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To comprehensively evaluate the impact of agricultural management practices on soil productivity, it is imperative to conduct a thorough analysis of soil bacterial ecology. Deep‐banding nutrient‐rich amendments is a soil management practice that aims to improve plant growth and soil structure by addressing the plant‐growth constraints posed by dense‐clay subsoils. However, the response of bacterial communities to deep‐banded amendments has not been thoroughly studied. To address this knowledge gap, we conducted a controlled‐environment column experiment to examine the effects of different types of soil amendments (poultry litter, wheat straw + chemical fertiliser and chemical fertiliser alone) on bacterial taxonomic composition in simulated dense‐clay subsoils. We evaluated the bacterial taxonomic and ecological group composition in soils beside and below the amendment using 16S rRNA amplicon sequencing and robust statistical methods. Our results indicate that deep‐banded amendments alter bacterial communities through direct and indirect mechanisms. All amendments directly facilitated a shift in bacterial communities in the absence of growing wheat. However, a combination of amendments with growing wheat led to a more pronounced bacterial community shift which was distinct from and eclipsed the direct impact of the amendments and plants alone. This indirect mechanism was evidenced to be mediated primarily by plant growth and hypothesised to result from an enhancement in wheat root distribution, density and rhizodeposition changes. Therefore, we propose that subsoil amendments regardless of type facilitated an expansion in the rhizosphere which engineered a substantial plant‐mediated bacterial community response within the simulated dense‐clay subsoils. Overall, our findings highlight the importance of considering the complex and synergistic interactions between soil physicochemical properties, plant growth and bacterial communities when assessing agricultural management strategies for improving soil and plant productivity. [ABSTRACT FROM AUTHOR]

Spatial and temporal variability in benthic flux denitrification efficiency occurs across Port Phillip Bay, Australia. Here, we assess the capacity for untargeted metatranscriptomics to resolve spatiotemporal differences in the microbial contribution to benthic nitrogen cycling. The most abundant sediment transcripts assembled were associated with the archaeal nitrifier Nitrosopumilus. In sediments close to external inputs of organic nitrogen, the dominant transcripts were associated with Nitrosopumilus nitric oxide nitrite reduction (nirK). The environmental conditions close to organic nitrogen inputs that select for increased transcription in Nitrosopumilus (amoCAB, nirK, nirS, nmo, hcp) additionally selected for increased transcription of bacterial nitrite reduction (nxrB) and transcripts associated with anammox (hzo) but not denitrification (bacterial nirS/nirk). In sediments that are more isolated from external inputs of organic nitrogen dominant transcripts were associated with nitrous oxide reduction (nosZ) and changes in nosZ transcript abundance were uncoupled from transcriptional profiles associated with archaeal nitrification. Coordinated transcription of coupled community‐level nitrification–denitrification was not well supported by metatranscriptomics. In comparison, the abundance of archaeal nirK transcripts were site‐ and season‐specific. This study indicates that the transcription of archaeal nirK in response to changing environmental conditions may be an important and overlooked feature of coastal sediment nitrogen cycling. [ABSTRACT FROM AUTHOR]

Most studies on soil N2O emissions have focused either on the quantifying of agricultural N2O fluxes or on the effect of environmental factors on N2O emissions. However, very limited information is available on how land-use will affect N2O production, and nitrifiers involved in N2O emissions in agricultural soil ecosystems. Therefore, this study aimed at evaluating the relative importance of nitrification and denitrification to N2O emissions from different land-use soils and identifying the potential underlying microbial mechanisms. A 15N-tracing experiment was conducted under controlled laboratory conditions on four agricultural soils collected from different land-use. We measured N2O fluxes, nitrate (NO-3), and ammonium (NH+4) concentration and 15N2O, 15NO−3, and 15NH+4 enrichment during the incubation. Quantitative PCR was used to quantify ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results showed that nitrification was the main contributor to N2O production in soils from sugarcane, dairy pasture and cereal cropping systems, while denitrification played a major role in N2O production in the vegetable soil under the experimental conditions. Nitrification contributed to 96.7% of the N2O emissions in sugarcane soil followed by 71.3% in the cereal cropping soil and 70.9% in the dairy pasture soil, while only around 20.0% of N2O was produced from nitrification in vegetable soil. The proportion of nitrified nitrogen as N2O (PN2O-value) varied across different soils, with the highest PN2O-value (0.26‰) found in the cereal cropping soil, which was around 10 times higher than that in other three systems. AOA were the abundant ammonia oxidizers, and were significantly correlated to N2O emitted from nitrification in the sugarcane soil, while AOB were significantly correlated with N2O emitted from nitrification in the cereal cropping soil. Our findings suggested that soil type and land-use might have strongly affected the relative contribution of nitrification and denitrification to N2O production from agricultural soils. [ABSTRACT FROM AUTHOR]

