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Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity.

The efficacy of nitrification inhibitors (NIs) dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP) varies with soil types. Understanding the microbial mechanisms for this variation may lead to better modelling of NI efficacy and therefore on-farm adoption. This study addressed the response patterns of mineral nitrogen, nitrous oxide (N2O) emission, abundances of N-cycling functional guilds and soil microbiota characteristics, in relation to urea application with or without DCD or DMPP in two arable soils (an alkaline and an acid soil). The inhibition of nitrification rate and N2O emission by NI application occurred by suppressing ammonia-oxidizing bacteria (AOB) abundances and increasing the abundances of nosZI-N2O reducers; however, abundances of ammonia-oxidizing archaea (AOA) were also stimulated with NIs-added in these two arable soils. DMPP generally had stronger inhibition efficiency than DCD, and both NIs' addition decreased Nitrobacter, while increased Nitrospira abundance only in alkaline soil. N2O emissions were positively correlated with AOB and negatively correlated with nosZI in both soils and AOA only in acid soil. Moreover, N2O emissions were also positively correlated with nirK-type denitrifiers in alkaline soil, and clade A comammox in acid soil. Amendment with DCD or DMPP altered soil microbiota community structure, but had minor effect on community composition. These results highlight a crucial role of the niche differentiation among canonical ammonia oxidizers (AOA/AOB), Nitrobacter and Nitrospira, as well as nosZI- and nosZII-N2O reducers in determining the varying efficacies of DCD and DMPP in different arable soils. [ABSTRACT FROM AUTHOR]

Ammonia-oxidising archaea (AOA) have recently been described as having an important role in soil nitrification. However, published data on factors which influence their distribution and their impact on a soil's potential nitrification rates (PNR) are sparse, particularly compared with the amount of information available regarding ammonia-oxidising bacteria (AOB). This study had two aims. First, to investigate which environmental factors affect the AOA : AOB ratio in soils from two agricultural regions, and second, to explore whether the abundance of either AOA or AOB correlated with PNR. Samples were collected from 45 sites within the cropping regions of Western Australia and South Australia. Soils were tested for pH, N[H.sub.4.sup.+]/N[O.sub.3.sup.-], organic carbon (C), total nitrogen (N), C : N ratio, PNR, and electrical conductivity. Climate data were obtained from the Queensland Climate Change Centre for Excellence SILO website. Abundances of AOA and AOB were measured using real-time PCR quantification of the gene encoding the ammonia monooxygenase enzyme (amoA). Multivariate statistical analysis was applied to assess correlations between PNR, soil properties, and abundance of AOA or AOB. In the majority samples AOA were present, but their abundance, and the AOA : AOB ratio, varied considerably between sites. Multivariate analysis showed that the distribution of AOA and AOB and the AOA : AOB ratio were strongly correlated with climatic and seasonal factors. Sites where samples were collected during dry, hot periods tended to be AOA-dominated, whereas samples collected during cool, wet periods tended to be AOB-dominated or have equal abundances of AOA and AOB. The PNRs were correlated with total N content, organic C content, and soil pH. There was no clear correlation between AOA or AOB and PNR. This study shows that both AOA and AOB are widespread in Western Australian and South Australian soils and their abundance and ratio are affected by climate and season. It also shows that PNR is more strongly influenced by soil fertility factors than by the AOA:AOB ratio. Additional keywords: ammonia-oxidising archaea, ammonia-oxidising bacteria, amoA, distribution, potential nitrification rate., Introduction Nitrification is the microbially mediated conversion of reduced forms of nitrogen, i.e. ammonia (N[H.sup.3]) and ammonium (N[H.sub.4.sup.+]), into oxidised forms, e.g. nitrate (N[O.sub.3.sup.-]) and nitrite (N[O.sub.2.sup.-]). The first and [...]

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 [...]

We explored the microbial ecology of water draining through the soil (lysimeter samples) and in the shallow aquifers (bore samples) underlying sugarcane and banana fields near the Great Barrier Reef (GBR), Australia. Lysimeter and bore water samples were collected and analysed chemically and with DNA fingerprinting methods (PCR-DGGE and clone library sequencing) to characterise the structure of the bacterial community. Bacterial communities in soil water and bore water were distinct (P < 0.05), and a primary factor linked with bacterial community structure was water pH (P < 0.05), particularly in water sampled from lysimeters. Irrespective of treatment, >80% of all rRNA gene sequences originated from proteobacteria. However, groundwater communities differed from those in soil water by greater occurrence of Neisseriales and Comamonadaceae (P< 0.01). qPCR was used to measure copy numbers of the nirK and nirS genes encoding NO-forming nitrite reductases. Copy numbers of both genes were greater in soil water samples than groundwater (P = 0.05), with the difference in nirK being greater under sugarcane than banana. These differences in nirK-gene abundance show that there is greater potential for denitrification in soil water under sugarcane, leading to low concentrations of nitrate in the underlying groundwater. This knowledge can be used towards development of soil and land-use management practices promoting bacterial denitrification in groundwater to lessen the undesirable ecological consequences where groundwater discharges lower in the GBR catchment zones., Introduction The Great Barrier Reef (GBR), off the north-east coast of Australia, is the largest coral-reef ecosystem in the world. It is of immense ecological and economic significance, and is [...]

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