School of Agriculture, Food and Ecosystem Sciences - Research Publications
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Item15N methodologies for quantifying the response of N2-fixing associations to elevated [CO2]: A review(ELSEVIER, 2016-11-15)Methodologies based on (15)N enrichment (E) and (15)N natural abundance (NA) have been used to obtain quantitative estimates of the response of biological N2 fixation (BNF) of legumes (woody, grain and forage) and actinorhizal plants grown in artificial media or in soil exposed to elevated atmospheric concentrations of carbon dioxide e[CO2] for extended periods of time, in growth rooms, greenhouses, open top chambers or free-air CO2 enrichment (FACE) facilities. (15)N2 has also been used to quantify the response of endophytic and free-living diazotrophs to e[CO2]. The primary criterion of response was the proportional dependence of the N2-fixing system on the atmosphere as a source of N. i.e. the symbiotic dependence (Patm). The unique feature of (15)N-based methods is their ability to provide time-integrated and yield-independent estimates of Patm. In studies conducted in artificial media or in soil using the E methodology there was either no response or a positive response of Patm to e[CO2]. The interpretation of results obtained in artificial media or with (15)N2 is straight forward, not being subject to the assumptions on which the E and NA soil-cultured methods are based. A variety of methods have been used to estimate isotopic fractionation attendant on the NA technique, the so-called 'B value', which attaches a degree of uncertainty to the results obtained. Using the NA technique, a suite of responses of Patm to e[CO2] has been published, from positive to neutral to sometimes negative effects. Several factors which interact with the response of N2-fixing species to e[CO2] were identified.
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ItemAmmonia deposition in the neighbourhood of an intensive cattle feedlot in Victoria, Australia(NATURE PORTFOLIO, 2016-09-07)Intensive cattle feedlots are large emission sources of ammonia (NH3), but NH3 deposition to the landscape downwind of feedlots is not well understood. We conducted the first study in Australia to measure NH3 dry deposition within 1 km of a commercial beef cattle feedlot in Victoria. NH3 concentrations and deposition fluxes decreased exponentially with distance away from the feedlot. The mean NH3 concentrations decreased from 419 μg N m(-3) at 50 m to 36 μg N m(-3) at 1 km, while the mean NH3 dry deposition fluxes decreased from 2.38 μg N m(-2) s(-1) at 50 m to 0.20 μg N m(-2) s(-1) at 1 km downwind from the feedlot. These results extrapolate to NH3 deposition of 53.9 tonne N yr(-1) in the area within 1 km from the feedlot, or 67.5 kg N ha(-1) yr(-1) as an area-weighted mean, accounting for 8.1% of the annual NH3-N emissions from the feedlot. Thus NH3 deposition around feedlots is a significant nitrogen input for surrounding ecosystems. Researches need be conducted to evaluate the impacts of NH3 deposition on the surrounding natural or semi-naturals ecosystems and to reduce N fertilizer application rate for the surrounding crops by considering nitrogen input from NH3 deposition.
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ItemNitrification Is a Primary Driver of Nitrous Oxide Production in Laboratory Microcosms from Different Land-Use Soils(FRONTIERS MEDIA SA, 2016-09-09)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 (15)N-tracing experiment was conducted under controlled laboratory conditions on four agricultural soils collected from different land-use. We measured N2O fluxes, nitrate ([Formula: see text]), and ammonium ([Formula: see text]) concentration and (15)N2O, (15)[Formula: see text], and (15)[Formula: see text] 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.
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ItemImpacts of reclaimed water irrigation on soil antibiotic resistome in urban parks of Victoria, Australia(ELSEVIER SCI LTD, 2016-04)UNLABELLED: The effluents from wastewater treatment plants have been recognized as a significant environmental reservoir of antibiotics and antibiotic resistance genes (ARGs). Reclaimed water irrigation (RWI) is increasingly used as a practical solution for combating water scarcity in arid and semiarid regions, however, impacts of RWI on the patterns of ARGs and the soil bacterial community remain unclear. Here, we used high-throughput quantitative PCR and terminal restriction fragment length polymorphism techniques to compare the diversity, abundance and composition of a broad-spectrum of ARGs and total bacteria in 12 urban parks with and without RWI in Victoria, Australia. A total of 40 unique ARGs were detected across all park soils, with genes conferring resistance to β-lactam being the most prevalent ARG type. The total numbers and the fold changes of the detected ARGs were significantly increased by RWI, and marked shifts in ARG patterns were also observed in urban parks with RWI compared to those without RWI. The changes in ARG patterns were paralleled by a significant effect of RWI on the bacterial community structure and a co-occurrence pattern of the detected ARG types. There were significant and positive correlations between the fold changes of the integrase intI1 gene and two β-lactam resistance genes (KPC and IMP-2 groups), but no significant impacts of RWI on the abundances of intI1 and the transposase tnpA gene were found, indicating that RWI did not improve the potential for horizontal gene transfer of soil ARGs. Taken together, our findings suggested that irrigation of urban parks with reclaimed water could influence the abundance, diversity, and compositions of a wide variety of soil ARGs of clinical relevance. ONE-SENTENCE SUMMARY: Irrigation of urban parks with treated wastewater significantly increased the abundance and diversity of various antibiotic resistance genes, but did not significantly enhance their potential for horizontal gene transfer.
