Impact of climate change on groundwater point discharge: backflooding of karstic springs (Loiret, France)

Under certain hydrological conditions it is possible for spring flow in karst systems to be reversed. When this occurs, the resulting invasion by surface water, i.e. the backflooding, represents a serious threat to groundwater quality because the surface water could well be contaminated. Here we examine the possible impact of future climate change on the occurrences of backflooding in a specific karst system, having first established the occurrence of such events in the selected study area over the past 40 years. It would appear that backflooding has been more frequent since the 1980s, and that it is apparently linked to river flow variability on the pluri-annual scale. The avenue that we adopt here for studying recent and future variations of these events is based on a downscaling algorithm relating large-scale atmospheric circulation to local precipitation spatial patterns. The large-scale atmospheric circulation is viewed as a set of quasi-stationary and recurrent states, called weather types, and its variability as the transition between them. Based on a set of climate model projections, simulated changes in weather-type occurrence for the end of the century suggests that backflooding events can be expected to decrease in 2075–2099. If such is the case, then the potential risk for groundwater quality in the area will be greatly reduced compared to the current situation. Finally, our results also show the potential interest of the weather-type based downscaling approach for examining the impact of climate change on hydrological systems

Mass balance of zinc redistribution during the pedogenesis of a soil developed on a natural geochemical anomaly

Pedogenetic processes that redistribute soil elements over time have been considerably investigated and clearly identified. Nevertheless, the quantification of their respective influences on element redistribution is still poorly known, while soil protection requires extensive knowledge of their long-time depending evolution. The quantitative redistribution of elements is of prime importance in polluted soils, since the long-term environmental hazards depend on their potential mobility and biodisponibility, thus speciation. Among the elements frequently encountered in polluted soils and exhibiting a well-established phytotoxic nature, zinc is of great concern. Nevertheless, pollutions are too recent to observe or even predict the long-term behavior of zinc in polluted soils. An alternative approach is to study paleosoil developed on natural geochemical anomalies. Indeed, such paleosoils display zinc concentrations equivalent to those of polluted soils with the advantage to involve long pedological time of contact between the elements and the different soil phases. Our study aims at quantifying the long-term redistribution of zinc during the pedogenesis of a soil developed upon a natural geochemical anomaly. We first determined zinc speciation both in the parental material and in the solum, then quantified redistribution by mass balance calculations. This approach permits to estimate Zn outputs or inputs in the solum and to quantify its redistribution along the profile and among the different mineral phases

Zinc Redistribution in a Soil Developed from Limestone During Pedogenesis

International audienceThe long-term redistribution of Zn in a naturally Zn-enriched soil during pedogenesis was quantified based on mass balance calculations. According to their fate, parent limestones comprised three Zn pools: bound to calcite and pyritesphalerite grains, bound to phyllosilicates and bound to goethite in the inherited phosphate nodules. Four pedological processes, i.e., carbonate dissolution, two stages of redox processes and eluviation, redistributed Zn during pedogenesis. The carbonate dissolution of limestones released Zn bound to calcite into soil solution. Due to residual enrichment, Zn concentrations in the soil are higher than those in parent limestones. Birnessite, ferrihydrite and goethite dispersed in soil horizon trapped high quantities of Zn during their formation. Afterwards, primary redox conditions induced the release of Zn and Fe into soil solution, and the subsequent individualization of Fe and Mn into Zn-rich concretions. Both processes and subsequent aging of the concretions formed induced significant exportation of Zn through the bottom water table. Secondary redox conditions promoted the weathering of Fe and Mn oxides in cements and concretions. This process caused other losses of Zn through lateral exportation in an upper water table. Concomitantly, eluviation occurred at the top of the solum. The lateral exportation of eluviated minerals through the upper water table limited illuviation. Eluviation was also responsible for Zn loss, but this Zn bound to phyllosilicates was not bioavailabl

Estrutura e propriedades hidráulicas em latossolos sob cultivo na região do Cerrado.

Na região do Cerrado, o potencial produtivo dos solos apresenta-se cada vez mais degradado devido à utilização de sistemas agrícolas extrativistas. Neste contexto, os Latossolos, que cobrem cerca de 50% da superfície do Cerrado, constituem um modelo bastante sensível. Suas propriedades químicas e físicas podem ser rapidamente transformadas pela utilização de práticas agrícolas inadequadas. As alterações na fertilidade química devido à utilização agrícola do solo são conhecidas, mas o mesmo não ocorre no que se concerne à fertilidade física. Na realidade, uma análise detalhada da literatura mostra que a diminuição da fertilidade global após a utilização do solo é atualmente perceptível na maioria dos agroecossistemas, mas a evolução das propriedades físicas é menos evidente. Os estudos revelam que a utilização do solo é acompanhada de uma importante e rápida evolução da sua porosidade em superfície, que se traduz freqüentemente por um aumento da massa volumétrica do solo, a qual sob vegetação natural apresenta valores baixos, particularmente nos Latossolos argilosos. Observa-se, também, diminuição da estabilidade estrutural, aumento do teor de argila dispersa em água, aumento da resistência à penetração e diminuição da condutividade hidráulica.bitstream/CNPAF/21730/1/bolpesq_8.pd

