Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir, Beijing, China

Abstract

Bacterial and archaeal assemblages are one of the most important contributors to the recycling of nutrients and the decomposition of organic matter in aquatic sediments. However, their spatiotemporal variation and its driving factors remain unclear, especially for drinking reservoirs, which are strongly affected by human consumption. Using quantitative PCR and Illumina MiSeq sequencing, we investigated the bacterial and archaeal communities in the sediments of a drinking reservoir, the Miyun Reservoir, one of the most important drinking sources for Beijing City. The abundance of bacteria and archaea presented no spatiotemporal variation. With respect to community diversity, visible spatial and temporal differences were observed in archaea, whereas the bacterial community showed minor variation. The bacterial communities in the reservoir sediment mainly included Proteobacteria, Bacteroidetes, Nitrospirae, Acidobacteria, and Verrucomicrobia. The bacterial community structure showed obvious spatial variation. The composition of the bacterial operational taxonomic units (OTUs) and main phyla were dam-specific; the composition of samples in front of the dam were significantly different from the composition of the other samples. The archaeal communities were mainly represented by Woesearchaeota and Euryarchaeota. Distinctly spatial and seasonal variation was observed in the archaeal community structure. The sediment NH-N, pH, and water depth were identified as the key driving factors of changes in the composition of the bacterial and archaeal communities. Water depth might have the greatest influence on the microbial community structure. The dam-specific community structure may be related to the greater water depth in front of the dam. This finding indicates that water depth might be the greatest contributor to the microbial community structure in the Miyun Reservoir.

Sediment Depth-Dependent Spatial Variations of Bacterial Communities in Mud Deposits of the Eastern China Marginal Seas

“…The proportions of these two genera were higher in several deep layer samples, which might be related to the general decrease in bacterial abundance with depth combined with their presence as contaminants in the extraction kit ( Salter et al, 2014 ). However, sampling and DNA extraction methods in the present study were in accordance with methods used in previous studies on different samples ( Nguyen and Landfald, 2015 ; Chen et al, 2017 ), in which case these potential contaminant genera were not detected. Thus, it is also possible that they might exist in deep layer sediments and feed on organics, such as remnants of marine animals.…”

“…Nitrospirae are nitrite oxidizing bacteria functioning in aerobic nitrite oxidization. However, they have been found to widely distribute in anaerobic marine sediments ( Liu et al, 2014 ; Nunoura et al, 2016 ; Chen et al, 2017 ). Whether sedimentary Nitrospirae are inactive or have other uncharacterized physiologies needs further investigation.…”

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

“…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.…”

“…A number of published data have illustrated spatial heterogeneity of bacterial communities in freshwater ecosystems 8 – 10 . Bacterial population’s seasonality in different water types and variant ecosystems, such as bacterioplankton communities 11 , 12 , bacterial communities in sediments 13 , wastewater treatment plants 14 , 15 , and drinking water works 16 , 17 , as well as in the estuarine ecosystems 18 , 19 , has repeatedly been observed. However, seasonal impacts on the lotic bacterial community structure remain sparsely addressed.…”

Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages

“…In combination with Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota, they form a monophyletic super-phylum proposed as DPANN [ 15 , 16 ]. Currently, Woesearchaeota are widely found in diverse environments, such as groundwater [ 15 ], surface water [ 17 ], inland soil [ 18 ], marine sediments [ 19 , 20 ], freshwater sediments [ 21 ], activated sludge [ 22 ], wetland [ 23 ], hypersaline lakes [ 24 ], estuaries [ 25 ], and deep-sea hydrothermal vents [ 26 ]. Several Woesearchaeotal genomes with different completeness have also been detected from groundwater [ 15 , 27 ], sediment [ 28 , 29 ], and freshwater [ 16 ].…”