Effects of Co-existing Heterotrophs on Physiology of and Nitrogen Metabolism in Autotrophic Nitrite-oxidizing Candidatus Nitrotoga.

Interactions between autotrophic nitrifiers and heterotrophs have attracted considerable attention in microbial ecology. However, the mechanisms by which heterotrophs affect the physiological activity of and nitrogen metabolism in autotrophic nitrite oxidizers remain unclear. We herein focused on nitrite-oxidizing Candidatus Nitrotoga and compared an axenic culture including only Ca. Nitrotoga with a co-culture of both Ca. Nitrotoga and Acidovorax in physiological experiments and transcriptomics. In the co-culture with Acidovorax, nitrite consumption by Ca. Nitrotoga was promoted, and some genes relevant to nitrogen metabolism in Ca. Nitrotoga were highly expressed. These results provide insights into the mechanisms by which co-existing heterotrophs affect autotrophic nitrifiers.

Characterisation of bacteria representing a novel Nitrosomonas clade: Physiology, genomics and distribution of missing ammonia oxidizer.

Members of the genus Nitrosomonas are major ammonia oxidizers that catalyse the first step of nitrification in various ecosystems. To date, six subgenus-level clades have been identified. We have previously isolated novel ammonia oxidizers from an additional clade (unclassified cluster 1) of the genus Nitrosomonas. In this study, we report unique physiological and genomic properties of the strain PY1, compared with representative ammonia-oxidising bacteria (AOB). The apparent half-saturation constant for total ammonia nitrogen and maximum velocity of strain PY1 were 57.9 ± 4.8 µM NH3 + NH4 + and 18.5 ± 1.8 µmol N (mg protein)-1 h-1 , respectively. Phylogenetic analysis based on genomic information revealed that strain PY1 belongs to a novel clade of the Nitrosomonas genus. Although PY1 contained genes to withstand oxidative stress, cell growth of PY1 required catalase to scavenge hydrogen peroxide. Environmental distribution analysis revealed that the novel clade containing PY1-like sequences is predominant in oligotrophic freshwater. Taken together, the strain PY1 had a longer generation time, higher yield and required reactive oxygen species (ROS) scavengers to oxidize ammonia, compared with known AOB. These findings expand our knowledge of the ecophysiology and genomic diversity of ammonia-oxidising Nitrosomonas.

Nitrite Production by Nitrifying Bacteria in Urban Groundwater Used in a Chlorinated Public Bath System in Japan.

In contrast to pathogens, the effects of environmental microbes on the water quality in baths have not yet been examined in detail. We herein focused on a public bath in which groundwater was pumped up as bath water and disinfected by chlorination. Ammonia in groundwater is oxidized to nitrite, thereby reducing residual chlorine. A batch-culture test and bacterial community ana-lysis revealed that ammonia-oxidizing bacteria accumulated nitrite and had higher resistance to chlorination than nitrite-oxidizing bacteria. These results demonstrate that the difference in resistance to chlorination between ammonia-oxidizing and nitrite-oxidizing bacteria may lead to the accumulation of nitrite in baths using groundwater.

Predissociation Dynamics of Br2 in the [2Π1/2]c5d; 0g + and [2Π3/2]c6d; 0g + Rydberg States by Velocity Map Imaging Study.

We investigated the predissociation dynamics from the [2Π1/2]c5d; 0g + and [2Π3/2]c6d; 0g + Rydberg states of Br2 using the velocity map imaging technique. Two-dimensional scattering images of the fragmented Br+ exhibited an isotropic feature upon the excitation of these Rydberg states. Analysis of the total kinetic energy release suggested the existence of the predissociation pathways to the dissociation limits of Br(5s, 4P3/2) + Br(4p, 2P3/2) and Br(5s, 4P5/2) + Br(4p, 2P3/2) via the 0g + ion-pair states that interact with the lower and/or excited-core Rydberg states lying at long internuclear distance regions thorough the avoided crossing.

Hafnium Oxide Nanostructured Thin Films: Electrophoretic Deposition Process and DUV Photolithography Patterning.

