Acidity constants and redox potentials of uranyl ions in hydrothermal solutions

Acknowledgements We thank Matthias Krack for supplying us with the pseudopotential and basis sets for U. We acknowledge the National Science Foundation of China (No. 41222015, 41273074, 41572027 and 21373166), Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase), the Foundation for the Author of National Excellent Doctoral Dissertation of PR China (No. 201228), Newton International Fellowship Program and the financial support from the State Key Laboratory at Nanjing University. We are grateful to the High Performance Computing Center of Nanjing University for allowing us to use the IBM Blade cluster system. Open access via RSC Gold 4 Gold.Peer reviewedPublisher PD

Redox potentials of aryl derivatives from hybrid functional based first principles molecular dynamics

Acknowledgements We acknowledge the National Science Foundation of China (No. 41222015, 41273074, 41572027 and 21373166), Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase), the Foundation for the Author of National Excellent Doctoral Dissertation of P. R. China (No. 201228), Newton International Fellowship Program and the financial support from the State Key Laboratory at Nanjing University. We are grateful to the High Performance Computing Center of Nanjing University for allowing us to use the IBM Blade cluster system. Open access via RSC Gold for GoldPeer reviewedPublisher PD

Acidity of edge surface sites of montmorillonite and kaolinite

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Examining geodetic glacier mass balance in the eastern Pamir transition zone

This research was supported by the Key Research Program of Frontier Sciences CAS [QYZDY-SSW-DQC026] and the National Natural Science Foundation of China [41590853]. SRTM DEM and NASA HMA DEM data were sourced from NASA Earthdata (https://earthdata.nasa.gov/), and the ALOS Global Digital Surface Model (AW3D30) was sourced from JAXA (https://www.eorc.jaxa.jp/ALOS/en/aw3d30/index.htm). ALOS PRISM level-1B1 products were ordered from http://en.alos-pasco.com/alos/prism/ under a 4th ALOS RA data grant awarded to Quincey (PI No. 1008). Landsat-7 and Landsat-8 images can be freely downloaded from http://glovis.usgs.gov. Randolph Glacier Inventory data were acquired from Global Land Ice Measurements from Space (GLIMS) (RGI Consortium, 2017). Lv acknowledges program B for outstanding PhD candidates of Nanjing University and the support from the Chinese Scholarship Council (CSC) for studying at the University of Leeds.Glaciers in the eastern Pamir have reportedly been gaining mass during recent decades, even though glaciers in most other regions in High Mountain Asia have been in recession. Questions still remain about whether the trend is strengthening or weakening, and how far the positive balances extend into the eastern Pamir. To address these gaps, we use three different digital elevation models to reconstruct glacier surface elevation changes over two periods (2000–09 and 2000–15/16). We characterize the eastern Pamir as a zone of transition from positive to negative mass balance with the boundary lying at the northern end of Kongur Tagh, and find that glaciers situated at higher elevations are those with the most positive balances. Most (67% of 55) glaciers displayed a net mass gain since the 21st century. This led to an increasing regional geodetic glacier mass balance from −0.06 ± 0.16 m w.e. a−1 in 2000–09 to 0.06 ± 0.04 m w.e. a−1 in 2000–15/16. Surge-type glaciers, which are prevalent in the eastern Pamir, showed fluctuations in mass balance on an individual scale during and after surges, but no statistical difference compared to non-surge-type glaciers when aggregated across the region.Publisher PDFPeer reviewe

Chromosomal DNA deletion confers phage resistance to Pseudomonas aeruginosa.

Bacteria develop a broad range of phage resistance mechanisms, such as prevention of phage adsorption and CRISPR/Cas system, to survive phage predation. In this study, Pseudomonas aeruginosa PA1 strain was infected with lytic phage PaP1, and phage-resistant mutants were selected. A high percentage (~30%) of these mutants displayed red pigmentation phenotype (Red mutant). Through comparative genomic analysis, one Red mutant PA1r was found to have a 219.6 kb genomic fragment deletion, which contains two key genes hmgA and galU related to the observed phenotypes. Deletion of hmgA resulted in the accumulation of a red compound homogentisic acid; while A galU mutant is devoid of O-antigen, which is required for phage adsorption. Intriguingly, while the loss of galU conferred phage resistance, it significantly attenuated PA1r in a mouse infection experiment. Our study revealed a novel phage resistance mechanism via chromosomal DNA deletion in P. aeruginosa

