Investigating bacterial coupled assimilation of fertilizer­nitrogen and crop residue­carbon in upland soils by DNA-qSIP.

Microbial immobilization of fertilizer nitrogen (N) can effectively reduce N losses in soil. However, the effects of crop residue on microbial assimilation of fertilizer-N and the underlying microbial mechanisms in upland soils are unclear. We evaluated the influence of maize residue (13C) addition on the microbial assimilation of ammonium-N (15N) in DNA from fertilizer, and quantified the bacterial 13C or 15N assimilation by quantitative stable isotope probing (DNA-qSIP). We found that the straw addition did increase total microbial assimilation of ammonium from fertilizer during the 2-week incubation. However, bacterial taxa varied in their responses to straw addition: Bacteriodetes and Proteobacteria accounted for large fractions of ammonium assimilation and their N assimilations were increased, while N assimilations of Acidobacteria were decreased. We revealed that highly 13C-labeled taxa were the main contributors of N assimilation under straw addition. The straw primarily enhanced the contributions of bacterial taxa to ammonium assimilation through increasing the extent of N assimilation, or enhancing the abundance of the N-assimilating bacterial taxa. Overall, our study elucidated an interaction between microbial assimilation of fertilizer-N and straw-C, showing a close element coupling of the keystone functional microbial taxa in N immobilization driven by organic carbon.

3D Nanoscale Mapping of Short-Range Order in GeSn Alloys.

GeSn on Si has attracted much research interest due to its tunable direct bandgap for mid-infrared applications. Recently, short-range order (SRO) in GeSn alloys has been theoretically predicted, which profoundly impacts the band structure. However, characterizing SRO in GeSn is challenging. Guided by physics-informed Poisson statistical analyses of k-nearest neighbors (KNN) in atom probe tomography (APT), a new approach is demonstrated here for 3D nanoscale SRO mapping and semi-quantitative strain mapping in GeSn. For GeSn with ≈14 at. % Sn, the SRO parameters of Sn-Sn 1NN in 10 × 10 × 10 nm3 nanocubes can deviate from that of the random alloys by ±15 %. The relatively large fluctuation of the SRO parameters contributes to band-edge softening observed optically. Sn-Sn 1NN also tends to be more favored toward the surface, less favored under strain relaxation or tensile strain, while almost independent of local Sn composition. An algorithm based on least square fit of atomic positions further verifies this Poisson-KNN statistical method. Compared to existing macroscopic spectroscopy or electron microscopy techniques, this new APT statistical analysis uniquely offers 3D SRO mapping at nanoscale resolution in a relatively large volume with millions of atoms. It can also be extended to investigate SRO in other alloy systems.

Decomposition of Microbial Necromass Is Divergent at the Individual Taxonomic Level in Soil.

The turnover of microbial biomass plays an important part in providing a significant source of carbon (C) to soil organic C. However, whether the decomposition of microbial necromass (non-living microbial biomass) in the soil varies at the individual taxa level remains largely unknown. To fill up these gaps, we compared the necromass decomposition of bacterial and archaeal taxa by separating live microbial biomass with 18O-stable isotope probing from dead microbial biomass in soil. Our results showed that most of the microbial necromass at the operational taxonomic unit level (88.51%), which mainly belong to Acidobacteria, Actinobacteria, Gemmatimonadetes, and Proteobacteria, decomposed significantly after 30 days. In addition, there were great variations in necromass decomposition within each phylum, such as the decomposition of operational taxonomic units in Proteobacteria that ranged from 51% (Beijerinckia) to 92% (Nitrosospira). More importantly, the necromass decomposition was not related to the chemical composition of the cell wall but might positively correlate with the guanine-cytosine content of DNA and negatively correlated with genome size. This study provided a new insight that the decomposition of microbial necromass in soil was divergent at the individual taxonomic level and could not be fully explained by previously proposed mechanisms.

Rewritable color nanoprints in antimony trisulfide films.

Materials that exhibit large and rapid switching of their optical properties in the visible spectrum hold the key to color-changing devices. Antimony trisulfide (Sb2S3) is a chalcogenide material that exhibits large refractive index changes of ~1 between crystalline and amorphous states. However, little is known about its ability to endure multiple switching cycles, its capacity for recording high-resolution patterns, nor the optical properties of the crystallized state. Unexpectedly, we show that crystalline Sb2S3 films that are just 20 nm thick can produce substantial birefringent phase retardation. We also report a high-speed rewritable patterning approach at subdiffraction resolutions (>40,000 dpi) using 780-nm femtosecond laser pulses. Partial reamorphization is demonstrated and then used to write and erase multiple microscale color images with a wide range of colors over a ~120-nm band in the visible spectrum. These solid-state, rapid-switching, and ultrahigh-resolution color-changing devices could find applications in nonvolatile ultrathin displays.

