Search Results (14)

With the rapid development of the global aquaculture industry, the issue of effluent pollution from aquaculture has become increasingly severe. Effective management of aquaculture effluent is an urgent requirement for the sustainable development of the aquaculture industry, with a key focus on the efficient removal of nitrogen. Heterotrophic bacteria assimilation technology offers advantages such as high efficiency and resource recovery; however, its application in effluent treatment remains limited. Therefore, this study aimed to identify the optimal carbon source for the heterotrophic bacteria assimilation process and to optimize its operating parameters using response surface methodology (RSM). The results revealed that the sucrose group achieved the highest total ammonia nitrogen (TAN) removal rate of 85.1%, significantly outperforming molasses (77.0%) and glucose (62.9%), with microbial biomass also significantly higher than in the other groups. Metagenomic analysis indicated that sucrose promotes the formation of efficient denitrifying microbial communities by enriching the phylum Bacteroidota and the denitrifying functional bacteria Xanthomarina, thereby significantly enhancing denitrification efficiency. The optimal carbon source was determined to be sucrose. Using the optimal parameters of microbial biomass at 1.7 g/L, a hydraulic retention time of 36 h, and a chemical oxygen demand-to-total nitrogen (COD/TN) ratio of 26, the removal rates of total nitrogen (TN), TAN, and nitrite nitrogen (NO₂⁻-N) exceeded 85%, while the removal rate of nitrate nitrogen (NO₃⁻-N) surpassed 60%. A significant interaction was observed between microbial biomass and hydraulic retention time, which notably affected denitrification efficiency (p < 0.05). This study provides theoretical support for the harmless and resourceful treatment of aquaculture effluent, contributing to the green and sustainable development of the aquaculture industry. Full article

Oyster mushrooms (Pleurotus ostreatus) are one of the most commonly grown edible mushrooms using compost, which contains high concentrations of ammonia. In this study, inoculation of the oyster mushroom culture substrate with ammonia-assimilating bacterium Enterobacter sp. B12, either before or after composting, reduced the ammonia nitrogen content, increased the total nitrogen content of the compost, and enhanced the mushroom yield. Co-cultivation with P. ostreatus mycelia on potato dextrose agar (PDA) plates containing 200 mM NH₄⁺, B12 reduced reactive oxygen species (ROS) accumulation in the mycelia and downregulated the expression of the ROS-generating enzymes NADPH oxidase A (NOXA) and the stress hormone ethylene synthase 1-aminocyclopropane-1-carboxylate oxidase (ACO). It also downregulated the expression of the ammonia-assimilating related genes in the mycelia, such as glutamate dehydrogenase (GDH), glutamate synthase (GOGAT), glutamine synthetase (GS), ammonia transporter protein (AMT), and amino acid transporter protein (AAT), while upregulating its own ammonia-assimilation genes. These findings suggest that the mechanism by which B12 promoted oyster mushroom growth was that B12 assimilated ammonia, alleviated ammonia stress, mitigated ROS accumulation in the mycelia, and supplied ammonia and amino acids to the mycelia. To our knowledge, ammonia-assimilating bacteria are a novel type of mushroom growth promoter (MGP). Full article

Nitrogen fertilizers in agriculture often suffer losses. Ammonia-assimilating bacteria can immobilize ammonia and reduce these losses, but they have not been used in agriculture. This study identified an ammonia-assimilating strain, Enterobacter sp. B12, which assimilated ammonia via the glutamate dehydrogenase (GDH) pathway at low levels (5 mM) and the glutamine synthetase (GS)-glutamine-2-oxoglutarate aminotransferase (GOGAT) pathway at high levels (10 mM). Inoculating wheat with B12 increased seedling dry weight, nitrogen accumulation, rhizosphere soil nitrogen content, and root enzyme activities, including GDH, superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD), under both conditions. However, root GS, GOGAT enzyme activities, and ammonia assimilation-related gene expressions were lower than the controls. The results suggest that the ammonia-assimilating bacterium promotes wheat growth, nitrogen accumulation, and soil nitrogen immobilization by establishing an ammonia and amino acid exchange with roots and enhancing root antioxidant capacity, making it a potential plant growth-promoting rhizobacteria (PGPR). Full article

