Drainage and drying of the shrimp earthen-pond at the end of each production cycle allows the aeration of pond bottom sediment and enhance microbial decomposition of the accumulated organic matter (Yang et al., 2017). However, pond drying is not always beneficial for the microbial communities as water stress could impaired the bacterial decomposition activities (Schimel 2018, Boyd and Pippopinyo, 1994). In New Caledonia, high parts of the internal earth dikes of shrimp farms are colonized by halophytic plants, able to thrive in extreme salinity conditions. The use of halophyte species as crops for remediation of shrimp pond sediment was explored. Plants interactions with soil environment can change surrounding soil microbial communities and thereby affect nutrient cycling and organic matter degradation. Thus, we aim to answer if 1) halophyte can change the composition of the microbial communities inhabiting the pond sediment, 2) microbial communities are different according to the halophyte species and moisture conditions, 3) distinct microbial communities differ functionally.
We conduct experimental greenhouse study where three halophyte species (Sarcocornia quinqueflora, Suaeda australis and Atriplex jubata) were separately grown in pots filled with shrimp earthen-pond sediments. At the end of the experiment, upper part of the sediments was collected to explore the active microbial diversity present in each soil condition. For that, RNA extractions, reverse-transcription and sequencing of the V4 region of the 16S rRNA molecule and bioinformatics analysis were done.
Our data highlight that dry sediment shares very few common taxa with sediment colonized by halophytes species. Venn diagram evidenced great proportion of specific taxa following moisture conditions and halophytes species. Thus, at family’s level, there is clear dissimilarities of sediment specific microbiome following sediment moistures condition and halophytes species.