Nitrogen Metabolism Research Articles

Whole Genome Analysis of Streptomyces spp. Strains Isolated from the Rhizosphere of Vitis vinifera L. Reveals Their Role in Nitrogen and Phosphorus Metabolism

The rhizospheric microorganisms of agricultural crops play a crucial role in plant growth and nutrient cycling. In this study, we isolated two Streptomyces strains, Streptomyces sp. LM32 and Streptomyces sp. LM65, from the rhizosphere of Vitis vinifera L. We then conducted genomic analysis by assembling, annotating, and inferring phylogenomic information from the whole genome sequences. Streptomyces sp. strain LM32 had a genome size of 8.1 Mb and a GC content of 72.14%, while Streptomyces sp. strain LM65 had a genome size of 7.3 Mb and a GC content of 71%. Through ANI results, as well as phylogenomic, pan-, and core-genome analysis, we found that strain LM32 was closely related to the species S. coelicoflavus, while strain LM65 was closely related to the species S. achromogenes subsp. achromogenes. We annotated the functional categories of genes encoded in both strains, which revealed genes involved in nitrogen and phosphorus metabolism. This suggests that these strains have the potential to enhance nutrient availability in the soil, promoting agricultural sustainability. Additionally, we identified gene clusters associated with nitrate and nitrite ammonification, nitrosative stress, allantoin utilization, ammonia assimilation, denitrifying reductase gene clusters, high-affinity phosphate transporter and control of PHO regulon, polyphosphate, and phosphate metabolism. These findings highlight the ecological roles of these strains in sustainable agriculture, particularly in grapevine and other agricultural crop systems.

Effects of Short-Term Nitrogen Additions on Biomass and Soil Phytochemical Cycling in Alpine Grasslands of Tianshan, China

The nitrogen deposition process, as an important phenomenon of global climate change and an important link in the nitrogen cycle, has had serious and far-reaching impacts on grassland ecosystems. This study aimed to investigate the survival adaptation strategies of plants of different functional groups under nitrogen deposition, and the study identified the following outcomes of differences in biomass changes by conducting in situ simulated nitrogen deposition experiments while integrating plant nutrient contents and soil physicochemical properties: (1) nitrogen addition enhanced the aboveground biomass of grassland communities, in which Poaceae were significantly affected by nitrogen addition. Additionally, nitrogen addition significantly influenced plant total nitrogen and total phosphorus; (2) nitrogen addition improved the plant growth environment, alleviated plant nitrogen limitation, and promoted plant phosphorus uptake; and (3) there was variability in the biomass responses of different functional groups to nitrogen addition. The level of nitrogen addition was the primary factor affecting differences in biomass changes, while nitrogen addition frequency was an important factor affecting changes in plant community structure.

Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments.

Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.

Partial root-zone drying combined with nitrogen treatments mitigates drought responses in rice

Drought is a major stress affecting rice yields. Combining partial root-zone drying (PRD) and different nitrogen fertilizers reduces the damage caused by water stress in rice. However, the underlying molecular mechanisms remain unclear. In this study, we combined treatments with PRD and ammonia:nitrate nitrogen at 0:100 (PRD0:100) and 50:50 (PRD50:50) ratios or PEG and nitrate nitrogen at 0:100 (PEG0:100) ratios in rice. Physiological, transcriptomic, and metabolomic analyses were performed on rice leaves to identify key genes involved in water stress tolerance under different nitrogen forms and PRD pretreatments. Our results indicated that, in contrast to PRD0:100, PRD50:50 elevated the superoxide dismutase activity in leaves to accelerate the scavenging of ROS accumulated by osmotic stress, attenuated the degree of membrane lipid peroxidation, stabilized photosynthesis, and elevated the relative water content of leaves to alleviate the drought-induced osmotic stress. Moreover, the alleviation ability was better under PRD50:50 treatment than under PRD0:100. Integrated transcriptome and metabolome analyses of PRD0:100 vs PRD50:50 revealed that the differences in PRD involvement in water stress tolerance under different nitrogen pretreatments were mainly in photosynthesis, oxidative stress, nitrogen metabolism process, phytohormone signaling, and biosynthesis of other secondary metabolites. Some key genes may play an important role in these pathways, including OsGRX4, OsNDPK2, OsGS1;1, OsNR1.2, OsSUS7, and YGL8. Thus, the osmotic stress tolerance mediated by PRD and nitrogen cotreatment is influenced by different nitrogen forms. Our results provide new insights into osmotic stress tolerance mediated by PRD and nitrogen cotreatment, demonstrate the essential role of nitrogen morphology in PRD-induced molecular regulation, and identify genes that contribute to further improving stress tolerance in rice.

