Global transcriptional response of Nitrosomonas europaea to chloroform and chloromethane

Ofloxacin weakened treatment performance of rural domestic sewage in an aerobic biofilm system by affecting biofilm resistance, bacterial community, and functional genes

Ofloxacin (OFL) is a typical fluoroquinolone antibiotic widely detected in rural domestic sewage, however, its effects on the performance of aerobic biofilm systems during sewage treatment process remain poorly understood. We carried out an aerobic biofilm experiment to explore how the OFL with different concentrations affects the pollutant removal efficiency of rural domestic sewage. Results demonstrated that the OFL negatively affected pollutant removal in aerobic biofilm systems. High OFL levels resulted in a decrease in removal efficiency: 9.33% for chemical oxygen demand (COD), 18.57% for ammonium (NH4+-N), and 8.49% for total phosphorus (TP) after 35 days. The findings related to the chemical and biological properties of the biofilm revealed that the OFL exposure triggered oxidative stress and SOS responses, decreased the live cell number and extracellular polymeric substance content of biofilm, and altered bacterial community composition. More specifically, the relative abundance of key genera linked to COD (e.g., Rhodobacter), NH4+-N (e.g., Nitrosomonas), and TP (e.g., Dechlorimonas) removal was decreased. Such the OFL-induced decrease of these genera might result in the down-regulation of carbon degradation (amyA), ammonia oxidation (hao), and phosphorus adsorption (ppx) functional genes. The conventional pollutants (COD, NH4+-N, and TP) removal was directly affected by biofilm resistance, functional genes, and bacterial community under OFL exposure, and the bacterial community played a more dominant role based on partial least-squares path model analysis. These findings will provide valuable insights into understanding how antibiotics impact the performance of aerobic biofilm systems during rural domestic sewage treatment.

Growth of the Nitrosomonas europaea cells in the biofilm and planktonic growth mode: Responses of extracellular polymeric substances production and transcriptome

Nitrosomonas europaea, an aerobic ammonia oxidizing bacterium, is responsible for the first and rate-limiting step of the nitrification process, and their ammonia oxidation activities are critical for the biogeochemical cycling and the biological nitrogen removal of wastewater treatment. In the present study, N. europaea cells were cultivated in the inorganic or organic media (the NBRC829 and the nutrient-rich, NR, media, respectively), and the cells proliferated in the form of planktonic and biofilm in those media, respectively. The N. europaea cells in the biofilm growth mode produced larger amounts of the extracellular polymeric substances (EPS), and the composition of the EPS was characterized by the chemical analyses including Fourier transform infrared spectroscopy (FT-IR) and 1H-nuclear magnetic resonance (NMR) measurements. The RNA-Seq analysis of N. europaea in the biofilm or planktonic growth mode revealed that the following gene transcripts involved in central nitrogen metabolisms were abundant in the biofilm growth mode; amo encoding ammonia monooxygenase, hao encoding hydroxylamine dehydrogenase, the gene encoding nitrosocyanine, nirK encoding copper-containing nitrite reductase. Additionally, the transcripts of the pepA and wza involved in the bacterial floc formation and the translocation of EPS, respectively, were also abundant in the biofilm-growth mode. Our study was first to characterize the EPS production and transcriptome of N. europaea in the biofilm and planktonic growth mode.

Effects of sulfoxaflor on greenhouse vegetable soil N2O emissions and its microbial driving mechanism

The wide application of pesticides ensures the safety of food production, but it also has a serious impact on soil ecosystem. Although sulfoxaflor as a pesticide has great potential for application due to its excellent insecticidal activity and low crossresistance, little is known about its soil environmental safety risks. In this study, the effects of sulfoxaflor on N₂O emissions and microorganisms in greenhouse vegetable soils were studied by indoor simulation culture experiments. Dynamic changes of soil main inorganic N and N₂O emission rate were tested, and the abundance and community of total bacteria and microorganisms related to N cycle were analyzed. The results indicated that soil microorganisms rapidly degraded sulfoxaflor, and the N₂O emissions rate and ammonium nitrogen (NH₄⁺-N) content significantly increased, while nitrate nitrogen (NO₃^--N) content was significantly decreased. Sulfoxaflor significantly changed the abundance and community of total bacteria, nitrite reducing and nitrous oxide reducing bacteria, but had no significant effect on ammoxidation microorganisms. The N₂O emission rate was positively correlated with gene abundance of denitrifying microorganisms. Under 65% soil maximum water holding capacity, sulfoxaflor may broke the dynamic balance of N₂O production and consumption in the denitrification process, which caused a significant increase in N₂O emission. Therefore, the application of sulfoxaflor had a certain effect on N cycling and utilization in greenhouse vegetable soil.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses

