483 results on '"Brajesh K. Singh"'
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2. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development
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Chao Xiong, Brajesh K. Singh, Yong-Guan Zhu, Hang-Wei Hu, Pei-Pei Li, Yan-Lai Han, Li-Li Han, Qin-Bing Zhang, Jun-Tao Wang, Si-Yi Liu, Chuan-Fa Wu, An-Hui Ge, Li-Mei Zhang, and Ji-Zheng He
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plant microbiome ,diazotrophs ,cereal crops ,microbial networks ,soil–plant continuum ,phyllosphere ,Microbiology ,QR1-502 - Abstract
ABSTRACTPlant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil–plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.
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- 2024
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3. Exploring the connectivity between rhizosphere microbiomes and the plant genes: A way forward for sustainable increase in primary productivity
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Ayomide E. Fadiji, Rutwik Barmukh, Rajeev K. Varshney, and Brajesh K. Singh
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microbe–plant genetic interaction ,microbiome ,plant genes ,rhizobiome engineering ,sustainable agriculture ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract The plant genome and its microbiome act together to enhance survival and promote host growth under various stresses. Plant microbiome plays an important role in plant productivity via a multitude of mechanisms including provision of nutrients and resistance against different biotic and abiotic factors. However, the molecular mechanisms responsible for plant microbiome interactions remain largely unknown. Nevertheless, gaining a deeper understanding of the plant genetic traits driving microbiome recruitments and assembly holds the potential to greatly enhance our capacity to utilize the microbiome effectively, leading to sustainable improvements in agricultural productivity and produce quality. This article explores the mutual influence of specific plant genes in modulating the rhizosphere (area around plant roots) microbiome, and how this rhizosphere microbiome impacts the plant genes, ultimately enhancing plant health and productivity. It further examines the effects of various rhizosphere microbiota, including Bacillus, Pseudomonas, Azospirillum, Trichoderma spp., on plant development, immunology and the expression of host functional genes. We conclude that the adoption of a hologenomics approach (i.e., considering both the plant genome and the genomes of all microorganisms colonizing the plant) can significantly advance our understanding of plant resistance and resilience to biotic and abiotic stresses. This approach can offer improved solutions for agronomic challenges in the future. Furthermore, within this context, we identify key knowledge gaps within the discipline and propose frameworks that may be employed in the future to harness plant–microbial interactions effectively, leading to a sustainable increase in farm productivity.
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- 2023
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4. Evidence of distinct response of soil viral community to a plant infection and the disease pathobiome
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Zhen‐Zhen Yan, Juntao Wang, Jinsong Liang, Bruna D. Batista, Hongwei Liu, Chao Xiong, Simranjit Kaur, Catriona A. Macdonald, and Brajesh K. Singh
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agricultural production ,network stability ,pathobiome ,Verticillium dahliae ,viral community ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Despite the abundance and ubiquity of viruses in terrestrial ecosystems, the roles of soil viruses in ecosystem functions and plant diseases remain understudied. Here, we used 42 pairs of bulk soil and rhizosphere samples collected from cotton fields with different Verticillium dahliae infection conditions to investigate the responses of soil viruses to soilborne fungal pathogen infections. We found that V. dahliae infection significantly impacted the characteristics of rhizosphere viral community but not bulk soil community. In addition, our results revealed that unlike current knowledge of the impacts of plant pathogens on soil bacterial and fungal communities, the soil viral community demonstrated a lower viral network vulnerability to infection. Importantly, we provided evidence that soil viruses are a potentially important component of the pathobiome of plant disease which may help pathogen invasion and promote disease symptoms. Our study highlights distinct response of viral community and has implications for future plant disease management and agricultural productivity.
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- 2023
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5. Seed biopriming for sustainable agriculture and ecosystem restoration
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Prachi Singh, Anukool Vaishnav, Hongwei Liu, Chao Xiong, Harikesh Bahadur Singh, and Brajesh K. Singh
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Biotechnology ,TP248.13-248.65 - Abstract
Abstract The utilization of microbial inoculants in the realm of sustainable agricultural and ecosystem restoration has witnessed a surge in recent decades. This rise is largely attributed to advancements in our understanding of plant–microbe interactions, the urgency to reduce the dependence on agrochemicals and the growing societal demand for sustainable strategies in ecosystem management. However, despite the rapid growth of bio‐inoculants sector, certain limitations persist concerning their efficacy and performance under the field condition. Here, we propose that seed biopriming, an effective microbial inoculant technique integrating both biological agents (the priming of beneficial microbes on seeds) and physiological aspects (hydration of seeds for improved metabolically activity), has a significant potential to mitigate these limitations. This method increases the protection of seeds against soil‐borne pathogens and soil pollutants, such as salts and heavy metals, while promoting germination rate and uniformity, leading to overall improved primary productivity and soil health. Furthermore, we argue that a microbial coating on seeds can facilitate transgenerational associations of beneficial microbes, refine plant and soil microbiomes, and maintain soil legacies of beneficial microflora. This review article aims to improve our understanding of the seed biopriming approach as a potent and valuable tool in achieving sustainable agriculture and successful ecosystem restoration.
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- 2023
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6. Plants and endophytes interaction: a 'secret wedlock' for sustainable biosynthesis of pharmaceutically important secondary metabolites
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Poonam Kumari, Nikky Deepa, Prabodh Kumar Trivedi, Brajesh K. Singh, Vaibhav Srivastava, and Akanksha Singh
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Core endomicrobiome ,Endophytes ,Medicinal plants ,Microbiome engineering ,Secondary Metabolites ,Microbiology ,QR1-502 - Abstract
Abstract Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.
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- 2023
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7. Getting to the Root of Tree Soil Microbiome Sampling
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Sarah L. Addison, Megan A. Rúa, Simeon J. Smaill, Kaitlyn J. Daley, Brajesh K. Singh, and Steve A. Wakelin
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metabarcoding ,microbial communities ,Pinus radiata ,plant–soil interactions ,rhizoplane ,rhizosphere ,Plant culture ,SB1-1110 ,Microbial ecology ,QR100-130 ,Plant ecology ,QK900-989 - Abstract
Microbiomes play critical roles in host functioning and, therefore, there is increasing interest in the microbiome assembly of plants. However, sampling strategies for long-lived perennial trees need to be standardized to produce robust data that accurately represent the microbiome over time. This issue is currently unresolved because there is little evidence indicating which portion of perennial tree species (e.g., root region or surrounding soil) is the best to sample to produce the most accurate measure of microbiome communities. Our aim was to sample different compartments of a plant's belowground microbiome to identify the optimal sampling strategy to account for the microbial community present. We found that the structure of the microbial community depends most strongly on the environment (site) and compartment of sample collected (bulk soil, rhizosphere, or rhizoplane), rather than the depth or cardinal direction of the sample. We also found that the microbial community increased in diversity with increased distance from the tree within the rhizoplane and rhizosphere. The data presented here provide systematic evidence for a pragmatic and robust sampling regime that was tested and validated across different environments and soil types while controlling for host genotype. This sampling regime will enable effective partitioning of root compartments when studying the microbiome associated with perennial tree species, allowing targeted questions about the microbiome to be explored with greater accuracy.
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- 2023
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8. Microbial inoculants with higher capacity to colonize soils improved wheat drought tolerance
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Jiayu Li, Juntao Wang, Hongwei Liu, Catriona A. Macdonald, and Brajesh K. Singh
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Biotechnology ,TP248.13-248.65 - Abstract
Abstract Microbial inoculants have gained increasing attention worldwide as an eco‐friendly solution for improving agriculture productivity. Several studies have demonstrated their potential benefits, such as enhanced resistance to drought, salinity, and pathogens. However, the beneficial impacts of inoculants remain inconsistent. This variability is attributed to limited knowledge of the mechanisms by which microbial inoculants affect crop growth and a lack of ecological characteristics of these inoculants that limit our ability to predict their beneficial effects. The first important step is believed to be the evaluation of the inoculant's ability to colonize new habitats (soils and plant roots), which could provide crops with beneficial functions and improve the consistency and efficiency of the inoculants. In this study, we aimed to investigate the impact of three microbial inoculants (two bacterial: P1 and P2, and one fungal: P3) on the growth and stress responses of three wheat varieties in two different soil types under drought conditions. Furthermore, we investigated the impact of microbial inoculants on soil microbial communities. Plant biomass and traits were measured, and high‐throughput sequencing was used to characterize bulk and rhizosphere soil microbiomes after exposure to drought stress. Under drought conditions, plant shoot weight significantly increased (11.37%) under P1 treatments compared to uninoculated controls. In addition, total nitrogen enzyme activity increased significantly under P1 in sandy soil but not in clay soil. Importantly, network analyses revealed that P1, consisting of Bacillus paralicheniformis and Bacillus subtilis, emerged as the keystone taxa in sandy soil. Conversely, P2 and P3 failed to establish as keystone taxa, which may explain their insignificant impact on wheat performance under drought conditions. In conclusion, our study emphasizes the importance of effective colonization by microbial inoculants in promoting crop growth under drought conditions. Our findings support the development of microbial inoculants that robustly colonize plant roots for improved agricultural productivity.
