Nitrate assimilation by bacteria

Phytoplankton biomass in northern lakes reveals a complex response to global change

Global change may introduce fundamental alterations in phytoplankton biomass and community structure that can alter the productivity of northern lakes. In this study, we utilized Swedish and Finnish monitoring data from lakes that are spatially (135 lakes) and temporally (1995-2019, 110 lakes) extensive to assess how phytoplankton biomass (PB) of dominant phytoplankton groups related to changes in water temperature, pH and key nutrients [total phosphorus (TP), total nitrogen (TN), total organic carbon (TOC), iron (Fe)] along spatial (Fennoscandia) and temporal (25 years) gradients. Using a machine learning approach, we found that TP was the most important determinant of total PB and biomass of a specific species of Raphidophyceae - Gonyostomum semen - and Cyanobacteria (both typically with adverse impacts on food-webs and water quality) in spatial analyses, while Fe and pH were second in importance for G. semen and TN and pH were second and third in importance for Cyanobacteria. However, in temporal analyses, decreasing Fe and increasing pH and TOC were associated with a decrease in G. semen and an increase in Cyanobacteria. In addition, in many lakes increasing TOC seemed to have generated browning to an extent that significantly reduced PB. The identified discrepancy between the spatial and temporal results suggests that substitutions of data for space-for-time may not be adequate to characterize long-term effects of global change on phytoplankton. Further, we found that total PB exhibited contrasting temporal trends (increasing in northern- and decreasing in southern Fennoscandia), with the decline in total PB being more pronounced than the increase. Among phytoplankton, G. semen biomass showed the strongest decline, while cyanobacterial biomass showed the strongest increase over 25 years. Our findings suggest that progressing browning and changes in Fe and pH promote significant temporal changes in PB and shifts in phytoplankton community structures in northern lakes.

Synergies of chemodenitrification and denitrification in a saline inland lake

The interconnection between biotic and abiotic pathways involving the nitrogen and iron biogeochemical cycles has recently gained interest. While lacustrine ecosystems are considered prone to the biotic nitrate reduction (denitrification), their potential for promoting the abiotic nitrite reduction (chemodenitrification) remains unclear. In the present study, batch incubations were performed to assess the potential for chemodenitrification and denitrification in the saline inland lake Gallocanta. Sulfidic conditions are found in top sediments of the system while below (5-9 cm), it presents low organic carbon and high sulfate and ferrous iron availability. Anoxic incubations of sediment (5-9 cm) and water from the lake with nitrite revealed potential for chemodenitrification, especially when external ferrous iron was added. The obtained isotopic fractionation values for nitrite (ɛ15NNO2) were -6.8 and -12.3 ‰ and therefore, fell in the range of those previously reported for the nitrite reduction. The more pronounced ɛ15NNO2 (-12.3 ‰) measured in the experiment containing additional ferrous iron was attributed to a higher contribution of the chemodenitrification over biotic denitrification. Incubations containing nitrate also confirmed the potential for denitrification under autotrophic conditions (low organic carbon, high ferrous iron). Higher reaction rate constants were found in the experiment containing 100 μM compared to 400 μM nitrate. The obtained ɛ15NNO3 values (-8.5 and -15.1 ‰) during nitrate consumption fell in the range of those expected for the denitrification. A more pronounced ɛ15NNO3 (-15.1 ‰) was determined in the experiment presenting a lower reaction rate constant (400 μM nitrate). Therefore, in Gallocanta lake, nitrite generated during nitrate reduction can be further reduced by both the abiotic and biotic pathways. These findings establish the significance of chemodenitrification in lacustrine systems and support further exploration in aquatic environments with different levels of C, N, S, and Fe. This might be especially useful in predicting nitrous oxide emissions in natural ecosystems.

Nitrate reduction to ammonium: a phylogenetic, physiological, and genetic aspects in Prokaryotes and eukaryotes

The microbe-mediated conversion of nitrate (NO3-) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3- reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3- -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3--reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3- assimilation genes in response to NO3- availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.

Temporal and spatial differences in nitrogen and phosphorus biogeochemistry and ecosystem functioning of a hypertrophic lagoon (Curonian Lagoon, SE Baltic Sea) revealed via Ecological Network Analysis

In coastal lagoons, eutrophication and hydrology are interacting factors that produce distortions in biogeochemical nitrogen (N) and phosphorus (P) cycles. Such distortions affect nutrient relative availability and produce cascade consequences on primary producer's community and ecosystem functioning. In this study, the seasonal functioning of a coastal lagoon was investigated with a multielement approach, via the construction and analysis of network models. Spring and summer networks, both for N and P flows, have been simultaneously compiled for the northern transitional and southern confined area of the hypertrophic Curonian Lagoon (SE Baltic Sea). Ecological Network Analysis was applied to address the combined effect of hydrology and seasonality on biogeochemical processes. Results suggest that the ecosystem is more active and presents higher N and P fluxes in summer compared to spring, regardless of the area. Furthermore, larger internal recycling characterizes the confined compared to the transitional area, regardless of the season. The two areas differed in the fate of available nutrients. The transitional area received large riverine inputs that were mainly transferred to the sea without the conversion into primary producers' biomass. The confined area had fewer inputs but proportionally larger conversion into phytoplankton biomass. In summer, particularly in the confined area, primary production was inefficiently consumed by herbivores. Most phytoplanktonic N and P, in the confined area more than in the transitional area, were conveyed to the detritus pathway where P, more than N, was recycled, contributing to the unbalance in N:P stoichiometry and favouring N-fixing cyanobacteria over other phytoplankton groups. The findings of this study provide a comprehensive understanding of N and P circulation patterns in lagoon areas characterized by different hydrology. They also support the importance of a stoichiometric approach to trace relative differences in N and P recycling and abundance, that promote blooms, drive algal communities and whole ecosystem functioning.

Expression Analysis of Nitrogen Metabolism Genes in Lelliottia amnigena PTJIIT1005, Comparison with Escherichia coli K12 and Validation of Nitrogen Metabolism Genes

Escherichia coli K12 and Lelliottia amnigena PTJIIT1005 bacteria were isolated from the polluted Yamuna River (Delhi, India) site, which can remediate nitrate from groundwater media under anaerobic conditions. BV-BRC (Bacterial and Viral Bioinformatics Resource Center) information system, RAST, and PGAP servers were used to annotate the nitrogen metabolism genes from the genome sequence of these microbes. Here we compared the strains L. amnigena PTJIIT1005 with E. coli K12 in the context of nitrogen metabolism genes. Sequence alignment, similarity percentage, and phylogenetic analysis were done to find similarities between the genes. Common nitrogen genes of these strains, like respiratory nitrate reductase, nitrite reductase, nitric oxide reductase, glutamine synthetase, and hydroxylamine reductase, have found good sequence similarity (83-94%) with each other. The PATRIC tool identified N-operons, and the nitrate reductase gene clusters were also determined as per literature survey. Protein-protein interaction network was constructed using STRING 12.0 database and Cytoscape v 3.10.0 software plug-in Network analyzer. On the basis of network topological parameters NarG, NarZ, NarY, NarH, NarI, NarV, NirB, NirD, NapA, and NapB are the key genes in network of E. coli K12 strain. Nar, NirB, NirD, NasA, NasB, NasC, NasD, NasE, and GlnA are the key genes in network of L. amnigena PTJIIT1005. Among these, NarG and NirB are the superhub genes because of having highest Betweenness centrality (BC) and node degree. The functional enrichment analysis was determined using PANTHER GENE ONTOLOGY and DAVID software exhibited their role in nitrogen metabolism pathway and nitrate assimilation. Further, SWISS-MODEL was used to predict the 3D protein structure of these enzymes, and after, these structures were validated by Ramachandran plot using the PROCHECK tool. The Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) method was used to determine the N-genes expression level in both strains. This study showed that E. coli K12 and L. amnigena PTJIIT1005 have common nitrogen metabolism genes involved in the same functional role, like the denitrification pathway. Additionally, operon arrangement study and PPI network revealed that E. coli K12 has only a denitrification pathway, while L. amnigena PTJIIT1005 has both an assimilation and denitrification pathway. PCR successfully amplified selected N-metabolizing genes, and the expression level of N-genes was high in strain L. amnigena PTJIIT1005. Our previous experimental study exhibited a better nitrate remediation rate in L. amnigena PTJIIT1005 over E. coli K12. This study confirmed the presence of assimilation and denitrification process through amplified N-metabolizing genes and showed high expression of N-genes in L. amnigena PTJIIT1005, which favor the evidence of better nitrate remediation in L. amnigena PTJIIT1005 over E. coli K12.

