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The abundances of ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB) in soils underlying pastures in the south-west of Western Australia (WA) were investigated. samples were collected from irrigated pastures and one unmanaged (driveway) area during December 2009. Archaeal and bacterial ammonia monooxygenase (amoA) genes were quantified using real-time PCR, and the diversity of the archaeal amoA genes was investigated using denaturing gradient gel electrophoresis (PCR-DGGE). AOA amoA gene copies outnumbered AOB in all samples. Numbers ofarchaeal amoA genes ranged from 4.1 E+01 to 1.34E+05 gene copies/ng soil DNA. Bacterial amoA genes were below detection limits at three of the four sample sites and ranged from 8.9E+01 to 6.7E+02 gene copies/rig soil DNA at the remaining site. Potential nitrification rates (PNR) were not correlated with AOA or AOB gene abundance, but high PNR only occurred at the site with measureable numbers of AOB. The DGGE analysis revealed that the AOA community was diverse and variability in banding patterns was significantly affected by both site and depth (P< 0.05). Statistical analysis matching biological variation (AOA amoA genotypes) to environmental variables (BEST analysis) revealed that pH was the key driver of AOA community structure (p-0.72; P = 0.005). Soil pH was also inversely correlated to abundance of AOA amoA genes in soil (p = 0.8; P=0.003). This study has shown that AOA are important members of the nitrogencycling community in acidic WA pasture soils, and likely in the wider agricultural soils of WA. Additional keywords: ammonia oxidation, acidic soils, ammonia-oxidising archaea, ammonia-oxidising bacteria, amoA, nitrification., Introduction The microbially mediated conversion of ammonium-nitrogen (N[H.sup.4.sup.+]-N) to nitrite-N (N[O.sub.2.sup.-]-N) is the first step in the process of nitrification, i.e. the oxidation of N[H.sup.4.sup.+] to nitrate (N[O.sub.3]) (Focht and [...]

Biofilms living on gold (Au) grains play a key role in the biogeochemical cycle of Au by promoting the dispersion of Au via the formation of Au nanoparticles as well as the formation of secondary biomorphic Au. Gold grains from Queensland, Australia, are covered by a polymorphic, organic-inorganic layer that is up to 40 [micro]m thick. It consists of a bacterial biofilm containing Au nanoparticles associated with extracellular polymeric substances as well as bacterioform Au. Focused ion beam (FIB) sectioning through the biofilm revealed that aggregates of nanoparticulate Au line open spaces beneath the active biofilm layer. These aggregates (bacterioform Au type 1) resulted from the reprecipitation of dissolved Au, and their internal growth structures provide direct evidence for coarsening of the Au grains. At the contact between the polymorphic layer and the primary Au, bacterioform Au type 2 is present. It consists of solid rounded forms into which crystal boundaries of underlying primary Au extend, and is the result of dealloying and Ag dissolution from the primary Au. This study demonstrates that (1) microbially driven dissolution, precipitation, and aggregation lead to the formation of bacterioform Au and contribute to the growth of Au grains under supergene conditions, and (2) the microbially driven mobilization of coarse Au into nanoparticles plays a key role in mediating the mobility of Au in surface environments, because the release of nanoparticulate Au upon biofilm disintegration greatly enhances environmental mobility compared to Au complexes only. doi: 10.1130/G31052.1

Background: The atyid shrimp Paratya australiensis occurs in surface freshwater habitats throughout eastern Australia and has been used to study the ecotoxicology of contaminants such as pesticides and metals. The acidification of surface water that can occur after acid sulfate material in soils and sediments is oxidised and subsequently re-wetted is a serious environmental issue in coastal regions and inland riverine floodplains worldwide. Solubilisation of soil-associated minerals can result in high waterborne concentrations of mineral salts and dissolved metals, which together with low pH represent a potential threat to aquatic ecosystems in affected regions. The aims of the present study were to gain insight into stress responses induced by exposure to acid drainage water (ADW) in P. australiensis by determining changes in the abundance of protein-coding transcripts and to generate a comprehensive transcriptomic resource to facilitate further research into gene regulation or protein structure and function in this species. Adult P. australiensis were exposed for 24 h to undiluted ADW, 50 % ADW diluted in river water, or to river water as control, and high-throughput mRNA sequencing (RNA-Seq) conducted on whole-body tissues. A reference transcriptome was generated using de novo assembly and putative protein-coding regions were identified and annotated. Changes in transcript abundance in response to ADW exposure were determined by aligning reads to the reference transcriptome and quantifying coverage. Results: A high proportion of arthropod benchmarking universal single-copy orthologues were present in the reference transcriptome. Functions associated with cuticle biosynthesis and oxidative stress were significantly enriched in the lists of transcripts exhibiting differential abundance in either direction after exposure to 50 % or 100 % ADW. Transcripts involved in osmoregulation exhibited decreased abundance following exposure to ADW. The transcriptome contained full-length coding sequences for numerous proteins known to be involved in environmental response pathways, including two putative metallothioneins, four glutathione peroxidases and 19 nuclear receptors. Conclusions: The results of the present study provide insight into stress response pathways induced in crustaceans by short-term exposure to multiple stressors present in ADW such as low pH, high salinity and dissolved metals, and represent a resource for future toxicogenomics and protein functional studies in P. australiensis [ABSTRACT FROM AUTHOR]

