UNIX for Dummies Questions & Answers

awk '
NR==FNR{a[$1]=0;next}
{for (i in a) {s=match($0,i);if (s>0) a[i]++}}
END {for (i in a) print i,a[i]}
' name_list input.txt

SALINISPORA 2
PROPIONIBACTERIUM 1
RHODOCOCCUS 1
AZORHIZOBIUM 0
NOCARDIOIDES 1
RUBROBACTER 1
CORYNEBACTERIUM 5
AZOTOBACTER 0

# for i in $(cat namelist); do echo "$i" $(sed -n "/$i/p" infile | sed '$=' | sed -n 'N;$s/\(.*\)\n\(.*\)/\1/;p' | sed -n '$p') ;done
PROPIONIBACTERIUM 1
RHODOCOCCUS 1
NOCARDIOIDES 1
RUBROBACTER 1
SALINISPORA 2
CORYNEBACTERIUM 5
AZORHIZOBIUM
AZOTOBACTER

for i in $(cat namelist)
  do
    if [[ $(sed -n "/$i/p" infile | sed '$=' | sed -n 'N;$s/\(.*\)\n\(.*\)/\1/;p' | sed -n '$p') == "" ]] ; then
         echo "$i 0" ; else echo "$i" $(sed -n "/$i/p" infile | sed '$=' | sed -n 'N;$s/\(.*\)\n\(.*\)/\1/;p' | sed -n '$p')
    fi
  done
PROPIONIBACTERIUM 1
RHODOCOCCUS 1
NOCARDIOIDES 1
RUBROBACTER 1
SALINISPORA 2
CORYNEBACTERIUM 5
AZORHIZOBIUM 0
AZOTOBACTER 0