ORCID Profile
0000-0002-3294-102X
Current Organisations
Karolinska Institutet
,
University of Melbourne
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Soil Biology | Microbial Ecology | Soil Sciences | Organic Chemistry | Organic Chemical Synthesis | Membrane and Separation Technologies | Ecological Impacts of Climate Change | Agricultural and Veterinary Sciences not elsewhere classified | Other Agricultural and Veterinary Sciences | Soil biology | Microbial ecology | Agricultural land management | Soil sciences |
ANZSRC Socio-Economic Objective (SEO)
Farmland, Arable Cropland and Permanent Cropland Soils | Chemical Fertilisers | Farmland, Arable Cropland and Permanent Cropland Land Management | Agricultural and Environmental Standards | Climate Change Mitigation Strategies | Environmentally Sustainable Plant Production not elsewhere classified | Forest and Woodlands Soils | Food Safety
Related Links
Publications
Altitudinal Distribution Patterns of Soil Bacterial and Archaeal Communities Along Mt. Shegyla on the Tibetan Plateau
Publisher: Springer Science and Business Media LLC
Date: 30-07-2015
DOI: 10.1007/S00248-014-0465-7
Abstract: Unraveling the distribution patterns of plants and animals along the elevational gradients has been attracting growing scientific interests of ecologists, whether the microbial communities exhibit similar elevational patterns, however, remains largely less documented. Here, we investigate the biogeographic distribution of soil archaeal and bacterial communities across three vertical climate zones (3,106-4,479 m.a.s.l.) in Mt. Shegyla on the Tibetan Plateau, by combining quantitative PCR and high-throughput barcoded pyrosequencing approaches. Our results found that the ratio of bacterial to archaeal 16S rRNA gene abundance was negatively related with elevation. Acidobacteria dominated in the bacterial communities, Marine benthic group A dominated in the archaeal communities, and the relative abundance of both taxa changed significantly with elevation. At the taxonomic levels of domain, phylum, and class, more bacterial taxa than archaeal exhibited declining trend in ersity along the increasing elevational gradient, as revealed by Shannon and Faith's phylogenetic ersity indices. Unweighted UniFrac distance clustering showed that the bacterial communities from the mountainous temperate zone clustered together, whereas those from the subalpine cool temperate zone clustered together. However, the partitioning effect of elevational zones on the archaeal community was much weaker compared to that on bacteria. Redundancy analysis revealed that soil geochemical factors explained 58.3 % of the bacterial community variance and 75.4 % of the archaeal community variance. Taken together, we provide evidence that soil bacteria exhibited more apparent elevational zonation feature and decreased ersity pattern than archaea with increasing elevation, and distribution patterns of soil microbes are strongly regulated by soil properties along elevational gradient in this plateau montane ecosystem.
Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
Publisher: Springer Science and Business Media LLC
Date: 17-11-2021
Fertilization alters protistan consumers and parasites in crop‐associated microbiomes
Publisher: Wiley
Date: 12-01-2021
Publisher Correction: Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide
Publisher: Springer Science and Business Media LLC
Date: 26-04-2023
Effects of long‐term mowing on leaf‐ and root‐associated bacterial community structures are linked to functional traits in 11 plant species from a temperate steppe
Publisher: Wiley
Date: 24-04-2023
Abstract: Long‐term mowing can cause morphological stuntedness of plants, thus reducing grassland productivity and exacerbating grassland degradation. Although plant microbiomes can enhance plant resistance against disturbance, considerable uncertainty exists regarding how mowing and mowing‐induced plant trait plasticity affect plant microbiomes in natural grasslands. Here we examined the responses of leaf/root‐associated bacterial (LAB/RAB) communities of 11 dominant herbaceous perennials (six replicates per species) to a 17‐year mowing treatment in a temperate grassland. We also measured leaf/root physiological and morphological traits, and analysed the relationships among mowing practice, bacterial community structures and leaf/root trait parameters. We found that both leaf and root functional traits showed interspecific variations (variations across different plant species), while only the leaf traits exhibited intraspecific variation (treatment‐induced variations within plant species) between the treatments. Similarly, the LAB community structure was more sensitive to mowing but less influenced by host species identity, compared to the RAB community. The RAB community structure was primarily shaped by host species identity, while mowing was a secondary influencing factor. The different patterns of LAB and RAB communities in response to mowing could be specifically explained by the inter/intraspecific variations of the related leaf and root traits. The LAB community was strongly correlated with the leaf traits which exhibited mowing‐induced plasticity (intraspecific variation), with the correlations with nitrogen resorption efficiency and above‐ground dry weight being the greatest. The root traits were important indicators of bacterial community structure in the root compartment across the hosts, rather than between the treatments. Root tissue density showed the strongest interspecific variation, and was identified as an overwhelming driver of the RAB community. The shifts in LAB/RAB communities under mowing were largely attributed to the increased proportions of Actinobacteria. The high mowing sensitivity of the LAB community was associated with the enrichment of soil‐derived Actinobacteria in leaves under mowing. Actinobacteria were also the main keystone taxa in the bacterial community networks under mowing. Our results demonstrate that the magnitude of plant‐associated microbial community response to long‐term mowing is plant compartment and trait variation dependent, and advance our understanding of the leaf/root microbiome‐trait relationships in complex plant communities. Read the free Plain Language Summary for this article on the Journal blog.
Termite mounds reduce soil microbial diversity by filtering rare microbial taxa
Publisher: Wiley
Date: 15-04-2021
Abstract: Termites are ubiquitous insects in tropical and subtropical habitats, and some of them construct massive nests (‘mounds’), which substantially promote substrate heterogeneity by altering soil properties. Yet, the role of termite nesting process in regulating the distribution and ersity of soil microbial communities remains poorly understood, which introduces uncertainty in predictions of ecosystem functions of termite mounds in a changing environment. Here, by using licon sequencing, we conducted a survey of 134 termite mounds across km in northern Australia and found that termite mounds significantly differed from bulk soils in the microbial ersity and community compositions. Compared with bulk soils, termite nesting process decreased the microbial ersity and the relative abundance of rare taxa. Rare taxa had a narrower habitat niche breadth than dominant taxa and might be easier to be filtered by the potential intensive microbial competition during the nesting processes. We further demonstrated that the shift in pH induced by termite nesting process was a major driver shaping the microbial community profiles in termite mounds. Together, our work provides novel evidence that termite nesting is an important process in regulating soil microbial ersity, which advances our understanding of the functioning of termite mounds.
Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19
Publisher: Springer Science and Business Media LLC
Date: 15-04-2023
DOI: 10.1038/S41467-023-37835-9
Abstract: Effective humoral immune responses require well-orchestrated B and T follicular helper (Tfh) cell interactions. Whether these interactions are impaired and associated with COVID-19 disease severity is unclear. Here, longitudinal blood s les across COVID-19 disease severity are analysed. We find that during acute infection SARS-CoV-2-specific circulating Tfh (cTfh) cells expand with disease severity. SARS-CoV-2-specific cTfh cell frequencies correlate with plasmablast frequencies and SARS-CoV-2 antibody titers, avidity and neutralization. Furthermore, cTfh cells but not other memory CD4 T cells, from severe patients better induce plasmablast differentiation and antibody production compared to cTfh cells from mild patients. However, virus-specific cTfh cell development is delayed in patients that display or later develop severe disease compared to those with mild disease, which correlates with delayed induction of high-avidity neutralizing antibodies. Our study suggests that impaired generation of functional virus-specific cTfh cells delays high-quality antibody production at an early stage, potentially enabling progression to severe disease.
