ORCID Profile
0000-0002-3301-0470
Current Organisation
University of South Australia
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Publisher: Springer Science and Business Media LLC
Date: 27-12-2019
DOI: 10.1038/S41598-019-56248-7
Abstract: There is increasing demand for safe and effective sanitizers for irrigation water disinfection to prevent transmission of foodborne pathogens to fresh produce. Here we compared the efficacy of pH-neutral electrolyzed oxidizing water (EOW), sodium hypochlorite (NaClO) and chlorine dioxide (ClO 2 ) against single and mixed populations of E. coli , Listeria and Salmonella under a range of pH and organic matter content. EOW treatment of the mixed bacterial suspension resulted in a dose-dependent ( mg/L free chlorine), rapid ( min) and effective (4–6 Log 10 ) reduction of the microbial load in water devoid of organic matter under the range of pH conditions tested (pH, 6.0, 7.0, 8.4 and 9.2). The efficacy of EOW containing 5 mg/L free chlorine was unaffected by increasing organic matter, and compared favourably with equivalent concentrations of NaClO and ClO 2 . EOW at 20 mg/L free chlorine was more effective than NaClO and ClO 2 in reducing bacterial populations in the presence of high (20–100 mg/L) dissolved organic carbon, and no regrowth or metabolic activity was observed for EOW-treated bacteria at this concentration upon reculturing in rich media. Thus, EOW is as effective or more effective than other common chlorine-based sanitizers for pathogen reduction in contaminated water. EOW’s other characteristics, such as neutral pH and ease of handling, indicate its suitability for fresh produce sanitation.
Publisher: Wiley
Date: 21-05-2009
Publisher: Elsevier BV
Date: 2008
Publisher: Wiley
Date: 08-2017
Abstract: Global change models indicate that rainfall patterns are likely to shift towards more extreme events concurrent with increasing atmospheric carbon dioxide concentration ([CO
Publisher: Elsevier BV
Date: 06-2012
Publisher: Elsevier BV
Date: 02-2021
Publisher: Elsevier BV
Date: 05-2022
Publisher: Frontiers Media SA
Date: 14-04-2021
DOI: 10.3389/FMICB.2021.644046
Abstract: The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more erse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type Arabidopsis thaliana plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, such effect on rhizosphere fungi was not confirmed for a salicylic acid-impaired A. thaliana mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using licon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots ( Fusarium, Trichoderma and Fusicolla spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.
Publisher: Wiley
Date: 18-03-2013
Publisher: Springer Science and Business Media LLC
Date: 02-02-2015
DOI: 10.1038/NG.3211
Publisher: Elsevier BV
Date: 03-2014
Publisher: Proceedings of the National Academy of Sciences
Date: 06-2010
Abstract: Rising atmospheric CO 2 levels are predicted to have major consequences on carbon cycling and the functioning of terrestrial ecosystems. Increased photosynthetic activity is expected, especially for C-3 plants, thereby influencing vegetation dynamics however, little is known about the path of fixed carbon into soil-borne communities and resulting feedbacks on ecosystem function. Here, we examine how arbuscular mycorrhizal fungi (AMF) act as a major conduit in the transfer of carbon between plants and soil and how elevated atmospheric CO 2 modulates the belowground translocation pathway of plant-fixed carbon. Shifts in active AMF species under elevated atmospheric CO 2 conditions are coupled to changes within active rhizosphere bacterial and fungal communities. Thus, as opposed to simply increasing the activity of soil-borne microbes through enhanced rhizodeposition, elevated atmospheric CO 2 clearly evokes the emergence of distinct opportunistic plant-associated microbial communities. Analyses involving RNA-based stable isotope probing, neutral hosphate lipid fatty acids stable isotope probing, community fingerprinting, and real-time PCR allowed us to trace plant-fixed carbon to the affected soil-borne microorganisms. Based on our data, we present a conceptual model in which plant-assimilated carbon is rapidly transferred to AMF, followed by a slower release from AMF to the bacterial and fungal populations well-adapted to the prevailing (myco-)rhizosphere conditions. This model provides a general framework for reappraising carbon-flow paths in soils, facilitating predictions of future interactions between rising atmospheric CO 2 concentrations and terrestrial ecosystems.
