Heterotrophic Nitrifying and Oxygen Tolerant Denitrifying Bacteria from Greenwater System of Coastal Aquaculture

Hydrogel and fish mucus mediated semi-biofloc formation, nitrogenous stress mitigation and growth performance of fish in integrated bioremediation system of aquaculture

Intensive aquaculture system tends to produce excessive ammonia and other nitrogenous metabolites and microbial load, which lead to abiotic and biotic stresses in fish. Eco-friendly alternatives such as probiotics are needed to prevent economically relevant infectious diseases for a successful disease-free harvest in aquaculture. In the present study, 90-days experiments were conducted at two stocking densities 80 and 160 per m3 fish (7.15 ± 0.05 g) coupled with xanthan gum (ED1) and sweet potato powder (ED2) for mitigation of priority stresses in Labeo rohita. Highest average body weight (17.71 ± 0.15 g), average daily gain (0.12 ± 0.01 g), specific growth rate (1.02 ± 0.01 g day-1), percentage weight gain (150.73 ± 1.01) and feed efficiency ratio (1.00 ± 0.01) were found in 80 fish per m3 coupled with ED2. Bacterial counts (2.6 × 106 CFU ml-1) and removal efficiency of total ammonia-N (97.6 %) and nitrite-N (99.99 %) were significantly(P < 0.05) higher in 160 fish per m3 coupled with ED2. Maturation of biofloc bacterial biomass and bio-stimulatory effects were found to be the major mechanism. Fish mucus was found to be bactericidal mostly against fish pathogenic bacteria Aeromonas hydrophila and Edwardsiella tarda due to antagonistic effect of probiotic microbiome of green slime. Bacteria as safe candidate probionts in fish health management have been isolated and identified as Bacillus spp based on 16S rDNA and FAME approaches. Low level of catalase and SOD was observed in gill, muscle and liver in treatments, indicating stress alleviation to the culture organisms. For the first time, coupling of fish green slime with hydrogel has newly been coined an integrated hydrogel-mucus-based bioremediation system. The investigation of fish mucus has a very important biological and environmental roles in potential applications in species diversification and climate-resilient aquaculture and culture-based fisheries.

Exploring the Potential of Candida sp. SW4-6 as a Probiotic for Enhancing Water Quality in Aquaculture

Aquaculture, a vital industry supplying a significant portion of the world's seafood, faces challenges such as the deterioration of the aquaculture environment. The objective of this study was to isolate and identify microorganisms with the capacity to eliminate nitrite in water from shrimp ponds and evaluate their potential as probiotics to improve water quality. Additionally, the study also determines the ideal conditions for the probiotic to effectively reduce nitrite-N and ammonia-N. Water samples were collected from four shrimp ponds (SW1, SW2, SW3, SW4) and isolates were obtained. Among all the samples, SW4 was the most effective in reducing the concentration of nitrite-N. Upon further isolation of SW4, the strain SW4-W6 showed significant nitrite-N reduction capabilities compared to the 19 other isolates tested. Through morphological, genetic (ITS sequence), and phylogenetic analyses, strain SW4-6 was identified as Candida sp. The isolation of Candida sp. SW4-6 showed superior nitrite-N and ammonia-N reduction capabilities, with sucrose as the carbon source and complete reduction observed at a C/N ratio of 15-20. Gene expression analysis revealed the up-regulation of nitrite reductase in SW4-6 after inoculation, with significantly higher expression observed with sucrose as the carbon source. Salinity and temperature significantly influenced nitrite-N and ammonia-N reduction by SW4-6, with higher temperatures (30 °C) and 0% NaCl favoring faster reduction rates. Candida sp. SW4-6 emerges as a promising probiotic candidate for aquaculture water quality management due to its efficient nitrite-N and ammonia-N reduction capabilities under optimal conditions. Its virulence profile and ability to thrive across various salinity and temperature conditions further support its potential applicability in aquaculture.

