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Soil biochemistry

Rafael Moreno-Sánchez, Sara Rodríguez-Enríquez, Ricardo Jasso-Chávez, Emma Saavedra, Jorge D García-García
Free-living microorganisms may become suitable models for removal of heavy metals from polluted water bodies, sediments, and soils by using and enhancing their metal accumulating abilities. The available research data indicate that protists of the genus Euglena are a highly promising group of microorganisms to be used in bio-remediation of heavy metal-polluted aerobic and anaerobic acidic aquatic environments. This chapter analyzes the variety of biochemical mechanisms evolved in E. gracilis to resist, accumulate and remove heavy metals from the environment, being the most relevant those involving (1) adsorption to the external cell pellicle; (2) intracellular binding by glutathione and glutathione polymers, and their further compartmentalization as heavy metal-complexes into chloroplasts and mitochondria; (3) polyphosphate biosynthesis; and (4) secretion of organic acids...
2017: Advances in Experimental Medicine and Biology
Carla Maldonado, Christopher J Barnes, Claus Cornett, Else Holmfred, Steen H Hansen, Claes Persson, Alexandre Antonelli, Nina Rønsted
Considerable inter- and intraspecific variation with respect to the quantity and composition of plant natural products exists. The processes that drive this variation remain largely unknown. Understanding which factors determine chemical diversity has the potential to shed light on plant defenses against herbivores and diseases and accelerate drug discovery. For centuries, Cinchona alkaloids were the primary treatment of malaria. Using Cinchona calisaya as a model, we generated genetic profiles of leaf samples from four plastid (trnL-F, matK, rps16, and ndhF) and one nuclear (ITS) DNA regions from twenty-two C...
2017: Frontiers in Plant Science
Yong Zhang, Shikui Dong, Qingzhu Gao, Shiliang Liu, Hasbagan Ganjurjav, Xuexia Wang, Xukun Su, Xiaoyu Wu
To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands...
March 6, 2017: Scientific Reports
Mirco Migliavacca, Oscar Perez-Priego, Micol Rossini, Tarek S El-Madany, Gerardo Moreno, Christiaan van der Tol, Uwe Rascher, Anna Berninger, Verena Bessenbacher, Andreas Burkart, Arnaud Carrara, Francesco Fava, Jin-Hong Guan, Tiana W Hammer, Kathrin Henkel, Enrique Juarez-Alcalde, Tommaso Julitta, Olaf Kolle, M Pilar Martín, Talie Musavi, Javier Pacheco-Labrador, Andrea Pérez-Burgueño, Thomas Wutzler, Sönke Zaehle, Markus Reichstein
Sun-induced fluorescence (SIF) in the far-red region provides a new noninvasive measurement approach that has the potential to quantify dynamic changes in light-use efficiency and gross primary production (GPP). However, the mechanistic link between GPP and SIF is not completely understood. We analyzed the structural and functional factors controlling the emission of SIF at 760 nm (F760 ) in a Mediterranean grassland manipulated with nutrient addition of nitrogen (N), phosphorous (P) or nitrogen-phosphorous (NP)...
February 9, 2017: New Phytologist
Julie M Grondin, Kazune Tamura, Guillaume Déjean, D Wade Abbott, Harry Brumer
The complex carbohydrates of terrestrial and marine biomass represent a rich nutrient source for free-living and mutualistic microbes alike. The enzymatic saccharification of these diverse substrates is of critical importance for fuelling a variety of complex microbial communities, including marine, soil, ruminant, and monogastric microbiota. Consequently, highly specific carbohydrate-active enzymes, recognition proteins, and transporters are enriched in the genomes of certain species, and are of critical importance in competitive environments...
January 30, 2017: Journal of Bacteriology
Takashi Yamaguchi, Min Gi, Shotarou Yamano, Masaki Fujioka, Kumiko Tatsumi, Satoko Kawachi, Naomi Ishii, Kenichiro Doi, Anna Kakehashi, Hideki Wanibuchi
Diphenylarsinic acid (DPAA), a chemical warfare-related neurotoxic organic arsenical, is present in the groundwater and soil in some regions of Japan due to illegal dumping after World War II. The purpose of the present study was to evaluate the potential toxicity of DPAA when administered to rats in their drinking water for 52 weeks. DPAA was administered to groups 1-4 at concentrations of 0, 5, 10, and 20ppm in their drinking water for 52 weeks. There were no significant differences in the final body weights between the control groups and the treatment groups in male or female rats...
