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Assembly Processes and Biogeographical Characteristics of Soil Bacterial Sub-communities of Different Habitats in Urban Green Spaces

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Abstract

The process of urbanization is one of the most important human-driven activities that reshape the natural distribution of soil microorganisms. However, it is still unclear about the effects of urbanization on the different taxonomic soil bacterial community dynamics. In this study, we collected soil samples from highly urbanized the regions of Yangtze River Delta, Beijing–Tianjin–Hebei in China, to explore the bio-geographic patterns, assembly processes, and symbiotic patterns of abundant, moderate, and rare bacterial communities. We found that the number of moderate and rare taxa species were lower than that of abundant taxa, but their α-diversity index was higher than abundant taxa. Proteobacteria, Acidobacteria, Actinobacteria, Bacterioidetes, and Chloroflexi were the dominant phylum across all three sub-communities. And the β-diversity value of rare taxa was significantly higher than those of moderate and abundant taxa. Abundant, moderate, and rare sub-communities showed a weak distance–decay relationship, and the moderate taxa had the highest turnover rate of microbial geography in the context of urbanization. Diffusion limitation was the dominant process of soil bacterial community assembly. The co-occurrence networks of abundant, moderate, and rare taxa were dominated by positive correlations. The network of moderate taxa had the highest modularity, followed by abundant taxa. The main functions of the abundant, moderate, and rare taxa were related to Chemoheterotrophy and N transformations. Redundancy analysis showed that the dispersal limitation, climate, and soil properties were the main factors dominating bio-geographic differences in soil bacterial community diversity. We conclude that human-dominated urbanization processes have generated more uncertain survival pressures on soil bacteria, which resulted in a stronger linkage but weak bio-geographic variation for soil bacteria. In the future urban planning process, we suggest that such maintenance of native vegetation and soil types should be considered to maintain the long-term stability of local microbial ecosystem functions.

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Data Availability

The 16S rRNA gene sequences from this experiment were submitted to the NCBI sequence read archive and are available under BioProject number PRJNA841243.

Code Availability

Not applicable.

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Funding

This work was supported by The Natural Science Foundation of China [No.32060011, 32160007]; “Hundred” Talent Projects of Guizhou Province [Qian Ke He [2020] 6005]; the Key Areas of Research and Development Program of Guangdong Province [No. 2018B020205003]; Construction Program of Biology First-class Discipline in Guizhou [GNYL [2017]009].

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Authors and Affiliations

  1. Institute of Fungus Resources, Department of Ecology, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025, Guizhou, China

    Yulian Ren, Qiuyu Shao, Wei Ge, Xin Li, Haiyan Wang, Chunbo Dong & Yanfeng Han

  2. School of Biological Sciences, Guizhou Education University, Guiyang, 550018, Guizhou, China

    Yanwei Zhang

  3. TERI-Deakin Nano Biotechnology Centre, The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi, 110003, India

    Sunil Kumar Deshmukh

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YH and YZ: conceptualization and funding acquisition. YR, QS, WG, XL, and HW: data acquisition. CD, QS, and WG: formal analysis. YR: writing the first draft. YH, YZ, and DSK: writing, reviewing, and editing the manuscript. All authors have read and agreed to the published version of the manuscript.

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Ren, Y., Shao, Q., Ge, W. et al. Assembly Processes and Biogeographical Characteristics of Soil Bacterial Sub-communities of Different Habitats in Urban Green Spaces. Curr Microbiol 80, 309 (2023). https://doi.org/10.1007/s00284-023-03428-4

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