Table 2.

Questions associated with ballast water monitoring, and applicable genetic tools. Different nucleic acids-based detection methods satisfy different criteria and are associated with different challenges to technology development and deployment.

Management/science question	Criteria that must be satisfied to answer question	Possible genetic tools	Most significant challenges
Single species approaches
Does the sample contain target species X?	Target specificity, sensitivity	PCR/qPCR or other probe-based detection methods	Managing false positive and negative errors
What is the abundance of target species X in the sample?	Target specificity, sensitivity, quantification	qPCR or other probe-based detection method calibrated for quantification of target	Managing false positive and negative errors, plus calibration for robust quantification of target
Does the sample comply with a standard?	Target specificity, sensitivity, quantification, viability	qPCR targeting transcripts associated with viability	Managing false positive and negative errors, calibration for robust quantification of target, plus identification of targets tightly associated with viability and possibly additional costs associated with handling RNA targets
Community approaches
What species are in the sample?	Broad community profiling, sensitivity	HTS metabarcoding	Gaps in reference databases, difficulty interpreting data from rare species, not amenable to fast turnaround
What is the overall biodiversity (species richness and abundance) in the sample?	Broad community profiling, sensitivity, quantification	HTS metabarcoding, calibration of sequence frequency data to relative abundance	Gaps in reference databases, difficulty interpreting data from rare species, not amenable to fast turnaround, plus calibration for robust quantification