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- 2023
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9. New microbial tools to boost restoration and soil organic matter
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Tadeo Sáez‐Sandino, Manuel Delgado‐Baquerizo, Eleonora Egidi, and Brajesh K. Singh
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Biotechnology ,TP248.13-248.65 - Abstract
Abstract Anthropogenic activities are causing unprecedented rates of soil and ecosystem degradation, and the current restoration practices take decades and are prone to high rates of failure. Here we propose, the development and application of emerging microbiome tools that can potentially improve the contents and diversity of soil organic matters, enhancing the efficacy and consistency of restoration outcomes.
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- 2023
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10. Impact of general incidence function on three-strain SEIAR model
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Manoj Kumar Singh, Anjali., Brajesh K. Singh, and Carlo Cattani
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general incidence rate ,reproduction number ,multi-strain ,asymptomatic ,liénard chipart criterion ,Biotechnology ,TP248.13-248.65 ,Mathematics ,QA1-939 - Abstract
We investigate the behavior of a complex three-strain model with a generalized incidence rate. The incidence rate is an essential aspect of the model as it determines the number of new infections emerging. The mathematical model comprises thirteen nonlinear ordinary differential equations with susceptible, exposed, symptomatic, asymptomatic and recovered compartments. The model is well-posed and verified through existence, positivity and boundedness. Eight equilibria comprise a disease-free equilibria and seven endemic equilibrium points following the existence of three strains. The basic reproduction numbers $ \mathfrak{R}_{01} $, $ \mathfrak{R}_{02} $ and $ \mathfrak{R}_{03} $ represent the dominance of strain 1, strain 2 and strain 3 in the environment for new strain emergence. The model establishes local stability at a disease-free equilibrium point. Numerical simulations endorse the impact of general incidence rates, including bi-linear, saturated, Beddington DeAngelis, non-monotone and Crowley Martin incidence rates.
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- 2023
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11. Impacts of biostimulants on crop yield and biological activity under drought conditions
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Jenendra Wadduwage, Eleonora Egidi, Brajesh K. Singh, and Catriona A. Macdonald
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biostimulant ,crop yield ,drought condition ,microbial activity ,soil health ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Introduction Biostimulants are proposed to have a role in sustainable food production and are being increasingly used strategies to limit the negative effects of drought stress on crop yield and soil health. However, how different biostimulants used alone, or in combination with conventional management approaches affect soil health and crop yield under drought in different soils is not well understood. Here we conducted a glasshouse experiment to investigate this. Materials and Methods Two soil types from fields maintained under intensive (IM) and extensive (EM) management practices were used with two commercial biostimulants [Universal Natural Plant food (UNP) and Converte Seed Primer (CSP)] on soil microbial populations and crop yield (lettuce) under well‐watered and drought stressed conditions. We examined the activity and biomass of soil microorganisms as well as seed germination and root and shoot biomass to examine the effect of application of biostimulants on parameters of soil health and crop yield. Results Biostimulants generally increased crop yield, basal soil respiration and microbial biomass, with effects stronger in EM soils than in IM soils, but effects on soil enzyme activities were variable. The combined use of biostimulant and inorganic fertiliser negated the benefits of the biostimulant on soil biological properties in some cases. Nevertheless, effects of biostimulants had a positive impact on crop yield with the combined use of soil‐applied and seed applied biostimulants have the greatest impact on plant biomass and also conferring some resistance in both soil microbial communities and plant growth to drought. Conclusions While biomass and activity of the microbial community and plant growth responses to biostimulant additions are both soil and biostimulant dependent, their combined use has potential to aid both plants and maintain promote microbial activity under of drought, compared to conventional fertiliser treatments in extensively managed soils.
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- 2024
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12. Streptomyces‐triggered coordination between rhizosphere microbiomes and plant transcriptome enables watermelon Fusarium wilt resistance
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An‐Hui Ge, Qi‐Yun Li, Hong‐Wei Liu, Zheng‐Kun Zhang, Yang Lu, Zhi‐Huai Liang, Brajesh K. Singh, Li‐Li Han, Ji‐Fang Xiang, Ji‐Ling Xiao, Si‐Yi Liu, and Li‐Mei Zhang
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Biotechnology ,TP248.13-248.65 - Abstract
Abstract The use of microbial inoculant is a promising strategy to improve plant health, but their efficiency often faces challenges due to difficulties in successful microbial colonization in soil environments. To this end, the application of biostimulation products derived from microbes is expected to resolve these barriers via direct interactions with plants or soil pathogens. However, their effectiveness and mechanisms for promoting plant growth and disease resistance remain elusive. In this study, we showed that root irrigation with the extracts of Streptomyces ahygroscopicus strain 769 (S769) solid fermentation products significantly reduced watermelon Fusarium wilt disease incidence by 30% and increased the plant biomass by 150% at a fruiting stage in a continuous cropping field. S769 treatment led to substantial changes in both bacterial and fungal community compositions, and induced a highly interconnected microbial association network in the rhizosphere. The root transcriptome analysis further suggested that S769 treatment significantly improved the expression of the MAPK signalling pathway, plant hormone signal transduction and plant–pathogen interactions, particular those genes related to PR‐1 and ethylene, as well as genes associated with auxin production and reception. Together, our study provides mechanistic and empirical evidences for the biostimulation products benefiting plant health through coordinating plant and rhizosphere microbiome interaction.
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- 2024
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13. Effects of biostimulant application on soil biological and physicochemical properties: A field study
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Jenendra Wadduwage, Hongwei Liu, Eleonora Egidi, Brajesh K. Singh, and Catriona A. Macdonald
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biostimulant ,field condition ,microbial communities ,soil health ,soil microbial activity ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Introduction Despite their potential benefits, it is not well understood how the application of biostimulants influences soil biological properties and their microbial communities in field conditions. In this study, we aimed to evaluate the impacts of biostimulants on soil biological and physicochemical properties relevant to soil health. Materials and Methods To achieve this, we conducted a field study to investigate the effects of two types of commercially available biostimulants, Universal Natural Plant food (UNP) and Converte Seed Primer (CSP), on microbial activity, bacterial and fungal abundance, community structure and diversity, and soil chemical and physical properties across two depths (0–10 and 10–20 cm) from five sites under either wheat or pasture cultivation. Results Our findings suggest that application of UNP stimulated microbial activity by 40.1% in surface (0–10 cm) and 36.4% in deeper (10–20 cm) soil, but was dependant on site. Effects were generally greater in grasslands compared with arable soils. At sites where UNP stimulated microbial respiration, substrate‐induced respiration was also stimulated in surface soils and was associated with increased soil moisture content and higher total carbon and nitrogen. At the one site where UNP was combined with CSP, soil enzymes associated with carbon and nitrogen cycling were stimulated in UNP and UNP + CSP treatments. Total bacterial and fungal abundance and their alpha diversity did not respond to biostimulant treatment. However, microbial indicator communities were identified that responded positively to UNP and CSP addition across the two depths. Bacterial indicator species included Elsterales, Propionibacteriales, Solibacterales, Candatus, Reyranellales and Sphingomonadales, but differed between depths. For the fungal indicator species Filobasidiales (Basidiomycota) and Pleosporales (Ascomycota) were strong responders and common across both depths. Conclusion Overall, our results suggest some positive effects of biostimulants on soil biological and physicochemical properties. Further long‐term studies should be conducted to evaluate the effects of biostimulants on crop yield and farm resilience.
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- 2023
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14. Tapping the rhizosphere metabolites for the prebiotic control of soil-borne bacterial wilt disease
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Tao Wen, Penghao Xie, Hongwei Liu, Ting Liu, Mengli Zhao, Shengdie Yang, Guoqing Niu, Lauren Hale, Brajesh K. Singh, George A. Kowalchuk, Qirong Shen, and Jun Yuan
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Science - Abstract
Abstract Prebiotics are compounds that selectively stimulate the growth and activity of beneficial microorganisms. The use of prebiotics is a well-established strategy for managing human gut health. This concept can also be extended to plants where plant rhizosphere microbiomes can improve the nutrient acquisition and disease resistance. However, we lack effective strategies for choosing metabolites to elicit the desired impacts on plant health. In this study, we target the rhizosphere of tomato (Solanum lycopersicum) suffering from wilt disease (caused by Ralstonia solanacearum) as source for potential prebiotic metabolites. We identify metabolites (ribose, lactic acid, xylose, mannose, maltose, gluconolactone, and ribitol) exclusively used by soil commensal bacteria (not positively correlated with R. solanacearum) but not efficiently used by the pathogen in vitro. Metabolites application in the soil with 1 µmol g−1 soil effectively protects tomato and other Solanaceae crops, pepper (Capsicum annuum) and eggplant (Solanum melongena), from pathogen invasion. After adding prebiotics, the rhizosphere soil microbiome exhibits enrichment of pathways related to carbon metabolism and autotoxin degradation, which were driven by commensal microbes. Collectively, we propose a novel pathway for mining metabolites from the rhizosphere soil and their use as prebiotics to help control soil-borne bacterial wilt diseases.