Cyclic di-GMP inhibits nitrate assimilation by impairing the antitermination function of NasT in Pseudomonas putida

The ubiquitous bacterial second messenger cyclic diguanylate (c-di-GMP) coordinates diverse cellular processes through its downstream receptors. However, whether c-di-GMP participates in regulating nitrate assimilation is unclear. Here, we found that NasT, an antiterminator involved in nitrate assimilation in Pseudomonas putida, specifically bound c-di-GMP. NasT was essential for expressing the nirBD operon encoding nitrite reductase during nitrate assimilation. High-level c-di-GMP inhibited the binding of NasT to the leading RNA of nirBD operon (NalA), thus attenuating the antitermination function of NasT, resulting in decreased nirBD expression and nitrite reductase activity, which in turn led to increased nitrite accumulation in cells and its export. Molecular docking and point mutation assays revealed five residues in NasT (R70, Q72, D123, K127 and R140) involved in c-di-GMP-binding, of which R140 was essential for both c-di-GMP-binding and NalA-binding. Three diguanylate cyclases (c-di-GMP synthetases) were found to interact with NasT and inhibited nirBD expression, including WspR, PP_2557, and PP_4405. Besides, the c-di-GMP-binding ability of NasT was conserved in the other three representative Pseudomonas species, including P. aeruginosa, P. fluorescens and P. syringae. Our findings provide new insights into nitrate assimilation regulation by revealing the mechanism by which c-di-GMP inhibits nitrate assimilation via NasT.

Insight into the metabolic pathways of Paracoccus sp. strain DMF: a non-marine halotolerant methylotroph capable of degrading aliphatic amines/amides

Paracoccus sp. strain DMF (P. DMF from henceforth) is a gram-negative heterotroph known to tolerate and utilize high concentrations of N,N-dimethylformamide (DMF). The work presented here elaborates on the metabolic pathways involved in the degradation of C1 compounds, many of which are well-known pollutants and toxic to the environment. Investigations on microbial growth and detection of metabolic intermediates corroborate the outcome of the functional genome analysis. Several classes of C1 compounds, such as methanol, methylated amines, aliphatic amides, and naturally occurring quaternary amines like glycine betaine, were tested as growth substrates. The detailed growth and kinetic parameter analyses reveal that P. DMF can efficiently aerobically degrade trimethylamine (TMA) and grow on quaternary amines such as glycine betaine. The results show that the mechanism for halotolerant adaptation in the presence of glycine betaine is dissimilar from those observed for conventional trehalose-mediated halotolerance in heterotrophic bacteria. In addition, a close genomic survey revealed the presence of a Co(I)-based substrate-specific corrinoid methyltransferase operon, referred to as mtgBC. This demethylation system has been associated with glycine betaine catabolism in anaerobic methanogens and is unknown in denitrifying aerobic heterotrophs. This report on an anoxic-specific demethylation system in an aerobic heterotroph is unique. Our finding exposes the metabolic potential for the degradation of a variety of C1 compounds by P. DMF, making it a novel organism of choice for remediating a wide range of possible environmental contaminants.

The behaviour of Escherichia coli and Pseudomonas aeruginosa in bottled mineral water

Microbial contamination of bottled water during the filling and capping procedure is a problem which should be avoided. The examination of the influence of carbon dioxide (CO2) on bacterial growth of Escherichia coli (E. coli) and Pseudomonas aeruginosa (P. aeruginosa) in bottled mineral water was the aim of this study. Commercially available glass bottles with plastic screw caps filled with natural mineral water (without additional CO2 "still" (StMW) and with CO2 "sparkling" (SpMW) were obtained from a manufacturer in the province of Styria, Austria. The artificial contamination was performed in the lab by opening the bottle with subsequent addition of a bacterial solution with a defined number of bacteria. For each bacterial strain, 12 bottles were prepared. Samples (100 mL) were taken after a specific number of days, filtrated and placed on Endo Agar for cultivation. After incubation for 24 h bacterial colonies were counted. In this study CO2 addition to bottled water reduced colony forming units of the two investigated bacterial strains over time.

Nitrogen removal characteristics of heterotrophic nitrification-aerobic denitrification bacterium Acinetobacter ZQ-A1 and community characteristics analysis of its application in pig farm wastewater

A heterotrophic nitrifying aerobic denitrifying (HN-AD) strain ZQ-A1 with excellent denitrification performance, identified as Acinetobacter, was isolated from simultaneous nitrification and denitrification (SND) craft. ZQ-A1 was capable of removing NH4+, NO2-, and NO3-; the 21-hour removal rates were 84.84%, 87.13%, and 92.63%. ZQ-A1 has the ability to treat mixed nitrogen sources. In addition, ZQ-A1 can be well applied to actual sewage. According to the analysis of microbial community characteristics, the relative abundance of Acinetobacter in the experimental group increased from 0.06% to 2.38%, which is an important reason for the removal rate of NH4+ exceeding 99% within 30 days. The results of KEGG function prediction showed that with the addition of ZQ-A1, the relative abundance of pathways related to bacterial metabolism, such as tricarboxylic acid cycle metabolism, was higher. The research expanded the thinking of HN-AD bacteria in actual production and laid a foundation for its application in sewage treatment.

Iron-modified biochar reduces nitrogen loss and improves nitrogen retention in Luvisols by adsorption and microbial regulation

Nitrogen (N) loss poses a great threat to global environmental sustainability. The application of modified biochar is a novel strategy to improve soil nitrogen retention and alleviate the negative effects caused by N fertilizers. Therefore, in this study iron modified biochar was used as a soil amendment to investigate the potential mechanisms of N retention in Luvisols. The experiment comprised five treatments i.e., CK (control), 0.5 % BC, 1 % BC, 0.5 % FBC and 1 % FBC. Our results showed that the intensity of functional groups and surface structure of FBC was improved. The 1 % FBC treatment showed a significant increment in soil NO₃^--N, dissolved organic nitrogen (DON), and total nitrogen (TN) content by 374.7 %, 51.9 %, and 14.4 %, respectively, compared with CK. The accumulation of N in cotton shoots and roots was increased by 28.6 % and 6.6 % with 1 % FBC addition. The application of FBC also stimulated the activities of soil enzymes related to C and N cycling i.e., β-glucosidase (βG), β-Cellobiohydrolase (CBH), and Leucine aminopeptidase (LAP). In the soil treated with FBC, a significant improvement in the structure and functions of the soil bacterial community was found. FBC addition altered the taxa involved in the N cycle by affecting soil chemical properties, especially for Achromobacte, Gemmatimonas, and Cyanobacteriales. In addition to direct adsorption, the regulation of FBC on organisms related to N-cycling also played an important role in soil nitrogen retention.

