Publications by authors named "Deng Ye"

Biodegradable mulch films (BDMs) are becoming increasingly popular in agriculture and are emerging as an alternative to conventional polyethylene (PE) films. However, the intricate details surrounding the establishment and growth of microorganisms on BDMs and PE during their degradation in agricultural fields remain unclear. In this study, the succession of bacterial communities in farmland soil and the plastispheres of PE and BDMs were compared through 16S rRNA gene high-throughput sequencing and real-time PCR.

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Alcohol-induced health damage has become an increasing global public health concern. Anthocyanins exhibit essential biological activities, including antioxidation, anti-inflammation, and lipid reduction. This study investigates the rapid intervention effects and mechanisms of anthocyanin-rich blueberry extract in mitigating acute alcohol exposure in mice, aiming to uncover its novel nutritional roles.

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  • This study examines how reseeding and fertilization affect rhizospheric bacterial communities in degraded grasslands in the Qinghai-Tibet Plateau using high-throughput sequencing technology.
  • Results show that fertilization alone reduced bacterial diversity, while the combination of reseeding and fertilization most significantly altered community structure, favoring certain bacterial phyla like Actinomycetota and Pseudomonadota.
  • Key environmental factors, including nitrogen and phosphorus levels, were found to influence bacterial community composition, offering insights for better management practices in restoring high-altitude grasslands.
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Phthalic acid esters (PAEs) are common organic contaminants in farmland soil throughout agricultural systems, posing significant threats to human health and thus closely associated with food safety concerns. Here, we consolidate the latest findings regarding the distribution, ecological effects, bioremediation methods, and microbial degradation pathways of PAEs in agricultural ecosystems. Generally, di(2-ethylhexyl) phthalate (DEHP), di--butyl phthalate (DnBP), and di-isobutyl phthalate (DiBP) exhibit the highest detection frequencies and concentrations in soil, air and agricultural products.

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Influence spread analysis, a critical component of social network studies, focuses on the patterns and effects of information dissemination among interconnected entities. The core of influence spread analysis is to identify influential nodes that involve two distinct aspects: influence maximization (IM) and influence blocking maximization (IBM). However, when IM and IBM occur simultaneously, identifying influential nodes becomes an intricate decision-making challenge.

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As a common environmental endocrine disruptor, phthalate exposure could affect the diabetes risk. However, it remains unclear whether phthalate exposure in the elderly population alters diabetes risk. We conducted a cross-sectional survey to explore the effect of urinary phthalate metabolites on diabetes in the elderly.

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Cover crop integration into grain crop rotations is a promising strategy for mitigating nematode-induced diseases in agriculture. However, the precise mechanisms underlying this phenomenon remain elusive. Here, we first assessed the impact of five commonly used cover crops on the suppression of rice root-knot nematodes (RKNs).

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  • Complex networks, which consist of interconnected nodes and edges, are vital in understanding various systems in nature and society, with a focus on shortest path calculations in network science.
  • The study extends the use of the adjacency matrix from counting walks to counting shortest paths, addressing the challenge of calculating both the number and length of these paths effectively.
  • The proposed algorithm, tested on both synthetic and real-world networks, is significantly faster and more efficient than traditional methods, with potential applications in areas like traffic optimization and social network analysis.
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  • The text discusses the introduction of the integrated Network Analysis Pipeline 2.0 (iNAP 2.0), a tool designed for studying microbial ecological networks through metagenomic sequencing data.
  • iNAP 2.0 includes a four-module process for analyzing metabolic interactions, which involves preparing metabolic models, inferring pairwise interactions, constructing networks, and performing detailed analyses.
  • Key features of iNAP 2.0 include methods for quantifying metabolic complementarity, identifying transferable metabolites, and using random matrix theory for network construction; the tool is freely available online for users.
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  • Mangrove sediment is a significant source of methane emissions, but the impact of restoration on methane production and archaea community dynamics is not well understood.
  • Microcosm experiments showed that methane production from sediment decreased as mangrove stands aged, with rates dropping from 0.42 ng g d in younger stands to 0.23 ng g d in older ones, and a notable loss of microbial diversity, particularly Bathyarchaeia in 64-year-old sediments.
  • The research highlights that older mangrove stands have more stable microbial networks and that factors affecting community assembly shift from deterministic in younger stands to stochastic in older ones, leading to reduced methane production potential due to decreased abundance and interactions among key microorganisms.
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Implementing temporary traffic control measures is a common strategy to prevent air pollution and alleviate traffic congestion during mega-events. Accurate assessment of event-time vehicular emissions is useful for local authorities to develop effective policies. However, many previous assessments were based on policy-based scenarios, which often failed to capture the synergistic impact from other sectors (e.

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Biological nitrogen fixation (BNF) is a crucial process that provides bioavailable nitrogen and supports primary production in freshwater lake ecosystems. However, the characteristics of diazotrophic community and nitrogenase activity in freshwater lake sediments remain poorly understood. Here, we investigated the diazotrophic communities and nitrogenase activities in the sediments of three large river-connected freshwater lakes in eastern China using N-isotope tracing and nifH sequencing.