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- 2023
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15. Host selection has a stronger impact on leaf microbiome assembly compared to land‐management practices
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Pankaj K. Singh, Eleonora Egidi, Catriona A. Macdonald, and Brajesh K. Singh
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fertilizer ,irrigation ,plant microbiome ,plant traits ,soil properties ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Introduction Plant microbiomes contribute directly to plant health and productivity, but mechanisms that underpin plant microbiome assembly in different compartments (e.g., root, leaf) are not fully understood. Identifying environmental and management factors that affect plant microbiome assembly is important to advance understanding of fundamental ecological processes, and to harness microbiome for improved primary productivity and environmental sustainability. Irrigation and fertilization are two common management practices in Australian tree plantations, but little is known about the effects of these treatments on soil, plant host and their microbiome. Here, we investigated the impact of decade‐long irrigation, fertilization and their combined application on soil, plant traits and microbiome of a Eucalyptus saligna plantation. Materials and Methods Microbial profiling of bulk soil, rhizosphere, root and leaves was performed using amplicon sequencing 16S ribosomal DNA and internal transcribed spacer (ITS) markers for bacteria and fungi, respectively, along with measurements of soil properties and plant traits. Results The results indicated that both management practices significantly affected soil properties and soil and root microbiomes. Irrigation increased but fertilizer treatment reduced microbial alpha diversity. However, neither irrigation nor fertilizer treatment impacted the leaf microbiome. Our findings suggest that management practices impact soil edaphic factors, which in turn influence the below‐ground microbiome (soil and root), but the leaf microbiome remains unaffected. In addition, the leaf microbiome was distinct from soil and root microbiomes, and a source tracker analysis suggested that root and bulk soils only contributed to 53% and 10% operational taxonomic units of the leaf bacterial community, suggesting strong and sequential host selection of the leaf microbiome. In addition, management practices had a limited impact on leaf traits and, consequently, the leaf microbiome maintained its distinct composition. Conclusion These findings provide mechanistic evidence for ecological processes that drive plant microbiome assembly and indicate that host selection plays a more important role than management practices in the leaf microbiome assembly.
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- 2023
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16. Interferon-independent processes constrain measles virus cell-to-cell spread in primary human airway epithelial cells
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Lorellin A. Durnell, Camilla E. Hippee, Roberto Cattaneo, Jennifer A. Bartlett, Brajesh K. Singh, and Patrick L. Sinn
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contagion ,cell-associated virus ,innate immunity ,morbillivirus ,paramyxoviridae ,Microbiology ,QR1-502 - Abstract
ABSTRACT Amplification of measles virus (MeV) in human airway epithelia may contribute to its extremely high contagious nature. We use well-differentiated primary cultures of human airway epithelial cells (HAE) to model ex vivo how MeV spreads in human airways. In HAE, MeV spreads cell-to-cell for 3–5 days, but then, infectious center growth is arrested. What stops MeV spread in HAE is not understood, but interferon (IFN) is known to slow MeV spread in other in vitro and in vivo models. Here, we assessed the role of type I and type III IFN in arresting MeV spread in HAE. The addition of IFN-β or IFN-λ1 to the medium of infected HAE slowed MeV infectious center growth, but when IFN receptor signaling was blocked, infectious center size was not affected. In contrast, blocking type-I IFN receptor signaling enhanced respiratory syncytial virus spread. HAE were also infected with MeV mutants defective for the V protein. The V protein has been demonstrated to interact with both MDA5 and STAT2 to inhibit activation of innate immunity; however, innate immune reactions were unexpectedly muted against the V-defective MeV in HAE. Minimal innate immunity activation was confirmed by deep sequencing, quantitative RT-PCR, and single-cell RNA-seq analyses of the transcription of IFN and IFN-stimulated genes. We conclude that in HAE, IFN-signaling can contribute to slowing infectious center growth; however, IFN-independent processes are most important for limiting cell-to-cell spread. Importance Fundamental biological questions remain about the highly contagious measles virus (MeV). MeV amplifies within airway epithelial cells before spreading to the next host. This final step likely contributes to the ability of MeV to spread host-to-host. Over the course of 3–5 days post-infection of airway epithelial cells, MeV spreads directly cell-to-cell and forms infectious centers. Infectious center formation is unique to MeV. In this study, we show that interferon (IFN) signaling does not explain why MeV cell-to-cell spread is ultimately impeded within the cell layer. The ability of MeV to spread cell-to-cell in airway cells without appreciable IFN induction may contribute to its highly contagious nature. This study contributes to the understanding of a significant global health concern by demonstrating that infectious center formation occurs independent of the simplest explanation for limiting viral transmission within a host.
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- 2023
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17. Under nonlinear prey-harvesting, effect of strong Allee effect on the dynamics of a modified Leslie-Gower predator-prey model
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Manoj K. Singh, Brajesh K. Singh, Poonam, and Carlo Cattani
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predator-prey model ,stability ,bifurcation ,harvesting ,allee effect ,Biotechnology ,TP248.13-248.65 ,Mathematics ,QA1-939 - Abstract
In the present study, the effects of the strong Allee effect on the dynamics of the modified Leslie-Gower predator-prey model, in the presence of nonlinear prey-harvesting, have been investigated. In our findings, it is seen that the behaviors of the described mathematical model are positive and bounded for all future times. The conditions for the local stability and existence for various distinct equilibrium points have been determined. The present research concludes that system dynamics are vulnerable to initial conditions. In addition, the presence of several types of bifurcations (e.g., saddle-node bifurcation, Hopf bifurcation, Bogdanov-Takens bifurcation, homoclinic bifurcation) has been investigated. The first Lyapunov coefficient has been evaluated to study the stability of the limit cycle that results from Hopf bifurcation. The presence of a homoclinic loop has been demonstrated by numerical simulation. Finally, possible phase drawings and parametric figures have been depicted to validate the outcomes.
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- 2023
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18. Correction: Plants and endophytes interaction: a 'secret wedlock' for sustainable biosynthesis of pharmaceutically important secondary metabolites
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Poonam Kumari, Nikky Deepa, Prabodh Kumar Trivedi, Brajesh K. Singh, Vaibhav Srivastava, and Akanksha Singh
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Microbiology ,QR1-502 - Published
- 2024
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19. Application of microbial inoculants significantly enhances crop productivity: A meta‐analysis of studies from 2010 to 2020
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Jiayu Li, Juntao Wang, Hongwei Liu, Catriona A. Macdonald, and Brajesh K. Singh
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crop yield ,meta‐analysis ,microbial inoculants ,PGPR ,sustainable agriculture ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Introduction With the rapid development of microbial technology, microbial inoculant is considered as a promising tool in sustainable agricultural systems. Mechanisms by which microbial inoculants improve crop yield include improving plant nutrient availability and alleviating abiotic/biotic stresses (e.g., drought, salt and disease). However, the field efficacy of microbial inoculants remains inconsistent, which constrains large‐scale adoptions. Identity of dominant mechanisms that underpin the positive impacts of different microbial inoculants is limited. Thus, a comprehensive quantitative assessment of known inoculants on crop performance is needed to provide guidance for the development of effective microbial tools from both research and commercial perspectives. Materials and Methods Based on 97 peer‐reviewed publications, we conducted a meta‐analysis to quantify the benefits of different microbial inoculants on crop yield, and to identify the key mechanisms that underpin enhanced crop yield. Results Result showed that (i) alleviation of stresses was the major mechanism (53.95%, n = 53) by which microbial inoculants enhance crop yield, while improving plant nutrient availability accounted for 22.25% (n = 58) of crop yield enhancement. (ii) Pseudomonas was the most effective microbial inoculant in enhancing crop yield through alleviating stresses (63.91%, n = 15), whereas Enterobacter was the most effective in improving plant nutrient availability (27.12%, n = 5). (iii) Considering both mechanisms together, Pseudomonas (49.94%, n = 21), Enterobacter (27.55%, n = 13) and Bacillus (25.66%, n = 32) were the largest sources of microbial inoculants to enhance crop yield, and the combination of diazotroph Burkholderia with its legume host had the highest effect on improving the yield (by 196.38%). Microbial inoculants also improve nutritional quality by enhancing mineral contents in the produce. Conclusion Our analysis provides evidence that microbial inoculants can enhance agricultural productivity and nutritional quality and can be used either alone or in combination with reduced amount of agrochemicals to promote sustainable agriculture.
