Diversity of culturable Gram-negative bacteria isolated from irrigation water of two rice crop regions in Southern Brazil Maria Helena Lima Ribeiro Reche & Catiusca Reali & Michele Pittol & Danilo de Athayde Saul & Vera Regina Mussoi Macedo & Victor Hugo Valiati & Vilmar Machado & Lidia Mariana Fiuza Received: 20 October 2015 /Accepted: 9 May 2016 # Springer International Publishing Switzerland 2016 Abstract In this study, we assessed the diversity of Gram-negative bacteria found in water used for irriga- tion of rice crops in two growing areas of southern Brazil. Samples were collected from the main irrigation channel and field drain area. Twenty-two bacterial spe- cies were found in Cachoeirinha and 28 in Camaquã. In both areas, the most frequent bacterial families were Enterobacteriaceae and Aeromonadaceae. Differences in microbial diversity were observed in both study areas. Thirty-five Gram-negative species were identified; how- ever, only 15 were common in both locations. In addi- tion, there were found pathogenic and drug-resistant species, such as Acinetobacter sp., Brucella spp., and Chryseobacterium meningosepticum. This study dem- onstrates the existence of a number of pathogenic species in aquatic ecosystems analyzed in three consec- utive crop years, especially water used for rice production. Keywords Crop management . Enterobacteriaceae . Pathogens . Water . 16S rRNA gene Introduction The presence of bacteria in freshwater systems is subject of many studies related to species diversity, which are essential for public health actions. Therefore, bacterial communities contribute to the maintenance of biochem- ical processes accountable for the stability of these ecosystems, specially associated with areas used for agriculture (Asakawa and Kimura 2008; Somura et al. 2009; Mayumi et al. 2010; Fang et al. 2011; Tago et al. 2011). In the specific case of irrigated crops, there are additional concerns since the water used for irrigation is often from rivers that pass through urban areas and which receive a large quantity of wastewater. Irrigation has as main positive effect that is the additional supply of nutrients for cultivated plants. However, excess of nutrients and contamination by pathogens are aspects that can affect both human health and the environment (Mara et al. 2007; Taylor et al. 2011; Hanjra et al. 2012). Among the known pathogens present in freshwater systems, there are fecal coliforms, belonging the family Enterobacteriaceae, which can be considered as indica- tors of water quality. Besides these, there are other Environ Monit Assess (2016) 188:359 DOI 10.1007/s10661-016-5357-5 M. H. L. R. Reche : C. Reali : M. Pittol : D. de Athayde Saul : V. R. M. Macedo : V. Machado : L. M. Fiuza Microbiology and Toxicology Laboratory, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil M. H. L. R. Reche : C. Reali : M. Pittol : D. de Athayde Saul : V. R. M. Macedo : V. H. Valiati : V. Machado : L. M. Fiuza Postgraduate Program in Biology, Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Brazil V. R. M. Macedo : V. H. Valiati (*) : V. Machado Molecular Biology Laboratory, PPG, Universidade do Vale do Rio dos Sinos (UNISINOS), Av. Unisinos, 950 - Bairro Cristo Rei – CEP, 93.022-750 São Leopoldo, Brazil e-mail: valiati@unisinos.br