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Traditionally, antifungal resistance (AFR) has received much less attention compared with bacterial resistance to antibiotics. However, global changes, pandemics, and emerging new fungal infections have highlighted global health consequences of AFR. The recent report of the World Health Organisation (WHO) has identified fungal priority pathogens, and recognised AFR among the greatest global health threats. This is particularly important given the significant increase in fungal infections linked to climate change and pandemics. Environmental factors play critical roles in AFR and fungal infections, as many clinically relevant fungal pathogens and AFR originate from the environment (mainly soil). In addition, the environment serves as a potential rich source for the discovery of new antifungal agents, including mycoviruses and bacterial probiotics, which hold promise for effective therapies. In this article, we summarise the environmental pathways of AFR development and spread among high priority fungal pathogens, and propose potential mechanisms of AFR development and spread. We identify a research priority list to address key knowledge gaps in our understanding of environmental AFR. Further, we propose an integrated roadmap for predictive risk management of AFR that is critical for effective surveillance and forecasting of public health outcomes under current and future climatic conditions., Competing Interests: Declaration of interests No interests are declared., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Application of essential oils to mitigate aflatoxin B 1 (AFB 1 ) contamination in food is a current research hotspot; however, their direct incorporation may cause toxic effects, and changes in food organoleptic properties. This work aimed to synthesize novel synergistic formulation of Pinus roxburghii, Juniperus communis, and Cupressus sempervirens essential oils by mixture design assay (PJC) and encapsulation of PJC formulation into chitosan nanocomposite (Nm-PJC) with an aim to protect stored rice (Oryza sativa L., prime staple food) against fungi and AFB 1 mediated loss of valuable minerals, macronutrients, and fatty acids. Nm-PJC was characterized through DLS, SEM, FTIR, and XRD analyses, along with controlled delivery from chitosan nanobiopolymer. Encapsulation of synergistic formulation into chitosan-nanomatrix improved antifungal (4.0 μL/mL), antiaflatoxigenic (3.5 μL/mL), and antioxidant activities (P < 0.05). Impairment in ergosterol and methylglyoxal biosynthesis along with in-silico-homology-modeling of major components with Ver-1 and Omt-A proteins advocated chemico-molecular interaction responsible for fungal growth inhibition and AFB 1 secretion. In addition, in-situ efficacy against lipid-peroxidation, fatty acid biodeterioration, and preservation of minerals, macronutrients without affecting organoleptic attributes in rice and high mammalian safety profile (9874.23 μL/kg) suggested practical application of synergistic nanoformulation as innovative smart, and green candidate to mitigate AFB 1 contamination, and shelf-life extension of stored food products., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e., Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized. Measured soil functions included surrogates of microbial respiration, enzyme activities and nutrient cycling. Using Permutation multivariate analysis of variance (PerMANOVA) and network analysis, we found that the identity of tree provenances regulated both structure and function of soil microbiomes. In some cases, tree provenances substantially affected the response of microbial communities to the temperature treatments. For example, we found significant interactions of temperature and tree provenance on bacterial community and relative abundances of Chloroflexi and Zygomycota, and inorganic nitrogen. Microbial abundance was altered in response to increasing temperature, but was not affected by tree provenances. Our study provides novel evidence that even a small variation in biotic components (i.e., intraspecies tree variation) can significantly influence the response of soil microbial community composition and specific soil functions to global warming., (© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome-based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane-associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the core microbiome that were influenced by YCS incidence. Our study revealed key hub microorganisms in the core microbiome networks of sugarcane leaves, stalks, roots and rhizosphere soil despite location and time-associated shifts in the community assemblages. Elucidating their functional roles and identification of the keystone core microbiota that sustain plant health could provide a technological breakthrough for a sustainable increase in crop productivity., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Globally, drylands represent the largest terrestrial biome and are projected to expand by 23% by the end of this century. Drylands are characterized by extremely low levels of water and nutrients and exhibit highly heterogeneous distribution in plants and biocrusts which make microbial processes shaping the dryland functioning rather unique compared with other terrestrial ecosystems. Nitrous oxide (N 2 O) is a powerful greenhouse gas with ozone depletion potential. Despite of the pivotal influences of microbial communities on the production and consumption of N 2 O, we have limited knowledge of the biological pathways and mechanisms underpinning N 2 O emissions from drylands, which are estimated to account for 30% of total gaseous nitrogen emissions on Earth. In this article, we describe the key microbial players and biological pathways regulating dryland N 2 O emissions, and discuss how these processes will respond to emerging global changes such as climate warming, extreme weather events and nitrogen deposition. We also provide a conceptual framework to precisely manipulate the dryland microbiome to mitigate N 2 O emissions in situ using emerging technologies with great specificity and efficacy. These cross-disciplinary efforts will enable the development of novel and environmental-friendly microbiome-based solutions to future mitigation strategies of climate change., (© 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.)