Nitrogen retention potentials of magnesium oxide- and sepiolite-modified biochars and their impacts on bacterial distribution under nitrogen fertilization

Mitigating the loss and negative impacts of reactive N from fertilized soils remains a global environmental challenge. To optimize N retention by biochar, bamboo and pig manure biochars were modified as MgO- and sepiolite-biochar composites and characterized. Novel soil application of the modified biochars and their raw forms were comparatively evaluated for N-retention in a fertilized soil leached for 90 days in a column experiment. Changes in N-cycling-related enzyme and bacterial structure were also reported after 90 days. Results revealed low leaching losses of NH₄⁺, which reduced over time across all the treatments. However, while sole fertilizer (F) increased the initial and cumulative NO₃^- leached from the soil, the MgO-bamboo biochar (MgOBF) and sepiolite-bamboo biochar (SBF) treatments reduced leachate NO₃^- by 22.1 % and 10.5 % compared to raw bamboo biochar (BBF) treatment. However, 15.5 % more NO₃^- was leached from the MgO-pig manure biochar-treated soil (MgOPF) compared to its raw biochar treatment (PMBF) after 90 days. Dissolved organic N leached was reduced by 9.2 % and 0.5 % in MgOBF and SBF, as well as 15.4 % and 40.5 % in MgOPF and SPF compared to their respective raw forms. The total N of the biochars, adjustment of surface charges, cation exchange capacity, surface area, pore filling effects, and the formation of potential MgN precipitates on the modified-biochar surfaces regulated N leaching/retention. In addition, the modified biochar treatments reduced the hydrolysis of urea and stimulated some nitrate-reduction-related bacteria crucial for NO₃^- retention. Hence, unlike the raw biochar and MgOPF treatments, MgOBF, SBF, and SPF hold promise in mitigating inorganic-N losses from fertilized soils while improving the soil's chemical properties.

The nitrite reductase encoded by nirBDs in Pseudomonas putida Y-9 influences ammonium transformation

It is unknown whether nirBDs, which conventionally encode an NADH nitrite reductase, play other novel roles in nitrogen cycling. In this study, we explored the role of nirBDs in the nitrogen cycling of Pseudomonas putida Y-9. nirBDs had no effect on organic nitrogen transformation by strain Y-9. The △nirBD strain exhibited higher ammonium removal efficiency (90.7%) than the wild-type strain (76.1%; P < 0.05) and lower end gaseous nitrogen (N2O) production. Moreover, the expression of glnA (control of the ammonium assimilation) in the △nirBD strain was higher than that in the wild-type strain (P < 0.05) after being cultured in ammonium-containing medium. Furthermore, nitrite noticeably inhibited the ammonium elimination of the wild-type strain, with a corresponding removal rate decreasing to 44.8%. However, no similar impact on ammonium transformation was observed for the △nirBD strain, with removal efficiency reaching 97.5%. In conclusion, nirBDs in strain Y-9 decreased the ammonium assimilation and increased the ammonium oxidation to nitrous oxide.

Antifungal Chitinase Production by Bacillus paramycoides B26 using Squid Pen Powder as a Carbon Source

This study aimed to optimize the medium compositions and cultural conditions for improved chitinase production by a potential strain of Bacillus isolated from the marine environment and determine the antifungal activity of its chitinase against plant pathogenic fungi. Five potential isolates were cultured for chitinase production by submerged fermentation using colloidal chitin in a liquid medium. In this study, chitinase activity was determined by measuring reducing sugars, which were determined by the 3,5-dinitrosalicylic acid (DNS) assay. The most potential isolate, B26, showed similarity to Bacillus paramycoides based on the 16S rRNA gene sequence. The maximum chitinase production was achieved at 6.52±0.02 U/mL after 72 h of incubation in a medium containing 2% squid pen powder, supplemented with 0.5% sodium nitrate and 2% NaCl, with an initial pH of 7. It was observed that the optimization of cultural conditions resulted in 2.83 times higher chitinase production than an unoptimized medium. The antifungal activity of crude chitinase against phytopathogenic fungi was evaluated by a well-diffusion method. The chitinase of B. paramycoides B26 effectively inhibited the growth of Fusarium solani TISTR 3436 (83.4%) and Penicillium chrysogenum TISTR 3554 (80.12%).

Transcript Profiling of Nitroxoline-Treated Biofilms Shows Rapid Up-regulation of Iron Acquisition Gene Clusters

Bacterial biofilms are surface-attached communities of slow- or non-replicating cells embedded within a protective matrix of biomolecules. Unlike free-floating planktonic bacteria, biofilms are innately tolerant to conventional antibiotics and are prevalent in recurring and chronic infections. Nitroxoline, a broad-spectrum biofilm-eradicating agent, was used to probe biofilm viability. Transcript profiling (RNA-seq) showed that 452 of 2594 genes (17.4%) in methicillin-resistant Staphylococcus aureus (MRSA) biofilms were differentially expressed after a 2 h treatment of nitroxoline. WoPPER analysis and time-course validation (RT-qPCR) revealed that gene clusters involved in iron acquisition (sbn, isd, MW2101, MW0695, fhu, and feo) were rapidly up-regulated following nitroxoline treatment, which is indicative of iron starvation in MRSA biofilms. In addition, genes related to oligopeptide transporters and riboflavin biosynthesis were found to be up-regulated, while genes related to carotenoid biosynthesis and nitrate assimilation were down-regulated. RT-qPCR experiments revealed that iron uptake transcripts were also up-regulated in established Staphylococcus epidermidis and Acinetobacter baumannii biofilms following nitroxoline treatment. Overall, we show RNA-seq to be an ideal platform to define cellular pathways critical for biofilm survival, in addition to demonstrating the need these bacterial communities have for iron.

Effect of sulfur sources on the competition between denitrification and DNRA

The fate of nitrogen is controlled by the competition between nitrate reduction pathways. Denitrification removes nitrogen in the system to the atmosphere, whereas dissimilatory nitrate reduction to ammonia (DNRA) retains nitrate in the form of ammonia. Different microbes specialize in the oxidation of different electron donors, thus electron donors might influence the outcomes of the competition. Here, we investigated the fate of nitrate with five forms of sulfur as electron donors. Chemoautotrophic nitrate reduction did not continue after the passages of the enrichments with sulfide, sulfite and pyrite. Nitrate reduction rate was the highest in the enrichment with thiosulfate. Denitrification was stimulated and no DNRA was observed with thiosulfate, while both denitrification and DNRA were stimulated with elemental sulfur. Metagenomes of the enrichments were assembled and binned into ten genomes. The enriched populations with thiosulfate included Thiobacillus, Lentimicrobium, Sulfurovum and Hydrogenophaga, all of which contained genes involved in sulfur oxidation. Elemental sulfur-based DNRA was performed by Thiobacillus (with NrfA and NirB) and Nocardioides (with only NirB). Our study established a link between sulfur sources, nitrate reduction pathways and microbial populations.

Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth

Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (N_Inorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and N_Inorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.

Nitrogen removal by a novel heterotrophic nitrification and aerobic denitrification bacterium Acinetobacter calcoaceticus TY1 under low temperatures

A new bacterial strain, Acinetobacter calcoaceticus TY1, was identified in activated sludge. This strain efficiently metabolized nitrogen from ammonium at low temperatures, utilizing NH₄⁺-N, NO₃^--N, and NO₂^--N as nitrogen sources. Of these, NH₄⁺-N was superior in terms of both assimilation and heterotrophic nitrification at 8 °C. The nitrogen metabolism-associated genes amoA, nirK, and nosZ were identified in TY1. Optimal requirements for growth and nitrogen removal were pH 7, shaking speed of 90 rpm, a C/N ratio of 10, and sodium citrate for the carbon supply. The ability to denitrify at low temperature suggests TY1's potential for wastewater management.

