Bacterial Community Profiling of Tropical Freshwaters in Bangladesh

Abstract

Seasonal and spatial variations in the bacterial communities of two tropical freshwater sources in Bangladesh, Lake Dhanmondi in central Dhaka, and a pond in the outskirts of Dhaka, were assessed and compared using PCR-DGGE and deep sequencing of 16S rRNA genes, as well as heterotrophic enrichments using water samples collected at nine different time points during 1 year. Temporal and spatial variations of common aquatic bacterial genera were observed, but no clear seasonal variations could be depicted. The major bacterial genera identified from these two sites were members of the Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Verrucomicrobia , and Firmicutes . Among the proteobacterial groups, members of the α - , β - , and γ - Proteobacteria predominated. γ - Proteobacteria belonging to the Escherichia coli/Shigella group even the diarrheagenic pathotypes of E. coli e.g., EPEC and ETEC were detected in most samples throughout the year, with no apparent correlations with other microbial groups. The other pathotypes, EHEC, EAEC, and EIEC/ Shigella spp. were also detected occasionally. This study represents the first thorough analysis of the microbial diversity of tropical freshwater systems in Bangladesh.

Seasonal dynamics of lotic bacterial communities assessed by 16S rRNA gene amplicon deep sequencing

“…Among them, α-, β-, and γ-Proteobacteria were dominant classes of Proteobacteria phylum, while Flavobacteriia and Sphingobacteriia were prevailing in the Bacteroidetes phylum. Similar findings were recently reported by Azmuda et al 20 , where these two phyla were among the major bacterial groups of lentic freshwater ecosystems and did not reveal seasonal variations. However, these findings somewhat deviated from discoveries of Lee et al 22 in marine ecosystems, where Proteobacteria and Bacteroidetes only dominated from June to November, while in December, the dominance switched to Firmicutes.…”

“…S1). Most of them are affiliated to Proteobacteria, which are ubiquitous, persistent and prevalent in freshwater ecosystems under various environmental conditions 16,20,21 . To focus in on the population discrepancy of the bacterial community between cold and warm seasons, a linear discriminant analysis (LDA) effect size (LEfSe) tool was performed on the bacterial class level for the two aligned groups (cold vs. warm), generated by merging all taxa from the same seasonal samples (Fig.…”

“…four in the first year, Warm_1 (Warm_1a/Jun.2015, Warm_1b/ Jul.2015, Warm_1c/Aug.2015, and Warm_1d/Sep.2015) and four in the second year, Warm_2 (Warm_2a/ Jun.2016, Warm_2b/Jul.2016, Warm_2c/Aug.2016, and Warm_2d/Sep.2016). The entire study duration and sampling sets were conceived based on similar settings reported in aquatic research worldwide, profiling microbial communities through seasonal and spatial variations 20,35,36 .…”

“…To investigate the aquatic microbial community structure and dynamics, various molecular approaches have been adopted to address specific targets of interest. For instance, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 16S rRNA deep sequencing have been applied to study bacterial communities in tropical freshwaters 20 . Also, an automated ribosomal intergenic spacer analysis (ARISA), as a DNA fingerprinting methodology, was utilized to investigate bacterial communities in lentic freshwater 8 .…”

Metagenomes from the Loxahatchee wildlife refuge in the Florida Everglades

“…2a). Proteobacteria are found in most freshwater environments, as they are able to withstand an array of different temperatures and pressures, emphasizing their role as one of the most versatile and abundant bacterial phyla 27 . Certain Proteobacteria have symbiotic relationships with plant roots, possibly contributing to their high frequencies within these sediment samples 28 .…”