Ectomycorrhizal fungi inoculation alleviates simulated acid rain effects on soil ammonia oxidizers and denitrifiers in Masson pine forest
Publisher: Wiley
Date: 28-11-2019
Abstract: Acid rain can cause severe effects on soil biota and nutrient biogeochemical cycles in the forest ecosystem, but how plant-symbiotic ectomycorrhizal fungi will modulate the effects remains unknown. Here, we conducted a full factorial field experiment in a Masson pine forest by simultaneously controlling the acidity of the simulated rain (pH 5.6 vs. pH 3.5) and the ectomycorrhizal fungi Pisolithus tinctorius inoculation (non-inoculation vs. inoculation), to investigate the effects on ammonia oxidizers and denitrifiers. After 10 months, compared with the control (rain pH 5.6, and non-inoculation), simulated acid rain (pH 3.5) reduced soil nutrient content, decreased archaeal amoA gene abundance and inhibited denitrification enzyme activity. Also, simulated acid rain altered the community compositions of all the examined functional genes (archaeal amoA, bacterial amoA, nirK, nirS and nosZ). However, inoculation with ectomycorrhizal fungi under acid rain stress recovered soil nutrient content, archaeal amoA gene abundance and denitrification enzyme activity to levels comparable to the control, suggesting that ectomycorrhizal fungi inoculation ameliorates simulated acid rain effects. Taken together, ectomycorrhizal fungi inoculation - potentially through improving soil substrate availability - could alleviate the deleterious effects of acid rain on nitrogen cycling microbes in forest soils.
Long-Term Nickel Contamination Increases the Occurrence of Antibiotic Resistance Genes in Agricultural Soils
Publisher: American Chemical Society (ACS)
Date: 23-12-2017
Abstract: Heavy metal contamination is assumed to be a selection pressure on antibiotic resistance, but to our knowledge, evidence of the heavy metal-induced changes of antibiotic resistance is lacking on a long-term basis. Using quantitative PCR array and Illumina sequencing, we investigated the changes of a wide spectrum of soil antibiotic resistance genes (ARGs) following 4-5 year nickel exposure (0-800 mg kg
Seasonality regulates the taxonomic and functional compositions of protists responding to climate warming in forest ecosystems
Publisher: Wiley
Date: 18-08-2023
DOI: 10.1002/SAE2.12068
Abstract: Protists are unicellular eukaryotes including important predators, parasites and phototrophs, and play pivotal roles in organic matter decomposition, biogeochemical nutrient cycling and various ecosystem functions. Unravelling the impact of climate warming on soil protists is paramount in predicting how these microorganisms will continue to provide essential ecosystem services in the face of changing climatic conditions. We examined the effects of 5‐year simulated climate warming scenario, with temperatures increased by 4°C above ambient levels, on the ersity and community composition of soil protists, as well as their interactions with other microorganisms in both natural and plantation forest ecosystems during three seasons: summer, autumn and winter. We found a season‐dependent response of protists to climate warming, with a significant decrease in protist ersity during winter in natural forests. Furthermore, we identified significant alterations in the community compositions of protists during summer in both natural and plantation forests, as well as during winter in both forest types, under warming. Our analysis pinpointed specific functional protist taxa, such as consumers, parasites and phototrophs, which exhibited significant shifts in their relative abundances under warming. Additionally, we found that warming facilitated trophic interactions between protists and bacteria, while also strengthening interactions between bacterial and fungal communities. Warming could induce direct modifications in protist community compositions or indirectly affect them by modifying bacterial and fungal communities, as revealed by structural equation modelling. These findings demonstrate the substantial impact of warming on the taxonomic and functional compositions of protists in forest ecosystems, with the magnitude of these effects varying across seasons. Our study implicates that ongoing climate warming could have significant consequences for the profiles of soil protists, as well as their trophic interactions with bacteria and fungi, highlighting the importance of considering these effects for the sustainable provision of ecosystem functions.
Response of ammonia oxidizing microbes to the stresses of arsenic and copper in two acidic alfisols
Publisher: Elsevier BV
Date: 05-2014
Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils
Publisher: Springer Science and Business Media LLC
Date: 12-04-2016
DOI: 10.1007/S00248-016-0762-4
Abstract: Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial ersity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil s les spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta ersity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil s les. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental ergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta ersity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta ersity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta ersity patterns in the grassland soils.
Cross-biome antibiotic resistance decays after millions of years of soil development
Publisher: Springer Science and Business Media LLC
Date: 30-03-2022
Influence of nitrogen fertilization on soil ammonia oxidizer and denitrifier abundance, microbial biomass, and enzyme activities in an alpine meadow
Publisher: Springer Science and Business Media LLC
Date: 30-11-2013
Long-term nickel exposure altered the bacterial community composition but not diversity in two contrasting agricultural soils
Publisher: Springer Science and Business Media LLC
Date: 03-03-2015
DOI: 10.1007/S11356-015-4232-1
Abstract: Nickel pollution imposes deleterious effects on soil ecosystem. The responses of soil microorganisms to long-term nickel pollution under field conditions remain largely unknown. Here, we used high-throughput sequencing to elucidate the impacts of long-term nickel pollution on soil bacterial communities in two contrasting agricultural soils. Our results found that the soil microbial biomass carbon consistently decreased along the nickel gradients in both soils. Nickel pollution selectively favored or impeded the prevalence of several dominant bacterial guilds, in particular, Actinobacteria showed tolerance, while Acidobacteria and Planctomycetes displayed sensitivity. Despite the apparent shifts in the bacterial community composition, no clear tendency in the bacterial ersity and abundance was identified along the nickel gradients in either soil. Collectively, we provide evidence that long-term nickel pollution shifted the soil bacterial communities, resulting in the decrease of microbial biomass although the bacterial ersity was not significantly changed.
Abundance and community structure of ammonia-oxidizingArchaeaandBacteriain response to fertilization and mowing in a temperate steppe in Inner Mongolia
Publisher: Oxford University Press (OUP)
Date: 28-04-2014
Abstract: Based on a 6-year field trial in a temperate steppe in Inner Mongolia, we investigated the effects of nitrogen (N) and phosphorus (P) fertilization and mowing on the abundance and community compositions of ammonia-oxidizing Bacteria (AOB) and Archaea (AOA) upon early (May) and peak (August) plant growth using quantitative PCR (qPCR), terminal-restriction fragment length polymorphism (T-RFLP), cloning and sequencing. The results showed that N fertilization changed AOB community composition and increased AOB abundance in both May and August, but significantly decreased AOA abundance in May. By contrast, P fertilization significantly influenced AOB abundance only in August. Mowing significantly decreased AOA abundance and had little effect on AOA community compositions in May, while significantly influencing AOB abundance in both May and August, Moreover, AOA and AOB community structures showed obvious seasonal variations between May and August. Phylogenetic analysis showed that all AOA sequences fell into the Nitrososphaera cluster, and the AOB community was dominated by Nitrosospira Cluster 3. The results suggest that fertilization and mowing play important roles in affecting the abundance and community compositions of AOA and AOB.
Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships
Publisher: Springer Science and Business Media LLC
Date: 10-05-2016
Effects of climate warming and elevated CO 2 on autotrophic nitrification and nitrifiers in dryland ecosystems
Publisher: Elsevier BV
Date: 2016
Unraveling Microbial Communities Associated with Methylmercury Production in Paddy Soils
Publisher: American Chemical Society (ACS)
Date: 17-10-2018
Abstract: Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically erse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and ersity of Hg methylators in microbial communities of rice paddy soils remain unclear. We characterized the abundance and distribution of hgcAB genes using third-generation PacBio long-read sequencing and Illumina short-read metagenomic sequencing, in combination with quantitative PCR analyses in several mine-impacted paddy soils from southwest China. Both Illumina and PacBio sequencing analyses revealed that Hg methylating communities were dominated by iron-reducing bacteria (i.e., Geobacter) and methanogens, with a relatively low abundance of hgcA
Dissimilatory nitrate reduction to ammonium dominates nitrate reduction in long-term low nitrogen fertilized rice paddies
Publisher: Elsevier BV
Date: 04-2019
Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems
Publisher: Springer Science and Business Media LLC
Date: 09-08-2022
DOI: 10.1038/S43705-022-00156-X
Abstract: Soil pollution is an important stressor affecting bio ersity and ecosystem functioning. However, we lack a holistic understanding of how soil microbial communities respond to heavy metal pollution in agricultural ecosystems. Here, we explored the distribution patterns and inter-kingdom interactions of entire soil microbiome (including bacteria, fungi, and protists) in 47 paired paddy and upland fields along a gradient of legacy mercury (Hg) pollution. We found that the richness and composition of protistan community had stronger responses to Hg pollution than those of bacterial and fungal communities in both paddy and upland soils. Mercury polluted soils harbored less protistan phototrophs but more protistan consumers. We further revealed that long-term Hg pollution greatly increased network complexity of protistan community than that of bacterial and fungal communities, as well as intensified the interactions between protists and the other microorganisms. Moreover, our results consistently indicated that protistan communities had stronger responses to long-term Hg pollution than bacterial and fungal communities in agricultural soils based on structural equation models and random forest analyses. Our study highlights that soil protists can be used as bioindicators of Hg pollution, with important implications for the assessment of contaminated farmlands and the sustainable management of agricultural ecosystems.
Effects of the nitrification inhibitor 3,4-dimethylpyrazole phosphate on nitrification and nitrifiers in two contrasting agricultural soils
Publisher: American Society for Microbiology
Date: 09-2016
DOI: 10.1128/AEM.01031-16
Abstract: The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is a powerful tool that can be used to promote nitrogen (N) use efficiency and reduce N losses from agricultural systems by slowing nitrification. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in nitrification and N 2 O production however, their responses to DMPP amendment and the microbial mechanisms underlying the variable efficiencies of DMPP across different soils remain largely unknown. Here we compared the impacts of DMPP on nitrification and the dynamics of ammonia oxidizers between an acidic pasture soil and an alkaline vegetable soil using a 15 N tracing and 13 CO 2 -DNA–stable-isotope probing (SIP) technique. The results showed that DMPP significantly inhibited nitrification and N 2 O production in the vegetable soil only, and the transient inhibition was coupled with a significant decrease in AOB abundance. No significant effects on the community structure of ammonia oxidizers or the abundances of total bacteria and denitrifiers were observed in either soil. The 15 N tracing experiment revealed that autotrophic nitrification was the predominant form of nitrification in both soils. The 13 CO 2 -DNA–SIP results indicated the involvement of AOB in active nitrification in both soils, but DMPP inhibited the assimilation of 13 CO 2 into AOB only in the vegetable soil. Our findings provide evidence that DMPP could effectively inhibit nitrification through impeding the abundance and metabolic activity of AOB in the alkaline vegetable soil but not in the acidic pasture soil, possibly due to the low AOB abundance or the adsorption of DMPP by organic matter. IMPORTANCE The combination of the 15 N tracing model and 13 CO 2 -DNA–SIP technique provides important evidence that the nitrification inhibitor DMPP could effectively inhibit nitrification and nitrous oxide emission in an alkaline soil through influencing the abundance and metabolic activity of AOB. In contrast, DMPP amendment has no significant effect on nitrification or nitrifiers in an acidic soil, potentially owing to the low abundance of AOB and the possible adsorption of DMPP by organic matter. Our findings have direct implications for improved agricultural practices through utilizing the nitrification inhibitor DMPP in appropriate situations, and they emphasize the importance of microbial communities to the efficacy of DMPP.
Differential response of archaeal groups to land use change in an acidic red soil
Publisher: Elsevier BV
Date: 09-2013
DOI: 10.1016/J.SCITOTENV.2013.05.070
Abstract: Land use management, one of the most important aspects of anthropogenic disturbance to terrestrial ecosystems, has exerted overriding impacts on soil biogeochemical cycling and inhabitant microorganisms. However, the knowledge concerning response of different archaeal groups to long-term land use changes is still limited in terrestrial environments. Here we used quantitative polymerase chain reaction (qPCR) and denaturing gradient gel electrophoresis (DGGE) approaches to investigate the response of archaeal communities to four different land use practices, i.e. cropland, pine forest, restoration land and degradation land. qPCR analyses showed that expression of the archaeal amoA gene responds more sensitively to changes of land use. In particular, we observed, occurring at significantly lower numbers of archaeal amoA genes in degradation land s les, while the abundance of total archaea and Group 1.1c based on 16S rRNA gene copy numbers remained constant among the different treatments examined. Soil nitrate content is significantly correlated with archaeal amoA gene abundance, but not their bacterial counterparts. The percentage of archaea among total prokaryote communities increases with increasing depth, but has no significant relationship with total carbon, total nitrogen or pH. Soil pH was significantly correlated with total bacterial abundance. Based on results from PCR-DGGE, three land use practices (i.e. cropland, pine forest, restoration land) showed distinct dominant bands, which were mostly affiliated with Group 1.1a. Degradation land, however, was dominated by sequences belonging to Group 1.1c. Results from this study suggest that community structure of ammonia oxidizing archaea were significantly impacted by land use practices.
Plant associated protists—Untapped promising candidates for agrifood tools
Publisher: Wiley
Date: 12-12-2022
Abstract: The importance of host‐associated microorganisms and their biotic interactions for plant health and performance has been increasingly acknowledged. Protists, main predators and regulators of bacteria and fungi, are abundant and ubiquitous eukaryotes in terrestrial ecosystems. Protists are considered to benefit plant health and performance, but the community structure and functions of plant‐associated protists remain surprisingly underexplored. Harnessing plant‐associated protists and other microbes can potentially enhance plant health and productivity and sustain healthy food and agriculture systems. In this review, we summarize the knowledge of multifunctionality of protists and their interactions with other microbes in plant hosts, and propose a future framework to study plant‐associated protists and utilize protists as agrifood tools for benefiting agricultural production.
Responses of ammonia-oxidizing bacteria and archaea to nitrogen fertilization and precipitation increment in a typical temperate steppe in Inner Mongolia
Publisher: Elsevier BV
Date: 06-2013
Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area
Publisher: Research Square Platform LLC
Date: 15-06-2020
DOI: 10.21203/RS.3.RS-34782/V1
Abstract: Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness 0.7) and normalized stochasticity ratio index ( NST ) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria ( NST = 45.23%) than on fungi ( NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.
