Microbial profiles of a drinking water resource based on different 16S rRNA V regions during a heavy cyanobacterial bloom in Lake Taihu, China

Abstract

Understanding of the bacterial community structure in drinking water resources helps to enhance the security of municipal water supplies. In this study, bacterial communities were surveyed in water and sediment during a heavy cyanobacterial bloom in a drinking water resource of Lake Taihu, China. A total of 325,317 high-quality sequences were obtained from different 16S ribosomal RNA (rRNA) regions (V3, V4, and V6) using the Miseq sequencing platform. A notable difference was shown between the water and sediment samples, as predominated by Cyanobacteria, Proteobacteria, and Actinobacteria in the water and Proteobacteria, Chloroflexi, and Verrucomicrobia in the sediment, respectively. The LD12 family dominated the water surface and was tightly associated with related indicators of cyanobacterial propagation, indicating involvement in the massive proliferation of cyanobacterial blooms. Alternatively, the genus Nitrospira dominated the sediment samples, which indicates that nitrite oxidation was very active in the sediment. Although pathogenic bacteria were not detected in a large amount, some genera such as Mycobacterium, Acinetobacter, and Legionella were still identified but in very low abundance. In addition, the effects of different V regions on bacterial diversity survey were evaluated. Overall, V4 and V3 were proven to be more promising V regions for bacterial diversity survey in water and sediment samples during heavy water blooms in Lake Taihu, respectively. As longer, cheaper, and faster DNA sequencing technologies become more accessible, we expect that bacterial community structures based on 16S rRNA amplicons as an indicator could be used alongside with physical and chemical indicators, to conduct comprehensive assessments for drinking water resource management.Electronic supplementary materialThe online version of this article (doi:10.1007/s11356-017-8693-2) contains supplementary material, which is available to authorized users.

Investigation of Detection Limits and the Influence of DNA Extraction and Primer Choice on the Observed Microbial Communities in Drinking Water Samples Using 16S rRNA Gene Amplicon Sequencing

“…This was not the case for samples amplified with the two other primers as all these samples had read abundances of at least 0.6% for these phyla. This is consistent with findings in a recent study by Zhang et al (2017) , which also indicated that some primer-sets are incapable of detecting specific phyla. The study by Zhang et al (2017) investigated the microbial profiles of DW using primer-sets targeting the V3, V4, and the V6 region.…”

“…This is consistent with findings in a recent study by Zhang et al (2017) , which also indicated that some primer-sets are incapable of detecting specific phyla. The study by Zhang et al (2017) investigated the microbial profiles of DW using primer-sets targeting the V3, V4, and the V6 region. It should also be emphasized that the results from the primer test do not give a complete understanding of the primer bias related to DW as any phyla absent from the samples would not be detectable.…”

Responses of Cyanobacterial Aggregate Microbial Communities to Algal Blooms

“…The real-time remote sensing image data of Lake Taihu showed the signi cantly different cyanobacterial blooming in different month. The seasonal dynamics of microbial communities is apparent, including the succession of dominant cyanobacterial genera [47][48][49] and the variation of attached bacteria [47,50,51]. Four OTUs of cyanobacterial genus Dolichospermum were enriched in Early-stage and Late-stage, while the cyanobacterial genus Microcystis was more enriched in Mid-stage than Early-stage, demonstrating the alternate succession of dominant cyanobacterial genera between Microcystis and Dolichospermum.…”

Spatial Modelling of Bacterial Diversity over the Selected Regions in Bangladesh by Next-Generation Sequencing: Role of Water Temperature

“…All primers are available in probeBase, a comprehensive online database for rRNA-targeted oligonucleotides (www.microbial-ecology.net/probebase/). PCR primer pairs had previously been validated in the literature [27,28], and we used 341F-5'CCTACGGGAGGCAGCAG3' and 534R-5'ATTACCG CGGCTGCTGG3'.…”