Publisher: Elsevier BV
Date: 02-2018
DOI: 10.1016/J.TREE.2017.11.005
Abstract: In agricultural and natural systems researchers have demonstrated large effects of plant-soil feedback (PSF) on plant growth. However, the concepts and approaches used in these two types of systems have developed, for the most part, independently. Here, we present a conceptual framework that integrates knowledge and approaches from these two contrasting systems. We use this integrated framework to demonstrate (i) how knowledge from complex natural systems can be used to increase agricultural resource-use efficiency and productivity and (ii) how research in agricultural systems can be used to test hypotheses and approaches developed in natural systems. Using this framework, we discuss avenues for new research toward an ecologically sustainable and climate-smart future.
Publisher: CSIRO Publishing
Date: 2021
DOI: 10.1071/MA21006
Abstract: Wastewater monitoring (WM) of SARS-CoV-2 from sewers was applied throughout the world early in the COVID-19 pandemic. Sharing of protocols and experiences in WM of SARS-CoV-2 by national and international researchers and practitioners has been vital to ensuring the sensitivity and specificity of the methods. WM has been a valuable adjunct to human clinical testing, and when positive results occur in sewage, community testing has been increased. WM findings allow public health officials to track and respond to the impacts of loosening lockdown restrictions, demonstrating when return to normal social activities might occur without a resurgence of rapid community transmission, and they are particularly useful in areas with low human case numbers and/or low clinical testing rates. New research is required to address several practical knowledge gaps, for ex le, s ling protocols, prediction of case prevalence from viral numbers by modelling, and determination of detection limits. Communication to the Australian public of WM of SARS-CoV-2 has been via interactive, visual dashboards. Once SARS-CoV-2 vaccinations are introduced, WM could help track the underlying circulation of the virus in the population, the spread of known variants and its future evolution.
Publisher: Springer Berlin Heidelberg
Date: 2006
Publisher: Elsevier BV
Date: 08-2021
Publisher: Microbiology Society
Date: 15-12-2021
Abstract: Escherichia coli ST131 is a globally dispersed extraintestinal pathogenic E. coli lineage contributing significantly to hospital and community acquired urinary tract and bloodstream infections. Here we describe a detailed phylogenetic analysis of the whole genome sequences of 284 Australian ST131 E. coli isolates from erse sources, including clinical, food and companion animals, wildlife and the environment. Our phylogeny and the results of single nucleotide polymorphism (SNP) analysis show the typical ST131 clade distribution with clades A, B and C clearly displayed, but no niche associations were observed. Indeed, interspecies relatedness was a feature of this study. Thirty-five isolates (29 of human and six of wild bird origin) from clade A (32 fimH 41, 2 fimH 89, 1 fimH 141) were observed to differ by an average of 76 SNPs. Forty-five isolates from clade C1 from four sources formed a cluster with an average of 46 SNPs. Within this cluster, human sourced isolates differed by approximately 37 SNPs from isolates sourced from canines, approximately 50 SNPs from isolates from wild birds, and approximately 52 SNPs from isolates from wastewater. Many ST131 carried resistance genes to multiple antibiotic classes and while 41 (14 %) contained the complete class one integron–integrase intI1 , 128 (45 %) isolates harboured a truncated intI1 (462–1014 bp), highlighting the ongoing evolution of this element. The module intI1–dfrA17–aadA5–qacEΔ1–sul1 –ORF –chrA–padR –IS 1600–mphR–mrx–mphA , conferring resistance to trimethoprim, aminoglycosides, quaternary ammonium compounds, sulphonamides, chromate and macrolides, was the most common structure. Most (73 %) Australian ST131 isolates carry at least one extended spectrum β-lactamase gene, typically bla CTX-M-15 and bla CTX-M-27 . Notably, dual parC -1aAB and gyrA -1AB fluoroquinolone resistant mutations, a unique feature of clade C ST131 isolates, were identified in some clade A isolates. The results of this study indicate that the the ST131 population in Australia carries erse antimicrobial resistance genes and plasmid replicons and indicate cross-species movement of ST131 strains across erse reservoirs.
Publisher: Informa UK Limited
Date: 19-12-2020
Publisher: Elsevier BV
Date: 08-2023
Publisher: Wiley
Date: 07-11-2013
DOI: 10.1111/GCB.12045
Abstract: Carbon (C) uptake by terrestrial ecosystems represents an important option for partially mitigating anthropogenic CO2 emissions. Short-term atmospheric elevated CO2 exposure has been shown to create major shifts in C flow routes and ersity of the active soil-borne microbial community. Long-term increases in CO2 have been hypothesized to have subtle effects due to the potential adaptation of soil microorganism to the increased flow of organic C. Here, we studied the effects of prolonged elevated atmospheric CO2 exposure on microbial C flow and microbial communities in the rhizosphere. Carex arenaria (a nonmycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown at defined atmospheric conditions differing in CO2 concentration (350 and 700 ppm) for 3 years. During this period, C flow was assessed repeatedly (after 6 months, 1, 2, and 3 years) by (13) C pulse-chase experiments, and label was tracked through the rhizosphere bacterial, general fungal, and arbuscular mycorrhizal fungal (AMF) communities. Fatty acid biomarker analyses and RNA-stable isotope probing (RNA-SIP), in combination with real-time PCR and PCR-DGGE, were used to examine microbial community dynamics and abundance. Throughout the experiment the influence of elevated CO2 was highly plant dependent, with the mycorrhizal plant exerting a greater influence on both bacterial and fungal communities. Biomarker data confirmed that rhizodeposited C was first processed by AMF and subsequently transferred to bacterial and fungal communities in the rhizosphere soil. Over the course of 3 years, elevated CO2 caused a continuous increase in the (13) C enrichment retained in AMF and an increasing delay in the transfer of C to the bacterial community. These results show that, not only do elevated atmospheric CO2 conditions induce changes in rhizosphere C flow and dynamics but also continue to develop over multiple seasons, thereby affecting terrestrial ecosystems C utilization processes.
Publisher: Elsevier BV
Date: 2015
Publisher: Elsevier BV
Date: 06-2020
Publisher: American Society for Microbiology
Date: 12-07-2022
DOI: 10.1128/AEM.00646-22
Abstract: Antimicrobial resistance (AMR) poses a global public health threat, and the increase in resistance to “last-resort drugs,” such as carbapenems, is alarming. Wastewater has been flagged as a hot spot for AMR evolution. Comamonas spp. are among the most common bacteria in wastewater and play a role in its bioaugmentation.
Publisher: Springer Science and Business Media LLC
Date: 08-2018
DOI: 10.1007/S00572-018-0865-5
Abstract: This Mycorrhiza issue groups topical papers based on presentations and discussions at the Mycorrhizal Microbiomes session at 9th International Conference on Mycorrhiza, Prague, Czech Republic, August 2017. The five articles that appear in this special issue advance the field of mycorrhizal microbiomes, not simply by importing ideas from an emerging area, but by using them to inform rich and methodologically grounded research. The aim of this special issue is to explore the interactions between mycorrhizal fungi and surrounding complex environments from a distinct but complementary point of view, highlighting the large spectrum of unknowns that still need to be explored. In this editorial, we first introduce the level of knowledge in this thematic area, then describe major results from the five manuscripts and characterise their importance to mycorrhizal research, and finally discuss the developing topics in this rapidly emerging thematic area.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 12-08-2011
Abstract: Plants and their associated fungi reward partners that offer the best resources to sustain mutualism in complex systems.
