What matters most? Assessment of within-canopy factors influencing the needle microbiome of the model conifer, Pinus radiata.

The assembly and function of the phyllosphere microbiome is important to the overall fitness of plants and, thereby, the ecosystems they inhabit. Presently, model systems for tree phyllosphere microbiome studies are lacking, yet forests resilient to pests, diseases, and climate change are important to support a myriad of ecosystem services impacting from local to global levels. In this study, we extend the development of model microbiome systems for trees species, particularly coniferous gymnosperms, by undertaking a structured approach assessing the phyllosphere microbiome of Pinus radiata. Canopy sampling height was the single most important factor influencing both alpha- and beta-diversity of bacterial and fungal communities (p < 0.005). Bacterial and fungal phyllosphere microbiome richness was lowest in samples from the top of the canopy, subsequently increasing in the middle and then bottom canopy samples. These differences maybe driven by either by (1) exchange of microbiomes with the forest floor and soil with the lower foliage, (2) strong ecological filtering in the upper canopy via environmental exposure (e.g., UV), (3) canopy density, (4) or combinations of factors. Most taxa present in the top canopy were also present lower in tree; as such, sampling strategies focussing on lower canopy sampling should provide good overall phyllosphere microbiome coverage for the tree. The dominant phyllosphere bacteria were Alpha-proteobacteria (Rhizobiales and Sphingomonas) along with Acidobacteria Gp1. However, the P. radiata phyllosphere microbiome samples were fungal dominated. From the top canopy samples, Arthoniomycetes and Dothideomycetes were highly represented, with abundances of Arthoniomycetes then reducing in lower canopy samples whilst abundances of Ascomycota increased. The most abundant fungal taxa were Phaeococcomyces (14.4% of total reads) and Phaeotheca spp. (10.38%). A second-order effect of canopy sampling direction was evident in bacterial community composition (p = 0.01); these directional influences were not evident for fungal communities. However, sterilisation of needles did impact fungal community composition (p = 0.025), indicating potential for community differences in the endosphere versus leaf surface compartments. Needle age was only important in relation to bacterial communities, but was canopy height dependant (interaction p = 0.008). By building an understanding of the primary and secondary factors related to intra-canopy phyllosphere microbiome variation, we provide a sampling framework to either explicitly minimise or capture variation in needle collection to enable ongoing ecological studies targeted at inter-canopy or other experimental levels.

Niche Differentiation Among Canonical Nitrifiers and N2O Reducers Is Linked to Varying Effects of Nitrification Inhibitors DCD and DMPP in Two Arable Soils.

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.

Gross N2O Production Process, Not Consumption, Determines the Temperature Sensitivity of Net N2O Emission in Arable Soil Subject to Different Long-Term Fertilization Practices.

Chronic amendment of agricultural soil with synthetic nitrogen fertilization and/or livestock manure has been demonstrated to enhance the feedback intensity of net N2O emission to temperature variation (i.e., temperature sensitivity, TS). Yet few studies have explored the relevance of changes in underlying gross N2O production and consumption processes toward explaining this phenomenon, in particular for the latter. Furthermore, the microbe-based mechanisms associated with the variation of N2O consumption process remain largely unexplored. To address this knowledge gap, a temperature- (15, 25, and 35°C) and moisture-controlled (50% water holding capacity) microcosm incubation experiment was established using an arable soil subject to long-term addition of synthetic fertilizer (NPK), a mixture of synthetic fertilizer with livestock manure (MNPK), or with no fertilizer treatment (CT). Over the incubation time period, the C2H2 inhibition method was adopted to monitor reaction rates of gross N2O production and consumption; the population sizes and community structures of nosZI- and nosZII-N2O reducers were analyzed using quantitative PCR (Q-PCR) and terminal restriction fragment length polymorphism (T-RFLP). The results indicated that only NPK significantly increased the TS of net N2O emission, and gross N2O consumption process consistently occurred under all treatment combinations (temperature and fertilization) at each sampling time point. The responses of gross N2O production and consumption processes to temperature elevation exhibited fertilization- and sampling time-dependent pattern, and the higher net N2O production TS in the NPK treatment was underlain by its higher TS of gross production process and insensitivity of gross consumption process to temperature. The size and structure of nosZII-N2O reducers, as well as the community structure of nosZI-N2O reducers, were positively correlated with variation of gross N2O production and consumption rates across all fertilization regimes. NosZII-N2O reducer abundance was less responsive to temperature change, and its community structure less susceptible to fertilization, as compared with nosZI-N2O reducers. Overall, our results demonstrate that the TS of the gross N2O production process, not gross consumption, is the key step regulating the TS of net N2O production, and both nosZI- and nosZII-N2O clades are likely active N2O reducers in the tested soil.

