The Role of Pseudomonas in Heterotrophic Nitrification: A Case Study on Shrimp Ponds (Litopenaeus vannamei) in Soc Trang Province

Application of a nitrifying bacterium Pseudomonas sp. HIB_D to reduce nitrogen waste in the Litopenaeus vannamei cultivation environment

Pseudomonas sp. HIB_D has been observed to have nitrification activity that can oxidize ammonia/ammonium to nitrite and nitrate. This bacterium was isolated from the aquaculture environment with Ancol Indonesian marine water sources. Pseudomonas sp. HIB_D was applied in the rearing water of Litopenaeus vannamei to decrease nitrogen pollution levels and support a sustainable cultivation environment. This present study was set up using a completely randomized design with four treatments and three replications, i.e., control (without bacterial application) and bacterial application with a cell density of 107, 108, and 109 CFU mL-1 in a volume of 100 mL for 90 L seawater treatment. Thirty-six individuals of 15-day-old postlarvae L. vannamei (PL 15) (a density of 120 PL m-2) were used in this study for an 8-week rearing period. Based on the water quality analysis, the ammonia level under the bacterial applications was lower than in the control after 8-week cultivation. Nitrate levels increased at week 6 and decreased at week 8, specifically in 109 CFU mL-1 treatment. L. vannamei with 109 CFU mL-1 bacterial application had the best production performance with a survival rate of 94.33 ± 2.78%, an absolute length gain of 10.59 ± 0.22 cm, an absolute weight gain of 8.16 ± 0.33 g, a specific growth rate of 14.12% ± 0.01% day-1, and a feed conversion ratio of 1.26 ± 0.03. The blood glucose level and total hemocyte count of shrimp under the bacterial application with a density of 109 CFU mL-1 showed the highest level (30.71 ± 13.9 mg dL-1) and the lowest level (15 × 106 cells mL-1), respectively. The results showed that all treatments performed better than the control, in which the 109 CFU mL-1 bacterial application was the best treatment.

Self-rescue of nitrogen-cycling bacteria under β-lactam antibiotics stress during managed aquifer recharge (MAR): Microbial collaboration and anti-resistance

Storing reclaimed water via managed aquifer recharge (MAR) is an effective strategy for alleviating groundwater overdraft and achieving water resource recycling simultaneously. However, β-lactam antibiotics in the reclaimed water can induce stress on aquifer system, reshape microbial community, and affect the emergence and prevalence of antibiotic resistance genes (ARGs). In this study, three sandy soil columns (H 1.5 m, ID 14 cm) were employed to simulate MAR, and synthetic reclaimed water containing either amoxicillin (AMO), ampicillin (AMP) or oxacillin (OXA) was continuously recharged for 120 d The temporal and spatial attenuation of β-lactams and nitrogen was studied, and microbial collaboration and the resistance mechanism were elaborated. Biodegradation is the main pathway for β-lactams elimination, AMO and AMP were eliminated when migrating 30 cm, while the attenuation of OXA experienced in the whole column with final removal efficiency of 82%. Moreover, refractory OXA induced more ARGs production, and approximately 10% and 13% higher than that of AMO and AMP columns. Efflux pump and antibiotics inactivation were the two major resistance mechanisms. NO₃^--N gradually decreased (by 26%, 38%, and 49% for AMO, AMP, and OXA, respectively) along the recharge direction. Microbial co-occurrence network revealed that nitrogen-cycling bacteria were the keystone species in aquifer community, and ammonation provided NH₄⁺-N for the nitrification process of ammonia-oxidizing archaea (AOA), promoting the further denitrification for nitrogen removal in MAR process. Nitrogen-cycling bacteria were the key and active ARG hosts, which could keep nitrogen transformation activity under antibiotics stress. In sum, nitrogen-cycling bacteria exhibited intimate collaboration and elastic resistance in response to the malnutrition environment and β-lactams exposure during MAR.

Comparative Genome Analysis of Two Heterotrophic Nitrifying Pseudomonas putida Strains Isolated from Freshwater Shrimp Ponds in Soc Trang Province

Nitrogen compounds, especially ammonia, are widely produced in aquaculture systems during cultivation. Ammonia has been investigated as a model compound for use by heterotrophic nitrifying bacteria. Pseudomonas TT321 and Pseudomonas TT322, isolated from shrimp pond water in Soc Trang province, Vietnam, are identified by comparing them with 31 of the closest genomes sequences from the NCBI nucleotide database. The genome sizes of strains TT321 and TT322 were 5,566,241 bp and 5,563,644 bp, respectively. No plasmids were evident in these strains. Genome analysis revealed that TT321 and TT322 belonged to Pseudomonas putida and shared a common ancestor with 33 genomes. Analysis based on the comparison of genomes showed that three genes, carbamate kinase (arcC), glutamine synthetase (Glul), and aminomethyltransferase (amt), are involved in three metabolic pathways. These pathways are: (i) arginine and proline metabolism, (ii) alanine, aspartate and glutamate metabolism, and (iii) glycine, serine and threonine metabolism. These genes may play important roles in ammonia reduction and support bacterial growth via ammonia assimilation.