In the frame of the nanoarchitectonic concept, the objective of this study was to develop simple and easy methods to ensure the preparation of polymorphic HfO2 thin film materials (<200 nm) having the best balance of patterning potential, reproducibility and stability to be used in optical, sensing or electronic fields. The nanostructured HfO2 thin films with micropatterns or continuous morphologies were synthesized by two different methods, i.e., the micropatterning of sol-gel solutions by deep ultraviolet (DUV) photolithography or the electrophoretic deposition (EPD) of HfO2 nanoparticles (HfO2-NPs). Amorphous and monoclinic HfO2 micropatterned nanostructured thin films (HfO2-DUV) were prepared by using a sol-gel solution precursor (HfO2-SG) and spin-coating process following by DUV photolithography, whereas continuous and dense monoclinic HfO2 nanostructured thin films (HfO2-EPD) were prepared by the direct EPD of HfO2-NPs. The HfO2-NPs were prepared by a hydrothermal route and studied through the changing aging temperature, pH and reaction time parameters to produce nanocrystalline particles. Subsequently, based on the colloidal stability study, suspensions of the monoclinic HfO2-NPs with morphologies near spherical, spindle- and rice-like shapes were used to prepare HfO2-EPD thin films on conductive indium-tin oxide-coated glass substrates. Morphology, composition and crystallinity of the HfO2-NPs and thin films were investigated by powder and grazing incidence X-ray diffraction, scanning electron microscopy, transmission electron microscopy and UV-visible spectrophotometry. The EPD and DUV photolithography performances were explored and, in this study, it was clearly demonstrated that these two complementary methods are suitable, simple and effective processes to prepare controllable and tunable HfO2 nanostructures as with homogeneous, dense or micropatterned structures.

Stable nitrogen removal by anammox process after rapid temperature drops: Insights from metagenomics and metaproteomics.

This study investigated the impacts of rapid temperature drops on anammox process performance and the metabolism of its core microbial populations through proteomic analysis. Over a 50-day period, the temperature of an up-flow granular bed anammox reactor was stepwise decreased from 35 °C to 15 °C and resulted in repeated transient increases in effluent nitrite concentrations. At 15 °C, a nitrogen removal rate of 2.71 ± 0.23 gN/(L·d) was maintained over 100 days operation. Total AnAOB population abundance (20.9%±4.9%) and AnAOB protein abundances (75.7% ± 3.3%) remained stable with decreased temperature. Key proteins of Ca. Brocadia for nitrogen metabolism, as well as for carbohydrate metabolism and primary metabolite biosynthesis were less expressed at 15 °C than 35 °C, while several proteins of heterotrophic Chloroflexi spp. involved in carbohydrate and metabolites metabolisms were expressed to a higher degree at 15 °C. Overall, metabolism of AnAOB responded at a higher degree to low temperatures than that of heterotrophs.

Genomic and Physiological Characteristics of a Novel Nitrite-Oxidizing Nitrospira Strain Isolated From a Drinking Water Treatment Plant.

Nitrite-oxidizing bacteria (NOB) catalyze the second step of nitrification, which is an important process of the biogeochemical nitrogen cycle and is exploited extensively as a biological nitrogen removal process. Members of the genus Nitrospira are often identified as the dominant NOB in a diverse range of natural and artificial environments. Additionally, a number of studies examining the distribution, abundance, and characterization of complete ammonia oxidation (comammox) Nitrospira support the ecological importance of the genus Nitrospira. However, niche differentiation between nitrite-oxidizing Nitrospira and comammox Nitrospira remains unknown due to a lack of pure cultures. In this study, we report the isolation, physiology, and genome of a novel nitrite-oxidizing Nitrospira strain isolated from a fixed-bed column at a drinking water treatment plant. Continuous feeding of ammonia led to the enrichment of Nitrospira-like cells, as well as members of ammonia-oxidizing genus Nitrosomonas. Subsequently, a microcolony sorting technique was used to isolate a novel nitrite-oxidizing Nitrospira strain. Sequences of strains showing the growth of microcolonies in microtiter plates were checked. Consequently, the most abundant operational taxonomic unit (OTU) exhibited high sequence similarity with Nitrospira japonica (98%) at the 16S rRNA gene level. The two other Nitrospira OTUs shared over 99% sequence similarities with N. japonica and Nitrospira sp. strain GC86. Only one strain identified as Nitrospira was successfully subcultivated and designated as Nitrospira sp. strain KM1 with high sequence similarity with N. japonica (98%). The half saturation constant for nitrite and the maximum nitrite oxidation rate of strain KM1 were orders of magnitude lower than the published data of other known Nitrospira strains; moreover, strain KM1 was more sensitive to free ammonia compared with previously isolated Nitrospira strains. Therefore, the new Nitrospira strain appears to be better adapted to oligotrophic environments compared with other known non-marine nitrite oxidizers. The complete genome of strain KM1 was 4,509,223 bp in length and contained 4,318 predicted coding sequences. Average nucleotide identities between strain KM1 and known cultured Nitrospira genome sequences are 76.7-78.4%, suggesting at least species-level novelty of the strain in the Nitrospira lineage II. These findings broaden knowledge of the ecophysiological diversity of nitrite-oxidizing Nitrospira.