The phylum Acidobacteria is widely distributed in soils, but few representatives have been cultured. In general, Acidobacteria are oligotrophs and exhibit slow growth under laboratory conditions. We sequenced the genome of Granulicella sp. WH15, a strain obtained from decaying wood, and determined the bacterial transcriptome and proteome under growth in poor medium with a low or high concentration of sugar. We detected the presence of 217 carbohydrate-associated enzymes in the genome of strain WH15. Integrated analysis of the transcriptomic and proteomic profiles showed that high sugar triggered a stress response. As part of this response, transcripts related to cell wall stress, such as sigma factor σW and toxin-antitoxin (TA) systems, were upregulated, as were several proteins involved in detoxification and repair, including MdtA and OprM. KEGG metabolic pathway analysis indicated the repression of carbon metabolism (especially the pentose phosphate pathway) and the reduction of protein synthesis, carbohydrate metabolism, and cell division, suggesting the arrest of cell activity and growth. In summary, the stress response of Granulicella sp. WH15 induced by the presence of a high sugar concentration in the medium resulted in the intensification of secretion functions to eliminate toxic compounds and the reallocation of resources to cell maintenance instead of growth.

Comparative analysis of the effects of five soil fumigants on the abundance of denitrifying microbes and changes in bacterial community composition

Soil fumigation is currently the most effective method for controlling soil-borne pests and diseases in high-value crops. To better understand the effect of chloropicrin (CP), dazomet (DZ), dimethyl disulfide (DMDS), allyl isothiocyanate (AITC) and 1,3-dichloropropene (1,3-D) fumigants on soil microorganisms, this study monitored changes in the diversity and community composition of soil bacteria involved in denitrification using real-time PCR and high-throughput gene sequencing techniques. These five fumigants significantly decreased the bacterial population size in some phyla including Proteobacteria, Chloroflexi and Acidobacteria, and increased the bacterial population size in other phyla such as Firmicutes, Gemmatimonadetes, Actinobacteria, Verrucomicrobia, Saccharibacteria and Parcubacteria. Although bacterial diversity declined after CP fumigation, it was briefly stimulated by the other four fumigants. Meanwhile, all five fumigants temporarily decreased populations of denitrifying bacteria containing the napA, narG, nirS or nirK enzyme-encoding genes. Denitrifiers bearing the cnorB, qnorB or nosZ genes were relatively stable following DZ and DMDS fumigation. However, cnorB and nosZ decreased initially following CP, AITC and 1,3-D fumigation. Simultaneously, the abundance of qnorB significantly increased in AITC and 1,3-D fumigated soils. These results showed that soil fumigation significantly shifted the abundance and community structure of denitrifying bacteria. This study will help to predict the response of different phyla of denitrifying bacteria to soil fumigation.

Transcriptomic Response of Nitrosomonas europaea Transitioned from Ammonia- to Oxygen-Limited Steady-State Growth

Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Ammonia-oxidizing microorganisms perform the first step of nitrification, the oxidation of ammonia to nitrite. The bacterium Nitrosomonas europaea is the best-characterized ammonia oxidizer to date. Exposure to hypoxic conditions has a profound effect on the physiology of N. europaea, e.g., by inducing nitrifier denitrification, resulting in increased nitric and nitrous oxide production. This metabolic shift is of major significance in agricultural soils, as it contributes to fertilizer loss and global climate change. Previous studies investigating the effect of oxygen limitation on N. europaea have focused on the transcriptional regulation of genes involved in nitrification and nitrifier denitrification. Here, we combine steady-state cultivation with whole-genome transcriptomics to investigate the overall effect of oxygen limitation on N. europaea. Under oxygen-limited conditions, growth yield was reduced and ammonia-to-nitrite conversion was not stoichiometric, suggesting the production of nitrogenous gases. However, the transcription of the principal nitric oxide reductase (cNOR) did not change significantly during oxygen-limited growth, while the transcription of the nitrite reductase-encoding gene (nirK) was significantly lower. In contrast, both heme-copper-containing cytochrome c oxidases encoded by N. europaea were upregulated during oxygen-limited growth. Particularly striking was the significant increase in transcription of the B-type heme-copper oxidase, proposed to function as a nitric oxide reductase (sNOR) in ammonia-oxidizing bacteria. In the context of previous physiological studies, as well as the evolutionary placement of N. europaea’s sNOR with regard to other heme-copper oxidases, these results suggest sNOR may function as a high-affinity terminal oxidase in N. europaea and other ammonia-oxidizing bacteria.