Large-Area Silver-Stibnite Nanoporous Plasmonic Films for Label-Free Biosensing.

The development of various plasmonic nanoporous materials has attracted much interest in different areas of research including bioengineering and biosensing because of their large surface area and versatile porous structure. Here, we introduce a novel technique for fabricating silver-stibnite nanoporous plasmonic films. Unlike conventional techniques that are usually used to fabricate nanoporous plasmonic films, we use a room-temperature growth method that is wet-chemistry free, which enables wafer-scale fabrication of nanoporous films on flexible substrates. We show the existence of propagating surface plasmon polaritons in nanoporous films and demonstrate the extreme bulk refractive index sensitivity of the films using the Goos-Hänchen shift interrogation scheme. In the proof-of-concept biosensing experiments, we functionalize the nanoporous films with biotin-thiol using a modified functionalization technique, to capture streptavidin. The fractal nature of the films increases the overlap between the local field and the immobilized biomolecules. The extreme sensitivity of the Goos-Hänchen shift allows femtomolar concentrations of streptavidin to be detected in real time, which is unprecedented using surface plasmons excited via the Kretschmann configuration.

Warming deferentially altered multidimensional soil legacy induced by past land use history.

The legacy effects of previous land use and climate history may affect current soil function. However, the manner in which these legacy effects of land use are modulated by the subsequent climate remains unclear. For this reason, we investigated how the legacies of soil multiple functions left by conversion of grassland to agricultural management were mediated by climate warming with a reciprocal transplant approach. The overall legacy was further separated into the contributions by changes in the abiotic properties of the soil (abiotic process) and microbial community (biotic process). We here hypothesized that warming may mediate the legacy effects of previous land use, mainly by changing biotic processes. Results indicated that warming significantly influenced the total legacies of soil respiration and three exoenzyme activities representing recalcitrant carbon, nitrogen, and phosphorus cycling, but did not affect the total legacy of ß-1,4-glucosidase activity, which is involved in labile carbon cycling. The relative contributions of abiotic and biotic processes to the warming effects on the total legacy depended on the type of soil function. The effects of warming on land use change legacies were derived from altered bacterial community structure. The results of the present study suggest that climate conditions could interact with land use legacy to determine the ecosystem functions in a process-specific way.

Effects of pyrite and sphalerite on population compositions, dynamics and copper extraction efficiency in chalcopyrite bioleaching process.

This study used an artificial microbial community with four known moderately thermophilic acidophiles (three bacteria including Acidithiobacillus caldus S1, Sulfobacillus thermosulfidooxidans ST and Leptospirillum ferriphilum YSK, and one archaea, Ferroplasma thermophilum L1) to explore the variation of microbial community structure, composition, dynamics and function (e.g., copper extraction efficiency) in chalcopyrite bioleaching (C) systems with additions of pyrite (CP) or sphalerite (CS). The community compositions and dynamics in the solution and on the ore surface were investigated by real-time quantitative PCR (qPCR). The results showed that the addition of pyrite or sphalerite changed the microbial community composition and dynamics dramatically during the chalcopyrite bioleaching process. For example, A. caldus (above 60%) was the dominant species at the initial stage in three groups, and at the middle stage, still dominated C group (above 70%), but it was replaced by L. ferriphilum (above 60%) in CP and CS groups; at the final stage, L. ferriphilum dominated C group, while F. thermophilum dominated CP group on the ore surface. Furthermore, the additions of pyrite or sphalerite both made the increase of redox potential (ORP) and the concentrations of Fe3+ and H+, which would affect the microbial community compositions and copper extraction efficiency. Additionally, pyrite could enhance copper extraction efficiency (e.g., improving around 13.2% on day 6) during chalcopyrite bioleaching; on the contrary, sphalerite restrained it.

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics.

Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes. We found no obvious intraspecific divergence with respect to predicted genes that are related to central metabolism and stress management strategies between these two groups. Although numerous highly homogeneous genes were observed, high genetic diversity was also detected. Preliminary inspection provided a first glimpse of the potential correlation between intraspecific diversity at the genome level and environmental variation, especially geochemical conditions. Evolutionary genetic analyses further showed evidence that the difference in environmental conditions might be a crucial factor to drive the divergent evolution of A. caldus species. We identified a diverse pool of mobile genetic elements including insertion sequences and genomic islands, which suggests a high frequency of genetic exchange in these harsh habitats. Comprehensive analysis revealed that gene gains and losses were both dominant evolutionary forces that directed the genomic diversification of A. caldus species. For instance, horizontal gene transfer and gene duplication events in group 2 strains might contribute to an increase in microbial DNA content and novel functions. Moreover, genomes undergo extensive changes in group 1 strains such as removal of potential non-functional DNA, which results in the formation of compact and streamlined genomes. Taken together, the findings presented herein show highly frequent gene turnover of A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles.

Comparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus.

Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 âˆ¼ 87.9 %), while Leptospirillum (48.6 âˆ¼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system.

This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2%, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.

A zero density change phase change memory material: GeTe-O structural characteristics upon crystallisation.

Oxygen-doped germanium telluride phase change materials are proposed for high temperature applications. Up to 8 at.% oxygen is readily incorporated into GeTe, causing an increased crystallisation temperature and activation energy. The rhombohedral structure of the GeTe crystal is preserved in the oxygen doped films. For higher oxygen concentrations the material is found to phase separate into GeO2 and TeO2, which inhibits the technologically useful abrupt change in properties. Increasing the oxygen content in GeTe-O reduces the difference in film thickness and mass density between the amorphous and crystalline states. For oxygen concentrations between 5 and 6 at.%, the amorphous material and the crystalline material have the same density. Above 6 at.% O doping, crystallisation exhibits an anomalous density change, where the volume of the crystalline state is larger than that of the amorphous. The high thermal stability and zero-density change characteristic of Oxygen-incorporated GeTe, is recommended for efficient and low stress phase change memory devices that may operate at elevated temperatures.

Monodispersed sulfur nanoparticles for lithium-sulfur batteries with theoretical performance.

While Li-S batteries are poised to be the next generation high-density energy storage devices, low sulfur utilization and slow rate performance have limited their practical applications. Here, we report the synthesis of monodispersed S8 nanoparticles (NPs) with different diameter and the nanosize dependent kinetic characteristics of the corresponding Li-S batteries. Most remarkably, 5 nm S NPs display the theoretical discharging/charging capacity of 1672 mAh g(-1) at 0.1 C rate and a discharge capacity of 1089 mAh g(-1) at 4 C.

Sulfur-amine chemistry-based synthesis of multi-walled carbon nanotube-sulfur composites for high performance Li-S batteries.

We report a sulfur-amine chemistry-based method to prepare multi-walled carbon nanotube-sulfur (MWNT-S) composites in a highly efficient and quantitative manner. The resulting MWNT-S composites exhibit excellent cycling stability at up to 400 cycles, with high sulfur loading. Developing this method also increases the number of research routes that could be pursued with respect to Li-S batteries.

Si/PEDOT hybrid core/shell nanowire arrays as photoelectrodes for photoelectrochemical water-splitting.

Si/poly(3,4-ethylenedioxythiophene) (PEDOT) core/shell nanowire arrays have been prepared by chemical etching of Si nanowires followed by vapor-phase polymerization of PEDOT as hybrid photoanodes for photoelectrochemical water-splitting. The PEDOT layer is employed as a multi-functional coating to prevent photocorrosion of Si nanowires, collect photogenerated holes and catalyze the water oxidation reaction. The amino silane modified Si nanowire surface improves PEDOT layer adhesion, and the resulting photoanode exhibits better photoresponse and improved stability. By tuning the length of the nanowires, we identify that the competition between the carrier recombination and catalytic water oxidation reaction is the primary factor determining the photoelectrocatalytic activity of the hybrid photoanode.

Ultrafine sulfur nanoparticles in conducting polymer shell as cathode materials for high performance lithium/sulfur batteries.

We report the synthesis of ultrafine S nanoparticles with diameter 10 ~ 20 nm via a membrane-assisted precipitation technique. The S nanoparticles were then coated with conducting poly (3,4-ethylenedioxythiophene) (PEDOT) to form S/PEDOT core/shell nanoparticles. The ultrasmall size of S nanoparticles facilitates the electrical conduction and improves sulfur utilization. The encapsulation of conducting PEDOT shell restricts the polysulfides diffusion, alleviates self-discharging and the shuttle effect, and thus enhances the cycling stability. The resulting S/PEDOT core/shell nanoparticles show initial discharge capacity of 1117 mAh g(-1) and a stable capacity of 930 mAh g(-1) after 50 cycles.