Physiological and genomic characterization of a new 'Candidatus Nitrotoga' isolate.

Oxidation of nitrite to nitrate is an important process in the global nitrogen cycle. Recent molecular biology-based studies have revealed that the widespread nitrite-oxidizing bacteria (NOB) belonging to the genus 'Candidatus Nitrotoga' may be highly important for the environment. However, the insufficient availability of pure Nitrotoga cultures has limited our understanding of their physiological and genomic characteristics. Here, we isolated the 'Ca. Nitrotoga' sp. strain AM1P, from a previously enriched Nitrotoga culture, using an improved isolation strategy. Although 'Ca. Nitrotoga' have been recognized as cold-adapted NOB, the strain AM1P had a slightly higher optimum growth temperature at 23°C. Strain AM1P showed a pH optimum of 8.3 and was not inhibited even at high nitrite concentrations (20 mM). We obtained the complete genome of the strain and compared the genome profile to five previously sequenced 'Ca. Nitrotoga' strains. Comparative genomics suggested that lactate dehydrogenase may be only encoded in the strain AM1P and closely related genomes. While the growth yield of AM1P did not change, we observed faster growth in the presence of lactate in comparison to purely chemolithoautotrophic growth. The characterization of the new strain AM1P sheds light on the physiological adaptation of this environmentally important, but understudied genus 'Ca. Nitrotoga'.

Dynamics of Strontium and geochemically correlated elements in soil during washing remediation with eco-complaint chelators.

In the study, the dynamics of Sr2+ and geochemically correlated elements (Ca2+, Ba2+, and Y3+) in soil with chelators in the mix (soil to chelator ratio, 1:10; matrix, H2O) were assessed to understand chemical-induced washing remediation of radiogenic waste solids. Specifically, EDTA (2,2',2″,2‴-(ethane-1,2-diyldinitrilo)tetraacetic acid), EDDS (2-[2-(1,2-dicarboxyethylamino)ethylamino]butanedioic acid), GLDA (2-[bis(carboxymethyl)amino]pentanedioic acid), and HIDS (2-(1,2-dicarboxyethylamino)-3-hydroxy-butanedioic acid) are chelators that are used as extractants. The effect of solution pH on chelator-induced extractions of the target elements (t-Es: Sr2+, Ca2+, Ba2+, or Y3+) from soil and stability constants of the t-Es complexes with chelators were used to explain the trends and magnitudes in interactions. Pre- and post-extractive solid-phase speciation was used to define the extent of the competence of each chelator in persuading dissolution of t-Es in the soil. The effects of ultrasonic energy, admixtures of biodegradable chelators, and excess chelators in solution (1:20) were also analyzed on the extractive removal of t-Es from soil. The results indicate that the Sr2+ removal with biodegradable chelators significantly exceeded (approximately 70%) when compared to that of environmentally-persistent EDTA at lower solution pHs and a higher soil to chelator ratio (GLDA > HIDS > EDDS ≈ EDTA). However, the extraction of the geochemically related element was significantly lower.

Solution-mediated nanometric growth of α-Fe2O3 with electrocatalytic activity for water oxidation.

