Bacterial communities and predicted nitrogen metabolism of heterotrophic‐ and probiotic‐based biofilms used for super‐intensive indoor shrimp culture

Abstract

Biofilm-based aquaculture systems constitute a promising alternative for intensive shrimp rearing. Microorganisms forming biofilms can recycle the nitrogen compounds the production units improving the water quality while using zero or limited water exchange. This study aimed to compare the taxonomic profiles and the predicted functions related to the transformation of nitrogenous compounds between a heterotrophic-(HtB) and a probiotic biofilm (PrB), and the effect of these on the water quality and the productive response of cultured shrimp. Libraries of the 16S-rRNA gene (V3-V4 region) were prepared and sequenced to be used as a taxonomic biomarker. Analysis of metagenomic datasets revelated that genera Halomonas, Planctomycetes and Rhodopirellula were the most abundant genera in HtB; meanwhile, Bacillus, Halobacillus and Flavobacterium dominated in PrB. Regarding nitrogen metabolism, the proportion of genes encoding enzymes catalyzing the six pathways shaping the nitrogen metabolism showed differences between biofilms, which could also explain the difference in water quality between treatments. Concerning the productive response of shrimp, no significant differences were detected except for survival, which was higher in PrB. Finally, the results suggest that biofilms harbour functions for nitrogen metabolism, including dissimilatory nitrate reduction, assimilatory nitrate reduction, denitrification, nitrification, nitrogen fixation and anammox; however, the balance of these functional capabilities seems to be relevant to maintain water quality.

Longitudinal variations in the gastrointestinal microbiome of the white shrimp, Litopenaeus vannamei

“…Previously there are reports of microbial sequences annotated to energy metabolism, xenobiotics biodegradation, membrane transport in intestinal microbiota from two cultured stages (30 d and 60 d) of L. vannamei ( Gao et al, 2019 ), even so, their implications in the intestine shrimp are not yet elucidated. However, regarding energy metabolism, such as nitrogen metabolism, Ortiz-Estrada et al (2021) reported genes encoding enzymes implicated in the nitrogen metabolism in probiotic biofilm from a zero recharge shrimp culture, which registered better water quality parameters than a heterotrophic biofilm. Nitrogenous metabolites, particularly unionized ammonia (NH 3 ) and nitrite (NO 2 ) are toxic for shrimp.…”

The role of probiotics in vannamei shrimp aquaculture performance – A review

“…This is especially important since the organic matter in the water can turn into ammonia, a highly toxic compound [ 29 ] that can cause a mortality rate of up to 100% in vannamei shrimp cultures [ 30 ]. Probiotics reduce the ammonia content of water through nitrification and denitrification [ 31 ]. In addition, the dissolved oxygen content in the water increases when probiotics are present since they break down organic matter that can then be used by oxygen producers as nutrients to facilitate photosynthesis [ 32 ].…”

Microorganisms as a sustainable aquafeed ingredient: A review

“…For example, due to their ability to utilize many organic substrates, microorganisms have been used to maintain water quality, particularly by the autotroph nitrifying bacteria. In addition, their role in controlling pathogens in disease management and minimizing environmental impacts in the system has also been widely documented (de Mello Júnior et al, 2021; Martínez‐Córdova et al, 2017; Ortiz‐Estrada et al, 2020).…”