Publisher: Springer Science and Business Media LLC
Date: 07-2017
Publisher: Springer Science and Business Media LLC
Date: 31-10-2018
DOI: 10.1007/S11356-017-0574-1
Abstract: Nitrogen (N) limitation is one of the major constrain factors for biochar in improving plant growth, the same for elevated atmospheric carbon dioxide (CO
Publisher: Elsevier BV
Date: 2018
Publisher: MDPI AG
Date: 24-10-2020
DOI: 10.3390/MICROORGANISMS8111647
Abstract: Pseudomonas aeruginosa is an opportunistic pathogen displaying high intrinsic antimicrobial resistance and the ability to thrive in different ecological environments. In this study, the ability of P. aeruginosa to develop simultaneous resistance to multiple antibiotics and disinfectants in different natural niches were investigated using strains collected from clinical s les, veterinary s les, and wastewater. The correlation between biocide and antimicrobial resistance was determined by employing principal component analysis. Molecular mechanisms linking biocide and antimicrobial resistance were interrogated by determining gene expression using RT-qPCR and identifying a potential genetic determinant for co- and cross-resistance using whole-genome sequencing. A subpopulation of P. aeruginosa isolates belonging to three sequence types was resistant against the common preservative benzalkonium chloride and showed cross-resistance to fluoroquinolones, cephalosporins, aminoglycosides, and multidrug resistance. Of these, the epidemiological high-risk ST235 clone was the most abundant. The overexpression of the MexAB-OprM drug efflux pump resulting from amino acid mutations in regulators MexR, NalC, or NalD was the major contributing factor for cross-resistance that could be reversed by an efflux pump inhibitor. This is the first comparison of antibiotic-biocide cross-resistance in s les isolated from different ecological niches and serves as a confirmation of laboratory-based studies on biocide adapted isolates. The isolates from wastewater had a higher incidence of multidrug resistance and biocide-antibiotic cross-resistance than those from clinical and veterinary settings.
Publisher: Frontiers Media SA
Date: 07-03-2018
Publisher: Springer Science and Business Media LLC
Date: 12-03-2008
Publisher: Elsevier BV
Date: 07-2016
DOI: 10.1016/J.SCITOTENV.2016.03.122
Abstract: The application of straw and biochar to soil has received great attention because of their potential benefits such as fertility improvement and carbon (C) sequestration. The abiotic effects of these materials on C and nitrogen (N) cycling in the soil ecosystem have been previously investigated, however, the effects of straw or its derived biochar on the soil microbial community structure and function are not well understood. For this purpose, a short-term incubation experiment was conducted using (13)C-labeled rice straw and its derived biochar ((13)C-labeled biochar) to deepen our understanding about soil microbial community dynamics and function in C sequestration and greenhouse gas emission in the acidic paddy soil amended with these materials. Regarding microbial function, biochar and straw applications increased CO2 emission in the initial stage of incubation and reached the highest level (0.52 and 3.96mgCkg(-1)soilh(-1)) at 1d and 3d after incubation, respectively. Straw amendment significantly (p<0.01) increased respiration rate, total phospholipid fatty acids (PLFAs) and (13)C-PLFA as compared to biochar amendment and the control. The amount and percent of Gram positive bacteria, fungi and actinomycetes were also significantly (p<0.05) higher in (13)C-labeled straw amended soil than the (13)C-labeled biochar amended soil. According to the (13)C data, 23 different PLFAs were derived from straw amended paddy soil, while only 17 PLFAs were derived from biochar amendments. The profile of (13)C-PLFAs derived from straw amendment was significantly (p<0.01) different from biochar amendment. The PLFAs18:1ω7c and cy17:0 (indicators of Gram negative bacteria) showed high relative abundances in the biochar amendment, while 10Me18:0, i17:0 and 18:2ω6,9c (indicators of actinomycetes, Gram positive bacteria and fungi, respectively) showed high relative abundance in the straw amendments. Our results suggest that the function, size and structure of the microbial community were strongly influenced by the substrate composition and availability.
Publisher: Elsevier BV
Date: 06-2022
Publisher: Springer Science and Business Media LLC
Date: 10-02-2015
DOI: 10.1007/S00248-015-0571-1
Abstract: Tephritid fruit fly species display a ersity of host plant specialisation on a scale from monophagy to polyphagy. Furthermore, while some species prefer ripening fruit, a few are restricted to damaged or rotting fruit. Such a ersity of host plant use may be reflected in the microbial symbiont ersity of tephritids and their grade of dependency on their microbiomes. Here, we investigated the microbiome of six tephritid species from three genera, including species that are polyphagous pests (Bactrocera tryoni, Bactrocera neohumeralis, Bactrocera jarvisi, Ceratitis capitata) and a monophagous specialist (Bactrocera cacuminata). These were compared with the microbiome of a non-pestiferous but polyphagous tephritid species that is restricted to damaged or rotting fruit (Dirioxa pornia). The bacterial community associated with whole fruit flies was analysed by 16S ribosomal DNA (rDNA) licon pyrosequencing to detect potential drivers of taxonomic composition. Overall, the dominant bacterial families were Enterobacteriaceae and Acetobacteraceae (both Proteobacteria), and Streptococcaceae and Enterococcaceae (both Firmicutes). Comparisons across species and genera found different microbial composition in the three tephritid genera, but limited consistent differentiation between Bactrocera species. Within Bactrocera species, differentiation of microbial composition seemed to be influenced by the environment, possibly including their diets beyond this, tephritid species identity or ecology also had an effect. The microbiome of D. pornia was most distinct from the other five species, which may be due to its ecologically different niche of rotting or damaged fruit, as opposed to ripening fruit favoured by the other species. Our study is the first licon pyrosequencing study to compare the microbiomes of tephritid species and thus delivers important information about the turnover of microbial ersity within and between fruit fly species and their potential application in pest management strategies.