Efficient heterotrophic nitrification by a novel bacterium Sneathiella aquimaris 216LB-ZA1-12T isolated from aquaculture seawater

High concentration of ammonia poses a common threat to the healthy breeding of marine aquaculture organisms. Since aquaculture water is rich in organic matter, heterotrophic nitrifying bacteria might play a crucial role in ammonia removal. However, their roles in ammonia oxidation remain unknown. Here, we report a novel strain isolated from shrimp aquaculture seawater, identified as Sneathiella aquimaris 216LB-ZA1-12T, capable of heterotrophic nitrification. It is the first characterized heterotrophic nitrifier of the order Sneathiellales in the class Alphaproteobacteria. It exhibits high activity in heterotrophic nitrification, removing nearly 94% of ammonium-N under carbon-constrained conditions in 8 days with no observed nitrite accumulation. The heterotrophic nitrification pathway, inferred based on detection and genomic data was as follows: NH4+→NH2OH→NO→NO2-→NO3-. While this pathway aligns with the classical nitrification pathway, while the significant difference lies in the absence of classical HAO and HOX encoding genes in the genome, which is common in heterotrophic nitrifying bacteria. In summary, this bacterium is not only valuable for studying the nitrifying mechanism, but also holds potential for practical applications in ammonia removal in marine aquaculture systems and saline wastewater.

Early activated quorum sensing enhanced a nosZ-deficient strain of Pseudomonas aeruginosa for stably recovering nitrous oxide from incineration leachate in microbial electrolysis cell

In this study, a quorum sensing (QS) signal molecule, 3-oxo-C12-HSL, was supplied into ΔnosZ Pseudomonas microbial electrolysis cell system for strengthening the N₂O recovery from incineration leachate. The resistance for high nitrite loading was strongly improved with nitrite removal efficiency of 80.35% compared to 67.07% from the control on day 13 due to the increasing biomass through early activated QS. Higher N₂O proportion in biogas (85.85% on average) was achieved in the QS early activated reactor, which indicated the better potential for N₂O recovery. Bacterial community analysis showed the purity of ΔnosZ strain with the abundance of 100% in the anode chamber at the end of the operation. This was plausibly related to the increased synthesis of phenazine derivatives by the early activated QS system. These results show a more promising way for N₂O recovery by a single engineering bacteria from the high nitrogen contained actual wastewater.

Isolation and Nitrogen Removal Efficiency of the Heterotrophic Nitrifying-Aerobic Denitrifying Strain K17 From a Rare Earth Element Leaching Site

K17, an indigenous and heterotrophic nitrifying-aerobic denitrifying bacterium, was isolated from the soil of a weathered crust elution-deposited rare earth ore leaching site in Longnan County, China. Strain K17 was identified as Pseudomonas mosselii. In this study, the morphological characteristics of strain K17 were observed and the optimal ammonia nitrogen removal conditions for the strain were studied using a single-factor experiment. Key enzyme activities were determined, and we also explored the ammonia nitrogen removal process of strain K17 on simulated leaching liquor of the rare earth element leaching site. Based on the determination of ammonia nitrogen removal and enzyme activity, it was found that strain K17 has both heterotrophic nitrifying and aerobic denitrifying activities. In addition, single-factor experiments revealed that the most appropriate carbon source for strain K17 was sodium citrate with a C/N ratio of 10 and an initial NH₄⁺-N concentration of 100 mg/l. Furthermore, the optimal initial pH and rotation speed were 7 and 165 r/min, respectively. Under optimal conditions, the ammonia nitrogen removal efficiency of strain K17 was greater than 95%. As an indigenous bacterium, strain K17 has great potential for treating residual ammonium leaching solutions from rare earth element leaching sites.

Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity

Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial communities. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation; however, the effect of antibiotic treatment on the diversity of indigenous microbial populations and the consequences on the performance of tissue culture is not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) shoots in vitro as well as the composition of the plant-associated microbiome. The study revealed that shoot cultivation on a medium supplemented with 250 mg L^-1 timentin resulted in 29 ± 4% reduced biomass accumulation and a 1.2-1.6-fold higher level of oxidative stress injury compared to the control samples. Moreover, the growth properties of shoots were only partially restored after transfer to a medium without the antibiotic. Microbiome analysis of the shoot samples using multivariable region-based 16S rRNA gene sequencing revealed a diverse microbial community in the control tobacco shoots, including 59 bacterial families; however, it was largely dominated by Mycobacteriaceae. Antibiotic treatment resulted in a decline in microbial diversity (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. These results imply that the diversity of the plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.

