Multi-method assessment of the intrinsic biodegradation potential of an aquifer contaminated with chlorinated ethenes at an industrial area in Barcelona (Spain)

The bioremediation potential of an aquifer contaminated with tetrachloroethene (PCE) was assessed by combining hydrogeochemical data of the site, microcosm studies, metabolites concentrations, compound specific-stable carbon isotope analysis and the identification of selected reductive dechlorination biomarker genes. The characterization of the site through 10 monitoring wells evidenced that leaked PCE was transformed to TCE and cis-DCE via hydrogenolysis. Carbon isotopic mass balance of chlorinated ethenes pointed to two distinct sources of contamination and discarded relevant alternate degradation pathways in the aquifer. Application of specific-genus primers targeting Dehalococcoides mccartyi species and the vinyl chloride-to-ethene reductive dehalogenase vcrA indicated the presence of autochthonous bacteria capable of the complete dechlorination of PCE. The observed cis-DCE stall was consistent with the aquifer geochemistry (positive redox potentials; presence of dissolved oxygen, nitrate, and sulphate; absence of ferrous iron), which was thermodynamically favourable to dechlorinate highly chlorinated ethenes but required lower redox potentials to evolve beyond cis-DCE to the innocuous end product ethene. Accordingly, the addition of lactate or a mixture of ethanol plus methanol as electron donor sources in parallel field-derived anoxic microcosms accelerated dechlorination of PCE and passed cis-DCE up to ethene, unlike the controls (without amendments, representative of field natural attenuation). Lactate fermentation produced acetate at near-stoichiometric amounts. The array of techniques used in this study provided complementary lines of evidence to suggest that enhanced anaerobic bioremediation using lactate as electron donor source is a feasible strategy to successfully decontaminate this site

Genetic divergence toward the selection of promising bean progenitors via mixed multivariate models

Abstract The genetic variability present in the bean (Phaseolus vulgaris L.) germplasm that is currently used as an agricultural crop has been shown to be stable in production and is acceptable for human sustenance. Accordingly, to maintain as much of the available variability as possible, this study aimed to examine the genetic divergence in the bean using multivariate analysis to identify the sources of genetic variability and enable breeders to recognize genetic combinations that have a greater chances of success before crossings are performed. This study was conducted in a randomized block design with three replications in the agricultural year 2015. The agronomic traits evaluated were the stem diameter (DIAM) in millimeters, plant height (PH) in centimeters, number of seedsper plant (NS), protein percentage (PROT), height of the first pod (HFP) in centimeters, pod number (PN), grain mass per plant (GM) in g plant−1, grain yield (GY) in kg ha−1, and straw yield (SY) in kg ha−1. To enable selection of the most divergent genotypes, twenty different genotypes were analyzed via clustering according to the average linkage criterion (UPGMA) using a matrix of the mean standardized Euclidean distances and principal component analysis based on the values predicted via a multivariate mixed model. The results obtained in this study revealed a high degree of genetic divergence and allowed the progenies to be allocated into different groups, as well as recommended crossings for future bean breeding programs.Resumen La variabilidad genética presente en el germoplasma de frijol (Phaseolus vulgaris L.) actualmente utilizada en la agricultura es la garantía más pronunciada de estabilidad de la producción y sustento humano en relación con este cultivo. En consecuencia, para mantener la mayor variabilidad disponible posible, este estudio tuvo como objetivo examinar la divergencia genética mediante análisis multivariante para identificar fuentes de variabilidad genética y permitir a los mejoradores reconocer las combinaciones genéticas con mayores posibilidades de éxito antes de que se realicen los cruces. El experimento se realizó en diseño de bloques al azar con tres repeticiones en el año agrícola 2015. Los caracteres agronómicos evaluados fueron: diámetro del tallo (DIAM) en mm; altura (ALT) en cm; cantidad de semillas (CS); porcentaje de proteína (PROT); altura de la primera vaina (APV) en cm; número de pod (NP); masa de grano por planta (MG) en g planta−1; rendimiento de grano (RG) en kg ha−1; y rendimiento de paja (RP) en kg ha−1. Para seleccionar los genotipos más divergentes, se analizaron 20 diferentes agrupando según el criterio de ligamiento promedio (UPGMA) usando la matriz de distancias euclidianas estandarizadas medias, y el análisis de componentes principales en base a los valores predichos mediante el modelo mixto multivariante. Los resultados obtenidos en este estudio revelaron un alto grado de divergencia genética y permitieron la asignación de las progenies en diferentes grupos, así como recomendaciones para cruces en futuros programas de mejoramiento de frijol

Lipopolysaccharide-induced apoptosis of macrophages determines the up-regulation of concentrative nucleoside transporters Cnt1 and Cnt2 through tumor necrosis factor-alpha-dependent and -independent mechanisms

