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.Many microbesMicrobes grownSequencing How do we know what microbes are in the soil? are visible underin the lab can bethe DNA in the There are a few different technologies that can shine a lighta microscope, butidentified usingsoil allows us they look identicaldifferent methods,to differentiate on the invisible world of microbes. Because it provides theand are impossiblebut the vast majoritybetween very most clear picture, Trace Genomics uses DNA sequencing toto tell apart. of microbes cannotsimilar microbes, be grown in the laband it also captures understand the soil microbiome. In order to understand how(sometimes calledthe unculturable that works, lets back up a little bit microbial darkorganisms.matter).What is DNA?DNA is known as the blueprint of life because it contains all the information necessary to build a living organism. It is a biological 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,Photos: Trace Genomicsanother biological molecule like a protein), and the DNA that codes for it is called a gene. All the DNA for a particular organism is called its genome, and the process thatso scientists can sequence all instances of that gene from scientists use to read a genome is called DNA sequencing. 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 Metagenomics difference between species). Sequencing all the DNA in an environment is known as metagenomics. In the past 20 years, this has been anDifferences between metagenomics and amplicon invaluable scientific discovery tool for understanding thesequencingtrue breadth of the tree of life. Because most microbes cantIf we think of a single organisms genome as a complete be cultured in the lab or differentiated under a microscope,puzzle, a soil metagenome is like having 10,000 different we had no idea how many different species there were.puzzles with their pieces all mixed into the same box. Since the development of metagenomics, scientists haveAmplicon sequencing is like looking for a specific piece that discovered a treasure trove of microorganisms from entireall the puzzles have in common, like the top left corner, and groups that were previously unknown. using that to identify which puzzles (genomes) are there. Metagenomics looks at all the pieces to try and find other Amplicon sequencing useful information, such as how many genomes contain Rather than sequencing all DNA in an environment,certain functional genes (like nitrogen or phosphorus scientists can also use fingerprint genes to see whatcycling).types of microbes are present. For each of the large groups of microbes (bacteria, archaea, fungi, and protists), thereAbout the author: Dr. Tuesday Simmons is the Science Writer are a few genes that are found in all the members (this isat Trace Genomics. She earned her Ph.D. in Microbiology called a conserved gene). For example, the 16S rRNA genefrom the University of California, Berkeley, studying the root (or just 16S) is conserved among bacteria and archaea,microbiome of cereal crops.Spring 2024 47'