Search results for "soil"
showing 10 items of 3493 documents
pcaH, a molecular marker for estimating the diversity of the protocatechuate-degrading bacterial community in the soil environment
2007
Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the -ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pai…
The evolution of substrate differentiation inMinuartiaseriesLaricifoliae(Caryophyllaceae) in the European Alps: In situ origin or repeated colonizati…
2013
Premise of the study Substrate specialization is often considered an important factor in evolutionary diversification. A classic example of divergence related to different substrate types is the dichotomy between calcicole and calcifuge plants on calcareous and siliceous substrates as found in the European Alps. When closely related species with contrasting substrate preferences are found in the same area, it is generally hypothesized that they diverged where they now occur. However, it is possible that Alpine edaphic diversity instead allows the coexistence of related species whose edaphic differentiation took place deeper in the phylogeny, in some other part of the range of their clades. …
The origin of the serpentine endemic Minuartia laricifolia subsp. ophiolitica by vicariance and competitive exclusion.
2013
Serpentine soils harbour a unique flora that is rich in endemics. We examined the evolution of serpentine endemism in Minuartia laricifolia, which has two ecologically distinct subspecies with disjunct distributions: subsp. laricifolia on siliceous rocks in the western Alps and eastern Pyrenees and subsp. ophiolitica on serpentine in the northern Apennines. We analysed AFLPs and chloroplast sequences from 30 populations to examine their relationships and how their current distributions and ecologies were influenced by Quaternary climatic changes. Minuartia laricifolia was divided into four groups with a BAPS cluster analysis of the AFLP data, one group consisted only of subsp. ophiolitica, …
Does metal contamination affect clonal diversity of the parthenogenetic earthworm Dendrobaena octaedra?
2007
Clonal diversity of the parthenogenetic earthworm Dendrobaena octaedra was studied in three metal contamination gradients in Finland. Metal concentrations in soils (both total and bioavailable fractions) and in earthworm tissues were analysed at each sampling site. Allozyme electrophoresis was used to determine clonal diversity and several genetic diversity measures were used to evaluate differences between populations at metal contaminated and uncontaminated sites. Cu and Zn in the soils and in the earthworms increased with decreasing distance from the emission sources in all areas. Metal contamination appeared to affect clonal diversity of D. octaedra only slightly, since clonal diversity…
Fingerprinting and diversity of bacterial copA genes in response to soil types, soil organic status and copper contamination
2007
A molecular fingerprinting assay was developed to assess the diversity of copA genes, one of the genetic determinants involved in bacterial resistance to copper. Consensus primers of the copA genes were deduced from an alignment of sequences from proteobacterial strains. A PCR detection procedure was optimized for bacterial strains and allowed the description of a novel copA genetic determinant in Pseudomonas fluorescens. The copA DNA fingerprinting procedure was optimized for DNA directly extracted from soils differing in their physico-chemical characteristics and in their organic status (SOS). Particular copA genetic structures were obtained for each studied soil and a coinertia analysis …
Quantitative Detection of the nosZ Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA, narG , nirK , and nosZ Genes…
2006
ABSTRACT Nitrous oxide (N 2 O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N 2 O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the nosZ gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of nosZ primers flanking the nosZ fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the nosZ gene present in six different …
Compatibility of Rhizobial Genotypes within Natural Populations of Rhizobium leguminosarum Biovar viciae for Nodulation of Host Legumes
2003
ABSTRACT Populations of Rhizobium leguminosarum biovar viciae were sampled from two bulk soils, rhizosphere, and nodules of host legumes, fava bean ( Vicia faba ) and pea ( Pisum sativum ) grown in the same soils. Additional populations nodulating peas, fava beans, and vetches ( Vicia sativa ) grown in other soils and fava bean-nodulating strains from various geographic sites were also analyzed. The rhizobia were characterized by repetitive extragenomic palindromic-PCR fingerprinting and/or PCR-restriction fragment length polymorphism (RFLP) of 16S-23S ribosomal DNA intergenic spacers as markers of the genomic background and PCR-RFLP of a nodulation gene region, nodD , as a marker of the sy…
Contamination Remediation with Soil Amendments by Immobilization of Heavy Metals
2015
Elektroniskā versija nesatur pielikumus
Isotope fractionation of zinc in the paddy rice soil-water environment and the role of 2’deoxymugineic acid (DMA) as zincophore under Zn limiting con…
2021
Non-traditional stable isotope systems are increasingly used to study micronutrient cycling and acquisition in terrestrial ecosystems. We previously proposed for zinc (Zn) a conceptual model linking observed isotope signatures and fractionations to biogeochemical processes occurring in the rice soil environment and we suggested that 2’deoxymugineic acid (DMA) could play an important role for rice during the acquisition of Zn when grown under Zn limiting conditions. This proposition was sustained by the extent and direction of isotope fractionation observed during the complexation of Zn with DMA synthesised in our laboratory. Here we report a new set of experimental data from field and labor…
Geogenic element behaviour in soil-rainwater interaction at Mt Etna, Sicily: preliminary results
2008
Active volcanoes emit considerable amounts of contaminants such as As, Se and V. Previous studies have shown that the volcanic activity at Mt Etna (Sicily) has a strong influence on local rainwater compositions. However to date, the behaviour of trace elements in the soils around Mt Etna is poorly understood. 4-hr batch experiments have been performed with 1:5 soil solutions of air-dried soil (fraction <2 mm) and synthetic (acid) rainwater (using either deionized water with a pH of ~6 or a ~500 ppm of sulphuric acid solution with a pH of ~2). In general trace element concentrations are more enriched in soil solutions with low pH (e.g. enrichment factor (EF) acid compared to neutral soil sol…