Yu Shi

• Dr
• Professor at Henan University

Climate warming and anthropogenic activities have led to an increase in the prevalence of non‐native plants in mountainous regions that previously exhibited limited occurrences. This phenomenon has resulted in detrimental effects on endemic plants and ecosystem functions. However, the variation in traits of non‐native plants that successfully sprea...

The Tibetan Plateau contains the world’s largest area of alpine wetlands, where coexisting water and sediment environments provide habitats for multitrophic microbial communities. However, the microbial food web (MFW) of coexisting water and sediment in wetland ecosystems and their responses to environmental changes remain unclear. In this study, w...

Long‐term climatic differences shape the ecological memory of soil bacterial communities, which refers to the ability of past events to influence current environmental responses. However, their ecological mechanisms and consequences for bacterial responses to current environmental changes remain largely unknown, particularly in terms of temporal dy...

Ecosystem multifunctionality (EMF) is influenced by rhizosphere microorganisms, and understanding how they regulate EMF has been an intriguing process to date. Here, amplicon sequencing was employed to investigate the diversity, assembly processes, and co-occurrence networks of rhizosphere bacteria and fungi in the topsoil (0-20 cm) across eight co...

Mulberries (genus Morus; Moraceae) hold significant economic value in sericulture and have great potential in the horticultural industry, food industry, and human health arenas worldwide. Since the advent of the genomic era, biological macromolecules of Morus species such as whole genome and plastome sequences have been reported, but mitochondrial...

Aboveground herbivores and belowground microbes have been interacting via terrestrial plants since their origins , but whether and how feeding guild affects root bacterial-fungal community structure, diversity, and co-occurrence patterns remains poorly understood. Here we examined the effect of chewing and sucking herbivory on bacterial and fungal...

Background Tiarella polyphylla D. Don has been traditionally used to cure asthma and skin eruptions. However, the sequence and the structure of the mitogenome of T. polyphylla remained elusive, limiting the genomic and evolution analysis based on the mitogenome. Results Using a combination of Illumina and Nanopore sequencing reads, we de novo asse...

Nitrogen (N) deposition affects ecosystem functions crucial to human health and well‐being. However, the consequences of this scenario for soil ecosystem multifunctionality (SMF) in forests are poorly understood. Here, we conducted a long‐term field experiment in a temperate forest in China, where N deposition was simulated by adding N above and un...

Foliar herbivory is known to directly affect phyllosphere microbiomes through altering plant phenotypes. However, how plant evolutionary responses to herbivory shape phyllosphere microbiomes is unclear. Here we use different invasive populations of the plant Ambrosia artemisiifolia that vary in reassociation timespan with a native specialist herbiv...

Insect herbivory can affect interactions between plants and arbuscular mycorrhizal (AM) fungi through herbivore‐modified root carbon pools, while the specific metabolic changes underlying fungal responses to herbivory are poorly understood. Here we explored the impacts of foliar herbivory and mechanical wounding on AM colonisation and AM community...

Pathogen genetic diversity varies in response to environmental changes. However, it remains unclear whether plant barriers to invasion could be considered a genetic bottleneck for phytopathogen populations. Here, we implement a barcoding approach to generate a pool of 90 isogenic and individually barcoded Ralstonia solanacearum strains. We used 90...

Coastal wetlands contribute to the mitigation of climate change through the sequestration of “blue carbon”. Microbial necromass, lignin, and glycoproteins (i.e., glomalin-related soil proteins (GRSP)), as important components of soil organic carbon (SOC), are sensitive to environmental change. However, their contributions to blue carbon formation a...

Phytopathogenic fungi threaten global food security but the ecological drivers of their global diversity and biogeography remain unknown. Here, we construct and analyse a global atlas of potential phytopathogenic fungi from 20,312 samples across all continents and major oceanic island regions, eleven land cover types, and twelve habitat types. We s...

As productive and essential ecosystems, coastal wetlands have experienced increased environmental impacts such as saltwater intrusion and eutrophication, resulting in significant shifts in microbially mediated ecosystem functions, such as carbon sequestration and nutrient transformations. The soil microbial respiration, a primary process in the tra...

Wheat sheath blight is a soil-borne fungal disease caused by Rhizoctonia cerealis and is a serious threat to wheat worldwide. A microbial fungicide is a promising alternative to a chemical fungicide for wheat disease control. In this study, strain RB5 against R. cerealis was isolated from wheat rhizosphere soil, which was identified as Pseudomonas...

Background Temperature shapes microbial functional genes associated with carbon (C) cycles. However, the effects of temperature on microbial C cycle genes associated with carcass-contaminated water remains poorly understood. To fill this gap, we explored the variation of microbial carbon cycling genes in polluted water caused by animal corpse decay...