Vertical distribution of Fe, P and correlation with organic carbon in coastal sediments of Yellow Sea, Eastern China

The coastal zone is considered as a major carbon pool. Iron minerals and phosphates are vital factors affecting the amounts and occurrence of total organic carbon (TOC) in sediments. However, coupling mechanisms of iron (Fe) and phosphorous (P) in the source-sink transition of TOC in coastal sediments is poorly understood. This study characterized the distribution of Fe, P and TOC contents of three independent 170 cm sediment cores sampled from a coastal aquaculture area in the eastern Jiangsu Province, and quantified the correlations among Fe, P, median grain diameter (Dx(50)), and TOC. The results showed total phosphorus (TP) content ranges in a scope of 337.4-578.0 mg/kg, and many depths recorded moderate P eutrophication. Inorganic phosphorus (DA + IP) and biogenic apatite were the primary components of TP, accounting for 25.19–55.00 and 26.71–49.62%, respectively. The Fe contents varied from 987.9 mg/kg to 2900.7 mg/kg, in which oxidized iron (Feox) accounted for about 62.2–79.4%. In the vertical profile, the TOC was positively correlated with the contents of low-crystallinity Fe-bearing carbonates (Fecarb), high crystallinity pyrite (FePy), iron-bound phosphorus (PCDB), manganeses (Mn), and nitrogen (N), while it was negatively correlated with DA + IP, organic phosphorus (OP), and Dx(50). Based on the the partial least squares (PLS) model, we proposed that the higher FePy, Mn, magnetite (FeMag), Fecarb, PCDB, amorphous exchangeable Fe (Ex-Fe), and authigenic apatite phosphorus (Bio-P) in sediments represent the high capacity for TOC sink, whereas, higher DA + IP, and OP indicate a TOC conversion to the source. The non-siginificat indication of Feox on TOC source-sink is due to its surplus and strong reactivity relative to TOC content. These revealed correlations provide a theoretical reference for understanding and regulating the burial rate and storage of TOC by changing the input of Fe minerals and P components into coastal sediments

Characterization and Genomic Analyses of Pseudomonas aeruginosa Podovirus TC6: Establishment of Genus Pa11virus

Phages have attracted a renewed interest as alternative to chemical antibiotics. Although the number of phages is 10-fold higher than that of bacteria, the number of genomically characterized phages is far less than that of bacteria. In this study, phage TC6, a novel lytic virus of Pseudomonas aeruginosa, was isolated and characterized. TC6 consists of an icosahedral head with a diameter of approximately 54 nm and a short tail with a length of about 17 nm, which are characteristics of the family Podoviridae. TC6 can lyse 86 out of 233 clinically isolated P. aeruginosa strains, thus showing application potentials for phage therapy. The linear double-stranded genomic DNA of TC6 consisted of 49796 base pairs and was predicted to contain 71 protein-coding genes. A total of 11 TC6 structural proteins were identified by mass spectrometry. Comparative analysis revealed that the P. aeruginosa phages TC6, O4, PA11, and IME180 shared high similarity at DNA sequence and proteome levels, among which PA11 was the first phage discovered and published. Meanwhile, these phages contain 54 core genes and have very close phylogenetic relationships, which distinguish them from other known phage genera. We therefore proposed that these four phages can be classified as Pa11virus, comprising a new phage genus of Podoviridae that infects Pseudomonas spp. The results of this work promoted our understanding of phage biology, classification, and diversity

Ecological networks of dissolved organic matter and microorganisms under global change

