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.

Gross NO Production Process, Not Consumption, Determines the Temperature Sensitivity of Net NO 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 NO emission to temperature variation (i.e., temperature sensitivity, TS).

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.

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.

Reduction of NO emission by biochar and/or 3,4-dimethylpyrazole phosphate (DMPP) is closely linked to soil ammonia oxidizing bacteria and nosZI-NO reducer populations.

Biochar has been demonstrated to reduce nitrous oxide (NO) emissions from soils, but its effect is highly soil-dependent. In particular, in soils with strong nitrification potential, biochar addition may increase NO 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 NO emissions than biochar alone.

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) 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.

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.

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.

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.

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 NO 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.

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

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 ( L.) Root Endophyte, sp. Strain C9.

sp. strain C9 is a plant growth-promoting bacterium isolated from the root tissue of L. grown in soil from Marlborough, New Zealand.

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.

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.

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.

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.

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.

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.

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.

Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia.

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.

Extent of copper tolerance and consequences for functional stability of the ammonia-oxidizing community in long-term copper-contaminated soils.

Adaptation of soil microbial communities to elevated copper (Cu) concentrations has been well documented. However, effects of long-term Cu exposure on adaptation responses associated with functional stability and structural composition within the nitrifying community are still unknown. Soils were sampled in three field sites (Denmark, Thailand, and Australia) where Cu gradients had been established from 3 to 80 years prior to sampling.

The abundance of microbial functional genes in grassy woodlands is influenced more by soil nutrient enrichment than by recent weed invasion or livestock exclusion.

A diverse soil microbial community is involved in nitrogen cycling, and these microbes can be affected by land management practices and weed invasion. We surveyed 20 woodlands with a history of livestock grazing, with livestock recently excluded from 10 sites. We investigated whether soil nutrients were lower when grazing was excluded and higher when exotic grasses dominated the understory.

Bacteria, not archaea, restore nitrification in a zinc-contaminated soil.

Biological ammonia oxidation had long been thought to be mediated solely by discrete clades of beta- and gamma-proteobacteria (ammonia-oxidizing bacteria; AOB). However, ammonia-oxidizing Crenarchaeota (ammonia-oxidizing archaea; AOA) have recently been identified and proposed to be the dominant agents of ammonia oxidation in soils. Nevertheless, the dynamics of AOB versus AOA, and their relative contribution to soil ammonia oxidation and ecosystem functioning on stress and environmental perturbation, remain unknown.

The effect of bacteria on the sensitivity of microalgae to copper in laboratory bioassays.

Although single-species laboratory toxicity tests with microalgae are sensitive and highly reproducible, they lack environmental realism. Interactions between algae and their associated bacteria, either in the plankton or in biofilms, may alter algal sensitivity to contaminants, which are not mimicked in laboratory toxicity tests. This study investigated the effects of simple algal-bacterial relationships on the sensitivity of laboratory-cultured algae to copper using 72-h algal growth-rate inhibition bioassays.