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The understanding of activated sludge microbial status and roles is imperative for improving and enhancing the performance of wastewater treatment plants (WWTPs). In this study, we conducted a deep analysis of activated sludge microbial communities across five compartments (inflow, effluent, and aerobic, anoxic, anaerobic tanks) over temporal scales, employing high-throughput sequencing of 16S rRNA amplicons and metagenome data. Clearly discernible seasonal patterns, exhibiting cyclic variations, were observed in microbial diversity, assembly, co-occurrence network, and metabolic functions.

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Microbial communities exhibit intricate interactions underpinned by metabolic dependencies. To elucidate these dependencies, we present a workflow utilizing random matrix theory on metagenome-assembled genomes to construct co-occurrence and metabolic complementarity networks. We apply this approach to a temperature gradient hot spring, unraveling the interplay between thermal stress and metabolic cooperation.

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  • Chromium (Cr) contamination negatively impacts soil fungi, yet the specific responses of these fungi in heavily affected areas are not well understood.
  • High-throughput sequencing was used to analyze fungal communities in soils with different Cr levels, revealing that hexavalent chromium (Cr(VI)) is a key factor altering fungal structure and abundance.
  • The study found that Cr contamination not only decreased certain fungal trophic types but also enhanced fungal interactions, resulting in more complex and stable fungal networks, with some fungi showing potential for reducing toxic heavy metals.
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Background: Microbial anaerobic metabolism is a key driver of biogeochemical cycles, influencing ecosystem function and health of both natural and engineered environments. However, the temporal dynamics of the intricate interactions between microorganisms and the organic metabolites are still poorly understood. Leveraging metagenomic and metabolomic approaches, we unveiled the principles governing microbial metabolism during a 96-day anaerobic bioreactor experiment.

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Soil organic matter has been well acknowledged as a natural solution to mitigate climate change and to maintain agricultural productivity. Microbial necromass is an important contributor to soil organic carbon (SOC) storage, and serves as a resource pool for microbial utilization. The trade-off between microbial births/deaths and resource acquisition might influence the fate of microbial necromass in the SOC pool, which remains poorly understood.

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  • Peanuts are a special type of plant that grow their seeds underground and are packed with nutrients like oil and protein.
  • Scientists found a gene that helps protect peanut seeds from diseases in the soil, focusing on parts of the seed called pericarp and testa.
  • By using this gene, they hope to make peanuts stronger against soil diseases, which can help in farming and ensure more food is available for everyone.
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Particulate matter pollution (PMP) has been identified as a substantial contributor to cancer. However, accurately delineating the evolving trends in cancer burden attributable to PMP remains an ongoing challenge. The 1990-2019 disability-adjusted life years (DALYs) were used for cancers attributable to PMP from the Global Burden and Disease Study (GBD) 2019, including ambient particulate matter pollution (APMP) and household air pollution from solid fuels (HAP).

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Objective: The current study aimed to explore the relationships between urinary metals and vital capacity index (VCI) in 380 children and adolescents in Northeast China using a variety of statistical methods.

Methods: A cross-sectional survey was conducted among 380 children and adolescents in Liaoning Province, China. To assess the relationships between urinary metals and VCI, Elastic-net (ENET) regression, multivariate linear regression, weighted quantile sum (WQS), bayesian kernel machine regression (BKMR) and quantile-based g computation (qgcomp) were adopted.

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Assessing the risk of human pathogens in the environment is crucial for controlling the spread of diseases and safeguarding human health. However, conducting a thorough assessment of low-abundance pathogens in highly complex environmental microbial communities remains challenging. This study compiled a comprehensive catalog of 247 human-pathogenic bacterial taxa from global biosafety agencies and identified more than 78 million genome-specific markers (GSMs) from their 17,470 sequenced genomes.

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Low-dosage nitrate pollutants can contribute to eutrophication in surface water bodies, such as lakes and reservoirs. This study employed assembled denitrifying bacterial-fungal communities as bio-denitrifiers, in combination with zero-valent iron (ZVI), to treat micro-polluted water. Immobilized bacterial-fungal mixed communities (IBFMC) reactors demonstrated their ability to reduce nitrate and organic carbon by over 43.

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The inoculum has a crucial impact on bioreactor initialization and performance. However, there is currently a lack of guidance on selecting appropriate inocula for applications in environmental biotechnology. In this study, we applied microbial electrolysis cells (MECs) as models to investigate the differences in the functional potential of electroactive microorganisms (EAMs) within anodic biofilms developed from four different inocula (natural or artificial), using shotgun metagenomic techniques.

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Complex networks describe a wide range of systems in nature and society. As a fundamental concept of graph theory, the path connecting nodes and edges plays a vital role in network science. Rather than focusing on the path length or path centrality, here we draw attention to the path multiplicity related to decision-making efficiency, which is defined as the number of shortest paths between node pairs and thus characterizes the routing choice diversity.

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  • The Microbiome Protocols eBook (MPB) connects researchers by providing essential protocols for microbiome experiments and data analysis.
  • The first edition, released in 2020, included 152 well-organized protocols and received positive feedback from the scientific community.
  • Researchers are now encouraged to contribute their own protocols for the upcoming 2nd edition to help further microbiome research.
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