Guanidine production by plant homoarginine-6-hydroxylases.

Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.

Guanidine production by plant homoarginine-6-hydroxylases

Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.

Measurement report: Characteristics of nitrogen-containing organics in PM2.5 in Ürümqi, northwestern China – differential impacts of combustion of fresh and aged biomass materials

Abstract. Nitrogen-containing organic compounds (NOCs) are abundant and important aerosol components deeply involved in the global nitrogen cycle. However, the sources and formation processes of NOCs remain largely unknown, particularly in the city (Ürümqi, China) farthest from the ocean worldwide. Here, NOCs in PM2.5 collected in Ürümqi over a 1-year period were characterized by ultra-high-resolution mass spectrometry. The abundance of CHON compounds (mainly oxygen-poor unsaturated aliphatic-like species) in the positive ion mode was higher in the warm period than in the cold period, which was largely attributed to the contribution of fresh biomass material combustion (e.g., forest fires) associated with amidation of unsaturated fatty acids in the warm period, rather than the oxidation processes. However, CHON compounds (mainly nitro-aromatic species) in the negative ion mode increased significantly in the cold period, which was tightly related to aged biomass combustion (e.g., dry straws) in wintertime Ürümqi. For CHN compounds, alkyl nitriles and aromatic species showed higher abundance in the warm and cold periods, respectively. Alkyl nitriles can be derived from fresh biomass material combustion associated with the dehydration of amides (the main CHON compounds in the warm period). In contrast, aromatic species were tightly related to aged biomass burning. These findings further suggested different impacts of the combustion of fresh and aged biomass materials on NOC compositions in different seasons. The overall results shed light on the mechanisms by which fresh and aged biomass materials release different NOCs during combustion.

Machine Learning-Driven Classification of Urease Inhibitors Leveraging Physicochemical Properties as Effective Filter Criteria

Urease, a pivotal enzyme in nitrogen metabolism, plays a crucial role in various microorganisms, including the pathogenic Helicobacter pylori. Inhibiting urease activity offers a promising approach to combating infections and associated ailments, such as chronic kidney diseases and gastric cancer. However, identifying potent urease inhibitors remains challenging due to resistance issues that hinder traditional approaches. Recently, machine learning (ML)-based models have demonstrated the ability to predict the bioactivity of molecules rapidly and effectively. In this study, we present ML models designed to predict urease inhibitors by leveraging essential physicochemical properties. The methodological approach involved constructing a dataset of urease inhibitors through an extensive literature search. Subsequently, these inhibitors were characterized based on physicochemical properties calculations. An exploratory data analysis was then conducted to identify and analyze critical features. Ultimately, 252 classification models were trained, utilizing a combination of seven ML algorithms, three attribute selection methods, and six different strategies for categorizing inhibitory activity. The investigation unveiled discernible trends distinguishing urease inhibitors from non-inhibitors. This differentiation enabled the identification of essential features that are crucial for precise classification. Through a comprehensive comparison of ML algorithms, tree-based methods like random forest, decision tree, and XGBoost exhibited superior performance. Additionally, incorporating the “chemical family type” attribute significantly enhanced model accuracy. Strategies involving a gray-zone categorization demonstrated marked improvements in predictive precision. This research underscores the transformative potential of ML in predicting urease inhibitors. The meticulous methodology outlined herein offers actionable insights for developing robust predictive models within biochemical systems.

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential

Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.

Optimal enzyme allocation leads to the constrained enzyme hypothesis: the Soil Enzyme Steady Allocation Model (SESAM; v3.1)

Abstract. Describing the coupling of nitrogen (N), phosphorus (P), and carbon (C) cycles of land ecosystems requires understanding microbial element use efficiencies of soil organic matter (SOM) decomposition. These efficiencies are studied by the Soil Enzyme Steady Allocation Model (SESAM) at the decadal scale. The model assumes that the soil microbial communities and their element use efficiencies develop towards an optimum where the growth of the entire community is maximized. Specifically, SESAM approximated this growth optimization by allocating resources to several SOM-degrading enzymes proportional to the revenue of these enzymes, called the Relative approach. However, a rigorous mathematical treatment of this approximation has been lacking so far. Therefore, in this study we derive explicit formulas of enzyme allocation that maximize the total return from enzymatic processing, called the Optimal approach. Further, we derive another heuristic approach that prescribes the change of allocation without the need of deriving a formulation for the optimal allocation, called the Derivative approach. When comparing predictions across these approaches, we found that the Relative approach was a special case of the Optimal approach valid at sufficiently high microbial biomass. However, at low microbial biomass, it overestimated allocation to the enzymes having lower revenues compared to the Optimal approach. The Derivative-based allocation closely tracked the Optimal allocation. These findings increase our confidence in conclusions drawn from SESAM studies. Moreover, the new developments extend the range of conditions at which valid conclusions can be drawn. Further, based on these findings we formulated the constrained enzyme hypothesis. This hypothesis provides a complementary explanation why some substrates in soil are preserved over decades, although they are often decomposed within a few years in incubation experiments. This study shows how optimality considerations lead to simplified models, new insights, and new hypotheses. This is another step in deriving a simple representation of an adaptive microbial community, which is required for coupled stoichiometric C–N–P dynamic models that are aimed to study decadal processes beyond the ecosystem scale.