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- 2022
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20. Sustainable agricultural practices contribute significantly to One Health
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Zhenzhen Yan, Chao Xiong, Hongwei Liu, and Brajesh K. Singh
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agrochemicals ,antibiotic resistance ,One Health ,soil microbiome ,sustainable agriculture ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract The One Health concept proposes that the health of humans, animals, and the environment are interconnected. Agricultural production is a critical component of One Health as food links the environment to human health. Food not only provides nutrients to humans but also represents an important pathway for human exposure to environmental microbes as well as potentially harmful agrochemicals. In addition, inappropriate agronomic practices can cause damage to the environment which can have unintended adverse impacts on human health. Therefore, improving agricultural production systems and protecting environmental health should not be viewed as isolated goals as they are strongly interlinked. Here, we used the nexus of soil, plant, and human microbiomes to discuss sustainable agricultural production from the One Health perspective. We highlighted three interconnected challenges faced by current agronomic practices: the transmissions of pathogens in soil‐human microbial loops, the dissemination of antibiotic resistance genes in agroecosystems, and the impacts of chemical pesticides on humans and environmental health. Finally, we propose the potential of utilising microbiomes for better sustainable agronomic practices to contribute to key goals of the One Health concept.
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- 2022
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21. Synthetic community improves crop performance and alters rhizosphere microbial communities
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Simranjit Kaur, Eleonora Egidi, Zhiguang Qiu, Catriona A. Macdonald, Jay Prakash Verma, Pankaj Trivedi, Juntao Wang, Hongwei Liu, and Brajesh K. Singh
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crop productivity ,microbial community ,seed dressings ,synthetic community ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Introduction Harnessing synthetic communities (SynCom) of plant growth‐promoting (PGP) microorganisms is considered a promising approach to improve crop fitness and productivity. However, biotic mechanisms that underpin improved plant performance and the effects of delivery mode of synthetic community are poorly understood. These are critical knowledge gaps that constrain field efficacy of SynCom and hence large‐scale adoption by the farming community. Material & Methods In this study, a SynCom of four PGP microbial species was constructed and applied to either as seed dressing (treatment T1, applied at the time of sowing) or to soil (treatment T2, applied in soil at true leaf stage) across five different cotton (Gossypium hirsutum) cultivars. The impact of SynCom on plant growth, rhizosphere microbiome and soil nutrient availability, and how this was modified by plant variety and mode of applications, was assessed. Results Results showed that the seed application of SynCom had the strongest positive impact on overall plant fitness, resulting in higher germination (14.3%), increased plant height (7.4%) and shoot biomass (5.4%). A significant increase in the number of flowers (10.4%) and yield (8.5%) was also observed in T1. The soil nitrate availability was enhanced by 28% and 55% under T1 and T2, respectively. Results further suggested that SynCom applications triggered enrichment of members from bacterial phyla Actinobacteria, Firmicutes and Cyanobacteria in the rhizosphere. A shift in fungal communities was also observed, with a significant increase in the relative abundance of fungi from phyla Chytridiomycota and Basidiomycota in SynCom treatments. A structural equation model suggested that SynCom directly increased crop productivity but also indirectly via impacting the alpha diversity of bacteria. Conclusion Overall, this study provides mechanistic evidence that SynCom applications can shift rhizosphere microbial communities and improve soil fertility, plant growth, and crop productivity, suggesting that their use could contribute toward sustainable increase in farm productivity.
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- 2022
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22. Individuality and stability of the koala (Phascolarctos cinereus) faecal microbiota through time
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Raphael Eisenhofer, Kylie L. Brice, Michaela DJ Blyton, Scott E. Bevins, Kellie Leigh, Brajesh K. Singh, Kristofer M. Helgen, Ian Hough, Christopher B. Daniels, Natasha Speight, and Ben D. Moore
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Time series ,Longitudinal ,16S rRNA ,Marsupial ,Eucalyptus ,Core microbiota ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
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- 2023
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23. Effective colonisation by a bacterial synthetic community promotes plant growth and alters soil microbial community
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Hongwei Liu, Zhiguang Qiu, Jun Ye, Jay Prakash Verma, Jiayu Li, and Brajesh K. Singh
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beneficial microbes ,Fusarium pseudograminearum ,microbial colonisation ,plant defence ,SynCom ,Agriculture (General) ,S1-972 ,Environmental sciences ,GE1-350 - Abstract
Abstract Introduction Plant‐associated microorganisms are widely explored for their use as bioinoculants in agriculture. However, the rate and ability of introduced microbes to colonise and interact with indigenous soil microbiomes are largely unknown. Materials & Methods In this study, we constructed a bacterial synthetic community (SynCom) using eight plant‐growth‐promoting bacteria isolated from the wheat (Triticum aestivum) rhizosphere, including three Bacillus spp., two Acinebacter spp., an Enterobacter sp., a Xanthomonas sp. and a Burkholderia sp., which all showed multiple plant growth‐promoting effects including indole‐3‐acetic acid and ammonia production and fungal pathogen suppression. We inoculated this SynCom in a soil with reduced microbial diversity, and investigated the ability of the SynCom to colonise wheat plants, and interact with soil microbes in the presence or absence of a soil‐borne pathogen Fusarium pseudograminearum (Fp). Results We found that SynCom significantly increased the wheat plant growth, root development and biomass production. Fp load in soil was significantly reduced and plant survival rates increased following the SynCom inoculation. Soil microbial community structure was altered by the SynCom, and noticeably, relative abundance of Pseudomonas spp. was induced in the soil. Conclusion This study provides novel evidence that colonisation of a beneficial SynCom promotes plant growth and alters soil microbial community.
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- 2022
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24. Soil initial bacterial diversity and nutrient availability determine the rate of xenobiotic biodegradation
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Ramesha H. Jayaramaiah, Eleonora Egidi, Catriona A. Macdonald, Jun‐Tao Wang, Thomas C. Jeffries, Mallavarapu Megharaj, and Brajesh K. Singh
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Biotechnology ,TP248.13-248.65 - Abstract
Summary Understanding the relative importance of soil microbial diversity, plants and nutrient management is crucial to implement an effective bioremediation approach to xenobiotics‐contaminated soils. To date, knowledge on the interactive effects of soil microbiome, plant and nutrient supply on influencing biodegradation potential of soils remains limited. In this study, we evaluated the individual and interactive effects of soil initial bacterial diversity, nutrient amendments (organic and inorganic) and plant presence on the biodegradation rate of pyrene, a polycyclic aromatic hydrocarbon. Initial bacterial diversity had a strong positive impact on soil biodegradation potential, with soil harbouring higher bacterial diversity showing ~ 2 times higher degradation rates than soils with lower bacterial diversity. Both organic and inorganic nutrient amendments consistently improved the degradation rate in lower diversity soils and had negative (inorganic) to neutral (organic) effect in higher diversity soils. Interestingly, plant presence/type did not show any significant effect on the degradation rate in most of the treatments. Structural equation modelling demonstrated that initial bacterial diversity had a prominent role in driving pyrene biodegradation rates. We provide novel evidence that suggests that soil initial microbial diversity, and nutrient amendments should be explicitly considered in the design and employment of bioremediation management strategies for restoring natural habitats disturbed by organic pollutants.