Publisher: Elsevier BV
Date: 08-2019
Publisher: Frontiers Media SA
Date: 18-12-2014
Publisher: Frontiers Media SA
Date: 07-04-2017
Publisher: Wiley
Date: 21-08-2007
Publisher: Elsevier BV
Date: 08-2022
DOI: 10.1016/J.JHAZMAT.2022.128943
Abstract: Ultrafiltration (UF) was assessed at chemical, microbiological, genetical and toxicological level and in terms of removing specific antibiotic-related microcontaminants from urban wastewater. The UF capacity to remove various antibiotics (clarithromycin, erythromycin, icillin, ofloxacin, sulfamethoxazole, trimethoprim, and tetracycline [A
Publisher: Springer Science and Business Media LLC
Date: 25-09-0012
Publisher: Springer Science and Business Media LLC
Date: 07-2014
DOI: 10.1038/NATURE13595
Publisher: Elsevier BV
Date: 10-2022
Publisher: Wiley
Date: 18-03-2013
Publisher: Elsevier BV
Date: 10-2018
Publisher: Elsevier
Date: 2017
Publisher: American Chemical Society (ACS)
Date: 07-12-2021
DOI: 10.1021/ACSSENSORS.1C01973
Abstract: The spread of antimicrobial resistance (AMR) is a rapidly growing threat to humankind on both regional and global scales. As countries worldwide prepare to embrace a One Health approach to AMR management, which is one that recognizes the interconnectivity between human, animal, and environmental health, increasing attention is being paid to identifying and monitoring key contributing factors and critical control points. Presently, AMR sensing technologies have significantly progressed phenotypic antimicrobial susceptibility testing (AST) and genotypic antimicrobial resistance gene (ARG) detection in human healthcare. For effective AMR management, an evolution of innovative sensing technologies is needed for tackling the unique challenges of interconnected AMR across various and different health domains. This review comprehensively discusses the modern state-of-play for innovative commercial and emerging AMR sensing technologies, including sequencing, microfluidic, and miniaturized point-of-need platforms. With a unique view toward the future of One Health, we also provide our perspectives and outlook on the constantly changing landscape of AMR sensing technologies beyond the human health domain.
Publisher: Wiley
Date: 09-05-2014
Abstract: Terrestrial arid and semi-arid ecosystems (drylands) constitute about 41% of the Earth's land surface and are predicted to experience increasing fluctuations in water and nitrogen availability. Mounting evidence has confirmed the significant importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in nitrification, plant nitrogen availability and atmospheric N2 O emissions, but their responses to environmental perturbations in drylands remain largely unknown. Here we evaluate how the factorial combinations of irrigation and fertilization in forests and land-use change from grassland to forest affects the dynamics of AOA and AOB following a 6-year dryland field study. Potential nitrification rates and AOA and AOB abundances were significantly higher in the irrigated plots, accompanied by considerable changes in community compositions, but their responses to fertilization alone were not significant. DNA-stable isotope probing results showed increased (13) CO2 incorporation into the amoA gene of AOA, but not of AOB, in plots receiving water addition, coupled with significantly higher net mineralization and nitrification rates. High-throughput microarray analysis revealed that active AOA assemblages belonging to Nitrosopumilus and Nitrosotalea were increasingly labelled by (13) CO2 following irrigation. However, no obvious effects of land-use changes on nitrification rates or metabolic activity of AOA and AOB could be observed under dry conditions. We provide evidence that water addition had more important roles than nitrogen fertilization in influencing the autotrophic nitrification in dryland ecosystems, and AOA are increasingly involved in ammonia oxidation when dry soils become wetted.