Precipitation seasonality and soil pH drive the large-scale distribution of soil invertebrate communities in agricultural ecosystems
Publisher: Oxford University Press (OUP)
Date: 14-10-2023
Organic fertilization regimes suppress fungal plant pathogens through modulating the resident bacterial and protistan communities
Publisher: Wiley
Date: 03-2022
DOI: 10.1002/SAE2.12011
Abstract: Fungal plant pathogens are an emerging threat to economically important crop production worldwide and a significant risk to global food security. However, we have limited knowledge of how agricultural management practices drive the emergence and spread of pathogens within crop microbiomes and the underlying ecological mechanisms. We characterized the profiles of potential fungal plant pathogens, as well as bacterial and protistan communities, in sorghum phyllosphere, root endosphere, and rhizosphere and bulk soils collected from a long‐term experiment with multiple inorganic and organic fertilization regimes. We found contrasting patterns of fungal plant pathogens across the four sorghum–soil compartments and that organic fertilization regime significantly reduced the ersity and proportions of fungal plant pathogens in rhizosphere and bulk soils. We further found that the changes in fungal plant pathogens were driven more by resident bacterial and protistan communities than by soil physicochemical parameters. There was a significantly negative relationship between the ersity of fungal plant pathogens in the rhizosphere and bulk soils with sorghum yield and protein contents. Structural equation modeling revealed that long‐term organic fertilization regimes contributed to the suppression of fungal plant pathogens mainly through modulating the resident bacterial and protistan communities. These findings advance our understanding of the responses of fungal plant pathogens in crop microbiomes to fertilization regimes, with implications for more targeted strategies to manage the impacts of fungal pathogens on plant health and economic losses.
Impacts of shelterbelt systems on pasture production and soil bacterial and fungal communities in agricultural fields
Publisher: Wiley
Date: 10-07-2023
DOI: 10.1002/SAE2.12059
Abstract: Shelterbelts, which provide protection for livestock and crops against severe weather conditions, have been recognised as important contributors to increased crop yields. Soil microorganisms play important roles in nutrient cycling, soil health and plant performance, thereby exerting significant influence on ecological services in terrestrial ecosystems. However, impacts of shelterbelts on soil microbial communities in pasture ecosystems remain poorly studied. Here, we assessed the effect of shelterbelts (composed of Eucalyptus and native shrubs) on the pasture and nutrient productivity as well as soil bacterial and fungal communities at four distances from the shelterbelts with two different heights in two fields during spring and summer by applying licon sequencing, physicochemical and nutritional value analyses. The results showed that the shelterbelt height, distances from shelterbelts, seasons and their interactive effects substantially affected pasture yield, neutral detergent fibre, metabolisable energy and crude protein yields, but did not increase the pasture productivity in the rows adjacent to the shelterbelts. We also identified that the alpha ersity of bacteria and fungi did not significantly change across distances from the shelterbelts in both fields, but the community structure of soil bacteria and fungi was significantly influenced by distances from the shelterbelts. Interestingly, soil calcium (Ca) and shelterbelts were identified as top predictors of fungal community while soil pH and Ca was key drivers of bacterial community. Our study provides novel knowledge in the impact of shelterbelts on pasture and nutritional production and soil microbial communities, which contributes to appropriate application and strategic management of the windbreak systems in agriculture production.
Diversity of herbaceous plants and bacterial communities regulates soil resistome across forest biomes
Publisher: Wiley
Date: 22-05-2018
Abstract: Antibiotic resistance is ancient and prevalent in natural ecosystems and evolved long before the utilization of synthetic antibiotics started, but factors influencing the large-scale distribution patterns of natural antibiotic resistance genes (ARGs) remain largely unknown. Here, a large-scale investigation over 4000 km was performed to profile soil ARGs, plant communities and bacterial communities from 300 quadrats across five forest biomes with minimal human impact. We detected erse and abundant ARGs in forests, including over 160 genes conferring resistance to eight major categories of antibiotics. The ersity of ARGs was strongly and positively correlated with the ersity of bacteria, herbaceous plants and mobile genetic elements (MGEs). The ARG composition was strongly correlated with the taxonomic structure of bacteria and herbs. Consistent with this strong correlation, structural equation modelling demonstrated that the positive effects of bacterial and herb communities on ARG patterns were maintained even when simultaneously accounting for multiple drivers (climate, spatial predictors and edaphic factors). These findings suggest a paradigm that the interactions between aboveground and belowground communities shape the large-scale distribution of soil resistomes, providing new knowledge for tackling the emerging environmental antibiotic resistance.
Next-generation enhanced-efficiency fertilizers for sustained food security
Publisher: Springer Science and Business Media LLC
Date: 21-07-2022
Effect of straw incorporation and nitrification inhibitor on nitrous oxide emission in three cropland soils
Publisher: Wiley
Date: 04-04-2022
DOI: 10.1002/SAE2.12013
Abstract: Nitrification inhibitors and straw incorporation are used to reduce microbial mediated nitrogen (N) losses, thereby increasing N use efficiency (NUE) in cropland soil, but their effects on nitrous oxide (N 2 O) emission across different soil types and the underlying molecular mechanisms remain less understood. In this study, we investigated how nitrification inhibitor nitrapyrin and straw incorporation affected soil N balance, N 2 O emission, nitrifiers and denitrifiers in three cropland soils (black, fluvo‐aquic and red soils). Compared with fertilization‐only treatment (N), nitrapyrin addition increased ammonium, while it decreased nitrate concentration in all soils however, the performance of straw incorporation was less significant. Nitrapyrin decreased N 2 O emission only in the fluvo‐aquic soil, while straw incorporation strongly increased N 2 O emission in the red soil. Terminal restriction fragment length polymorphism analysis revealed that the denitrifier community was distinct across the three soils, but not strongly structured by nitrapyrin or straw incorporation. Compared with the N treatment, straw incorporation and nitrapyrin increased nosZ gene abundance only in the black soil. Structural equational modelling further confirmed that, after accounting for different soil properties, straw incorporation significantly increased N 2 O emission from black and red soils, and a decrease in nosZ gene abundance was the main biological factor for increased N 2 O emission in red soil. Taken together, our work provides new knowledge that the performance of nitrification inhibitor and straw incorporation on N 2 O emission is soil type‐dependent, and management practices should be used as per soil type to balance NUE and N 2 O emission.
Assembly processes lead to divergent soil fungal communities within and among 12 forest ecosystems along a latitudinal gradient
Publisher: Wiley
Date: 06-06-2021
DOI: 10.1111/NPH.17457
Abstract: Latitudinal gradients provide opportunities to better understand soil fungal community assembly and its relationship with vegetation, climate, soil and ecosystem function. Understanding the mechanisms underlying community assembly is essential for predicting compositional responses to changing environments. We quantified the relative importance of stochastic and deterministic processes in structuring soil fungal communities using patterns of community dissimilarity observed within and between 12 natural forests and related these to environmental variation within and among sites. The results revealed that whole fungal communities and communities of arbuscular and ectomycorrhizal fungi consistently exhibited ergent patterns but with less ergence for ectomycorrhizal fungi at most sites. Within those forests, no clear relationships were observed between the degree of ergence within fungal and plant communities. When comparing communities at larger spatial scales, among the 12 forests, we observed distinct separation in all three fungal groups among tropical, subtropical and temperate climatic zones. Soil fungal β‐ ersity patterns between forests were also greater when comparing forests exhibiting high environmental heterogeneity. Taken together, although large‐scale community turnover could be attributed to specific environmental drivers, the differences among fungal communities in soils within forests was high even at local scales.