Boosting nitrogen fertilization by a slow releasing nitrate-intercalated biocompatible layered double hydroxide-hydrogel composite loaded with Azospirillum brasilense

Indiscriminate use of chemical fertilizers leads to soil environmental disbalance and therefore, preparation and application of environment-friendly slow-release multifunctional fertilizers are of paramount importance for sustainable crop production in the present scenario. In this study, we propose a slow-release multifunctional composite nitrogen (N) fertilizer, which possesses the ability to supply plant accessible N in the form of ammonium (NH₄⁺) and nitrate (NO₃⁻) to improve nitrate assimilation coupled with zinc (Zn, a major micronutrient for plants in the soil) after its degradation. For this purpose, NO₃⁻-intercalated zinc–aluminum (Zn–Al) layered double hydroxide (LDH) was synthesized using a co-precipitation protocol. The prepared LDH was added as 25.45% of total polymer weight to a sodium carboxymethyl cellulose/hydroxyethyl cellulose citric acid (NaCMC/HEC-CA) biodegradable hydrogel. A. brasilense, commonly used nitrogen-fixing bacteria in soils, was added to the LDH–hydrogel composite along with LDH alone to augment the availability of NH₄⁺ and NO₃⁻. Adjusting the pH under acidic (pH 5.25) and neutral (pH 7) conditions, the release pattern of NO₃⁻ from LDH and the composite was monitored for 30 days at normal temperature. The pH was selected based on the soil analysis data of North East India. The LDH-composite released 90% (w/w) and 85.45% (w/w) of intercalated NO₃⁻ at pH 5.25 and 7.00 respectively in 30 days. However, 100% (w/w) and 87% (w/w) of intercalated NO₃⁻ at pH 5.25 and 7.00 respectively were released in 30 days when only LDH was applied, which indicated the lower performance of LDH alone in comparison to the LDH-composite for the nitrate holding pattern. The pH of the bacteria-loaded system was observed to be acidic (pH = 5–6) during the study of nitrate assimilation and Zn²⁺ release. A. brasilense improved nitrate assimilation and increased the NH₄⁺ ion concentration in the studied system. A significant increase in Zn²⁺ release was observed from day 5 in the presence of A. brasilense in the LDH-composite compared with that in the absence of A. brasilense. In conclusion, the prepared LDH–hydrogel–A. brasilense composite fertilizer system increases the availability of plant accessible N form (both NO₃⁻ and NH₄⁺) and can potentially improve soil fertility with the addition of Zn and bacteria to the soil in the extended course.

Indiscriminate use of chemical fertilizers leads to soil environmental disbalance, therefore, use of environment-friendly slow-release multifunctional fertilizers are of paramount importance for sustainable crop production in the present scenario.

The Enzymology of Ocean Global Change

A small subset of marine microbial enzymes and surface transporters have a disproportionately important influence on the cycling of carbon and nutrients in the global ocean. As a result, they largely determine marine biological productivity and have been the focus of considerable research attention from microbial oceanographers. Like all biological catalysts, the activity of these keystone biomolecules is subject to control by temperature and pH, leaving the crucial ecosystem functions they support potentially vulnerable to anthropogenic environmental change. We summarize and discuss both consensus and conflicting evidence on the effects of sea surface warming and ocean acidification for five of these critical enzymes [carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), nitrogenase, nitrate reductase, and ammonia monooxygenase] and one important transporter (proteorhodopsin). Finally, we forecast how the responses of these few but essential biocatalysts to ongoing global change processes may ultimately help to shape the microbial communities and biogeochemical cycles of the future greenhouse ocean.

Understanding the effects of Moringa oleifera in chronic unpredictable stressed zebrafish using metabolomics analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Moringa leaves have been used for thousands of years to maintain skin health and mental fitness. People also use it to relieves pain and stress.

AIM OF THE STUDY

To determine the effects of Moringa oleifera leaves ethanol-aqueous (ratio 7:3) extract (MOLE) on the chronically stressed zebrafish.

METHOD

The changes in the stress-related behaviour and the metabolic pathways in response to MOLE treatment in zebrafish were studied. A chronic unpredictable stress model was adopted in which zebrafish were induced with different stressors for 14 days. Stress-related behaviour was assessed using a depth-preference test and a light and dark test. Three doses of MOLE (500, 1000, and 2000 mg/L) were administered to the zebrafish. Upon sacrifice, the brains were harvested and processed for LC-MS QTOF based, global metabolomics analysis.

RESULTS

We observed significant changes in the behavioural parameters, where the swimming time at the light phase and upper phase of the tank were increased in the chronically stressed zebrafish treated with MOLE compared to those zebrafish which were not treated. Further, distinctive metabolite profiles were observed in zebrafish with different treatments. Several pathways that shed light on effects of MOLE were identified. MOLE is believed to relieve stress by regulating pathways that are involved in the metabolism of purine, glutathione, arginine and proline, D-glutamine, and D-glutamate.

CONCLUSION

MOLE is potentially an effective stress reliever. However, its effects in human needs to be confirmed with a systematic randomised control trial.

Role for nitrate assimilatory genes in virulence of Ustilago maydis

Ustilago maydis can utilize nitrate as a sole source of nitrogen. This process is initiated by transporting nitrate from the extracellular environment into the cell by a nitrate transporter and followed by a two-step reduction of nitrate to ammonium via nitrate reductase and nitrite reductase enzymes, respectively. Here, we characterize the genes encoding nitrate transporter, um03849 and nitrite reductase, um03848 in U. maydis based on their roles in mating and virulence. The deletion mutants for um03848, um03849 or both genes were constructed in mating compatible haploid strains 1/2 and 2/9. In addition, CRISPR-Cas9 gene editing technique was used for um03849 gene to create INDEL mutations in U. maydis mating strains. For all the mutants, phenotypes such as growth ability, mating efficiency and pathogenesis were examined. The growth of all the mutants was diminished when grown in a medium with nitrate as the source of nitrogen. Although no clear effects on haploid filamentation or mating were observed for either single mutant, double Δum03848 Δum03849 mutants showed reduction in mating, but increased filamentation on low ammonium, particularly in the 1/2 background. With respect to pathogenesis on the host, all the mutants showed reduced degrees of disease symptoms. Further, when the deletion mutants were paired with wild type of opposite mating-type, reduced virulence was observed, in a manner specific to the genetic background of the mutant's progenitor. This background specific reduction of plant pathogenicity was correlated with differential expression of genes for the mating program in U. maydis.

Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community

A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant.

Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.

IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.

Metagenomic Insight Into Patterns and Mechanism of Nitrogen Cycle During Biocrust Succession

The successional ecology of nitrogen cycling in biocrusts and the linkages to ecosystem processes remains unclear. To explore this, four successional stages of natural biocrust with five batches of repeated sampling and three developmental stages of simulated biocrust were studied using relative and absolute quantified multi-omics methods. A consistent pattern across all biocrust was found where ammonium assimilation, mineralization, dissimilatory nitrite to ammonium (DNiRA), and assimilatory nitrate to ammonium were abundant, while denitrification medium, N-fixation, and ammonia oxidation were low. Mathematic analysis showed that the nitrogen cycle in natural biocrust was driven by dissolved organic N and NO₃^–. pH and SO₄^2– were the strongest variables affecting denitrification, while C:(N:P) was the strongest variable affecting N-fixation, DNiRA, nitrite oxidation, and dissimilatory nitrate to nitrite. Furthermore, N-fixation and DNiRA were closely related to elemental stoichiometry and redox balance, while assimilatory nitrite to ammonium (ANiRA) and mineralization were related to hydrological cycles. Together with the absolute quantification and network models, our results suggest that responsive ANiRA and mineralization decreased during biocrust succession; whereas central respiratory DNiRA, the final step of denitrification, and the complexity and interaction of the whole nitrogen cycle network increased. Therefore, our study stresses the changing environmental functions in the biocrust N-cycle, which are succession-dependent.

