In legacy blast (blastall) it was easy to do a remote BLAST query from the command line that only returned hits for a single organism:
blastall -u "[Arabidopsis thaliana[organism]" -p blastp -d nr -i my_protein_input.fas -o my_protein_input_vs_nr_Athaliana.blastout.txt
However, this seems to have been removed with the release of BLAST+. Aside from filtering hits after they are returned, is it possible to perform a query on the 'nr' database that only returns hits for a single specified taxon?