Ye Deng

Ye Deng
Chinese Academy of Sciences | CAS · Research Center for Eco-Environmental Sciences

Ph.D

About

394
Publications
110,138
Reads
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17,327
Citations
Additional affiliations
April 2014 - present
Chinese Academy of Sciences
Position
  • Professor (Full)
December 2005 - April 2014
University of Oklahoma
Position
  • Research Associate

Publications

Publications (394)
Article
Full-text available
Understanding the impact of long-term fertilization in different soil types and its effect on soil bacteria and crop production is critical for designing sustainable agricultural practices across diverse landscapes. Here, we investigated the impact of 25–37 years of continuous fertilizer treatments in three parent materials (Phaeozem, Cambisol, and...
Article
Root rot caused by Fusarium sp., a ubiquitous soilborne disease, leads to huge economic losses for tobacco cultivation in China. However, comprehensive knowledge about the interactions between this fungal pathogen and other members of soil and endophytic fungal communities is very limited. In this study, how the invasion process of root rot disease...
Article
Forage monoculture and grass (Gramineae)-legume mixtures are the two most commonly used planting patterns for establishing farming grasslands, but the effects of these planting patterns on the rhizosphere bacterial community and forage production are still unclear. In this study, we carried out a field experiment on the Tibetan Plateau, and observe...
Article
Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soi...
Article
Insect-associated bacteria play an important role in the resistance to pesticides, yet bacterial community compositions in wild insect host populations and the environmental factors that shape them are mostly elusive. In this study, Sitobion miscanthi (Takahashi) populations were collected from major wheat growing regions in China. Following high-t...
Article
A better understanding of how nitrogen (N) cycling genes are involved in ecological processes is one of the crucial areas of microbial ecology. Currently, most molecular biological techniques investigating N cycling genes in the environment heavily rely on the accuracy of the polymerase chain reaction (PCR) primers; however, their specificity and c...
Article
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The effects of organic fertilizer application on the soil microbial community in grassland systems have been extensively studied. However, the effects of organic fertilizers on the structure of rhizosphere microbial communities are still limited. In this study, the diversity and composition of rhizosphere microbial communities of a gramineous grass...
Article
Quantitative real‐time PCR (qPCR) has been widely used in quantifying bacterial and fungal populations in various ecosystems, as well as the fungi to bacteria ratio (F:B ratio). Recently, researchers have begun to apply droplet digital PCR (ddPCR) to this area, however, no study has systematically compared qPCR and ddPCR for quantitating both bacte...
Article
Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms i...
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Soil microbes assemble in highly complex and diverse microbial communities, and microbial diversity patterns and their drivers have been studied extensively. However, diversity correlations and co-occurrence patterns between bacterial, fungal, and archaeal domains and between microbial functional groups in arid regions remain poorly understood. Her...
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Fungi could play an important role during anaerobic digestion (AD), but have received less attention than prokaryotes. Here AD bioreactors of food waste were performed to explore fungal succession and their potential ecological and engineering value. We found that similar patterns in fungal biomass and diversity, decreasing from the initial time po...
Article
The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1...
Article
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Although autotrophic phytoplankton and heterotrophic zooplankton both play important roles in the food web of marine ecosystem, their comprehensive interactions and spatial patterns at continental scale remain poorly studied. Here, we collected 251 seawater samples along 13,000 km of Chinese coastline, and microscopically investigated the latitudin...
Article
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Integrated network analysis pipeline (iNAP) is an online analysis pipeline for generating and analyzing comprehensive ecological networks in microbiome studies. It is implemented in two sections, that is, network construction and network analysis, and integrates many open‐access tools. Network construction contains multiple feasible alternatives, i...
Article
Objective: To explore the differences of oral mycobiome and bacteriome between the healthy controls (H) and oral lichen planus (OLP) patients, and the co-occurrence patterns of the salivary mycobiome and bacteriome and the association with host immunity. Methods: Saliva samples were collected from clinical OLP patients (n=35) and healthy volunte...
Article
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Global warming is likely to affect the underground microbial communities in various ecosystems, but the response of soil microbial communities along a vertical depth profile to global warming has been elusive. Herein, we leveraged a warming field experiment in Qinghai-Tibet Plateau grassland and investigated the community structure of prokaryotes a...
Article
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Ecological restoration is essential to reverse land degradation worldwide. Most studies have assessed the restoration of ecosystem functions individually, as opposed to a holistic view. Here we developed a network‐based ecosystem multifunctionality (EMF) framework to identify key functions in evaluating EMF restoration. Through synthesizing 293 res...
Article
The levels of organic pollutants, in particular polycyclic aromatic hydrocarbons (PAHs), are increasing worldwide, yet we lack clarity on how these pollutants affect microbial communities of different trophic levels, including protists, fungi, and bacteria. Herein, we conducted soil microcosm incubation experiments to investigate the effects of pyr...
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Despite the increasing application of biodegradable plastic mulches (BDMs) in agriculture, the colonization and succession of the attached microbial community on BDMs during their degradation processes remain poorly characterized. Here, we buried four types of commonly used BDMs, including pure polylactic acid (PLA), pure polybutylene adipate terep...
