Metagenomic profiling of the microbial freshwater communities in two Bulgarian reservoirs

Abstract

Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA). Analysis of the metagenomic amplicon datasets, including quality filtering, clustering of Operational Taxonomic Units and taxonomy assignment revealed that 78.45% of the microbial communities between the two reservoirs were overlapping. The diversity (H) and Pielou's evenness (J) indices declined along the longitudinal axis of both reservoirs. The estimated values for the Shannon diversity index are typically observed in oligotrophic lakes. The microbial communities of both reservoirs were dominated by Proteobacteria, followed by Actinobacteria and Bacteroidetes all comprised over 95% of the relative abundance, regardless of the reservoir's large hydrogeological differences. The bacterioplankton was characterized by high phylogenetic heterogeneity in the taxonomic structure, being distributed among 211 genera. The genera Limnohabitans and Rhodoferax held the absolute predominance, implying their significance in the aquatic food webs. The obtained data can contribute to the better systematic understanding of the microbial diversity of freshwater environments.

Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry

“…Findings from Lee et al (2018) show similar results. In our study, the four strongest increasing phyla, i.e., Verrucomicrobia, Actinobacteria, Cyanobacteria, and Bacteroidetes, are all considered typical freshwater bacteria ( Newton et al, 2011 ) and have also been found previously in freshwater by Iliev et al (2017) and Kim et al (2018) and others. Patescibacteria were first reported in groundwater and sediments of anoxic environments ( Elshahed et al, 2005 ; Youssef et al, 2011 ; Wrighton et al, 2012 ), but showed to be widespread in most semiaquatic habitats ( Sánchez-Osuna et al, 2017 ).…”

Intensive allochthonous inputs along the Ganges River and their effect on microbial community composition and dynamics

“…In any case, as revealed and quantified by metagenomics, these variable allochthonous inputs in the Ganges River distinguish its microbial communities from their counterparts elsewhere, and dramatically alter both the taxonomic and functional composition in the river. While typical freshwater bacteria in rivers, including Betaproteobacteria , Actinobacteria , Bacteroidetes and Verrucomicrobia (Savio et al ., ; Newton et al ., ; Iliev et al ., ) were also detected, the Ganges River was distinct by possessing a higher abundance of Gammaproteobacteria , which often have fast growth rates on high organic substrate conditions (copiotrophs) such as sewage lagoons (Newton et al ., ). The higher allochthonous inputs rates of sludge/sewage altered microbial communities in Ganges River, especially in samples from the wet season and upstream.…”

Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan

“…Bacteroidetes is the most dominant bacterial group in mesotrophic water bodies ( 29 , 53 ). Among Bacteroidetes , the distribution of Flavobacteriia and Sediminibacterium in YYL waters and their absence from TFL waters suggest that they thrive better in this environment.…”

“…Microbiological studies have focused on the bacterial composition of lakes ( 29 , 34 , 39 , 55 ), in addition to other freshwater systems, such as rivers ( 32 ) and ponds ( 13 ). A recent review by Newton et al ( 38 ) provided detailed information on the bacterial communities of the epilimnetic waters of lakes worldwide, with Proteobacteria , Actinobacteria , Bacteroidetes , Cyanobacteria , and Verrucomicrobia being the dominant phyla.…”