IMPORTANCE Nitrification is a ubiquitous microbially mediated process in the environment and an essential process in engineered systems such as wastewater and drinking water treatment plants. However, nitrification also contributes to fertilizer loss from agricultural environments, increasing the eutrophication of downstream aquatic ecosystems, and produces the greenhouse gas nitrous oxide. As ammonia-oxidizing bacteria are the most dominant ammonia-oxidizing microbes in fertilized agricultural soils, understanding their responses to a variety of environmental conditions is essential for curbing the negative environmental effects of nitrification. Notably, oxygen limitation has been reported to significantly increase nitric oxide and nitrous oxide production during nitrification. Here, we investigate the physiology of the best-characterized ammonia-oxidizing bacterium, Nitrosomonas europaea, growing under oxygen-limited conditions.

Changes in the abundance and community composition of different nitrogen cycling groups in response to fumigation with 1,3-dichloropropene

The fumigant 1,3-dichloropropene (1,3-D) is widely-used to control pathogenic bacteria, fungi, nematodes and insects in soil before a crop is planted. Although fumigants in general have been reported to have a 'fertilizer effect' in the soil by increasing nitrogen availability, little is known of how a specific fumigant such as 1,3-D affects available nitrogen. This study used real-time quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing techniques to investigate the effects of 1,3-D on microorganisms involved in nitrogen cycling that were present in 2 soils: Jiangxi lateritic red soil and Beijing fluvo-aquic soil. The fumigant 1,3-D temporarily decreased the abundance of 11 functional genes involved in nitrogen-fixing, nitrification and denitrification in both soil types. Different nitrogen cycling groups recovered to the unfumigated level in various incubation phases. Microorganisms containing nifH, nxrB, napA and qnorB genes were most vulnerable to 1,3-D fumigation. However, a stronger and longer inhibition effect of 1,3-D on these 11 functional genes was observed in Jiangxi soil than in Beijing soil. At the same time, the abundance of nifH, AOBamoA, nirS, qnorB and cnorB genes was significantly increased 59 days after 1,3-D fumigation. Fumigation with 1,3-D significantly reduced the nitrogen-fixing bacteria Azospirillum and Paenibacillus; the nitrifiers Nitrosomonas and Nitrospira; and the denitrifiers Pseudomonas, Paracoccus and Sphingomonas. Conversely, fumigation with 1,3-D increased the nitrogen-fixing bacteria Bradyrhizobium and Rhizobium; the nitrification bacteria Nitrosospira and Nitrolancea; and the denitrification bacteria Sphingobium, Alcanivorax, Bacillus, Streptomyces and Aeromonas. Fumigation with 1,3-D therefore caused significant shifts in the species composition and number of microbes directly involved in nitrogen cycling in the short-term. These results contribute toward a better understanding of the impact of 1,3-D fumigation on various types of soil nitrogen-cycling groups.

Adaption and recovery of Nitrosomonas europaea to chronic TiO2 nanoparticle exposure

Although the adverse impacts of emerging nanoparticles (NPs) on the biological nitrogen removal (BNR) process have been broadly reported, the adaptive responses of NP-impaired nitrifiers and the related mechanisms have seldom been addressed to date. Here, we systematically explored the adaption and recovery capacities of the ammonia oxidizer Nitrosomonas europaea under chronic TiO₂ NP exposure and different dissolved oxygen (DO) conditions at the physiological and transcriptional levels in a chemostat reactor. N. europaea cells adapted to 50 mg/L TiO₂ NP exposure after 40-d incubation and the inhibited cell growth, membrane integrity, nitritation rate, and ammonia monooxygenase activity all recovered regardless of the DO concentrations. Transmission electron microscope imaging indicated the remission of the membrane distortion after the cells' 40-d adaption to the NP exposure. The microarray results further suggested that the metabolic processes associated with the membrane repair were pivotal for cellular adaption/recovery, such as the membrane efflux for toxicant exclusion, the structural preservation or stabilization, and the osmotic equilibrium adjustment. In addition, diverse metabolic and stress-defense pathways, including aminoacyl-tRNA biosynthesis, respiratory chain, ATP production, toxin-antitoxin 'stress-fighting', and DNA repair were activated for the cellular adaption coupled with the metabolic activity recovery, probably via recovering the energy production/conversion efficiency and mediating the non-photooxidative stress. Finally, low DO (0.5 mg/L) incubated cells were more susceptible to TiO₂ NP exposure and required more time to adapt to and recover from the stress, which was probably due to the stimulation limitation of the oxygen-dependent energy metabolism with a lower oxygen supply. The findings of this study provide new insights into NP contamination control and management adjustments during the BNR process.

