Xiaoyu Cheng

Xiaoyu Cheng BSc

PhD Student
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Visiting Address

Droevendaalsesteeg 10
6708 PB Wageningen

+31 (0) 317 47 34 00

The Netherlands


I concentrate more on the methane functional taxa, long-term monitoring of greenhouse gas, and would like to evaluate the consumption capacity of methane in karst caves, which are proposed as a a potential methane sink for atmospheric methane.


2021.11- 2023. 1
Joint PhD in Microbial Ecology, the Netherlands Institute of Ecology, the Netherlands. (Advisor: Dr Paul L.E. Bodelier)

2017. 9- to date
PhD in Environmental Science and Engineering, China University of Geosciences, China. Thesis: Spatial and temporal distribution of methane functional taxa in Heshang Cave and their responses to environmental changes. (Advisor: Prof. Hongmei Wang)

2013.9- 2017.6
BSc in Bioscience, China University of Geosciences, China. Thesis: Actinobacterial diversity in weathered rock of Heshang Cave and its role of biomineralization. (Advisor: Prof. Hongmei Wang)

Research groups



  • 2013–2017
    bachelor, China University of Geosciences
  • 2017–Present
    doctor, China University of Geosciences

PhD students

China University of Geosciences
Promotors and Copromotors: Prof. Hongmei Wang, dr. Paul L.E. Bodelier


Key publications

  • Science of the Total Environment

    Contrasting bacterial communities and their assembly processes in karst soils under different land use

    Xiaoyu Cheng, Yuan Yun, Hongmei Wang, Liyuan Ma, Wen Tian, Baiying Man, Chaoyang Liu
    Structure and assembly processes of soil bacterial communities under different land use at karst areas remained poorly understood to date. To address this issue, soil samples from arable land and pristine forest over a karst cave, located in the acid rain impacted area, Hubei province, were collected and subjected to high-throughput sequencing and multivariate statistical analysis. Bacterial communities and functions remarkably distinguished between soils under different land use. Both edaphic properties (the content of SO4 2−, C/N, pH, TN) and weathering processes, such as Si concentration, Mg/Al and Ca/Al, significantly impacted on soil bacterial community structures. Variable selections were predominant ecological processes, and pH and SO4 2− concentrationwere of significance in community assembly. Random molecular ecological network analysis revealed a more stable and complex microbial network in the forest ecosystem, which can quickly response to environmental change. Forest soil bacteria were mainly phototrophs, involving in C and N cycles, whereas those in arable soils were mainly chemoheterotrophs, capable of degrading organic fertilizers due to anthropogenic activities as confirmed by the analysis of keystone taxa, indicators and functional prediction. These results reveal that land use constructed soil bacterial communities in different aspects such as the structure, potential functions, microbial interactions and correlations with environmental variables. To our knowledge, this is the first report on bacterial community assembly in karst soils under different land usewhich enhances our understanding about howland use impact on microbial interaction and community assembly processes.
  • Microbiology Spectrum

    USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves

    Xiao-Yu Cheng, Xiao-Yan Liu, Hong-Mei Wang, Chun-Tian Su, Rui Zhao, Paul L. E. Bodelier, Wei-Qi Wang, Li-Yuan Ma, Xiao-Lu Lu
    Karst caves have recently been demonstrated to act as a sink for atmospheric methane, due in part to consumption by microbes residing in caves that can oxidize methane at atmospheric levels. However, our knowledge about the responsible atmospheric methane-oxidizing bacteria (atmMOB) in this vast habitat remains limited to date. To address this issue, weathered rock samples from three karst caves were collected in Guilin City and subjected to high-throughput sequencing of pmoA and 16S rRNA genes. The results showed that members of the high-affinity upland soil cluster (USC), especially upland soil cluster gamma (USCg), with absolute abundances of 104 to 109 copies  g21 dry sample, dominated the atmMOB communities, while Proteobacteria and Actinobacteria dominated the overall bacterial communities. Moreover, USCg was a keystone taxon in cooccurrence networks of both the atmMOB and the total bacterial community, whereas keystone taxa in the bacterial network also included Gaiella and Aciditerrimonas. Positive links overwhelmingly dominated the cooccurrence networks of both atmMOB and the total bacterial community, indicating a consistent response to environmental disturbances. Our study shed new insights on the diversity and abundances underlining atmMOB and total bacterial communities and on microbial interactions in subterranean karst caves, which increased our understanding about USC and supported karst caves as a methane sink.
  • Environmental Pollution

    Different responses of bacteria and fungi to environmental variables and corresponding community assembly in Sb-contaminated soi

    Weiqi Wang, Hongmei Wang, Xiaoyu Cheng, Mengxiaojun Wu, Yuyang Song, Xiaoyan Liu, Prakash C.Loni, Olli H.Tuovinen
    Bacterial communities in antimony (Sb) polluted soils have been well addressed, whereas the important players fungal communities are far less studied to date. Here, we report different responses of bacterial and fungal communities to Sb contamination and the ecological processes controlling their community assembly. Soil samples in the Xikuangshan mining area were collected and subjected to high through-put sequencing of 16S rRNA and ITS1 to investigate bacterial and fungal communities, respectively, along an Sb gradient. Sb speciation in the soil samples and other physicochemical parameters were analyzed as well. Bacterial communities were dominated by Deltaproteobacteria in the soil with highest Sb concentration, whereas Chloroflexi were dominant in the soil with lowest Sb concentration. Fungal communities in high-Sb soils were predominated by unclassified Fungi, whilst Leotiomycetes were dominant in low-Sb soil samples. Multivariate analysis indicated that Sb, pH and soil texture were the main drivers to strongly impact microbial communities. We further identified Sb-resistant microbial groups via correlation analysis. In total, 18 bacterial amplicon sequence variants (ASVs) were found to potentially involve in biogeochemical cycles such as Sb oxidation, sulfur oxidation or nitrate reduction, whereas 12 fungal ASVs were singled out for potential heavy metal resistance and plant growth promotion. Community assembly analysis revealed that variable selection contributed 100% to bacterial community assembly under acidic or high Sb concentration conditions, whereas homogeneous selection dominated fungal community assembly with a contribution over 78.9%. The community assembly of Sb-resistant microorganisms was mainly controlled by stochastic process. The results offer new insights into microbial ecology in Sb-contaminated soils, especially on the different responses of microbial communities under identical environmental stress and the different ecological processes underlining bacterial and fungal community assembly.
  • Frontiers in Microbiology

    The characterization of microbiome and interactions on weathered rocks in a subsurface karst cave, central China

    Yiheng Wang, Xiaoyu Cheng, Hongmei Wang, Jianping Zhou, Xiaoyan Liu and Olli H. Tuovinen
    Karst caves are natural oligotrophic subsurface biosphere widely distributed in southern China. Despite of the progress in bacterial and fungal diversity, the knowledge about interactions among bacteria, fungi and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxylapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations offer new knowledge about microbial interactions among bacteria, fungi and minerals in the subterranean biosphere.