The investigation of metabolic pathways and regulatory mechanisms in newly discovered species can offer valuable insights into the nitrogen removal function of heterotrophic nitrification–aerobic denitrification (HN-AD) bacteria. To investigate the nitrogen removal mechanism of a new genus, Delftia, we analyzed the complete genome, metabolic pathways, and the related genes of Delftia sp. B7. We further examined the nitrogen removal capacity of Delftia sp. B7 under various nitrogen sources and real wastewater. Our results demonstrate the presence of several genes in Delftia sp. B7, including narGHI, nasAB, nirK, nirS, nirBD, norBC, nosZ, nxrAB, gdhA, glnA, gltBD, amt, and nrt. These genes encode enzymes that facilitate ammonia assimilation, assimilatory nitrate reduction to nitrite, HN-AD, and dissimilatory nitrate reduction (DNRA) in Delftia sp. B7. Specifically, we propose an HN-AD pathway in Delftia sp. B7, NH₄⁺-N → NH₂OH → NO₂⁻-N → NO₃⁻-N → NO₂⁻-N → NO → N₂O → N₂, which accounts for the majority of nitrogen removal. Here, the transformation of NH₄⁺-N to NO₂⁻-N was achieved by unknown enzymes or by another pathway. When treating municipal wastewater, Delftia sp. B7 was able to remove 45.62 ± 1.29% of TN. These findings provide a theoretical basis for utilizing microbial resources to mitigate nitrogen contamination. Full article

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants. Full article

Heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria are the key functional microorganisms needed to achieve simultaneous nitrification and denitrification (SND). In this study, 25 strains of HN-AD bacteria were successfully isolated from a stable landfill leachate biochemical treatment system, of which 10 strains belonged to Firmicutes and 15 strains belonged to Proteobacteria. Bacillus subtilis F4 and Alcaligenes faecalis P4 displayed good tolerance at a wide range of ammonia nitrogen (NH₄⁺-N) concentrations. When the C/N ratio was 20, the removal rates of ammonia nitrogen were 90.1% and 89.5%, and the chemical oxygen demand (COD) removal rates were 92.4% and 93.9%, respectively. The napA gene encoding periplasmic nitrate reductase (Nap) and the nirS gene encoding nitrite reductase (Nir) were detected, and nitrogen balance showed assimilation and HN-AD was the main nitrogen metabolism mode in both strains. The use of immobilization materials could increase removal rate of ammonia nitrogen by 21.1% and 29.6%, respectively. The research results of this work can provide theoretical basis and technical support for the practical application of HN-AD bacteria to enhance the treatment of high ammonia nitrogen wastewater with high efficiency and low consumption. Full article

As methane fermentation is inhibited by ammonia derived from organic waste, anaerobic microbial communities tolerant to enriched wastewater with high concentrations of ammonia and salt must be obtained for methane fermentation. Therefore, acclimation cultures were prepared in bottles for 60–80 weeks with artificial wastewater medium added every 2 weeks, using three types of sludge from wastewater treatment plants in food factories. These cultures were maintained without substantially decreasing methanogenesis and gradually increasing NH₄-N and salt concentrations to 5 and 34 g/L, respectively, via the accumulation of ammonia and salt through anaerobic digestion and direct addition. The culture did not show the severe inhibition of methanogenesis or the accumulation of volatile fatty acids (VFAs) such as acetic and propionic acids. The analysis of bacterial consortia in the acclimated sludge based on the 16S rRNA sequence showed that hydrogenotrophic methanogenic bacteria of the genus Methanoculleus were dominant among archaea, whereas bacteria from the orders Clostridiales and Bacteroidales were dominant among eubacteria. Further, VFA-assimilating bacteria, including synthetic acetate-oxidizing bacteria coupled with hydrogenotrophic Methanoculleus to convert methane from acetate, were present to prevent the excessive accumulation of VFAs in the acclimation culture. The proposed acclimation process can enhance the anaerobic digestion of wastewater for methane production. Full article

