Role of Organic Amendments to Mitigate Cd Toxicity and Its Assimilation in <i>Triticum aestivum</i> L.

In soil biota, higher and enduring concentration of heavy metals like cadmium (Cd) is hazardous and associated with great loss in growth, yield, and quality parameters of most of the crop plants. Recently, in-situ applications of eco-friendly stabilizing agents in the form of organic modifications have been utilized to mitigate the adverse effects of Cd-toxicity. This controlled experiment was laid down to appraise the imprints of various applied organic amendments namely poultry manure (PM), farmyard manure (FYM), and sugarcane press mud (PS) to immobilize Cd in polluted soil. Moreover, phytoavailability of Cd in wheat was also accessed under an alkaline environment. Results revealed that the addition of FYM (5–10 ton ha^-1 ) in Cd-contaminated soil significantly increased germination rate, leaf chlorophyll content, plant height, spike length, biological and grain yield amongst all applied organic amendments. Moreover, the addition of FYM (5–10 ton ha^-1 ) also reduced the phytoavailability of Cd by 73–85% in the roots, 57–83% in the shoots, and 81–90% in grains of wheat crop. Thus, it is affirmed that incorporation of FYM (5–10 ton ha^-1 ) performed better to enhance wheat growth and yield by remediating Cd. Thus, the application of FYM (5–10 ton ha^-1 ) reduced the toxicity induced by Cd to plants by declining its uptake and translocation as compared to all other applied organic amendments to immobilize Cd under sandy alkaline polluted soil.     

As old as the hills: Pliocene palaeogeographical processes influence patterns of genetic structure in the widespread,common shrub Banksia sessilis

The impact of Quaternary glaciation on the development of phylogeographic structure in plant species is well documented. In unglaciated landscapes, phylogeographic patterns tend to reflect processes relating to persistence and stochasticity, yet other factors, associated with the palaeogeographical history of the landscape, including geomorphological events, can also have a significant influence. The unglaciated landscape of south‐western Western Australia is an ideal location to observe these ancient drivers of lineage diversification, with tectonic activity associated with the Darling Fault in the late Pliocene attributed to patterns of deep phylogeographic divergence in a widespread tree from this region. Interestingly, other species within this region have not shown this pattern and this palaeogeographical boundary therefore presents an opportunity to examine age and historical distribution of plant species endemic to this region. In this study, we assess patterns of genetic diversity and structure across 28 populations of the widespread shrub Banksia sessilis using three cpDNA markers and nine nuclear microsatellite markers. Sixteen cpDNA haplotypes were identified, comprising two major chloroplast DNA lineages that are estimated to have diverged in the Pliocene, approximately 3.3 million years ago. This timing coincides with major geomorphological processes in the landscape, including the separation of the Darling Plateau from the adjacent Swan Coastal Plain, as well as eustatic changes on the Swan Coastal Plain that are likely to have resulted in the physical isolation of historical plant lineages. Chloroplast lineages were broadly aligned with populations associated with older lateritic soils of the Darling Plateau and Geraldton sandplains or the younger sandy soils associated with the Swan Coastal Plain and Southern Coastline. This structural pattern of lateritic versus non‐lateritic division was not observed in the nuclear microsatellite data that identified three genetic clades that roughly corresponded to populations in the North, South, and Central portions of the distributions.     

Composition of the pollinator community,pollination and the mating system for a shrub in fragments of species rich kwongan in south-west Western Australia

In this study we investigate the composition of the potential honeyeater pollinator community, patterns of honeyeater visitation, pollination and the mating system in a range of population fragments for the bird-pollinated mixed mating system shrub Calothamnus quadrifidus R.Br. Specifically, we aimed to answer the following questions. For smaller and more isolated population fragments are honeyeater species lost from the pollinator community, patterns of visitation different, levels of pollination lower and rates of selfing, biparental inbreeding and correlated paternity higher. The composition of the honeyeater community was similar across population fragments and there was no relationship between the abundance of birds and population fragment size. Honeyeaters were most commonly observed visiting numerous inflorescences within single plants in all populations, but as population fragments became larger movements between plants were more commonly observed. Our observations of honeyeater visitation were generally consistent with our measurements of pollination and patterns in the mating system across population fragments. We found no significant relationship between population fragment size and levels of pollination. Mating system studies showed outcrossing rates (t _m) comparable to those found in other bird-pollinated Myrtaceae, and ranged from 0.54 to 0.90 across populations. Outcrossing rates were not significantly correlated with log population size, but correlations of outcrossed paternity indicate a clear trend from low correlated paternity in larger populations to significantly higher correlated paternities in smaller populations. As a consequence mating in small populations will occur between much smaller groups of plants, and this may affect population fitness in subsequent generations.     

