Environmental Management https://doi.org/10.1007/s00267-020-01357-7 Contrasting the Water Quality and Bacterial Community Patterns in Shallow and Deep Lakes: Manyas vs. Iznik E. Gozde Ozbayram 1 ● Latife Koker 1 ● Reyhan Akçaalan 1 ● Fatih Aydın 1 ● Ali Ertürk 1 ● Orhan Ince 2 ● Meriç Albay 1 Received: 12 May 2020 / Accepted: 28 August 2020 © Springer Science+Business Media, LLC, part of Springer Nature 2020 Abstract The objectives of this study are to monitor the physicochemical properties of two freshwater lakes with different chemical characteristics and trophic status over a year (2019) and assess the bacterial diversity by a high-throughput sequencing method for a certain time. Carlson Trophic Index analysis revealed that, whereas the deep lake, Iznik Lake, (TSI mean = 48.9) has mesotrophic characteristics, the shallow lake Manyas Lake (TSI mean = 74.2) was found at a hypertrophic status. The most important parameters controlling water qualities in the lakes were temperature, alkalinity, and phosphate levels. Although the bacterial communities were dominated by the same phyla (Cyanobacteria, Bacteroidetes, Actinomicrobia, Proteobacteria, and Verrucomicrobia) in both lakes, the communities differed distinctly at the lower levels. Whereas Sporichthyaceae in Manyas Lake accounted for 10% of the total reads, the major share of the sequences was assigned to Cyanobacteria Family I (8%) in Iznik Lake. The hypertrophic Manyas Lake had a more diverse bacterial community rather than Iznik Lake and contained higher numbers of unique Operational Taxonomic Units. Keywords Bacterial community ● Illumina ® MiSeq™ ● Water quality ● 16S rRNA ● Manyas Lake ● İznik Lake Introduction Freshwater lakes have critical roles in ecological and eco- nomic perspectives, whereas it is a habitat for a diverse biological community, it is also a resource for human consumption (Ma et al. 2018). In these ecosystems, bacteria play a vital role in ecosystem services and have an impact on water quality (Newton et al. 2011) in which the profile is highly dependent on biotic factors and physicochemical characterization of the water (Zwirglmaier et al. 2015). Although, the bacterial community is fundamental for ecosystem processes, much uncertainty still exists about the diversity and function in the lake ecosystems. Determination of water quality is a great concern for the lakes indicating the health of the ecosystem as well as the source of nutrient and pollutant loads (Wang et al. 2019). Lakes can be classified into three trophic status regarding their biological activity namely; oligotrophic, mesotrophic, and eutrophic lakes (Feng et al. 2019) in which the trophic status of the lakes gives information about the function and current structure of the lakes and enables to predict future trends (Wang et al. 2019). Moreover water quality is a key factor affecting the bacterial community patterns and diversity. Environmental variables such as temperature, pH, nutrient concentrations alter bacterial community structure in the freshwater lakes (Feng et al. 2019). Recent developments on next-generation sequencing methods resulted to have high-quality data, which enables deep characterization of complex microbial communities and considerable literature has grown up to increase our understanding of the microbial community compositions of freshwater habitats by metagenomic analyses (Diao et al. 2017; Ji et al. 2018). There are 200 natural lakes in Turkey. Although water quality and cyanobacterial diversity monitoring have been conducted in some of those lakes (Albay and Akcaalan 2003; Akcaalan et al. 2009), much less is known about the * E. Gozde Ozbayram gozde.ozbayram@istanbul.edu.tr 1 Department of Marine and Freshwater Resources Management, Faculty of Aquatic Sciences, Istanbul University, Fatih, 34134 Istanbul, Turkey 2 Department of Environmental Engineering, Faculty of Civil Engineering, Istanbul Technical University, Maslak, 34469 Istanbul, Turkey 1234567890();,: 1234567890();,: