Contributed by Shawn Higdon
Biological Nitrogen fixation energy-intensive process carried out by Bacteria and Archaebacteria that have been classified across many phyla. While there is an overwhelming amount of research that describes and characterizes the process of biological nitrogen fixation by microbes that have been proven to convert atmospheric dinitrogen into the organic form of ammonia, one question that comes to mind is whether or not the described mechanism that involves the nitrogenase enzyme complex is the only strategy that has evolved in nature.
The focus of my PhD research is heavily centered around understanding how an isolated variety of maize is capable of completing its life cycle without the addition of synthetic nitrogen fertilizers on fields that are essentially N-depleted. I have sequenced the genomes of over 600 microbial samples that derive from the corn plant’s root exudate. These cultures were isolated on growth media that lacked the addition of nitrogen sources and streaked in a serial fashion as an attempt to isolate pure cultures. Furthermore, all of the isolates that were sequenced were also subjected to nitrogen fixing assays and scored based on their ability to assimilate atmospheric nitrogen in metabolites.
My approach to bioinformatic analysis so far involves the use of Hidden Markov Models for proteins involved in nitrogen fixation. While these models serve the purpose of screening the identified proteins within each isolate’s whole genome sequence for gene products that match known nitrogen fixation proteins, the possibility that unknown nitrogen fixation proteins within our population of putative diazotrophs certainly exists. Today, it was brought to my attention that I should also consider the administration of a sequence alignment-based approach to identify any nitrogen fixation proteins present within the genomes of isolates I have sequenced. My next step will be to carry out this analysis in order to corroborate any findings that suggest isolates may be fixing nitrogen with mechanisms that are yet to have been discovered or described by the scientific community. So far, we have a hypothesis and the data is propelling us forward in our pursuit of an answer; but, the road ahead appears to be at a steep incline and we must persevere to uncover the truth…