Simultaneous Heterotrophic Nitrification and Aerobic Denitrification of Water after Sludge Dewatering in Two Sequential Moving Bed Biofilm Reactors (MBBR)

Water after sludge dewatering, also known as reject water from anaerobic digestion, is recycled back to the main wastewater treatment inlet in the wastewater treatment plant Porsgrunn, Norway, causing periodic process disturbance due to high ammonium of 568 (±76.7) mg/L and total chemical oxygen demand (tCOD) of 2825 (±526) mg/L. The main aim of this study was the simultaneous treatment of reject water ammonium and COD using two pilot-scale sequential moving bed biofilm reactors (MBBR) implemented in the main wastewater treatment stream. The two pilot MBBRs each had a working volume of 67.4 L. The biofilm carriers used had a protected surface area of 650 m²/m³ with a 60% filling ratio. The results indicate that the combined ammonia removal efficiency (ARE) in both reactors was 65.9%, while the nitrite accumulation rate (NAR) and nitrate production rate (NPR) were 80.2 and 19.8%, respectively. Over 28% of the reject water’s tCOD was removed in both reactors. The heterotrophic nitrification and oxygen tolerant aerobic denitrification were the key biological mechanisms found for the ammonium removal in both reactors. The dominant bacterial family in both reactors was Alcaligenaceae, capable of simultaneous heterotrophic nitrification and denitrification. Moreover, microbial families that were found with equal potential for application of simultaneous heterotrophic nitrification and aerobic denitrification including Cloacamonaceae, Alcaligenaceae, Comamonadaceae, Microbacteriaceae, and Anaerolinaceae.

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.

Intermittent aeration of landfill simulation bioreactors: Effects on emissions and microbial community

Landfill simulation experiments were run at lab-scale to compare the effects of intermittent and continuous aeration on the evolution of leachate composition and biogas production. The experiments were carried out using six reactors; two of them under continuous aeration, two under intermitted aeration and two anaerobic as a control. Different aeration regimes produced different effects on reactors. As expected, carbon discharge via biogas was higher in reactors under continuous aeration than under intermittent aeration. The evolution of leachate quality was affected by the aeration regimes; however, at test end very similar concentration were ascertained for relevant leachate parameters in all aerated reactors. A comprehensive description of the aerobic and anaerobic landfill microbiome is provided, using a metagenomic approach focused on the microbial genome reconstruction. A time course investigation evidenced the modification of the microbiome and revealed taxa and specific microbes more strictly connected to the environmental parameters of the reactors. Methanoculleus, Syntrophomonas and Parabacteroides were identified as the genera more strictly connected to biogas production, while numerous species belonging to Thiomonas, Nitrosomonas, Xanthomonadaceae, Myxococcales and Alcaligenaceae were found to be connected with NH₄⁺ oxidation.

Selective enrichment of heterotrophic nitrifiers Alcaligenaceae and Alcanivorax spp. from industrial wastewaters

Removal of nitrogen from wastewaters (WW) represents a global problem. The low nitrification rate during WW treatment is often caused by ecotoxicity. This problem is attributed mostly to the industrial WW. Our study was focused on the testing of industrial WW and activated sludge (AS) with the aim to reveal the abundance of nitrifiers and increase their biomass, thus, providing the additional step, i.e., bioaugmentation, within the technological process of WW treatment. Plating of AS on the selective solidified media designated for the 1st and 2nd nitrification stages, resulted in the shift in bacterial community structure with dominated Alcaligenaceae and Alcanivorax for the 1st stage, and Alcanivorax-for the 2nd stage of nitrification, respectively. Incubation of AS in the presence of real WW and selective nitrification broth resulted in a considerable increase (one or two magnitudes in the presence of the 1st and 2nd stage nitrification broth, respectively) of culturable nitrifiers after 5 days incubation under aerated conditions. The obtained data provide with evidence about a possibility to strengthen the role of heterotrophic nitrifiers in the treatment of industrial WW, where toxicity obstacles inhibited nitrification under conventional conditions.

Characterization of an aerobic denitrifier Pseudomonas stutzeri strain XL-2 to achieve efficient nitrate removal

An aerobic denitrifier was newly isolated and identified as Pseudomonas stutzeri strain XL-2. Strain XL-2 removed 97.9% of nitrate with an initial concentration about 100 mg/L. Nitrogen balance indicates that 12.4% of the initial nitrogen was converted to N₂O, and 62.4% was converted to N₂. Single factor experiments indicate that the optimal conditions for nitrate removal were C/N ratio of 10, temperature of 30 °C and shaking speed of 120 rpm. Sequence amplification indicates that the denitrification genes of napA, nirS, norB and nosZ were present in strain XL-2. Combined with nitrogen balance, strain XL-2 presents the metabolic pathway of NO₃^- → NO₂^- → NO  →  N₂O → N₂ under aerobic conditions. The expression of napA and nirS might be responsible for the tolerance of dissolved oxygen by strain XL-2 during denitrification process.