Availability, Quality, and Relevance of Toxicogenomics Data for Human Health Risk Assessment: A Scoping Review of the Literature on Trihalomethanes

Human health risk assessment (HHRA) must be adapted to the challenges of the 21st century, and the use of toxicogenomics data in HHRA is among the changes that regulatory agencies worldwide are trying to implement. However, the use of toxicogenomics data in HHRA is still limited. The purpose of this study was to explore the availability, quality, and relevance to HHRA of toxicogenomics publications as potential barriers to their use in HHRA. We conducted a scoping review of available toxicogenomics literature, using trihalomethanes as a case study. Four bibliographic databases (including the Comparative Toxicogenomics Database) were assessed. An evaluation table was developed to characterize quality and relevance of studies included on the basis of criteria proposed in the literature. Studies were selected and analyzed by 2 independent reviewers. Only 9 studies, published between 1997 and 2015, were included in the analysis. Based on the selected criteria, critical methodological details were often missing; in fact, only 3 out of 9 studies were considered to be of adequate quality for HHRA. No studies met >3 (out of 7) criteria of relevance to HHRA (eg, adequate number of doses and sample size). This first scoping review of toxicogenomics publications on trihalomethanes shows that low availability, quality, and relevance to HHRA of toxicogenomics publications presents potential barriers to their use in HHRA. Improved reporting of methodological details and study design is needed in the future so that toxicogenomics studies can be appropriately assessed regarding their quality and value for HHRA.

Mechanisms of Persistence of the Ammonia-Oxidizing Bacteria Nitrosomonas to the Biocide Free Nitrous Acid

Free nitrous acid (FNA) exerts a broad range of antimicrobial effects on bacteria, although susceptibility varies considerably among microorganisms. Among nitrifiers found in activated sludge of wastewater treatment processes (WWTPs), nitrite-oxidizing bacteria (NOB) are more susceptible to FNA compared to ammonia-oxidizing bacteria (AOB). This selective inhibition of NOB over AOB in WWTPs bypasses nitrate production and improves the efficiency and costs of the nitrogen removal process in both the activated sludge and anaerobic ammonium oxidation (Anammox) system. However, the molecular mechanisms governing this atypical tolerance of AOB to FNA have yet to be understood. Herein we investigate the varying effects of the antimicrobial FNA on activated sludge containing AOB and NOB using an integrated metagenomics and label-free quantitative sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS) metaproteomic approach. The Nitrosomonas genus of AOB, on exposure to FNA, maintains internal homeostasis by upregulating a number of known oxidative stress enzymes, such as pteridine reductase and dihydrolipoyl dehydrogenase. Denitrifying enzymes were upregulated on exposure to FNA, suggesting the detoxification of nitrite to nitric oxide. Interestingly, proteins involved in stress response mechanisms, such as DNA and protein repair enzymes, phage prevention proteins, and iron transport proteins, were upregulated on exposure to FNA. In addition enzymes involved in energy generation were also upregulated on exposure to FNA. The total proteins specifically derived from the NOB genus Nitrobacter was low and, as such, did not allow for the elucidation of the response mechanism to FNA exposure. These findings give us an understanding of the adaptive mechanisms of tolerance within the AOB Nitrosomonas to the biocidal agent FNA.

AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea

Nitrosomonas europaea carries numerous toxin-antitoxin systems. However, despite the abundant representation in its chromosome, studies have not surveyed the underlying molecular functions in detail, and their biological roles remain enigmatic. In the present study, we found that a chromosomally-encoded MazF family member, predicted at the locus NE1181, is a functional toxin endoribonuclease, and constitutes a toxin-antitoxin system, together with its cognate antitoxin, MazE. Massive parallel sequencing provided strong evidence that this toxin endoribonuclease exhibits RNA cleavage activity, primarily against the AAU triplet. This sequence-specificity was supported by the results of fluorometric assays. Our results indicate that N. europaea alters the translation profile and regulates its growth using the MazF family of endoribonuclease under certain stressful conditions.

Transcriptional responses of bacterial amoA gene to dimethyl sulfide inhibition in complex microbial communities

This study presented an approach by combining the real-time reverse transcription polymerase chain reaction with the terminal restriction fragment length polymorphism (T-RFLP) to investigate transcriptional responses of ammonia-oxidizing bacteria (AOB) to dimethyl sulfide (DMS) inhibition. Batch experiments with added ammonium and DMS were conducted using three activated sludges and Nitrosomonas europaea, and the transcriptional responses of the amo subunit A (amoA) mRNA were evaluated. It was found that DMS inhibited ammonium oxidation and amoA mRNA expression in all batch experiments but the inhibition degree observed was different for different sludges examined. It is likely that the different inhibitory effects of DMS on ammonium oxidation and amoA mRNA expression stemmed from different dominant AOB populations in the sludges. The T-RFLP results for amoA mRNA suggested that inhibition of ammonium oxidation by DMS to Nm. europaea-like AOB with T-RF 219/270 is relatively minor compared to other AOB populations in the examined sludges, such as Nm. europaea-like AOB with T-RF 491/491.

