Nitrogen Metabolism Research Articles

New insight into protective effect against oxidative stress and biosynthesis of exopolysaccharides produced by Lacticaseibacillus paracasei NC4 from fermented eggplant.

Fermented eggplant is a traditional fermented food, however lactic acid bacteria capable of producing exopolysaccharide (EPS) have not yet been exploited. The present study focused on the production and protective effects against oxidative stress of an EPS produced by Lacticaseibacillus paracasei NC4 (NC4-EPS), in addition to deciphering its genomic features and EPS biosynthesis pathway. Among 54 isolates tested, strain NC4 showed the highest EPS yield and antioxidant activity. The maximum EPS production (2.04 ± 0.11g/L) was achieved by culturing in MRS medium containing 60g/L sucrose at 37°C for 48h. Under 2mM H2O2 stress, the survival of a yeast model Saccharomyces cerevisiae treated with 0.4mg/mL NC4-EPS was 2.4-fold better than non-treated cells, which was in agreement with the catalase and superoxide dismutase activities measured from cell lysates. The complete genome of NC4 composed of a circular chromosome of 2,888,896bp and 3 circular plasmids. The NC4 genome comprises more genes with annotated function in nitrogen metabolism, phosphorus metabolism, cell division and cell cycle, and iron acquisition and metabolism as compared to other reported L. paracasei. Of note, the eps gene cluster is not conserved across L. paracasei. Pathways of sugar metabolism for EPS biosynthesis were proposed for the first time, in which gdp pathway only present in few plant-derived bacteria was identified. These findings shed new light on the cell-protective activity and biosynthesis of EPS produced by L. paracasei, paving the way for future efforts to enhance yield and tailor-made EPS production for food and pharmaceutical industries.

Seawater intrusion effects on nitrogen cycling in the regulated Nakdong River Estuary, South Korea

Seawater intrusion effects on nitrogen cycling in the regulated Nakdong River Estuary, South Korea

Catalysts for C-N coupling in urea electrosynthesis under ambient conditions from carbon dioxide and nitrogenous species.

Urea is an indispensable nitrogen-containing organic compound in modern human life. However, the current industrial synthesis of urea involves ammonia, which is produced through the Haber-Bosch process under harsh reaction conditions, causing huge energy consumption and heavy environmental pollution. Electrochemical reduction of carbon dioxide (CO2) and nitrogenous species (N2, NOx- and NO) have achieved significant progress, offering a promising approach for the electrochemical C-N coupling to produce urea under ambient conditions. Urea synthesis driven by renewable electricity represents a suitable alternative to the traditional process, contributing to the goal of carbon neutrality and nitrogen cycles. However, challenges such as low yield rate, poor selectivity and unveiled reaction mechanisms still need to be addressed. This review provides a summary of the latest catalysts utilized in urea electrosynthesis, aiming to provide guidance and prospects for the development of high-performance catalysts.

Census of below-ground biota associated with permafrost affected soils of western Greenland, with a focus on trophic structure

Large amounts of terrestrial organic carbon (OC) are stored in Arctic permafrost-affected soils. Through processes of cryoturbation and solifluction, the subsoils can contain subducted topsoil material, which largely contribute to the large OC storage in these soils. While the bacterial, archaeal, and fungal communities in such soils have been studied to some degree, information about protists and meso- and macrofauna is scarce, although these groups might substantially contribute to OC processing, through e.g., food web interactions. Different organic and mineral horizons, including subducted topsoil material, of Arctic soils were investigated using a metatranscriptomics three-domain community profiling approach. Soil horizons were compared in regards to their total microbial community composition including all three domains of life. Furthermore, abundances of different pro- and eukaryotic micropredators were examined and a variety of functional groups involved in the carbon (C) and the nitrogen (N) cycle were analyzed in relation to specific taxonomic groups and abiotic soil parameters. Our study showed that RNA yields positively correlated with the OC content of the horizon and that the composition of the microbial community in subducted topsoil material rather matched that of mineral subsoils instead of organic top horizons. Horizon-resolved profiling revealed heterogeneity in the associated microbiomes and showed major differences in microbiomes of topsoil and subducted topsoil. The abundance of protist and nematode micropredators decreased in subducted topsoil, while predatory myxobacteria remained remarkably constant and comprised high proportions of the total communities in all horizons. Correlations analysis between functional guilds and biotic and abiotic parameters suggest a major impact of predatory myxobacteria on carbon and nitrogen cycles of subducted topsoils. The study adds urgently needed information about the total biota structure in permafrost soils and first insights into the associated soil microbial food webs.

