Background: The Vistula River is Poland's longest river, and its section called the Lesser Poland Gorge of the Vistula (Polish: Małopolski Przełom Wisły) belongs to two Natura 2000 Areas. The waters of the Vistula River periodically flood neighbouring areas during winter or summer floods. Among studies on the microbiome of river waters, sanitary analyses to control drinking water dominate. The most frequently determined bacteria are Escherichia coli and Enterobacter, Citrobacter and Klebsiella. In this study we decided to determine the composition of the bacterial community and its metabolic potential in Vistula River water.

Methods: The water was taken from the Vistula River in Janowiec in the Lublin Province. The water was taken from the river flow at a distance of about 27 m from the shore into a 50 L sterile container. In order to analyse the structure of bacterial communities, the next generation V3/V4 16S rDNA region sequencing (NGS) using Miseq (Ilumina) and the community-level physiological profiles (CLPP) method using the Biolog® EcoPlate™ system were applied.

Results: A total of 413 operational taxonomic units (OTU) were obtained, of which 377 could not be classified to type. Among those identified, Arenimonas (2.13%), Brevundimonas (1.44%) and Flavobacterium (1.05%) predominated. Of the OTUs present above 1% in the water, 23 were unclassified, including the dominant Unclassified_CL0182 (5.05%).

The analysis of the metabolic potential of river water community microorganisms showed that they were most active after 120 h incubation of EcoPlate™ plates. The most intensively degraded group of substrates were carbohydrates (30.93%) and the least amines and amides (6.44%).

While searching for bacteria pathogenic to humans, there were a few representatives of Legionella sp. (0.03%) and Rickettsia sp. (0.03 %). Additionally, the presence of bacteria from the genus Brevundimonas (1.44%) and from the family Oxalobacteraceae (0.09%) were detected, which may cause opportunistic infections. The results obtained are surprising, as it is commonly believed that river waters are contaminated with pathogenic microorganisms.

Conclusion: The NGS analysis did not indicate a sanitary risk to humans. A large number of unclassified bacteria indicate a still low level of knowledge and limitations concerning the world of bacteria.