Introduction Aquatic ecosystems in floodplains provide homes for a variety of active bacterial populations. However, the coexistence pattern of bacterial communities of water and sediment in these ecosystems is unclear. Methods In the present study, Illumina Mi-Seq sequencing were to assess bacteria's co-occurrence patterns in the water and sedime...

Microbial inoculation was an effective way to improve product quality of composting and solve traditional composting shortage. However, the effect mechanism of microbial inoculation on compost microorganisms remains unclear. Here, Shifts in bacterial community, metabolic function and co-occurrence network during the primary and secondary fermentati...

Release from enemies can lead to rapid evolution in invasive plants, including reduced metabolic investment in defence. Conversely, reassociation with enemies leads to renewed evolution of defence, but the potential costs of this evolution are poorly documented. We report increased resistance of the invader Ambrosia artemisiifolia after reassociati...

Interactions between plants and arbuscular mycorrhizal fungi (AMF) are strongly affected by soil phosphorus (P) availability. However, how P forms impact rhizosphere AMF diversity, community composition, and the co-occurrence network associated with native and invasive plants, and whether these changes in turn influence the invasiveness of alien sp...

Introduction Rhizosphere microbes perform critical functions for their hosts, and their structure is strongly influenced by vegetation type. Although studies on the effects of vegetation on rhizosphere microbial community structure have been conducted at large and global environment scales, studies at local environment scales would eliminate numero...

Rational cropping maintains high soil fertility and a healthy ecosystem. Soil microorganism is the controller of soil fertility. Meanwhile, soil microbial communities also respond to different cropping patterns. The mechanisms by which biotic and abiotic factors were affected by different cropping sequences remain unclear in the major grain-produci...

A workflow has been compiled as “qcmi” R package—the quantifying community‐level microbial interactions—to identify and quantify the putative biotic associations of microbes at the community level from ecological networks.

Long-term deposition of atmospheric pollutants emitted from coal combustion and their effects on the eco-environment have been extensively studied around coal-fired power plants. However, the effects of coal-fired power plants on soil microbial communities have received little attention through atmospheric pollutant deposition and coal-stacking. He...

Understanding how the network structure of plant and microbiota interactions differ along ecological gradients is of great interest. We studied network patterns at 60 sites across the Tibetan Plateau, representing a gradient in both precipitation and plant species richness. The number of fungal OTUs that were uniquely connected to each plant specie...

Introduction Climate change and anthropogenic activities are the greatest threats to floodplain ecosystems. A growing body of literature shows that floodplain ecosystems have experienced increased chemical fertilizer and pesticide loads, which will disturb the above and belowground ecosystems. However, we lack knowledge regarding the effects of suc...

Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody...

Soil microbiomes are characterized by their composition and networks, which are linked to soil nitrogen (N) availability. In nature, inorganic N dominates at one end and organic N dominates at the other end along soil N gradients; however, little is known about how this shift influences soil microbiome composition and co-occurrence networks, as wel...

Coastal reclamation is a global threat to coastal wetland ecosystems, but the impacts of coastal reclamation on belowground biodiversity and their consequences for ecosystem nutrient cycling remain poorly understood. In this study, we examined soil bacterial communities, bacterial co-occurrence pattern and soil multi-nutrient cycling index after na...

The floodplain ecosystem is crucial for facilitating or regulating regional ecological functions (biodiversity conservation, contamination filtration, soil erosion prevention, flood control and so on). The intensified use of floodplains may significantly influence the soil's potential to handle ecosystem functions by changing key biotic groups such...

Black soils (Mollisols) are among the most important soil resources for crop production and food security. In China, they are mainly distributed in the northeastern region. To investigate soil antibiotic resistance distribution patterns and monitor soil quality, we randomly chose nine corn fields in Northeast China and analyzed the antibiotic resis...

Archaeal ammonia oxidizers (AOA) are important in converting ammonia into nitrates in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has been poorly understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogen...

Microbial community assembly contributes to the restoration and rehabilitation of the disturbed ecosystems. However, the viral assembly mechanism and its difference from bacterial communities under soil contamination have not been previously reported. Here, clean, light and heavy chromium (Cr)-contaminated soils were collected from two Cr slag site...

Revegetation is an important restoration approach after reclamation in coal mining subsidence area. However, few studies have paid attention to the impacts of different vegetation species on soil fertility and bacterial community composition in the reclamation area filled with fly ash for a long time. In this study, soil fertility and bacterial com...