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ItemField-based evidence for copper contamination induced changes of antibiotic resistance in agricultural soils(WILEY, 2016-11)Bacterial resistance to antibiotics and heavy metals are frequently linked, suggesting that exposure to heavy metals might select for bacterial assemblages conferring resistance to antibiotics. However, there is a lack of clear evidence for the heavy metal-induced changes of antibiotic resistance in a long-term basis. Here, we used high-capacity quantitative PCR array to investigate the responses of a broad spectrum of antibiotic resistance genes (ARGs) to 4-5 year copper contamination (0-800 mg kg-1 ) in two contrasting agricultural soils. In total, 157 and 149 unique ARGs were detected in the red and fluvo-aquic soil, respectively, with multidrug and β-lactam as the most dominant ARG types. The highest diversity and abundance of ARGs were observed in medium copper concentrations (100-200 mg kg-1 ) of the red soil and in high copper concentrations (400-800 mg kg-1 ) of the fluvo-aquic soil. The abundances of total ARGs and several ARG types had significantly positive correlations with mobile genetic elements (MGEs), suggesting mobility potential of ARGs in copper-contaminated soils. Network analysis revealed significant co-occurrence patterns between ARGs and microbial taxa, indicating strong associations between ARGs and bacterial communities. Structural equation models showed that the significant impacts of copper contamination on ARG patterns were mainly driven by changes in bacterial community compositions and MGEs. Our results provide field-based evidence that long-term Cu contamination significantly changed the diversity, abundance and mobility potential of environmental antibiotic resistance, and caution the un-perceived risk of the ARG dissemination in heavy metal polluted environments.
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ItemEffects of 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and the abundance and community composition of soil ammonia oxidizers in three land uses(SPRINGER, 2016-10)The application of the nitrification inhibitor, 3,4-dimethylpyrazole-phosphate (DMPP), is considered as an effective strategy to mitigate agricultural nitrogen loss. However, the inhibitory effect of DMPP on nitrification is variable and the importance of the soil microbial community composition to the variability is poorly understood. In this study, nine soils were collected across three land uses to investigate the impact of DMPP on nitrification and associated dynamics of ammonia oxidizers in a 28-day microcosm incubation. The results showed that the efficacy of DMPP at inhibiting net nitrification rates varied highly from no effect to 63.6 % during the first week of incubation. The abundance of ammonia-oxidizing bacteria (AOB), rather than ammonia-oxidizing archaea (AOA), was significantly correlated with nitrate concentrations across three land uses and significantly inhibited by DMPP addition. DMPP had higher efficacy in neutral and alkaline wheat and vegetable soils, compared with pasture soils. Canonical correspondence analysis suggested that soil pH was the most influential factor explaining the community composition of AOB and AOA in the collected soils. However, neither ammonium nitrate nor DMPP addition had a significant effect on the community composition of AOB or AOA during the incubation indicated by non-metric multidimensional scaling ordination. Taken together, our findings indicated that DMPP slowed nitrification by inhibiting the growth of AOB, and DMPP application affected the abundance of AOB more than the ammonia oxidizer community composition.
