Standard Water Tests
overview with a comparison chart similar to lu’s:
DNA Sequencing and Analysis
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.
Knowledge of DNA sequences has become indispensable for basic biological research, and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of complete DNA sequences, or genomes of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, plant, and microbial species.
The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography. Following the development of fluorescence-based sequencing methods with a DNA sequencer, DNA sequencing has become easier and orders of magnitude faster.
DNA in Water
The key, as microbiologist Per Halkjaer Nielsen explains, is to link the identity of a microbe with its function. Nielsen borrowed the tools and lessons from the decade-long, US$3 billion undertaking to map the human genome, and began applying and further developing them in order to identify the bacteria in treatment plants, the better to feed, nurture, and cater to their needs. In a process called metagenomics, his team extracts DNA from a water or sludge sample, chops it into pieces, sequences it and by using bioinformatics tools, puts it together in genomes for the individual species.
“By looking into the DNA of the microbes in wastewater treatment plants, or any other ecosystem, we can get two types of important info: identification of the microorganisms and some understanding of their function,” says Nielsen.
Indeed, the DNA revolution may irreversibly alter our relation with the water systems we depend on. Nielsen speaks of unlocking the “circular economy” by augmenting the traditional treatment process. “All parts of this circle consist of microbes–influent, primary sludge and external sources, activated sludge, digester, recovery of nutrients, and polishing of the effluent–in all cases a surveillance of the microbiology will help optimise the plant and the entire circular economy,” he says.
A microbiome has a particular metabolic function unique to a treatment plant, whether it’s located in northern China, eastern Brazil, or southern Portugal. Wherever there had been a mystery over the content of wastewater, it can now be affordably and accurately unlocked. The DNA sequencing process–giving a name tag to hundreds of microorganisms– can turn a mysterious liquid into a clearly identifiable table of contents. They can serve as “knowledge banks, like a Google for wastewater”.
Metagenomic shotgun sequencing samples all genes, including viruses and results in a very large dataset.
DNA amplicon sequencing of the 16S rRNA gene, identifying nearly all Bacteria and Archaea at the genus level or above and their relative percentage abundance.
DNA amplicon sequencing of the 18S rRNA gene, identifying nearly all Eukarya at the genus level or above and their relative percentage abundance.
DNA amplicon sequencing to identify methanogens at the species level and measurement of the percentage relative abundance in your system.
Polymerase Chain Reaction uses primers to test for the presence of a specific microbe. qPCR provides a count of microbes (quantification).