Influence of geogenic factors on microbial communities in metallogenic Australian soils

Links between microbial community assemblages and geogenic factors were assessed in 187 soil samples collected from four metal-rich provinces across Australia. Field-fresh soils and soils incubated with soluble Au(III) complexes were analysed using three-domain multiplex-terminal restriction fragment length polymorphism, and phylogenetic (PhyloChip) and functional (GeoChip) microarrays. Geogenic factors of soils were determined using lithological-, geomorphological- and soil-mapping combined with analyses of 51 geochemical parameters. Microbial communities differed significantly between landforms, soil horizons, lithologies and also with the occurrence of underlying Au deposits. The strongest responses to these factors, and to amendment with soluble Au(III) complexes, was observed in bacterial communities. PhyloChip analyses revealed a greater abundance and diversity of Alphaproteobacteria (especially Sphingomonas spp.), and Firmicutes (Bacillus spp.) in Au-containing and Au(III)-amended soils. Analyses of potential function (GeoChip) revealed higher abundances of metal-resistance genes in metal-rich soils. For example, genes that hybridised with metal-resistance genes copA, chrA and czcA of a prevalent aurophillic bacterium, Cupriavidus metallidurans CH34, occurred only in auriferous soils. These data help establish key links between geogenic factors and the phylogeny and function within soil microbial communities. In particular, the landform, which is a crucial factor in determining soil geochemistry, strongly affected microbial community structures.     

Structural characterisation of bisintercalation in higher-order DNA at a junction-like quadruplex

We report the single-crystal X-ray structure for the complex of the bisacridine bis-(9-aminooctyl(2-(dimethylaminoethyl)acridine-4-carboxamide)) with the oligonucleotide d(CGTACG)(2) to a resolution of 2.4A. Solution studies with closed circular DNA show this compound to be a bisintercalating threading agent, but so far we have no crystallographic or NMR structural data conforming to the model of contiguous intercalation within the same duplex. Here, with the hexameric duplex d(CGTACG), the DNA is observed to undergo a terminal cytosine base exchange to yield an unusual guanine quadruplex intercalation site through which the bisacridine threads its octamethylene linker to fuse two DNA duplexes. The 4-carboxamide side-chains form anchoring hydrogen-bonding interactions with guanine O6 atoms on each side of the quadruplex. This higher-order DNA structure provides insight into an unexpected property of bisintercalating threading agents, and suggests the idea of targeting such compounds specifically at four-way DNA junctions.     

The effect of the expulsion phase of Trichinella spiralis on Hymenolepis diminuta infection in rats.

The effect of the intestinal changes brought about by the expulsion of Trichinella spiralis in rats was studied in relation to the growth and survival of a concurrent infection with Hymenolepis diminuta, a cestode not normally rejected by the rat in low-level infections. Growth of H. diminuta was stunted in rats given T. spiralis just before, or after, infection with H. diminuta, the stunting being more pronounced when the cestode was given closer to the period of inflammation. There was no loss of the cestode from dual-infected rats and no evidence for destrobilation was found. Lower T. spiralis burdens had a correspondingly weaker effect on growth of H. diminuta, and stunting was abolished by administration of the anti-inflammatory drug cortisone acetate. It is concluded that the stunting of H. diminuta is probably due to the non-specific inflammatory component of the rat's response to T. spiralis infection.     

Predicting the efficacy of the nitrification inhibitor dicyandiamide in pastoral soils

Aims

Identification of soil, environmental, or microbial properties linked with efficacy of the nitrification inhibitor dicyandiamide (DCD) in high and low-input pastoral farming system soils.

Methods

Soils were collected from under 25 pastures. Potential nitrification rate (PRN) was quantified in the presence and absence of DCD, and percentage efficacy of DCD in reducing PNR calculated. PNR and %DCD efficacy were statistically tested (REML analysis) for relationships to a suite of edaphic (33), environmental (5), and microbiological (8) variables. Microbiological properties included measurement of bacterial and archaeal ammonia monooxygenase genes (amoA qPCR) and soil DNA content.

Results

DCD reduced PRN by an average of 36 %. The percent DCD efficacy was not related to system intensity, soil type, nor PNR (all P?>?0.05). However the numbers of bacterial amoA genes (r?=?0.46; P?<?0.05), and ratios of bacterial:archaeal amoA (r?=??0.53; P?<?0.05), were strongly correlated to %DCD efficacy. In both high and low input systems, models best explaining variance in %DCD efficacy fitted AOA: AOB g soil^?1 as the first varaible (P?<?0.05).

Conclusions

Characterisation of soils based on ammonia oxidising communities may increase the ability to predict the % efficacy of DCD between sites and provide for more targeted application of this nitrification inhibitor.     