Specific protistan consumers and parasites are responsive to inorganic fertilization in rhizosphere and bulk soils
Publisher: Springer Science and Business Media LLC
Date: 18-08-2021
Effects of 3,4-dimethylpyrazole phosphate (DMPP) on nitrification and the abundance and community composition of soil ammonia oxidizers in three land uses
Publisher: Springer Science and Business Media LLC
Date: 15-07-2016
Activity, abundance and community structure of anammox bacteria along depth profiles in three different paddy soils
Publisher: Elsevier BV
Date: 12-2015
Optimizing cropping systems to close the gap between economic profitability and environmental health
Publisher: Wiley
Date: 16-10-2023
DOI: 10.1111/NPH.19310
The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance, and climatic factors
Publisher: Frontiers Media SA
Date: 04-09-2015
Impacts of reclaimed water irrigation on soil antibiotic resistome in urban parks of Victoria, Australia
Publisher: Elsevier BV
Date: 04-2016
DOI: 10.1016/J.ENVPOL.2015.12.033
Abstract: The effluents from wastewater treatment plants have been recognized as a significant environmental reservoir of antibiotics and antibiotic resistance genes (ARGs). Reclaimed water irrigation (RWI) is increasingly used as a practical solution for combating water scarcity in arid and semiarid regions, however, impacts of RWI on the patterns of ARGs and the soil bacterial community remain unclear. Here, we used high-throughput quantitative PCR and terminal restriction fragment length polymorphism techniques to compare the ersity, abundance and composition of a broad-spectrum of ARGs and total bacteria in 12 urban parks with and without RWI in Victoria, Australia. A total of 40 unique ARGs were detected across all park soils, with genes conferring resistance to β-lactam being the most prevalent ARG type. The total numbers and the fold changes of the detected ARGs were significantly increased by RWI, and marked shifts in ARG patterns were also observed in urban parks with RWI compared to those without RWI. The changes in ARG patterns were paralleled by a significant effect of RWI on the bacterial community structure and a co-occurrence pattern of the detected ARG types. There were significant and positive correlations between the fold changes of the integrase intI1 gene and two β-lactam resistance genes (KPC and IMP-2 groups), but no significant impacts of RWI on the abundances of intI1 and the transposase tnpA gene were found, indicating that RWI did not improve the potential for horizontal gene transfer of soil ARGs. Taken together, our findings suggested that irrigation of urban parks with reclaimed water could influence the abundance, ersity, and compositions of a wide variety of soil ARGs of clinical relevance. Irrigation of urban parks with treated wastewater significantly increased the abundance and ersity of various antibiotic resistance genes, but did not significantly enhance their potential for horizontal gene transfer.
Contrasting patterns and drivers of soil bacterial and fungal diversity across a mountain gradient
Publisher: Wiley
Date: 08-06-2020
Ammonia oxidizers and denitrifiers in response to reciprocal elevation translocation in an alpine meadow on the Tibetan Plateau
Publisher: Springer Science and Business Media LLC
Date: 18-02-2014
Fungal richness contributes to multifunctionality in boreal forest soil
Publisher: Elsevier BV
Date: 09-2019
Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems
Publisher: Springer Science and Business Media LLC
Date: 19-01-2016
DOI: 10.1038/SREP19561
Abstract: The belowground soil prokaryotic community plays a cardinal role in sustaining the stability and functions of forest ecosystems. Yet, the nature of how soil prokaryotic ersity co-varies with aboveground plant ersity along a latitudinal gradient remains elusive. By establishing three hundred 400-m 2 quadrats from tropical rainforest to boreal forest in a large-scale parallel study on both belowground soil prokaryote and aboveground tree and herb communities, we found that soil prokaryotic ersity couples with the ersity of herbs rather than trees. The ersity of prokaryotes and herbs responds similarly to environmental factors along the latitudinal gradient. These findings revealed that herbs provide a good predictor of belowground bio ersity in forest ecosystems and provide new perspective on the aboveground and belowground interactions in forest ecosystems.
Precipitation increases the abundance of fungal plant pathogens in Eucalyptus phyllosphere
Publisher: Wiley
Date: 28-08-2021
Abstract: Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large‐scale investigation of Eucalyptus phyllospheric microbiomes in Australia and the multiple linear regression model, we show that precipitation is the most important predictor of fungal taxonomic ersity and abundance. The abundance of fungal plant pathogens in phyllosphere exhibited a positive linear relationship with precipitation. With this empirical dataset, we constructed current and future atlases of phyllosphere plant pathogens to estimate their spatial distributions under different climate change scenarios. Our atlases indicate that the abundance of fungal plant pathogens would increase especially in the coastal regions with up to 100‐fold increase compared with the current abundance. These findings advance our understanding of the distributions of fungal plant pathogens in phyllospheric microbiomes under the climate change, which can improve our ability to predict and mitigate their impacts on plant productivity and economic losses.
Full substitution of chemical fertilizer by organic manure decreases soil N2O emissions driven by ammonia oxidizers and gross nitrogen transformations
Publisher: Wiley
Date: 06-10-2023
DOI: 10.1111/GCB.16957
Comammox Nitrospira play an active role in nitrification of agricultural soils amended with nitrogen fertilizers
Publisher: Elsevier BV
Date: 11-2019
pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing
Publisher: Springer Science and Business Media LLC
Date: 11-06-2013
Current insights into the autotrophic thaumarchaeal ammonia oxidation in acidic soils
Publisher: Elsevier BV
Date: 12-2012
Ammonia-Oxidizing Archaea Play a Predominant Role in Acid Soil Nitrification
Publisher: Elsevier
Date: 2014
Generation of plasma cells and CD27−IgD− B cells during hantavirus infection is associated with distinct pathological findings
Publisher: Wiley
Date: 2021
DOI: 10.1002/CTI2.1313
Abstract: Human hantavirus infections can cause haemorrhagic fever with renal syndrome (HFRS). The pathogenic mechanisms are not fully understood, nor if they affect the humoral immune system. The objective of this study was to investigate humoral immune responses to hantavirus infection and to correlate them to the typical features of HFRS: thrombocytopenia and transient kidney dysfunction. We performed a comprehensive characterisation of longitudinal antiviral B‐cell responses of 26 hantavirus patients and combined this with paired clinical data. In addition, we measured extracellular adenosine triphosphate (ATP) and its breakdown products in circulation and performed in vitro stimulations to address its effect on B cells. We found that thrombocytopenia was correlated to an elevated frequency of plasmablasts in circulation. In contrast, kidney dysfunction was indicative of an accumulation of CD27 − IgD − B cells and CD27 −/low plasmablasts. Finally, we provide evidence that high levels of extracellular ATP and matrix metalloproteinase 8 can contribute to shedding of CD27 during human hantavirus infection. Our findings demonstrate that thrombocytopenia and kidney dysfunction associate with distinctly different effects on the humoral immune system. Moreover, hantavirus‐infected in iduals have significantly elevated levels of extracellular ATP in circulation.
Oxytetracycline and Ciprofloxacin Exposure Altered the Composition of Protistan Consumers in an Agricultural Soil
Publisher: American Chemical Society (ACS)
Date: 10-07-2020
Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces
Publisher: Springer Science and Business Media LLC
Date: 09-01-2023
Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China
Publisher: Springer Science and Business Media LLC
Date: 10-12-2014
Application of nano-scale secondary ion mass spectrometry to microbial ecology study
Publisher: Acta Ecologica Sinica
Date: 2013
Biotic and abiotic factors distinctly drive contrasting biogeographic patterns between phyllosphere and soil resistomes in natural ecosystems
Publisher: Springer Science and Business Media LLC
Date: 14-04-2021
DOI: 10.1038/S43705-021-00012-4
Abstract: The phyllosphere and soil are two of the most important reservoirs of antibiotic resistance genes (ARGs) in terrestrial ecosystems. However, comparative studies on the biogeographic patterns of ARGs in these two habitats are lacking. Based on the construction of ARG abundance atlas across a 4,000 km transect in eastern and northern Australia, we found contrasting biogeographic patterns of the phyllosphere and soil resistomes, which showed their distinct responses to the biotic and abiotic stresses. The similarity of ARG compositions in soil, but not in the phyllosphere, exhibited significant distance-decay patterns. ARG abundance in the phyllosphere was mainly correlated with the compositions of co-occurring bacterial, fungal and protistan communities, indicating that biotic stresses were the main drivers shaping the phyllosphere resistome. Soil ARG abundance was mainly associated with abiotic factors including mean annual temperature and precipitation as well as soil total carbon and nitrogen. Our findings demonstrated the distinct roles of biotic and abiotic factors in shaping resistomes in different environmental habitats. These findings constitute a major advance in our understanding of the current environmental resistomes and contribute to better predictions of the evolution of environmental ARGs by highlighting the importance of habitat difference in shaping environmental resistomes.