The microbial community structure of bacteria, archaea and fungi is described in an Australian native grassland soil after more than 5 years exposure to different atmospheric CO2 concentrations ([ CO2]) (ambient, + 550 ppm) and temperatures (ambient, + 2°C) under different plant functional types ( C3 and C4 grasses) and at two soil depths (0-5 cm and 5-10 cm). Archaeal community diversity was influenced by elevated [ CO2], while under warming archaeal 16S rRNA gene copy numbers increased for C4 plant Themeda triandra and decreased for the C3 plant community ( P < 0.05). Fungal community diversity resulted in three groups based upon elevated [ CO2], elevated [ CO2] plus warming and ambient [ CO2]. Overall bacterial community diversity was influenced primarily by depth. Specific bacterial taxa changed in richness and relative abundance in response to climate change factors when assessed by a high-resolution 16 S rRNA microarray ( PhyloChip). Operational taxonomic unit signal intensities increased under elevated [ CO2] for both Firmicutes and Bacteroidetes, and increased under warming for Actinobacteria and Alphaproteobacteria. For the interaction of elevated [ CO2] and warming there were 103 significant operational taxonomic units ( P < 0.01) representing 15 phyla and 30 classes. The majority of these operational taxonomic units increased in abundance for elevated [ CO2] plus warming plots, while abundance declined in warmed or elevated [ CO2] plots. Bacterial abundance (16 S rRNA gene copy number) was significantly different for the interaction of elevated [ CO2] and depth ( P < 0.05) with decreased abundance under elevated [ CO2] at 5-10 cm, and for Firmicutes under elevated [ CO2] ( P < 0.05). Bacteria, archaea and fungi in soil responded differently to elevated [ CO2], warming and their interaction. Taxa identified as significantly climate-responsive could show differing trends in the direction of response ('+' or '−') under elevated CO2 or warming, which could then not be used to predict their interactive effects supporting the need to investigate interactive effects for climate change. The approach of focusing on specific taxonomic groups provides greater potential for understanding complex microbial community changes in ecosystems under climate change. [ABSTRACT FROM AUTHOR]

The population genetic structure of the fungal pathogen Leptosphaeria maculans was determined in Australia using six microsatellite and two minisatellite markers. Ascospores were sampled from Brassica napus stubble in disease nurseries and commercial fields in different sites over 2 years. The 13 subpopulations of L. maculans exhibited high gene (H = 0.393 to 0.563) and genotypic diversity, with 357 haplotypes identified among 513 isolates. Although the majority of genetic variation was distributed within subpopulations (85%), 10% occurred between the regions of eastern and Western Australia, and 5% within regions. FST analysis of subpopulation pairs also showed the east-west genetic differentiation, whereas factorial correspondence analysis separated Western Australian subpopulations from eastern ones. Bayesian model-based population structure analyses of multilocus haplotypes inferred three distinct populations, one in Western Australia and an admixture of two in eastern Australia. These two regions are separated by 1,200 km of arid desert that may act as a natural barrier to gene flow, resulting in differentiation by random genetic drift. The genetic differentiation of L. maculans isolates between eastern and Western Australia means that these regions can be treated as different management units, and reinforces the need for widespread disease nurseries in each region to screen breeding lines against a range of genetic and pathogenic populations of L. maculans. [ABSTRACT FROM AUTHOR]

Seven polymorphic microsatellite markers suitable for population genetic studies and genetic mapping were developed for Leptosphaeria maculans, a fungal pathogen of canola ( Brassica napus). Polymorphism was evaluated using 14 isolates from diverse geographical locations. Each locus had either two or three alleles. Cross-species amplification was observed for almost all loci in L. biglobosa ‘brassicae’ and L. maculans ‘lepidii’. [ABSTRACT FROM AUTHOR]

The suppression of soilborne crop pathogens such as Rhizoctonia solani AG8 may offer a sustainable and enduring method for disease control, though soils with these properties are difficult to identify. In this study, we analysed the soil metabolic profiles of suppressive and non-suppressive soils over 2 years of cereal production. We collected bulk and rhizosphere soil at different cropping stages and subjected soil extracts to liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy ( 1 H NMR) analyses. Community analyses of suppressive and non-suppressive soils using principal component analyses and predictive modelling of LC-MS and NMR datasets respectively, revealed distinct biochemical profiles for the two soil types with clustering based on suppressiveness and cropping stage. NMR spectra revealed the suppressive soils to be more abundant in sugar molecules than non-suppressive soils, which were more abundant in lipids and terpenes. LC-MS features that were significantly more abundant in the suppressive soil were identified and assessed as potential biomarkers for disease suppression. The structures of a potential class of LC-MS biomarkers were elucidated using accurate mass data and MS fragmentation spectrum information. The most abundant compound found in association with suppressive soils was confirmed to be a macrocarpal, which is an antimicrobial secondary metabolite. Our study has demonstrated the utility of environmental metabolomics for the study of disease suppressive soils, resulting in the discovery of a macrocarpal biomarker for R. solani AG8 suppressive soil which can be further studied functionally in association with suppression pot trials and microbial isolation studies., (Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.)