Effects of manganese oxide amendments on greenhouse gas emissions and the methanogenic archaeal community in paddy soil

Description

In this study, three manganese oxides—birnessite, vernadite and lithiophorite, commonly found in manganese slag—were added to paddy soil in an indoor incubation experiment under alternating light-dark conditions. The fluxes of greenhouse gas emissions and the composition of the archaeal community were analyzed.

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Greenhouse gases were collected on days 3, 6, 9, 12, 15, 18, 21, 24, and 27 of the soil culture experiment. Samples were taken from the outlet valve at the top of each culture bottle through a rubber hose using a polypropylene syringe. The collected gases were immediately transferred into a 300 mL aluminum foil gas collection bag, which was then filled with nitrogen to equalize the air pressure within the culture bottles. The gas samples were subsequently analyzed using a gas chromatograph. Soil samples were collected from the culture bottles at the end of incubation period. Total DNA was extracted using Omega Soil DNA Kit (D5635-02, Omega Bio-Tek, USA). The size of the DNA fragments was determined via 0.8% agarose gel electrophoresis, and DNA concentration was quantified using a Nanodrop spectrophotometer. The 16s rRNA V8-V9 region of Archaea methanogenes was amplified by polymerase chain reaction (PCR) using the primers 1106F (5'-TTTWAGTCAGGCAACAAGC-3') and 1378R (5'-TGTGCAAGGAGCAGGGAC-3'). he PCR products were subjected to bipartite sequencing at Parsonage Bioscience and Technology (Shanghai) Co.Ltd. Microbiome analysis was performed using QIIME2 2019.4. The raw sequence data were decoded using the Demux plugin, with primer sequences removed using the Cutadapt plugin. Quality filtering, denoising, sequence splicing, and chimera removal were conducted using the DADA2 plugin. The resulting sequences were clustered at 100% sequence similarity to generate Amplicon Sequence Variants (ASVs) and abundance data tables. Reference sequences from the Greengenes database were used to annotate the ASVs. ASVs with an abundance lower than 0.001% of the total sequences across all samples were removed prior to further analysis.

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