When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD

DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB Homology 1 and 2). Despite strong sequence divergence, many of the DNA-binding and oligomerization properties of these domains have been conserved. Although eluding simple sequence comparisons, the DDBH2 domains share the only strong sequence motif; an extremely highly conserved YxxxIxxxW sequence that contributes to DNA binding. Sequence alignments of DnaD alone fail to identify another key part of the DNA-binding module, since it includes a poorly conserved sequence, a solvent-exposed and somewhat unstable helix and a mobile segment. We show by NMR, in vitro mutagenesis and in vivo complementation experiments that the DNA-binding module of Bacillus subtilis DnaD comprises the YxxxIxxxW motif, the unstable helix and a portion of the mobile region, the latter two being essential for viability. These structural insights lead us to a re-evaluation of the oligomerization and DNA-binding properties of the DnaD and DnaB proteins

Co-directional replication-transcription conflicts lead to replication restart

August 24, 2011Head-on encounters between the replication and transcription machineries on the lagging DNA strand can lead to replication fork arrest and genomic instability1, 2. To avoid head-on encounters, most genes, especially essential and highly transcribed genes, are encoded on the leading strand such that transcription and replication are co-directional. Virtually all bacteria have the highly expressed ribosomal RNA genes co-directional with replication3. In bacteria, co-directional encounters seem inevitable because the rate of replication is about 10–20-fold greater than the rate of transcription. However, these encounters are generally thought to be benign2, 4, 5, 6, 7, 8, 9. Biochemical analyses indicate that head-on encounters10 are more deleterious than co-directional encounters8 and that in both situations, replication resumes without the need for any auxiliary restart proteins, at least in vitro. Here we show that in vivo, co-directional transcription can disrupt replication, leading to the involvement of replication restart proteins. We found that highly transcribed rRNA genes are hotspots for co-directional conflicts between replication and transcription in rapidly growing Bacillus subtilis cells. We observed a transcription-dependent increase in association of the replicative helicase and replication restart proteins where head-on and co-directional conflicts occur. Our results indicate that there are co-directional conflicts between replication and transcription in vivo. Furthermore, in contrast to the findings in vitro, the replication restart machinery is involved in vivo in resolving potentially deleterious encounters due to head-on and co-directional conflicts. These conflicts probably occur in many organisms and at many chromosomal locations and help to explain the presence of important auxiliary proteins involved in replication restart and in helping to clear a path along the DNA for the replisome.Biotechnology and Biological Sciences Research Council (Great Britain) (Grant BB/E006450/1)Wellcome Trust (London, England) (Grant 091968/Z/10/Z)National Institutes of Health (U.S.) (Grant GM41934)National Institutes of Health (U.S.) (Postdoctoral Fellowship GM093408)Biotechnology and Biological Sciences Research Council (Great Britain) (Sabbatical Visit

The conserved C-terminus of the PcrA/UvrD helicase interacts directly with RNA polymerase

Copyright: © 2013 Gwynn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by a Wellcome Trust project grant to MD (Reference: 077368), an ERC starting grant to MD (Acronym: SM-DNA-REPAIR) and a BBSRC project grant to PM, NS and MD (Reference: BB/I003142/1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Classification and evolutionary history of the single-strand annealing proteins, RecT, Redβ, ERF and RAD52

BACKGROUND: The DNA single-strand annealing proteins (SSAPs), such as RecT, Redβ, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. Recently, they have been shown to form similar helical quaternary superstructures. However, despite the functional similarities between these diverse SSAPs, their actual evolutionary affinities are poorly understood. RESULTS: Using sensitive computational sequence analysis, we show that the RecT and Redβ proteins, along with several other bacterial proteins, form a distinct superfamily. The ERF and Rad52 families show no direct evolutionary relationship to these proteins and define novel superfamilies of their own. We identify several previously unknown members of each of these superfamilies and also report, for the first time, bacterial and viral homologs of Rad52. Additionally, we predict the presence of aberrant HhH modules in RAD52 that are likely to be involved in DNA-binding. Using the contextual information obtained from the analysis of gene neighborhoods, we provide evidence of the interaction of the bacterial members of each of these SSAP superfamilies with a similar set of DNA repair/recombination protein. These include different nucleases or Holliday junction resolvases, the ABC ATPase SbcC and the single-strand-binding protein. We also present evidence of independent assembly of some of the predicted operons encoding SSAPs and in situ displacement of functionally similar genes. CONCLUSIONS: There are three evolutionarily distinct superfamilies of SSAPs, namely the RecT/Redβ, ERF, and RAD52, that have different sequence conservation patterns and predicted folds. All these SSAPs appear to be primarily of bacteriophage origin and have been acquired by numerous phylogenetically distant cellular genomes. They generally occur in predicted operons encoding one or more of a set of conserved DNA recombination proteins that appear to be the principal functional partners of the SSAPs