Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes

Abstract

Sediment bacterial community is the main driving force for nutrient cycling and energy transfer in aquatic ecosystem. A thorough understanding of the community's spatiotemporal variation is critical for us to understand the mechanisms of cycling and transfer. Here, we investigated the sediment bacterial community structures and their relations with environmental factors, using Lake Taihu as a model system to explore the dependence of biodiversity upon trophic level and seasonality. To combat the limitations of conventional techniques, we employed Illumina MiSeq Sequencing and LeFSe cladogram to obtain a more comprehensive view of the bacterial taxonomy and their variations of spatiotemporal distribution. The results uncovered a 1,000-fold increase in the total amount of sequences harvested and a reverse relationship between trophic level and the bacterial diversity in most seasons of a year. A total of 65 phyla, 221 classes, 436 orders, 624 families, and 864 genera were identified in the study area. Delta-proteobacteria and gamma-proteobacteria prevailed in spring/summer and winter, respectively, regardless trophic conditions; meanwhile, the two classes dominated in the eutrophication and mesotrophication lake regions, respectively, but exclusively in the Fall. For LEfSe analysis, bacterial taxon that showed the strongest seasonal or spatial variation, majority had the highest abundance in spring/summer or medium eutrophication region, respectively. Pearson's correlation analysis indicated that 5 major phyla and 18 sub-phylogenetic groups showed significant correlation with trophic status. Canonical correspondence analysis further revealed that porewater NH₄⁺ -N as well as sediment TOM and NO_x -N are likely the dominant environmental factors affecting bacterial community compositions.

Keywords: Illumina Sequencing; Lake Taihu; bacteria communities and biodiversity; sediment; trophic status of aquatic ecosystem.

Figure 1

The 21 sampling sites in the different trophic statuses regions of Lake Taihu. Water quality classification of the lake regions referred to the Standard GB3838‐2002 of China. The data of total nitrogen concentration in the figure is from the Health Status Report of Taihu Lake 2015 in Water Resources Department of Jiangsu Province. Sites 1 to 10, sites 11 to 16, and sites 17 to 21 were located in the Meiliang Bay (A‐1), Gonghu Bay (A‐2), and Xukou Bay (A‐3), respectively. Site 5, 8, 11, 15, 18, and 19 were performed further analysis by Illumina MiSeq sequencing

Figure 2

Physiochemical properties of the overlying water, pore water and sediment in different trophic statuses lake in four seasons. A monitoring index concentration of each lake was calculated by taking average value of the monitoring index concentration of the all sample site in this lake

Figure 3

The relative abundance of 19 major bacterial phyla in all sampling sites

Figure 4

Composition of the top‐10 taxa at the class, order, family, and genus level for all samples

Figure 5

The temporal and spatial variations characteristics of bacterial community structure in different bacterial taxonomical levels (only shown the sequence of bacteria >1% of all sequences). The size of the circle represented the relative abundance of bacteria at each site, and the color of the circle represents bacterial taxonomical levels, red is phylum, blue is class, black is order, family and genus

Figure 6

Cladograms indicating the phylogenetic distribution of bacterial lineages associated with the 4 seasons of a year. The phylum, class, order, family, and genus levels are listed in order from inside to outside of the cladogram and the labels for levels of order, family, and genus are abbreviated by a single letter. The green, blue, red, and purple circles represent the bacteria enriched in the sediment of spring, summer, fall, and winter, respectively, whereas the yellow circles represent the taxa with no significant differences between 4 seasons of a year

Figure 7

Cladograms indicating the phylogenetic distribution of bacterial lineages associated with the sediments of 3 lake regions. The phylum, class, order, family, and genus levels are listed in order from inside to outside of the cladogram and the labels for levels of order, family, and genus are abbreviated by a single letter. The green, red, and blue circles represent the bacteria enriched in the sediment of Meiliang Bay (A‐1), Gonghu Bay (A‐2), and Xukou Bay (A‐3), respectively, whereas the yellow circles represent the taxa with no significant differences between the sediments of 3 lake regions

Figure 8

Canonical correspondence analysis (CCA) ordination diagram of bacterial communities associated with environmental variables based on Illumina MiSeq sequencing of the 24 sampling sites in the 4 seasons. The samples were marked as ‘Season‐Lake Region‐Site number’, for example, Spr‐Mei‐1 was one of the sampling site of Meiliang Bay in spring