbes (bacteria,About the author: Dr. Tuesday Simmons is the Science Writer at archaea, fungi, and protists), there are a few genes that are foundTrace Genomics. She earned her Ph.D. in Microbiology from the in all the members (this is called a conserved gene). For example,University of California, Berkeley, studying the root microbiome of the 16S rRNA gene (or just 16S) is conserved among bacteriacereal crops.NOVEMBER 2023GERMINATION.CA 25'