Evaluation of Potential Probiotic Properties of a Strain of Lactobacillus plantarum for Shrimp Farming: From Beneficial Functions to Safety Assessment

In recent years the safety of probiotics has received increasing attention due to the possible transfer and spread of virulence factors (VFs) and antibiotic resistance genes (ARGs) among microorganisms. The safety of a strain of Lactobacillus plantarum named W2 was evaluated in phenotype and genotype in the present study. Its probiotic properties were also evaluated both in vivo and in vitro, including adherence properties, antibacterial properties and beneficial effects on the growth and immunity of Pacific white shrimp, Penaeus vannamei. Hemolysis tests, antibiotic resistance tests and whole genome sequence analysis showed that W2 had no significant virulence effects and did not carry high virulence factors. W2 was found to be sensitive to chloramphenicol, clindamycin, gentamicin, kanamycin and tetracycline, and to be resistant to ampicillin and erythromycin. Most ARGs have no transfer risk and a few have transfer risk but no significant enrichment in human-associated environments. The autoaggregation of W2 was 82.6% and the hydrophobicity was 81.0%. Coaggregation rate with Vibrio parahaemolyticus (24.9%) was significantly higher than Vibrio's autoaggregation rate (17.8%). This suggested that W2 had adhesion potential to mucosal/intestinal surfaces and was able to attenuate the adherence of V. parahaemolyticus. In addition, several adhesion-related protein genes, including 1 S-layer protein, 1 collagen-binding protein and 9 mucus-binding proteins were identified in the W2 genome. W2 had efficiently antagonistic activity against 7 aquatic pathogenic strains. Antagonistic components analysis indicated that active antibacterial substances might be organic acids. W2 can significantly promote the growth of shrimp when supplemented with 1 × 10¹⁰ cfu/kg live cells. Levels of 7 serological immune indicators and expression levels of 12 hepatopancreatic immune-related genes were up-regulated, and the mortality of shrimp exposed to V. parahaemolyticus was significantly reduced. Based on the above, L. plantarum W2 can be applied safely as a potential probiotic to enhance the growth performance, immunity capacity and disease resistance of P. vannamei.

Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu

To explore the effects of Microcystis blooms on nitrogen (N) cycling in the water column, the community structures of the Microcystis-attached and free-living bacteria in Lake Taihu were assessed and a mesocosm experiment was further conducted on the shore of Lake Taihu. The bacterial communities of Microcystis-attached and free-living bacteria were dominated by heterotrophic bacteria, such as Pseudomonas and Massilia, while the relative abundances of the genera related to traditional autotrophic nitrification were surprisingly low. However, the dramatic increase in nitrate (NO₃^-) levels at the daytime suggested that in the mesocosms nitrification did occur, during which the heterotrophic nitrifiers played a predominant role as revealed by the acetylene inhibition experiment. The ammonium (NH₄⁺) concentrations were always maintained at a low level, indicating that most of the substrates for daytime nitrification originated from organic N. The total N being removed during the experiment was much less than the sum of daily NO₃^- reduction, while the decrease in NO₃^- concentration was much higher than the increase in NH₄⁺ concentration during the night, indicating that assimilation was the main explanation for nocturnal NO₃^- reduction. Thus, the cycling of organic N (remineralization) - heterotrophic nitrification - NO₃^- assimilation (reduction) promoted by Microcystis blooms aggravates the diurnal variation of NO₃^- in the water column.

Comparison of the Performance and Microbial Community Structure of Two Outdoor Pilot-Scale Photobioreactors Treating Digestate

This study aimed at examining and comparing the nutrient removal efficiency, biomass productivity and microbial community structure of two outdoor pilot-scale photobioreactors, namely a bubble column and a raceway pond, treating the liquid fraction of an agricultural digestate. Bacterial and eukaryotic communities were characterized using a metabarcoding approach and quantitative PCR. The abundance, composition, diversity, and dynamics of the main microbes were then correlated to the environmental conditions and operational parameters of the reactors. Both photobioreactors were dominated either by Chlorella sp. or Scenedesmus sp. in function of temperature, irradiance and the nitrogen compounds derived by nitrification. Other species, such as Chlamydomonas and Planktochlorella, were sporadically present, demonstrating that they have more specific niche requirement. Pseudomonas sp. always dominated the bacterial community in both reactors, except in summertime, when a bloom of Calothrix occurred in the raceway pond. In autumn, the worsening of the climate conditions decreased the microalgal growth, promoting predation by Vorticella sp. The study highlights the factors influencing the structure and dynamics of the microbial consortia and which ecological mechanisms are driving the microbial shifts and the consequent reactor performance. On these bases, control strategies could be defined to optimize the management of the microalgal-based technologies.