The endocrine responses in male Murray rainbowfish ( Melanotaenia fluviatilis) were evaluated after exposures to biologically active concentrations of the nonsteroidal pharmaceutical, flutamide. Fish were exposed to nominal concentrations of 125 µg/L, 250 µg/L, 500 µg/L, and 1000 µg/L of flutamide for 7 d, after which plasma vitellogenin concentration; brain aromatase activity; and hepatic expression of the genes for vitellogenin, choriogenin, and androgen and estrogen receptors were assessed. Qualitative assessment of the testes of the fish exposed to flutamide exhibited hindrance in the transformation of spermatogonia to spermatozoa and increased testicular anomalies, such as multinucleated and pyknotic cells and interstitial fibrosis. An increase in the hepatosomatic index with respect to the controls was noted after treating the fish with flutamide at all concentrations. Vitellogenin was induced in plasma in the 1000 µg/L flutamide group. The activity of aromatase in the brain declined significantly after exposures to flutamide at all concentrations. Males exposed to 1000 µg/L of flutamide showed a downregulation in the genes encoding androgen receptors α and β. The expression of the gene for the estrogen receptor α was induced and of vitellogenin was downregulated after treatment with 250 µg/L to 1000 µg/L of flutamide. The results suggest that 7-d exposures to 125 µg/L to 1000 µg/L flutamide can impair the reproductive endocrine system in male Murray rainbowfish at multiple levels by an antiandrogenic mode of action. Environ Toxicol Chem 2014;33:1098-1107. © 2014 SETAC [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We investigated bacterial community assemblages and functions down a hill slope contaminated by tailings from a volcanogenic massive sulphide mine in arid Western Australia. Weathering of waste rock, high in S and Fe, had resulted in a varying elemental dispersal down a face of the tailings hill. Bacterial community assemblage, characterised by PCR- DGGE fingerprinting, was significantly associated with electrical conductivity ( E. C.) (ρ = 0.664; P < 0.01). Analysis of mobile salts showed that E. C. values were driven by ionic S, Zn, Cl and Al. The bacterial community assemblage was directly characterised across an E. C. gradient using an oligonucleotide microarray ( Phylo Chip). The dominant taxa at the site were P roteobacteria, A ctinobacteria and F irmicutes; however, 37 phyla were detected. The most responsive taxa to variation in E. C. was A cidobacteria (negative correlation). Patterns of heterotrophic processes ( Bio Log analysis) were also best explained by variation in E. C. (ρ = 0.53; P < 0.01), showing a link between primary mineral weathering by lithotrophic bacteria and abiotic processes, and secondary biogeochemical processes by heterotrophic taxa. These data significantly broaden our knowledge of the bacteria present in metallomorphic ecosystems, establish that mobile phase elements are key drivers of community structure, and that primary biogeochemical cycling is directly influencing other geochemical interactions in the samples. [ABSTRACT FROM AUTHOR]

This study shows that the geogenic factors landform, lithology, and underlying mineral deposits (expressed by elevated metal concentrations in overlying soils) are key drivers of microbial community diversity in naturally metal-rich Australian soils with different land uses, i.e., agriculture versus natural bushland. One hundred sixty-eight soil samples were obtained from two metal-rich provinces in Australia, i.e., the Fifield Au-Pt field (New South Wales) and the Hillside Cu-Au-U rare-earth-element (REE) deposit (South Australia). Soils were analyzed using three-domain multiplex terminal-restriction-fragment-length-polymorphism (M-TRFLP) and PhyloChip microarrays. Geogenic factors were determined using field-mapping techniques and analyses of >50 geochemical parameters. At Fifield, microbial communities differed significantly with geogenic factors and equally with land use (P < 0.05). At Hillside, communities in surface soils (0.03- to 0.2-m depth) differed significantly with landform and land use (P < 0.05). Communities in deeper soils (>0.2 m) differed significantly with lithology and mineral deposit (P < 0.05). Across both sites, elevated metal contents in soils overlying mineral deposits were selective for a range of bacterial taxa, most importantly Acidobacteria, Bacilli, Betaproteobacteria, and Epsilonproteobacteria. In conclusion, long-term geogenic factors can be just as important as land use in determining soil microbial community diversity. [ABSTRACT FROM AUTHOR]