Functional capabilities of bacterial biofilms on gold particles.

Gold particles contain gold and other toxic, heavy metals, making them 'extreme' geochemical microenvironments. To date, the functional capabilities of bacterial biofilms to deal with these conditions have been inferred from taxonomic analyses. The aims of this study are to evaluate the functional capabilities of bacterial communities on gold particles from six key locations using GeoChip 5.0 and to link functional and taxonomic data. Biofilm communities displayed a wide range of functional capabilities, with up to 53 505 gene probes detected. The capability of bacterial communities to (re)cycle carbon, nitrogen, and sulphur were detected. The cycling of major nutrients is important for maintaining the biofilm community as well as enabling the biogeochemical cycling and mobilisation of heavy and noble metals. Additionally, a multitude of stress- and heavy metal resistance capabilities were also detected, most notably from the α/ß/γ-Proteobacteria and Actinobacteria. The multi-copper-oxidase gene copA, which is directly involved in gold resistance and biomineralisation, was the 15th most intense response and was detected in 246 genera. The Parker Road and Belle Brooke sites were consistently the most different from other sites, which may be a result of local physicochemical conditions (extreme nutrient poverty and sulphur-richness, respectively). In conclusion, biofilms on gold particles display wide-ranging metabolic and stress-related capabilities, which may enable them to survive in these niche environments and drive biotransformation of gold particles.

Stakeholder valuation of soil ecosystem services from New Zealand's planted forests.

The goal of this study was to determine if there were differences among stakeholders in the values they attribute to soil ecosystem services from plantation forests in New Zealand. Groups of forest-associated stakeholders were identified (e.g. land owners, forest owners, wood processors, and recreational forest users) and surveyed to assess their cultural background (indigenous New Zealand Maori or not) and then the relative importance they placed on 10 forest soil ecosystem services. Across all survey respondents, very high importance was placed on the ability of soils to sustain forest growth across multiple plantings/rotations (sustainable production). Interestingly, this was more highly valued than maximising short-term production. Maori placed greater importance on forest ecosystem resilience, provenance and kaitiakitanga (sensu stewardship of resources), water quality, and harvest of food and/or medicines from forests than non-Maori. These results demonstrate inherent cultural differences in valuing the range of forest ecosystem services that soils support. It is important that cultural views are understood and integrated into future soil health testing schemes to reflect the needs of all stakeholders. Ultimately, this work will help increase the sustainability of planted forest ecosystems in New Zealand, ensure the forestry sectors social licence to operate, and add value to forest products by demonstrating environmental and cultural stewardship of forest products.

Reduction of N2O emission by biochar and/or 3,4-dimethylpyrazole phosphate (DMPP) is closely linked to soil ammonia oxidizing bacteria and nosZI-N2O reducer populations.

Biochar has been demonstrated to reduce nitrous oxide (N2O) emissions from soils, but its effect is highly soil-dependent. In particular, in soils with strong nitrification potential, biochar addition may increase N2O emissions. Thus, in soils with strong nitrification potential, the combination of biochar with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) may be more effective in reducing N2O emissions than biochar alone. However, the combined use of biochar and DMPP on soil N2O emissions is relatively unexplored, and underlying microbial mechanisms of how biochar and/or DMPP amendment affect N2O emissions is still largely unknown. Here, a 30-day incubation experiment was established with four treatments: CK (control), BC (biochar), DMPP, and BD (biochar and DMPP), all at agronomically recommended rates, and N cycling assessed following addition of urea. Treatment of soil with BC, DMPP and BD reduced N2O emissions (compared with urea alone) by 59.1%, 95.5% and 74.1%, respectively. Quantification of N cycling genes (amoA, nirS, nirK, and nosZ) indicated that biochar stimulated growth of ammonia oxidizing archaea (AOA) and bacteria (AOB), while DMPP alone inhibited the activity and growth of AOB. In the BD treatment, DMPP was absorbed onto biochar reducing its efficacy in inhibiting AOB growth. The response patterns of nirS/nirK nitrite-reducing denitrifiers to biochar and/or DMPP addition varied among clades. Notably, biochar and/or DMPP increased the abundance of nosZI and nosZII-N2O reducers, but nosZI-clade taxa were more closely associated with reducing N2O emission than nosZII taxa. Overall, our findings proved that the dynamics of AOB and nosZI-N2O reducers resulting from the addition of biochar and/or DMPP played a key role in governing soil N2O emissions.