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- 2022
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25. Plant developmental stage drives the differentiation in ecological role of the maize microbiome
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Chao Xiong, Brajesh K. Singh, Ji-Zheng He, Yan-Lai Han, Pei-Pei Li, Li-Hua Wan, Guo-Zhong Meng, Si-Yi Liu, Jun-Tao Wang, Chuan-Fa Wu, An-Hui Ge, and Li-Mei Zhang
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Crop microbiomes ,Temporal dynamics ,Soil–plant continuum ,Microbiome assembly ,Microbial interkingdom networks ,Phylloplane microbiome ,Microbial ecology ,QR100-130 - Abstract
Abstract Background Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics. Results Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage. Conclusions Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract
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- 2021
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26. Realities and hopes in the application of microbial tools in agriculture
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Bruna D. Batista and Brajesh K. Singh
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Biotechnology ,TP248.13-248.65 - Abstract
Summary The use of microbial tools to sustainably increase agricultural production has received significant attention from researchers, industries and policymakers. Over the past decade, the market access and development of microbial products have been accelerated by (i) the recent advances in plant‐associated microbiome science, (ii) the pressure from consumers and policymakers for increasing crop productivity and reducing the use of agrochemicals, (iii) the rising threats of biotic and abiotic stresses, (iv) the loss of efficacy of some agrochemicals and plant breeding programs and (v) the calls for agriculture to contribute towards mitigating climate change. Although the sector is still in its infancy, the path towards effective microbial products is taking shape and the global market of these products has increased faster than that of agrochemicals. Promising results from using microbes either as biofertilizers or biopesticides have been continually reported, fuelling optimism and high expectations for the sector. However, some limitations, often related to low efficacy and inconsistent performance in field conditions, urgently need to be addressed to promote a wider use of microbial tools. We propose that advances in in situ microbiome manipulation approaches, such as the use of products containing synthetic microbial communities and novel prebiotics, have great potential to overcome some of these current constraints. Much more progress is expected in the development of microbial inoculants as areas such as synthetic biology and nano‐biotechnology advance. If key technical, translational and regulatory issues are addressed, microbial tools will not only play an important role in sustainably boosting agricultural production over the next few decades but also contribute towards other sustainable development goals, including job creation and mitigation of the impacts of climate change.
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- 2021
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27. Establishing a quality management framework for commercial inoculants containing arbuscular mycorrhizal fungi
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Matthias J. Salomon, Stephanie J. Watts-Williams, Michael J. McLaughlin, Heike Bücking, Brajesh K. Singh, Imke Hutter, Carolin Schneider, Francis M. Martin, Miroslav Vosatka, Liangdong Guo, Tatsuhiro Ezawa, Masanori Saito, Stéphane Declerck, Yong-Guan Zhu, Timothy Bowles, Lynette K. Abbott, F. Andrew Smith, Timothy R. Cavagnaro, and Marcel G.A. van der Heijden
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Environmental science ,Environmental health ,Biological sciences ,Biotechnology ,Plant biology ,Interaction of plants with organisms ,Science - Abstract
Summary: Microbial inoculants containing arbuscular mycorrhizal (AM) fungi are potential tools in increasing the sustainability of our food production systems. Given the demand for sustainable agriculture, the production of such inoculants has potential economic value and has resulted in a variety of commercial inoculants currently being advertised. However, their use is limited by inconsistent product efficacy and lack of consumer confidence. Here, we propose a framework that can be used to assess the quality and reliability of AM inoculants. First, we set out a range of basic quality criteria which are required to achieve reliable inoculants. This is followed by a standardized bioassay which can be used to test inoculum viability and efficacy under controlled conditions. Implementation of these measurements would contribute to the adoption of AM inoculants by producers with the potential to increase sustainability in food production systems.
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- 2022
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28. Study of Time-Fractional Nonlinear Model Governing Unsteady Flow of Polytropic Gas
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Brajesh K. Singh, Haci Mehmet Baskonus, Neetu Singh, Mukesh Gupta, and D. G. Prakasha
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caputo derivative ,polytropic gas ,?-transform ,variational calculus ,optimal homotopy analysis method ,Mathematics ,QA1-939 - Abstract
The present study is concerned with studying the dynamical behavior of two space-dimensional nonlinear time-fractional models governing the unsteady-flow of polytropic-gas (in brief, pGas) that occurred in cosmology and astronomy. For this purpose, two efficient hybrid methods so-called optimal homotopy analysis J-transform method (OHAJTM) and J-variational iteration transform method (J-VITM) have been adopted. The OHAJTM is the hybrid method, where optimal-homotopy analysis method (OHAM) is utilized after implementing the properties of J-transform (JT), and in J-VITM is the J-transform-based variational iteration method. Banach’s fixed point approach is adopted to analyze the convergence of these methods. It is demonstrated that J-VITM is T-stable, and the evaluated dynamics of pGas are described in terms of Mittag–Leffler functions. The proposed evaluation confirms that the implemented methods perform better for the referred model equation of pGas. In addition, for a given iteration, the proposed behavior via OHAJTM performs better in producing more accurate behavior in comparison to J-VITM and the methods introduced recently.
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- 2023
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29. Blind spots in global soil biodiversity and ecosystem function research
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Carlos A. Guerra, Anna Heintz-Buschart, Johannes Sikorski, Antonis Chatzinotas, Nathaly Guerrero-Ramírez, Simone Cesarz, Léa Beaumelle, Matthias C. Rillig, Fernando T. Maestre, Manuel Delgado-Baquerizo, François Buscot, Jörg Overmann, Guillaume Patoine, Helen R. P. Phillips, Marten Winter, Tesfaye Wubet, Kirsten Küsel, Richard D. Bardgett, Erin K. Cameron, Don Cowan, Tine Grebenc, César Marín, Alberto Orgiazzi, Brajesh K. Singh, Diana H. Wall, and Nico Eisenhauer
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Science - Abstract
Soil organism biodiversity contributes to ecosystem function, but biodiversity and function have not been equivalently studied across the globe. Here the authors identify locations, environment types, and taxonomic groups for which there is currently a lack of biodiversity and ecosystem function data in the existing literature.
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- 2020
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30. Visualizing the invisible: class excursions to ignite children’s enthusiasm for microbes
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Terry J. McGenity, Amare Gessesse, John E. Hallsworth, Esther Garcia Cela, Carol Verheecke‐Vaessen, Fengping Wang, Max Chavarría, Max M. Haggblom, Søren Molin, Antoine Danchin, Eddy J. Smid, Cédric Lood, Charles S. Cockell, Corinne Whitby, Shuang‐Jiang Liu, Nancy P. Keller, Lisa Y. Stein, Seth R. Bordenstein, Rup Lal, Olga C. Nunes, Lone Gram, Brajesh K. Singh, Nicole S. Webster, Cindy Morris, Sharon Sivinski, Saskia Bindschedler, Pilar Junier, André Antunes, Bonnie K. Baxter, Paola Scavone, and Kenneth Timmis
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Biotechnology ,TP248.13-248.65 - Abstract
Summary We have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology‐literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513‐1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public‐health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well‐being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of ‘germs’ and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination‐capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision‐making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology‐centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre‐occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.
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- 2020
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31. Microbiome definition re-visited: old concepts and new challenges
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Gabriele Berg, Daria Rybakova, Doreen Fischer, Tomislav Cernava, Marie-Christine Champomier Vergès, Trevor Charles, Xiaoyulong Chen, Luca Cocolin, Kellye Eversole, Gema Herrero Corral, Maria Kazou, Linda Kinkel, Lene Lange, Nelson Lima, Alexander Loy, James A. Macklin, Emmanuelle Maguin, Tim Mauchline, Ryan McClure, Birgit Mitter, Matthew Ryan, Inga Sarand, Hauke Smidt, Bettina Schelkle, Hugo Roume, G. Seghal Kiran, Joseph Selvin, Rafael Soares Correa de Souza, Leo van Overbeek, Brajesh K. Singh, Michael Wagner, Aaron Walsh, Angela Sessitsch, and Michael Schloter
- Subjects
Microbial ecology ,QR100-130 - Abstract
Abstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract
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- 2020
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32. Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems
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Jun-Tao Wang, Ju-Pei Shen, Li-Mei Zhang, Brajesh K. Singh, Manuel Delgado-Baquerizo, Hang-Wei Hu, Li-Li Han, Wen-Xue Wei, Yun-Ting Fang, and Ji-Zheng He
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coexistence pattern ,niche differentiation ,functional traits ,soil fungi ,community structure ,cropland soil ,Microbiology ,QR1-502 - 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 >35% 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.
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- 2021
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33. A few Ascomycota taxa dominate soil fungal communities worldwide
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Eleonora Egidi, Manuel Delgado-Baquerizo, Jonathan M. Plett, Juntao Wang, David J. Eldridge, Richard D. Bardgett, Fernando T. Maestre, and Brajesh K. Singh
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Science - Abstract
Soil fungi play essential roles in ecosystems worldwide. Here, the authors sequence and analyze 235 soil samples collected from across the globe, and identify dominant fungal taxa and their associated environmental attributes.