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.

Environmental microbes are a major source of drug discovery, and several microbial products (antibiotics, anti-tumour products, immunosuppressants and others) are used routinely for human therapies. Most of these products were obtained from cultivable (<1%) environmental microbes, and this means that the vast majority of microbes were not targeted for drug discovery. With the advent of new and emerging technologies, we are poised to harvest novel drugs from the so-called 'uncultivable' microbes. In this article, we propose how a multidisciplinary approach combining different technologies can expedite and revolutionize drug discovery from uncultivable microbes and examine the current limitations of technologies and strategies to overcome such limitations that might further expand the promise of drugs from environmental microbes., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

Olive mill wastewater (OMW) is rich in potentially toxic organics precluding its disposal into water receptors. However, land application of diluted OMW may result in safe disposal and fertilization. In order to investigate the effects of OMW on the structure of soil fungal groups, OMW was applied daily to pepper plants growing in a loamy sand and a sandy loam at two doses for a period of 3 months (total OMW equivalents 900 and 1800 m(3) ha(-1)). Nitrogen (N) fertilization alleviated N scarcity and considerably enhanced plant biomass production; however, when applied in combination with the high OMW dose, it induced plant stress. OMW applications resulted in marked changes in the denaturing gradient gel electrophoresis patterns of soil basidiomycete communities, while concurrent N fertilization reduced these effects. In contrast, the ascomycete communities required N fertilization to respond to OMW addition. Cloning libraries for the basidiomycete communities showed that Cryptococcus yeasts and Ceratobasidium spp. dominated in the samples treated with OMW. In contrast, certain plant pathogenic basidiomycetes such as Thanatephorus cucumeris and Athelia rolfsii were suppressed. The observed changes may be reasonably explained by the capacity of OMW to enrich soils in organic substrates, to induce N immobilization and to directly introduce OMW-derived basidiomycetous yeasts.

In grazed pastures, soil pH is raised in urine patches, causing dissolution of organic carbon and increased ammonium and nitrate concentrations, with potential effects on the structure and functioning of soil microbial communities. Here we examined the effects of synthetic sheep urine (SU) in a field study on dominant soil bacterial and fungal communities associated with bulk soil and plant roots (rhizoplane), using culture-independent methods and a new approach to investigate the ureolytic community. A differential response of bacteria and fungal communities to SU treatment was observed. The bacterial community showed a clear shift in composition after SU treatment, which was more pronounced in bulk soil than on the rhizoplane. The fungal community did not respond to SU treatment; instead, it was more affected by the time of sampling. Redundancy analysis of data indicated that the variation in the bacterial community was related to change in soil pH, while fungal community was more responsive to dissolution of organic carbon. Like the universal bacterial community, the ureolytic community was influenced by the SU treatment. However, different taxa within the ureolytic bacterial community responded differentially to the treatment. The ureolytic community comprised of members from a range of phylogenetically different taxa and could be used to measure the effect of environmental perturbations on the functional diversity of natural ecosystems.

The long-term impacts of Cu- and Zn-rich sewage sludge additions on the structure of the microbial community in a field under pasture were investigated using a combination of multiplex-terminal restriction fragment length polymorphism (M-TRFLP) and T-RFLP profiling approaches. Changes in the community structure of bacteria, fungi, archaea and actinobacteria were observed in soils that had previously received Cu- (50-200 mg kg(-1) soil) and Zn- (150-450 mg kg(-1) soil) rich sewage sludge additions. Changes in the structure of all microbial groups measured were observed at Cu and Zn rates below the current EU guidelines (135 mg kg(-1) Cu and 300 mg kg(-1) Zn). The response of the fungal community, and to a lesser extent the bacterial and archaeal community, to Cu was dose dependent. The fungal community also showed a dose-dependent response to Zn, which was not observed in the other microbial groups assessed. Redundancy analysis demonstrated that individual terminal restriction fragments responded to both Cu and Zn and these may have potential as genetic markers of long-term metal effects in soil.