Analysis of nearly 3000 archaeal genomes from terrestrial geothermal springs sheds light on interconnected biogeochemical processes

Terrestrial geothermal springs are physicochemically diverse and host abundant populations of Archaea. However, the diversity, functionality, and geological influences of these Archaea are not well understood. Here we explore the genomic diversity of Archaea in 152 metagenomes from 48 geothermal springs in Tengchong, China, collected from 2016 to 2021. Our dataset is comprised of 2949 archaeal metagenome-assembled genomes spanning 12 phyla and 392 newly identified species, which increases the known species diversity of Archaea by ~48.6%. The structures and potential functions of the archaeal communities are strongly influenced by temperature and pH, with high-temperature acidic and alkaline springs favoring archaeal abundance over Bacteria. Genome-resolved metagenomics and metatranscriptomics provide insights into the potential ecological niches of these Archaea and their potential roles in carbon, sulfur, nitrogen, and hydrogen metabolism. Furthermore, our findings illustrate the interplay of competition and cooperation among Archaea in biogeochemical cycles, possibly arising from overlapping functional niches and metabolic handoffs. Taken together, our study expands the genomic diversity of Archaea inhabiting geothermal springs and provides a foundation for more incisive study of biogeochemical processes mediated by Archaea in geothermal ecosystems.

Investigating gene signatures associated with immunity in colon adenocarcinoma to predict the immunotherapy effectiveness using NFM and WGCNA algorithms.

Colon adenocarcinoma (COAD), a frequently encountered and highly lethal malignancy of the digestive system, has been the focus of intensive research regarding its prognosis. The intricate immune microenvironment plays a pivotal role in the pathological progression of COAD; nevertheless, the underlying molecular mechanisms remain incompletely understood. This study aims to explore the immune gene expression patterns in COAD, construct a robust prognostic model, and delve into the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby providing critical support for individualized treatment strategies and prognostic evaluation. Initially, we curated a comprehensive dataset by screening 2600 immune-related genes (IRGs) from the ImmPort and InnateDB databases, successfully obtaining a rich data resource. Subsequently, the COAD patient cohort was classified using the non-negative matrix factorization (NMF) algorithm, enabling accurate categorization. Continuing on, utilizing the weighted gene co-expression network analysis (WGCNA) method, we analyzed the top 5000 genes with the smallest p-values among the differentially expressed genes (DEGs) between immune subtypes. Through this rigorous screening process, we identified the gene modules with the strongest correlation to the COAD subpopulation, and the intersection of genes in these modules with DEGs (COAD vs COAD vs Normal colon tissue) is referred to as Differentially Expressed Immune Genes Associated with COAD (DEIGRC). Employing diverse bioinformatics methodologies, we successfully developed a prognostic model (DPM) consisting of six genes derived from the DEIGRC, which was further validated across multiple independent datasets. Not only does this predictive model accurately forecast the prognosis of COAD patients, but it also provides valuable insights for formulating personalized treatment regimens. Within the constructed DPM, we observed a downregulation of CALB2 expression levels in COAD tissues, whereas NOXA1, KDF1, LARS2, GSR, and TIMP1 exhibited upregulated expression levels. These genes likely play indispensable roles in the initiation and progression of COAD and thus represent potential therapeutic targets for patient management. Furthermore, our investigation into the molecular mechanisms and therapeutic targets for COAD liver metastasis revealed associations with relevant processes such as fat digestion and absorption, cancer gene protein polysaccharides, and nitrogen metabolism. Consequently, genes including CAV1, ANXA1, CPS1, EDNRA, and GC emerge as promising candidates as therapeutic targets for COAD liver metastasis, thereby providing crucial insights for future clinical practices and drug development. In summary, this study uncovers the immune gene expression patterns in COAD, establishes a robust prognostic model, and elucidates the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby possessing significant theoretical and clinical implications. These findings are anticipated to offer substantial support for both the treatment and prognosis management of COAD patients.