The global nitrogen regulator GlnR is a direct transcriptional repressor of the key gluconeogenic gene pckA in actinomycetes.

The GlnR regulator of actinomycetes controls nitrogen metabolism genes and many other genes involved in carbon, phosphate, and secondary metabolisms. Currently, the known GlnR-regulated genes in carbon metabolism are involved in the transport of carbon sources, the assimilation of short-chain fatty acid, and the 2-methylcitrate cycle, although little is known about the relationship between GlnR and the TCA cycle and gluconeogenesis. Here, based on the biochemical and genetic results, we identified GlnR as a direct transcriptional repressor of pckA, the gene that encodes phosphoenolpyruvate carboxykinase, a key enzyme for gluconeogenesis, thus highlighting that GlnR plays a central and complex role for dynamic orchestration of cellular carbon, nitrogen, and phosphate fluxes and bioactive secondary metabolites in actinomycetes to adapt to changing surroundings.

Combining association with linkage mapping to dissect the phenolamides metabolism of the maize kernel

Phenolamides are important secondary metabolites in plant species. They play important roles in plant defense responses against pathogens and insect herbivores, protection against UV irradiation and floral induction and development. However, the accumulation and variation in phenolamides content in diverse maize lines and the genes responsible for their biosynthesis remain largely unknown. Here, we combined genetic mapping, protein regulatory network and bioinformatics analysis to further enhance the understanding of maize phenolamides biosynthesis. Sixteen phenolamides were identified in multiple populations, and they were all significantly correlated with one or several of 19 phenotypic traits. By linkage mapping, 58, 58, 39 and 67 QTLs, with an average of 3.9, 3.6, 3.6 and 4.2 QTLs for each trait were mapped in BBE1, BBE2, ZYE1 and ZYE2, explaining 9.47%, 10.78%, 9.51% and 11.40% phenotypic variation for each QTL on average, respectively. By GWAS, 39 and 36 significant loci were detected in two different environments, 3.3 and 2.8 loci for each trait, explaining 10.00% and 9.97% phenotypic variation for each locus on average, respectively. Totally, 58 unique candidate genes were identified, 31% of them encoding enzymes involved in amine and derivative metabolic processes. Gene Ontology term analysis of the 358 protein-protein interrelated genes revealed significant enrichment in terms relating to cellular nitrogen metabolism, amine metabolism. GRMZM2G066142, GRMZM2G066049, GRMZM2G165390 and GRMZM2G159587 were further validated involvement in phenolamides biosynthesis. Our results provide insights into the genetic basis of phenolamides biosynthesis in maize kernels, understanding phenolamides biosynthesis and its nutritional content and ability to withstand biotic and abiotic stress.

Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica

Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3−) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3− via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via 13C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.

Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses

Abstract The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.

Ru-Induced Defect Engineering in Co3O4 Lattice for High Performance Electrochemical Reduction of Nitrate to Ammonium.

Amidst these growing sustainability concerns, producing NH4 + via electrochemical NO3 - reduction reaction (NO3RR) emerges as a promising alternative to the conventional Haber-Bosch process. In a pioneering approach, this study introduces Ru incorporation into Co3O4 lattices at the nanoscale and further couples it with electroreduction conditioning (ERC) treatment as a strategy to enhance metal oxide reducibility and induce oxygen vacancies, advancing NH4 + production from NO3RR. Here, supported by a suite of ex situ and in situ characterization measurements, the findings reveal that Ru enrichment promotes Co species reduction and oxygen vacancy formation. Further, as evidenced by the theoretical calculations, Ru integration lowers the energy barrier for oxygen vacancy formation, thereby facilitating a more energy-efficient NO3RR-to-NH4 + pathway. Optimal catalytic activity is realized with a Ru loading of 10 at.% (named 10Ru/Co3O4), achieving a high NH4 + production rate (98nmols-1cm-2), selectivity (97.5%) and current density (≈100mAcm-2) at -1.0V vs RHE. The findings not only provide insights into defect engineering via the incorporation of secondary sites but also lay the groundwork for innovative catalyst design aimed at improving NH4 + yield from NO3RR. This research contributes to the ongoing efforts to develop sustainable electrochemical processes for nitrogen cycle management.