Removal of NH3 and H2S from odor causing tannery emissions using biological filters: Impact of operational strategy on the performance of a pilot-scale bio-filter

Deodorization of gases emitted from Tanneries using eco-friendly and cost-effective approaches is necessary for the safe disposal of industrial emissions. There is limited research available on the treatment of odorous gases emitted from tanneries using bio-filter. In this endeavor, pilot-scale studies were performed in a 2.7 m³ bio-filter with synthetic gas mixture containing hydrogen sulfide (H₂S) and ammonia (NH₃) as input gas to study the impact of bedding material for the removal of H₂S and NH₃ using bio-filter and identification of various design parameters for scale-up. The pilot-scale studies showed that the removal efficacy of both NH₃ and H₂S was about 90-99% at an empty bed residence time of 55 seconds at an inlet concentration (NH₃ and H₂S) of 200 to 210 ppmV and microbial count enhanced from 3.5 × 10³ to 8.9 × 10⁹ in 210 days. The microbial biodiversity analysis revealed the dominance of proteobacteriaas as well as Firmicutes and Acinetobacter. A full-scale bio-filter (13.75 m³) was designed, installed, and commissioned in a tannery and observed that the removal efficiency of >99% since last three years.

Endophytic Lifestyle of Global Clones of Extended-Spectrum β-Lactamase-Producing Priority Pathogens in Fresh Vegetables: a Trojan Horse Strategy Favoring Human Colonization?

The global spread of antibiotic-resistant bacteria and their resistance genes is a critical issue that is no longer restricted to hospital settings, but also represents a growing problem involving environmental and food safety. In this study, we have performed a microbiological and genomic investigation of critical priority pathogens resistant to broad-spectrum cephalosporins and showing endophytic lifestyles in fresh vegetables sold in a country with high endemicity of extended-spectrum β-lactamases (ESBLs). We report the isolation of international high-risk clones of CTX-M-15-producing Escherichia coli, belonging to clonal complexes CC38 and CC648, and Klebsiella pneumoniae of complex CC307 from macerated tissue of surface-sterilized leaves of spinach, cabbage, arugula, and lettuce. Regardless of species, all ESBL-positive isolates were able to endophytically colonize common bean (Phaseolus vulgaris) seedlings, showed resistance to acid pH, and had a multidrug-resistant (MDR) profile to clinically relevant antibiotics (i.e., broad-spectrum cephalosporins, aminoglycosides, and fluoroquinolones). Genomic analysis of CTX-M-producing endophytic Enterobacterales revealed a wide resistome (antibiotics, biocides, disinfectants, and pesticides) and virulome, and genes for endophytic fitness and for withstanding acidic conditions. Transferable IncFIB and IncHI2A plasmids carried bla _CTX-M-15 genes and, additionally, an IncFIB plasmid (named pKP301cro) also harbored genes encoding resistance to heavy metals. These data support the hypothesis that fresh vegetables marketed for consumption can act as a figurative Trojan horse for the hidden spread of international clones of critical WHO priority pathogens producing ESBLs, and/or their resistance genes, to humans and other animals, which is a critical issue within a food safety and broader public and environmental health perspective.IMPORTANCE Extended-spectrum β-lactamases (ESBL)-producing Enterobacterales are a leading cause of human and animal infections, being classified as critical priority pathogens by the World Health Organization. Epidemiological studies have shown that spread of ESBL-producing bacteria is not a problem restricted to hospitals, but also represents a growing problem involving environmental and food safety. In this regard, CTX-M-type β-lactamases have become the most widely distributed and clinically relevant ESBLs worldwide. Here, we have investigated the occurrence and genomic features of ESBL-producing Enterobacterales in surface-sterilized fresh vegetables. We have uncovered that international high-risk clones of CTX-M-15-producing Escherichia coli and Klebsiella pneumoniae harboring a wide resistome and virulome, carry additional genes for endophytic fitness and resistance to acidic conditions. Furthermore, we have demonstrated that these CTX-M-15-positive isolates are able to endophytically colonize plant tissues. Therefore, we believe that fresh vegetables can act as a figurative Trojan horse for the hidden spread of critical priority pathogens exhibiting endophytic lifestyles.

Genomics Analysis of Bacillus megaterium 1259 as a Probiotic and Its Effects on Performance in Lactating Dairy Cows

In this study, we isolated a novel bacterium, Bacillus megaterium 1259 (BM1259), from chicken manure. Whole-genome sequencing analysis showed that the BM1259 complete genome is composed of a 5,043,095 bp circular chromosome and three circular plasmids, and it encodes 5379 coding genes and 182 RNA genes. Among these genes, a series of nitrate assimilation-related genes and pathways were identified, implying a potential role of BM1259 in nitrate metabolism. In addition, 24 lactating Holstein dairy cows were randomly assigned to four groups that were fed a total mixed ration (TMR) diet only (C), a TMR diet supplemented with 5 g/day of BM1259 (T1), a TMR diet supplemented with 10 g/day of BM1259 (T2), or a TMR diet supplemented with 15 g/day of BM1259 (T3). The results showed that supplementing dairy cows with 15 g/day of BM1259 increased 4% fat-corrected milk production. The molar proportion of propionate (C3) was significantly higher in T2 than in C. The C2:C3 ratio of T3 was higher than those of C and T2. No negative effect of BM1259 on blood indicators was detected. This study demonstrates BM1259 can be applied as a potential probiotic to improve nitrogen utilization and milk production in lactating dairy cows.

Biological nitrogen and phosphorus removal by a phosphorus-accumulating bacteria Acinetobacter sp. strain C-13 with the ability of heterotrophic nitrification-aerobic denitrification

Strain C-13, identified as an Acinetobacter sp. by homology searches, exhibited efficient simultaneous heterotrophic nitrification-aerobic denitrification phosphorus removal (SNDPR) abilities by nitrogen balance analysis and further confirmation of successful amplification of functional genes ppk, napA, and nirS. In addition, strain C-13 could utilize NH₄⁺-N, NO₃^--N, and NO₂^--N as nitrogen sources, among which NH₄⁺-N was indicated to be an excellent nitrogen source for assimilation and heterotrophic nitrification. Besides, the optimum conditions for nutrient removal were determined as follows: sodium acetate as the sole carbon source, C/N/P ratio of 100/10/2, pH = 7.5, and temperature of 30 °C. Meanwhile, the strain also showed the traditional features, such as release and the excess uptake of phosphate under anaerobic/aerobic conditions, with the highest phosphorus content of 5.01% after cultivation. Strain C-13 presents promising prospects for application in biologicalnutrient removal in wastewater treatment.

Transcriptomic Approach for Understanding the Adaptation of Salmonella enterica to Contaminated Produce

Salmonellosis is a form of gastroenteritis caused by Salmonella infection. The main transmission route of salmonellosis has been identified as poorly cooked meat and poultry products contaminated with Salmonella. However, in recent years, the number of outbreaks attributed to contaminated raw produce has increased dramatically. To understand how Salmonella adapts to produce, transcriptomic analysis was conducted on Salmonella enterica serovar Virchow exposed to fresh-cut radish greens. Considering the different Salmonella lifestyles in contact with fresh produce, such as motile and sessile lifestyles, total RNA was extracted from planktonic and epiphytic cells separately. Transcriptomic analysis of S. Virchow cells revealed different transcription profiles between lifestyles. During bacterial adaptation to fresh-cut radish greens, planktonic cells were likely to shift toward anaerobic metabolism, exploiting nitrate as an electron acceptor of anaerobic respiration, and utilizing cobalamin as a cofactor for coupled metabolic pathways. Meanwhile, Salmonella cells adhering to plant surfaces showed coordinated upregulation in genes associated with translation and ribosomal biogenesis, indicating dramatic cellular reprogramming in response to environmental changes. In accordance with the extensive translational response, epiphytic cells showed an increase in the transcription of genes that are important for bacterial motility, nucleotide transporter/metabolism, cell envelope biogenesis, and defense mechanisms. Intriguingly, Salmonella pathogenicity island (SPI)-1 and SPI-2 displayed up- and downregulation, respectively, regardless of lifestyles in contact with the radish greens, suggesting altered Salmonella virulence during adaptation to plant environments. This study provides molecular insights into Salmonella adaptation to plants as an alternative environmental reservoir.