- Published
- 2019
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34. Soil Biogeochemical Cycle Couplings Inferred from a Function-Taxon Network
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Bin Ma, Erinne Stirling, Yuanhui Liu, Kankan Zhao, Jizhong Zhou, Brajesh K. Singh, Caixian Tang, Randy A. Dahlgren, and Jianming Xu
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Science - Abstract
Soil biogeochemical cycles and their interconnections play a critical role in regulating functions and services of environmental systems. However, the coupling of soil biogeochemical processes with their mediating microbes remains poorly understood. Here, we identified key microbial taxa regulating soil biogeochemical processes by exploring biomarker genes and taxa of contigs assembled from metagenomes of forest soils collected along a latitudinal transect (18° N to 48° N) in eastern China. Among environmental and soil factors, soil pH was a sensitive indicator for functional gene composition and diversity. A function-taxon bipartite network inferred from metagenomic contigs identified the microbial taxa regulating coupled biogeochemical cycles between carbon and phosphorus, nitrogen and sulfur, and nitrogen and iron. Our results provide novel evidence for the coupling of soil biogeochemical cycles, identify key regulating microbes, and demonstrate the efficacy of a new approach to investigate the processes and microbial taxa regulating soil ecosystem functions.
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- 2021
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35. Plant Microbiomes: Do Different Preservation Approaches and Primer Sets Alter Our Capacity to Assess Microbial Diversity and Community Composition?
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Zhiguang Qiu, Juntao Wang, Manuel Delgado-Baquerizo, Pankaj Trivedi, Eleonora Egidi, Yi-Min Chen, Haiyang Zhang, and Brajesh K. Singh
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plant microbiome ,sampling ,preservation methods ,amplicon sequencing ,soil ,sequencing primers ,Plant culture ,SB1-1110 - Abstract
The microbial communities associated with plants (the plant microbiome) play critical roles in regulating plant health and productivity. Because of this, in recent years, there have been significant increase in studies targeting the plant microbiome. Amplicon sequencing is widely used to investigate the plant microbiome and to develop sustainable microbial agricultural tools. However, performing large microbiome surveys at the regional and global scales pose several logistic challenges. One of these challenges is related with the preservation of plant materials for sequencing aiming to maintain the integrity of the original diversity and community composition of the plant microbiome. Another significant challenge involves the existence of multiple primer sets used in amplicon sequencing that, especially for bacterial communities, hampers the comparability of datasets across studies. Here, we aimed to examine the effect of different preservation approaches (snap freezing, fresh and kept on ice, and air drying) on the bacterial and fungal diversity and community composition on plant leaves, stems and roots from seven plant species from contrasting functional groups (e.g. C3, C4, N-Fixers, etc.). Another major challenge comes when comparing plant to soil microbiomes, as different primers sets are often used for plant vs. soil microbiomes. Thus, we also investigated if widely used 16S rRNA primer set (779F/1193R) for plant microbiome studies provides comparable data to those often used for soil microbiomes (341F/805R) using 86 soil samples. We found that the community composition and diversity of bacteria or fungi were robust to contrasting preservation methods. The primer sets often used for plants provided similar results to those often used for soil studies suggesting that simultaneous studies on plant and soil microbiomes are possible. Our findings provide novel evidence that preservation approaches do not significantly impact plant microbiome data interpretation and primer differences do not impact the treatment effect, which has significant implication for future large-scale and global surveys of plant microbiomes.
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- 2020
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36. Measles Virus Ribonucleoprotein Complexes Rapidly Spread across Well-Differentiated Primary Human Airway Epithelial Cells along F-Actin Rings
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Brajesh K. Singh, Christian K. Pfaller, Roberto Cattaneo, and Patrick L. Sinn
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actin ,airways ,lungs ,measles ,paramyxovirus ,Microbiology ,QR1-502 - Abstract
ABSTRACT Measles virus (MeV) is a highly contagious human pathogen that continues to be a worldwide health burden. One of the challenges for the study of MeV spread is the identification of model systems that accurately reflect how MeV behaves in humans. For our studies, we use unpassaged, well-differentiated primary cultures of airway epithelial cells from human donor lungs to examine MeV infection and spread. Here, we show that the main components of the MeV ribonucleoprotein complex (RNP), the nucleocapsid and phosphoprotein, colocalize with the apical and circumapical F-actin networks. To better understand how MeV infections spread across the airway epithelium, we generated a recombinant virus incorporating chimeric fluorescent proteins in its RNP complex. By live cell imaging, we observed rapid movement of RNPs along the circumapical F-actin rings of newly infected cells. This strikingly rapid mechanism of horizontal trafficking across epithelia is consistent with the opening of pores between columnar cells by the viral membrane fusion apparatus. Our work provides mechanistic insights into how MeV rapidly spreads through airway epithelial cells, contributing to its extremely contagious nature. IMPORTANCE The ability of viral particles to directly spread cell to cell within the airways without particle release is considered to be highly advantageous to many respiratory viruses. Our previous studies in well-differentiated, primary human airway epithelial cells suggest that measles virus (MeV) spreads cell to cell by eliciting the formation of intercellular membrane pores. Based on a newly generated ribonucleoprotein complex (RNP) “tracker” virus, we document by live-cell microscopy that MeV RNPs move along F-actin rings before entering a new cell. Thus, rather than diffusing through the cytoplasm of a newly infected columnar cell, RNPs take advantage of the cytoskeletal infrastructure to rapidly spread laterally across the human airway epithelium. This results in rapid horizontal spread through the epithelium that does not require particle release.
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- 2019
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37. Extracellular release of virulence factor major surface protease via exosomes in Leishmania infantum promastigotes
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Skye Marshall, Patrick H. Kelly, Brajesh K. Singh, R. Marshall Pope, Peter Kim, Bayan Zhanbolat, Mary E. Wilson, and Chaoqun Yao
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Leishmania ,Exosome ,Major surface protease ,Virulence factors ,Promastigotes ,Infectious and parasitic diseases ,RC109-216 - Abstract
Abstract Background The Leishmania spp. protozoa are introduced into humans through a sand fly blood meal, depositing the infectious metacyclic promastigote form of the parasite into human skin. Parasites enter a variety of host cells, although a majority are found in macrophages where they replicate intracellularly during chronic leishmaniasis. Symptomatic leishmaniasis causes considerable human morbidity in endemic regions. The Leishmania spp. evade host microbicidal mechanisms partially through virulence-associated proteins such as the major surface protease (MSP or GP63), to inactivate immune factors in the host environment. MSP is a metalloprotease encoded by a tandem array of genes belonging to three msp gene classes, whose mRNAs are differentially expressed in different life stages of the parasite. Like other cells, Leishmania spp. release small membrane-bound vesicles called exosomes into their environment. The purpose of this study was to detect MSP proteins in exosomal vesicles of Leishmania spp. protozoa. Methods Using mass spectrometry data we determined the profile of MSP class proteins released in L. infantum exosomes derived from promastigotes in their avirulent procyclic (logarithmic) stage and virulent stationary and metacyclic stages. MSP protein isoforms belonging to each of the three msp gene classes could be identified by unique peptides. Results Metacyclic promastigote exosomes contained the highest, and logarithmic exosomes had the lowest abundance of total MSP. Among the MSP classes, MSPC class had the greatest variety of isoforms, but was least abundant in all exosomes. Nonetheless, all MSP classes were present at higher levels in exosomes released from stationary or metacyclic promastigotes than logarithmic promastigotes. Conclusions The data suggest the efficiency of exosome release may be more important than the identity of MSP isoform in determining the MSP content of Leishmania spp. exosomes.
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- 2018
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38. A numerical scheme for the generalized Burgers–Huxley equation
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Brajesh K. Singh, Geeta Arora, and Manoj K. Singh
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Modified cubic B-spline ,gBH equation ,SSP-RK43 scheme ,Thomas algorithm ,Mathematics ,QA1-939 - Abstract
In this article, a numerical solution of generalized Burgers–Huxley (gBH) equation is approximated by using a new scheme: modified cubic B-spline differential quadrature method (MCB-DQM). The scheme is based on differential quadrature method in which the weighting coefficients are obtained by using modified cubic B-splines as a set of basis functions. This scheme reduces the equation into a system of first-order ordinary differential equation (ODE) which is solved by adopting SSP-RK43 scheme. Further, it is shown that the proposed scheme is stable. The efficiency of the proposed method is illustrated by four numerical experiments, which confirm that obtained results are in good agreement with earlier studies. This scheme is an easy, economical and efficient technique for finding numerical solutions for various kinds of (non)linear physical models as compared to the earlier schemes.
