Spatial variations and bioaccumulation of heavy metals in intertidal zone of the Yellow River estuary, China

Nine units in new-born intertidal zone of the Yellow River estuary, China were examined for concentrations of heavy metals (Pb, Cr, Cu, Zn and Ni) in sediments and plants. Heavy metal levels in surface sediments were in the order of Zn > Pb approximate to Cr > Cu approximate to Ni and generally increased in a seaward direction except for Z6 (Tamarix chinensis-Suaeda salsa zone) and Z7 (S. salsa-T. chinensis zone) units. Significant differences in metal concentrations of the 9 units were observed in the profiles (p < 0.01). Heavy metal levels in the shoots or roots of different plants decreased in the order of Zn > Cu > Pb > Ni > Cr and differed among plants or tissues. The roots at Z2 (Calamagrostis pseudophragmites zone), Z3 (Imperata cylindrical zone) and Z4 (Phramites australis zone) units accumulated greater metals than shoots [TFs (translocation factors) < 1], while the shoots at Z1 (Sparganium minimum-Potentilla supina zone), Z7 and Z8 (S. salsa zone) units accumulated greater metals than roots (TFs > 1), implying that intertidal plants showed different pathways in metal accumulation and internal transportation. Except for Pb, the concentrations of Cr, Cu, Zn and Ni in sediments were lower than the criteria of Class I recommended by the Environmental Quality Standard for Soils of China, Although heavy metal levels in intertidal zone were generally the lowest (Cr, Cu, Zn and Ni) or relatively moderate (Pb) compared with other estuaries or bays in Asia and Europe, high eco-toxic risk of Pb and Ni exposure still could be observed at Z4, Z6 and Z9 (mudflat zone) units. S. salsa was more suitable for the potential biomonitor or phytoremediation of all five heavy metals if intertidal sediments was seriously contaminated with increasing of pollutants loading in the Yellow River estuary. (C) 2014 Elsevier B.V. All rights reserved

Physiological and transcriptional responses of two contrasting Populus clones to nitrogen stress

The aim of this study was to reveal mechanisms responsible for nitrogen (N) stress in two contrasting Populus clones. Leaves of Nanlin 1388 (N stress-insensitive clone hybrids of Populus deltoides Bart.CV.aEuro...xaEuro...Populus euramericana (Dode) Guineir CV) and Nanlin 895 (N stress-sensitive clone hybrids of Populus deltoides Bart.CV.aEuro...xaEuro...Populus euramericana (Dode) Guineir CV) were harvested and analyzed. Different responses visible in photosynthesis, N and carbon contents, physiological traits, and chlorophyll were observed. The Solexa/Illumina's digital gene expression system was used to investigate differentially expressed miRNAs and mRNAs under N stress. Target profiling, and biological network and function analyses were also performed. Randomly selected mRNAs and miRNAs were validated by quantitative reverse transcription polymerase chain reaction. In all, 110 Nanlin 1388 and 122 Nanlin 895 miRNAs were differentially expressed, among which 34 and 23 miRNAs were newly found in the two clones, respectively. Under N stress, a total of 329 and 98 mRNAs were regulated in N stress-insensitive and -sensitive clones, respectively. Notably, the miR396 family and its regulated mRNAs were altered in both clones under N stress, while miR646 was regulated only in the N stress-insensitive clone (Nanlin 1388), and miR156, miR319 and miR393 in the N stress-sensitive clone (Nanlin 895). Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses also proved several clone-specific functions and pathways. These findings may be significant for understanding the genetic responses of Populus to N stress

Assessing adsorption of polycyclic aromatic hydrocarbons on Rhizopus oryzae cell wall components with water-methanol cosolvent model

The contribution of different fungal cell wall components in adsorption of polycyclic aromatic hydrocarbons (PAHs) is still unclear. We isolated Rhizopus oryzae cell walls components with sequential extraction, characterized functional groups with NEXAFS spectra, and determined partition coefficients of PAHs on cell walls and cell wall components with cosolvent model. Spectra of NEXAFS indicated that isolated cell walls components were featured with peaks at similar to 532.7 and similar to 534.5 eV energy. The lipid cosolvent partition coefficients were approximately one order of magnitude higher than the corresponding carbohydrate cosolvent partition coefficients. The partition coefficients for four tested carbohydrates varied at approximate 0.5 logarithmic units. Partition coefficients between biosorbents and water calculated based cosolvent models ranged from 0.8 to 4.2. The present study proved the importance of fungal cell wall components in adsorption of PAHs, and consequently the role of fungi in PAHs bioremediation. (C) 2015 Elsevier Inc. All rights reserved

Species-specific competition and N fertilization regulate non-structural carbohydrate contents in two Larix species

Non-structural carbohydrates (NSC) are critical to plant signaling, gene transcription, physiological processes, survival and growth. Previous studies have demonstrated that species differing in NSC contents have various responses to stressful environments. However, effects of intra- and interspecific competition or N fertilization on NSC have not been previously studied. We employed two coniferous tree species, Larix kaempferi and Larix olgensis, to investigate the effects of intra- and interspecific competition on NSC under two N supply levels, with and without N fertilization. N fertilization significantly promoted the growth rates, biomass accumulation, carbon isotope composition and N concentration of leaves of the two species. Competition patterns significantly affected the average root diameter. Interspecific competition tended to increase the specific root length and specific root tip density. Also, interspecific competition significantly increased the N concentration of leaves but declined their C:N ratio under no N fertilization (N) treatments. L. kaempferi greatly benefited from the presence of L. olgensis, particularly under N fertilization (N+) treatments. Competition patterns, N fertilization and their interactions promoted N and carbohydrate storage. Our results demonstrated that N was a crucial factor to drive and regulate carbon balance. Differences between species in carbohydrate metabolism may contribute to their coexistence or niche differentiation. (C) 2016 Elsevier B.V. All rights reserved

