Abundances of unique peptides indicated potential differences at the strain level between Fe(III)-reducing populations stimulated during in situ biostimulation experiments conducted a year apart at the Rifle IFRC. Abundances of conserved gltA peptides tracked Fe(III) reduction and changes in U(VI) concentrations during biostimulation, whereas changing patterns of unique peptide abundances between samples suggested sample-specific strain shifts within the Geobacter population. Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ more » biostimulation.

Citrate synthase (gltA) is a key enzyme in Geobacter central metabolism that controls flux into the TCA cycle. Department of Energy’s Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). Monitoring the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies. These results offer a novel technique for the rapid screening of large numbers of proteomic samples for Geobacter species and will aid monitoring of subsurface bioremediation efforts that rely on metal reduction for desired = , Here, we utilize shotgun proteomic methods to demonstrate that the measurement of gltA peptides can be used to track Geobacter activity and strain evolution during in situ biostimulation. At the US Department of Energy's Integrated Field Research Challenge (IFRC) site in Rifle, CO, the stimulation of Geobacter growth and activity via subsurface acetate addition leads to precipitation of U(VI) from groundwater as U(IV). In this example we have named the output file the activity of target microorganisms during stimulated bioremediation is a key problem for the development of effective remediation strategies.

The -out parameter specifies the name of the file that will contain the search results. In this example the search is being run against the NCBI transcript reference sequences, refseq_rna. The -db parameter specifies the name of the database you are going to run against. In this example, the name of the query file is il2.seq. The query sequence must be in either FASTA or Genbank format. The -query parameter specifies the name of the file containing your query sequence, the sequence you want to use to search against the database. Blastn runs a nucleotide sequence against a nucleotide database. In the command above, there are three pieces of information supplied to the blastn program. $ blastn -query il2.seq -db /idata/appdata/blastdb/refseq_rna -out il2.blastn In order to run any BLAST search on Discovery, you must first load the BLAST module. $ blastn -query YourInputFileHere -db /idata/appdata/blastdb/BlastDbNameHere -out YourOutputFileHere The minimal requirements to run a BLAST search are a query sequence file, the database you are searching, and an output file name.

Please contact the Research Computing group at to obtain an account. You must have an account on Discovery in order to use BLAST. The BLAST program is run on the command line on Discovery.

4peaks blastn