Biochar-fertilizer interaction modifies N-sorption, enzyme activities and microbial functional abundance regulating nitrogen retention in rhizosphere soil

The impact of the excessive use of N fertilizer remains an environmental problem of global concern. The effect of biochar on soil N retention is still unclear, and knowledge on how a mixture of biochar and fertilizer (B-F) influence N-sorption, N-cycling enzymes activities, diversity and functional abundance of organisms regulating N-retention in rhizosphere soil is poorly understood. Therefore, biochars derived from bamboo, rice straw, cow and pig manure were characterized, and their interactions with NPK fertilizer were evaluated. Results showed that while the effect of biochar on N retention varied among biochar types, such variations increased after B-F. Unlike NH₄⁺ retention, NO₃^- retention by biochar in fertilized soil was poor (<8 weeks), but were however increased after longer periods (15 weeks) in B-F due to plant uptake, sorption and stimulation of N-cycling enzymes activities. This stimulation proved that N-fertilizer provided substrates for N-cycling organisms which was confirmed by the dominance of Proteobacteria, Chloroflexi, Actinobacteria, and Gemmatimonadetes which are important in soil N-cycling, despite the reductions in total diversity, class, phyla and genera abundance of bacterial 16SrRNA genes by B-F. This suggested that B-F induced specific organisms involved in N-cycling, which out-competed other organisms not involved in N-cycling. The provision of substrates by N-fertilizer in B-F for bacterial groups involved in N-cycling modified the rhizosphere microbial structure. The abundance of N-cycling organisms was regulated by the persistence among dominant groups, soil pH, total N, and microbial colonization induced by different biochars interacting with fertilizer which led to enhanced N-retention.

Expression of Formate-Tetrahydrofolate Ligase Did Not Improve Growth but Interferes With Nitrogen and Carbon Metabolism of Synechocystis sp. PCC 6803

The introduction of alternative CO2-fixing pathways in photoautotrophic organism may improve the efficiency of biological carbon fixation such as minimizing the carbon loss due to photorespiration. Here, we analyzed the effects of creating a formate entry point into the primary metabolism of the cyanobacterium Synechocystis sp. PCC 6803. The formate-tetrahydrofolate ligase (FTL) from Methylobacterium extorquens AM1 was expressed in Synechocystis to enable formate assimilation and reducing the loss of fixed carbon in the photorespiratory pathway. Transgenic strains accumulated serine and 3-phosphoglycerate, and consumed more 2-phosphoglycolate and glycine, which seemed to reflect an efficient utilization of formate. However, labeling experiments showed that the serine accumulation was not due to the expected incorporation of formate. Subsequent DNA-microarray analysis revealed profound changes in transcript abundance due to ftl expression. Transcriptome changes were observed in relation to serine and glycine metabolism, C1-metabolism and particularly nitrogen assimilation. The data implied that ftl expression interfered with the signaling the carbon/nitrogen ratio in Synechocystis. Our results indicate that the expression of new enzymes could have a severe impact on the cellular regulatory network, which potentially hinders the establishment of newly designed pathways.

Nitrogen Source Governs Community Carbon Metabolism in a Model Hypersaline Benthic Phototrophic Biofilm

Increasing anthropogenic inputs of fixed nitrogen are leading to greater eutrophication of aquatic environments, but it is unclear how this impacts the flux and fate of carbon in lacustrine and riverine systems. Here, we present evidence that the form of nitrogen governs the partitioning of carbon among members in a genome-sequenced, model phototrophic biofilm of 20 members. Consumption of NO₃ ^- as the sole nitrogen source unexpectedly resulted in more rapid transfer of carbon to heterotrophs than when NH₄ ⁺ was also provided, suggesting alterations in the form of carbon exchanged. The form of nitrogen dramatically impacted net community nitrogen, but not carbon, uptake rates. Furthermore, this alteration in nitrogen form caused very large but focused alterations to community structure, strongly impacting the abundance of only two species within the biofilm and modestly impacting a third member species. Our data suggest that nitrogen metabolism may coordinate coupled carbon-nitrogen biogeochemical cycling in benthic biofilms and, potentially, in phototroph-heterotroph consortia more broadly. It further indicates that the form of nitrogen inputs may significantly impact the contribution of these communities to carbon partitioning across the terrestrial-aquatic interface.IMPORTANCE Anthropogenic inputs of nitrogen into aquatic ecosystems, and especially those of agricultural origin, involve a mix of chemical species. Although it is well-known in general that nitrogen eutrophication markedly influences the metabolism of aquatic phototrophic communities, relatively little is known regarding whether the specific chemical form of nitrogen inputs matter. Our data suggest that the nitrogen form alters the rate of nitrogen uptake significantly, whereas corresponding alterations in carbon uptake were minor. However, differences imposed by uptake of divergent nitrogen forms may result in alterations among phototroph-heterotroph interactions that rewire community metabolism. Furthermore, our data hint that availability of other nutrients (i.e., iron) might mediate the linkage between carbon and nitrogen cycling in these communities. Taken together, our data suggest that different nitrogen forms should be examined for divergent impacts on phototrophic communities in fluvial systems and that these anthropogenic nitrogen inputs may significantly differ in their ultimate biogeochemical impacts.

Nitrates as a Potential N Supply for Microbial Ecosystems in a Hyperarid Mars Analog System

Nitrate is common in Mars sediments owing to long-term atmospheric photolysis, oxidation, and potentially, impact shock heating. The Atacama Desert in Chile, which is the driest region on Earth and rich in nitrate deposits, is used as a Mars analog in this study to explore the potential effects of high nitrate levels on growth of extremophilic ecosystems. Seven study sites sampled across an aridity gradient in the Atacama Desert were categorized into 3 clusters—hyperarid, middle, and arid sites—as defined by essential soil physical and chemical properties. Intriguingly, the distribution of nitrate concentrations in the shallow subsurface suggests that the buildup of nitrate is not solely controlled by precipitation. Correlations of nitrate with SiO₂/Al₂O₃ and grain sizes suggest that sedimentation rates may also be important in controlling nitrate distribution. At arid sites receiving more than 10 mm/yr precipitation, rainfall shows a stronger impact on biomass than nitrate does. However, high nitrate to organic carbon ratios are generally beneficial to N assimilation, as evidenced both by soil geochemistry and enriched culturing experiments. This study suggests that even in the absence of precipitation, nitrate levels on a more recent, hyperarid Mars could be sufficiently high to benefit potentially extant Martian microorganisms.

Methanogenesis in animals with foregut and hindgut fermentation: a review

Methane is the main greenhouse-gas contributor to global warming in the livestock sector; it is generated by anaerobic fermentation in the different sections of the gut, and the methane concentration differs significantly among species. Methane is produced only by certain types of microorganisms called methanogens. The species composition of methanogenic archaea population is largely affected by the diet, geographical location, host and the section of the gut. Consequently, methane production, either measured as total grams emitted per day or per bodyweight mass, differs greatly among animal species. The main difference in methanogenic activity among different gut sections and animal species is the substrate fermented and the metabolic pathway to complete anaerobic fermentation of plant material. The three main substrates used by methanogens are CO2, acetate and compounds containing methyl groups. The three dominant orders of methanogens in gut environments are Methanomicrobiales, Methanobacteriales and Methanosarcinales. They normally are present in low numbers (below 3% of total microbiome). The present review will describe the main metabolic pathways and methanogens involved in CH4 production in the gut of different host-animal species, as well as discuss general trends that influence such emissions, such as geographical distribution, feed composition, section of the gut, host age and diurnal and season variation. Finally, the review will describe animal species (large and small domestic ruminants, wild ruminants, camelids, pigs, rabbits, horses, macropods, termites and humans) specificities in the methanogen diversity and their effects on methane emission.

In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle

The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H₂ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H₂ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.