Silver Toxicity Thresholds for Multiple Soil Microbial Biomarkers.

Material flow analysis shows that soil is a key repository for silver (Ag) from (nano)silver-functionalized consumer products, but the potential effects of Ag toxicity, via Ag+ release, on soil microbial communities and their ecosystem services remains largely unknown. We examined the responses of multiple microbial biomarkers to increasing Ag+ doses (nine concentrations, 0-2000 mg kg-1) in nine different soils representing a wide range of soil properties. Analyses included substrate-induced microbial respiration, nine different soil enzyme activities, and quantification of bacterial 16S-rRNA (SSU) and fungal intergenic spacer (ITS) copies. The resulting half-maximal effective concentrations (EC50) for Ag ranged from ∼1 to >500 mg kg -1 and showed soil-specific responses, including some hormesis-type responses. Carbon cycle-associated enzyme activities (e.g., cellobiohydrolase, xylosidase, and α/ß-glucosidase) responded similarly to Ag. Sulfatase and leucine-aminopeptidase activities (linked to the sulfur and nitrogen cycles) were the most sensitive to Ag. Total organic carbon, and to a lesser extent pH, were identified as potentially useful response predictors, but only for some biomarkers; this reflects the complexity of soil Ag chemistry. Our results show Ag toxicity is highly dependent on soil characteristics and the specific microbial parameter under investigation, but end point redundancies also indicated that representative parameters for key microbial functions can be identified for risk assessment purposes. Sulfatase activity may be an important Ag toxicity biomarker; its response was highly sensitive and not correlated with that of other biomarkers.

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression.

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.

Dynamics of bacterial composition and the fate of antibiotic resistance genes and mobile genetic elements during the co-composting with gentamicin fermentation residue and lovastatin fermentation residue.

Dynamics in bacterial community composition, along with 13 antibiotic resistance genes (ARGs) and eight mobile genetic elements (MGEs), were assessed during co-composting with gentamicin and lovastatin fermentation residue (GFR and LFR, respectively). Using next generation sequencing, the key bacterial taxa associated with the different stages of composting were identified. Most importantly, Bacillus, belonging to Phylum Firmicutes, was associated with enhanced degradation of gentamicin, decomposition of organic matter (OM) and dissolved organic carbon (DOC), and also extension of the thermophilic phase of the composting cycle. During the course of composting, the patterns of different ARGs/MGEs varied. However, the total and the normalized (to bacterial numbers) copies both remained high. The abundance of various ARGs was related to bacterial abundance and community composition, and the changing pattern of individual ARGs was influenced by the selectivity of MGEs and bacteria.

High spatial variation in population size and symbiotic performance of Rhizobium leguminosarum bv. trifolii with white clover in New Zealand pasture soils.

Biological nitrogen fixation through the legume-rhizobia symbiosis is important for sustainable pastoral production. In New Zealand, the most widespread and valuable symbiosis occurs between white clover (Trifolium repens L.) and Rhizobium leguminosarum bv. trifolii (Rlt). As variation in the population size (determined by most probable number assays; MPN) and effectiveness of N-fixation (symbiotic potential; SP) of Rlt in soils may affect white clover performance, the extent in variation in these properties was examined at three different spatial scales: (1) From 26 sites across New Zealand, (2) at farm-wide scale, and (3) within single fields. Overall, Rlt populations ranged from 95 to >1 x 108 per g soil, with variation similar at the three spatial scales assessed. For almost all samples, there was no relationship between rhizobia population size and ability of the population to fix N during legume symbiosis (SP). When compared with the commercial inoculant strain, the SP of soils ranged between 14 to 143% efficacy. The N-fixing ability of rhizobia populations varied more between samples collected from within a single hill country field (0.8 ha) than between 26 samples collected from diverse locations across New Zealand. Correlations between SP and calcium and aluminium content were found in all sites, except within a dairy farm field. Given the general lack of association between SP and MPN, and high spatial variability of SP at single field scale, provision of advice for treating legume seed with rhizobia based on field-average MPN counts needs to be carefully considered.