Microbes regulate the composition and turnover of organic matter. Here we developed a framework called Energy-Diversity-Trait integrative Analysis to quantify how dissolved organic matter and microbes interact along global change drivers of temperature and nutrient enrichment. Negative and positive interactions suggest decomposition and production processes of organic matter, respectively. We applied this framework to manipulative field experiments on mountainsides in subarctic and subtropical climates. In both climates, negative interactions of bipartite networks were more specialized than positive interactions, showing fewer interactions between chemical molecules and bacterial taxa. Nutrient enrichment promoted specialization of positive interactions, but decreased specialization of negative interactions, indicating that organic matter was more vulnerable to decomposition by a greater range of bacteria, particularly at warmer temperatures in the subtropical climate. These two global change drivers influenced specialization of negative interactions most strongly via molecular traits, while molecular traits and bacterial diversity similarly affected specialization of positive interactions. Microbes are intimately linked with the fate of organic matter. Here the authors develop an ecological network framework and show how microbes and dissolved organic matter interact along global change drivers of temperature and nutrient enrichment via manipulative field experiments on mountains.Peer reviewe

Mediation of Extracellular Polymeric Substances in Microbial Reduction of Hematite by Shewanella oneidensis MR-1

Extracellular electron transfer (EET) plays a fundamental role in microbial reduction/oxidation of minerals. Extracellular polymeric substances (EPS) surrounding the cells constitute a matrix that separates the cell’s outer membrane from insoluble minerals and environmental fluid. This study investigated the effects of EPS on EET processes during microbial reduction of hematite by the iron-reducing strain Shewanella oneidensis MR-1 (MR-1). Electrochemical characterization techniques were employed to determine the influence of EPS components on the redox ability of MR-1. Cells with removed EPS exhibited approximately 30% higher hematite reduction than regular MR-1 cells, and produced a current density of 56 μA cm-2, corresponding to 3–4 fold that of regular MR-1. The superior EET of EPS-deprived cells could be attributed to direct contact between outer membrane proteins and hematite surface, as indicated by more redox peaks being detected by cyclic voltammetry and differential pulse voltammetry. The significantly reduced current density of MR-1 cells treated with proteinase K and deoxyribonuclease suggests that the electron transfer capacity across the EPS layer depends mainly on the spatial distribution of specific proteins and electron shuttles. Exopolysaccharides in EPS tend to inhibit electron transfer, however they also favor the attachment of cells onto hematite surfaces. Consistently, the charge transfer resistance of cells lacking EPS was only 116.3 Ω, approximately 44 times lower than that of regular cells (5,139.1 Ω). These findings point to a negative influence of EPS on EET processes for microbial reduction/oxidation of minerals

bifA Regulates Biofilm Development of Pseudomonas putida MnB1 as a Primary Response to H2O2 and Mn2+

Pseudomonas putida (P. putida) MnB1 is a widely used model strain in environment science and technology for determining microbial manganese oxidation. Numerous studies have demonstrated that the growth and metabolism of P. putida MnB1 are influenced by various environmental factors. In this study, we investigated the effects of hydrogen peroxide (H2O2) and manganese (Mn2+) on proliferation, Mn2+ acquisition, anti-oxidative system, and biofilm formation of P. putida MnB1. The related orthologs of 4 genes, mco, mntABC, sod, and bifA, were amplified from P. putida GB1 and their involvement were assayed, respectively. We found that P. putida MnB1 degraded H2O2, and quickly recovered for proliferation, but its intracellular oxidative stress state was maintained, with rapid biofilm formation after H2O2 depletion. The data from mco, mntABC, sod and bifA expression levels by qRT-PCR, elucidated a sensitivity toward bifA-mediated biofilm formation, in contrary to intracellular anti-oxidative system under H2O2 exposure. Meanwhile, Mn2+ ion supply inhibited biofilm formation of P. putida MnB1. The expression pattern of these genes showed that Mn2+ ion supply likely functioned to modulate biofilm formation rather than only acting as nutrient substrate for P. putida MnB1. Furthermore, blockade of BifA activity by GTP increased the formation and development of biofilms during H2O2 exposure, while converse response to Mn2+ ion supply was evident. These distinct cellular responses to H2O2 and Mn2+ provide insights on the common mechanism by which environmental microorganisms may be protected from exogenous factors. We postulate that BifA-mediated biofilm formation but not intracellular anti-oxidative system may be a primary protective strategy adopted by P. putida MnB1. These findings will highlight the understanding of microbial adaptation mechanisms to distinct environmental stresses