Quantification of the effects of various soil fumigation treatments on nitrogen mineralization and nitrification in laboratory incubation and field studies

Better quantification of nitrogen mineralization and nitrification after fumigation would indicate if any adjustment is needed in fertilizer application. The effects of chloropicrin (Pic), 1,3-dichloropropene (1,3-D), dimethyl disulfide (DMDS) and metham sodium (MS) fumigation on soil nitrogen dynamics were evaluated in lab incubation and field studies. Although some differences were observed in NH(4)(+)-N and NO(3)(-)-N concentrations in lab incubation and field experiments, both studies led to the same conclusions: (1) Soil fumigation was shown to increase soil mineral nitrogen only during the first 2 weeks after fumigation (WAF). In particular, Pic significantly increased soil mineral nitrogen in both studies at 1 WAF. However, for all fumigant treatments the observed effect was temporary; the soil mineral content of treated samples recovered to the general level observed in the untreated control. (2) All the fumigation treatments depressed nitrification temporarily, although the treatments exhibited significant differences in the duration of nitrification inhibition. In both studies, for a limited period of time, Pic showed a stronger inhibitory effect on nitrification compared to other fumigant treatments. An S-shaped function was fitted to the concentrations of NO(3)(-)-N in lab incubation samples. The times of maximum nitrification (t(max)) in DMDS and MS treatments were 0.97 week and 1.03 week, which is similar to the untreated control (t(max)=1.02 week). While Pic has the longest effect on nitrifying bacteria, nitrification appears to restart at a later time (t(max)=14.37 week).

Insights into glycogen metabolism in chemolithoautotrophic bacteria from distinctive kinetic and regulatory properties of ADP-glucose pyrophosphorylase from Nitrosomonas europaea

Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO(2) via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms.

Inhibition and gene expression of Nitrosomonas europaea biofilms exposed to phenol and toluene

Pure culture biofilms of the ammonia-oxidizing bacterium Nitrosomonas europaea were grown in a Drip Flow Biofilm Reactor and exposed to the aromatic hydrocarbons phenol and toluene. Ammonia oxidation rates, as measured by nitrite production in the biofilms, were inhibited 50% when exposed to 56 µM phenol or 100 µM toluene, while 50% inhibition of suspended cells occurred at 8 µM phenol or 20 µM toluene. Biofilm-grown cells dispersed into liquid medium and immediately exposed to phenol or toluene experienced similar inhibition levels as batch grown cells, indicating that mass transfer may be a factor in N. europaea biofilm resistance. Whole genome microarray analysis of gene expression was used to detect genes up-regulated in biofilms during toluene and phenol exposure. Two genes, a putative pirin protein (NE1545) and a putative inner membrane protein (NE1546) were up-regulated during phenol exposure, but no genes were up-regulated during toluene exposure. Using qRT-PCR, up-regulation of NE1545 was detected in biofilms and suspended cells exposed to a range of phenol concentrations and levels of inhibition. In the biofilms, NE1545 expression was up-regulated an average of 13-fold over the range of phenol concentrations tested, and was essentially independent of phenol concentration. However, the expression of NE1545 in suspended cells increased from 20-fold at 7 µM phenol up to 80-fold at 30 µM phenol. This study demonstrates that biofilms of N. europaea are more resistant than suspended cells to inhibition of ammonia oxidation by phenol and toluene, even though the global transcriptional responses to the inhibitors do not differ in N. europaea between the suspended and attached growth states.

Computational prediction and transcriptional analysis of sRNAs in Nitrosomonas europaea

Bacterial small noncoding RNAs (sRNAs) have been discovered in many genetically well-studied microorganisms and have been shown to regulate critical cellular processes at the post-transcriptional level. In this study, we used comparative genomics and microarray data to analyze the genome of the ammonia-oxidizing bacterium Nitrosomonas europaea for the presence and expression of sRNAs. Fifteen genes encoding putative sRNAs (psRNAs) were identified. Most of these genes showed altered expression in a variety of experimental conditions. The transcripts of two psRNAs were further characterized by mapping their 5'- and 3'-ends and by real-time PCR. The results of these analyses suggested that one of them, psRNA11, is involved in iron homeostasis in N. europaea.