Effect of Zn2+ on halohydrin dehalogenase expression and accumulation through multi-parameter correlation research with Escherichia coli P84A/MC1061

Using 5 Zn²⁺ supplementation strategies in a 50 L batch bioreactor named FUS-50L(A), possible correlations among Zn²⁺ content and addition timing, physiologic activity (PA), halohydrin dehalogenase (HheC) accumulation of Escherichia coli P84A/MC1061 were systematically investigated. First, Zn²⁺ was confirmed as the significant factor, and its optimal concentration for HheC expression was 3.87 mg/L through fermentation experiments in shaking flasks. Second, based on experimental results from the different strategies, it was found that PA, nutrient consumption rate (NCR) and specific growth rate (μ) for E. coli P84A/MC1061 were promoted in the log phase (4-8 h) under appropriate Zn²⁺ concentrations in the lag phase and late log phase. Furthermore cell biomass was also increased to a higher level and the maximum HheC activity (i.e. HheC_max) was increased by 9.80%, and the time to reach HheC_max was reduced from 16 to 12 hours. Furthermore, appropriate supplementation of Zn²⁺ caused higher μ for E. coli P84A/MC1061, which resulted in more rapid accumulation of increased acetic acid concentrations, leading to higher acetic acid consumption avoiding any negative effects on producing HheC because of carbon source being exhausted prematurely and acetic acid being consumed rapidly.

Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment

Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of "Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (K_m ) and the generation time were determined to be 25 μM NO₂^- and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH₄Cl but completely inhibited at 50 mM NH₄Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of NitrotogaIMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification.

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.

Effect of molybdenum and tungsten on the reduction of nitrate in nitrate reductase, a DFT study

The molybdenum and tungsten active site model complexes, derived from the protein X-ray crystal structure of the first W-containing nitrate reductase isolated from Pyrobaculum aerophilum, were computed for nitrate reduction at the COSMO-B3LYP/SDDp//B3LYP/Lanl2DZ(p) energy level of density functional theory. The molybdenum containing active site model complex (Mo–Nar) has the largest activation energy (34.4 kcal/mol) for the oxygen atom transfer from the nitrate to the metal center as compared to the tungsten containing active site model complex (W–Nar) (12.0 kcal/mol). Oxidation of the educt complex is close to thermoneutral (−1.9 kcal/mol) for the Mo active site model complex but strongly exothermic (−34.7 kcal/mol) for the W containing active site model complex, however, the M^VI to M^IV reduction requires equal amount of reductive power for both metal complexes, Mo–Nar or W–Nar.

Heterologous expression and biochemical characterization of assimilatory nitrate and nitrite reductase reveals adaption and potential of Bacillus megaterium NCT-2 in secondary salinization soil

Large accumulation of nitrate in soil has resulted in "salt stress" and soil secondary salinization. Bacillus megaterium NCT-2 which was isolated from secondary salinization soil showed high capability of nitrate reduction. The genes encoding assimilatory nitrate and nitrite reductase from NCT-2 were cloned and over-expressed in Escherichia coli. The optimum co-expression condition was obtained with E. coli BL21 (DE3) and 0.1mM IPTG for 10h when expression was carried out at 20°C and 120rpm in Luria-Bertani (LB) medium. The molecular mass of nitrate reductase was 87.3kDa and 80.5kDa for electron transfer and catalytic subunit, respectively. The large and small subunit of nitrite reductase was 88kDa and 11.7kDa, respectively. The purified recombinant enzymes showed broad activity range of temperature and pH. The maximum activities were obtained at 35°C and 30°C, pH 6.2 and 6.5, which was similar to the condition of greenhouse soils. Maximum stimulation of the enzymes occurred with addition of Fe³⁺, while Cu²⁺ caused the maximum inhibition. The optimum electron donor was MV+Na₂S₂O₄+EDTA and MV+Na₂S₂O₄, respectively. Kinetic parameters of K_m and V_max were determined to be 670μM and 58U/mg for nitrate reductase, and 3100μM and 5.2U/mg for nitrite reductase. Results of quantitative real-time PCR showed that the maximum expression levels of nitrate and nitrite reductase were obtained at 50mM nitrate for 8h and 12h, respectively. These results provided information on novel assimilatory nitrate and nitrite reductase and their properties presumably revealed adaption of B. megaterium NCT-2 to secondary salinization condition. This study also shed light on the role played by the nitrate assimilatory pathway in B. megaterium NCT-2.

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillusthermosulfidooxidans Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.

Gene Expression and Silencing Studies in Phytophthora infestans Reveal Infection-Specific Nutrient Transporters and a Role for the Nitrate Reductase Pathway in Plant Pathogenesis

To help learn how phytopathogens feed from their hosts, genes for nutrient transporters from the hemibiotrophic potato and tomato pest Phytophthora infestans were annotated. This identified 453 genes from 19 families. Comparisons with a necrotrophic oomycete, Pythium ultimum var. ultimum, and a hemibiotrophic fungus, Magnaporthe oryzae, revealed diversity in the size of some families although a similar fraction of genes encoded transporters. RNA-seq of infected potato tubers, tomato leaves, and several artificial media revealed that 56 and 207 transporters from P. infestans were significantly up- or down-regulated, respectively, during early infection timepoints of leaves or tubers versus media. About 17 were up-regulated >4-fold in both leaves and tubers compared to media and expressed primarily in the biotrophic stage. The transcription pattern of many genes was host-organ specific. For example, the mRNA level of a nitrate transporter (NRT) was about 100-fold higher during mid-infection in leaves, which are nitrate-rich, than in tubers and three types of artificial media, which are nitrate-poor. The NRT gene is physically linked with genes encoding nitrate reductase (NR) and nitrite reductase (NiR), which mobilize nitrate into ammonium and amino acids. All three genes were coregulated. For example, the three genes were expressed primarily at mid-stage infection timepoints in both potato and tomato leaves, but showed little expression in potato tubers. Transformants down-regulated for all three genes were generated by DNA-directed RNAi, with silencing spreading from the NR target to the flanking NRT and NiR genes. The silenced strains were nonpathogenic on leaves but colonized tubers. We propose that the nitrate assimilation genes play roles both in obtaining nitrogen for amino acid biosynthesis and protecting P. infestans from natural or fertilization-induced nitrate and nitrite toxicity.

Little is known of how plant pathogens adapt to different growth conditions and host tissues. To understand the interaction between the filamentous eukaryotic microbe Phytophthora infestans and its potato and tomato hosts, we mined the genome for genes encoding proteins involved in nutrient uptake and measured their expression in leaves, tubers, and three artificial media. We observed dynamic changes between the growth conditions, and identified transporters expressed mainly in the biotrophic stage, leaves, tubers, or artificial media. When we blocked the expression of a nitrate transporter and two other genes involved in assimilating nitrate, we observed that those genes were required for successful colonization of nitrate-rich leaves but not nitrate-poor tissues, and that nitrate had become toxic to the silenced strains. We therefore hypothesize that the nitrate assimilation pathway may help the pathogen use inorganic nitrogen for nutrition and/or detoxify nitrate when its levels may become damaging.

Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

Pseudomonas stutzeri A1501 is an endophytic bacterium capable of nitrogen fixation. This strain has been isolated from the rice rhizosphere and provides the plant with fixed nitrogen and phytohormones. These interesting features encouraged us to study the metabolism of this microorganism at the systems-level. In this work, we present the first genome-scale metabolic model (iPB890) for P. stutzeri, involving 890 genes, 1135 reactions, and 813 metabolites. A combination of automatic and manual approaches was used in the reconstruction process. Briefly, using the metabolic networks of Pseudomonas aeruginosa and Pseudomonas putida as templates, a draft metabolic network of P. stutzeri was reconstructed. Then, the draft network was driven through an iterative and curative process of gap filling. In the next step, the model was evaluated using different experimental data such as specific growth rate, Biolog substrate utilization data and other experimental observations. In most of the evaluation cases, the model was successful in correctly predicting the cellular phenotypes. Thus, we posit that the iPB890 model serves as a suitable platform to explore the metabolism of P. stutzeri.