The effect of Plasmodium berghei and Trypanosoma brucei infections on the immune expulsion of the nematode Trichuris muris from mice

The effects of concurrent P. berghei or T. brucei infections on the immune expulsion of primary and challenge infections of T. muris from CFLP strain mice have been examined. CFLP mice usually expel the nematode 18–21 days after a primary infection and within 4–6 days after a challenge infection. Both acute malaria and trypanosome infections initiated at the same time as the T. muris infection suppressed worm expulsion; when the protozoal infections were started 7 days after the T. muris infection worm expulsion was suppressed in a proportion of the mice. Acute trypanosome and malaria infections delayed the expulsion of a challenge infection from immune mice, but in the case of P. berghei the delay was short-lived.     

Distribution of an endogenous lectin in the developing chick optic tectum

We determined the cellular localization of an endogenous lectin at various times during the development of a well-characterized region of chick brain, the optic tectum. This lectin is a carbohydrate-binding protein that interacts with lactose and other saccharides, undergoes striking changes in specific activity with development, and has previously been purified by affinity chromatography from extracts of embryonic chick brain and muscle. Cellular localization in the tectum was done by indirect immunofluoresecent staining, using immunoglobulin G derived from an antiserum raised against pure lectin. No lectin was detectable in the optic tectum examined at 5 days of embryonic development. From approximately 7 days of development, neuronal cell bodies and fibers were labeled by the antibody; and extracts of tectum contained hemagglutination activity that could be inhibited by lactose or by the antiserum. Lectin remained present in many tectal neuronal layers after hatching; but in 2-month-old chicks it was sparse or absent in most of the tectum except for prominent labeling of fibers in the stratum album centrale. The initial appearance of lectin in the optic tectum was not dependent on innervation by optic nerve fibers since bilateral enucleation during embryogenesis did not affect it. Lectin was detectable on the surface of embryonic optic tectal neurons dissociated with a buffer containing EDTA.     

The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize

The effects of agronomic management practices on the soil microbial community were investigated in a maize production system in New South Wales, Australia. The site has been intensively studied to measure the impact of stubble management and N-fertilizer application on greenhouse gas emissions (CO(2) and N(2)O), N-cycling, pathology, soil structure and yield. As all of these endpoints can be regulated by microbial processes, the microbiology of the system was examined. Soil samples were taken after a winter fallow period and the diversity of the bacterial and fungal communities was measured using PCR-denaturing gradient gel electrophoresis. Stubble and N shifted the structure of bacterial and fungal communities with the primary driver being stubble addition on the fungal community structure (P<0.05 for all effects). Changes in C, N (total and NO(3)), K and Na, were correlated (P<0.05) with variation in the microbial community structure. Quantitative PCR showed that nifH (nitrogen fixation) and napA (denitrification) gene abundance increased upon stubble retention, whereas amoA gene numbers were increased by N addition. These results showed that the management of both stubble and N have significant and long-term impacts on the size and structure of the soil microbial community at phylogenetic and functional levels.     

Alkyl-linked diquinolines are monofunctional AT-selective DNA-intercalating agents

The binding of a homologous series of alkyl-linked 4-aminodiquinolines to circular and linear DNAs was studied using viscometric titrations and equilibrium dialysis. The compounds are monofunctional intercalators with the capacity for intercalative binding reaching a peak for the heptane homologue. They show marked AT-base pair selectivity, which suggests that the non-intercalated quinoline ring may lie in the DNA minor groove. Affinities for calf thymus DNA increase as the alkyl chain is lengthened, falling in the range 6 to greater than 250 X 10(4) M-1 in a buffer of I 0.01. The association constant of the heptane diquinoline decreases with increasing ionic strength, 2.1 cations being released per bound dipositive ligand molecule. All the agents are growth inhibitory towards mouse leukemia cells in culture with IC50 values in the range 0.06-18 microM.     

The interaction of substituted and rigidly linked diquinolines with DNA

Viscometric measurements with circular and sonicated rodlike DNA fragments were used to explore whether ring substituents or conformationally restricted linkers promote bifunctional intercalation amongst a series of binuclear 4-aminoquinolines bridged via their 4-amino group. We find that ligands comprising unsubstituted quinolines and piperazine or pyrazole linkages bisintercalate. Quinoline-substituted alkyl-linked dimers intercalate in either a mixed monofunctional-bifunctional mode or bind with only one of their chromophores intercalated depending on the nature of the substituents. Equilibrium dialysis measurements show that the binding affinity for calf thymus DNA of the compounds studied ranges from (1.2-12) . 10(4) M-1 in buffer of ionic strength 0.1. Both co-operative and antico-operative binding isotherms were obtained and there is evidence for a second binding mode for the piperazine-linked diquinoline at saturating binding levels. For this compound the high-affinity association constant decreases with increasing ionic strength, 3.4 cations being released per bound ligand molecule. Partition dialysis measurements with DNAs of differing base composition indicate that the compounds studied are either AT selective or sequence neutral depending on ligand structure. For example, the pyrazole linker imparts a marked specificity for binding to AT-rich DNA, whereas the piperazine linker does not. Kinetic measurements using the surfactant-sequestration method reveal that DNA-diquinoline complexes dissociate very rapidly by complex mechanisms with rate constants greater than 100 s-1 in buffer of ionic strength 0.1.