Methanotrophic abundance and community fingerprint in pine and tea plantation soils as revealed by molecular methods

Understanding the community structure of methane-oxidizing bacteria (methanotrophs) is important to assess the microbial oxidation of the greenhouse gas methane (CH4) in soil under different land uses. Soil samples were collected from two plantation plots of pine and tea in southern China. Methanotrophic abundance was quantified with quantitative real-time polymerase chain reaction (qPCR) based on the 16S rRNA and pmoA genes, and the community fingerprint was characterized with denaturing gradient gel electrophoresis (DGGE) targeting the pmoA gene. No significant difference in the gene copy numbers of methanotrophs was found between the pine and tea land-use, regardless of 16S rRNA and pmoA genes. Higher abundance of type I (1.35 vs 1.66×108 copie g-1 soil) over type II methanotrophs (8.59 vs 10.9 × 107) were found both in pine and tea plantation soils. Apparent differences in methanotrophic community fingerprint were observed between the pine and tea treatments. Correlations analysis between methanotrophic abundance and soil characteristics, combining with canonial correspondence analysis (CCA) regarding community fingerprint and environmental parameters indicated that soil pH and available phosphorus were the most important factors potentially affecting the methanotrophic community diversity in the acidic red soil.Key words: Denaturing gradient gel electrophoresis (DGGE), land use, methanotrophs, pmoA gene, quantitative real-time PCR (qPCR)

A review of ammonia-oxidizing bacteria and archaea in Chinese soils

Ammonia (NH3) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing) methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizer in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N2O) emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA

AOB Nitrosospira cluster 3a.2 (D11) dominates N2O emissions in fertilised agricultural soils.

CRediT authorship contribution statement Na Deng: Writing – review & editing, Methodology, Investigation, Data curation. Cecile Gubry-Rangin: Writing – review & editing, Methodology, Conceptualization. Xiao-Tong Song: Writing – review & editing, Methodology, Data curation. Xiao-Tang Ju: Writing – review & editing, Conceptualization. Si-Yi Liu: Methodology, Data curation. Ju-Pei Shen: Writing – review & editing, Data curation. Hong-jie Di: Writing – review & editing. Li-Li Han: Writing – review & editing, Methodology. Li-Mei Zhang: Writing – review & editing, Methodology, Data curation, Conceptualization.Peer reviewe

AHRNet: Attention and heatmap-based regressor for hand pose estimation and mesh recovery

Estimating 3D hand pose and recovering the full hand surface mesh from a single RGB image is a challenging task due to self-occlusions, viewpoint changes, and the complexity of hand articulations. In this paper, we propose a novel framework that combines an attention mechanism with heatmap regression to accurately and efficiently predict 3D joint locations and reconstruct the hand mesh. We adopt a pooling attention module that learns to focus on relevant regions in the input image to extract better features for handling occlusions, while greatly reducing the computational cost. The multi-scale 2D heatmaps provide spatial constraints to guide the 3D vertex predictions. By exploiting the complementary strengths of sparse 2D supervision and dense mesh regression, our method accurately reconstructs hand meshes with realistic details. Extensive experiments on standard benchmarks demonstrate that the proposed method efficiently improves the performance of 3D hand pose estimation and mesh recovery. The reproducible recipes are available at https://github.com/SDiannn/AHRNET-Heatmap

Primary succession of nitrogen cycling microbial communities along the deglaciated forelands of Tianshan Mountain, China

Structural succession and its driving factors for nitrogen (N) cycling microbial communities during the early stages of soil development (0-44 years) were studied along a chronosequence in the glacial forelands of the Tianshan Mountain No.1 glacier in the arid and semi-arid region of central Asia. We assessed the abundance and population of functional genes affiliated with N-fixation (nifH), nitrification (bacterial and archaeal amoA), and denitrification (nirK/S and nosZ) in a glacier foreland using molecular methods. The abundance of functional genes significantly increased with soil development. N cycling community compositions were also significantly shifted within 44 years and were structured by successional age. Cyanobacterial nifH gene sequences were the most dominant N fixing bacteria and its relative abundance increased from 56.8-93.2% along the chronosequence. Ammonia-oxidizing communities shifted from the Nitrososphaera cluster (AOA-amoA) and the Nitrosospira cluster ME (AOB-aomA) in younger soils (0 and 5 years) to communities dominated by soil and sediment 1 (AOA-amoA) and Nitrosospira Cluster 2 Related (AOB-aomA) in older soils (=17 years). Most of the denitrifers closest relatives were potential aerobic denitrifying bacteria, and some other types of denitrifying bacteria (like autotrophic nitrate-reducing, sulfide-oxidizing bacteria and denitrifying phosphorus removing bacteria) were also detected in all soil samples. The regression analysis showed that N cycling microbial communities were dominant in younger soils (0-5 years) and significantly correlated with soil total carbon, while communities that were most abundant in older soils were significantly correlated with soil total nitrogen. These results suggested that the shift of soil C and N contents during the glacial retreat significantly influenced the abundance, composition and diversity of N cycling microbial communities. © 2016 Zeng, Lou, Zhang, Wang, Hu, Shen, Zhang, Han, Zhang, Lin, Chalk and He

The cardiomyocyte disrupts pyrimidine biosynthesis in non-myocytes to regulate heart repair

Various populations of cells are recruited to the heart after cardiac injury, but little is known about whether cardiomyocytes directly regulate heart repair. Using a murine model of ischemic cardiac injury, we demonstrate that cardiomyocytes play a pivotal role in heart repair by regulating nucleotide metabolism and fates of nonmyocytes. Cardiac injury induced the expression of the ectonucleotidase ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which hydrolyzes extracellular ATP to form AMP. In response to AMP, cardiomyocytes released adenine and specific ribonucleosides that disrupted pyrimidine biosynthesis at the orotidine monophosphate (OMP) synthesis step and induced genotoxic stress and p53-mediated cell death of cycling nonmyocytes. As nonmyocytes are critical for heart repair, we showed that rescue of pyrimidine biosynthesis by administration of uridine or by genetic targeting of the ENPP1/AMP pathway enhanced repair after cardiac injury. We identified ENPP1 inhibitors using small molecule screening and showed that systemic administration of an ENPP1 inhibitor after heart injury rescued pyrimidine biosynthesis in nonmyocyte cells and augmented cardiac repair and postinfarct heart function. These observations demonstrate that the cardiac muscle cell regulates pyrimidine metabolism in nonmuscle cells by releasing adenine and specific nucleosides after heart injury and provide insight into how intercellular regulation of pyrimidine biosynthesis can be targeted and monitored for augmenting tissue repair

Synthesis and catalysis of chemically reduced metal–metalloid amorphous alloys

This is the published version. Copyright 2012 Royal Society of ChemistryAmorphous alloys structurally deviate from crystalline materials in that they possess unique short-range ordered and long-range disordered atomic arrangement. They are important catalytic materials due to their unique chemical and structural properties including broadly adjustable composition, structural homogeneity, and high concentration of coordinatively unsaturated sites. As chemically reduced metal–metalloid amorphous alloys exhibit excellent catalytic performance in applications such as efficient chemical production, energy conversion, and environmental remediation, there is an intense surge in interest in using them as catalytic materials. This critical review summarizes the progress in the study of the metal–metalloid amorphous alloy catalysts, mainly in recent decades, with special focus on their synthetic strategies and catalytic applications in petrochemical, fine chemical, energy, and environmental relevant reactions. The review is intended to be a valuable resource to researchers interested in these exciting catalytic materials. We concluded the review with some perspectives on the challenges and opportunities about the future developments of metal–metalloid amorphous alloy catalysts