Nitrous oxide emission and denitrifier communities in drip-irrigated calcareous soil as affected by chemical and organic fertilizers.

The effects of consecutive application of chemical fertilizer with or without organic fertilizer on soil N2O emissions and denitrifying community structure in a drip-irrigated field were determined. The four fertilizer treatments were (i) unfertilized, (ii) chemical fertilizer, (iii) 60% chemical fertilizer plus cattle manure, and (iv) 60% chemical fertilizer plus biofertilizer. The treatments with organic amendments (i.e. cattle manure and biofertilizer) reduced cumulative N2O emissions by 4.9-9.9%, reduced the N2O emission factor by 1.3-42%, and increased denitrifying enzyme activities by 14.3-56.2%. The nirK gene copy numbers were greatest in soil which received only chemical fertilizer. In contrast, nirS- and nosZ-copy numbers were greatest in soil amended with chemical fertilizer plus biofertilizer. Chemical fertilizer application with or without organic fertilizer significantly changed the community structure of nirK-type denitrifiers relative to the unfertilized soil. In comparison, the nirS- and nosZ-type denitrifier genotypes varied in treatments receiving organic fertilizer but not chemical fertilizer alone. The changes in the denitrifier communities were closely associated with soil organic carbon (SOC), NO3-, NH4+, water holding capacity, and soil pH. Modeling indicated that N2O emissions in this soil were primarily associated with the abundance of nirS type denitrifying bacteria, SOC, and NO3-. Overall, our findings indicate that (i) the organic fertilizers increased denitrifying enzyme activity, increased denitrifying-bacteria gene copy numbers, but reduced N2O emissions, and (ii) nirS- and nosZ-type denitrifiers were more sensitive than nirK-type denitrifiers to the organic fertilizers.

Draft Genome Sequence of the Clover (Trifolium repens L.) Root Endophyte Paraburkholderia sp. Strain A27.

Paraburkholderia sp. strain A27, isolated from the root material of white clover, has plant growth-promoting activity on a range of agriculturally important plants. The draft genome of this bacterium is 7,393,089 bp and harbors a range of genes putatively involved in host colonization.

Draft Genome Sequence of a Kale (Brassica oleracea L.) Root Endophyte, Pseudomonas sp. Strain C9.

Pseudomonas sp. strain C9 is a plant growth-promoting bacterium isolated from the root tissue of Brassica oleracea L. grown in soil from Marlborough, New Zealand. Its draft genome of 6,350,161 bp contains genes associated with plant growth promotion and biological control.

Geogenic Factors as Drivers of Microbial Community Diversity in Soils Overlying Polymetallic Deposits.

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.

Effects of climate change on the delivery of soil-mediated ecosystem services within the primary sector in temperate ecosystems: a review and New Zealand case study.

Future human well-being under climate change depends on the ongoing delivery of food, fibre and wood from the land-based primary sector. The ability to deliver these provisioning services depends on soil-based ecosystem services (e.g. carbon, nutrient and water cycling and storage), yet we lack an in-depth understanding of the likely response of soil-based ecosystem services to climate change. We review the current knowledge on this topic for temperate ecosystems, focusing on mechanisms that are likely to underpin differences in climate change responses between four primary sector systems: cropping, intensive grazing, extensive grazing and plantation forestry. We then illustrate how our findings can be applied to assess service delivery under climate change in a specific region, using New Zealand as an example system. Differences in the climate change responses of carbon and nutrient-related services between systems will largely be driven by whether they are reliant on externally added or internally cycled nutrients, the extent to which plant communities could influence responses, and variation in vulnerability to erosion. The ability of soils to regulate water under climate change will mostly be driven by changes in rainfall, but can be influenced by different primary sector systems' vulnerability to soil water repellency and differences in evapotranspiration rates. These changes in regulating services resulted in different potentials for increased biomass production across systems, with intensively managed systems being the most likely to benefit from climate change. Quantitative prediction of net effects of climate change on soil ecosystem services remains a challenge, in part due to knowledge gaps, but also due to the complex interactions between different aspects of climate change. Despite this challenge, it is critical to gain the information required to make such predictions as robust as possible given the fundamental role of soils in supporting human well-being.

Mechanisms of pollution induced community tolerance in a soil microbial community exposed to Cu.