Turbulence and stratification in Priest Pot,a productive pond in a sheltered environment

Priest Pot is an example of the abundant ponds that, collectively, contribute crucially to species diversity. Despite extensive biological study, little has been reported about the physical framework that supports its ecological richness. This article elucidates the physical character of Priest Pot’s water column and thus that of similar water bodies. Vertical thermal microstructure profiles were recorded during summer 2003 and analyzed alongside concurrent meteorological data. During summer stratification, the thermal structure appeared to be dominated by surface heat fluxes. Surface wind stress, limited by sheltering vegetation, caused turbulent overturns once a surface mixed layer was present but appeared to contribute little to setting up the thermal structure. Variations in full-depth mean stratification occurred predominantly over seasonal and ∼5-day time scales, the passage of atmospheric pressure systems being posited as the cause of the latter. In the uppermost ∼0.5 m, where the stratification varied at subdaily time scales, turbulence was active (sensu Ivey and Imberger 1991) when this layer was mixed, with dissipation values ε ∼ 10⁻⁸ m² s⁻³ and vertical diffusivity K_Z = 10⁻⁴ — 10⁻⁶ m² s⁻¹. Where the water column was stratified, turbulence was strongly damped by both buoyancy and viscosity, and K_Z was an order of magnitude smaller. Vertical transport in the mixed layer occurred via many small overturns (Thorpe scale r.m.s. and maximum values were typically 0.02 m and 0.10 m, respectively), and seston were fully mixed through the water column.     

Phenotypic and Genotypic Description of Sedimenticola selenatireducens Strain CUZ,a Marine (Per)Chlorate-Respiring Gammaproteobacterium,and Its Close Relative the Chlorate-Respiring Sedimenticola Strain NSS

Two (per)chlorate-reducing bacteria, strains CUZ and NSS, were isolated from marine sediments in Berkeley and San Diego, CA, respectively. Strain CUZ respired both perchlorate and chlorate [collectively designated (per)chlorate], while strain NSS respired only chlorate. Phylogenetic analysis classified both strains as close relatives of the gammaproteobacterium Sedimenticola selenatireducens. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) preparations showed the presence of rod-shaped, motile cells containing one polar flagellum. Optimum growth for strain CUZ was observed at 25 to 30°C, pH 7, and 4% NaCl, while strain NSS grew optimally at 37 to 42°C, pH 7.5 to 8, and 1.5 to 2.5% NaCl. Both strains oxidized hydrogen, sulfide, various organic acids, and aromatics, such as benzoate and phenylacetate, as electron donors coupled to oxygen, nitrate, and (per)chlorate or chlorate as electron acceptors. The draft genome of strain CUZ carried the requisite (per)chlorate reduction island (PRI) for (per)chlorate respiration, while that of strain NSS carried the composite chlorate reduction transposon responsible for chlorate metabolism. The PRI of strain CUZ encoded a perchlorate reductase (Pcr), which reduced both perchlorate and chlorate, while the genome of strain NSS included a gene for a distinct chlorate reductase (Clr) that reduced only chlorate. When both (per)chlorate and nitrate were present, (per)chlorate was preferentially utilized if the inoculum was pregrown on (per)chlorate. Historically, (per)chlorate-reducing bacteria (PRB) and chlorate-reducing bacteria (CRB) have been isolated primarily from freshwater, mesophilic environments. This study describes the isolation and characterization of two highly related marine halophiles, one a PRB and the other a CRB, and thus broadens the known phylogenetic and physiological diversity of these unusual metabolisms.     

Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short‐day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome‐wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co‐located with a QTL mapped in the RIL population.     

