Cyanobacterial
blooms produce hazardous toxins, deplete oxygen,
and secrete compounds that confer undesirable organoleptic properties
to water. To prevent bloom appearance, the World Health Organization
has established an alert level between 500 and 2000 cells·mL–1, beyond the capabilities of most optical sensors
detecting the cyanobacteria fluorescent pigments. Flow cytometry,
cell culturing, and microscopy may reach these detection limits, but
they involve both bulky and expensive laboratory equipment or long
and tedious protocols. Thus, no current technology allows fast, sensitive,
and in situ detection of cyanobacteria. Here, we
present a simple, user-friendly, low-cost, and portable photonic system
for in situ detection of low cyanobacterial concentrations
in water samples. The system integrates high-performance preconcentration
elements and optical components for fluorescence measurement of specific
cyanobacterial pigments, that is, phycocyanin. Phycocyanin has demonstrated
to be more selective to cyanobacteria than other pigments, such as
chlorophyll-a, and to present an excellent linear
correlation with bacterial concentration from 102 to 104 cell·mL–1 (R
2 = 0.99). Additionally, the high performance of the preconcentration
system leads to detection limits below 435 cells·mL–1 after 10 min in aquaponic water samples. Due to its simplicity,
compactness, and sensitivity, we envision the current technology as
a powerful tool for early warning and detection of low pathogen concentrations
in water samples.