Dynamic of active microbial diversity in rhizosphere sediments of halophytes used for bioremediation of earthen shrimp ponds

Abstract

Background In New-Caledonia, at the end of each shrimp production cycle, earthen ponds are drained and dried to enhance microbial decomposition of nutrient-rich waste trapped in the sediment during the rearing. However, excessive ponds drying may not be suitable for the decomposition activities of microorganisms. Halophytes, salt tolerant plants, naturally grow at vicinity of shrimp ponds; due to their specificity, we explored whether halophytes cultivation during the pond drying period may be suitable for pond bioremediation. In addition, plants are closely associated with microorganisms, which may play a significant role in organic matter decomposition and therefore in bioremediation. Thus, in this study we aimed to determine the impact of 3 halophyte species (Suaeda australis, Sarcocornia quinqueflora and Atriplex jubata) on active sediment microbial communities and their implications on organic matter degradation. Results Drying significantly decreased the microbial diversity index compared to those of wet sediment or sediment with halophytes. Microbial profiles varied significantly over time and according to the experimental conditions (wet, dry sediment or sediment with halophyte species). Halophytes species seemed to promote putative microbial metabolism activities in the sediment. Taxa related to nitrogen removal, carbon mineralisation, sulphur reduction and sulphide oxidation were significant biomarkers in sediment harbouring halophytes and may be relevant for bioremediation. Whereas microbial communities of dry sediment were marked by soil limited-moisture taxa with no identification of microbial metabolic functions. Nitrogen reduction in sediments was evidenced in wet sediment and in sediments with halophytes cultures, along with putative microbial denitrification activities. The greatest nitrogen reduction was observed in halophytes culture. Conclusion The efficiency of sediment bioremediation by halophytes appears to be the result of both rhizosphere microbial communities and plant nutrition. Their cultures during the pond drying period may be used as aquaculture diversification by being a sustainable system.

Active Microbiota of Penaeus stylirostris Larvae: Partially Shaped via Vertical and Horizontal Transmissions and Larval Ontogeny

“…Core microbiota from the Venn diagram was used to infer putative microbial functions in larvae according to their stage, using FRAPROTAX: Functional Annotation of Prokaryotic Taxa [ 39 ] in the microeco package [ 37 ]. As described in Colette et al, 2023 [ 40 ], FAPROTAX is a tool that predicts metabolic phenotypes and ecological features and functions based on published data [ 39 , 41 ].…”

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

“…The experimental greenhouse is located on a shrimp farm (Aigue Marine) in Boulouparis, New Caledonia, bordering Saint-Vincent Bay. The experiment extended from September (2021) to February (2022) in the same meteorological and watering conditions as in our previous study described in ( Colette et al, 2023 ). Sediments from four different shrimp farms were collected with a medium-sized excavator at the end of the shrimp rearing, on the first days of the drying period of the ponds.…”

“…Two-month-old seedlings of Suaeda australis were planted on these sediments. The seedlings were obtained from germinations of seeds from mother plants grown in another experimental greenhouse in New Caledonia ( Colette et al, 2023 ). Then, to avoid drastic change, the young seedlings were transplanted with a part of their initial growth substrate in the 42 L pots filled with sediment.…”

“…In addition, halophytic species rapidly colonize pond sediments when they are abandoned or left empty for several months (Della Patrona, personal communication). Thus, the cultivation of halophytes has recently been explored as a means of improving the quality of pond bottoms by reducing the organic waste accumulated in the sediments at the end of a shrimp rearing cycle ( Colette et al, 2022 , 2023 ). The integration of plant cultivation into aquaculture farming systems to limit eutrophication of the aquaculture ecosystem use waste product derived from aquaculture activities to produce plant biomass, and therefore reduce waste concentrations in farming system (e.g., water or sediment) ( Miranda et al, 2008 ; Mariscal-Lagarda et al, 2014 ; Mariscal-Lagarda and Páez-Osuna, 2014 ; Yaobin et al, 2019 ).…”

“…Thus, to evaluate the nutrient removal effectiveness of shrimp sediments by halophytes, the microbiota associated with the rhizosphere of plant species must be taken into account ( Li et al, 2022 ). In a previous study, we have demonstrated that the microbiota associated with the rhizosphere of halophytes growing in shrimp sediments varied according to halophyte species ( Sarcocornia quinqueflora, Atriplex jubata, and Suaeda australis ) ( Colette et al, 2023 ). In addition, microbial guilds selected by the plants were differently involved in functions linked to the N, C and S biogeochemical cycles in the sediment.…”