January 2017: Experimental and Toxicologic Pathology: Official Journal of the Gesellschaft Für Toxikologische Pathologie
Lorenzo Rossi, Weilan Zhang, Leonardo Lombardini, Xingmao Ma
Dwindling high quality water resources and growing population are forcing growers to irrigate crops with water of high salinity. It is well recognized that salinity negatively affects plant physiology and biochemistry, and represents one of the most serious threats to crop production and food security. Meanwhile, engineered nanoparticles (ENPs) are increasingly detected in irrigation water and agricultural soils due to the rapid advancement of nanotechnology. Previous research has demonstrated that ENPs such as cerium oxide nanoparticles (CeO2-NPs) exert significant impact on plant growth and production...
December 2016: Environmental Pollution
Ola F A Talkhan, Safaa A E Abd Elwahab, Ebtessam M Shalapy
Low concentration of a heavy metal is toxic and can be classified as one of the pollution sources. Industrial and human waste can pollute water with heavy metals and soils breaking down under the effect of acidic rain, which release heavy metals into river, streams, lakes, and ground water. Bioaccumulation of heavy metals in vital organs of the human body damages these organs, including the liver and kidney, which are the main organs for metabolism, detoxification, and excretion. The present study aims to investigate into concentrations of such heavy metals (Fe, Cu, Zn, and Pb) in both ground and tap water samples collected from different areas in Hail region, KSA...
August 2016: Environmental Monitoring and Assessment
Jingxin Li, Qian Wang, Ronald S Oremland, Thomas R Kulp, Christopher Rensing, Gejiao Wang
Antimony (Sb) is a toxic metalloid that occurs widely at trace concentrations in soil, aquatic systems, and the atmosphere. Nowadays, with the development of its new industrial applications and the corresponding expansion of antimony mining activities, the phenomenon of antimony pollution has become an increasingly serious concern. In recent years, research interest in Sb has been growing and reflects a fundamental scientific concern regarding Sb in the environment. In this review, we summarize the recent research on bacterial antimony transformations, especially those regarding antimony uptake, efflux, antimonite oxidation, and antimonate reduction...
September 15, 2016: Applied and Environmental Microbiology
Yunuen Tapia-Torres, Maria Dolores Rodríguez-Torres, James J Elser, Africa Islas, Valeria Souza, Felipe García-Oliva, Gabriela Olmedo-Álvarez
UNLABELLED: Phosphorus (P) plays a fundamental role in the physiology and biochemistry of all living things. Recent evidence indicates that organisms in the oceans can break down and use P forms in different oxidation states (e.g., +5, +3, +1, and -3); however, information is lacking for organisms from soil and sediment. The Cuatro Ciénegas Basin (CCB), Mexico, is an oligotrophic ecosystem with acute P limitation, providing a great opportunity to assess the various strategies that bacteria from soil and sediment use to obtain P...
August 1, 2016: Applied and Environmental Microbiology
Vilja Siitonen, Kaj Räty, Mikko Metsä-Ketelä
The "Streptomyces genetics and secondary metabolism" laboratory course gives an introduction to the versatile soil dwelling Gram-positive bacteria Streptomyces and their secondary metabolism. The course combines genetic modification of Streptomyces; growing of the strain and protoplast preparation, plasmid isolation by alkaline lysis and phenol precipitation, digestions, and ligations prior to protoplast transformation, as well as investigating the secondary metabolites produced by the strains. Thus, the course is a combination of microbiology, molecular biology, and chemistry...
September 10, 2016: Biochemistry and Molecular Biology Education
Lianghua Chen, Danju Zhang, Wanqin Yang, Yang Liu, Li Zhang, Shun Gao
The positive effects of arbuscular mycorrhizal fungi (AM) on the survival, growth and physiology of plants under various stress conditions have been widely recognized. However, whether sex-dependent susceptibility to AM colonization exists, which can induce a differential tolerance between the sexes to stress conditions, is still unclear. In this study, we investigated the effects of Glomus intraradices on Cd-stressed males and females of Populus deltoides (spiked with 10 mg Cd per kg dry substrate) in terms of morphology, physiology, biochemistry, ultrastructure, and toxin storage and translocation...
