Microbial community dynamics and methane, carbon dioxide, oxygen, and nitrous oxide concentrations in upland forest and riparian soils across a seasonal gradient of fully saturated soils to completely dried soils

Abstract:

Gas concentrations (CH₄, CO₂, N₂O, and O₂), soil properties (soil water content and pH), and microbial community composition were measured from soils at 32 sites across the Stringer Creek Watershed in the Tenderfoot Creek Experimental Forest 7 times between June 3, 2013 and September 20, 2013. Soils were fully saturated during the initial sampling period and dried down over the course of the summer. Soils and gas were sampled from 5cm and 20cm at each site and also at 50cm at eight riparian sites. In total, 496 individual soil samples were collected. Soil moisture ranged from 3.7% to fully saturated; soil pH ranged from 3.60 to 6.68. Methane concentrations in soils ranged from 0.426 ppm to 218 ppm; Carbon dioxide concentrations ranged from 550 ppm to 42,990 ppm; Nitrous oxide concentrations ranged from 0.220 ppm to 2.111 ppm; Oxygen concentrations ranged from 10.2% to 21.5%. Soil microbial communities were characterized by DNA sequences covering the V4 region of the 16S rRNA gene. DNA sequences were generated (~30,000,000 sequences) from the 496 soil samples using the Illumina MiSeq platform. Operational Taxonomic Units were generated using USEARCH, and representative sequences were taxonomically classified according the Ribosomal Database Project’s taxonomy scheme. Analysis of similarity revealed that microbial communities found within a landscape type (high upland forest, low upland forest, riparian) were more similar than among landscape types (R = 0.600; p<0.001). Similarly, communities from unique site x depths were similar across the 7 collection periods (R = 0.646; p<0.001) despite changes in soil moisture. Euclidean distances of soil properties and gas concentrations were compared to Bray-Curtis community dissimilarity matrices using Mantel tests to determine how community structure co-varies with the soil environment and gas concentrations. All variables measured significantly co-varied with microbial community membership (pH: R = 0.712, p < 0.001; CO₂: R = 0.578, p < 0.001; O₂: R = 0.517, p < 0.001; Soil moisture: R = 0.408, p < 0.001; N₂O: R = 0.218, p = 0.003; CH₄: R = 0.195, p = 0.008). Despite the rather low co-variation between methane concentrations and microbial community composition, relative abundances of methanotrophic and methanogenic lineages did co-vary strongly with methane concentrations.