Response Patterns of Soil Nitrogen Cycling to Crop Residue Addition: A Review

Response Patterns of Soil Nitrogen Cycling to Crop Residue Addition: A Review

Ammonia-oxidizing archaea adapted better to the dark, alkaline oligotrophic karst cave than their bacterial counterparts

Subsurface karst caves provide unique opportunities to study the deep biosphere, shedding light on microbial contribution to elemental cycling. Although ammonia oxidation driven by both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) is well explored in soil and marine environments, our understanding in the subsurface biosphere still remained limited to date. To address this gap, weathered rock and sediment samples were collected from the Xincuntun Cave in Guilin City, an alkaline karst cave, and subjected to high-throughput sequencing and quantification of bacterial and archaeal amoA, along with determination of the potential nitrification rates (PNR). Results revealed that AOA dominated in ammonia oxidation, contributing 48–100% to the PNR, and AOA amoA gene copies outnumbered AOB by 2 to 6 orders. Nitrososphaera dominated in AOA communities, while Nitrosopira dominated AOB communities. AOA demonstrated significantly larger niche breadth than AOB. The development of AOA communities was influenced by deterministic processes (50.71%), while AOB communities were predominantly influenced by stochastic processes. TOC, NH4+, and Cl− played crucial roles in shaping the compositions of ammonia oxidizers at the OTU level. Cross-domain co-occurrence networks highlighted the dominance of AOA nodes in the networks and positive associations between AOA and AOB, especially in the inner zone, suggesting collaborative effort to thrive in extreme environments. Their high gene copies, dominance in the interaction with ammonia oxidizing bacteria, expansive niche breadth and substantial contribution to PNR collectively confirmed that AOA better adapted to alkaline, oligotrophic karst caves environments, and thus play a fundamental role in nitrogen cycling in subsurface biosphere.

Nitrogen cycling process and application in different prawn culture modes

AbstractNitrogenous waste is a global concern in aquatic ecosystems. In the shrimp farming system, feeding is the main input of nitrogen, which leads to the accumulation of nitrogenous waste, such as ammonia, nitrite, and nitrate. Nitrogen cycling is crucial for nitrogenous waste removal and for the stability of the aquaculture system. Under the action of different functional microorganisms, a variety of nitrogen cycling pathways can be used for the transformation and removal of nitrogenous waste. Understanding the complexity of the nitrogen cycle is necessary for improving the aquaculture environment. This review examines the many components and mechanisms involved in the nitrogen cycle in shrimp farming system, including nitrification, denitrification, anammox, heterotrophic assimilation, and autotrophic assimilation. Because of the difference in aquaculture characteristics, nitrogen cycling pathways in different shrimp culture modes are diverse. The current application of the nitrogen cycle in shrimp farming system, including the outdoor pond mode and indoor industrialized mode, was presented in combination with the requirements for dissolved oxygen (DO), organic matter, carbon–nitrogen ratio, light, and other environmental factors. Overall, nitrification, heterotrophic assimilation, autotrophic assimilation, and heterotrophic denitrification are the main nitrogen cycle processes in the shrimp culture system. According to the characteristics of aquaculture modes and microorganisms, utilizing different nitrogen cycle processes can enhance the efficiency of the nitrogen cycle, facilitate the elimination of nitrogenous waste, optimize the aquaculture water environment, and improve overall aquaculture benefits.

Biomineralized manganese oxide mediated nitrogen-contained wastewater treatment

In recent years, manganese (Mn) has emerged as an accelerator for nitrogen metabolism. However, the bioactivity of manganese is limited by the restricted contact between microbes and manganese minerals in the solid phase and by the toxicity of manganese to microbes. To enhance the bioactivity of solid-phase manganese, biomineralized manganese oxide (MnOx) modified by Lactobacillus was introduced. Nitrogen removal performance have confirmed the effective role of biomineralized MnOx in accelerating the removal of total inorganic nitrogen (TIN). Metagenomic analysis has confirmed the enhancement of the nitrogen metabolic pathway and microbial extracellular electron transfer (MEET) in biomineralized MnOx treatment group (BIOA group). Additionally, the enrichment of manganese oxidation and denitrification genus indicates a coupling between nitrogen metabolism and manganese metabolism. One point of views is that biomineralized MnOx-mediated nitrogen transformation processes could serve as a substitute for traditional nitrogen removal processes.

Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland

The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.