High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation

In this paper, we provide direct evidence of the importance of root hairs on pore structure development at the root-soil interface during the early stage of crop establishment. This was achieved by use of high resolution (~5 μm) synchrotron radiation computed tomography (SRCT) to visualise both the structure of root hairs and the soil pore structure in plant-soil microcosms. Two contrasting genotypes of barley (Hordeum vulgare L.), with and without root hairs, were grown for 8 days in microcosms packed with sandy loam soil at 1.2 g cm-3 36 dry bulk density. Root hairs were visualised within air filled pore spaces, but not in the fine-textured soil regions. - We found that the genotype with root hairs significantly altered the porosity and connectivity of the detectable pore space (> 5 μm) in the rhizosphere, as compared with the no-hair mutants. Both genotypes showed decreasing pore-space between 0.8 mm and 0.1 mm from the root surface. Interestingly the root-hair-bearing genotype had a significantly greater soil pore volume-fraction at the root-soil interface. - Effects of pore structure on diffusion and permeability were estimated to be functionally insignificant under saturated conditions when simulated using image based modelling

Behavior and Impact of Zirconium in the Soil–Plant System: Plant Uptake and Phytotoxicity

Because of the large number of sites they pollute, toxic metals that contaminate terrestrial ecosystems are increasingly of environmental and sanitary concern (Uzu et al. 2010, 2011; Shahid et al. 2011a, b, 2012a). Among such metals is zirconium (Zr), which has the atomic number 40 and is a transition metal that resembles titanium in physical and chemical properties (Zaccone et al. 2008). Zr is widely used in many chemical industry processes and in nuclear reactors (Sandoval et al. 2011; Kamal et al. 2011), owing to its useful properties like hardness, corrosion-resistance and permeable to neutrons (Mushtaq 2012). Hence, the recent increased use of Zr by industry, and the occurrence of the Chernobyl and Fukashima catastrophe have enhanced environmental levels in soil and waters (Yirchenko and Agapkina 1993; Mosulishvili et al. 1994 ; Kruglov et al. 1996)

Methane fluxes during the initiation of a large-scale water table manipulation experiment in the Alaskan Arctic tundra

Much of the 191.8 Pg C in the upper 1 m of Arctic soil of Arctic soil organic mater is, or is at risk of, being released to the atmosphere as CO2 and/or CH4. Global warming will further alter the rate of emission of these gases to the atmosphere. Here we quantify the effect of major environmental variables affected by global climate change on CH4 fluxes in the Alaskan Arctic. Soil temperature best predicts CH4 fluxes and explained 89% of the variability in CH4 emissions. Water table depth has a nonlinear impact on CH4 efflux. Increasing water table height above the surface retards CH4 efflux. Decreasing water table depth below the surface has a minor effect on CH4 release once an aerobic layer is formed at the surface. In contrast with several other studies, we found that CH4 emissions are not driven by net ecosystem exchange (NEE) and are not limited by labile carbon supply

Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years

The native shrub, Piliostigma reticulatum , as an ecological “resource island” for mango trees in the Sahel

African farmers are increasingly adopting sustainable agricultural practices including use of native shrub intercropping approaches. In one village of Sénégal (near Thiès) it was reported that farmers planted mango (Mangifera indica) seedlings within the canopies of a native shrub (Piliostigma reticulatum). Anecdotal information and qualitative observations suggested that the presence of P. reticulatum promoted soil quality and a competitive advantage for establishing mango plantations. We hypothesized that soil chemical and microbial properties of mango rhizosphere soil growing in the presence of P. reticulatum would be significantly improved over soils associated with mango growing outside the influence of P. reticulatum. The results showed that mango-shrub interplanting significantly lowered pH, and increased arbuscular mycorrhizal fungi (AMF) colonization of mango roots, enzyme activities, and microbial biomass compared to mango alone. Phylogenetic analyses by PCR-denaturing gradient gel electrophoresis (DGGE) showed that community structures of fungi, bacteria, and bacterial genes responsible for denitrification (nirK) of the soil from the rooting zone of the mango-shrub intercropping system were distinct from all other soil outside the influence of P. reticulatum. It is concluded that P. reticulatum enhances soil biological functioning and that there is a synergistic effect of intercropping mango with the native shrub, P. reticulatum, in soil quality with a more diverse community, greater AMF infection rates, and greater potential to perform decomposition and mineralize nutrients

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed