Assembly of a Benthic Microbial Community in a Eutrophic Bay with a Long History of Oyster Culturing

Abstract

The introduction of oysters to a waterbody is an efficient method for decreasing levels of eutrophication. Oysters affect sedimental environments and benthic microbes via their roles in nutrient cycling. However, little is known about how long-term oyster culturing affects benthic microbial community assembly. In the present study, top and bottom sediments from an oyster-culture area and non-culture area, in a eutrophic bay with a long history of oyster culturing, were obtained for environmental parameter measurement and microbe identification. Deterministic and stochastic processes in microbial community assembly were assessed. In particular, keystone species identification through network analysis was combined with measured environmental parameters to determine the factors related to community assembly processes. Our results suggest that oyster culturing relates to greater variation in both biological and non-biological sediment profiles. In benthic communities, Proteobacteria and Chloroflexi were the most abundant phyla, and community compositions were significantly different between sample groups. We also found that community assembly was more affected by deterministic factors than stochastic ones, when oysters were present. Moisture, or water content, and pH were identified as affecting deterministic and stochastic processes, respectively, but only water content was a driver associated with oyster culturing. Additionally, although keystone species presented a similar pattern of composition to peripheral species, they responded to their environments differently. Furthermore, model selection, fitting keystone species to community assembly processes, indicates their role in shaping microbial communities.

Keywords: benthic microbial community; keystone species; oyster culturing; stochastic and deterministic processes.

Figure 1

Location of the sampling sites. More detailed satellite images are inset on the right-hand side to show that there are many oyster-culturing rafts at the oyster-culturing site and no oysters being cultured at the control–non-oyster-culture site.

Figure 2

Environmental parameters. (A–F) Environmental parameters of the four groups. Groups sharing the same letter were not significantly different according to that parameter (n = 8, p < 0.05. Error bars, mean ± standard deviation); (G) PCA. Each point is one sample. Environmental parameters are shown as red arrows. Percentages in parentheses are proportional differences between parameters represented by the PC axis.

Figure 3

Diversity of benthic communities. (A) The α-diversity; (B) the non-phylogenetic β-diversity, visualized through NMDS based on Bray–Curtis distance; (C) the phylogenetic β-diversity, shown by PCoA. Each point in B and C represents one sample.

Figure 4

Contributions of different processes to community assembly. Sample groups are indicated by squares. Pie charts located at the four corners of the figure depict the relative contribution of processes in community turnover within groups. The pie charts on dark-blue double-headed arrows show the contribution proportions of various processes to the difference between the two groups connected by the arrow. The pie chart in the center indicates the contribution of processes in overall community assembly. (TO: the top layer of the oyster-culturing area; BO: the bottom layer of the oyster-culturing area; TN: the top layer of the non-culture area; BN: the bottom layer of the non-culture area).

Figure 5

(A) Phylogenetic β-diversity based on keystone species only shown by NMDS; (B) keystone species based on phylogenetic β-diversity in the PCoA. Each point represents one sample.

Figure 6

The contributions of different processes in keystone -pecies composition. Sample groups are indicated by squares. The pie charts located at each of the four corners depicts the relative contribution of processes in assemblies of keystone species within groups. The pie charts overlaying the midpoints of the dark-blue double-headed arrows show the contribution of various processes to the differences between the two groups (squares) connected by the aforementioned arrows. The center pie chart indicates the contribution of each process in the overall turnover of keystone species in the study. (TO: the top layer of the oyster-culturing area; BO: the bottom layer of the oyster-culturing area; TN: the top layer of the non-culture area; BN: the bottom layer of the non-culture area).