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- 2016
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39. Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes
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Yu-Jing Zhang, Hang-Wei Hu, Qing-Lin Chen, Brajesh K. Singh, Hui Yan, Deli Chen, and Ji-Zheng He
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Environmental sciences ,GE1-350 - Abstract
The increasing antimicrobial resistance in manure-amended soil can potentially enter food chain, representing an important vehicle for antibiotic resistance genes (ARGs) transmission into human microbiome. However, the pathways for transmission of ARGs from soil to plant remain unclear. Here, we explored the impacts of poultry and cattle manure application on the patterns of resistome in soil and lettuce microbiome including rhizosphere, root endosphere, leaf endosphere and phyllosphere, to identify the potential transmission routes of ARGs in the soil-plant system. After 90 days of cultivation, a total of 144 ARGs were detected in all samples using high-throughput quantitative PCR. Rhizosphere soil samples harbored the most diverse ARGs compared with other components of lettuce. Cattle manure application increased the abundance of ARGs in root endophyte, while poultry manure application increased ARGs in rhizosphere, root endophyte and phyllosphere, suggesting that poultry manure may have a stronger impact on lettuce resistomes. The ARG profiles were significantly correlated with the bacterial community, and the enrichment of soil and plant resistomes was strongly affected by the bacterial taxa including Solibacteres, Chloroflexi, Acidobacteria, Gemm-1 and Gemmatimonadetes, as revealed by the network analyses. Moreover, the overlaps of ARGs between lettuce tissues and soil were identified, which indicated that plant and environmental resistomes are interconnected. Our findings provide insights into the transmission routes of ARGs from manured soil to vegetables, and highlight the potential risks of plant resistome migration to the human food chain. Keywords: Antibiotic resistance genes, Manure-amended soil, Plant resistome, Endophyte, Phyllosphere
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- 2019
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40. The Koala (Phascolarctos cinereus) faecal microbiome differs with diet in a wild population
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Kylie L. Brice, Pankaj Trivedi, Thomas C. Jeffries, Michaela D.J. Blyton, Christopher Mitchell, Brajesh K. Singh, and Ben D. Moore
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Marsupial ,Folivore ,Microbiome ,Plant secondary metabolites (PSMs) ,Dietary specialist ,Formylated phloroglucinol compounds (FPCs) ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Background The diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genus Eucalyptus (family Myrtaceae). Eucalyptus produces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet. Method The 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (n = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious species Eucalyptus viminalis, the other comprising the less preferred and less digestible species Eucalyptus obliqua. Results Alpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eating E. viminalis. Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, the E. viminalis diet produced communities dominated by the genera Parabacteroides and/or Bacteroides, whereas the E. obliqua-associated diets were dominated by unidentified genera from the family Ruminococcaceae. Discussion We show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut microbiome of a specialist folivorous mammal, even amongst individuals in the same population. We identify key microbiota associated with each diet type and predict functions within the microbial community based on 80 previously identified Parabacteroides and Ruminococcaceae genomes.
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- 2019
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41. Microbial diversity drives multifunctionality in terrestrial ecosystems
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Manuel Delgado-Baquerizo, Fernando T. Maestre, Peter B. Reich, Thomas C. Jeffries, Juan J. Gaitan, Daniel Encinar, Miguel Berdugo, Colin D. Campbell, and Brajesh K. Singh
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Science - Abstract
The role of microbial diversity in ecosystems is less well understood than, for example, that of plant diversity. Analysing two independent data sets at a global and regional scale, Delgado-Baquerizo et al. show positive effects of soil diversity on multiple terrestrial ecosystem functions.
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- 2016
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42. Correction to: Microbiome definition re-visited: old concepts and new challenges
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Gabriele Berg, Daria Rybakova, Doreen Fischer, Tomislav Cernava, Marie-Christine Champomier Vergès, Trevor Charles, Xiaoyulong Chen, Luca Cocolin, Kellye Eversole, Gema Herrero Corral, Maria Kazou, Linda Kinkel, Lene Lange, Nelson Lima, Alexander Loy, James A. Macklin, Emmanuelle Maguin, Tim Mauchline, Ryan McClure, Birgit Mitter, Matthew Ryan, Inga Sarand, Hauke Smidt, Bettina Schelkle, Hugo Roume, G. Seghal Kiran, Joseph Selvin, Rafael Soares Correa de Souza, Leo van Overbeek, Brajesh K. Singh, Michael Wagner, Aaron Walsh, Angela Sessitsch, and Michael Schloter
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Microbial ecology ,QR100-130 - Abstract
An amendment to this paper has been published and can be accessed via the original article.
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- 2020
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43. Extracellular Vesicle-Mediated siRNA Delivery, Protein Delivery, and CFTR Complementation in Well-Differentiated Human Airway Epithelial Cells
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Brajesh K. Singh, Ashley L. Cooney, Sateesh Krishnamurthy, and Patrick L. Sinn
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exosomes ,microvesicles ,cystic fibrosis ,lung ,primary cells ,Genetics ,QH426-470 - Abstract
Extracellular vesicles (EVs) are a class of naturally occurring secreted cellular bodies that are involved in long distance cell-to-cell communication. Proteins, lipids, mRNA, and miRNA can be packaged into these vesicles and released from the cell. This information is then delivered to target cells. Since EVs are naturally adapted molecular messengers, they have emerged as an innovative, inexpensive, and robust method to deliver therapeutic cargo in vitro and in vivo. Well-differentiated primary cultures of human airway epithelial cells (HAE) are refractory to standard transfection techniques. Indeed, common strategies used to overexpress or knockdown gene expression in immortalized cell lines simply have no detectable effect in HAE. Here we use EVs to efficiently deliver siRNA or protein to HAE. Furthermore, EVs can deliver CFTR protein to cystic fibrosis donor cells and functionally correct the Cl− channel defect in vitro. EV-mediated delivery of siRNA or proteins to HAE provides a powerful genetic tool in a model system that closely recapitulates the in vivo airways.
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- 2020
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44. Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils
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Thomas C. Jeffries, Smriti Rayu, Uffe N. Nielsen, Kaitao Lai, Ali Ijaz, Loic Nazaries, and Brajesh K. Singh
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metagenomics ,bioremediation ,pesticides ,soil microbiology ,biodegradation ,environmental ,Microbiology ,QR1-502 - Abstract
Chemical contamination of natural and agricultural habitats is an increasing global problem and a major threat to sustainability and human health. Organophosphorus (OP) compounds are one major class of contaminant and can undergo microbial degradation, however, no studies have applied system-wide ecogenomic tools to investigate OP degradation or use metagenomics to understand the underlying mechanisms of biodegradation in situ and predict degradation potential. Thus, there is a lack of knowledge regarding the functional genes and genomic potential underpinning degradation and community responses to contamination. Here we address this knowledge gap by performing shotgun sequencing of community DNA from agricultural soils with a history of pesticide usage and profiling shifts in functional genes and microbial taxa abundance. Our results showed two distinct groups of soils defined by differing functional and taxonomic profiles. Degradation assays suggested that these groups corresponded to the organophosphorus degradation potential of soils, with the fastest degrading community being defined by increases in transport and nutrient cycling pathways and enzymes potentially involved in phosphorus metabolism. This was against a backdrop of taxonomic community shifts potentially related to contamination adaptation and reflecting the legacy of exposure. Overall our results highlight the value of using holistic system-wide metagenomic approaches as a tool to predict microbial degradation in the context of the ecology of contaminated habitats.
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- 2018
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45. Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences
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Ali Z. Ijaz, Thomas C. Jeffries, Umer Z. Ijaz, Kelly Hamonts, and Brajesh K. Singh
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Environmental ,Annotations ,16S rDNA ,SEQenv ,Taxa centric ,Biogeography ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients.
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- 2017
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46. Aboveground and belowground biodiversity have complementary effects on ecosystem functions across global grasslands.
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Catarina S C Martins, Manuel Delgado-Baquerizo, Ramesha H Jayaramaiah, Dongxue Tao, Jun-Tao Wang, Tadeo Sáez-Sandino, Hongwei Liu, Fernando T Maestre, Peter B Reich, and Brajesh K Singh
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Biology (General) ,QH301-705.5 - Abstract
Grasslands are integral to maintaining biodiversity and key ecosystem services and are under threat from climate change. Plant and soil microbial diversity, and their interactions, support the provision of multiple ecosystem functions (multifunctionality). However, it remains virtually unknown whether plant and soil microbial diversity explain a unique portion of total variation or shared contributions to supporting multifunctionality across global grasslands. Here, we combine results from a global survey of 101 grasslands with a novel microcosm study, controlling for both plant and soil microbial diversity to identify their individual and interactive contribution to support multifunctionality under aridity and experimental drought. We found that plant and soil microbial diversity independently predict a unique portion of total variation in above- and belowground functioning, suggesting that both types of biodiversity complement each other. Interactions between plant and soil microbial diversity positively impacted multifunctionality including primary production and nutrient storage. Our findings were also climate context dependent, since soil fungal diversity was positively associated with multifunctionality in less arid regions, while plant diversity was strongly and positively linked to multifunctionality in more arid regions. Our results highlight the need to conserve both above- and belowground diversity to sustain grassland multifunctionality in a drier world and indicate climate change may shift the relative contribution of plant and soil biodiversity to multifunctionality across global grasslands.