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The relationship between plants and their associated soil microbial communities plays a crucial role in maintaining ecosystem processes and function. However, identifying these complex relationships is challenging. In this study, we constructed an interdomain ecology network (IDEN) of plant–bacteria based on SparCC pairwise associations using synch...
Article
The alpine meadow ecosystem, as the main ecosystem of the Qinghai-Tibet Plateau, has been heavily degraded over the past several decades due to overgrazing and climate change. Although soil microorganisms play key roles in the stability and succession of grassland ecosystems, their response to grassland degradation has not been investigated at spat...
Article
The functioning of microbial communities in response to elevated atmospheric carbon dioxide (eCO2) is one of the most important, but poorly understood, contributors to climate change feedbacks. The effect of soil moisture caused by eCO2 on soil microbial communities and functioning may be of high importance in water limited ecosystems. To address t...
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Understanding biogeographical patterns and underlying processes of belowground community assembly is crucial for predicting soil functions and their responses to global environmental change. However, little is known about potential differences of belowground community assembly among bacteria, fungi, protists and soil animals, particularly for alpin...
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The facultative anaerobic and strict anaerobic microorganisms enriched and acclimated during the anaerobic digestion process are crucial for the efficiency of the anaerobic digestion system. Most of the problems encountered during running anaerobic digestion processes could be effectively improved via stimulation of microbial metabolic activity. Be...
Article
Although fungi are regarded as the important degraders of aromatic hydrocarbons (AHs) in various environments, the dynamic succession and interaction of their community under aromatic hydrocarbon stress has been rarely reported. In this study, we systematically investigated the responses of the fungal community and the associations among fungal spe...
Article
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Changes in species composition across communities, i.e., β-diversity, is a central focus of ecology. Compared to macroorganisms, the β-diversity of soil microbes and its drivers are less studied. Whether the determinants of soil microbial β-diversity are consistent between soil depths and between abundant and rare microorganisms remains controversi...
Article
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In the plant rhizosphere and endosphere, some fungal and bacterial species regularly co-exist, however, our knowledge about their co-existence patterns is quite limited, especially during invasion by bacterial wilt pathogens. In this study, the fungal communities from soil to endophytic compartments were surveyed during an outbreak of tobacco wilt...
Article
Global warming may alter microbially mediated ecosystem functions through reshaping of microbial diversity and modified microbial interactions. Here, we examined the effects of 5‐years experimental warming on different microbial hierarchical groups in a coastal non‐tidal soil ecosystem, including prokaryotes (i.e. bacteria and archaea), fungi and C...
Article
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Due to the tremendous diversity of microbial organisms in topsoil, the estimation of saturated richness in a belowground ecosystem is still challenging. Here, we intensively surveyed the 16S rRNA gene in four 1 m2 sampling quadrats in a typical grassland, with 141 biological or technical replicates generating over 11 million sequences per quadrat....
Article
A mature cathodic biofilm plays the key role in biocathode electron transfer. The physiological transitions of it were of great interests as the sessile and dispersed (planktonic) work in a balance while it is still lack of understanding. In this study, an improved sampling method was used for detecting sessile, detached, and dispersed microorganis...
Article
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Elucidating the relative importance of species interactions and assembly mechanisms in regulating bacterial community structure and functions, especially the abundant and rare subcommunities, is crucial for understanding the influence of environmental disturbance in shaping ecological functions. However, little is known about how polycyclic aromati...
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The pollution of plastics and microplastics in the soil environment attracted lots of attentions in recent years. This paper reviewed the latest research progresses on the interaction between microorganisms and soil plastics. The main contents included, (i) the source and migration of soil plastics and their basic characteristics of long-term stora...
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Dams represent the most significant anthropogenic disturbance to global rivers. Previous studies have shown that free-living and particle-attached microbes exhibited differentially in river and reservoir ecosystems. However, little is known about the dam’s effect on their co-occurrence patterns. Here, a random matrix theory (RMT)-based network appr...
Article
Temperature sensitivity (Q10) of soil organic matter (SOM) decomposition is a crucial parameter to predict the fate of soil carbon (C) under global warming. Nonetheless, the response pattern of Q10 to continuous warming and the underlying mechanisms are still under debate, especially considering the complex interactions between Q10, SOM quality and...
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Organic and inorganic materials migrate downstream and have important roles in regulating environmental health in the river networks. However, it remains unclear whether and how a mixture of materials (i.e., microbial species) from various upstream habitats contribute to microbial community coalescence upstream of a dam. Here we track the spatial v...
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Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fung...
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It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil – their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly...
Article
Due to the massive quantity and broad phylogeny, an accurate measurement of microbial diversity is highly challenging in soil ecosystems. Initially, the deviation caused by sampling should be adequately considered. Here, we attempted to uncover the effect of different sampling strategies on α diversity measurement of soil prokaryotes. Four 1 m² sam...
Article
Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here...
Article