Publisher: Elsevier BV
Date: 2022
Publisher: Frontiers Media SA
Date: 09-07-2021
DOI: 10.3389/FMICB.2021.678290
Abstract: Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for & % of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.
Publisher: Oxford University Press (OUP)
Date: 03-10-2013
Abstract: Soil microbial processes have a central role in global fluxes of the key biogenic greenhouse gases and are likely to respond rapidly to climate change. Whether climate change effects on microbial processes lead to a positive or negative feedback for terrestrial ecosystem resilience is unclear. In this study, we investigated the interactive effects of [CO(2)] and temperature on soil fungi associated with faster-growing Eucalyptus saligna and slower-growing Eucalyptus sideroxylon, and fungi that colonised hyphal in-growth bags. Plants were grown in native soil under controlled soil moisture conditions, while subjecting the above-ground compartment to defined atmospheric conditions differing in CO(2) concentrations (290, 400, 650 μL L(-1)) and temperature (26 and 30 °C). Terminal restriction fragment length polymorphism and sequencing methods were used to examine effects on the structure of the soil fungal communities. There was no significant effect of host plant or [CO(2)]/temperature treatment on fungal species richness (α ersity) however, there was a significant effect on soil fungal community composition (β ersity) which was strongly influenced by eucalypt species. Interestingly, β ersity of soil fungi associated with both eucalypt species was significantly influenced by the elevated [CO(2) ]/high temperature treatment, suggesting that the combination of future predicted levels of atmospheric [CO(2)] and projected increases in global temperature will significantly alter soil fungal community composition in eucalypt forest ecosystems, independent of eucalypt species composition. These changes may arise through direct effects of changes in [CO(2)] and temperature on soil fungi or through indirect effects, which is likely the case in this study given the plant-dependent nature of our observations. This study highlights the role of plant species in moderating below-ground responses to future predicted changes to [CO(2)] and temperature and the importance of considering integrated plant-soil system responses.
Publisher: Springer Science and Business Media LLC
Date: 05-10-2015
DOI: 10.1038/NCOMMS9444
Abstract: The continuum hypothesis states that both deterministic and stochastic processes contribute to the assembly of ecological communities. However, the contextual dependency of these processes remains an open question that imposes strong limitations on predictions of community responses to environmental change. Here we measure community and habitat turnover across multiple vertical soil horizons at 183 sites across Scotland for bacteria and fungi, both dominant and functionally vital components of all soils but which differ substantially in their growth habit and dispersal capability. We find that habitat turnover is the primary driver of bacterial community turnover in general, although its importance decreases with increasing isolation and disturbance. Fungal communities, however, exhibit a highly stochastic assembly process, both neutral and non-neutral in nature, largely independent of disturbance. These findings suggest that increased focus on dispersal limitation and biotic interactions are necessary to manage and conserve the key ecosystem services provided by these assemblages.
Publisher: Elsevier BV
Date: 11-2022
DOI: 10.1016/J.CHEMOSPHERE.2022.135820
Abstract: Pesticides are known to affect non-targeted soil microorganisms. Still, studies comparing the effect of multiple pesticides on a wide range of microbial endpoints associated with carbon cycling are scarce. Here, we employed fluorescence enzymatic assay and real-time PCR to evaluate the effect of 20 commercial pesticides, applied at their recommended dose and five times their recommended dose, on soil carbon cycling related enzymatic activities (α-1,4-glucosidase, β-1,4-glucosidase, β-d-cellobiohydrolase and β-xylosidase), and on the absolute abundance of functional genes (cbhl and chiA), in three different South Australian agricultural soils. The effects on cellulolytic and chitinolytic microorganisms, and the total microbial community composition were determined using shotgun metagenomic sequencing in selected pesticide-treated and untreated s les. The application of insecticides significantly increased the cbhl and chiA genes absolute abundance in the acidic soil. At the community level, insecticide fipronil had the greatest stimulating effect on cellulolytic and chitinolytic microorganisms, followed by fungicide metalaxyl-M and insecticide imidacloprid. A shift towards a fungal dominated microbial community was observed in metalaxyl-M treated soil. Overall, our results suggest that the application of pesticides might affect the soil carbon cycle and may disrupt the formation of soil organic matter and structure stabilisation.