Ammonia-oxidizing archaea have more important role than ammonia-oxidizing bacteria in ammonia oxidation of strongly acidic soils
Publisher: Springer Science and Business Media LLC
Date: 12-2012
Conversion of natural grassland to cropland alters microbial community assembly across northern China
Publisher: Wiley
Date: 26-07-2022
Abstract: To feed the growing human population, natural grasslands are being converted to agricultural use at a massive scale. This conversion may have negative consequences for soil bio ersity, but its impact on the community assembly of differentially microbial groups remains largely unknown. Here, we investigated the ersity and community compositions of bacteria, archaea, fungi and protists, using a paired s ling of grassland and cropland soils across the agro‐pastoral ecotone of northern China. Land‐use conversion decreased α ersity of bacteria, fungi and protists, and altered the structures of the entire soil microbial community (archaea, bacteria, fungi and protists). The community assembly of archaea and bacteria was dominated by stochastic processes, and that of protists dominated by deterministic processes in both land‐use types. By contrast, the fungal community was governed more strongly by stochastic processes in grassland soil, than by deterministic processes in cropland soil. Our findings support the ʻsize‐plasticityʼ hypothesis that smaller body‐sized microorganisms (archaea and bacteria) are more structured by stochastic processes, and larger one (protist) is more influenced by deterministic processes. Our study demonstrates that distinct ecological processes govern microbial community assembly, and land‐use change regulates the balance between determinism and stochasticity.
Soil pH determines the alpha diversity but not beta diversity of soil fungal community along altitude in a typical Tibetan forest ecosystem
Publisher: Springer Science and Business Media LLC
Date: 05-02-2015
Salinity as a predominant factor modulating the distribution patterns of antibiotic resistance genes in ocean and river beach soils
Publisher: Elsevier BV
Date: 06-2019
DOI: 10.1016/J.SCITOTENV.2019.02.454
Abstract: Growing evidence points to the pivotal role of the environmental factors in influencing the transmission of antibiotic resistance genes (ARGs) and the propagation of resistant human pathogens. However, our understanding of the ecological and evolutionary environmental factors that contribute to development and dissemination of antibiotic resistance is lacking. Here, we profiled a wide variety of ARGs using the high-throughput quantitative PCR analysis in 61 soil s les collected from ocean and river beaches, which are hotspots for human activities and platforms for potential transmission of environmental ARGs to human pathogens. We identified the dominant abiotic and biotic factors influencing the ersity, abundance and composition of ARGs in these ecosystems. A total of 110 ARGs conferring resistance to eight major categories of antibiotics were detected. The core resistome was mainly affiliated into β-lactam and multidrug resistance, accounting for 66.9% of the total abundance of ARGs. The oprJ gene conferring resistance to multidrug was the most widespread ARG subtype detected in all the s les. The relative abundances of total ARGs and core resistome were significantly correlated with salinity-related properties including electrical conductivity and concentrations of sodium and chloride. Random forest analysis and structural equation modelling revealed that salinity was the most important factor modulating the distribution patterns of beach soil ARGs after accounting for multiple drivers. These findings suggest that beach soil is a rich reservoir of ARGs and that salinity is a predominant factor shaping the distribution patterns of soil resistome.
Potential of indigenous crop microbiomes for sustainable agriculture
Publisher: Springer Science and Business Media LLC
Date: 21-04-2021
2022 taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
Publisher: Springer Science and Business Media LLC
Date: 28-11-2022
DOI: 10.1007/S00705-022-05546-Z
Abstract: In March 2022, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by two new families (bunyaviral Discoviridae and Tulasviridae), 41 new genera, and 98 new species. Three hundred forty-nine species were renamed and/or moved. The accidentally misspelled names of seven species were corrected. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
Termite mound formation reduces the abundance and diversity of soil resistomes
Publisher: Wiley
Date: 15-06-2021
Abstract: Termites are pivotal ecosystem engineers in tropical and subtropical habitats, where they construct massive nests (‘mounds’) that substantially modify soil properties and promote nutrient cycling. Yet, little is known about the roles of termite nesting activity in regulating the spread of antimicrobial resistance (AMR), one of the major Global Health challenges. Here, we conducted a large‐scale ( 1500 km) investigation in northern Australia and found distinct resistome profiles in termite mounds and bulk soils. By profiling a wide spectrum of ARGs, we found that the abundance and ersity of antibiotic resistance genes (ARGs) were significantly lower in termite mounds than in bulk soils ( P 0.001). The proportion of efflux pump ARGs was significantly lower in termite mound resistome than in bulk soil resistome ( P 0.001). The differences in resistome profiles between termite mounds and bulk soils may result from the changes in microbial interactions owing to the substantial increase in pH and nutrient availability induced by termite nesting activities. These findings advance our understanding of the profile of ARGs in termite mounds, which is a crucial step to evaluate the roles of soil faunal activity in regulating soil resistome under global environmental change.
Trophic interrelationships of bacteria are important for shaping soil protist communities
Publisher: Wiley
Date: 29-03-2023
Abstract: Protists occupy multiple trophic positions in soil food webs and significantly contribute to organic matter decomposition and biogeochemical cycling. Protists can ingest bacteria and fungi as main food sources while being subjected to predation of invertebrates, but our understanding of how bottom‐up and top‐down regulations structure protists in natural soil habitats is limited. Here, we disentangle the effects of trophic regulations to the ersity and structure of soil protists in natural settings across northern and eastern Australia. Bacterial and invertebrate ersity were identified as important drivers of the ersity of functional groups of protists. Moreover, the compositions of protistan taxonomic and functional groups were better predicted by bacteria and fungi, than by soil invertebrates. There were strong trophic interconnections between protists and bacteria in multiple organismic network analysis. Altogether, the study provided new evidence that, bottom‐up control of bacteria played an important role in shaping the soil protist community structure, which can be derived from feeding preferences of protists on microbial prey, and their intimate relationships in soil functioning or environmental adaptation. Our findings advance our knowledge about the impacts of different trophic groups on key soil organismic communities, with implications for ecosystem functions and services.