Phylogeography and population differentiation in terrestrial island populations of Banksia arborea (Proteaceae)

The Banded Iron Formations (BIFs) of south‐western Australia are terrestrial islands characterized by high species richness and endemism. Regional endemics occur across multiple formations without inhabiting the intervening landscape matrix. We investigated whether the occurrence on BIF terrestrial islands has led to genetic differentiation among the eight known populations of the regional endemic, Banksia arborea. Genetic structure was assessed using three chloroplast DNA sequence markers and 11 nuclear microsatellite loci. Phylogenetic relationships were assessed with statistical parsimony and Bayesian methods. Dates of haplotype divergence were estimated using the time to most recent common ancestor of B. arborea and Banksia purdieana, as well as a conservative angiosperm chloroplast (cp)DNA mutation rate. Population genetic diversity and structure was assessed amongst and within populations by genotyping 24 geographically clustered individuals from each BIF and three subpopulations within the Die Hardy Range BIF. Indirect gene flow estimates were determined using a method based on the frequency of private alleles. Banksia arborea showed low genetic diversity in (cp)DNA and a complex structural pattern, with genetic differentiation of some BIF populations and an absence of differentiation amongst others, reflecting either retention of ancestral polymorphism across northern BIF populations or more recent connectivity of these populations. There was little evidence of pollen dispersal both between BIFs and within the large BIF known as Die Hardy Range. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 860–872.     

Fossil juvenile coelacanths from the Devonian of South Africa shed light on the order of character acquisition in actinistians

A new coelacanth genus from the Famennian (Upper Devonian) of South Africa is described, principally from presumed juveniles. S erenichthys kowiensis gen. et sp. nov. uniquely shares with Diplocercides a ventral expansion of the elbow‐like lachrymojugal, as well as a symmetrical diphycercal tail supported by expanded neural and haemal spines and radials. Serenichthys is distinguished from Diplocercides by a number of derived characters, including possession of longer anterior parietals, a more crescent‐shaped postorbital with a more anteriorly positioned infraorbital canal, and a far smaller squamosal, which is well separated from the skull roof. By contrast, Serenichthys appears to lacks a second dorsal fin lobe, a derived feature present in Diplocercides. Most specimens of Serenichthys are between 3 and 6 cm in length. They have large eyes, and dermal bones of the skull ornamented with long wavy ridges, similar to the dermal ornament of other Devonian coelacanths such as Gavinia. Larger isolated operculae also collected from the Waterloo Farm locality and attributed to Serenichthys indicate that with growth the ridges on the dermal bones transformed into elongate tubercles, reminiscent of those of Diplocercides and Carboniferous taxa. Phylogenetic analysis resolves Serenichthys as the sister group of Holopterygius and all known post‐Devonian coelacanths. The clade including the unusual leaf‐shaped coelacanths, the Devonian Holopterygius and Carboniferous Allenypterus, branches from the coelacanth lineage immediately crownward of Serenichthys. The presence of abundant juveniles within an estuarine setting strongly parallels the discovery of similarly sized juveniles of Rhabdoderma exiguus together with eggs and yolk‐sack larvae in the Upper Carboniferous Mazon Creek biota. It is therefore argued that Serenichthys, like Rhabdoderma, was using the sheltered estuarine environment as a nursery. © 2015 The Linnean Society of London     

Horizontal transfer of a non-autonomous Helitron among insect and viral genomes

Background

The movement of mobile elements among species by horizontal transposon transfer (HTT) influences the evolution of genomes through the modification of structure and function. Helitrons are a relatively new lineage of DNA-based (class II) transposable elements (TEs) that propagate by rolling-circle replication, and are capable of acquiring host DNA. The rapid spread of Helitrons among animal lineages by HTT is facilitated by shuttling in viral particles or by unknown mechanisms mediated by close organism associations (e.g. between hosts and parasites).

Results

A non-autonomous Helitron independently annotated as BmHel-2 from Bombyx mori and the MITE01 element from Ostrinia nubilalis was predicted in the genomes of 24 species in the insect Order Lepidoptera. Integrated Helitrons retained ≥ 65% sequence identity over a 250 bp consensus, and were predicted to retain secondary structures inclusive of a 3′-hairpin and a 5′-subterminal inverted repeat. Highly similar Hel-2 copies were predicted in the genomes of insects and associated viruses, which along with a previous documented case of real-time virus-insect cell line transposition suggests that this Helitron has likely propagated by HTT.

Conclusions

These findings provide evidence that insect virus may mediate the HTT of Helitron-like TEs. This movement may facilitate the shuttling of DNA elements among insect genomes. Further sampling is required to determine the putative role of HTT in insect genome evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1318-6) contains supplementary material, which is available to authorized users.