Soil microeukaryotes play a pivotal role in soil nutrient cycling and crop growth in agroecosystems. However, knowledge of microeukaryotic community distribution patterns, assembly processes, and co-existence networks is greatly limited. Here, microbial eukaryotes in bulk and rhizosphere soils of the North China Plain were investigated. The results...

Extracellular DNA (eDNA) and intracellular DNA (iDNA) extensively exist in both terrestrial and aquatic environment systems and have been found to play a significant role in the nutrient cycling and genetic information transmission between the environment and microorganisms. As inert DNA sequences, eDNA is able to present stability in the environme...

There has been little study on the biogeographical patterns of microbial co-occurrence, especially in agricultural soils. Here we investigated the biogeographical patterns and major drivers of co-occurrence network topological structure, and the relative abundance of keystone taxa for soil bacterial and fungal communities using high-throughput sequ...

Theory and experiments support that plant invasions largely impact aboveground biodiversity and function. Yet, much less is known on the influence of plant invasions on the structure and function of the soil microbiome of coastal wetlands, one of the largest major reservoirs of biodiversity and carbon on Earth. We studied the continental‐scale inva...

Background: Keystone genes exert great influence on maintaining microbiome stability and functional recovery irrespective of their environmental abundance. Elucidating the effects of environmental stresses on their variation is vital for identifying the recovery potential of ecosystems and regulating microbial adaptation within. Extracellular and i...

The soil microbial community is an essential biotic component in plant-soil feedback processes that can alter plant fitness, growth, and reproduction. Further, they may exert an influence on plants by forming a microbial association network. Accordingly, pronounced changes in the soil microbial community induced by climate warming is vital when eva...

Insect herbivores can adversely impact terrestrial plants throughout ontogeny and across various ecosystems. Simultaneously, the effects of foliar herbivory may extend belowground, to the soil microbial community. However, the responses in terms of the diversity, assembly, and stability of rhizosphere fungi to aboveground herbivory remain understud...

Revealing the responses of rare and abundant bacteria to environmental change is crucial for understanding microbial community assembly and ecosystem function. However, both the environmental adaptability and the ecological assembly processes exhibited by rare and abundant soil bacteria remain poorly understood. Here we investigated the assembly pr...

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of b...

Studies of methane-oxidizing bacteria are updating our views of their composition and function in paddy and natural wetlands. However, few studies have characterized differences in the methane-oxidizing bacterial communities between paddy and natural wetlands. Here, we conducted a 13 C stable isotope-probing experiment and high-throughput sequencin...

Viruses significantly influence local and global biogeochemical cycles and help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance and degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched in organochl...

Metagenomic sequencing revealed the variation of functional genes in the microbial community in soil and earthworm gut with increasing vanadium concentrations, which provided a new insight to explore the effect of vanadium stress on microbial community assembly from the perspective of functional genes. Our results reinforced the view that functiona...

Soil aggregate structure mediates the impacts of long-term fertilization on soil organic carbon (OC) accrual and microbiome. Recent studies have shown that microbiome structure and functioning are driven by keystone taxa irrespective of their abundance. However, whether and how carbon accrual relates to keystone taxa at the aggregate level remains...

Aim An important research question in ecology is how climate and the biodiversity of aboveground plants and belowground microbiomes affect ecosystem functions such as nutrient pools. However, little is studied on the concurrent role of above‐ and belowground species composition in shaping the spatial distribution patterns of ecosystem functions acr...

The elevational distributions of bacterial communities in natural mountain forests, especially along large elevational gradients, have been studied for many years. However, the distributional patterns that underlie variations in soil bacterial communities along small-scale elevational gradients in urban ecosystems are not yet well understood. Using...

It is well known that the interactive effect of nitrogen (N) fertilizer and plant root would cause distinct microbial communities and associations between root surface and bulk soil. However, little is known about the continuous changes of these microbial parameters along an increasing distance from roots under different N forms. Ammonium (NH4⁺) an...

Fertilization has been shown to exert a significant influence on soil microorganisms and directly and indirectly influences plant growth and survival in agroecosystems. However, it is unknown whether fertilization affects endophytic microbial communities, which are ubiquitous and intimately associated with plant growth and health. Herein, we invest...

Soil pH plays a pivotal role in shaping microbial diversity and community composition in terrestrial ecosystems. Soil microbes clearly do not exist independently and instead form complex interaction networks, but little is known about the effect of soil pH upon those microbial co-occurrence networks. In this study, 62 alkaline and 61 acidic soil sa...

