Improved methane mitigation potential and modulated methane cycling microbial communities in arable soil by compost addition

The global atmospheric concentration of the potent greenhouse gas methane
(CH4) is rising rapidly, and agriculture is responsible for 30-50% of the
yearly CH4 emissions. To limit its global warming effects, strong and
sustained reductions are needed. Sustainable agricultural management
strategies, as the use of organic amendments like compost, have previously
proven to have a potent CH4 mitigation effect in laboratory experiments.
Here we investigated, using an extensive field study, the effect of
organic amendments on the CH4 mitigation potential of agricultural soils
and the CH4 cycling microbial communities. Organic-amended soils had
higher potential CH4 uptake rates and an improved potential to oxidize CH4
to sub-atmospheric concentrations. Also, we showed for the first time that
the methanotrophic and methanogenic microbial communities of arable soils
were unequivocally altered after organic amendment application by
increasing in size while getting less diverse. Compost-amended soils
became dominated by the compost-originating methanotroph Methylocaldum
szegediense and methanogen Methanosarcina horonobensis, replacing the
indigenous methane cycling community members. However, multivariate
analyses did not point out type Ib methanotrophs like M. szegediense as
significant driving factors for the observed improved soil CH4 uptake
potential. Conventional type IIa methanotrophs like Methylocystis sp. also
had higher differential abundances in organic-amended soils and are
speculated to be contributing to the improved CH4 uptake potential.
Altogether, the results showed that compost serves as a vector for the
introduction of CH4 cycling microbes and improves the soil’s CH4 uptake
potential, which emphasizes the potential of organic fertilization with
compost to contribute to CH4 mitigation in agricultural soils.

# Improved methane mitigation potential and modulated methane cycling
microbial communities in arable soil by compost addition Dataset DOI:
[10.5061/dryad.dz08kps8h](10.5061/dryad.dz08kps8h) ## Description of the
data and file structure To assess the effect of organic fertilization on
the methane uptake potential and methane cycling microbial communities of
agricultural soils, an extensive field screening was performed. To this
end, soil samples (0-15cm depth) were collected at 6 sites in the
Netherlands, Belgium and Switzerland. The following physicochemical
properties were determined: Moisture content, organic matter content, pH,
NO3+NO2-N-, NH4-N, Al-, Co-, Cu-, Fe-, K-, Mg-, Mn-, Mo-, Na-, Ni-, P-,
S-, and Zn-content. Also, the potential methane uptake rates and lag
phases were determined in incubations with 10 or 10.000 ppmv CH4 in the
headspace, and the capacity to oxidize to sub-atmospheric CH4
concentrations. Furthermore, the gene copy numbers of the bacterial 16S
rRNA, *pmoA* (total, type Ib, and type II), and *mcrA* were determined.
Also, amplicon sequencing was performed, targetting *pmoA*, using a nested
multiplex-reverse approach, of which the ASV matrix is also provided. ###
Files and variables #### File:
Amplicon_sequencing_pmoA_and_environmental_data_0-15cm_(incl_metadata).xlsx Description: All environmental data and *pmoA* amplicon sequencing results for agricultural soils (0-15 cm depth). #### File: Amplicon_sequencing_pmoA_and_environmental_data_0-7_5cm_(incl_metadata).xlsx Description: All environmental data and *pmoA* amplicon sequencing results for upper-top layer of agricultural soils (0-7.5 cm depth). #### File: Amplicon_sequencing_pmoA_and_environmental_data_7_5-15cm_(incl_metadata).xlsx Description: All environmental data and *pmoA* amplicon sequencing results for subtop layer of agricultural soils (7.5-15 cm depth). #### File: Amplicon_sequencing_mcrA_(incl_metadata).xlsx Description: All *mcrA* amplicon sequencing results for agricultural soils (0-15 cm depth), upper-top layer of agricultural soils (0-7.5 cm depth), and subtop layer of agricultural soils (7.5-15 cm depth). #### File: Amplicon_sequencing_16S_(incl_metadata).xlsx Description: All 16S amplicon sequencing results for agricultural soils (0-15 cm depth), upper-top layer of agricultural soils (0-7.5 cm depth), and subtop layer of agricultural soils (7.5-15 cm depth). ##### Variables General overview of metadata. See for data-specific metadata the accompanying sheet "Metadata" in each data file. | Sheet | Column | Name | Unit | Description | | :----------------- | :----- | :------------- | :--------------- | :----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | ASV matrix | A | ASV | n.a. | ASV id. Corresponding with "Taxonomy