Nitrification and degradation of halogenated hydrocarbons--a tenuous balance for ammonia-oxidizing bacteria

The process of nitrification has the potential for the in situ bioremediation of halogenated compounds provided a number of challenges can be overcome. In nitrification, the microbial process where ammonia is oxidized to nitrate, ammonia-oxidizing bacteria (AOB) are key players and are capable of carrying out the biodegradation of recalcitrant halogenated compounds. Through industrial uses, halogenated compounds often find their way into wastewater, contaminating the environment and bodies of water that supply drinking water. In the reclamation of wastewater, halogenated compounds can be degraded by AOB but can also be detrimental to the process of nitrification. This minireview considers the ability of AOB to carry out cometabolism of halogenated compounds and the consequent inhibition of nitrification. Possible cometabolism monitoring methods that were derived from current information about AOB genomes are also discussed. AOB expression microarrays have detected mRNA of genes that are expressed at higher levels during stress and are deemed "sentinel" genes. Promoters of selected "sentinel" genes have been cloned and used to drive the expression of gene-reporter constructs. The latter are being tested as early warning biosensors of cometabolism-induced damage in Nitrosomonas europaea with promising results. These and other biosensors may help to preserve the tenuous balance that exists when nitrification occurs in waste streams containing alternative AOB substrates such as halogenated hydrocarbons.

RelB and RelE of Escherichia coli form a tight complex that represses transcription via the ribbon-helix-helix motif in RelB

RelB, the ribbon–helix–helix (RHH) repressor encoded by the relBE toxin–antitoxin locus of Escherichia coli, interacts with RelE and thereby counteracts the mRNA cleavage activity of RelE. In addition, RelB dimers repress the strong relBE promoter and this repression by RelB is enhanced by RelE; that is, RelE functions as a transcriptional co-repressor. RelB is a Lon protease substrate, and Lon is required both for activation of relBE transcription and for activation of the mRNA cleavage activity of RelE. Here we characterize the molecular interactions important for transcriptional control of the relBE model operon. Using an in vivo screen for relB mutants, we identified multiple nucleotide changes that map to important amino acid positions within the DNA-binding domain formed by the N-terminal RHH motif of RelB. Analysis of DNA binding of a subset of these mutant RHH proteins by gel-shift assays, transcriptional fusion assays and a structure model of RelB–DNA revealed amino acid residues making crucial DNA–backbone contacts within the operator (relO) DNA. Mutational and footprinting analyses of relO showed that RelB dimers bind on the same face of the DNA helix and that the RHH motif recognizes four 6-bp repeats within the bipartite binding site. The spacing between each half-site was found to be essential for cooperative interactions between adjacently bound RelB dimers stabilized by the co-repressor RelE. Kinetic and stoichiometric measurements of the interaction between RelB and RelE confirmed that the proteins form a high-affinity complex with a 2:1 stoichiometry. Lon degraded RelB in vitro and degradation was inhibited by RelE, consistent with the proposal that RelE protects RelB from proteolysis by Lon in vivo.

Construction of recombinant Nitrosomonas europaea expressing green fluorescent protein in response to co-oxidation of chloroform

Transcriptional fusions with gfp driven by the promoter region of mbla (NE2571) in pPRO/mbla4 and clpB (NE2402) in pPRO/clpb7 were used to transform the ammonia-oxidizing bacterium Nitrosomonas europaea (ATCC 19718). The two genes were chosen because their transcript levels were found at much higher levels in N. europaea in response to oxidation of chloroform and chloromethane. In N. europaea transformed with pPRO/mbla4, green fluorescent protein (GFP)-dependent fluorescence increased from 3- to 18-fold above control levels in response to increasing chloroform concentrations (7 to 28 microM), and from 8- to 10-fold in response to increasing hydrogen peroxide concentrations (2.5-7.5 mM). The GFP-dependent fluorescence of N. europaea transformed with pPRO/clpb7 also showed an increase of 6- to 10-fold in response to chloroform (28-100 microM) but did not respond to H(2)O(2). Our data provide proof of concept that biosensors can be fabricated in ammonia-oxidizing bacteria using "sentinel" genes that up-regulate in response to stress caused either by co-oxidation of chlorinated solvents or by the presence of H(2)O(2). The fabricated biosensors had a consistent concentration-dependent response to chloroform; however, these did not respond to other chlorinated compounds that cause similar cellular stress.

HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea

Toxin-antitoxin (TA) loci are common in free-living bacteria and archaea. TA loci encode a stable toxin that is neutralized by a metabolically unstable antitoxin. The antitoxin can be either a protein or an antisense RNA. So far, six different TA gene families, in which the antitoxins are proteins, have been identified. Recently, Makarova et al. (K. S. Makarova, N. V. Grishin, and E. V. Koonin, Bioinformatics 22:2581-2584, 2006) suggested that the hicAB loci constitute a novel TA gene family. Using the hicAB locus of Escherichia coli K-12 as a model system, we present evidence that supports this inference: expression of the small HicA protein (58 amino acids [aa]) induced cleavage in three model mRNAs and tmRNA. Concomitantly, the global rate of translation was severely reduced. Using tmRNA as a substrate, we show that HicA-induced cleavage does not require the target RNA to be translated. Expression of HicB (145 aa) prevented HicA-mediated inhibition of cell growth. These results suggest that HicB neutralizes HicA and therefore functions as an antitoxin. As with other antitoxins (RelB and MazF), HicB could resuscitate cells inhibited by HicA, indicating that ectopic production of HicA induces a bacteriostatic rather than a bactericidal condition. Nutrient starvation induced strong hicAB transcription that depended on Lon protease. Mining of 218 prokaryotic genomes revealed that hicAB loci are abundant in bacteria and archaea.

Translation affects YoeB and MazF messenger RNA interferase activities by different mechanisms

Prokaryotic toxin–antitoxin loci encode mRNA cleaving enzymes that inhibit translation. Two types are known: those that cleave mRNA codons at the ribosomal A site and those that cleave any RNA site specifically. RelE of Escherichia coli cleaves mRNA at the ribosomal A site in vivo and in vitro but does not cleave pure RNA in vitro. RelE exhibits an incomplete RNase fold that may explain why RelE requires its substrate mRNA to presented by the ribosome. In contrast, RelE homologue YoeB has a complete RNase fold and cleaves RNA independently of ribosomes in vitro. Here, we show that YoeB cleavage of mRNA is strictly dependent on translation of the mRNA in vivo. Non-translated model mRNAs were not cleaved whereas the corresponding wild-type mRNAs were cleaved efficiently. Model mRNAs carrying frameshift mutations exhibited a YoeB-mediated cleavage pattern consistent with the reading frameshift thus giving strong evidence that YoeB cleavage specificity was determined by the translational reading frame. In contrast, site-specific mRNA cleavage by MazF occurred independently of translation. In one case, translation seriously influenced MazF cleavage efficiency, thus solving a previous apparent paradox. We propose that translation enhances MazF-mediated cleavage of mRNA by destabilization of the mRNA secondary structure.

Candidate stress genes of Nitrosomonas europaea for monitoring inhibition of nitrification by heavy metals

Heavy metals have been shown to be strong inhibitors of nitrification in wastewater treatment plants. In this research, the effects of cadmium, copper, and mercury on Nitrosomonas europaea were studied in quasi-steady-state batch reactors. When cells were exposed to 1 microM CdCl2, 6 microM HgCl2, or 8 microM CuCl2, ammonia oxidation rates were decreased by about 90%. Whole-genome transcriptional and proteomic responses of N. europaea to cadmium were used to identify heavy metal stress response genes. When cells were exposed to 1 microM CdCl2 for 1 h, 66 genes (of the total of 2,460 genes) were upregulated, and 50 genes were downregulated more than twofold. Of these, the mercury resistance genes (merTPCADE) averaged 277-fold upregulation under 1 microM CdCl2, with merA (mercuric reductase) showing 297-fold upregulation. In N. europaea cells exposed to 6 microM HgCl2 or to 8 microM CuCl2, merA showed 250-fold and 1.7-fold upregulation, respectively. Cells showed the ability to recover quickly from Hg2+-related toxic effects, apparently associated with upregulation of the mercury resistance genes and amoA, but no such recovery was evident in Cd2+-exposed cells even though merTPCADE were highly upregulated. We suggest that the upregulation of merA in response to CdCl2 and HgCl2 exposure may provide a means to develop an early-warning indicator for inhibition of nitrification by these metals.

Messenger RNA interferase RelE controls relBE transcription by conditional cooperativity

Prokaryotic toxin-antitoxin (TA) loci consist of two genes in an operon that encodes a metabolically stable toxin and an unstable antitoxin. The antitoxin neutralizes its cognate toxin by forming a tight complex with it. In all cases known, the antitoxin autoregulates TA operon transcription by binding to one or more operators in the promoter region while the toxin functions as a co-repressor of transcription. Interestingly, the toxin can also stimulate TA operon transcription. Here we analyse mechanistic aspects of how RelE of Escherichia coli can function both as a co-repressor and as a derepressor of relBE transcription. When RelB was in excess to RelE, two trimeric RelB(2)*RelE complexes bound cooperatively to two adjacent operator sites in the relBE promoter region and repressed transcription. In contrast, RelE in excess stimulated relBE transcription and released the RelB(2)*RelE complex from operator DNA. A mutational analysis of the operator sites showed that RelE in excess counteracted cooperative binding of the RelB(2)*RelE complexes to the operator sites. Thus, RelE controls relBE transcription by conditional cooperativity.