Soils support an enormous microbial diversity, but the ecological drivers of this diversity are poorly understood. Interactions between the roots of individual grass species and the arbuscular mycorrhizal (AM) fungi and bacteria in their rhizoplane were studied in a grazed, unimproved upland pasture. Individual root fragments were isolated from soil cores, DNA extracted and used to identify plant species and assess rhizoplane bacterial and AM fungal assemblages, by amplifying part of the small-subunit ribosomal RNA gene, followed by terminal restriction fragment length polymorphism analysis. For the first time we showed that AM fungal and bacterial assemblages are related in situ and that this relationship occurred at the community level. Principal coordinate analyses of the data show that the AM fungi were a major factor determining the bacterial assemblage on grass roots. We also report a strong influence of the composition of the plant community on AM fungal assemblage. The bacterial assemblage was also influenced by soil pH and was spatially structured, whereas AM fungi were influenced neither by the bacteria nor by soil pH. Our study shows that linkages between plant roots and their microbial communities exist in a complex web of interactions that act at individual and at community levels, with AM fungi influencing the bacterial assemblage, but not the other way round.

A multiplex terminal restriction fragment length polymorphism (M-TRFLP) fingerprinting method was developed and validated for simultaneous analysis of the diversity and community structure of two or more microbial taxa (up to four taxa). The reproducibility and robustness of the method were examined using soil samples collected from different habitats. DNA was PCR amplified separately from soil samples using individual taxon-specific primers for bacteria, archaea, and fungi. The same samples were also subjected to a multiplex PCR with the primers for all three taxa. The terminal restriction fragment length polymorphism profiles generated for the two sets of PCR products were almost identical not only in terms of the presence of peaks but also in terms of the relative peak intensity. The M-TRFLP method was then used to investigate rhizosphere bacterial, fungal, and rhizobial/agrobacterial communities associated with the dwarf shrub Calluna vulgaris growing in either open moorland, a mature pine forest, or a transition zone between these two habitats containing naturally regenerating pine trees. Rhizosphere microbial communities associated with Vaccinium myrtillus collected from the native pine forest were also investigated. In this study, individual PCR products from the three taxa were also pooled before restriction digestion and fragment size analysis. The terminal restriction fragment length polymorphism profiles obtained with PCR products amplified individually and with multiplexed and pooled PCR products were found to be consistent with each other in terms of the number, position, and relative intensity of peaks. The results presented here confirm that M-TRFLP analysis is a highly reproducible and robust molecular tool for simultaneous investigation of multiple taxa, which allows more complete and higher resolution of microbial communities to be obtained more rapidly and economically.

Synthetic organophosphorus compounds are used as pesticides, plasticizers, air fuel ingredients and chemical warfare agents. Organophosphorus compounds are the most widely used insecticides, accounting for an estimated 34% of world-wide insecticide sales. Contamination of soil from pesticides as a result of their bulk handling at the farmyard or following application in the field or accidental release may lead occasionally to contamination of surface and ground water. Several reports suggest that a wide range of water and terrestrial ecosystems may be contaminated with organophosphorus compounds. These compounds possess high mammalian toxicity and it is therefore essential to remove them from the environments. In addition, about 200,000 metric tons of nerve (chemical warfare) agents have to be destroyed world-wide under Chemical Weapons Convention (1993). Bioremediation can offer an efficient and cheap option for decontamination of polluted ecosystems and destruction of nerve agents. The first micro-organism that could degrade organophosphorus compounds was isolated in 1973 and identified as Flavobacterium sp. Since then several bacterial and a few fungal species have been isolated which can degrade a wide range of organophosphorus compounds in liquid cultures and soil systems. The biochemistry of organophosphorus compound degradation by most of the bacteria seems to be identical, in which a structurally similar enzyme called organophosphate hydrolase or phosphotriesterase catalyzes the first step of the degradation. organophosphate hydrolase encoding gene opd (organophosphate degrading) gene has been isolated from geographically different regions and taxonomically different species. This gene has been sequenced, cloned in different organisms, and altered for better activity and stability. Recently, genes with similar function but different sequences have also been isolated and characterized. Engineered microorganisms have been tested for their ability to degrade different organophosphorus pollutants, including nerve agents. In this article, we review and propose pathways for degradation of some organophosphorus compounds by microorganisms. Isolation, characterization, utilization and manipulation of the major detoxifying enzymes and the molecular basis of degradation are discussed. The major achievements and technological advancements towards bioremediation of organophosphorus compounds, limitations of available technologies and future challenge are also discussed.