table" column A. | | ASV matrix | B-BK | plot81-plot510 | n.a. | ASV matrix, how many amplicons per ASV id (column A) are found in the corresponding sample (column B-BK). MiSeq sequencing performed on samples plot81-plot334, NextSeq sequencing performed on samples plot401-plot510. | | Taxonomy table | A | ASV | n.a. | ASV id. Corresponding with "ASV matrix" column A. | | Taxonomy table | B | Kingdom | n.a. | Corresponding taxonomic identity of said ASV. | | Taxonomy table | C | Phylum | n.a. | Corresponding taxonomic identity of said ASV. | | Taxonomy table | D | Class | n.a. | Corresponding taxonomic identity of said ASV. | | Taxonomy table | E | Order | n.a. | Corresponding taxonomic identity of said ASV. | | Taxonomy table | F | Family | n.a. | Corresponding taxonomic identity of said ASV. | | Taxonomy table | G | Genus | n.a. | Corresponding taxonomic identity of said ASV. | | Taxonomy table | H | Species | n.a. | Corresponding taxonomic identity of said ASV. | | Environmental data | A | Sample | n.a. | Sample id. Corresponding with "ASV matrix" columns B-BK. | | Environmental data | B | Location | n.a. | Location of visited field site. | | Environmental data | C | Practice | n.a. | No-tillage (notil) or tillage (til) practice. | | Environmental data | D | Treatment | n.a. | Organic-amended (oa) or unamended (control). | | Environmental data | E | Oa | n.a. | Organic amendment used (compost/cover crops) or unamended. | | Environmental data | F | Moistgrav | % | Gravimetric moisture content. | | Environmental data | G | Moistwhc | % | Moisture content as % of water holding capacity. | | Environmental data | H | OM | % | Organic matter content. | | Environmental data | I | pH | n.a. | pH. | | Environmental data | J | Chemnox | mg/kg | (NO3- + NO2)-N  content. | | Environmental data | K | Chemnh4 | mg/kg | NH4+ content. | | Environmental data | L | Chemal | mg/kg | Al content. | | Environmental data | M | Chemco | µg/kg | Co content. | | Environmental data | N | Chemcu | µg/kg | Cu content. | | Environmental data | O | Chemfe | µg/kg | Fe content. | | Environmental data | P | Chemk | mg/kg | K content. | | Environmental data | Q | Chemmg | mg/kg | Mg content. | | Environmental data | R | Chemmn | mg/kg | Mn content. | | Environmental data | S | Chemmo | µg/kg | Mo content. | | Environmental data | T | Chemna | mg/kg | Na content. | | Environmental data | U | Chemni | mg/kg | Ni content. | | Environmental data | V | Chemp | mg/kg | P content. | | Environmental data | W | Chems | mg/kg | S content. | | Environmental data | X | Chemzn | mg/kg | Zn content. | | Environmental data | Y | ratelow | pmol/d/g dw soil | Potential CH4 uptake rate of soil sample in incubation with \~10 ppmv CH4. | | Environmental data | Z | laglow | d | Lag phase of soil sample before active CH4 oxidation activity in incubation with \~10 ppmv CH4. | | Environmental data | AA | ratehigh | nmol/h/g dw soil | Potential CH4 uptake rate of soil sample in incubation with \~10.000 ppmv CH4. | | Environmental data | AB | laghigh | d | Lag phase of soil sample before active CH4 oxidation activity in incubation with \~10.000 ppmv CH4. | | Environmental data | AC | belowatmlow | n.a. | Did sample oxidize to <1.89 ppmv (=sub-atmospheric) during incubation with \~10 ppmv CH4. | | Environmental data | AD | below10high | n.a. | Did sample oxidize to <10 ppmv during incubation with \~10.000 ppmv CH4. | | Environmental data | AE | belowatmhigh | n.a. | Did sample oxidize to <1.89 ppmv (=sub-atmospheric) during incubation with \~10.000 ppmv CH4. | | Environmental data | AF | 16S | copies/g dw soil | total 16S copy number in sample as determined with qPCR. | | Environmental data | AG | pmoAtot | copies/g dw soil | total pmoA copy number in sample as determined with qPCR. | | Environmental data | AH | pmoA1b | copies/g dw soil | pmoA type 1b copy number in sample as determined with qPCR. | | Environmental data | AI | pmoA2 | copies/g dw soil | pmoA type 2 copy number in sample as determined with qPCR. | | Environmental data | AJ | mcrA | copies/g dw soil | total mcrA copy number in sample as determined with qPCR. | Missing values are left as blank cells. ## Access information Other publicly accessible locations of the data: * Sequencing data can be found at the European Nucleotide Archive (ENA) under the accession number PRJEB75729 ([http://www.ebi.ac.uk/ena/data/view/PRJEB75729](http://www.ebi.ac.uk/ena/data/view/PRJEB75729)). Data was derived from the following sources: * Agricultural soils, locations: WUR Open Teelten location Vredepeel, WUR Open Teelten location Valthermond, WUR Open Teelten location Lelystad, Proefhoeve Melle - UGent, Unifarm (Wageningen University), and Agroscope Reckenholz Zürich.