Soil fungi play an important role in promoting nutrient cycling and maintaining ecosystem stability. Yet, there has been little understanding of how fungal co-occurrence networks differ along elevational climate gradients, a topic of interest to both macroecology and climate change studies. Based on high-throughput sequencing technology, we investi...

Aim Most existing studies that examined the biotic mechanisms of ecosystem stability have focused on aboveground biodiversity. Whether and how belowground biodiversity affects the stability of natural ecosystems is largely unknown. In the present study, we investigated the relationships between above‐ and belowground biodiversity and the temporal s...

Glacier-fed aquatic ecosystems provide habitats for diverse and active bacterial communities. However, the environmental vulnerabilities of co-existing water and sediment bacterial communities in these ecosystems remain unclear. Here, 16S rRNA gene sequencing was used to investigate co-existing bacterial communities in paired water and sediment sam...

Earthworms play an important role in the organic matter decomposition in terrestrial ecosystems. Earthworms interact directly with the microorganisms to affect the organic matter decomposition via gut transit, i.e., the digestion and assimilation of organic matter in the foregut and midgut and its excretion by the hindgut. However, how the microbia...

Nitrogen (N) enrichment has been reported to affect the soil bacteria community in natural temperate grasslands. However, it remains unknown how the bacteria community responds to N enrichment in degraded grasslands. Here, we established multi‐level N enrichment experiments in temperate grasslands under non‐degraded (ND), moderately degraded (MD),...

The evolution of contact performance of electrical connectors, as an expression of service performance, played a significant role in various electronic equipment or system. However, very few methods had been used to detect the evolution of contact performance effectively and accurately. Hence, in this research, reliability accelerated testing was c...

Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, the trends of co-occurrence networks across similar gradients remain elusive. Here, we constructed co-occurrence networks for fungal community along a 2300 m elevation gradient on Mt Norikura, Japan, hypothesizing a prog...

Urban soils harbor billions of bacterial cells and millions of species. However, the distribution patterns and assembly processes of bacterial communities remain largely uncharacterized in urban soils. It is also unknown if we can use the bacteria to track soil sources to certain cities and districts. Here, Illumina MiSeq sequencing was used to sur...

In environmental forensic investigations, soil is often considered as the evidence associated with a crime scene in court. A major challenge is minimizing the uncertainty in linking sets of matched soil to a suspected offender. This article examined the potential methods of analyzing soil bacterial communities via high throughput sequencing, which...

Microbial taxa within complex ecological networks can be classified by their universal roles based on their level of connectivity with other taxa. Highly connected taxa within an ecological network (kinless hubs) are theoretically expected to support higher levels of ecosystem functions than less connected taxa (peripherals). Empirical evidence of...

Background: Ammonium (NH4⁺) and nitrate (NO3⁻) are two major inorganic nitrogen (N) forms available for plant growth. Soil microbes affect the availability and transformation of these N forms in the rhizosphere, and this affects the N-use efficiency of plants. However, little is known about the responses of the rhizosphere bacterial community struc...

Soil fungi represent a major component of below‐ground biodiversity that determines the succession and recovery of forests after disturbance. However, their successional trajectories and driving mechanisms following wildfire remain unclear. We examined fungal biomass, richness, composition and enzymes across three soil horizons (Oe, A1 and A2) alon...

The last decade has witnessed an explosion of interest in the cutting load analysis for multifarious tools, especially in experiments and classical 2D model. But the cutting load model for broaching tool with grooves is still not clear and functional. In this paper, a new cutting load model applied to the broaching tool, which has some grooves on t...

Depth patterns of soil microbial distribution have not been well characterized and little is known about the balance between stochastic and deterministic processes in shaping microbial community through soil profiles. We examined how the composition, diversity, and assembly processes of bacterial communities change to a depth of 4 m along three cor...

Understanding the processes that regulate communities of microorganisms is a key issue and focus in microbial ecology. Although fungi play a critical role in soil biogeochemical cycling, their community assembly processes remain largely unknown, especially in agricultural soils. In this study, we investigated the relative importance of five communi...

Microbial co‐occurrence is a ubiquitous ecological phenomenon, yet we know surprisingly little of the relative importance of bacteria, fungi, and archaea for structuring their co‐occurrence network, especially in natural ecosystems. Here, we present a visualization of the soil microbial co‐occurrence network pattern based on a sampling from across...

The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production. Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services, thus providing valuable insights to improve food production. The North China Plain (NCP) i...

It has been widely accepted that there is a distance‐decay pattern in the soil microbiome. However, few studies have attempted to interpret the microbial distance‐decay pattern from the perspective of quantifying underlying processes. In this study, we examined the processes governing bacterial community assembly at multiple spatial scales in maize...