Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species

Abstract

Nitrogen species such as ammonia and nitrite are considered as major stressors in modern aquaculture practices. We developed enrichments of ammonia oxidising bacteria (AOB) and nitrite oxidising bacteria (NOB) for effective mitigation of nitrogenous wastes in the shrimp culture operations. The objective of this study was to understand the microbial community composition of AoB and noB enrichments using the V3-V4 region of the 16S rDNA gene by Illumina MiSeq sequencing. The analysis revealed 2948 and 1069 OTUs at 97% similarity index and Shannon alpha diversity index of 7.64 and 4.85 for AOB and NOB enrichments, respectively. Comparative analysis showed that a total of 887 OTUs were common among AOB and NOB enrichments. The AOB and NOB enrichment were dominated by Eubacteria at 96% and 99.7% respectively. Proteobacterial phylum constituted 31.46% (AOB) and 39.75% (NOB) and dominated by α-Proteobacteria (20%) in AOB and γ-Proteobacteria (16%) in NOB. Among the species in AOB enrichment (2,948) two sequences were assigned to ammonia oxidising bacterial group belonging to Nitrosomonas, and Nitrosococcus genera and two belonged to archaeon group comprising Nitrosopumilus and candidatus Nitrososphaeraea genera. The NOB enrichment was predominated by Nitrospiraceae and Thermodesulfovibrionaceae. further, the data revealed the presence of heterotrophic bacteria contributing to the process of nitrification and form microcosm with the AOB and NOB. PICRUSt analysis predicted the presence of 24 different nitrogen cycling genes involved in nitrification, denitrification, ammonia and nitrogen transporter family, nitrate reduction and ammonia assimilation. The study confirms the presence of many lesser known nitrifying bacteria along with well characterised nitrifiers. Aquaculture is an important economic activity supplying quality animal protein, generating employment and providing foreign exchange. Fish and fishery products are the most traded food items in the world, and an estimated 45% of the fish produced enters the international market. In terms of value, shrimp/prawn is the second most traded item next only to salmon in the USD 152 billion global seafood market 1. In the modern-day intensive and semi-intensive shrimp aquaculture, management of accumulating metabolic wastes, especially in zero water exchange systems has been a major challenge. Accumulation of nitrogenous wastes generated by animal excreta and degradation of uneaten feed leads to deterioration of culture environment and stress to farmed animals 2-4. Ammonia is the primary end product of protein metabolism in most aquatic animals 5 and is also produced following microbial decomposition of organic wastes. Increase in the levels of nitrogenous species in the shrimp haemolymph leads to reduced food intake, increased oxygen consumption, increased excretion of nitrogen, and altered protein concentrations cause moderate to high mortality 6. Further, the ammonia (>5 ppm) and nitrite

Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms

“…In the same study, as well as in a study by Keeley et al (2018) , also Thermodesulfovibrionaceae, which can utilize nitrate, sulfite, thiosulfate, and sulfate as terminal electron acceptors, were characterized as indicative of far-field, unenriched sites. Thermodesulfovibrionaceae and Nitrospiraceae often co-occur in benthic marine nitrogen-metabolizing communities ( Baskaran et al, 2020 ). Likewise, Ectothiorhodospiraceae include widely distributed aerobic and anaerobic bacteria capable of nitrite and sulfur oxidation ( Oren, 2014 ), which were previously reported as indicators of high-to-good environmental quality in coastal sediments ( Aylagas et al, 2017 ).…”

Water quality assessment of East Kolkata Wetland with a special focus on bioremediation by nitrifying bacteria

“…Nitrifying bacteria along with lactobacillus is one of the best probiotic for enhancing fish production and maintenance of water quality parameters like temperature, DO, pH, ammonia, nitrite and nitrate (Karthik et al 2016). Small scale experiments in different aquaculture farms using nitrifying bacteria as probiotics to promote the water quality and reduction in load of pathogenic bacteria were conducted (Padmavathi et al 2012;Barik et al 2018;Baskaran et al 2020). Consequently, nitrifying bacteria can be used extensively as water probiotics in aquaculture for bioremediation.…”

Abundance, community structure and diversity of nitrifying bacterial enrichments from low and high saline brackishwater environments

“…The study showed the presence of microbial groups involved in nitrification, denitrification and establishing a microcosm with dissimilatory nitrate reduction to ammonium (DNRA) and assimilatory nitrate reduction in addition to ammonia‐ and nitrite‐oxidizing autotrophs (Baskaran et al . 2020).…”

“…The enrichment developed from brackishwater environment (18–35‰) performs efficiently in brackishwater aquaculture (Baskaran et al . 2020), whereas low saline (LS) aquaculture needs microbes enriched from LS environments, which can perform well. The present study aims to understand the abundance and diversity of nitrifying bacteria in the enrichments developed from LS environments in comparison with brackishwater environments.…”