In murine bone marrow macrophages, lipopolysaccharide (LPS) induces apoptosis through the autocrine production of tumor necrosis factor-alpha (TNF-alpha), as demonstrated by the fact that macrophages from TNF-alpha receptor I knock-out mice did not undergo early apoptosis. In these conditions LPS up-regulated the two concentrative high affinity nucleoside transporters here shown to be expressed in murine bone marrow macrophages, concentrative nucleoside transporter (CNT) 1 and 2, in a rapid manner that is nevertheless consistent with the de novo synthesis of carrier proteins. This effect was not dependent on the presence of macrophage colony-stimulating factor, although LPS blocked the macrophage colony-stimulating factor-mediated up-regulation of the equilibrative nucleoside transport system es. TNF-alpha mimicked the regulatory response of nucleoside transporters triggered by LPS, but macrophages isolated from TNF-alpha receptor I knock-out mice similarly up-regulated nucleoside transport after LPS treatment. Although NO is produced by macrophages after LPS treatment, NO is not involved in these regulatory responses because LPS up-regulated CNT1 and CNT2 transport activity and expression in macrophages from inducible nitric oxide synthase and cationic amino acid transporter (CAT) 2 knock-out mice, both of which lack inducible nitric oxide synthesis. These data indicate that the early proapoptotic responses of macrophages, involving the up-regulation of CNT transporters, follow redundant regulatory pathways in which TNF-alpha-dependent- and -independent mechanisms are involved. These observations also support a role for CNT transporters in determining extracellular nucleoside availability and modulating macrophage apoptosis

Genome-wide analysis of the lignin toolbox of Eucalyptus grandis

Lignin, a major component of secondary cell walls, hinders the optimal processing of wood for industrial uses. The recent availability of the Eucalyptus grandis genome sequence allows comprehensive analysis of the genes encoding the 11 protein families specific to the lignin branch of the phenylpropanoid pathway and identification of those mainly involved in xylem developmental lignification. We performed genome-wide identification of putative members of the lignin gene families, followed by comparative phylogenetic studies focusing on bona fide clades inferred from genes functionally characterized in other species. RNA-seq and microfluid real-time quantitative PCR (RT-qPCR) expression data were used to investigate the developmental and environmental responsive expression patterns of the genes. The phylogenetic analysis revealed that 38 E. grandis genes are located in bona fide lignification clades. Four multigene families (shikimate O-hydroxycinnamoyltransferase (HCT), p-coumarate 3-hydroxylase (C3H), caffeate/5-hydroxyferulate O-methyltransferase (COMT) and phenylalanine ammonia-lyase (PAL)) are expanded by tandem gene duplication compared with other plant species. Seventeen of the 38 genes exhibited strong, preferential expression in highly lignified tissues, probably representing the E. grandis core lignification toolbox. The identification of major genes involved in lignin biosynthesis in E. grandis, the most widely planted hardwood crop world-wide, provides the foundation for the development of biotechnology approaches to develop tree varieties with enhanced processing qualities.This work, part of the LABEX project TULIP (ANR-10-LABX-41), was supported by grants from the Project Tree For Joules (ANR-2010-KBBE-007-01 and FCT-PKBBE/ AGR_GPL/0001/2010), the CNRS, the Toulouse III University (UPS), and the FCT project microEGo (PTDC/AGR-GPL/098179/2008). V.C. was supported by a FCT PhD grant (SFRH/BD/72982/2010). M.S. received a postdoctoral fellowship ‘Beatriu de Pinós’ from the DURSI de la Generalitat de Catalunya. J.A.P.P. acknowledges FCT for the research contract Ciência 2008 program and the postdoctoral fellowship SFRH/BPD/92207/2013. We are grateful to C. Araujo and L. Neves (Altri Florestal, Portugal), C. Marques (RAIZ, Portugal) and L. Harvengt (FCBA, France) for kindly providing and/or allowing collection of Eucalyptus samples, and C. Graça (IBET, IICT), N. Saidi, H. Yu and E. Camargo (all LRSV) for help with sample design/collection and RNA extraction. We also thank N. Ladouce (LRSV) and the Genotoul Genomic platform http://get.genotoul.fr/ for technical assistance with the Biomark Fluidigm RT-qPCR amplifications, and E. Mizrachi for assistance with RNA-seq data analysis. RNA-seq was funded by Mondi and Sappi through the FMG Program, the THRIP Program (UID 80118), the NRF (UID 71255 and 86936) and the DST of South Africa.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1469-8137hb2016Genetic

Silencing of StKCS6 in potato periderm leads to reduced chain lengths of suberin and wax compounds and increased peridermal transpiration

Very long chain aliphatic compounds occur in the suberin polymer and associated wax. Up to now only few genes involved in suberin biosynthesis have been identified. This is a report on the isolation of a potato (Solanum tuberosum) 3-ketoacyl-CoA synthase (KCS) gene and the study of its molecular and physiological relevance by means of a reverse genetic approach. This gene, called StKCS6, was stably silenced by RNA interference (RNAi) in potato. Analysis of the chemical composition of silenced potato tuber periderms indicated that StKCS6 down-regulation has a significant and fairly specific effect on the chain length distribution of very long-chain fatty acids (VLCFAs) and derivatives, occurring in the suberin polymer and peridermal wax. All compounds with chain lengths of C28 and higher were significantly reduced in silenced periderms, whereas compounds with chain lengths of C26 and lower accumulated. Thus, StKCS6 is preferentially involved in the formation of suberin and wax lipidic monomers with chain lengths of C28 and higher. As a result, peridermal transpiration of the silenced lines was about 1.5-times higher than that of the wild type. Our results convincingly show that StKCS6 is involved in both suberin and wax biosynthesis and that a reduction of the monomeric carbon chain lengths leads to increased rates of peridermal transpiration

