There is nothing to automate if all the contigs are in a single file.

blastn -query contigs.fna -db nr -task blastn -out contigs_vs_nr.txt -evalue 1e-10 -num_threads 10

If you have the contigs in individual files that end in .fna:

for i in *.fna
do
blastn -query $i -db nr -task blastn -out ${i%.fna}_vs_nr.out -evalue 1e-10 -num_threads 10
done

For metagenomes I do not use contigs smaller than 2,000 bp. As you seem to have a pure isolate, a 1,000 cutoff could be used as well.