July 2016: Chemosphere
Fiorela L Nievas, Pablo C Bogino, Walter Giordano
Biochemistry courses in the Department of Molecular Biology at the National University of Río Cuarto, Argentina, are designed for undergraduate students in biology, microbiology, chemistry, agronomy, and veterinary medicine. Microbiology students typically have previous coursework in general, analytical, and organic chemistry. Programmed sequences of lab experiments allow these students to investigate biochemical problems whose solution is feasible within the context of their knowledge and experience. We previously designed and reported a programmed lab experiment that familiarizes microbiology students with techniques for detection and characterization of quorum-sensing (QS) and quorum-quenching (QQ) signal molecules...
May 6, 2016: Biochemistry and Molecular Biology Education
Gaspare Cesarano, Guido Incerti, Giuliano Bonanomi
Soil water repellency (SWR, i.e. reduced affinity for water owing to the presence of organic hydrophobic coatings on soil particles) has relevant hydrological implications because low rates of infiltration enhance water runoff, and untargeted diffusion of fertilizers and pesticides. Previous studies investigated the occurrence of SWR in ecosystems with different vegetation cover but did not clarify its relationships with litter biochemical quality. Here, we investigated the capability of different plant litter types to induce SWR by using fresh and decomposed leaf materials from 12 species, to amend a model sandy soil over a year-long microcosm experiment...
2016: PloS One
Claudia-Nicole Meisrimler, Stefanie Wienkoop, David Lyon, Christoph-Martin Geilfus, Sabine Lüthje
UNLABELLED: Iron deficiency (-Fe) is one of the major problems in crop production. Dicots, like pea (Pisum sativum L.), are Strategy I plants, which induce a group of specific enzymes such as Fe(III)-chelate reductase (FRO), Fe responsive transporter (IRT) and H(+)-ATPase (HA) at the root plasma membrane under -Fe. Different species and cultivars have been shown to react diversely to -Fe. Furthermore, different kinds of experimental set-ups for -Fe have to be distinguished: i) short-term vs...
May 17, 2016: Journal of Proteomics
Lee H Bergstrand, Erick Cardenas, Johannes Holert, Jonathan D Van Hamme, William W Mohn
UNLABELLED: Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments...
March 8, 2016: MBio
Lauren C Cline, Donald R Zak
Although we understand the ecological processes eliciting changes in plant community composition during secondary succession, we do not understand whether co-occurring changes in plant detritus shape saprotrophic microbial communities in soil. In this study, we investigated soil microbial composition and function across an old-field chronosequence ranging from 16 to 86 years following agricultural abandonment, as well as three forests representing potential late-successional ecosystems. Fungal and bacterial community composition was quantified from ribosomal DNA, and insight into the functional potential of the microbial community to decay plant litter was gained from shotgun metagenomics and extracellular enzyme assays...
December 2015: Ecology
John A Raven, Timothy D Colmer
Mosses are among the earliest branching embryophytes and probably originated not later than the early Ordovician when atmospheric CO2 was higher and O2 was lower than today. The C3 biochemistry and physiology of their photosynthesis suggests, by analogy with tracheophytes, that growth of extant bryophytes in high CO2 approximating Ordovician values would increase the growth rate. This occurs for many mosses, including Physcomitrella patens in suspension culture, although recently published transcriptomic data on this species at high CO2 and present-day CO2 show down-regulation of the transcription of several genes related to photosynthesis...
March 2016: Journal of Experimental Botany
Xiao-Feng Zhang, Mark Thompson, Yi-Hua Xu
Laboratory studies involving repeated exposure to paraquat (PQ) in different animal models can induce many of the pathological features of Parkinson's disease (PD), such as the loss of dopaminergic neurons in the nigrostriatal dopamine system. Epidemiological studies identify an increased risk of developing PD in human populations living in areas where PQ exposure is likely to occur and among workers lacking appropriate protective equipment. The mechanisms involved in developing PD may not be due to any single cause, but rather a multifactorial situation may exist where PQ exposure may cause PD in some circumstances...
May 2016: Laboratory Investigation; a Journal of Technical Methods and Pathology
Zunwei Guo, Jun Yao, Fei Wang, Zhimin Yuan, P Bararunyeretse, Yue Zhao
The sulfide mineral flotation collectors are wildly used in China, whereas their toxic effect on soil microbial activity remains largely unexplored. In this study, isothermal microcalorimetric technique and soil enzyme assay techniques were employed to investigate the toxic effect of typical sulfide mineral flotation collectors on soil microbial activity. Soil samples were treated with different concentrations (0-100 μg•g - 1 soil) of butyl xanthate, butyl dithiophosphate, and sodium diethyldithiocarbamate...
April 2016: Environmental Science and Pollution Research International
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