Exploiting the roles of nitrogen sources for HEA increment in Cordyceps cicadae

Cordyceps cicadae, as a new food ingredient, is a valuable edible and medicinal fungi. However, its resources are severely depleted due to environmental limitations and excessive harvesting practices. N6-(2-hydroxyethyl) adenosine (HEA), as an important product of Cordyceps cicadae, has the potential to be used in medical industry due to its diverse disease curing potential. However, the disclosure of HEA synthesis still severely limited its application until now. In this study, the kinetic curves for adenosine and HEA under shaker fermentation were explored. The kinetics of HEA and adenosine production exhibited a competitive pattern, implicating a possibility of sharing a same step during their synthesis. Due to HEA as a derivative of nitrogen metabolism, the effect of different nitrogen sources (peptone, yeast extract, ammonium sulfate, diammonium oxalate monohydrate, ammonium citrate dibasic, and ammonium citrate tribasic) on HEA production in Cordyceps cicadae strain AH 10-4 had been explored under different incubation conditions (shaker fermentation, stationary fermentation, and submerged fermentation). Our results indicated that the complex organic nitrogen sources were found to improve the accumulation of HEA content under shaker fermentation. In contrast, the optimal nitrogen source for the accumulation of HEA under stationary fermentation and submerged fermentation was ammonium citrate tribasic. But submerged fermentation obviously shortened the incubation time and had a comparable capacity of HEA accumulation by 2.578 mg/g compared with stationary fermentation of 2.535 mg/g, implicating a possibility of scaled-up production of HEA in industry by submerged fermentation. Based on the dramatic HEA production by ammonium sulfate as nitrogen resources between stationary and shaker fermentations, alanine, aspartate and glutamate as well as arginine metabolic pathway were related to the production of HEA by comparative transcriptome. Further investigation indicated that glutamic acid, which is an analog of Asp, showed an optimum production of HEA in comparison with other amino acids.

Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence

BackgroundBoreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing.ResultsFungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion.ConclusionsMicrobial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.

Ca(H2PO4)2 and MgSO4 activated nitrogen-related bacteria and genes in thermophilic stage of compost

This study was conducted to investigate the effects of Ca(H2PO4)2 and MgSO4 on the bacterial community and nitrogen metabolism genes in the aerobic composting of pig manure. The experimental treatments were set up as control (C), 1% Ca(H2PO4)2 + 2% MgSO4 (CaPM1), and 1.5% Ca(H2PO4)2 + 3% MgSO4 (CaPM2), which were used at the end of composting for potting trials. The results showed that Ca(H2PO4)2 and MgSO4 played an excellent role in retaining nitrogen and increasing the alkali-hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK) contents of the composts. Adding Ca(H2PO4)2 and MgSO4 changed the microbial community structure of the compost. The microorganisms associated with nitrogen retention were activated. The complexity of the microbial network was enhanced. Genetic prediction analysis showed that the addition of Ca(H2PO4)2 and MgSO4 reduced the accumulation of nitroso-nitrogen and the process of denitrification. At the same time, despite the reduction of genes related to nitrogen fixation, the conversion of ammonia to nitrogenous organic compounds was promoted and the stability of nitrogen was increased. Mantel test analysis showed that Ca(H2PO4)2 and MgSO4 can affect nitrogen transformation-related bacteria and thus indirectly affect nitrogen metabolism genes by influencing the temperature, pH, and organic matter (OM) of the compost and also directly affected nitrogen metabolism genes through PO43− and Mg2+. The pot experiment showed that composting with 1.5% Ca(H2PO4)2 + 3% MgSO4 produced the compost product that improved the growth yield and nutrient content of cilantro and increased the fertility of the soil. In conclusion, Ca(H2PO4)2 and MgSO4 reduces the loss of nitrogen from compost, activates nitrogen-related bacteria and genes in the thermophilic phase of composting, and improves the fertilizer efficiency of compost products.Key points• Ca(H2PO4)2 and MgSO4 reduced the nitrogen loss and improved the compost effect• Activated nitrogen-related bacteria and altered nitrogen metabolism genes• Improved the yield and quality of cilantro and fertility of soil