Bacteria, designated as A1.1 and A1.2, were isolated from poultry waste based on the ability to form ammonia on LB nutrient medium. Whole genome sequencing identified the studied strains as Peribacillus frigoritolerans VKM B-3700D (A1.1) and Bacillus subtilis VKM B-3701D (A1.2) with genome sizes of 5462638 and 4158287 bp, respectively. In the genome of B. subtilis VKM B-3701D, gene clusters of secondary metabolites of bacillin, subtilisin, bacilisin, surfactin, bacilliacin, fengycin, sactipeptide, and ratipeptide (spore killing factor) with potential antimicrobial activity were identified. Clusters of coronimine and peninodin production genes were found in P. frigoritolerans VKM B-3700D. Information on coronimine in bacteria is extremely limited. The study of the individual properties of the strains showed that the cultures are capable of biosynthesis of a number of enzymes, including amylases. The B. subtilis VKM V-3701D inhibited the growth of bacterial test cultures and reduced the growth rate of the mold fungus Aspergillus unguis VKM F-1754 by 70% relative to the control. The antimicrobial activity of P. frigoritolerans VKM V-3700D was insignificant. At the same time, a mixture of cultures P. frigoritolerans VKM B-3700D/B. subtilis VKM B-3701D reduced the growth rate of A. unguis VKM F-1754 by 24.5%. It has been shown that strain A1.1 is able to use nitrogen compounds for assimilation processes. It can be assumed that P. frigoritolerans VKM V-3700D belongs to the group of nitrifying or denitrifying microorganisms, which may be important in developing methods for reducing nitrogen load and eutrophication. Full article

Nitrogen is one of the most important elements involved in ecosystem biogeochemical cycling. However, little is known about the characteristics of nitrogen cycling during the ice-covered period in seasonally frozen lakes. In this study, shotgun metagenomic sequencing of subglacial water and sediment from Lake Ulansuhai was performed to identify and compare nitrogen metabolism pathways and microbes involved in these pathways. In total, ammonia assimilation was the most prominent nitrogen transformation pathway, and Bacteria and Proteobacteria (at the domain and phylum levels, respectively) were the most abundant portion of microorganisms involved in nitrogen metabolism. Gene sequences devoted to nitrogen fixation, nitrification, denitrification, dissimilatory nitrate reduction to ammonium, and ammonia assimilation were significantly higher in sediment than in surface and subsurface water. In addition, 15 biomarkers of nitrogen-converting microorganisms, such as Ciliophora and Synergistetes, showed significant variation between sampling levels. The findings of the present study improve our understanding of the nitrogen cycle in seasonally frozen lakes. Full article

Feed input leads to a large amount of nitrogen-containing sediment accumulating in the substrate in the pond culture process, threatening the safety of aquaculture production. Planting lotus roots (Nelumbo nucifera Gaertn.) in ponds can accelerate the removal of bottom nitrogen, while the role of nitrogen cycle-related microorganisms in the removal is still unclear. In this study, eight yellow catfish (Pelteobagrus fulvidraco) culture ponds with the same basic situation were divided into fishponds with planted lotus roots and ponds with only fish farming. Sediment samples were taken from the fishponds with planted lotus roots and the ponds with only fish farming before and after fish farming, marked as FPB, FPA, FOB, and FOA, respectively, and subjected to physicochemical and metagenomic sequencing analyses. The results show that the contents of NH₄⁺, NO₂⁻, TN, TP, and OM were significantly lower (p < 0.05) in FPA than in FOA. The abundance of metabolic pathways for inorganic nitrogen transformation and ammonia assimilation increased considerably after culture compared to the sediments before culture. A total of eight ammonia production pathways and two ammonia utilization pathways were annotated in the sediments of the experimental ponds, with a very high abundance of ammonia assimilation. Acinetobacter and Pseudomonas (34.67%, 18.02%) were the dominant bacteria in the pond sediments before culture, which changed to Thiobacillus (12.16%) after culture. The FPA had significantly higher relative abundances of Thiobacillus denitrificans and Sulfuricella denitrificans, and the FOA had significantly a higher abundance of Microcystis aeruginosa compared to other samples. The massive growth of Microcystis aeruginosa provided two new inorganic nitrogen metabolic pathways and one organic nitrogen metabolic pathway for FOA. The relative abundances of these three microorganisms were negatively correlated with NH₄⁺ content (p < 0.01) and significantly positively correlated with AP, OM content, and pH value. Compared with ponds with only fish farming, lotus root–fish co-culture can significantly reduce the nitrogen content in sediment, increase the abundance of denitrifying bacteria, and inhibit algae growth. Still, it has little effect on the abundance of nitrogen cycle-related enzymes and genes. In summary, it is shown that, although lotus roots promote the growth of denitrifying microorganisms in the sediment, nitrogen removal relies mainly on nutrient uptake by lotus roots. Full article