Physiological and transcriptional responses of Nitrosomonas europaea to toluene and benzene inhibition

Ammonia oxidizing bacteria (AOB) are inhibited by many compounds found in wastewater treatment plant (WWTP) influent, including aromatic hydrocarbons. The detection of "sentinel genes" to identify the presence of aromatic hydrocarbons could be useful to WWTP operators. In this study, the transcriptomic responses of Nitrosomonas europaea during the cometabolism of benzene to phenol and toluene to benzyl alcohol and benzaldehyde were evaluated using whole genome Affymetrix microarrays and qRT-PCR. Benzyl alcohol and benzaldehyde were found not to inhibit N. europaea. However, phenol concentrations as low as 5 microM directly inhibited ammonia oxidation. Surprisingly, there were no significant up- or down-regulation of genes in N. europaea cells exposed to 20 microM toluene, which caused 50% inhibition of ammonia oxidation. Exposing N. europaea to 40 microM benzene, which caused a similar degree of inhibition, resulted in the up-regulation of seven adjacent genes, including NE 1545 (a putative pirin protein) and NE 1546 (a putative membrane protein), that appear to be involved with fatty-acid metabolism, lipid biosynthesis, and membrane protein synthesis. qRT-PCR analysis revealed that NE 1545 and NE 1546 were significantly up-regulated upon exposure to benzene and phenol, but not upon exposure to toluene. Transmission electron microscope images revealed a shift in outer cell structure in response to benzene exposure.

Physiological responses of Pseudomonas putida to formaldehyde during detoxification

Pseudomonas putida KT2440 exhibits two formaldehyde dehydrogenases and two formate dehydrogenase complexes that allow the strain to stoichiometrically convert formaldehyde into CO(2). The strain tolerated up to 1.5 mM formaldehyde and died in the presence of 10 mM. In the presence of 0.5 mM formaldehyde, a sublethal concentration of this chemical, the growth rate decreased by about 40% with respect to growth in the absence of the toxicant. Transcriptomic analysis revealed that in response to low formaldehyde concentrations, a limited number of genes (52) were upregulated. Based on the function of these genes it seems that sublethal concentrations of HCOH trigger responses to overcome DNA and protein damage, extrude this toxic compound, and detoxify it by converting the chemical to CO(2). In strains bearing mutations of the upregulated genes we analysed growth inhibition by 1.5 mM HCOH and killing rates by 10 mM HCOH. Mutants in the MexEF/OprN efflux pump and in the DNA repair genes recA and uvrB were hypersensitive to 10 mM HCOH, the killing rate being three to four orders of magnitude higher than those in the wild-type strain. Mutants in other upregulated genes died at slightly higher or at similar rates to the parental strain. Regarding growth inhibition, we found that mutants in glutathione biosynthesis, stress response mediated by 2-hydroxy acid dehydrogenases and two efflux pumps of the MSF family were unable to grow in the presence of 1.5 mM HCOH. In an independent screening test we searched for mutants which were hypersensitive to formaldehyde, but whose expression did not change in response to this chemical. Two mutants with insertions in recD and fhdA were found which were unable to grow in the presence of 1.5 mM HCOH. The recD mutant was hypersensitive to 10 mM HCOH and died at a higher rate than the parental strain.

Genome-wide transcriptional responses of Nitrosomonas europaea to zinc

Nitrosomonas europaea, a Gram-negative obligate chemolithoautotroph, participates in global nitrogen cycling by carrying out nitrification and derives energy for growth through oxidation of ammonia. In this work, the physiological, proteomic, and transcriptional responses of N. europaea to zinc stress were studied. The nitrite production rate and ammonia-dependent oxygen uptake rate of the cells exposed to 3.4 microM ZnCl2 decreased about 61 and 69% within 30 min, respectively. Two proteins were notably up regulated in zinc treatment and the mRNA levels of their encoding genes started to increase by 1 h after the addition of zinc. A total of 27 genes were up regulated and 30 genes were down regulated. Up-regulated genes included mercury resistance genes (merTPCAD), inorganic ion transport genes, oxidative stress genes, toxin-antitoxin genes, and two-component signal transduction systems genes. merTPCAD was the highest up-regulated operon (46-fold). Down-regulated genes included the RubisCO operon (cbbO), biosynthesis (mrsA), and amino acid transporter.