Stress Responses and Ammonia Nitrogen Removal Efficiency of Oocystis lacustris in Saline Ammonium-Contaminated Wastewater Treatment

The increasing concern over climate change has spurred significant interest in exploring the potential of microalgae for wastewater treatment. Among the various types of industrial wastewaters, high-salinity NH4+-N wastewater stands out as a common challenge. Investigating microalgae’s resilience to NH4+-N under high-salinity conditions and their efficacy in NH4+-N utilization is crucial for advancing industrial wastewater microalgae treatment technologies. This study evaluated the effectiveness of employing nitrogen-efficient microalgae, specifically Oocystis lacustris, for NH4+-N removal from saline wastewater. The results revealed Oocystis lacustris’s tolerance to a Na2SO4 concentration of 5 g/L. When the Na2SO4 concentration reached 10 g/L, the growth inhibition experienced by Oocystis lacustris began to decrease on the 6th day of cultivation, with significant alleviation observed by the 7th day. Additionally, the toxic mechanism of saline NH4+-N wastewater on Oocystis lacustris was analyzed through various parameters, including chlorophyll-a, soluble protein, oxidative stress indicators, key nitrogen metabolism enzymes, and microscopic observations of algal cells. The results demonstrated that when the Oocystis lacustris was in the stationary growth phase with an initial density of 2 × 107 cells/L, NH4+-N concentrations of 1, 5, and 10 mg/L achieved almost 100% removal of the microalgae on the 1st, 2nd, and 4th days of treatment, respectively. On the other hand, saline NH4+-N wastewater minimally impacted photosynthesis, protein synthesis, and antioxidant systems within algal cells. Additionally, NH4+-N within the cells was assimilated into glutamic acid through glutamate dehydrogenase-mediated pathways besides the conventional pathway involving NH4+-N conversion into glutamine and assimilation amino acids.

Simultaneous methane mitigation and nitrogen removal by denitrifying anaerobic methane oxidation in lake sediments

Methane (CH4) is a potent greenhouse gas, with lake ecosystems significantly contributing to its global emissions. Denitrifying anaerobic methane oxidation (DAMO) process, mediated by NC10 bacteria and ANME-2d archaea, links global carbon and nitrogen cycles. However, their potential roles in mitigating methane emissions and removing nitrogen from lake ecosystems remain unclear. This study explored the spatial variations in activities of nitrite- and nitrate-DAMO and their functional microbes in Changdanghu Lake sediments (Jiangsu Province, China). The results showed that although the average abundance of ANME-2d archaea (5.0 × 106 copies g−1) was significantly higher than that of NC10 bacteria (2.1 × 106 copies g−1), the average potential rates of nitrite-DAMO (4.59 nmol 13CO2 g−1 d−1) and nitrate-DAMO (5.01 nmol 13CO2 g−1 d−1) showed no significant difference across all sampling sites. It is estimated that nitrite- and nitrate-DAMO consumed approximately 6.46 and 7.05 mg CH4 m−2 d−1, respectively, which accordingly achieved 15.07–24.95 mg m−2 d−1 nitrogen removal from the studied lake sediments. Statistical analyses found that nitrite- and nitrate-DAMO activities were both significantly related to sediment nitrate contents and ANME-2d archaeal abundance. In addition, NC10 bacterial and ANME-2d archaeal community compositions showed significant correlations with sediment organic carbon content and water depth. Overall, this study underscores the dual roles of nitrite- and nitrate-DAMO processes in CH4 mitigation and nitrogen elimination and their key environmental impact factors (sediment organic carbon and inorganic nitrogen contents, and water depth) in shallow lake, enhancing the understanding of carbon and nitrogen cycles in freshwater aquatic ecosystems.

Feeding strategy and feed protein level affect the gut microbiota of common carp (Cyprinus carpio).