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- 2024
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47. Approximate series solution of multi-dimensional, time fractional-order (heat-like) diffusion equations using FRDTM
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Brajesh K. Singh and Vineet K. Srivastava
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multi-dimensional diffusion equation ,caputo time-fractional derivative ,mittag–leffler function ,fractional-order reduced differential transform method ,exact solution ,Science - Abstract
The main goal of this paper is to present a new approximate series solution of the multi-dimensional (heat-like) diffusion equation with time-fractional derivative in Caputo form using a semi-analytical approach: fractional-order reduced differential transform method (FRDTM). The efficiency of FRDTM is confirmed by considering four test problems of the multi-dimensional time fractional-order diffusion equation. FRDTM is a very efficient, effective and powerful mathematical tool which provides exact or very close approximate solutions for a wide range of real-world problems arising in engineering and natural sciences, modelled in terms of differential equations.
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- 2015
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48. Ensuring societal considerations are met when translating science into policy for sustainable food system transformation
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Brajesh K. Singh, Evan D.G. Fraser, Tom Arnold, Patricia Biermayr-Jenzano, Jacqueline E.W. Broerse, Gianluca Brunori, Patrick Caron, Olivier De Schutter, Karen Fabbri, Shenggen Fan, Jessica Fanzo, Magdalena Gajdzinska, Mirjana Gurinovic, Marta Hugas, Jacqueline McGlade, Christine Nellemann, Jemimah Njuki, Hanna L. Tuomisto, Seta Tutundjian, Justus Wesseler, Roberta Sonnino, and Patrick Webb
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Food Science ,Biotechnology - Abstract
Background: A food system transformation is needed to address food and nutrition security, minimise impacts on planetary health, reduce climate change emissions, and contribute to equity, diversity, and the Sustainable Development Goals. Scope and approach: This paper summarizes findings of the European Commission's High Level Expert Group on Food Systems Science, which reviewed obstacles that prevent food systems policy from achieving society-wide impacts. These barriers include knowledge and translation gaps in food-related science-policy-interfaces (SPIs), insufficient attention to the priorities of diverse stakeholders, and a failure to adequately consider equity, diversity, political economy, and societal engagements. Key findings & conclusions: Three potential pathways can ensure science and policy support food systems transformation: (1) Adapt the current SPI landscape with extra resources and a wider mandate to ensure coordinated action across the full food system, (2) Enhance the current policy landscape with a range of multisectoral taskforces designed to fulfill specific functions such as creating an enhanced food systems data portal, and (3) Establish a “network of networks” to provide both global coordination as well as organize defined agendas at global through to regional scales. In embarking on these pathways, a revised science-policy-society landscape (SPSIs) should deliver the following core functions: (1) Engage and empower multi-stakeholder dialogue; (2) Build capacity at multiple scales to translate evidence into tangible real-world outcomes; (3) Ensure access to openly accessible data for the entire food system; (4) Use models, forecasts, and scenario building exercises to explore the potential future of food systems; (5) Produce assessment reports and policy publications; and (6) Establish fora for diplomacy that will be empowered to create standards set targets and establish policy.
- Published
- 2023
49. Water availability creates global thresholds in multidimensional soil biodiversity and functions
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Jianwei Zhang, Youzhi Feng, Fernando T. Maestre, Miguel Berdugo, Juntao Wang, Claudia Coleine, Tadeo Sáez-Sandino, Laura García-Velázquez, Brajesh K. Singh, Manuel Delgado-Baquerizo, National Natural Science Foundation of China, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), European Commission, Junta de Andalucía, Generalitat Valenciana, Feng, Youzhi, Maestre, Fernando T., Berdugo, Miguel, Wang, Jun-Tao, Coleine, Claudia, Sáez-Sandino, Tadeo, García-Velázquez, Laura, Singh, Brajesh K., and Delgado-Baquerizo, Manuel
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Ecology ,Ecology, Evolution, Behavior and Systematics - Abstract
21 páginas.- 3 figuras.- 75 referencias.- Additional information Extended data is available for this paper at https://doi.org/10.1038/s41559-023-02071-3 .- Supplementary information The online version contains supplementary material available at https://doi.org/10.1038/s41559-023-02071-3, Soils support an immense portion of Earth’s biodiversity and maintain multiple ecosystem functions which are essential for human well-being. Environmental thresholds are known to govern global vegetation patterns, but it is still unknown whether they can be used to predict the distribution of soil organisms and functions across global biomes. Using a global field survey of 383 sites across contrasting climatic and vegetation conditions, here we showed that soil biodiversity and functions exhibited pervasive nonlinear patterns worldwide and are mainly governed by water availability (precipitation and potential evapotranspiration). Changes in water availability resulted in drastic shifts in soil biodiversity (bacteria, fungi, protists and invertebrates) and soil functions including plant–microbe interactions, plant productivity, soil biogeochemical cycles and soil carbon sequestration. Our findings highlight that crossing specific water availability thresholds can have critical consequences for the provision of essential ecosystem services needed to sustain our planet., Y.F. is supported by National Natural Science Foundation of China (42177297) and CAS Strategic Priority Research Program (XDA28010302). M.D.-B. acknowledges support from the Spanish Ministry of Science and Innovation for the I+D+i project PID2020-115813RA-I00 funded by MCIN/AEI/10.13039/501100011033. M.D.-B. is also supported by a project of the Fondo Europeo de Desarrollo Regional (FEDER) and the Consejería de Transformación Económica, Industria, Conocimiento y Universidades of the Junta de Andalucía (FEDER Andalucía 2014-2020 Objetivo temático ‘01—Refuerzo de la investigación, el desarrollo tecnológico y la innovación’) associated with the research project P20_00879 (ANDABIOMA). F.T.M. is supported by Generalitat Valenciana grant CIDEGENT/2018/041 and the Horizon Europe programme of the European Union (SOILGUARD, grant agreement no. 101000371). M.B. acknowledges funding from Spanish Ministry of Science and Innovation through a Ramón y Cajal Fellowship (no. RYC2021-031797-I). C.C. is supported by the European Commission under the Marie Sklodowska-Curie grant agreement no. 702057 (DRYLIFE). The survey of dryland areas was supported by the European Research Council (BIODESERT project, grant agreement no. 647038).
- Published
- 2023
50. <scp>UV</scp> index and climate seasonality explain fungal community turnover in global drylands
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Eleonora Egidi, Manuel Delgado‐Baquerizo, Miguel Berdugo, Emilio Guirado, Davide Albanese, Brajesh K. Singh, Claudia Coleine, Universidad de Alicante. Instituto Multidisciplinar para el Estudio del Medio 'Ramón Margalef', and Laboratorio de Ecología de Zonas Áridas y Cambio Global (DRYLAB)
- Subjects
Global and Planetary Change ,Ecology ,Settore BIO/07 - ECOLOGIA ,Drylands ,Fungal traits ,Fungi ,Climate change ,climate change ,drylands ,environmental predictors ,fungal traits ,fungi ,Ecology, Evolution, Behavior and Systematics ,Environmental predictors - Abstract
Aim Fungi are major drivers of ecosystem functioning. Increases in aridity are known to negatively impact fungal community composition in dryland ecosystems globally; yet, much less is known on the potential influence of other environmental drivers, and whether these relationships are linear or nonlinear. Time period 2017–2021. Location Global. Major taxa studied Fungi. Methods We re-analysed multiple datasets from different dryland biogeographical regions, for a total of 912 samples and 1,483 taxa. We examined geographical patterns in community diversity and composition, and spatial, edaphic and climatic factors driving them. Results UV index, climate seasonality, and sand content were the most important environmental predictors of community shifts, showing the strongest association with the richness of putative plant pathogens and saprobes. Important nonlinear relationships existed with each of these fungal guilds, with increases in UV and temperature seasonality above 7.5 and 900 SD (standard deviation x 100 of the mean monthly temperature), respectively, being associated with an increased probability of plant pathogen and unspecified saprotroph occurrence. Conversely, these environmental parameters had a negative relationship with litter and soil saprotroph richness. Consequently, these ecological groups might be particularly sensitive to shifts in UV radiation and climate seasonality, which is likely to disturb current plant–soil dynamics in drylands. Main conclusions Our synthesis integrates fungal community data from drylands across the globe, allowing the investigation of fungal distribution and providing the first evidence of shifts in fungal diversity and composition of key fungal ecological groups along diverse spatial, climatic and edaphic gradients in these widely distributed ecosystems. Our findings imply that shifts in soil structure and seasonal climatic patterns induced by global change will have disproportionate consequences for the distribution of fungal groups linked to vegetation and biogeochemical cycling in drylands, with implications for plant–soil interactions in drylands., Global Ecology and Biogeography, 32 (1), ISSN:1466-822X, ISSN:1466-8238
- Published
- 2022
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