Water addition regulates the metabolic activity of ammonia oxidizers responding to environmental perturbations in dry subhumid ecosystems
Publisher: Wiley
Date: 09-05-2014
Abstract: Terrestrial arid and semi-arid ecosystems (drylands) constitute about 41% of the Earth's land surface and are predicted to experience increasing fluctuations in water and nitrogen availability. Mounting evidence has confirmed the significant importance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in nitrification, plant nitrogen availability and atmospheric N2 O emissions, but their responses to environmental perturbations in drylands remain largely unknown. Here we evaluate how the factorial combinations of irrigation and fertilization in forests and land-use change from grassland to forest affects the dynamics of AOA and AOB following a 6-year dryland field study. Potential nitrification rates and AOA and AOB abundances were significantly higher in the irrigated plots, accompanied by considerable changes in community compositions, but their responses to fertilization alone were not significant. DNA-stable isotope probing results showed increased (13) CO2 incorporation into the amoA gene of AOA, but not of AOB, in plots receiving water addition, coupled with significantly higher net mineralization and nitrification rates. High-throughput microarray analysis revealed that active AOA assemblages belonging to Nitrosopumilus and Nitrosotalea were increasingly labelled by (13) CO2 following irrigation. However, no obvious effects of land-use changes on nitrification rates or metabolic activity of AOA and AOB could be observed under dry conditions. We provide evidence that water addition had more important roles than nitrogen fertilization in influencing the autotrophic nitrification in dryland ecosystems, and AOA are increasingly involved in ammonia oxidation when dry soils become wetted.
NK cells are activated and primed for skin-homing during acute dengue virus infection in humans
Publisher: Springer Science and Business Media LLC
Date: 29-08-2019
DOI: 10.1038/S41467-019-11878-3
Abstract: Despite animal models showing that natural killer (NK) cells are important players in the early defense against many viral infections, the NK cell response is poorly understood in humans. Here we analyze the phenotype, temporal dynamics, regulation and trafficking of NK cells in a patient cohort with acute dengue virus infection. NK cells are robustly activated and proliferate during the first week after symptom debut. Increased IL-18 levels in plasma and in induced skin blisters of DENV-infected patients, as well as concomitant signaling downstream of the IL-18R, suggests an IL-18-dependent mechanism in driving the proliferative NK cell response. Responding NK cells have a less mature phenotype and a distinct chemokine-receptor imprint indicative of skin-homing. A corresponding NK cell subset can be localized to skin early during acute infection. These data provide evidence of an IL-18-driven NK cell proliferation and priming for skin-homing during an acute viral infection in humans.
Protistan predation selects for antibiotic resistance in soil bacterial communities
Publisher: Springer Science and Business Media LLC
Date: 04-10-2023
Contrasting Euryarchaeota communities between upland and paddy soils exhibited similar pH-impacted biogeographic patterns
Publisher: Elsevier BV
Date: 09-2013
The global contribution of soil mosses to ecosystem services
Publisher: Springer Science and Business Media LLC
Date: 05-2023
Soil contamination in nearby natural areas mirrors that in urban greenspaces worldwide
Publisher: Springer Science and Business Media LLC
Date: 27-03-2023
DOI: 10.1038/S41467-023-37428-6
Abstract: Soil contamination is one of the main threats to ecosystem health and sustainability. Yet little is known about the extent to which soil contaminants differ between urban greenspaces and natural ecosystems. Here we show that urban greenspaces and adjacent natural areas (i.e., natural/semi-natural ecosystems) shared similar levels of multiple soil contaminants (metal(loid)s, pesticides, microplastics, and antibiotic resistance genes) across the globe. We reveal that human influence explained many forms of soil contamination worldwide. Socio-economic factors were integral to explaining the occurrence of soil contaminants worldwide. We further show that increased levels of multiple soil contaminants were linked with changes in microbial traits including genes associated with environmental stress resistance, nutrient cycling, and pathogenesis. Taken together, our work demonstrates that human-driven soil contamination in nearby natural areas mirrors that in urban greenspaces globally, and highlights that soil contaminants have the potential to cause dire consequences for ecosystem sustainability and human wellbeing.
Field-based evidence for consistent responses of bacterial communities to copper contamination in two contrasting agricultural soils
Publisher: Frontiers Media SA
Date: 02-02-2015
Hantavirus Gn and Gc Glycoproteins Self-Assemble into Virus-Like Particles
Publisher: American Society for Microbiology
Date: 15-02-2013
DOI: 10.1128/JVI.03118-13
Abstract: How hantaviruses assemble and exit infected cells remains largely unknown. Here, we show that the expression of Andes (ANDV) and Puumala (PUUV) hantavirus Gn and Gc envelope glycoproteins lead to their self-assembly into virus-like particles (VLPs) which were released to cell supernatants. The viral nucleoprotein was not required for particle formation. Further, a Gc endodomain deletion mutant did not abrogate VLP formation. The VLPs were pleomorphic, exposed protrusions and reacted with patient sera.
The end of hunger: fertilizers, microbes and plant productivity
Publisher: Wiley
Date: 12-11-2022
Abstract: It is a grand challenge to ensure the food security for a predicted world population of exceeding 9.7 billion by 2050, especially in an era of global climate change, land degradation and bio ersity loss. Current agricultural productions are mainly relying on synthetic chemical fertilisers to boost plant productivity but have undesirable effects on the environment and soil bio ersity. A promising direction in sustainable agriculture is to harness naturally occurring processes of beneficial plant‐associated microbiomes to ensure sustained crop production and global food security. Despite the significant progress made in the development of beneficial microbes as inoculants to enhance plant performance, challenges remain with the translation of knowledge of plant and soil microbiomes to successful microbial products in the agricultural sector. Here, we highlight how fertilizer technology should be renovated by harnessing microbiome‐based innovations to promote plant productivity and contribute to the end of hunger.
Microbial hydrogen cycling in agricultural systems – plant beneficial or detrimental?
Publisher: Wiley
Date: 24-06-2023
Abstract: Hydrogen‐oxidising bacteria play a key role in maintaining the composition of gases within the atmosphere and are ubiquitous in agricultural soils. While studies have shown that hydrogen accumulates in soil surrounding legume nodules and the soil surface, soils as a whole act as a net sink for hydrogen, raising questions about how hydrogen is internally recycled by soils. Can the energy derived from hydrogen oxidation be directly funnelled into plants to promote their growth or does it only act as a booster for other plant‐growth promoting bacteria? Moreover, while the fertilisation effect of hydrogen on plants has previously been shown to be beneficial, questions remain about the upper limit of hydrogen uptake by plants before it becomes detrimental. Agricultural practices such as fertilisation may impact the balance of hydrogen‐oxidisers and hydrogen‐producers in these ecosystems, potentially having detrimental effects on not only agricultural land but also global biogeochemical cycles. In this perspectives piece, we highlight the importance of understanding the contribution of hydrogen to agricultural soils and the effects of agricultural practices on the ability for bacteria to cycle hydrogen in agricultural soils. We propose a framework to gain better insights into microbial hydrogen cycling within agroecosystems, which could contribute to the development of new agricultural biotechnologies.
Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils
Publisher: Elsevier BV
Date: 2018
DOI: 10.1016/J.SCITOTENV.2017.09.028
Abstract: Composting has been suggested as a potential strategy to eliminate antibiotic residues and pathogens in livestock manure before its application as an organic fertilizer in agro-ecosystems. However, the impacts of composting on antibiotic resistance genes (ARGs) in livestock manure and their temporal succession following the application of compost to land are not well understood. We examined how aerobic composting affected the resistome profiles of cattle manure, and by constructing laboratory microcosms we compared the effects of manure and compost application to agricultural soils on the temporal succession of a wide spectrum of ARGs. The high-throughput quantitative PCR array detected a total of 144 ARGs across all the soil, manure and compost s les, with Macrolide-Lincosamide-Streptogramin B, aminoglycoside, multidrug, tetracycline, and β-lactam resistance as the most dominant types. Composting significantly reduced the ersity and relative abundance of ARGs and mobile genetic elements (MGEs) in the cattle manure. In the 120-day microcosm incubation, the ersity and abundance of ARGs in manure-treated soils were significantly higher than those in compost-treated soils at the beginning of the experiment. The level of antibiotic resistance rapidly declined over time in all manure- and compost-treated soils, coupled with similar temporal patterns of manure- and compost-derived bacterial communities as revealed by SourceTracker analysis. The network analysis revealed more intensive interactions/associations among ARGs and MGEs in manure-treated soils than in compost-treated soils, suggesting that mobility potential of ARGs was lower in soils amended with compost. Our results provide evidence that aerobic composting of cattle manure may be an effective approach to mitigate the risk of antibiotic resistance propagation associated with land application of organic wastes.
