DOI: 10.5281/zenodo.11648114
title: Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau

description:  



This project repository associated with the following manuscript:




Luyao Kang, Yutong Song, Rachel Mackelprang, Dianye Zhang, Shuqi Qin, Leiyi Chen, Linwei Wu, Yunfeng Peng and Yuanhe Yang*. Metagenomic insights into microbial community structure and metabolism in alpine permafrost on the Tibetan Plateau.
description: Permafrost, characterized by its frozen soil, serves as a unique habitat for diverse microorganisms. Understanding these microbial communities is crucial for predicting the response of permafrost ecosystems to climate change. However, large-scale evidence regarding stratigraphic variations in microbial profiles remains limited. Here, we analyze microbial community structure and functional potential based on 16S rRNA gene amplicon sequencing and metagenomic data obtained from a ∼1,000 km permafrost transect on the Tibetan Plateau. We find that microbial alpha diversity declines and beta diversity increases down the soil profile. Microbial assemblages are primarily governed by dispersal limitation and drift; the importance of drift decreases and that of dispersal limitation increases with soil depth. Moreover, genes related to reduction reactions (e.g., ferric iron reduction, dissimilatory nitrate reduction, and denitrification) are enriched in the subsurface and permafrost layers. In addition, microbial groups involved in alternative electron accepting processes are more diverse and contribute highly to community-level metabolic profiles in the subsurface and permafrost layers, likely reflecting the lower redox potential and more complicated trophic strategies for microorganisms in deeper soils. Overall, these findings provide comprehensive insights into the large-scale stratigraphic profiles of microbial community structure and functional potentials in permafrost regions.
description: ├── data1
    ├── 16S
        ├── metadata.txt                                            <--metadata including the climatic, vegetable for samples
        ├── otus.nwk                                                <--phylogenetic tree for ASVs
        ├── otutab.txt                                              <--ASV table
        ├── otutab_rare.txt                                         <--Rarefy ASV table
        └── taxonomy.txt                                            <--Taxonomic table
    ├── Functional genes
        ├── eggnog.KEGG_ko.raw.counts.txt                           <-- KEGG KO table with row counts
        └── eggnog.KEGG_ko.raw.tpm.txt                              <-- KEGG KO table with TPM tansformation
    ├── Metabolic
        ├── Metabolic_Sankey_diagram                                <-- Resuts of metabolic weighted scores for the metagenomic assembly genomes 
            ├── Metabolic_Sankey_diagram_sur_input_rare.txt         <-- The contributions of microbial groups to individual biogeochemical processes in surface layer
            ├── Metabolic_Sankey_diagram_sub_input_rare.txt         <-- The contributions of microbial groups to individual biogeochemical processes in subsurface layer
            └── Metabolic_Sankey_diagram_pl_input_rare.txt          <-- The contributions of microbial groups to individual biogeochemical processes in permafrost layer 
        ├── bin_abundance_table.tab                                 <-- Abundance table for each bin
        ├── METABOLIC_result.xlsx                                   <-- Summary of the presence/absence of functional genes on each genome
        ├── MW_score_result.csv                                     <-- Resuts of metabolic weighted scores for the metagenomic assembly genomes
        └── tax.txt                                                 <-- Taxnomic identificcation for each bin
    └── Supplementary Data
        ├── Supplementary Data 1.xlsx                               <-- Characteristics of recovered metagenomic assembly genomes (MAGs)
        ├── Supplementary Data 2.xlsx                               <-- Custom selected KEGG genes used to define metabolic pathways
        └── Supplementary Data 3.xlsx                               <-- The metabolic profiles of all MAGs annotated by METABOLIC v4.0
└── script
    ├── read_data.R                                                 <-- codes for data input
    ├── amplicon_analysis.Rmd                                       <-- microbial diversity and composition analysis based on the amplicon data
    ├── SPEC-OCCU.Rmd                                               <-- specificity-occupancy analysis
    ├── env_effect_on_diver_comp.Rmd                                <-- test the environmentaL effects on the microbial community
    ├── iCAMP_analysis.R                                            <-- null model analysis using iCAMP framework
    ├── selected_ko_analysis.Rmd                                    <-- codes for the difference analysis in genes involved in C, N, S, and other elements among soil layers
    └── Metagenome_analysis.Rmd                                     <-- codes for reproducing the results about the MAGs


All .html files in script folder are produced by Rmarkdown files (.Rmd files) using knitr package in R.