Common carp (Cyprinus carpio) were fed food with different protein concentrations following different feeding regimes, which were previously shown to affect growth, nitrogen excretion and amino acid catabolism. 16S rRNA gene amplicon sequencing was performed to investigate the gut microbiota of these fish. Lower dietary protein content increased microbial richness, while the combination of demand feeding and dietary protein content affected the composition of the gut microbiota. Hepatic glutamate dehydrogenase (GDH) activity was correlated to the composition of the gut microbiota in all dietary treatments. We found that demand-fed carp fed a diet containing 39% protein had a significantly higher abundance of Beijerinckiaceae compared to other dietary groups. Network analysis identified this family and two Rhizobiales families as hubs in the microbial association network. In demand-fed carp, the microbial association network had significantly fewer connections than in batch-fed carp. In contrast to the large effects of the feeding regime and protein content of the food on growth and nitrogen metabolism, it had only limited effects on gut microbiota composition. However, correlations between gut microbiota composition and liver GDH activity showed that host physiology and gut microbiota are connected, which warrants functional studies into the role of the gut microbiota in fish physiology.

Metabolomics analysis of different diameter classes of Taxus chinensis reveals that the resource allocation is related to carbon and nitrogen metabolism

Taxus chinensis (Taxus cuspidata Sieb. et Zucc.) is a traditional medicinal plant known for its anticancer substance paclitaxel, and its growth age is also an important factor affecting its medicinal value. However, how age affects the physiological and metabolic characteristics and active substances of T. chinensis is still unclear. In this study, carbon and nitrogen accumulation, contents of active substances and changes in primary metabolites in barks and annual leaves of T. chinensis of different diameter classes were investigated by using diameter classes instead of age. The results showed that leaves and barks of small diameter class (D1) had higher content of non-structural carbohydrates and C, which were effective in enhancing defense capacity, while N content was higher in medium (D2) and large diameter classes (D3). Active substances such as paclitaxel, baccatin III and cephalomannine also accumulated significantly in barks of large diameter classes. Moreover, 21 and 25 differential metabolites were identified in leaves and barks of different diameter classes, respectively. The differential metabolites were enhanced the TCA cycle and amino acid biosynthesis, accumulate metabolites such as organic acids, and promote the synthesis and accumulation of active substances such as paclitaxel in the medium and large diameter classes. These results revealed the carbon and nitrogen allocation mechanism of different diameter classes of T. chinensis, and its relationship with medicinal components, providing a guidance for the harvesting and utilization of wild T. chinensis.

Shrub effects on the decomposition microenvironment and changes in litter quality have opposing effects on litter decomposition

Increasing abundance of tall deciduous shrubs has been shown to affect tundra soil properties, which may further affect carbon and nitrogen cycling in these soils, including through effects on litter decomposition. These tall deciduous shrubs produce a higher quantity of litter, and also a different quality of litter, than tundra species in non-shrub dominated tundra, both of which may affect community-wide decomposition rates. We examined how presence of tall deciduous shrubs, including resulting increases in litter quantity, affects litter decomposition through effects on both the decomposition environment and on litter composition. In a factorial experiment, we modified the decomposition environment by manipulating both the abundance of tall deciduous shrubs (present/absent) and their litter (absent, natural, and doubled). In each environment we decomposed litter of the tall deciduous shrub, Betula glandulosa and two other dominant species in our study area; Salix reticulata, a dwarf deciduous shrub, and Carex consimilis, a graminoid. We report that while tall Betula shrub presence reduced decomposition rates, decomposition was not affected by manipulations of litter quantity. Although litter decomposed slower under deciduous shrubs, B. glandulosa litter decomposed faster than the litter of the other dominant tundra plant species. However, the reduction in decomposition rates due to tall deciduous shrub presence and higher decomposition rates of B. glandulosa litter in comparison to other plant species were of the same magnitude and these opposing effects may result in little to no change of shrub encroachment on litter decomposition rate overall.

