Page 206 - Microbial methane cycling in a warming world From biosphere to atmosphere Michiel H in t Zandt

Chapter 9. Long-term warming effects on permafrost soil microbial communities
Therefore, it was used as an alternative approach to analyze the general change of microbial community composition upon warming. However, the reference database is less extensive for rpS3 than for the SSU rRNA, and the analysis is more sensitive to the quality of the assembly process than that of the SSU rRNA. Details on this analysis can be found in Supplementary Document 1.
Data visualization. Microbial community visualization was performed in R (R Core Team 2014). Community data were collapsed at higher taxonomic level with the R package otuSummary (Yang 2018). Ordination analyses of microbial community structure were performed with the R package vegan (v2.5-2) (Oksanen et al. 2018). Heatmaps were generated with the package ggplot2 (v3.1.0) (Wickham 2009). In addition, the fold-changes in relative abundance of taxonomic composition for the initial and incubated samples were used to semi- quantitatively estimate the extent of abundance shifts for various microbial taxa. The fold changes were visualized via bubble plot with ggplot2 (v3.1.0) (Wickham 2016). PCoA plots and symmetric procrustes analysis on the functional and taxonomic profiles were performed by using Bray-Curtis dissimilarity with package vegan (v2.5-2) (Oksanen et al. 2018). Permutational anova on the CH4 production rates over layers were performed with the kruskal.test function in R (R Core Team 2014).
Data deposition
The data were deposited at EMBL-EBI under accession number ERS4594325-ERS4594330 (Bioproject PRJEB38557).
Results
CO2 and CH4 production rates
The CO2 and CH4 production rates were monitored within the active layer (AL), transition layer (TL), and permafrost layer (PF) over the course of 1163 days to gain insights into GHG gas production rates under anoxic thaw conditions on the long-term (Fig. 1). The CO2 production rates peaked during the first 50-100 days of incubation, after which a rapid decrease was observed for all layers. Afterwards, CO2 production rates were similar in the different layers,
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