Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium

Abstract

Background: The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the ability of this host to cope with complex and changing marine environments. In this study, the coral Pocillopora damicornis was inoculated with a beneficial microorganisms for corals (BMC) consortium to investigate how the coral host and its associated microbial community would respond.

Results: High-throughput 16S rRNA gene sequencing revealed no significant differences in bacterial community α-diversity. However, the bacterial community structure differed significantly between the BMC and placebo groups at the end of the experiment. Addition of the BMC consortium significantly increased the relative abundance of potentially beneficial bacteria, including the genera Mameliella and Endozoicomonas. Energy reserves and calcification rates of the coral host were also improved by the addition of the BMC consortium. Co-occurrence network analysis indicated that inoculation of coral with the exogenous BMC consortium improved the physiological status of the host by shifting the coral-associated microbial community structure.

Conclusions: Manipulating the coral-associated microbial community may enhance the physiology of coral in normal aquarium conditions (no stress applied), which may hypothetically contribute to resilience and resistance in this host.

Keywords: Beneficial bacterial consortium; Endozoicomonas; High-throughput sequencing; Pocillopora damicornis.

Fig. 1

Coral gross energy reserves and calcification rates following exposure to a bacterial consortium. a Changes in coral gross energy reserves on days 7, 14 and 21. b Changes in average daily calcification rates in the placebo (purple boxes) and BMC (orange boxes) groups. * and ** indicate significant differences at P < 0.05 and P < 0.01, respectively. Bars represent the standard deviation of the mean. Number of coral fragments: gross energy reserves, n = 6; calcification rate, n = 9

Fig. 2

Relative abundances of the coral microbiome of placebo and BMC groups at the phylum level (except Proteobacteria, which is represented at the class level). Bubble size indicates relative abundance, and different colors represent different treatments. Numbers 7, 14 and 21 represent days 7, 14 and 21, respectively. Placebo: received no bacterial consortium; BMC: received the bacterial consortium

Fig. 3

Subsystems enriched or depleted with the bacterial genera between the placebo and BMC groups. Data from days 7 (a), 14 (b) and 21 (c). Subsystems overrepresented in the added bacterial consortium treatment community with positive (negative) differences between proportions are indicated by different colors (black is placebo group; purple is BMC group). Red font: P < 0.05

Fig. 4

Co-occurrence patterns of markedly changing genera and physiological parameters of the coral. Network analysis was conducted on data from days 7 (a), 14 (b), and 21 (c). Each connection indicates a strong significant correlation, with Spearman’s correlation coefficient ≥ 0.5 and P < 0.05. Each node represents a microbial genus, and the size is proportional to the node connectivity. Each edge represents a linkage between two co-occurring nodes, and the color represents a correlation (red is positive; purple is negative). All nodes are labeled with annotated genera, which are colored at the phylum level except Proteobacteria, which is at the class level)

Fig. 5

Experimental design flowchart. Placebo and BMC groups, which each comprised two aquariums containing 12 coral nubbins, were used to explore the effects of addition of a bacterial consortium on coral physiology and microbial community structure. Buoyancy weighing and coral sampling were conducted every 6 days, and three corals were collected per aquarium at time point. After each sampling, the BMC group was inoculated with the bacterial consortium, and the placebo group received FSW. Water-flow exchange with the outside of the aquarium was stopped for 24 h after each inoculation