Metagenome-assembled genomes involved in methane cycling from agricultural soils and compost¶

Narrative created by: Gabriel Silvestre Rocha & Stijn van den Bergh¶

We report 14 metagenome-assembled genomes (MAGs) recovered from agricultural soils, composts, and enrichment cultures enriched therefrom, originating from the Netherlands, Belgium and Switzerland. Recovered MAGs constitute methane-cycling related organisms sequenced from isolated cultures or environmental DNA, elucidating their metabolic potential in important ecological processes like the oxidation or production of atmospheric trace gases as methane, hydrogen, and carbon monoxide.

1. Brief sample description¶

Environmental sampling was conducted at field sites in the Netherlands, Belgium and Switzerland as described by van den Bergh et al. (2024), and at Dutch composting companies as described by van den Bergh et al. (2023). Methanotrophic cultures were enriched from soil and compost samples in NMS medium with 20% methane and subsequently cultured on polycarbonate nuclepore membranes (0.2 µm pore size) on NMS-agar plates or in liquid NMS medium. Environmental DNA was isolated from soil and compost samples and enrichment culture DNA from methanotrophic liquid cultures, both using the DNeasy PowerSoil Pro Kit. Further processing of the extracted DNA, library construction, shotgun metagenomics and sequencing (NovaSeq PE150) was done by Novogene (Cambridge, UK). Further analysis was done using the SqueezeMeta pipeline, after which 14 MAGs were selected for subsequent analysis.

Sample IDs:¶

MbctrC_maxbin.001.fasta.contigs.fa: Metagenome assembled from enrichment culture of Methylobacter sp., originally enriched from green compost (Van Iersel; pile 2).

MbctrS_maxbin.001.fasta.contigs.fa: Metagenome assembled from enrichment culture of Methylobacter sp., originally enriched from compost-amended Vredepeel soil.

McldmC_maxbin.001.fasta.contigs.fa: Metagenome assembled from enrichment culture of Methylocaldum szegediense, originally enriched from green compost (Van Iersel; pile 2).

McldmS_maxbin.002.fasta.contigs.fa: Metagenome assembled from enrichment culture of Methylocaldum szegediense, originally enriched from compost-amended Lelystad soil.

McystS_maxbin.001.fasta.contigs.fa: Metagenome assembled from enrichment culture of Methylocystis sp., originally enriched from compost-amended Valthermond soil.

MelSoi_Bin2: Metagenome assembled from compost-amended Melle soil.

CompC33_Bin3: Metagenome assembled from green compost (Van Iersel; pile 3).

CompC5_Bin3: Metagenome assembled from green compost (Den Ouden, pile 2).

CompC33_Bin8: Metagenome assembled from green compost (Van Iersel; pile 3).

CompC5_Bin9: Metagenome assembled from green compost (Den Ouden, pile 2).

CompC33_Bin10: Metagenome assembled from green compost (Van Iersel; pile 3).

CompC33_Bin12: Metagenome assembled from green compost (Van Iersel; pile 3).

CompC5_Bin15: Metagenome assembled from green compost (Den Ouden, pile 2).

CompC5_Bin24: Metagenome assembled from green compost (Den Ouden, pile 2).

2. Data upload¶

from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fasta_as_assembly_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "staging_file_subdir_path": "MbctrC_maxbin.001.fasta.contigs.fa",
            "assembly_name": "MbctrC_maxbin.001.fasta.contigs.fa_assembly"
        }, {
            "staging_file_subdir_path": "McldmS_maxbin.002.fasta.contigs.fa",
            "assembly_name": "McldmS_maxbin.002.fasta.contigs.fa_assembly"
        }, {
            "staging_file_subdir_path": "McldmC_maxbin.001.fasta.contigs.fa",
            "assembly_name": "McldmC_maxbin.001.fasta.contigs.fa_assembly"
        }, {
            "staging_file_subdir_path": "MbctrS_maxbin.001.fasta.contigs.fa",
            "assembly_name": "MbctrS_maxbin.001.fasta.contigs.fa_assembly"
        }, {
            "staging_file_subdir_path": "McystS_maxbin.001.fasta.contigs.fa",
            "assembly_name": "McystS_maxbin.001.fasta.contigs.fa_assembly"
        }],
        "shared_params": {
            "type": "draft isolate",
            "min_contig_length": 500
        }
    }],
    cell_id="b6b167ce-60cf-4977-b9a2-89b22e444860",
    run_id="6a2e1247-2734-4341-a685-44c173a8a631"
)

from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_app_batch(
    [{
        "app_id": "kb_uploadmethods/import_fasta_as_assembly_from_staging",
        "tag": "release",
        "version": "5b9346463df88a422ff5d4f4cba421679f63c73f",
        "params": [{
            "staging_file_subdir_path": "MelSoi_Bin2.fa",
            "assembly_name": "MelSoi_Bin2.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC5_Bin24.fa",
            "assembly_name": "CompC5_Bin24.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC33_Bin8.fa",
            "assembly_name": "CompC33_Bin8.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC5_Bin15.fa",
            "assembly_name": "CompC5_Bin15.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC5_Bin3.fa",
            "assembly_name": "CompC5_Bin3.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC33_Bin10.fa",
            "assembly_name": "CompC33_Bin10.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC33_Bin12.fa",
            "assembly_name": "CompC33_Bin12.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC33_Bin3.fa",
            "assembly_name": "CompC33_Bin3.fa_assembly"
        }, {
            "staging_file_subdir_path": "CompC5_Bin9.fa",
            "assembly_name": "CompC5_Bin9.fa_assembly"
        }],
        "shared_params": {
            "type": "mag",
            "min_contig_length": 500
        }
    }],
    cell_id="3deb9858-9770-48c5-8c99-de4c2e0a210d",
    run_id="6f9ee3f0-c318-4325-a93e-4b72b8964371"
)

3. Genome functional annotation¶

4. References¶

van den Bergh, S. G., Chardon, I., Meima-Franke, M., Costa, O. Y., Korthals, G. W., de Boer, W., & Bodelier, P. L. (2023). The intrinsic methane mitigation potential and associated microbes add product value to compost. Waste Management, 170, 17-32.

van den Bergh, S. G., Chardon, I., Leite, M. F., Korthals, G. W., Mayer, J., Cougnon, M., ... & Bodelier, P. L. (2024). Soil aggregate stability governs field greenhouse gas fluxes in agricultural soils. Soil Biology and Biochemistry, 191, 109354.