Expression and functional characterization of a gene associated with retinoid-interferon-induced mortality 19 (GRIM-19) from orange-spotted grouper (Epinephelus coioides)

GRIM-19 is a nuclear encoded subunit of complex I that has been implicated in apoptosis. The protein participates in multiple functions including the innate immune response. GRIM-19 has been studied in humans and other mammals; however, fish GRIM-19 has not been well characterized. In this study, a new GRIM-19 gene, EcGRIM-19, was isolated from the orange-spotted grouper (Epinephelus coioides) cDNA library, which was constructed following LPS treatment. EcGRIM-19 is a 582-bp gene that encodes a 144-amino acid protein. The gene is a true ortholog of mammalian GRIM-19. EcGRIM-19 exhibits ubiquitous and constitutive expression in the different tissues of the orange-spotted grouper. The expression levels of EcGRIM-19 are altered in the gill, spleen, kidney and liver after induction with LPS. The subcellular localization analysis demonstrated that the EcGRIM-19 protein is localized predominantly in the mitochondria. In addition, amino acids 30-50 of the protein are responsible for the mitochondrial localization of EcGRIM-19. The caspase assay demonstrated that the overexpression of GRIM-19 enhanced the cellular sensitivity to interferon(IFN)-beta- and retinoic acid (RA)-induced death in HeLa cells. The data presented in this study are important for further understanding the EcGRIM-19 gene function in fish. (c) 2012 Elsevier Ltd. All rights reserved.GRIM-19 is a nuclear encoded subunit of complex I that has been implicated in apoptosis. The protein participates in multiple functions including the innate immune response. GRIM-19 has been studied in humans and other mammals; however, fish GRIM-19 has not been well characterized. In this study, a new GRIM-19 gene, EcGRIM-19, was isolated from the orange-spotted grouper (Epinephelus coioides) cDNA library, which was constructed following LPS treatment. EcGRIM-19 is a 582-bp gene that encodes a 144-amino acid protein. The gene is a true ortholog of mammalian GRIM-19. EcGRIM-19 exhibits ubiquitous and constitutive expression in the different tissues of the orange-spotted grouper. The expression levels of EcGRIM-19 are altered in the gill, spleen, kidney and liver after induction with LPS. The subcellular localization analysis demonstrated that the EcGRIM-19 protein is localized predominantly in the mitochondria. In addition, amino acids 30-50 of the protein are responsible for the mitochondrial localization of EcGRIM-19. The caspase assay demonstrated that the overexpression of GRIM-19 enhanced the cellular sensitivity to interferon(IFN)-beta- and retinoic acid (RA)-induced death in HeLa cells. The data presented in this study are important for further understanding the EcGRIM-19 gene function in fish. (c) 2012 Elsevier Ltd. All rights reserved

Succinic acid production from duckweed (Landoltia punctata) hydrolysate by batch fermentation of Actinobacillus succinogenes GXAS137

Duckweed is potentially an ideal succinic acid (SA) feedstock due to its high proportion of starch and low lignin content. Pretreatment methods, substrate content and nitrogen source were investigated to enhance the bioconversion of duckweed to SA and to reduce the costs of production. Results showed that acid hydrolysis was an effective pretreatment method because of its high SA yield. The optimum substrate concentration was 140 g/L. The optimum substrate concentration was 140 g/L. Corn steep liquor powder could be considered a feasible and inexpensive alternative to yeast extract as a nitrogen source. Approximately 57.85 g/L of SA was produced when batch fermentation was conducted in a 1.3 L stirred bioreactor. Therefore, inexpensive duckweed can be a promising feedstock for the economical and efficient production of SA through fermentation by Actinobacillus succinogenes GXAS137. (C) 2016 Published by Elsevier Ltd

Reconstructed metagenomes reveal changes of microbial functional profiling during PAHs degradation along a rice (Oryza sativa) rhizosphere gradient

AimsThe response of microbial metagenome to polycyclic aromatic hydrocarbons (PAHs) degradation in the rice rhizosphere remains poorly understood. We investigated the spatial and temporal variations of microbial communities and reconstructed metagenomes along the rice rhizosphere gradient during PAHs degradation. Methods and ResultsThe experiment was performed in rhizoboxes, in which the rhizosphere region was divided into five 1-mm thick layers. Based on denaturant gradient gel electrophoresis profiling and sequencing of bacterial and archaeal 16S rRNA genes, predicted metagenomes were reconstructed. The microbial communities in the rice rhizosphere were influenced by the PAHs concentration and distance from the root surface during PAHs degradation. Correlation network analysis showed that archaea played an important role in PAHs degradation. Predicted metagenomes can be clustered into two groups with high and low PAHs degrading potential, respectively. The relative abundance of genes for defense mechanisms, replication, recombination and reparation was significantly higher in samples with high PAHs degrading potentials. The relative abundance of the dioxygenase gene was greater near the root surface of the rice. However, the abundance of aldolase and dehydrogenase was constant in rhizosphere soils at different distances from the root surface. ConclusionsDistance from root surface and PAH concentrations affected the microbial communities and metagenomes in rice rhizosphere. The abundance of dioxygenase genes relating to PAH degradation in metagenomes mirrored the PAH degradation potential in rice rhizosphere. Significance and Impact of the StudyOur findings suggested that the predicted metagenomes reconstructed from 16S rRNA marker gene sequences provide further insights into the spatial variation and dynamics of microbial functioning that occur during bioremediation