Publisher: Frontiers Media SA
Date: 25-01-2023
DOI: 10.3389/FMICB.2023.1058350
Abstract: Currently there are sparse regulations regarding the discharge of antibiotics from wastewater treatment plants (WWTP) into river systems, making surface waters a latent reservoir for antibiotics and antibiotic resistance genes (ARGs). To better understand factors that influence the fate of ARGs in the environment and to foster surveillance of antibiotic resistance spreading in such habitats, several indicator genes have been proposed, including the integrase gene intI1 and the sulfonamide resistance genes sul1 and sul2 . Here we used quantitative PCR and long-read nanopore sequencing to monitor the abundance of these indicator genes and ARGs present as class 1 integron gene cassettes in a river system from pristine source to WWTP-impacted water. ARG abundance was compared with the dynamics of the microbial communities determined via 16S rRNA gene licon sequencing, conventional water parameters and the concentration of sulfamethoxazole (SMX), sulfamethazine (SMZ) and sulfadiazine (SDZ). Our results show that WWTP effluent was the principal source of all three sulfonamides with highest concentrations for SMX (median 8.6 ng/l), and of the indicator genes sul1 , sul2 and intI1 with median relative abundance to 16S rRNA gene of 0.55, 0.77 and 0.65%, respectively. Downstream from the WWTP, water quality improved constantly, including lower sulfonamide concentrations, decreasing abundances of sul1 and sul2 and lower numbers and ersity of ARGs in the class 1 integron. The riverine microbial community partially recovered after receiving WWTP effluent, which was consolidated by a microbiome recovery model. Surprisingly, the relative abundance of intI1 increased 3-fold over 13 km of the river stretch, suggesting an internal gene multiplication. We found no evidence that low amounts of sulfonamides in the aquatic environment stimulate the maintenance or even spread of corresponding ARGs. Nevertheless, class 1 integrons carrying various ARGs were still present 13 km downstream from the WWTP. Therefore, limiting the release of ARG-harboring microorganisms may be more crucial for restricting the environmental spread of antimicrobial resistance than attenuating ng/L concentrations of antibiotics.
Publisher: Frontiers Media SA
Date: 14-06-2016
Publisher: Springer Science and Business Media LLC
Date: 18-06-2009
Abstract: Soil community responses to increased atmospheric CO(2) concentrations are expected to occur mostly through interactions with changing vegetation patterns and plant physiology. To gain insight into the effects of elevated atmospheric CO(2) on the composition and functioning of microbial communities in the rhizosphere, Carex arenaria (a non-mycorrhizal plant species) and Festuca rubra (a mycorrhizal plant species) were grown under defined atmospheric conditions with either ambient (350 p.p.m.) or elevated (700 p.p.m.) CO(2) concentrations. PCR-DGGE (PCR-denaturing gradient gel electrophoresis) and quantitative-PCR were carried out to analyze, respectively, the structure and abundance of the communities of actinomycetes, Fusarium spp., Trichoderma spp., Pseudomonas spp., Burkholderia spp. and Bacillus spp. Responses of specific functional groups, such as phloroglucinol, phenazine and pyrrolnitrin producers, were also examined by quantitative-PCR, and HPLC (high performance liquid chromatography) was employed to assess changes in exuded sugars in the rhizosphere. Multivariate analysis of group-specific community profiles showed disparate responses to elevated CO(2) for the different bacterial and fungal groups examined, and these responses were dependent on plant type and soil nutrient availability. Within the bacterial community, the genera Burkholderia and Pseudomonas, typically known as successful rhizosphere colonizers, were significantly influenced by elevated CO(2), whereas the genus Bacillus and actinomycetes, typically more dominant in bulk soil, were not. Total sugar concentrations in the rhizosphere also increased in both plants in response to elevated CO(2). The abundances of phloroglucinol-, phenazine- and pyrrolnitrin-producing bacterial communities were also influenced by elevated CO(2), as was the abundance of the fungal genera Fusarium and Trichoderma.