This paper describes a simple, low-temperature, and environmentally friendly aqueous route for the layer-by-layer nanometric growth of crystalline α-Fe2O3. The formation mechanism involves alternative sequences of the electrostatic adsorption of Fe2+ ions on the surface and the subsequent onsite oxidation to Fe3+. A combination analysis of X-ray diffraction, scanning electron microscopy, UV-Vis spectroscopy, and X-ray photoelectron spectroscopy revealed that α-Fe2O3 is directly formed without post-growth annealing via designed chemical reactions with a growth rate of ca. 1.7 nm per deposition cycle. The obtained α-Fe2O3 layer exhibits electrocatalytic activity for water oxidation and, at the same time, insignificant photo-electrocatalytic response, indicating its defective nature. The electrocatalytic activity was tailored by annealing up to 500 °C in air, where thermal diffusion of Sn4+ into the α-Fe2O3 lattice from the substrate probably provides an increased electrical conductivity. The subsequent surface-modification with Ni(OH)2 lowers the overpotential (250 mV at 0.5 mA cm-2) in a 1 M KOH solution. These findings open direct growth pathways to functional metal oxide nanolayers via liquid phase atomic layer deposition.

Draft Genome Sequence of Acidovorax sp. Strain NB1, Isolated from a Nitrite-Oxidizing Enrichment Culture.

Here, we report the draft genome sequence of Acidovorax sp. strain NB1, isolated from an enrichment culture of nitrite-oxidizing bacteria (NOB). Genes involved in denitrification were found in the draft genome of NB1. The closest strain to NB1 based on genomic relatedness is Acidovorax sp. strain GW101-3H11, with 91.5% average nucleotide identity.

Arsenic biotransformation potential of six marine diatom species: effect of temperature and salinity.

Temperature and salinity effects on marine diatom species growth has been studied extensively; however, their effect on arsenic (As) biotransformation has been imprecise. This study reports the growth, and As biotransformation and speciation patterns at various temperatures and salinities of six marine diatom species: Asteroplanus karianus, Thalassionema nitzschioides, Nitzschia longissima, Skeletonema sp., Ditylum brightwellii, and Chaetoceros didymus. The growth rate and As biotransformation potentials of these species during three weeks of culture in f/2 based medium were significantly affected by wide temperature (0-35 °C) and salinity (0.3-50‰) ranges. Growth and As biotransformation were higher at optimum temperatures of 10-25 °C, and salinity of 10-35‰, whereas growth and arsenic biotransformation were lower at <5 °C and 5‰ and >25 °C and 35‰, respectively. The results showed that As(V) to As(III) biotransformation differed significantly (p < 0.05) between day 10 and 17. At optimum temperature and salinity levels, the cell size and As biotransformation were higher for all the species. A conceptual model on temperature and salinity effects on growth and As uptake and biotransformation mechanisms by these species has been proposed based on the findings of this study.

Structural optimization of cyclic peptides that efficiently detect denatured collagen.

To develop a facile method for detecting denatured collagen, we investigated the structure-activity relationship of cyclic collagen-mimetic peptides (cCMPs). Reported cCMP prototypes tend to self-assemble and they must be disassembled just before use. Introducing charge repulsion and a deformation in the peptide backbone structure enabled cCMPs to detect denatured collagen without a pre-treatment for disassembly. Using the optimized cCMP, types I-V collagen were detected by western blotting and denatured collagen fibrils were visualized in a cell culture system.

Assessment of health risks associated with potentially toxic element contamination of soil by end-of-life ship dismantling in Bangladesh.

