DOI: 10.5061/dryad.6wwpzgn52
title: Unraveling community adaption and survival strategy of soil microbiome under vanadium stress in nationwide mining environments

description: The vanadium (V) smelters soil harbor wide ranges of microorganisms, whose
 survival relies on their metabolic activities under
 stress. Nonetheless, the characteristics and functions of soil
 microbiome in V mining environments have not been recognized at a
 continental scale. This study investigates microbial diversity, community
 assembly and metabolic traits of soil microbiome across 90 V smelters in
 China. A decrease in alpha diversity is observed, along with
 community variation, which is also jointly explained by other
 environmental, climatic and geographic factors. Null model shows that V
 promotes homogeneous selection. V also mediates co-occurrence
 patterns, with increased positive interspecific associations under higher
 V concentrations (＞559.6 mg/kg), e.g., f_Gemmatimonadaceae, Nocardioides,
 Micromonospora, Rubrobacter. In addition, 67 metagenome assembled genomes
 are retrieved via metagenomic analysis. The metabolic pathways of
 keystone taxa are disentangled to reveal their putative involvement in the
 V(V) reduction process. Nitrate and nitrite reductase (nirK, narG), and
 mtrABC are found to be taxonomically affiliated with Micromonospora. sp,
 FEN-1250. sp, Nocardioides. sp, etc. Additionally, reverse citric acid
 cycle (rTCA) serves the main carbon fixation pathway, synthetizing
 alternative energy for putative V reducers, highlighting a synergistic
 relationship between autotrophic and heterotrophic processes to support
 the microbial survival. Our findings comprehensively reveal the driving
 forces for soil community variation under V stress, suggesting the robust
 strategies adopted by indigenous microorganisms to alleviate V impact,
 which can be exploited for bioremediation application.
description: The datasets herein serve as the basis to
 perform data analysis for this article. Physicochemical data was obtained
 from actual measurements, which was used to perform analysis to uncover
 the key driving factors for shaping the community structure, and
 implemented in models such as Variation partitioning analysis (VPA),
 Mantel’s test, and Random forest (RF). Community assembling process was
 characterized using Neutral community modeling (NCM) and Null model (NM)
 using 16S rRNA data. All mentioned models were performed by executing the
 R script, which were also provided here. Functional genes were obtained
 from metagenomic investigations. 67 qualified Metagenome assembled genome
 (MAG) were also retrieved from metagenomic binning, among which keystone
 taxa were focused and their functional potential were
 annotated.
description: # Unraveling community adaption and survival strategy of soil microbiome
 under vanadium stress in nationwide mining environments
 Four types of datasets are
 included herein: 1\. Sites information (physicochemical measurements) 2\.
 16S rRNA (community profile at OTU and genera level) 3\. Metagenome
 (functional genes profile, MAG results, annotation tables for keystone
 taxa, carbon fixation marker genes, naming convention) 4\. R script 5\.
 fastq files for metagenome sequence for binning ## Description of the data
 and file structure The datasets herein serve as the basis to perform data
 analysis for this article. Physicochemical data was obtained from actual
 measurements, which was used to perform analysis to uncover the key
 driving factors for shaping the community structure, and implemented in
 models such as Variation partitioning analysis (VPA), Mantel’s test, and
 Random forest (RF). Community assembling process was characterized using
 Neutral community modeling (NCM) and Null model (NM) using 16S rRNA data.
 All mentioned models were performed by executing the R script, which were
 also provided here. Functional genes were obtained from metagenomic
 investigations. 67 qualified Metagenome assembled genome (MAG) were also
 retrieved from metagenomic binning, among which keystone taxa were focused
 and their functional potential were annotated. The detailed description of
 each uploaded datasets and software is provided below: 1\. Physicochemical
 parameter Physicochemical parameter measurements of soil samples collected
 from smelter sites. 2\. Sequence data The webpage link to obtain the 16S
 rRNA sequence data from NCBI Sequence Read Archive (SRA) database
 () 3\. Metagenome data, including:
 * KO summary, the functional profile of metagenome investigation. * MAG
 quality, the results of binning process, including all qualified
 metagenome assembled genomes * Annotation tables, provide the full
 annotation of functional genes for all keystone genera identified,
 bin6/11/22/54/70/136/267/302/305/310/431. * Carbon fixation marker genes,
 provide all genes related with carbon fixation process and central
 metanolism process for all keystone genera, with the marker genes
 highlighted. * All fastq data files for 13 MAGs retrieved (2 subfiles per
 1 MAG) from binning process of metagenomic sequence. For fastq file, old
 file names were used, therefore we have attachd a separate csv file to
 provide with new sample names) * SML-1 (L1HFI240433) * SML-2 (L1HFI240431)
 * SML-3 (L1HFI240425) * SMM-1 (L1HFI240428) * SMM-2 (L1HFI240427) * SMM-3
 (L1HFI240429) * SMM-4 (L1EFI270346) * SMM-5 (L1HFI240426) * SMH-1
 (L1HFI240422) * SMH-2 (L1HFI240430) * SMH-3 (L1HFI240421) * SMH-4
 (L1HFI240423) * SMH-5 (L1HFI240424) 4\. R scripts (software), including: *
 RF_0130, random forest analysis using "RandomForest" function to
 support the creation of sample groups by screening the important driving
 factors for community structure based on percentage increases in the MSE
 (mean squared error). * VPA1, variable partitioning analysis using
 "Vegan" package to quantify the relative contribution of
 explanatory variables on community variation. * Mantel7, Mantel's
 test using "Vegan" package to associate influence variables with
 community structure and disentangle the interactive patterns between
 individual determinants. * NCM_0111, using R package “Hmisc, stat4 and
 minpack.lm” to predict the relationship between OTU detection frequency
 and their relative abundance. * bNTI_Rscript_0116, using “picante” to
 calculate the standardized effect size measure of the mean nearest taxon
 distance (SES.MNTD) and β mean nearest taxon distance (βMNTD). * Beta_RC,
 using “raup_crick.dist” function to partitioning the relative influence of
 stochastic process (dispersal limitation, undominated, homogeneous
 dispersal). ## Sharing/Access information Links to other publicly
 accessible locations of the data: *
 ## Code/Software List of software
 and R script used for data analysis:   R scripts: 1. R (version 4.2.1)
 package “RandomForest” was used for performing Random Forest analysis. 2.
 R (version 4.2.1) package “Vegan” was used for conducting Mantel’s test
 and variable partitioning analysis. 3. R (version 4.2.1) package “Hmisc,
 stat4 and minpack.lm” were used to examine the influence of neutral
 process on community assembling process. 4. R (version 4.2.1) package
 “picante” and ““raup_crick.dist” were used to characterize the community
 assembling process. All abovementioned script were provided herein.