Gastric microbiota and predicted gene functions are altered after subtotal gastrectomy in patients with gastric cancer

Subtotal gastrectomy (i.e., partial removal of the stomach), a surgical treatment for early-stage distal gastric cancer, is usually accompanied by highly selective vagotomy and Billroth II reconstruction, leading to dramatic changes in the gastric environment. Based on accumulating evidence of a strong link between human gut microbiota and host health, a 2-year follow-up study was conducted to characterize the effects of subtotal gastrectomy. Gastric microbiota and predicted gene functions inferred from 16S rRNA gene sequencing were analyzed before and after surgery. The results demonstrated that gastric microbiota is significantly more diverse after surgery. Ralstonia and Helicobacter were the top two genera of discriminant abundance in the cancerous stomach before surgery, while Streptococcus and Prevotella were the two most abundant genera after tumor excision. Furthermore, N-nitrosation genes were prevalent before surgery, whereas bile salt hydrolase, NO and N2O reductase were prevalent afterward. To our knowledge, this is the first report to document changes in gastric microbiota before and after surgical treatment of stomach cancer.

Succinic Semialdehyde Promotes Prosurvival Capability of Agrobacterium tumefaciens

Succinic semialdehyde (SSA), an important metabolite of γ-aminobutyric acid (GABA), is a ligand of the repressor AttJ regulating the expression of the attJ-attKLM gene cluster in the plant pathogen Agrobacterium tumefaciens. While the response of A. tumefaciens to GABA and the function of attKLM have been extensively studied, genetic and physiological responses of A. tumefaciens to SSA remain unknown. In combination with microarray and genetic approaches, this study sets out to explore new roles of the SSA-AttJKLM regulatory mechanism during bacterial infection. The results showed that SSA plays a key role in regulation of several bacterial activities, including C4-dicarboxylate utilization, nitrate assimilation, and resistance to oxidative stress. Interestingly, while the SSA relies heavily on the functional AttKLM in mediating nitrate assimilation and oxidative stress resistance, the compound could regulate utilization of C4-dicarboxylates independent of AttJKLM. We further provide evidence that SSA controls C4-dicarboxylate utilization through induction of an SSA importer and that disruption of attKLM attenuates the tumorigenicity of A. tumefaciens. Taken together, these findings indicate that SSA could be a potent plant signal which, together with AttKLM, plays a vital role in promoting the bacterial prosurvival abilities during infection.

IMPORTANCE

Agrobacterium tumefaciens is a plant pathogen causing crown gall diseases and has been well known as a powerful tool for plant genetic engineering. During the long history of microbe-host interaction, A. tumefaciens has evolved the capabilities of recognition and response to plant-derived chemical metabolites. Succinic semialdehyde (SSA) is one such metabolite. Previous results have demonstrated that SSA functions to activate a quorum-quenching mechanism and thus to decrease the level of quorum-sensing signals, thereby avoiding the elicitation of a plant defense. Here, we studied the effect of SSA on gene expression at a genome-wide level and reported that SSA also promotes bacterial survival during infection. These findings provide a new insight on the biological significance of chemical signaling between agrobacteria and plant hosts.

An integrated biochemical system for nitrate assimilation and nitric oxide detoxification in Bradyrhizobium japonicum

Rhizobia are recognized to establish N2-fixing symbiotic interactions with legume plants. Bradyrhizobium japonicum, the symbiont of soybeans, can denitrify and grow under free-living conditions with nitrate (NO3 (-)) or nitrite (NO2 (-)) as sole nitrogen source. Unlike related bacteria that assimilate NO3 (-), genes encoding the assimilatory NO3 (-) reductase (nasC) and NO2 (-) reductase (nirA) in B. japonicum are located at distinct chromosomal loci. The nasC gene is located with genes encoding an ABC-type NO3 (-) transporter, a major facilitator family NO3 (-)/NO2 (-) transporter (NarK), flavoprotein (Flp) and single-domain haemoglobin (termed Bjgb). However, nirA clusters with genes for a NO3 (-)/NO2 (-)-responsive regulator (NasS-NasT). In the present study, we demonstrate NasC and NirA are both key for NO3 (-) assimilation and that growth with NO3 (-), but not NO2 (-) requires flp, implying Flp may function as electron donor to NasC. In addition, bjgb and flp encode a nitric oxide (NO) detoxification system that functions to mitigate cytotoxic NO formed as a by-product of NO3 (-) assimilation. Additional experiments reveal NasT is required for NO3 (-)-responsive expression of the narK-bjgb-flp-nasC transcriptional unit and the nirA gene and that NasS is also involved in the regulatory control of this novel bipartite assimilatory NO3 (-)/NO2 (-) reductase pathway.

Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

BACKGROUND

Bacteria of the genus Sulfobacillus are found worldwide as members of microbial communities that accelerate sulfide mineral dissolution in acid mine drainage environments (AMD), acid-rock drainage environments (ARD), as well as in industrial bioleaching operations. Despite their frequent identification in these environments, their role in biogeochemical cycling is poorly understood.

RESULTS

Here we report draft genomes of five species of the Sulfobacillus genus (AMDSBA1-5) reconstructed by cultivation-independent sequencing of biofilms sampled from the Richmond Mine (Iron Mountain, CA). Three of these species (AMDSBA2, AMDSBA3, and AMDSBA4) have no cultured representatives while AMDSBA1 is a strain of S. benefaciens, and AMDSBA5 a strain of S. thermosulfidooxidans. We analyzed the diversity of energy conservation and central carbon metabolisms for these genomes and previously published Sulfobacillus genomes. Pathways of sulfur oxidation vary considerably across the genus, including the number and type of subunits of putative heterodisulfide reductase complexes likely involved in sulfur oxidation. The number and type of nickel-iron hydrogenase proteins varied across the genus, as does the presence of different central carbon pathways. Only the AMDSBA3 genome encodes a dissimilatory nitrate reducatase and only the AMDSBA5 and S. thermosulfidooxidans genomes encode assimilatory nitrate reductases. Within the genus, AMDSBA4 is unusual in that its electron transport chain includes a cytochrome bc type complex, a unique cytochrome c oxidase, and two distinct succinate dehydrogenase complexes.

CONCLUSIONS

Overall, the results significantly expand our understanding of carbon, sulfur, nitrogen, and hydrogen metabolism within the Sulfobacillus genus.

A novel A3 group aconitase tolerates oxidation and nitric oxide

Achromobacter denitrificans YD35 is an NO2 (-)-tolerant bacterium that expresses the aconitase genes acnA3, acnA4, and acnB, of which acnA3 is essential for growth tolerance against 100 mm NO2 (-). Atmospheric oxygen inactivated AcnA3 at a rate of 1.6 × 10(-3) min(-1), which was 2.7- and 37-fold lower compared with AcnA4 and AcnB, respectively. Stoichiometric titration showed that the [4Fe-4S](2+) cluster of AcnA3 was more stable against oxidative inactivation by ferricyanide than that of AcnA4. Aconitase activity of AcnA3 persisted against high NO2 (-) levels that generate reactive nitrogen species with an inactivation rate constant of k = 7.8 × 10(-3) min(-1), which was 1.6- and 7.8-fold lower than those for AcnA4 and AcnB, respectively. When exposed to NO2 (-), the acnA3 mutant (AcnA3Tn) accumulated higher levels of cellular citrate compared with the other aconitase mutants, indicating that AcnA3 is a major producer of cellular aconitase activity. The extreme resistance of AcnA3 against oxidation and reactive nitrogen species apparently contributes to bacterial NO2 (-) tolerance. AcnA3Tn accumulated less cellular NADH and ATP compared with YD35 under our culture conditions. The accumulation of more NO by AcnA3Tn suggested that NADH-dependent enzymes detoxify NO for survival in a high NO2 (-) milieu. This novel aconitase is distributed in Alcaligenaceae bacteria, including pathogens and denitrifiers, and it appears to contribute to a novel NO2 (-) tolerance mechanism in this strain.