Publisher: Elsevier BV
Date: 02-2022
DOI: 10.1016/J.SCITOTENV.2021.150734
Abstract: The extensive application of pesticides in agriculture raises concerns about their potential negative impact on soil microorganisms, being the key drivers of nutrient cycling. Most studies have investigated the effect of a single pesticide on a nutrient cycling in single soil type. We, for the first time, investigated the effect of 20 commercial pesticides with different mode of actions, applied at their recommended dose and five times their recommended dose, on nitrogen (N) microbial cycling in three different agricultural soils from southern Australian. Functional effects were determined by measuring soil enzymatic activities of β-1,4-N-acetyliglucosaminidase (NAG) and l-leucine aminopeptidase (LAP), potential nitrification (PN), and the abundance of functional genes involved in N cycling (amoA and nifH). Effects on nitrifiers ersity were determined with licon sequencing. Overall, the pesticides effect on N microbial cycling was dose-independent and soil specific. The fungicides flutriafol and azoxystrobin, the herbicide chlorsulfuron and the insecticide fipronil induced a significant reduction in PN and β-1,4-N-acetylglucosaminidase activity (P < 0.05) (NAG) in the alkaline loam soil with low organic carbon content i.e. a soil with properties which typically favors pesticide bioavailability and therefore potential toxicity. For the nitrifier community, the greatest pesticide effects were on the most dominant Nitrososphaeraceae (ammonia-oxidizing archaea AOA) whose abundance increased significantly compared to the less dominant AOA and other nitrifiers. The inhibiting effects were more evident in the soil s les treated with fungicides. By testing multiple pesticides in a single study, our findings provide crucial information that can be used for pesticide hazard assessment.
Publisher: Wiley
Date: 12-08-2008
DOI: 10.1111/J.1462-2920.2008.01644.X
Abstract: Climatic changes will not only result in higher overall temperature, but also in greater variability in weather conditions. Antarctic soils are subjected to extremely variable conditions in the form of frequent freeze-thaw cycles (FTCs), but the importance of alteration in FTC frequency, compared with increases in average temperature and indirect vegetation-mediated effects on soil microorganisms, is still unknown. We therefore designed two complementary microcosm experiments using undisturbed soil cores from Signy Island (60 degrees 43'S, 45 degrees 38'W) in the maritime Antarctic. The experiments consisted of soil core incubations with or without the overlying vegetation at four different temperatures and six different FTC regimes. We assessed bacterial and fungal density and community structure, as well as the density of several key genes in microbial nutrient cycles using a combination of RNA- and DNA-based molecular fingerprinting and quantitative PCR approaches in addition to enzymatic activity assays. Results showed that bacteria were more affected by warming than by changes in FTC frequency. In contrast, fungal community structure and abundance were mostly influenced by FTC frequency, as well as the presence of vegetation cover. The relative densities of several bacterial gene families involved in key steps of the N-cycle were affected by FTCs, while warming had little or no effect. The FTCs and incubation temperature also strongly influenced laccase enzymatic activity in soil. In total, our results suggest that, in addition to climatic warming, increased climatic variability may also have a profound impact on Antarctic microbial communities. Although these effects are difficult to detect with assays of total bacterial community structure, they do become manifest in the analysis of key functional gene densities.
Publisher: American Psychological Association (APA)
Date: 03-2022
DOI: 10.1037/MAC0000030
Publisher: Elsevier
Date: 2017
Publisher: Elsevier BV
Date: 11-2020
Location: Australia
Start Date: 2020
End Date: 2027
Funder: Australian Centre for International Agricultural Research
View Funded ActivityStart Date: 2017
End Date: 2020
Funder: Hort Innovation
View Funded ActivityStart Date: 2020
End Date: 2021
Funder: University of South Australia
View Funded ActivityStart Date: 2023
End Date: 2025
Funder: South Australian Grain Industry Trust Fund
View Funded ActivityStart Date: 2019
End Date: 2020
Funder: Water Research Australia
View Funded ActivityStart Date: 2019
End Date: 2019
Funder: Environmental Protection Agency
View Funded ActivityStart Date: 2019
End Date: 2019
Funder: University of South Australia
View Funded ActivityStart Date: 2020
End Date: 2021
Funder: University of South Australia
View Funded ActivityStart Date: 2020
End Date: 2021
Funder: Water Research Australia
View Funded ActivityStart Date: 2021
End Date: 2021
Funder: Water Research Australia
View Funded Activity