Pollution induced community tolerance (PICT) to Cu(2+), and co-tolerance to nanoparticulate Cu, ionic silver (Ag(+)), and vancomycin were measured in field soils treated with Cu(2+) 15 years previously. EC50 values were determined using substrate induced respiration and correlations made against soil physicochemical properties, microbial community structure, physiological status (qCO2; metabolic quotient), and abundances of genes associated with metal and antibiotic resistance. Previous level of exposure to copper was directly (P < 0.05) associated with tolerance to addition of new Cu(2+), and also of nanoparticle Cu. However, Cu-exposed communities had no co-tolerance to Ag(+) and had increased susceptibly to vancomycin. Increased tolerance to both Cu correlated (P < 0.05) with increased metabolic quotient, potentially indicating that the community directed more energy towards cellular maintenance rather than biomass production. Neither bacterial or fungal community composition nor changes in the abundance of genes involved with metal resistance were related to PICT or co-tolerance mechanisms.

Links between sulphur oxidation and sulphur-oxidising bacteria abundance and diversity in soil microcosms based on soxB functional gene analysis.

Sulphur-oxidising bacteria (SOB) play a key role in the biogeochemical cycling of sulphur in soil ecosystems. However, the ecology of SOB is poorly understood, and there is little knowledge about the taxa capable of sulphur oxidation, their distribution, habitat preferences and ecophysiology. Furthermore, as yet there are no conclusive links between SOB community size or structure and rates of sulphur oxidation. We have developed a molecular approach based on primer design targeting the soxB functional gene of nonfilamentous chemolithotrophic SOB that allows assessment of both abundance and diversity. Cloning and sequencing revealed considerable diversity of known soxB genotypes from agricultural soils and also evidence for previously undescribed taxa. In a microcosm experiment, abundance of soxB genes increased with sulphur oxidation rate in soils amended with elemental sulphur. Addition of elemental sulphur to soil had a significant effect in the soxB gene diversity, with the chemolithotrophic Thiobacillus-like Betaproteobacteria sequences dominating clone libraries 6 days after sulphur application. Using culture-independent methodology, the study provides evidence for links between abundance and diversity of SOB and sulphur oxidation. The methodology provides a new tool for investigation of the ecology and role of SOB in soil sulphur biogeochemistry.

Application of MicroResp™ for soil ecotoxicology.

MicroResp™ is a miniaturised method for measuring substrate induced respiration (SIR) in soil. We modified the MicroResp™ method to develop a rapid tool for quantifying the ecotoxicological impact of contaminants. The method is based on reduction in SIR across a gradient of contaminant, allowing for determination of dose-response curves EC-values. Contaminants are mixed into soil samples at a range of concentrations; each sample is then dispensed into a column of eight wells in 96 well format (deep) plates. Moisture and glucose are added to the samples at levels to provide maximum response. Released CO2 from the soils is then measured using colorimetric gel-traps, following the standard MicroResp™ methodology. Examination revealed that this method works over a range of soil types and is insensitive to minor variations in assay length (2-7 h), alteration of moisture content (±20 µL from optimum), and soil storage conditions (4 °C versus fresh).

Effect of nitrogen and waterlogging on denitrifier gene abundance, community structure and activity in the rhizosphere of wheat.

Microbial denitrification plays a key role in determining the availability of soil nitrogen (N) to plants. However, factors influencing the structure and function of denitrifier communities in the rhizosphere remain unclear. Waterlogging can result in root anoxia and increased denitrification, leading to significant N loss from soil and potential nitrous oxide (N(2)O) emissions. This study investigated denitrifier gene abundance, community structure and activity in the rhizosphere of wheat in response to anoxia and N limitation. Denitrifier community structure in the rhizosphere differed from that in bulk soil, and denitrifier gene copy numbers (nirS, nirK, nosZ) and potential denitrification activity were greater in the rhizosphere. Anoxia and N limitation, and in particular a combination of both, reduced the magnitude of this effect on gene abundance (in particular nirS) and activity, with N limitation having greater impact than waterlogging in rhizosphere soil, in contrast to bulk soil where the impact of waterlogging was greater. Increased N supply to anoxic plants improved plant health and increased rhizosphere soil pH, which resulted in enhanced reduction of N(2)O. Both anoxia and N limitation significantly influenced the structure and function of denitrifier communities in the rhizosphere, with reduced root-derived carbon postulated to play an important role.

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.