Suaeda australis and its associated rhizosphere microbiota: a comparison of the nutrient removal potential between different shrimp farm sediments in New Caledonia

Abstract

Shrimp rearing generate organic waste that is trapped in the pond sediment. In excess, these wastes may impair aquaculture ecosystem and shrimps' health. To promote the biological oxidation of accumulated organic waste, the pond is drained and dried at the end of each production cycle. However, this practice is not always conducive to maintaining microbial decomposition activities in sediments. Shrimp production in New Caledonia is no exception to this problem of pollution of pond bottoms. One promising way of treating this waste would be bioremediation, using a native halophyte plant and its microbiota. Thus, this study explored the nutrient removal potential of Suaeda australis and its microbiota on sediments from four shrimp farms. Suaeda australis was grown in an experimental greenhouse for 6 months. In order to mimic the drying out of the sediments, pots containing only sediments were left to dry in the open air without halophytes. An analysis of the chemical composition and active microbiota was carried out initially and after 6 months in the sediments of the halophyte cultures and in the dry sediments for each farm, respectively. In the initial state, the chemical parameters and the microbial diversity of the sediment varied considerably from one farm to another. Growing Suaeda australis reduced the nitrogen, phosphorus and sulfur content in all type of sediment. However, this reduction varied significantly from one sediment to another. The rhizosphere of Suaeda australis is mainly composed of micro-organisms belonging to the Alphaproteobacteria class. However, the families recruited from this class vary depending on the farm in question. Depending on the sediment, the variation in microbiota leads to different putative biochemical functions. For two of the farms, a similar reduction in nitrogen concentration was observed in both dry and cultivated sediments. This suggests that certain initial chemical characteristics of the sediments influence the nutrient removal efficiency of Suaeda australis. Our study therefore highlights the need to control the pH of sediments before cultivation or in dry sediments in order to ensure optimal microbial decomposition of organic waste and nutrient cycling.

Keywords: active rhizosphere microbiota; earthen pond sediment; halophyte; metabarcoding; nutrient removal.

Figure 1

Principle coordinate analysis (PCoA) plot, of the microbial diversity in the sediments from the farms A, D, F, and P following the different modalities (D0, dry, S. australis), made using the Bray-Curtis distance.

Figure 2

Venn diagrams of shared and specific ASVs in the sediment of farms A, D, F and P, in (A) the sediment at the beginning of the experiment (D0), (B) in the dry sediment. The relative abundance of the specific ASVs at the bacterial family level found in each farms sediments was represented in (C) at the beginning of the experiment and in (D) dry sediment.

Figure 3

(A) Venn diagram of shared and specific ASVs in the sediments with S. australis from the farms A, D, F, and P. (B) Stacked bar plot represent relative abundance of the 10 main bacterial classes and the 5 main families per class, of the specific ASVs found in each farm.

Figure 4

Correlation heatmap of putative ecological function associated with the specific microbiota of S. australis according to the farm sediment. Heatmap color gradient is linked to Pearson correlation coefficient intensity with in red the positive correlation and in blue the negative correlation. Significant correlations between ecological function and farms are indicated by an asterisk (*).

Figure 5

Pie charts of the 15 main bacterial classes representing at least 84% of the relative abundance found in the microbiota of the sediment at (A) D0, (B) in the dry sediment, and (C) in the rhizosphere of S. australis, all farms combined.