Datasets and metadata for reproduction of taxonomic analyses using the RMarkdown report.

ABSTRACT

Soil microbial communities respond quickly to natural and/or anthropic-induced changes in environmental conditions, with potential impacts in terms of soil functioning. However, most studies are limited to specific microbial groups, mainly bacteria and fungi, thus the in situ dynamics of the whole microbial community remains to be documented. Here, we investigated the response of the soil microbial community (archaea, bacteria, fungi, protists and viruses) to wheat straw input in a 4-month in-situ field study. We employed global metagenomics to characterise the whole soil microbial diversity, and compared the results with those previously obtained using high throughput amplicon sequencing on the same soil samples. Taxonomic patterns at the community, phyla and genus levels, were concordant between the two methodologies but global metagenomics was more sensitive and allowed studying all the microbial groups simultaneously, showing the considerable potential of this approach for the fine analysis of microbial population dynamics in situ. Microorganisms from each taxonomic group were affected directly or indirectly by the amendment. Land-use histories impacted the soil communities and their responses to amendment. Lastly, both inter and intra-domain trophic interactions could be inferred from our dataset. In particular, we observed the multiplication of viral sequences in the early phase of straw decomposition, in parallel to that of copiotrophic bacteria, suggesting a “kill-the-winner” dynamic that, to our knowledge, had not been observed before in soils. Our study highlights that top-down regulation by microbial predators or viruses might play a key role in soil microbiota dynamics and structure.

File structure:

counts_per_sample_16S.tsv: Table of amplicon sequencing data for 16S rRNA genes. Bacterial and archaeal data. Originally obtained in https://doi.org/10.1371/journal.pone.0130672.

Each line corresponds to one sample, and each column corresponds to each detected genus. The first column is the sample ID.

counts_per_sample_18S.tsv: Table of amplicon sequencing data for 18S rRNA genes. Fungal data. Originally obtained in https://doi.org/10.1371/journal.pone.0130672. Each line corresponds to one sample, and each column corresponds to each detected genus. The first column is the sample ID.

FONCTIOMIC_taxonomy_sample_metadata.tab: Tabulated file giving the complete metadata details for each sample.

submitted_sample_name: Name of the sample chosen for the publication. laboratory_sample_name: Internal sample name used in the laboratory and for the deposit in public databases (NCBI, EBI, DDBJ). Site: Location of the sampling survey. geo_loc_name: geo_loc_name needed for NCBI. sampling_date: Sampling year of soils. sampling_operator: Laboratory name that performed the sampling. extraction_operator: Laboratory name that performed the extraction. User_name: Used method to determine the DNA concentration and quality. Date_and_Time: Date when the Nanodrop quantification was realized. Nucleic_Acid_Conc: Nucleic Acid Concentration with Nanodrop. Unit_Conc: Nucleic Acid Concentration Unit with Nanodrop. A260: Absorbance at 260nm. A280: Absorbance at 280nm. X260.280: Absorbance ratio at 260/280nm. X260.230: Absorbance ratio at 260/230nm. Tecan: Nucleic Acid Concentration with TECAN. Unit_Tecan: Nucleic Acid Concentration Unit with TECAN. land_use: Observed land use during the sampling survey. wheat_straw_amendment: Wheat straw amendment status (control: no, amended: yes). time: Time of sampling after wheat straw amendment. Unit_time: Time of sampling unit (day). subplot: Subplot numbers defined during the sampling survey.

FONCTIOMIC_taxo_physeq.rds: Phyloseq object containing taxonomic data for each sample. It contains counts of each taxon found by Kaiju, a detailed taxonomy for each taxon, and the metadata of the samples.

manual_taxonomy_replacement.txt: Table of manually corrected taxonomy for metagenomic data. Includes replacement of NA values for phyla by other placeholder taxonomic ranks.

Class_or_Order_or_Family_or_genus : Taxonomic reference used to improve the taxonomy. original_Phylum : Original phylum in the taxonomic results. new_Phylum : Chosen phylum in the taxonomic results after curation.

ref_taxo_genus_16S_corrected.tsv: Manually corrected taxonomy for 16S rRNA gene data, to allow comparison with metagenomic dataset.

ref_taxo_genus_18S_corrected.tsv: Manually corrected taxonomy for 18S rRNA gene data, to allow comparison with metagenomic dataset.