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ItemBeef and coal are key drivers of Australia's high nitrogen footprint(NATURE PORTFOLIO, 2016-12-23)Anthropogenic release of reactive nitrogen (Nr; all species of N except N2) to the global nitrogen (N) cycle is substantial and it negatively affects human and ecosystem health. A novel metric, the N footprint, provides a consumer-based perspective for Nr use efficiency and connects lifestyle choices with Nr losses. Here we report the first full-scale assessment of the anthropogenic Nr loss by Australians. Despite its 'clean and green' image, Australia has the largest N footprint (47 kg N cap-1 yr-1) both in food and energy sectors among all countries that have used the N-Calculator model. About 69% of the Australia's N footprint is attributed to food consumption and the associated food production, with the rest from energy consumption. Beef consumption and production is the major contributor of the high food N footprint, while the heavy dependence on coal for electricity explains the large energy N footprint. Our study demonstrates opportunities for managing Nr loss and lifestyle choices to reduce the N footprint.
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ItemEffects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate on Nitrification and Nitrifiers in Two Contrasting Agricultural Soils(AMER SOC MICROBIOLOGY, 2016-09)UNLABELLED: The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is a powerful tool that can be used to promote nitrogen (N) use efficiency and reduce N losses from agricultural systems by slowing nitrification. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrification and N2O production; however, their responses to DMPP amendment and the microbial mechanisms underlying the variable efficiencies of DMPP across different soils remain largely unknown. Here we compared the impacts of DMPP on nitrification and the dynamics of ammonia oxidizers between an acidic pasture soil and an alkaline vegetable soil using a (15)N tracing and (13)CO2-DNA-stable-isotope probing (SIP) technique. The results showed that DMPP significantly inhibited nitrification and N2O production in the vegetable soil only, and the transient inhibition was coupled with a significant decrease in AOB abundance. No significant effects on the community structure of ammonia oxidizers or the abundances of total bacteria and denitrifiers were observed in either soil. The (15)N tracing experiment revealed that autotrophic nitrification was the predominant form of nitrification in both soils. The (13)CO2-DNA-SIP results indicated the involvement of AOB in active nitrification in both soils, but DMPP inhibited the assimilation of (13)CO2 into AOB only in the vegetable soil. Our findings provide evidence that DMPP could effectively inhibit nitrification through impeding the abundance and metabolic activity of AOB in the alkaline vegetable soil but not in the acidic pasture soil, possibly due to the low AOB abundance or the adsorption of DMPP by organic matter. IMPORTANCE: The combination of the (15)N tracing model and (13)CO2-DNA-SIP technique provides important evidence that the nitrification inhibitor DMPP could effectively inhibit nitrification and nitrous oxide emission in an alkaline soil through influencing the abundance and metabolic activity of AOB. In contrast, DMPP amendment has no significant effect on nitrification or nitrifiers in an acidic soil, potentially owing to the low abundance of AOB and the possible adsorption of DMPP by organic matter. Our findings have direct implications for improved agricultural practices through utilizing the nitrification inhibitor DMPP in appropriate situations, and they emphasize the importance of microbial communities to the efficacy of DMPP.
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ItemNo Preview AvailableLong-term effects of elevated CO2 on carbon and nitrogen functional capacity of microbial communities in three contrasting soils(PERGAMON-ELSEVIER SCIENCE LTD, 2016-06)Elevated atmospheric CO2 (eCO2) affects soil-plant systems by stimulating plant growth, rhizosphere processes and altering the amount and quality of organic matter inputs. This study examined whether these plant-mediated processes indirectly influence the structure and function of soil microbial communities and soil carbon (C) and nitrogen (N) cycling. Surface soils (0–5 and 5–10 cm) of Calcarosol, Chromosol and Vertosol were sampled after 5 years' exposure to either ambient CO2 (aCO2; 390 ppm) or eCO2 (550 ppm) using free-air CO2 enrichment (SoilFACE). Changes in microbial community structure were not detected using automated ribosomal intergenic spacer analyses (ARISA). However, quantitative PCR of targeted organic C decomposition (cu, cbh), N mineralisation (apr, npr), nitrification (amoB, amoA, norA) and denitrification (nirK, narG, nosZ) genes showed that eCO2 reduced the abundance of half of the functional genes in the Chromosol and Vertosol and their abundance was tightly coupled with total C and N pools. In the Chromosol, total N and C of soil (<2 mm particles) was reduced by up to 20% and was associated with enhanced microbial activity (soil respiration). Soil C was also reduced in the Vertosol (15%, 5–10 cm); however greater laccase, reduced cellulase and lower microbial activity indicated that organic matter decomposition was currently limited by N. The loss of soil organic N and C under eCO2 was likely driven by greater N demand. This study highlighted that the indirect effects of eCO2 on functional capacity of soil microbial communities in dryland agricultural system depended on the soil type.