Terrestrial species are predicted to migrate northward under global warming conditions, yet little is known about the direction and magnitude of change in microbial distribution patterns. In this continental-scale study with more than 1600 forest soil samples, we verify the existence of core microbiota and lump them into a manageable number of eco-...
Article
In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-facete...
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Although many studies have investigated the spatial scaling of microbial communities living in surface soils, very little is known about the patterns within deeper strata, nor is the mechanism behind them. Here, we systematically assessed spatial scaling of prokaryotic biodiversity within three different strata (Upper: 0-20 cm, Middle: 20-40 cm, an...
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The microbiota colonizing the root endophytic compartment and surrounding rhizosphere soils contribute to plant growth and health. However, the key members of plant soil and endophytic microbial communities involved in inhibiting or assisting pathogen invasion remain elusive. By utilizing 16S high-throughput sequencing and a molecular ecological ne...
Preprint
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Background The marine autotrophic phytoplankton is responsible for approximately half of global primary production on Earth, and as the planktonic consumers, the heterotrophic zooplankton could link the phytoplankton and higher trophic level to complete the aquatic Food Web. Despite the interaction between phytoplankton and zooplankton has played i...
Article
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Atmospheric CO2 concentration is increasing, largely due to anthropogenic activities. Previous studies of individual free-air CO2 enrichment (FACE) experimental sites have shown significant impacts of elevated CO2 (eCO2) on soil microbial communities; however, no common microbial response patterns have yet emerged, challenging our ability to predic...
Article
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Background: Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO...
Preprint
Full-text available
Background: Nitrification in the soil is dominated by ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and the newly discovered complete nitrifiers, which are members of complex communities. Complicated relations have been found in microbial communities, but the relations between heterotrophic bacteria and autotrophic ammonia oxidi...
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The survey of microbial diversity in various environments has relied upon the widespread use of well-evaluated amplification primers for taxonomic marker genes (e.g., prokaryotic 16S and fungal ITS). However, it is urgent to develop a fast and accurate bioinformatic program to design primers for microbial functional genes to explore more mechanisms...
Article
Excessive nitrate in water systems is prevailing and a global risk of human health. Polluted river sediments are dominated by anaerobes and often the hotspot of denitrification. So far, little is known about the ecological effects of nitrate pollution on microbial dynamics, especially those in sulfide-rich sediments. Here we simulated a nitrate sur...
Article
Rather than simple accumulation of individual populations, microorganisms in natural ecosystems form complex ecological networks that are critical to maintain ecosystem functions and services. Although various studies have examined the patterns of microbial community diversity and composition across spatial gradients, whether microbial co-occurrenc...
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AimsSoil bacterial communities play vital roles in subtropical broad-leaved forests (SBFs), however, the mechanisms regulating their formation remain poorly understood. The present work aimed to address this question.Methods We used dIVI (Important Value Index of deciduous canopy trees) to quantitively classify three SBFs. Soil bacterial traits suc...
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The rise of oxygen on the early Earth about 2.4 billion years ago reorganized the redox cycle of harmful metal(loids), including that of arsenic, which doubtlessly imposed substantial barriers to the physiology and diversification of life. Evaluating the adaptive biological responses to these environmental challenges is inherently difficult because...
Article
Biodiversity is the foundation of all ecosystems across the planet, and better understanding of its global distribution mechanism could be important for biodiversity conservation under global change world. A niche width model, combined with metabolic theory, has successfully predicted the increase of a‐diversity and decrease of b‐diversity in the b...
Article
The accelerated development and application of graphene-family nanomaterials (GFNs) have increased their release to various environments and converged in wastewater treatment plants (WWTPs). However, little is known about the interactions between GFNs and microbes in WWTPs. In this study, the interaction of graphene oxide (GO) or graphene (G) at di...
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Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used...
Article
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Understanding the effects of pollution on ecological communities and the underlying mechanisms that drive them will helpful for selecting a method to mediate polluted ecosystems. Quantifying the relative importance of deterministic and stochastic processes is a very important issue in ecology. However, little is known about their effects on the suc...
Preprint
Full-text available
In a field experiment we investigated the influence of the environmental filters soil type and plant species identity on rhizosphere community assembly of Cercozoa, a dominant group of (mostly bacterivorous) soil protists. The experiment was set up with two plant species, lettuce and potato, grown in an experimental plot system with three contrasti...
Article
To investigate the influence of antibiotics on microbial interactions in a biofilm community, we set up eight replicate reactors of microbial electrolysis cell (MEC) and applied a broad-spectrum antibiotic florfenical (FLO) as an environmental disturbance. According to the results, exposure to FLO resulted in degradation of reactor performance. The...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Soil microbiomes contribute to plant growth, health and agricultural production. However, the influence of long-term application of different fertilizers on soil microbial diversity and community structure of tea (Camellia sinensis) plantations remains unclear. Here it was hypothesized that organic fertilizer treatment (OF) would significantly impr...