Use of dual element isotope analysis and microcosm studies to determine the origin and potential anaerobic biodegradation of dichloromethane in two multi-contaminated aquifers

Many aquifers around the world are impacted by toxic chlorinated methanes derived from industrial processes due to accidental spills. Frequently, these contaminants co-occur with chlorinated ethenes and/or chlorinated benzenes in groundwater, forming complex mixtures that become very difficult to remediate. In this study, a multi-method approach was used to provide lines of evidence of natural attenuation processes and potential setbacks in the implementation of bioremediation strategies in multi-contaminated aquifers. First, this study determined i) the carbon and chlorine isotopic compositions (δ¹³C, δ³⁷Cl) of several commercial pure phase chlorinated compounds, and ii) the chlorine isotopic fractionation (εCl = −5.2 ± 0.6‰) and the dual CCl isotope correlation (ΛC/Cl = 5.9 ± 0.3) during dichloromethane (DCM) degradation by a Dehalobacterium-containing culture. Such data provide valuable information for practitioners to support the interpretation of stable isotope analyses derived from polluted sites. Second, the bioremediation potential of two industrial sites contaminated with a mixture of organic pollutants (mainly DCM, chloroform (CF), trichloroethene (TCE), and mono-chlorobenzene (MCB)) was evaluated. Hydrochemistry, dual (CCl) isotope analyses, laboratory microcosms, and microbiological data were used to investigate the origin, fate and biodegradation potential of chlorinated methanes. At Site 1, δ¹³C and δ³⁷Cl compositions from field samples were consistent with laboratory microcosms, which showed complete degradation of CF, DCM and TCE, while MCB remained. Identification of Dehalobacter sp. in CF-enriched microcosms further supported the biodegradation capability of the aquifer to remediate chlorinated methanes. At Site 2, hydrochemistry and δ¹³C and δ³⁷Cl compositions from field samples suggested little DCM, CF and TCE transformation; however, laboratory microcosms evidenced that their degradation was severely inhibited, probably by co-contamination. A dual CCl isotopic assessment using results from this study and reference values from the literature allowed to determine the extent of degradation and elucidated the origin of chlorinated methanes

Repeatability analysis of guava fruit and leaf characteristics

Psidium guajava L. (guava) is an important species that presents high genetic variability due to its mixed reproductive system, which is desired in breeding programs. Repeatability is an important tool for the selection of genotypes in pre-breeding studies. When genetic variability is present, the knowledge regarding the number of samples to be used in repeatability studies is indispensable. This study aims to determine the number of necessary measures while optimizing resources and maintaining the reliability of the results for the variables evaluated in P. guajava. The experiment was carried out with genotypes from three Brazilian States: Espírito Santo, São Paulo, and Minas Gerais, and a total of 79 P. guajava genotypes were collected. The following characteristics were evaluated: young leaf length and width; developed leaf length and width; fruit length; fruit diameter and fruit cavity diameter; and fruit weight and pulp weight. For the evaluated characteristics, deviance, permanent phenotypic and temporary environment variance, coefficients of repeatability and determination, accuracy and the number of estimated measurements required were determined. We established that the number of measurements required in repeatability analysis for a coefficient of repeatability with a reliability of 80% is four, for the measurements of developed leaf width, pulp weight, fruit diameter, and fruit cavity diameter

Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus

BackgroundNitrogen (N) is a main nutrient required for tree growth and biomass accumulation. In this study, we analyzed the effects of contrasting nitrogen fertilization treatments on the phenotypes of fast growing Eucalyptus hybrids (E. urophylla x E. grandis) with a special focus on xylem secondary cell walls and global gene expression patterns.ResultsHistological observations of the xylem secondary cell walls further confirmed by chemical analyses showed that lignin was reduced by luxuriant fertilization, whereas a consistent lignin deposition was observed in trees grown in N-limiting conditions. Also, the syringyl/guaiacyl (S/G) ratio was significantly lower in luxuriant nitrogen samples. Deep sequencing RNAseq analyses allowed us to identify a high number of differentially expressed genes (1,469) between contrasting N treatments. This number is dramatically higher than those obtained in similar studies performed in poplar but using microarrays. Remarkably, all the genes involved the general phenylpropanoid metabolism and lignin pathway were found to be down-regulated in response to high N availability. These findings further confirmed by RT-qPCR are in agreement with the reduced amount of lignin in xylem secondary cell walls of these plants.ConclusionsThis work enabled us to identify, at the whole genome level, xylem genes differentially regulated by N availability, some of which are involved in the environmental control of xylogenesis. It further illustrates that N fertilization can be used to alter the quantity and quality of lignocellulosic biomass in Eucalyptus, offering exciting prospects for the pulp and paper industry and for the use of short coppices plantations to produce second generation biofuels.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0256-9) contains supplementary material, which is available to authorized users