Microbial structure and nitrogen compound conversions in aerobic granular sludge reactors with non-aeration phases and acetate pulse feeding

A technological system was developed for efficient nitrogen removal from real digester supernatant in a single reactor with shortened aeration to increase the economical aspects of wastewater treatment. The supernatant (600 mg TKN/L, low COD/N ratio of 2.2) was treated in batch reactors with aerobic granules (GSBRs) to test how one, two, or three non-aeration phases and acetate pulse feeding in the cycle affect the morphological and microbial properties of biomass. Introduction of one non-aeration phase in the cycle increased nitrogen removal efficiency by 11 % in comparison with constantly aerated GSBR. The additional non-aeration phases did not diminish the efficiency of ammonia oxidation but did favor nitrification to nitrate. Acetate pulse feeding in the reactor with three non-aeration phases raised the efficiency of nitrogen removal to 77 %; in parallel, the number of denitrifiers possessing nosZ genes and performing denitrification to N₂ increased. Ammonia was oxidized by aerobic and anaerobic ammonia-oxidizing bacteria and heterotrophic nitrifiers (Pseudomonas sp. and Alcaligenes faecalis) that coexisted in granules. Azoarcus sp., Rhizobium sp., and Thauera sp. were core genera of denitrifiers in granules. An increase in the number of non-aeration phases diminished EPS content in the biomass and granule diameters and increased granule density.

Unanticipated Geochemical and Microbial Community Structure under Seasonal Ice Cover in a Dilute, Dimictic Arctic Lake

Despite most lakes in the Arctic being perennially or seasonally frozen for at least 40% of the year, little is known about microbial communities and nutrient cycling under ice cover. We assessed the vertical microbial community distribution and geochemical composition in early spring under ice in a seasonally ice-covered lake in southwest Greenland using amplicon-based sequencing that targeted 16S rRNA genes and using a combination of field and laboratory aqueous geochemical methods. Microbial communities changed consistently with changes in geochemistry. Composition of the abundant members responded strongly to redox conditions, shifting downward from a predominantly heterotrophic aerobic community in the suboxic waters to a heterotrophic anaerobic community in the anoxic waters. Operational taxonomic units (OTUs) of Sporichthyaceae, Comamonadaceae, and the SAR11 Clade had higher relative abundances above the oxycline and OTUs within the genus Methylobacter, the phylum Lentisphaerae, and purple sulfur bacteria (PSB) below the oxycline. Notably, a 13-fold increase in sulfide at the oxycline was reflected in an increase and change in community composition of potential sulfur oxidizers. Purple non-sulfur bacteria were present above the oxycline and green sulfur bacteria and PSB coexisted below the oxycline, however, PSB were most abundant. For the first time we show the importance of PSB as potential sulfur oxidizers in an Arctic dimictic lake.

Membrane bioreactors fed with different COD/N ratio wastewater: impacts on microbial community, microbial products, and membrane fouling

It is known that an increase of COD/N ratio can result in an enhanced removal of nutrients in membrane bioreactors (MBRs); however, impacts of doing so on membrane filtration performance remain unclear. In this work, comparison of membrane filtration performance, microbial community, and microbial products under low temperature was carried out in anoxic/oxic (A/O) MBRs with COD/N ratios of 9.9 and 5.5 g COD/g N in influent. There was no doubt that an improvement of nitrogen removal under high COD/N ratio was observed; however, severer membrane fouling was found compared to the MBR fed with low COD/N ratio wastewater. The increase of COD/N ratio resulted in an elevated production of humic acids in soluble microbial product (SMP) and carbohydrates, proteins, and humic acids in loosely bound extracellular polymeric substance (LB-EPS). Quartz crystal microbalance with dissipation monitoring (QCM-D) analysis showed that the adsorption capability of SMP and LB-EPS was higher in the MBR with higher COD/N ratio. Four hundred fifty four high-throughput pyrosequencing revealed that the higher COD/N ratio led to the enrichment of Bacteroidetes at phylum level and Azospira, Thauera, Zoogloea, etc. at genus level. Bacteroidetes are considered to potentially release EPS, and Azospira, Thauera, and Zoogloea, etc. have denitrification activity. The change in microbial communities is consistent with MBR performance.