Copper pollution decreases the resistance of soil microbial community to subsequent dry-rewetting disturbance
Publisher: Elsevier BV
Date: 2016
DOI: 10.1016/J.JES.2015.10.009
Abstract: Dry-rewetting (DW) disturbance frequently occurs in soils due to rainfall and irrigation, and the frequency of DW cycles might exert significant influences on soil microbial communities and their mediated functions. However, how microorganisms respond to DW alternations in soils with a history of heavy metal pollution remains largely unknown. Here, soil laboratory microcosms were constructed to explore the impacts of ten DW cycles on the soil microbial communities in two contrasting soils (fluvo-aquic soil and red soil) under three copper concentrations (zero, medium and high). Results showed that the fluctuations of substrate induced respiration (SIR) decreased with repeated cycles of DW alternation. Furthermore, the resistance values of substrate induced respiration (RS-SIR) were highest in non-copper-stressed (zero) soils. Structural equation model (SEM) analysis ascertained that the shifts of bacterial communities determined the changes of RS-SIR in both soils. The rate of bacterial community variance was significantly lower in non-copper-stressed soil compared to the other two copper-stressed (medium and high) soils, which might lead to the higher RS-SIR in the fluvo-aquic soil. As for the red soil, the substantial increase of the dominant group WPS-2 after DW disturbance might result in the low RS-SIR in the high copper-stressed soil. Moreover, in both soils, the bacterial ersity was highest in non-copper-stressed soils. Our results revealed that initial copper stress could decrease the resistance of soil microbial community structure and function to subsequent DW disturbance.
2020 taxonomic update for phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales
Publisher: Springer Science and Business Media LLC
Date: 04-09-2020
Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China
Publisher: Frontiers Media SA
Date: 30-08-2016
Temporal changes of antibiotic-resistance genes and bacterial communities in two contrasting soils treated with cattle manure
Publisher: Oxford University Press (OUP)
Date: 27-12-2016
Abstract: The emerging environmental spread of antibiotic-resistance genes (ARGs) and their subsequent acquisition by clinically relevant microorganisms is a major threat to public health. Animal manure has been recognized as an important reservoir of ARGs however, the dissemination of manure-derived ARGs and the impacts of manure application on the soil resistome remain obscure. Here, we conducted a microcosm study to assess the temporal succession of total bacteria and a broad spectrum of ARGs in two contrasting soils following manure application from cattle that had not been treated with antibiotics. High-capacity quantitative PCR detected 52 unique ARGs across all the s les, with β-lactamase as the most dominant ARG type. Several genes of soil indigenous bacteria conferring resistance to β-lactam, which could not be detected in manure, were found to be highly enriched in manure-treated soils, and the level of enrichment was maintained over the entire course of 140 days. The enriched β-lactam resistance genes had significantly positive relationships with the relative abundance of the integrase intI1 gene, suggesting an increasing mobility potential in manure-treated soils. The changes in ARG patterns were accompanied by a significant effect of cattle manure on the total bacterial community compositions. Our study indicates that even in the absence of selective pressure imposed by agricultural use of antibiotics, manure application could still strongly impact the abundance, ersity and mobility potential of a broad spectrum of soil ARGs. Our findings are important for reliable prediction of ARG behaviors in soil environment and development of appropriate strategies to minimize their dissemination.
Initial Copper Stress Strengthens the Resistance of Soil Microorganisms to a Subsequent Copper Stress
Publisher: Springer Science and Business Media LLC
Date: 28-02-2014
DOI: 10.1007/S00248-014-0391-8
Abstract: To improve the prediction of essential ecosystem functioning under future environmental disturbances, it is of significance to identify responses of soil microorganisms to environmental stresses. In this study, we collected polluted soil s les from field plots with eight copper levels ranging from 0 to 3,200 mg Cu kg(-1) soil. Then, the soils with 0 and 3,200 mg Cu kg(-1) were selected to construct a microcosm experiment. Four treatments were set up including Cu0-C and Cu3200-C without further Cu addition, and Cu0-A and Cu3200-A with addition of 57.5 mg Cu kg(-1) soil. We measured substrate-induced respiration (SIR) and potential nitrification rate (PNR). Furthermore, the abundance of bacterial, archaeal 16S rRNA genes, ammonia-oxidizing bacteria and archaea amoA genes were determined through quantitative PCR. The soil microbial communities were investigated by terminal restriction fragment length polymorphism (T-RFLP). For the field s les, the SIR and PNR as well as the abundance of soil microorganisms varied significantly between eight copper levels. Soil microbial communities highly differed between the low and high copper stress. In the microcosm experiment, the PNR and SIR both recovered while the abundance of soil microorganisms varied irregularly during the 90-day incubation. The differences of microbial communities measured by pairwise Bray-Curtis dissimilarities between Cu0-A and Cu0-C on day 0 were significantly higher after subsequent stress than before. However, the differences of microbial communities between Cu3200-A and Cu3200-C on day 0 changed little between after subsequent stress and before. Therefore, initial copper stress could increase the resistance of soil microorganisms to subsequent copper stress.
Influence of Legacy Mercury on Antibiotic Resistomes: Evidence from Agricultural Soils with Different Cropping Systems
Publisher: American Chemical Society (ACS)
Date: 06-10-2021
Microbial regulation of terrestrial nitrous oxide formation: Understanding the biological pathways for prediction of emission rates
Publisher: Oxford University Press (OUP)
Date: 30-04-2015
Abstract: The continuous increase of the greenhouse gas nitrous oxide (N2O) in the atmosphere due to increasing anthropogenic nitrogen input in agriculture has become a global concern. In recent years, identification of the microbial assemblages responsible for soil N2O production has substantially advanced with the development of molecular technologies and the discoveries of novel functional guilds and new types of metabolism. However, few practical tools are available to effectively reduce in situ soil N2O flux. Combating the negative impacts of increasing N2O fluxes poses considerable challenges and will be ineffective without successfully incorporating microbially regulated N2O processes into ecosystem modeling and mitigation strategies. Here, we synthesize the latest knowledge of (i) the key microbial pathways regulating N2O production and consumption processes in terrestrial ecosystems and the critical environmental factors influencing their occurrence, and (ii) the relative contributions of major biological pathways to soil N2O emissions by analyzing available natural isotopic signatures of N2O and by using stable isotope enrichment and inhibition techniques. We argue that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling in order to increase the estimation reliability of N2O emissions. We further propose a molecular methodology oriented framework from gene to ecosystem scales for more robust prediction and mitigation of future N2O emissions.
Annual (2023) taxonomic update of RNA-directed RNA polymerase-encoding negative-sense RNA viruses (realm Riboviria: kingdom Orthornavirae: phylum Negarnaviricota)
Publisher: Microbiology Society
Date: 25-08-2023
DOI: 10.1099/JGV.0.001864
Rare microbial taxa as the major drivers of ecosystem multifunctionality in long-term fertilized soils
Publisher: Elsevier BV
Date: 02-2020
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