Enhancing bioretention efficiency for pollutant mitigation in stormwater runoff: Exploring ecosystem cycling dynamics amidst temporal variability

In this study, three distinct bioretention setups incorporating fillers, plants, and earthworms were established to evaluate the operational efficiency under an ecosystem concept across varying time scales. The results revealed that under short-term operating conditions, extending the drying period led to a notable increase in the removal of NO3–-N, total phosphorus (TP), and chemical oxygen demand (COD) by 5 %–7%, 4 %–12 %, and 5 %–10 %, respectively. Conversely, under long-time operating conditions, the introduction of plants resulted in a significant boost in COD removal by 10 %–20 %, while the inclusion of earthworms improved NH4+-N and NO3–-N removal, especially TP removal by 9 %–16 %. Microbial community analysis further indicated the favorable impact of the bioretention system on biological nitrogen and phosphorus metabolism, particularly with the incorporation of plants and earthworms. This study provides a reference for the operational performance of bioretention systems on different time scales.

Response of different plants to ecological floating bed-microbial fuel cells: Decontamination and power generation

Screening suitable plants that can facilitate decontamination and sustainably harvest electricity plays a crucial role in phyto-power integrated with bioelectrochemical systems (BES). Here, four plant-integrated microbial fuel cell (PMFCs) were assembled to assess decontamination and power generation performance within micro-contaminated water. The results demonstrated the Hydrocotyle vulgaris L.-MFC exhibited exceptional performance, achieving optimal removal rates of 53.17% for COD, 88.35% for TN, 80.51% for NO3−-N, 98.56% for NO2−-N, and 99.89% for NH4+-N, respectively. The same tendency is observed for power generation performance. It is attributed that plant introduction could enhance the enrichment of the exoelectrogen in the rhizosphere. Furthermore, the dominant functional bacteria such as Proteobacteria, Actinobacteriota, Firmicutes, Bacteroidota and Chloroflexi contributing to nitrogen cycle, autotrophic denitrification, and organic matters degradation were observed in PMFCs significantly more than that of single MFC. The present study could provide brandnew technique reference for micro-polluted water remediation in real-world scenarios.

Climate determines diversity but not abundance of nitrogen-cycling microorganisms in rivers across a latitudinal gradient

A central goal in microecology is to understand the ecological factors shaping spatial patterns of microbial communities and the underlying mechanisms. However, the biogeographical patterns of microbial functional groups involved in nitrogen cycling (e.g., nitrifiers and denitrifiers) and their drivers at a large scale remain poorly understood. In this study, we evaluated the geographical distributions of nitrifiers and denitrifiers in riparian rhizosphere soils, riparian bulk soils, and channel sediments of 30 river regions along a latitudinal gradient from 21.8°N to 45.1°N across eastern China. We found that the diversity of nitrifiers and denitrifiers exhibited a gradual latitudinal gradient, in direct contrast to no significant changes observed for their abundance along the same latitudinal gradient. Statistical analyses suggested that climatic factors (mean annual temperature and mean annual precipitation) were the major drivers for the diversity of nitrifiers and denitrifiers, whereas soil properties were the key environmental factors shaping the abundance of nitrifiers and denitrifiers. Overall, these results provide new insights into the biogeographical distributions and ecological drivers for nitrogen-cycling microorganisms in river ecosystems at a large scale and can help us to improve the simulation models of the nitrogen cycle for accurately predicting the diversity of nitrogen-cycling microbes under ongoing climate changes.

Bacterial Community Characteristics and Roles in Nitrogen Transformation in Industrial Farming Systems of Litopenaeus vannamei

