Table 2.

Detection of microorganisms in surface water by qPCR assays

Microorganisms	Country	Type of surface water	Type of assay	Gene/genome amplified	Concentration	% Positive samples	Reference
Mycobacterium avium subsp. paratuberculosis	USA	Drinking water	TaqMan	IS900 gene	82 % < than 10,00 target copies/L and 68 % < 500 target copies/L	81 % for first-pull water and 88 % for standard water	[208]
Salmonella spp.	Australia	Rainwater	SYBR Green	InvA gene	2 GC logs/100 mL	3 %	[74]
Campylobacter jejuni	Australia	Rainwater	SYBR Green	16S rRNA	1 GC logs/100 mL	25 %	[74]
JC polyomavirus (JCPyV)	Spain	River water	Taqman	Regions of early and late viral genes	0–3 GC logs/L	90 %	[7]
	Japan	River water	AmpliTaq	Regions of early and late viral genes	2–3 logs/L for JCPyV	11 %	[48]
Adenovirus	Spain	Seawater		Hexon gene	1–3 GC logs/L		[209]
	Japan	River water	AmpliTaq	Fiber gene	3–5 GC logs/L	61 %	[48]
	Spain	River water	SYBR Green	Ad hexon gene	1–4 GC logs/L	90 %	[7]
Schistosoma japonicum cercariae	China	Surface water	TaqMan	Deoxyribodipyrimidine photolyase (PL) gene	500 cercariae	6.48 %	[152]
Helicobacter pylori	USA	Groundwater	RT-PCR; SYBR Green	vacA gene			[22]
Bacteroidetes	Northern Calcareous Alps	Surface water	TaqMan	16S rRNA	4.1 × 109 marker equivalents/g	100 %	[4]
Enterococcus spp.	Racine, WI, USA	Lake water	TaqMan	rRNA subunit	3 GC logs/100 mL		[210]
	Lake Michigan	Lake water	TaqMan	rRNA subunit	27 cells per extract	98 % and 97 %	[25]
	Lake Erie
Candida spp.	Ohio, Lake water, USA	Drinking and surface water	TaqMan	Nuclear large subunit ribosomal gene			[6]
E. coli spp.	USA	Surface water	Triplex qPCR, minor groove binding probes	Eae, stx1 and stx2 genes	3–4 cells/L	100 %	[119]
	China	Surface water	SYBR Green	16s rRNA	Low level river pollution 1.8 GC logs/100 mL		[211]
					High level river pollution 3.7 GC logs/100 mL
					2 urban lakes 2.7–3.3 GC logs/100 mL
Vibrio spp.	USA	Seawater	TaqMan	Hemolysin genes (vvhA and vvhB)	2 and 91 cells/100 mL		[212]
Cryptosporidium spp.	France	River water	TaqMan	Genomic DNA	8 Oocyts		[135]
	Japan	River water	Quenching probe	18S rRNA	1 Oocyst		[136]

Results are expressed as genome copy logs (GC logs) or cell logs