Warming and wetting-induced soil acidification triggers methanotrophic diversity loss and species turnover in an alpine ecosystem

Li, Chaonan; Wang, Changting; Zou, Ping; Xu, Lin; Liao, Haijun; Lan, Nan; Lei, Li; Xiong, Wenjun; Kong, Weidong; Wang, Junming; Li, Xiangzhen

doi:10.1016/j.catena.2023.107700

CATENA

2024

DOI: 10.1016/j.catena.2023.107700

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Warming and wetting-induced soil acidification triggers methanotrophic diversity loss and species turnover in an alpine ecosystem

Chaonan Li,

Changting Wang,

Ping Zou

et al.

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The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps

Li,

Liu,

et al. 2024

FEMS Microbiology Ecology

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Many R packages provide statistical approaches for elucidating the diversity of soil microbes, yet they still struggle to visualize microbial traits on a geographical map. This creates challenges in interpreting microbial biogeography on a regional scale, especially when the spatial scale is large or the distribution of sampling sites is uneven. Here, we developed a lightweight, flexible, and user-friendly R package called microgeo. This package integrates many functions involved in reading, manipulating, and visualizing geographical boundary data; downloading spatial datasets; and calculating microbial traits and rendering them onto a geographical map using grid-based visualization, spatial interpolation, or machine learning. Using this R package, users can visualize any trait calculated by microgeo or other tools on a map and can analyze microbiome data in conjunction with metadata derived from a geographical map. In contrast to other R packages that statistically analyze microbiome data, microgeo provides more-intuitive approaches in illustrating the biogeography of soil microbes on a large geographical scale, serving as an important supplement to statistically driven comparisons and facilitating the biogeographic analysis of publicly accessible microbiome data at a large spatial scale in a more convenient and efficient manner. The microgeo R package can be installed from the Gitee (https://gitee.com/bioape/microgeo) and GitHub (https://github.com/ChaonanLi/microgeo) repositories. Detailed tutorials for the microgeo R package are available at https://chaonanli.github.io/microgeo.

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The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps

Li,

Liu,

et al. 2024

FEMS Microbiology Ecology

Self Cite

View full text Add to dashboard Cite

show abstract

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Warming and wetting-induced soil acidification triggers methanotrophic diversity loss and species turnover in an alpine ecosystem

Cited by 1 publication

References 42 publications

The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps

The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps

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