Ship breaking and recycling industry (SBRI) loops back scarce ferrous and non-ferrous materials from dismantled ships and also renews the global shipping fleet by treating the end-of-life (EoL) ships. Currently, SBRIs in Bangladesh, India, and Pakistan are dismantling the majority of the EoL ships by open beaching method. Accordingly, ship dismantling carries the blame of releasing potentially toxic elements (PTEs) to the coastal and marine environment risking the food chain through potential bioaccumulation and biomagnification. Health risk assessment associated with PTEs from open beach ship dismantling is scarce. This study aimed at assessing concentrations and seasonal variations of PTEs in soils exposed to the activities of SBRIs for their source apportionment by using contamination factor (CF) and multivariate statistical analysis, while carcinogenic and non-carcinogenic health risks due to the PTEs have also been determined. Soil samples were collected twice-during pre-monsoon and post-monsoon seasons-from three working zones of each of the 15 different ship breaking yards spanning the entire SBRI zone in Bangladesh. Soil contamination was assessed by using the CF, and inverse distance weighting interpolation mapping showed the spatial distribution of metals at SBRI zone in Bangladesh. Multivariate statistical analysis, principal component analysis, and correlation matrix yielded the source apportionment of PTEs. Subsequently, carcinogenic and non-carcinogenic health risks were assessed following the approach recommended by the United States Environmental Protection Agency (USEPA) with uncertainty estimation through Monte Carlo simulation. Contamination levels of PTEs followed Cd > Zn > Cr > Cu > Pb > Ni > Mn > As. Concentrations of Cd, Cr, Mn, and Zn were higher than the maximum allowable regulatory limits at storage zone and also higher as compared with the beaching and cutting zones in general. The contamination index indicated extreme Cd contamination in the area with elevated levels in pre-monsoon. Two principal components (PC) were identified-PC1 (Cd, Cu, Mn, Pb, Zn) and PC2 (As, Cr, Ni) inferring their source segmentation. Indirect soil ingestion is the major possible exposure path to PTEs. The health index indicated the absence of any obvious health effects on the people active at SBRI yards in Bangladesh. The carcinogenic risk was for 6 to 7 persons per 100,000 people which was within the USEPA acceptable range.

Chelator-induced recovery of rare earths from end-of-life fluorescent lamps with the aid of mechano-chemical energy.

Rare-earths (REs) are key components for the transition to a greener energy profile and low carbon society. The elements turn out to be of limited availability in the market, due to the supply-demand issues, exponential price rises, or geopolitics, which has led to a focus on the exploration of secondary sources for RE reclamation. End-of-life (EoL) nickel-metal hydride batteries, permanent magnets, and fluorescent lamps (FL) have been the primary sources for recyclable REs, while the recovery of REs in EoL FL (Ce, Eu, La, Tb, or Y) includes comparatively fewer processing steps than the other potential sources. In the current work, we proposed a simple, energy-efficient protocol for EoL FL processing, using chelators in combination with ball milling. The parameters for optimum chelator-assisted recovery (chelator concentration, solid-to-liquid ratio, solution pH), and milling variables (ball size, ball weight, milling speed, milling duration), were evaluated at room temperature (RT, 25 ±â€¯2 °C). The dissolution of REs with ethylenediaminetetraacetic acid (EDTA), ethylenediaminedisuccinic acid, methylglycinediacetic Acid, or 3-hydroxy-2,2'-iminodisuccinic acid, was compared at RT, while EDTA was used as the reference chelator throughout. Increasing the system temperature from 25 to 135 °C achieved at least double Eu and Y recovery, relative to that at RT, whereas the recovery rate improvement for Ce, La or Tb was insignificant. Mechano-chemical treatment at RT, via wet milling of EoL FL, with chelators, yielded a five order of magnitude increase in Ce, La and Tb recovery, however, plus a two-order increase for Eu or Y, compared with non-abetted operating conditions. It was also found that higher impact energy achieved improved recovery over a reduced milling duration with this technique having the added advantage of minimal acid consumption and reduced effluent production.

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 (Km ) 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.

Synthesis and characterization of monodispersed polymer/polydiacetylene nanocrystal composite particles.

Monodispersed polymer/polydiacetylenecomposite particles were synthesized by soap-free seeded emulsion polymerization of styrene andmethyl methacrylate; the products were characterized by XRD, SEM, TEM, UV-visible spectroscopy, and single particle scattering spectroscopy. In the synthesis process, polydiacetylene nanocrystals were found to act as inhibitor, and consequently a relatively low concentration was necessary. Different monomers lead to the differences in reaction condition and particle morphology; the PMMA composite particles were simpler in preparation than polystyrene particles, but the latter havebetter spherical morphology. The composite particles were composed of polymer shells and polydiacetylene cores, which kept their crystal structure and optical properties. A high percentage of cored particles could be achieved with optimized reaction conditions where the amount of seed was sufficient and the oily oligomer by-product was suppressed.