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. Full article

This study aimed to characterize the rumen microbiota structure of cattle grazing in tropical rangelands throughout seasons and their responses in rumen ecology and productivity to a N-based supplement during the dry season. Twenty pregnant heifers grazing during the dry season of northern Australia were allocated to either N-supplemented or un-supplemented diets and monitored through the seasons. Rumen fluid, blood, and feces were analyzed before supplementation (mid-dry season), after two months supplementation (late-dry season), and post supplementation (wet season). Supplementation increased average daily weight gain (ADWG), rumen NH₃–N, branched fatty acids, butyrate and acetic:propionic ratio, and decreased plasma δ¹⁵N. The supplement promoted bacterial populations involved in hemicellulose and pectin degradation and ammonia assimilation: Bacteroidales BS11, Cyanobacteria, and Prevotella spp. During the dry season, fibrolytic populations were promoted: the bacteria Fibrobacter, Cyanobacteria and Kiritimatiellaeota groups; the fungi Cyllamyces; and the protozoa Ostracodinium. The wet season increased the abundances of rumen protozoa and fungi populations, with increases of bacterial families Lachnospiraceae, Ruminococcaceae, and Muribaculaceae; the protozoa Entodinium and Eudiplodinium; the fungi Pecoramyces; and the archaea Methanosphera. In conclusion, the rumen microbiota of cattle grazing in a tropical grassland is distinctive from published studies that mainly describe ruminants consuming better quality diets. Full article

RpoN (or σ⁵⁴) is the key sigma factor for the regulation of transcription of nitrogen fixation genes in diazotrophic bacteria, which include α- and β-rhizobia. Our previous studies showed that an rpoN mutant of the β-rhizobial strain Paraburkholderia phymatum STM815^T formed root nodules on Phaseolus vulgaris cv. Negro jamapa, which were unable to reduce atmospheric nitrogen into ammonia. In an effort to further characterize the RpoN regulon of P. phymatum, transcriptomics was combined with a powerful metabolomics approach. The metabolome of P. vulgaris root nodules infected by a P. phymatum rpoN Fix⁻ mutant revealed statistically significant metabolic changes compared to wild-type Fix⁺ nodules, including reduced amounts of chorismate and elevated levels of flavonoids. A transcriptome analysis on Fix⁻ and Fix⁺ nodules—combined with a search for RpoN binding sequences in promoter regions of regulated genes—confirmed the expected control of σ⁵⁴ on nitrogen fixation genes in nodules. The transcriptomic data also allowed us to identify additional target genes, whose differential expression was able to explain the observed metabolite changes in numerous cases. Moreover, the genes encoding the two-component regulatory system NtrBC were downregulated in root nodules induced by the rpoN mutant, and contained a putative RpoN binding motif in their promoter region, suggesting direct regulation. The construction and characterization of an ntrB mutant strain revealed impaired nitrogen assimilation in free-living conditions, as well as a noticeable symbiotic phenotype, as fewer but heavier nodules were formed on P. vulgaris roots. Full article

During the last 10 years, systems biology has matured from a fuzzy concept combining omics, mathematical modeling and computers into a scientific field on its own right. In spite of its incredible potential, the multilevel complexity of its objects of study makes it very difficult to establish a reliable connection between data and models. The great number of degrees of freedom often results in situations, where many different models can explain/fit all available datasets. This has resulted in a shift of paradigm from the initially dominant, maybe naive, idea of inferring the system out of a number of datasets to the application of different techniques that reduce the degrees of freedom before any data set is analyzed. There is a wide variety of techniques available, each of them can contribute a piece of the puzzle and include different kinds of experimental information. But the challenge that remains is their meaningful integration. Here we show some theoretical results that enable some of the main modeling approaches to be applied sequentially in a complementary manner, and how this workflow can benefit from evolutionary reasoning to keep the complexity of the problem in check. As a proof of concept, we show how the synergies between these modeling techniques can provide insight into some well studied problems: Ammonia assimilation in bacteria and an unbranched linear pathway with end-product inhibition. Full article