Industrial farming is one of the main farming systems used for L. vannamei, and it is also the main direction of development in the future. To investigate the role of the bacterial community in nitrogen transformation in industrial L. vannamei farming systems, we studied the concentration of nitrogen compounds, the bacterial community using 16S rRNA sequencing, and nitrogen cycling genes’ abundance using absolute quantitative PCR in aquaculture water (using seawater (WD) and groundwater mixed with seawater (CY)) and analyzed the correlations between them using a person analysis. The results showed that the bacterial α-diversity index (ACE, Shannon, and Sobs) significantly changed during culture in WD but not in CY. Bacterial community species composition analysis and linear discriminant analysis effect size (LEfSe analysis) revealed that Cyanobiaceae and Microbacteriaceae were the dominant bacteria and biomarkers in WD. Vibrionaceae, Ateromonadaceae, Microbacteriaceae, Saprospiraceae, and Cryomorphaceae were the dominant bacteria and biomarkers in CY. A functional annotation of procaryotic taxa (FAPROTAX) analysis revealed that the bacterial community in WD exhibited a greater phototrophic activity at early culture stages, while at the same stage, CY exhibited strong nitrate reduction. A correlation analysis of nitrogen cycling genes and environmental factors revealed that napA, narG, ureC, amoA, and nirK were significantly correlated with the concentrations of total ammonia nitrogen (TAN), nitrite (NO2−-N), nitrate (NO3−-N), and total nitrogen (TN) in WD. In CY, amoA was positively correlated and napA and nirK were negatively correlated with TAN and TN concentrations. A correlation analysis between bacterial abundance and environmental factors revealed that Flavobacteriaceae, Saprospiraceae, Cryomorphaceae, Cyanobiaceae, Halieaceae, and Cyclobacteriaceae were significantly correlated with the concentrations of TAN and NO2−-N. The above results indicated that the bacterial community in industrial shrimp farming systems changed under different conditions, with consequent changes in the abundance of genes being involved in the nitrogen cycle and in this biogeochemical process in the water. Our study facilitates further understanding of microbes and their functions in nitrogen cycling in industrial shrimp farming systems.

Environmental specificity of karst cave habitats evidenced by diverse symbiotic bacteria in Opiliones

BackgroundKarst caves serve as natural laboratories, providing organisms with extreme and constant conditions that promote isolation, resulting in a genetic relationship and living environment that is significantly different from those outside the cave. However, research on cave creatures, especially Opiliones, remains scarce, with most studies focused on water, soil, and cave sediments.ResultsThe structure of symbiotic bacteria in different caves were compared, revealing significant differences. Based on the alpha and beta diversity, symbiotic bacteria abundance and diversity in the cave were similar, but the structure of symbiotic bacteria differed inside and outside the cave. Microorganisms in the cave play an important role in material cycling and energy flow, particularly in the nitrogen cycle. Although microbial diversity varies inside and outside the cave, Opiliones in Beijing caves and Hainan Island exhibited a strong similarity, indicating that the two environments share commonalities.ConclusionsThe karst cave environment possesses high microbial diversity and there are noticeable differences among different caves. Different habitats lead to significant differences in the symbiotic bacteria in Opiliones inside and outside the cave, and cave microorganisms have made efforts to adapt to extreme environments. The similarity in symbiotic bacteria community structure suggests a potential similarity in host environments, providing an explanation for the appearance of Sinonychia martensi in caves in the north.

A study on nickel application methods for optimizing soybean growth

Fertilization with nickel (Ni) can positively affect plant development due to the role of this micronutrient in nitrogen (N) metabolism, namely, through urease and NiFe-hydrogenase. Although the application of Ni is an emerging practice in modern agriculture, its effectiveness strongly depends on the chosen application method, making further research in this area essential. The individual and combined effects of different Ni application methods—seed treatment, leaf spraying and/or soil fertilization—were investigated in soybean plants under different edaphoclimatic conditions (field and greenhouse). Beneficial effects of the Soil, Soil + Leaf and Seed + Leaf treatments were observed, with gains of 7 to 20% in biological nitrogen fixation, 1.5-fold in ureides, 14% in shoot dry weight and yield increases of up to 1161 kg ha−1. All the Ni application methods resulted in a 1.1-fold increase in the SPAD index, a 1.2-fold increase in photosynthesis, a 1.4-fold increase in nitrogenase, and a 3.9-fold increase in urease activity. Edaphoclimatic conditions exerted a significant influence on the treatments. The integrated approaches, namely, leaf application in conjunction with soil or seed fertilization, were more effective for enhancing yield in soybean cultivation systems. The determination of the ideal method is crucial for ensuring optimal absorption and utilization of this micronutrient and thus a feasible and sustainable management technology. Further research is warranted to establish official guidelines for the application of Ni in agricultural practices.